Nat Methods , IF:30.822 , 2019 Sep , V16 (9) : P866-869 doi: 10.1038/s41592-019-0512-x
An efficient auxin-inducible degron system with low basal degradation in human cells.
Department of Anatomy and Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland.; Minerva Foundation Institute for Medical Research, Helsinki, Finland.; Department of Physics, University of Helsinki, Helsinki, Finland.; Computational Physics Laboratory, Tampere University, Tampere, Finland.; Department of Anatomy and Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland. elina.ikonen@helsinki.fi.; Minerva Foundation Institute for Medical Research, Helsinki, Finland. elina.ikonen@helsinki.fi.
Auxin-inducible degron technology allows rapid and controlled protein depletion. However, basal degradation without auxin and inefficient auxin-inducible depletion have limited its utility. We have identified a potent auxin-inducible degron system composed of auxin receptor F-box protein AtAFB2 and short degron miniIAA7. The system showed minimal basal degradation and enabled rapid auxin-inducible depletion of endogenous human transmembrane, cytoplasmic and nuclear proteins in 1 h with robust functional phenotypes.
PMID: 31451765
Trends Plant Sci , IF:14.416 , 2019 Sep , V24 (9) : P826-839 doi: 10.1016/j.tplants.2019.06.015
Lateral Root Formation in Arabidopsis: A Well-Ordered LRexit.
Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, UK.; Unite Mixte de Recherche (UMR) Diversite, Adaptation, et Developpement des Plantes (DIADE), Institut de Recherche pour le Developpement (IRD), Universite de Montpellier, Montpellier, France.; Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma 630-0192, Japan.; Unite Mixte de Recherche (UMR) Diversite, Adaptation, et Developpement des Plantes (DIADE), Institut de Recherche pour le Developpement (IRD), Universite de Montpellier, Montpellier, France. Electronic address: laurent.laplaze@ird.fr.; Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, UK. Electronic address: mMalcolm.bennett@nottingham.ac.uk.
Lateral roots (LRs) are crucial for increasing the surface area of root systems to explore heterogeneous soil environments. Major advances have recently been made in the model plant arabidopsis (Arabidopsis thaliana) to elucidate the cellular basis of LR development and the underlying gene regulatory networks (GRNs) that control the morphogenesis of the new root organ. This has provided a foundation for understanding the sophisticated adaptive mechanisms that regulate how plants pattern their root branching to match the spatial availability of resources such as water and nutrients in their external environment. We review new insights into the molecular, cellular, and environmental regulation of LR development in arabidopsis.
PMID: 31362861
Angew Chem Int Ed Engl , IF:12.959 , 2019 Sep , V58 (37) : P12778-12786 doi: 10.1002/anie.201901626
Strigolactones: Plant Hormones with Promising Features.
Plant Hormone Biology group, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands.; Syngenta Crop Protection Research, Stein, CH-4334, Switzerland.
Almost 80 years after the discovery of the first plant hormone, auxin, a few years ago a new class of plant hormones, the strigolactones, was discovered. These molecules have unprecedented biological activity in a number of highly important biological processes in plants but also outside the plant in the rhizosphere, the layer of soil surrounding the roots of plants and teeming with life. The exploitation of this amazing biological activity is not without challenges: the synthesis of strigolactones is complicated and designing the desired activity a difficult task. This minireview describes the current state of knowledge about the strigolactones and how synthetic analogs can be developed that can potentially contribute to the development of a sustainable agriculture.
PMID: 31282086
Nat Commun , IF:12.121 , 2019 Sep , V10 (1) : P4417 doi: 10.1038/s41467-019-12369-1
UVR8 disrupts stabilisation of PIF5 by COP1 to inhibit plant stem elongation in sunlight.
School of Biological Sciences, Life Sciences Building, University of Bristol, Bristol, BS8 1TQ, UK.; Centro Nacional de Biotecnologia (CNB-CSIC), Calle Darwin 3, Madrid, 28049, Spain.; Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), Biocenter, University of Cologne, Cologne, Germany.; Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK.; School of Biological Sciences, Life Sciences Building, University of Bristol, Bristol, BS8 1TQ, UK. kerry.franklin@bristol.ac.uk.
Alterations in light quality significantly affect plant growth and development. In canopy shade, phytochrome photoreceptors perceive reduced ratios of red to far-red light (R:FR) and initiate stem elongation to enable plants to overtop competitors. This shade avoidance response is achieved via the stabilisation and activation of PHYTOCHROME INTERACTING FACTORs (PIFs) which elevate auxin biosynthesis. UV-B inhibits shade avoidance by reducing the abundance and activity of PIFs, yet the molecular mechanisms controlling PIF abundance in UV-B are unknown. Here we show that the UV-B photoreceptor UVR8 promotes rapid PIF5 degradation via the ubiquitin-proteasome system in a response requiring the N terminus of PIF5. In planta interactions between UVR8 and PIF5 are not observed. We further demonstrate that PIF5 interacts with the E3 ligase COP1, promoting PIF5 stabilisation in light-grown plants. Binding of UVR8 to COP1 in UV-B disrupts this stabilisation, providing a mechanism to rapidly lower PIF5 abundance in sunlight.
PMID: 31562307
Nat Commun , IF:12.121 , 2019 Sep , V10 (1) : P4021 doi: 10.1038/s41467-019-12002-1
Auxin-sensitive Aux/IAA proteins mediate drought tolerance in Arabidopsis by regulating glucosinolate levels.
Section of Cell and Developmental Biology and Howard Hughes Medical Institute, University of California, San Diego, La Jolla CA., 92093, USA.; Department of Plant Sciences, University of California, Davis, CA, 95616, USA.; Genomic Analysis Laboratory, Howard Hughes Medical Institute and The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA.; Section of Cell and Developmental Biology and Howard Hughes Medical Institute, University of California, San Diego, La Jolla CA., 92093, USA. mestelle@ucsd.edu.
A detailed understanding of abiotic stress tolerance in plants is essential to provide food security in the face of increasingly harsh climatic conditions. Glucosinolates (GLSs) are secondary metabolites found in the Brassicaceae that protect plants from herbivory and pathogen attack. Here we report that in Arabidopsis, aliphatic GLS levels are regulated by the auxin-sensitive Aux/IAA repressors IAA5, IAA6, and IAA19. These proteins act in a transcriptional cascade that maintains expression of GLS levels when plants are exposed to drought conditions. Loss of IAA5/6/19 results in reduced GLS levels and decreased drought tolerance. Further, we show that this phenotype is associated with a defect in stomatal regulation. Application of GLS to the iaa5,6,19 mutants restores stomatal regulation and normal drought tolerance. GLS action is dependent on the receptor kinase GHR1, suggesting that GLS may signal via reactive oxygen species. These results provide a novel connection between auxin signaling, GLS levels and drought response.
PMID: 31492889
Nucleic Acids Res , IF:11.501 , 2019 Sep , V47 (17) : P9216-9230 doi: 10.1093/nar/gkz712
RNA degradomes reveal substrates and importance for dark and nitrogen stress responses of Arabidopsis XRN4.
Delaware Biotechnology Institute and Department of Plant and Soil Sciences, University of Delaware, Newark, DE 19711, USA.
XRN4, the plant cytoplasmic homolog of yeast and metazoan XRN1, catalyzes exoribonucleolytic degradation of uncapped mRNAs from the 5' end. Most studies of cytoplasmic XRN substrates have focused on polyadenylated transcripts, although many substrates are likely first deadenylated. Here, we report the global investigation of XRN4 substrates in both polyadenylated and nonpolyadenylated RNA to better understand the impact of the enzyme in Arabidopsis. RNA degradome analysis demonstrated that xrn4 mutants overaccumulate many more decapped deadenylated intermediates than those that are polyadenylated. Among these XRN4 substrates that have 5' ends precisely at cap sites, those associated with photosynthesis, nitrogen responses and auxin responses were enriched. Moreover, xrn4 was found to be defective in the dark stress response and lateral root growth during N resupply, demonstrating that XRN4 is required during both processes. XRN4 also contributes to nonsense-mediated decay (NMD) and xrn4 accumulates 3' fragments of select NMD targets, despite the lack of the metazoan endoribonuclease SMG6 in plants. Beyond demonstrating that XRN4 is a major player in multiple decay pathways, this study identified intriguing molecular impacts of the enzyme, including those that led to new insights about mRNA decay and discovery of functional contributions at the whole-plant level.
PMID: 31428786
Dev Cell , IF:10.092 , 2019 Sep , V50 (5) : P599-609.e4 doi: 10.1016/j.devcel.2019.06.010
TRANSPORTER OF IBA1 Links Auxin and Cytokinin to Influence Root Architecture.
Department of Biology, Washington University, St. Louis, MO 63130, USA.; Institute for Molecular Physiology, Heinrich Heine Universitat Dusseldorf, Institute for Biotransformative Molecules (WPI-ITbM), Nagoya University, Nagoya, Japan; Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan.; Donald Danforth Plant Science Center, St. Louis, MO 63132, USA.; Institute for Molecular Physiology, Heinrich Heine Universitat Dusseldorf, Institute for Biotransformative Molecules (WPI-ITbM), Nagoya University, Nagoya, Japan.; Department of Biology, Washington University, St. Louis, MO 63130, USA; Center for Engineering MechanoBiology, Washington University, St. Louis, MO 63130, USA; Center for Science & Engineering of Living Systems, Washington University, St. Louis, MO 63130, USA. Electronic address: strader@wustl.edu.
Developmental processes that control root system architecture are critical for soil exploration by plants, allowing for uptake of water and nutrients. Conversion of the auxin precursor indole-3-butyric acid (IBA) to active auxin (indole-3-acetic acid; IAA) modulates lateral root formation. However, mechanisms governing IBA-to-IAA conversion have yet to be elucidated. We identified TRANSPORTER OF IBA1 (TOB1) as a vacuolar IBA transporter that limits lateral root formation. Moreover, TOB1, which is transcriptionally regulated by the phytohormone cytokinin, is necessary for the ability of cytokinin to exert inhibitory effects on lateral root production. The increased production of lateral roots in tob1 mutants, TOB1 transport of IBA into the vacuole, and cytokinin-regulated TOB1 expression provide a mechanism linking cytokinin signaling and IBA contribution to the auxin pool to tune root system architecture.
PMID: 31327740
Plant Cell , IF:9.618 , 2019 Sep , V31 (9) : P2070-2088 doi: 10.1105/tpc.18.00929
Differential UVR8 Signal across the Stem Controls UV-B-Induced Inflorescence Phototropism.
Laboratory of Functional Plant Biology, Department of Biology, Faculty of Sciences, Ghent University, KL Ledeganckstraat 35, B-9000 Gent, Belgium.; Institute of Plant Biology, Biological Research Centre, Temesvari korut 62, H-6726 Szeged, Hungary.; Department of Biology, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium.; Doctoral School in Biology, Faculty of Science and Informatics, University of Szeged, Szeged, H-6726, Hungary.; IADIZA, Av. Ruiz Leal s/n Parque Gral. San Martin, Casilla de Correo 507, Mendoza, 5500, Argentina (CONICET).; Instituto de Investigaciones Forestales y Agropecuarias Bariloche, (CONICET-INTA), Modesta Victoria 4450, San Carlos de Bariloche Rio Negro R8403DVZ, Argentina.; IFEVA Universidad de Buenos Aires, Av. San Martin 4453, C1417DSE, Buenos Aires, Argentina.; IIBIO-INTECH, Universidad Nacional de San Martin, B1650HMP, Buenos Aires, Argentina.; Laboratory of Functional Plant Biology, Department of Biology, Faculty of Sciences, Ghent University, KL Ledeganckstraat 35, B-9000 Gent, Belgium filip.vandenbussche@ugent.be.
In the course of evolution, plants have developed mechanisms that orient their organs toward the incoming light. At the seedling stage, positive phototropism is mainly regulated by phototropin photoreceptors in blue and UV wavelengths. Contrasting with this, we report that UV RESISTANCE LOCUS8 (UVR8) serves as the predominant photoreceptor of UV-B-induced phototropic responses in Arabidopsis (Arabidopsis thaliana) inflorescence stems. We examined the molecular mechanisms underlying this response and our findings support the Blaauw theory (Blaauw, 1919), suggesting rapid differential growth through unilateral photomorphogenic growth inhibition. UVR8-dependent UV-B light perception occurs mainly in the epidermis and cortex, but deeper tissues such as endodermis can also contribute. Within stems, a spatial difference of UVR8 signal causes a transcript and protein increase of transcription factors ELONGATED HYPOCOTYL5 (HY5) and its homolog HY5 HOMOLOG at the UV-B-exposed side. The irradiated side shows (1) strong activation of flavonoid synthesis genes and flavonoid accumulation; (2) increased gibberellin (GA)2-oxidase expression, diminished GA1 levels, and accumulation of the DELLA protein REPRESSOR OF GA1; and (3) increased expression of the auxin transport regulator PINOID, contributing to diminished auxin signaling. Together, the data suggest a mechanism of phototropin-independent inflorescence phototropism through multiple, locally UVR8-regulated hormone pathways.
PMID: 31289115
Proc Natl Acad Sci U S A , IF:9.412 , 2019 Sep , V116 (39) : P19736-19742 doi: 10.1073/pnas.1907071116
NEEDLE1 encodes a mitochondria localized ATP-dependent metalloprotease required for thermotolerant maize growth.
Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ 08854-8020.; Dipartimento di Biotecnologie e Bioscienze, Universita di Milano Bicocca, 20126 Milan, Italy.; Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093-0116.; Division of Biological Sciences, University of Missouri Columbia, Columbia, MO 65211.; Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ 08854-8020; agallavotti@waksman.rutgers.edu.; Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901.
Meristems are highly regulated structures ultimately responsible for the formation of branches, lateral organs, and stems, and thus directly affect plant architecture and crop yield. In meristems, genetic networks, hormones, and signaling molecules are tightly integrated to establish robust systems that can adapt growth to continuous inputs from the environment. Here we characterized needle1 (ndl1), a temperature-sensitive maize mutant that displays severe reproductive defects and strong genetic interactions with known mutants affected in the regulation of the plant hormone auxin. NDL1 encodes a mitochondria-localized ATP-dependent metalloprotease belonging to the FILAMENTATION TEMPERATURE-SENSITIVE H (FTSH) family. Together with the hyperaccumulation of reactive oxygen species (ROS), ndl1 inflorescences show up-regulation of a plethora of stress-response genes. We provide evidence that these conditions alter endogenous auxin levels and disrupt primordia initiation in meristems. These findings connect meristem redox status and auxin in the control of maize growth.
PMID: 31501327
Plant Physiol , IF:6.902 , 2019 Sep , V181 (1) : P353-366 doi: 10.1104/pp.19.00496
Mutation of a Conserved Motif of PP2C.D Phosphatases Confers SAUR Immunity and Constitutive Activity.
Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota 55108.; Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota 55108 grayx051@umn.edu.
The phytohormone auxin promotes the growth of plant shoots by stimulating cell expansion via plasma membrane (PM) H(+)-ATPase activation, which facilitates cell wall loosening and solute uptake. Mechanistic insight was recently obtained by demonstrating that auxin-induced SMALL AUXIN UP RNA (SAUR) proteins inhibit D-CLADE TYPE 2C PROTEIN PHOSPHATASE (PP2C.D) activity, thereby trapping PM H(+)-ATPases in the phosphorylated, activated state, but how SAURs bind PP2C.D proteins and inhibit their activity is unknown. Here, we identified a highly conserved motif near the C-terminal region of the PP2C.D catalytic domain that is required for SAUR binding in Arabidopsis (Arabidopsis thaliana). Missense mutations in this motif abolished SAUR binding but had no apparent effect on catalytic activity. Consequently, mutant PP2C.D proteins that could not bind SAURs exhibited constitutive activity, as they were immune to SAUR inhibition. In planta expression of SAUR-immune pp2c.d2 or pp2c.d5 derivatives conferred severe cell expansion defects and corresponding constitutively low levels of PM H(+)-ATPase phosphorylation. These growth defects were not alleviated by either auxin treatment or 35S:StrepII-SAUR19 coexpression. In contrast, a PM H(+)-ATPase gain-of-function mutation that results in a constitutively active H(+) pump partially suppressed SAUR-immune pp2c.d5 phenotypes, demonstrating that impaired PM H(+)-ATPase function is largely responsible for the reduced growth of the SAUR-immune pp2c.d5 mutant. Together, these findings provide crucial genetic support for SAUR-PP2C.D regulation of cell expansion via modulation of PM H(+)-ATPase activity. Furthermore, SAUR-immune pp2c.d derivatives provide new genetic tools for elucidating SAUR and PP2C.D functions and manipulating plant organ growth.
PMID: 31311832
Plant Physiol , IF:6.902 , 2019 Sep , V181 (1) : P161-178 doi: 10.1104/pp.19.00064
An Auxin Transport Inhibitor Targets Villin-Mediated Actin Dynamics to Regulate Polar Auxin Transport.
Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Science, Beijing Normal University, Beijing 100875, China.; Key Laboratory of Cell Proliferation and Regulation of Ministry of Education, College of Life Science, Beijing Normal University, Beijing 100875, China.; Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Science, Beijing Normal University, Beijing 100875, China jiejieli@bnu.edu.cn.
Auxin transport inhibitors are essential tools for understanding auxin-dependent plant development. One mode of inhibition affects actin dynamics; however, the underlying mechanisms remain unclear. In this study, we characterized the action of 2,3,5-triiodobenzoic acid (TIBA) on actin dynamics in greater mechanistic detail. By surveying mutants for candidate actin-binding proteins with reduced TIBA sensitivity, we determined that Arabidopsis (Arabidopsis thaliana) villins contribute to TIBA action. By directly interacting with the C-terminal headpiece domain of villins, TIBA causes villin to oligomerize, driving excessive bundling of actin filaments. The resulting changes in actin dynamics impair auxin transport by disrupting the trafficking of PIN-FORMED auxin efflux carriers and reducing their levels at the plasma membrane. Collectively, our study provides mechanistic insight into the link between the actin cytoskeleton, vesicle trafficking, and auxin transport.
PMID: 31311831
Plant Physiol , IF:6.902 , 2019 Sep , V181 (1) : P112-126 doi: 10.1104/pp.19.00695
PI4KIIIbeta Activity Regulates Lateral Root Formation Driven by Endocytic Trafficking to the Vacuole.
Plant Molecular Biology Centre, Department of Biology, Faculty of Sciences, Universidad de Chile, Santiago, Chile.; Plant Molecular Biology Centre, Department of Biology, Faculty of Sciences, Universidad de Chile, Santiago, Chile lnorambuena@uchile.cl.
Lateral roots (LRs) increase the contact area of the root with the rhizosphere and thereby improve water and nutrient uptake from the soil. LRs are generated either via a developmentally controlled mechanism or through induction by external stimuli, such as water and nutrient availability. Auxin regulates LR organogenesis via transcriptional activation by an auxin complex receptor. Endocytic trafficking to the vacuole positively regulates LR organogenesis independently of the auxin complex receptor in Arabidopsis (Arabidopsis thaliana). Here, we demonstrate that phosphatidylinositol 4-phosphate (PI4P) biosynthesis regulated by the phosphatidylinositol 4-kinases PI4KIIIbeta1 and PI4KIIIbeta2 is essential for the LR organogenesis driven by endocytic trafficking to the vacuole. Stimulation with Sortin2, a biomodulator that promotes protein targeting to the vacuole, altered PI4P abundance at both the plasma membrane and endosomal compartments, a process dependent on PI4K activity. These findings suggest that endocytic trafficking to the vacuole regulated by the enzymatic activities of PI4KIIIbeta1 and PI4KIIIbeta2 participates in a mechanism independent of the auxin complex receptor that regulates LR organogenesis in Arabidopsis. Surprisingly, loss-of-function of PI4KIIIbeta1 and PI4KIIIbeta2 induced both LR primordium formation and endocytic trafficking toward the vacuole. This LR primordium induction was alleviated by exogenous PI4P, suggesting that PI4KIIIbeta1 and PI4KIIIbeta2 activity constitutively negatively regulates LR primordium formation. Overall, this research demonstrates a dual role of PI4KIIIbeta1 and PI4KIIIbeta2 in LR primordium formation in Arabidopsis.
PMID: 31285293
Plant Physiol , IF:6.902 , 2019 Sep , V181 (1) : P179-194 doi: 10.1104/pp.19.00248
Wheat TaSPL8 Modulates Leaf Angle Through Auxin and Brassinosteroid Signaling.
State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, 100193, China.; Key Laboratory of Crop Heterosis and Utilization (Ministry of Education), China Agricultural University, Beijing, 100193, China.; Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China.; Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, I-24126 Bergamo, Italy.; State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, 100193, China yingyin@cau.edu.cn.
In grass crops, leaf angle is determined by development of the lamina joint, the tissue connecting the leaf blade and sheath, and is closely related to crop architecture and yield. In this study, we identified a mutant generated by fast neutron radiation that exhibited an erect leaf phenotype caused by defects in lamina joint development. Map-based cloning revealed that the gene TaSPL8, encoding a SQUAMOSA PROMOTER BINDING-LIKE (SPL) protein, is deleted in this mutant. TaSPL8 knock-out mutants exhibit erect leaves due to loss of the lamina joint, compact architecture, and increased spike number especially in high planting density, suggesting similarity with its LIGULESS1 homologs in maize (Zea mays) and rice (Oryza sativa). Hence, LG1 could be a robust target for plant architecture improvement in grass species. Common wheat (Triticum aestivum, 2n = 6x = 42; BBAADD) is an allohexaploid containing A, B, and D subgenomes and the homeologous gene of TaSPL8 from the D subgenome contributes to the length of the lamina joint to a greater extent than that from the A and B subgenomes. Comparison of the transcriptome between the Taspl8 mutant and the wild type revealed that TaSPL8 is involved in the activation of genes related to auxin and brassinosteroid pathways and cell elongation. TaSPL8 binds to the promoters of the AUXIN RESPONSE FACTOR gene and of the brassinosteroid biogenesis gene CYP90D2 and activates their expression. These results indicate that TaSPL8 might regulate lamina joint development through auxin signaling and the brassinosteroid biosynthesis pathway.
PMID: 31209125
Environ Pollut , IF:6.792 , 2019 Sep , V252 (Pt A) : P706-714 doi: 10.1016/j.envpol.2019.05.159
Effect of low-dose, repeated exposure of contaminants of emerging concern on plant development and hormone homeostasis.
Department of Environmental Sciences, University of California Riverside, CA, 92521, United States.; Department of Environmental Sciences, University of California Riverside, CA, 92521, United States; Graduate Program in Environmental Toxicology, University of California, Riverside, CA, 92521, United States.; Department of Environmental Sciences, University of California Riverside, CA, 92521, United States. Electronic address: jgan@ucr.edu.
Treated wastewater is increasingly used to meet agriculture's water needs; however, treated wastewater contains numerous contaminants of emerging concern (CECs). With exposure and uptake of CECs, phytotoxicity and health of crop plants is of concern, but is poorly understood. This study evaluated the effect of low-dose, chronic exposure to a mixture of 10 CECs, including 4 antibiotics, 3 anti-inflammatory drugs, 1 antiepileptic, 1 beta-blocker, and 1 antimicrobial, on lettuce (Lactuca sativa) and cucumber (Cucumis sativa L.) plants. The CEC mixture was added in nutrient media at 1 to 20X of their typical levels in treated wastewater effluents. Biological endpoints including germination, growth, phytohormone homeostasis, and CEC bioaccumulation were determined. Exposure to the CEC mixture did not affect the germination rate of lettuce seeds, but stimulated root elongation and increased the root-to-shoot biomass ratio during a 7d cultivation. A dose-dependent decrease in biomass was observed in cucumber seedling after a 30d exposure, with the highest rate CEC treatment resulting in decreases of 51.2+/-20.9, 26.3+/-34.1, and 33.2+/-41.7% in the below-ground, above-ground, and total biomass, respectively. Levels of abscisic acid were significantly elevated (p<0.05) in the leaves, but decreased (p<0.05) in the roots. The dose-response of auxin was characterized by a hormesis effect. A significant 6-fold increase in the stem auxin level was observed at the 1X CEC rate, followed by a decrease to 2-fold the control at the 20X rate. Leaf auxin concentrations also significantly increased at the 1X CEC rate to 16-fold, followed by a decrease at the highest CEC rate. The results of this study suggeste that chronic exposure to low levels of CEC mixtures may compromise the fitness of plants, and the impairments are underlined by alterations in hormone balances.
PMID: 31185360
Plant J , IF:6.141 , 2019 Sep , V99 (6) : P1159-1171 doi: 10.1111/tpj.14412
Rosa hybrida RhERF1 and RhERF4 mediate ethylene- and auxin-regulated petal abscission by influencing pectin degradation.
Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, 100193, China.; Robert W. Holley Center for Agriculture and Health, United States Department of Agriculture, Agricultural Research Service, Ithaca, 14853, NY, USA.; Boyce Thompson Institute, Ithaca, 14853, NY, USA.; Crops Pathology and Genetic Research Unit, United States Department of Agriculture, Agricultural Research Service, Davis, 95616, CA, USA.; Department of Plant Sciences, University of California at Davis, Davis, 95616, CA, USA.
The timing of plant organ abscission is modulated by the balance of two hormones, ethylene and auxin, while the mechanism of organ shedding depends on the loss of middle lamella pectin in the abscission zone (AZ). However, the mechanisms involved in sensing the balance of auxin and ethylene and that affect pectin degradation during abscission are not well understood. In this study, we identified two members of the APETALA2/ethylene-responsive factor (AP2/ERF) transcription factor family in rose (Rosa hybrida), RhERF1 and RhERF4 which play a role in petal abscission. The expression of RhERF1 and RhERF4 was influenced by ethylene and auxin, respectively. Reduced expression of RhERF1 or RhERF4 was observed to accelerate petal abscission. Global expression analysis and real-time PCR assays revealed that RhERF1 and RhERF4 modulate the expression of genes encoding pectin-metabolizing enzymes. A reduction in the abundance of pectin epitopes was detected in the AZs of RhERF1 and RhERF4-silenced plants by immunofluorescence microscopy analysis. In addition, RhERF1 and RhERF4 were shown to bind to the promoter of the pectin-metabolizing gene beta-GALACTOSIDASE 1 (RhBGLA1), and reduced expression of RhBGLA1 delayed petal abscission. We conclude that during petal abscission, RhERF1 and RhERF4 integrate and coordinate ethylene and auxin signals to modulate pectin metabolism, in part by regulating the expression of RhBGLA1.
PMID: 31111587
Ying Yong Sheng Tai Xue Bao , IF:5.84 , 2019 Sep , V30 (9) : P3137-3144 doi: 10.13287/j.1001-9332.201909.030
[Effects of partial root-zone irrigation and rational close planting on yield and water productivity of cotton in arid area.]
Cotton Research Center/Shandong Key Laboratory for Cotton Culture and Physio-logy/Shandong Academy of Agricultural Sciences, Ji'nan 250100, China.
The objective of this study was to evaluate the effects and underlying physiological mecha-nisms of partial root zone irrigation (PRI) and rational close planting, as well as their interaction on yield and water productivity (WP) of cotton and to explore new alternatives of water-saving irrigation in dry land areas. A factorial field experiment with irrigation mode (normal irrigation, partial root-zone irrigation and deficient irrigation) and plant population density (135000, 180000 and 225000 plants.hm(-2)) was conducted in the west of Inner Mongolia to examine their effects on cotton growth, yield, water productivity and related physiological characters. The results showed that the irrigation mode and plant density as well as their interaction significantly affected the biomass, yield, yield components and harvest index. Under normal irrigation, the biomass and the number of bolls per unit area increased with the increasing of plant density, but the harvest index and boll weight significantly reduced. The yield of high plant density was comparable to that of medium plant density, both of which were increased significantly compared with that of low plant density. The content of abscisic acid (ABA) significantly increased and that of auxin (IAA) significantly reduced in cotton leaves under partial root-zone irrigation, which significantly increased the harvest index by improving the partitioning of assimilates to reproductive organs under partial root-zone irrigation. The number of bolls per unit area increased and boll mass remained unchanged with the increasing of density under partial root-zone irrigation. The yield of high density increased by 6.7% and 11.5% compared with that of medium and low density under partial root zone irrigation. The pre-frost seed cotton increased by 22.5%, the amount of irrigation reduced by 30%, and water productivity increased by 49.3% under partial root zone irrigation compared with that under normal irrigation at high plant density. Plant density did not affect photosynthetic rate (Pn) of functional leaves, but irrigation mode significantly affected Pn. Deficient irrigation significantly reduced the Pn of the main-stem functional leaves, but the Pn under partial root-zone irrigation was comparable to that of normal irrigation. The jasmonate (JA) content and the expression level of plasma membrane intrinsic protein (PIP) gene were significantly increased in the hydrated root under partial root-zone irrigation compared with those under normal irrigation. The results suggested that the increased JA content, as a signal molecule, up-regulated the expression level of PIP gene in dehydrated root and increased water uptake capacity of roots and guaranteed water balance of leaves, and then contributed to a relatively high Pn. Partial root-zone irrigation combined with relatively high plant density (225000 plants.hm(-2)) is an important agronomic alternative for water saving in cotton plantation in the dry land areas.
PMID: 31529889
Development , IF:5.611 , 2019 Sep , V146 (17) doi: 10.1242/dev.183590
The people behind the papers - Qiang Zhu, Marcal Gallemi and Eva Benkova.
The apical hook is a transient structure that functions to protect the vulnerable apical meristem from damage when the seedling penetrates the soil. Although some of the molecular players regulating its development have been identified, many aspects have remained opaque, including how an early auxin asymmetry in the hypocotyl is established. A paper in Development now provides a link between hormone signalling and the gravitropic response of the seedling's growing root in apical hook development. We caught up with co-first authors Qiang Zhu and Marcal Gallemi and their supervisor Eva Benkova, Professor at the Institute of Science and Technology Austria in Klosterneuberg, to find out more about the project.
PMID: 31515442
Development , IF:5.611 , 2019 Sep , V146 (17) doi: 10.1242/dev.177097
Abiotic stress modulates root patterning via ABA-regulated microRNA expression in the endodermis initials.
School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv 6997801, Israel.; The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, The Hebrew University of Jerusalem, Rehovot 7610001, Israel.; School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv 6997801, Israel shauly@tauex.tau.ac.il.
Patterning of the root xylem into protoxylem (PX) and metaxylem is regulated by auxin-cytokinin signaling and microRNA miR165a/166b-mediated suppression of genes encoding Class III HOMEODOMAIN LEU-ZIPPER (HD-ZIPIII) proteins. We found that, in Arabidopsis, osmotic stress via core abscisic acid (ABA) signaling in meristematic endodermal cells induces differentiation of PX in radial and longitudinal axes in association with increased VND7 expression. Similarly, in tomato, ABA enhanced PX differentiation longitudinally and radially, indicating an evolutionarily conserved mechanism. ABA increased expression of miR165a/166b and reduced expression of the miR165a/166b repressor ZWILLE (ZLL) (also known as ARGONAUTE10), resulting in reduced levels of all five HD-ZIPIII RNAs. ABA treatments failed to induce additional PX files in a miR165a/166b-resistant PHB mutant, phb1-d, and in scr and shr mutants, in which miR165a/166b expression is strongly reduced. Thus, ABA regulates xylem patterning and maturation via miR165a/166b-regulated expression of HD-ZIPIII mRNAs and associated VND7 levels. In lateral root initials, ABA induced an increase in miR165a levels in endodermal precursors and inhibited their reduction in the future quiescent center specifically at pre-emergence stage. Hence, ABA-induced inhibition of lateral root is associated with reduced HD-ZIPIII levels.
PMID: 31399468
Development , IF:5.611 , 2019 Sep , V146 (17) doi: 10.1242/dev.175919
Root gravity response module guides differential growth determining both root bending and apical hook formation in Arabidopsis.
Basic Forestry & Proteomics Center (BFPC), College of Forestry, Fujian Agriculture and Forestry University, 350002 Fuzhou, China.; Institute of Science and Technology Austria, Klosterneuburg, 3400, Austria.; Laboratory of Growth Regulators, Institute of Experimental Botany ASCR & Palacky University Olomouc, CZ-771 47, Czech Republic.; Department of Plant Systems Biology, VIB, 9052 Gent, Belgium.; Institute of Science and Technology Austria, Klosterneuburg, 3400, Austria eva.benkova@ist.ac.at.
The apical hook is a transiently formed structure that plays a protective role when the germinating seedling penetrates through the soil towards the surface. Crucial for proper bending is the local auxin maxima, which defines the concave (inner) side of the hook curvature. As no sign of asymmetric auxin distribution has been reported in embryonic hypocotyls prior to hook formation, the question of how auxin asymmetry is established in the early phases of seedling germination remains largely unanswered. Here, we analyzed the auxin distribution and expression of PIN auxin efflux carriers from early phases of germination, and show that bending of the root in response to gravity is the crucial initial cue that governs the hypocotyl bending required for apical hook formation. Importantly, polar auxin transport machinery is established gradually after germination starts as a result of tight root-hypocotyl interaction and a proper balance between abscisic acid and gibberellins.This article has an associated 'The people behind the papers' interview.
PMID: 31391194
PLoS Genet , IF:5.174 , 2019 Sep , V15 (9) : Pe1008400 doi: 10.1371/journal.pgen.1008400
Evolution of the Auxin Response Factors from charophyte ancestors.
Laboratoire de Reproduction et Developpement des Plantes, Univ. Lyon, ENS de Lyon, UCB Lyon1, CNRS, INRA, Lyon, France.; Univ. Grenoble Alpes, CNRS, CEA, INRA, IRIG-DBSCI-LPCV, Grenoble, France.
Auxin is a major developmental regulator in plants and the acquisition of a transcriptional response to auxin likely contributed to developmental innovations at the time of water-to-land transition. Auxin Response Factors (ARFs) Transcription Factors (TFs) that mediate auxin-dependent transcriptional changes are divided into A, B and C evolutive classes in land plants. The origin and nature of the first ARF proteins in algae is still debated. Here, we identify the most 'ancient' ARF homologue to date in the early divergent charophyte algae Chlorokybus atmophyticus, CaARF. Structural modelling combined with biochemical studies showed that CaARF already shares many features with modern ARFs: it is capable of oligomerization, interacts with the TOPLESS co-repressor and specifically binds Auxin Response Elements as dimer. In addition, CaARF possesses a DNA-binding specificity that differs from class A and B ARFs and that was maintained in class C ARF along plants evolution. Phylogenetic evidence together with CaARF biochemical properties indicate that the different classes of ARFs likely arose from an ancestral proto-ARF protein with class C-like features. The foundation of auxin signalling would have thus happened from a pre-existing hormone-independent transcriptional regulation together with the emergence of a functional hormone perception complex.
PMID: 31553720
PLoS Genet , IF:5.174 , 2019 Sep , V15 (9) : Pe1008366 doi: 10.1371/journal.pgen.1008366
Natural variation in Arabidopsis shoot branching plasticity in response to nitrate supply affects fitness.
Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom.; Department of Biology, University of York, York, United Kingdom.; Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, United Kingdom.
The capacity of organisms to tune their development in response to environmental cues is pervasive in nature. This phenotypic plasticity is particularly striking in plants, enabled by their modular and continuous development. A good example is the activation of lateral shoot branches in Arabidopsis, which develop from axillary meristems at the base of leaves. The activity and elongation of lateral shoots depends on the integration of many signals both external (e.g. light, nutrient supply) and internal (e.g. the phytohormones auxin, strigolactone and cytokinin). Here, we characterise natural variation in plasticity of shoot branching in response to nitrate supply using two diverse panels of Arabidopsis lines. We find extensive variation in nitrate sensitivity across these lines, suggesting a genetic basis for variation in branching plasticity. High plasticity is associated with extreme branching phenotypes such that lines with the most branches on high nitrate have the fewest under nitrate deficient conditions. Conversely, low plasticity is associated with a constitutively moderate level of branching. Furthermore, variation in plasticity is associated with alternative life histories with the low plasticity lines flowering significantly earlier than high plasticity lines. In Arabidopsis, branching is highly correlated with fruit yield, and thus low plasticity lines produce more fruit than high plasticity lines under nitrate deficient conditions, whereas highly plastic lines produce more fruit under high nitrate conditions. Low and high plasticity, associated with early and late flowering respectively, can therefore be interpreted alternative escape vs mitigate strategies to low N environments. The genetic architecture of these traits appears to be highly complex, with only a small proportion of the estimated genetic variance detected in association mapping.
PMID: 31539368
J Integr Plant Biol , IF:4.885 , 2019 Sep , V61 (9) : P966-967 doi: 10.1111/jipb.12860
A defect in the PINOID serine/threonine kinase affects leaf shape in cucumber.
Science Editor, Peridot Scientific Communications, 2958 North Kilbourn Ave., Chicago, 60641, USA.
Leaf shape has important implications for optimizing plant architecture for grain crops and horticultural crops. Examination of the cucumber (Cucumis sativus L.) round leaf (rl) mutant by Song et al. (2019) revealed that the PINOID protein kinase affects leaf shape by altering auxin biosynthesis, transport, and signaling.
PMID: 31359619
J Integr Plant Biol , IF:4.885 , 2019 Sep , V61 (9) : P968-973 doi: 10.1111/jipb.12760
ESCRT-dependent vacuolar sorting and degradation of the auxin biosynthetic enzyme YUC1 flavin monooxygenase.
National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.; Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA 92093-0116, USA.; School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China.; Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou 510631, China.
YUC flavin monooxygenases catalyze the rate-limiting step of auxin biosynthesis. Here we report the vacuolar targeting and degradation of GFP-YUC1. GFP-YUC1 fusion expressed in Arabidopsis protoplasts or transgenic plants was primarily localized in vacuoles. Surprisingly, we established that GFP-YUC1, a soluble protein, was sorted to vacuoles through the ESCRT pathway, which has long been recognized for sorting and targeting integral membrane proteins. We further show that GFP-YUC1 was ubiquitinated and in this form GFP-YUC1 was targeted for degradation, a process that was also stimulated by elevated auxin levels. Our findings revealed a molecular mechanism of GFP-YUC1 degradation and demonstrate that the ESCRT pathway can recognize both soluble and integral membrane proteins as cargoes.
PMID: 30565393
J Integr Plant Biol , IF:4.885 , 2019 Sep , V61 (9) : P1000-1014 doi: 10.1111/jipb.12739
A leaf shape mutant provides insight into PINOID Serine/Threonine Kinase function in cucumber (Cucumis sativus L.).
State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
Optimizing leaf shape is a major challenge in efforts to develop an ideal plant type. Cucumber leaf shapes are diverse; however, the molecular regulatory mechanisms underlying leaf shape formation are unknown. In this study, we obtained a round leaf mutant (rl) from an ethyl methanesulfonate-induced mutagenesis population. Genetic analysis revealed that a single recessive gene, rl, is responsible for this mutation. A modified MutMap analysis combined linkage mapping identified a single nucleotide polymorphism within a candidate gene, Csa1M537400, as the mutation underlying the trait. Csa1M537400 encodes a PINOID kinase protein involved in auxin transport. Expression of Csa1M537400 was significantly lower in the rl mutant than in wild type, and it displayed higher levels of IAA (indole-3-acetic acid) in several tissues. Treatment of wild-type plants with an auxin transport inhibitor induced the formation of round leaves, similar to those in the rl mutant. Altered expression patterns of several auxin-related genes in the rl mutant suggest that rl plays a key role in auxin biosynthesis, transport, and response in cucumber. These findings provide insight into the molecular mechanism underlying the regulation of auxin signaling pathways in cucumber, and will be valuable in the development of an ideal plant type.
PMID: 30421569
J Integr Plant Biol , IF:4.885 , 2019 Sep , V61 (9) : P1015-1031 doi: 10.1111/jipb.12735
Arabidopsis ANAC092 regulates auxin-mediated root development by binding to the ARF8 and PIN4 promoters.
State Key Laboratory of Genetic Engineering, Institute of Genetics, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China.
Auxin is an important plant hormone that is essential for growth and development due to its effects on organogenesis, morphogenesis, tropisms, and apical dominance. The functional diversity of auxin highlights the importance of its biosynthesis, transport, and associated responses. In this study, we show that a NAC transcription factor, ANAC092 (also named AtNAC2 and ORESARA1), known to positively regulate leaf senescence and contribute to abiotic stress responses, also affects primary root development. Plants overexpressing ANAC092 had altered root meristem lengths and shorter primary roots compared with the wild-type control. Additionally, expression of the proANAC092::GUS was strongly induced by indole-3-acetic acid. Quantitative real-time RT-PCR (qRT-PCR) analysis revealed that the YUCCA2, PIN, and ARF expression levels were downregulated in ANAC092-overexpressing plants. Moreover, yeast one-hybrid and chromatin immunoprecipitation assays confirmed that ANAC092 binds to the promoters of AUXIN RESPONSE FACTOR 8 (ARF8) and PIN-FORMED 4 (PIN4). Furthermore, a dual-luciferase assay indicated that ANAC092 decreases ARF8 and PIN4 promoter activities. We also applied a CRISPR/Cas9 system to mutate ANAC092. The roots of three of the analyzed mutants were longer than normal. Collectively, our findings indicate that ANAC092 negatively affects root development by controlling the auxin pathway.
PMID: 30415491
Int J Mol Sci , IF:4.556 , 2019 Sep , V20 (19) doi: 10.3390/ijms20194817
Auxin-Induced Adventitious Root Formation in Nodal Cuttings of Camellia sinensis.
Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, National Center for Tea Improvement, Tea Research Institute Chinese Academy of Agricultural Sciences (TRICAAS), Hangzhou 310008, China. weikang@tricaas.com.; Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, National Center for Tea Improvement, Tea Research Institute Chinese Academy of Agricultural Sciences (TRICAAS), Hangzhou 310008, China. ruanli@tricaas.com.; Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, National Center for Tea Improvement, Tea Research Institute Chinese Academy of Agricultural Sciences (TRICAAS), Hangzhou 310008, China. wangly@tricaas.com.; Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, National Center for Tea Improvement, Tea Research Institute Chinese Academy of Agricultural Sciences (TRICAAS), Hangzhou 310008, China. chenghao@tricaas.com.
Adventitious root (AR) formation is essential for the successful propagation of Camellia sinensis and auxins play promotive effects on this process. Nowadays, the mechanism of auxin-induced AR formation in tea cuttings is widely studied. However, a lack of global view of the underlying mechanism has largely inhibited further studies. In this paper, recent advances including endogenous hormone changes, nitric oxide (NO) and hydrogen peroxide (H2O2) signals, secondary metabolism, cell wall reconstruction, and mechanisms involved in auxin signaling are reviewed. A further time course analysis of transcriptome changes in tea cuttings during AR formation is also suggested to deepen our understanding. The purpose of this paper is to offer an overview on the most recent developments especially on those key aspects affected by auxins and that play important roles in AR formation in tea plants.
PMID: 31569758
Int J Mol Sci , IF:4.556 , 2019 Sep , V20 (19) doi: 10.3390/ijms20194816
Expression and Distribution of the Auxin Response Factors in Sorghum bicolor During Development and Temperature Stress.
School of Life Science and Technology, Xidian University, Xi'an 710126, China. dchen@xidian.edu.cn.; School of Life Science and Technology, Xidian University, Xi'an 710126, China. weian02.wang@gmail.com.; School of Life Science and Technology, Xidian University, Xi'an 710126, China. wuyq@ascend-bio.com.; School of Life Science and Technology, Xidian University, Xi'an 710126, China. hxie@xidian.edu.cn.; School of Life Science and Technology, Xidian University, Xi'an 710126, China. linfeizhao1@gmail.com.; School of Life Science and Technology, Xidian University, Xi'an 710126, China. qizeng@xidian.edu.cn.; School of Life Science and Technology, Xidian University, Xi'an 710126, China. yhzhan@xidian.edu.cn.
Auxin response factor (ARF) is a transcription factor that can specifically bind to the promoter of auxin-responsive genes in plants and plays an important regulatory role in plant growth and development. The previous studies have predicted 25 ARF genes in Sorghum bicolor (SbARFs) and indicated that SbARFs play complex roles in salt and drought stresses. In this study, we reclassified and analyzed the structures of ARFs in three plants, including sorghum, rice, and Arabidopsis. Phylogenetic analyses categorized 73 ARF into five classes. By studying the characterization of the structures, it was found that SbARFs from the same evolutionary branches showed similar motif patterns. Furthermore, the expression patterns of SbARF genes during development and temperature stress were investigated in sorghum. Quantitative transcription-quantitative polymerase chain reaction (qRT-PCR) results suggested that they had different expression patterns in vegetative and reproductive organs at various developmental stages. High and low-temperature treatments and qRT-PCR demonstrated some of them changed dramatically along with the increase of treatment time. Additionally, in situ hybridization results displayed that SbARF genes were accumulated in vascular tissues under temperature stress. These findings provide evidence that SbARFs may play important roles in sorghum vegetative development, reproductive development, and auxin response to temperature stress.
PMID: 31569745
Int J Mol Sci , IF:4.556 , 2019 Sep , V20 (19) doi: 10.3390/ijms20194806
Molecular Characterization of the Transcription Factors in Susceptible Poplar Infected with Virulent Melampsora larici-populina.
School of Forestry, Northeast Forestry University, Harbin 150040, China. qiaolichen@nefu.edu.cn.; School of Forestry, Northeast Forestry University, Harbin 150040, China. wangjianan@nefu.edu.cn.; School of Forestry, Northeast Forestry University, Harbin 150040, China. danleili@nefu.edu.cn.; Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, Northeast Forestry University, Harbin 150040, China. danleili@nefu.edu.cn.; School of Forestry, Northeast Forestry University, Harbin 150040, China. zhiyingwang@nefu.edu.cn.; School of Forestry, Northeast Forestry University, Harbin 150040, China. fengwang@nefu.edu.cn.; Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, Northeast Forestry University, Harbin 150040, China. fengwang@nefu.edu.cn.; School of Forestry, Northeast Forestry University, Harbin 150040, China. zhangruizhi1993@163.com.
Transcription factors (TFs) have been shown to play important roles in determining poplar susceptibility. In this study, the transcript profiles of five resistance-related TF groups at different time points were investigated to study the roles of TFs in the compatible interaction between 'Robusta' (Populus nigra x P. deltoides) and the virulent E4 race of Melampsora larici-populina. The susceptibility test indicated that the parasitic process of E4 could be divided into two representative time periods: the infection phase and the production phase. Bioinformatics analysis showed that in these two phases, E4 infection induced a network of TFs in 'Robusta'. Although some TFs responded rapidly and positively, most TFs did not respond to E4, especially during the infection phase. The ethylene, jasmonic acid, and auxin pathways were downregulated, while a calcium-binding protein was upregulated. No other significantly changed phytohormone-related genes were found, which was consistent with the pathological process in the absence of an immune response, suggesting that the lack of response of most TFs during the infection phase of E4 is related to the susceptibility of 'Robusta'.
PMID: 31569685
Int J Mol Sci , IF:4.556 , 2019 Sep , V20 (19) doi: 10.3390/ijms20194703
Genome-Wide Analysis and Identification of the Aux/IAA Gene Family in Peach.
Beijing Key Laboratory of New Technique in Agricultural Application, Beijing University of Agriculture, Beijing 102206, China. guanadan@hotmail.com.; College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China. guanadan@hotmail.com.; Beijing Key Laboratory of New Technique in Agricultural Application, Beijing University of Agriculture, Beijing 102206, China. hxiao_0323@sina.com.; College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China. hxiao_0323@sina.com.; College of Bioscience and Resources Environment, Beijing University of Agriculture, Beijing 102206, China. 18210853628@163.com.; Food science and Engineering College, Beijing University of Agriculture, Beijing 102206, China. fangwang1973@sina.com.; College of Bioscience and Resources Environment, Beijing University of Agriculture, Beijing 102206, China. liuyueping@bua.edu.cn.; Key Laboratory for Northern Urban Agriculture Ministry of Agriculture and Rural Affairs, Beijing University of Agriculture, Beijing 102206, China. liuyueping@bua.edu.cn.
The Auxin/indole-3-acetic acid (Aux/IAA) repressor genes down-regulate the auxin response pathway during many stages of plant and fruit development. In order to determine if and how Aux/IAAs participate in governing texture and hardness in stone fruit maturation, we identified 23 Aux/IAA genes in peach, confirmed by the presence of four conserved domains. In this work, we used fluorescence microscopy with PpIAA-GFP fusion reporters to observe their nuclear localization. We then conducted PCR-based differential expression analysis in "melting" and "stony hard" varieties of peach, and found that in the "melting" variety, nine PpIAAs exhibited peak expression in the S4-3 stage of fruit maturation, with PpIAA33 showing the highest (>120-fold) induction. The expression of six PpIAAs peaked in the S4-2 stage, with PpIAA14 expressed the most highly. Only PpIAA15/16 showed higher expression in the "stony hard" variety than in the "melting" variety, both peaking in the S3 stage. In contrast, PpIAA32 had the highest relative expression in buds, flowers, young and mature leaves, and roots. Our study provides insights into the expression patterns of Aux/IAA developmental regulators in response to auxin during fruit maturation, thus providing insight into their potential development as useful markers for quantitative traits associated with fruit phenotype.
PMID: 31547521
Int J Mol Sci , IF:4.556 , 2019 Sep , V20 (18) doi: 10.3390/ijms20184586
The miRNA-mRNA Networks Involving Abnormal Energy and Hormone Metabolisms Restrict Tillering in a Wheat Mutant dmc.
National Centre of Engineering and Technological Research for Wheat/Key Laboratory of Physiological Ecology and Genetic Improvement of Food Crops in Henan Province, Henan Agricultural University, Zhengzhou 450046, China. jhan68@163.com.; Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China. m15927306510@163.com.; Shangqiu Academy of Agricultural and Forestry Sciences, Shangqiu 476000, China. nyj317@163.com.; National Centre of Engineering and Technological Research for Wheat/Key Laboratory of Physiological Ecology and Genetic Improvement of Food Crops in Henan Province, Henan Agricultural University, Zhengzhou 450046, China. nxyjym@henau.edu.cn.; National Centre of Engineering and Technological Research for Wheat/Key Laboratory of Physiological Ecology and Genetic Improvement of Food Crops in Henan Province, Henan Agricultural University, Zhengzhou 450046, China. 13253817312@stu.henau.edu.cn.; National Centre of Engineering and Technological Research for Wheat/Key Laboratory of Physiological Ecology and Genetic Improvement of Food Crops in Henan Province, Henan Agricultural University, Zhengzhou 450046, China. guomai301@163.com.; National Centre of Engineering and Technological Research for Wheat/Key Laboratory of Physiological Ecology and Genetic Improvement of Food Crops in Henan Province, Henan Agricultural University, Zhengzhou 450046, China. chang_top@163.com.; National Centre of Engineering and Technological Research for Wheat/Key Laboratory of Physiological Ecology and Genetic Improvement of Food Crops in Henan Province, Henan Agricultural University, Zhengzhou 450046, China. zxjiao2018@163.com.; National Centre of Engineering and Technological Research for Wheat/Key Laboratory of Physiological Ecology and Genetic Improvement of Food Crops in Henan Province, Henan Agricultural University, Zhengzhou 450046, China. jzhang1023@126.com.; National Centre of Engineering and Technological Research for Wheat/Key Laboratory of Physiological Ecology and Genetic Improvement of Food Crops in Henan Province, Henan Agricultural University, Zhengzhou 450046, China. lhj19960901@163.com.; National Centre of Engineering and Technological Research for Wheat/Key Laboratory of Physiological Ecology and Genetic Improvement of Food Crops in Henan Province, Henan Agricultural University, Zhengzhou 450046, China. liqiaoyun@henau.edu.cn.; National Centre of Engineering and Technological Research for Wheat/Key Laboratory of Physiological Ecology and Genetic Improvement of Food Crops in Henan Province, Henan Agricultural University, Zhengzhou 450046, China. jsniu@263.net.
Tillers not only determine plant architecture but also influence crop yield. To explore the miRNA regulatory network restraining tiller development in a dwarf-monoculm wheat mutant (dmc) derived from Guomai 301 (wild type, WT), we employed miRNome and transcriptome integrative analysis, real-time qRT-PCR, histochemistry, and determinations of the key metabolites and photosynthesis parameters. A total of 91 differentially expressed miRNAs (DEMs) were identified between dmc and WT. Among them, 40 key DEMs targeted 45 differentially expressed genes (DEGs) including the key DEGs encode growth-regulating factors (GRF), auxin response factors (ARF), and other proteins involved in the metabolisms of hormones and carbohydrates, etc. Compared with WT, both the chlorophyll contents and the photosynthesis rate were lower in dmc. The contents of glucose, sucrose, fructose, and maltose were lower in dmc. The contents of auxin (IAA) and zeatin (ZA) were significantly lower, but gibberellin (GA) was significantly higher in the tiller tissues of dmc. This research demonstrated that the DEMs regulating hormone and carbohydrate metabolisms were important causes for dmc to not tiller. A primary miRNA-mRNA regulatory model for dmc tillering was established. The lower photosynthesis rate, insufficient energy, and abnormal hormone metabolisms restrict tillering in dmc.
PMID: 31533225
Int J Mol Sci , IF:4.556 , 2019 Sep , V20 (18) doi: 10.3390/ijms20184469
Jasmonic Acid Methyl Ester Induces Xylogenesis and Modulates Auxin-Induced Xylary Cell Identity with NO Involvement.
Department of Environmental Biology, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy. federica.dellarovere@uniroma1.it.; Department of Environmental Biology, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy. laura.fattorini@uniroma1.it.; Department of Environmental Biology, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy. marilena.ronzan@uniroma1.it.; Department of Environmental Biology, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy. giuseppina.falasca@uniroma1.it.; Department of Environmental Biology, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy. mariamaddalena.altamura@uniroma1.it.; Department of Medicine, University of Perugia, Piazzale Menghini 8/9, 06132 Perugia, Italy. camilla.betti@unipg.it.
In Arabidopsis basal hypocotyls of dark-grown seedlings, xylary cells may form from the pericycle as an alternative to adventitious roots. Several hormones may induce xylogenesis, as Jasmonic acid (JA), as well as indole-3-acetic acid (IAA) and indole-3-butyric acid (IBA) auxins, which also affect xylary identity. Studies with the ethylene (ET)-perception mutant ein3eil1 and the ET-precursor 1-aminocyclopropane-1-carboxylic acid (ACC), also demonstrate ET involvement in IBA-induced ectopic metaxylem. Moreover, nitric oxide (NO), produced after IBA/IAA-treatments, may affect JA signalling and interact positively/negatively with ET. To date, NO-involvement in ET/JA-mediated xylogenesis has never been investigated. To study this, and unravel JA-effects on xylary identity, xylogenesis was investigated in hypocotyls of seedlings treated with JA methyl-ester (JAMe) with/without ACC, IBA, IAA. Wild-type (wt) and ein3eil1 responses to hormonal treatments were compared, and the NO signal was quantified and its role evaluated by using NO-donors/scavengers. Ectopic-protoxylem increased in the wt only after treatment with JAMe(10 muM), whereas in ein3eil1 with any JAMe concentration. NO was detected in cells leading to either xylogenesis or adventitious rooting, and increased after treatment with JAMe(10 muM) combined or not with IBA(10 muM). Xylary identity changed when JAMe was applied with each auxin. Altogether, the results show that xylogenesis is induced by JA and NO positively regulates this process. In addition, NO also negatively interacts with ET-signalling and modulates auxin-induced xylary identity.
PMID: 31510080
Int J Mol Sci , IF:4.556 , 2019 Sep , V20 (18) doi: 10.3390/ijms20184429
IBR5 Regulates Leaf Serrations Development via Modulation of the Expression of PIN1.
Plant Biotechnology Research Center, School of Agriculture and Life Sciences, Shanghai Jiao Tong University, Shanghai 200240, China. kzxiuzhen@163.com.; State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China. huang19880901@126.com.; Plant Biotechnology Research Center, School of Agriculture and Life Sciences, Shanghai Jiao Tong University, Shanghai 200240, China. tianruoyou@sjtu.edu.cn.; Plant Biotechnology Research Center, School of Agriculture and Life Sciences, Shanghai Jiao Tong University, Shanghai 200240, China. zhao13817438337@sjtu.edu.cn.; Plant Biotechnology Research Center, School of Agriculture and Life Sciences, Shanghai Jiao Tong University, Shanghai 200240, China. rexue997@126.com.; Plant Biotechnology Research Center, School of Agriculture and Life Sciences, Shanghai Jiao Tong University, Shanghai 200240, China. songxiaoyun67@163.com.; National Institute of Plant Genome Research, New Delhi 110067, India. jitender@nipgr.ac.in.; Plant Biotechnology Research Center, School of Agriculture and Life Sciences, Shanghai Jiao Tong University, Shanghai 200240, China. kjzuo@sjtu.edu.cn.
Biodiversity in plant shape is mainly attributable to the diversity of leaf shape, which is largely determined by the transient morphogenetic activity of the leaf margin that creates leaf serrations. However, the precise mechanism underlying the establishment of this morphogenetic capacity remains poorly understood. We report here that INDOLE-3-BUTYRIC ACID RESPONSE 5 (IBR5), a dual-specificity phosphatase, is a key component of leaf-serration regulatory machinery. Loss-of-function mutants of IBR5 exhibited pronounced serrations due to increased cell area. IBR5 was localized in the nucleus of leaf epidermis and petiole cells. Introducing a C129S mutation within the highly conserved VxVHCx2GxSRSx5AYLM motif of IBR5 rendered it unable to rescue the leaf-serration defects of the ibr5-3 mutant. In addition, auxin reporters revealed that the distribution of auxin maxima was expanded ectopically in ibr5-3. Furthermore, we found that the distribution of PIN1 on the plasma membrane of the epidermal and cells around the leaf vein was compromised in ibr5-3. We concluded that IBR5 is essential for the establishment of PIN-FORMED 1 (PIN1)-directed auxin maxima at the tips of leaf serration, which is vital for the elaborated regulation during its formation.
PMID: 31505781
Int J Mol Sci , IF:4.556 , 2019 Sep , V20 (18) doi: 10.3390/ijms20184428
A DAO1-Mediated Circuit Controls Auxin and Jasmonate Crosstalk Robustness during Adventitious Root Initiation in Arabidopsis.
Umea Plant Science Centre, Department of Plant Physiology, Umea University, SE-90736 Umea, Sweden.; Laboratory of Growth Regulators, Faculty of Science, Palacky University and Institute of Experimental Botany, The Czech Academy of Sciences, 78371 Olomouc, Czech Republic.; Umea Plant Science Centre, Department of Forest Genetics and Physiology, Swedish Agriculture University, SE-90183 Umea, Sweden.; Umea Plant Science Centre, Department of Plant Physiology, Umea University, SE-90736 Umea, Sweden. Catherine.Bellini@umu.se.; Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Universite Paris-Saclay, FR-78000 Versailles, France. Catherine.Bellini@umu.se.
Adventitious rooting is a post-embryonic developmental program governed by a multitude of endogenous and environmental cues. Auxin, along with other phytohormones, integrates and translates these cues into precise molecular signatures to provide a coherent developmental output. Auxin signaling guides every step of adventitious root (AR) development from the early event of cell reprogramming and identity transitions until emergence. We have previously shown that auxin signaling controls the early events of AR initiation (ARI) by modulating the homeostasis of the negative regulator jasmonate (JA). Although considerable knowledge has been acquired about the role of auxin and JA in ARI, the genetic components acting downstream of JA signaling and the mechanistic basis controlling the interaction between these two hormones are not well understood. Here we provide evidence that COI1-dependent JA signaling controls the expression of DAO1 and its closely related paralog DAO2. In addition, we show that the dao1-1 loss of function mutant produces more ARs than the wild type, probably due to its deficiency in accumulating JA and its bioactive metabolite JA-Ile. Together, our data indicate that DAO1 controls a sensitive feedback circuit that stabilizes the auxin and JA crosstalk during ARI.
PMID: 31505771
iScience , IF:4.447 , 2019 Sep , V19 : P1179-1188 doi: 10.1016/j.isci.2019.09.004
Arabidopsis JANUS Regulates Embryonic Pattern Formation through Pol II-Mediated Transcription of WOX2 and PIN7.
State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, China.; State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, China; Department of Plant Biology and Ecology, College of Life Sciences, Nankai University, Tianjin, China. Electronic address: shali@sdau.edu.cn.
Embryonic pattern formation relies on positional coordination of cell division and specification. Early axis formation during Arabidopsis embryogenesis requires WUSCHEL RELATED HOMEOBOX (WOX)-mediated transcription activation and PIN-FORMED7 (PIN7)-mediated auxin asymmetry. How these events are regulated is obscure. We report that Arabidopsis JANUS, a putative subunit of spliceosome, is essential for embryonic pattern formation. Significantly reduced transcription but not mRNA processing of WOX2 and PIN7 in janus suggested its role in transcriptional regulation. JANUS interacts with RNA polymerase II (Pol II) through a region outside of its spliceosome-association domain. We further show that Pol II mediates the transcription of WOX2 and PIN7 in a JANUS-dependent way and is essential for embryonic pattern formation. These findings reveal that JANUS recruits Pol II for the activation of two parallel pathways to ensure proper pattern formation during embryogenesis.
PMID: 31542701
Theor Appl Genet , IF:4.439 , 2019 Sep , V132 (9) : P2663-2676 doi: 10.1007/s00122-019-03380-7
QTL analysis and candidate gene identification for plant height in cotton based on an interspecific backcross inbred line population of Gossypium hirsutum x Gossypium barbadense.
State Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, 455000, Henan, China.; College of Agriculture, Northwest A&F University, Yangling, 712100, Shanxi, China.; Xinjiang Research Base, State Key Laboratory of Cotton Biology, Xinjiang Agricultural University, Urumqi, 830001, China.; Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, 880033, USA. jinzhang@nmsu.edu.; State Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, 455000, Henan, China. ysx195311@163.com.; College of Agriculture, Northwest A&F University, Yangling, 712100, Shanxi, China. ysx195311@163.com.; State Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, 455000, Henan, China. yujw666@hotmail.com.
KEY MESSAGE: We constructed the first high-quality and high-density genetic linkage map for an interspecific BIL population in cotton by specific-locus amplified fragment sequencing for QTL mapping. A novel gene GhPIN3 for plant height was identified in cotton. Ideal plant height (PH) is important for improving lint yield and mechanized harvesting in cotton. Most published genetic studies on cotton have focused on fibre yield and quality traits rather than PH. To facilitate the understanding of the genetic basis in PH, an interspecific backcross inbred line (BIL) population of 250 lines derived from upland cotton (Gossypium hirsutum L.) CRI36 and Egyptian cotton (G. barbadense L.) Hai7124 was used to construct a high-density genetic linkage map for quantitative trait locus (QTL) mapping. The high-density genetic map harboured 7,709 genotyping-by-sequencing (GBS)-based single nucleotide polymorphism (SNP) markers that covered 3,433.24 cM with a mean marker interval of 0.67 cM. In total, ten PH QTLs were identified and each explained 4.27-14.92% of the phenotypic variation, four of which were stable as they were mapped in at least two tests or based on best linear unbiased prediction in seven field tests. Based on functional annotation of orthologues in Arabidopsis and transcriptome data for the genes within the stable QTL regions, GhPIN3 encoding for the hormone auxin efflux carrier protein was identified as a candidate gene located in the stable QTL qPH-Dt1-1 region. A qRT-PCR analysis showed that the expression level of GhPIN3 in apical tissues was significantly higher in four short-statured cotton genotypes than that in four tall-statured cotton genotypes. Virus-induced gene silencing cotton has significantly increased PH when the expression of the GhPIN3 gene was suppressed.
PMID: 31236630
J Agric Food Chem , IF:4.192 , 2019 Sep , V67 (37) : P10489-10497 doi: 10.1021/acs.jafc.9b03109
Design and Synthesis of Novel 4-Hydroxyl-3-(2-phenoxyacetyl)-pyran-2-one Derivatives for Use as Herbicides and Evaluation of Their Mode of Action.
School of Pharmacy , Liaocheng University , Liaocheng 252059 , China.; State Key Laboratory of Elemento-Organic Chemistry, Institute of Elemento-Organic Chemistry , Nankai University , Tianjin 300071 , China.; College of Agriculture , Shanxi Agricultural University , Jinzhong , Shanxi 030800 , China.
In order to develop a novel herbicide containing the beta-triketone motif, a series of 4-hydroxyl-3-(2-phenoxyacetyl)-pyran-2-one derivatives were designed and synthesized. The bioassay results showed that compound II15 had good pre-emergent herbicidal activity even at a dosage of 187.5 g ha(-1). Moreover, compound II15 showed a broader spectrum of weed control when compared with a commercial herbicide 2,4-dichlorophenoxyacetic acid (2,4-D), and displayed good crop safety to Triticum aestivum L. and Zea mays Linn. when applied at 375 g ha(-1) under pre-emergence conditions, which indicated its great potential as a herbicide. More importantly, studying the molecular mode of action of compound II15 revealed that the novel triketone structure is a proherbicide of its corresponding phenoxyacetic acid auxin herbicide, which has a herbicidal mechanism similar to that of 2,4-D. The present work indicates that the 4-hydroxyl-3-(2-phenoxyacetyl)-pyran-2-one motif may be a potential lead structure for further development of novel auxin-type herbicides.
PMID: 31452371
J Agric Food Chem , IF:4.192 , 2019 Sep , V67 (36) : P10010-10017 doi: 10.1021/acs.jafc.9b03988
Multiple Resistance to Synthetic Auxin Herbicides and Glyphosate in Parthenium hysterophorus Occurring in Citrus Orchards.
Department of Agricultural Chemistry and Edaphology , University of Cordoba , 14071 Cordoba , Spain.; Universidad Catolica Tecnologica del Cibao-UCATECI , La Vega 41000 , Republica Dominicana.; Department d'Hortofructicultura, Botanica i Jardineria, Agrotecnio , Universitat de Lleida , 25198 Lleida , Spain.; Departamento de Quimica , Universidade Federal de Sao Carlos , 13565-905 Sao Carlos , Brasil.
Dominican farmers have started to apply synthetic auxin herbicides (SAHs) as the main alternative to mitigate the impacts of the occurrence of glyphosate-resistant (GR) Parthenium hysterophorus populations in citrus orchards. A GR P. hysterophorus population survived field labeled rates of glyphosate, 2,4-dichlorophenoxyacetic acid (2,4-D), dicamba, and picloram, which showed poor control (<50%). In in vivo assays, resistance levels were high for glyphosate and moderate for picloram, dicamba, and 2,4-D. Sequencing the 5-enolpyruvylshikimate-3-phosphate synthase gene revealed the double Thr-102-Ile and Pro-106-Ser amino acid substitution, conferring resistance to glyphosate. Additionally, reduced absorption and impaired translocation contributed to this resistance. Regarding SAH, impaired 2,4-D transport and enhanced metabolism were confirmed in resistant plants. The application of malathion improved the efficacy of SAHs (control >50%), showing that metabolism of these herbicides was mediated by cytochrome P450 enzymes. This study reports, for the first time, multiple resistance to SAHs and glyphosate in P. hysterophorus.
PMID: 31414816
Microorganisms , IF:4.152 , 2019 Sep , V7 (10) doi: 10.3390/microorganisms7100403
Bacterial IAA-Delivery into Medicago Root Nodules Triggers a Balanced Stimulation of C and N Metabolism Leading to a Biomass Increase.
Institute of Biosciences and BioResources, via P. Castellino 111, 80131 Naples, Italy. roberto.defez@ibbr.cnr.it.; Institute of Biosciences and BioResources, via P. Castellino 111, 80131 Naples, Italy. anna.andreozzi@ibbr.cnr.it.; Institute of Biosciences and BioResources, via P. Castellino 111, 80131 Naples, Italy. silvia.romano@ibbr.cnr.it.; Institute of Biosciences and BioResources, via P. Castellino 111, 80131 Naples, Italy. gabriella.pocsfalvi@ibbr.cnr.it.; Institute of Biosciences and BioResources, via P. Castellino 111, 80131 Naples, Italy. immacolata.fiume@ibbr.cnr.it.; Institute of Genetics and Biophysics "A.B.T.", CNR, via P. Castellino 111, 80131 Naples, Italy. roberta.esposito@dbmr.unibe.ch.; Institute for Applied Mathematics "Mauro Picone" IAC, CNR, via P. Castellino 111, 80131 Naples, Italy. claudia.angelini@cnr.it.; Institute of Biosciences and BioResources, via P. Castellino 111, 80131 Naples, Italy. carmen.bianco@ibbr.cnr.it.
Indole-3-acetic acid (IAA) is the main auxin acting as a phytohormone in many plant developmental processes. The ability to synthesize IAA is widely associated with plant growth-promoting rhizobacteria (PGPR). Several studies have been published on the potential application of PGPR to improve plant growth through the enhancement of their main metabolic processes. In this study, the IAA-overproducing Ensifer meliloti strain RD64 and its parental strain 1021 were used to inoculate Medicago sativa plants. After verifying that the endogenous biosynthesis of IAA did not lead to genomic changes during the initial phases of the symbiotic process, we analyzed whether the overproduction of bacterial IAA inside root nodules influenced, in a coordinated manner, the activity of the nitrogen-fixing apparatus and the photosynthetic function, which are the two processes playing a key role in legume plant growth and productivity. Higher nitrogen-fixing activity and a greater amount of total nitrogen (N), carbon (C), Rubisco, nitrogen-rich amino acids, soluble sugars, and organic acids were measured for RD64-nodulated plants compared to the plants nodulated by the wild-type strain 1021. Furthermore, the RD64-nodulated plants showed a biomass increase over time, with the highest increment (more than 60%) being reached at six weeks after infection. Our findings show that the RD64-nodulated plants need more substrate derived from photosynthesis to generate the ATP required for their increased nitrogenase activity. This high carbohydrate demand further stimulates the photosynthetic function with the production of molecules that can be used to promote plant growth. We thus speculate that the use of PGPR able to stimulate both C and N metabolism with a balanced C/N ratio represents an efficient strategy to obtain substantial gains in plant productivity.
PMID: 31569530
Microorganisms , IF:4.152 , 2019 Sep , V7 (9) doi: 10.3390/microorganisms7090329
Maize Inoculation with Microbial Consortia: Contrasting Effects on Rhizosphere Activities, Nutrient Acquisition and Early Growth in Different Soils.
Institute of Crop Science (340h), Universitat Hohenheim, Fruwirthstrasse 20, 70593 Stuttgart, Germany. klara.bradacova@uni-hohenheim.de.; Julius Kuhn-Institut, Institute for Biological Control, Heinrichstrasse 243, 64287 Darmstadt, Germany. maximilian.sittinger@julius-kuehn.de.; Institute of Crop Science (340h), Universitat Hohenheim, Fruwirthstrasse 20, 70593 Stuttgart, Germany. katharina.tietz95@googlemail.com.; Institute of Crop Science (340h), Universitat Hohenheim, Fruwirthstrasse 20, 70593 Stuttgart, Germany. benjamin.neuhaeuser@uni-hohenheim.de.; Institute of Soil Science and Land Evaluation, Soil Biology Department, Universitat Hohenheim, Emil-Wolff-Strasse 27, 70593 Stuttgart, Germany. kandeler@uni-hohenheim.de.; EuroChem Agro GmbH, 8165 Mannheim, Germany. nils.berger@eurochemgroup.com.; Institute of Crop Science (340h), Universitat Hohenheim, Fruwirthstrasse 20, 70593 Stuttgart, Germany. u.ludewig@uni-hohenheim.de.; Institute of Crop Science (340h), Universitat Hohenheim, Fruwirthstrasse 20, 70593 Stuttgart, Germany. guenter.neumann@uni-hohenheim.de.
The benefit of plant growth-promoting microorganisms (PGPMs) as plant inoculants is influenced by a wide range of environmental factors. Therefore, microbial consortia products (MCPs) based on multiple PGPM strains with complementary functions, have been proposed as superior, particularly under challenging environmental conditions and for restoration of beneficial microbial communities in disturbed soil environments. To test this hypothesis, the performance of a commercial MCP inoculant based on 22 PGPM strains was investigated in greenhouse experiments with maize on three soils with contrasting pH, organic matter content and microbial activity, under different P and N fertilization regimes. Interestingly, the MCP inoculant stimulated root and shoot growth and improved the acquisition of macronutrients only on a freshly collected field soil with high organic matter content, exclusively in combination with stabilized ammonium fertilization. This was associated with transiently increased expression of AuxIAA5 in the root tissue, a gene responsive to exogenous auxin supply, suggesting root growth promotion by microbial auxin production as a major mode of action of the MCP inoculant. High microbial activity was indicated by intense expression of soil enzyme activities involved in C, N and P cycling in the rhizosphere (cellulase, leucine peptidase, alkaline and acid phosphatases) but without MCP effects. By contrast, the MCP inoculation did not affect maize biomass production or nutrient acquisition on soils with very little Corg and low microbial activity, although moderate stimulation of rhizosphere enzymes involved in N and P cycling was recorded. There was also no indication for MCP-induced solubilization of Ca-phosphates on a calcareous sub-soil fertilized with rock-phosphate. The results demonstrate that the combination of multiple PGPM strains with complementary properties as MCP inoculants does not necessarily translate into plant benefits in challenging environments. Thus, a better understanding of the conditions determining successful MCP application is mandatory.
PMID: 31500269
Biomolecules , IF:4.082 , 2019 Sep , V9 (10) doi: 10.3390/biom9100526
Two Auxin Response Elements Fine-Tune PINOID Expression During Gynoecium Development in Arabidopsis thaliana.
Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK. andre.kuhn@jic.ac.uk.; Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK. b.runciman@aol.co.uk.; Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK. billy.tasker-brown@jic.ac.uk.; Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK. lars.ostergaard@jic.ac.uk.
The plant hormone auxin controls almost all aspects of plant development through the gene regulatory properties of auxin response factors (ARFs) which bind so-called auxin responsive elements (AuxREs) in regulatory regions of their target genes. It has been proposed that ARFs interact and cooperate with other transcription factors (TFs) to bind to complex DNA-binding sites harboring cis-elements for several TFs. Complex DNA-binding sites have not been studied systematically for ARF target genes. ETTIN (ETT; ARF3) is a key regulator of gynoecium development. Cooperatively with its interacting partner INDEHISCENT (IND), ETT regulates PINOID (PID), a gene involved in the regulation gynoecium apical development (style development). Here, we mutated two ETT-bound AuxREs within the PID promoter and observed increased style length in gynoecia of plants carrying mutated promoter variants. Furthermore, mutating the AuxREs led to ectopic repression of PID in one developmental context while leading to ectopically upregulated PID expression in another stage. Our data also show that IND associates with the PID promoter in an auxin-sensitive manner. In summary, we demonstrate that targeted mutations of cis-regulatory elements can be used to dissect the importance of single cis-regulatory elements within complex regulatory regions supporting the importance of the ETT-IND interaction for PID regulation. At the same time, our work also highlights the challenges of such studies, as gene regulation is highly robust, and mutations within gene regulatory regions may only display subtle phenotypes.
PMID: 31557840
Biomolecules , IF:4.082 , 2019 Sep , V9 (10) doi: 10.3390/biom9100523
Combination of Transcriptomic, Proteomic, and Metabolomic Analysis Reveals the Ripening Mechanism of Banana Pulp.
Key Laboratory of Post-Harvest Handling of Fruits, Ministry of Agriculture/Guangdong Provincial Key Laboratory of Applied Botany/Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China. taotaoli@scbg.ac.cn.; Key Laboratory of Post-Harvest Handling of Fruits, Ministry of Agriculture/Guangdong Provincial Key Laboratory of Applied Botany/Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China. yunze@scbg.ac.cn.; Key Laboratory of Post-Harvest Handling of Fruits, Ministry of Agriculture/Guangdong Provincial Key Laboratory of Applied Botany/Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China. wuqixian@scbg.ac.cn.; University of Chinese Academy of Sciences, Beijing 100039, China. wuqixian@scbg.ac.cn.; Key Laboratory of Post-Harvest Handling of Fruits, Ministry of Agriculture/Guangdong Provincial Key Laboratory of Applied Botany/Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China. q-hxia@scbg.ac.cn.; Key Laboratory of Post-Harvest Handling of Fruits, Ministry of Agriculture/Guangdong Provincial Key Laboratory of Applied Botany/Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China. xwduan@scbg.ac.cn.; Key Laboratory of Post-Harvest Handling of Fruits, Ministry of Agriculture/Guangdong Provincial Key Laboratory of Applied Botany/Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China. ymjiang@scbg.ac.cn.
The banana is one of the most important fruits in the world. Bananas undergo a rapid ripening process after harvest, resulting in a short shelf. In this study, the mechanism underlying pulp ripening of harvested bananas was investigated using integrated transcriptomic, proteomic, and metabolomic analysis. Ribonucleic acid sequencing (RNA-Seq) revealed that a great number of genes related to transcriptional regulation, signal transduction, cell wall modification, and secondary metabolism were up-regulated during pulp ripening. At the protein level, 84 proteins were differentially expressed during pulp ripening, most of which were associated with energy metabolism, oxidation-reduction, cell wall metabolism, and starch degradation. According to partial least squares discriminant analysis, 33 proteins were identified as potential markers for separating different ripening stages of the fruit. In addition to ethylene's central role, auxin signal transduction might be involved in regulating pulp ripening. Moreover, secondary metabolism, energy metabolism, and the protein metabolic process also played an important role in pulp ripening. In all, this study provided a better understanding of pulp ripening of harvested bananas.
PMID: 31548496
Plant Cell Physiol , IF:4.062 , 2019 Sep , V60 (9) : P2000-2014 doi: 10.1093/pcp/pcz154
Nonsense-Mediated mRNA Decay Deficiency Affects the Auxin Response and Shoot Regeneration in Arabidopsis.
Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan.; RIKEN Center for Sustainable Resource Science, Yokohama, Japan.; Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan.; Department of Biological Science, Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan.; Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan.
Plants generally possess a strong ability to regenerate organs; for example, in tissue culture, shoots can regenerate from callus, a clump of actively proliferating, undifferentiated cells. Processing of pre-mRNA and ribosomal RNAs is important for callus formation and shoot regeneration. However, our knowledge of the roles of RNA quality control via the nonsense-mediated mRNA decay (NMD) pathway in shoot regeneration is limited. Here, we examined the shoot regeneration phenotypes of the low-beta-amylase1 (lba1)/upstream frame shift1-1 (upf1-1) and upf3-1 mutants, in which the core NMD components UPF1 and UPF3 are defective. These mutants formed callus from hypocotyl explants normally, but this callus behaved abnormally during shoot regeneration: the mutant callus generated numerous adventitious root structures instead of adventitious shoots in an auxin-dependent manner. Quantitative RT-PCR and microarray analyses showed that the upf mutations had widespread effects during culture on shoot-induction medium. In particular, the expression patterns of early auxin response genes, including those encoding AUXIN/INDOLE ACETIC ACID (AUX/IAA) family members, were significantly affected in the upf mutants. Also, the upregulation of shoot apical meristem-related transcription factor genes, such as CUP-SHAPED COTYLEDON1 (CUC1) and CUC2, was inhibited in the mutants. Taken together, these results indicate that NMD-mediated transcriptomic regulation modulates the auxin response in plants and thus plays crucial roles in the early stages of shoot regeneration.
PMID: 31386149
Plant Cell Physiol , IF:4.062 , 2019 Sep , V60 (9) : P2100-2112 doi: 10.1093/pcp/pcz108
The Control of Zealactone Biosynthesis and Exudation is Involved in the Response to Nitrogen in Maize Root.
Department of Agronomy, Food, Natural resources, Animals and Environment, DAFNAE, University of Padova, Viale dell'Universiti inverted question mark(1/2) 16, Legnaro, Padova, Italy.; Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Universiti inverted question mark(1/2) Paris-Saclay, Versailles, France.
Nitrate acts as a signal in regulating plant development in response to environment. In particular nitric oxide, auxin and strigolactones (SLs) were supposed to cooperate to regulate the maize root response to this anion. In this study, a combined approach based on liquid chromatography-quadrupole/time-of-flight tandem mass spectrometry and on physiological and molecular analyses was adopted to specify the involvement of SLs in the maize response to N. Our results showed that N deficiency strongly induces SL exudation, likely through stimulating their biosynthesis. Nitrate provision early counteracts and also ammonium lowers SL exudation, but less markedly. Exudates obtained from N-starved and ammonium-provided seedlings stimulated Phelipanche germination, whereas when seeds were treated with exudates harvested from nitrate-provided plants no germination was observed. Furthermore, our findings support the idea that the inhibition of SL production observed in response to nitrate and ammonium would contribute to the regulation of lateral root development. Moreover, the transcriptional regulation of a gene encoding a putative maize WBC transporter, in response to various nitrogen supplies, together with its mRNA tissue localization, supported its role in SL allocation. Our results highlight the dual role of SLs as molecules able to signal outwards a nutritional need and as endogenous regulators of root architecture adjustments to N, thus synchronizing plant growth with nitrogen acquisition.
PMID: 31147714
Plant Cell Physiol , IF:4.062 , 2019 Sep , V60 (9) : P1961-1973 doi: 10.1093/pcp/pcz048
Genome-Wide Analysis of Long Intergenic Noncoding RNAs Responding to Low-Nutrient Conditions in Arabidopsis thaliana: Possible Involvement of Trans-Acting siRNA3 in Response to Low Nitrogen.
Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Japan.; Graduate School of Biosphere Science, Hiroshima University, 1-4-4 Kagamiyama, Higashi-hiroshima, Japan.; Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan.; Institute of Vegetable and Floriculture Science, NARO, Tsu, Japan.
Long intergenic noncoding RNAs (lincRNAs) play critical roles in transcriptional and post-transcriptional regulation of gene expression in a wide variety of organisms. Thousands of lincRNAs have been identified in plant genomes, although their functions remain mostly uncharacterized. Here, we report a genome-wide survey of lincRNAs involved in the response to low-nutrient conditions in Arabidopsis thaliana. We used RNA sequencing data derived from A. thaliana roots exposed to low levels of 12 different nutrients. Using bioinformatics approaches, 60 differentially expressed lincRNAs were identified that were significantly upregulated or downregulated under deficiency of at least one nutrient. To clarify their roles in nutrient response, correlations of expression patterns between lincRNAs and reference genes were examined across the 13 conditions (12 low-nutrient conditions and control). This analysis allowed us to identify lincRNA-RNA pairs with highly positive or negative correlations. In addition, calculating interaction energies of those pairs showed lincRNAs that may act as regulatory interactors; e.g. small interfering RNAs (siRNAs). Among them, trans-acting siRNA3 (TAS3), which is known to promote lateral root development by producing siRNA against Auxin response factor 2, 3, and 4, was revealed as a nitrogen (N)-responsive lincRNA. Furthermore, nitrate transporter 2 was identified as a potential target of TAS3-derived siRNA, suggesting that TAS3 participates in multiple pathways by regulating N transport and root development under low-N conditions. This study provides the first resource for candidate lincRNAs involved in multiple nutrient responses in plants.
PMID: 30892644
Genes (Basel) , IF:3.759 , 2019 Sep , V10 (10) doi: 10.3390/genes10100743
Physiological and Transcriptomic Analysis Reveals Distorted Ion Homeostasis and Responses in the Freshwater Plant Spirodela polyrhiza L. under Salt Stress.
Institute of Tropical Bioscience and Biotechnology, MOA Key Laboratory of Tropical Crops Biology and Genetic Resources, Hainan Academy of Tropical Agricultural Resource, Hainan Bioenergy Center, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou 571101, China. fulili@itbb.org.cn.; Institute of Tropical Bioscience and Biotechnology, MOA Key Laboratory of Tropical Crops Biology and Genetic Resources, Hainan Academy of Tropical Agricultural Resource, Hainan Bioenergy Center, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou 571101, China. dingzehong@itbb.org.cn.; Institute of Tropical Bioscience and Biotechnology, MOA Key Laboratory of Tropical Crops Biology and Genetic Resources, Hainan Academy of Tropical Agricultural Resource, Hainan Bioenergy Center, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou 571101, China. sunxuepiao@itbb.org.cn.; Institute of Tropical Bioscience and Biotechnology, MOA Key Laboratory of Tropical Crops Biology and Genetic Resources, Hainan Academy of Tropical Agricultural Resource, Hainan Bioenergy Center, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou 571101, China. zhangjiaming@itbb.org.cn.
Duckweeds are a family of freshwater angiosperms with morphology reduced to fronds and propagation by vegetative budding. Unlike other angiosperm plants such as Arabidopsis and rice that have physical barriers between their photosynthetic organs and soils, the photosynthetic organs of duckweeds face directly to their nutrient suppliers (waters), therefore, their responses to salinity may be distinct. In this research, we found that the duckweed Spirodela polyrhiza L. accumulated high content of sodium and reduced potassium and calcium contents in large amounts under salt stress. Fresh weight, Rubisco and AGPase activities, and starch content were significantly decreaseded in the first day but recovered gradually in the following days and accumulated more starch than control from Day 3 to Day 5 when treated with 100 mM and 150 mM NaCl. A total of 2156 differentially expressed genes were identified. Overall, the genes related to ethylene metabolism, major CHO degradation, lipid degradation, N-metabolism, secondary metabolism of flavonoids, and abiotic stress were significantly increased, while those involved in cell cycle and organization, cell wall, mitochondrial electron transport of ATP synthesis, light reaction of photosynthesis, auxin metabolism, and tetrapyrrole synthesis were greatly inhibited. Moreover, salt stress also significantly influenced the expression of transcription factors that are mainly involved in abiotic stress and cell differentiation. However, most of the osmosensing calcium antiporters (OSCA) and the potassium inward channels were downregulated, Na(+)/H(+) antiporters (SOS1 and NHX) and a Na(+)/Ca(2+) exchanger were slightly upregulated, but most of them did not respond significantly to salt stress. These results indicated that the ion homeostasis was strongly disturbed. Finally, the shared and distinct regulatory networks of salt stress responses between duckweeds and other plants were intensively discussed. Taken together, these findings provide novel insights into the underlying mechanisms of salt stress response in duckweeds, and can be served as a useful foundation for salt tolerance improvement of duckweeds for the application in salinity conditions.
PMID: 31554307
Genes (Basel) , IF:3.759 , 2019 Sep , V10 (10) doi: 10.3390/genes10100730
Genome-Wide Analysis of Cotton Auxin Early Response Gene Families and Their Roles in Somatic Embryogenesis.
State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China. sunruibin@caas.cn.; State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China. wangshaohui@caas.cn.; State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China. madan@caas.cn.; Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou 450001, China. 16638246238@163.com.; State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China. liuchuanliang@caas.cn.; Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou 450001, China. liuchuanliang@caas.cn.
Auxin is well known to regulate growth and development processes. Auxin early response genes serve as a critical component of auxin signaling and mediate auxin regulation of diverse physiological processes. In the present study, a genome-wide identification and comprehensive analysis of auxin early response genes were conducted in upland cotton. A total of 71 auxin response factor (ARF), 86 Auxin/Indole-3-Acetic Acid (Aux/IAA), 63 Gretchen Hagen3 (GH3), and 194 small auxin upregulated RNA (SAUR) genes were identified in upland cotton, respectively. Phylogenetic analysis revealed that the ARF, GH3, and SAUR families were likely subject to extensive evolutionary divergence between Arabidopsis and upland cotton, while the Aux/IAA family was evolutionary conserved. Expression profiles showed that the ARF, Aux/IAA, GH3, and SAUR family genes were extensively involved in embryogenic competence acquisition of upland cotton callus. The Aux/IAA family genes generally showed a higher expression level in the non-embryogenic callus (NEC) of highly embryogenic cultivar CCRI24 than that of recalcitrant cultivar CCRI12, which may be conducive to initializing the embryogenic transformation. Auxin early response genes were tightly co-expressed with most of the known somatic embryogenesis (SE) related genes, indicating that these genes may regulate upland cotton SE by interacting with auxin early response genes.
PMID: 31547015
Pest Manag Sci , IF:3.75 , 2019 Sep , V75 (9) : P2490-2504 doi: 10.1002/ps.5405
Transcriptome responses to the natural phytotoxin t-chalcone in Arabidopsis thaliana L.
Department of Plant Biology and Soil Science, University of Vigo, Vigo, Spain.; Genomics and Bioinformatics Research Unit, USDA, ARS, Athens, GA, USA.; Natural Products Utilization Research Unit, USDA, ARS, Oxford, MS, USA.; Genomics and Bioinformatics Research, USDA, ARS, Stoneville, MS, USA.
BACKGROUND: New modes of action are needed for herbicides. The flavonoid synthesis intermediate t-chalcone causes apoptosis-like symptoms in roots and bleaching of shoots of Arabidospsis, suggesting a unique mode of action as a phytotoxin. RESULTS: Using RNA-Seq, transcriptome changes were monitored in Arabidopsis seedlings during the first 24 h of exposure (at 1, 3, 6, 12 and 24 h) to 21 mum t-chalcone (I50 dose), examining effects on roots and shoots separately. Expression of 892 and 1000 genes was affected in roots and shoots, respectively. According to biological classification, many of the affected genes were transcription factors and genes associated with oxidative stress, heat shock proteins, xenobiotic detoxification, ABA and auxin biosynthesis, and primary metabolic processess. These are secondary effects found with most phytotoxins. Potent phytotoxins usually act by inhibiting enzymes of primary metabolism. KEGG pathway analysis of transcriptome results from the first 3 h of t-chalcone exposure indicated several potential primary metabolism target sites for t-chalcone. Of these, p-hydroxyphenylpyruvate dioxygenase (HPPD) and tyrosine amino transferase were consistent with the bleaching effect of the phytotoxin. Supplementation studies with Lemna paucicostata and Arabidiopsis supported HPPD as the target, although in vitro enzyme inhibition was not found. CONCLUSIONS: t-Chalcone is possibly a protoxin that is converted to a HPPD inhibitor in vivo. (c) 2019 Society of Chemical Industry.
PMID: 30868714
Plant Physiol Biochem , IF:3.72 , 2019 Sep , V142 : P303-311 doi: 10.1016/j.plaphy.2019.07.021
The barley miR393 has multiple roles in regulation of seedling growth, stomatal density, and drought stress tolerance.
Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Institute of Genetics and Regenerative Biology, College of Life Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China.; Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Institute of Genetics and Regenerative Biology, College of Life Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China. Electronic address: ninghan@zju.edu.cn.
microRNA393 (miR393) and its target module have been implicated as comprising a conserved mechanism to regulate developmental processes and plant growth in response to environmental signals through the auxin signaling pathway. Our previous work identified miR393 and its two targets in barley. In this study, we further investigated the expression pattern of miR393 and its biological functions in seedling growth and drought tolerance. We showed that the miR393 overexpressing line (OE) exhibited increased stomatal density with decreased guard cell length, while the miR393 knockdown line (MIM) displayed the opposite phenotype, which might be due to the effects of miR393 on AUXIN RESPONSE FACTOR5 (ARF5) and three stomatal development-related genes, such as EPIDERMAL PATTERNING FACTOR1 (EPF1), SPEECHLESS (SPCH), and MUTE. In addition, the MIM line conferred enhanced drought tolerance, with alleviated leaf chlorosis and lipid peroxidation after 22 days drought treatment. In contrast, the OE line was more sensitive to drought stress and accumulated more malondialdehyde and hydrogen peroxide than the wild type. Furthermore, polyethylene glycol (PEG) treatment-induced abscisic acid (ABA) accumulation in leaves was suppressed in the OE line, indicating that miR393 might regulate drought stress response and tolerance through its interaction with ABA biosynthesis. Overall, these data suggest that miR393 might be a potential target for manipulation of stomatal density and improvement of drought tolerance in barley.
PMID: 31351321
Plant Physiol Biochem , IF:3.72 , 2019 Sep , V142 : P193-201 doi: 10.1016/j.plaphy.2019.05.006
Regulation of cadmium toxicity in roots of tomato by indole acetic acid with special emphasis on reactive oxygen species production and their scavenging.
Department of Biotechnology, Motilal Nehru National Institute of Technology Allahabad, Prayagraj, Uttar Pradesh, India.; D D Pant Interdisciplinary Research Laboratory, Department of Botany, University of Allahabad, Allahabad, 211002, India.; Ranjan Plant Physiology and Biochemistry Laboratory, Department of Botany, University of Allahabad, Allahabad, 211002, India.; Amity Institute of Organic Agriculture, Amity University Uttar Pradesh, I 2 Block, 5th Floor, AUUP Campus Sector-125, Noida, 201313, India.; Department of Botany, C.M.P. Degree College, A Constituent PG College of University of Allahabad, Allahabad, 211002, India. Electronic address: vijaypratap.au@gmail.com.; Amity Institute of Organic Agriculture, Amity University Uttar Pradesh, I 2 Block, 5th Floor, AUUP Campus Sector-125, Noida, 201313, India. Electronic address: dktripathiau@gmail.com.; Department of Biotechnology, Motilal Nehru National Institute of Technology Allahabad, Prayagraj, Uttar Pradesh, India. Electronic address: shiveshs@mnnit.ac.in.
Toxic impact of cadmium (Cd) on plants is well known which affects their productivity. To mitigate toxic impact of metals such as Cd, exogenous application of phytohormones like indole acetic acid (IAA) has been well recognized in the recent past. But, mechanisms related to the IAA-mediated mitigation of metal toxicity remain elusive. Therefore, in this study, effect of IAA on growth and photosynthetic attributes, nitric oxide, cell viability, reactive oxygen species (ROS) and ascorbate-glutathione cycle (AsA-GSH cycle) was investigated in tomato roots exposed to Cd stress. Cd declined growth and photosynthetic attributes which were accompanied by the excess accumulation of Cd and decreased level of nitric oxide (NO). Among photosynthetic attributes, quantum yield parameters were more sensitive to Cd and these results were in parallel of photosynthetic pigments. However, exogenously applied IAA together with Cd significantly improved level of NO, growth and photosynthetic attributes together with reduced accumulation of Cd. Cd enhanced level of superoxide radical and hydrogen peroxide leading to severe damage to lipids and membranes as indicated by increased level of lipid peroxidation and electrolyte leakage which collectively reduced cell viability of roots. Moreover, components of the AsA-GSH cycle i.e. enzymes (ascorbate peroxidase, monodehydroascorbate reducatse, dehydroascorbate reducatse and glutathione reductase) and metabolites (ascorbate and glutathione) were declined by the Cd. However, addition of IAA with Cd had up-regulated components of the AsA-GSH cycle. Interestingly, application of 2,4,6-triiodobenzoic acid (TIBA, a polar auxin transport inhibitor) diminished growth attributes and its combination with Cd worsened its toxicity and these events were in parallel with decline in NO content and enhancement in Cd accumulation. The results also showed that IAA was also able in mitigating Cd toxicity in tomato roots even in the presence of TIBA. Overall results show the essentiality of IAA in mitigating Cd stress in tomato roots through NO that up-regulates components of the AsA-GSH cycle for balancing ROS and their associated damages and hence much improved growth and photosynthetic attributes were noticed.
PMID: 31301530
Tree Physiol , IF:3.655 , 2019 Sep doi: 10.1093/treephys/tpz101
Changes in Phytohormone Content and Associated Gene Expression Throughout the Stages of Pear (Pyrus pyrifolia Nakai) Dormancy.
Institute of Fruit Tree and Tea Science, NARO, 2-1 Fujimoto, Tsukuba, Ibaraki 305-8605, Japan.; Department of Plant Science, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada.; Graduate School of Horticulture, Chiba University, Matsudo, Chiba 271-8510, Japan.; Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Hangzhou, Zhejiang 310058, China.
To elucidate the role of phytohormones during bud dormancy progression in Japanese pear (Pyrus pyrifolia Nakai), we investigated changes in phytohormone levels of indole acetic acid (IAA), gibberellic acid (GA), abscisic acid (ABA) and t-zeatin (tZ). Using ultra-performance liquid chromatography/mass spectrometry/mass spectrometry (UPLC/MS/MS), we monitored phytohormone levels in the buds of field-grown and potted trees that were artificially heated to modify the timing of dormancy and flowering (spring flush) progression. We also analyzed the expression of GA- and ABA- metabolic genes during dormancy. IAA and tZ levels were low during dormancy and increased toward the flowering stage. GA levels were maintained at relatively high concentrations during the dormancy induction stage, then decreased before slightly increasing prior to flowering. The low GA concentration in potted trees compared with field-grown trees indicated that GA functions in regulating tree vigor. ABA levels increased from the dormancy induction stage, peaked near endodormancy release, and steadily decreased before increasing again before the flowering stage. ABA peak levels did not always coincide with endodormancy release, but peak height correlated with flowering uniformity, suggesting that a decline in ABA concentration was not necessary for resumption of growth but the abundance of ABA might be associated with dormancy depth. From monitoring the expression of genes related to GA- and ABA- metabolism, we inferred that phytohormone metabolism changed significantly during dormancy, even though the levels of bioactive molecules were consistently low. Phytohormones regulate dormancy progression not only upon the reception of internal signals but also upon sensing ambient conditions.
PMID: 31595966
Plant Sci , IF:3.591 , 2019 Sep , V286 : P37-48 doi: 10.1016/j.plantsci.2019.06.002
Alternative responses to fungal attack on a metalliferous soil: Phytohormone levels and structural changes in Silene paradoxa L. growing under copper stress.
Department of Biology, Universita di Firenze, via Micheli 1, 50121, Firenze, Italy. Electronic address: alessio.papini@unifi.it.; Department of Biomedical Experimental and Clinical Sciences, Universita di Firenze, Viale Morgagni 50, 50134, Firenze, Italy. Electronic address: simone.luti@unifi.it.; Department of Biology, Universita di Firenze, via Micheli 1, 50121, Firenze, Italy. Electronic address: ilaria.colzi@unifi.it.; Department of Biomedical Experimental and Clinical Sciences, Universita di Firenze, Viale Morgagni 50, 50134, Firenze, Italy. Electronic address: lorenzo.mazzoli@unifi.it.; Department of Biology, Universita di Firenze, via Micheli 1, 50121, Firenze, Italy. Electronic address: betti_days@hotmail.it.; Department of Biomedical Experimental and Clinical Sciences, Universita di Firenze, Viale Morgagni 50, 50134, Firenze, Italy. Electronic address: luigia.pazzagli@unifi.it.; Department of Biology, Universita di Firenze, via Micheli 1, 50121, Firenze, Italy. Electronic address: cristina.gonnelli@unifi.it.
In this work, a non-metallicolous and a metallicolous population of S. paradoxa were exposed to copper excess and fungal elicitation, and investigated for phytohormone production and cytological alterations. Under the stress applied separately and in combination, S. paradoxa plants varied phytohormone concentration in a population-specific way, suggesting a different signalling in response to biotic and abiotic stimuli according to the environment of origin. Generally, the stress responses consisted in increased levels of salicylic acid, auxin, and gibberellin in the non-metallicolous population, and of jasmonic and abscisic acid in the metallicolous one. Interestingly, the metallicolous population increased the level of such phytohormones following exposure to the fungal elicitor only in the presence of copper. This alternative hormonal signalling could derive from the incompatibility between the ordinary ROS-mediated response to pathogens and the acquired mechanisms that prevent oxidative stress in the population from the metal-rich soil. Furthermore, stress-induced autophagic phenomena were more evident in the non-metallicolous plants than in the metallicolous ones, suggesting that the adaptation to the metalliferous environment has also affected autophagy intensity and signalling in response to copper excess and fungal elicitation.
PMID: 31300140
J Biotechnol , IF:3.503 , 2019 Sep , V303 : P8-15 doi: 10.1016/j.jbiotec.2019.07.004
Synthesis of indole-3-acetic acid and indole-3-butyric acid loaded zinc oxide nanoparticles: Effects on rhizogenesis.
Ankara University, Chemical Engineering Department, Tandogan, Ankara, 06100, Turkey. Electronic address: akarakecili@eng.ankara.edu.tr.; Ankara University, Biotechnology Institute, Tandogan, Ankara, 06100, Turkey.; Ankara University, Faculty of Agriculture, Department of Horticulture, 06110, Ankara, Turkey.
The aim of this work was to investigate the use of zinc oxide nanoparticles (nZnO) as nanocarriers for plant auxins indole-3-acetic acid (IAA) and indole-3-butyric acid (IBA) and determine the effects on rhizogenesis in micro cuttings of different Pyrus species. Auxin loaded nanoparticles (IAA-nZnO and IBA-nZnO) were characterized for particle size, morphology, thermal behavior and chemical structure. A high loading capacity was observed for both auxins ( 90%). Bioactivity assays were performed by using micro cuttings of Pyrus genotypes (Pyrus elaeagrifolia Pall and Pyrus communis L.) under aseptic conditions by dilute solution soaking method. In vitro rooting efficiency was increased at least two folds for the difficult-to-root wild pear (Pyrus elaeagrifolia Pallas) with IAA or IBA loaded ZnO nanoparticles. In this genotype, the highest rooting percentage was achieved for IBA-nZnO and IAA-nZnO at 400mgL(-1) concentration as 50.0% and 41.7%, respectively. Thus, auxin loaded ZnO nanoparticles could be used as efficient nanocarriers in agricultural applications.
PMID: 31301312
BMC Plant Biol , IF:3.497 , 2019 Sep , V19 (1) : P395 doi: 10.1186/s12870-019-2007-4
NAL8 encodes a prohibitin that contributes to leaf and spikelet development by regulating mitochondria and chloroplasts stability in rice.
National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology & Ecology, Shanghai Institute for Biological Sciences, Chinese Academic of Sciences, Shanghai, 200032, China.; University of the Chinese Academy of Sciences, Beijing, 100049, China.; National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology & Ecology, Shanghai Institute for Biological Sciences, Chinese Academic of Sciences, Shanghai, 200032, China. hxlin@sibs.ac.cn.; University of the Chinese Academy of Sciences, Beijing, 100049, China. hxlin@sibs.ac.cn.; School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China. hxlin@sibs.ac.cn.
BACKGROUND: Leaf morphology and spikelet number are two important traits associated with grain yield. To understand how genes coordinating with sink and sources of cereal crops is important for grain yield improvement guidance. Although many researches focus on leaf morphology or grain number in rice, the regulating molecular mechanisms are still unclear. RESULTS: In this study, we identified a prohibitin complex 2alpha subunit, NAL8, that contributes to multiple developmental process and is required for normal leaf width and spikelet number at the reproductive stage in rice. These results were consistent with the ubiquitous expression pattern of NAL8 gene. We used genetic complementation, CRISPR/Cas9 gene editing system, RNAi gene silenced system and overexpressing system to generate transgenic plants for confirming the fuctions of NAL8. Mutation of NAL8 causes a reduction in the number of plastoglobules and shrunken thylakoids in chloroplasts, resulting in reduced cell division. In addition, the auxin levels in nal8 mutants are higher than in TQ, while the cytokinin levels are lower than in TQ. Moreover, RNA-sequencing and proteomics analysis shows that NAL8 is involved in multiple hormone signaling pathways as well as photosynthesis in chloroplasts and respiration in mitochondria. CONCLUSIONS: Our findings provide new insights into the way that NAL8 functions as a molecular chaperone in regulating plant leaf morphology and spikelet number through its effects on mitochondria and chloroplasts associated with cell division.
PMID: 31510917
Proteomics , IF:3.254 , 2019 Sep , V19 (17) : Pe1900199 doi: 10.1002/pmic.201900199
Auxin Induces Widespread Proteome Remodeling in Arabidopsis Seedlings.
Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 92093, USA.; Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, 92093, USA.; Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, 50011, USA.
It is known that auxin induces rapid gene expression changes throughout plant development, but how these transcriptional responses relate to changes in protein abundance is not well characterized. This report identifies early auxin responsive proteins in whole Arabidopsis seedlings using an isobaric tags for relative and absolute quantification-based quantitative proteomics approach. Approximately 25% of the detected proteins (1045 out of 4257 proteins) are auxin responsive, which is in line with the central role of auxin in the regulation of plant growth and development. Several well-known auxin pathway proteins are identified as differentially expressed, validating this quantitative proteomics approach. Additionally, functional categorization of these auxin responsive proteins indicates that rapid and complex metabolic changes occur in seedlings in response to auxin, including lipid metabolism. Altogether, these data describe novel auxin-regulated proteins and are an excellent resource for identifying new downstream signaling components related to auxin-mediated plant growth and development.
PMID: 31381813
J Plant Physiol , IF:3.013 , 2019 Sep , V240 : P153010 doi: 10.1016/j.jplph.2019.153010
PGPR-induced OsASR6 improves plant growth and yield by altering root auxin sensitivity and the xylem structure in transgenic Arabidopsis thaliana.
Plant Gene Expression Lab, CSIR- National Botanical Research Institute, Lucknow, 226001, India; Integral University, Lucknow, India.; Microbiology Division, CSIR- National Botanical Research Institute, Lucknow, 226001, India.; Plant Physiology, CSIR- National Botanical Research Institute, Lucknow, 226001, India.; Genetics and Molecular Biology Division, CSIR- National Botanical Research Institute, Lucknow-226001, India.; Integral University, Lucknow, India.; Plant Gene Expression Lab, CSIR- National Botanical Research Institute, Lucknow, 226001, India.; Plant Gene Expression Lab, CSIR- National Botanical Research Institute, Lucknow, 226001, India. Electronic address: va.sane@nbri.res.in.
Plant-growth-promoting rhizobacteria (PGPR) improve plant growth by altering the root architecture, although the mechanisms underlying this alteration have yet to be unravelled. Through microarray analysis of PGPR-treated rice roots, a large number of differentially regulated genes were identified. Ectopic expression of one of these genes, OsASR6 (ABA STRESS RIPENING6), had a remarkable effect on plant growth in Arabidopsis. Transgenic lines over-expressing OsASR6 had larger leaves, taller inflorescence bolts and greater numbers of siliques and seeds. The most prominent effect was observed in root growth, with the root biomass increasing four-fold compared with the shoot biomass increase of 1.7-fold. Transgenic OsASR6 over-expressing plants showed higher conductance, transpiration and photosynthesis rates, leading to an 30% higher seed yield compared with the control. Interestingly, OsASR6 expression led to alterations in the xylem structure, an increase in the xylem vessel size and altered lignification, which correlated with higher conductance. OsASR6 is activated by auxin and, in turn, increases auxin responses and root auxin sensitivity, as observed by the increased expression of auxin-responsive genes, such as SAUR32 and PINOID, and the key auxin transcription factor, ARF5. Collectively, these phenomena led to an increased root density. The effects of OsASR6 expression largely mimic the beneficial effects of PGPRs in rice, indicating that OsASR6 activation may be a key factor governing PGPR-mediated changes in rice. OsASR6 is a potential candidate for the manipulation of rice for improved productivity.
PMID: 31352021
J Plant Physiol , IF:3.013 , 2019 Sep , V240 : P152990 doi: 10.1016/j.jplph.2019.152990
Characterization the role of a UFC homolog, AtAuxRP3, in the regulation of Arabidopsis seedling growth and stress response.
National Maize Improvement Center, China Agricultural University, 2 West Yuanmingyuan Road, Beijing 100193, China; State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, 100871, China.; National Maize Improvement Center, China Agricultural University, 2 West Yuanmingyuan Road, Beijing 100193, China.; National Maize Improvement Center, China Agricultural University, 2 West Yuanmingyuan Road, Beijing 100193, China. Electronic address: yejr2006@cau.edu.cn.
Auxin is a well-known, crucial regulator of the entire plant lifecycle, not only orchestrating many aspects of plant growth and development, but also playing various roles in biotic and abiotic stress. This study reports the isolation and functional characterization of a DUF-966 domain-containing gene, At3g46110, re-named AtAuxRP3. AtAuxRP3 overexpression in Arabidopsis increased the levels of endogenous indole-3-acetic acid, enhanced expression of the auxin-responsive reporter DR5:GUS near the vegetative shoot apex, and led to ectopic activation of auxin signaling, including dysmorphic (narrow, asymmetric) rosette leaves, abnormal emergence of inflorescence, inhibition of primary root elongation and arrest of dark-grown hypocotyls. AtAuxRP3-OX lines also showed decreased tolerance to NaCl and osmotic stress during Arabidopsis seeds germination and young seedling growth. Genome-wide transcriptomic analysis showed AtAuxRP3-OX seedlings displayed increases in the expression of genes that group in a variety of developmental categories, while other downregulated genes were associated with stress responses. Our results provide evidence for a regulatory role of AtAuxRP3 in endogenous auxin levels, leaf development, and initiation of inflorescence stems early in reproductive development during Arabidopsis seedling growth.
PMID: 31207460
Plants (Basel) , IF:2.762 , 2019 Sep , V8 (10) doi: 10.3390/plants8100391
Reactive Carbonyl Species: A Missing Link in ROS Signaling.
Science Research Center, Organization of Research Initiatives, Yamaguchi University, Yamaguchi 753-8511, Japan. mano@yamaguchi-u.ac.jp.; Graduate School of Science and Technology for Innovation, Yamaguchi University, Yamaguchi 753-8511, Japan. mano@yamaguchi-u.ac.jp.; Department of Horticulture, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh. sanaullahbiswas@gmail.com.; Science Research Center, Organization of Research Initiatives, Yamaguchi University, Yamaguchi 753-8511, Japan. sugimok@yamaguchi-u.ac.jp.
As reactive oxygen species (ROS) play critical roles in plants to determine cell fate in various physiological situations, there is keen interest in the biochemical processes of ROS signal transmission. Reactive carbonyl species (RCS), the ,-unsaturated aldehydes and ketones produced from lipid peroxides, due to their chemical property to covalently modify protein, can mediate ROS signals to proteins. Comprehensive carbonyl analysis in plants has revealed that more than a dozen different RCS, e.g., acrolein, 4-hydroxy-(E)-2-nonenal and malondialdehyde, are produced from various membranes, and some of them increase and modify proteins in response to oxidative stimuli. At early stages of response, specific subsets of proteins are selectively modified with RCS. The involvement of RCS in ROS signaling can be judged on three criteria: (1) A stimulus to increase the ROS level in plants leads to the enhancement of RCS levels. (2) Suppression of the increase of RCS by scavenging enzymes or chemicals diminishes the ROS-induced response. (3) Addition of RCS to plants evokes responses similar to those induced by ROS. On these criteria, the RCS action as damaging/signaling agents has been demonstrated for root injury, programmed cell death, senescence of siliques, stomata response to abscisic acid, and root response to auxin. RCS thus act as damage/signal mediators downstream of ROS in a variety of physiological situations. A current picture and perspectives of RCS research are presented in this article.
PMID: 31575078
Plants (Basel) , IF:2.762 , 2019 Sep , V8 (10) doi: 10.3390/plants8100382
Target-Site Mutations Conferring Herbicide Resistance.
Department of Crop Sciences, University of Illinois, Urbana, IL 61801, USA. brentpm2@illinois.edu.; Department of Crop Sciences, University of Illinois, Urbana, IL 61801, USA. tranel@illinois.edu.
Mutations conferring evolved herbicide resistance in weeds are known in nine different herbicide sites of action. This review summarizes recently reported resistance-conferring mutations for each of these nine target sites. One emerging trend is an increase in reports of multiple mutations, including multiple amino acid changes at the glyphosate target site, as well as mutations involving two nucleotide changes at a single amino acid codon. Standard reference sequences are suggested for target sites for which standards do not already exist. We also discuss experimental approaches for investigating cross-resistance patterns and for investigating fitness costs of specific target-site mutations.
PMID: 31569336
J Biomol NMR , IF:2.634 , 2019 Sep , V73 (8-9) : P493-507 doi: 10.1007/s10858-019-00258-0
Tuning a timing device that regulates lateral root development in rice.
Department of Molecular Biology & Genetics, Cornell University, Ithaca, NY, 14853, USA.; Department of Biochemistry and Biophysics and the Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.; Department of Molecular Biology & Genetics, Cornell University, Ithaca, NY, 14853, USA. lkn2@cornell.edu.
Peptidyl Prolyl Isomerases (PPIases) accelerate cis-trans isomerization of prolyl peptide bonds. In rice, the PPIase LRT2 is essential for lateral root initiation. LRT2 displays in vitro isomerization of a highly conserved W-P peptide bond ((104)W-P(105)) in the natural substrate OsIAA11. OsIAA11 is a transcription repressor that, in response to the plant hormone auxin, is targeted to ubiquitin-mediated proteasomal degradation via specific recognition of the cis isomer of its (104)W-P(105) peptide bond. OsIAA11 controls transcription of specific genes, including its own, that are required for lateral root development. This auxin-responsive negative feedback circuit governs patterning and development of lateral roots along the primary root. The ability to tune LRT2 activity via mutagenesis is crucial for understanding and modeling the role of this bimodal switch in the auxin circuit and lateral root development. We present characterization of the thermal stability and isomerization rates of several LRT2 mutants acting on the OsIAA11 substrate. The thermally stable mutants display activities lower than that of wild-type (WT) LRT2. These include binding diminished but catalytically active P125K, binding incompetent W128A, and binding capable but catalytically incompetent H133Q mutations. Additionally, LRT2 homologs hCypA from human, TaCypA from Triticum aestivum (wheat) and PPIB from E. coli were shown to have 110, 50 and 60% of WT LRT2 activity on the OsIAA11 substrate. These studies identify several thermally stable LRT2 mutants with altered activities that will be useful for establishing relationships between cis-trans isomerization, auxin circuit dynamics, and lateral root development in rice.
PMID: 31407206
Prog Biophys Mol Biol , IF:2.175 , 2019 Sep , V146 : P134-141 doi: 10.1016/j.pbiomolbio.2019.03.006
Genome-wide identification and expression analysis of dormancy-associated gene 1/auxin repressed protein (DRM1/ARP) gene family in Glycine max.
Departamento de Bioquimica e Biologia Molecular, Universidade Federal de Vicosa, Avenida PH Rolfs s/n, Campus Universitario, 36571-000, Vicosa, MG, Brazil.; Departamento de Bioquimica e Biologia Molecular, Universidade Federal de Vicosa, Avenida PH Rolfs s/n, Campus Universitario, 36571-000, Vicosa, MG, Brazil. Electronic address: murilo.alves@ufc.br.; Departamento de Bioquimica e Biologia Molecular, Universidade Federal de Vicosa, Avenida PH Rolfs s/n, Campus Universitario, 36571-000, Vicosa, MG, Brazil. Electronic address: lgfietto@ufv.br.
Dormancy-Associated gene 1/Auxin Repressed protein (DRM1/ARP) genes are responsive to hormones involved in defense response to biotic stress, such as salicylic acid (SA) and methyl jasmonate (MeJA), as well as to hormones that regulate plant growth and development, including auxins. These characteristics suggest that this gene family may be an important link between the response to pathogens and plant growth and development. In this investigation, the DRM1/ARP genes were identified in the genome of four legume species. The deduced proteins were separated into three distinct groups, according to their sequence conservation. The expression profile of soybean genes from each group was measured in different organs, after treatment with auxin and MeJA and in response to the nematode Meloidogyne javanica. The results demonstrated that this soybean gene family is predominantly expressed in root. The time auxin takes to alter DRM1/ARP expression suggests that these genes can be classified as a late response to auxin. Nevertheless, only the groups 1 and 3 are induced in roots infected by M. javanica and only group 3 is induced by MeJA, which indicates a high level of complexity in expression control mechanisms of DRM1/ARP family in soybean.
PMID: 30914276
Genome , IF:2.037 , 2019 Sep , V62 (9) : P597-608 doi: 10.1139/gen-2018-0161
Genome-wide identification and characterization of Gretchen Hagen3 (GH3) family genes in Brassica napus.
Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, P.R. China.
The hormone auxin is involved in many biological processes throughout a plant's lifecycle. However, genes in the GH3 (Gretchen Hagen3) family, one of the three major auxin-responsive gene families, have not yet been identified in oilseed rape (Brassica napus). In this study, we identified 63 BnaGH3 genes in oilseed rape using homology searches. We analyzed the chromosome locations, gene structures, and phylogenetic relationships of the BnaGH3 genes, as well as the cis-elements in their promoters. Most BnaGH3 genes are located on chromosomes A03, A09, C02, C03, and C09, each with 4-7 members. In addition, we analyzed the expression patterns of BnaGH3 genes in seven tissues by transcriptome sequencing and quantitative RT-PCR analysis of plants under exogenous IAA treatment. The BnaGH3 genes showed different expression patterns in various tissues. BnaA.GH3.2-1 and BnaC.GH3.2-1 were expressed in the seed and seed coat during development and in response to IAA treatment. These results shed light on the possible roles of the GH3 gene family in oilseed rape.
PMID: 31271724
Physiol Mol Biol Plants , IF:2.005 , 2019 Sep , V25 (5) : P1185-1196 doi: 10.1007/s12298-019-00693-1
Chilli leaf curl virus infection downregulates the expression of the genes encoding chloroplast proteins and stress-related proteins.
1Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067 India.0000 0004 0498 924Xgrid.10706.30; 2National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067 India.0000 0001 2217 5846grid.419632.b
Virus infection alters the expression of several host genes involved in various cellular and biological processes in plants. Most of the studies performed till now have mainly focused on genes which are up-regulated and later projected them as probable stress tolerant/susceptible genes. Nevertheless, genes which are down-regulated during plant-virus interaction could also play a critical role on disease development as well as in combating the virus infection. Hence, to identify such down-regulated genes and pathway, we performed reverse suppression subtractive hybridization in Capsicum annuum var. Punjab Lal following Chilli leaf curl virus (ChiLCV) infection. The screening and further processing suggested that majority of the genes (approximately 35% ESTs) showed homology with the genes encoding chloroplast proteins and 16% genes involved in the biotic and abiotic stress response. Additionally, we identified several genes, functionally known to be involved in metabolic processes, protein synthesis and degradation, ribosomal proteins, energy production, DNA replication and transcription, and transporters. We also found 3% transcripts which did not show homology with any known genes. The redundancy analysis revealed the maximum percentage of chlorophyll a-b binding protein (15/96) and auxin-binding proteins (13/96). We developed a protein interactome network to characterise the relationships between proteins and pathway involved during the ChiLCV infection. We identified that the most of the interaction occurs either among the chloroplast proteins (Arabidopsis proteins interactive map) or biotic and abiotic stress responsive proteins (Solanum lycopersicum interactome). Taken together, our study provides the first transcriptome and protein interactome of the down-regulated genes during C. annuum-ChiLCV interaction. These resources could be exploited in deciphering the steps involved in the process of virus infection.
PMID: 31564781
Genesis , IF:1.76 , 2019 Sep , V57 (9) : Pe23307 doi: 10.1002/dvg.23307
The Ha-ROXL gene is required for initiation of axillary and floral meristems in sunflower.
Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy.; Department of Agriculture, Food and Environment (DAFE), University of Pisa, Pisa, Italy.; Department of Biology, University of Pisa, Pisa, Italy.
Axillary meristems (AMs) contribute to the growth of a plant, determining adult architecture and reproductive success in response to environmental stimuli. The missing flowers (mf) mutant of sunflower (Helianthus annuus) is defective in AM development. mf lacks shoot branching and ray flowers, occasionally producing few disk flowers. Here we demonstrated that a point mutation in the REGULATOR OF AXILLARY MERISTEM FORMATION-LIKE (Ha-ROXL) gene of mf generates a premature stop codon and therefore a nonfunctional bHLH transcription factor, no longer localized in the nucleus, where it should exert its function. Virus-induced gene silencing of Ha-ROXL also causes defects in disk and ray flower development. Ha-ROXL mRNA accumulates at the adaxial boundaries of leaves and AMs. During inflorescence development, Ha-ROXL is expressed in small arcs of cells before a clear separation between abaxial bracts and disk flower primordia. No Ha-ROXL mRNA accumulates in mf inflorescences. Several genes known to play roles in plant architecture, auxin transport, and flower development are differentially expressed in mf and Ha-ROXL-silenced plants. These results highlight the predominant role of Ha-ROXL in regulating AMs in sunflower. In dicot, mf is the first mutant for which the ROXL gene is also required for initiation of flower meristems.
PMID: 31140735
Plant Direct , IF:1.725 , 2019 Sep , V3 (9) : Pe00166 doi: 10.1002/pld3.166
Auxin promotion of seedling growth via ARF5 is dependent on the brassinosteroid-regulated transcription factors BES1 and BEH4.
Department of Biology University of Washington Seattle WA USA.; Present address: Max Planck Institute for Plant Breeding Research Carl-von-Linne-Weg 10 Cologne 50829 Germany.
Seedlings must continually calibrate their growth in response to the environment. Auxin and brassinosteroids (BRs) are plant hormones that work together to control growth responses during photomorphogenesis. We used our previous analysis of promoter architecture in an auxin and BR target gene to guide our investigation into the broader molecular bases and biological relevance of transcriptional co-regulation by these hormones. We found that the auxin-regulated transcription factor Auxin Responsive Factor 5 (ARF5) and the brassinosteroid-regulated transcription factor BRI1-EMS-Suppressor 1/Brassinazole Resistant 2 (BES1) co-regulated a subset of growth-promoting genes via conserved bipartite cis-regulatory elements. Moreover, ARF5 binding to DNA could be enriched by increasing BES1 levels. The evolutionary loss of bipartite elements in promoters results in loss of hormone responsiveness. We also identified another member of the BES1/BZR1 family called BEH4 that acts partially redundantly with BES1 to regulate seedling growth. Double mutant analysis showed that BEH4 and not BZR1 were required alongside BES1 for normal auxin response during early seedling development. We propose that an ARF5-BES1/BEH4 transcriptional module acts to promote growth via modulation of a diverse set of growth-associated genes.
PMID: 31508562
Plant Direct , IF:1.725 , 2019 Sep , V3 (9) : Pe00165 doi: 10.1002/pld3.165
Mechanisms underlying the enhanced biomass and abiotic stress tolerance phenotype of an Arabidopsis MIOX over-expresser.
Arkansas Biosciences Institute Arkansas State University State University AR USA.; INBIOTECA Universidad Veracruzana Xalapa Mexico.; Department of Chemistry and Physics Arkansas State University State University AR USA.
Myo-inositol oxygenase (MIOX) is the first enzyme in the inositol route to ascorbate (L-ascorbic acid, AsA, vitamin C). We have previously shown that Arabidopsis plants constitutively expressing MIOX have elevated foliar AsA content and displayed enhanced growth rate, biomass accumulation, and increased tolerance to multiple abiotic stresses. In this work, we used a combination of transcriptomics, chromatography, microscopy, and physiological measurements to gain a deeper understanding of the underlying mechanisms mediating the phenotype of the AtMIOX4 line. Transcriptomic analysis revealed increased expression of genes involved in auxin synthesis, hydrolysis, transport, and metabolism, which are supported by elevated auxin levels both in vitro and in vivo, and confirmed by assays demonstrating their effect on epidermal cell elongation in the AtMIOX4 over-expressers. Additionally, we detected up-regulation of transcripts involved in photosynthesis and this was validated by increased efficiency of the photosystem II and proton motive force. We also found increased expression of amylase leading to higher intracellular glucose levels. Multiple gene families conferring plants tolerance/expressed in response to cold, water limitation, and heat stresses were found to be elevated in the AtMIOX4 line. Interestingly, the high AsA plants also displayed up-regulation of transcripts and hormones involved in defense including jasmonates, defensin, glucosinolates, and transcription factors that are known to be important for biotic stress tolerance. These results overall indicate that elevated levels of auxin and glucose, and enhanced photosynthetic efficiency in combination with up-regulation of abiotic stresses response genes underly the higher growth rate and abiotic stresses tolerance phenotype of the AtMIOX4 over-expressers.
PMID: 31497751
Neuroreport , IF:1.394 , 2019 Sep , V30 (13) : P908-913 doi: 10.1097/WNR.0000000000001299
Auxin-mediated rapid degradation of target proteins in hippocampal neurons.
Laboratory of Chemical Pharmacology.; Molecular Cell Engineering Laboratory, National Institute of Genetics, Research Organization of Information and Systems (ROIS).; Department of Genetics, The Graduate University for Advanced Studies (SOKENDAI), Mishima, Shizuoka, Japan.; Center for Information and Neural Networks, National Institute of Information and Communications Technology, Suita, Osaka, Japan.; Social Cooperation Program of evolutional chemical safety assessment system, LECSAS, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.
Genetic manipulation of protein levels is a promising approach to identify the function of a specific protein in living organisms. Previous studies demonstrated that the auxin-inducible degron strategy provides rapid and reversible degradation of various proteins in fungi and mammalian mitotic cells. In this study, we employed this technology to postmitotic neurons to address whether the auxin-inducible degron system could be applied to the nervous system. Using adeno-associated viruses, we simultaneously introduced enhanced green fluorescent protein (EGFP) fused with an auxin-inducible degron tag and an F-box family protein, TIR1 from Oryza sativa (OsTIR1), into hippocampal neurons from mice. In dissociated hippocampal neurons, EGFP enhanced green fluorescent protein fluorescence signals rapidly decreased when adding a plant hormone, auxin. Furthermore, auxin-induced enhanced green fluorescent protein degradation was also observed in hippocampal acute slices. Taken together, these results open the door for neuroscientists to manipulate protein expression levels by the auxin-inducible degron system in a temporally controlled manner.
PMID: 31373971
Acta Crystallogr F Struct Biol Commun , IF:0.968 , 2019 Sep , V75 (Pt 9) : P616-624 doi: 10.1107/S2053230X19011488
Structure of the dihydrolipoamide succinyltransferase catalytic domain from Escherichia coli in a novel crystal form: a tale of a common protein crystallization contaminant.
National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY 11973-5000, USA.
The crystallization of amidase, the ultimate enzyme in the Trp-dependent auxin-biosynthesis pathway, from Arabidopsis thaliana was attempted using protein samples with at least 95% purity. Cube-shaped crystals that were assumed to be amidase crystals that belonged to space group I4 (unit-cell parameters a = b = 128.6, c = 249.7 A) were obtained and diffracted to 3.0 A resolution. Molecular replacement using structures from the PDB containing the amidase signature fold as search models was unsuccessful in yielding a convincing solution. Using the Sequence-Independent Molecular replacement Based on Available Databases (SIMBAD) program, it was discovered that the structure corresponded to dihydrolipoamide succinyltransferase from Escherichia coli (PDB entry 1c4t), which is considered to be a common crystallization contaminant protein. The structure was refined to an Rwork of 23.0% and an Rfree of 27.2% at 3.0 A resolution. The structure was compared with others of the same protein deposited in the PDB. This is the first report of the structure of dihydrolipoamide succinyltransferase isolated without an expression tag and in this novel crystal form.
PMID: 31475929
Curr Protoc Mol Biol , 2019 Sep , V128 (1) : Pe104 doi: 10.1002/cpmb.104
Auxin-Inducible Degron System for Depletion of Proteins in Saccharomyces cerevisiae.
Department of Genetics, Harvard Medical School, Boston, Massachusetts.
The auxin-inducible degron (AID) is a powerful tool that is used for depletion of proteins to study their function in vivo. This method can conditionally induce the degradation of any protein by the proteasome simply by the addition of the plant hormone auxin. This approach is particularly valuable to study the function of essential proteins. The protocols provided here describe the steps to construct the necessary strains and to optimize auxin-inducible depletion in Saccharomyces cerevisiae. (c) 2019 by John Wiley & Sons, Inc. Basic Protocol 1: Construction of TIR1-expressing strains by transformation Basic Protocol 2: Tagging a yeast protein of interest with an auxin-inducible degron Support Protocol: Construction of depletion strains by genetic crosses Basic Protocol 3: Optimization for depletion of the auxin-inducible-degron-tagged protein.
PMID: 31503416