Nat Commun , IF:12.121 , 2019 Dec , V10 (1) : P5516 doi: 10.1038/s41467-019-13543-1
Brassinosteroid signaling delimits root gravitropism via sorting of the Arabidopsis PIN2 auxin transporter.
Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna (BOKU), Muthgasse 18, 1190, Wien, Austria.; Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojova 263 Praha 6, 165 02, Praha, Czech Republic.; Institute of Science and Technology Austria (IST Austria), Am Campus 1, 3400, Klosterneuburg, Austria.; Boehringer Ingelheim RCV, Doktor-Boehringer-Gasse 5-11, 1120, Wien, Austria.; Department of Experimental Plant Biology, Faculty of Science, Charles University, 128 44, Prague 2, Prague, Czech Republic.; Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna (BOKU), Muthgasse 18, 1190, Wien, Austria. christian.luschnig@boku.ac.at.
Arabidopsis PIN2 protein directs transport of the phytohormone auxin from the root tip into the root elongation zone. Variation in hormone transport, which depends on a delicate interplay between PIN2 sorting to and from polar plasma membrane domains, determines root growth. By employing a constitutively degraded version of PIN2, we identify brassinolides as antagonists of PIN2 endocytosis. This response does not require de novo protein synthesis, but involves early events in canonical brassinolide signaling. Brassinolide-controlled adjustments in PIN2 sorting and intracellular distribution governs formation of a lateral PIN2 gradient in gravistimulated roots, coinciding with adjustments in auxin signaling and directional root growth. Strikingly, simulations indicate that PIN2 gradient formation is no prerequisite for root bending but rather dampens asymmetric auxin flow and signaling. Crosstalk between brassinolide signaling and endocytic PIN2 sorting, thus, appears essential for determining the rate of gravity-induced root curvature via attenuation of differential cell elongation.
PMID: 31797871
Proc Natl Acad Sci U S A , IF:9.412 , 2019 Dec , V116 (50) : P25343-25354 doi: 10.1073/pnas.1911694116
HISTONE DEACETYLASE 9 stimulates auxin-dependent thermomorphogenesis in Arabidopsis thaliana by mediating H2A.Z depletion.
Molecular Plant Physiology, Institute of Environmental Biology, Utrecht University, 3584 CH Utrecht, The Netherlands.; Institute of Molecular, Cell & Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, G12 8QQ Glasgow, United Kingdom.; Trisaia Research Centre, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, 75026 Rotondella (Matera), Italy.; Theoretical Biology and Bioinformatics, Institute of Biodynamics and Biocomplexity, Utrecht University, 3584 CH Utrecht, The Netherlands.; Laboratory of Plant Physiology, Wageningen University, 6708 PB Wageningen, The Netherlands.; Umea Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-901 83 Umea, Sweden.; Laboratory of Growth Regulators, Institute of Experimental Botany, The Czech Academy of Sciences & Faculty of Science, Palacky University, 78371 Olomouc, Czech Republic.; Plant Microbe Interactions, Institute of Environmental Biology, Utrecht University, 3584 CH Utrecht, The Netherlands.; Laboratory of Molecular Biology, Wageningen University, 6708 PB Wageningen, The Netherlands.; School of Biological Sciences, Monash University, VIC 3800, Melbourne, Australia.; Molecular Plant Physiology, Institute of Environmental Biology, Utrecht University, 3584 CH Utrecht, The Netherlands; m.vanzanten@uu.nl.
Many plant species respond to unfavorable high ambient temperatures by adjusting their vegetative body plan to facilitate cooling. This process is known as thermomorphogenesis and is induced by the phytohormone auxin. Here, we demonstrate that the chromatin-modifying enzyme HISTONE DEACETYLASE 9 (HDA9) mediates thermomorphogenesis but does not interfere with hypocotyl elongation during shade avoidance. HDA9 is stabilized in response to high temperature and mediates histone deacetylation at the YUCCA8 locus, a rate-limiting enzyme in auxin biosynthesis, at warm temperatures. We show that HDA9 permits net eviction of the H2A.Z histone variant from nucleosomes associated with YUCCA8, allowing binding and transcriptional activation by PHYTOCHROME INTERACTING FACTOR 4, followed by auxin accumulation and thermomorphogenesis.
PMID: 31767749
Curr Opin Plant Biol , IF:8.356 , 2019 Dec , V52 : P155-163 doi: 10.1016/j.pbi.2019.10.001
Nitrate and hormonal signaling crosstalk for plant growth and development.
FONDAP Center for Genome Regulation, Millennium Institute for Integrative Biology (iBio), Chile; Departamento de Genetica Molecular y Microbiologia, Facultad de Ciencias Biologicas, Pontificia Universidad Catolica de Chile, Avda. Libertador Bernardo O'Higgins 340, Santiago, 8331150, Chile.; Departamento de Genetica Molecular y Microbiologia, Facultad de Ciencias Biologicas, Pontificia Universidad Catolica de Chile, Avda. Libertador Bernardo O'Higgins 340, Santiago, 8331150, Chile; Departamento de Fruticultura y Enologia, Facultad de Agronomia e Ingenieria Forestal, Pontificia Universidad Catolica de Chile, Chile.; FONDAP Center for Genome Regulation, Millennium Institute for Integrative Biology (iBio), Chile; Departamento de Genetica Molecular y Microbiologia, Facultad de Ciencias Biologicas, Pontificia Universidad Catolica de Chile, Avda. Libertador Bernardo O'Higgins 340, Santiago, 8331150, Chile. Electronic address: rgutierrez@bio.puc.cl.
Nitrate is an essential macronutrient for plants, a primary nitrogen source in natural and human-made ecosystems. Nitrate can also act as a signaling molecule that directs genome-wide gene expression changes with an impact on plant metabolism, physiology, growth and development. Nitrate and phytohormone signaling pathways crosstalk to modulate growth and developmental programs in a multifactorial manner. Nitrate-signaling controls plant growth and development using molecular mechanisms that involve phytohormone-signaling pathways. In contrast, many phytohormones modulate or impact nitrate signaling in interconnected pathways. In this review, we explore recent progress in our understanding of well-documented connections between nitrate and phytohormones such as auxin, cytokinin and abscisic acid. We also discuss recent studies connecting nitrate to other phytohormones such as ethylene, salicylic acid, gibberellins and brassinosteroids. While many molecular details remain to be elucidated, a number of core signaling components at the intersection between nitrate and the major hormonal pathways have been described. We focus on established interactions of nitrate and different hormonal pathways to bring about cellular, growth and developmental processes in Arabidopsis thaliana.
PMID: 31726384
Curr Opin Plant Biol , IF:8.356 , 2019 Dec , V52 : P54-60 doi: 10.1016/j.pbi.2019.07.005
Bridging the gap between amyloplasts and directional auxin transport in plant gravitropism.
Division of Plant Environmental Responses, National Institute for Basic Biology, Okazaki, 444-8585, Japan.; Division of Plant Environmental Responses, National Institute for Basic Biology, Okazaki, 444-8585, Japan; Department of Basic Biology, School of Life Sciences, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, 444-8585, Japan.; Division of Plant Environmental Responses, National Institute for Basic Biology, Okazaki, 444-8585, Japan; Department of Basic Biology, School of Life Sciences, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, 444-8585, Japan. Electronic address: mimorita@nibb.ac.jp.
Gravitropism is the directional control of plant organ growth in response to gravity. Specialized gravity-sensing cells contain amyloplasts that can change their position according to the direction of gravity. Gravity signaling, which is elicited by the relocation of amyloplasts, is a key process that redirects auxin transport from gravity-sensing cells to the lower flank of gravity-responsive organs. Despite the long history of research on plant gravitropism, a molecular detail of gravity signaling remained unexplained. Recent studies have characterized the Arabidopsis LAZY1 family genes to be key factors of gravity signaling. Furthermore, studies regarding Arabidopsis AGCVIII kinases have demonstrated the requirement of auxin transporter PIN-FORMED3 (PIN3) phosphorylation in plant gravitropism.
PMID: 31446250
Plant Biotechnol J , IF:8.154 , 2019 Dec , V17 (12) : P2325-2340 doi: 10.1111/pbi.13143
Comprehensive characterization of a floral mutant reveals the mechanism of hooked petal morphogenesis in Chrysanthemum morifolium.
State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, China.
The diversity of form of the chrysanthemum flower makes this species an ideal model for studying petal morphogenesis, but as yet, the molecular mechanisms underlying petal shape development remain largely unexplored. Here, a floral mutant, which arose as a bud sport in a plant of the variety 'Anastasia Dark Green', and formed straight, rather than hooked petals, was subjected to both comparative morphological analysis and transcriptome profiling. The hooked petals only became discernible during a late stage of flower development. At the late stage of 'Anastasia Dark Green', genes related to chloroplast, hormone metabolism, cell wall and microtubules were active, as were cell division-promoting factors. Auxin concentration was significantly reduced, and a positive regulator of cell expansion was down-regulated. Two types of critical candidates, boundary genes and adaxial-abaxial regulators, were identified from 7937 differentially expressed genes in pairwise comparisons, which were up-regulated at the late stage in 'Anastasia Dark Green' and another two hooked varieties. Ectopic expression of a candidate abaxial gene, CmYAB1, in chrysanthemum led to changes in petal curvature and inflorescence morphology. Our findings provide new insights into the regulatory networks underlying chrysanthemum petal morphogenesis.
PMID: 31050173
Elife , IF:7.08 , 2019 Dec , V8 doi: 10.7554/eLife.51061
Coordination of tissue cell polarity by auxin transport and signaling.
Department of Biological Sciences, University of Alberta, Edmonton, Canada.
Plants coordinate the polarity of hundreds of cells during vein formation, but how they do so is unclear. The prevailing hypothesis proposes that GNOM, a regulator of membrane trafficking, positions PIN-FORMED auxin transporters to the correct side of the plasma membrane; the resulting cell-to-cell, polar transport of auxin would coordinate tissue cell polarity and induce vein formation. Contrary to predictions of the hypothesis, we find that vein formation occurs in the absence of PIN-FORMED or any other intercellular auxin-transporter; that the residual auxin-transport-independent vein-patterning activity relies on auxin signaling; and that a GNOM-dependent signal acts upstream of both auxin transport and signaling to coordinate tissue cell polarity and induce vein formation. Our results reveal synergism between auxin transport and signaling, and their unsuspected control by GNOM in the coordination of tissue cell polarity during vein patterning, one of the most informative expressions of tissue cell polarization in plants.
PMID: 31793881
Plant J , IF:6.141 , 2019 Dec , V100 (6) : P1224-1236 doi: 10.1111/tpj.14511
AtHB23 participates in the gene regulatory network controlling root branching, and reveals differences between secondary and tertiary roots.
Instituto de Agrobiotecnologia del Litoral, Universidad Nacional del Litoral, CONICET, FBCB, Centro Cientifico Tecnologico CONICET Santa Fe, Colectora Ruta Nacional No 168 km. 0, Paraje El Pozo, 3000, Santa Fe, Argentina.
In Arabidopsis, lateral root (LR) development is mainly controlled by several known auxin-regulated transcription factors (TFs). Here, we show that AtHB23 (a homeodomain-leucine zipper I TF) participates in this intricate network. Our study of the expression pattern of AtHB23 revealed that it is transcriptionally activated in the early stages of secondary LR primordium (LRP). We found that AtHB23 directly limits the expression of LBD16, a key factor in LR initiation, and also directly induces the auxin transporter gene LAX3. We propose that this HD-Zip I mediates the regulation of LAX3 by ARF7/19. Furthermore, AtHB23 plays distinct roles during the formation of secondary and tertiary roots, exhibiting differential expression patterns. ATHB23 is expressed throughout the tertiary root primordium, whereas it is restricted to early stages in secondary primordia, likely later repressing LBD16 in tertiary LR development and further inhibiting root emergence. Our results suggest that different genetic programs govern the formation of LRP from the main or secondary roots, thereby shaping the global dynamic architecture of the root system.
PMID: 31444832
Plant J , IF:6.141 , 2019 Dec , V100 (5) : P954-968 doi: 10.1111/tpj.14487
Inference of the gene regulatory network acting downstream of CROWN ROOTLESS 1 in rice reveals a regulatory cascade linking genes involved in auxin signaling, crown root initiation, and root meristem specification and maintenance.
UMR DIADE, Universite de Montpellier, IRD, 911 Avenue Agropolis, 34394, Montpellier Cedex 5, France.; Centre de Recherches de Chappes, Biogemma, Route d'Ennezat, 63720, Chappes, France.
Crown roots (CRs) are essential components of the rice root system. Several genes involved in CR initiation or development have been identified but our knowledge about how they organize to form a gene regulatory network (GRN) is still limited. To characterize the regulatory cascades acting during CR formation, we used a systems biology approach to infer the GRN controlling CR formation downstream of CROWN ROOTLESS 1 (CRL1), coding for an ASL (asymmetric leaves-2-like)/LBD (LOB domain) transcription factor necessary for CR initiation. A time-series transcriptomic dataset was generated after synchronized induction of CR formation by dexamethasone-mediated expression of CRL1 expression in a crl1 mutant background. This time series revealed three different genome expression phases during the early steps of CR formation and was further exploited to infer a GRN using a dedicated algorithm. The predicted GRN was confronted with experimental data and 72% of the inferred links were validated. Interestingly, this network revealed a regulatory cascade linking CRL1 to other genes involved in CR initiation, root meristem specification and maintenance, such as QUIESCENT-CENTER-SPECIFIC HOMEOBOX, and in auxin signalling. This predicted regulatory cascade was validated in vivo using transient activation assays. Thus, the CRL1-dependant GRN reflects major gene regulation events at play during CR formation and constitutes a valuable source of discovery to better understand this developmental process.
PMID: 31369175
J Exp Bot , IF:5.908 , 2019 Dec doi: 10.1093/jxb/erz554
NRT1.1 in plants: functions beyond nitrate transporter.
State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, the Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China.
Arabidopsis AtNRT1.1 (CHL1/AtNPF6.3) is the first identified nitrate transporter in plants and initially featured in nitrate uptake and transport. It is also found that AtNRT1.1 displays auxin transport activity and thus mediates nitrate-modulated root development, suggesting that it has transport capacities of multiple substrates. Subsequent work revealed that AtNRT1.1 can respond to the environmental nitrate fluctuation via altering its nitrate transport activity modulated by phosphorylation, leading to the critical finding that AtNRT1.1 actually acts as a transceptor for nitrate sensing. Recent studies further revealed how OsNRT1.1B, the functional homologue of AtNRT1.1 in rice, mediates the nitrate signal transduction from the plasma membrane to the nucleus, and how OsNRT1.1B integrates nitrate and phosphate signaling network. It is also shown that OsNRT1.1B is involved in regulating the root microbiota to facilitate organic nitrogen mineralization in soil, thus mediating the plant-microbe interaction. Furthermore, the divergent functions of rice OsNRT1.1A and OsNRT1.1B in regulating nitrogen utilization suggest that the function of NRT1.1 is still far from fully understood. In this review, we focus on the most recent progress on molecular mechanisms of NRT1.1s in plants, with the aim to provide an evolved view for the versatile functions of NRT1.1 in nitrogen utilization in plants.
PMID: 31832669
Int J Mol Sci , IF:4.556 , 2019 Dec , V20 (24) doi: 10.3390/ijms20246343
The Roles of Auxin Biosynthesis YUCCA Gene Family in Plants.
College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212003, China.; Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agricultural and Rural Areas, Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang 212018, China.
Auxin plays essential roles in plant normal growth and development. The auxin signaling pathway relies on the auxin gradient within tissues and cells, which is facilitated by both local auxin biosynthesis and polar auxin transport (PAT). The TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS (TAA)/YUCCA (YUC) pathway is the most important and well-characterized pathway that plants deploy to produce auxin. YUCs function as flavin-containing monooxygenases (FMO) catalyzing the rate-limiting irreversible oxidative decarboxylation of indole-3-pyruvate acid (IPyA) to form indole-3-acetic acid (IAA). The spatiotemporal dynamic expression of different YUC gene members finely tunes the local auxin biosynthesis in plants, which contributes to plant development as well as environmental responses. In this review, the recent advances in the identification, evolution, molecular structures, and functions in plant development and stress response regarding the YUC gene family are addressed.
PMID: 31888214
Int J Mol Sci , IF:4.556 , 2019 Dec , V21 (1) doi: 10.3390/ijms21010179
Analysis of the Barley Malt Rootlet Proteome.
USDA-ARS, Cereal Crops Research Unit, Madison, WI 53726, USA.
Barley seeds are one of the main ingredients of the malting industry for brewing beer. The barley rootlets that are separated from the kilned seeds at the end of the malting process and used as animal feed are one of the byproducts of this industry. In this study, the proteome of rootlets derived from two stages of the malting process, germination and kilning, from a popular malting barley variety were analyzed. A label-free shotgun proteomics strategy was used to identify more than 800 proteins from the barley rootlets. A high coverage and high confidence Gene Ontology annotations of the barley genome was used to facilitate the functional annotation of the proteins that were identified in the rootlets. An analysis of these proteins using Kellogg Encyclopedia of Genes and Genomes (KEGG) and Plant Reactome databases indicated the enrichment of pathways associated with phytohormones, protein biosynthesis, secondary metabolism, and antioxidants. Increased levels of jasmonic acid and auxin in the rootlets further supported the in silico analysis. As a rich source of proteins and amino acids use of these by-products of the malting industry for animal feed is validated. This study also indicates rootlets as a potential source of naturally occurring phenylpropanoids and antioxidants that can be further exploited in the development of functional foods.
PMID: 31887991
Int J Mol Sci , IF:4.556 , 2019 Dec , V21 (1) doi: 10.3390/ijms21010014
Genome-Wide Characterization and Gene Expression Analyses of GATA Transcription Factors in Moso Bamboo (Phyllostachys edulis).
Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China.; Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.; College of Biopharmaceutical and Food Engineering, Shangluo University, Shangluo 726000, China.; Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095, USA.
Moso bamboo is well-known for its rapid-growth shoots and widespread rhizomes. However, the regulatory genes of these two processes are largely unexplored. GATA transcription factors regulate many developmental processes, but their roles in moso bamboo height control and rhizome development remains unexplored. Here, thirty-one bamboo GATA factors (PeGATAs) were identified, which are evolutionarily closer to rice than Arabidopsis, and their gene expression patterns were analyzed in bamboo development and phytohormone response with bioinformatics and molecular methods. Interestingly, PeGATAs could only be classified into three groups. Phytohormone responsive cis-elements were found in PeGATA promoters and the expression profiles showed that PeGATA genes might respond to gibberellin acid and abscisic acid but not to auxin at the transcriptional level. Furthermore, PeGATA genes have a tissue-specific expression pattern in bamboo rhizomes. Interestingly, most PeGATA genes were down-regulated during the rapid-growth of bamboo shoots. In addition, over-expressing one of the PeGATA genes, PeGATA26, significantly repressed the primary root length and plant height of transgenic Arabidopsis plants, which may be achieved by promoting the gibberellin acid turnover. Overall, our results provide insight into the function of GATA transcription factors in bamboo, and into genetic resources for engineering plant height.
PMID: 31861396
Int J Mol Sci , IF:4.556 , 2019 Dec , V20 (24) doi: 10.3390/ijms20246270
Comparing and Contrasting the Multiple Roles of Butenolide Plant Growth Regulators: Strigolactones and Karrikins in Plant Development and Adaptation to Abiotic Stresses.
Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China.
Strigolactones (SLs) and karrikins (KARs) are both butenolide molecules that play essential roles in plant growth and development. SLs are phytohormones, with SLs having known functions within the plant they are produced in, while KARs are found in smoke emitted from burning plant matter and affect seeds and seedlings in areas of wildfire. It has been suggested that SL and KAR signaling may share similar mechanisms. The alpha/beta hydrolases DWARF14 (D14) and KARRIKIN INSENSITIVE 2 (KAI2), which act as receptors of SL and KAR, respectively, both interact with the F-box protein MORE AXILLARY GROWTH 2 (MAX2) in order to target SUPPRESSOR OF MAX2 1 (SMAX1)-LIKE/D53 family members for degradation via the 26S proteasome. Recent reports suggest that SLs and/or KARs are also involved in regulating plant responses and adaptation to various abiotic stresses, particularly nutrient deficiency, drought, salinity, and chilling. There is also crosstalk with other hormone signaling pathways, including auxin, gibberellic acid (GA), abscisic acid (ABA), cytokinin (CK), and ethylene (ET), under normal and abiotic stress conditions. This review briefly covers the biosynthetic and signaling pathways of SLs and KARs, compares their functions in plant growth and development, and reviews the effects of any crosstalk between SLs or KARs and other plant hormones at various stages of plant development. We also focus on the distinct responses, adaptations, and regulatory mechanisms related to SLs and/or KARs in response to various abiotic stresses. The review closes with discussion on ways to gain additional insights into the SL and KAR pathways and the crosstalk between these related phytohormones.
PMID: 31842355
Int J Mol Sci , IF:4.556 , 2019 Dec , V20 (24) doi: 10.3390/ijms20246138
Comparative Transcriptome Profiling of Resistant and Susceptible Sugarcane Cultivars in Response to Infection by Xanthomonas albilineans.
National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou 350002, China.; BGPI, INRA, CIRAD, SupAgro, Univ Montpellier, 34398 Montpellier, France.; Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD 4072, Australia.
Sugarcane (Saccharum spp. hybrids) is a major source of sugar and renewable bioenergy crop worldwide and suffers serious yield losses due to many pathogen infections. Leaf scald caused by Xanthomonas albilineans is a major bacterial disease of sugarcane in most sugarcane-planting countries. The molecular mechanisms of resistance to leaf scald in this plant are, however, still unclear. We performed a comparative transcriptome analysis between resistant (LCP 85-384) and susceptible (ROC20) sugarcane cultivars infected by X. albilineans using the RNA-seq platform. 24 cDNA libraries were generated with RNA isolated at four time points (0, 24, 48, and 72 h post inoculation) from the two cultivars with three biological replicates. A total of 105,783 differentially expressed genes (DEGs) were identified in both cultivars and the most upregulated and downregulated DEGs were annotated for the processes of the metabolic and single-organism categories, respectively. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of the 7612 DEGs showed that plant-pathogen interaction, spliceosome, glutathione metabolism, protein processing in endoplasmic reticulum, and plant hormone signal transduction contributed to sugarcane's response to X. albilineans infection. Subsequently, relative expression levels of ten DEGs determined by quantitative reverse transcription-PCR (qRT-PCR), in addition to RNA-Seq data, indicated that different plant hormone (auxin and ethylene) signal transduction pathways play essential roles in sugarcane infected by X. albilineans. In conclusion, our results provide, for the first time, valuable information regarding the transcriptome changes in sugarcane in response to infection by X. albilineans, which contribute to the understanding of the molecular mechanisms underlying the interactions between sugarcane and this pathogen and provide important clues for further characterization of leaf scald resistance in sugarcane.
PMID: 31817492
Int J Mol Sci , IF:4.556 , 2019 Dec , V20 (24) doi: 10.3390/ijms20246120
CRK5 Protein Kinase Contributes to the Progression of Embryogenesis of Arabidopsis thaliana.
Institute of Plant Biology, Biological Research Centre, 6726 Szeged, Hungary.; Doctoral School in Biology, Faculty of Science and Informatics, University of Szeged, 6720 Szeged, Hungary.; Department of Botany, Bhavan's College Andheri West, Mumbai 400058, India.; Developmental and Cell Biology of Plants, CEITEC Masaryk University, 62500 Brno, Czech Republic.; Department of Plant Biology, University of Szeged, 52. Kozepfasor, H-6726 Szeged, Hungary.; Proteomics Research Group, Biological Research Centre, 6726 Szeged, Hungary.
The fine tuning of hormone (e.g., auxin and gibberellin) levels and hormone signaling is required for maintaining normal embryogenesis. Embryo polarity, for example, is ensured by the directional movement of auxin that is controlled by various types of auxin transporters. Here, we present pieces of evidence for the auxin-gibberellic acid (GA) hormonal crosstalk during embryo development and the regulatory role of the Arabidopsis thaliana Calcium-Dependent Protein Kinase-Related Kinase 5 (AtCRK5) in this regard. It is pointed out that the embryogenesis of the Atcrk5-1 mutant is delayed in comparison to the wild type. This delay is accompanied with a decrease in the levels of GA and auxin, as well as the abundance of the polar auxin transport (PAT) proteins PIN1, PIN4, and PIN7 in the mutant embryos. We have previously showed that AtCRK5 can regulate the PIN2 and PIN3 proteins either directly by phosphorylation or indirectly affecting the GA level during the root gravitropic and hypocotyl hook bending responses. In this manuscript, we provide evidence that the AtCRK5 protein kinase can in vitro phosphorylate the hydrophilic loops of additional PIN proteins that are important for embryogenesis. We propose that AtCRK5 can govern embryo development in Arabidopsis through the fine tuning of auxin-GA level and the accumulation of certain polar auxin transport proteins.
PMID: 31817249
Theor Appl Genet , IF:4.439 , 2019 Dec , V132 (12) : P3321-3331 doi: 10.1007/s00122-019-03427-9
Characterization and fine mapping of qkrnw4, a major QTL controlling kernel row number in maize.
Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.; College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China.; Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China. liyongxiang@caas.cn.; Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China. shiyunsu@caas.cn.
KEY MESSAGE: A major QTL controlling kernel row number, qkrnw4, was identified by combining linkage analysis and association mapping. Within qkrnw4, on the basis of its expression and bioinformatics analysis, Zm00001d052910 was supposed to be the candidate gene for kernel row number. Kernel row number (KRN) is an important yield-related trait that affects kernel number in maize. Understanding the genetic basis of KRN is important for increasing maize yields. In the present study, by the use of a near-isogenic line (NIL) that has a B73 background and that consistently displays a low KRN across environments, qkrnw4, a major quantitative trait locus (QTL) associated with KRN within a yield trait-related QTL hotspot in bin 4.08, was finely mapped to an ~ 33-kb interval. Regional association analysis of a nested association mapping population comprising 5000 recombinant inbred lines revealed Zm00001d052910, which encodes a protein with an unknown function, as the important candidate gene responsible for qkrnw4. Different expression levels of this candidate gene in immature ears were detected between the NIL and its recurrent parent. Moreover, the expression of several auxin-related genes was consistent with that of the candidate gene. Furthermore, the potential associations of this candidate gene with well-known inflorescence-related genes were discussed. The results of this study provide important information for the genetic elucidation of KRN variation in maize.
PMID: 31555888
J Biol Chem , IF:4.238 , 2019 Dec , V294 (52) : P19923-19933 doi: 10.1074/jbc.RA119.010480
A phenotype-directed chemical screen identifies ponalrestat as an inhibitor of the plant flavin monooxygenase YUCCA in auxin biosynthesis.
Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology (SUSTech), Shenzhen, Guangdong 518055, China.; State Key Laboratory of Protein and Plant Gene Research, College of Life Science, Peking University, Beijing 100871, China.; Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education and Beijing National Laboratory for Molecular Science (BNLMS), and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China.; Max-Planck Institute for Plant Breeding Research, Cologne 50829, Germany.; Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037.; Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology (SUSTech), Shenzhen, Guangdong 518055, China jiangk@sustech.edu.cn.; SUSTech Academy for Advanced and Interdisciplinary Studies, Southern University of Science and Technology (SUSTech), Shenzhen, Guangdong 518055, China.; Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology (SUSTech), Shenzhen, Guangdong 518055, China guohw@sustech.edu.cn.
Plant development is regulated by both synergistic and antagonistic interactions of different phytohormones, including a complex crosstalk between ethylene and auxin. For instance, auxin and ethylene synergistically control primary root elongation and root hair formation. However, a lack of chemical agents that specifically modulate ethylene or auxin production has precluded precise delineation of the contribution of each hormone to root development. Here, we performed a chemical genetic screen based on the recovery of root growth in ethylene-related Arabidopsis mutants with constitutive "short root" phenotypes (eto1-2 and ctr1-1). We found that ponalrestat exposure recovers root elongation in these mutants in an ethylene signal-independent manner. Genetic and pharmacological investigations revealed that ponalrestat inhibits the enzymatic activity of the flavin-containing monooxygenase YUCCA, which catalyzes the rate-limiting step of the indole-3-pyruvic acid branch of the auxin biosynthesis pathway. In summary, our findings have identified a YUCCA inhibitor that may be useful as a chemical tool to dissect the distinct steps in auxin biosynthesis and in the regulation of root development.
PMID: 31732559
Plant Cell Physiol , IF:4.062 , 2019 Dec , V60 (12) : P2648-2659 doi: 10.1093/pcp/pcz201
Jasmonate Signaling during Arabidopsis Stamen Maturation.
Max Planck Institute for Plant Breeding Research, Carl-von-Linni inverted question mark(1/2)-Weg 10, 50829 Cologne, Germany.
The last stages of stamen development, collectively called stamen maturation, encompass pollen viability, filament elongation and anther dehiscence or opening. These processes are essential for male fertility in Arabidopsis and require the function of jasmonate signaling. There is a good understanding of jasmonate synthesis, perception and transcriptional outputs in Arabidopsis stamens. In addition, the spatiotemporal localization of jasmonate signaling components at the tissue and cellular levels has started to emerge in recent years. However, the ultimate cellular functions activated by jasmonate to promote stamen maturation remain unknown. The hormones auxin and gibberellin have been proposed to control the activation of jasmonate synthesis to promote stamen maturation, although we hypothesize that this action is rather indirect. In this review, we examine these different areas, attempt to clarify some confusing aspects found in the literature and raise testable hypothesis that may help to further understand how jasmonate controls male fertility in Arabidopsis.
PMID: 31651948
Plant Cell Physiol , IF:4.062 , 2019 Dec , V60 (12) : P2720-2732 doi: 10.1093/pcp/pcz159
Functional Divergence of PIN1 Paralogous Genes in Rice.
State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China.
Auxin is a phytohormone that plays an important role in plant growth and development by forming local concentration gradients. The regulation of auxin levels is determined by the activity of auxin efflux carrier protein PIN-formed (PIN). In Arabidopsis thaliana, PIN-formed1 (PIN1) functions in inflorescence and root development. In rice (Oryza sativa L.), there are four PIN1 homologs (OsPIN1a-1d), but their functions remain largely unexplored. Hence, in this study, we created mutant alleles of PIN1 gene-pin1a, pin1b, pin1c, pin1d, pin1a pin1b and pin1c pin1d- using CRISPR/Cas9 technology and used them to study the functions of the four OsPIN1 paralogs in rice. In wild-type rice, all four OsPIN1 genes were relatively highly expressed in the root than in other tissues. Compared with the wild type, the OsPIN1 single mutants had no dramatic phenotypes, but the pin1a pin1b double mutant had shorter shoots and primary roots, fewer crown roots, reduced root gravitropism, longer root hairs and larger panicle branch angle. Furthermore, the pin1c pin1d double mutant showed no observable phenotype at the seedling stage, but showed naked, pin-shape inflorescence at flowering. These data suggest that OsPIN1a and OsPIN1b are involved in root, shoot and inflorescence development in rice, whereas OsPIN1c and OsPIN1d mainly function in panicle formation. Our study provides basic knowledge that will facilitate the study of auxin transport and signaling in rice.
PMID: 31410483
Plant Cell Physiol , IF:4.062 , 2019 Dec , V60 (12) : P2684-2691 doi: 10.1093/pcp/pcz156
A Positive Feedback Loop Comprising LHW-TMO5 and Local Auxin Biosynthesis Regulates Initial Vascular Development in Arabidopsis Roots.
Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan.; Plant Productivity Systems Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045 Japan.; Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, 464-8601 Japan.
The phytohormone auxin governs various developmental processes in plants including vascular formation. Auxin transport and biosynthesis are important factors in determining auxin distribution in tissues. Although the role of auxin transport in vein pattern formation is widely recognized, that of auxin biosynthesis in vascular development is poorly understood. Heterodimer complexes comprising two basic helix-loop-helix protein families, LONESOME HIGHWAY (LHW) and TARGET OF MONOPTEROS5 (TMO5)/TMO5-LIKE1 (T5L1), are master transcriptional regulators of the initial process of vascular development. The LHW-TMO5/T5L1 dimers regulate vascular initial cell production, vascular cell proliferation and xylem fate determination in the embryo and root apical meristem (RAM). In this study, we investigated the function of local auxin biosynthesis in initial vascular development in RAM. Results showed that LHW-T5L1 upregulated the expression of YUCCA4 (YUC4), a key auxin biosynthesis gene. The expression of YUC4 was essential for promoting xylem differentiation and vascular cell proliferation in RAM. Conversely, auxin biosynthesis was required for maintaining the expression levels of LHW, TMO5/T5L1 and their targets. Our results suggest that local auxin biosynthesis forms a positive feedback loop for fine-tuning the level of LHW-TMO5/T5L1, which is necessary for initiating vascular development.
PMID: 31392340
Sci Rep , IF:3.998 , 2019 Dec , V9 (1) : P18645 doi: 10.1038/s41598-019-55195-7
Deletion in the Promoter of PcPIN-L Affects the Polar Auxin Transport in Dwarf Pear (Pyrus communis L.).
College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China.; Qingdao Key Laboratory of Genetic Improvement and Breeding in Horticulture Plants, Qingdao, 266109, China.; College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China. chw6068@126.com.; Qingdao Key Laboratory of Genetic Improvement and Breeding in Horticulture Plants, Qingdao, 266109, China. chw6068@126.com.
Dwarf cultivars or dwarfing rootstocks enable high-density planting and are therefore highly desirable in modern pear production. Previously, we found that the dwarf growth habit of pear is controlled by a single dominant gene PcDw. In this study, PcPIN-L (PCP021016) was cloned from dwarf-type and standard-type pears. PcPIN-L expression was significantly lower in the dwarf-type pears than in standard-type pears, which was caused by the CT repeat deletion in the promoter of dwarf-type pears. PcPIN-L overexpression in tobacco plants enhanced the growth of the stems and the roots. Notably, the indole acetic acid (IAA) content decreased in the shoot tips and increased in the stems of transgenic lines compared with wild type, which is consistent with the greater IAA content in the shoot tips and lower IAA content in the stems of dwarf-type pears than in standard-type pears. The CT repeat deletion in the promoter that causes a decrease in promoter activity is associated with lower PcPIN-L expression in the dwarf-type pears, which might limit the polar auxin transport and in turn result in the dwarf phenotype. Taken together, the results provide a novel dwarfing molecular mechanism in perennial woody plants.
PMID: 31819123
Sci Rep , IF:3.998 , 2019 Dec , V9 (1) : P18191 doi: 10.1038/s41598-019-54340-6
Expressivity of the key genes associated with seed and pod development is highly regulated via lncRNAs and miRNAs in Pigeonpea.
ICAR- National Research Centre on Plant Biotechnology, New Delhi, India.; Division of Genetics, ICAR-IARI, New Delhi, India.; ICAR- National Research Centre on Plant Biotechnology, New Delhi, India. kish2012@gmail.com.
Non-coding RNA's like miRNA, lncRNA, have gained immense importance as a significant regulatory factor in different physiological and developmental processes in plants. In an effort to understand the molecular role of these regulatory agents, in the present study, 3019 lncRNAs and 227 miRNAs were identified from different seed and pod developmental stages in Pigeonpea, a major grain legume of Southeast Asia and Africa. Target analysis revealed that 3768 mRNAs, including 83 TFs were targeted by lncRNAs; whereas 3060 mRNA, including 154 TFs, were targeted by miRNAs. The targeted transcription factors majorly belong to WRKY, MYB, bHLH, etc. families; whereas the targeted genes were associated with the embryo, seed, and flower development. Total 302 lncRNAs interact with miRNAs and formed endogenous target mimics (eTMs) which leads to sequestering of the miRNAs present in the cell. Expression analysis showed that notably, Cc_lncRNA-2830 expression is up-regulated and sequestrates miR160h in pod leading to higher expression of the miR160h target gene, Auxin responsive factor-18. A similar pattern was observed for SPIKE, Auxin signaling F-box-2, Bidirectional sugar transporter, and Starch synthetase-2 eTMs. All the identified target mRNAs code for transcription factor and genes are involved in the processes like cell division, plant growth and development, starch synthesis, sugar transportation and accumulation of storage proteins which are essential for seed and pod development. On a combinatorial basis, our study provides a lncRNA and miRNA based regulatory insight into the genes governing seed and pod development in Pigeonpea.
PMID: 31796783
Rice (N Y) , IF:3.912 , 2019 Dec , V12 (1) : P92 doi: 10.1186/s12284-019-0357-z
OsIAGT1 Is a Glucosyltransferase Gene Involved in the Glucose Conjugation of Auxins in Rice.
The Key Lab of Plant Development and Environment Adaptation Biology, Ministry of Education of China, School of Life Sciences, Shandong University, Qingdao, 266237, China.; Present Address: Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.; The Key Lab of Plant Development and Environment Adaptation Biology, Ministry of Education of China, School of Life Sciences, Shandong University, Qingdao, 266237, China. bkhou@sdu.edu.cn.
BACKGROUND: In cereal crop rice, auxin is known as an important class of plant hormone that regulates a plethora of plant growth and development. Glycosylation of auxin is known to be one of the important mechanisms mediating auxin homeostasis. However, the relevant auxin glucosyltransferase (GT) in rice still remains largely unknown. RESULTS: In this study, using known auxin glucosyltransferases from other species as queries, twelve putative auxin UDP-glycosyltransferase (UGT) genes were cloned from rice and the one showing highest sequence similarity, named as OsIAGT1, was expressed as recombinant protein. In vitro enzymatic analysis showed that recombinant OsIAGT1 was capable of catalyzing glucosylation of IAA, IBA and other auxin analogs, and that OsIAGT1 is quite tolerant to a broad range of reaction conditions with peak activity at 30 degrees capital ES, Cyrillic and pH 8.0. OsIAGT1 showed favorite activity towards native auxins over artificially synthesized ones. Further study indicated that expression of OsIAGT1 can be upregulated by auxin in rice, and with OsIAGT1 overexpressing lines we confirmed that OsIAGT1 is indeed able to glucosylate IAA in vivo. Consistently, ectopic expression of OsIAGT1 leads to declined endogenous IAA content, as well as upregulated auxin synthesis genes and reduced expression of auxin-responsive genes, which likely leads to the reduced plant stature and root length in OsIAGT1 overexpression lines. CONCLUSION: Our result indicated that OsIAGT1 plays an important role in mediating auxin homeostasis by catalyzing auxin glucosylation, and by which OsIAGT1 regulates growth and development in rice.
PMID: 31853664
Rice (N Y) , IF:3.912 , 2019 Dec , V12 (1) : P91 doi: 10.1186/s12284-019-0344-4
The Rice G Protein gamma Subunit DEP1/qPE9-1 Positively Regulates Grain-Filling Process by Increasing Auxin and Cytokinin Content in Rice Grains.
Department of Biology, Southern University of Science and Technology, Shenzhen, 518055, China.; Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China.; Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China. ricegb@yzu.edu.cn.; Department of Biology, Southern University of Science and Technology, Shenzhen, 518055, China. liangjs@sustech.edu.cn.
Heterotrimeric G protein-mediated signal transduction is one of the most important and highly conserved signaling pathways in eukaryotes, which involves in the regulation of many important biological processes. As compared with those in mammals and Arabidopsis thaliana, the functions of rice heterotrimeric G protein and their molecular mechanisms are largely unknown. The rice genome contains a single Galpha (RGA1) and Gbeta (RGB1), and five Ggamma (RGG1, RGG2, GS3, DEP1/qPE9-1, and GGC2) subunits. Recent genetic studies have shown that DEP1/qPE9-1, an atypical putative Ggamma protein, is responsible for the grain size as well as the dense and erect panicles, but the biochemical and molecular mechanisms underlying the control of grain size are not well understood. Here, we report that rice plants carrying DEP1/qPE9-1 have more endosperm cells per grain than plants contain the dep1/qpe9-1 allele. The DEP1/qPE9-1 line has a higher rate and more prolonged period of starch accumulation than the dep1/qpe9-1 line. Additionally, the expression of several essential genes encoding enzymes catalyzing sucrose metabolism and starch biosynthesis is higher in the DEP1/qPE9-1 line than in the dep1/qpe9-1 line, especially from the mid to late grain-filling stage. Grains of the DEP1/qPE9-1 line also have higher contents of three phytohormones, ABA, auxin and cytokinin. Exogenous application of auxin or cytokinin enhanced the starch accumulation and the expression of genes encoding grain-filling-related enzymes in the grains of dep1/qpe9-1, whereas ABA produced no effects. Based on these results, we conclude that DEP1/qPE9-1 positively regulates starch accumulation primarily through auxin and cytokinin, which enhance the expression of genes encoding starch biosynthesis during the mid to late grain-filling stage, resulting in increased duration of the grain-filling process.
PMID: 31844998
Genes (Basel) , IF:3.759 , 2019 Dec , V11 (1) doi: 10.3390/genes11010026
Sugar Transporter, CmSWEET17, Promotes Bud Outgrowth in Chrysanthemum Morifolium.
State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
We previously demonstrated that 20 mM sucrose promotes the upper axillary bud outgrowth in two-node stems of Chrysanthemum morifolium. In this study, we aimed to screen for potential genes involved in this process. Quantitative reverse transcription (qRT)-PCR analysis of sugar-related genes in the upper axillary bud of plants treated with 20 mM sucrose revealed the specific expression of the gene CmSWEET17. Expression of this gene was increased in the bud, as well as the leaves of C. morifolium, following exogenous sucrose treatment. CmSWEET17 was isolated from C. morifolium and a subcellular localization assay confirmed that the protein product was localized in the cell membrane. Overexpression of CmSWEET17 promoted upper axillary bud growth in the two-node stems treatment as compared with the wild-type. In addition, the expression of auxin transporter genes CmAUX1, CmLAX2, CmPIN1, CmPIN2, and CmPIN4 was upregulated in the upper axillary bud of CmSWEET17 overexpression lines, while indole-3-acetic acid content decreased. The results suggest that CmSWEET17 could be involved in the process of sucrose-induced axillary bud outgrowth in C. morifolium, possibly via the auxin transport pathway.
PMID: 31878242
Genes (Basel) , IF:3.759 , 2019 Dec , V10 (12) doi: 10.3390/genes10121034
Identification of Shoot Differentiation-Related Genes in Populus euphratica Oliv.
Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China.; Center for Statistical Genetics, The Pennsylvania State University, Hershey, PA 17033, USA.
De novo shoot regeneration is one of the important manifestations of cell totipotency in organogenesis, which reflects a survival strategy organism evolved when facing natural selection. Compared with tissue regeneration, and somatic embryogenesis, de novo shoot regeneration denotes a shoot regeneration process directly from detatched or injured tissues of plant. Studies on plant shoot regeneration had identified key genes mediating shoot regeneration. However, knowledge was derived from Arabidopsis; the regeneration capacity is hugely distinct among species. To achieve a comprehensive understanding of the shoot regeneration mechanism from tree species, we select four genetic lines of Populus euphratica from a natural population to be sequenced at transcriptome level. On the basis of the large difference of differentiation capacity, between the highly differentiated (HD) and low differentiated (LD) groups, the analysis of differential expression identified 4920 differentially expressed genes (DEGs), which were revealed in five groups of expression patterns by clustering analysis. Enrichment showed crucial pathways involved in regulation of regeneration difference, including "plant hormone signal transduction", "cell differentiation", "cellular response to auxin stimulus", and "auxin-activated signaling pathway". The expression of nine genes reported to be associated with shoot regeneration was validated using quantitative real-time PCR (qRT-PCR). For the specificity of regeneration mechanism with P. euphratica, large amount of DEGs involved in "plant-pathogen interaction", ubiquitin-26S proteosome mediated proteolysis pathway, stress-responsive DEGs, and senescence-associated DEGs were summarized to possibly account for the differentiation difference with distinct genotypes of P. euphratica. The result in this study helps screening of key regulators in mediating the shoot differentiation. The transcriptomic characteristic in P. euphratica further enhances our understanding of key processes affecting the regeneration capacity of de novo shoots among distinct species.
PMID: 31835855
Genes (Basel) , IF:3.759 , 2019 Dec , V10 (12) doi: 10.3390/genes10121012
Plant Hormones Differentially Control the Sub-Cellular Localization of Plasma Membrane Microdomains during the Early Stage of Soybean Nodulation.
Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA.; Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA.; Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Beadle Center, Lincoln, NE 68503, USA.
Phytohormones regulate the mutualistic symbiotic interaction between legumes and rhizobia, nitrogen-fixing soil bacteria, notably by controlling the formation of the infection thread in the root hair (RH). At the cellular level, the formation of the infection thread is promoted by the translocation of plasma membrane microdomains at the tip of the RH. We hypothesize that phytohormones regulate the translocation of plasma membrane microdomains to regulate infection thread formation. Accordingly, we treated with hormone and hormone inhibitors transgenic soybean roots expressing fusions between the Green Fluorescent Protein (GFP) and GmFWL1 or GmFLOT2/4, two microdomain-associated proteins translocated at the tip of the soybean RH in response to rhizobia. Auxin and cytokinin treatments are sufficient to trigger or inhibit the translocation of GmFWL1 and GmFLOT2/4 to the RH tip independently of the presence of rhizobia, respectively. Unexpectedly, the application of salicylic acid, a phytohormone regulating the plant defense system, also promotes the translocation of GmFWL1 and GmFLOT2/4 to the RH tip regardless of the presence of rhizobia. These results suggest that phytohormones are playing a central role in controlling the early stages of rhizobia infection by regulating the translocation of plasma membrane microdomains. They also support the concept of crosstalk of phytohormones to control nodulation.
PMID: 31817452
Plant Physiol Biochem , IF:3.72 , 2019 Dec , V145 : P164-173 doi: 10.1016/j.plaphy.2019.10.033
Melatonin application reduces fluoride uptake and toxicity in rice seedlings by altering abscisic acid, gibberellin, auxin and antioxidant homeostasis.
Post Graduate Department of Biotechnology, St. Xavier's College (Autonomous), 30, Mother Teresa Sarani, Kolkata, 700016, West Bengal, India.; Post Graduate Department of Biotechnology, St. Xavier's College (Autonomous), 30, Mother Teresa Sarani, Kolkata, 700016, West Bengal, India. Electronic address: aryadeep.rc@gmail.com.
The manuscript presents an elaborate report on the ameliorative effects of exogenous melatonin in soil-grown seedlings of the rice variety, IR-64 subjected to prolonged fluoride stress. Exogenous melatonin stimulated the physiological growth of the stressed seedlings by triggering high accumulation of gibberellic acid (GA) and melatonin via up regulation of the biosynthetic genes like GA3ox, TDC, SNAT and ASMT. The endogenous abscisic acid (ABA) content increased via induction of NCED3 and suppression of ABA8ox1. However, the ABA-dependent genes like TRAB1, WRKY71 and OSBZ8 were down regulated in presence of high endogenous GA and melatonin. High melatonin level led to low indole-3-acetic acid accumulation in the treated seedlings during fluoride stress. Melatonin significantly decreased fluoride bioaccumulation by suppressing its uptake via CLC1 and CLC2, and also restored P-H(+)/ATPase expression. The damage indices like chlorosis (accompanied by low RuBisCo), malondialdehyde, electrolyte leakage, methylglyoxal (detoxified by glyoxalase II) and protein carbonylation were greatly reduced. Increased proline synthesis, activation of the ascorbate-glutathione cycle and enhanced activity of glutathione peroxidase, catalase and guaiacol peroxidase led to low ROS accumulation and localization in the melatonin-treated plants exposed to stress. Overall, melatonin treatment alleviated fluoride-mediated injuries by restricting fluoride uptake, refining the defence machinery and altering the phytohormone homeostasis.
PMID: 31698329
Tree Physiol , IF:3.655 , 2019 Dec , V39 (11) : P1880-1895 doi: 10.1093/treephys/tpz093
High-efficient utilization and uptake of N contribute to higher NUE of 'Qinguan' apple under drought and N-deficient conditions compared with 'Honeycrisp'.
State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A & F University, Yangling, 712100, China.
Drought and nitrogen (N) deficiency are common factors that limit apple production in the Loess Plateau region of China. Different apple cultivars respond to drought and low N differently; however, the mechanism that underlies the difference in nitrogen-use efficiency (NUE) under drought conditions is not well understood. In this study, by comparing the physiological responses of two apple (Malus domestica Borkh.) cultivars with contrasting NUE, 'Qinguan' (higher NUE) and 'Honeycrisp' (lower NUE), under low N and drought conditions, we discovered that, 'Qinguan' had larger stomatal apertures, higher chlorophyll fluorescence levels, more active N metabolism and antioxidant enzymes, higher abscisic acid and auxin concentrations, larger root size and more efficient N uptake mediated by higher expression of MdNRT2.4 in rootstock than that of 'Honeycrisp'. Additionally, we experimentally confirmed that MdNRT2.4 enhanced low N and osmotic stress tolerance in Arabidopsis when being overexpressed. Taken together, our findings shed light on the mechanism that underlies the difference in NUE of apple under drought and N-deficient conditionss and provide MdNRT2.4 as a candidate gene for future genetic engineering.
PMID: 31711215
Tree Physiol , IF:3.655 , 2019 Dec , V39 (11) : P1922-1936 doi: 10.1093/treephys/tpz085
MiRNA-target pairs regulate adventitious rooting in Populus: a functional role for miR167a and its target Auxin response factor 8.
Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China.; College of Forestry, Nanjing Forestry University, Nanjing 210037, China.; Jiangxi Academy of Forestry, Nanchang 330013, China.
The ability of a plant to form roots from its non-root tissues is ecologically advantageous during rapid adaptation to a changing environment. Although this biological phenomenon has been widely utilized for cuttings in many economically important agronomic and tree species, its genetic and developmental mechanisms have been poorly understood. In this study, we conducted an association analysis of small RNAs, the degradome and the transcriptome of adventitious rooting in poplar softwood cuttings, which revealed that 373 miRNA-target pairs were detected. Of these, 72 significantly differentially expressed targets were screened as likely to modulate adventitious root (AR) development, in conjunction with plant hormone signal transduction. Poplar miR167a and its targets PeARF6s and PeARF8s were subjected to functional verification of their ability to mediate plant growth and hormone signal transduction. Overexpression of miR167a inhibited target transcripts and improved lateral root (LR) development in poplar, while overexpressing PeARF8.1mut increased AR numbers and slightly inhibited LR development. Taken together, these results suggest that miR167a-PeARF8.1 modules play crucial roles in regulating AR and LR development in poplar and improve the adaptation of poplar to more complex environments.
PMID: 31504994
Plant Sci , IF:3.591 , 2019 Dec , V289 : P110248 doi: 10.1016/j.plantsci.2019.110248
ZmGLR, a cell membrane localized microtubule-associated protein, mediated leaf morphogenesis in maize.
State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, 100193, Beijing, China.; State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, 100193, Beijing, China. Electronic address: zhaoqian@cau.edu.cn.
Microtubule arrays play notable roles in cell division, cell movement, cell morphogenesis and signal transduction. Due to their important regulation of microtubule dynamic instability and array-ordering processes, microtubule-associated proteins have been a cutting-edge issue in research. Here, a new maize microtubule-associated protein, ZmGLR (Zea mays glutamic acid- and lysine-rich), was found. ZmGLR bundles microtubules in vitro and targets the cell membrane through an interaction between 24 conserved N-terminal amino acids and specific phosphatidylinositol phosphates (PtdInsPs). Increased Ca(2+) levels in the cytoplasm lead to ZmGLR partially dissociating from the cell membrane and moving into the cytoplasm to associate with microtubule. Overexpression and RNAi of ZmGLR both resulted in misoriented microtubule arrays, which led to dwarf maize plants and curved leaves. In addition, the expression of ZmGLR was regulated by BR and auxin through ZmBES1 and ZmARF9, respectively. This study reveals that the microtubule-associated protein ZmGLR plays a crucial role in cortical microtubule reorientation and maize leaf morphogenesis.
PMID: 31623783
Plant Sci , IF:3.591 , 2019 Dec , V289 : P110269 doi: 10.1016/j.plantsci.2019.110269
Different regulatory modules of two mango ERS1 promoters modulate specific gene expression in response to phytohormones in transgenic model plants.
University of Hohenheim, Institute of Crop Science, Section Crop Physiology of Specialty Crops, Stuttgart, Germany. Electronic address: p.winterhagen@uni-hohenheim.de.; University of Hohenheim, Institute of Crop Science, Section Crop Physiology of Specialty Crops, Stuttgart, Germany.
Ethylene is a key element of plant physiology, thus ethylene research is important for both, fundamental research and agriculture. Previous work on ethylene receptors focused on expression level and protein interaction, but knowledge on regulation of gene transcription is scarce. Promoters of mango ethylene receptor genes (pMiERS1a, pMiERS1b) were analysed particularly regarding responsiveness to hormones. The promoter sequences reveal some variation and they were characterized by identifying functional regulatory candidate modules via truncated-promoter approach. Based on ectopic gene expression studies in transgenic Arabidopsis and Nicotiana it is demonstrated that both promoters are positively responsive to ethylene. For pMiERS1a the AHBP/DOFF1 module is linked to ethylene responsiveness, while for pMiERS1b it is the module MYBL/OPAQ1. A negative gene regulation in response to abscisic acid (ABA) is linked to MYBL/DOFF2. A positive response to indole-3-acetic acid (IAA) was found for GTBX/MYCL1, containing the motifs IBOX/IDDF/TEFB, which are present in this combination only in pMiERS1b, but not in pMiERS1a. Conclusively, the general response of the ethylene receptor genes is conserved, but similar regulation can be linked to different modules. Further, a minor variation in a transcription factor binding site (TFBS) motif within an overall conserved module type can lead to a different expression.
PMID: 31623779
BMC Plant Biol , IF:3.497 , 2019 Dec , V19 (1) : P589 doi: 10.1186/s12870-019-2200-5
Maize brachytic2 (br2) suppresses the elongation of lower internodes for excessive auxin accumulation in the intercalary meristem region.
State Key Laboratory of Crop Genetics of Disease Resistance and Disease Control, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.; College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.; College of Agriculture and Food Engineering, Baise University, Baise, 533000, Guangxi, China.; Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.; College of Life Science, Sichuan Agricultural University, Ya'an, 625014, Sichuan, China.; National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450000, Henan, China. tangjihua1@163.com.; State Key Laboratory of Crop Genetics of Disease Resistance and Disease Control, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China. yubihuang@sohu.com.; College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China. yubihuang@sohu.com.
BACKGROUND: Short internodes contribute to plant dwarfism, which is exceedingly beneficial for crop production. However, the underlying mechanisms of internode elongation are complicated and have been not fully understood. RESULTS: Here, we report a maize dwarf mutant, dwarf2014 (d2014), which displays shortened lower internodes. Map-based cloning revealed that the d2014 gene is a novel br2 allele with a splicing variation, resulting in a higher expression of BR2-T02 instead of normal BR2-T01. Then, we found that the internode elongation in d2014/br2 exhibited a pattern of inhibition-normality-inhibition (transient for the ear-internode), correspondingly, at the 6-leaf, 12-leaf and 14-leaf stages. Indeed, BR2 encodes a P-glycoprotein1 (PGP1) protein that functions in auxin efflux, and our in situ hybridization assay showed that BR2 was mainly expressed in vascular bundles of the node and internode. Furthermore, significantly higher auxin concentration was detected in the stem apex of d2014 at the 6-leaf stage and strictly in the node region for the ear-internode at the 14-leaf stage. In such context, we propose that BR2/PGP1 transports auxin from node to internode through the vascular bundles, and excessive auxin accumulation in the node (immediately next to the intercalary meristem) region suppresses internode elongation of d2014. CONCLUSIONS: These findings suggest that low auxin levels mediated by BR2/PGP1 in the intercalary meristem region are crucial for internode elongation.
PMID: 31881837
BMC Plant Biol , IF:3.497 , 2019 Dec , V19 (1) : P573 doi: 10.1186/s12870-019-2176-1
Mepiquat chloride promotes cotton lateral root formation by modulating plant hormone homeostasis.
College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China.; Institute of Agricultural Information, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China.; Plant Phenomics Research Center, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.; Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.; College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China. lifangjun@cau.edu.cn.
BACKGROUND: Mepiquat chloride (MC), a plant growth regulator, enhances root growth by promoting lateral root formation in cotton. However, the underlying molecular mechanisms of this phenomenon is still unknown. METHODS: In this study, we used 10 cotton (Gossypium hirsutum Linn.) cultivars to perform a seed treatment with MC to investigate lateral root formation, and selected a MC sensitive cotton cultivar for dynamic monitor of root growth and transcriptome analysis during lateral root development upon MC seed treatment. RESULTS: The results showed that MC treated seeds promotes the lateral root formation in a dosage-depended manner and the effective promotion region is within 5 cm from the base of primary root. MC treated seeds induce endogenous auxin level by altering gene expression of both gibberellin (GA) biosynthesis and signaling and abscisic acid (ABA) signaling. Meanwhile, MC treated seeds differentially express genes involved in indole acetic acid (IAA) synthesis and transport. Furthermore, MC-induced IAA regulates the expression of genes related to cell cycle and division for lateral root development. CONCLUSIONS: Our data suggest that MC orchestrates GA and ABA metabolism and signaling, which further regulates auxin biosynthesis, transport, and signaling to promote the cell division responsible for lateral root formation.
PMID: 31864311
BMC Plant Biol , IF:3.497 , 2019 Dec , V19 (1) : P567 doi: 10.1186/s12870-019-2158-3
Direct comparison of Arabidopsis gene expression reveals different responses to melatonin versus auxin.
Department of Animal, Plant and Soil Sciences, AgriBio, La Trobe University, Bundoora, VIC, 3086, Australia.; ARC Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, VIC, 3086, Australia.; Department of Animal, Plant and Soil Sciences, AgriBio, La Trobe University, Bundoora, VIC, 3086, Australia. f.bedon@latrobe.edu.au.; Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora, VIC, 3086, Australia.; Centre for Future Landscapes, La Trobe University, Bundoora, VIC, 3086, Australia.; Department of Animal, Plant and Soil Sciences, AgriBio, La Trobe University, Bundoora, VIC, 3086, Australia. k.plummer@latrobe.edu.au.
BACKGROUND: Melatonin (N-acetyl-5-methoxytryptamine) in plants, regulates shoot and root growth and alleviates environmental stresses. Melatonin and the phyto-hormone auxin are tryptophan-derived compounds. However, it largely remains controversial as to whether melatonin and auxin act through similar or overlapping signalling and regulatory pathways. RESULTS: Here, we have used a promoter-activation study to demonstrate that, unlike auxin (1-naphthalene acetic acid, NAA), melatonin neither induces Direct repeat 5 DR5 expression in Arabidopsis thaliana roots under normal growth conditions nor suppresses the induction of Alternative oxidase 1a AOX1a in leaves upon Antimycin A treatment, both of which are the hallmarks of auxin action. Additionally, comparative global transcriptome analysis conducted on Arabidopsis treated with melatonin or NAA revealed differences in the number and types of differentially expressed genes. Auxin (4.5 muM) altered the expression of a diverse and large number of genes whereas melatonin at 5 muM had no significant effect but melatonin at 100 muM had a modest effect on transcriptome compared to solvent-treated control. Interestingly, the prominent category of genes differentially expressed upon exposure to melatonin trended towards biotic stress defence pathways while downregulation of key genes related to photosynthesis was observed. CONCLUSION: Together these findings indicate that though they are both indolic compounds, melatonin and auxin act through different pathways to alter gene expression in Arabidopsis thaliana. Furthermore, it appears that effects of melatonin enable Arabidopsis thaliana to prioritize biotic stress defence signalling rather than growth. These findings clear the current confusion in the literature regarding the relationship of melatonin and auxin and also have greater implications of utilizing melatonin for improved plant protection.
PMID: 31856719
BMC Plant Biol , IF:3.497 , 2019 Dec , V19 (1) : P565 doi: 10.1186/s12870-019-2197-9
Full-length transcriptome analysis of shade-induced promotion of tuber production in Pinellia ternata.
Key Laboratory of Resource Plant Biology of Anhui Province, College of Life Sciences, Huaibei Normal University, Huaibei, 235000, China.; Key Laboratory of Resource Plant Biology of Anhui Province, College of Life Sciences, Huaibei Normal University, Huaibei, 235000, China. yboduan@163.com.; Key Laboratory of Resource Plant Biology of Anhui Province, College of Life Sciences, Huaibei Normal University, Huaibei, 235000, China. xuejp@163.com.
BACKGROUND: Pinellia ternata is native to China and has been used as a traditional herb due to its antiemetic, antitussive, analgesic, and anxiolytic effects. When exposed to strong light intensity and high temperature during the reproductive growth process, P. ternata withers in a phenomenon known as "sprout tumble", which largely limits tuber production. Shade was previously found to delay sprout tumble formation (STF); however, no information exists regarding this process at the molecular level. Hence, we determined the genes involved in tuber development and STF in P. ternata. RESULTS: Compared to that with natural sun-light (control), shade significantly induced chlorophyll accumulation, increased chlorophyll fluorescence parameters including initial fluorescence, maximal fluorescence, and qP, and dramatically repressed chlorophyll a:b and NPQ. Catalase (CAT) activity was largely induced by shade, and tuber products were largely increased in this environment. Transcriptome profiles of P. ternata grown in natural sun-light and shaded environments were analyzed by a combination of next generation sequencing (NGS) and third generation single-molecule real-time (SMRT) sequencing. Corrections of SMRT long reads based on NGS short reads yielded 136,163 non-redundant transcripts, with an average N50 length of 2578 bp. In total, 6738 deferentially-expressed genes (DEGs) were obtained from the comparisons, specifically D5S vs D5CK, D20S vs D20CK, D20S vs D5S, and D20CK vs D5CK, of which, 6384 DEGs (94.8%) were generated from the D20S vs D20CK comparison. Gene annotation and functional analyses revealed that these genes were related to auxin signal transduction, polysaccharide and sugar metabolism, phenylpropanoid biosynthesis, and photosynthesis. Moreover, the expression of genes enriched in photosynthesis appeared to be significantly altered by shade. The expression patterns of 16 candidate genes were consistent with changes in their transcript abundance as identified by RNA-Seq, and these might contribute to STF and tuber production. CONCLUSION: The full-length transcripts identified in this study have provided a more accurate depiction of P. ternata gene transcription. Further, we identified potential genes involved in STF and tuber growth. Such data could serve as a genetic resource and a foundation for further research on this important traditional herb.
PMID: 31852442
BMC Plant Biol , IF:3.497 , 2019 Dec , V19 (1) : P554 doi: 10.1186/s12870-019-2081-7
Anatomy and RNA-Seq reveal important gene pathways regulating sex differentiation in a functionally Androdioecious tree, Tapiscia sinensis.
Key Laboratory of Resource Biology and Biotechnology in Western China (Northwest University), Ministry of Education, School of Life Science, Northwest University, Xi'an, 710069, Shaanxi, China.; Key Laboratory of Resource Biology and Biotechnology in Western China (Northwest University), Ministry of Education, School of Life Science, Northwest University, Xi'an, 710069, Shaanxi, China. lwenzhe@nwu.edu.cn.
BACKGROUND: Gametogenesis is a key step in the production of ovules or pollen in higher plants. The sex-determination aspects of gametogenesis have been well characterized in the model plant Arabidopsis. However, little is known about this process in androdioecious plants. Tapiscia sinensis Oliv. is a functionally androdioecious tree, with both male and hermaphroditic individuals. Hermaphroditic flowers (HFs) are female-fertile flowers that can produce functional pollen and set fruits. However, compared with male flowers (MFs), the pollen viability and number of pollen grains per flower are markedly reduced in HFs. MFs are female-sterile flowers that fail to set fruit and that eventually drop. RESULTS: Compared with HF, a notable cause of MF female sterility in T. sinensis is when the early gynoecium meristem is disrupted. During the early stage of HF development (stage 6), the ring meristem begins to form as a ridge around the center of the flower. At this stage, the internal fourth-whorl organ is stem-like rather than carpelloid in MF. A total of 52,945 unigenes were identified as transcribed in MF and HF. A number of differentially expressed genes (DEGs) and metabolic pathways were detected as involved in the development of the gynoecium, especially the ovule, carpel and style. At the early gynoecium development stage, DEGs were shown to function in the metabolic pathways regulating ethylene biosynthesis and signal transduction (upstream regulator), auxin, cytokinin transport and signalling, and sex determination (or flower meristem identity). CONCLUSIONS: Pathways for the female sterility model were initially proposed to shed light on the molecular mechanisms of gynoecium development at early stages in T. sinensis.
PMID: 31842763
BMC Plant Biol , IF:3.497 , 2019 Dec , V19 (1) : P551 doi: 10.1186/s12870-019-2134-y
Wheat straw increases the defense response and resistance of watermelon monoculture to Fusarium wilt.
College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, Heilongjiang, 150030, People's Republic of China.; Institute of Cash Crops, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, Heilongjiang, China.; Institute of Crop Cultivation and Tillage, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, Heilongjiang, China.; College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, Heilongjiang, 150030, People's Republic of China. mugonglin@163.com.
BACKGROUND: Wheat straw is a rich resource worldwide. Straw return is an effective strategy to alleviate soil-borne diseases on monoculture watermelon. Previous studies focus on soil structure, physical and chemical properties; however, little is known about the molecular responses on host plant. RESULTS: No significant difference on the population of Fusarium oxysporum f.sp. niveum race 1(Fon1) in rhizosphere soil was found between control (no addition of wheat straw) and the treated groups (addition of 1% (T1) or 2% (T2) wheat straw). RNA-Seq analysis showed that 3419 differentially expressed genes were clustered into 8 profiles. KEGG analysis revealed that phenylpropanoid biosynthesis and plant hormone signal transduction were involved in wheat straw induced response in monoculture watermelon. Genes in lignin biosynthesis were found to be upregulated, and the lignin and auxin contents were higher in T1 and T2 compared to the control. Lignin was also enriched and the Fon1 population decreased in watermelon roots treated with wheat straw. The enzyme activities of phenylalanine ammonia-lyase and peroxidase were increased. CONCLUSIONS: Our data suggest that the addition of wheat straw enhances the defense response to Fon1 infection in watermelon through increasing lignin and auxin biosynthesis.
PMID: 31829140
BMC Plant Biol , IF:3.497 , 2019 Dec , V19 (1) : P545 doi: 10.1186/s12870-019-2169-0
Differential gene expression among three sex types reveals a MALE STERILITY 1 (CpMS1) for sex differentiation in papaya.
Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.; Hawaii Agriculture Research Center, Kunia, HI, 96759, USA.; Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA. rayming@illinois.edu.
BACKGROUND: Carica papaya is a trioecious plant species with a genetic sex-determination system defined by sex chromosomes. Under unfavorable environmental conditions male and hermaphrodite exhibit sex-reversal. Previous genomic research revealed few candidate genes for sex differentiation in this species. Nevertheless, more analysis is still needed to identify the mechanism responsible for sex flower organ development in papaya. RESULTS: The aim of this study was to identify differentially expressed genes among male, female and hermaphrodite flowers in papaya during early (pre-meiosis) and later (post-meiosis) stages of flower development. RNA-seq was used to evaluate the expression of differentially expressed genes and RT-qPCR was used to verify the results. Putative functions of these genes were analyzed based on their homology with orthologs in other plant species and their expression patterns. We identified a Male Sterility 1 gene (CpMS1) highly up-regulated in male and hermaphrodite flower buds compared to female flower buds, which expresses in small male flower buds (3-8 mm), and that might be playing an important role in male flower organ development due to its homology to MS1 genes previously identified in other plants. This is the first study in which the sex-biased expression of genes related to tapetum development in the anther developmental pathway is being reported in papaya. Besides important transcription factors related to flower organ development and flowering time regulation, we identified differential expression of genes that are known to participate in ABA, ROS and auxin signaling pathways (ABA-8-hydroxylases, AIL5, UPBEAT 1, VAN3-binding protein). CONCLUSIONS: CpMS1 was expressed in papaya male and hermaphrodite flowers at early stages, suggesting that this gene might participate in male flower organ development processes, nevertheless, this gene cannot be considered a sex-determination gene. Due to its homology with other plant MS1 proteins and its expression pattern, we hypothesize that this gene participates in anther development processes, like tapetum and pollen development, downstream gender specification. Further gene functional characterization studies in papaya are required to confirm this hypothesis. The role of ABA and ROS signaling pathways in papaya flower development needs to be further explored as well.
PMID: 31818257
Enzyme Microb Technol , IF:3.448 , 2019 Dec , V131 : P109381 doi: 10.1016/j.enzmictec.2019.109381
Phytohormones as stimulators to improve arachidonic acid biosynthesis in Mortierella alpina.
CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Shandong Engineering Laboratory of Single Cell Oil, Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, Shandong, China.; CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Shandong Engineering Laboratory of Single Cell Oil, Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, Shandong, China; University of Chinese Academy of Sciences, Beijing, 100049, China.; CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Shandong Engineering Laboratory of Single Cell Oil, Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, Shandong, China. Electronic address: cuiqiu@qibebt.ac.cn.; CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Shandong Engineering Laboratory of Single Cell Oil, Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, Shandong, China. Electronic address: songxj@qibebt.ac.cn.
Phytohormones are chemical messengers that have a positive effect at low concentrations on the biosynthesis of high-value compounds. Therefore, the effects of phytohormones on lipid and arachidonic acid (ARA) biosynthesis in Mortierella alpina were investigated in this study. At proper concentrations, the stimulatory effects of phytohormones on lipid production were determined to be as follows: 6-benzyl adenine (BA) > indole-3-acetic acid (IAA) > furfuryl adenine (KT) > gibberellin (GA) > indole-3-butyric acid (IBA) > abscisic acid (ABA). The results show that in the presence of 15 mg L(-1) BA, the best positive effect was obtained, in which the lipid and ARA yields of M. alpina increased by 20.34% and 29.17%, respectively. Surprisingly, there was no synergy between the addition of two cytokinins (KT and BA), while adding cytokinins (KT or BA) and auxin (IAA) inhibited the growth of M. alpina and the ARA yield decreased by approximately 64%. Additional studies, such as those involving enzyme activity detection and quantitative real time polymerase chain reaction were carried out to check the fatty acid and lipid biosynthesis when the phytohormones were present. The activity of the main NADPH-supplying enzyme, 6-phosphoglucose dehydrogenase (G6PDH), increased by 19.52%. Moreover, the transcription levels of fatty acid synthase (FAS), Delta9-desaturase, and diacylglycerolacyltransferase (DGAT) increased by 9.3, 9.6 and 7.7 times, respectively, when only one type of phytohormone was present, indicating the enhancement of fatty acid and lipid biosynthesis in M. alpina. This study demonstrates the potential application of phytohormones for improving ARA yields of M. alpina.
PMID: 31615662
Chromosome Res , IF:3.413 , 2019 Dec , V27 (4) : P287-298 doi: 10.1007/s10577-019-09611-3
Global epigenetic changes of histone modification under environmental stresses in rice root.
Indonesian Center for Agricultural Biotechnology and Genetic Resource Research and Development (ICABIOGRD), Bogor, Indonesia.; Graduate School of Human Development and Environment, Kobe University, Kobe, Japan.; Graduate School of Human Development and Environment, Kobe University, Kobe, Japan. ohmido@kobe-u.ac.jp.
Abiotic stresses are non-living factors with negative morphological and physiological effects on living organisms. Substantial evidence exists that gene expression changes during plant cell growth are regulated by chromatin reconfiguration and histone modification. Several types of histone modifications are dramatically transformed in stress-responsive gene regions under drought stress conditions. Environmental stresses also cause the root apical meristem (RAM) region to decelerate root growth. In this study, we investigated how quantitative changes in epigenetic markers in this region influence rice morphology and physiology. Both iron and salinity treatments changed the epigenetic landscape from euchromatic to heterochromatic according to heterochromatin (H3K9me2) and euchromatin (H3K4me) markers, especially in the proximal meristem region. Moreover, supplementation with external abscisic acid (ABA) was able to mimic the effect of environmental stresses on global epigenetic changes. In contrast, the addition of external auxin (IAA) to rice under saline conditions affected heterochromatin formation without influencing euchromatin transformation. Chromatin dynamics is therefore believed to be directly connected to plant growth regulator signaling. We discuss insights into the role of plant growth regulators: ABA and IAA, peroxide signaling, and their effects on the global epigenetic change of histone modification under abiotic stresses.
PMID: 31280458
Planta , IF:3.39 , 2019 Dec , V250 (6) : P2147-2158 doi: 10.1007/s00425-019-03271-7
Analysis of the MIR160 gene family and the role of MIR160a_A05 in regulating fiber length in cotton.
Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture, Zhengzhou University, Anyang, 455000, Henan, 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, Box 30003, Las Cruces, NM, 88003, USA.; Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture, Zhengzhou University, Anyang, 455000, Henan, China. yu@cricaas.com.cn.; Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture, Zhengzhou University, Anyang, 455000, Henan, China. wuman@cricaas.com.cn.; Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture, Zhengzhou University, Anyang, 455000, Henan, China. yujw@cricaas.com.cn.
MAIN CONCLUSION: The MIR160 family in Gossypium hirsutum and G. barbadense was characterized, and miR160a_A05 was found to increase cotton-fiber length by downregulating its target gene (ARF17) and several GH3 genes. Cotton fiber is the most important raw material for the textile industry. MicroRNAs are involved in regulating cotton-fiber development, but a role in fiber elongation has not been demonstrated. In this study, miR160a was found to be differentially expressed in elongating fibers between two interspecific (between Gossypium hirsutum and G. barbadense) backcross inbred lines (BILs) with different fiber lengths. The gene MIR160 colocalized with a previously mapped fiber-length quantitative trait locus. Its target gene ARF17 was differentially expressed between the two BILs during fiber elongation, but in the inverse fashion. Bioinformatics was used to analyze the MIR160 family in both G. hirsutum and G. barbadense. Moreover, qRT-PCR analysis identified MIR160a as the functional MIR160 gene encoding the miR160a precursor during fiber elongation. Using virus-induced gene silencing and overexpression, overexpressed MIR160a_A05 resulted in significantly longer fibers compared with wild type, whereas suppression of miR160 resulted in significantly shorter fibers. Expression levels of the target gene auxin-response factor 17 (ARF17) and related genes GH3 in the two BILs and/or the virus-infected plants demonstrated similar changes in response to modulation of miR160a level. Finally, overexpression or suppression of miR160 increased or decreased, respectively, the cellular level of indole-3-acetic acid, which is involved in fiber elongation. These results describe a specific regulatory mechanism for fiber elongation in cotton that can be utilized for future crop improvement.
PMID: 31620865
Mol Genet Genomics , IF:2.797 , 2019 Dec , V294 (6) : P1511-1525 doi: 10.1007/s00438-019-01593-5
Indole-3-acetic acid has long-term effects on long non-coding RNA gene methylation and growth in Populus tomentosa.
National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, People's Republic of China.; National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, People's Republic of China. DeqiangZhang@bjfu.edu.cn.; Xining Forestry Science Research Institute, No. 18-2, Haihu Avenue Chengbei District, Xining, 810003, Qinghai, People's Republic of China. DeqiangZhang@bjfu.edu.cn.
DNA methylation and long non-coding RNAs (lncRNAs) regulate plant growth and development, but their relationship and effect on responses to the auxin phytohormone indole-3-acetic acid (IAA) remain largely unknown, particularly in woody plants such as poplar (Populus tomentosa). Following treatment of 1-year-old clonal plants with 100 microM IAA, key poplar lncRNA genes showed changes in methylation, but whole-genome methylation levels showed no significant change. Moreover, 100 microM IAA inhibited growth of the 1-year-old poplar clones, possibly through the suppression of photosynthesis. This inhibition had a long-term effect, persisting at 1 month after removal of the exogenous IAA. Transcriptome analysis identified two candidate lncRNA genes that show changes in expression following IAA treatment, TCONS_00003480 and TCONS_00004832. TCONS_00003480 contains the same microRNA target sites of ptc-miR6464 as the 4-coumarate: CoA ligase 2 transcript, which encodes a lignin biosynthesis enzyme. And TCONS_00004832 shares the same target sites of ptc-miR6437a with the Photosystem II reaction center protein D and Cytochrome C Oxidase 17 transcripts, which are related to photosynthesis. The two lncRNAs as the mimics to corresponding target genes of miRNAs to prevent them from degrading. Examination of lncRNA gene expression and methylation revealed a negative relationship (r = - 0.29, P < 0.05); moreover, hypermethylation of the two candidate lncRNA genes remained 1 month after IAA treatment, suggesting that changes in methylation might be involved in the long-term effects of plant hormones. Therefore, our study reveals a long-term effect of IAA on the growth of P. tomentosa, possibly via methylation-mediated epigenetic changes in lncRNA gene expression and the interaction with corresponding miRNAs, leading to regulation of genes related to photosynthesis and growth.
PMID: 31324970
Plants (Basel) , IF:2.762 , 2019 Dec , V9 (1) doi: 10.3390/plants9010049
Comparison of the Androgenic Response of Spring and Winter Wheat (Triticum aestivum L.).
Department of Genetics and Plant Breeding, Poznan University of Life Sciences, 11 Dojazd St, 60-637 Poznan, Poland.; Department of Mathematical and Statistical Method, Poznan University of Life Sciences, 28 Wojska Polskiego St, 60-637 Poznan, Poland.
Androgenesis is potentially the most effective technique for doubled haploid production of wheat. It is not however widely used in breeding programmes due to its main limitation: the genotype dependence. Due to genetic differences between spring and winter wheat, it was assumed that both phenotypes are different in their capacity to conduct androgenesis. And so, the aim of this investigation was to verify the effectiveness of androgenesis induction and plant regeneration of spring and winter wheat genotypes while considering varying amounts of growth hormones in the induction medium. Fifteen genotypes of spring wheat and fifteen of winter wheat were used in the experiment. Six hundred anthers of each of the 30 genotypes were plated and analysed. Previous studies have allowed selection of the best medium for wheat androgenesis and a combination of growth hormones that are the most effective in stimulating microspore proliferation. Therefore, C17 induction media with two combinations of growth hormones were used: I-supplemented only by auxins (2,4-D and dicamba), and II-supplemented by auxin and cytokinin (2,4-D and kinetin). Data was recorded according to the efficiency of androgenic structure formation (ASF), green plant regeneration (GPR), and albino plant regeneration (APR). The results showed that the induction and regeneration of androgenesis in the spring wheat were more efficient than in the winter ones. The spring genotypes formed more androgenic structures and green plants on anthers plated on the medium supplemented only by auxins, in contrast to the winter genotypes which were better induced and regenerated on the medium supplemented by auxin and cytokinin. The study showed that to increase the efficiency of androgenesis, it is necessary to select appropriate factors such as concentration and type of hormones in medium composition, affecting the course of the culturing procedure according to the winter or spring phenotype of donor plants.
PMID: 31906148
Plants (Basel) , IF:2.762 , 2019 Dec , V9 (1) doi: 10.3390/plants9010025
Characterization and Expression Analysis of the Ca(2+)/Cation Antiporter Gene Family in Tomatoes.
Graduate School of Agricultural Science, Tohoku University, Aoba-ku, Sendai 980-8572, Japan.; Faculty of Life and Environmental Science, Shimane University, Matsue 690-8504, Japan.
The Ca(2+)/cation antiporter (CaCA) superfamily plays an important role in the regulation of the essential element Ca(2+) and cation concentrations. Characterization and expression analyses of CaCA superfamily genes were performed in the tomato (Solanum lycopersicum) as a representative of dicotyledonous plants and fruit crops. Sixteen CaCA candidate genes were found and identified as tomato CaCA, SlCaCA, by a domain search. In a phylogenetic analysis of the SlCaCA superfamily, the 16 genes were classified into SlCAX, SlNCL, SlCCX, and SlMHX families. Among them, Solyc12g011070, belonging to the SlCAX family, had four splice variants, three of which were predicted to be nonfunctional because of a lack of important motifs. EF-hand domains were only found in SlNCL, in addition to consensus Na_Ca_ex domains, and the region containing EF-hand domains was characteristically long in some members of SlNCL. Furthermore, four genes of the SlCCX family were found to be intronless. As for intracellular localization, one SlCCX member was predicted to be localized to the plasma membrane, while other SlCCXs, SlCAXs, and SlMHXs were predicted to be localized to the vacuolar membrane. The expression patterns of SlCaCAs in various organs, including during several developmental stages of fruit, were classified into four groups. Genes involved in each of the SlCAX, SlNCL, and SlCCX gene families were categorized into three or four groups according to expression patterns, suggesting role sharing within each family. The main member in each subfamily and the members with characteristic fruit expression patterns included genes whose expression was regulated by sugar or auxin and that were highly expressed in a line having metabolite-rich fruit.
PMID: 31878106
Plants (Basel) , IF:2.762 , 2019 Dec , V8 (12) doi: 10.3390/plants8120614
Transcriptomic Analysis of Dark-Induced Senescence in Bermudagrass (Cynodon dactylon).
College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China.; CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China.; Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China.; National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment, Shandong Agricultural University, Daizong Road, Tai'an 271018, China.; College of Horticulture, Agricultural University of Hebei, Baoding 071001, China.
Leaf senescence induced by prolonged light deficiency is inevitable whenever turfgrass is cultivated in forests, and this negatively influences the survival and aesthetic quality of the turfgrass. However, the mechanism underlying dark-induced senescence in turfgrass remained obscure. In this study, RNA sequencing was performed to analyze how genes were regulated in response to dark-induced leaf senescence in bermudagrass. A total of 159,207 unigenes were obtained with a mean length of 948 bp. The differential expression analysis showed that a total of 59,062 genes, including 52,382 up-regulated genes and 6680 down-regulated genes were found to be differentially expressed between control leaves and senescent leaves induced by darkness. Subsequent bioinformatics analysis showed that these differentially expressed genes (DEGs) were mainly related to plant hormone (ethylene, abscisic acid, jasmonic acid, auxin, cytokinin, gibberellin, and brassinosteroid) signal transduction, N-glycan biosynthesis, and protein processing in the endoplasmic reticulum. In addition, transcription factors, such as WRKY, NAC, HSF, and bHLH families were also responsive to dark-induced leaf senescence in bermudagrass. Finally, qRT-PCR analysis of six randomly selected DEGs validated the accuracy of sequencing results. Taken together, our results provide basic information of how genes respond to darkness, and contribute to the understanding of comprehensive mechanisms of dark-induced leaf senescence in turfgrass.
PMID: 31861053
Plants (Basel) , IF:2.762 , 2019 Dec , V8 (12) doi: 10.3390/plants8120603
Conjunctive Analyses of BSA-Seq and BSR-Seq to Reveal the Molecular Pathway of Leafy Head Formation in Chinese Cabbage.
State Key Laboratory of Crop Genetics and Germplasm Enhancement, and Key laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.; Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China.
As the storage organ of Chinese cabbage, the leafy head was harvested as a commercial product due to its edible value. In this study, the bulked segregant analysis (BSA) and bulked segregant RNA-Seq (BSR) were performed with F2 separation progeny to study the molecular mechanism of leafy head formation in Chinese cabbage. BSA-Seq analysis located four candidate regions containing 40 candidate genes, while BSR-Seq analysis revealed eight candidate regions containing 607 candidate genes. The conjunctive analyses of these two methods identified that Casein kinase gene BrCKL8 (Bra035974) is the common candidate gene related with leafy head formation in Chinese cabbage, and it showed high expression levels at the three segments of heading type plant leaves. The differentially expressed genes (DEGs) between two set pairs of cDNA sequencing bulks were divided into two categories: one category was related with five hormone pathways (Auxin, Ethylene, Abscisic acid, Jasmonic acid and Gibberellin), the other category was composed of genes that associate with the calcium signaling pathway. Moreover, a series of upregulated transcriptional factors (TFs) were also identified by the association analysis of BSR-Seq analysis. The leafy head development was regulated by various biological processes and effected by diverse external environment factors, so our research will contribute to the breeding of perfect leaf-heading types of Chinese cabbage.
PMID: 31847231
Bioengineered , IF:2.205 , 2019 Dec , V10 (1) : P668-678 doi: 10.1080/21655979.2019.1692610
Identification and bioinformatic analysis of Aux/IAA family based on transcriptome data of Bletilla striata.
Department of Cell Biology, Zunyi Medical University, Zunyi, China.; Sesame Research Institute, Chinese Academy of Agriculture Sciences, Zheng Zhou, China.; Department of Pharmacy, Zunyi Medical University, Zunyi, China.
Auxin/Indole-3-Acetic Acid (Aux/IAA) genes are involved in auxin signaling pathway and play an important role in plant growth and development. However, many studies focus on Aux/IAA gene families and much less known in Bletilla striata. In this study, a total of 27 Aux/IAA genes (BsIAA1-27) were cloned from the transcriptome of Bletilla striata. Based on a phylogenetic analysis of the Aux/IAA protein sequences from B. striata, Arabidopsis thaliana and Dendrobium officinale, the Aux/IAA genes of B. striata (BsIAAs) were categorized into 2 subfamilies and 9 groups. While BsIAAs were more closer to those of D. officinale compared to A. thaliana. EST-SSR marker mining test showed that 4 markers could be stably amplified with obvious polymorphisms among 4 landraces. Our results suggested that BsIAAs were involved in the process of tuber development and provided insights into functional roles of Aux/IAA genes in B. striata and other plants.
PMID: 31722607
Genome , IF:2.037 , 2019 Dec , V62 (12) : P769-783 doi: 10.1139/gen-2019-0013
Assessment of germination, phytochemicals, and transcriptional responses to ethephon priming in soybean [Glycine max (L.) Merrill].
ITC Limited, ITC Life Sciences and Technology Centre (LSTC), Peenya Industrial Area, 1 Phase, Bengaluru-560058, Karnataka, India.
The present work aims to dissect the underlying signaling pathways associated with soybean [Glycine max (L.) Merrill] seed hormo-priming with ethephon (Eth). Our results demonstrated that soybean germination improved significantly upon Eth priming (Ethp). Phytohormone quantification shows relative enhanced endogenous gibberellin A4 (GA4) levels concomitant with impaired biogenesis and signaling of auxin, viz., indole acetic acid (IAA) and abscisic acid (ABA). Phytochemical analysis revealed relative reduced levels of individual and total raffinose family oligosaccharide (RFO) components, starch, soluble sugars, and sucrose concomitant with enhanced levels of reducing sugars, glucose, cellular ATP, and acetyl-CoA pools. Secondary metabolite analysis revealed the activation of the mevalonate (MVA) pathway with a concomitant suppression of the plastidal 2-methyl-d-erythritol-4-phosphate/1-deoxy-d-xylulose-5-phosphate (MEP/DOX) and phenylpropanoid pathways, substantiated by relative reduced levels of total phenolics, tannins, and proanthocyanidin. Ethp also enhances the in vitro antioxidative activity (viz., 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging ability and ferric reducing antioxidant power (FRAP)) and endogenous antioxidants levels (viz., flavonoids, isoflavones, beta-carotene, vitamin C, and vitamin E). Further quantitative real-time polymerase chain reaction (qRT-PCR) analysis showed transcriptional pattern of representative genes in agreement with these metabolic alterations.
PMID: 31479624
Comput Biol Chem , IF:1.85 , 2019 Dec , V83 : P107100 doi: 10.1016/j.compbiolchem.2019.107100
Identification of miRNA, their targets and miPEPs in peanut (Arachis hypogaea L.).
Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, 835 215, Jharkhand, India.; Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, 835 215, Jharkhand, India. Electronic address: dmpandey@bitmesra.ac.in.
MicroRNAs (miRNAs) are one of the major cytoplasmic tools employed by the eukaryotes for post-transcriptional gene regulation. These 21nt small non-coding RNA molecules are highly conserved among species which forms a base for identification of new miRNAs. In this study, we used previously known mature miRNAs to search their homologs in Arachis hypogaea ESTs. A total of 50 non-protein coding sequences showing homology with no more than 3 mismatches were folded back to hairpin stem-loop structures using mfold. These predicted structures were passed through strict filtration criteria to obtain 18 miRNAs, all of which were other than those reported in miRBase. Out of 18 miRNAs, 7 were found to be new. These miRNAs belonged to miR156, miR166, miR167, miR319, miR398, miR399, miR482 and miR1507 family. These miRNAs were found to target a total of 118 genes in Arabidopsis. These targets included disease resistant proteins, auxin responsive proteins, squamosa promoter binding like proteins, co-transporter protein, transposable element genes, NAD(P) binding protein and topoisomerase II. KEGG pathway analysis showed potential involvement of these miRNAs in regulating different pathways. Apart from miRNA and their targets, microRNA encoded peptides (miPEPs) for 14 miRNAs were also identified. These findings can be used in the appropriate manipulation of miRNAs and corresponding miPEPs that will be helpful towards the peanut crop improvement.
PMID: 31446369
Plant Direct , IF:1.725 , 2019 Dec , V3 (12) : Pe00193 doi: 10.1002/pld3.193
The regulation of ZCT1, a transcriptional repressor of monoterpenoid indole alkaloid biosynthetic genes in Catharanthus roseus.
Department of Biology Northeastern University Boston MA USA.; Department of Chemistry and Chemical Biology Northeastern University Boston MA USA.; Department of Bioengineering Northeastern University Boston MA USA.; Department of Chemical Engineering Northeastern University Boston MA USA.
Cys2/His2-type (C2H2) zinc finger proteins, such as ZCT1, are an important class of transcription factors involved in growth, development, and stress responses in plants. In the medicinal plant Catharanthus roseus, the zinc finger Catharanthus transcription factor (ZCT) family represses monoterpenoid indole alkaloid (MIA) biosynthetic gene expression. Here, we report the analysis of the ZCT1 promoter, which contains several hormone-responsive elements. ZCT1 is responsive to not only jasmonate, as was previously known, but is also induced by the synthetic auxin, 1-naphthalene acetic acid (1-NAA). Through promoter deletion analysis, we show that an activation sequence-1-like (as-1-like)-motif and other motifs contribute significantly to ZCT1 expression in seedlings. We also show that the activator ORCA3 does not transactivate the expression of ZCT1 in seedlings, but ZCT1 represses its own promoter, suggesting a feedback mechanism by which the expression of ZCT1 can be limited.
PMID: 31909362
Plant Biotechnol (Tokyo) , IF:0.901 , 2019 Dec , V36 (4) : P223-231 doi: 10.5511/plantbiotechnology.19.0830a
Multiplex exome sequencing reveals genome-wide frequency and distribution of mutations in the 'Micro-Tom' Targeting Induced Local Lesions in Genomes (TILLING) mutant library.
Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan.; Advanced Analysis Center, NARO, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan.; JST PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan.; Tsukuba Plant Innovation Research Center (T-PIRC), University of Tsukuba, 1-1-1Tennodai, Tsukuba, Ibaraki 305-8572, Japan.; Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan.
While the 'Micro-Tom' TILLING mutant library is used for a wide range of purposes, including both basic research of gene function and breeding of commercial cultivars, genome-wide distribution and frequency of mutations have not yet been thoroughly elucidated on a population scale. In this study, we developed a 96-plex exome sequencing method to identify and analyze mutations within the TILLING mutants that were developed in the University of Tsukuba. First, an Illumina paired-end sequencing coupled with 96-plex exome capture resulted in the acquisition of an exome sequence dataset with an average read count of 5.6 million for the 95 mutants. Over 98% of the capture target region could be covered by the short reads with an averaged read depth of 12.8, which enabled us to identify single nucleotide polymorphisms and Indels in a genome-wide manner. By subtracting intra-cultivar DNA variations that are present between wild-type 'Micro-Tom' lines, we identified 241,391 mutation candidates in 95 mutant individuals. Of these, 64,319 and 6,480 mutations were expected to cause protein amino acid substitutions or premature stop codon, respectively. Based on the exome mutation dataset, a mutant line designated 'TOMJPW601' was found to carry a premature stop codon mutation (W261*) in a putative auxin influx carrier gene SlLAX1 (Solyc09G014380), consistent with our previous report of its curly leaf phenotype. Our results suggested that a population-scale mutation database developed by multiplexed exome sequencing could be used for in silico mutant screening, which in turn could contribute to both gene function research and breeding programs.
PMID: 31983876