Mol Plant , IF:12.084 , 2019 Jun , V12 (6) : P863-878 doi: 10.1016/j.molp.2019.05.003
Systems Biology Approach Pinpoints Minimum Requirements for Auxin Distribution during Fruit Opening.
Crop Genetics, John Innes Centre, Norwich NR4 7UH, UK.; Computational and Systems Biology, John Innes Centre, Norwich NR4 7UH, UK; Centre of Excellence in Computational and Experimental Developmental Biology, Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland.; Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK.; Computational and Systems Biology, John Innes Centre, Norwich NR4 7UH, UK; School of Biosciences, Cardiff University, Cardiff CF10 3AX, Wales, UK.; Crop Genetics, John Innes Centre, Norwich NR4 7UH, UK. Electronic address: lars.ostergaard@jic.ac.uk.; Computational and Systems Biology, John Innes Centre, Norwich NR4 7UH, UK; School of Biosciences, Cardiff University, Cardiff CF10 3AX, Wales, UK. Electronic address: marees@cardiff.ac.uk.
The phytohormone auxin is implied in steering various developmental decisions during plant morphogenesis in a concentration-dependent manner. Auxin maxima have been shown to maintain meristematic activity, for example, of the root apical meristem, and position new sites of outgrowth, such as during lateral root initiation and phyllotaxis. More recently, it has been demonstrated that sites of auxin minima also provide positional information. In the developing Arabidopsis fruit, auxin minima are required for correct differentiation of the valve margin. It remains unclear, however, how this auxin minimum is generated and maintained. Here, we employ a systems biology approach to model auxin transport based on experimental observations. This allows us to determine the minimal requirements for its establishment. Our simulations reveal that two alternative processes-which we coin "flux-barrier" and "flux-passage"-are both able to generate an auxin minimum, but under different parameter settings. Both models are in principle able to yield similar auxin profiles but present qualitatively distinct patterns of auxin flux. The models were tested by tissue-specific inducible ablation, revealing that the auxin minimum in the fruit is most likely generated by a flux-passage process. Model predictions were further supported through 3D PIN localization imaging and implementing experimentally observed transporter localization. Through such an experimental-modeling cycle, we predict how the auxin minimum gradually matures during fruit development to ensure timely fruit opening and seed dispersal.
PMID: 31128274
Mol Plant , IF:12.084 , 2019 Jun , V12 (6) : P784-803 doi: 10.1016/j.molp.2019.03.015
The Systems Biology of Lateral Root Formation: Connecting the Dots.
Computational Developmental Biology Group, Department of Biology, Utrecht University, Utrecht, the Netherlands.; Computational Developmental Biology Group, Department of Biology, Utrecht University, Utrecht, the Netherlands. Electronic address: k.h.w.j.tentusscher@uu.nl.
The root system is a major determinant of a plant's access to water and nutrients. The architecture of the root system to a large extent depends on the repeated formation of new lateral roots. In this review, we discuss lateral root development from a systems biology perspective. We focus on studies combining experiments with computational modeling that have advanced our understanding of how the auxin-centered regulatory modules involved in different stages of lateral root development exert their specific functions. Moreover, we discuss how these regulatory networks may enable robust transitions from one developmental stage to the next, a subject that thus far has received limited attention. In addition, we analyze how environmental factors impinge on these modules, and the different manners in which these environmental signals are being integrated to enable coordinated developmental decision making. Finally, we provide some suggestions for extending current models of lateral root development to incorporate multiple processes and stages. Only through more comprehensive models we can fully elucidate the cooperative effects of multiple processes on later root formation, and how one stage drives the transition to the next.
PMID: 30953788
Mol Plant , IF:12.084 , 2019 Jun , V12 (6) : P822-832 doi: 10.1016/j.molp.2018.09.010
Capturing Auxin Response Factors Syntax Using DNA Binding Models.
Univ. Grenoble Alpes, CNRS, CEA, INRA, BIG-LPCV, 38000 Grenoble, France.; Univ. Grenoble Alpes, CNRS, CEA, INRA, BIG-LPCV, 38000 Grenoble, France; Laboratoire de Reproduction et Developpement des Plantes, Univ. Lyon, ENS de Lyon, UCB Lyon1, CNRS, INRA, 46 allee d'Italie, 69364, Lyon, France.; Novosibirsk State University, Pirogova Street 2, Novosibirsk, Russia; Institute of Cytology and Genetics SB RAS, Lavrentyeva Avenue 10, Novosibirsk, Russia.; Laboratoire de Reproduction et Developpement des Plantes, Univ. Lyon, ENS de Lyon, UCB Lyon1, CNRS, INRA, 46 allee d'Italie, 69364, Lyon, France.; Univ. Grenoble Alpes, CNRS, CEA, INRA, BIG-LPCV, 38000 Grenoble, France. Electronic address: francois.parcy@cea.fr.
Auxin is a key hormone performing a wealth of functions throughout the life cycle of plants. It acts largely by regulating genes at the transcriptional level through a family of transcription factors called auxin response factors (ARFs). Even though all ARF monomers analyzed so far bind a similar DNA sequence, there is evidence that ARFs differ in their target genomic regions and regulated genes. Here, we report the use of position weight matrices (PWMs) to model ARF DNA binding specificity based on published DNA affinity purification sequencing (DAP-seq) data. We found that the genome binding of two ARFs (ARF2 and ARF5/Monopteros [MP]) differ largely because these two factors have different preferred ARF binding site (ARFbs) arrangements (orientation and spacing). We illustrated why PWMs are more versatile to reliably identify ARFbs than the widely used consensus sequences and demonstrated their power with biochemical experiments in the identification of the regulatory regions of IAA19, an well-characterized auxin-responsive gene. Finally, we combined gene regulation by auxin with ARF-bound regions and identified specific ARFbs configurations that are over-represented in auxin-upregulated genes, thus deciphering the ARFbs syntax functional for regulation. Our study provides a general method to exploit the potential of genome-wide DNA binding assays and to decode gene regulation.
PMID: 30336329
Mol Biol Evol , IF:11.062 , 2019 Jun , V36 (6) : P1239-1253 doi: 10.1093/molbev/msz063
Paternally Expressed Imprinted Genes under Positive Darwinian Selection in Arabidopsis thaliana.
Genetics & Biotechnology Lab, Plant & AgriBiosciences Research Centre (PABC), School of Natural Sciences, Ryan Institute, National University of Ireland Galway, Galway, Ireland.; Center for Genomics and Systems Biology, New York University, New York, NY.; School of Biotechnology, Faculty of Biological Sciences, Dublin City University, Dublin, Ireland.; Division of Diabetes, Endocrinology and Metabolism, Imperial College London, London, United Kingdom.; Memorial Sloan Kettering Cancer Center, New York, NY.; Computational and Molecular Evolutionary Biology Research Group, School of Biology, Faculty of Biological Sciences, The University of Leeds, Leeds, United Kingdom.; Computational and Molecular Evolutionary Biology Group, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom.
Genomic imprinting is an epigenetic phenomenon where autosomal genes display uniparental expression depending on whether they are maternally or paternally inherited. Genomic imprinting can arise from parental conflicts over resource allocation to the offspring, which could drive imprinted loci to evolve by positive selection. We investigate whether positive selection is associated with genomic imprinting in the inbreeding species Arabidopsis thaliana. Our analysis of 140 genes regulated by genomic imprinting in the A. thaliana seed endosperm demonstrates they are evolving more rapidly than expected. To investigate whether positive selection drives this evolutionary acceleration, we identified orthologs of each imprinted gene across 34 plant species and elucidated their evolutionary trajectories. Increased positive selection was sought by comparing its incidence among imprinted genes with nonimprinted controls. Strikingly, we find a statistically significant enrichment of imprinted paternally expressed genes (iPEGs) evolving under positive selection, 50.6% of the total, but no such enrichment for positive selection among imprinted maternally expressed genes (iMEGs). This suggests that maternally- and paternally expressed imprinted genes are subject to different selective pressures. Almost all positively selected amino acids were fixed across 80 sequenced A. thaliana accessions, suggestive of selective sweeps in the A. thaliana lineage. The imprinted genes under positive selection are involved in processes important for seed development including auxin biosynthesis and epigenetic regulation. Our findings support a genomic imprinting model for plants where positive selection can affect paternally expressed genes due to continued conflict with maternal sporophyte tissues, even when parental conflict is reduced in predominantly inbreeding species.
PMID: 30913563
Autophagy , IF:9.77 , 2019 Jun , V15 (6) : P941-959 doi: 10.1080/15548627.2019.1569915
A facile forward-genetic screen for Arabidopsis autophagy mutants reveals twenty-one loss-of-function mutations disrupting six ATG genes.
a Department of Biosciences , Rice University , Houston , TX , USA.; b Department of Biology , University of Mary Hardin-Baylor , Belton , TX , USA.
Macroautophagy is a process through which eukaryotic cells degrade large substrates including organelles, protein aggregates, and invading pathogens. Over 40 autophagy-related (ATG) genes have been identified through forward-genetic screens in yeast. Although homology-based analyses have identified conserved ATG genes in plants, only a few atg mutants have emerged from forward-genetic screens in Arabidopsis thaliana. We developed a screen that consistently recovers Arabidopsis atg mutations by exploiting mutants with defective LON2/At5g47040, a protease implicated in peroxisomal quality control. Arabidopsis lon2 mutants exhibit reduced responsiveness to the peroxisomally-metabolized auxin precursor indole-3-butyric acid (IBA), heightened degradation of several peroxisomal matrix proteins, and impaired processing of proteins harboring N-terminal peroxisomal targeting signals; these defects are ameliorated by preventing autophagy. We optimized a lon2 suppressor screen to expedite recovery of additional atg mutants. After screening mutagenized lon2-2 seedlings for restored IBA responsiveness, we evaluated stabilization and processing of peroxisomal proteins, levels of several ATG proteins, and levels of the selective autophagy receptor NBR1/At4g24690, which accumulates when autophagy is impaired. We recovered 21 alleles disrupting 6 ATG genes: ATG2/At3g19190, ATG3/At5g61500, ATG5/At5g17290, ATG7/At5g45900, ATG16/At5g50230, and ATG18a/At3g62770. Twenty alleles were novel, and 3 of the mutated genes lack T-DNA insertional alleles in publicly available repositories. We also demonstrate that an insertional atg11/At4g30790 allele incompletely suppresses lon2 defects. Finally, we show that NBR1 is not necessary for autophagy of lon2 peroxisomes and that NBR1 overexpression is not sufficient to trigger autophagy of seedling peroxisomes, indicating that Arabidopsis can use an NBR1-independent mechanism to target peroxisomes for autophagic degradation. Abbreviations: ATG: autophagy-related; ATI: ATG8-interacting protein; Col-0: Columbia-0; DSK2: dominant suppressor of KAR2; EMS: ethyl methanesulfonate; GFP: green fluorescent protein; IAA: indole-3-acetic acid; IBA: indole-3-butyric acid; ICL: isocitrate lyase; MLS: malate synthase; NBR1: Next to BRCA1 gene 1; PEX: peroxin; PMDH: peroxisomal malate dehydrogenase; PTS: peroxisomal targeting signal; thiolase: 3-ketoacyl-CoA thiolase; UBA: ubiquitin-associated; WT: wild type.
PMID: 30734619
Plant Cell , IF:9.618 , 2019 Jun , V31 (6) : P1289-1307 doi: 10.1105/tpc.18.00905
A Functional Allele of CsFUL1 Regulates Fruit Length through Repressing CsSUP and Inhibiting Auxin Transport in Cucumber.
Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, MOE Joint International Research Laboratory of Crop Molecular Breeding, China Agricultural University, Beijing 100193, China.; Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706.; Department of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.; Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences, Shanghai 201602, China.; Department of Plant Nutrition, China Agricultural University, Beijing 100193, China.; College of Horticulture Science and Technology, Hebei Normal University of Science & Technology, Qinhuangdao 066004, China.; College of Horticultural and Landscape Architecture, Northeast Agricultural University, 600 Changjiang Road, Harbin 150030, China.; USDA-ARS, Vegetable Crops Research Unit, 1575 Linden Drive, Madison, Wisconsin 53706.; Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, MOE Joint International Research Laboratory of Crop Molecular Breeding, China Agricultural University, Beijing 100193, China zhxiaolan@cau.edu.cn.
Fruit length is a prominent agricultural trait during cucumber (Cucumis sativus) domestication and diversifying selection; however, the regulatory mechanisms of fruit elongation remain elusive. We identified two alleles of the FRUITFULL (FUL)-like MADS-box gene CsFUL1 with 3393(C/A) Single Nucleotide Polymorphism variation among 150 cucumber lines. Whereas CsFUL1(A) was specifically enriched in the long-fruited East Asian type cucumbers (China and Japan), the CsFUL1(C) allele was randomly distributed in cucumber populations, including wild and semiwild cucumbers. CsFUL1(A) knockdown led to further fruit elongation in cucumber, whereas elevated expression of CsFUL1(A) resulted in significantly shorter fruits. No effect on fruit elongation was detected when CsFUL1(C) expression was modulated, suggesting that CsFUL1(A) is a gain-of-function allele in long-fruited cucumber that acts as a repressor during diversifying selection of East Asian cucumbers. Furthermore, CsFUL1(A) binds to the CArG-box in the promoter region of SUPERMAN, a regulator of cell division and expansion, to repress its expression. Additionally, CsFUL1(A) inhibits the expression of auxin transporters PIN-FORMED1 (PIN1) and PIN7, resulting in decreases in auxin accumulation in fruits. Together, our work identifies an agriculturally important allele and suggests a strategy for manipulating fruit length in cucumber breeding that involves modulation of CsFUL1(A) expression.
PMID: 30979795
Curr Biol , IF:9.601 , 2019 Jun , V29 (11) : P1746-1759.e5 doi: 10.1016/j.cub.2019.04.047
Multiple Auxin-Response Regulators Enable Stability and Variability in Leaf Development.
The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Hebrew University, PO Box 12, Rehovot 76100, Israel.; The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Hebrew University, PO Box 12, Rehovot 76100, Israel; Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 76100, Israel.; Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 76100, Israel.; The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Hebrew University, PO Box 12, Rehovot 76100, Israel; Department of Plant Pathology and Weed Research, Agricultural Research Organization, Volcani Center, 68 HaMaccabim Road, Rishon LeZion 7505101, Israel.; The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Hebrew University, PO Box 12, Rehovot 76100, Israel. Electronic address: naomi.ori@mail.huji.ac.il.
Auxin-signal transduction is mediated by the antagonistic activity of transcriptional activators and repressors. Both activators and repressors belong to gene families, but the biological importance of this complexity is not clear. Here, we addressed this question using tomato leaf development as a model by generating and analyzing mutants in multiple auxin-response components. In developing compound tomato leaves, auxin promotes leaflet formation and blade growth, and in the intercalary regions between leaflets, auxin response is inhibited by the Aux/IAA protein ENTIRE (E). e mutants form simple leaves due to ectopic blade growth in the intercalary domain. Using this unique loss-of-function phenotype and genome editing of auxin-response factor (ARF) genes, encoding auxin-response activators, we identified the contribution of specific ARFs to the e phenotype. Mutations in the related ARFs SlMP, SlARF19A, and SlARF19B, but not SlARF7, reduced the leaf blade and suppressed the e phenotype in a dosage-dependent manner that correlated with their relative expression, leading to a continuum of shapes. While single e and slmp mutants affected blade growth in an opposite manner, leaves of e slmp double mutants were similar to those of the wild type. However, the leaf shape of e slmp was more variable than that of the wild type, and it showed increased sensitivity to auxin. Our findings demonstrate that the existence of multiple auxin-response repressors and activators stabilizes the developmental output of auxin and that tuning their activity enables shape variability. The increased complexity of the auxin response therefore balances stability and flexibility in leaf patterning.
PMID: 31104930
Plant Physiol , IF:6.902 , 2019 Jun , V180 (2) : P708 doi: 10.1104/pp.19.00464
Pinstatic Acid as a Dissection Tool-Kit for Transcriptional and Nontranscriptional Auxin Responses.
Biological and Environmental Sciences and Engineering, King Abdullah University for Science & Technology (KAUST), 23955-6900 Thuwal, Saudi Arabia magdalena.julkowska@kaust.edu.sa.
PMID: 31160529
Plant Physiol , IF:6.902 , 2019 Jun , V180 (2) : P757-766 doi: 10.1104/pp.18.01377
A Mobile Auxin Signal Connects Temperature Sensing in Cotyledons with Growth Responses in Hypocotyls.
Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany.; Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany.; German Centre for Integrative Biodiversity Research Halle-Jena-Leipzig, 04103 Leipzig, Germany.; Institute of Computer Science, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany.; Developmental and Cell Biology of Plants, Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria.; Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, 1190 Vienna, Austria.; Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany carolin.delker@landw.uni-halle.de.
Plants have a remarkable capacity to adjust their growth and development to elevated ambient temperatures. Increased elongation growth of roots, hypocotyls, and petioles in warm temperatures are hallmarks of seedling thermomorphogenesis. In the last decade, significant progress has been made to identify the molecular signaling components regulating these growth responses. Increased ambient temperature utilizes diverse components of the light sensing and signal transduction network to trigger growth adjustments. However, it remains unknown whether temperature sensing and responses are universal processes that occur uniformly in all plant organs. Alternatively, temperature sensing may be confined to specific tissues or organs, which would require a systemic signal that mediates responses in distal parts of the plant. Here, we show that Arabidopsis (Arabidopsis thaliana) seedlings show organ-specific transcriptome responses to elevated temperatures and that thermomorphogenesis involves both autonomous and organ-interdependent temperature sensing and signaling. Seedling roots can sense and respond to temperature in a shoot-independent manner, whereas shoot temperature responses require both local and systemic processes. The induction of cell elongation in hypocotyls requires temperature sensing in cotyledons, followed by the generation of a mobile auxin signal. Subsequently, auxin travels to the hypocotyl, where it triggers local brassinosteroid-induced cell elongation in seedling stems, which depends upon a distinct, permissive temperature sensor in the hypocotyl.
PMID: 31000634
Plant Physiol , IF:6.902 , 2019 Jun , V180 (2) : P986-997 doi: 10.1104/pp.19.00317
Down-regulation of the Sucrose Transporter CsSUT1 Causes Male Sterility by Altering Carbohydrate Supply.
Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing 100193, China.; Department of Plant Biology, College of Biological Sciences, University of California, Davis, California 95616.; Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing 100193, China zhangzx@cau.edu.cn.
In plants, male sterility is an important agronomic trait, especially in hybrid crop production. Many factors are known to affect crop male sterility, but it remains unclear whether Suc transporters (SUTs) participate directly in this process. Here, we identified and functionally characterized the cucumber (Cucumis sativus) CsSUT1, a typical plasma membrane-localized energy-dependent high-affinity Suc-H(+) symporter. CsSUT1 is expressed in male flowers and encodes a protein that is localized primarily in the tapetum, pollen, and companion cells of the phloem of sepals, petals, filaments, and pedicel. The male flowers of CsSUT1-RNA interference (RNAi) lines exhibited a decrease in Suc, hexose, and starch content, relative to those of the wild type, during the later stages of male flower development, a finding that was highly associated with male sterility. Transcriptomic analysis revealed that numerous genes associated with sugar metabolism, transport, and signaling, as well as with auxin signaling, were down-regulated, whereas most myeloblastosis (MYB) transcription factor genes were up-regulated in these CsSUT1-RNAi lines relative to wild type. Our findings demonstrate that male sterility can be induced by RNAi-mediated down-regulation of CsSUT1 expression, through the resultant perturbation in carbohydrate delivery and subsequent alteration in sugar and hormone signaling and up-regulation of specific MYB transcription factors. This knowledge provides a new approach for bioengineering male sterility in crop plants.
PMID: 30967482
Plant Physiol , IF:6.902 , 2019 Jun , V180 (2) : P1185-1197 doi: 10.1104/pp.19.00139
Developmental Programming of Thermonastic Leaf Movement.
Department of Chemistry, Seoul National University, Seoul 08826, Korea.; Department of Biological Sciences, Seoul National University, Seoul 08826, Korea.; Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium.; VIB Center for Plant Systems Biology, B-9052 Ghent, Belgium.; Department of Biomolecular Medicine, Ghent University, B-9000 Ghent, Belgium.; VIB Center for Medical Biotechnology, B-9000 Ghent, Belgium.; Department of Chemistry, Seoul National University, Seoul 08826, Korea cmpark@snu.ac.kr.; Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Korea.
Plants exhibit diverse polar behaviors in response to directional and nondirectional environmental signals, termed tropic and nastic movements, respectively. The ways in which plants incorporate directional information into tropic behaviors is well understood, but it is less well understood how nondirectional stimuli, such as ambient temperatures, specify the polarity of nastic behaviors. Here, we demonstrate that a developmentally programmed polarity of auxin flow underlies thermo-induced leaf hyponasty in Arabidopsis (Arabidopsis thaliana). In warm environments, PHYTOCHROME-INTERACTING FACTOR4 (PIF4) stimulates auxin production in the leaf. This results in the accumulation of auxin in leaf petioles, where PIF4 directly activates a gene encoding the PINOID (PID) protein kinase. PID is involved in polarization of the auxin transporter PIN-FORMED3 to the outer membranes of petiole cells. Notably, the leaf polarity-determining ASYMMETRIC LEAVES1 (AS1) directs the induction of PID to occur predominantly in the abaxial petiole region. These observations indicate that the integration of PIF4-mediated auxin biosynthesis and polar transport, and the AS1-mediated developmental shaping of polar auxin flow, coordinate leaf thermonasty, which facilitates leaf cooling in warm environments. We believe that leaf thermonasty is a suitable model system for studying the developmental programming of environmental adaptation in plants.
PMID: 30948554
Plant Physiol , IF:6.902 , 2019 Jun , V180 (2) : P1152-1165 doi: 10.1104/pp.19.00201
Pinstatic Acid Promotes Auxin Transport by Inhibiting PIN Internalization.
Department of Biochemistry, Okayama University of Science, Okayama 700-0005, Japan.; Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria.; Laboratory of Growth Regulators, The Czech Academy of Sciences, Institute of Experimental Botany & Palacky University, CZ-78371 Olomouc, Czech Republic.; School of Life Sciences, University of Warwick, Coventry, CV4 7AL, United Kingdom.; Graduate School of Science, Nagoya University, Chikusa, Nagoya, 464-8602 Japan.; Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya, 464-8601, Japan.; Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.; Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, Fuchu-shi, Tokyo 183-8509, Japan.; RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045 Japan.; Department of Biochemistry, Okayama University of Science, Okayama 700-0005, Japan hayashi@dbc.ous.ac.jp.
Polar auxin transport plays a pivotal role in plant growth and development. PIN-FORMED (PIN) auxin efflux carriers regulate directional auxin movement by establishing local auxin maxima, minima, and gradients that drive multiple developmental processes and responses to environmental signals. Auxin has been proposed to modulate its own transport by regulating subcellular PIN trafficking via processes such as clathrin-mediated PIN endocytosis and constitutive recycling. Here, we further investigated the mechanisms by which auxin affects PIN trafficking by screening auxin analogs and identified pinstatic acid (PISA) as a positive modulator of polar auxin transport in Arabidopsis (Arabidopsis thaliana). PISA had an auxin-like effect on hypocotyl elongation and adventitious root formation via positive regulation of auxin transport. PISA did not activate SCF(TIR1/AFB) signaling and yet induced PIN accumulation at the cell surface by inhibiting PIN internalization from the plasma membrane. This work demonstrates PISA to be a promising chemical tool to dissect the regulatory mechanisms behind subcellular PIN trafficking and auxin transport.
PMID: 30936248
Plant Physiol , IF:6.902 , 2019 Jun , V180 (2) : P837-858 doi: 10.1104/pp.19.00266
Unusual Roles of Secretory SNARE SYP132 in Plasma Membrane H(+)-ATPase Traffic and Vegetative Plant Growth.
Plant Science Group, Laboratory of Plant Physiology and Biophysics, Institute of Molecular, Cell, and Systems Biology, University of Glasgow, Glasgow G12 8QQ, United Kingdom.; Plant Science Group, Laboratory of Plant Physiology and Biophysics, Institute of Molecular, Cell, and Systems Biology, University of Glasgow, Glasgow G12 8QQ, United Kingdom rucha.karnik@glasgow.ac.uk.
The plasma membrane proton (H(+))-ATPases of plants generate steep electrochemical gradients and activate osmotic solute uptake. H(+)-ATPase-mediated proton pumping orchestrates cellular homeostasis and is a prerequisite for plastic cell expansion and plant growth. All evidence suggests that the population of H(+)-ATPase proteins at the plasma membrane reflects a balance of their roles in exocytosis, endocytosis, and recycling. Auxin governs both traffic and activation of the plasma membrane H(+)-ATPase proteins already present at the membrane. As in other eukaryotes, in plants, SNARE-mediated membrane traffic influences the density of several proteins at the plasma membrane. Even so, H(+)-ATPase traffic, its relationship with SNAREs, and its regulation by auxin have remained enigmatic. Here, we identify the Arabidopsis (Arabidopsis thaliana) Qa-SNARE SYP132 (Syntaxin of Plants132) as a key factor in H(+)-ATPase traffic and demonstrate its association with endocytosis. SYP132 is a low-abundant, secretory SNARE that primarily localizes to the plasma membrane. We find that SYP132 expression is tightly regulated by auxin and that augmented SYP132 expression reduces the amount of H(+)-ATPase proteins at the plasma membrane. The physiological consequences of SYP132 overexpression include reduced apoplast acidification and suppressed vegetative growth. Thus, SYP132 plays unexpected and vital roles in auxin-regulated H(+)-ATPase traffic and associated functions at the plasma membrane.
PMID: 30926657
Plant Physiol , IF:6.902 , 2019 Jun , V180 (2) : P952-965 doi: 10.1104/pp.18.01385
OsPINOID Regulates Stigma and Ovule Initiation through Maintenance of the Floral Meristem by Auxin Signaling.
Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Agricultural College of Yangzhou University, Yangzhou 225009, China.; State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.; Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan 430064, China.; Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Agricultural College of Yangzhou University, Yangzhou 225009, China hxyu@yzu.edu.cn.
Stigma and ovule initiation is essential for sexual reproduction in flowering plants. However, the mechanism underlying the initiation of stigma and ovule primordia remains elusive. We identified a stigma-less mutant of rice (Oryza sativa) and revealed that it was caused by the mutation in the PINOID (OsPID) gene. Unlike the pid mutant that shows typical pin-like inflorescences in maize (Zea mays) and Arabidopsis (Arabidopsis thaliana), the ospid mutant does not display any defects in inflorescence development and flower initiation, and fails to develop normal ovules in most spikelets. The auxin activity in the young pistil of ospid was lower than that in the wild-type pistil. Furthermore, the expression of most auxin response factor genes was down-regulated, and OsETTIN1, OsETTIN2, and OsMONOPTEROS lost their rearrangements of expression patterns during pistil and stamen primordia development in ospid Moreover, the transcription of the floral meristem marker gene, OSH1, was down-regulated and FLORAL ORGAN NUMBER4, the putative ortholog of Arabidopsis CLAVATA3, was up-regulated in the pistil primordium of ospid These results suggested that the meristem proliferation in the pistil primordium might be arrested prematurely in ospid Based on these results, we propose that the OsPID-mediated auxin signaling pathway plays a crucial role in the regulation of rice stigma and ovule initiation by maintaining the floral meristem.
PMID: 30926655
Plant Physiol , IF:6.902 , 2019 Jun , V180 (2) : P926-936 doi: 10.1104/pp.18.01389
PINOID Is Required for Formation of the Stigma and Style in Rice.
National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.; Section of Cell and Developmental Biology, University of California San Diego, La Jolla, California 92093-0116.; Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.; School of Life Sciences, Centre for Cell and Developmental Biology and State Key Laboratory of Agrobiotechnology, Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.; National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China yundezhao@ucsd.edu.
The stigma is the entry point for sexual reproduction in plants, but the mechanisms underlying stigma development are largely unknown. Here, we disrupted putative auxin biosynthetic and signaling genes to evaluate their roles in rice (Oryza sativa) development. Disruption of the rice PINOID (OsPID) gene completely eliminated the development of stigmas, and overexpression of OsPID led to overproliferation of stigmas, suggesting that OsPID is a key determinant for stigma development. Interestingly, ospid mutants did not display defects in flower initiation, nor did they develop any pin-like inflorescences, a characteristic phenotype observed in pid mutants in Arabidopsis (Arabidopsis thaliana) and maize (Zea mays). We constructed double mutants of OsPID and its closest homolog, OsPIDb, yet the double mutants still did not develop any pin-like inflorescences, indicating that either ospid is compensated by additional homologous genes or OsPID has different functions in rice compared with PID in other organisms. We then knocked out one of the NAKED PINS IN YUC MUTANTS (NPY) genes, which cause the formation of pin-like inflorescences in Arabidopsis when compromised, in the ospid background. The ospid osnpy2 double mutants developed pin-like inflorescences, which were phenotypically similar to pid mutants in Arabidopsis and maize, demonstrating that the roles of OsPID in inflorescence development are likely masked by redundant partners. This work identified a key determinant for stigma development in rice and revealed a complex picture of the PID gene in rice development. Furthermore, the stigma-less ospid mutants are potentially useful in producing hybrid rice.
PMID: 30918083
Plant Physiol , IF:6.902 , 2019 Jun , V180 (2) : P1119-1131 doi: 10.1104/pp.19.00206
Deetiolation Enhances Phototropism by Modulating NON-PHOTOTROPIC HYPOCOTYL3 Phosphorylation Status.
Institute of Molecular, Cell, and Systems Biology, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom.; Department of Botany, St. Edmund's College, Shillong 793003, Meghalaya, India.; Institute of Science and Technology, Niigata University, Ikarashi, Nishiku, Niigata 950-2181, Japan.; Institute of Molecular, Cell, and Systems Biology, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom john.christie@glasgow.ac.uk.
Phototropin (phot) receptor kinases play important roles in promoting plant growth by controlling light-capturing processes, such as phototropism. Phototropism is mediated through the action of NON-PHOTOTROPIC HYPOCOTYL3 (NPH3), which is dephosphorylated following phot activation. However, the functional significance of this early signaling event remains unclear. Here, we show that the onset of phototropism in dark-grown (etiolated) seedlings of Arabidopsis (Arabidopsis thaliana) and tomato (Solanum lycopersicum) is enhanced by greening (deetiolation). Red and blue light were equally effective in promoting phototropism in Arabidopsis, consistent with our observations that deetiolation by phytochrome or cryptochrome was sufficient to enhance phototropism. Increased responsiveness did not result from an enhanced sensitivity to the phytohormone auxin, nor does it involve the phot-interacting protein, ROOT PHOTOTROPISM2. Instead, deetiolated seedlings showed attenuated levels of NPH3 dephosphorylation and diminished relocalization of NPH3 from the plasma membrane during phototropism. Likewise, etiolated seedlings that lack the PHYTOCHROME-INTERACTING FACTORS (PIFs) PIF1, PIF3, PIF4, and PIF5 displayed reduced NPH3 dephosphorylation and enhanced phototropism, consistent with their constitutive photomorphogenic phenotype in darkness. Phototropic enhancement could also be achieved in etiolated seedlings by lowering the light intensity to diminish NPH3 dephosphorylation. Thus, phototropism is enhanced following deetiolation through the modulation of a phosphorylation rheostat, which in turn sustains the activity of NPH3. We propose that this dynamic mode of regulation enables young seedlings to maximize their establishment under changing light conditions, depending on their photoautotrophic capacity.
PMID: 30918082
Plant Physiol , IF:6.902 , 2019 Jun , V180 (2) : P896-909 doi: 10.1104/pp.18.01460
Mitochondrial Pyruvate Dehydrogenase Contributes to Auxin-Regulated Organ Development.
College of Life Sciences, Fujian Agriculture and Forestry University, No.15 Shangxiadian Road, Cangshan District, Fuzhou City, Fujian 350002, China.; FAFU-UCR Joint Center and Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, No.15 Shangxiadian Road, Cangshan District, Fuzhou City, Fujian 350002, China.; School of Molecular Science and ARC Centre of Excellence in Plant Energy Biology, Bayliss Building, M316, The University of Western Australia, 35 Stirling Highway, Crawley, Washington 6009, Western Australia, Australia.; Department of Biology, Graduate School of Science, Kobe University, Rokkodai 1-1, Kobe 657-8501, Japan.; Division of Plant Environmental Responses, National Institute for Basic Biology, Myodaiji, Okazaki 444-8556, Japan.; Graduate School of Biological Sciences, Nara Institute of Science and Technology (NAIST), Takayama 8916-5, Ikoma, Nara 630-0192, Japan.; College of Life Sciences, Fujian Agriculture and Forestry University, No.15 Shangxiadian Road, Cangshan District, Fuzhou City, Fujian 350002, China ma-furut@fafu.edu.cn.
Pyruvate dehydrogenase is the first enzyme (E1) of the PDH complex (PDC). This multienzyme complex contains E1, E2, and E3 components and controls the entry of carbon into the mitochondrial tricarboxylic acid cycle to enable cellular energy production. The E1 component of the PDC is composed of an E1alpha catalytic subunit and an E1beta regulatory subunit. In Arabidopsis (Arabidopsis thaliana), there are two mitochondrial E1alpha homologs encoded by IAA-CONJUGATE-RESISTANT 4 (IAR4) and IAR4-LIKE (IAR4L), and one mitochondrial E1beta homolog. Although IAR4 was reported to be involved in auxin conjugate sensitivity and auxin homeostasis in root development, its precise role remains unknown. Here, we provide experimental evidence that mitochondrial PDC E1 contributes to polar auxin transport during organ development. We performed genetic screens for factors involved in cotyledon development and identified an uncharacterized mutant, macchi-bou 1 (mab1). MAB1 encodes a mitochondrial PDC E1beta subunit that can form both a homodimer and a heterodimer with IAR4. The mab1 mutation impaired MAB1 homodimerization, reduced the abundance of IAR4 and IAR4L, weakened PDC enzymatic activity, and diminished mitochondrial respiration. A metabolomics analysis showed significant changes in metabolites including amino acids in mab1 and, in particular, identified an accumulation of Ala. These results suggest that MAB1 is a component of the Arabidopsis mitochondrial PDC E1. Furthermore, in mab1 mutants and seedlings where the TCA cycle was pharmacologically blocked, we found reduced abundance of the PIN-FORMED (PIN) auxin efflux carriers, possibly due to impaired PIN recycling and enhanced PIN degradation in vacuoles. Therefore, we suggest that mab1 induces defective polar auxin transport via metabolic abnormalities.
PMID: 30894418
Plant Physiol , IF:6.902 , 2019 Jun , V180 (2) : P882-895 doi: 10.1104/pp.19.00142
A Transcription Factor, OsMADS57, Regulates Long-Distance Nitrate Transport and Root Elongation.
State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China.; Henan Key Laboratory of Tea Plant Comprehensive Utilization in South Henan, Xinyang Agriculture and Forestry University, Xinyang 464000, China.; College of Agronomy, Collaborative Innovation Center of Henan Grain Crops, Key Laboratory of Rice Biology in Henan Province, Henan Agricultural University, Zhengzhou 450002, China.; Institute of Food Crops of Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China.; State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China ylzhang@njau.edu.cn.
Root nitrate uptake adjusts to the plant's nitrogen demand for growth. Here, we report that OsMADS57, a MADS-box transcription factor, modulates nitrate translocation from rice (Oryza sativa) roots to shoots under low-nitrate conditions. OsMADS57 is abundantly expressed in xylem parenchyma cells of root stele and is induced by nitrate. Compared with wild-type rice plants supplied with 0.2 mM nitrate, osmads57 mutants had 31% less xylem loading of nitrate, while overexpression lines had 2-fold higher levels. Shoot-root (15)N content ratios were 40% lower in the mutants and 76% higher in the overexpression lines. Rapid NO3 (-) root influx experiments showed that mutation of OsMADS57 did not affect root nitrate uptake. Reverse transcription quantitative PCR analysis of OsNRT2 nitrate transporter genes showed that after 5 min in 0.2 mM nitrate, only OsNRT2.3a (a vascular-specific high-affinity nitrate transporter) had reduced (by two-thirds) expression levels. At 60 min of nitrate treatment, lower expression levels were also observed for three additional NRT2 genes (OsNRT2.1/2.2/2.4). Conversely, in the overexpression lines, four NRT2 genes had much higher expression profiles at all time points tested. As previously reported, OsNRT2.3a functions in nitrate translocation, indicating the possible interaction between OsMADS57 and OsNRT2.3a Yeast one-hybrid and transient expression assays demonstrated that OsMADS57 binds to the CArG motif (CATTTTATAG) within the OsNRT2.3a promoter. Moreover, seminal root elongation was inhibited in osmads57 mutants, which may be associated with higher auxin levels in and auxin polar transport to root tips of mutant plants. Taken together, these results suggest that OsMADS57 has a role in regulating nitrate translocation from root to shoot via OsNRT2.3a.
PMID: 30886113
Plant Physiol , IF:6.902 , 2019 Jun , V180 (2) : P718-731 doi: 10.1104/pp.19.00051
Tandem Fluorescent Protein Timers for Noninvasive Relative Protein Lifetime Measurement in Plants.
Plant Sciences Department, Rothamsted Research, Harpenden AL5 2JQ, United Kingdom.; Centre for Organismal Studies, University of Heidelberg, Heidelberg 69120, Germany.; Plant Sciences Department, Rothamsted Research, Harpenden AL5 2JQ, United Kingdom freddie.theodoulou@rothamsted.ac.uk.
Targeted protein degradation is an important and pervasive regulatory mechanism in plants, required for perception and response to the environment as well as developmental signaling. Despite the significance of this process, relatively few studies have assessed plant protein turnover in a quantitative fashion. Tandem fluorescent protein timers (tFTs) offer a powerful approach for the assessment of in vivo protein turnover in distinct subcellular compartments of single or multiple cells. A tFT is a fusion of two different fluorescent proteins with distinct fluorophore maturation kinetics, which enable protein age to be estimated from the ratio of fluorescence intensities of the two fluorescent proteins. Here, we used short-lived auxin signaling proteins and model N-end rule (N-recognin) pathway reporters to demonstrate the utility of tFTs for studying protein turnover in living plant cells of Arabidopsis (Arabidopsis thaliana) and Nicotiana benthamiana We present transient expression of tFTs as an efficient screen for relative protein lifetime, useful for testing the effects of mutations and different genetic backgrounds on protein stability. This work demonstrates the potential for using stably expressed tFTs to study native protein dynamics with high temporal resolution in response to exogenous or endogenous stimuli.
PMID: 30872425
Plant J , IF:6.141 , 2019 Jun , V98 (5) : P767-782 doi: 10.1111/tpj.14349
The genome of cowpea (Vigna unguiculata [L.] Walp.).
Department of Computer Science and Engineering, University of California, Riverside, CA, 92521, USA.; Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA.; US Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA.; Natural Resources Institute Finland (Luke), Helsinki, Finland.; Institute of Biotechnology, University of Helsinki, Helsinki, Finland.; Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland.; Department of Plant Sciences, University of California, Davis, CA, 95616, USA.; Institut de Recherche en Horticulture et Semences, INRA, Universite d'Angers, 49071, Beaucouze, France.; Department of Nematology, University of California, Riverside, CA, 92521, USA.; Departamento de Fitopatologia, Instituto de Ciencias Biologicas, Universidade de Brasilia, Brasilia, DF, Brazil.; Centre of the Region Hana for Biotechnological and Agricultural Research, Institute of Experimental Botany, Olomouc, Czech Republic.; National Center for Genome Resources, Santa Fe, NM, 87505, USA.; US Department of Agriculture-Agricultural Research Service, Ames, IA, USA.
Cowpea (Vigna unguiculata [L.] Walp.) is a major crop for worldwide food and nutritional security, especially in sub-Saharan Africa, that is resilient to hot and drought-prone environments. An assembly of the single-haplotype inbred genome of cowpea IT97K-499-35 was developed by exploiting the synergies between single-molecule real-time sequencing, optical and genetic mapping, and an assembly reconciliation algorithm. A total of 519 Mb is included in the assembled sequences. Nearly half of the assembled sequence is composed of repetitive elements, which are enriched within recombination-poor pericentromeric regions. A comparative analysis of these elements suggests that genome size differences between Vigna species are mainly attributable to changes in the amount of Gypsy retrotransposons. Conversely, genes are more abundant in more distal, high-recombination regions of the chromosomes; there appears to be more duplication of genes within the NBS-LRR and the SAUR-like auxin superfamilies compared with other warm-season legumes that have been sequenced. A surprising outcome is the identification of an inversion of 4.2 Mb among landraces and cultivars, which includes a gene that has been associated in other plants with interactions with the parasitic weed Striga gesnerioides. The genome sequence facilitated the identification of a putative syntelog for multiple organ gigantism in legumes. A revised numbering system has been adopted for cowpea chromosomes based on synteny with common bean (Phaseolus vulgaris). An estimate of nuclear genome size of 640.6 Mbp based on cytometry is presented.
PMID: 31017340
Plant J , IF:6.141 , 2019 Jun , V98 (6) : P1048-1059 doi: 10.1111/tpj.14301
Genetic screen for factors mediating PIN polarization in gravistimulated Arabidopsis thaliana hypocotyls.
Institute of Science and Technology (IST) Austria, 3400, Klosterneuburg, Austria.
Gravitropism is an adaptive response that orients plant growth parallel to the gravity vector. Asymmetric distribution of the phytohormone auxin is a necessary prerequisite to the tropic bending both in roots and shoots. During hypocotyl gravitropic response, the PIN3 auxin transporter polarizes within gravity-sensing cells to redirect intercellular auxin fluxes. First gravity-induced PIN3 polarization to the bottom cell membranes leads to the auxin accumulation at the lower side of the organ, initiating bending and, later, auxin feedback-mediated repolarization restores symmetric auxin distribution to terminate bending. Here, we performed a forward genetic screen to identify regulators of both PIN3 polarization events during gravitropic response. We searched for mutants with defective PIN3 polarizations based on easy-to-score morphological outputs of decreased or increased gravity-induced hypocotyl bending. We identified the number of hypocotyl reduced bending (hrb) and hypocotyl hyperbending (hhb) mutants, revealing that reduced bending correlated typically with defective gravity-induced PIN3 relocation whereas all analyzed hhb mutants showed defects in the second, auxin-mediated PIN3 relocation. Next-generation sequencing-aided mutation mapping identified several candidate genes, including SCARECROW and ACTIN2, revealing roles of endodermis specification and actin cytoskeleton in the respective gravity- and auxin-induced PIN polarization events. The hypocotyl gravitropism screen thus promises to provide novel insights into mechanisms underlying cell polarity and plant adaptive development.
PMID: 30821050
J Exp Bot , IF:5.908 , 2019 Jun , V70 (12) : P3021-3023 doi: 10.1093/jxb/erz183
Optimization of polar distribution of GhPIN3a in the ovule epidermis improves cotton fiber development.
State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing, China.; Crop Science Institute, Agronomy Department, College of Agriculture and Biotechnology, Zhejiang University, Zhejiang, China.
PMID: 31250905
J Exp Bot , IF:5.908 , 2019 Jun , V70 (11) : P2937-2949 doi: 10.1093/jxb/erz212
Establishing a framework for female germline initiation in the plant ovule.
Department of Subtropical Fruits, Instituto de Hortofruticultura Subtropical y Mediterranea 'La Mayora' (IHSM-UMA-CSIC), Algarrobo-Costa, Malaga, Spain.; School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, Glen Osmond, SA, Australia.
Female gametogenesis in flowering plants initiates in the ovule, where a single germline progenitor differentiates from a pool of somatic cells. Germline initiation is a fundamental prerequisite for seed development but is poorly understood at the molecular level due to the location of the cells deep within the flower. Studies in Arabidopsis have shown that regulators of germline development include transcription factors such as NOZZLE/SPOROCYTELESS and WUSCHEL, components of the RNA-dependent DNA methylation pathway such as ARGONAUTE9 and RNA-DEPENDENT RNA POLYMERASE 6, and phytohormones such as auxin and cytokinin. These factors accumulate in a range of cell types from where they establish an environment to support germline differentiation. Recent studies provide fresh insight into the transition from somatic to germline identity, linking chromatin regulators, cell cycle genes, and novel mobile signals, capitalizing on cell type-specific methodologies in both dicot and monocot models. These findings are providing unique molecular and compositional insight into the mechanistic basis and evolutionary conservation of female germline development in plants.
PMID: 31063548
J Exp Bot , IF:5.908 , 2019 Jun , V70 (12) : P3139-3151 doi: 10.1093/jxb/erz162
Cytokinin inhibits cotton fiber initiation by disrupting PIN3a-mediated asymmetric accumulation of auxin in the ovule epidermis.
Biotechnology Research Center, Southwest University, Beibei, Chongqing, P. R. China.
Auxin-dependent cell expansion is crucial for initiation of fiber cells in cotton (Gossypium hirsutum), which ultimately determines fiber yield and quality. However, the regulation of this process is far from being well understood. In this study, we demonstrate an antagonistic effect between cytokinin (CK) and auxin on cotton fiber initiation. In vitro and in planta experiments indicate that enhanced CK levels can reduce auxin accumulation in the ovule integument, which may account for the defects in the fiberless mutant xu142fl. In turn, supplementation with auxin can recover fiber growth of CK-treated ovules and mutant ovules. We further found that GhPIN3a is a key auxin transporter for fiber-cell initiation and is polarly localized to the plasma membranes of non-fiber cells, but not to those of fiber cells. This polar localization allows auxin to be transported within the ovule integument while specifically accumulating in fiber cells. We show that CKs antagonize the promotive effect of auxin on fiber cell initiation by undermining asymmetric accumulation of auxin in the ovule epidermis through down-regulation of GhPIN3a and disturbance of the polar localization of the protein.
PMID: 30970146
J Exp Bot , IF:5.908 , 2019 Jun , V70 (12) : P3165-3176 doi: 10.1093/jxb/erz144
GmYUC2a mediates auxin biosynthesis during root development and nodulation in soybean.
State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, PR China.; Centre for Integrative Legume Research, School of Agriculture and Food Sciences, The University of Queensland, St. Lucia, QLD, Australia.; Key State Laboratory of Plant Cell & Chromosome Engineering, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei, China.
Auxin plays central roles in rhizobial infection and nodule development in legumes. However, the sources of auxin during nodulation are unknown. In this study, we analyzed the YUCCA (YUC) gene family of soybean and identified GmYUC2a as an important regulator of auxin biosynthesis that modulates nodulation. Following rhizobial infection, GmYUC2a exhibited increased expression in various nodule tissues. Overexpression of GmYUC2a (35S::GmYUC2a) increased auxin production in soybean, resulting in severe growth defects in root hairs and root development. Upon rhizobial infection, 35S::GmYUC2a hairy roots displayed altered patterns of root hair deformation and nodule formation. Root hair deformation occurred mainly on primary roots, and nodules formed exclusively on primary roots of 35S::GmYUC2a plants. Moreover, transgenic 35S::GmYUC2a composite plants showed delayed nodule development and a reduced number of nodules. Our results suggest that GmYUC2a plays an important role in regulating both root growth and nodulation by modulating auxin balance in soybean.
PMID: 30958883
J Exp Bot , IF:5.908 , 2019 Jun , V70 (11) : P2965-2978 doi: 10.1093/jxb/ery464
Microspore embryogenesis: targeting the determinant factors of stress-induced cell reprogramming for crop improvement.
Pollen Biotechnology of Crop Plants group, Biological Research Center, CIB-CSIC, Ramiro de Maeztu, Madrid, Spain.
Under stress, isolated microspores are reprogrammed in vitro towards embryogenesis, producing doubled haploid plants that are useful biotechnological tools in plant breeding as a source of new genetic variability, fixed in homozygous plants in only one generation. Stress-induced cell death and low rates of cell reprogramming are major factors that reduce yield. Knowledge gained in recent years has revealed that initiation and progression of microspore embryogenesis involve a complex network of factors, whose roles are not yet well understood. Here, I review recent findings on the determinant factors underlying stress-induced microspore embryogenesis, focusing on the role of autophagy, cell death, auxin, chromatin modifications, and the cell wall. Autophagy and cell death proteases are crucial players in the response to stress, while cell reprogramming and acquisition of totipotency are regulated by hormonal and epigenetic mechanisms. Auxin biosynthesis, transport, and action are required for microspore embryogenesis. Initial stages involve DNA hypomethylation, H3K9 demethylation, and H3/H4 acetylation. Cell wall remodelling, with pectin de-methylesterification and arabinogalactan protein expression, is necessary for embryo development. Recent reports show that treatments with small modulators of autophagy, proteases, and epigenetic marks reduce cell death and enhance embryogenesis initiation in several crops, opening up new possibilities for improving in vitro embryo production in breeding programmes.
PMID: 30753698
J Integr Plant Biol , IF:4.885 , 2019 Jun , V61 (6) : P658-674 doi: 10.1111/jipb.12797
Genome-wide association study dissects the genetic bases of salt tolerance in maize seedlings.
National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.; College of Plant Science, Tarim University, Alaer, 843300, China.; Department of Biology, Wilkes University, Wilkes-Barre, Pennsylvania, 18766, USA.
Excess salinity is a natural stress that causes crop yield losses worldwide. The genetic bases of maize salt tolerance remain largely unknown. Here we investigated the survival rates of 445 maize natural accessions after salt treatments. A skewed distribution of the salt-tolerant phenotypes was observed in this population. Genome-wide association studies (GWAS) revealed 57 loci significantly associated with salt tolerance. Forty-nine candidate genes were detected from these loci. About 10% of these genes were co-localized with loci from QTL mapping. Forty four percent of the candidate genes were involved in stress responses, ABA signaling, stomata division, DNA binding/transcription regulation and auxin signaling, suggesting that they are key genetic mechanisms of maize salt tolerance. Transgenic studies showed that two genes, the salt-tolerance-associated-gene 4 (SAG4, GRMZM2G077295) and SAG6 (GRMZM2G106056), which encode a protein transport protein and the double-strand break repair protein MRE11, respectively, had positive roles in plant salt tolerance, and their salt-tolerant haplotypes were revealed. The genes we identified in this study provide a list of candidate targets for further study of maize salt tolerance, and of genetic markers and materials that may be used for breeding salt-tolerance in maize.
PMID: 30803125
Mol Cell Proteomics , IF:4.87 , 2019 Jun , V18 (6) : P1157-1170 doi: 10.1074/mcp.RA119.001378
Quantitative Early Auxin Root Proteomics Identifies GAUT10, a Galacturonosyltransferase, as a Novel Regulator of Root Meristem Maintenance.
From the Departments of double daggerGenetics, Development and Cell Biology.; paragraph signPlant Pathology and Microbiology, Iowa State University, Ames, IA.; section signSection of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA.; From the Departments of double daggerGenetics, Development and Cell Biology, dkelley@iastate.edu.
Auxin induces rapid gene expression changes throughout root development. How auxin-induced transcriptional responses relate to changes in protein abundance is not well characterized. This report identifies early auxin responsive proteins in roots at 30 min and 2 h after hormone treatment using a quantitative proteomics approach in which 3,514 proteins were reliably quantified. A comparison of the >100 differentially expressed proteins at each the time point showed limited overlap, suggesting a dynamic and transient response to exogenous auxin. Several proteins with established roles in auxin-mediated root development exhibited altered abundance, providing support for this approach. While novel targeted proteomics assays demonstrate that all six auxin receptors remain stable in response to hormone. Additionally, 15 of the top responsive proteins display root and/or auxin response phenotypes, demonstrating the validity of these differentially expressed proteins. Auxin signaling in roots dictates proteome reprogramming of proteins enriched for several gene ontology terms, including transcription, translation, protein localization, thigmatropism, and cell wall modification. In addition, we identified auxin-regulated proteins that had not previously been implicated in auxin response. For example, genetic studies of the auxin responsive protein galacturonosyltransferase 10 demonstrate that this enzyme plays a key role in root development. Altogether these data complement and extend our understanding of auxin response beyond that provided by transcriptome studies and can be used to uncover novel proteins that may mediate root developmental programs.
PMID: 30918009
Int J Mol Sci , IF:4.556 , 2019 Jun , V20 (13) doi: 10.3390/ijms20133185
Morphological, Transcriptomic and Hormonal Characterization of Trimonoecious and Subandroecious Pumpkin (Cucurbita maxima) Suggests Important Roles of Ethylene in Sex Expression.
Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture/Northeast Agricultural University, Harbin 150030, China. wangyunlii@163.com.; College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China. wangyunlii@163.com.; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture/Northeast Agricultural University, Harbin 150030, China. yanchundong177@163.com.; College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China. yanchundong177@163.com.; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture/Northeast Agricultural University, Harbin 150030, China. 15046782102@139.com.; College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China. 15046782102@139.com.; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture/Northeast Agricultural University, Harbin 150030, China. chaojiewang1992@163.com.; College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China. chaojiewang1992@163.com.; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture/Northeast Agricultural University, Harbin 150030, China. xwl1973@163.com.; College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China. xwl1973@163.com.; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture/Northeast Agricultural University, Harbin 150030, China. Chongshicui9@163.com.; College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China. Chongshicui9@163.com.; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture/Northeast Agricultural University, Harbin 150030, China. spqu@neau.edu.cn.; College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China. spqu@neau.edu.cn.
: Sex expression is a complex process, and in-depth knowledge of its mechanism in pumpkin is important. In this study, young shoot apices at the one-true-leaf stage and 10-leaf stage in Cucurbita maxima trimonoecious line '2013-12' and subandroecious line '9-6' were collected as materials, and transcriptome sequencing was performed using an Illumina HiSeq(TM) 2000 System. 496 up-regulated genes and 375 down-regulated genes were identified between shoot apices containing mostly male flower buds and only female flower buds. Based on gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, the differentially expressed genes were mainly enriched in the ethylene and auxin synthesis and signal transduction pathways. In addition, shoot apices at the 4-leaf stage were treated with the ethylene-releasing agent 2-chloroethylphosphonic acid (Ethrel), aminoethoxyvinyl glycine (AVG), AgNO3 and indoleacetic acid (IAA). The number of female flowers up to node 20 on the main stem of '2013-12' increased significantly after Ethrel and IAA treatment and decreased significantly after AVG and AgNO3 treatment. The female flowers in '9-6' showed slight changes after treatment with the exogenous chemicals. The expression of key genes in ethylene synthesis and signal transduction (CmaACS7, CmaACO1, CmaETR1 and CmaEIN3) was determined using quantitative RT-PCR, and the expression of these four genes was positively correlated with the number of female flowers in '2013-12'. The variations in gene expression, especially that of CmaACS7, after chemical treatment were small in '9-6'. From stage 1 (S1) to stage 7 (S7) of flower development, the expression of CmaACS7 in the stamen was much lower than that in the ovary, stigma and style. These transcriptome data and chemical treatment results indicated that IAA might affect pumpkin sex expression by inducing CmaACS7 expression and indirectly affecting ethylene production, and the ethylene synthesis and signal transduction pathways play crucial roles in pumpkin flower sex expression. A possible reason for the differences in sex expression between pumpkin lines '2013-12' and '9-6' was proposed based on the key gene expression. Overall, these transcriptome data and chemical treatment results suggest important roles for ethylene in pumpkin sex expression.
PMID: 31261811
J Agric Food Chem , IF:4.192 , 2019 Jun , V67 (25) : P6911-6920 doi: 10.1021/acs.jafc.9b00907
Enhanced Properties of Chitosan Microparticles over Bulk Chitosan on the Modulation of the Auxin Signaling Pathway with Beneficial Impacts on Root Architecture in Plants.
UNMdP, CONICET, Instituto de Investigaciones Biologicas, UE-CONICET-UNMdP, Facultad de Ciencias Exactas y Naturales , Universidad Nacional de Mar del Plata , Funes 3250 , B7600 Mar del Plata , Argentina.; Gihon Laboratorios Quimicos SRL , Calle 4 y 5 Parque Industrial General Salvio , B7600 Mar del Plata , Argentina.; UNMdP, CONICET, Instituto Investigacion de Ciencia & Tecnologia de Materiales INTEMA, UE-CONICET-UNMDP, Grupo Materiales Compuestos Termoplasticos, Facultad de Ingenieria , Universidad Nacional de Mar del Plata , Avenida Colon 10850 , B7600 Mar del Plata , Argentina.
Improving the root system architecture (RSA) under adverse environmental conditions by using biostimulants is emerging as a new way to boost crop productivity. Recently, we have reported the characterization of novel chitosan-based microparticles (CS-MPs) with promising biological properties as rooting agents in lettuce. In this work, we demonstrated that in contrast to bulk chitosan (CS), which exerts root growth inhibition, CS-MPs promoted root growth and development from 1 to 10 mug mL(-1) without cytotoxicity effects at higher doses in Arabidopsis and lettuce seedlings. In addition, we studied the mechanistic mode of action of CS-MPs in the development of early RSA in the Arabidopsis model. CS-MPs unchained accurate and sustained spatio-temporal activation of the nuclear auxin signaling pathway. Our findings validated a promising scenario for the application of CS-MPs in the modulation of RSA to respond to changing soil environments and improve crop performance.
PMID: 31194542
Physiol Plant , IF:4.148 , 2019 Jun , V166 (2) : P663-676 doi: 10.1111/ppl.12817
Inhibition of adventitious root development in apple rootstocks by cytokinin is based on its suppression of adventitious root primordia formation.
Department of Horticulture College, Northwest Agriculture & Forestry University, Yangling, 712100, China.
Cytokinin (CK) inhibits adventitious root (AR) formation in stem cuttings. Little is known, however, about the mechanism underlying the inhibitory effect. In this study, 2 mg l(-1) of exogenous 6-benzyl adenine (6-BA) was administered to 3 and 7-day-old apple rootstocks 'M.26' cuttings (3 and 7 days 6-BA) by transferring them from a rooting medium containing indole-3-butanoic acid to the medium containing 6-BA. Anatomical and morphological observations revealed that the exogenous application of 6-BA inhibited primordia formation in the 3 days 6-BA but not the 7 days 6-BA group. The concentration of auxin (IAA), the ratios of IAA/CK and IAA/abscisic acid were lower in 3 days 6-BA than in 7 days 6-BA. Expression analysis of genes known to be associated with AR formation was also analyzed. In the 3 days 6-BA group, high level of CK inhibited the synthesis and transport of auxin, as a result, low endogenous auxin level suppressed the auxin signaling pathway genes, as were other AR development and cell cycle related genes; all of which had an inhibitory impact on AR primordium formation. On the contrary, low CK level in the 7 days 6-BA, reduced the inhibitory impact on auxin levels, leading to an upregulated expression of genes known to promote AR primordia formation. Collectively, our data indicated that 3-7 days is the time period in which AR primordia formation occurs in cuttings of 'M.26' and that the inhibition of AR development by CK is due to the suppression of AR primordia development over 3-7 days period after culturing in rooting medium.
PMID: 30098023
Biomolecules , IF:4.082 , 2019 Jun , V9 (6) doi: 10.3390/biom9060222
PIN2 Polarity Establishment in Arabidopsis in the Absence of an Intact Cytoskeleton.
Institute of Science and Technology Austria (IST Austria), 3400 Klosterneuburg, Austria. matous.glanc@psb.vib-ugent.be.; Department of Experimental Plant Biology, Faculty of Science, Charles University, 12844 Prague, Czech Republic. matous.glanc@psb.vib-ugent.be.; Institute of Science and Technology Austria (IST Austria), 3400 Klosterneuburg, Austria. fendryc1@natur.cuni.cz.; Department of Experimental Plant Biology, Faculty of Science, Charles University, 12844 Prague, Czech Republic. fendryc1@natur.cuni.cz.; Institute of Science and Technology Austria (IST Austria), 3400 Klosterneuburg, Austria. jiri.friml@ist.ac.at.
Cell polarity is crucial for the coordinated development of all multicellular organisms. In plants, this is exemplified by the PIN-FORMED (PIN) efflux carriers of the phytohormone auxin: The polar subcellular localization of the PINs is instructive to the directional intercellular auxin transport, and thus to a plethora of auxin-regulated growth and developmental processes. Despite its importance, the regulation of PIN polar subcellular localization remains poorly understood. Here, we have employed advanced live-cell imaging techniques to study the roles of microtubules and actin microfilaments in the establishment of apical polar localization of PIN2 in the epidermis of the Arabidopsis root meristem. We report that apical PIN2 polarity requires neither intact actin microfilaments nor microtubules, suggesting that the primary spatial cue for polar PIN distribution is likely independent of cytoskeleton-guided endomembrane trafficking.
PMID: 31181636
Ann Bot , IF:4.005 , 2019 Jun , V123 (6) : P929-949 doi: 10.1093/aob/mcy234
Molecular and physiological control of adventitious rooting in cuttings: phytohormone action meets resource allocation.
Leibniz Institute of Vegetable and Ornamental Crops, Erfurt, Germany.; Leibniz Institute of Plant Genetics and Crop Plant Research, OT Gatersleben, Stadt Seeland, Germany.; Instituto de Bioingenieria, Universidad Miguel Hernandez de Elche, Elche, Spain.; Universidad de Murcia, Facultad de Biologia, Campus de Espinardo, Murcia, Spain.
BACKGROUND: Adventitious root (AR) formation in excised plant parts is a bottleneck for survival of isolated plant fragments. AR formation plays an important ecological role and is a critical process in cuttings for the clonal propagation of horticultural and forestry crops. Therefore, understanding the regulation of excision-induced AR formation is essential for sustainable and efficient utilization of plant genetic resources. SCOPE: Recent studies of plant transcriptomes, proteomes and metabolomes, and the use of mutants and transgenic lines have significantly expanded our knowledge concerning excision-induced AR formation. Here, we integrate new findings regarding AR formation in the cuttings of diverse plant species. These findings support a new system-oriented concept that the phytohormone-controlled reprogramming and differentiation of particular responsive cells in the cutting base interacts with a co-ordinated reallocation of plant resources within the whole cutting to initiate and drive excision-induced AR formation. Master control by auxin involves diverse transcription factors and mechanically sensitive microtubules, and is further linked to ethylene, jasmonates, cytokinins and strigolactones. Hormone functions seem to involve epigenetic factors and cross-talk with metabolic signals, reflecting the nutrient status of the cutting. By affecting distinct physiological units in the cutting, environmental factors such as light, nitrogen and iron modify the implementation of the genetically controlled root developmental programme. CONCLUSION: Despite advanced research in the last decade, important questions remain open for future investigations on excision-induced AR formation. These concern the distinct roles and interactions of certain molecular, hormonal and metabolic factors, as well as the functional equilibrium of the whole cutting in a complex environment. Starting from model plants, cell type- and phase-specific monitoring of controlling processes and modification of gene expression are promising methodologies that, however, need to be integrated into a coherent model of the whole system, before research findings can be translated to other crops.
PMID: 30759178
Sci Rep , IF:3.998 , 2019 Jun , V9 (1) : P8734 doi: 10.1038/s41598-019-45427-1
Network analysis of noncoding RNAs in pepper provides insights into fruit ripening control.
Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing, Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China. zuojinhua@126.com.; Boyce Thompson Institute for Plant Research, Cornell University Campus, Ithaca, NY, 14853, USA. zuojinhua@126.com.; Beijing Academy of Forestry and Pomology Sciences, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100093, China.; Laboratory of Postharvest Molecular Biology of Fruits and Vegetables, Department of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China.; Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing, Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China. wangqing@nercv.org.; Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing, Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China. gaolipu@nercv.org.
Pepper is an important vegetable worldwide and is a model plant for nonclimacteric fleshy fruit ripening. Drastic visual changes and internal biochemical alterations are involved in fruit coloration, flavor, texture, aroma, and palatability to animals during the pepper fruit ripening process. To explore the regulation of bell pepper fruit ripening by noncoding RNAs (ncRNAs), we examined their expression profiles; 43 microRNAs (miRNAs), 125 circular RNAs (circRNAs), 366 long noncoding RNAs (lncRNAs), and 3266 messenger RNAs (mRNAs) were differentially expressed (DE) in mature green and red ripe fruit. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed that the targets of the DE ncRNAs and DE mRNAs included several kinds of transcription factors (TFs) (ERF, bHLH, WRKY, MYB, NAC, bZIP, and ARF), enzymes involved in cell wall metabolism (beta-galactosidase, beta-glucosidase, beta-amylase, chitinase, pectate lyase (PL), pectinesterase (PE) and polygalacturonase (PG)), enzymes involved in fruit color accumulation (bifunctional 15-cis-phytoene synthase, 9-cis-epoxycarotenoid dioxygenase, beta-carotene hydroxylase and carotene epsilon-monooxygenase), enzymes associated with fruit flavor and aroma (glutamate-1-semialdehyde 2,1-aminomutase, anthocyanin 5-aromatic acyltransferase, and eugenol synthase 1) and enzymes involved in the production of ethylene (ET) (ACO1/ACO4) as well as other plant hormones such as abscisic acid (ABA), auxin (IAA), and gibberellic acid (GA). Based on accumulation profiles, a network of ncRNAs and mRNAs associated with bell pepper fruit ripening was developed that provides a foundation for further developing a more refined understanding of the molecular biology of fruit ripening.
PMID: 31217463
Plant Reprod , IF:3.957 , 2019 Jun , V32 (2) : P141-151 doi: 10.1007/s00497-018-0349-y
Comparative transcriptome analysis highlights the hormone effects on somatic embryogenesis in Catalpa bungei.
Key Laboratory of Three Gorges Regional Plant Genetics and Germplasm Enhancement (CTGU)/Biotechnology Research Center, China Three Gorges University, Yichang, 443002, Hubei Province, People's Republic of China.; Key Laboratory of Three Gorges Regional Plant Genetics and Germplasm Enhancement (CTGU)/Biotechnology Research Center, China Three Gorges University, Yichang, 443002, Hubei Province, People's Republic of China. chenfj616@163.com.
KEY MESSAGE: The major pathways and key events related to somatic embryo development in Catalpa bungei were illustrated by deep analysis of DEGs and quantification of hormone contents. Catalpa bungei C.A. Meyer is a valuable timber species, known as "The king of wood" in China. Due to the low propagation rate, somatic embryogenesis-based rapid propagation can regenerate a large number of new plants in a very short period of time and thus has great commercial value for this timber species. However, the mechanisms of somatic embryogenesis in C. bungei remain largely unclear so far. In our previous study, we established the vegetative propagation system in C. bungei using immature zygotic embryo as explants. Here, we further compared the transcriptional profiles and hormones contents between the embryogenic callus (EC) and non-embryogenic callus (NEC). RNA-seq analysis showed a total assembly of 73038 unigenes, and identified 12310 differentially expressed genes (DEGs) between EC and NEC. Also, six DEGs were chosen to verify the authenticity of the transcriptome sequencing results by qRT-PCR. Moreover, by using LC-MS approaches, we quantified various plant hormone contents and found that auxin and ABA were dramatically higher in EC than those in NEC. Accordingly, DEGs were enriched in plant hormone signaling pathways. Taken together, we highlight the hormone effects on somatic embryogenesis in a tree species, C. bungei. The use of certain genes as markers of embryogenesis induction in C. bungei regeneration process will provide new tools to pre-screen genotypes or tissue culture hormone combinations suitable for somatic embryo production. Our results provide theoretical references for the somatic embryogenesis mechanism and experimental bases for breeding and rapid propagation of C. bungei.
PMID: 30421145
Rice (N Y) , IF:3.912 , 2019 Jun , V12 (1) : P45 doi: 10.1186/s12284-019-0303-0
Characterization of Jasmonoyl-Isoleucine (JA-Ile) Hormonal Catabolic Pathways in Rice upon Wounding and Salt Stress.
Institut de Biologie Moleculaire des Plantes (IBMP) du CNRS, Universite de Strasbourg, Strasbourg, France.; Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Centre (ARC), Giza, 12619, Egypt.; Karlsruhe Institute of Technology, Botanical Institute, Karlsruhe, Germany.; Synthese Organique et Phytochimie (SOPhy), Institut de Chimie, Universite de Strasbourg, CNRS, Strasbourg, France.; Karlsruhe Institute of Technology, Botanical Institute, Karlsruhe, Germany. michael.riemann@kit.edu.; Institut de Biologie Moleculaire des Plantes (IBMP) du CNRS, Universite de Strasbourg, Strasbourg, France. thierry.heitz@ibmp-cnrs.unistra.fr.
BACKGROUND: Jasmonate (JA) signaling and functions have been established in rice development and response to a range of biotic or abiotic stress conditions. However, information on the molecular actors and mechanisms underlying turnover of the bioactive jasmonoyl-isoleucine (JA-Ile) is very limited in this plant species. RESULTS: Here we explored two gene families in rice in which some members were described previously in Arabidopsis to encode enzymes metabolizing JA-Ile hormone, namely cytochrome P450 of the CYP94 subfamily (CYP94, 20 members) and amidohydrolases (AH, 9 members). The CYP94D subclade, of unknown function, was most represented in the rice genome with about 10 genes. We used phylogeny and gene expression analysis to narrow the study to candidate members that could mediate JA-Ile catabolism upon leaf wounding used as mimic of insect chewing or seedling exposure to salt, two stresses triggering jasmonate metabolism and signaling. Both treatments induced specific transcriptional changes, along with accumulation of JA-Ile and a complex array of oxidized jasmonate catabolites, with some of these responses being abolished in the JASMONATE RESISTANT 1 (jar1) mutant. However, upon response to salt, a lower dependence on JAR1 was evidenced. Dynamics of CYP94B5, CYP94C2, CYP94C4 and AH7 transcripts matched best the accumulation of JA-Ile catabolites. To gain direct insight into JA-Ile metabolizing activities, recombinant expression of some selected genes was undertaken in yeast and bacteria. CYP94B5 was demonstrated to catalyze C12-hydroxylation of JA-Ile, whereas similarly to its Arabidopsis bi-functional homolog IAR3, AH8 performed cleavage of JA-Ile and auxin-alanine conjugates. CONCLUSIONS: Our data shed light on two rice gene families encoding enzymes related to hormone homeostasis. Expression data along with JA profiling and functional analysis identifies likely actors of JA-Ile catabolism in rice seedlings. This knowledge will now enable to better understand the metabolic fate of JA-Ile and engineer optimized JA signaling under stress conditions.
PMID: 31240493
Plant Cell Rep , IF:3.825 , 2019 Jun , V38 (6) : P731-739 doi: 10.1007/s00299-019-02402-4
Overexpression of OsIAAGLU reveals a role for IAA-glucose conjugation in modulating rice plant architecture.
College of Life Sciences, South China Agricultural University, Guangzhou, 510642, People's Republic of China.; School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand.; College of Life Sciences, South China Agricultural University, Guangzhou, 510642, People's Republic of China. eeliu70@scau.edu.cn.
KEY MESSAGE: OsIAAGLU could catalyze the reaction of IAA with glucose to generate IAA-glucose. Overexpression of OsIAAGLU in rice resulted in altered rice shoot architecture and root gravitropism. The distribution and levels of indole-3-acetic acid (IAA) within plant tissues are well known to play vital roles in plant growth and development. An important mechanism of regulating free IAA levels in monocots is formation of IAA ester conjugates. In this study, a cytosol-localized protein encoded by the rice gene of indole-3-acetic acid glucosyltransferase (OsIAAGLU) was found to catalyze the reaction of free IAA with glucose to generate IAA-glucose. Expression of OsIAAGLU could be induced by IAA and NAA. The number of tillers and leaf angle was significantly increased with a concomitant decrease in plant height and panicle length in the transgenic rice lines overexpressing OsIAAGLU compared to the wild-type (WT) plants. Phenotypes of iaaglu mutants constructed using the CRISPR/Cas9 system had no obvious differences with WT plants. Furthermore, overexpression of OsIAAGLU resulted in reduced sensitivity to IAA/NAA and altered gravitropic response of the roots in the transgenic plants. Free IAA contents in the leaves, root tips, and lamina joint of OsIAAGLU-overexpressing transgenic lines were lower than those of WT plants. These results support that OsIAAGLU could play a regulatory role in IAA homeostasis and rice architecture.
PMID: 30903268
Plant Cell Rep , IF:3.825 , 2019 Jun , V38 (6) : P681-698 doi: 10.1007/s00299-019-02395-0
Auxins in potato: molecular aspects and emerging roles in tuber formation and stress resistance.
Laboratory of Signaling Systems, Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, 127276, Russia.; Laboratory of Signaling Systems, Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, 127276, Russia. gromanov@yahoo.com.; Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia. gromanov@yahoo.com.
The study of the effects of auxins on potato tuberization corresponds to one of the oldest experimental systems in plant biology, which has remained relevant for over 70 years. However, only recently, in the postgenomic era, the role of auxin in tuber formation and other vital processes in potatoes has begun to emerge. This review describes the main results obtained over the entire period of auxin-potato research, including the effects of exogenous auxin; the content and dynamics of endogenous auxins; the effects of manipulating endogenous auxin content; the molecular mechanisms of auxin signaling, transport and inactivation; the role and position of auxin among other tuberigenic factors; the effects of auxin on tuber dormancy; the prospects for auxin use in potato biotechnology. Special attention is paid to recent insights into auxin function in potato tuberization and stress resistance. Taken together, the data discussed here leave no doubt on the important role of auxin in potato tuberization, particularly in the processes of tuber initiation, growth and sprouting. A new integrative model for the stage-dependent auxin action on tuberization is presented. In addition, auxin is shown to differentially affects the potato resistance to biotrophic and necrotrophic biopathogens. Thus, the modern auxin biology opens up new perspectives for further biotechnological improvement of potato crops.
PMID: 30739137
Genes (Basel) , IF:3.759 , 2019 Jun , V10 (7) doi: 10.3390/genes10070497
Screening the Reference Genes for Quantitative Gene Expression by RT-qPCR During SE Initial Dedifferentiation in Four Gossypium hirsutum Cultivars that Have Different SE Capability.
Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, College of Life Sciences, Shihezi University, Shihezi 832003, China.; Key Laboratory of Oasis Eco-Agriculture, Shihezi University, Shihezi 832003, China.; Key Laboratory of Oasis Eco-Agriculture, Shihezi University, Shihezi 832003, China. sunjie@shzu.edu.cn.; Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, College of Life Sciences, Shihezi University, Shihezi 832003, China. lihb@shzu.edu.cn.
RNA sequencing (RNA-Seq)-based gene expression analysis is applicable to a wide range of biological purposes in various species. Reverse transcription quantitative PCR (RT-qPCR) is also used to assess target gene expression utilizing stably expressed reference genes as internal control under a given set of conditions. However, investigations of the reference genes for RT-qPCR normalization in the process of somatic embryogenesis (SE) initial dedifferentiation in Gossypium hirsutum are rarely reported. In this study, on the basis of our previous transcriptome data of three different induction stages during SE initial dedifferentiation process in four G. hirsutum cultivars that have different SE capability, 15 candidate genes were selected during SE initial dedifferentiation process, and their expression stability was evaluated by geNorm, NormFinder, and BestKeeper. The results indicated that the two genes of endonuclease 4 (ENDO4) and 18S ribosomal RNA (18S rRNA) showed stable expression in the four different G. hirsutum cultivars, endowing them to be appropriate reference genes during three induction stages in the four cotton cultivars. In addition, the stability and reliability of the two reference genes of ENDO4 and 18S rRNA were further verified by comparing the expressions of auxin-responsive protein 22 (AUX22) and ethylene-responsive transcription factor 17 (ERF17) between RT-qPCR results and the RNA-seq data, which showed strong positive correlation coefficient (R(2) = 0.8396-0.9984), validating again the steady expression of ENDO4 and 18S rRNA as the reliable reference genes. Our results provide effective reference genes for RT-qPCR normalization during SE process in different G. hirsutum cultivars.
PMID: 31261792
Plant Physiol Biochem , IF:3.72 , 2019 Jun , V139 : P521-527 doi: 10.1016/j.plaphy.2019.04.017
Phenotypic and molecular traits determine the tolerance of olive trees to drought stress.
Department of Soil Microbiology and Symbiotic Systems, Estacion Experimental del Zaidin (CSIC), C/Profesor Albareda 1, 18008, Granada, Spain. Electronic address: mcalvopolanco@gmail.com.; Department of Soil Microbiology and Symbiotic Systems, Estacion Experimental del Zaidin (CSIC), C/Profesor Albareda 1, 18008, Granada, Spain.; Department of Cellular Biology, Genetics and Physiology, Campus de Teatinos, University of Malaga, 29010, Malaga, Spain.; Department of Plant Biotechnnology, Instituto de Recursos Naturales y Agrobiologia (CSIC), Av. Reina Mercedes, 10 41012, Sevilla, Spain.
Olive trees are known for their capacity to adapt to drought through several phenotypic and molecular variations, although this can vary according to the different provenances of the same olive cultivar. We confronted the same olive cultivar from two different location in Spain: Freila, in the Granada province, with low annual precipitation, and Grazalema, in the Cadiz province, with high annual precipitation, and subjected them to five weeks of severe drought stress. We found distinctive physiological and developmental adaptations among the two provenances. Thus, trees from Freila subjected to drought stress exhibited increasing root dry weights and decreasing leaf numbers and relative stem heights. On the other hand, the treatment with drought in Grazalema trees reduced their leaf chlorophyll contents, but increased their relative stem diameter and their root hydraulic conductivity. The physiological responses of Freila tree roots to drought were linked to different molecular adaptations that involved the regulation of genes related to transcription factors induced by ABA, auxin and ethylene signaling, as well as, the action of a predicted membrane intrinsic protein (MIP). On the other hand, the responses of Grazalema trees were related with different root genes related to oxidation-reduction, ATP synthesis, transduction and posttranslational regulation, with a special mention to the cytokinins signaling through the transcript predicted as a histidine-containing phosphotransfer protein. Our results show that olive trees adapted to dry environments will adjust their growth and water uptake capacity through transcription factors regulation, and this will influence the different physiological responses to drought stress.
PMID: 31015091
Plant Physiol Biochem , IF:3.72 , 2019 Jun , V139 : P738-745 doi: 10.1016/j.plaphy.2019.04.020
Weisiensin B inhibits primary and lateral root development by interfering with polar auxin transport in Arabidopsis thaliana.
College of Life Science, Northwest Normal University, China.; College of Life Science, Northwest Normal University, China. Electronic address: dinglan@nwnu.edu.cn.
Weisiensin B, a new ent-kaurene diterpenoid isolated from Isodon weisiensis (C. Y. Wu) H. Hara, exhibited phytotoxic effects on root growth and lateral root development in Arabidopsis thaliana seedlings. Primary root growth and lateral root formation in A. thaliana seedlings were significantly inhibited by 10-20muM weisiensin B. Additionally, the role of weisiensin B in response to polar auxin transport in A. thaliana roots was investigated using a PIN promoter (PIN::GUS), a green fluorescent protein (GFP) fusion protein reporter (PINs::PINs:GFP), and DR5::GUS and DR5::GFP reporter genes. The results indicated that weisiensin B reduced the expression of PIN2, PIN3, PIN4, PIN7, and AUX1 genes and significantly decreased the abundance of PIN2-GFP, PIN3-GFP, PIN4-GFP, PIN7-GFP, and AUX1-GFP fusion proteins at their respective cellular locations, simultaneously causing auxin accumulation in the root apex. These results suggest that weisiensin B interferes with polar auxin transport in A. thaliana roots, resulting in auxin accumulation in the root meristematic cells and the inhibition of root growth and lateral root development.
PMID: 31010613
Plant Physiol Biochem , IF:3.72 , 2019 Jun , V139 : P239-245 doi: 10.1016/j.plaphy.2019.03.026
The non-DNA binding bHLH transcription factor Paclobutrazol Resistances are involved in the regulation of ABA and salt responses in Arabidopsis.
Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China; Key Laboratory of Molecular Epigenetics of MOE, Institute of Genetics and Cytology, Northeast Normal University, Changchun, China.; Key Laboratory of Molecular Epigenetics of MOE, Institute of Genetics and Cytology, Northeast Normal University, Changchun, China.; Key Laboratory of Molecular Epigenetics of MOE, Institute of Genetics and Cytology, Northeast Normal University, Changchun, China; College of Life Science, Linyi University, Linyi, China. Electronic address: wangsc550@nenu.edu.cn.
Abscisic acid (ABA) is the key hormone that regulating plant responses to abiotic stresses. Several basic helix-loop-helix (bHLH) transcription factors have been reported to regulate ABA signaling in Arabidopsis. Paclobutrazol Resistances (PREs) are non-DNA binding bHLH transcription factors involved in the regulation of plant response to several different plant hormones including gibberellin, brassinosteroid and auxin. Here, we show that PREs are involved in the regulation of ABA and salt responses in Arabidopsis. Quantitative RT-PCR results showed that the expression levels of PRE6 as well as several other PRE genes were reduced in response to ABA treatment, but increased to salt treatment. Seed germination assays indicated that ABA sensitivity is reduced in the pre6 mutants, but increased in transgenic plants overexpressing PRE6. On the other hand, the 35S:PRE6 transgenic plants showed enhanced tolerance to salt, whereas little, if any changes were observed in the pre6 mutants. Similar responses to ABA and salt treatments were observed in the pre2 mutants and the transgenic plants overexpressing PRE2, and a slight increased resistance to ABA in seed germination was observed in the pre2 pre6 double mutants. Taken together, our results suggest that at least some of the PRE genes are ABA responsive genes, and PREs may function redundantly to regulate ABA and salt responses in Arabidopsis.
PMID: 30921735
Plant Physiol Biochem , IF:3.72 , 2019 Jun , V139 : P66-81 doi: 10.1016/j.plaphy.2019.03.006
miRNAs associated with auxin signaling, stress response, and cellular activities mediate adventitious root formation in apple rootstocks.
Department of Horticulture College, Northwest Agriculture & Forestry University, Yangling, 712100, China. Electronic address: keli505@163.com.; Department of Horticulture College, Northwest Agriculture & Forestry University, Yangling, 712100, China. Electronic address: zlhieun@nwafu.edu.cn.; Department of Horticulture College, Northwest Agriculture & Forestry University, Yangling, 712100, China. Electronic address: libo_xing@nwafu.edu.cn.; Department of Horticulture College, Northwest Agriculture & Forestry University, Yangling, 712100, China. Electronic address: 1551882256@qq.com.; Department of Horticulture College, Northwest Agriculture & Forestry University, Yangling, 712100, China. Electronic address: mjp588@nwafu.edu.cn.; Department of Horticulture College, Northwest Agriculture & Forestry University, Yangling, 712100, China. Electronic address: myhh0430@nwafu.edu.cn.; Department of Horticulture College, Northwest Agriculture & Forestry University, Yangling, 712100, China. Electronic address: baolu@nwsuaf.edu.cn.; Department of Horticulture College, Northwest Agriculture & Forestry University, Yangling, 712100, China. Electronic address: hanmy@nwsuaf.edu.cn.; Department of Horticulture College, Northwest Agriculture & Forestry University, Yangling, 712100, China. Electronic address: zhcc@nwsuaf.edu.cn.; Department of Horticulture College, Northwest Agriculture & Forestry University, Yangling, 712100, China. Electronic address: afant@nwsuaf.edu.cn.
Adventitious root (AR) formation is essential for the vegetative propagation of apple rootstocks. miRNAs play a significant role in regulating AR development, however, large-scale transcriptomic data on miRNA mediated AR formation in apple rootstocks is lacking. Therefore, in order to identify the molecular mechanisms underlying AR formation in 'M9-T337' apple rootstocks, transcriptomic changes occurring during key time points of AR formation (0, 3, and 16 days) were analyzed using high-throughput sequencing with a focus on miRNAs. A total of 84 known miRNAs and 56 novel miRNAs have differentially expressed were identified. Additionally, a total of 88 target genes of known miRNAs and 76 target genes of novel miRNAs were identified by degradome sequencing. The expression levels of the miRNAs and target genes were quantified by RT-qPCR. Results indicate that miRNAs and their target genes are associated with auxin signal-related (miR160 and miR390), stress response-related (miR398, miR395 and miR408), cell fate transformation-, proliferation- and enlargement-related (miR171, miR156, miR166, miR319 and miR396). These all involve pathways that participate in AR formation in 'M9-T337' apple rootstock. In addition, hormones (AUX, CTK, GA3, BR, JA, and ABA) are also involved in regulating AR formation. The candidate genes belonging to pathways associated with AR formation exhibited significantly higher expression levels, providing evidence that they may be involved in the regulation of AR development. The collective results of the present study indicate that the developmental process associated with AR formation in apple rootstock is extremely complex. The known and novel miRNAs and target genes that were identified by high-throughput and degradome sequencing, respectively, provide a framework for the future analysis of miRNAs associated with AR development in apple rootstocks, and provide new information that can be used to better understand AR development in woody plants.
PMID: 30878839
BMC Genomics , IF:3.594 , 2019 Jun , V20 (1) : P519 doi: 10.1186/s12864-019-5902-z
Dual species transcript profiling during the interaction between banana (Musa acuminata) and the fungal pathogen Fusarium oxysporum f. sp. cubense.
Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China. liwenbin@itbb.org.cn.; Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China.; Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China. pengming@itbb.org.cn.
BACKGROUND: Banana wilt disease, caused by Fusarium oxysporum f. sp. cubense Tropical Race 4 (Foc TR4), is one of the most devastating diseases in banana (Musa spp.). Foc is a soil borne pathogen that causes rot of the roots or wilt of leaves by colonizing the xylem vessels. The dual RNA sequencing is used to simultaneously assess the transcriptomes of pathogen and host. This method greatly helps to understand the responses of pathogen and host to each other and discover the potential pathogenic mechanism. RESULTS: Plantlets of two economically important banana cultivars, Foc TR4 less susceptible cultivar NK and susceptible cultivar BX, were used to research the Foc-banana interaction mechanism. Notably, the infected NK had more significantly up-regulated genes on the respiration machinery including TCA cycle, glyoxylate, glycerol, and glycolysis compared to BX at 27 h post inoculation (hpi). In addition, genes involved in plant-pathogen interaction, starch, sucrose, linolenic acid and sphingolipid metabolisms were uniquely more greatly induced in BX than those in NK during the whole infection. Genes related to the biosynthesis and metabolism of SA and JA were greatly induced in the infected NK; while auxin and abscisic acid metabolisms related genes were strongly stimulated in the infected BX at 27 hpi. Furthermore, most of fungal genes were more highly expressed in the roots of BX than in those of NK. The fungal genes related to pathogenicity, pectin and chitin metabolism, reactive oxygen scavenging played the important roles during the infection of Foc. CCP1 (cytochrome c peroxidase 1) was verified to involve in cellulose utilization, oxidative stress response and pathogenicity of fungus. CONCLUSION: The transcriptome indicated that NK had much faster defense response against Foc TR4 than BX and the expression levels of fungal genes were higher in BX than those in NK. The metabolisms of carbon, nitrogen, and signal transduction molecular were differentially involved in pathogen infection in BX and NK. Additionally, the putative virulence associated fungal genes involved in colonization, nutrition acquirement and transport provided more insights into the infection process of Foc TR4 in banana roots.
PMID: 31234790
BMC Genomics , IF:3.594 , 2019 Jun , V20 (1) : P487 doi: 10.1186/s12864-019-5881-0
Small RNA-seq reveals novel regulatory components for apomixis in Paspalum notatum.
Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR, CONICET-UNR), Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Zavalla, Argentina.; Institut de Recherche pour le Developpement (IRD), Universite de Montpellier, Montpellier, France.; Instituto de Agrobiotecnologia de Rosario (INDEAR), Rosario, Argentina.; Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR, CONICET-UNR), Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Zavalla, Argentina. pessino@arnet.com.ar.
BACKGROUND: Apomixis is considered an evolutionary deviation of the sexual reproductive pathway leading to the generation of clonal maternal progenies by seeds. Recent evidence from model and non-model species suggested that this trait could be modulated by epigenetic mechanisms involving small RNAs (sRNAs). Here we profiled floral sRNAs originated from apomictic and sexual Paspalum notatum genotypes in order to identify molecular pathways under epigenetic control that might be involved in the transition from sexuality to agamospermy. RESULTS: The mining of genes participating in sRNA-directed pathways from floral Paspalum transcriptomic resources showed these routes are functional during reproductive development, with several members differentially expressed in apomictic and sexual plants. Triplicate floral sRNA libraries derived from apomictic and a sexual genotypes were characterized by using high-throughput sequencing technology. EdgeR was apply to compare the number of sRNA reads between sexual and apomictic libraries that map over all Paspalum floral transcripts. A total of 1525 transcripts showed differential sRNA representation, including genes related to meiosis, plant hormone signaling, biomolecules transport, transcription control and cell cycle. Survey for miRNA precursors on transcriptome and genome references allowed the discovery of 124 entities, including 40 conserved and 8 novel ones. Fifty-six clusters were differentially represented in apomictic and sexual plants. All differentially expressed miRNAs were up-regulated in apomictic libraries but miR2275, which showed different family members with opposed representation. Examination of predicted miRNAs targets detected 374 potential candidates. Considering sRNA, miRNAs and target surveys together, 14 genes previously described as related with auxin metabolism, transport and signaling were detected, including AMINO ACID/AUXIN PERMEASE 15, IAA-AMIDO SYNTHETASE GH3-8, IAA30, miR160, miR167, miR164, miR319, ARF2, ARF8, ARF10, ARF12, AFB2, PROLIFERATING CELL FACTOR 6 and NITRATE TRANSPORTER 1.1. CONCLUSIONS: This work provides a comprehensive survey of the sRNA differential representation in flowers of sexual and apomictic Paspalum notatum plants. An integration of the small RNA profiling data presented here and previous transcriptomic information suggests that sRNA-mediated regulation of auxin pathways is pivotal in promoting apomixis. These results will underlie future functional characterization of the molecular components mediating the switch from sexuality to apomixis.
PMID: 31195966
Plant Sci , IF:3.591 , 2019 Jun , V283 : P177-188 doi: 10.1016/j.plantsci.2019.02.011
Auxin and GA signaling play important roles in the maize response to phosphate deficiency.
School of Life Sciences, Shandong University, 27 Shanda South Road, Jinan 250100, PR China. Electronic address: zhxinrui@163.com.; School of Life Sciences, Shandong University, 27 Shanda South Road, Jinan 250100, PR China. Electronic address: baomeiaijia@163.com.; School of Life Sciences, Shandong University, 27 Shanda South Road, Jinan 250100, PR China. Electronic address: 198591yy@163.com.; School of Life Sciences, Shandong University, 27 Shanda South Road, Jinan 250100, PR China. Electronic address: jrzhang@sdu.edu.cn.; School of Life Sciences, Shandong University, 27 Shanda South Road, Jinan 250100, PR China. Electronic address: zhaoxia_1019@126.com.
Phytohormone signaling is involved in the low-phosphate (LP) response and causes root system changes. To understand the roles of auxin and gibberellic acid (GA) in the maize response to LP stress, inbred line Q319 was used to identify the changes in root morphology and the gene expression response to LP stress with or without exogenous auxin, GA or their inhibitors. The root morphology, IAA and GAs concentration and genes related to the LP response, cell elongation and division, auxin transport and signaling, and GA synthesis and signaling were analyzed. The LP-induced maize root morphological adaption was dependent on changes in the expression of related genes, like IPS1, pht1;1 LPR1b, KRPs, and EXPB1-4. The altered local auxin concentration and signaling were involved in promoting axial root elongation and reducing lateral root density and length under LP conditions, which were regulated by PID and PP2A activity and the auxin signaling pathway. The upregulation of the GA synthesis genes AN1, GA20ox1, and GA20ox2 and the downregulation of the GA inactive genes GA2ox1 and GA2ox2 were observed in maize roots subjected to LP stress, and the increased GA biosynthesis and signaling were involved in root growth. Both hormones participate in LP stress response and jointly regulated root modification and LP acclimation in maize.
PMID: 31128687
Plant Sci , IF:3.591 , 2019 Jun , V283 : P165-176 doi: 10.1016/j.plantsci.2019.01.015
A low temperature promotes anthocyanin biosynthesis but does not accelerate endogenous abscisic acid accumulation in red-skinned grapes.
Faculty of Bioresources and Environmental Sciences, Ishikawa Prefectural University, 1-308 Suematsu, Nonoichi, Ishikawa 921-8836, Japan. Electronic address: mtakai@ishikawa-pu.ac.jp.; Faculty of Bioresources and Environmental Sciences, Ishikawa Prefectural University, 1-308 Suematsu, Nonoichi, Ishikawa 921-8836, Japan.; Ishikawa Agriculture and Forestry Research Center, Agricultural Experiment Station, Sand Hill Place Agriculture Research Center, Kahoku 929-1126, Japan.
The effect of temperature on the concentrations of anthocyanins and endogenous plant hormones [abscisic acid (ABA), auxin, and cytokinin] were investigated using the detached berries of two related red-skinned cultivars cv. 'Aki Queen' and 'Ruby Roman' of the table grape Vitis labrusca L. x Vitis vinifera L. The total anthocyanin concentration of both cultivars was lower when exposed to high rather than low temperatures after veraison (the onset of ripening). However, the responses to temperature differed between the two cultivars, and anthocyanin accumulation could occur in 'Ruby Roman' at a higher temperature than in 'Aki Queen'. High temperatures increased the expression of VlMybA1-2 and VlMybA1-3, which encode myeloblastosis (MYB)-related transcription factors; however, the expression of the anthocyanin biosynthesis-related structural genes uridine diphosphate-d-glucose: flavonoid 3-O-glucosyltransferase, flavonoid 3'5' hydroxylase, and flavonoid O-methyltransferase at different temperatures did not correspond with that of the expression of MybAs. The concentration of ABA and its derivatives increased under high temperatures, but that of auxin and cytokinin decreased. The observation that high temperatures induced the accumulation of ABA and expression of VlMybA1s but not the expression of anthocyanin biosynthesis-related structural genes implied the operation of a mechanism different from up-regulation of anthocyanin synthesis by VlMybA1s in the temperature response of grape berries.
PMID: 31128686
BMC Plant Biol , IF:3.497 , 2019 Jun , V19 (1) : P264 doi: 10.1186/s12870-019-1866-z
A transcriptome analysis reveals a role for the indole GLS-linked auxin biosynthesis in secondary dormancy in rapeseed (Brassica napus L.).
Jiangsu Key Laboratory for Eco-agriculture Biotechnology around Hongze Lake, Huaiyin Normal University, Huai'an, 223300, China.; Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environment Protection, Huaiyin Normal University, Huai'an, 223300, China.; National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.; School of Food Science and Engineering, Yangzhou University, Yangzhou, 225127, China.; Jiangsu Key Laboratory for Eco-agriculture Biotechnology around Hongze Lake, Huaiyin Normal University, Huai'an, 223300, China. xxzhao2013@163.com.; Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environment Protection, Huaiyin Normal University, Huai'an, 223300, China. xxzhao2013@163.com.
BACKGROUND: Brassica napus L. has little or no primary dormancy, but exhibits great variation in secondary dormancy. Secondary dormancy potential in oilseed rape can lead to the emergence of volunteer plants that cause genetic contamination, reduced quality and biosafety issues. However, the mechanisms underlying secondary dormancy are poorly understood. In this study, cultivars Huaiyou-WSD-H2 (H) and Huaiyou-SSD-V1 (V), which exhibit low (approximately 5%) and high (approximately 95%) secondary dormancy rate, respectively, were identified. Four samples, before (Hb and Vb) and after (Ha and Va) secondary dormancy induction by polyethylene glycol (PEG), were collected to identify the candidate genes involved in secondary dormancy via comparative transcriptome profile analysis. RESULTS: A total of 998 differentially expressed genes (DEGs), which are mainly involved in secondary metabolism, transcriptional regulation, protein modification and signaling pathways, were then detected. Among these DEGs, the expression levels of those involved in the sulfur-rich indole glucosinolate (GLS)-linked auxin biosynthesis pathway were markedly upregulated in the dormant seeds (Va), which were validated by qRT-PCR and subsequently confirmed via detection of altered concentrations of indole-3-acetic acid (IAA), IAA conjugates and precursors. Furthermore, exogenous IAA applications to cultivar H enhanced secondary dormancy. CONCLUSION: This study first (to our knowledge) elucidated that indole GLS-linked auxin biosynthesis is enhanced during secondary dormancy induced by PEG, which provides valuable information concerning secondary dormancy and expands the current understanding of the role of auxin in rapeseed.
PMID: 31215396
BMC Plant Biol , IF:3.497 , 2019 Jun , V19 (1) : P262 doi: 10.1186/s12870-019-1875-y
Effect of wet storage conditions on potato tuber transcriptome, phytohormones and growth.
Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland.; Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark.; Department of Biosciences, University of Helsinki, Helsinki, Finland.; Viikki Metabolomics Unit, Department of Biosciences, University of Helsinki, Helsinki, Finland.; Present address: Department of Biology, Lund University, Lund, Sweden.; Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland. minna.pirhonen@helsinki.fi.
BACKGROUND: Stored potato (Solanum tuberosum L.) tubers are sensitive to wet conditions that can cause rotting in long-term storage. To study the effect of water on the tuber surface during storage, microarray analysis, RNA-Seq profiling, qRT-PCR and phytohormone measurements were performed to study gene expression and hormone content in wet tubers incubated at two temperatures: 4 degrees C and 15 degrees C. The growth of the plants was also observed in a greenhouse after the incubation of tubers in wet conditions. RESULTS: Wet conditions induced a low-oxygen response, suggesting reduced oxygen availability in wet tubers at both temperatures when compared to that in the corresponding dry samples. Wet conditions induced genes coding for heat shock proteins, as well as proteins involved in fermentative energy production and defense against reactive oxygen species (ROS), which are transcripts that have been previously associated with low-oxygen stress in hypoxic or anoxic conditions. Wet treatment also induced senescence-related gene expression and genes involved in cell wall loosening, but downregulated genes encoding protease inhibitors and proteins involved in chloroplast functions and in the biosynthesis of secondary metabolites. Many genes involved in the production of phytohormones and signaling were also affected by wet conditions, suggesting altered regulation of growth by wet conditions. Hormone measurements after incubation showed increased salicylic acid (SA), abscisic acid (ABA) and auxin (IAA) concentrations as well as reduced production of jasmonate 12-oxo-phytodienoic acid (OPDA) in wet tubers. After incubation in wet conditions, the tubers produced fewer stems and more roots compared to controls incubated in dry conditions. CONCLUSIONS: In wet conditions, tubers invest in ROS protection and defense against the abiotic stress caused by reduced oxygen due to excessive water. Changes in ABA, SA and IAA that are antagonistic to jasmonates affect growth and defenses, causing induction of root growth and rendering tubers susceptible to necrotrophic pathogens. Water on the tuber surface may function as a signal for growth, similar to germination of seeds.
PMID: 31208336
BMC Plant Biol , IF:3.497 , 2019 Jun , V19 (1) : P233 doi: 10.1186/s12870-019-1840-9
A family of auxin conjugate hydrolases from Solanum lycopersicum and analysis of their roles in flower pedicel abscission.
Horticulture Department, Shenyang Agricultural University, No. 120 Dongling Road, Shenhe District, Shenyang, 110866, Liaoning, China.; Key Laboratory of Protected Horticulture of Ministry of Education, No.120 Dongling Road, Shenhe District, Shenyang, 110866, Liaoning, China.; Shenyang Entry-exit Inspection and Quarantine Bureau, No.433 Danan street, Shenhe District, Shenyang, 110016, Liaoning, China.; Horticulture Department, Shenyang Agricultural University, No. 120 Dongling Road, Shenhe District, Shenyang, 110866, Liaoning, China. syauxutao@qq.com.; Key Laboratory of Protected Horticulture of Ministry of Education, No.120 Dongling Road, Shenhe District, Shenyang, 110866, Liaoning, China. syauxutao@qq.com.; Horticulture Department, Shenyang Agricultural University, No. 120 Dongling Road, Shenhe District, Shenyang, 110866, Liaoning, China. 15702414552@163.com.; Key Laboratory of Protected Horticulture of Ministry of Education, No.120 Dongling Road, Shenhe District, Shenyang, 110866, Liaoning, China. 15702414552@163.com.
BACKGROUND: Auxin conjugates are hydrolyzed to release free auxin to ensure defined cellular auxin levels or gradients within tissues for proper development or response to environmental signals. The auxin concentration in the abscission zone (AZ) is thought to play an important role in mediating the abscission lag phase. RESULTS: In this study, the full cDNA sequences of seven tomato ILR1-like SlILL genes were identified and characterized, All SlILLs were found to have auxin conjugate hydrolysis activity. The effects of different auxin conjugates on abscission identified IAA-Ile as a candidate to determine the auxin conjugate and auxin conjugate hydrolysis functions in abscission. Treatment of pedicel explants with IAA-Ile for different times showed that application before 6 h could effectively delay abscission. IAA-Ile pre-incubation for 2 h was sufficient to inhibit abscission. These results showed that there is not sufficient auxin conjugates in the AZ to inhibit abscission, and the optimal time to inhibit abscission by the application of exogenous auxin conjugates is before 6 h. Treatment with cycloheximide (CHX, a protein biosynthesis inhibitor) indicated that de novo synthesis of auxin conjugate hydrolases is also required to delay abscission. During abscission, SlILL1, 5, and 6 showed abscission-related gene expression patterns, and SlILL1, 3, 5, 6, and 7 showed increasing expression trends, which collectively might contribute to delay abscission. Silencing the expression of SlILL1, 3, 5, 6, and 7 using virus-induced gene silencing showed that SlILL1, 5, and 6 are major mediators of abscission in tomato. CONCLUSIONS: In the process of abscission, auxin inhibition is concentration dependent, and the concentration of auxin in the AZ was regulated by hydrolyzed auxin conjugates. SlILR1, 5, and 6 play a key role in flower pedicel abscission.
PMID: 31159738
Molecules , IF:3.267 , 2019 Jun , V24 (11) doi: 10.3390/molecules24112112
Production of Stilbenes in Callus Cultures of the Maltese Indigenous Grapevine Variety, Gellewza.
Division of Rural Sciences and Food Systems, Institute of Earth Systems, University of Malta, Msida MSD 2080, Malta. mary-anne.bonello@gov.mt.; University of Belgrade, Faculty of Chemistry, Studentski trg 12-16, P.O. Box 51, 11158 Belgrade, Serbia. urosgasic@chem.bg.ac.rs.; University of Belgrade, Faculty of Chemistry, Studentski trg 12-16, P.O. Box 51, 11158 Belgrade, Serbia. ztesic@chem.bg.ac.rs.; Division of Rural Sciences and Food Systems, Institute of Earth Systems, University of Malta, Msida MSD 2080, Malta. everaldo.attard@um.edu.mt.
The production of secondary metabolites in tissue culture has been considered as an alternative to the cultivation and harvesting of crops intended for this purpose. The present study was aimed at the growth of callus and production of polyphenolic compound of callus derived from a Maltese indigenous grapevine variety, Gellewza. Callus was inoculated onto plant growth regulators-enriched Murashige Skoog media (MSm) to determine whether polyphenols are produced in vitro as well as to determine the best combination of plant growth regulators needed for the production of these metabolites. From results obtained, it was observed that the best callus production was obtained by auxin-enriched MSm. In fact, indole acetic acid and indole acetic acid /6-benzyl aminopurine enhanced biomass accumulation (3.04 g and 3.39 g) as opposed to the others (<1.97 g). On the other hand, parameters showing the presence of flavonoids (tonality, 3.80), particularly anthocyanins (24.09 mg/kg) and total polyphenols (1.42 mg/g), were optimum in the presence of cytokinins, particularly 6-benzyl aminopurine. Analysis for single polyphenols revealed a high amount a particular stilbene: polydatin (glucoside of resveratrol). Resveratrol and other typical polyphenols, found in mature berries, were also found in significant quantities, while the other polyphenolic compounds were found in minimal quantities. This is the first study to describe the production and composition of polyphenols in Gellewza callus cultures. From the results obtained, it can be seen that this grape tissue is an excellent alternative for the production of polyphenols from the stilbene group, which can be upscaled and exploited commercially.
PMID: 31167390
Plants (Basel) , IF:2.762 , 2019 Jun , V8 (6) doi: 10.3390/plants8060158
Annotation and Expression of IDN2-like and FDM-like Genes in Sexual and Aposporous Hypericum perforatum L. accessions.
Laboratory of Genetics and Genomics, DAFNAE, University of Padova, Campus of Agripolis, Viale dell' Universita, 1635020 Legnaro, Italy. andrea.basso@unipd.it.; Laboratory of Genetics and Genomics, DAFNAE, University of Padova, Campus of Agripolis, Viale dell' Universita, 1635020 Legnaro, Italy. gianni.barcaccia@unipd.it.; Laboratory of Genetics and Genomics, DAFNAE, University of Padova, Campus of Agripolis, Viale dell' Universita, 1635020 Legnaro, Italy. giulio.galla@unipd.it.
The protein IDN2, together with the highly similar interactors FDM1 and FDM2, is required for RNA-directed DNA methylation (RdDM) and siRNA production. Epigenetic regulation of gene expression is required to restrict cell fate determination in A. thaliana ovules. Recently, three transcripts sharing high similarity with the A. thaliana IDN2 and FDM1-2 were found to be differentially expressed in ovules of apomictic Hypericum perforatum L. accessions. To gain further insight into the expression and regulation of these genes in the context of apomixis, we investigated genomic, transcriptional and functional aspects of the gene family in this species. The H. perforatum genome encodes for two IDN2-like and 7 FDM-like genes. Differential and heterochronic expression of FDM4-like genes was found in H. perforatum pistils. The involvement of these genes in reproduction and seed development is consistent with the observed reduction of the seed set and high variability in seed size in A. thaliana IDN2 and FDM-like knockout lines. Differential expression of IDN2-like and FDM-like genes in H. perforatum was predicted to affect the network of potential interactions between these proteins. Furthermore, pistil transcript levels are modulated by cytokinin and auxin but the effect operated by the two hormones depends on the reproductive phenotype.
PMID: 31181659
Funct Plant Biol , IF:2.617 , 2019 Jun , V46 (7) : P670-683 doi: 10.1071/FP18295
Comparative transcriptome analysis reveals unique genetic adaptations conferring salt tolerance in a xerohalophyte.
State Key Laboratory of Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, PR China.; State Key Laboratory of Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, PR China; and Department of Biology, Institute of Biochemistry, Carleton University, Ottawa, ON, Canada.; State Key Laboratory of Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, PR China; and Corresponding author. Email: smwang@lzu.edu.cn.
Most studies on salt tolerance in plants have been conducted using glycophytes like Arabidopsis thaliana (L.) Heynh., with limited resistance to salinity. The xerohalophyte Zygophyllum xanthoxylum (Bunge) Engl. is a salt-accumulating desert plant that efficiently transports Na+ into vacuoles to manage salt and exhibits increased growth under salinity conditions, suggesting a unique transcriptional response compared with glycophytes. We used transcriptome profiling by RNA-seq to compare gene expression in roots of Z. xanthoxylum and A. thaliana under 50 mM NaCl treatments. Gene Ontology (GO) functional annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathway analysis suggested that 50 mM NaCl was perceived as a stimulus for Z. xanthoxylum whereas a stress for A. thaliana. Exposure to 50 mM NaCl caused metabolic shifts towards gluconeogenesis to stimulate growth of Z. xanthoxylum, but triggered defensive systems in A. thaliana. Compared with A. thaliana, a vast array of ion transporter genes was induced in Z. xanthoxylum, revealing an active strategy to uptake Na+ and nutrients from the environment. An ascorbate-glutathione scavenging system for reactive oxygen species was also crucial in Z. xanthoxylum, based on high expression of key enzyme genes. Finally, key regulatory genes for the biosynthesis pathways of abscisic acid and gibberellin showed distinct expression patterns between the two species and auxin response genes were more active in Z. xanthoxylum compared with A. thaliana. Our results provide an important framework for understanding unique patterns of gene expression conferring salt resistance in Z. xanthoxylum.
PMID: 31064640
Funct Plant Biol , IF:2.617 , 2019 Jun , V46 (6) : P493-506 doi: 10.1071/FP18323
Hormonal regulation of cereal endosperm development with a focus on rice (Oryza sativa).
School of Science and Technology, University of New England, Armidale, NSW 2350, Australia.; School of Science and Technology, University of New England, Armidale, NSW 2350, Australia; and Corresponding author. Email: hnonheb2@une.edu.au.
The endosperm of cereal grain forms the staple diet for most of the world's population, and feeds much of their stock. Grain size and quality are determined largely by events taking place during coenocytic nuclear division, endosperm cellularisation and cell differentiation, and the production of storage molecules. Thus, understanding the complex signalling processes occurring at each of these steps is essential for maintaining and improving our food supply. Here, we critically review evidence for the effects of phytohormones on grain size, as well as hormone homeostasis, signalling and crosstalk. We focus on rice endosperm due to the importance of rice as a food crop and a model grass, as well as its relative neglect in recent reviews; however, data from other cereals are also discussed due to strong evidence for conserved signalling networks operating during grain development. Discussion is restricted to auxin, cytokinin, ethylene, abscisic acid and gibberellin. Our review highlights the need for accurate hormone determinations combined with information on gene expression. We present evidence for separate, localised signalling roles for auxin at different stages of grain development and highlight key research questions for other hormones where much less data are available.
PMID: 30955506
World J Microbiol Biotechnol , IF:2.477 , 2019 Jun , V35 (7) : P97 doi: 10.1007/s11274-019-2671-4
Identification and characterization of Populus microRNAs in response to plant growth-promoting endophytic Streptomyces sp. SSD49.
Department of Microbiology, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China.; Department of Microbiology, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China. mayuchao@bjfu.edu.cn.
Endophytic Streptomyces sp. SSD49 inhibited eight pathogens, including the human opportunistic pathogenic microorganisms, the plant pathogenic fungi and bacteria. The growth of soybeans, tomatoes, peppers and Populus tomentosa seedings inoculated with SSD49 are remarkably promoted. Here, we constructed two P. tomentosa seedling microRNA (miRNA) libraries inoculated with (PS30d) and without SSD49 (PC30d) to explore the molecular regulatory roles in the plant response to the beneficial bacteria. Totals of 314 known and 144 novel miRNAs were identified, among which 27 known and 11 novel miRNA had significantly different expression. The targets of up-regulated miR160, miR156, ptc114 and down-regulated miR319 and other differential expressed miRNAs primarily regulated genes encoding transcription factors (auxin response factor, small auxin-up RNA, and GRAS proteins), disease resistance proteins, phytohormone oxidase, and response regulators, which could promote plant growth, influence disease resistance and miRNA biosynthesis in P. tomentosa. This is the first report on the genome-wide identification of biocontrol endophytic Streptomyces inoculation-responsive miRNAs using small RNA sequencing in P. tomentosa and these findings provide new insight into understanding the biocontrol effects of endophytic Streptomyces.
PMID: 31222457
Appl Biochem Biotechnol , IF:2.277 , 2019 Jun , V188 (2) : P450-459 doi: 10.1007/s12010-018-02937-4
Gibberellin Promotes Cell Growth and Induces Changes in Fatty Acid Biosynthesis and Upregulates Fatty Acid Biosynthetic Genes in Chlorella vulgaris UMT-M1.
Institute of Marine Biotechnology, Universiti Malaysia Terengganu, 21030, Kuala Terengganu, Terengganu, Malaysia.; School of Fundamental Sciences, Universiti Malaysia Terengganu, 21030, Kuala Terengganu, Terengganu, Malaysia.; School of Marine and Environmental Sciences, Universiti Malaysia Terengganu, 21030, Kuala Terengganu, Terengganu, Malaysia.; Institute of Marine Biotechnology, Universiti Malaysia Terengganu, 21030, Kuala Terengganu, Terengganu, Malaysia. cha_ts@umt.edu.my.; School of Fundamental Sciences, Universiti Malaysia Terengganu, 21030, Kuala Terengganu, Terengganu, Malaysia. cha_ts@umt.edu.my.
Microalgae lipids and oils are potential candidates for renewable biofuels and nutritional inventions. Recent studies from our lab have shown that two plant hormones, auxin and jasmonic acid, influence microalgae growth and fatty acid accumulation. Therefore, in this study, a high oil-producing strain Chlorella vulgaris UMT-M1 was selected for hormonal study using gibberellin (GA). Exogenous GA3 was applied to early stationary culture of C. vulgaris UMT-M1. Results showed that GA3 gradually increases the cell density of C. vulgaris to up to 42% on days after treatment (DAT)-8 and also capable of delaying the algal senescence. However, the increment in cell density did not enhance the total oil production albeit transient modification of fatty acid compositions was observed for saturated (SFA) and polyunsaturated (PUFA) fatty acids. This illustrates that GA3 only promotes cell division and growth but not the oil accumulation. In addition, application of GA3 in culture medium was shown to promote transient increment of palmitic (C16:0) and stearic (C18:0) acids from DAT-4 to DAT-6 and these changes are correlated with the expression of beta-ketoacyl ACP synthase I (KAS I) gene.
PMID: 30536033
J Membr Biol , IF:1.877 , 2019 Jun , V252 (2-3) : P183-194 doi: 10.1007/s00232-019-00065-6
Potassium Stimulation of IAA Transport Mediated by the Arabidopsis Importer AUX1 Investigated in a Heterologous Yeast System.
Department of Life Science and Institute of Bioinformatics and Structural Biology, College of Life Science, National Tsing Hua University, No. 101, Sec. 2, Guangfu Rd. East Dist., Hsin Chu, 30013, Taiwan, Republic of China.; Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, 701, Taiwan, Republic of China.; Department of Life Science and Institute of Bioinformatics and Structural Biology, College of Life Science, National Tsing Hua University, No. 101, Sec. 2, Guangfu Rd. East Dist., Hsin Chu, 30013, Taiwan, Republic of China. d934245@oz.nthu.edu.tw.; Department of Life Science and Institute of Bioinformatics and Structural Biology, College of Life Science, National Tsing Hua University, No. 101, Sec. 2, Guangfu Rd. East Dist., Hsin Chu, 30013, Taiwan, Republic of China. rlpan@life.nthu.edu.tw.
Auxin regulates diverse processes involved in plant growth and development. AUX1 is the first identified and most widely investigated auxin importer, and plays an important role in root gravitropism and the development of lateral root and root hair. However, the regulation of auxin transport by AUX1 is still not well understood. In this study, we examined the effect of metal ions on AUX1 transport function and found that the activity could be specifically stimulated four times by K(+). Further experiments revealed the preference of KF on the enhancement of transport activity of AUX1 over KCl, KBr, and KI. In addition, the interaction between K(+) and AUX1 confers AUX1 more resistant to thermal stress but more vulnerable to proteolysis. Conventional chemical modification indicated that the extracellular acidic amino acids of AUX1 play a key role in the K(+) stimulation. Site-specific mutagenesis showed that the replacement of Asp(166), Asp(293), and Asp(312) of AUX1 to alanine deteriorated the K(+)-stimulated auxin transport. By contrast, when these residues were mutated to glutamate, lysine, or asparagine, only the D312E variant restored the IAA transport activity to the wild-type level. It is thus convinced that D312 is presumably the most promising residue for the K(+) stimulation on AUX1.
PMID: 31053903