Nat Commun , IF:12.121 , 2019 Feb , V10 (1) : P886 doi: 10.1038/s41467-019-08861-3
Auxin Response Factors promote organogenesis by chromatin-mediated repression of the pluripotency gene SHOOTMERISTEMLESS.
Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA.; Bayer Crop Science, St. Louis, MO, 63146, USA.; Crop Genetics Dept, John Innes Centre, Norwich Research Park, NR4 7UH, Norwich, Norfolk, UK.; Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, CH-8008, Zurich, Switzerland.; Laboratorio Nacional de Genomica para la Biodiversidad (Langebio), Unidad de Genomica Avanzada, Centro de Investigacion y de Estudios Avanzados del Instituto Politecnico Nacional (CINVESTAV-IPN), Irapuato C.P., 36824, Guanajuato, Mexico.; Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA. wagnerdo@sas.upenn.edu.
Specification of new organs from transit amplifying cells is critical for higher eukaryote development. In plants, a central stem cell pool maintained by the pluripotency factor SHOOTMERISTEMLESS (STM), is surrounded by transit amplifying cells competent to respond to auxin hormone maxima by giving rise to new organs. Auxin triggers flower initiation through Auxin Response Factor (ARF) MONOPTEROS (MP) and recruitment of chromatin remodelers to activate genes promoting floral fate. The contribution of gene repression to reproductive primordium initiation is poorly understood. Here we show that downregulation of the STM pluripotency gene promotes initiation of flowers and uncover the mechanism for STM silencing. The ARFs ETTIN (ETT) and ARF4 promote organogenesis at the reproductive shoot apex in parallel with MP via histone-deacetylation mediated transcriptional silencing of STM. ETT and ARF4 directly repress STM, while MP acts indirectly, through its target FILAMENTOUS FLOWER (FIL). Our data suggest that - as in animals- downregulation of the pluripotency program is important for organogenesis in plants.
PMID: 30792395
Nat Commun , IF:12.121 , 2019 Feb , V10 (1) : P726 doi: 10.1038/s41467-019-08575-6
Calcium signals are necessary to establish auxin transporter polarity in a plant stem cell niche.
Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA, 91125, USA.; Howard Hughes Medical Institute, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA, 91125, USA.; School of Life and Environmental Sciences, The University of Sydney, Darlington, NSW, 2008, Australia.; Machine Learning and Instrument Autonomy, NASA Jet Propulsion Laboratory, California Institute of Technology, 4800 Oak Grove Drive, Pasadena, CA, 91109, USA.; Division of Biological Sciences, Cell and Developmental Biology Section, University of California, San Diego, La Jolla, CA, 92093, USA.; School of Life and Environmental Sciences, The University of Sydney, Darlington, NSW, 2008, Australia. marcus.heisler@sydney.edu.au.; Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA, 91125, USA. meyerow@caltech.edu.; Howard Hughes Medical Institute, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA, 91125, USA. meyerow@caltech.edu.
In plants mechanical signals pattern morphogenesis through the polar transport of the hormone auxin and through regulation of interphase microtubule (MT) orientation. To date, the mechanisms by which such signals induce changes in cell polarity remain unknown. Through a combination of time-lapse imaging, and chemical and mechanical perturbations, we show that mechanical stimulation of the SAM causes transient changes in cytoplasmic calcium ion concentration (Ca(2+)) and that transient Ca(2+) response is required for downstream changes in PIN-FORMED 1 (PIN1) polarity. We also find that dynamic changes in Ca(2+) occur during development of the SAM and this Ca(2+) response is required for changes in PIN1 polarity, though not sufficient. In contrast, we find that Ca(2+) is not necessary for the response of MTs to mechanical perturbations revealing that Ca(2+) specifically acts downstream of mechanics to regulate PIN1 polarity response.
PMID: 30760714
Curr Biol , IF:9.601 , 2019 Feb , V29 (3) : P520-529.e6 doi: 10.1016/j.cub.2018.12.041
DOF2.1 Controls Cytokinin-Dependent Vascular Cell Proliferation Downstream of TMO5/LHW.
Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium; Wageningen University, Laboratory of Biochemistry, Stippeneng 4, 6708 WE Wageningen, the Netherlands.; Institute of Biotechnology, HiLIFE, University of Helsinki, Viikinkaari 5d, 00014 Helsinki, Finland; Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, 00014 Helsinki, Finland.; Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, USA.; Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium.; Institute of Biotechnology, HiLIFE, University of Helsinki, Viikinkaari 5d, 00014 Helsinki, Finland; Graduate School of Sciences and Technology, Nara Institute of Science and Technology, Nara, 630-0192 Japan.; Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge CB2 1LR, UK.; Institute of Biotechnology, HiLIFE, University of Helsinki, Viikinkaari 5d, 00014 Helsinki, Finland; Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge CB2 1LR, UK.; Wageningen University, Division of Human Nutrition and Health, Nutrition, Metabolism and Genomics group, Stippeneng 4, 6708 WE Wageningen, the Netherlands.; Institute of Biotechnology, HiLIFE, University of Helsinki, Viikinkaari 5d, 00014 Helsinki, Finland; Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, 00014 Helsinki, Finland; Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge CB2 1LR, UK. Electronic address: yrjo.helariutta@slcu.cam.ac.uk.; Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium; Wageningen University, Laboratory of Biochemistry, Stippeneng 4, 6708 WE Wageningen, the Netherlands. Electronic address: beryb@psb.vib-ugent.be.
To create a three-dimensional structure, plants rely on oriented cell divisions and cell elongation. Oriented cell divisions are specifically important in procambium cells of the root to establish the different vascular cell types [1, 2]. These divisions are in part controlled by the auxin-controlled TARGET OF MONOPTEROS5 (TMO5) and LONESOME HIGHWAY (LHW) transcription factor complex [3-7]. Loss-of-function of tmo5 or lhw clade members results in strongly reduced vascular cell file numbers, whereas ectopic expression of both TMO5 and LHW can ubiquitously induce periclinal and radial cell divisions in all cell types of the root meristem. TMO5 and LHW interact only in young xylem cells, where they promote expression of two direct target genes involved in the final step of cytokinin (CK) biosynthesis, LONELY GUY3 (LOG3) and LOG4 [8, 9] Therefore, CK was hypothesized to act as a mobile signal from the xylem to trigger divisions in the neighboring procambium cells [3, 6]. To unravel how TMO5/LHW-dependent cytokinin regulates cell proliferation, we analyzed the transcriptional responses upon simultaneous induction of both transcription factors. Using inferred network analysis, we identified AT2G28510/DOF2.1 as a cytokinin-dependent downstream target gene. We further showed that DOF2.1 controls specific procambium cell divisions without inducing other cytokinin-dependent effects such as the inhibition of vascular differentiation. In summary, our results suggest that DOF2.1 and its closest homologs control vascular cell proliferation, thus leading to radial expansion of the root.
PMID: 30686737
Proc Natl Acad Sci U S A , IF:9.412 , 2019 Feb , V116 (9) : P3893-3898 doi: 10.1073/pnas.1814015116
PILS6 is a temperature-sensitive regulator of nuclear auxin input and organ growth in Arabidopsis thaliana.
Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, 1190 Vienna, Austria elena.feraru@boku.ac.at juergen.kleine-vehn@boku.ac.at.; Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, 1190 Vienna, Austria.
Temperature modulates growth and development throughout the entire lifecycle of a plant. High temperature (HT) triggers the auxin biosynthesis-dependent growth in aerial tissues. On the other hand, the contribution of auxin to HT-induced root growth is currently under debate. Here we show that the putative intracellular auxin carrier PIN-LIKES 6 (PILS6) is a negative regulator of organ growth and that its abundance is highly sensitive to HT. PILS6 localizes to the endoplasmic reticulum and limits the nuclear availability of auxin, consequently reducing the auxin signaling output. HT represses the PILS6 protein abundance, which impacts on PILS6-dependent auxin signaling in roots and root expansion. Accordingly, we hypothesize that PILS6 is part of an alternative mechanism linking HT to auxin responses in roots.
PMID: 30755525
Proc Natl Acad Sci U S A , IF:9.412 , 2019 Feb , V116 (7) : P2589-2594 doi: 10.1073/pnas.1817038116
Quantification of reaction cycle parameters for an essential molecular switch in an auxin-responsive transcription circuit in rice.
Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853.; Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853 lkn2@cornell.edu.
Protein-based molecular switches play critical roles in biological processes. The importance of the prolyl cis-trans switch is underscored by the ubiquitous presence of peptidyl prolyl isomerases such as cyclophilins that accelerate the intrinsically slow isomerization rate. In rice, a tryptophan-proline (W-P) cis-trans switch in transcription repressor protein OsIAA11 along with its associated cyclophilin LRT2 are essential components in a negative feedback gene regulation circuit that controls lateral root initiation in response to the plant hormone auxin. Importantly, no quantitative characterizations of the individual (microscopic) thermodynamic and kinetic parameters for any cyclophilin-catalyzed W-P isomerization have been reported. Here we present NMR studies that determine and independently validate these parameters for LRT2 catalysis of the W-P motif in OsIAA11, providing predictive power for understanding the role of this switch in the auxin-responsive circuit and the resulting lateral rootless phenotype in rice. We show that the observed isomerization rate is linearly dependent on LRT2 concentration but is independent of OsIAA11 concentration over a wide range, and LRT2 is optimally tuned to maintain OsIAA11 at its cis-trans equilibrium to supply the slower downstream cis-specific proteasomal degradation with maximal OsIAA11 substrate. This indicates that accelerating the LRT2-catalyzed isomerization would not accelerate OsIAA degradation, whereas decreasing this rate via targeted mutation could reveal relationships between circuit dynamics and lateral root development. Moreover, we show that sequences flanking the highly conserved Aux/IAA W-P motif do not impact LRT2 catalysis, suggesting that the parameters determined here are broadly applicable across highly conserved cyclophilins and their Aux/IAA targets.
PMID: 30696765
Proc Natl Acad Sci U S A , IF:9.412 , 2019 Feb , V116 (6) : P2354-2363 doi: 10.1073/pnas.1819971116
Phosphoproteomics of Arabidopsis Highly ABA-Induced1 identifies AT-Hook-Like10 phosphorylation required for stress growth regulation.
Institute of Plant and Microbial Biology, Academia Sinica, 115 Taipei, Taiwan.; Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung-Hsing University, 402 Taichung, Taiwan, and Academia Sinica, 115 Taipei, Taiwan.; Graduate Institute of Biotechnology, Biotechnology Center, National Chung-Hsing University, 402 Taichung, Taiwan.; Institute of Plant and Microbial Biology, Academia Sinica, 115 Taipei, Taiwan; paulv@gate.sinica.edu.tw.; Biotechnology Center, National Chung-Hsing University, 402 Taichung, Taiwan.
The clade A protein phosphatase 2C Highly ABA-Induced 1 (HAI1) plays an important role in stress signaling, yet little information is available on HAI1-regulated phosphoproteins. Quantitative phosphoproteomics identified phosphopeptides of increased abundance in hai1-2 in unstressed plants and in plants exposed to low-water potential (drought) stress. The identity and localization of the phosphoproteins as well as enrichment of specific phosphorylation motifs indicated that these phosphorylation sites may be regulated directly by HAI1 or by HAI1-regulated kinases including mitogen-activated protein kinases, sucrose non-fermenting-related kinase 2, or casein kinases. One of the phosphosites putatively regulated by HAI1 was S313/S314 of AT-Hook-Like10 (AHL10), a DNA-binding protein of unclear function. HAI1 could directly dephosphorylate AHL10 in vitro, and the level of HAI1 expression affected the abundance of phosphorylated AHL10 in vivo. AHL10 S314 phosphorylation was critical for restriction of plant growth under low-water potential stress and for regulation of jasmonic acid and auxin-related gene expression as well as expression of developmental regulators including Shootmeristemless These genes were also misregulated in hai1-2 AHL10 S314 phosphorylation was required for AHL10 complexes to form foci within the nucleoplasm, suggesting that S314 phosphorylation may control AHL10 association with the nuclear matrix or with other transcriptional regulators. These data identify a set of HAI1-affected phosphorylation sites, show that HAI1-regulated phosphorylation of AHL10 S314 controls AHL10 function and localization, and indicate that HAI1-AHL10 signaling coordinates growth with stress and defense responses.
PMID: 30670655
New Phytol , IF:8.512 , 2019 Feb , V221 (3) : P1260-1267 doi: 10.1111/nph.15491
Getting closer: vein density in C4 leaves.
Donald Danforth Plant Science Center, St Louis, MO, 63132, USA.
Contents Summary 1260 I. Introduction 1260 II. Molecular and genetic mechanisms of C4 leaf venation 1262 III. Conclusions and future perspectives 1266 Acknowledgements 1266 References 1266 SUMMARY: C4 grasses are major contributors to the world's food supply. Their highly efficient method of carbon fixation is a unique adaptation that combines close vein spacing and distinct photosynthetic cell types. Despite its importance, the molecular genetic basis of C4 leaf development is still poorly understood. Here we summarize current knowledge of leaf venation and review recent progress in understanding molecular and genetic regulation of vascular patterning events in C4 plants. Evidence points to the interplay of auxin, brassinosteroids, SHORTROOT/SCARECROW and INDETERMINATE DOMAIN transcription factors. Identification and functional characterization of candidate regulators acting early in vascular development will be essential for further progress in understanding the precise regulation of these processes.
PMID: 30368826
Plant Biotechnol J , IF:8.154 , 2019 Feb , V17 (2) : P451-460 doi: 10.1111/pbi.12989
Genome sequence and genetic transformation of a widely distributed and cultivated poplar.
State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China.; Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China.
Populus alba is widely distributed and cultivated in Europe and Asia. This species has been used for diverse studies. In this study, we assembled a de novo genome sequence of P. alba var. pyramidalis (= P. bolleana) and confirmed its high transformation efficiency and short transformation time by experiments. Through a process of hybrid genome assembly, a total of 464 M of the genome was assembled. Annotation analyses predicted 37 901 protein-coding genes. This genome is highly collinear to that of P. trichocarpa, with most genes having orthologs in the two species. We found a marked expansion of gene families related to histone and the hormone auxin but loss of disease resistance genes in P. alba if compared with the closely related P. trichocarpa. The genome sequence presented here represents a valuable resource for further molecular functional analyses of this species as a new tree model, poplar breeding practices and comparative genomic analyses across different poplars.
PMID: 30044051
Plant Biotechnol J , IF:8.154 , 2019 Feb , V17 (2) : P338-349 doi: 10.1111/pbi.12980
The auxin receptor TIR1 homolog (PagFBL 1) regulates adventitious rooting through interactions with Aux/IAA28 in Populus.
State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China.; Guangxi Academy of Forestry, Nanning, Guangxi, China.; US Forest Service, Pacific Southwest Research Station, Davis, CA, USA.
Adventitious roots occur naturally in many species and can also be induced from explants of some tree species including Populus, providing an important means of clonal propagation. Auxin has been identified as playing a crucial role in adventitious root formation, but the associated molecular regulatory mechanisms need to be elucidated. In this study, we examined the role of PagFBL1, the hybrid poplar (Populus alba x P. glandulosa clone 84K) homolog of Arabidopsis auxin receptor TIR1, in adventitious root formation in poplar. Similar to the distribution pattern of auxin during initiation of adventitious roots, PagFBL1 expression was concentrated in the cambium and secondary phloem in stems during adventitious root induction and initiation phases, but decreased in emerging adventitious root primordia. Overexpressing PagFBL1 stimulated adventitious root formation and increased root biomass, while knock-down of PagFBL1 transcript levels delayed adventitious root formation and decreased root biomass. Transcriptome analyses of PagFBL1 overexpressing lines indicated that an extensive remodelling of gene expression was stimulated by auxin signalling pathway during early adventitious root formation. In addition, PagIAA28 was identified as downstream targets of PagFBL1. We propose that the PagFBL1-PagIAA28 module promotes adventitious rooting and could be targeted to improve Populus propagation by cuttings.
PMID: 29949229
Plant Physiol , IF:6.902 , 2019 Feb , V179 (2) : P686-699 doi: 10.1104/pp.18.00782
Modulation of Auxin Signaling and Development by Polyadenylation Machinery.
Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.; University of Chinese Academy of Sciences, Beijing 100049, China.; Section of Cell and Developmental Biology, University of California, San Diego, California 92093-0116.; State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.; College of Life Sciences, Tianjin Normal University, Tianjin 300387, China.; Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China yfcheng@ibcas.ac.cn.
Polyadenylation influences gene expression by affecting mRNA stability, transport, and translatability. Here, we report that Cleavage stimulation Factor 77 (AtCstF77), a component of the pre-mRNA 3'-end polyadenylation machinery, affects polyadenylation site (PAS) selection in transcripts of some auxin signaling genes in Arabidopsis (Arabidopsis thaliana). Disruption of AtCstF77 reduced auxin sensitivity and decreased the expression of the auxin reporter DR5-GFP Null mutations of cstf77 caused severe developmental defects, but were not lethal as previously reported. cstf77-2 genetically interacted with transport inhibitor response 1 auxin signaling f-box 2 auxin receptor double mutants, further supporting that polyadenylation affects auxin signaling. AtCstF77 was ubiquitously expressed in embryos, seedlings, and adult plants. The AtCstF77 protein was localized in the nucleus, which is consistent with its function in pre-mRNA processing. We observed that PASs in transcripts from approximately 2,400 genes were shifted in the cstf77-2 mutant. Moreover, most of the PAS shifts were from proximal to distal sites. Auxin treatment also caused PAS shifts in transcripts from a small number of genes. Several auxin signaling or homeostasis genes had different PASs in their transcripts in the cstf77-2 mutant. The expression levels of AUXIN RESISTANT 2/INDOLE-3-ACETIC ACID 7 were significantly increased in the cstf77-2 mutant, which can partially account for the auxin resistance phenotype of this mutant. Our results demonstrate that AtCstF77 plays pleiotropic and critical roles in Arabidopsis development. Moreover, disruption of AtCstF64, another component of the polyadenylation machinery, led to developmental defects and reduced auxin response, similar to those of the cstf77-2 mutant. We conclude that AtCstF77 affects auxin responses, likely by controlling PAS selection of transcripts of some auxin signaling components.
PMID: 30487141
Plant Physiol , IF:6.902 , 2019 Feb , V179 (2) : P391-401 doi: 10.1104/pp.18.01119
The Role of Auxin in the Pattern Formation of the Asteraceae Flower Head (Capitulum).
Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester M13 9PT UK.; Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester M13 9PT UK minsung.kim@manchester.ac.uk.
Nature often creates complex structures by rearranging pre-existing units. One such example is the flower head (capitulum) in daisies, where a group of flowers (florets) and phyllaries (modified bracts) are arranged to superficially mimic a single flower. The capitulum is a key taxonomical innovation that defines the daisy family (Asteraceae), the largest flowering plant group. However, patterning mechanisms underlying its structure remain elusive. Here, we show that auxin, a plant hormone, provides a developmental patterning cue for the capitulum. During capitulum development, a temporal auxin gradient occurs, regulating the successive and centripetal formation of distinct florets and phyllaries. Disruption of the endogenous auxin gradient led to homeotic conversions of florets and phyllaries in the capitulum. Furthermore, auxin regulates floral meristem identity genes, such as Matricaria inodora RAY2 and M inodora LEAFY, which determine floret and phyllary identity. This study reveals the mechanism of capitulum patterning and highlights how common developmental tools, such as hormone gradients, have independently evolved in plants and animals.
PMID: 30459264
Sci Total Environ , IF:6.551 , 2019 Feb , V651 (Pt 2) : P2671-2678 doi: 10.1016/j.scitotenv.2018.09.365
Effects of Ciprofloxacin and Roundup on seed germination and root development of maize.
Laboratorio de Fisiologia de Plantas sob Estresse, Departamento de Botanica, Setor de Ciencias Biologicas, Universidade Federal do Parana, Avenida Coronel Francisco H. dos Santos, 100, Centro Politecnico Jardim das Americas, C.P. 19031, 81531-980, Curitiba, Parana, Brazil; Pos-Graduacao em Ciencias do Solo, Departamento de Solos e Engenharia Agricola, Setor de Ciencias Agrarias, Universidade Federal do Parana, Rua dos Funcionarios, 1540, Juveve, 80035-050, Curitiba, Parana, Brazil. Electronic address: marcelo.gomes@ufpr.br.; Laboratorio de Morfologia e Fisiologia de Culicidae e Chironomidae, Departamento de Zoologia, Setor de Ciencias Biologicas, Universidade Federal do Parana, Avenida Coronel Francisco H. dos Santos, 100, Centro Politecnico Jardim das Americas, C.P. 19031, 81531-980, Curitiba, Parana, Brazil.; Laboratorio de Crescimento e Desenvolvimento de Plantas, Setor de Fisiologia Vegetal, Departamento de Botanica, Universidade Federal de Lavras, Campus UFLA, C.P. 3037, 37200-000, Lavras, Minas Gerais, Brazil.; Pos-Graduacao em Ciencias do Solo, Departamento de Solos e Engenharia Agricola, Setor de Ciencias Agrarias, Universidade Federal do Parana, Rua dos Funcionarios, 1540, Juveve, 80035-050, Curitiba, Parana, Brazil.; Laboratorio de Anatomia e Biomecanica Vegetal, Departamento de Botanica, Setor de Ciencias Biologicas, Universidade Federal do Parana, Avenida Coronel Francisco H. dos Santos, 100, Centro Politecnico Jardim das Americas, C.P. 19031, 81531-980, Curitiba, Parana, Brazil.; Laboratorio de Fisiologia Vegetal, Departamento de Botanica, Instituto de Ciencias Biologicas, Universidade Federal de Minas Gerais, Avenida Antonio Carlos 6627, Pampulha, C.P. 486, Belo Horizonte, Minas Gerais, Brazil.
Their continuous release into the environment, associated with their inherent biological activity, has motivated investigations into the detrimental effects of antibiotics and herbicides in natural and agricultural ecosystems. In this study, the interactive effects of the antibiotic ciprofloxacin (Cipro) and the herbicide Roundup on seed germination and root development were investigated. Although both compounds act as inhibitors of the mitochondrial electron transport chain in seeds, neither Cipro nor Roundup disrupted germinability of maize seeds. However, Cipro accelerated germination by promoting ROS accumulation in seeds, while the stimulatory effect of Roundup on ROS-scavenging enzymes (catalase and ascorbate peroxidase) seems to prevent ROS-signaling, delaying the germination process. Roundup reduced root elongation, possibly due to its interference with auxin production, thereby preventing cell division, while Cipro stimulated root elongation by increasing root oxidative status. Cipro and Roundup showed antagonistic effects on maize seeds and root physiology. The presence of the antibiotic is likely not to disturb plant development; however, its stimulatory effects were not sufficient to overcome the deleterious effects of Roundup. According to our results, glyphosate-based herbicides must be carefully used during maize cropping and although antibiotics such as Cipro may not negatively impact agricultural production, their accumulation by crops must be investigated since this can be a pathway of antibiotic-insertion into the food chain.
PMID: 30463122
Plant Cell Environ , IF:6.362 , 2019 Feb , V42 (2) : P448-465 doi: 10.1111/pce.13413
Modulation of auxin signalling through DIAGETROPICA and ENTIRE differentially affects tomato plant growth via changes in photosynthetic and mitochondrial metabolism.
Departamento de Biologia Vegetal, Universidade Federal de Vicosa, Vicosa, Minas Gerais, Brazil.; Max-Planck Partner Group at the Departamento de Biologia Vegetal, Universidade Federal de Vicosa, Vicosa, Minas Gerais, Brazil.; Central Metabolism Group, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany.; Departmento de Ciencias Biologicas, Escola Superior de Agricultura Luiz de Queiroz, Universidade de Sao Paulo, Piracicaba, Brazil.
Auxin modulates a range of plant developmental processes including embryogenesis, organogenesis, and shoot and root development. Recent studies have shown that plant hormones also strongly influence metabolic networks, which results in altered growth phenotypes. Modulating auxin signalling pathways may therefore provide an opportunity to alter crop performance. Here, we performed a detailed physiological and metabolic characterization of tomato (Solanum lycopersicum) mutants with either increased (entire) or reduced (diageotropica-dgt) auxin signalling to investigate the consequences of altered auxin signalling on photosynthesis, water use, and primary metabolism. We show that reduced auxin sensitivity in dgt led to anatomical and physiological modifications, including altered stomatal distribution along the leaf blade and reduced stomatal conductance, resulting in clear reductions in both photosynthesis and water loss in detached leaves. By contrast, plants with higher auxin sensitivity (entire) increased the photosynthetic capacity, as deduced by higher Vcmax and Jmax coupled with reduced stomatal limitation. Remarkably, our results demonstrate that auxin-sensitive mutants (dgt) are characterized by impairments in the usage of starch that led to lower growth, most likely associated with decreased respiration. Collectively, our findings suggest that mutations in different components of the auxin signalling pathway specifically modulate photosynthetic and respiratory processes.
PMID: 30066402
Plant J , IF:6.141 , 2019 Feb , V97 (3) : P500-516 doi: 10.1111/tpj.14137
Cold stress response in Arabidopsis thaliana is mediated by GNOM ARF-GEF.
United Graduate School of Agricultural Sciences, Iwate University, Morioka, 020-8550, Japan.; Department of Plant Bio Sciences, Faculty of Agriculture, Iwate University, Morioka, 020-8550, Japan.; Agro-Innovation Center, Iwate University, Morioka, Japan.
Endosomal trafficking plays an important role in regulating plant growth and development both at optimal and stressed conditions. Cold stress response in Arabidopsis root is directly linked to inhibition of the endosomal trafficking of auxin efflux carriers. However, the cellular components that link cold stress and the endosomal trafficking remain elusive. By screening available endosomal trafficking mutants against root growth recovery response under cold stress, we identified GNOM, a SEC7 containing ARF-GEF, as a major modulator of cold response. Contrasting response of partial loss of function mutant gnom(B4049/emb30-1) and the engineered Brefeldin A (BFA)-resistant GNOM line, both of which contain mutations within SEC7 domain, to cold stress at the whole-plant level highlights the importance of this domain in modulating the cold response pathway of plants. Cold stress selectively and transiently inhibits GNOM expression. The engineered point mutation at 696 amino acid position (Methionine to Leucine) that makes GNOM resistant to BFA in fact results in overexpression of GNOM both at transcriptional and translational levels, and also alters its subcellular localization. Overexpression and altered cellular localization of GNOM were found to be directly linked to conferring striking cold-resistant phenotype in Arabidopsis. Collectively, these results provide a mechanistic link between GNOM, BFA-sensitive GNOM-regulated trafficking and cold stress.
PMID: 30362633
J Exp Bot , IF:5.908 , 2019 Feb , V70 (4) : P1239-1253 doi: 10.1093/jxb/ery456
TIR1 auxin receptors are implicated in the differential response to 4-Cl-IAA and IAA in developing pea fruit.
Plant BioSystems, Department of Agricultural, Food and Nutritional Science University of Alberta, Edmonton, Alberta, Canada.
The auxins indole-3-acetic acid (IAA) and 4-chloroindole-3-acetic acid (4-Cl-IAA) occur naturally in pea (Pisum sativum); however, only 4-Cl-IAA mimics the presence of seeds in stimulating pericarp growth. To examine if this differential auxin effect is mediated through TIR1/AFB auxin receptors, pea TIR1 and AFB2 homologs were functionally characterized in Arabidopsis, and receptor expression, and auxin distribution and action were profiled in developing pea fruits. PsTIR1a, PsTIR1b, and PsAFB2 restored the auxin-sensitive root growth response to the mutant Arabidopsis seedlings Attir1-10 and/or Attir1-10 afb2-3. Expression of PsTIR1 or AtTIR1 in Attir1-10 afb2-3 mutants also restored the greater root inhibitory response of 4-Cl-IAA compared to that of IAA, implicating TIR1 receptors in this response. The ability of 4-Cl-IAA to stimulate a stronger DR5::GUS auxin response than IAA at the same concentration in pea pericarps was associated with its ability to enrich the auxin-receptor transcript pool with PsTIR1a and PsAFB2 by decreasing the transcript abundance of PsTIR1b (mimicking results in pericarps with developing seeds). Therefore, the markedly different effect of IAA and 4-Cl-IAA on pea fruit growth may at least partially involve TIR1/AFB receptors and the differential modulation of their population, resulting in specific Aux/IAA protein degradation that leads to an auxin-specific tissue response.
PMID: 30715391
J Exp Bot , IF:5.908 , 2019 Feb , V70 (4) : P1255-1265 doi: 10.1093/jxb/erz005
Developmental plasticity of Arabidopsis hypocotyl is dependent on exocyst complex function.
Institute of Experimental Botany, Academy of Sciences of the Czech Republic, Prague 6, Czech Republic.; Department of Experimental Plant Biology, Faculty of Science, Charles University, Prague 2, Czech Republic.; Institute of Animal Physiology and Genetics, Academy of Sciences of the Czech Republic, Libechov, Czech Republic.
The collet (root-hypocotyl junction) region is an important plant transition zone between soil and atmospheric environments. Despite its crucial importance for plant development, little is known about how this transition zone is specified. Here we document the involvement of the exocyst complex in this process. The exocyst, an octameric tethering complex, participates in secretion and membrane recycling and is central to numerous cellular and developmental processes, such as growth of root hairs, cell expansion, recycling of PIN auxin efflux carriers and many others. We show that dark-grown Arabidopsis mutants deficient in exocyst subunits can form a hair-bearing ectopic collet-like structure above the true collet, morphologically resembling the true collet but also retaining some characteristics of the hypocotyl. The penetrance of this phenotypic defect is significantly influenced by cultivation temperature and carbon source, and is related to a defect in auxin regulation. These observations provide new insights into the regulation of collet region formation and developmental plasticity of the hypocotyl.
PMID: 30649396
PLoS Genet , IF:5.174 , 2019 Feb , V15 (2) : Pe1007988 doi: 10.1371/journal.pgen.1007988
The CIN-TCP transcription factors promote commitment to differentiation in Arabidopsis leaf pavement cells via both auxin-dependent and independent pathways.
Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India.
Cells in organ primordia undergo active proliferation at an early stage to generate sufficient number, before exiting proliferation and entering differentiation. However, how the actively proliferating cells are developmentally reprogrammed to acquire differentiation potential during organ maturation is unclear. Here, we induced a microRNA-resistant form of TCP4 at various developmental stages of Arabidopsis leaf primordium that lacked the activity of TCP4 and its homologues and followed its effect on growth kinematics. By combining this with spatio-temporal gene expression analysis, we show that TCP4 commits leaf cells within the transition zone to exit proliferation and enter differentiation. A 24-hour pulse of TCP4 activity was sufficient to impart irreversible differentiation competence to the actively dividing cells. A combination of biochemical and genetic analyses revealed that TCP4 imparts differentiation competence by promoting auxin response as well as by directly activating HAT2, a HD-ZIP II transcription factor-encoding gene that also acts downstream to auxin response. Our study offers a molecular link between the two major organ maturation factors, CIN-like TCPs and HD-ZIP II transcription factors and explains how TCP activity restricts the cell number and final size in a leaf.
PMID: 30742619
J Integr Plant Biol , IF:4.885 , 2019 Feb , V61 (2) : P182-196 doi: 10.1111/jipb.12724
Streptomyces lydicus A01 affects soil microbial diversity, improving growth and resilience in tomato.
The Key laboratory of Urban (South) Agriculture, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China.; Laboratory of Biological Microbiology, Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.
The actinomycete Streptomyces lydicus A01 promotes tomato seedling growth; however, the underlying mechanism is unclear. In this study, we investigated whether changes in soil microbial diversity, following Streptomyces lydicus A01 treatment, were responsible for the increased tomato seedling growth. Eukaryotic 18S ribosomal DNA (rDNA) sequencing showed that S. lydicus A01-treated and untreated soil shared 193 operational taxonomic units (OTUs), whereas bacterial 16S rDNA sequencing identified 1,219 shared OTUs between the treated and untreated soil. Of the 42 dominant eukaryotic OTUs, eight were significantly increased and six were significantly decreased after A01 treatment. Of the 25 dominant bacterial OTUs, 12 were significantly increased and eight were significantly decreased after A01 treatment. Most of the eukaryotes and bacteria that increased in abundance exhibited growth promoting characteristics, which were mainly predicted to be associated with mineralization of nitrogen and phosphorus, phosphate solubilization, nutrient accumulation, and secretion of auxin, whereas some were related to plant protection, such as the degradation of toxic and hazardous substances. Soil composition tests showed that S. lydicus A01 treatment enhanced the utilization of nitrogen, phosphorus, and potassium in tomato seedlings. Thus, microbial fertilizers based on S. lydicus A01 may improve plant growth, without the detriment effects of chemical fertilizers.
PMID: 30255551
Int J Mol Sci , IF:4.556 , 2019 Feb , V20 (4) doi: 10.3390/ijms20040936
Molecular Communication for Coordinated Seed and Fruit Development: What Can We Learn from Auxin and Sugars?
Mendel Centre for Genomics and Proteomics of Plants Systems, CEITEC MU-Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic. helene.robert.boisivon@ceitec.muni.cz.
Seed development in flowering plants is a critical part of plant life for successful reproduction. The formation of viable seeds requires the synchronous growth and development of the fruit and the three seed structures: the embryo, the endosperm, the seed coat. Molecular communication between these tissues is crucial to coordinate these developmental processes. The phytohormone auxin is a significant player in embryo, seed and fruit development. Its regulated local biosynthesis and its cell-to-cell transport capacity make of auxin the perfect candidate as a signaling molecule to coordinate the growth and development of the embryo, endosperm, seed and fruit. Moreover, newly formed seeds need nutrients and form new carbon sink, generating high sugar flow from vegetative tissues to the seeds. This review will discuss how auxin and sugars may be considered as signaling molecules to coordinate seed and fruit development.
PMID: 30795528
Int J Mol Sci , IF:4.556 , 2019 Feb , V20 (3) doi: 10.3390/ijms20030761
Transcriptome Analysis Reveals New Insights into the Bacterial Wilt Resistance Mechanism Mediated by Silicon in Tomato.
College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China. jnhskip@hotmail.com.; Institute of Tropical and Subtropical Ecology, South China Agricultural University, Guangzhou 510642, China. jnhskip@hotmail.com.; College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China. fanxueying19@163.com.; Institute of Tropical and Subtropical Ecology, South China Agricultural University, Guangzhou 510642, China. fanxueying19@163.com.; College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China. linweipeng1986@163.com.; Tea Research Institute, Guangdong Academy of Agricultural Science/Guangdong Key Laboratory of Tea Plant Resources Innovation & Utilization, Guangzhou 510640, China. linweipeng1986@163.com.; College of Horticulture, South China Agricultural University, Guangzhou 510642, China. gpwang@scau.edu.cn.; College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China. kzcai@scau.edu.cn.; Institute of Tropical and Subtropical Ecology, South China Agricultural University, Guangzhou 510642, China. kzcai@scau.edu.cn.
Bacterial wilt is a devastating disease of tomato caused by soilborne pathogenic bacterium Ralstonia solanacearum. Previous studies found that silicon (Si) can increase tomato resistance against R. solanacearum, but the exact molecular mechanism remains unclear. RNA sequencing (RNA-Seq) technology was used to investigate the dynamic changes of root transcriptome profiles between Si-treated (+Si) and untreated (-Si) tomato plants at 1, 3, and 7 days post-inoculation with R. solanacearum. The contents of salicylic acid (SA), ethylene (ET), and jasmonic acid (JA) and the activity of defense-related enzymes in roots of tomato in different treatments were also determined. The burst of ET production in roots was delayed, and SA and JA contents were altered in Si treatment. The transcriptional response to R. solanacearum infection of the +Si plants was quicker than that of the untreated plants. The expression levels of differentially-expressed genes involved in pathogen-associated molecular pattern-triggered immunity (PTI), oxidation resistance, and water-deficit stress tolerance were upregulated in the Si-treated plants. Multiple hormone-related genes were differentially expressed in the Si-treated plants. Si-mediated resistance involves mechanisms other than SA- and JA/ET-mediated stress responses. We propose that Si-mediated tomato resistance to R. solanacearum is associated with activated PTI-related responses and enhanced disease resistance and tolerance via several signaling pathways. Such pathways are mediated by multiple hormones (e.g., SA, JA, ET, and auxin), leading to diminished adverse effects (e.g., senescence, water-deficit, salinity and oxidative stress) normally caused by R. solanacearum infection. This finding will provide an important basis to further characterize the role of Si in enhancing plant resistance against biotic stress.
PMID: 30754671
Int J Mol Sci , IF:4.556 , 2019 Feb , V20 (3) doi: 10.3390/ijms20030671
Signaling Crosstalk between Salicylic Acid and Ethylene/Jasmonate in Plant Defense: Do We Understand What They Are Whispering?
State Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha 410004, China. nli@csuft.edu.cn.; College of Biological Science and Engineering, Fuzhou University, Fuzhou 350116, China. hanxiao@caas.cn.; Biotechnology Research Institute, Chinese Academy of Agricultural Science, Beijing 100081, China. hanxiao@caas.cn.; College of Biological Science and Engineering, Fuzhou University, Fuzhou 350116, China. gygzgzyx@126.com.; Biotechnology Research Institute, Chinese Academy of Agricultural Science, Beijing 100081, China. gygzgzyx@126.com.; State Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha 410004, China. yuan-deyi@163.com.; State Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha 410004, China. nghua@126.com.
During their lifetime, plants encounter numerous biotic and abiotic stresses with diverse modes of attack. Phytohormones, including salicylic acid (SA), ethylene (ET), jasmonate (JA), abscisic acid (ABA), auxin (AUX), brassinosteroid (BR), gibberellic acid (GA), cytokinin (CK) and the recently identified strigolactones (SLs), orchestrate effective defense responses by activating defense gene expression. Genetic analysis of the model plant Arabidopsis thaliana has advanced our understanding of the function of these hormones. The SA- and ET/JA-mediated signaling pathways were thought to be the backbone of plant immune responses against biotic invaders, whereas ABA, auxin, BR, GA, CK and SL were considered to be involved in the plant immune response through modulating the SA-ET/JA signaling pathways. In general, the SA-mediated defense response plays a central role in local and systemic-acquired resistance (SAR) against biotrophic pathogens, such as Pseudomonas syringae, which colonize between the host cells by producing nutrient-absorbing structures while keeping the host alive. The ET/JA-mediated response contributes to the defense against necrotrophic pathogens, such as Botrytis cinerea, which invade and kill hosts to extract their nutrients. Increasing evidence indicates that the SA- and ET/JA-mediated defense response pathways are mutually antagonistic.
PMID: 30720746
Plant Cell Physiol , IF:4.062 , 2019 Feb , V60 (2) : P255-273 doi: 10.1093/pcp/pcz001
Root Adaptation to H2O2-Induced Oxidative Stress by ARF-GEF BEN1- and Cytoskeleton-Mediated PIN2 Trafficking.
Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, Brno, Czech Republic.; Institute of Experimental Botany Czech Acad. Sci, Laboratory of Hormonal Regulations in Plants, Rozvojovi inverted question mark(1/2) 263, Prague 6, Czech Republic.; Institute of Science and Technology Austria, Klosterneuburg, Austria.
Abiotic stress poses constant challenges for plant survival and is a serious problem for global agricultural productivity. On a molecular level, stress conditions result in elevation of reactive oxygen species (ROS) production causing oxidative stress associated with oxidation of proteins and nucleic acids as well as impairment of membrane functions. Adaptation of root growth to ROS accumulation is facilitated through modification of auxin and cytokinin hormone homeostasis. Here, we report that in Arabidopsis root meristem, ROS-induced changes of auxin levels correspond to decreased abundance of PIN auxin efflux carriers at the plasma membrane (PM). Specifically, increase in H2O2 levels affects PIN2 endocytic recycling. We show that the PIN2 intracellular trafficking during adaptation to oxidative stress requires the function of the ADP-ribosylation factor (ARF)-guanine-nucleotide exchange factor (GEF) BEN1, an actin-associated regulator of the trafficking from the PM to early endosomes and, presumably, indirectly, trafficking to the vacuoles. We propose that H2O2 levels affect the actin dynamics thus modulating ARF-GEF-dependent trafficking of PIN2. This mechanism provides a way how root growth acclimates to stress and adapts to a changing environment.
PMID: 30668780
Plant Cell Physiol , IF:4.062 , 2019 Feb , V60 (2) : P243-254 doi: 10.1093/pcp/pcz004
An Historical Review of Phenylacetic Acid.
Institute of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Japan.; JSPS International Research Fellow.
Plant hormone biology is an ever-evolving field and as such, novel avenues of research must always be sought. Technological and theoretical advancement can also allow for previously dismissed research to yield equally interesting insights into processes now that they are better understood. The auxin phenylacetic acid (PAA) is an excellent example of this. PAA is a plant auxin that also possesses substantial antimicrobial activity. It has a broad distribution and has been studied in bacteria, fungi, algae and land plants. Research on this compound in plants was prominent in the 1980s, where its bioactivity and broad distribution were frequently examined. Unfortunately, due to the strong interest in the quintessential auxin, indole-3-acetic acid (IAA), research on PAA quickly petered out. Recently, several groups have resumed investigations on this hormone in plants, yet, little is known about PAA biology and its physiological role is unclear. PAA biosynthesis from the amino acid Phe invites direct comparisons with previously studied IAA biosynthesis pathways, and recent work has shown that PAA metabolism and signaling appears to be similar to that of IAA. However, given the large gap between previous work and recent investigations, a historical review of this auxin is required to renew our understanding of PAA. Here, previous work on PAA is reassessed in light of recent research in plants and serves as a synthesis of current knowledge on PAA biology.
PMID: 30649529
Ann Bot , IF:4.005 , 2019 Feb , V123 (3) : P429-439 doi: 10.1093/aob/mcy180
Auxin transport and stem vascular reconnection - has our thinking become canalized?
Discipline of Biological Sciences, University of Tasmania, Hobart, Tasmania, Australia.
BACKGROUND: The presence of a polar auxin transport stream has long been correlated with the differentiation and patterning of vascular cells across vascular plants. As our understanding of auxin transport and vascular development has grown, so too has evidence for the correlation between these processes. However, a clear understanding of the cellular and molecular mechanisms driving this correlation has not been elucidated. SCOPE: This article examines the hypothesis that canalization via polar auxin transport regulates vascular reconnection and patterning in the stem after wounding or grafting. We examine the evidence for the causal nature of the relationship and the suggested role that other hormones may play. Data are presented indicating that in grafted plants the degree of auxin transport may not always correlate with vascular reconnection. Furthermore, data on grafting success using plants with a range of hormone-related mutations indicate that these hormones may not be critical for vascular reconnection. CONCLUSIONS: In the past, excellent work examining elements of auxin synthesis, transport and response in relation to vascular development has been carried out. However, new experimental approaches are required to test more directly the hypothesis that auxin transport regulates stem vascular reconnection after wounding or grafting. This could include studies on the timing of the re-establishment of auxin transport and vascular reconnection after grafting and the influence of auxin transport mutants and inhibitors on these processes using live imaging.
PMID: 30380009
Sci Rep , IF:3.998 , 2019 Feb , V9 (1) : P2935 doi: 10.1038/s41598-019-39264-5
Analysis of Differentially Expressed Genes in Tissues of Camellia sinensis during Dedifferentiation and Root Redifferentiation.
Zhejiang University Tea Research Institute, Hangzhou, 310058, P.R. China.; The World Vegetable Centre, Guwahati, Assam, India.; Zhejiang University Tea Research Institute, Hangzhou, 310058, P.R. China. jllu@zju.edu.cn.
Tissue culture is very important for identifying the gene function of Camellia sinensis (L.) and exploiting novel germplasm through transgenic technology. Regeneration system of tea plant has been explored but not been well established since the molecular mechanism of tea plant regeneration is not clear yet. In this study, transcriptomic analysis was performed in the initial explants of tea plant and their dedifferentiated and redifferentiated tissues. A total of 93,607 unigenes were obtained through de novo assembly, and 7,193 differentially expressed genes (DEGs) were screened out from the 42,417 annotated unigenes. Much more DEGs were observed during phase transition rather than at growth stages of callus. Our KOG and KEGG analysis, and qPCR results confirmed that phase transition of tea plant was closely related to the mechanism that regulate expression of genes encoding the auxin- and cytokinin-responsive proteins, transcription factor MYB15 and ethylene-responsive transcription factor ERF RAP2-12. These findings provide a reliable foundation for elucidating the mechanism of the phase transition and may help to optimize the regeneration system by regulating the gene expression pattern.
PMID: 30814540
Sci Rep , IF:3.998 , 2019 Feb , V9 (1) : P2832 doi: 10.1038/s41598-019-39397-7
The interaction between miR160 and miR165/166 in the control of leaf development and drought tolerance in Arabidopsis.
National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops/College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, P. R. China.; Department of Biological Sciences, Michigan Technological University, Houghton, Michigan, 49931, USA.; Department of Biotechnology, Sharda University, Greater Noida, 201306, India.; National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops/College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, P. R. China. amair0534@163.com.; National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops/College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, P. R. China. gtang1@mtu.edu.; Department of Biological Sciences, Michigan Technological University, Houghton, Michigan, 49931, USA. gtang1@mtu.edu.
MicroRNAs (miRNAs) are a class of non-coding RNAs that play important roles in plant development and abiotic stresses. To date, studies have mainly focused on the roles of individual miRNAs, however, a few have addressed the interactions among multiple miRNAs. In this study, we investigated the interplay and regulatory circuit between miR160 and miR165/166 and its effect on leaf development and drought tolerance in Arabidopsis using Short Tandem Target Mimic (STTM). By crossing STTM160 Arabidopsis with STTM165/166, we successfully generated a double mutant of miR160 and miR165/166. The double mutant plants exhibited a series of compromised phenotypes in leaf development and drought tolerance in comparison to phenotypic alterations in the single STTM lines. RNA-seq and qRT-PCR analyses suggested that the expression levels of auxin and ABA signaling genes in the STTM-directed double mutant were compromised compared to the two single mutants. Our results also suggested that miR160-directed regulation of auxin response factors (ARFs) contribute to leaf development via auxin signaling genes, whereas miR165/166- mediated HD-ZIP IIIs regulation confers drought tolerance through ABA signaling. Our studies further indicated that ARFs and HD-ZIP IIIs may play opposite roles in the regulation of leaf development and drought tolerance that can be further applied to other crops for agronomic traits improvement.
PMID: 30808969
Sci Rep , IF:3.998 , 2019 Feb , V9 (1) : P2184 doi: 10.1038/s41598-018-37824-9
Transcriptional profiling of wheat (Triticum aestivum L.) during a compatible interaction with the cereal cyst nematode Heterodera avenae.
State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.; NIBIO - Norwegian Institute of Bioeconomy Research, P.O. Box 115, N-1431, Oslo, As, Norway.; State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China. dlpeng@ippcaas.cn.
Cereal cyst nematode (CCN, Heterodera avenae) presents severe challenges to wheat (Triticum aestivum L.) production worldwide. An investigation of the interaction between wheat and CCN can greatly improve our understanding of how nematodes alter wheat root metabolic pathways for their development and could contribute to new control strategies against CCN. In this study, we conducted transcriptome analyses of wheat cv. Wen 19 (Wen19) by using RNA-Seq during the compatible interaction with CCN at 1, 3 and 8 days past inoculation (dpi). In total, 71,569 transcripts were identified, and 10,929 of them were examined as differentially expressed genes (DEGs) in response to CCN infection. Based on the functional annotation and orthologous findings, the protein phosphorylation, oxidation-reduction process, regulation of transcription, metabolic process, transport, and response process as well as many other pathways previously reported were enriched at the transcriptional level. Plant cell wall hydrolysis and modifying proteins, auxin biosynthesis, signalling and transporter genes were up-regulated by CCN infection to facilitate penetration, migration and syncytium establishment. Genes responding to wounding and jasmonic acid stimuli were enriched at 1 dpi. We found 16 NBS-LRR genes, 12 of which were down-regulated, indicating the repression of resistance. The expression of genes encoding antioxidant enzymes, glutathione S-transferases and UDP-glucosyltransferase was significantly up-regulated during CCN infection, indicating that they may play key roles in the compatible interaction of wheat with CCN. Taken together, the results obtained from the transcriptome analyses indicate that the genes involved in oxidation-reduction processes, induction and suppression of resistance, metabolism, transport and syncytium establishment may be involved in the compatible interaction of Wen 19 with CCN. This study provides new insights into the responses of wheat to CCN infection. These insights could facilitate the elucidation of the potential mechanisms of wheat responses to CCN.
PMID: 30778126
Sci Rep , IF:3.998 , 2019 Feb , V9 (1) : P1755 doi: 10.1038/s41598-018-37923-7
Genome-wide Identification, Expression Profiling and Evolutionary Analysis of Auxin Response Factor Gene Family in Potato (Solanum tuberosum Group Phureja).
College of Plant Protection, Yunnan Agricultural University, Kunming, 650201, China.; State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.; School of Agriculture, Ningxia University, Yinchuan, 750021, China.; College of Plant Protection, Yunnan Agricultural University, Kunming, 650201, China. zhanghongji111@163.com.; State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China. liuning@im.ac.cn.
Auxin response factors (ARFs) play central roles in conferring auxin-mediated responses through selection of target genes in plants. Despite their physiological importance, systematic analysis of ARF genes in potato have not been investigated yet. Our genome-wide analysis identified 20 StARF (Solanum tuberosum ARF) genes from potato and found that they are unevenly distributed in all the potato chromosomes except chromosome X. Sequence alignment and conserved motif analysis suggested the presence of all typical domains in all but StARF18c that lacks B3 DNA-binding domain. Phylogenetic analysis indicated that potato ARF could be clustered into 3 distinct subgroups, a result supported by exon-intron structure, consensus motifs, and domain architecture. In silico expression analysis and quantitative real-time PCR experiments revealed that several StARFs were expressed in tissue-specific, biotic/abiotic stress-responsive or hormone-inducible manners, which reflected their potential roles in plant growth, development or under various stress adaptions. Strikingly, most StARFs were identified as highly abiotic stress responsive, indicating that auxin signaling might be implicated in mediating environmental stress-adaptation responses. Taken together, this analysis provides molecular insights into StARF gene family, which paves the way to functional analysis of StARF members and will facilitate potato breeding programs.
PMID: 30742001
Genes (Basel) , IF:3.759 , 2019 Feb , V10 (2) doi: 10.3390/genes10020165
Genome-Wide Analysis of Auxin Receptor Family Genes in Brassica juncea var. tumida.
College of Life Science and Technology, Yangtze Normal University, Chongqing 408100, China. caizhaoming-2000@163.com.; School of Life Sciences, Provincial Key Laboratory of the Biodiversity Study and Ecology Conservation in Southwest Anhui, Anqing Normal University, Anqing 246133, China. qiuyizeng@163.com.; College of Life Science and Technology, Yangtze Normal University, Chongqing 408100, China. 10091123@163.com.; College of Life Science and Technology, Yangtze Normal University, Chongqing 408100, China. xiaobei15109217512@163.com.; State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetic and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China. sahito_zulfiqarali@yahoo.com.; College of Life Science and Technology, Yangtze Normal University, Chongqing 408100, China. 18323997970@163.com.; College of Life Science and Technology, Yangtze Normal University, Chongqing 408100, China. FUMIN55555@126.com.; College of Life Science and Technology, Yangtze Normal University, Chongqing 408100, China. 17729647355@163.com.; College of Life Science and Technology, Yangtze Normal University, Chongqing 408100, China. wangdiandongyznu@163.com.
Transport inhibitor response 1/auxin signaling f-box proteins (TIR1/AFBs) play important roles in the process of plant growth and development as auxin receptors. To date, no information has been available about the characteristics of the TIR1/AFB gene family in Brassica juncea var. tumida. In this study, 18 TIR1/AFB genes were identified and could be clustered into six groups. The genes are located in 11 of 18 chromosomes in the genome of B. juncea var. tumida, and similar gene structures are found for each of those genes. Several cis-elements related to plant response to phytohormones, biotic stresses, and abiotic stresses are found in the promoter of BjuTIR1/AFB genes. The results of qPCR analysis show that most genes have differential patterns of expression among six tissues, with the expression levels of some of the genes repressed by salt stress treatment. Some of the genes are also responsive to pathogen Plasmodiophora brassicae treatment. This study provides valuable information for further studies as to the role of BjuTIR1/AFB genes in the regulation of plant growth, development, and response to abiotic stress.
PMID: 30791673
Plant Physiol Biochem , IF:3.72 , 2019 Feb , V135 : P341-347 doi: 10.1016/j.plaphy.2018.12.022
Exposure of Catasetum fimbriatum aerial roots to light coordinates carbon partitioning between source and sink organs in an auxin dependent manner.
Departamento de Botanica, Instituto de Biociencias, Universidade de Sao Paulo, 05508-900, Sao Paulo, SP, Brazil. Electronic address: paulorayner@usp.br.; Departamento de Botanica, Instituto de Biociencias, Universidade de Sao Paulo, 05508-900, Sao Paulo, SP, Brazil.
Light energy is essential for carbon metabolism in plants, as well as controlling the transport of metabolites between the organs. While terrestrial plants have a distinct structural and functional separation between the light exposed aerial parts and the non-exposed roots, epiphytic plants, such as orchids, have shoots and roots simultaneously fully exposed to light. The roots of orchids differ mainly from non-orchidaceous plants in their ability to photosynthesize. Since the roots of Catasetum fimbriatum can synthesize auxin which is acropetally transported to the shoot region, we decided to investigate whether: (1) light treatment of C. fimbriatum roots raises the auxin levels in the plant; and (2) distinct auxin concentrations can change the source-sink relationships, altering the amounts of sugars and organic acids in leaves, pseudobulbs and roots. Among the organs studied, the roots accumulated the highest concentrations of indole-3-acetic-acid (IAA); and when roots were exposed to light, IAA accumulated in the leaves. However, when polar auxin transport (PAT) was blocked with N-(1-Naphthyl)phthalamic acid (NPA) treatment, a significant accumulation of sugars and organic acids occurred in the pseudobulbs and leaves, respectively, suggesting that auxin flux from roots to shoots was involved in carbon partitioning of the aerial organs. Considering that C. fimbriatum plants lose all their leaves seasonally, it is possible the roots are a substituting influence on the growth and development of this orchid during its leafless period.
PMID: 30605871
Plant Physiol Biochem , IF:3.72 , 2019 Feb , V135 : P215-223 doi: 10.1016/j.plaphy.2018.12.008
In seedlings of Pinus radiata, jasmonic acid and auxin are differentially distributed on opposite sides of tilted stems affecting lignin monomer biosynthesis and composition.
Instituto de Ciencias Biologicas, Campus Talca, Universidad de Talca, Avda. Lircay s/, Talca, Chile.; Centro de Biotecnologia y Genomica de Plantas, Universidad Politecnica de Madrid (UPM) - Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria (INIA), Pozuelo de Alarcon, Spain.; Multidisciplinary Agroindustry Research Laboratory, Universidad Autonoma de Chile, Chile.; Centre for Research in Agricultural Genomics (CRAG) Consorci CSIC-IRTA-UAB-UB Edifici CRAG Campus de Bellaterra de la UAB, 08193, Cerdanyola del Valles, Barcelona, Spain.; Instituto de Ciencias Biologicas, Campus Talca, Universidad de Talca, Avda. Lircay s/, Talca, Chile. Electronic address: pramoscampos76@gmail.com.
Plants respond to the loss of vertical growth re-orientating their affected organs. In trees, this phenomenon has received the scientific attention due to its importance for the forestry industry. Nowadays it is accepted that auxin distribution is involved in the modulation of the tilting response, but how this distribution is controlled is not fully clear. Auxin transporters that determine the spatio-temporal auxin distribution in radiate pine seedlings exposed to 45 degrees of tilting were identified. Additionally, based on indications for an intimate plant hormone crosstalk in this process, IAA and JA contents were evaluated. The experiments revealed that expression of the auxin transporters was down-regulated in the upper half of the tilted stem, while being induced in the lower half. Moreover, transporter-coding genes were first induced at the apical zone of the stem. IAA was consistently redistributed toward the lower half, which is in accordance with the expression profile of the auxin transporters. In contrast, JA was mainly accumulated in the upper half of tilted stems. Finally, lignin content and monomeric composition were analyzed in both sides of stem and along the time course of tilting. As expected, lignin accumulation was higher at the lower half of stem at longer times of tilting. However, the most marked difference was the accumulation of the H-lignin monomer in the lower half, while the G-lignin unit was more dominant in the upper half. Here, we provide detailed insight in the distribution of IAA and JA, affecting the lignin composition during the tilting response in Pinus radiata seedlings.
PMID: 30576980
BMC Genomics , IF:3.594 , 2019 Feb , V20 (1) : P108 doi: 10.1186/s12864-019-5486-7
De novo assembly of Persea americana cv. 'Hass' transcriptome during fruit development.
Facultad de Ciencias de la Vida, Centro de Biotecnologia Vegetal, Universidad Andres Bello, Avenida Republica 330, 8370035, Santiago, RM, Chile.; Instituto de Investigaciones Agropecuarias, INIA-La Platina, Santa Rosa 11610, La Pintana, 831314, Santiago, RM, Chile.; Escuela de Agronomia, Pontificia Universidad Catolica de Valparaiso, Quillota, Chile.; Instituto de Investigaciones Agropecuarias, INIA-La Platina, Santa Rosa 11610, La Pintana, 831314, Santiago, RM, Chile. bdefilip@inia.cl.; Facultad de Ciencias de la Vida, Centro de Biotecnologia Vegetal, Universidad Andres Bello, Avenida Republica 330, 8370035, Santiago, RM, Chile. claudio.meneses@unab.cl.; FONDAP Center for Genome Regulation, Santiago, Chile. claudio.meneses@unab.cl.
BACKGROUND: Avocado (Persea americana Mill.) is a basal angiosperm from the Lauraceae family. This species has a diploid genome with an approximated size of ~ 920 Mbp and produces a climacteric, fleshy and oily fruit. The flowering and fruit set are particularly prolonged processes, lasting between one to three months, generating important differences in physiological ages of the fruit within the same tree. So far there is no detailed genomic information regarding this species, being the cultivar 'Hass' especially important for avocado growers worldwide. With the aim to explore the fruit avocado transcriptome and to identify candidate biomarkers to monitore fruit development, we carried out an RNA-Seq approach during 4 stages of 'Hass' fruit development: 150 days after fruit set (DAFS), 240 DAFS, 300 DAFS (harvest) and 390 DAFS (late-harvest). RESULTS: The 'Hass' de novo transcriptome contains 62,203 contigs (x=988 bp, N50 = 1050 bp). We found approximately an 85 and 99% of complete ultra-conserved genes in eukaryote and plantae database using BUSCO (Benchmarking Universal Single-Copy Orthologs) and CEGMA (Core Eukaryotic Gene Mapping Approach), respectively. Annotation was performed with BLASTx, resulting in a 58% of annotated contigs (90% of differentially expressed genes were annotated). Differentially expressed genes analysis (DEG; with False Discovery Rate
PMID: 30727956
BMC Plant Biol , IF:3.497 , 2019 Feb , V19 (1) : P88 doi: 10.1186/s12870-019-1686-1
Transcriptome analysis reveals regulatory framework for salt and osmotic tolerance in a succulent xerophyte.
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, People's Republic of China. yinhj@lzu.edu.cn.; 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, People's Republic of China.; 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, People's Republic of China. smwang@lzu.edu.cn.
BACKGROUND: Zygophyllum xanthoxylum is a succulent xerophyte with remarkable tolerance to diverse abiotic stresses. Previous studies have revealed important physiological mechanisms and identified functional genes associated with stress tolerance. However, knowledge of the regulatory genes conferring stress tolerance in this species is poorly understood. RESULTS: Here, we present a comprehensive analysis of regulatory genes based on the transcriptome of Z. xanthoxylum roots exposed to osmotic stress and salt treatments. Significant changes were observed in transcripts related to known and obscure stress-related hormone signaling pathways, in particular abscisic acid and auxin. Significant changes were also found among key classes of early response regulatory genes encoding protein kinases, transcription factors, and ubiquitin-mediated proteolysis machinery. Network analysis shows a highly integrated matrix formed by these conserved and novel gene products associated with osmotic stress and salt in Z. xanthoxylum. Among them, two previously uncharacterized NAC (NAM/ATAF/CUC) transcription factor genes, ZxNAC083 (Unigene16368_All) and ZxNAC035 (CL6534.Contig1_All), conferred tolerance to salt and drought stress when constitutively overexpressed in Arabidopsis plants. CONCLUSIONS: This study provides a unique framework for understanding osmotic stress and salt adaptation in Z. xanthoxylum including novel gene targets for engineering stress tolerance in susceptible crop species.
PMID: 30819118
BMC Plant Biol , IF:3.497 , 2019 Feb , V19 (1) : P72 doi: 10.1186/s12870-019-1664-7
Transcriptomic response is more sensitive to water deficit in shoots than roots of Vitis riparia (Michx.).
McFadden BioStress Laboratory, Agronomy, Horticulture, and Plant Science Department, South Dakota State University, Brookings, SD, 57006, USA.; JABSOM Bioinformatics Core, Department of Complementary & Integrative Medicine, University of Hawaii, Honolulu, HI, USA.; South Dakota State University, Brookings, SD, 57006, USA.; Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, USA.; McFadden BioStress Laboratory, Agronomy, Horticulture, and Plant Science Department, South Dakota State University, Brookings, SD, 57006, USA. anne.fennell@sdstate.edu.; South Dakota State University, Brookings, SD, 57006, USA. anne.fennell@sdstate.edu.
BACKGROUND: Drought is an important constraint on grapevine sustainability. Vitis riparia, widely used in rootstock and scion breeding, has been studied in isolated leaf drying response studies; however, it is essential to identify key root and shoot water deficit signaling traits in intact plants. This information will aid improved scion and rootstock selection and management practices in grapevine. RNAseq data were generated from V. riparia roots and shoots under water deficit and well-watered conditions to determine root signaling and shoot responses to water deficit. RESULTS: Shoot elongation, photosynthetic rate, and stomatal conductance were significantly reduced in water deficit (WD) treated than in well-watered grapevines. RNAseq analysis indicated greater transcriptional differences in shoots than in roots under WD, with 6925 and 1395 genes differentially expressed, respectively (q-value < 0.05). There were 50 and 25 VitisNet pathways significantly enriched in WD relative to well-watered treatments in grapevine shoots and roots, respectively. The ABA biosynthesis genes beta-carotene hydroxylase, zeaxanthin epoxidase, and 9-cis-epoxycarotenoid dioxygenases were up-regulated in WD root and WD shoot. A positive enrichment of ABA biosynthesis genes and signaling pathways in WD grapevine roots indicated enhanced root signaling to the shoot. An increased frequency of differentially expressed reactive oxygen species scavenging (ROS) genes were found in the WD shoot. Analyses of hormone signaling genes indicated a strong ABA, auxin, and ethylene network and an ABA, cytokinin, and circadian rhythm network in both WD shoot and WD root. CONCLUSIONS: This work supports previous findings in detached leaf studies suggesting ABA-responsive binding factor 2 (ABF2) is a central regulator in ABA signaling in the WD shoot. Likewise, ABF2 may have a key role in V. riparia WD shoot and WD root. A role for ABF3 was indicated only in WD root. WD shoot and WD root hormone expression analysis identified strong ABA, auxin, ethylene, cytokinin, and circadian rhythm signaling networks. These results present the first ABA, cytokinin, and circadian rhythm signaling network in roots under water deficit. These networks point to organ specific regulators that should be explored to further define the communication network from soil to shoot.
PMID: 30760212
BMC Plant Biol , IF:3.497 , 2019 Feb , V19 (1) : P61 doi: 10.1186/s12870-019-1632-2
First RNA-seq approach to study fruit set and parthenocarpy in zucchini (Cucurbita pepo L.).
Genomics and Biotechnology Department, IFAPA Research Centre La Mojonera, Camino de San Nicolas, 1, 04745 La Mojonera, Almeria, Spain.; Genomics and Biotechnology Department, IFAPA Research Centre Alameda del Obispo, Avd. Menendez Pidal s/n, 14004, Cordoba, Spain.; Genetics Department, University of Cordoba, Av. de Medina Azahara, 5, 14071, Cordoba, Spain.; Institute for the Conservation and Breeding of Agricultural Biodiversity (COMAV-UPV), Universitat Politecnica de Valencia, Camino de Vera s/n, 46022, Valencia, Spain.; Genomics and Biotechnology Department, IFAPA Research Centre La Mojonera, Camino de San Nicolas, 1, 04745 La Mojonera, Almeria, Spain. pedro.gomez.j@juntadeandalucia.es.
BACKGROUND: Zucchini fruit set can be limited due to unfavourable environmental conditions in off-seasons crops that caused ineffective pollination/fertilization. Parthenocarpy, the natural or artificial fruit development without fertilization, has been recognized as an important trait to avoid this problem, and is related to auxin signalling. Nevertheless, differences found in transcriptome analysis during early fruit development of zucchini suggest that other complementary pathways could regulate fruit formation in parthenocarpic cultivars of this species. The development of next-generation sequencing technologies (NGS) as RNA-sequencing (RNA-seq) opens a new horizon for mapping and quantifying transcriptome to understand the molecular basis of pathways that could regulate parthenocarpy in this species. The aim of the current study was to analyze fruit transcriptome of two cultivars of zucchini, a non-parthenocarpic cultivar and a parthenocarpic cultivar, in an attempt to identify key genes involved in parthenocarpy. RESULTS: RNA-seq analysis of six libraries (unpollinated, pollinated and auxin treated fruit in a non-parthenocarpic and parthenocarpic cultivar) was performed mapping to a new version of C. pepo transcriptome, with a mean of 92% success rate of mapping. In the non-parthenocarpic cultivar, 6479 and 2186 genes were differentially expressed (DEGs) in pollinated fruit and auxin treated fruit, respectively. In the parthenocarpic cultivar, 10,497 in pollinated fruit and 5718 in auxin treated fruit. A comparison between transcriptome of the unpollinated fruit for each cultivar has been performed determining that 6120 genes were differentially expressed. Annotation analysis of these DEGs revealed that cell cycle, regulation of transcription, carbohydrate metabolism and coordination between auxin, ethylene and gibberellin were enriched biological processes during pollinated and parthenocarpic fruit set. CONCLUSION: This analysis revealed the important role of hormones during fruit set, establishing the activating role of auxins and gibberellins against the inhibitory role of ethylene and different candidate genes that could be useful as markers for parthenocarpic selection in the current breeding programs of zucchini.
PMID: 30727959
Plant Mol Biol , IF:3.302 , 2019 Feb , V99 (3) : P205-217 doi: 10.1007/s11103-018-0812-z
The regulatory mechanism of chilling-induced dormancy transition from endo-dormancy to non-dormancy in Polygonatum kingianum Coll.et Hemsl rhizome bud.
College of Agronomy and Biotechnology, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, China.; College of Agronomy and Biotechnology, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, China. xuehuidong@cau.edu.cn.
KEY MESSAGE: We identified three dormant stages of Polygonatum kingianum and changes that occurred during dormancy transition in the following aspects including cell wall and hormones, as well as interaction among them. Polygonatum kingianum Coll.et Hemsl (P. kingianum) is an important traditional Chinese medicine, but the mechanism of its rhizome bud dormancy has not yet been studied systematically. In this study, three dormancy phases were induced under controlled conditions, and changes occurring during the transition were examined, focusing on phytohormones and the cell wall. As revealed by HPLC-MS (High Performance Liquid Chromatography-Mass Spectrometry) analysis, the endo- to non-dormancy transition was association with a reduced abscisic acid (ABA)/gibberellin (GA3) ratio, a decreased level of auxin (IAA) and an increased level of trans-zeatin (tZR). Transmission electron microscopy showed that plasmodesmata (PDs) and the cell wall of the bud underwent significant changes between endo- and eco-dormancy. A total of 95,462 differentially expressed genes (DEGs) were identified based on transcriptomics, and clustering and principal component analysis confirmed the different physiological statuses of the three types of bud samples. Changes in the abundance of transcripts associated with IAA, cytokinins (CTKs), GA, ABA, brassinolide (BR), jasmonic acid (JA), ethylene, salicylic acid (SA), PDs and cell wall-loosening factors were analysed during the bud dormancy transition in P. kingianum. Furthermore, nitrilase 4 (NIT4) and tryptophan synthase alpha chain (TSA1), which are related to IAA synthesis, were identified as hub genes of the co-expression network, and strong interactions between hormones and cell wall-related factors were observed. This research will provide a good model for chilling-treated rhizome bud dormancy in P. kingianum and cultivation of this plant.
PMID: 30627860
Molecules , IF:3.267 , 2019 Feb , V24 (4) doi: 10.3390/molecules24040717
Analysis of Metabolite Accumulation Related to Pod Color Variation of Caragana intermedia.
College of Life Sciences, Inner Mongolia Agricultural University, Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Hohhot 010018, China. yangfeiyun@imau.edu.cn.; College of Food Science and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China. yangfeiyun@imau.edu.cn.; College of Life Sciences, Inner Mongolia Agricultural University, Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Hohhot 010018, China. yang_tianrui@163.com.; College of Life Sciences, Inner Mongolia Agricultural University, Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Hohhot 010018, China. liukun261@163.com.; College of Life Sciences, Inner Mongolia Agricultural University, Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Hohhot 010018, China. atp_yangqi@163.com.; College of Life Sciences, Inner Mongolia Agricultural University, Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Hohhot 010018, China. livgreen176@163.com.; College of Life Sciences, Inner Mongolia Agricultural University, Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Hohhot 010018, China. ruigangwang@126.com.; College of Life Sciences, Inner Mongolia Agricultural University, Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Hohhot 010018, China. liguojing@imau.edu.cn.
Caragana intermedia, a leguminous shrub widely distributed in cold and arid regions, is rich in secondary metabolites and natural active substances, with high nutritional and medical values. It is interesting that the pods of C. intermedia often show different colors among individual plants. In this study, 10-, 20- and 30-day-old red and green pods of C. intermedia were used to identify and characterize important metabolites associated with pod color. A total 557 metabolites, which could be classified into 21 groups, were detected in the pod extracts using liquid chromatography coupled with ESI-triple quadrupole-linear ion trap mass spectrometer (LC-ESI-MS/MS). Metabolomics analysis revealed significant differences in 15 groups of metabolites between red and green pods, including amino acids, nucleotide derivatives, flavonoids, and phytohormones. Metabolic pathway analysis showed that the shikimic acid and the phytohormone metabolic pathways were extraordinarily active in red pods, and the difference between red and green pods was obvious. Moreover, red pods showed remarkable flavonoids, cytokinins, and auxin accumulation, and the content of total flavonoids and proanthocyanidins in 30-day-old red pods was significantly higher than that in green pods. This metabolic profile contributes to valuable insights into the metabolic regulation mechanism in different color pods.
PMID: 30781495
Gene , IF:2.984 , 2019 Feb , V685 : P96-105 doi: 10.1016/j.gene.2018.10.066
Transcriptomics profiling in response to cold stress in cultivated rice and weedy rice.
Rice Research Institute, College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China; Key Laboratory of Agricultural Biotechnology of Liaoning Province, College of Biosciences and Biotechnology, Shenyang Agricultural University, Shenyang, Liaoning 110866, China.; Rice Research Institute, College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China.; Rice Research Institute, College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China. Electronic address: zmh560@163.com.; Rice Research Institute, College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China; Key Laboratory of Agricultural Biotechnology of Liaoning Province, College of Biosciences and Biotechnology, Shenyang Agricultural University, Shenyang, Liaoning 110866, China. Electronic address: zfguo@syau.edu.cn.
Weedy rice is an important germplasm resource for rice improvement because it has useful genes for many abiotic stresses including cold tolerance. We identified the cold tolerance and cold sensitivity of two weedy rice lines (WR 03-35 and WR 03-26) and two cultivated rice lines (Kongyu 131 and 9311). During the seedling stage of these lines, we used RNA-seq to measure changes in weedy rice and cultivated rice whole-genome transcriptome before and after cold treatment. We identified 14,213 and 14,730 differentially expressed genes (DEGs) in cold-tolerant genotypes (WR 03-35, Kongyu 131), and 9219 and 720 DEGs were observed in two cold-sensitive genotypes (WR 03-26, 9311). Many common and special DEGs were analyzed in cold-tolerant and cold-sensitive genotypes, respectively. Some typical genes related to cold stress such as the basic helix-loop-helix (bHLH) gene and leucine-rich repeat (LRR) domain gene etc. The number of these DEGs in cold-tolerant genotypes is more than those found in cold-sensitive genotypes. The gene ontology (GO) enrichment analyses showed significantly enriched terms for biological processes, cellular components and molecular functions. In addition, some genes related to several plant hormones such as abscisic acid (ABA), gibberellic acid (GA), auxin and ethylene were identified. To confirm the RNA-seq data, semi-quantitative RT-PCR and qRT-PCR were performed on 12 randomly selected DEGs. The expression patterns of RNA-seq on these genes corresponded with the semi-quantitative RT-PCR and qRT-PCR method. This study suggests the gene resources related to cold stress from weedy rice could be valuable for understanding the mechanisms involved in cold stress and rice breeding for improving cold tolerance.
PMID: 30389557
Photochem Photobiol Sci , IF:2.831 , 2019 Feb , V18 (2) : P434-447 doi: 10.1039/c8pp00567b
Responses of flavonoid profile and associated gene expression to solar blue and UV radiation in two accessions of Vicia faba L. from contrasting UV environments.
Viikki Plant Science Centre (ViPS), Department of Biosciences, University of Helsinki, Uusimaa, Finland. yan.z.yan@helsinki.fi.
Blue light and UV radiation shape a plant's morphology and development, but accession-dependent responses under natural conditions are unclear. Here we tested the hypothesis that two faba bean (Vicia faba L.) accessions adapted to different latitudes and altitudes vary in their responses to solar blue and UV light. We measured growth, physiological traits, phenolic profiles and expression of associated genes in a factorial experiment combining two accessions (Aurora, a Swedish cultivar adapted to high latitude and low altitude; ILB938, from the Andean region of Colombia and Ecuador, adapted to low latitude and high altitude) and four filter treatments created with plastic sheets: 1. transparent as control; 2. attenuated short UV (290-350 nm); 3. attenuated UV (290-400 nm); 4. attenuated blue and UV light. In both accessions, the exclusion of blue and UV light increased plant height and leaf area, and decreased transcript abundance of ELONGATED HYPOCOTYL 5 (HY5) and TYROSINE AMINOTRANSFERASE 3 (TAT3). Blue light and short UV induced the accumulation of epidermal and whole-leaf flavonoids, mainly quercetins, and the responses in the two accessions were through different glycosides. Filter treatments did not affect kaempferol concentration, but there were more tri-glycosides in Aurora and di-glycosides in ILB938. Furthermore, fewer quercetin glycosides were identified in ILB938. The transcript abundance was consistently higher in Aurora than in ILB938 for all seven investigated genes: HY5, TAT3, CHALCONE SYNTHASE (CHS), CHALCONE ISOMERASE (CHI), DON-GLUCOSYLTRANSFERASE 1 (DOGT1), ABA INSENSITIVE 2 (ABI2), AUXIN-INDUCIBLE 2-27 (IAA5). The two largest differences in transcript abundance between the two accessions across treatments were 132-fold in CHS and 30-fold in DOGT1 which may explain the accession-dependent glycosylation patterns. Our findings suggest that agronomic selection for adaptation to high altitude may favour phenotypes with particular adaptations to the light environment, including solar UV and blue light.
PMID: 30629071
Life Sci Space Res (Amst) , IF:2.453 , 2019 Feb , V20 : P1-11 doi: 10.1016/j.lssr.2018.11.001
Polar auxin transport is essential to maintain growth and development of etiolated pea and maize seedlings grown under 1g conditions: Relevance to the international space station experiment.
Faculty of Liberal Arts and Sciences, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan; Graduate School of Science, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan. Electronic address: miyamoto@las.osakafu-u.ac.jp.; Graduate School of Science, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan.; Faculty of Agriculture, Tottori University, 4-101 Koyamacho-minami, Tottori 680-8553, Japan.; Future Development Division, Advanced Engineering Services Co., Ltd., 1-6-1 Takezono, Tsukuba, Ibaraki 305-0032, Japan.; Technology and Research Promotion Department, Japan Space Forum, Shin-Otemachi Bldg. 7F, 2-2-1 Otemachi, Chiyoda-ku, Tokyo 100-0004, Japan.; Utilization Engineering Department, Japan Manned Space System Corporation, Space Station Test Building, Tsukuba Space Center, 2-1-1 Sengen, Tsukuba, Ibaraki 305-8505, Japan.; Kibo Utilization Center, Human Spaceflight Technology Directorate, Japan Aerospace Exploration Agency, 2-1-1 Sengen, Tsukuba, Ibaraki 305-8505, Japan.; Graduate School of Science, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan. Electronic address: ueda@b.s.osakafu-u.ac.jp.
We conducted "Auxin Transport" space experiments in 2016 and 2017 in the Japanese Experiment Module (JEM) on the International Space Station (ISS), with the principal objective being integrated analyses of the growth and development of etiolated pea (Pisum sativum L. cv Alaska) and maize (Zea mays L. cv Golden Cross Bantam) seedlings under true microgravity conditions in space relative to auxin dynamics. Etiolated pea seedlings grown under microgravity conditions in space for 3 days showed automorphogenesis. Epicotyls and roots bent ca. 45 degrees and 20 degrees toward the direction away from the cotyledons, respectively, whereas those grown under artificial 1g conditions produced by a centrifuge in the Cell Biology Experimental Facility (CBEF) in space showed negative and positive gravitropic response in epicotyls and in roots, respectively. On the other hand, the coleoptiles of 4-day-old etiolated maize seedlings grew almost straight, but the mesocotyls curved and grew toward a random direction under microgravity conditions in space. In contrast, the coleoptiles and mesocotyls of etiolated maize seedlings grown under 1g conditions on Earth were almost straight and grew upward or toward the direction against the gravity vector. The polar auxin transport activity in etiolated pea epicotyls and in maize shoots was significantly inhibited and enhanced, respectively, under microgravity conditions in space as compared with artificial 1g conditions in space or 1g conditions on Earth. An inhibitor of polar auxin transport, 2,3,5-triiodobenzoic acid (TIBA) substantially affected the growth direction and polar auxin transport activity in etiolated pea seedlings grown under both artificial 1g and microgravity conditions in space. These results strongly suggest that adequate polar auxin transport is essential for gravitropic response in plants. Possible mechanisms enhancing polar auxin transport in etiolated maize seedlings grown under microgravity conditions in space are also proposed.
PMID: 30797426
Plant Direct , IF:1.725 , 2019 Feb , V3 (2) : Pe00121 doi: 10.1002/pld3.121
Antagonistic activity of auxin and cytokinin in shoot and root organs.
Department of Plant and Soil Sciences University of Kentucky Lexington Kentucky.
The hormones auxin and cytokinin are essential for plant growth and development. Because of the central importance of root and shoot apical meristems in plant growth, auxin/cytokinin interactions have been predominantly analyzed in relation to apical meristem formation and function. In contrast, the auxin/cytokinin interactions during organ growth have remained largely unexplored. Here, we show that a specific interaction between auxin and cytokinin operates in both the root and the shoot where it serves as an additional determinant of plant development. We found that auxin at low concentrations limits the action of cytokinin. An increase in cytokinin level counteracts this inhibitory effect and leads to an inhibition of auxin signaling. At higher concentrations of both hormones, these antagonistic interactions between cytokinin and auxin are absent. Thus, our results reveal a bidirectional and asymmetrical interaction of auxin and cytokinin beyond the bounds of apical meristems. The relation is bidirectional in that both hormones exert inhibitory effects on each other's signaling mechanisms. However, this relation is also asymmetrical because under controlled growth conditions, auxin present in nontreated plants suppresses cytokinin signaling, whereas the reverse is not the case.
PMID: 31245764
Plant Direct , IF:1.725 , 2019 Feb , V3 (2) : Pe00116 doi: 10.1002/pld3.116
ARF5/MONOPTEROS directly regulates miR390 expression in the Arabidopsis thaliana primary root meristem.
Center for Organismal Studies (COS) University of Heidelberg Heidelberg Germany.; Present address: PsiOxus Therapeutics Abingdon UK.; Present address: Max Planck Institute for Plant Breeding Research Cologne Germany.
The root meristem is organized around a quiescent center (QC) surrounded by stem cells that generate all cell types of the root. In the transit-amplifying compartment, progeny of stem cells further divides prior to differentiation. Auxin controls the size of this transit-amplifying compartment via auxin response factors (ARFs) that interact with auxin response elements (AuxREs) in the promoter of their targets. The microRNA miR390 regulates abundance of ARF2, ARF3, and ARF4 by triggering the production of trans-acting (ta)-siRNA from the TAS3 precursor. This miR390/TAS3/ARF regulatory module confers sensitivity and robustness to auxin responses in diverse developmental contexts and organisms. Here, we show that miR390 is expressed in the transit-amplifying compartment of the root meristem where it modulates response to exogenous auxin. We show that a single AuxRE located in miR390 promoter is necessary for miR390 expression in this compartment and identify that ARF5/MONOPTEROS (MP) binds miR390 promoter via the AuxRE. We show that interfering with ARF5/MP-dependent auxin signaling attenuates miR390 expression in the transit-amplifying compartment of the root meristem. Our results show that ARF5/MP regulates directly the expression of miR390 in the root meristem. We propose that ARF5, miR390, and the ta-siRNAs-regulated ARFs modulate the response of the transit-amplifying region of the meristem to exogenous auxin.
PMID: 31245759
Mol Biol Rep , IF:1.402 , 2019 Feb , V46 (1) : P933-945 doi: 10.1007/s11033-018-4549-1
Transcriptome-based gene expression profiling of diploid radish (Raphanus sativus L.) and the corresponding autotetraploid.
National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.; National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China. nauliulw@njau.edu.cn.
Polyploidy is an important evolutionary factor in most land plant lineages which possess more than two complete sets of chromosomes. Radish (Raphanus sativus L.) is an economically annual/biennial root vegetable crop worldwide. However, the expression patterns of duplicated homologs involved in the autopolyploidization remains unclear. In present study, the autotetraploid radish plants (2n = 4x = 36) were produced with colchicine and exhibited an increase in the size of flowers, leaves, stomata and pollen grains. The differential gene expression (DGE) profiling was performed to investigate the differences in gene expression patterns between diploid and its corresponding autotetraploid by RNA-Sequencing (RNA-Seq). Totally, 483 up-regulated differentially expressed genes (DEGs) and 408 down-regulated DEGs were detected in diploid and autotetraploid radishes, which majorly involved in the pathways of hormones, photosynthesis and stress response. Moreover, the xyloglucan endotransglucosylase/hydrolase (XTH) and pectin methylesterases (PME) family members related to cell enlargement and cell wall construction were found to be enriched in GO enrichment analysis, of which XTH family members enriched in "apoplast" and "cell wall" terms, while PME family members enriched in "cell wall" term. Reverse-transcription quantitative PCR (RT-qPCR) analysis indicated that the expression profile of DEGs were consistent with results from the RNA-Seq analysis. The DEGs involved in cell wall construction and auxin metabolism were predicted to be associated with organs size increase of autotetraploid radishes in the present study. These results could provide valuable information for elucidating the molecular mechanism underlying polyploidization and facilitating further genetic improvements of important traits in radish breeding programs.
PMID: 30560406
Mol Biol Rep , IF:1.402 , 2019 Feb , V46 (1) : P1107-1115 doi: 10.1007/s11033-018-4570-4
High accumulation of tilianin in in-vitro cultures of Agastache mexicana and its potential vasorelaxant action.
Centro de Investigacion en Biotecnologia, Universidad Autonoma del Estado de Morelos, Av. Universidad 1001, Col. Chamilpa, C.P. 62209, Cuernavaca, MOR, Mexico.; Facultad de Farmacia, Universidad Autonoma del Estado de Morelos, Av. Universidad 1001. Col. Chamilpa, C.P. 62209, Cuernavaca, MOR, Mexico.; Centro de Investigacion en Biotecnologia, Universidad Autonoma del Estado de Morelos, Av. Universidad 1001, Col. Chamilpa, C.P. 62209, Cuernavaca, MOR, Mexico. iperea@uaem.mx.
Agastache mexicana has gained importance during the last decade as a natural source of bioactive compounds, mainly due to the antidiabetic, antihyperlipidemic, and vasorelaxant effects derived from its flavonoids, particularly tilianin. The goal of this work was to evaluate the production of tilianin during the in-vitro process of morphogenesis leading to plant regeneration and to investigate the vasorelaxant activity of its methanolic extracts. The cultures were established from nodal segments and leaf explants, inoculated on Murashige and Skoog (MS) media supplemented with various concentrations of benzyl aminopurine (BAP) alone or in combination with 2,4-Dichlorophenoxyacetic acid (2,4-D). Callus inductions were obtained in all treatments from both types of explants, but the presence of auxin was essential. Maximal shoot multiplication and elongation was achieved with 0.1 mg/l 2,4-D and 1.0 mg/l BAP from nodal- segment explants. Shoots were rooted in 75% MS medium and the plantlets were transferred to a greenhouse with 33% average survival. Analysis of tilianin production in methanolic extracts from calli (0.15-2.01 +/- 0.06 mg/g dry weight), shoots (4.45 +/- 0.01 mg/g DW), and whole plants (9.77 +/- 0.02 mg/g DW) derived from in-vitro cultured nodal segments reveals that tilianin accumulation is associated with high cell differentiation and morphogenetic response to the plant-growth regulators. All of the extracts showed strong vasorelaxant activity, as compared to those of wild plant extracts. These results indicate that plant-tissue cultures of A. mexicana possess vast potential as a source of tilianin and other bioactive compounds.
PMID: 30554312
Microscopy (Oxf) , IF:1.394 , 2019 Feb , V68 (1) : P4-12 doi: 10.1093/jmicro/dfy135
Long-term live-cell imaging approaches to study lateral root formation in Arabidopsis thaliana.
Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Japan.
Lateral roots comprise the majority of the branching root system and are important for acquiring nutrients and water from soil in addition to providing anchorage. Lateral roots develop post-embryonically from existing root parts and originate from a subset of specified pericycle cells (lateral root founder cells) located deep inside roots. Small numbers of these specified pericycle cells undergo several rounds of cell division to create a dome-shaped primordium, which eventually organizes a meristem, an essential region for plant growth with active cell division, and emerges from its parental root as a lateral root. Observing cellular and molecular processes for an extended time at various scales are crucial for understanding biological processes during organogenesis. Lateral root formation is an example of the successful application of live-cell imaging approaches to understand various aspects of developmental events in plants, including cell fate determination, cell proliferation, cell-to-cell interaction and cell wall modification. Here I review the recent progress in understanding the molecular mechanisms of lateral root formation and the contribution of live-cell imaging approaches.
PMID: 30476201