Trends Plant Sci , IF:14.416 , 2021 Jan doi: 10.1016/j.tplants.2020.12.017
Auxin Response by the Numbers.
Laboratory of Biochemistry, Wageningen University, Stippeneng 4, 6708WE Wageningen, The Netherlands.; Laboratory of Biochemistry, Wageningen University, Stippeneng 4, 6708WE Wageningen, The Netherlands. Electronic address: dolf.weijers@wur.nl.; Laboratory of Biochemistry, Wageningen University, Stippeneng 4, 6708WE Wageningen, The Netherlands. Electronic address: janwillem.borst@wur.nl.
Auxin is fundamental to the growth and development of land plants, and acts in large part through the control of gene activity. Genetic and biochemical analysis of the nuclear auxin signaling pathway (NAP) has led to the establishment of a generic model for auxin-dependent gene regulation. To understand how this dynamic system operates in living cells, quantitative data are needed. For this, the liverwort Marchantia polymorpha provides a useful model system. Its limited number of NAP components, combined with experimental approaches to determine concentrations, binding affinities, and turnover rates, will enable a new, quantitative view on the mechanisms that allow auxin to control plant growth and development.
PMID: 33500193
Trends Plant Sci , IF:14.416 , 2021 Jan doi: 10.1016/j.tplants.2020.12.006
Shade Avoidance: Expanding the Color and Hormone Palette.
Instituto de Investigaciones Fisiologicas y Ecologicas Vinculadas a la Agricultura (IFEVA), Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Universidad de Buenos Aires, Avenida San Martin 4453, C1417DSE, Buenos Aires, Argentina.; Instituto de Investigaciones Fisiologicas y Ecologicas Vinculadas a la Agricultura (IFEVA), Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Universidad de Buenos Aires, Avenida San Martin 4453, C1417DSE, Buenos Aires, Argentina; Instituto de Investigaciones Biotecnologicas (IIBIO), CONICET, Universidad Nacional de San Martin, B1650HMP Buenos Aires, Argentina. Electronic address: ballare@ifeva.edu.ar.
Major strides have been made over the past decade in elucidating the mechanisms that mediate shade-avoidance responses. The canonical PHYTOCHROME INTERACTING FACTOR (PIF)-auxin pathway that begins with inactivation of phytochrome B (phyB) by a low red:far-red (R:FR) ratio, and that leads to increased elongation, has been thoroughly characterized in arabidopsis (Arabidopsisthaliana) seedlings. Nevertheless, studies in other life stages and plant species have demonstrated the role of other wavelengths, photoreceptors, and hormones in the orchestration of shade-avoidance responses. We highlight recent developments that illustrate how canopy light cues regulate signaling through auxin, gibberellins (GAs), jasmonic acid (JA), salicylic acid (SA), abscisic acid (ABA), and strigolactones (SLs) to modulate key aspects of plant growth, metabolism, and defense.
PMID: 33461868
Mol Plant , IF:12.084 , 2021 Jan , V14 (1) : P61-76 doi: 10.1016/j.molp.2020.11.021
Control of Plant Growth and Defense by Photoreceptors: From Mechanisms to Opportunities in Agriculture.
Plant Ecophysiology, Department of Biology, Utrecht University, Padualaan 8, Utrecht 3584 CH, the Netherlands. Electronic address: r.pierik@uu.nl.; IFEVA, Consejo Nacional de Investigaciones Cientificas y Tecnicas, Universidad de Buenos Aires, Ave. San Martin 4453, C1417DSE, Buenos Aires, Argentina; IIBIO-INTECH, Consejo Nacional de Investigaciones Cientificas y Tecnicas, Universidad Nacional de San Martin, B1650HMP, Buenos Aires, Argentina. Electronic address: ballare@ifeva.edu.ar.
Plants detect and respond to the proximity of competitors using light signals perceived by photoreceptor proteins. A low ratio of red to far-red radiation (R:FR ratio) is a key signal of competition that is sensed by the photoreceptor phytochrome B (phyB). Low R:FR ratios increase the synthesis of growth-related hormones, including auxin and gibberellins, promoting stem elongation and other shade-avoidance responses. Other photoreceptors that help plants to optimize their developmental configuration and resource allocation patterns in the canopy include blue light photoreceptors, such as cryptochromes and phototropins, and UV receptors, such as UVR8. All photoreceptors act by directly or indirectly controlling the activity of two major regulatory nodes for growth and development: the COP1/SPA ubiquitin E3 ligase complex and the PIF transcription factors. phyB is also an important modulator of hormonal pathways that regulate plant defense against herbivores and pathogens, including the jasmonic acid signaling pathway. In this Perspective, we discuss recent advances on the studies of the mechanisms that link photoreceptors with growth and defense. Understanding these mechanisms is important to provide a functional platform for breeding programs aimed at improving plant productivity, stress tolerance, and crop health in species of agronomic interest, and to manipulate the light environments in protected agriculture.
PMID: 33276158
Mol Plant , IF:12.084 , 2021 Jan , V14 (1) : P151-165 doi: 10.1016/j.molp.2020.11.004
Pho-view of Auxin: Reversible Protein Phosphorylation in Auxin Biosynthesis, Transport and Signaling.
Institute of Science and Technology Austria (IST Austria), Am Campus 1, 3400 Klosterneuburg, Austria.; Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna (BOKU), Muthgasse 18, 1190 Wien, Austria.; Institute of Science and Technology Austria (IST Austria), Am Campus 1, 3400 Klosterneuburg, Austria. Electronic address: jiri.friml@ist.ac.at.
The phytohormone auxin plays a central role in shaping plant growth and development. With decades of genetic and biochemical studies, numerous core molecular components and their networks, underlying auxin biosynthesis, transport, and signaling, have been identified. Notably, protein phosphorylation, catalyzed by kinases and oppositely hydrolyzed by phosphatases, has been emerging to be a crucial type of post-translational modification, regulating physiological and developmental auxin output at all levels. In this review, we comprehensively discuss earlier and recent advances in our understanding of genetics, biochemistry, and cell biology of the kinases and phosphatases participating in auxin action. We provide insights into the mechanisms by which reversible protein phosphorylation defines developmental auxin responses, discuss current challenges, and provide our perspectives on future directions involving the integration of the control of protein phosphorylation into the molecular auxin network.
PMID: 33186755
Dev Cell , IF:10.092 , 2021 Jan , V56 (1) : P67-80.e3 doi: 10.1016/j.devcel.2020.12.008
External Mechanical Cues Reveal a Katanin-Independent Mechanism behind Auxin-Mediated Tissue Bending in Plants.
Umea Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 901 87 Umea, Sweden. Electronic address: abaral1986@gmail.com.; Umea Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 901 87 Umea, Sweden; Beijing Advanced Innovation Centre for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China.; Umea Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 901 87 Umea, Sweden.; Centre for Plant Integrative Biology, University of Nottingham, Nottingham LE12 SRD, UK.; Laboratoire de Reproduction et Developpement des Plantes, Universite de Lyon, ENS de Lyon, UCBL, INRAE, CNRS, 46 Allee d'Italie, 69364 Lyon, Cedex 07, France.; FAFU-Joint Centre, Horticulture and Metabolic Biology Centre, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China.; Umea Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 901 87 Umea, Sweden. Electronic address: rishi.bhalerao@slu.se.
Tissue folding is a central building block of plant and animal morphogenesis. In dicotyledonous plants, hypocotyl folds to form hooks after seedling germination that protects their aerial stem cell niche during emergence from soil. Auxin response factors and auxin transport are reported to play a key role in this process. Here, we show that the microtubule-severing enzyme katanin contributes to hook formation. However, by exposing hypocotyls to external mechanical cues mimicking the natural soil environment, we reveal that auxin response factors ARF7/ARF19, auxin influx carriers, and katanin are dispensable for apical hook formation, indicating that these factors primarily play the role of catalyzers of tissue bending in the absence of external mechanical cues. Instead, our results reveal the key roles of the non-canonical TMK-mediated auxin pathway, PIN efflux carriers, and cellulose microfibrils as components of the core pathway behind hook formation in the presence or absence of external mechanical cues.
PMID: 33434527
EMBO J , IF:9.889 , 2021 Jan : Pe106862 doi: 10.15252/embj.2020106862
Modulation of plant root growth by nitrogen source-defined regulation of polar auxin transport.
Institute of Science and Technology (IST) Austria, Klosterneuburg, Austria.; Bioresources Unit, Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria.; Centro de Biotecnologia y Genomica de Plantas (CBGP, UPM-INIA) Universidad Politecnica de Madrid (UPM)-Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria (INIA), Madrid, Spain.; Pontifical Catholic University of Chile, Santiago, Chile.; BPMP, CNRS, INRAE, Institut Agro, Univ Montpellier, Montpellier, France.
Availability of the essential macronutrient nitrogen in soil plays a critical role in plant growth, development, and impacts agricultural productivity. Plants have evolved different strategies for sensing and responding to heterogeneous nitrogen distribution. Modulation of root system architecture, including primary root growth and branching, is among the most essential plant adaptions to ensure adequate nitrogen acquisition. However, the immediate molecular pathways coordinating the adjustment of root growth in response to distinct nitrogen sources, such as nitrate or ammonium, are poorly understood. Here, we show that growth as manifested by cell division and elongation is synchronized by coordinated auxin flux between two adjacent outer tissue layers of the root. This coordination is achieved by nitrate-dependent dephosphorylation of the PIN2 auxin efflux carrier at a previously uncharacterized phosphorylation site, leading to subsequent PIN2 lateralization and thereby regulating auxin flow between adjacent tissues. A dynamic computer model based on our experimental data successfully recapitulates experimental observations. Our study provides mechanistic insights broadening our understanding of root growth mechanisms in dynamic environments.
PMID: 33399250
EMBO J , IF:9.889 , 2021 Jan , V40 (1) : Pe104416 doi: 10.15252/embj.2020104416
Flavonol-mediated stabilization of PIN efflux complexes regulates polar auxin transport.
Institute of Biology II, University of Freiburg, Freiburg, Germany.; Institute of Physiology II, Faculty of Medicine, University of Freiburg, Freiburg, Germany.; Institute for Computer Science, University of Freiburg, Freiburg, Germany.; Department of Agronomy, Food, Natural resources, Animals and Environment-DAFNAE, University of Padova, Padova, Italy.; High-Throughput Binder Selection Facility, Department of Biochemistry, University of Zurich, Zurich, Switzerland.; Sino German Joint Research Center for Agricultural Biology, and State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, China.; Logopharm GmbH, Freiburg, Germany.; Signalling Research Centres BIOSS and CIBSS, Freiburg, Germany.
The transport of auxin controls the rate, direction and localization of plant growth and development. The course of auxin transport is defined by the polar subcellular localization of the PIN proteins, a family of auxin efflux transporters. However, little is known about the composition and regulation of the PIN protein complex. Here, using blue-native PAGE and quantitative mass spectrometry, we identify native PIN core transport units as homo- and heteromers assembled from PIN1, PIN2, PIN3, PIN4 and PIN7 subunits only. Furthermore, we show that endogenous flavonols stabilize PIN dimers to regulate auxin efflux in the same way as does the auxin transport inhibitor 1-naphthylphthalamic acid (NPA). This inhibitory mechanism is counteracted both by the natural auxin indole-3-acetic acid and by phosphomimetic amino acids introduced into the PIN1 cytoplasmic domain. Our results lend mechanistic insights into an endogenous control mechanism which regulates PIN function and opens the way for a deeper understanding of the protein environment and regulation of the polar auxin transport complex.
PMID: 33185277
Curr Biol , IF:9.601 , 2021 Jan doi: 10.1016/j.cub.2020.12.016
Mechanochemical feedback mediates tissue bending required for seedling emergence.
Umea Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 90187 Umea, Sweden. Electronic address: kristoffer.jonsson@slu.se.; Umea Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 90187 Umea, Sweden.; IRBV, Department of Biological Sciences, University of Montreal, 4101 Sherbrooke Est, Montreal H1X 2B2, QC, Canada.; Laboratoire Reproduction et Developpement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, Lyon, France.; Umea Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 90187 Umea, Sweden. Electronic address: rishi.bhalerao@slu.se.
Tissue bending is vital to plant development, as exemplified by apical hook formation during seedling emergence by bending of the hypocotyl. How tissue bending is coordinated during development remains poorly understood, especially in plants where cells are attached via rigid cell walls. Asymmetric distribution of the plant hormone auxin underlies differential cell elongation during apical hook formation. Yet the underlying mechanism remains unclear. Here, we demonstrate spatial correlation between asymmetric auxin distribution, methylesterified homogalacturonan (HG) pectin, and mechanical properties of the epidermal layer of the hypocotyl in Arabidopsis. Genetic and cell biological approaches show that this mechanochemical asymmetry is essential for differential cell elongation. We show that asymmetric auxin distribution underlies differential HG methylesterification, and conversely changes in HG methylesterification impact the auxin response domain. Our results suggest that a positive feedback loop between auxin distribution and HG methylesterification underpins asymmetric cell wall mechanochemical properties to promote tissue bending and seedling emergence.
PMID: 33417884
Curr Biol , IF:9.601 , 2021 Jan , V31 (1) : P228-237.e10 doi: 10.1016/j.cub.2020.10.011
Auxin-Regulated Reversible Inhibition of TMK1 Signaling by MAKR2 Modulates the Dynamics of Root Gravitropism.
Laboratoire Reproduction et Developpement des Plantes, Universite de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, 69342 Lyon, France; Department of Molecular Genetics, Center for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra (Cerdanyola del Valles), 08193 Barcelona, Spain.; Laboratoire Reproduction et Developpement des Plantes, Universite de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, 69342 Lyon, France.; Institute of Science and Technology Austria (IST Austria), Am Campus 1, 3400 Klosterneuburg, Austria.; Center for Plant Systems Biology, VIB, Technologiepark 71, 9052 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium.; Center for Plant Systems Biology, VIB, Technologiepark 71, 9052 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium; Lab of Plant Growth Analysis, Ghent University Global Campus, Songdomunhwa-Ro, 119, Yeonsu-gu, Incheon 21985, Republic of Korea.; Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.; Department of Molecular Genetics, Center for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra (Cerdanyola del Valles), 08193 Barcelona, Spain.; Laboratoire Reproduction et Developpement des Plantes, Universite de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, 69342 Lyon, France. Electronic address: yvon.jaillais@ens-lyon.fr.
Plants are able to orient their growth according to gravity, which ultimately controls both shoot and root architecture.(1) Gravitropism is a dynamic process whereby gravistimulation induces the asymmetric distribution of the plant hormone auxin, leading to asymmetric growth, organ bending, and subsequent reset of auxin distribution back to the original pre-gravistimulation situation.(1-3) Differential auxin accumulation during the gravitropic response depends on the activity of polarly localized PIN-FORMED (PIN) auxin-efflux carriers.(1-4) In particular, the timing of this dynamic response is regulated by PIN2,(5)(,)(6) but the underlying molecular mechanisms are poorly understood. Here, we show that MEMBRANE ASSOCIATED KINASE REGULATOR2 (MAKR2) controls the pace of the root gravitropic response. We found that MAKR2 is required for the PIN2 asymmetry during gravitropism by acting as a negative regulator of the cell-surface signaling mediated by the receptor-like kinase TRANSMEMBRANE KINASE1 (TMK1).(2)(,)(7-10) Furthermore, we show that the MAKR2 inhibitory effect on TMK1 signaling is antagonized by auxin itself, which triggers rapid MAKR2 membrane dissociation in a TMK1-dependent manner. Our findings suggest that the timing of the root gravitropic response is orchestrated by the reversible inhibition of the TMK1 signaling pathway at the cell surface.
PMID: 33157019
Curr Biol , IF:9.601 , 2021 Jan , V31 (1) : P220-227.e5 doi: 10.1016/j.cub.2020.10.008
CLAVATA Signaling Ensures Reproductive Development in Plants across Thermal Environments.
Department of Biology, University of North Carolina at Chapel Hill, 250 Bell Tower Drive, Chapel Hill, NC 27599, USA.; Department of Biology, University of North Carolina at Chapel Hill, 250 Bell Tower Drive, Chapel Hill, NC 27599, USA; Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. Electronic address: zackn@email.unc.edu.
The ability to thrive in diverse environments requires that species maintain development and reproduction despite dynamic conditions. Many developmental processes are stabilized through robust signaling pathways that cooperatively ensure proper development.(1) During reproduction, plants like Arabidopsis thaliana continuously generate flowers on growing indeterminate inflorescences.(2) Flower primordia initiation and outgrowth depends on the hormone auxin and is robust across diverse environments.(3-6) Here, we show that reproductive development under different thermal conditions requires the integration of multiple pathways regulating auxin-dependent flower production. In colder/ambient temperatures, the receptor complex CLAVATA2/CORYNE (CLV2/CRN) is necessary for continuous flower outgrowth during inflorescence development. CLV2/CRN signaling is independent of CLAVATA1 (CLV1)-related receptor signaling but involves the CLAVATA3 INSENSITIVE RECEPTOR KINASE (CIK) family co-receptors, with higher order cik mutant combinations phenocopying clv2/crn flower outgrowth defects. Developing crn inflorescences display reduced auxin signaling, and restoration of auxin biosynthesis is sufficient to restore flower outgrowth in colder and ambient temperatures. In contrast, at higher temperatures, both clv2/crn signaling and heat-induced auxin biosynthesis via YUCCA family genes are synergistically required to maintain flower development. Our work reveals a novel mechanism integrating peptide hormone and auxin signaling in the regulation of flower development across diverse thermal environments.
PMID: 33157018
Proc Natl Acad Sci U S A , IF:9.412 , 2021 Jan , V118 (1) doi: 10.1073/pnas.2020857118
Naphthylphthalamic acid associates with and inhibits PIN auxin transporters.
Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences (BOKU), 1190 Vienna, Austria; melinda.abas@boku.ac.at ulrich.hammes@wzw.tum.de.; Plant Systems Biology, School of Life Sciences Weihenstephan, Technical University of Munich, 85354 Freising, Germany.; Department of Chemistry, University of Natural Resources and Life Sciences (BOKU), 1190 Vienna, Austria.; Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria.; Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences (BOKU), 1190 Vienna, Austria.; Plant Systems Biology, School of Life Sciences Weihenstephan, Technical University of Munich, 85354 Freising, Germany; melinda.abas@boku.ac.at ulrich.hammes@wzw.tum.de.
N-1-naphthylphthalamic acid (NPA) is a key inhibitor of directional (polar) transport of the hormone auxin in plants. For decades, it has been a pivotal tool in elucidating the unique polar auxin transport-based processes underlying plant growth and development. Its exact mode of action has long been sought after and is still being debated, with prevailing mechanistic schemes describing only indirect connections between NPA and the main transporters responsible for directional transport, namely PIN auxin exporters. Here we present data supporting a model in which NPA associates with PINs in a more direct manner than hitherto postulated. We show that NPA inhibits PIN activity in a heterologous oocyte system and that expression of NPA-sensitive PINs in plant, yeast, and oocyte membranes leads to specific saturable NPA binding. We thus propose that PINs are a bona fide NPA target. This offers a straightforward molecular basis for NPA inhibition of PIN-dependent auxin transport and a logical parsimonious explanation for the known physiological effects of NPA on plant growth, as well as an alternative hypothesis to interpret past and future results. We also introduce PIN dimerization and describe an effect of NPA on this, suggesting that NPA binding could be exploited to gain insights into structural aspects of PINs related to their transport mechanism.
PMID: 33443187
ISME J , IF:9.18 , 2021 Jan doi: 10.1038/s41396-020-00866-x
Functional mutants of Azospirillum brasilense elicit beneficial physiological and metabolic responses in Zea mays contributing to increased host iron assimilation.
Missouri Research Reactor Center, University of Missouri, Columbia, MO, 65211, USA.; Chemistry Department, University of Missouri, Columbia, MO, 65211, USA.; Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA.; Department of Chemical Engineering, University of Missouri, Columbia, MO, 65211, USA.; Burns & McDonnell, Inc. 425 S, Woods Mill Rd., Chesterfield, MO, USA, 63017.; Idaho State Police 5255 S. 5th Ave, Pocatello, ID, 83204, USA.; Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA.; School of Natural Resources, University of Missouri, Columbia, MO, 65211, USA.; Missouri Research Reactor Center, University of Missouri, Columbia, MO, 65211, USA. ferrierir@missouri.edu.; Chemistry Department, University of Missouri, Columbia, MO, 65211, USA. ferrierir@missouri.edu.; Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA. ferrierir@missouri.edu.; Interdisciplinary Plant Group, University of Missouri, Columbia, MO, 65211, USA. ferrierir@missouri.edu.
Iron (Fe), an essential element for plant growth, is abundant in soil but with low bioavailability. Thus, plants developed specialized mechanisms to sequester the element. Beneficial microbes have recently become a favored method to promote plant growth through increased uptake of essential micronutrients, like Fe, yet little is known of their mechanisms of action. Functional mutants of the epiphytic bacterium Azospirillum brasilense, a prolific grass-root colonizer, were used to examine mechanisms for promoting iron uptake in Zea mays. Mutants included HM053, FP10, and ipdC, which have varying capacities for biological nitrogen fixation and production of the plant hormone auxin. Using radioactive iron-59 tracing and inductively coupled plasma mass spectrometry, we documented significant differences in host uptake of Fe(2+/3+) correlating with mutant biological function. Radioactive carbon-11, administered to plants as (11)CO2, provided insights into shifts in host usage of 'new' carbon resources in the presence of these beneficial microbes. Of the mutants examined, HM053 exhibited the greatest influence on host Fe uptake with increased plant allocation of (11)C-resources to roots where they were transformed and exuded as (11)C-acidic substrates to aid in Fe-chelation, and increased C-11 partitioning into citric acid, nicotianamine and histidine to aid in the in situ translocation of Fe once assimilated.
PMID: 33408368
New Phytol , IF:8.512 , 2021 Jan doi: 10.1111/nph.17205
The Arabidopsis R-SNARE VAMP714 is essential for polarization of PIN proteins and auxin responses.
Department of Biosciences, Durham University, South Road, Durham, DH1 3LE, UK.; Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China.
The plant hormone auxin and its directional intercellular transport plays a major role in diverse aspects of plant growth and development. The establishment of auxin gradients requires the asymmetric distribution of members of the auxin efflux carrier PIN-FORMED (PIN) protein family to the plasma membrane. An endocytic pathway regulates the recycling of PIN proteins between the plasma membrane and endosomes, providing a mechanism for dynamic localization. N-ethylmaleimide-sensitive factor adaptor protein receptors (SNAP receptors, SNAREs) mediate fusion between vesicles and target membranes and are classed as Q- or R-SNAREs based on their sequence. We analysed gain- and loss-of-function mutants, dominant negative transgenics and localization of the Arabidopsis R-SNARE VAMP714 protein to understand its function. We demonstrate that VAMP714 is essential for the insertion of PINs into the plasma membrane, for polar auxin transport, root gravitropism and morphogenesis. VAMP714 gene expression is upregulated by auxin, and the VAMP714 protein co-localizes with ER and Golgi vesicles and with PIN proteins at the plasma membrane. It is proposed that VAMP714 mediates the delivery of PIN-carrying vesicles to the plasma membrane, and that this forms part of a positive regulatory loop in which auxin activates a VAMP714-dependent PIN/auxin transport system to control development.
PMID: 33454983
New Phytol , IF:8.512 , 2021 Jan doi: 10.1111/nph.17183
New fluorescent auxin probes visualize tissue-specific and subcellular distributions of auxin in Arabidopsis.
Laboratory of Growth Regulators, Faculty of Science, Palacky University and Institute of Experimental Botany, The Czech Academy of Sciences, Slechtitelu 27, CZ-78371, Olomouc, Czech Republic.; Department of Forest Genetics and Plant Physiology, Umea Plant Science Centre, Swedish University of Agricultural Sciences, SE-90183, Umea, Sweden.; School of Life Sciences, The University of Warwick, Coventry, CV4 7AL, United Kingdom.; Centre for Plant Sciences, University of Leeds, Leeds, LS2 9JT, United Kingdom.; Department of Chemical Biology, Faculty of Science, Palacky University, Slechtitelu 27, CZ-78371, Olomouc, Czech Republic.
In a world that will rely increasingly on efficient plant growth for sufficient food, it is important to learn about natural mechanisms of phytohormone action. In this work, the introduction of a fluorophore to an auxin molecule represents a sensitive and non-invasive method to directly visualize auxin localization with high spatiotemporal resolution. The state-of-the-art multidisciplinary approaches of genetic and chemical biology analysis together with live cell imaging, liquid chromatography-mass spectrometry (LC-MS) and surface plasmon resonance (SPR) methods were employed for the characterization of auxin-related biological activity, distribution and stability of the presented compounds in Arabidopsis thaliana. Despite partial metabolization in vivo, these fluorescent auxins display an uneven and dynamic distribution leading to the formation of fluorescence maxima in tissues known to concentrate natural auxin, such as the concave side of the apical hook. Importantly, their distribution is altered in response to different exogenous stimuli in both roots and shoots. Moreover, we characterized the subcellular localization of the fluorescent auxin analogues as being present in the endoplasmic reticulum and endosomes. Our work provides powerful tools to visualize auxin distribution within different plant tissues at cellular or subcellular levels and in response to internal and environmental stimuli during plant development.
PMID: 33438224
New Phytol , IF:8.512 , 2021 Jan doi: 10.1111/nph.17180
Root growth responses to mechanical impedance are regulated by a network of ROS, ethylene and auxin signalling in Arabidopsis.
Department of Biosciences, Durham University, Durham, DH1 3LE, UK.; Department of Plant Systems Physiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands.; Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore, 117543, Singapore.
The growth and development of root systems is influenced by mechanical properties of the substrate in which the plants grow. Mechanical impedance, such as by compacted soil, can reduce root elongation and limit crop productivity. To understand better the mechanisms involved in plant root responses to mechanical impedance stress, we investigated changes in the root transcriptome and hormone signalling responses of Arabidopsis to artificial root barrier systems in vitro. We demonstrate that upon encountering a barrier, reduced Arabidopsis root growth and a characteristic 'step-like' growth pattern is due to a reduction in cell elongation associated with changes in signalling gene expression. Data from RNA-sequencing combined with reporter line and mutant studies identified essential roles for reactive oxygen species, ethylene and auxin signalling during the barrier response. We propose a model in which early responses to mechanical impedance include reactive oxygen signalling integrated with ethylene and auxin responses to mediate root growth changes. Inhibition of ethylene responses allows improved growth in response to root impedance, an observation that may inform future crop breeding programmes.
PMID: 33428776
Plant Biotechnol J , IF:8.154 , 2021 Jan doi: 10.1111/pbi.13549
High-Spatiotemporal-Resolution Transcriptomes Provide Insights into Fruit Development and Ripening in Citrus sinensis.
Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, PR China.
Citrus fruit has a unique structure with soft leathery peel and pulp containing vascular bundles and several segments with many juice sacs. The function and morphology of each fruit tissue are different. Therefore, analysis at the organ-wide or mixed-tissue level inevitably obscures many tissue-specific phenomena. High-throughput RNA sequencing was used to profile Citrus sinensis fruit development based on four fruit tissue types and six development stages from young fruits to ripe fruits. Using a coexpression network analysis, modules of coexpressed genes and hub genes of tissue-specific networks were identified. Of particular importance is the discovery of the regulatory network of phytohormones during citrus fruit development and ripening. A model was proposed to illustrate how ABF2 mediates the ABA signalling involved in sucrose transport, chlorophyll degradation, auxin homeostasis, carotenoid and ABA biosynthesis, and cell wall metabolism during citrus fruit development. Moreover, we depicted the detailed spatiotemporal expression patterns of the genes involved in sucrose and citric acid metabolism in citrus fruit and identified several key genes that may play crucial roles in sucrose and citric acid accumulation in the juice sac, such as SWEET15 and CsPH8. The high spatial and temporal resolution of our data provide important insights into the molecular networks underlying citrus fruit development and ripening.
PMID: 33471410
Cold Spring Harb Perspect Biol , IF:7.64 , 2021 Jan doi: 10.1101/cshperspect.a040030
Auxin-Environment Integration in Growth Responses to Forage for Resources.
Universidad de Buenos Aires, Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Instituto de Investigaciones Fisiologicas y Ecologicas Vinculadas a la Agricultura (IFEVA), Facultad de Agronomia, Buenos Aires 1417, Argentina.; Fundacion Instituto Leloir and IIBBA-CONICET, Buenos Aires C1405BWE, Argentina.; Centro de Biotecnologia Vegetal, Facultad de Ciencias de la Vida, Universidad Andres Bello and Millennium Institute for Integrative Biology (iBio), Santiago 8370146, Chile.
Plant fitness depends on the adequate morphological adjustment to the prevailing conditions of the environment. Therefore, plants sense environmental cues through their life cycle, including the presence of full darkness, light, or shade, the range of ambient temperatures, the direction of light and gravity vectors, and the presence of water and mineral nutrients (such as nitrate and phosphate) in the soil. The environmental information impinges on different aspects of the auxin system such as auxin synthesis, degradation, transport, perception, and downstream transcriptional regulation to modulate organ growth. Although a single environmental cue can affect several of these points, the relative impacts differ significantly among the various growth processes and cues. While stability in the generation of precise auxin gradients serves to guide the basic developmental pattern, dynamic changes in the auxin system fine-tune body shape to optimize the capture of environmental resources.
PMID: 33431585
Cold Spring Harb Perspect Biol , IF:7.64 , 2021 Jan doi: 10.1101/cshperspect.a040055
Auxin Biology in Bryophyta: A Simple Platform with Versatile Functions.
Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan.
Bryophytes, including liverworts, mosses, and hornworts, are gametophyte-dominant land plants that are derived from a common ancestor and underwent independent evolution from the sporophyte-dominant vascular plants since their divergence. The plant hormone auxin has been shown to play pleiotropic roles in the haploid bodies of bryophytes. Pharmacological and chemical studies identified conserved auxin molecules, their inactivated forms, and auxin transport in bryophyte tissues. Recent genomic and molecular biological studies show deep conservation of components and their functions in auxin biosynthesis, inactivation, transport, and signaling in land plants. Low genetic redundancy in model bryophytes enable unique assays, which are elucidating the design principles of the auxin signaling pathway. In this article, the physiological roles of auxin and regulatory mechanisms of gene expression and development by auxin in Bryophyta are reviewed.
PMID: 33431584
Cold Spring Harb Perspect Biol , IF:7.64 , 2021 Jan doi: 10.1101/cshperspect.a039917
Noncanonical Auxin Signaling.
Crop Genetics Department, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom.
Auxin influences all aspects of plant growth and development and exerts its function at scales ranging from the subcellular to the whole-organism level. A canonical mechanism for auxin signaling has been elucidated, which is based on derepression of downstream genes via ubiquitin-mediated degradation of transcriptional repressors. While the combinatorial nature of this canonical pathway provides great potential for specificity in the auxin response, alternative noncanonical signaling pathways required to mediate certain processes have been identified. One such pathway affects gene regulation in a manner that is reminiscent of mechanisms employed in animal hormone signaling, while another triggers transcriptional changes through auxin perception at the plasma membrane and the stabilization of transcriptional repressors. In some cases, the exact perception mechanisms and the nature of the receptors involved are yet to be revealed. In this review, we describe and discuss current knowledge on noncanonical auxin signaling and highlight unresolved questions surrounding auxin biology.
PMID: 33431583
Cold Spring Harb Perspect Biol , IF:7.64 , 2021 Jan doi: 10.1101/cshperspect.a039958
Of Cells, Strands, and Networks: Auxin and the Patterned Formation of the Vascular System.
Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada.
Throughout plant development, vascular cells continually form from within a population of seemingly equivalent cells. Vascular cells connect end to end to form continuous strands, and vascular strands connect at both or either end to form networks of exquisite complexity and mesmerizing beauty. Here we argue that experimental evidence gained over the past few decades implicates the plant hormone auxin-its production, transport, perception, and response-in all the steps that lead to the patterned formation of the plant vascular system, from the formation of vascular cells to their connection into vascular networks. We emphasize the organizing principles of the cell- and tissue-patterning process, rather than its molecular subtleties. In the picture that emerges, cells compete for an auxin-dependent, cell-polarizing signal; positive feedback between cell polarization and cell-to-cell movement of the polarizing signal leads to gradual selection of cell files; and selected cell files differentiate into vascular strands that drain the polarizing signal from the neighboring cells. Although the logic of the patterning process has become increasingly clear, the molecular details remain blurry; the future challenge will be to bring them into razor-sharp focus.
PMID: 33431582
Cold Spring Harb Perspect Biol , IF:7.64 , 2021 Jan doi: 10.1101/cshperspect.a040105
Chemical Biology in Auxin Research.
Department of Biochemistry, Okayama University of Science, Okayama City 700-0005, Japan hayashi@dbc.ous.ac.jp.
Molecular genetic and structural studies have revealed the mechanisms of fundamental components of key auxin regulatory pathways consisting of auxin biosynthesis, transport, and signaling. Chemical biology methods applied in auxin research have been greatly expanded through the understanding of auxin regulatory pathways. Many small-molecule modulators of auxin metabolism, transport, and signaling have been generated on the basis of the outcomes of genetic and structural studies on auxin regulatory pathways. These chemical modulators are now widely used as essential tools for dissecting auxin biology in diverse plants. This review covers the structures, primary targets, modes of action, and applications of chemical tools in auxin biosynthesis, transport, and signaling.
PMID: 33431581
Cold Spring Harb Perspect Biol , IF:7.64 , 2021 Jan doi: 10.1101/cshperspect.a039966
An Essential Function for Auxin in Embryo Development.
Mendel Centre for Genomics and Proteomics of Plants Systems, CEITEC MU - Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic.
Embryogenesis in seed plants is the process during which a single cell develops into a mature multicellular embryo that encloses all the modules and primary patterns necessary to build the architecture of the new plant after germination. This process involves a series of cell divisions and coordinated cell fate determinations resulting in the formation of an embryonic pattern with a shoot-root axis and cotyledon(s). The phytohormone auxin profoundly controls pattern formation during embryogenesis. Auxin functions in the embryo through its maxima/minima distribution, which acts as an instructive signal for tissue specification and organ initiation. In this review, we describe how disruptions of auxin biosynthesis, transport, and response severely affect embryo development. Also, the mechanism of auxin action in the development of the shoot-root axis and the three-tissue system is discussed with recent findings. Biological tools that can be implemented to study the auxin function during embryo development are presented, as they may be of interest to the reader.
PMID: 33431580
Cold Spring Harb Perspect Biol , IF:7.64 , 2021 Jan doi: 10.1101/cshperspect.a039867
Auxin Metabolism in Plants.
Umea Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-901 83 Umea, Sweden.
The major natural auxin in plants, indole-3-acetic acid (IAA), orchestrates a plethora of developmental responses that largely depend on the formation of auxin concentration gradients within plant tissues. Together with inter- and intracellular transport, IAA metabolism-which comprises biosynthesis, conjugation, and degradation-modulates auxin gradients and is therefore critical for plant growth. It is now very well established that IAA is mainly produced from Trp and that the IPyA pathway is a major and universally conserved biosynthetic route in plants, while other redundant pathways operate in parallel. Recent findings have shown that metabolic inactivation of IAA is also redundantly performed by oxidation and conjugation processes. An exquisite spatiotemporal expression of the genes for auxin synthesis and inactivation have been shown to drive several plant developmental processes. Moreover, a group of transcription factors and epigenetic regulators controlling the expression of auxin metabolic genes have been identified in past years, which are illuminating the road to understanding the molecular mechanisms behind the coordinated responses of local auxin metabolism to specific cues. Besides transcriptional regulation, subcellular compartmentalization of the IAA metabolism and posttranslational modifications of the metabolic enzymes are emerging as important contributors to IAA homeostasis. In this review, we summarize the current knowledge on (1) the pathways for IAA biosynthesis and inactivation in plants, (2) the influence of spatiotemporally regulated IAA metabolism on auxin-mediated responses, and (3) the regulatory mechanisms that modulate IAA levels in response to external and internal cues during plant development.
PMID: 33431579
Plant Cell Environ , IF:6.362 , 2021 Jan doi: 10.1111/pce.14001
An Auxin-Mediated Regulatory Framework for Wound-Induced Adventitious Root Formation in Tomato Shoot Explants.
Instituto de Bioingenieria, Universidad Miguel Hernandez, Elche, Spain.; Instituto Murciano de Investigacion y Desarrollo Agrario y Alimentario (IMIDA), La Alberca, Spain.; Departamento de Biologia Vegetal, Universidad de Murcia, Murcia, Spain.
Adventitious roots (ARs) are produced from non-root tissues in response to different environmental signals, such as abiotic stresses, or after wounding, in a complex developmental process that requires hormonal crosstalk. Here, we characterized AR formation in young seedlings of Solanum lycopersicum cv. 'Micro-Tom' after whole root excision by means of physiological, genetic and molecular approaches. We found that a regulated basipetal auxin transport from the shoot and local auxin biosynthesis triggered by wounding are both required for the re-establishment of internal auxin gradients within the vasculature. This promotes cell proliferation at the distal cambium near the wound in well-defined positions of the basal hypocotyl and during a narrow developmental window. In addition, a pre-established pattern of differential auxin responses along the apical-basal axis of the hypocotyl and an as of yet unknown cell-autonomous inhibitory pathway contribute to the temporal and spatial patterning of the newly formed ARs on isolated hypocotyl explants. Our work provides an experimental outline for the dissection of wound-induced AR formation in tomato, a species that is suitable for molecular identification of gene regulatory networks via forward and reverse genetics approaches. This article is protected by copyright. All rights reserved.
PMID: 33464573
J Exp Bot , IF:5.908 , 2021 Jan doi: 10.1093/jxb/erab034
Roles of various Phytohormones and Their Cross-talk in Regulating Stomatal Development and Patterning.
School of Life Sciences, Southwest University, Chongqing, China.; College of Life Sciences, South China Agricultural University, Guangzhou, China.; College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China.
Phytohormones play important roles in regulating various aspects of plant growth and development as well as in biotic and abiotic stress responses. Stomata are openings on the surface of land plants that control gas exchange with their environment. Accumulating evidence shows that various phytohormones, including abscisic acid, jasmonic acid, brassinosteroids, auxin, cytokinin, ethylene and gibberellic acid, play many roles in regulating stomatal development and patterning, and that the cotyledons/leaves and hypocotyls/stems of Arabidopsis exhibit differential responsiveness to phytohormones. In this review, we first discuss the shared regulatory mechanisms of stomatal development and patterning in Arabidopsis cotyledons and hypocotyls and those that are distinct, and then summarize current knowledge of how distinct hormonal signaling circuits are integrated into the core stomatal development pathways and how different phytohormones crosstalk to tailor stomatal density and spacing patterns. Knowledge obtained from Arabidopsis may pave the way for future research to elucidate the effects of phytohormones in regulating stomatal development and patterning in cereal grasses, for the purpose of increasing crop adaptive responses.
PMID: 33512461
J Exp Bot , IF:5.908 , 2021 Jan doi: 10.1093/jxb/erab025
Coordination between MIDASIN 1-mediated ribosome biogenesis and auxin for modulating plant development.
Biotechnology Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, PR China.; College of Life Science, Shandong University, Qingdao, PR China.; College of Life Sciences, Shandong Normal University, Jinan, PR China.
Ribosomes are required for plant growth and development, and ribosome-biogenesis-deficiency mutants generally display auxin-related phenotypes. Although the relationship between ribosome dysfunction and auxin has been raised, many aspects of this subject remain to be understood. We previously reported that MIDASIN 1 (MDN1) is an essential pre-60S ribosome biogenesis factor (RBF) in Arabidopsis. In this study, we further characterized the aberrant auxin-related phenotypes of mdn1-1, a weak mutant allele of MDN1. Auxin response is disturbed in both shoots and roots of mdn1-1 indicated by the DR5:GUS reporter. Through combining transcriptomic profiling analysis and reporter detection, we found that expression of genes involved in auxin biosynthesis, transport, and signaling is changed. Furthermore, the MDN1 deficiency affects both the posttranscriptional regulation and protein distribution of PIN2 (an auxin efflux facilitator) in mdn1-1 roots. These results indicate that MDN1 is required for maintaining the auxin system. More interestingly, MDN1 is an auxin-responsive gene, and its promoter can be targeted by multiple AUXIN RESPONSE FACTORs (ARFs), including ARF7 and ARF19, in vitro. Indeed, in arf7 arf19, the auxin sensitivity of MDN1 expression is significantly reduced. Together, our results reveal a coordination mechanism between the auxin system with the MDN1-dependent ribosome biogenesis for regulating plant development.
PMID: 33476386
J Exp Bot , IF:5.908 , 2021 Jan doi: 10.1093/jxb/erab009
The production of auxin by dying cells.
20 Willow Road, London, UK.
In this review, I discuss the possibility that dying cells produce much of the auxin in vascular plants. The natural auxin, indole-3-acetic acid (IAA), is derived from tryptophan by a two-step pathway via indole pyruvic acid. The first enzymes in the pathway, tryptophan aminotransferases, have a low affinity for tryptophan and break it down only when tryptophan levels rise far above normal intracellular concentrations. Such increases occur when tryptophan is released from proteins by hydrolytic enzymes as cells autolyse and die. Many sites of auxin production are in and around dying cells: in differentiating tracheary elements; in root cap cells; in nutritive tissues that break down in developing flowers and seeds; in senescent leaves; and in wounds. Living cells also produce auxin, such as those transformed genetically by the crown gall pathogen. IAA may first have served as an exogenous indicator of the presence of nutrient-rich decomposing organic matter, stimulating the production of rhizoids in bryophytes. As cell death was internalized in bryophytes and in vascular plants, IAA may have taken on a new role as an endogenous hormone.
PMID: 33460445
J Exp Bot , IF:5.908 , 2021 Jan , V72 (1) : P70-91 doi: 10.1093/jxb/eraa479
Regulation of glucosinolate biosynthesis.
Institute for Plant Sciences and Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany.
Glucosinolates are secondary defense metabolites produced by plants of the order Brassicales, which includes the model species Arabidopsis and many crop species. In the past 13 years, the regulation of glucosinolate synthesis in plants has been intensively studied, with recent research revealing complex molecular mechanisms that connect glucosinolate production with responses to other central pathways. In this review, we discuss how the regulation of glucosinolate biosynthesis is ecologically relevant for plants, how it is controlled by transcription factors, and how this transcriptional machinery interacts with hormonal, environmental, and epigenetic mechanisms. We present the central players in glucosinolate regulation, MYB and basic helix-loop-helix transcription factors, as well as the plant hormone jasmonate, which together with other hormones and environmental signals allow the coordinated and rapid regulation of glucosinolate genes. Furthermore, we highlight the regulatory connections between glucosinolates, auxin, and sulfur metabolism and discuss emerging insights and open questions on the regulation of glucosinolate biosynthesis.
PMID: 33313802
Development , IF:5.611 , 2021 Jan , V148 (1) doi: 10.1242/dev.190033
Conserved LBL1-ta-siRNA and miR165/166-RLD1/2 modules regulate root development in maize.
National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India.; Centre of Experimental Medicine and Surgery, Institute of Medical Sciences, Banaras Hindu University, Varanasi 221005, India.; Department of Botany and Forestry, Vidyasagar University, Midnapore, WB 721104, India.; National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India aksarkar@nipgr.ac.in.
Root system architecture and anatomy of monocotyledonous maize is significantly different from dicotyledonous model Arabidopsis The molecular role of non-coding RNA (ncRNA) is poorly understood in maize root development. Here, we address the role of LEAFBLADELESS1 (LBL1), a component of maize trans-acting short-interfering RNA (ta-siRNA), in maize root development. We report that root growth, anatomical patterning, and the number of lateral roots (LRs), monocot-specific crown roots (CRs) and seminal roots (SRs) are significantly affected in lbl1-rgd1 mutant, which is defective in production of ta-siRNA, including tasiR-ARF that targets AUXIN RESPONSE FACTOR3 (ARF3) in maize. Altered accumulation and distribution of auxin, due to differential expression of auxin biosynthesis and transporter genes, created an imbalance in auxin signalling. Altered expression of microRNA165/166 (miR165/166) and its targets, ROLLED1 and ROLLED2 (RLD1/2), contributed to the changes in lbl1-rgd1 root growth and vascular patterning, as was evident by the altered root phenotype of Rld1-O semi-dominant mutant. Thus, LBL1/ta-siRNA module regulates root development, possibly by affecting auxin distribution and signalling, in crosstalk with miR165/166-RLD1/2 module. We further show that ZmLBL1 and its Arabidopsis homologue AtSGS3 proteins are functionally conserved.
PMID: 33168582
Cell Biosci , IF:5.026 , 2021 Jan , V11 (1) : P17 doi: 10.1186/s13578-021-00528-1
Comparative transcriptome analysis revealed differential gene expression in multiple signaling pathways at flowering in polyploid Brassica rapa.
School of Life Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China.; Henan International Joint Laboratory of Crop Gene Resources and Improvements, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China.; Institute of Horticultural Research, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, China.; School of Life Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China. fangwei@zzu.edu.cn.; Henan International Joint Laboratory of Crop Gene Resources and Improvements, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China. fangwei@zzu.edu.cn.; Henan International Joint Laboratory of Crop Gene Resources and Improvements, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China. tianbm@zzu.edu.cn.
BACKGROUND: Polyploidy is widespread in angiosperms and has a significant impact on plant evolution, diversity, and breeding program. However, the changes in the flower development regulatory mechanism in autotetraploid plants remains relatively limited. In this study, RNA-seq analysis was used to investigate changes in signaling pathways at flowering in autotetraploid Brassica rapa. RESULTS: The study findings showed that the key genes such as CO, CRY2, and FT which promotes floral formation were down-regulated, whereas floral transition genes FPF1 and FD were up-regulated in autotetraploid B. rapa. The data also demonstrated that the positive regulators GA1 and ELA1 in the gibberellin's biosynthesis pathway were negatively regulated by polyploidy in B. rapa. Furthermore, transcriptional factors (TFs) associated with flower development were significantly differentially expressed including the up-regulated CIB1 and AGL18, and the down-regulated AGL15 genes, and by working together such genes affected the expression of the down-stream flowering regulator FLOWERING LOCUS T in polyploid B. rapa. Compared with that in diploids autotetrapoid plants consist of differential expression within the signaling transduction pathway, with 13 TIFY gens up-regulated and 17 genes related to auxin pathway down-regulated. CONCLUSION: Therefore, polyploidy is more likely to integrate multiple signaling pathways to influence flowering in B. rapa after polyploidization. In general, the present results shed new light on our global understanding of flowering regulation in polyploid plants during breeding program.
PMID: 33436051
J Integr Plant Biol , IF:4.885 , 2021 Jan doi: 10.1111/jipb.13073
Functional assembly of root-associated microbial consortia improves nutrient efficiency and yield in soybean.
Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
Root-associated microbes are critical for plant growth and nutrient acquisition. However, scant information exists on optimizing communities of beneficial root-associated microbes or the mechanisms underlying their interactions with host plants. In this report, we demonstrate that root-associated microbes are critical influencers of host plant growth and nutrient acquisition. Three synthetic communities (SynComs) were constructed based on functional screening of 1893 microbial strains isolated from root-associated compartments of soybean plants. Functionally assemblage of SynComs promoted significant plant growth and nutrient acquisition under both N/P nutrient deficiency and sufficiency conditions. Field trials further revealed that application of SynComs stably and significantly promoted plant growth, facilitated N and P acquisition, and subsequently increased soybean yield. Among the tested communities, SynCom 1 exhibited the greatest promotion effect, with yield increases of up to 36.1% observed in two field sites. Further RNA-seq implied that SynCom application systemically regulates N and P signaling networks at the transcriptional level, which leads to increased representation of important growth pathways, especially those related to auxin responses. Overall, this study details a promising strategy for constructing SynComs based on functional screening, which are capable of enhancing nutrient acquisition and crop yield through the activities of beneficial root-associated microbes. This article is protected by copyright. All rights reserved.
PMID: 33491865
Int J Mol Sci , IF:4.556 , 2021 Jan , V22 (2) doi: 10.3390/ijms22020975
The Protein Phosphatase PP2A Plays Multiple Roles in Plant Development by Regulation of Vesicle Traffic-Facts and Questions.
Department of Botany, Faculty of Science and Technology, University of Debrecen, H-4032 Debrecen, Hungary.
The protein phosphatase PP2A is essential for the control of integrated eukaryotic cell functioning. Several cellular and developmental events, e.g., plant growth regulator (PGR) mediated signaling pathways are regulated by reversible phosphorylation of vesicle traffic proteins. Reviewing present knowledge on the relevant role of PP2A is timely. We discuss three aspects: (1) PP2A regulates microtubule-mediated vesicle delivery during cell plate assembly. PP2A dephosphorylates members of the microtubule associated protein family MAP65, promoting their binding to microtubules. Regulation of phosphatase activity leads to changes in microtubule organization, which affects vesicle traffic towards cell plate and vesicle fusion to build the new cell wall between dividing cells. (2) PP2A-mediated inhibition of target of rapamycin complex (TORC) dependent signaling pathways contributes to autophagy and this has possible connections to the brassinosteroid signaling pathway. (3) Transcytosis of vesicles transporting PIN auxin efflux carriers. PP2A regulates vesicle localization and recycling of PINs related to GNOM (a GTP-GDP exchange factor) mediated pathways. The proper intracellular traffic of PINs is essential for auxin distribution in the plant body, thus in whole plant development. Overall, PP2A has essential roles in membrane interactions of plant cell and it is crucial for plant development and stress responses.
PMID: 33478110
Int J Mol Sci , IF:4.556 , 2021 Jan , V22 (2) doi: 10.3390/ijms22020898
Transcriptome Analysis Revealed GhWOX4 Intercedes Myriad Regulatory Pathways to Modulate Drought Tolerance and Vascular Growth in Cotton.
State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.; Institute of Cotton Research, Henan Normal University Research Base of State Key Laboratory of Cotton Biology, Xinxiang 453000, China.
Cotton is a paramount cash crop around the globe. Among all abiotic stresses, drought is a leading cause of cotton growth and yield loss. However, the molecular link between drought stress and vascular growth and development is relatively uncharted. Here, we validated a crucial role of GhWOX4, a transcription factor, modulating drought stress with that of vasculature growth in cotton. Knock-down of GhWOX4 decreased the stem width and severely compromised vascular growth and drought tolerance. Conversely, ectopic expression of GhWOX4 in Arabidopsis enhanced the tolerance to drought stress. Comparative RNAseq analysis revealed auxin responsive protein (AUX/IAA), abscisic acid (ABA), and ethylene were significantly induced. Additionally, MYC-bHLH, WRKY, MYB, homeodomain, and heat-shock transcription factors (HSF) were differentially expressed in control plants as compared to GhWOX4-silenced plants. The promotor zone of GhWOX4 was found congested with plant growth, light, and stress response related cis-elements. differentially expressed genes (DEGs) related to stress, water deprivation, and desiccation response were repressed in drought treated GhWOX4-virus-induced gene silencing (VIGS) plants as compared to control. Gene ontology (GO) functions related to cell proliferation, light response, fluid transport, and flavonoid biosynthesis were over-induced in TRV: 156-0 h/TRV: 156-1 h (control) in comparison to TRV: VIGS-0 h/TRV: VIGS-1 h (GhWOX4-silenced) plants. This study improves our context for elucidating the pivotal role of GhWOX4 transcription factors (TF), which mediates drought tolerance, plays a decisive role in plant growth and development, and is likely involved in different regulatory pathways in cotton.
PMID: 33477464
Int J Mol Sci , IF:4.556 , 2021 Jan , V22 (1) doi: 10.3390/ijms22010454
RNA-Seq Provides New Insights into the Molecular Events Involved in "Ball-Skin versus Bladder Effect" on Fruit Cracking in Litchi.
State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China.; Ministry of Agriculture and Rural Affairs Key Laboratory of South China Horticultural Crop Biology and Germplasm Enhancement, College of Horticulture, South China Agricultural University, Guangzhou 510642, China.
Fruit cracking is a disorder of fruit development in response to internal or external cues, which causes a loss in the economic value of fruit. Therefore, exploring the mechanism underlying fruit cracking is of great significance to increase the economic yield of fruit trees. However, the molecular mechanism underlying fruit cracking is still poorly understood. Litchi, as an important tropical and subtropical fruit crop, contributes significantly to the gross agricultural product in Southeast Asia. One important agricultural concern in the litchi industry is that some famous varieties with high economic value such as 'Nuomici' are susceptible to fruit cracking. Here, the cracking-susceptible cultivar 'Nuomici' and cracking-resistant cultivar 'Huaizhi' were selected, and the samples including pericarp and aril during fruit development and cracking were collected for RNA-Seq analysis. Based on weighted gene co-expression network analysis (WGCNA) and the "ball-skin versus bladder effect" theory (fruit cracking occurs upon the aril expanding pressure exceeds the pericarp strength), it was found that seven co-expression modules genes (1733 candidate genes) were closely associated with fruit cracking in 'Nuomici'. Importantly, we propose that the low expression level of genes related to plant hormones (Auxin, Gibberellins, Ethylene), transcription factors, calcium transport and signaling, and lipid synthesis might decrease the mechanical strength of pericarp in 'Nuomici', while high expression level of genes associated with plant hormones (Auxin and abscisic acid), transcription factors, starch/sucrose metabolism, and sugar/water transport might increase the aril expanding pressure, thereby resulting in fruit cracking in 'Nuomici'. In conclusion, our results provide comprehensive molecular events involved in the "ball-skin versus bladder effect" on fruit cracking in litchi.
PMID: 33466443
Int J Mol Sci , IF:4.556 , 2021 Jan , V22 (1) doi: 10.3390/ijms22010437
Membrane Sterol Composition in Arabidopsis thaliana Affects Root Elongation via Auxin Biosynthesis.
Department of Plant Biology and Ecology, College of Life Sciences, Nankai University and Tianjin Key Laboratory of Protein Sciences, Tianjin 300071, China.; Institute of Biochemistry and Biology, Plant Physiology, University of Potsdam, D-14476 Potsdam-Golm, Germany.
Plant membrane sterol composition has been reported to affect growth and gravitropism via polar auxin transport and auxin signaling. However, as to whether sterols influence auxin biosynthesis has received little attention. Here, by using the sterol biosynthesis mutant cyclopropylsterol isomerase1-1 (cpi1-1) and sterol application, we reveal that cycloeucalenol, a CPI1 substrate, and sitosterol, an end-product of sterol biosynthesis, antagonistically affect auxin biosynthesis. The short root phenotype of cpi1-1 was associated with a markedly enhanced auxin response in the root tip. Both were neither suppressed by mutations in polar auxin transport (PAT) proteins nor by treatment with a PAT inhibitor and responded to an auxin signaling inhibitor. However, expression of several auxin biosynthesis genes TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS1 (TAA1) was upregulated in cpi1-1. Functionally, TAA1 mutation reduced the auxin response in cpi1-1 and partially rescued its short root phenotype. In support of this genetic evidence, application of cycloeucalenol upregulated expression of the auxin responsive reporter DR5:GUS (beta-glucuronidase) and of several auxin biosynthesis genes, while sitosterol repressed their expression. Hence, our combined genetic, pharmacological, and sterol application studies reveal a hitherto unexplored sterol-dependent modulation of auxin biosynthesis during Arabidopsis root elongation.
PMID: 33406774
Front Plant Sci , IF:4.402 , 2020 , V11 : P619953 doi: 10.3389/fpls.2020.619953
The Physiological and Molecular Mechanism of Abscisic Acid in Regulation of Fleshy Fruit Ripening.
College of Horticulture, China Agricultural University, Beijing, China.; College of Plant Science and Technology, Beijing University of Agriculture, Beijing, China.
The ripening of fleshy fruits is coupled with the degradation of both chlorophyll and cell walls, as well as changes in the metabolism of phenylpropanoids, flavonoids, starch/sucrose, and carotenoids. These processes are controlled by phytohormones and other factors, including abscisic acid (ABA), ethylene, auxin, polyamines, sugar, and reactive oxygen species. The ripening of climacteric fruits is controlled by ethylene and non-climacteric fruit ripening is regulated mainly by ABA. Also, ABA and ethylene may interact in both types of fruit ripening. ABA concentrations in fleshy fruits are regulated in response to developmental and environmental cues and are controlled by the relative rates of ABA biosynthesis and catabolism, the former mainly via 9-cis-epoxycarotenoid dioxygenases (NCEDs) and beta-glucosidases and the latter via ABA 8'-hydroxylases (CYP707As) and beta-glycosyltransferases. In strawberry fruit ripening, ABA is perceived via at least two receptors, Pyrabactin resistance (PYR)/PYR-like (PYL) and putative abscisic acid receptor (ABAR), which are linked separately to the conserved signaling pathway ABA-FaPYR1-FaABIl-FaSnRK2 and the novel signaling pathway ABA-FaABAR-FaRIPK1-FaABI4. Downstream signaling components include important transcription factors, such as AREB (ABA responsive element binding protein)/ABF (ABRE binding factors ABA responsive factor), ethylene response factor (ERF), and V-myb Myeloblastosis viral oncogene homolog (MYB), as well as ripening-related genes. Finally, a comprehensive model of ABA linked to ethylene, sugar, polyamines, auxin and reactive oxygen species in the regulation of strawberry fruit ripening is proposed. Next, new integrated mechanisms, including two ABA signaling pathways, ABA and ethylene signaling pathways, and ABA/ethylene to other phytohormones are interesting and important research topics in ripening, especially in non-climacteric fruits.
PMID: 33505417
J Agric Food Chem , IF:4.192 , 2021 Jan , V69 (1) : P101-111 doi: 10.1021/acs.jafc.0c05541
Comparison of Efficacy and Detection of Clethodim and Glyphosate Applied with Dicamba and 2,4-D through Tank Mixture and Sequential Applications.
Department of Plant and Soil Science, Mississippi State University, Mississippi State, Mississippi 39762, United States.; Department of Crop Sciences, University of Illinois, Urbana, Illinois 61801, United States.; Mississippi State Chemical Laboratory, Mississippi State, Mississippi 39762, United States.
Greenhouse studies were planted at the R.R. Foil Plant Science Research Center in Starkville, MS. In the efficacy trial, pots were seeded with barnyardgrass (Echinochloa crus-galli), broadleaf signalgrass (Urochloa platyphylla), and giant foxtail (Setaria faberi). In the lab detection trial, only barnyardgrass was seeded. Both studies consisted of 16 treatments with four replications per treatment. The treatments consisted of clethodim, glyphosate, dicamba, and 2,4-D applied singularly and in combination with each other. Each herbicide combination was applied with three application methods: tank mixture, sequential applications where the synthetic auxin was applied first (auxin applied first), and sequential applications where glyphosate or clethodim was applied first (auxin applied second). The auxin applied second method had higher visual estimations of control ratings and lower biomass weights compared to the other two methods. The auxin applied second method had more glyphosate and clethodim detected with the use of liquid chromatography tandem mass spectrometry.
PMID: 33395522
Biomolecules , IF:4.082 , 2021 Jan , V11 (1) doi: 10.3390/biom11010077
Jasmonates, Ethylene and Brassinosteroids Control Adventitious and Lateral Rooting as Stress Avoidance Responses to Heavy Metals and Metalloids.
Department of Medicine, University of Perugia, Piazzale Menghini 8/9, 06132 Perugia, Italy.; Department of Environmental Biology, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy.
Developmental and environmental signaling networks often converge during plant growth in response to changing conditions. Stress-induced hormones, such as jasmonates (JAs), can influence growth by crosstalk with other signals like brassinosteroids (BRs) and ethylene (ET). Nevertheless, it is unclear how avoidance of an abiotic stress triggers local changes in development as a response. It is known that stress hormones like JAs/ET and BRs can regulate the division rate of cells from the first asymmetric cell divisions (ACDs) in meristems, suggesting that stem cell activation may take part in developmental changes as a stress-avoidance-induced response. The root system is a prime responder to stress conditions in soil. Together with the primary root and lateral roots (LRs), adventitious roots (ARs) are necessary for survival in numerous plant species. AR and LR formation is affected by soil pollution, causing substantial root architecture changes by either depressing or enhancing rooting as a stress avoidance/survival response. Here, a detailed overview of the crosstalk between JAs, ET, BRs, and the stress mediator nitric oxide (NO) in auxin-induced AR and LR formation, with/without cadmium and arsenic, is presented. Interactions essential in achieving a balance between growth and adaptation to Cd and As soil pollution to ensure survival are reviewed here in the model species Arabidopsis and rice.
PMID: 33435585
Plant Cell Physiol , IF:4.062 , 2021 Jan doi: 10.1093/pcp/pcab014
Strigolactones And Auxin Cooperate To Regulate Maize Root Development and Response to Nitrate.
Dept. of Agronomy, Food, Natural resources, Animals and Environment, University of Padova, viale dell'universita 16, 35020, Legnaro, Italy.; Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Universite Paris-Saclay, 78000, Versailles, France.; Department of Agricultural and Food Sciences (DISTAL), University of Bologna, viale Fanin 44, Bologna, 40127, Italy.
In maize, nitrate regulates root development thanks to the coordinated action of many players. In this study, the involvement of SLs and auxin as putative components of the nitrate regulation of lateral root was investigated. To this aim, the endogenous SL content of maize root in response to nitrate was assessed by LC-MS/MS and measurements of lateral root density in the presence of analogues or inhibitors of auxin and strigolactones were performed. Furthermore, an untargeted RNA-seq based approach was used to better characterize the participation of auxin and strigolactones to the transcriptional signature of maize root response to nitrate. Our results suggested that N deprivation induces zealactone and carlactonoic acid biosynthesis in root, to a higher extent if compared to P-deprived roots. Moreover, data on lateral root density led to hypothesise that the induction of LR development early occurring upon nitrate supply involves the inhibition of SL biosynthesis, but that the downstream target of SL shutdown, beside auxin, includes also additional unknown players. Furthermore, RNA-seq results provided a set of putative markers for the auxin- or SL-dependent action of nitrate, meanwhile allowing to identify also novel components of the molecular regulation of maize root response to nitrate. Globally the existence of at least four different pathways was hypothesised, one dependent on auxin, a second one mediated by SLs, a third deriving from the SL-auxin interplay and one last attributable to nitrate itself through further downstream signals. Further work will be necessary to better assess the reliability of the model proposed.
PMID: 33508105
Plant Cell Physiol , IF:4.062 , 2021 Jan doi: 10.1093/pcp/pcab002
S-nitrosoglutathione Reductase-Mediated nitric oxide affects axillary buds outgrowth of solanum lycopersicum L. by regulating auxin and cytokinin signaling.
State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Taian 271018, P.R. China.
Auxin and cytokinin are two kinds of important phytohormones that mediate outgrowth of axillary buds in plants. How nitric oxide and its regulator of S-nitrosoglutathione reductase (GSNOR) taking part in auxin and cytokinin signaling for controlling axillary buds outgrowth remains elusive. We explained roles of GSNOR during tomato axillary buds outgrowth by physiological, biochemical and genetic approach. GSNOR negatively regulated NO homeostasis. Suppression of GSNOR promoted axillary buds outgrowth via inhibiting the expression of FZY in both apical and axillary buds. Meanwhile, AUX1 and PIN1 were down-regulated in apical buds but up-regulated in axillary buds in GSNOR-suppressed plants. Thus, reduced IAA accumulation was shown in both apical buds and axillary buds of GSNOR-suppressed plants. GSNOR-mediated changes of NO and auxin affected cytokinin biosynthesis, transport, and signaling. And a decreased ratio of auxin: cytokinin was shown in axillary buds of GSNOR-suppressed plants, leading to buds dormancy breaking. We also found that the original NO signaling was generated by nitrate reductase (NR) catalyzing nitrate as substrate. NR-mediated NO reduced the GSNOR activity through S-nitrosylation of Cys-10, then induced a further NO burst, which played the above roles to promote axillary buds outgrowth. Together, GSNOR-mediated NO played important roles in controlling axillary buds outgrowth via altering the homeostasis and signaling of auxin and cytokinin in tomato plants.
PMID: 33493306
Sci Rep , IF:3.998 , 2021 Jan , V11 (1) : P1154 doi: 10.1038/s41598-021-81016-x
The ectopic expression of Arabidopsis glucosyltransferase UGT74D1 affects leaf positioning through modulating indole-3-acetic acid homeostasis.
College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, China.; The Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, College of Life Sciences, Shandong University, Qingdao, 266237, China.; School of Pharmacy, College of Pharmacy, Linyi University, Shuangling Road, Lanshan District, Linyi, 276000, China. guizhizhang11@163.com.; The Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, College of Life Sciences, Shandong University, Qingdao, 266237, China. guizhizhang11@163.com.
Leaf angle is an important agronomic trait affecting photosynthesis efficiency and crop yield. Although the mechanisms involved in the leaf angle control are intensively studied in monocots, factors contribute to the leaf angle in dicots are largely unknown. In this article, we explored the physiological roles of an Arabidopsis glucosyltransferase, UGT74D1, which have been proved to be indole-3-acetic acid (IAA) glucosyltransferase in vitro. We found that UGT74D1 possessed the enzymatic activity toward IAA glucosylation in vivo and its expression was induced by auxins. The ectopically expressed UGT74D1 obviously reduced the leaf angle with an altered IAA level, auxin distribution and cell size in leaf tissues. The expression of several key genes involved in the leaf shaping and leaf positioning, including PHYTOCHROME KINASE SUBSTRATE (PKS) genes and TEOSINTE BRANCHED1, CYCLOIDEA, and PCF (TCP) genes, were dramatically changed by ectopic expression of UGT74D1. In addition, clear transcription changes of YUCCA genes and other auxin related genes can be observed in overexpression lines. Taken together, our data indicate that glucosyltransferase UGT74D1 could affect leaf positioning through modulating auxin homeostasis and regulating transcription of PKS and TCP genes, suggesting a potential new role of UGT74D1 in regulation of leaf angle in dicot Arabidopsis.
PMID: 33441983
Rice (N Y) , IF:3.912 , 2021 Jan , V14 (1) : P13 doi: 10.1186/s12284-021-00454-3
Decreased Vascular Bundle 1 affects mitochondrial and plant development in rice.
Rice Research Institute, Key Laboratory of Application and Safety Control of Genetically Modified Crops, College of Agronomy and Biotechnology, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China.; Rice Research Institute, Key Laboratory of Application and Safety Control of Genetically Modified Crops, College of Agronomy and Biotechnology, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China. heghswu@163.com.; Rice Research Institute, Key Laboratory of Application and Safety Control of Genetically Modified Crops, College of Agronomy and Biotechnology, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China. wangnan_xndx@126.com.
BACKGROUND: Mitochondria are vital regulators of plant growth and development, constitute the predominant source of ATP, and participate in multiple anabolic and catabolic metabolic pathways. But the mechanism by which dysfunctional mitochondria affect plant growth remains unknown, and more mitochondria-defective mutants need to be identified. RESULTS: A mitochondria-defective mutant decreased vascular bundle 1 (dvb1) was isolated from rice mutant library mutagenized by EMS (ethylmethane sulfonate), which shows dwarfism, narrow leaves, short branches, few vascular bundles, and low fertility. Map-based cloning, genetic complementation, and phylogenetic analysis revealed that DVB1 encodes a structural protein classified in the Mic10 family and is required for the formation of cristae in mitochondria, and was primarily expressed in vascular bundles. The DVB1 protein is partially localized in the mitochondria and capable of forming dimers and polymers. Comparing with the wild type, disruption of amino acid metabolism and increased auxin synthesis were observed in dvb1 mutant which also showed increased sensitivity to the mitochondrial electron transport inhibitors. CONCLUSIONS: DVB1 belongs to Mic10 family and DVB1 is partially localized in the mitochondria. Further studies indicated that DVB1 is important for mitochondrial and plant development in rice.
PMID: 33492479
Rice (N Y) , IF:3.912 , 2021 Jan , V14 (1) : P2 doi: 10.1186/s12284-020-00446-9
The Amino Acid Transporter OsAAP4 Contributes to Rice Tillering and Grain Yield by Regulating Neutral Amino Acid Allocation through Two Splicing Variants.
Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Agricultural Sciences, Guizhou University, Guiyang, 550025, China. zmfang@gzu.edu.cn.; National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China. zmfang@gzu.edu.cn.; Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Agricultural Sciences, Guizhou University, Guiyang, 550025, China.; National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
BACKGROUND: Amino acids, which are transported by amino acid transporters, are the major forms of organic nitrogen utilized by higher plants. Among the 19 Amino Acid Permease transporters (AAPs) in rice, only a small number of these genes have been reported to influence rice growth and development. However, whether other OsAAPs are responsible for rice growth and development is unclear. RESULTS: In this study, we demonstrate that OsAAP4 promoter sequences are divergent between Indica and Japonica, with higher expression in the former, which produces more tillers and higher grain yield than does Japonica. Overexpression of two different splicing variants of OsAAP4 in Japonica ZH11 significantly increased rice tillering and grain yield as result of enhancing the neutral amino acid concentrations of Val, Pro, Thr and Leu. OsAAP4 RNA interference (RNAi) and mutant lines displayed opposite trends compared with overexpresing (OE) lines. In addition, exogenous Val or Pro at 0.5 mM significantly promoted the bud outgrowth of lines overexpressing an OsAAP4a splicing variant compared with ZH11, and exogenous Val or Pro at 2.0 mM significantly enhanced the bud outgrowth of lines overexpressing splicing variant OsAAP4b compared with ZH11. Of note, the results of a protoplast amino acid-uptake assay showed that Val or Pro at different concentrations was specifically transported and accumulated in these overexpressing lines. Transcriptome analysis further demonstrated that OsAAP4 may affect nitrogen transport and metabolism, and auxin, cytokinin signaling in regulating rice tillering. CONCLUSION: Our results suggested that OsAAP4 contributes to rice tiller and grain yield by regulating neutral amino acid allocation through two different splicing variants and that OsAAP4 might have potential applications in rice breeding.
PMID: 33409665
Plant Cell Rep , IF:3.825 , 2021 Jan doi: 10.1007/s00299-020-02643-8
ZEITLUPE enhances expression of PIF4 and YUC8 in the upper aerial parts of Arabidopsis seedlings to positively regulate hypocotyl elongation.
Graduate Course in Life Science, Graduate School of Science, Gakushuin University, 1-5-1 Mejiro, Toshima-Ku, Tokyo, 171-8588, Japan. ayasaito0126@gmail.com.; Graduate Course in Life Science, Graduate School of Science, Gakushuin University, 1-5-1 Mejiro, Toshima-Ku, Tokyo, 171-8588, Japan.; Experimental Plant Division, Department of Biological Systems, RIKEN, BioResource Center, Tsukuba-shi, Ibaraki, 305-0074, Japan.; Faculty of Science, Division of Biological Sciences, Hokkaido University, Kitaku Kita 10 Nishi 8, Sapporo, 060-0810, Japan.
KEY MESSAGE: Microarray and genetic analyses reveal that ZTL induces the expression of genes related to auxin synthesis, thereby promoting hypocotyl elongation. ZTL is a blue-light receptor that possesses a light-oxygen-voltage-sensing (LOV) domain, an F-box motif, and a kelch repeat domain. ZTL promotes hypocotyl elongation under high temperature (28 degrees C) in Arabidopsis thaliana; however, the mechanism of this regulation is unknown. Here, we divided seedlings into hypocotyls and upper aerial parts, and performed microarray analyses. In hypocotyl, 1062 genes were down-regulated in ztl mutants (ztl-3 and ztl-105) compared with wild type; some of these genes encoded enzymes involved in cell wall modification, consistent with reduced hypocotyl elongation. In upper aerial parts, 1038 genes were down-regulated in the ztl mutants compared with wild type; these included genes involved in auxin synthesis and auxin response. Furthermore, the expression of the PHYTOCHROME INTERACTING FACTOR 4 (PIF4) gene, which encodes a transcription factor known to positively regulate YUCCA genes (YUCs), was also decreased in the ztl mutants. Genetic analysis revealed that overexpression of PIF4 and YUC8 could restore the suppressed hypocotyl length in the ztl mutants. Our results suggest that ZTL induces expression of YUC8 via PIF4 in upper aerial parts and promotes hypocotyl elongation.
PMID: 33386962
Plant Physiol Biochem , IF:3.72 , 2021 Jan , V160 : P51-61 doi: 10.1016/j.plaphy.2021.01.007
Cytochrome P450 metabolism-based herbicide resistance to imazamox and 2,4-D in Papaver rhoeas.
Department d'Hortofructicultura, Botanica i Jardineria, Agrotecnio, Universitat de Lleida, 25198, Lleida, Spain. Electronic address: joel.torra@udl.cat.; Department of Agricultural Chemistry and Soil Science, University of Cordoba, Campus Rabanales, 14014, Cordoba, Spain.; Departamento de Ciencias Agroforestales, Escuela Politecnica Superior, Campus Universitario de La Rabida, 21071, Palos de la Frontera, Huelva, Spain.; Crop Protection, Corteva Agriscience, 782808, Guyancourt, France.
Papaver rhoeas biotypes displaying multiple herbicide resistance to ALS inhibitors and synthetic auxin herbicides (SAH) are spreading across Europe. In Spain, enhanced metabolism to imazamox was confirmed in one population, while cytochrome-P450 (P450) based metabolism to 2,4-D in another two. The objectives of this research were to further confirm the presence of P450 mediated enhanced metabolism and, if so, to confirm whether a putative common P450 is responsible of metabolizing both 2,4-D and imazamox. Metabolism studies were undertaken in five P. rhoeas populations with contrasted HR profiles (herbicide susceptible, only HR to ALS inhibitors, only HR to SAH, or multiple HR to both), and moreover, three different P450 inhibitors were used. The presence of enhanced metabolism to these SoA was confirmed in three more HR P. rhoeas populations. This study provides the first direct evidence that imazamox metabolism in these biotypes is P450-mediated, also in one population without an altered target site. Additionally, it was further confirmed that enhanced metabolism of 2,4-D in biotypes only HR to SAH or multiple HR to ALS inhibitors and SAH involves P450 as well. No metabolism was detected using the three inhibitors in all the herbicide-metabolizing P. rhoeas biotypes, suggesting that a common metabolic system involving P450s is responsible of degrading herbicides affecting both SoAs. Thus, selection pressure with either SAH or imidazolinone ALS inhibitors can select not only for resistance to each of them, but it can also confer cross-resistance between them in P. rhoeas.
PMID: 33454636
Mol Plant Microbe Interact , IF:3.696 , 2021 Jan doi: 10.1094/MPMI-08-20-0240-R
Proteomic analysis demonstrates a molecular dialog between Trichoderma guizhouense NJAU 4742 and cucumber (Cucumis sativus L) roots: role in promoting plant growth.
Nanjing Agricultural University, 70578, Nanjing, Jiangsu, China; 2016203055@njau.edu.cn.; Nanjing Agricultural University, 70578, Nanjing, Jiangsu, China; 2018103144@njau.edu.cn.; Nanjing Agricultural University, 70578, Nanjing, Jiangsu, China; 2015203032@njau.edu.cn.; Nanjing Agricultural University, 70578, Nanjing, Jiangsu, China; 2018103120@njau.edu.cn.; Nanjing Agricultural University, 70578, Nanjing, Jiangsu, China; yiyong1973@njau.edu.cn.; Nanjing Agricultural University, 70578, Nanjing, Jiangsu, China; liudongyang@njau.edu.cn.; Nanjing Agricultural University, 70578, Nanjing, Jiangsu, China; 281633954@qq.com.
Trichoderma is a genus of filamentous fungi that play notable roles in stimulating plant growth after colonizing the root surface. However, the key proteins and molecular mechanisms governing this stimulation have not been completely elucidated. In this study, Trichoderma guizhouense NJAU 4742 was investigated in a hydroponic culture system after interacting with cucumber roots. The total proteins of the fungus were characterized, and the key metabolic pathways along with related genes were analyzed through proteomic and transcriptomic analyses. The roles played by the regulated proteins during the interaction between plants and NJAU 4742 were further examined. The intracellular/extracellular proteins from NJAU 4742 and extracellular proteins from the cucumbers were quantified, and the high-abundance proteins were determined which primarily involved in the shikimate pathway (tryptophan, tyrosine, and phenylalanine metabolism, auxin biosynthesis and secondary metabolite synthesis). Moreover, 15N-KNO3 labeling analysis indicated that NJAU 4742 had a strong ability to convert nitrogenous amino acids, nitrate, nitrile and amines into ammonia. The auxin synthesis and ammonification metabolism pathways of NJAU 4742 significantly contribute to plant growth. The results of this study demonstrated the crucial metabolic pathways involved in the interactions between Trichoderma and plants.
PMID: 33496609
Tree Physiol , IF:3.655 , 2021 Jan doi: 10.1093/treephys/tpaa180
UV-B induced molecular mechanisms of stress physiology responses in the major Northern Chinese conifer Pinus tabuliformis Carr.
Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.; Department of Ecology and Environmental Science, UPSC, Umea University, Sweden.; Qigou State-owned Forest Farm, Pingquan, Hebei, 067509, China.; Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.; Department des Sciences du Bois et de la Foret, Faculte de Foresterie, de Geographie et Geomatique, Universite Laval Quebec, QC, G1V 0A6, Canada.
During their lifetimes, plants are exposed to different abiotic stress factors eliciting various physiological responses and triggering important defense processes. For UV-B radiation responses in forest trees, the genetics and molecular regulation remain to be elucidated. Here, we exposed Pinus tabuliformis Carr., a major conifer from Northern China, to short-term high-intensity UV-B and employed a systems biology approach to characterize the early physiological processes and the hierarchical gene regulation, which revealed a temporal transition from primary to secondary metabolism, the buildup of enhanced antioxidant capacity, and stress-signaling activation. Our findings showed that photosynthesis and biosynthesis of photosynthetic pigments were inhibited, while flavonoids and their related derivates biosynthesis as well as glutathione and glutathione S-transferase mediated antioxidant processes were enhanced. Likewise, stress related phytohormones (jasmonic acid, salicylic acid, and ethylene), kinase, and ROS signal transduction pathways were activated. Biological processes regulated by auxin and karrikin were, for the first time, found to be involved in plant defense against UV-B by promoting the biosynthesis of flavonoids and the improvement of antioxidant capacity in our research system. Our work evaluated the physiological and transcriptome perturbations in a conifer's response to UV-B, and generally, highlighted the necessity of a systems biology approach in addressing plant stress biology.
PMID: 33416074
BMC Genomics , IF:3.594 , 2021 Jan , V22 (1) : P85 doi: 10.1186/s12864-021-07378-8
Genome-wide characterization of the WAK gene family and expression analysis under plant hormone treatment in cotton.
School of Chemistry and Chemical Engineering, Xianyang Normal University, Xianyang, 712000, Shaanxi, China.; State Key Laboratory of Cotton Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng, 475001, Henan, China.; State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.; College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China.; Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China.; College of Life Sciences, Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Shihezi University, Shihezi, 832003, China.; College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China. guanghuix@snnu.edu.cn.
BACKGROUND: Wall-associated kinases (WAK), one of the receptor-like kinases (RLK), function directly in the connection and communication between the plant cell wall and the cytoplasm. WAK genes are highly conserved and have been identified in plants, such as rice, but there is little research on the WAK gene family in cotton. RESULTS: In the present study, we identified 29 GhWAK genes in Gossypium hirsutum. Phylogenetic analysis showed that cotton WAK proteins can be divided into five clades. The results of synteny and Ka/Ks analysis showed that the GhWAK genes mainly originated from whole genome duplication (WGD) and were then mainly under purifying selection. Transcriptome data and real-time PCR showed that 97% of GhWAK genes highly expressed in cotton fibers and ovules. beta-glucuronidase (GUS) staining assays showed that GhWAK5 and GhWAK16 expressed in Arabidopsis leaf trichomes. Fourteen GhWAK genes were found to possess putative gibberellin (GA) response elements in the promoter regions, 13 of which were significantly induced by GA treatment. Ten GhWAK genes contained auxin (IAA) response elements and the expression level of nine GhWAKs significantly increased under auxin treatment. CONCLUSIONS: We provide a preliminary analysis of the WAK gene family in G. hirsutum, which sheds light on the potantial roles of GhWAK genes in cotton fiber cell development. Our data also provides a useful resource for future studies on the functional roles of GhWAK genes.
PMID: 33509085
BMC Genomics , IF:3.594 , 2021 Jan , V22 (1) : P22 doi: 10.1186/s12864-020-07345-9
Genome-wide identification of GH3 genes in Brassica oleracea and identification of a promoter region for anther-specific expression of a GH3 gene.
Department of Biological Sciences, College of Biological Science and Biotechnology, Chungnam National University, Daejeon, 34134, Republic of Korea.; Department of Biological Sciences, College of Biological Science and Biotechnology, Chungnam National University, Daejeon, 34134, Republic of Korea. hankuil.yi@cnu.ac.kr.
BACKGROUND: The Gretchen Hagen 3 (GH3) genes encode acyl acid amido synthetases, many of which have been shown to modulate the amount of active plant hormones or their precursors. GH3 genes, especially Group III subgroup 6 GH3 genes, and their expression patterns in economically important B. oleracea var. oleracea have not been systematically identified. RESULTS: As a first step to understand regulation and molecular functions of Group III subgroup 6 GH3 genes, 34 GH3 genes including four subgroup 6 genes were identified in B. oleracea var. oleracea. Synteny found around subgroup 6 GH3 genes in B. oleracea var. oleracea and Arabidopsis thaliana indicated that these genes are evolutionarily related. Although expression of four subgroup 6 GH3 genes in B. oleracea var. oleracea is not induced by auxin, gibberellic acid, or jasmonic acid, the genes show different organ-dependent expression patterns. Among subgroup 6 GH3 genes in B. oleracea var. oleracea, only BoGH3.13-1 is expressed in anthers when microspores, polarized microspores, and bicellular pollens are present, similar to two out of four syntenic A. thaliana subgroup 6 GH3 genes. Detailed analyses of promoter activities further showed that BoGH3.13-1 is expressed in tapetal cells and pollens in anther, and also expressed in leaf primordia and floral abscission zones. CONCLUSIONS: Sixty-two base pairs (bp) region (- 340 ~ - 279 bp upstream from start codon) and about 450 bp region (- 1489 to - 1017 bp) in BoGH3.13-1 promoter are important for expressions in anther and expressions in leaf primordia and floral abscission zones, respectively. The identified anther-specific promoter region can be used to develop male sterile transgenic Brassica plants.
PMID: 33407107
J Biotechnol , IF:3.503 , 2021 Jan , V325 : P179-185 doi: 10.1016/j.jbiotec.2020.10.029
Azospirillum brasilense reduces oxidative stress in the green microalgae Chlorella sorokiniana under different stressors.
Biosystems Engineering, Auburn University, Auburn, AL 36849, USA.; Bashan Institute of Science, Dadeville, AL 36853, USA; Environmental Microbiology Group, Northwestern Center for Biological Research (CIBNOR), Av. IPN 195, 23096, La Paz, BCS, Mexico; Dept. of Entomology and Plant Pathology, 301 Funchess Hall, Auburn University, Auburn, AL 36849, USA.; Biosystems Engineering, Auburn University, Auburn, AL 36849, USA. Electronic address: bth0023@auburn.edu.
In this study, we investigated oxidative stress in the green microalgae, Chlorella sorokiniana, in co-culture with the plant growth promoting bacteria (PGPB), Azospirillum brasilense. This relationship was studied in the absence of an exogenous stressor, under copper stress, and under nitrogen limitation stress. We confirmed that copper and nitrogen limitation induced algal oxidative stress and reductions in chlorophyll content. In all cases, the presence of A. brasilense lowered the accumulation of intracellular reactive oxygen species (ROS) while promoting chlorophyll content. This effect was driven, in part, by A. brasilense's secretion of the auxin hormone, indole-3-acetic acid, which is known to mitigate stress in higher plants. The findings of the present study show that stress mitigation by A. brasilense resulted in suppressed starch accumulation under nitrogen limitation stress and neutral lipid accumulation under copper stress. In fact, A. brasilense could almost completely mitigate oxidative stress in C. sorokiniana resulting from nitrogen limitation, with ROS accumulation rates comparable to the axenic control cultures. The biotechnological implication of these findings is that co-culture strategies with A. brasilense (and similar PGPB) are most effective for high growth applications. A second growth stage may be needed to induce accumulation of desired products.
PMID: 33147514
BMC Plant Biol , IF:3.497 , 2021 Jan , V21 (1) : P57 doi: 10.1186/s12870-021-02839-4
Heterologous expression of Arabidopsis thaliana rty gene in strawberry (Fragaria x ananassa Duch.) improves drought tolerance.
Beijing Academy of Forestry and Pomology Sciences, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100093, P. R. China.; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, 100093, P. R. China.; Beijing Engineering Research Center for Deciduous Fruit Trees, Beijing, 100093, P. R. China.; Key Laboratory of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Wuhan, 430062, P. R. China.; Beijing Academy of Forestry and Pomology Sciences, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100093, P. R. China. jwm0809@163.com.; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, 100093, P. R. China. jwm0809@163.com.
BACKGROUND: Strawberry (Fragaria x ananassa Duch.) is an important fruit crop worldwide. It was particularly sensitive to drought stress because of their fibrous and shallow root systems. Mutant rty of Arabidopsis thaliana ROOTY (RTY) results in increased endogenous auxin levels, more roots, and shoot growth. It is still unclear whether the rty gene improves stress tolerance in strawberry. RESULTS: rty gene was isolated from Arabidopsis thaliana and placed under the control of the cauliflower mosaic virus (CaMV) 35S promoter in the pBI121-rty binary vector carrying the selectable marker of neomycin phosphotransferase II (NPT II). Seven transgenic lines were confirmed by PCR and western blot analysis. Accumulations of IAA and ABA were significantly increased in the transgenic plants. The endogenous IAA contents were 46.5 ng g(- 1) and 66.0 ng g(- 1)in control and transgenic plants respectively. The endogenous ABA contents in the control plant were 236.3 ng g(- 1) and in transgenic plants were 543.8 ng g(- 1). The production of adventitious roots and trichomes were enhanced in the transgenic plants. Furthermore, transcript levels of the genes including IAA and ABA biosynthetic, and stress-responsive genes, were higher in the transgenic plants than in the control plants under drought conditions. Water use efficiency and a reduced water loss rate were enhanced in the transgenic strawberry plants. Additionally, peroxidase and catalase activities were significantly higher in the transgenic plants than in the control plants. The experiment results revealed a novel function for rty related to ABA and drought responses. CONCLUSIONS: The rty gene improved hormone-mediated drought tolerance in transgenic strawberry. The heterologous expression of rty in strawberry improved drought tolerance by promoting auxin and ABA accumulation. These phytohormones together brought about various physiological changes that improved drought tolerance via increased root production, trichome density, and stomatal closure. Our results suggested that a transgenic approach can be used to overcome the inherent trade-off between plant growth and drought tolerance by enhancing water use efficiency and reducing water loss rate under water shortage conditions.
PMID: 33478380
BMC Plant Biol , IF:3.497 , 2021 Jan , V21 (1) : P48 doi: 10.1186/s12870-020-02817-2
Auxin is involved in arbuscular mycorrhizal fungi-promoted tomato growth and NADP-malic enzymes expression in continuous cropping substrates.
College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.; College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, 471023, China.; College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China. shusheng@njau.edu.cn.; College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China. sunj72@163.com.
BACKGROUND: Despite significant limitations of growth medium reuse, a large amount of organic substrate is reused in soilless cultivation of horticultural crops in China. Arbuscular mycorrhizal fungi (AMF) can promote nutrient absorption and improve plant tolerance to biotic and abiotic stresses. However, the mechanisms governing the effects of AMF on crop growth in organic continuous cropping substrates have not been elucidated. RESULTS: In this study, we showed that the inoculation of AMF in continuous cropping substrates promoted growth and root development, and increased the root and NADP-malic enzyme (NADP-ME) activity of tomato seedlings. Root transcriptome analysis demonstrated that the plant hormone signal transduction pathway was highly enriched, and 109 genes that positively correlated with the AMF-inoculated plant phenotype were obtained by gene set enrichment analysis (GSEA), which identified 9 genes related to indole acetic acid (IAA). Importantly, the levels of endogenous IAA in tomato seedlings significantly increased after AMF inoculation. Furthermore, the application of AMF significantly increased the expression levels of NADP-ME1 and NADP-ME2, as well as the activity of NADP-ME, and enhanced the root activity of tomato seedlings in comparison to that observed without inoculation of AMF. However, these effects were blocked in plants treated with 2,3,5-triiodobenzoic acid (TIBA), a polar transport inhibitor of IAA. CONCLUSIONS: These results suggest that IAA mediates the AMF-promoted tomato growth and expression of NADP-MEs in continuous cropping substrates. The study provides convincing evidence for the reuse of continuous cropping substrates by adding AMF as an amendment.
PMID: 33461504
BMC Plant Biol , IF:3.497 , 2021 Jan , V21 (1) : P47 doi: 10.1186/s12870-020-02803-8
Genome-wide identification and characterization of NBS-encoding genes in Raphanus sativus L. and their roles related to Fusarium oxysporum resistance.
Molecular Genetics and Genomics Laboratory, Department of Horticulture, College of Agriculture and Life Science, Chungnam National University, Daejeon, 34134, Republic of Korea.; Department of Crop Science, College of Agricultural and Life Sciences, Chungnam National University, Daejeon, 34134, Republic of Korea.; Neo Seed Co., 256-45 Jingeonjung-gil, Gongdo-eup, Anseong, Gyeonggi Province, 17565, Republic of Korea.; Center for Eco-friendly New Materials, Korea Research Institute of Chemical Technology, Daejeon, 34114, Republic of Korea.; Molecular Genetics and Genomics Laboratory, Department of Horticulture, College of Agriculture and Life Science, Chungnam National University, Daejeon, 34134, Republic of Korea. yplim@cnu.ac.kr.; Molecular Genetics and Genomics Laboratory, Department of Horticulture, College of Agriculture and Life Science, Chungnam National University, Daejeon, 34134, Republic of Korea. srchoi@cnu.ac.kr.
BACKGROUND: The nucleotide-binding site-leucine-rich repeat (NBS-LRR) genes are important for plant development and disease resistance. Although genome-wide studies of NBS-encoding genes have been performed in several species, the evolution, structure, expression, and function of these genes remain unknown in radish (Raphanus sativus L.). A recently released draft R. sativus L. reference genome has facilitated the genome-wide identification and characterization of NBS-encoding genes in radish. RESULTS: A total of 225 NBS-encoding genes were identified in the radish genome based on the essential NB-ARC domain through HMM search and Pfam database, with 202 mapped onto nine chromosomes and the remaining 23 localized on different scaffolds. According to a gene structure analysis, we identified 99 NBS-LRR-type genes and 126 partial NBS-encoding genes. Additionally, 80 and 19 genes respectively encoded an N-terminal Toll/interleukin-like domain and a coiled-coil domain. Furthermore, 72% of the 202 NBS-encoding genes were grouped in 48 clusters distributed in 24 crucifer blocks on chromosomes. The U block on chromosomes R02, R04, and R08 had the most NBS-encoding genes (48), followed by the R (24), D (23), E (23), and F (17) blocks. These clusters were mostly homogeneous, containing NBS-encoding genes derived from a recent common ancestor. Tandem (15 events) and segmental (20 events) duplications were revealed in the NBS family. Comparative evolutionary analyses of orthologous genes among Arabidopsis thaliana, Brassica rapa, and Brassica oleracea reflected the importance of the NBS-LRR gene family during evolution. Moreover, examinations of cis-elements identified 70 major elements involved in responses to methyl jasmonate, abscisic acid, auxin, and salicylic acid. According to RNA-seq expression analyses, 75 NBS-encoding genes contributed to the resistance of radish to Fusarium wilt. A quantitative real-time PCR analysis revealed that RsTNL03 (Rs093020) and RsTNL09 (Rs042580) expression positively regulates radish resistance to Fusarium oxysporum, in contrast to the negative regulatory role for RsTNL06 (Rs053740). CONCLUSIONS: The NBS-encoding gene structures, tandem and segmental duplications, synteny, and expression profiles in radish were elucidated for the first time and compared with those of other Brassicaceae family members (A. thaliana, B. oleracea, and B. rapa) to clarify the evolution of the NBS gene family. These results may be useful for functionally characterizing NBS-encoding genes in radish.
PMID: 33461498
BMC Plant Biol , IF:3.497 , 2021 Jan , V21 (1) : P4 doi: 10.1186/s12870-020-02781-x
Genome-wide identification and characterization of small auxin-up RNA (SAUR) gene family in plants: evolution and expression profiles during normal growth and stress response.
Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai, 200234, China.; Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai, 200234, China. fming@shnu.edu.cn.; Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai, 200234, China. jinyue@shnu.edu.cn.
BACKGROUND: Auxin is critical to plant growth and development, as well as stress responses. Small auxin-up RNA (SAUR) is the largest family of early auxin responsive genes in higher plants. However, the function of few SAUR genes is known owing to functional redundancy among the many family members. RESULTS: In this study, we conducted a phylogenetic analysis using protein sequences of 795 SAURs from Anthoceros angustus, Marchantia polymorpha, Physcomitrella patens, Selaginella moellendorffii, Ginkgo biloba, Gnetum montanum, Amborella trichopoda, Arabidopsis thaliana, Oryza sativa, Zea mays, Glycine max, Medicago truncatula and Setaria italica. The phylogenetic trees showed that the SAUR proteins could be divided into 10 clades and three subfamilies, and that SAUR proteins of three bryophyte species were only located in subfamily III, which suggested that they may be ancestral. From bryophyta to anthophyta, SAUR family have appeared very large expansion. The number of SAUR gene in Fabaceae species was considerably higher than that in other plants, which may be associated with independent whole genome duplication event in the Fabaceae lineages. The phylogenetic trees also showed that SAUR genes had expanded independently monocotyledons and dicotyledons in angiosperms. Conserved motif and protein structure prediction revealed that SAUR proteins were highly conserved among higher plants, and two leucine residues in motif I were observed in almost all SAUR proteins, which suggests the residues plays a critical role in the stability and function of SAUR proteins. Expression analysis of SAUR genes using publicly available RNA-seq data from rice and soybean indicated functional similarity of members in the same clade, which was also further confirmed by qRT-PCR. Summarization of SAUR functions also showed that SAUR functions were usually consistent within a subclade. CONCLUSIONS: This study provides insights into the evolution and function of the SAUR gene family from bryophyta to anthophyta, particularly in Fabaceae plants. Future investigation to understand the functions of SAUR family members should employ a clade as the study unit.
PMID: 33407147
Gene , IF:2.984 , 2021 Jan , V774 : P145424 doi: 10.1016/j.gene.2021.145424
Relative expression of putative genes involved in galanthamine and other Amaryllidaceae alkaloids biosynthesis in Narcissus field and in vitro tissues.
Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom. Electronic address: aferdausi.gpb@bau.edu.bd.; Associate Pro-Vice Chancellor and Senior Lecturer, Crop Production Technology, Royal Agricultural University, Cirencester Gloucestershire, GL7 6JS, United Kingdom. Electronic address: Xianmin.Chang@rau.ac.uk.; Head of Plant Genomics, Anthony Hall Group, Earlham Institute, Norwich Research Park, Norwich NR4 7UG, United Kingdom. Electronic address: anthony.hall@earlham.ac.uk.; Honorary Senior Lecturer, Functional and Comparative Genomics, Institute of Integrative Biology, The Biosciences Building, Crown Street, The University of Liverpool, Liverpool L69 7ZB, United Kingdom. Electronic address: m.g.jones@liverpool.ac.uk.
The Narcissus pseudonarcissus cv. Carlton contains Amaryllidaceae alkaloids namely galanthamine, lycorine, homolycorine, narciclasine, which are noted for their pharmaceutical properties such as for the treatment of early to mid-stage Alzheimer's diseases, cancer, tumor etc. Alkaloid biosynthesis using plant in vitro systems has been considered as a tool for drug discovery and the pathways are starting to be understood but still far from complete. Therefore, the study was emphasized to observe the relative expressions of putative genes involved in the biosynthetic pathway leading to the Amaryllidaceae alkaloids in field grown bulbs and developing cell culture systems in Narcissus. MS media fortified with growth regulators were used for the development of tissue culture from Carlton twin-scale explants. MS medium with high auxin, 20 mg/l NAA was the best medium for callus growth and maintenance while media with low auxin, 4 mg/l NAA and MS basal media gave the maximum bulblets. Field tissues showed a higher amount of galanthamine content; i.e. basal plate (1050-1310 microg Gal/g FW) and bulb (980-1150 microg Gal/g FW) than the culture derived samples; callus (1.0-7.0 microg Gal/g FW) and bulblets (12-215 microg Gal/g FW) on a fresh weight (FW) basis. GC-MS chromatograms of samples under study also showed the presence of other important alkaloids i.e. lycorine, homolycorine, lycorenine, haemanthamine, crinamine, lycoramine and tazettine. RNA extracted from in vitro callus, bulblets and field grown bulb, basal plate were used for PCR to detect the relative expression of putative genes; P450, PAL, TYDC and NpO4OMT normalized to actin. The selected transcripts for P450s and TYDC were expressed in both field and in vitro tissues. Higher expressions of PAL were observed in calli than field samples. The expression of NpN4OMT was notably higher in field samples than in vitro tissues. Therefore, in vitro tissues could be a good source for the reproducible and easy extraction of alkaloids from plants.
PMID: 33434626
Gene , IF:2.984 , 2021 Jan , V772 : P145355 doi: 10.1016/j.gene.2020.145355
Transcriptome sequencing and differential gene expression analysis reveal the mechanisms involved in seed germination and protocorm development of Calanthe tsoongiana.
Research Institution of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, Zhejiang, China.; Research Institution of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, Zhejiang, China. Electronic address: tmin115@126.com.
Calanthe tsoongiana is a rare orchid species native to China. Asymbiotic seed germination is of great importance in the ex situ conservation of this species. Based on morphological characteristics and anatomical structures, the C. tsoongiana developmental process from seeds to seedlings was divided into four stages (SA, PB, PC and PD), and subsequently, changes in endogenous hormone contents and gene expression were assessed using RNA-seq analysis. K-means analysis divided the DEGs into eight clusters. The gene expression decreased markedly between the imbibed seed and globular protocorm stages, with this being the most notably enriched cluster. During the seed germination period, DEGs were dominated by ATP metabolic processes, respiration and photosynthesis. A small change in gene expression was found in the globular protocorm versus the finger-like protocorm stages. During the last developmental stage, DEGs were significantly enriched in lignin catabolic processes and plant-type secondary cell wall biogenesis. DEG homologs, such as TSA1, DAO, NCED1, STM, and CUC2, were related to phytohormones and the morphogenesis of shoots, leaves and roots. Particularly, interactions between CUC2 and STM as well as AS1 and STM were likely involved in protocorm formation and development. Furthermore, TSA1 and DAO were distinctly validated and implicated in the synthesis and metabolism of auxin, which has a pivotal role in plant development. Our study is the first to combine morphological and transcriptome analysis to examine the process of protocorm formation and development. The results provide a foundation for understanding the mechanisms of seed germination and protocorm development of C. tsoongiana.
PMID: 33340562
Plants (Basel) , IF:2.762 , 2021 Jan , V10 (2) doi: 10.3390/plants10020208
Enhancement of In Vitro Production of Volatile Organic Compounds by Shoot Differentiation in Artemisia spicigera.
Department of Plant Sciences, Faculty of Natural Sciences, University of Tabriz, Tabriz 5166616471, Iran.; Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz 5165665811, Iran.; Department of Biological Sciences, Faculty of Basic Sciences, Higher Education Institute of Rab-Rashid, Tabriz 5155958316, Iran.; Research Center for Agriculture and Natural Resources, East Azerbaijan, Tabriz 5153715898, Iran.; School of Pharmacy, University of Camerino, 62032 Camerino, Italy.
Callus initiation, shoot formation and plant regeneration were established for Artemisia spicigera, a traditional medicinal plant growing in Armenia, Middle-Anatolia and Iran, and producing valuable volatile organic compounds (VOCs) that are mostly represented by monoterpenoids. Optimal callus initiation and shoot production were obtained by culture of hypocotyl and cotyledon explants on MS medium comprising 0.5 mg L(-1) naphthalene acetic acid (NAA) and 0.5 mg L(-1) 6-benzyladenine (BA). Consequently, the shoots were transferred onto the MS media supplemented with 1 mg L(-1) of indole-3-butyric acid (IBA) or 1 mg L(-1) of NAA. Both types of auxin induced root formation on the shoots and the resulting plantlets were successfully grown in pots. The production of VOCs in callus tissues and regenerated plantlets was studied by gas chromatography-mass spectrometry (GC-MS) analysis. Although the potential of undifferentiated callus to produce VOCs was very low, an increased content of bioactive volatile components was observed at the beginning of shoot primordia differentiation. Intriguingly, the volatiles obtained from in vitro plantlets showed quantitative and qualitative variation depending on the type of auxins used for the rooting process. The acquired quantities based on total ion current (TIC) showed that the regenerated plantlets using 1 mg L(-1) NAA produced higher amounts of oxygenated monoterpenes such as camphor (30.29%), cis-thujone (7.07%), and 1,8-cineole (6.71%) and sesquiterpene derivatives, namely germacrene D (8.75%), bicyclogermacrene (4.0%) and spathulenol (1.49%) compared with the intact plant. According to these findings, in vitro generation of volatile organic compounds in A. spicigera depends on the developmental stages of tissues and may enhance with the formation of shoot primordia and regeneration of plantlets.
PMID: 33499135
Plants (Basel) , IF:2.762 , 2021 Jan , V10 (1) doi: 10.3390/plants10010150
The TOR-Auxin Connection Upstream of Root Hair Growth.
Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany, Czech Academy of Sciences, 165 02 Prague, Czech Republic.; Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, 1010 Vienna, Austria.; Vienna Metabolomics Center (VIME), University of Vienna, 1010 Vienna, Austria.
Plant growth and productivity are orchestrated by a network of signaling cascades involved in balancing responses to perceived environmental changes with resource availability. Vascular plants are divided into the shoot, an aboveground organ where sugar is synthesized, and the underground located root. Continuous growth requires the generation of energy in the form of carbohydrates in the leaves upon photosynthesis and uptake of nutrients and water through root hairs. Root hair outgrowth depends on the overall condition of the plant and its energy level must be high enough to maintain root growth. TARGET OF RAPAMYCIN (TOR)-mediated signaling cascades serve as a hub to evaluate which resources are needed to respond to external stimuli and which are available to maintain proper plant adaptation. Root hair growth further requires appropriate distribution of the phytohormone auxin, which primes root hair cell fate and triggers root hair elongation. Auxin is transported in an active, directed manner by a plasma membrane located carrier. The auxin efflux carrier PIN-FORMED 2 is necessary to transport auxin to root hair cells, followed by subcellular rearrangements involved in root hair outgrowth. This review presents an overview of events upstream and downstream of PIN2 action, which are involved in root hair growth control.
PMID: 33451169
Plants (Basel) , IF:2.762 , 2021 Jan , V10 (1) doi: 10.3390/plants10010111
Dissecting Hierarchies between Light, Sugar and Auxin Action Underpinning Root and Root Hair Growth.
Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany, Czech Academy of Sciences, 165 02 Prague, Czech Republic.; Department of Experimental Plant Biology, Faculty of Science, Charles University, 128 00 Prague, Czech Republic.
Plant roots are very plastic and can adjust their tissue organization and cell appearance during abiotic stress responses. Previous studies showed that direct root illumination and sugar supplementation mask root growth phenotypes and traits. Sugar and light signaling where further connected to changes in auxin biosynthesis and distribution along the root. Auxin signaling underpins almost all processes involved in the establishment of root traits, including total root length, gravitropic growth, root hair initiation and elongation. Root hair plasticity allows maximized nutrient uptake and therefore plant productivity, and root hair priming and elongation require proper auxin availability. In the presence of sucrose in the growth medium, root hair emergence is partially rescued, but the full potential of root hair elongation is lost. With our work we describe a combinatory study showing to which extent light and sucrose are antagonistically influencing root length, but additively affecting root hair emergence and elongation. Furthermore, we investigated the impact of the loss of PIN-FORMED2, an auxin efflux carrier mediating shootward auxin transporter, on the establishment of root traits in combination with all growth conditions.
PMID: 33430437
Biol Open , IF:2.029 , 2021 Jan doi: 10.1242/bio.057992
Auxin confers protection against ER stress in Caenorhabditis elegans.
Laboratory of Biology and Modelling of the Cell, Ecole Normale Superieure de Lyon, CNRS UMR5239, INSERM U1210, Universite de Lyon, France.; Laboratory of Biology and Modelling of the Cell, Ecole Normale Superieure de Lyon, CNRS UMR5239, INSERM U1210, Universite de Lyon, France paola.fabrizio@ens-lyon.fr.
Auxins are plant growth regulators that influence most aspects of plant development through complex mechanisms. The development of an auxin-inducible degradation (AID) system has enabled rapid, conditional protein depletion in yeast and cultured cells. More recently, the system was successfully adapted to C. elegans to achieve auxin-dependent degradation of targets in all tissues and developmental stages. Whether auxin treatment alone has an impact on nematode physiology is an open question. Here we show that indole-3-acetic acid (IAA), the auxin most commonly used to trigger AID in worms, functions through the conserved IRE-1/XBP-1 branch of the Unfolded Protein Response (UPR) to promote resistance to Endoplasmic Reticulum (ER) stress. Because the UPR not only plays a central role in restoring ER homeostasis, but also promotes lipid biosynthesis and regulates lifespan, we suggest that extreme caution should be exercised when using the AID system to study these and related processes.
PMID: 33495210
Genet Mol Biol , IF:1.876 , 2021 , V44 (1) : Pe20200130 doi: 10.1590/1678-4685-GMB-2020-0130
Genome sequencing and analysis of plant growth-promoting attributes from Leclercia adecarboxylata.
Universidade Federal do Parana, Labiogen-Laboratorio de Bioquimica e Genetica, Palotina, PR, Brazil.; Universidade Federal do Parana, Departamento de Biociencias, Palotina, PR, Brazil.; Universidade Federal do Parana, Departamento de Bioquimica, Centro Politecnico, Jardim das Americas, Curitiba, PR, Brazil.
Plant growth-promoting bacteria are ecological alternatives for fertilization, mainly for gramineous. Since plant x bacteria interaction is genotype and strain dependent, searching for new strains may contribute to the development of new biofertilizers. We aim to characterize plant growth-promoting capacity of Leclercia adecarboxylata strain Palotina, formerly isolated by our group in corn. A single isolated colony was taken and its genome was sequenced using Illumina technology. The whole genome was compared to other Leclercia adecarboxylata strains, and their biological and growth-promoting traits, such as P solubilization and auxin production, were tested. Following that, a 4.8 Mb genome of L. adecarboxylata strain Palotina was assembled and the functional annotation was carried out. This paper is the first to report the genes associated with plant growth promotion demonstrating in vitro indole acid production by this strain. These results project the endophyte as a potential biofertilizer for further commercial exploitation.
PMID: 33503198
Plant Signal Behav , IF:1.671 , 2021 Jan , V16 (1) : P1837544 doi: 10.1080/15592324.2020.1837544
Phytohormones: structural and functional relationship to purine nucleotides and some pharmacologic agents.
Faculty of Life Sciences & Education, University of South Wales , Cardiff, UK.
Structural components of second messenger signaling (nucleotides and associated enzyme systems) within plant and animal cells have more in common than the hormones that initiate metabolic and functional changes. Neurotransmitters and hormones of mammalian pharmacologic classes relate to purine nucleotides in respect of chemical structure and the molecular changes they initiate. This study compares the molecular structures of purine nucleotides with compounds from the abscisic acid, auxin, brassinosteroid, cytokinin, gibberellin, and jasmonate classes by means of a computational program. The results illustrate how phytohomones relate to each other through the structures of nucleotides and cyclic nucleotides. Molecular similarity within the phytohormone structures relates to synergism, antagonism and the modulation of nucleotide function that regulates germination and plant development. As with the molecular evolution of mammalian hormones, cell signaling and cross-talk within the phytohormone classes is purine nucleotide centered.
PMID: 33100143
Plant Commun , 2021 Jan , V2 (1) : P100136 doi: 10.1016/j.xplc.2020.100136
Developmental and genomic architecture of plant embryogenesis: from model plant to crops.
Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK S7N 4J8, Canada.; Laboratorio Nacional de Genomica para la Biodiversidad (Langebio), Unidad de Genomica Avanzada, Centro de Investigacion y Estudios Avanzados del IPN (CINVESTAV-IPN), Irapuato, Guanajuato, Mexico.; National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada.
Embryonic development represents an important reproductive phase of sexually reproducing plant species. The fusion of egg and sperm produces the plant zygote, a totipotent cell that, through cell division and cell identity specification in early embryogenesis, establishes the major cell lineages and tissues of the adult plant. The subsequent morphogenesis phase produces the full-sized embryo, while the late embryogenesis maturation process prepares the seed for dormancy and subsequent germination, ensuring continuation of the plant life cycle. In this review on embryogenesis, we compare the model eudicot Arabidopsis thaliana with monocot crops, focusing on genome activation, paternal and maternal regulation of early zygote development, and key organizers of patterning, such as auxin and WOX transcription factors. While the early stages of embryo development are apparently conserved among plant species, embryo maturation programs have diversified between eudicots and monocots. This diversification in crop species reflects the likely effects of domestication on seed quality traits that are determined during embryo maturation, and also assures seed germination in different environmental conditions. This review describes the most important features of embryonic development in plants, and the scope and applications of genomics in plant embryo studies.
PMID: 33511346
Plant Commun , 2021 Jan , V2 (1) : P100092 doi: 10.1016/j.xplc.2020.100092
The maternally expressed polycomb group gene OsEMF2a is essential for endosperm cellularization and imprinting in rice.
Jiangsu Key Laboratory of Crop Genetics and Physiology, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Agricultural College of Yangzhou University, Yangzhou, China.; Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China.
Cellularization is a key event in endosperm development. Polycomb group (PcG) genes, such as Fertilization-Independent Seed 2 (FIS2), are vital for the syncytium-to-cellularization transition in Arabidopsis plants. In this study, we found that OsEMF2a, a rice homolog of the Arabidopsis PcG gene Embryonic Flower2 (EMF2), plays a role similar to that of FIS2 in regard to seed development, although there is limited sequence similarity between the genes. Delayed cellularization was observed in osemf2a, associated with an unusual activation of type I MADS-box genes. The cell cycle was persistently activated in osemf2a caryopses, which was likely caused by cytokinin overproduction. However, the overaccumulation of auxin was not found to be associated with the delayed cellularization. As OsEMF2a is a maternally expressed gene in the endosperm, a paternally inherited functional allele was unable to recover the maternal defects of OsEMF2a. Many imprinted rice genes were deregulated in the defective hybrid seeds of osemf2a (female symbol)/9311 (male symbol) (m9). The paternal expression bias of some paternally expressed genes was disrupted in m9 due to either the activation of maternal alleles or the repression of paternal alleles. These findings suggest that OsEMF2a-PRC2-mediated H3K27me3 is necessary for endosperm cellularization and genomic imprinting in rice.
PMID: 33511344