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Cho HT, Lee M, Choi HS, Maeng KH, Lee K, Lee HY, Ganguly A, Park H, Ho CH. A dose-dependent bimodal switch by homologous Aux/IAA transcriptional repressors. MOLECULAR PLANT 2024; 17:1407-1422. [PMID: 39095993 DOI: 10.1016/j.molp.2024.07.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 07/15/2024] [Accepted: 07/30/2024] [Indexed: 08/04/2024]
Abstract
Combinatorial interactions between different regulators diversify and enrich the chance of transcriptional regulation in eukaryotic cells. However, a dose-dependent functional switch of homologous transcriptional repressors has rarely been reported. Here, we show that SHY2, an auxin/indole-3-acetic acid (Aux/IAA) repressor, exhibits a dose-dependent bimodal role in auxin-sensitive root-hair growth and gene transcription in Arabidopsis, whereas other Aux/IAA homologs consistently repress the auxin responses. The co-repressor (TOPLESS [TPL])-binding affinity of a bimodal Aux/IAA was lower than that of a consistently repressing Aux/IAA. The switch of a single amino acid residue in the TPL-binding motif between the bimodal form and the consistently repressing form switched their TPL-binding affinity and transcriptional and biological roles in auxin responses. Based on these data, we propose a model whereby competition between homologous repressors with different co-repressor-binding affinities could generate a bimodal output at the transcriptional and developmental levels.
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Affiliation(s)
- Hyung-Taeg Cho
- Department of Biological Sciences, Seoul National University, Seoul, Korea.
| | - Minsu Lee
- Department of Biological Sciences, Seoul National University, Seoul, Korea
| | - Hee-Seung Choi
- Department of Biological Sciences, Seoul National University, Seoul, Korea
| | - Kwang-Ho Maeng
- Department of Biological Sciences, Seoul National University, Seoul, Korea
| | - Kyeonghoon Lee
- Department of Biological Sciences, Seoul National University, Seoul, Korea
| | - Ha-Yeon Lee
- Department of Biological Sciences, Seoul National University, Seoul, Korea
| | - Anindya Ganguly
- Department of Biological Sciences, Seoul National University, Seoul, Korea
| | - Hoonyoung Park
- School of Earth and Environmental Sciences, Seoul National University, Seoul, Korea
| | - Chang-Hoi Ho
- School of Earth and Environmental Sciences, Seoul National University, Seoul, Korea; Department of Climate and Energy Systems Engineering, Ewha Womans University, Seoul, Korea
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2
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Morffy N, Van den Broeck L, Miller C, Emenecker RJ, Bryant JA, Lee TM, Sageman-Furnas K, Wilkinson EG, Pathak S, Kotha SR, Lam A, Mahatma S, Pande V, Waoo A, Wright RC, Holehouse AS, Staller MV, Sozzani R, Strader LC. Identification of plant transcriptional activation domains. Nature 2024; 632:166-173. [PMID: 39020176 DOI: 10.1038/s41586-024-07707-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 06/12/2024] [Indexed: 07/19/2024]
Abstract
Gene expression in Arabidopsis is regulated by more than 1,900 transcription factors (TFs), which have been identified genome-wide by the presence of well-conserved DNA-binding domains. Activator TFs contain activation domains (ADs) that recruit coactivator complexes; however, for nearly all Arabidopsis TFs, we lack knowledge about the presence, location and transcriptional strength of their ADs1. To address this gap, here we use a yeast library approach to experimentally identify Arabidopsis ADs on a proteome-wide scale, and find that more than half of the Arabidopsis TFs contain an AD. We annotate 1,553 ADs, the vast majority of which are, to our knowledge, previously unknown. Using the dataset generated, we develop a neural network to accurately predict ADs and to identify sequence features that are necessary to recruit coactivator complexes. We uncover six distinct combinations of sequence features that result in activation activity, providing a framework to interrogate the subfunctionalization of ADs. Furthermore, we identify ADs in the ancient AUXIN RESPONSE FACTOR family of TFs, revealing that AD positioning is conserved in distinct clades. Our findings provide a deep resource for understanding transcriptional activation, a framework for examining function in intrinsically disordered regions and a predictive model of ADs.
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Affiliation(s)
| | - Lisa Van den Broeck
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, USA
| | - Caelan Miller
- Department of Biology, Duke University, Durham, NC, USA
| | - Ryan J Emenecker
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, USA
| | - John A Bryant
- Biological Systems Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Tyler M Lee
- Department of Biology, Duke University, Durham, NC, USA
| | | | | | - Sunita Pathak
- Department of Biology, Duke University, Durham, NC, USA
| | - Sanjana R Kotha
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Angelica Lam
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Saloni Mahatma
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, USA
| | - Vikram Pande
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, USA
| | - Aman Waoo
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, USA
| | - R Clay Wright
- Biological Systems Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Alex S Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, USA
| | - Max V Staller
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Rosangela Sozzani
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, USA
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3
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Liu L, Yahaya BS, Li J, Wu F. Enigmatic role of auxin response factors in plant growth and stress tolerance. FRONTIERS IN PLANT SCIENCE 2024; 15:1398818. [PMID: 38903418 PMCID: PMC11188990 DOI: 10.3389/fpls.2024.1398818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Accepted: 05/23/2024] [Indexed: 06/22/2024]
Abstract
Abiotic and biotic stresses globally constrain plant growth and impede the optimization of crop productivity. The phytohormone auxin is involved in nearly every aspect of plant development. Auxin acts as a chemical messenger that influences gene expression through a short nuclear pathway, mediated by a family of specific DNA-binding transcription factors known as Auxin Response Factors (ARFs). ARFs thus act as effectors of auxin response and translate chemical signals into the regulation of auxin responsive genes. Since the initial discovery of the first ARF in Arabidopsis, advancements in genetics, biochemistry, genomics, and structural biology have facilitated the development of models elucidating ARF action and their contributions to generating specific auxin responses. Yet, significant gaps persist in our understanding of ARF transcription factors despite these endeavors. Unraveling the functional roles of ARFs in regulating stress response, alongside elucidating their genetic and molecular mechanisms, is still in its nascent phase. Here, we review recent research outcomes on ARFs, detailing their involvement in regulating leaf, flower, and root organogenesis and development, as well as stress responses and their corresponding regulatory mechanisms: including gene expression patterns, functional characterization, transcriptional, post-transcriptional and post- translational regulation across diverse stress conditions. Furthermore, we delineate unresolved questions and forthcoming challenges in ARF research.
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Affiliation(s)
- Ling Liu
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, Sichuan, China
| | - Baba Salifu Yahaya
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Wenjiang, Sichuan, China
| | - Jing Li
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Wenjiang, Sichuan, China
| | - Fengkai Wu
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Wenjiang, Sichuan, China
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4
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Prigge MJ, Morffy N, de Neve A, Szutu W, Abraham-Juárez MJ, Johnson K, Do N, Lavy M, Hake S, Strader L, Estelle M, Richardson AE. Comparative mutant analyses reveal a novel mechanism of ARF regulation in land plants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.09.566459. [PMID: 38014308 PMCID: PMC10680667 DOI: 10.1101/2023.11.09.566459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
A major challenge in plant biology is to understand how the plant hormone auxin regulates diverse transcriptional responses throughout development, in different environments, and in different species. The answer may lie in the specific complement of auxin signaling components in each cell. The balance between activators (class-A AUXIN RESPONSE FACTORS) and repressors (class-B ARFs) is particularly important. It is unclear how this balance is achieved. Through comparative analysis of novel, dominant mutants in maize and the moss Physcomitrium patens , we have discovered a ∼500-million-year-old mechanism of class-B ARF protein level regulation, important in determining cell fate decisions across land plants. Thus, our results add a key piece to the puzzle of how auxin regulates plant development.
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Ying C, Meng Z, Wenli Z, Yamin W, Hua Z, Liu Y, Longjiang Y, Chunhua F. miR5298b regulated taxol biosynthesis by acting on TcNPR3, resulting in an alleviation of the strong inhibition of the TcNPR3-TcTGA6 complex in Taxus chinensis. Int J Biol Macromol 2023; 248:125909. [PMID: 37482165 DOI: 10.1016/j.ijbiomac.2023.125909] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 06/28/2023] [Accepted: 07/11/2023] [Indexed: 07/25/2023]
Abstract
Taxol, a valuable but rare secondary metabolite of the genus Taxus, is an effective anticancer drug. Understanding the regulation of taxol biosynthesis may provide a means to increase taxol content. The microRNA miR5298b was found to promote the accumulation of taxol and upregulate several taxol biosynthesis genes, including DBAT, TASY, and T5H, as demonstrated by experiments using the overexpression and mimicry of transient leaves. Moreover, miR5298b cleaves the mRNA sequence of TcNPR3, a homolog of the salicylic acid receptor AtNPR3/4. Overexpression and knockdown by RNA interference of TcNPR3 confirmed that it repressed taxol biosynthesis. These results indicate that miR5298b enhances taxol biosynthesis via the cleavage of TcNPR3. Yeast two-hybrid bimolecular fluorescence complementation and pull-down assays revealed that TcTGA6, a TGA transcription factor, physically interacted with TcNPR3. Functional experiments showed that TcTGA6 negatively regulates taxol biosynthesis by directly combining with the TGACG motif in the promoters of TASY, T5H, and T10H. TcNPR3 enhances TcTGA6 inhibition Luciferase assays showed that miR5298b alleviated the repression of the TcNPR3-TcTGA6 complex. In summary, miR5298b can cleave TcNPR3, thereby alleviating the inhibition of the TcNPR3-TcTGA6 complex to upregulate taxol biosynthesis genes.
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Affiliation(s)
- Chen Ying
- Institute of Resource Biology and Biotechnology, Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, No.1037 Luoyu Road, Wuhan 430074, PR China; Key Laboratory of Molecular Biophysics Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, No.1037 Luoyu Road, Wuhan 430074, PR China; Hubei Food and medicine Resources Engineering Research Center, College of Life Science and Technology, Huazhong University of Science and Technology, No.1037 Luoyu Road, Wuhan 430074, PR China
| | - Zhang Meng
- Institute of Resource Biology and Biotechnology, Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, No.1037 Luoyu Road, Wuhan 430074, PR China; Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha, 410082, PR China
| | - Zhang Wenli
- Institute of Resource Biology and Biotechnology, Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, No.1037 Luoyu Road, Wuhan 430074, PR China; Key Laboratory of Molecular Biophysics Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, No.1037 Luoyu Road, Wuhan 430074, PR China; Hubei Food and medicine Resources Engineering Research Center, College of Life Science and Technology, Huazhong University of Science and Technology, No.1037 Luoyu Road, Wuhan 430074, PR China
| | - Wang Yamin
- Institute of Resource Biology and Biotechnology, Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, No.1037 Luoyu Road, Wuhan 430074, PR China; Key Laboratory of Molecular Biophysics Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, No.1037 Luoyu Road, Wuhan 430074, PR China; Hubei Food and medicine Resources Engineering Research Center, College of Life Science and Technology, Huazhong University of Science and Technology, No.1037 Luoyu Road, Wuhan 430074, PR China
| | - Zhang Hua
- Institute of Resource Biology and Biotechnology, Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, No.1037 Luoyu Road, Wuhan 430074, PR China; Key Laboratory of Molecular Biophysics Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, No.1037 Luoyu Road, Wuhan 430074, PR China; Hubei Food and medicine Resources Engineering Research Center, College of Life Science and Technology, Huazhong University of Science and Technology, No.1037 Luoyu Road, Wuhan 430074, PR China
| | - Yang Liu
- Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha, 410082, PR China
| | - Yu Longjiang
- Institute of Resource Biology and Biotechnology, Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, No.1037 Luoyu Road, Wuhan 430074, PR China; Key Laboratory of Molecular Biophysics Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, No.1037 Luoyu Road, Wuhan 430074, PR China; Hubei Food and medicine Resources Engineering Research Center, College of Life Science and Technology, Huazhong University of Science and Technology, No.1037 Luoyu Road, Wuhan 430074, PR China
| | - Fu Chunhua
- Institute of Resource Biology and Biotechnology, Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, No.1037 Luoyu Road, Wuhan 430074, PR China; Key Laboratory of Molecular Biophysics Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, No.1037 Luoyu Road, Wuhan 430074, PR China; Hubei Food and medicine Resources Engineering Research Center, College of Life Science and Technology, Huazhong University of Science and Technology, No.1037 Luoyu Road, Wuhan 430074, PR China.
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6
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Seo PJ, Lee HG, Choi HY, Lee S, Park CM. Complexity of SMAX1 signaling during seedling establishment. TRENDS IN PLANT SCIENCE 2023; 28:902-912. [PMID: 37069002 DOI: 10.1016/j.tplants.2023.03.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 03/12/2023] [Accepted: 03/18/2023] [Indexed: 06/19/2023]
Abstract
Karrikins (KARs) are small butenolide compounds identified in the smoke of burning vegetation. Along with the stimulating effects on seed germination, KARs also regulate seedling vigor and adaptive behaviors, such as seedling morphogenesis, root hair development, and stress acclimation. The pivotal KAR signaling repressor, SUPPRESSOR OF MAX2 1 (SMAX1), plays central roles in these developmental and morphogenic processes through an extensive signaling network that governs seedling responses to endogenous and environmental cues. Here, we summarize the versatile roles of SMAX1 reported in recent years and discuss how SMAX1 integrates multiple growth hormone signals into optimizing seedling establishment. We also discuss the evolutionary relevance of the SMAX1-mediated signaling pathways during the colonization of aqueous plants to terrestrial environments.
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Affiliation(s)
- Pil Joon Seo
- Department of Chemistry, Seoul National University, Seoul 08826, Korea; Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Korea.
| | - Hong Gil Lee
- Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Korea
| | - Hye-Young Choi
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - Sangmin Lee
- Bio/Energy R&D Center, Korea Institute of Energy Research, Gwangju 61003, Korea
| | - Chung-Mo Park
- Department of Chemistry, Seoul National University, Seoul 08826, Korea; Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Korea.
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7
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El Mamoun I, Bouzroud S, Zouine M, Smouni A. The Knockdown of AUXIN RESPONSE FACTOR 2 Confers Enhanced Tolerance to Salt and Drought Stresses in Tomato ( Solanum lycopersicum L.). PLANTS (BASEL, SWITZERLAND) 2023; 12:2804. [PMID: 37570958 PMCID: PMC10420960 DOI: 10.3390/plants12152804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 07/19/2023] [Accepted: 07/25/2023] [Indexed: 08/13/2023]
Abstract
Auxin response factors (ARFs) act as key elements of the auxin-signaling pathway and play important roles in the process of a plant's growth, development, and response to environmental conditions. We studied the implication of the SlARF2 gene in the tomato response to salt (150 mM of NaCl) and drought (15% PEG 20000) stresses. The functional characterization of SlARF2 knockdown tomato mutants revealed that the downregulation of this gene enhanced primary root length and root branching and reduced plant wilting. At the physiological level, the arf2 mutant line displayed higher chlorophyll, soluble sugars, proline, and relative water contents as well as lower stomatal conductance and a decreased malondialdehyde content. Moreover, SlARF2 knockdown tomato mutants demonstrated higher activities of the antioxidant enzymes superoxide dismutase (SOD) and catalase (CAT) under salt and drought stresses than the wild type. Indeed, the stress tolerance of the arf2 mutant was also reflected by the upregulation of stress-related genes involved in ROS scavenging and plant defense, including SOD, CAT, dehydration-responsive element-binding protein, and early responsive to dehydration, which can ultimately result in a better resistance to salt and drought stresses. Furthermore, the transcriptional levels of the Δ1-pyrroline-5-carboxylate synthase (P5CS) gene were upregulated in the arf2 mutant after stress, in correlation with the higher levels of proline. Taken together, our findings reveal that SlARF2 is implicated in salt and drought tolerance in tomato and provides some considerable elements for improving the abiotic stress tolerance and increasing the crop yields of tomato.
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Affiliation(s)
- Ibtihaj El Mamoun
- Laboratoire de Biotechnologie et de Physiologie Végétales, Center of Plant and Microbial Biotechnology, Biodiversity and Environment, Faculty of Sciences, Mohammed V University in Rabat, Rabat 10000, Morocco;
- Laboratoire de Recherche en Sciences Végétales, UMR5546, Université de Toulouse, Centre National de la Recherche Scientifique (CNRS), Université Toulouse Paul Sabatier (UPS), Toulouse-INP, 31320 Auzeville-Tolosane, France
| | - Sarah Bouzroud
- Microbiology and Molecular Biology Team, Center of Plant and Microbial Biotechnology, Biodiversity and Environment, Faculty of Sciences, Mohammed V University in Rabat, Rabat 10000, Morocco;
| | - Mohamed Zouine
- Laboratoire de Recherche en Sciences Végétales, UMR5546, Université de Toulouse, Centre National de la Recherche Scientifique (CNRS), Université Toulouse Paul Sabatier (UPS), Toulouse-INP, 31320 Auzeville-Tolosane, France
| | - Abdelaziz Smouni
- Laboratoire de Biotechnologie et de Physiologie Végétales, Center of Plant and Microbial Biotechnology, Biodiversity and Environment, Faculty of Sciences, Mohammed V University in Rabat, Rabat 10000, Morocco;
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8
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Sun H, Hu K, Wei S, Yao G, Zhang H. ETHYLENE RESPONSE FACTORS 4.1/4.2 with an EAR motif repress anthocyanin biosynthesis in red-skinned pears. PLANT PHYSIOLOGY 2023; 192:1892-1912. [PMID: 36732887 PMCID: PMC10315276 DOI: 10.1093/plphys/kiad068] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 12/06/2022] [Accepted: 12/22/2022] [Indexed: 06/18/2023]
Abstract
Red-skinned pears (Pyrus L.) are preferred to consumers for their attractive color and abundant anthocyanins. Pyrus ETHYLENE RESPONSE FACTOR 3 (PyERF3) positively regulates anthocyanin biosynthesis through interacting with Pyrus myeloblastosis family 114 (PyMYB114) and Pyrus basic helix-loop-helix 3 (PybHLH3) in red-skinned pears. However, the role of APETALA2/ethylene response factors (AP2/ERFs), which negatively regulate anthocyanin biosynthesis, remains unclear in red-skinned pears. Here, we validated that 2 AP2/ERFs, PyERF4.1 and PyERF4.2, screened from the transcriptome data of 'Starkrimson' pear (Pyrus communis L.) and its green mutant, inhibit anthocyanin biosynthesis in transgenic pear calli, as well as in overexpression and gene-edited tomato (Solanum lycopersicum) fruits. Meanwhile, the co-transformation of PyERF4.1/PyERF4.2 with PyERF3-PyMYB114-PybHLH3 inhibited anthocyanin biosynthesis in pear fruits and strawberry (Fragaria vesca) receptacles. Further assays showed that PyMYB114 activated the transcription of PyERF4.1/PyERF4.2; PyERF4.1/PyERF4.2 then interacted with PyERF3 to affect the stability of the PyERF3-PyMYB114-PybHLH3 complex, thereby inhibiting the transcription of the anthocyanin biosynthesis gene Pyrus anthocyanidin synthase (PyANS). Furthermore, deletion of the ERF-associated-amphiphilic repression (EAR) motif eliminated the inhibitory effect of PyERF4.1/PyERF4.2 on anthocyanin biosynthesis, and a mutation of the PyERF4.2-EAR motif (LxLxM to LxLxL) strengthened the inhibitory effect, demonstrating that the EAR motif is indispensable for the inhibitory effect of PyERF4.1/PyERF4.2 on anthocyanin biosynthesis in pears. Our study has shed light on a feedback regulatory loop mechanism that balances the excessive accumulation of anthocyanins in red-skinned pears, providing insights into the regulatory mechanism of anthocyanin biosynthesis and the regulatory network of coloration in red-skinned pears.
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Affiliation(s)
- Hongye Sun
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Kangdi Hu
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Shuwei Wei
- Shandong Institute of Pomology, Tai’an 271000, China
| | - Gaifang Yao
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Hua Zhang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
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9
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Bascom C, Prigge MJ, Szutu W, Bantle A, Irmak S, Tu D, Estelle M. Clade-D auxin response factors regulate auxin signaling and development in the moss Physcomitrium patens. PLoS Biol 2023; 21:e3002163. [PMID: 37315060 PMCID: PMC10299833 DOI: 10.1371/journal.pbio.3002163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 06/27/2023] [Accepted: 05/12/2023] [Indexed: 06/16/2023] Open
Abstract
Auxin response factors (ARFs) are a family of transcription factors that are responsible for regulating gene expression in response to changes in auxin level. The analysis of ARF sequence and activity indicates that there are 2 major groups: activators and repressors. One clade of ARFs, clade-D, is sister to clade-A activating ARFs, but are unique in that they lack a DNA-binding domain. Clade-D ARFs are present in lycophytes and bryophytes but absent in other plant lineages. The transcriptional activity of clade-D ARFs, as well as how they regulate gene expression, is not well understood. Here, we report that clade-D ARFs are transcriptional activators in the model bryophyte Physcomitrium patens and have a major role in the development of this species. Δarfddub protonemata exhibit a delay in filament branching, as well as a delay in the chloronema to caulonema transition. Additionally, leafy gametophore development in Δarfddub lines lags behind wild type. We present evidence that ARFd1 interacts with activating ARFs via their PB1 domains, but not with repressing ARFs. Based on these results, we propose a model in which clade-D ARFs enhance gene expression by interacting with DNA bound clade-A ARFs. Further, we show that ARFd1 must form oligomers for full activity.
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Affiliation(s)
- Carlisle Bascom
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, San Diego, California, United States of America
| | - Michael J. Prigge
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, San Diego, California, United States of America
| | - Whitnie Szutu
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, San Diego, California, United States of America
| | - Alexis Bantle
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, San Diego, California, United States of America
| | - Sophie Irmak
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, San Diego, California, United States of America
| | - Daniella Tu
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, San Diego, California, United States of America
| | - Mark Estelle
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, San Diego, California, United States of America
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10
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Singh D, Debnath P, Sane AP, Sane VA. Tomato (Solanum lycopersicum) WRKY23 enhances salt and osmotic stress tolerance by modulating the ethylene and auxin pathways in transgenic Arabidopsis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 195:330-340. [PMID: 36669348 DOI: 10.1016/j.plaphy.2023.01.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 12/13/2022] [Accepted: 01/04/2023] [Indexed: 06/17/2023]
Abstract
Osmotic stress is one of the biggest problems in agriculture, which adversely affects crop productivity. Plants adopt several strategies to overcome osmotic stresses that include transcriptional reprogramming and activation of stress responses mediated by different transcription factors and phytohormones. We have identified a WRKY transcription factor from tomato, SlWRKY23, which is induced by mannitol and NaCl treatment. Over-expression of SlWRKY23 in transgenic Arabidopsis enhances osmotic stress tolerance to mannitol and NaCl and affects root growth and lateral root number. Transgenic Arabidopsis over-expressing SlWRKY23 showed reduced electrolyte leakage and higher relative water content than Col-0 plants upon mannitol and NaCl treatment. These lines also showed better membrane integrity with lower MDA content and higher proline content than Col-0. Responses to mannitol were governed by auxin as treatment with TIBA (auxin transport inhibitor) negatively affected the osmotic tolerance in transgenic lines by inhibiting lateral root growth. Similarly, responses to NaCl were controlled by ethylene as treatment with AgNO3 (ethylene perception inhibitor) inhibited the stress response to NaCl by suppressing primary and lateral root growth. The study shows that SlWRKY23, a osmotic stress inducible gene in tomato, imparts tolerance to mannitol and NaCl stress through interaction of the auxin and ethylene pathways.
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Affiliation(s)
- Deepika Singh
- Plant Gene Expression Lab, CSIR-National Botanical Research Institute, Lucknow, 226001, India
| | - Pratima Debnath
- Plant Gene Expression Lab, CSIR-National Botanical Research Institute, Lucknow, 226001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Aniruddha P Sane
- Plant Gene Expression Lab, CSIR-National Botanical Research Institute, Lucknow, 226001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Vidhu A Sane
- Plant Gene Expression Lab, CSIR-National Botanical Research Institute, Lucknow, 226001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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11
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Liu B, Liu K, Chen X, Xiao D, Wang T, Yang Y, Shuai H, Wu S, Yuan L, Chen L. Comparative Transcriptome Analysis Reveals the Interaction of Sugar and Hormone Metabolism Involved in the Root Hair Morphogenesis of the Endangered Fir Abies beshanzuensis. PLANTS (BASEL, SWITZERLAND) 2023; 12:276. [PMID: 36678989 PMCID: PMC9862426 DOI: 10.3390/plants12020276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/26/2022] [Accepted: 12/29/2022] [Indexed: 06/17/2023]
Abstract
Abies beshanzuensis, an extremely rare and critically endangered plant with only three wild adult trees globally, is strongly mycorrhizal-dependent, leading to difficulties in protection and artificial breeding without symbiosis. Root hair morphogenesis plays an important role in the survival of mycorrhizal symbionts. Due to the lack of an effective genome and transcriptome of A. beshanzuensis, the molecular signals involved in the root hair development remain unknown, which hinders its endangered mechanism analysis and protection. Herein, transcriptomes of radicles with root hair (RH1) and without root hair (RH0) from A. beshanzuensis in vitro plantlets were primarily established. Functional annotation and differentially expressed gene (DEG) analysis showed that the two phenotypes have highly differentially expressed gene clusters. Transcriptome divergence identified hormone and sugar signaling primarily involved in root hair morphogenesis of A. beshanzuensis. Weighted correlation network analysis (WGCNA) coupled with quantitative real-time PCR (qRT-PCR) found that two hormone-sucrose-root hair modules were linked by IAA17, and SUS was positioned in the center of the regulation network, co-expressed with SRK2E in hormone transduction and key genes related to root hair morphogenesis. Our results contribute to better understanding of the molecular mechanisms of root hair development and offer new insights into deciphering the survival mechanism of A. beshanzuensis and other endangered species, utilizing root hair as a compensatory strategy instead of poor mycorrhizal growth.
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Affiliation(s)
- Bin Liu
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Ke Liu
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Xiaorong Chen
- Qingyuan Conservation Center of Qianjiangyuan-Baishanzu National Park, Qingyuan 323800, China
| | - Duohong Xiao
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Tingjin Wang
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Yang Yang
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Hui Shuai
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Sumei Wu
- Qingyuan Conservation Center of Qianjiangyuan-Baishanzu National Park, Qingyuan 323800, China
| | - Lu Yuan
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Liping Chen
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
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12
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Zhang Y, Yu J, Xu X, Wang R, Liu Y, Huang S, Wei H, Wei Z. Molecular Mechanisms of Diverse Auxin Responses during Plant Growth and Development. Int J Mol Sci 2022; 23:ijms232012495. [PMID: 36293351 PMCID: PMC9604407 DOI: 10.3390/ijms232012495] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 10/13/2022] [Accepted: 10/15/2022] [Indexed: 11/16/2022] Open
Abstract
The plant hormone auxin acts as a signaling molecule to regulate numerous developmental processes throughout all stages of plant growth. Understanding how auxin regulates various physiological and developmental processes has been a hot topic and an intriguing field. Recent studies have unveiled more molecular details into how diverse auxin responses function in every aspect of plant growth and development. In this review, we systematically summarized and classified the molecular mechanisms of diverse auxin responses, and comprehensively elaborated the characteristics and multilevel regulation mechanisms of the canonical transcriptional auxin response. On this basis, we described the characteristics and differences between different auxin responses. We also presented some auxin response genes that have been genetically modified in plant species and how their changes impact various traits of interest. Finally, we summarized some important aspects and unsolved questions of auxin responses that need to be focused on or addressed in future research. This review will help to gain an overall understanding of and some insights into the diverse molecular mechanisms of auxin responses in plant growth and development that are instrumental in harnessing genetic resources in molecular breeding of extant plant species.
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Affiliation(s)
- Yang Zhang
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin 150500, China
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Jiajie Yu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Xiuyue Xu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Ruiqi Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Yingying Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Shan Huang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Hairong Wei
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931, USA
| | - Zhigang Wei
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin 150500, China
- Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region, School of Life Sciences, Heilongjiang University, Harbin 150080, China
- Correspondence: or
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13
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Cancé C, Martin-Arevalillo R, Boubekeur K, Dumas R. Auxin response factors are keys to the many auxin doors. THE NEW PHYTOLOGIST 2022; 235:402-419. [PMID: 35434800 DOI: 10.1111/nph.18159] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 03/22/2022] [Indexed: 06/14/2023]
Abstract
In plants, most developmental programs depend on the action of auxin. The best described model of the auxin signaling pathway, which explains most, but not all, of the auxin transcriptional responses, relies on a de-repression mechanism. The auxin/indole-3-acetic acid repressors (Aux/IAAs) interact with the auxin response factors (ARFs), the transcription factors of the auxin signaling pathway, leading to repression of the ARF-controlled genes. Auxin induces Aux/IAA degradation, releases ARFs and activates transcription. However, this elegant model is not suitable for all ARFs. Indeed, in Arabidopsis, which has 22 ARFs, only five of them fit into the model since they are the ones able to interact with Aux/IAAs. The remaining 17 have a limited capacity to interact with the repressors, and their mechanisms of action are still unclear. The differential interactions between ARF and Aux/IAA proteins constitute one of many examples of the biochemical and structural diversification of ARFs that affect their action and therefore affect auxin transcriptional responses. A deeper understanding of the structural properties of ARFs is fundamental to obtaining a better explanation of the action of auxin in plants.
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Affiliation(s)
- Coralie Cancé
- Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 38000, Grenoble, France
| | - Raquel Martin-Arevalillo
- Laboratoire de Reproduction et Développement des Plantes, ENS de Lyon, UCB Lyon 1, CNRS, INRA, Univ. Lyon, Lyon, France
| | - Kenza Boubekeur
- Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 38000, Grenoble, France
| | - Renaud Dumas
- Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 38000, Grenoble, France
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14
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Abstract
Auxin signaling regulates growth and developmental processes in plants. The core of nuclear auxin signaling relies on just three components: TIR1/AFBs, Aux/IAAs, and ARFs. Each component is itself made up of several domains, all of which contribute to the regulation of auxin signaling. Studies of the structural aspects of these three core signaling components have deepened our understanding of auxin signaling dynamics and regulation. In addition to the structured domains of these components, intrinsically disordered regions within the proteins also impact auxin signaling outcomes. New research is beginning to uncover the role intrinsic disorder plays in auxin-regulated degradation and subcellular localization. Structured and intrinsically disordered domains affect auxin perception, protein degradation dynamics, and DNA binding. Taken together, subtle differences within the domains and motifs of each class of auxin signaling component affect signaling outcomes and specificity.
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Affiliation(s)
- Nicholas Morffy
- Department of Biology, Duke University, Durham, North Carolina 27708, USA
- Center for Science and Engineering Living Systems (CSELS), Washington University, St. Louis, Missouri 63130, USA
| | - Lucia C Strader
- Department of Biology, Duke University, Durham, North Carolina 27708, USA
- Center for Science and Engineering Living Systems (CSELS), Washington University, St. Louis, Missouri 63130, USA
- Center for Engineering Mechanobiology, Washington University, St. Louis, Missouri 63130, USA
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15
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Yi C, Wang X, Chen Q, Callahan DL, Fournier-Level A, Whelan J, Jost R. Diverse phosphate and auxin transport loci distinguish phosphate tolerant from sensitive Arabidopsis accessions. PLANT PHYSIOLOGY 2021; 187:2656-2673. [PMID: 34636851 PMCID: PMC8644285 DOI: 10.1093/plphys/kiab441] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 08/18/2021] [Indexed: 05/11/2023]
Abstract
Phosphorus (P) is an essential element for plant growth often limiting agroecosystems. To identify genetic determinants of performance under variable phosphate (Pi) supply, we conducted genome-wide association studies on five highly predictive Pi starvation response traits in 200 Arabidopsis (Arabidopsis thaliana) accessions. Pi concentration in Pi-limited organs had the strongest, and primary root length had the weakest genetic component. Of 70 trait-associated candidate genes, 17 responded to Pi withdrawal. The PHOSPHATE TRANSPORTER1 gene cluster on chromosome 5 comprises PHT1;1, PHT1;2, and PHT1;3 with known impact on P status. A second locus featured uncharacterized endomembrane-associated auxin efflux carrier encoding PIN-LIKES7 (PILS7) which was more strongly suppressed in Pi-limited roots of Pi-starvation sensitive accessions. In the Col-0 background, Pi uptake and organ growth were impaired in both Pi-limited pht1;1 and two pils7 T-DNA insertion mutants, while Pi -limited pht1;2 had higher biomass and pht1;3 was indistinguishable from wild-type. Copy number variation at the PHT1 locus with loss of the PHT1;3 gene and smaller scale deletions in PHT1;1 and PHT1;2 predicted to alter both protein structure and function suggest diversification of PHT1 is a key driver for adaptation to P limitation. Haplogroup analysis revealed a phosphorylation site in the protein encoded by the PILS7 allele from stress-sensitive accessions as well as additional auxin-responsive elements in the promoter of the "stress tolerant" allele. The former allele's inability to complement the pils7-1 mutant in the Col-0 background implies the presence of a kinase signaling loop controlling PILS7 activity in accessions from P-rich environments, while survival in P-poor environments requires fine-tuning of stress-responsive root auxin signaling.
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Affiliation(s)
- Changyu Yi
- Department of Animal, Plant and Soil Sciences and La Trobe Institute for Agriculture and Food (LIAF), ARC Centre of Excellence in Plant Energy Biology, School of Life Sciences, La Trobe University, Bundoora VIC 3086, Australia
| | - Xinchao Wang
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture and Rural Affairs, Tea Research Institute, Chinese Academy of Agricultural Sciences, Zhejiang 31008, China
| | - Qian Chen
- Department of Animal, Plant and Soil Sciences and La Trobe Institute for Agriculture and Food (LIAF), ARC Centre of Excellence in Plant Energy Biology, School of Life Sciences, La Trobe University, Bundoora VIC 3086, Australia
| | - Damien L Callahan
- Centre for Chemistry and Biotechnology, School of Life and Environmental Sciences, Deakin University (Burwood Campus), Burwood VIC 3125, Australia
| | | | - James Whelan
- Department of Animal, Plant and Soil Sciences and La Trobe Institute for Agriculture and Food (LIAF), ARC Centre of Excellence in Plant Energy Biology, School of Life Sciences, La Trobe University, Bundoora VIC 3086, Australia
| | - Ricarda Jost
- Department of Animal, Plant and Soil Sciences and La Trobe Institute for Agriculture and Food (LIAF), ARC Centre of Excellence in Plant Energy Biology, School of Life Sciences, La Trobe University, Bundoora VIC 3086, Australia
- Author for communication:
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16
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Zhao H, Wang Y, Zhao S, Fu Y, Zhu L. HOMEOBOX PROTEIN 24 mediates the conversion of indole-3-butyric acid to indole-3-acetic acid to promote root hair elongation. THE NEW PHYTOLOGIST 2021; 232:2057-2070. [PMID: 34480752 DOI: 10.1111/nph.17719] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 08/26/2021] [Indexed: 06/13/2023]
Abstract
Indole-3-acetic acid (IAA) is a predominant form of active auxin in plants. In addition to de novo biosynthesis and release from its conjugate forms, IAA can be converted from its precursor indole-3-butyric acid (IBA). The IBA-derived IAA may help drive root hair elongation in Arabidopsis thaliana seedlings, but how the IBA-to-IAA conversion is regulated and affects IAA function requires further investigation. In this study, HOMEOBOX PROTEIN 24 (HB24), a transcription factor in the zinc finger-homeodomain family (ZF-HD family) of proteins, was identified. With loss of HB24 function, defective growth occurred in root hairs. INDOLE-3-BUTYRIC ACID RESPONSE 1 (IBR1), which encodes an enzyme involved in the IBA-to-IAA conversion, was identified as a direct target of HB24 for the control of root hair elongation. The exogenous IAA or auxin analogue 1-naphthalene acetic acid (NAA) both rescued the root hair growth phenotype of hb24 mutants, but IBA did not, suggesting a role for HB24 in the IBA-to-IAA conversion. Therefore, HB24 participates in root hair elongation by upregulating the expression of IBR1 and subsequently promoting the IBA-to-IAA conversion. Moreover, IAA also elevated the expression of HB24, suggesting a feedback loop is involved in IBA-to-IAA conversion-mediated root hair elongation.
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Affiliation(s)
- Huan Zhao
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Yutao Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Shuai Zhao
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Ying Fu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Lei Zhu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
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17
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Gomes GLB, Scortecci KC. Auxin and its role in plant development: structure, signalling, regulation and response mechanisms. PLANT BIOLOGY (STUTTGART, GERMANY) 2021; 23:894-904. [PMID: 34396657 DOI: 10.1111/plb.13303] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 05/04/2021] [Indexed: 05/28/2023]
Abstract
Auxins are plant hormones that play a central role in controlling plant growth and development across different environmental conditions. Even at low concentrations, auxins can regulate gene expression through specific transcription factors and proteins that are modulated to environmental responses in the signalling cascade. Auxins are synthesized in tissues with high cell division activity and distributed by specific transmembrane proteins that regulate efflux and influx. This review presents recent advances in understanding the biosynthetic pathways, both dependent and independent of tryptophan, highlighting the intermediate indole compounds (indole-3-acetamide, indole-3-acetaldoxime, indole-3-pyruvic acid and tryptamine) and the key enzymes for auxin biosynthesis, such as YUCs and TAAs. In relation to the signalling cascade, it has been shown that auxins influence gene expression regulation by the connection between synthesis and distribution. Moreover, the molecular action of the auxin response factors and auxin/indole-3-acetic acid transcription factors with the F-box TIR1/AFB auxin receptors regulates gene expression. In addition, the importance of microRNAs in the auxin signalling pathway and their influence on plant plasticity to environmental fluctuations is also demonstrated. Finally, this review describes the chemical and biological processes involving auxins in plants.
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Affiliation(s)
- G L B Gomes
- Programa de Pós-Graduação em Bioquímica, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Natal, Brazil
- Laboratório de Transformação de Plantas e Análises em Microscopia, Departamento de Biologia Celular e Genética, Universidade Federal do Rio Grande do Norte, Natal, Brazil
| | - K C Scortecci
- Programa de Pós-Graduação em Bioquímica, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Natal, Brazil
- Laboratório de Transformação de Plantas e Análises em Microscopia, Departamento de Biologia Celular e Genética, Universidade Federal do Rio Grande do Norte, Natal, Brazil
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18
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Kim Y, Kim SH, Shin DM, Kim SH. ATBS1-INTERACTING FACTOR 2 Negatively Modulates Pollen Production and Seed Formation in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2021; 12:704958. [PMID: 34386030 PMCID: PMC8353282 DOI: 10.3389/fpls.2021.704958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 07/02/2021] [Indexed: 06/13/2023]
Abstract
ATBS1-INTERACTING FACTOR 2 (AIF2) is a non-DNA-binding basic-helix-loop-helix (bHLH) transcription factor. Here, we demonstrate that AIF2 negatively modulates brassinosteroid (BR)-induced, BRASSINAZOLE RESISTANT 1 (BZR1)-mediated pollen and seed formation. AIF2-overexpressing Arabidopsis plants (AIF2ox) showed defective pollen grains and seed production while two AIF2 knockout mutants, aif2-1 and aif2-1/aif4-1, displayed opposite phenotypes. Genes encoding BZR1-regulated positive factors of seed size determination (SHB1, IKU1, MINI3) were suppressed in AIF2ox and genes for negative factors (AP2 and ARF2) were enhanced. Surprisingly, BZR1-regulated pollen genes such as SPL, MS1, and TDF1 were aberrantly up-regulated in AIF2ox plants. This stage-independent abnormal expression may lead to a retarded and defective progression of microsporogenesis, producing abnormal tetrad microspores and pollen grains with less-effective pollen tube germination. Auxin plays important roles in proper development of flower and seeds: genes for auxin biosynthesis such as TCPs and YUCCAs as well as for positive auxin signalling such as ARFs were suppressed in AIF2ox flowers. Moreover, lipid biosynthesis- and sucrose transport-related genes were repressed, resulting in impaired starch accumulation. Contrarily, sucrose and BR repressed ectopic accumulation of AIF2, thereby increasing silique length and the number of seeds. Taken together, we propose that AIF2 is negatively involved in pollen development and seed formation, and that sucrose- and BR-induced repression of AIF2 positively promotes pollen production and seed formation in Arabidopsis.
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19
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Bowman JL, Flores Sandoval E, Kato H. On the Evolutionary Origins of Land Plant Auxin Biology. Cold Spring Harb Perspect Biol 2021; 13:cshperspect.a040048. [PMID: 33558368 DOI: 10.1101/cshperspect.a040048] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Indole-3-acetic acid, that is, auxin, is a molecule found in a broad phylogenetic distribution of organisms, from bacteria to eukaryotes. In the ancestral land plant auxin was co-opted to be the paramount phytohormone mediating tropic responses and acting as a facilitator of developmental decisions throughout the life cycle. The evolutionary origins of land plant auxin biology genes can now be traced with reasonable clarity. Genes encoding the two enzymes of the land plant auxin biosynthetic pathway arose in the ancestral land plant by a combination of horizontal gene transfer from bacteria and possible neofunctionalization following gene duplication. Components of the auxin transcriptional signaling network have their origins in ancestral alga genes, with gene duplication and neofunctionalization of key domains allowing integration of a portion of the preexisting transcriptional network with auxin. Knowledge of the roles of orthologous genes in extant charophycean algae is lacking, but could illuminate the ancestral functions of both auxin and the co-opted transcriptional network.
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Affiliation(s)
- John L Bowman
- School of Biological Science, Monash University, Melbourne, Victoria 3800, Australia
| | | | - Hirotaka Kato
- Graduate School of Science, Kobe University, Kobe 657-8501, Japan
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20
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Sharma M, Singh D, Saksena HB, Sharma M, Tiwari A, Awasthi P, Botta HK, Shukla BN, Laxmi A. Understanding the Intricate Web of Phytohormone Signalling in Modulating Root System Architecture. Int J Mol Sci 2021; 22:ijms22115508. [PMID: 34073675 PMCID: PMC8197090 DOI: 10.3390/ijms22115508] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/11/2021] [Accepted: 05/13/2021] [Indexed: 12/12/2022] Open
Abstract
Root system architecture (RSA) is an important developmental and agronomic trait that is regulated by various physical factors such as nutrients, water, microbes, gravity, and soil compaction as well as hormone-mediated pathways. Phytohormones act as internal mediators between soil and RSA to influence various events of root development, starting from organogenesis to the formation of higher order lateral roots (LRs) through diverse mechanisms. Apart from interaction with the external cues, root development also relies on the complex web of interaction among phytohormones to exhibit synergistic or antagonistic effects to improve crop performance. However, there are considerable gaps in understanding the interaction of these hormonal networks during various aspects of root development. In this review, we elucidate the role of different hormones to modulate a common phenotypic output, such as RSA in Arabidopsis and crop plants, and discuss future perspectives to channel vast information on root development to modulate RSA components.
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21
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Kato H, Mutte SK, Suzuki H, Crespo I, Das S, Radoeva T, Fontana M, Yoshitake Y, Hainiwa E, van den Berg W, Lindhoud S, Ishizaki K, Hohlbein J, Borst JW, Boer DR, Nishihama R, Kohchi T, Weijers D. Design principles of a minimal auxin response system. NATURE PLANTS 2020; 6:473-482. [PMID: 32415296 DOI: 10.1038/s41477-020-0662-y] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 04/09/2020] [Indexed: 06/11/2023]
Abstract
Auxin controls numerous growth processes in land plants through a gene expression system that modulates ARF transcription factor activity1-3. Gene duplications in families encoding auxin response components have generated tremendous complexity in most land plants, and neofunctionalization enabled various unique response outputs during development1,3,4. However, it is unclear what fundamental biochemical principles underlie this complex response system. By studying the minimal system in Marchantia polymorpha, we derive an intuitive and simple model where a single auxin-dependent A-ARF activates gene expression. It is antagonized by an auxin-independent B-ARF that represses common target genes. The expression patterns of both ARF proteins define developmental zones where auxin response is permitted, quantitatively tuned or prevented. This fundamental design probably represents the ancestral system and formed the basis for inflated, complex systems.
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Affiliation(s)
- Hirotaka Kato
- Laboratory of Biochemistry, Wageningen University, Wageningen, The Netherlands
- Graduate School of Science, Kobe University, Kobe, Japan
| | - Sumanth K Mutte
- Laboratory of Biochemistry, Wageningen University, Wageningen, The Netherlands
| | - Hidemasa Suzuki
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Isidro Crespo
- Alba Synchrotron, Cerdanyola del Vallès, Barcelona, Spain
| | - Shubhajit Das
- Laboratory of Biochemistry, Wageningen University, Wageningen, The Netherlands
| | - Tatyana Radoeva
- Laboratory of Biochemistry, Wageningen University, Wageningen, The Netherlands
| | - Mattia Fontana
- Laboratory of Biochemistry, Wageningen University, Wageningen, The Netherlands
- Laboratory of Biophysics, Wageningen University, Wageningen, The Netherlands
| | | | - Emi Hainiwa
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Willy van den Berg
- Laboratory of Biochemistry, Wageningen University, Wageningen, The Netherlands
| | - Simon Lindhoud
- Laboratory of Biochemistry, Wageningen University, Wageningen, The Netherlands
| | | | - Johannes Hohlbein
- Laboratory of Biophysics, Wageningen University, Wageningen, The Netherlands
| | - Jan Willem Borst
- Laboratory of Biochemistry, Wageningen University, Wageningen, The Netherlands
| | - D Roeland Boer
- Alba Synchrotron, Cerdanyola del Vallès, Barcelona, Spain
| | | | - Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Dolf Weijers
- Laboratory of Biochemistry, Wageningen University, Wageningen, The Netherlands.
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22
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Vissenberg K, Claeijs N, Balcerowicz D, Schoenaers S. Hormonal regulation of root hair growth and responses to the environment in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:2412-2427. [PMID: 31993645 PMCID: PMC7178432 DOI: 10.1093/jxb/eraa048] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 01/23/2020] [Indexed: 05/04/2023]
Abstract
The main functions of plant roots are water and nutrient uptake, soil anchorage, and interaction with soil-living biota. Root hairs, single cell tubular extensions of root epidermal cells, facilitate or enhance these functions by drastically enlarging the absorptive surface. Root hair development is constantly adapted to changes in the root's surroundings, allowing for optimization of root functionality in heterogeneous soil environments. The underlying molecular pathway is the result of a complex interplay between position-dependent signalling and feedback loops. Phytohormone signalling interconnects this root hair signalling cascade with biotic and abiotic changes in the rhizosphere, enabling dynamic hormone-driven changes in root hair growth, density, length, and morphology. This review critically discusses the influence of the major plant hormones on root hair development, and how changes in rhizosphere properties impact on the latter.
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Affiliation(s)
- Kris Vissenberg
- Integrated Molecular Plant Physiology Research, Department of Biology, University of Antwerp, Antwerp, Belgium
- Plant Biochemistry and Biotechnology Lab, Department of Agriculture, Hellenic Mediterranean University, Stavromenos PC, Heraklion, Crete, Greece
| | - Naomi Claeijs
- Integrated Molecular Plant Physiology Research, Department of Biology, University of Antwerp, Antwerp, Belgium
| | - Daria Balcerowicz
- Integrated Molecular Plant Physiology Research, Department of Biology, University of Antwerp, Antwerp, Belgium
| | - Sébastjen Schoenaers
- Integrated Molecular Plant Physiology Research, Department of Biology, University of Antwerp, Antwerp, Belgium
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Schwarz B, Azodi CB, Shiu SH, Bauer P. Putative cis-Regulatory Elements Predict Iron Deficiency Responses in Arabidopsis Roots. PLANT PHYSIOLOGY 2020; 182:1420-1439. [PMID: 31937681 PMCID: PMC7054882 DOI: 10.1104/pp.19.00760] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 12/22/2019] [Indexed: 05/03/2023]
Abstract
Plant iron deficiency (-Fe) activates a complex regulatory network that coordinates root Fe uptake and distribution to sink tissues. In Arabidopsis (Arabidopsis thaliana), FER-LIKE FE DEFICIENCY-INDUCED TRANSCRIPTION FACTOR (FIT), a basic helix-loop-helix (bHLH) transcription factor (TF), regulates root Fe acquisition genes. Many other -Fe-induced genes are FIT independent, and instead regulated by other bHLH TFs and by yet unknown TFs. The cis-regulatory code, that is, the cis-regulatory elements (CREs) and their combinations that regulate plant -Fe-responses, remains largely elusive. Using Arabidopsis root transcriptome data and coexpression clustering, we identified over 100 putative CREs (pCREs) that predicted -Fe-induced gene expression in computational models. To assess pCRE properties and possible functions, we used large-scale in vitro TF binding data, positional bias, and evolutionary conservation. As one example, our approach uncovered pCREs resembling IDE1 (iron deficiency-responsive element 1), a known grass -Fe response CRE. Arabidopsis IDE1-likes were associated with FIT-dependent gene expression, more specifically with biosynthesis of Fe-chelating compounds. Thus, IDE1 seems to be conserved in grass and nongrass species. Our pCREs matched among others in vitro binding sites of B3, NAC, bZIP, and TCP TFs, which might be regulators of -Fe responses. Altogether, our findings provide a comprehensive source of cis-regulatory information for -Fe-responsive genes that advance our mechanistic understanding and inform future efforts in engineering plants with more efficient Fe uptake or transport systems.
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Affiliation(s)
- Birte Schwarz
- Institute of Botany, Heinrich Heine University, Düsseldorf 40225 Germany
| | - Christina B Azodi
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
- DOE-Great Lake Bioenergy Research Center, Michigan State University, East Lansing, Michigan 48824
| | - Shin-Han Shiu
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
- DOE-Great Lake Bioenergy Research Center, Michigan State University, East Lansing, Michigan 48824
- Department of Computational, Mathematics, Science, and Engineering, Michigan State University, East Lansing, Michigan 48824
| | - Petra Bauer
- Institute of Botany, Heinrich Heine University, Düsseldorf 40225 Germany
- Cluster of Excellence on Plant Science (CEPLAS), Heinrich Heine University, Düsseldorf 40225 Germany
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Molecular Evidences for the Interactions of Auxin, Gibberellin, and Cytokinin in Bent Peduncle Phenomenon in Rose ( Rosa sp.). Int J Mol Sci 2020; 21:ijms21041360. [PMID: 32085472 PMCID: PMC7072929 DOI: 10.3390/ijms21041360] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 02/08/2020] [Accepted: 02/14/2020] [Indexed: 12/03/2022] Open
Abstract
In roses (Rosa sp.), peduncle morphology is an important ornamental feature. The common physiological abnormality known as the bent peduncle phenomenon (BPP) seriously decreases the quality of rose flowers and thus the commercial value. Because the molecular mechanisms underlying this condition are poorly understood, we analysed the transcriptional profiles and cellular structures of bent rose peduncles. Numerous differentially expressed genes involved in the auxin, cytokinin, and gibberellin signaling pathways were shown to be associated with bent peduncle. Paraffin sections showed that the cell number on the upper sides of bent peduncles was increased, while the cells on the lower sides were larger than those in normal peduncles. We also investigated the large, deformed sepals that usually accompany BPP and found increased expression level of some auxin-responsive genes and decreased expression level of genes that are involved in cytokinin and gibberellin synthesis in these sepals. Furthermore, removal of the deformed sepals partially relieved BPP. In summary, our findings suggest that auxin, cytokinin, and gibberellin all influence the development of BPP by regulating cell division and expansion. To effectively reduce BPP in roses, more efforts need to be devoted to the molecular regulation of gibberellins and cytokinins in addition to that of auxin.
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Evolution of the Auxin Response Factors from charophyte ancestors. PLoS Genet 2019; 15:e1008400. [PMID: 31553720 PMCID: PMC6797205 DOI: 10.1371/journal.pgen.1008400] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 10/17/2019] [Accepted: 09/04/2019] [Indexed: 01/08/2023] Open
Abstract
Auxin is a major developmental regulator in plants and the acquisition of a transcriptional response to auxin likely contributed to developmental innovations at the time of water-to-land transition. Auxin Response Factors (ARFs) Transcription Factors (TFs) that mediate auxin-dependent transcriptional changes are divided into A, B and C evolutive classes in land plants. The origin and nature of the first ARF proteins in algae is still debated. Here, we identify the most ‘ancient’ ARF homologue to date in the early divergent charophyte algae Chlorokybus atmophyticus, CaARF. Structural modelling combined with biochemical studies showed that CaARF already shares many features with modern ARFs: it is capable of oligomerization, interacts with the TOPLESS co-repressor and specifically binds Auxin Response Elements as dimer. In addition, CaARF possesses a DNA-binding specificity that differs from class A and B ARFs and that was maintained in class C ARF along plants evolution. Phylogenetic evidence together with CaARF biochemical properties indicate that the different classes of ARFs likely arose from an ancestral proto-ARF protein with class C-like features. The foundation of auxin signalling would have thus happened from a pre-existing hormone-independent transcriptional regulation together with the emergence of a functional hormone perception complex. Plants transition from water to land was determining for the history of our planet, since it led to atmospheric and soil condition changes that promoted the appearance of other life forms. This transition initiated around 1 billion years ago from a Charophyte algae lineage that acquired features allowing it to adapt to the very different terrestrial conditions. Land plants coordinate their development with external stimuli through signalling mechanisms triggered by plant hormones. Therefore, evolution of these molecules and their signalling pathways likely played an important role in the aquatic to terrestrial move. In this manuscript we study the origin of auxin signalling, a plant hormone implicated in all plant developmental steps. Our studies suggest that out of the three families of proteins originally proposed to trigger auxin signalling in land plants, only one existed in Charophyte ancestors as a likely transcriptional repressor independent of auxin. We show that despite millions of years of evolution, this family of proteins has conserved its biochemical and structural properties that are found today in land plants. The results presented here provide an insight on how hormone signalling pathways could have evolved by co-opting a pre-existing hormone-independent transcriptional regulatory mechanism.
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Shibata M, Sugimoto K. A gene regulatory network for root hair development. JOURNAL OF PLANT RESEARCH 2019; 132:301-309. [PMID: 30903397 PMCID: PMC7082380 DOI: 10.1007/s10265-019-01100-2] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 03/06/2019] [Indexed: 05/21/2023]
Abstract
Root hairs play important roles for the acquisition of nutrients, microbe interaction and plant anchorage. In addition, root hairs provide an excellent model system to study cell patterning, differentiation and growth. Arabidopsis root hairs have been thoroughly studied to understand how plants regulate cell fate and growth in response to environmental signals. Accumulating evidence suggests that a multi-layered gene regulatory network is the molecular secret to enable the flexible and adequate response to multiple signals. In this review, we describe the key transcriptional regulators controlling cell fate and/or cell growth of root hairs. We also discuss how plants integrate phytohormonal and environmental signals, such as auxin, ethylene and phosphate availability, and modulate the level of these transcriptional regulators to tune root hair development.
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Affiliation(s)
- Michitaro Shibata
- RIKEN Center for Sustainable Resource Science, 230-0045, Yokohama, Japan.
| | - Keiko Sugimoto
- RIKEN Center for Sustainable Resource Science, 230-0045, Yokohama, Japan
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Wang L, Xu K, Li Y, Cai W, Zhao Y, Yu B, Zhu Y. Genome-Wide Identification of the Aux/IAA Family Genes (MdIAA) and Functional Analysis of MdIAA18 for Apple Tree Ideotype. Biochem Genet 2019; 57:709-733. [PMID: 30997626 DOI: 10.1007/s10528-019-09919-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 04/01/2019] [Indexed: 11/26/2022]
Abstract
The Aux/IAA (auxin/indole-3-acetic acid) gene family is one of the early auxin-responsive gene families, which play a central role in auxin response. Few reports are involved in Aux/IAA genes in fruit trees, especially in apple (Malus × domestica Borkh.). A total of 33 MdIAA members were identified, of which 27 members contained four conserved domains, whereas the others lost one or two conserved domains. Several cis-elements in promoters of MdIAAs were predicted responsive to hormones and abiotic stress. Tissue-specific expression patterns of MdIAAs in different apple tree ideotypes were investigated by quantitative real-time PCR. A large number of MdIAAs were highly expressed in leaf buds and reproductive organs, and MdIAAs clustered in same group showed similar expression profiles. Overexpression of MdIAA18 in Arabidopsis resulted in compact phenotype. These results indicated that MdIAA genes may be involved in vegetative and reproductive growth of apple. Taken together, the results provide useful clues to reveal the function of MdIAAs in apple and control apple tree architecture by manipulation of MdIAAs.
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Affiliation(s)
- Limin Wang
- Department of Pomology, College of Horticulture, China Agricultural University, Yuanmingyuan West Road No. 2, Haidian District, Beijing, 100193, People's Republic of China
| | - Ke Xu
- Department of Pomology, College of Horticulture, China Agricultural University, Yuanmingyuan West Road No. 2, Haidian District, Beijing, 100193, People's Republic of China
| | - Yongzhou Li
- Department of Pomology, College of Horticulture, China Agricultural University, Yuanmingyuan West Road No. 2, Haidian District, Beijing, 100193, People's Republic of China
| | - Wenbo Cai
- Department of Pomology, College of Horticulture, China Agricultural University, Yuanmingyuan West Road No. 2, Haidian District, Beijing, 100193, People's Republic of China
| | - Yanan Zhao
- Department of Pomology, College of Horticulture, China Agricultural University, Yuanmingyuan West Road No. 2, Haidian District, Beijing, 100193, People's Republic of China
| | - Boyang Yu
- Department of Pomology, College of Horticulture, China Agricultural University, Yuanmingyuan West Road No. 2, Haidian District, Beijing, 100193, People's Republic of China
| | - Yuandi Zhu
- Department of Pomology, College of Horticulture, China Agricultural University, Yuanmingyuan West Road No. 2, Haidian District, Beijing, 100193, People's Republic of China.
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Yang J, Liu Y, Yan H, Tian T, You Q, Zhang L, Xu W, Su Z. PlantEAR: Functional Analysis Platform for Plant EAR Motif-Containing Proteins. Front Genet 2018; 9:590. [PMID: 30555515 PMCID: PMC6283911 DOI: 10.3389/fgene.2018.00590] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Accepted: 11/15/2018] [Indexed: 01/05/2023] Open
Abstract
The Ethylene-responsive element binding factor-associated Amphiphilic Repression (EAR) motifs, which were initially identified in members of the Arabidopsis ethylene response factor (ERF) family, are transcriptional repression motifs in plants and are defined by the consensus sequence patterns of either LxLxL or DLNxxP. EAR motif-containing proteins can function as transcription repressors, thus interacting with co-repressors, such as TOPLESS and AtSAP18, affecting the structure of chromatin by histone modifications and thereby repressing gene transcription. EAR motif-containing proteins are highly conserved across diverse plant species and play important roles in hormone signal transduction, stress responses and development, but they have not been identified in most plants. In this study, we identified 20,542 EAR motif-containing proteins from 71 plant species based on a Hidden Markov Model and orthologous gene search, and then we constructed a functional analysis platform for plant EAR motif-containing proteins (PlantEAR, http://structuralbiology.cau.edu.cn/plantEAR) by integrating a variety of functional annotations and processed data. Several tools were provided as functional support for EAR motif-containing proteins, such as browse, search, co-expression and protein-protein interaction (PPI) network analysis as well as cis-element analysis and gene set enrichment analysis (GSEA). In addition, basing on the identified EAR motif-containing proteins, we also explored their distribution in various species and found that the numbers of EAR motif-containing proteins showed an increasing trend in evolution from algae to angiosperms.
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Affiliation(s)
- Jiaotong Yang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Yue Liu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Hengyu Yan
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Tian Tian
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Qi You
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Liwei Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Wenying Xu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Zhen Su
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
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