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Xu C, Xiang L, Huang W, Zhang X, Mao C, Wu S, Li T, Wang S, Wang S. Unraveling a Small Secreted Peptide SUBPEP3 That Positively Regulates Salt-Stress Tolerance in Pyrus betulifolia. Int J Mol Sci 2024; 25:4612. [PMID: 38731831 PMCID: PMC11083645 DOI: 10.3390/ijms25094612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 04/17/2024] [Accepted: 04/19/2024] [Indexed: 05/13/2024] Open
Abstract
Small secreted peptides (SSPs) play important roles in regulating plants' growth and development in response to external stimulus, but the genes and functions of SSPs in many species are still unknown. Therefore, it is particularly significant to characterize and annotate SSP genes in plant genomes. As a widely used stock of pears, Pyrus betulifolia has strong resistance to biotic and abiotic stresses. In this study, we analyzed the SSPs genes in the genome of P. betulifolia according to their characteristics and homology. A total of 1195 SSP genes were identified, and most of them are signaling molecules. Among these, we identified a new SSP, subtilase peptide 3 (SUBPEP3), which derived from the PA region of preSUBPEP3, increasing the expression level under salt stress. Both adding synthetic peptide SUBPEP3 to the culture medium of pears and the overexpression of SUBPEP3 in tobacco can improve the salt tolerance of plants. In summary, we annotated the SSP genes in the P. betulifolia genome and identified a small secreted peptide SUBPEP3 that regulates the salt tolerance of P. betulifolia, which provides an important theoretical basis for further revealing the function of SSPs.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Shengnan Wang
- College of Horticulture, China Agricultural University, Beijing 100080, China
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Kim EJ, Kim JH, Hong WJ, Kim EY, Kim MH, Lee SK, Min CW, Kim ST, Park SK, Jung KH, Kim YJ. Rice pollen-specific OsRALF17 and OsRALF19 are essential for pollen tube growth. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:2218-2236. [PMID: 37195059 DOI: 10.1111/jipb.13508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 05/16/2023] [Indexed: 05/18/2023]
Abstract
Pollen tube growth is essential for successful double fertilization, which is critical for grain yield in crop plants. Rapid alkalinization factors (RALFs) function as ligands for signal transduction during fertilization. However, functional studies on RALF in monocot plants are lacking. Herein, we functionally characterized two pollen-specific RALFs in rice (Oryza sativa) using multiple clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated protein 9-induced loss-of-function mutants, peptide treatment, expression analyses, and tag reporter lines. Among the 41 RALF members in rice, OsRALF17 was specifically expressed at the highest level in pollen and pollen tubes. Exogenously applied OsRALF17 or OsRALF19 peptide inhibited pollen tube germination and elongation at high concentrations but enhanced tube elongation at low concentrations, indicating growth regulation. Double mutants of OsRALF17 and OsRALF19 (ralf17/19) exhibited almost full male sterility with defects in pollen hydration, germination, and tube elongation, which was partially recovered by exogenous treatment with OsRALF17 peptide. This study revealed that two partially functionally redundant OsRALF17 and OsRALF19 bind to Oryza sativa male-gene transfer defective 2 (OsMTD2) and transmit reactive oxygen species signals for pollen tube germination and integrity maintenance in rice. Transcriptomic analysis confirmed their common downstream genes, in osmtd2 and ralf17/19. This study provides new insights into the role of RALF, expanding our knowledge of the biological role of RALF in regulating rice fertilization.
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Affiliation(s)
- Eui-Jung Kim
- Graduate School of Green Bio-Science & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Ji-Hyun Kim
- Department of Life Science and Environmental Biochemistry, Life and Industry Convergence Research Institute, Pusan National University, Miryang, 50463, Republic of Korea
| | - Woo-Jong Hong
- Department of Smart Farm Science, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Eun Young Kim
- School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Myung-Hee Kim
- School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
- Genomics Division, Department of Agricultural Bio-Resources, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, 54874, Republic of Korea
| | - Su Kyoung Lee
- Graduate School of Green Bio-Science & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Cheol Woo Min
- Department of Plant Bioscience, Pusan National University, Miryang, 50463, Republic of Korea
| | - Sun Tae Kim
- Department of Plant Bioscience, Pusan National University, Miryang, 50463, Republic of Korea
| | - Soon Ki Park
- School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Ki-Hong Jung
- Graduate School of Green Bio-Science & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Republic of Korea
- Research Center for Plant Plasticity, Seoul National University, Seoul, 08826, Republic of Korea
| | - Yu-Jin Kim
- Department of Life Science and Environmental Biochemistry, Life and Industry Convergence Research Institute, Pusan National University, Miryang, 50463, Republic of Korea
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Zhang Z, Gangurde SS, Chen S, Mandlik RR, Liu H, Deshmukh R, Xu J, Wu Z, Hong Y, Li Y. Overexpression of peanut ( Arachis hypogaea L.) AhGRFi gene enhanced root growth inhibition under exogenous NAA treatment in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2023; 14:1184058. [PMID: 37416889 PMCID: PMC10321354 DOI: 10.3389/fpls.2023.1184058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 05/24/2023] [Indexed: 07/08/2023]
Abstract
The 14-3-3 protein is a kind of evolutionary ubiquitous protein family highly conserved in eukaryotes. Initially, 14-3-3 proteins were reported in mammalian nervous tissues, but in the last decade, their role in various metabolic pathways in plants established the importance of 14-3-3 proteins. In the present study, a total of 22 14-3-3 genes, also called general regulatory factors (GRF), were identified in the peanut (Arachis hypogaea) genome, out of which 12 belonged to the ε group, whereas 10 of them belonged to the non- ε-group. Tissue-specific expression of identified 14-3-3 genes were studied using transcriptome analysis. The peanut AhGRFi gene was cloned and transformed into Arabidopsis thaliana. The investigation of subcellular localization indicated that AhGRFi is localized in the cytoplasm. Overexpression of the AhGRFi gene in transgenic Arabidopsis showed that under exogenous 1-naphthaleneacetic acid (NAA) treatment, root growth inhibition in transgenic plants was enhanced. Further analysis indicated that the expression of auxin-responsive genes IAA3, IAA7, IAA17, and SAUR-AC1 was upregulated and GH3.2 and GH3.3 were downregulated in transgenic plants, but the expression of GH3.2, GH3.3, and SAUR-AC1 showed opposite trends of change under NAA treatment. These results suggest that AhGRFi may be involved in auxin signaling during seedling root development. An in-depth study of the molecular mechanism of this process remains to be further explored.
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Affiliation(s)
- Zhou Zhang
- Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Sunil S. Gangurde
- Department of Plant Pathology, University of Georgia, Tifton, GA, United States
| | - Songbin Chen
- Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Rushil Ramesh Mandlik
- Department of Agriculture Biotechnology, National Agri-food Biotechnology Institute (NABI), Mohali, India
| | - Haiyan Liu
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Rupesh Deshmukh
- Department of Agriculture Biotechnology, National Agri-food Biotechnology Institute (NABI), Mohali, India
| | - Jialing Xu
- Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Zhongkang Wu
- Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yanbin Hong
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Yin Li
- Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
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4
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Fedoreyeva LI. Molecular Mechanisms of Regulation of Root Development by Plant Peptides. PLANTS (BASEL, SWITZERLAND) 2023; 12:1320. [PMID: 36987008 PMCID: PMC10053774 DOI: 10.3390/plants12061320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 02/14/2023] [Accepted: 03/01/2023] [Indexed: 06/19/2023]
Abstract
Peptides perform many functions, participating in the regulation of cell differentiation, regulating plant growth and development, and also involved in the response to stress factors and in antimicrobial defense. Peptides are an important class biomolecules for intercellular communication and in the transmission of various signals. The intercellular communication system based on the ligand-receptor bond is one of the most important molecular bases for creating complex multicellular organisms. Peptide-mediated intercellular communication plays a critical role in the coordination and determination of cellular functions in plants. The intercellular communication system based on the receptor-ligand is one of the most important molecular foundations for creating complex multicellular organisms. Peptide-mediated intercellular communication plays a critical role in the coordination and determination of cellular functions in plants. The identification of peptide hormones, their interaction with receptors, and the molecular mechanisms of peptide functioning are important for understanding the mechanisms of both intercellular communications and for regulating plant development. In this review, we drew attention to some peptides involved in the regulation of root development, which implement this regulation by the mechanism of a negative feedback loop.
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Affiliation(s)
- Larisa I Fedoreyeva
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya 42, 127550 Moscow, Russia
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5
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Xie M, Zhao C, Song M, Xiang Y, Tong C. Genome-wide identification and comparative analysis of CLE family in rapeseed and its diploid progenitors. FRONTIERS IN PLANT SCIENCE 2022; 13:998082. [PMID: 36340404 PMCID: PMC9632860 DOI: 10.3389/fpls.2022.998082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
Crop genomics and breeding CLAVATA3/EMBRYO SURROUNDING REGION-RELATED (CLE) proteins belong to a small peptide family in plants. During plant development, CLE gene family members play a pivotal role in regulating cell-to-cell communication and stem cell maintenance. However, the evolutionary process and functional importance of CLEs are unclear in Brassicaceae. In this study, a total of 70 BnCLEs were identified in Brassica napus (2n = 4x = 38, AnCn): 32 from the An subgenome, 36 from the Cn subgenome, and 2 from the unanchored subgenome. Meanwhile, 29 BrCLE and 32 BoCLE genes were explored in Brassica rapa (2n = 2x = 20, Ar) and Brassica oleracea (2n = 2x = 18, Co). Phylogenetic analysis revealed that 163 CLEs derived from three Brassica species and Arabidopsis thaliana can be divided into seven subfamilies. Homology and synteny analyses indicated whole-genome triplication (WGT) and segmental duplication may be the major contributors to the expansion of CLE family. In addition, RNA-seq and qPCR analysis indicated that 19 and 16 BnCLEs were more highly expressed in immature seeds and roots than in other tissues. Some CLE gene pairs exhibited different expression patterns in the same tissue, which indicated possible functional divergence. Furthermore, genetic variations and regional association mapping analysis indicated that 12 BnCLEs were potential genes for regulating important agronomic traits. This study provided valuable information to understand the molecular evolution and biological function of CLEs in B. napus and its diploid progenitors, which will be helpful for genetic improvement of high-yield breeding in B. napus.
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Affiliation(s)
- Meili Xie
- Guizhou Rapeseed Institute, Guizhou Academy of Agricultural Sciences, Guiyang, China
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Chuanji Zhao
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Min Song
- Guizhou Rapeseed Institute, Guizhou Academy of Agricultural Sciences, Guiyang, China
- College of Life Science, Qufu Normal University, Qufu, China
| | - Yang Xiang
- Guizhou Rapeseed Institute, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Chaobo Tong
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
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Huang P, Li Z, Guo H. New Advances in the Regulation of Leaf Senescence by Classical and Peptide Hormones. FRONTIERS IN PLANT SCIENCE 2022; 13:923136. [PMID: 35837465 PMCID: PMC9274171 DOI: 10.3389/fpls.2022.923136] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 06/02/2022] [Indexed: 06/15/2023]
Abstract
Leaf senescence is the last stage of leaf development, manifested by leaf yellowing due to the loss of chlorophyll, along with the degradation of macromolecules and facilitates nutrient translocation from the sink to the source tissues, which is essential for the plants' fitness. Leaf senescence is controlled by a sophisticated genetic network that has been revealed through the study of the molecular mechanisms of hundreds of senescence-associated genes (SAGs), which are involved in multiple layers of regulation. Leaf senescence is primarily regulated by plant age, but also influenced by a variety of factors, including phytohormones and environmental stimuli. Phytohormones, as important signaling molecules in plant, contribute to the onset and progression of leaf senescence. Recently, peptide hormones have been reported to be involved in the regulation of leaf senescence, enriching the significance of signaling molecules in controlling leaf senescence. This review summarizes recent advances in the regulation of leaf senescence by classical and peptide hormones, aiming to better understand the coordinated network of different pathways during leaf senescence.
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Affiliation(s)
- Peixin Huang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Research Center for Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Zhonghai Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Research Center for Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Hongwei Guo
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Research Center for Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, Southern University of Science and Technology, Shenzhen, China
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7
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Zhang Z, Liu C, Li K, Li X, Xu M, Guo Y. CLE14 functions as a "brake signal" to suppress age-dependent and stress-induced leaf senescence by promoting JUB1-mediated ROS scavenging in Arabidopsis. MOLECULAR PLANT 2022; 15:179-188. [PMID: 34530165 DOI: 10.1016/j.molp.2021.09.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 09/09/2021] [Accepted: 09/12/2021] [Indexed: 06/13/2023]
Abstract
Leaf senescence is an important developmental process in the plant life cycle and has a significant impact on agriculture. When facing harsh environmental conditions, monocarpic plants often initiate early leaf senescence as an adaptive mechanism to ensure a complete life cycle. Upon initiation, the senescence process is fine-tuned through the coordination of both positive and negative regulators. Here, we report that the small secreted peptide CLAVATA3/ESR-RELATED 14 (CLE14) functions in the suppression of leaf senescence by regulating ROS homeostasis in Arabidopsis. Expression of the CLE14-encoding gene in leaves was significantly induced by age, high salinity, abscisic acid (ABA), salicylic acid, and jasmonic acid. CLE14 knockout plants displayed accelerated progression of both natural and salinity-induced leaf senescence, whereas increased CLE14 expression or treatments with synthetic CLE14 peptides delayed senescence. CLE14 peptide treatments also delayed ABA-induced senescence in detached leaves. Further analysis showed that overexpression of CLE14 led to reduced ROS levels in leaves, where higher expression of ROS scavenging genes was detected. Moreover, CLE14 signaling resulted in transcriptional activation of JUB1, a NAC family transcription factor previously identified as a negative regulator of senescence. Notably, the delay of leaf senescence, reduction in H2O2 level, and activation of ROS scavenging genes by CLE14 peptides were dependent on JUB1. Collectively, these results suggest that the small peptide CLE14 serves as a novel "brake signal" to regulate age-dependent and stress-induced leaf senescence through JUB1-mediated ROS scavenging.
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Affiliation(s)
- Zenglin Zhang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, Shandong 266101, China
| | - Cheng Liu
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, Shandong 266101, China
| | - Kui Li
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, Shandong 266101, China
| | - Xiaoxu Li
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, Shandong 266101, China
| | - Mengmeng Xu
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, Shandong 266101, China
| | - Yongfeng Guo
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, Shandong 266101, China.
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8
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Kim MJ, Jeon BW, Oh E, Seo PJ, Kim J. Peptide Signaling during Plant Reproduction. TRENDS IN PLANT SCIENCE 2021; 26:822-835. [PMID: 33715959 DOI: 10.1016/j.tplants.2021.02.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 02/02/2021] [Accepted: 02/17/2021] [Indexed: 05/08/2023]
Abstract
Plant signaling peptides are involved in cell-cell communication networks and coordinate a wide range of plant growth and developmental processes. Signaling peptides generally bind to receptor-like kinases, inducing their dimerization with co-receptors for signaling activation to trigger cellular signaling and biological responses. Fertilization is an important life event in flowering plants, involving precise control of cell-cell communications between male and female tissues. Peptide-receptor-like kinase-mediated signaling plays an important role in male-female interactions for successful fertilization in flowering plants. Here, we describe the recent findings on the functions and signaling pathways of peptides and receptors involved in plant reproduction processes including pollen germination, pollen tube growth, pollen tube guidance to the embryo sac, and sperm cell reception in female tissues.
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Affiliation(s)
- Min-Jung Kim
- Department of Bioenergy Science and Technology, Chonnam National University, Gwangju 61186, Korea; Department of Integrative Food, Bioscience, and Technology, Chonnam National University, Gwangju 61186, Korea
| | - Byeong Wook Jeon
- Department of Bioenergy Science and Technology, Chonnam National University, Gwangju 61186, Korea; Department of Integrative Food, Bioscience, and Technology, Chonnam National University, Gwangju 61186, Korea
| | - Eunkyoo Oh
- Department of Life Sciences, Korea University, Seoul 02841, Korea
| | - Pil Joon Seo
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - Jungmook Kim
- Department of Bioenergy Science and Technology, Chonnam National University, Gwangju 61186, Korea; Department of Integrative Food, Bioscience, and Technology, Chonnam National University, Gwangju 61186, Korea; Kumho Life Science Laboratory, Chonnam National University, Buk-Gu, Gwangju 61186, Korea.
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9
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Furumizu C, Krabberød AK, Hammerstad M, Alling RM, Wildhagen M, Sawa S, Aalen RB. The sequenced genomes of non-flowering land plants reveal the innovative evolutionary history of peptide signaling. THE PLANT CELL 2021; 33:2915-2934. [PMID: 34240188 PMCID: PMC8462819 DOI: 10.1093/plcell/koab173] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 06/08/2021] [Indexed: 12/20/2022]
Abstract
An understanding of land plant evolution is a prerequisite for in-depth knowledge of plant biology. Here we extract and explore information hidden in the increasing number of sequenced plant genomes, from bryophytes to angiosperms, to elucidate a specific biological question - how peptide signaling evolved. To conquer land and cope with changing environmental conditions, plants have gone through transformations that must have required innovations in cell-to-cell communication. We discuss peptides mediating endogenous and exogenous changes by interaction with receptors activating intracellular molecular signaling. Signaling peptides were discovered in angiosperms and operate in tissues and organs such as flowers, seeds, vasculature, and 3D meristems that are not universally conserved across land plants. Nevertheless, orthologs of angiosperm peptides and receptors have been identified in non-angiosperms. These discoveries provoke questions regarding co-evolution of ligands and their receptors, and whether de novo interactions in peptide signaling pathways may have contributed to generate novel traits in land plants. The answers to such questions will have profound implications for the understanding of the evolution of cell-to-cell communication and the wealth of diversified terrestrial plants. Under this perspective we have generated, analyzed, and reviewed phylogenetic, genomic, structural, and functional data to elucidate the evolution of peptide signaling.
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Affiliation(s)
- Chihiro Furumizu
- Graduate School of Science and Technology, Kumamoto University, Kumamoto, Japan
| | - Anders K Krabberød
- Section for Evolutionary Biology and Genetics, Department of Biosciences, University of Oslo, Norway
| | - Marta Hammerstad
- Section for Biochemistry and Molecular Biology, Department of Biosciences, University of Oslo, Norway
| | - Renate M Alling
- Section for Evolutionary Biology and Genetics, Department of Biosciences, University of Oslo, Norway
| | - Mari Wildhagen
- Section for Evolutionary Biology and Genetics, Department of Biosciences, University of Oslo, Norway
| | - Shinichiro Sawa
- Graduate School of Science and Technology, Kumamoto University, Kumamoto, Japan
| | - Reidunn B Aalen
- Section for Evolutionary Biology and Genetics, Department of Biosciences, University of Oslo, Norway
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Jeon BW, Kim MJ, Pandey SK, Oh E, Seo PJ, Kim J. Recent advances in peptide signaling during Arabidopsis root development. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:2889-2902. [PMID: 33595615 DOI: 10.1093/jxb/erab050] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 02/01/2021] [Indexed: 06/12/2023]
Abstract
Roots provide the plant with water and nutrients and anchor it in a substrate. Root development is controlled by plant hormones and various sets of transcription factors. Recently, various small peptides and their cognate receptors have been identified as controlling root development. Small peptides bind to membrane-localized receptor-like kinases, inducing their dimerization with co-receptor proteins for signaling activation and giving rise to cellular signaling outputs. Small peptides function as local and long-distance signaling molecules involved in cell-to-cell communication networks, coordinating root development. In this review, we survey recent advances in the peptide ligand-mediated signaling pathways involved in the control of root development in Arabidopsis. We describe the interconnection between peptide signaling and conventional phytohormone signaling. Additionally, we discuss the diversity of identified peptide-receptor interactions during plant root development.
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Affiliation(s)
- Byeong Wook Jeon
- Kumho Life Science Laboratory, Chonnam National University, Buk-Gu, Gwangju 61186, Korea
| | - Min-Jung Kim
- Department of Bioenergy Science and Technology, Chonnam National University, Gwangju 61186, Korea
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju 61186, Korea
| | - Shashank K Pandey
- Department of Bioenergy Science and Technology, Chonnam National University, Gwangju 61186, Korea
| | - Eunkyoo Oh
- Department of Life Sciences, Korea University, Seoul 02841, Korea
| | - Pil Joon Seo
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - Jungmook Kim
- Kumho Life Science Laboratory, Chonnam National University, Buk-Gu, Gwangju 61186, Korea
- Department of Bioenergy Science and Technology, Chonnam National University, Gwangju 61186, Korea
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju 61186, Korea
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11
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Song Y, Yang S, Wang J. In vitro and in vivo activity analysis of poplar CLE dodecapeptides that are most divergent from Arabidopsis counterparts. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 305:110832. [PMID: 33691966 DOI: 10.1016/j.plantsci.2021.110832] [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: 10/12/2020] [Revised: 01/20/2021] [Accepted: 01/22/2021] [Indexed: 06/12/2023]
Abstract
Intercellular communication mediated by the plant-specific CLAVATA3/ENDOSPERM SURROUNDING REGION (ESR)-related (CLE) family members is one of the fundamental mechanisms coordinating the development of complex bodies of plants. In this work, we chose 8 out of 38 putative CLE dodecapeptides encoded in the genome of P. trichocarpa based on their lowest sequence similarity with Arabidopsis CLE peptides, and investigated how such sequence variations affect their functional characteristics. In group 1, PtCLE16p faithfully retained the AtCLE1-7p activity, while PtCLE49p reversed the root-enhancing effect to an inhibitory one with two extra amino acid substitutions, which might have disrupted the capacity of PtCLE49p to recognize the corresponding receptors. In group 2, PtCLE9p conferred Arabidopsis with retarded root growth and suppressed phloem differentiation in a negative dominant manner just like AtCLE25G6T did. PtCLE9p enhanced the vegetative growth in both basal and aerial rosettes by regulating the expression of AERIAL ROSETTE 1 (ART1) and FRIGIDA (FRI) as well as the downstream FLOWERING LOCUS C (FLC) genes. In group 3, PtCLE34p and PtCLE5p slightly promoted primary root growth, while PtCLE40p revealed CLV3p-like and TDIF activity in root and hypocotyls, respectively. The remaining PtCLE18p in group 4 dramatically disturbed the expression of WOX5 and promoted the development of root hairs by repressing the expression of GLABRA2 (GL2) gene, which encoded a negative regulator of epidermal cells differentiation towards root hairs. In summary, our data indicated that with significant functional conservation and common signaling machinery existing for CLE families of land plants, unique and diverse activities of CLE peptides have evolved to perform specific functions in different plant species.
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Affiliation(s)
- Yawen Song
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Shaohui Yang
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Jiehua Wang
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, China.
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12
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Shao Y, Yu X, Xu X, Li Y, Yuan W, Xu Y, Mao C, Zhang S, Xu J. The YDA-MKK4/MKK5-MPK3/MPK6 Cascade Functions Downstream of the RGF1-RGI Ligand-Receptor Pair in Regulating Mitotic Activity in Root Apical Meristem. MOLECULAR PLANT 2020; 13:1608-1623. [PMID: 32916336 DOI: 10.1016/j.molp.2020.09.004] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 08/16/2020] [Accepted: 09/07/2020] [Indexed: 05/26/2023]
Abstract
The mitotic activity of root apical meristem (RAM) is critical to primary root growth and development. Previous studies have identified the roles of ROOT GROWTH FACTOR 1 (RGF1), a peptide ligand, and its receptors, RGF1 INSENSITIVEs (RGIs), a clade of five leucine-rich-repeat receptor-like kinases, in promoting cell division in the RAM, which determines the primary root length. However, the downstream signaling components remain elusive. In this study, we identify a complete mitogen-activated protein kinase (MAPK or MPK) cascade, composed of YDA, MKK4/MKK5, and MPK3/MPK6, that functions downstream of the RGF1-RGI ligand-receptor pair. Similar to the rgi1/2/3/4/5 quintuple mutant, loss-of-function mutants of MPK3 and MPK6, MKK4 and MKK5, or YDA show a short-root phenotype, which is associated with reduced mitotic activity and lower expression of PLETHORA 1 (PLT1)/PLT2 in the RAM. Furthermore, MPK3/MPK6 activation in response to exogenous RGF1 treatment is impaired in the rgi1/2/3/4/5 quintuple, yda single, and mkk4 mkk5 double mutants. Epistatic analyses demonstrated that the expression of constitutively active MKK4, MKK5, or YDA driven by the RGI2 promoter can rescue the short-root phenotype of the rgi1/2/3/4/5 mutant. Taken together, these results suggest that the YDA-MKK4/MKK5-MPK3/MPK6 cascade functions downstream of the RGF1-RGI ligand-receptor pair and upstream of PLT1/PLT2 to modulate the stem cell population and primary root growth in Arabidopsis.
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Affiliation(s)
- Yiming Shao
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Xinxing Yu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Xuwen Xu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yong Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Wenxin Yuan
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yan Xu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Chuanzao Mao
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Shuqun Zhang
- Division of Biochemistry, University of Missouri, Columbia, MO 65211, USA.
| | - Juan Xu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China.
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13
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Aggarwal S, Kumar A, Jain M, Sudan J, Singh K, Kumari S, Mustafiz A. C-terminally encoded peptides (CEPs) are potential mediators of abiotic stress response in plants. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2020; 26:2019-2033. [PMID: 33088046 PMCID: PMC7548271 DOI: 10.1007/s12298-020-00881-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 08/18/2020] [Accepted: 09/04/2020] [Indexed: 05/13/2023]
Abstract
Intracellular signaling is a critical determinant of the normal growth and development of plants. Signaling peptides, also known as peptide hormones, along with classical phytohormones, are the significant players of plant intracellular signaling. C-terminally encoded peptide (CEP), a 15-amino acid post-translationally peptide identified in Arabidopsis, plays a pivotal role in lateral root formation, nodulation, and act as long-distance root to shoot signaling molecule in N-starvation conditions. Expression of CEP gene members in Arabidopsis is perturbed by nitrogen starvation; however, not much is known regarding their role in other abiotic stress conditions. To gain a comprehensive insight into CEP biology, we identified CEP genes across diverse plant genera (Glycine max, Sorghum bicolor, Brassica rapa, Zea mays, and Oryza sativa) using bioinformatics tools. In silico promoter analysis revealed that CEP gene promoters show an abundance of abiotic stress-responsive elements suggesting a possible role of CEPs in abiotic stress signaling. Spatial and temporal expression patterns of CEP via RNA seq and microarray revealed that various CEP genes are transcriptionally regulated in response to abiotic stresses. Validation of rice CEP genes expression by qRT-PCR showed that OsCEP1, OsCEP8, OsCEP9, and OsCEP10 were highly upregulated in response to different abiotic stress conditions. Our findings suggest these CEP genes might be important mediators of the abiotic stress response and warrant further overexpression/knockout studies to delineate their precise role in abiotic stress response.
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Affiliation(s)
- Sakshi Aggarwal
- Plant Molecular Biology Laboratory, Faculty of Life Sciences and Biotechnology, South Asian University, New Delhi, 110021 India
| | - Ashish Kumar
- Plant Molecular Biology Laboratory, Faculty of Life Sciences and Biotechnology, South Asian University, New Delhi, 110021 India
| | - Muskan Jain
- Plant Molecular Biology Laboratory, Faculty of Life Sciences and Biotechnology, South Asian University, New Delhi, 110021 India
| | - Jebi Sudan
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology, Jammu, 180009 India
| | - Kapil Singh
- Plant Molecular Biology Laboratory, Faculty of Life Sciences and Biotechnology, South Asian University, New Delhi, 110021 India
| | - Sumita Kumari
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology, Jammu, 180009 India
| | - Ananda Mustafiz
- Plant Molecular Biology Laboratory, Faculty of Life Sciences and Biotechnology, South Asian University, New Delhi, 110021 India
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14
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Luo JS, Xiao Y, Yao J, Wu Z, Yang Y, Ismail AM, Zhang Z. Overexpression of a Defensin-Like Gene CAL2 Enhances Cadmium Accumulation in Plants. FRONTIERS IN PLANT SCIENCE 2020; 11:217. [PMID: 32174951 PMCID: PMC7057248 DOI: 10.3389/fpls.2020.00217] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 02/12/2020] [Indexed: 05/15/2023]
Abstract
Accumulation and detoxification of cadmium in rice shoots are of great importance for adaptation to grow in cadmium contaminated soils and for limiting the transport of Cd to grains. However, the molecular mechanisms behind the processes involved in this regulation remain largely unknown. Defensin proteins play important roles in heavy metal tolerance and accumulation in plants. In rice, the cell wall-localized defensin protein (CAL1) is involved in Cd efflux and partitioning to the shoots. In the present study, we functionally characterized the CAL2 defensin protein and determined its contribution to Cd accumulation. CAL2 shared 66% similarity with CAL1, and its mRNA accumulation is mainly observed in roots and is unaffected by Cd stress, but its transcription level was lower than that of CAL1 based on the relative expression of CAL2/Actin1 observed in this study and that reported previously. A promoter-GUS assay revealed that CAL2 is expressed in root tips. Stable expression of the CAL2-mRFP fusion protein indicated that CAL2 is also localized in the cell walls. An in vitro Cd binding experiment revealed that CAL2 has Cd chelation activity. Overexpression of CAL2 increased Cd accumulation in Arabidopsis and rice shoots, but it had no effect on the accumulation of other essential elements. Heterologous expression of CAL2 enhanced Cd sensitivity in Arabidopsis, whereas overexpression of CAL2 had no effect on Cd tolerance in rice. These findings indicate that CAL2 positively regulates Cd accumulation in ectopic overexpression lines of Arabidopsis and rice. We have identified a new gene regulating Cd accumulation in rice grain, which would provide a new genetic resource for molecular breeding.
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Affiliation(s)
- Jin-Song Luo
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, College of Resources and Environmental Sciences, Hunan Agricultural University, Changsha, China
- Hunan Provincial Key Laboratory of Farmland Pollution Control and Agricultural Resources Use, Hunan Provincial Key Laboratory of Nutrition in Common University, National Engineering Laboratory on Soil and Fertilizer Resources Efficient Utilization, Changsha, China
| | - Yan Xiao
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, College of Resources and Environmental Sciences, Hunan Agricultural University, Changsha, China
- Hunan Provincial Key Laboratory of Farmland Pollution Control and Agricultural Resources Use, Hunan Provincial Key Laboratory of Nutrition in Common University, National Engineering Laboratory on Soil and Fertilizer Resources Efficient Utilization, Changsha, China
| | - Junyue Yao
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, College of Resources and Environmental Sciences, Hunan Agricultural University, Changsha, China
- Hunan Provincial Key Laboratory of Farmland Pollution Control and Agricultural Resources Use, Hunan Provincial Key Laboratory of Nutrition in Common University, National Engineering Laboratory on Soil and Fertilizer Resources Efficient Utilization, Changsha, China
| | - Zhimin Wu
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, College of Resources and Environmental Sciences, Hunan Agricultural University, Changsha, China
- Hunan Provincial Key Laboratory of Farmland Pollution Control and Agricultural Resources Use, Hunan Provincial Key Laboratory of Nutrition in Common University, National Engineering Laboratory on Soil and Fertilizer Resources Efficient Utilization, Changsha, China
| | - Yong Yang
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, College of Resources and Environmental Sciences, Hunan Agricultural University, Changsha, China
- Hunan Provincial Key Laboratory of Farmland Pollution Control and Agricultural Resources Use, Hunan Provincial Key Laboratory of Nutrition in Common University, National Engineering Laboratory on Soil and Fertilizer Resources Efficient Utilization, Changsha, China
| | | | - Zhenhua Zhang
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, College of Resources and Environmental Sciences, Hunan Agricultural University, Changsha, China
- Hunan Provincial Key Laboratory of Farmland Pollution Control and Agricultural Resources Use, Hunan Provincial Key Laboratory of Nutrition in Common University, National Engineering Laboratory on Soil and Fertilizer Resources Efficient Utilization, Changsha, China
- *Correspondence: Zhenhua Zhang,
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15
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Ren SC, Song XF, Chen WQ, Lu R, Lucas WJ, Liu CM. CLE25 peptide regulates phloem initiation in Arabidopsis through a CLERK-CLV2 receptor complex. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2019; 61:1043-1061. [PMID: 31127689 DOI: 10.1111/jipb.12846] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 05/24/2019] [Indexed: 05/29/2023]
Abstract
The phloem, located within the vascular system, is critical for delivery of nutrients and signaling molecules throughout the plant body. Although the morphological process and several factors regulating phloem differentiation have been reported, the molecular mechanism underlying its initiation remains largely unknown. Here, we report that the small peptide-coding gene, CLAVATA 3 (CLV3)/EMBEYO SURROUNDING REGION 25 (CLE25), the expression of which begins in provascular initial cells of 64-cell-staged embryos, and continues in sieve element-procambium stem cells and phloem lineage cells, during post-embryonic root development, facilitates phloem initiation in Arabidopsis. Knockout of CLE25 led to delayed protophloem formation, and in situ expression of an antagonistic CLE25G6T peptide compromised the fate-determining periclinal division of the sieve element precursor cell and the continuity of the phloem in roots. In stems of CLE25G6T plants the phloem formation was also compromised, and procambial cells were over-accumulated. Genetic and biochemical analyses indicated that a complex, consisting of the CLE-RESISTANT RECEPTOR KINASE (CLERK) leucine-rich repeat (LRR) receptor kinase and the CLV2 LRR receptor-like protein, is involved in perceiving the CLE25 peptide. Similar to CLE25, CLERK was also expressed during early embryogenesis. Taken together, our findings suggest that CLE25 regulates phloem initiation in Arabidopsis through a CLERK-CLV2 receptor complex.
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Affiliation(s)
- Shi-Chao Ren
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Fragrant Hill, Beijing, 100093, China
| | - Xiu-Fen Song
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Fragrant Hill, Beijing, 100093, China
| | - Wen-Qiang Chen
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Fragrant Hill, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ran Lu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Fragrant Hill, Beijing, 100093, China
| | - William J Lucas
- Department of Plant Biology, College of Biological Sciences, University of California, Davis, CA, 95616, USA
| | - Chun-Ming Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Fragrant Hill, Beijing, 100093, China
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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16
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Li Z, Liu D, Xia Y, Li Z, Niu N, Ma S, Wang J, Song Y, Zhang G. Identification and Functional Analysis of the CLAVATA3/EMBRYO SURROUNDING REGION (CLE) Gene Family in Wheat. Int J Mol Sci 2019; 20:E4319. [PMID: 31484454 PMCID: PMC6747155 DOI: 10.3390/ijms20174319] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 08/25/2019] [Accepted: 09/01/2019] [Indexed: 12/13/2022] Open
Abstract
CLAVATA3/EMBRYO SURROUNDING REGION (CLE) peptides are post-translationally cleaved and modified peptides from their corresponding pre-propeptides. Although they are only 12 to 13 amino acids in length, they are important ligands involved in regulating cell proliferation and differentiation in plant shoots, roots, vasculature, and other tissues. They function by interacting with their corresponding receptors. CLE peptides have been studied in many plants, but not in wheat. We identified 104 TaCLE genes in the wheat genome based on a genome-wide scan approach. Most of these genes have homologous copies distributed on sub-genomes A, B, and D. A few genes are derived from tandem duplication and segmental duplication events. Phylogenetic analysis revealed that TaCLE genes can be divided into five different groups. We obtained functional characterization of the peptides based on the evolutionary relationships among the CLE peptide families of wheat, rice, and Arabidopsis, and expression pattern analysis. Using chemically synthesized peptides (TaCLE3p and TaCLE34p), we found that TaCLE3 and TaCLE34 play important roles in regulating wheat and Arabidopsis root development, and wheat stem development. Overexpression analysis of TaCLE3 in Arabidopsis revealed that TaCLE3 not only affects the development of roots and stems, but also affects the development of leaves and fruits. These data represent the first comprehensive information on TaCLE family members.
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Affiliation(s)
- Zheng Li
- College of Agronomy, Northwest A&F University, National Yangling Agricultural Biotechnology & Breeding Center, Yangling Branch of State Wheat Improvement Centre, Wheat Breeding Engineering Research Center, Ministry of Education, Key Laboratory of Crop Heterosis of Shaanxi Province, Yangling 712100, China
| | - Dan Liu
- College of Agronomy, Northwest A&F University, National Yangling Agricultural Biotechnology & Breeding Center, Yangling Branch of State Wheat Improvement Centre, Wheat Breeding Engineering Research Center, Ministry of Education, Key Laboratory of Crop Heterosis of Shaanxi Province, Yangling 712100, China
| | - Yu Xia
- College of Agronomy, Northwest A&F University, National Yangling Agricultural Biotechnology & Breeding Center, Yangling Branch of State Wheat Improvement Centre, Wheat Breeding Engineering Research Center, Ministry of Education, Key Laboratory of Crop Heterosis of Shaanxi Province, Yangling 712100, China
| | - Ziliang Li
- College of Agronomy, Northwest A&F University, National Yangling Agricultural Biotechnology & Breeding Center, Yangling Branch of State Wheat Improvement Centre, Wheat Breeding Engineering Research Center, Ministry of Education, Key Laboratory of Crop Heterosis of Shaanxi Province, Yangling 712100, China
| | - Na Niu
- College of Agronomy, Northwest A&F University, National Yangling Agricultural Biotechnology & Breeding Center, Yangling Branch of State Wheat Improvement Centre, Wheat Breeding Engineering Research Center, Ministry of Education, Key Laboratory of Crop Heterosis of Shaanxi Province, Yangling 712100, China
| | - Shoucai Ma
- College of Agronomy, Northwest A&F University, National Yangling Agricultural Biotechnology & Breeding Center, Yangling Branch of State Wheat Improvement Centre, Wheat Breeding Engineering Research Center, Ministry of Education, Key Laboratory of Crop Heterosis of Shaanxi Province, Yangling 712100, China
| | - Junwei Wang
- College of Agronomy, Northwest A&F University, National Yangling Agricultural Biotechnology & Breeding Center, Yangling Branch of State Wheat Improvement Centre, Wheat Breeding Engineering Research Center, Ministry of Education, Key Laboratory of Crop Heterosis of Shaanxi Province, Yangling 712100, China
| | - Yulong Song
- College of Agronomy, Northwest A&F University, National Yangling Agricultural Biotechnology & Breeding Center, Yangling Branch of State Wheat Improvement Centre, Wheat Breeding Engineering Research Center, Ministry of Education, Key Laboratory of Crop Heterosis of Shaanxi Province, Yangling 712100, China
| | - Gaisheng Zhang
- College of Agronomy, Northwest A&F University, National Yangling Agricultural Biotechnology & Breeding Center, Yangling Branch of State Wheat Improvement Centre, Wheat Breeding Engineering Research Center, Ministry of Education, Key Laboratory of Crop Heterosis of Shaanxi Province, Yangling 712100, China.
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17
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Basu U, Narnoliya L, Srivastava R, Sharma A, Bajaj D, Daware A, Thakro V, Malik N, Upadhyaya HD, Tripathi S, Hegde VS, Tyagi AK, Parida SK. CLAVATA signaling pathway genes modulating flowering time and flower number in chickpea. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:2017-2038. [PMID: 30929032 DOI: 10.1007/s00122-019-03335-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Accepted: 03/20/2019] [Indexed: 05/26/2023]
Abstract
A combinatorial genomic strategy delineated functionally relevant natural allele of a CLAVATA gene and its marker (haplotype)-assisted introgression led to development of the early-flowering chickpea cultivars with high flower number and enhanced yield/productivity. Unraveling the genetic components involved in CLAVATA (CLV) signaling is crucial for modulating important shoot apical meristem (SAM) characteristics and ultimately regulating diverse SAM-regulated agromorphological traits in crop plants. A genome-wide scan identified 142 CLV1-, 28 CLV2- and 6 CLV3-like genes, and their comprehensive genomic constitution and phylogenetic relationships were deciphered in chickpea. The QTL/fine mapping and map-based cloning integrated with high-resolution association analysis identified SNP loci from CaCLV3_01 gene within a major CaqDTF1.1/CaqFN1.1 QTL associated with DTF (days to 50% flowering) and FN (flower number) traits in chickpea, which was further ascertained by quantitative expression profiling. Molecular haplotyping of CaCLV3_01 gene, expressed specifically in SAM, constituted two major haplotypes that differentiated the early-DTF and high-FN chickpea accessions from late-DTF and low-FN. Enhanced accumulation of transcripts of superior CaCLV3_01 gene haplotype and known flowering promoting genes was observed in the corresponding haplotype-introgressed early-DTF and high-FN near-isogenic lines (NILs) with narrow SAM width. The superior haplotype-introgressed NILs exhibited early-flowering, high-FN and enhanced seed yield/productivity without compromising agronomic performance. These delineated molecular signatures can regulate DTF and FN traits through SAM proliferation and differentiation and thereby will be useful for translational genomic study to develop early-flowering cultivars with enhanced yield/productivity.
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Affiliation(s)
- Udita Basu
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Laxmi Narnoliya
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Rishi Srivastava
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Akash Sharma
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Deepak Bajaj
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Anurag Daware
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Virevol Thakro
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Naveen Malik
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Hari D Upadhyaya
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, 502324, India
| | - Shailesh Tripathi
- Division of Genetics, Indian Agricultural Research Institute (IARI), New Delhi, 110012, India
| | - V S Hegde
- Division of Genetics, Indian Agricultural Research Institute (IARI), New Delhi, 110012, India
| | - Akhilesh K Tyagi
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
- Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, 110021, India
| | - Swarup K Parida
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India.
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18
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Loss of function mutation of the Rapid Alkalinization Factor (RALF1)-like peptide in the dandelion Taraxacum koksaghyz entails a high-biomass taproot phenotype. PLoS One 2019; 14:e0217454. [PMID: 31125376 PMCID: PMC6534333 DOI: 10.1371/journal.pone.0217454] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 05/13/2019] [Indexed: 12/16/2022] Open
Abstract
The Russian dandelion (Taraxacum koksaghyz) is a promising source of inulin and natural rubber because large amounts of both feedstocks can be extracted from its roots. However, the domestication of T. koksaghyz requires the development of stable agronomic traits such as higher yields of inulin and natural rubber, a higher root biomass, and an agronomically preferable root morphology which is more suitable for cultivation and harvesting. Arabidopsis thaliana Rapid Alkalinisation Factor 1 (RALF1) has been shown to suppress root growth. We identified the T. koksaghyz orthologue TkRALF-like 1 and knocked out the corresponding gene (TkRALFL1) using the CRISPR/Cas9 system to determine its impact on root morphology, biomass, and inulin and natural rubber yields. The TkRALFL1 knockout lines more frequently developed a taproot phenotype which is easier to cultivate and harvest, as well as a higher root biomass and greater yields of both inulin and natural rubber. The TkRALFL1 gene could therefore be suitable as a genetic marker to support the breeding of profitable new dandelion varieties with improved agronomic traits. To our knowledge, this is the first study addressing the root system of T. koksaghyz to enhance the agronomic performance.
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19
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Chen YL, Chang WH, Lee CY, Chen YR. An improved scoring method for the identification of endogenous peptides based on the Mascot MS/MS ion search. Analyst 2019; 144:3045-3055. [PMID: 30912770 DOI: 10.1039/c8an02141d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
To identify endogenous peptides using MS/MS analysis and searching against a polypeptide sequence database, a non-enzyme specific (NES) search considering all of the possible proteolytic cleavages is required. However, the use of a NES search generates more false positive hits than an enzyme specific search, and therefore shows lower identification performance. In this study, the use of the sub-ranked matches for improving the identification performance of the Mascot NES search was investigated and a new scoring method was developed that considered the contribution of all sub-ranked random match probabilities, named the contribution score (CS). The CS showed the highest identification sensitivity using the Mascot NES search with a full protein database when compared to the use of the Mascot first ranked score and the delta score (DS). The confident peptides identified by DS and CS were shown to be complementary. When applied to plant endogenous peptide identification, the identification numbers of tomato endogenous peptides using DS and CS were 176.3% and 184.2%, respectively, higher than the use of the first ranked score of Mascot. The combination of DS and CS identified 200.0% and 8.6% more tomato endogenous peptides compared to the use of Mascot and DS, respectively. This method by combining the CS and DS can significantly improve the identification performance of endogenous peptides without complex computational steps and is also able to improve the identification performance of the enzyme specific search. In addition to the application in the plant peptidomics analysis, this method may be applied to the improvement of peptidomics studies in different species. A web interface for calculating the DS and CS based on Mascot search results was developed herein.
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Affiliation(s)
- Ying-Lan Chen
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan 11529.
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20
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Shinohara H, Yasue N, Onuki T, Kondoh Y, Yoshida M, Matsubayashi Y. Screening and identification of a non-peptide antagonist for the peptide hormone receptor in Arabidopsis. Commun Biol 2019; 2:61. [PMID: 30793040 PMCID: PMC6377654 DOI: 10.1038/s42003-019-0307-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 01/15/2019] [Indexed: 12/12/2022] Open
Abstract
Intercellular signaling mediated by peptide hormones and membrane-localized receptor kinases plays crucial roles in plant developmental processes. Because of their diverse functions, agonistic or antagonistic modulation of peptide signaling holds enormous promise for agricultural applications. Here we established a high-throughput screening system using a bead-immobilized receptor kinase and fluorescent-labeled peptide ligand to identify small molecules that bind peptide hormone receptors in competition with natural ligands. We used the Arabidopsis CLE9-BAM1 ligand-receptor pair to screen a library of ≈30,000 chemicals and identified NPD12704 as an antagonist for BAM1. NPD12704 also inhibited CLV3 binding to BAM1 but only minimally interfered with CLV3 binding to CLV1, the closest homolog of BAM1, demonstrating preferential receptor specificity. Treatment of clv1-101 mutant seedlings with NPD12704 enhanced the enlarged shoot apical meristem phenotype. Our results provide a technological framework enabling high-throughput identification of small non-peptide chemicals that specifically control receptor kinase–mediated peptide hormone signaling in plants. Hidefumi Shinohara and colleagues used the CLE9-BAM1 ligand-receptor pair as a model system for screening peptide hormone receptor-binding small molecules in plants. They identified the small molecule NPD12704 as an antagonist for BAM1 and demonstrated the specific regulatory activity of NPD12704 in shoot apical meristem.
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Affiliation(s)
- Hidefumi Shinohara
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya, 464-8602, Japan
| | - Naoko Yasue
- National Institute for Basic Biology, Myodaiji, Okazaki, 444-8585, Japan
| | - Tetsuo Onuki
- RIKEN Center for Sustainable Resource Science, Hirosawa 2-1, Wako, 351-0198, Japan
| | - Yasumitsu Kondoh
- RIKEN Center for Sustainable Resource Science, Hirosawa 2-1, Wako, 351-0198, Japan
| | - Minoru Yoshida
- RIKEN Center for Sustainable Resource Science, Hirosawa 2-1, Wako, 351-0198, Japan
| | - Yoshikatsu Matsubayashi
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya, 464-8602, Japan.
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21
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Gordon-Kamm B, Sardesai N, Arling M, Lowe K, Hoerster G, Betts S, Jones AT. Using Morphogenic Genes to Improve Recovery and Regeneration of Transgenic Plants. PLANTS (BASEL, SWITZERLAND) 2019; 8:E38. [PMID: 30754699 PMCID: PMC6409764 DOI: 10.3390/plants8020038] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 01/29/2019] [Accepted: 01/31/2019] [Indexed: 12/31/2022]
Abstract
Efficient transformation of numerous important crops remains a challenge, due predominantly to our inability to stimulate growth of transgenic cells capable of producing plants. For years, this difficulty has been partially addressed by tissue culture strategies that improve regeneration either through somatic embryogenesis or meristem formation. Identification of genes involved in these developmental processes, designated here as morphogenic genes, provides useful tools in transformation research. In species from eudicots and cereals to gymnosperms, ectopic overexpression of genes involved in either embryo or meristem development has been used to stimulate growth of transgenic plants. However, many of these genes produce pleiotropic deleterious phenotypes. To mitigate this, research has been focusing on ways to take advantage of growth-stimulating morphogenic genes while later restricting or eliminating their expression in the plant. Methods of controlling ectopic overexpression include the use of transient expression, inducible promoters, tissue-specific promoters, and excision of the morphogenic genes. These methods of controlling morphogenic gene expression have been demonstrated in a variety of important crops. Here, we provide a review that highlights how ectopic overexpression of genes involved in morphogenesis has been used to improve transformation efficiencies, which is facilitating transformation of numerous recalcitrant crops. The use of morphogenic genes may help to alleviate one of the bottlenecks currently slowing progress in plant genome modification.
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Affiliation(s)
- Bill Gordon-Kamm
- Corteva Agriscience™, Agriculture Division of DowDuPont, Johnston, IA 50131, USA.
| | - Nagesh Sardesai
- Corteva Agriscience™, Agriculture Division of DowDuPont, Johnston, IA 50131, USA.
| | - Maren Arling
- Corteva Agriscience™, Agriculture Division of DowDuPont, Johnston, IA 50131, USA.
| | - Keith Lowe
- Corteva Agriscience™, Agriculture Division of DowDuPont, Johnston, IA 50131, USA.
| | - George Hoerster
- Corteva Agriscience™, Agriculture Division of DowDuPont, Johnston, IA 50131, USA.
| | - Scott Betts
- Corteva Agriscience™, Agriculture Division of DowDuPont, Johnston, IA 50131, USA.
| | - And Todd Jones
- Corteva Agriscience™, Agriculture Division of DowDuPont, Johnston, IA 50131, USA.
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DiGennaro P, Grienenberger E, Dao TQ, Jun J, Fletcher JC. Peptide signaling molecules CLE5 and CLE6 affect Arabidopsis leaf shape downstream of leaf patterning transcription factors and auxin. PLANT DIRECT 2018; 2:e00103. [PMID: 31245702 PMCID: PMC6508849 DOI: 10.1002/pld3.103] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 11/20/2018] [Accepted: 11/23/2018] [Indexed: 05/18/2023]
Abstract
Intercellular signaling mediated by small peptides is critical to coordinate organ formation in animals, but whether extracellular polypeptides play similar roles in plants is unknown. Here we describe a role in Arabidopsis leaf development for two members of the CLAVATA3/ESR-RELATED peptide family, CLE5 and CLE6, which lie adjacent to each other on chromosome 2. Uniquely among the CLE genes, CLE5 and CLE6 are expressed specifically at the base of developing leaves and floral organs, adjacent to the boundary with the shoot apical meristem. During vegetative development CLE5 and CLE6 transcription is regulated by the leaf patterning transcription factors BLADE-ON-PETIOLE1 (BOP1) and ASYMMETRIC LEAVES2 (AS2), as well as by the WUSCHEL-RELATED HOMEOBOX (WOX) transcription factors WOX1 and PRESSED FLOWER (PRS). Moreover, CLE5 and CLE6 transcript levels are differentially regulated in various genetic backgrounds by the phytohormone auxin. Analysis of loss-of-function mutations generated by genome engineering reveals that CLE5 and CLE6 independently and together have subtle effects on rosette leaf shape. Our study indicates that the CLE5 and CLE6 peptides function downstream of leaf patterning factors and phytohormones to modulate the final leaf morphology.
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Affiliation(s)
- Peter DiGennaro
- Plant Gene Expression CenterUSDA‐ARS/UC BerkeleyAlbanyCalifornia
- Department of Plant and Microbial BiologyUniversity of CaliforniaBerkeleyCalifornia
- Present address:
Department of Entomology and NematologyUniversity of FloridaGainesvilleFlorida
| | - Etienne Grienenberger
- Plant Gene Expression CenterUSDA‐ARS/UC BerkeleyAlbanyCalifornia
- Department of Plant and Microbial BiologyUniversity of CaliforniaBerkeleyCalifornia
- Present address:
Centre National de la Recherche Scientifique (CNRS)Institute of Plant Molecular BiologyUniversity of StrasbourgStrasbourgFrance
| | - Thai Q. Dao
- Plant Gene Expression CenterUSDA‐ARS/UC BerkeleyAlbanyCalifornia
- Department of Plant and Microbial BiologyUniversity of CaliforniaBerkeleyCalifornia
| | - Ji Hyung Jun
- Plant Gene Expression CenterUSDA‐ARS/UC BerkeleyAlbanyCalifornia
- Department of Plant and Microbial BiologyUniversity of CaliforniaBerkeleyCalifornia
- Present address:
BioDiscovery Institute and Department of Biological SciencesUniversity of North TexasDentonTexas
| | - Jennifer C. Fletcher
- Plant Gene Expression CenterUSDA‐ARS/UC BerkeleyAlbanyCalifornia
- Department of Plant and Microbial BiologyUniversity of CaliforniaBerkeleyCalifornia
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Fujita H, Kawaguchi M. Spatial regularity control of phyllotaxis pattern generated by the mutual interaction between auxin and PIN1. PLoS Comput Biol 2018; 14:e1006065. [PMID: 29614066 PMCID: PMC5882125 DOI: 10.1371/journal.pcbi.1006065] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 03/02/2018] [Indexed: 11/19/2022] Open
Abstract
Phyllotaxis, the arrangement of leaves on a plant stem, is well known because of its beautiful geometric configuration, which is derived from the constant spacing between leaf primordia. This phyllotaxis is established by mutual interaction between a diffusible plant hormone auxin and its efflux carrier PIN1, which cooperatively generate a regular pattern of auxin maxima, small regions with high auxin concentrations, leading to leaf primordia. However, the molecular mechanism of the regular pattern of auxin maxima is still largely unknown. To better understand how the phyllotaxis pattern is controlled, we investigated mathematical models based on the auxin-PIN1 interaction through linear stability analysis and numerical simulations, focusing on the spatial regularity control of auxin maxima. As in previous reports, we first confirmed that this spatial regularity can be reproduced by a highly simplified and abstract model. However, this model lacks the extracellular region and is not appropriate for considering the molecular mechanism. Thus, we investigated how auxin maxima patterns are affected under more realistic conditions. We found that the spatial regularity is eliminated by introducing the extracellular region, even in the presence of direct diffusion between cells or between extracellular spaces, and this strongly suggests the existence of an unknown molecular mechanism. To unravel this mechanism, we assumed a diffusible molecule to verify various feedback interactions with auxin-PIN1 dynamics. We revealed that regular patterns can be restored by a diffusible molecule that mediates the signaling from auxin to PIN1 polarization. Furthermore, as in the one-dimensional case, similar results are observed in the two-dimensional space. These results provide a great insight into the theoretical and molecular basis for understanding the phyllotaxis pattern. Our theoretical analysis strongly predicts a diffusible molecule that is pivotal for the phyllotaxis pattern but is yet to be determined experimentally.
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Affiliation(s)
- Hironori Fujita
- National Institute for Basic Biology, Okazaki, Aichi, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi, Japan
- * E-mail:
| | - Masayoshi Kawaguchi
- National Institute for Basic Biology, Okazaki, Aichi, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi, Japan
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24
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Oh E, Seo PJ, Kim J. Signaling Peptides and Receptors Coordinating Plant Root Development. TRENDS IN PLANT SCIENCE 2018; 23:337-351. [PMID: 29366684 DOI: 10.1016/j.tplants.2017.12.007] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 12/15/2017] [Accepted: 12/21/2017] [Indexed: 05/03/2023]
Abstract
Small peptides mediate cell-cell communication to coordinate a variety of plant developmental processes. Signaling peptides specifically bind to the extracellular domains of receptors that belong to the receptor-like kinase family, and the peptide-receptor interaction activates a range of biochemical and physiological processes. The plant root is crucial for the anchorage of plants in soil as well as for the uptake of water and nutrients. Over recent years great progress has been made in the identification of receptors, structural analysis of peptide-receptor pairs, and characterization of their signaling pathways during plant root development. We review here recent advances in the elucidation of the functions and molecular mechanisms of signaling peptides, the peptide-receptor pairs that activate signal initiation, and their signaling pathways during root development.
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Affiliation(s)
- Eunkyoo Oh
- Department of Bioenergy Science and Technology, Chonnam National University, Buk-Gu, Gwangju 61186, Korea; These authors contributed equally to this work
| | - Pil Joon Seo
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea; These authors contributed equally to this work
| | - Jungmook Kim
- Department of Bioenergy Science and Technology, Chonnam National University, Buk-Gu, Gwangju 61186, Korea.
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25
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Hastwell AH, de Bang TC, Gresshoff PM, Ferguson BJ. CLE peptide-encoding gene families in Medicago truncatula and Lotus japonicus, compared with those of soybean, common bean and Arabidopsis. Sci Rep 2017; 7:9384. [PMID: 28839170 PMCID: PMC5570945 DOI: 10.1038/s41598-017-09296-w] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 07/25/2017] [Indexed: 01/08/2023] Open
Abstract
CLE peptide hormones are critical regulators of many cell proliferation and differentiation mechanisms in plants. These 12-13 amino acid glycosylated peptides play vital roles in a diverse range of plant tissues, including the shoot, root and vasculature. CLE peptides are also involved in controlling legume nodulation. Here, the entire family of CLE peptide-encoding genes was identified in Medicago truncatula (52) and Lotus japonicus (53), including pseudogenes and non-functional sequences that were identified. An array of bioinformatic techniques were used to compare and contrast these complete CLE peptide-encoding gene families with those of fellow legumes, Glycine max and Phaseolus vulgaris, in addition to the model plant Arabidopsis thaliana. This approach provided insight into the evolution of CLE peptide families and enabled us to establish putative M. truncatula and L. japonicus orthologues. This includes orthologues of nodulation-suppressing CLE peptides and AtCLE40 that controls the stem cell population of the root apical meristem. A transcriptional meta-analysis was also conducted to help elucidate the function of the CLE peptide family members. Collectively, our analyses considerably increased the number of annotated CLE peptides in the model legume species, M. truncatula and L. japonicus, and substantially enhanced the knowledgebase of this critical class of peptide hormones.
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Affiliation(s)
- April H Hastwell
- Centre for Integrative Legume Research, School of Agriculture and Food Sciences, The University of Queensland, St Lucia, Brisbane, Queensland, 4072, Australia
| | - Thomas C de Bang
- Plant Biology Division, Noble Research Institute LLC, Ardmore, Oklahoma, 73401, USA
- Department of Plant and Environmental Sciences, Section for Plant and Soil Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark
| | - Peter M Gresshoff
- Centre for Integrative Legume Research, School of Agriculture and Food Sciences, The University of Queensland, St Lucia, Brisbane, Queensland, 4072, Australia
| | - Brett J Ferguson
- Centre for Integrative Legume Research, School of Agriculture and Food Sciences, The University of Queensland, St Lucia, Brisbane, Queensland, 4072, Australia.
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26
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Hirakawa Y, Torii KU, Uchida N. Mechanisms and Strategies Shaping Plant Peptide Hormones. PLANT & CELL PHYSIOLOGY 2017; 58:1313-1318. [PMID: 28961990 PMCID: PMC5914377 DOI: 10.1093/pcp/pcx069] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 04/30/2017] [Indexed: 05/09/2023]
Abstract
Plant genomes encode a variety of short peptides acting as signaling molecules. Since the discovery of tomato systemin, a myriad of peptide signals, ranging in size, structure and modifications, have been found in plants. Moreover, new peptides are still being identified. Surprisingly, non-plant organisms, especially pathogens, also produce peptides which exert hormonal activities against host plants by hijacking their endogenous reception systems. In this review, we focus on short secretory peptides ranging from five to 20 amino acids. We first summarize recent advances in understanding relationships between the bioactivities and structures of plant peptide hormones. Subsequently, we introduce the topic of peptides produced by non-plant organisms. Lastly, we describe artificial peptides synthesized in laboratories, which possess intriguing bioactive properties beyond those of natural peptide hormones.
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Affiliation(s)
- Yuki Hirakawa
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601 Japan
- Corresponding authors: Yuki Hirakawa, E-mail, ; Keiko U. Torii, E-mail, ; Naoyuki Uchida, E-mail,
| | - Keiko U. Torii
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601 Japan
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya, 464-8602 Japan
- Department of Biology, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
- Corresponding authors: Yuki Hirakawa, E-mail, ; Keiko U. Torii, E-mail, ; Naoyuki Uchida, E-mail,
| | - Naoyuki Uchida
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601 Japan
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya, 464-8602 Japan
- Corresponding authors: Yuki Hirakawa, E-mail, ; Keiko U. Torii, E-mail, ; Naoyuki Uchida, E-mail,
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27
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Liao H, Tang R, Zhang X, Luan S, Yu F. FERONIA Receptor Kinase at the Crossroads of Hormone Signaling and Stress Responses. PLANT & CELL PHYSIOLOGY 2017; 58:1143-1150. [PMID: 28444222 DOI: 10.1093/pcp/pcx048] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 03/28/2017] [Indexed: 05/04/2023]
Abstract
Plant receptor-like kinases (RLKs) are involved in nearly all aspects of plant life including growth, development and stress response. Recent studies show that FERONIA (FER), a CrRLK1L subfamily member, is a versatile regulator of cell expansion and serves as a signaling node mediating cross-talk among multiple phytohormones. As a receptor for the RALF (Rapid Alkalinization Factor) peptide ligand, FER triggers a downstream signaling cascade that leads to a rapid cytoplasmic calcium increase and inhibition of cell elongation in plants. Moreover, FER recruits and activates small G proteins through the guanine nucleotide exchange factor-Rho-like GTPase (GEF-ROP) network to regulate both auxin and ABA responses that cross-talk with the RALF signaling pathway. One of the downstream processes is NADPH oxidase-dependent ROS (reactive oxygen species) production that modulates cell expansion and responses to both abiotic and biotic stress responses. Intriguingly, some pathogenic fungi produce RALF-like peptides to activate the host FER-mediated pathway and thus increase their virulence and cause plant disease. Studies so far indicate that FER may serve as a central node of the cell signaling network that integrates a number of regulatory pathways targeting cell expansion, energy metabolism and stress responses. This review focuses on recent findings and their implications in the context of FER action as a modulator that is crucial for hormone signaling and stress responses.
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Affiliation(s)
- Hongdong Liao
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, and State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, PR China
| | - Renjie Tang
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Xin Zhang
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, and State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, PR China
| | - Sheng Luan
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Feng Yu
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, and State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, PR China
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28
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Zhang H, Han Z, Song W, Chai J. Structural Insight into Recognition of Plant Peptide Hormones by Receptors. MOLECULAR PLANT 2016; 9:1454-1463. [PMID: 27743937 DOI: 10.1016/j.molp.2016.10.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 09/29/2016] [Accepted: 10/01/2016] [Indexed: 05/26/2023]
Abstract
Secreted signaling peptides or peptide hormones play crucial roles in plant growth and development through coordination of cell-cell communication. Perception of peptide hormones in plants generally relies on membrane-localized receptor kinases (RKs). Progress has recently been made in structural elucidation of interactions between posttranslationally modified peptide hormones and RKs. The structural studies suggest conserved receptor binding and activation mechanisms of this type of peptide hormones involving their conserved C-termini. Here, we review these structural data and discuss how the conserved mechanisms can be used to match peptide-RK pairs.
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Affiliation(s)
- Heqiao Zhang
- Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Zhifu Han
- Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Wen Song
- Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jijie Chai
- Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.
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29
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Palovaara J, de Zeeuw T, Weijers D. Tissue and Organ Initiation in the Plant Embryo: A First Time for Everything. Annu Rev Cell Dev Biol 2016; 32:47-75. [PMID: 27576120 DOI: 10.1146/annurev-cellbio-111315-124929] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Land plants can grow to tremendous body sizes, yet even the most complex architectures are the result of iterations of the same developmental processes: organ initiation, growth, and pattern formation. A central question in plant biology is how these processes are regulated and coordinated to allow for the formation of ordered, 3D structures. All these elementary processes first occur in early embryogenesis, during which, from a fertilized egg cell, precursors for all major tissues and stem cells are initiated, followed by tissue growth and patterning. Here we discuss recent progress in our understanding of this phase of plant life. We consider the cellular basis for multicellular development in 3D and focus on the genetic regulatory mechanisms that direct specific steps during early embryogenesis.
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Affiliation(s)
- Joakim Palovaara
- Laboratory of Biochemistry, Wageningen University, 6703 HA Wageningen, The Netherlands;
| | - Thijs de Zeeuw
- Laboratory of Biochemistry, Wageningen University, 6703 HA Wageningen, The Netherlands;
| | - Dolf Weijers
- Laboratory of Biochemistry, Wageningen University, 6703 HA Wageningen, The Netherlands;
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30
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Abstract
A significant part of the communication between plant cells is mediated by signaling peptides and their corresponding plasma membrane-localized receptor-like kinases. This communication mechanism serves as a key regulatory unit for coordination of plant growth and development. In the past years more peptide–receptor signaling pathways have been shown to regulate developmental processes, such as shoot and root meristem maintenance, seed formation, and floral abscission. More detailed understanding of the processes behind this regulation might also be helpful to increase the yield of crop plants.
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Affiliation(s)
- Maike Breiden
- Institute for Developmental Genetics, Heinrich-Heine-Universität Düsseldorf, University Street, D-40225, Düsseldorf, Germany
| | - Rüdiger Simon
- Cluster of Excellence on Plant Sciences and Institute for Developmental Genetics, Heinrich-Heine University, University Street 1, D-40225, Düsseldorf, Germany.
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31
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Abstract
Root meristem growth factors (RGFs), a family of "orphan" peptides, control root growth by altering the expression and gradient of transcription factors PLETHORAS (PLTs) that maintain stem cell niche. However, the receptors for RGFs remain unknown until recently when three groups independently reported the identification of a group of receptor-like kinases (RLKs) as cell surface receptors for RGFs.
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Affiliation(s)
- Feng Yu
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, Hunan 410082, China
| | - Sheng Luan
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
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32
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Song W, Liu L, Wang J, Wu Z, Zhang H, Tang J, Lin G, Wang Y, Wen X, Li W, Han Z, Guo H, Chai J. Signature motif-guided identification of receptors for peptide hormones essential for root meristem growth. Cell Res 2016; 26:674-85. [PMID: 27229311 PMCID: PMC4897187 DOI: 10.1038/cr.2016.62] [Citation(s) in RCA: 110] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 04/11/2016] [Accepted: 04/20/2016] [Indexed: 11/09/2022] Open
Abstract
Peptide-mediated cell-to-cell signaling has crucial roles in coordination and definition of cellular functions in plants. Peptide-receptor matching is important for understanding the mechanisms underlying peptide-mediated signaling. Here we report the structure-guided identification of root meristem growth factor (RGF) receptors important for plant development. An assay based on a signature ligand recognition motif (Arg-x-Arg) conserved in a subfamily of leucine-rich repeat receptor kinases (LRR-RKs) identified the functionally uncharacterized LRR-RK At4g26540 as a receptor of RGF1 (RGFR1). We further solved the crystal structure of RGF1 in complex with the LRR domain of RGFR1 at a resolution of 2.6 Å, which reveals that the Arg-x-Gly-Gly (RxGG) motif is responsible for specific recognition of the sulfate group of RGF1 by RGFR1. Based on the RxGG motif, we identified additional four RGFRs. Participation of the five RGFRs in RGF-induced signaling is supported by biochemical and genetic data. We also offer evidence showing that SERKs function as co-receptors for RGFs. Taken together, our study identifies RGF receptors and co-receptors that can link RGF signals with their downstream components and provides a proof of principle for structure-based matching of LRR-RKs with their peptide ligands.
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Affiliation(s)
- Wen Song
- Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Li Liu
- The State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Joint Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, College of Life Sciences, Peking University, Beijing 100871, China
| | - Jizong Wang
- Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Zhen Wu
- Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Heqiao Zhang
- Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jiao Tang
- Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Guangzhong Lin
- Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yichuan Wang
- The State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Joint Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, College of Life Sciences, Peking University, Beijing 100871, China
- Department of Biology, South University of Science and Technology of China, Shenzhen, Guangdong 518055, China
| | - Xing Wen
- The State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Joint Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, College of Life Sciences, Peking University, Beijing 100871, China
| | - Wenyang Li
- The State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Joint Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, College of Life Sciences, Peking University, Beijing 100871, China
| | - Zhifu Han
- Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Hongwei Guo
- The State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Joint Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, College of Life Sciences, Peking University, Beijing 100871, China
- Department of Biology, South University of Science and Technology of China, Shenzhen, Guangdong 518055, China
| | - Jijie Chai
- Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
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RGF1 INSENSITIVE 1 to 5, a group of LRR receptor-like kinases, are essential for the perception of root meristem growth factor 1 in Arabidopsis thaliana. Cell Res 2016; 26:686-98. [PMID: 27229312 DOI: 10.1038/cr.2016.63] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 05/02/2016] [Accepted: 05/04/2016] [Indexed: 11/08/2022] Open
Abstract
RGF1, a secreted peptide hormone, plays key roles in root meristem development in Arabidopsis. Previous studies indicated that a functional RGF1 needs to be sulfated at a tyrosine residue by a tyrosylprotein sulfotransferase and that RGF1 regulates the root meristem activity mainly via two downstream transcription factors, PLETHORA 1 (PLT1) and PLT2. How extracellular RGF1 is perceived by a plant cell, however, is unclear. Using genetic approaches, we discovered a clade of leucine-rich repeat receptor-like kinases, designated as RGF1 INSENSITIVE 1 (RGI1) to RGI5, serving as receptors of RGF1. Two independent rgi1 rgi2 rgi3 rgi4 rgi5 quintuple mutants display a consistent short primary root phenotype with a small size of meristem. An rgi1 rgi2 rgi3 rgi4 quadruple mutant shows a significantly reduced sensitivity to RGF1, and the quintuple mutant is completely insensitive to RGF1. The expression of PLT1 and PLT2 is almost undetectable in the quintuple mutant. Ectopic expression of PLT2 driven by an RGI2 promoter in the quintuple mutant greatly rescued its root meristem defects. One of the RGIs, RGI1, was subsequently analyzed biochemically in detail. In vitro dot blotting and pull-down analyses indicated that RGI1 can physically interact with RGF1. Exogenous application of RGF1 can quickly and simultaneously induce the phosphorylation and ubiquitination of RGI1, indicating that RGI1 can perceive and transduce the RGF1 peptide signal. Yet, the activated RGI1 is likely turned over rapidly. These results demonstrate that RGIs, acting as the receptors of RGF1, play essential roles in RGF1-PLT-mediated root meristem development in Arabidopsis thaliana.
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34
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Xu Z, Jiang Y, Jia B, Zhou G. Elevated-CO2 Response of Stomata and Its Dependence on Environmental Factors. FRONTIERS IN PLANT SCIENCE 2016; 7:657. [PMID: 27242858 PMCID: PMC4865672 DOI: 10.3389/fpls.2016.00657] [Citation(s) in RCA: 117] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2015] [Accepted: 04/29/2016] [Indexed: 05/18/2023]
Abstract
Stomata control the flow of gases between plants and the atmosphere. This review is centered on stomatal responses to elevated CO2 concentration and considers other key environmental factors and underlying mechanisms at multiple levels. First, an outline of general responses in stomatal conductance under elevated CO2 is presented. Second, stomatal density response, its development, and the trade-off with leaf growth under elevated CO2 conditions are depicted. Third, the molecular mechanism regulating guard cell movement at elevated CO2 is suggested. Finally, the interactive effects of elevated CO2 with other factors critical to stomatal behavior are reviewed. It may be useful to better understand how stomata respond to elevated CO2 levels while considering other key environmental factors and mechanisms, including molecular mechanism, biochemical processes, and ecophysiological regulation. This understanding may provide profound new insights into how plants cope with climate change.
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Affiliation(s)
- Zhenzhu Xu
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of SciencesBeijing, China
| | - Yanling Jiang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of SciencesBeijing, China
| | - Bingrui Jia
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of SciencesBeijing, China
| | - Guangsheng Zhou
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of SciencesBeijing, China
- Chinese Academy of Meteorological SciencesBeijing, China
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Xu Z, Jiang Y, Jia B, Zhou G. Elevated-CO2 Response of Stomata and Its Dependence on Environmental Factors. FRONTIERS IN PLANT SCIENCE 2016. [PMID: 27242858 DOI: 10.3389/fpls.20116.00657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Stomata control the flow of gases between plants and the atmosphere. This review is centered on stomatal responses to elevated CO2 concentration and considers other key environmental factors and underlying mechanisms at multiple levels. First, an outline of general responses in stomatal conductance under elevated CO2 is presented. Second, stomatal density response, its development, and the trade-off with leaf growth under elevated CO2 conditions are depicted. Third, the molecular mechanism regulating guard cell movement at elevated CO2 is suggested. Finally, the interactive effects of elevated CO2 with other factors critical to stomatal behavior are reviewed. It may be useful to better understand how stomata respond to elevated CO2 levels while considering other key environmental factors and mechanisms, including molecular mechanism, biochemical processes, and ecophysiological regulation. This understanding may provide profound new insights into how plants cope with climate change.
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Affiliation(s)
- Zhenzhu Xu
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences Beijing, China
| | - Yanling Jiang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences Beijing, China
| | - Bingrui Jia
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences Beijing, China
| | - Guangsheng Zhou
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of SciencesBeijing, China; Chinese Academy of Meteorological SciencesBeijing, China
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Fernandez A, Drozdzecki A, Hoogewijs K, Vassileva V, Madder A, Beeckman T, Hilson P. The GLV6/RGF8/CLEL2 peptide regulates early pericycle divisions during lateral root initiation. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:5245-56. [PMID: 26163695 PMCID: PMC4526922 DOI: 10.1093/jxb/erv329] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Small peptides of the Arabidopsis GLV/RGF/CLEL family are involved in different developmental programmes, including meristem maintenance and gravitropic responses. In addition, our previous report suggested that they also participate in the formation of lateral roots. Specifically, GLV6 is transcribed during the first stages of primordium development and GLV6 overexpression results in a strong reduction of emerged lateral roots. To investigate the cause of this phenotype we analysed primordium development in gain-of-function (gof) mutants and found that GLV6 induces supernumerary pericycle divisions, hindering the formation of a dome-shaped primordium, a prerequisite for successful emergence. The GLV6 phenotype could be reproduced by ectopic expression of the gene only in xylem-pole pericycle cells. Furthermore, GLV6 seems to function at the very beginning of lateral root initiation because GLV6 excess-either gene overexpression or peptide treatment-disrupts the first asymmetric cell divisions required for proper primordium formation. Our results suggest that GLV6 acts during lateral root initiation controlling the patterning of the first pericycle divisions.
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Affiliation(s)
- Ana Fernandez
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium. Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
| | - Andrzej Drozdzecki
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium. Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
| | - Kurt Hoogewijs
- Department of Organic Chemistry, Ghent University, 9000 Ghent, Belgium
| | - Valya Vassileva
- Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Annemieke Madder
- Department of Organic Chemistry, Ghent University, 9000 Ghent, Belgium
| | - Tom Beeckman
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium. Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium.
| | - Pierre Hilson
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium. Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium. INRA, UMR1318, Institut Jean-Pierre Bourgin, RD10, F-78000 Versailles, France. AgroParisTech, Institut Jean-Pierre Bourgin, RD10, F-78000 Versailles, France
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Ghorbani S, Lin YC, Parizot B, Fernandez A, Njo MF, Van de Peer Y, Beeckman T, Hilson P. Expanding the repertoire of secretory peptides controlling root development with comparative genome analysis and functional assays. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:5257-69. [PMID: 26195730 PMCID: PMC4526923 DOI: 10.1093/jxb/erv346] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Plant genomes encode numerous small secretory peptides (SSPs) whose functions have yet to be explored. Based on structural features that characterize SSP families known to take part in postembryonic development, this comparative genome analysis resulted in the identification of genes coding for oligopeptides potentially involved in cell-to-cell communication. Because genome annotation based on short sequence homology is difficult, the criteria for the de novo identification and aggregation of conserved SSP sequences were first benchmarked across five reference plant species. The resulting gene families were then extended to 32 genome sequences, including major crops. The global phylogenetic pattern common to the functionally characterized SSP families suggests that their apparition and expansion coincide with that of the land plants. The SSP families can be searched online for members, sequences and consensus (http://bioinformatics.psb.ugent.be/webtools/PlantSSP/). Looking for putative regulators of root development, Arabidopsis thaliana SSP genes were further selected through transcriptome meta-analysis based on their expression at specific stages and in specific cell types in the course of the lateral root formation. As an additional indication that formerly uncharacterized SSPs may control development, this study showed that root growth and branching were altered by the application of synthetic peptides matching conserved SSP motifs, sometimes in very specific ways. The strategy used in the study, combining comparative genomics, transcriptome meta-analysis and peptide functional assays in planta, pinpoints factors potentially involved in non-cell-autonomous regulatory mechanisms. A similar approach can be implemented in different species for the study of a wide range of developmental programmes.
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Affiliation(s)
- Sarieh Ghorbani
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Yao-Cheng Lin
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Boris Parizot
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Ana Fernandez
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Maria Fransiska Njo
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Yves Van de Peer
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium Genomics Research Institute, University of Pretoria, Hatfield Campus, Pretoria 0028, South Africa
| | - Tom Beeckman
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Pierre Hilson
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Saclay Plant Sciences, INRA, route de Saint-Cyr, 78026 Versailles, France
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Hastwell AH, Gresshoff PM, Ferguson BJ. Genome-wide annotation and characterization of CLAVATA/ESR (CLE) peptide hormones of soybean (Glycine max) and common bean (Phaseolus vulgaris), and their orthologues of Arabidopsis thaliana. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:5271-87. [PMID: 26188205 PMCID: PMC4526924 DOI: 10.1093/jxb/erv351] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
CLE peptides are key regulators of cell proliferation and differentiation in plant shoots, roots, vasculature, and legume nodules. They are C-terminally encoded peptides that are post-translationally cleaved and modified from their corresponding pre-propeptides to produce a final ligand that is 12-13 amino acids in length. In this study, an array of bionformatic and comparative genomic approaches was used to identify and characterize the complete family of CLE peptide-encoding genes in two of the world's most important crop species, soybean and common bean. In total, there are 84 CLE peptide-encoding genes in soybean (considerably more than the 32 present in Arabidopsis), including three pseudogenes and two multi-CLE domain genes having six putative CLE domains each. In addition, 44 CLE peptide-encoding genes were identified in common bean. In silico characterization was used to establish all soybean homeologous pairs, and to identify corresponding gene orthologues present in common bean and Arabidopsis. The soybean CLE pre-propeptide family was further analysed and separated into seven distinct groups based on structure, with groupings strongly associated with the CLE domain sequence and function. These groups provide evolutionary insight into the CLE peptide families of soybean, common bean, and Arabidopsis, and represent a novel tool that can aid in the functional characterization of the peptides. Transcriptional evidence was also used to provide further insight into the location and function of all CLE peptide-encoding members currently available in gene atlases for the three species. Taken together, this in-depth analysis helped to identify and categorize the complete CLE peptide families of soybean and common bean, established gene orthologues within the two legume species, and Arabidopsis, and provided a platform to help compare, contrast, and identify the function of critical CLE peptide hormones in plant development.
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Affiliation(s)
- April H Hastwell
- Centre for Integrative Legume Research, School of Agricultural and Food Sciences, The University of Queensland, St Lucia, Brisbane, Queensland, 4072, Australia
| | - Peter M Gresshoff
- Centre for Integrative Legume Research, School of Agricultural and Food Sciences, The University of Queensland, St Lucia, Brisbane, Queensland, 4072, Australia
| | - Brett J Ferguson
- Centre for Integrative Legume Research, School of Agricultural and Food Sciences, The University of Queensland, St Lucia, Brisbane, Queensland, 4072, Australia
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Estornell LH, Wildhagen M, Pérez-Amador MA, Talón M, Tadeo FR, Butenko MA. The IDA Peptide Controls Abscission in Arabidopsis and Citrus. FRONTIERS IN PLANT SCIENCE 2015; 6:1003. [PMID: 26635830 PMCID: PMC4652038 DOI: 10.3389/fpls.2015.01003] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 10/30/2015] [Indexed: 05/22/2023]
Abstract
Organ abscission is an important process in plant development and reproduction. During abscission, changes in cellular adhesion of specialized abscission zone cells ensure the detachment of infected organs or those no longer serving a function to the plant. In addition, abscission also plays an important role in the release of ripe fruits. Different plant species display distinct patterns and timing of organ shedding, most likely adapted during evolution to their diverse life styles. However, it appears that key regulators of cell separation may have conserved function in different plant species. Here, we investigate the functional conservation of the citrus ortholog of the Arabidopsis peptide ligand INFLORESCENCE DEFICIENT IN ABSCISSION (AtIDA), controlling floral organ abscission. We discuss the possible implications of modifying the citrus IDA ortholog for citrus fruit production.
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Affiliation(s)
| | - Mari Wildhagen
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of OsloOslo, Norway
| | - Miguel A. Pérez-Amador
- Instituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia–Consejo Superior de Investigaciones CientíficasValència, Spain
| | - Manuel Talón
- Centre de Genómica, Institut Valencià d’Investigacions AgràriesMontcada, Spain
| | - Francisco R. Tadeo
- Centre de Genómica, Institut Valencià d’Investigacions AgràriesMontcada, Spain
- *Correspondence: Franscisco R. Tadeo, ; Melinka A. Butenko,
| | - Melinka A. Butenko
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of OsloOslo, Norway
- *Correspondence: Franscisco R. Tadeo, ; Melinka A. Butenko,
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