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Han GZ. Origin and evolution of the plant immune system. THE NEW PHYTOLOGIST 2019; 222:70-83. [PMID: 30575972 DOI: 10.1111/nph.15596] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 11/02/2018] [Indexed: 05/11/2023]
Abstract
Contents Summary 70 I. Introduction 70 II. Ancient associations between plants and microbes 72 III. Evolutionary dynamics of plant-pathogen interactions 74 IV. Evolutionary signature of plant-pathogen interactions 74 V. Origin and evolution of RLK proteins 75 VI. Origin and evolution of NLR proteins 77 VII. Origin and evolution of SA signaling 78 VIII. Origin and evolution of RNA-based defense 79 IX. Perspectives 79 Acknowledgements 80 References 80 SUMMARY: Microbes have engaged in antagonistic associations with plants for hundreds of millions of years. Plants, in turn, have evolved diverse immune strategies to combat microbial pathogens. The conflicts between plants and pathogens result in everchanging coevolutionary cycles known as 'Red Queen' dynamics. These ancient and ongoing plant-pathogen interactions have shaped the evolution of both plant and pathogen genomes. With the recent explosion of plant genome-scale data, comparative analyses provide novel insights into the coevolutionary dynamics of plants and pathogens. Here, we discuss the ancient associations between plants and microbes as well as the evolutionary principles underlying plant-pathogen interactions. We synthesize and review the current knowledge on the origin and evolution of key components of the plant immune system. We also highlight the importance of studying algae and nonflowering land plants in understanding the evolution of the plant immune system.
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Affiliation(s)
- Guan-Zhu Han
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, 210023, China
- College of Life Sciences, Shandong Normal University, Jinan, Shandong, 250014, China
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Wu S, Wang W, Xu X, Wu X. Commentary: Leucine-rich Repeat Receptor-Like Gene Screen Reveals that Nicotiana RXEG1 Regulates Glycoside Hydrolase 12 MAMP Detection. Front Genet 2019; 10:162. [PMID: 30899275 PMCID: PMC6416172 DOI: 10.3389/fgene.2019.00162] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 02/14/2019] [Indexed: 11/20/2022] Open
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van der Burgh AM, Postma J, Robatzek S, Joosten MHAJ. Kinase activity of SOBIR1 and BAK1 is required for immune signalling. MOLECULAR PLANT PATHOLOGY 2019; 20:410-422. [PMID: 30407725 PMCID: PMC6637861 DOI: 10.1111/mpp.12767] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Leucine-rich repeat-receptor-like proteins (LRR-RLPs) and LRR-receptor-like kinases (LRR-RLKs) trigger immune signalling to promote plant resistance against pathogens. LRR-RLPs lack an intracellular kinase domain, and several of these receptors have been shown to constitutively interact with the LRR-RLK Suppressor of BIR1-1/EVERSHED (SOBIR1/EVR) to form signalling-competent receptor complexes. Ligand perception by LRR-RLPs initiates recruitment of the co-receptor BRI1-Associated Kinase 1/Somatic Embryogenesis Receptor Kinase 3 (BAK1/SERK3) to the LRR-RLP/SOBIR1 complex, thereby activating LRR-RLP-mediated immunity. We employed phosphorylation analysis of in planta-produced proteins, live cell imaging, gene silencing and co-immunoprecipitation to investigate the roles of SOBIR1 and BAK1 in immune signalling. We show that Arabidopsis thaliana (At) SOBIR1, which constitutively activates immune responses when overexpressed in planta, is highly phosphorylated. Moreover, in addition to the kinase activity of SOBIR1 itself, kinase-active BAK1 is essential for AtSOBIR1-induced constitutive immunity and for the phosphorylation of AtSOBIR1. Furthermore, the defence response triggered by the tomato LRR-RLP Cf-4 on perception of Avr4 from the extracellular pathogenic fungus Cladosporium fulvum is dependent on kinase-active BAK1. We argue that, in addition to the trans-autophosphorylation of SOBIR1, it is likely that SOBIR1 and BAK1 transphosphorylate, and thereby activate the receptor complex. The signalling-competent cell surface receptor complex subsequently activates downstream cytoplasmic signalling partners to initiate RLP-mediated immunity.
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Affiliation(s)
- Aranka M. van der Burgh
- Laboratory of PhytopathologyWageningen UniversityDroevendaalsesteeg 16708 PBWageningenthe Netherlands
| | - Jelle Postma
- The Sainsbury LaboratoryNorwich Research Park, NorwichNR4 7UHUK
| | - Silke Robatzek
- The Sainsbury LaboratoryNorwich Research Park, NorwichNR4 7UHUK
- Ludwig‐Maximilians‐Universität MünchenGeneticsGroßhaderner Str. 2–482152MartinsriedGermany
| | - Matthieu H. A. J. Joosten
- Laboratory of PhytopathologyWageningen UniversityDroevendaalsesteeg 16708 PBWageningenthe Netherlands
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Vaattovaara A, Brandt B, Rajaraman S, Safronov O, Veidenberg A, Luklová M, Kangasjärvi J, Löytynoja A, Hothorn M, Salojärvi J, Wrzaczek M. Mechanistic insights into the evolution of DUF26-containing proteins in land plants. Commun Biol 2019; 2:56. [PMID: 30775457 PMCID: PMC6368629 DOI: 10.1038/s42003-019-0306-9] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 01/14/2019] [Indexed: 01/01/2023] Open
Abstract
Large protein families are a prominent feature of plant genomes and their size variation is a key element for adaptation. However, gene and genome duplications pose difficulties for functional characterization and translational research. Here we infer the evolutionary history of the DOMAIN OF UNKNOWN FUNCTION (DUF) 26-containing proteins. The DUF26 emerged in secreted proteins. Domain duplications and rearrangements led to the appearance of CYSTEINE-RICH RECEPTOR-LIKE PROTEIN KINASES (CRKs) and PLASMODESMATA-LOCALIZED PROTEINS (PDLPs). The DUF26 is land plant-specific but structural analyses of PDLP ectodomains revealed strong similarity to fungal lectins and thus may constitute a group of plant carbohydrate-binding proteins. CRKs expanded through tandem duplications and preferential retention of duplicates following whole genome duplications, whereas PDLPs evolved according to the dosage balance hypothesis. We propose that new gene families mainly expand through small-scale duplications, while fractionation and genetic drift after whole genome multiplications drive families towards dosage balance.
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Affiliation(s)
- Aleksia Vaattovaara
- Organismal and Evolutionary Biology Research Programme, Viikki Plant Science Centre, VIPS, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 1 (POB65), FI-00014 Helsinki, Finland
| | - Benjamin Brandt
- Structural Plant Biology Laboratory, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland
| | - Sitaram Rajaraman
- Organismal and Evolutionary Biology Research Programme, Viikki Plant Science Centre, VIPS, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 1 (POB65), FI-00014 Helsinki, Finland
| | - Omid Safronov
- Organismal and Evolutionary Biology Research Programme, Viikki Plant Science Centre, VIPS, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 1 (POB65), FI-00014 Helsinki, Finland
| | - Andres Veidenberg
- Institute of Biotechnology, University of Helsinki, Viikinkaari 5 (POB56), FI-00014 Helsinki, Finland
| | - Markéta Luklová
- Organismal and Evolutionary Biology Research Programme, Viikki Plant Science Centre, VIPS, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 1 (POB65), FI-00014 Helsinki, Finland
- Present Address: Laboratory of Plant Molecular Biology, Institute of Biophysics AS CR, v.v.i. and CEITEC—Central European Institute of Technology, Mendel University in Brno, Zemědělská 1, 613 00 Brno, Czech Republic
| | - Jaakko Kangasjärvi
- Organismal and Evolutionary Biology Research Programme, Viikki Plant Science Centre, VIPS, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 1 (POB65), FI-00014 Helsinki, Finland
| | - Ari Löytynoja
- Institute of Biotechnology, University of Helsinki, Viikinkaari 5 (POB56), FI-00014 Helsinki, Finland
| | - Michael Hothorn
- Structural Plant Biology Laboratory, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland
| | - Jarkko Salojärvi
- Organismal and Evolutionary Biology Research Programme, Viikki Plant Science Centre, VIPS, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 1 (POB65), FI-00014 Helsinki, Finland
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551 Singapore
| | - Michael Wrzaczek
- Organismal and Evolutionary Biology Research Programme, Viikki Plant Science Centre, VIPS, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 1 (POB65), FI-00014 Helsinki, Finland
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Mou S, Gao F, Shen L, Yang S, He W, Cheng W, Wu Y, He S. CaLRR-RLK1, a novel RD receptor-like kinase from Capsicum annuum and transcriptionally activated by CaHDZ27, act as positive regulator in Ralstonia solanacearum resistance. BMC PLANT BIOLOGY 2019; 19:28. [PMID: 30654746 PMCID: PMC6337819 DOI: 10.1186/s12870-018-1609-6] [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: 12/04/2018] [Accepted: 12/19/2018] [Indexed: 05/13/2023]
Abstract
BACKGROUND Bacterial wilt caused by Ralstonia solanacearum is one of the most important diseases in pepper worldwide, however, the molecular mechanism underlying pepper resistance to bacterial wilt remains poorly understood. RESULTS Herein, a novel RD leucine-rich repeat receptor-like kinase, CaLRR-RLK1, was functionally characterized in immunity against R. solanacearum. CaLRR-RLK1 was targeted exclusively to plasma membrane and was up-regulated by R. solanacearum inoculation (RSI) as well as by the exogenous application of salicylic acid (SA), methyl jasmonate (MeJA) or ethephon (ETH). The silencing of CaLRR-RLK1 led to enhanced susceptibility of pepper plants to RSI, accompanied by down-regulation of immunity-related genes including CaACO1, CaHIR1, CaPR4 and CaPO2. In contrast, transient overexpression of CaLRR-RLK1 triggered hypersensitive response (HR)-like cell death and H2O2 accumulation in pepper leaves, manifested by darker trypan blue and DAB staining respectively. In addition, the ectopic overexpression of CaLRR-RLK1 in tobacco plants enhanced resistance R. solanacearum, accompanied with the immunity associated marker genes including NtPR2, NtPR2, NtHSR203 and NtHSR515. Furthermore, it was found that CaHDZ27, a positive regulator in pepper response to RSI in our previous study, transcriptionally activated CaLRR-RLK1 by direct targeting its promoter probably in a CAATTATTG dependent manner. CONCLUSION The study revealed that CaLRR-RLK1 confers pepper resistance to R. solanacearum as the direct targeting of CaHDZ27.
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Affiliation(s)
- Shaoliang Mou
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 People’s Republic of China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 People’s Republic of China
- National Education Ministry Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 People’s Republic of China
| | - Feng Gao
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 People’s Republic of China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 People’s Republic of China
- National Education Ministry Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 People’s Republic of China
| | - Lei Shen
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 People’s Republic of China
- National Education Ministry Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 People’s Republic of China
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 People’s Republic of China
| | - Sheng Yang
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 People’s Republic of China
- National Education Ministry Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 People’s Republic of China
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 People’s Republic of China
| | - Weihong He
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 People’s Republic of China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 People’s Republic of China
- National Education Ministry Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 People’s Republic of China
| | - Wei Cheng
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 People’s Republic of China
- National Education Ministry Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 People’s Republic of China
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 People’s Republic of China
| | - Yang Wu
- College of Life Science, Jinggangshan University, Ji’an, Jiangxi 343000 People’s Republic of China
| | - Shuilin He
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 People’s Republic of China
- National Education Ministry Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 People’s Republic of China
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 People’s Republic of China
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Evolution of Disease Defense Genes and Their Regulators in Plants. Int J Mol Sci 2019; 20:ijms20020335. [PMID: 30650550 PMCID: PMC6358896 DOI: 10.3390/ijms20020335] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 12/28/2018] [Accepted: 01/10/2019] [Indexed: 02/06/2023] Open
Abstract
Biotic stresses do damage to the growth and development of plants, and yield losses for some crops. Confronted with microbial infections, plants have evolved multiple defense mechanisms, which play important roles in the never-ending molecular arms race of plant–pathogen interactions. The complicated defense systems include pathogen-associated molecular patterns (PAMP) triggered immunity (PTI), effector triggered immunity (ETI), and the exosome-mediated cross-kingdom RNA interference (CKRI) system. Furthermore, plants have evolved a classical regulation system mediated by miRNAs to regulate these defense genes. Most of the genes/small RNAs or their regulators that involve in the defense pathways can have very rapid evolutionary rates in the longitudinal and horizontal co-evolution with pathogens. According to these internal defense mechanisms, some strategies such as molecular switch for the disease resistance genes, host-induced gene silencing (HIGS), and the new generation of RNA-based fungicides, have been developed to control multiple plant diseases. These broadly applicable new strategies by transgene or spraying ds/sRNA may lead to reduced application of pesticides and improved crop yield.
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Cenci A, Chantret N, Rouard M. Glycosyltransferase Family 61 in Liliopsida (Monocot): The Story of a Gene Family Expansion. FRONTIERS IN PLANT SCIENCE 2018; 9:1843. [PMID: 30619412 PMCID: PMC6297846 DOI: 10.3389/fpls.2018.01843] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 11/28/2018] [Indexed: 06/09/2023]
Abstract
Plant cell walls play a fundamental role in several plant traits and also influence crop use as livestock nutrition or biofuel production. The Glycosyltransferase family 61 (GT61) is involved in the synthesis of cell wall xylans. In grasses (Poaceae), a copy number expansion was reported for the GT61 family, and raised the question of the evolutionary history of this gene family in a broader taxonomic context. A phylogenetic study was performed on GT61 members from 13 species representing the major angiosperm clades, in order to classify the genes, reconstruct the evolutionary history of this gene family and study its expansion in monocots. Four orthogroups (OG) were identified in angiosperms with two of them displaying a copy number expansion in monocots. These copy number expansions resulted from both tandem and segmental duplications during the genome evolution of monocot lineages. Positive selection footprints were detected on the ancestral branch leading to one of the orthogroups suggesting that the gene number expansion was accompanied by functional diversification, at least partially. We propose an OG-based classification framework for the GT61 genes at different taxonomic levels of the angiosperm useful for any further functional or translational biology study.
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Affiliation(s)
- Alberto Cenci
- Bioversity International, Parc Scientifique Agropolis II, Montpellier, France
| | | | - Mathieu Rouard
- Bioversity International, Parc Scientifique Agropolis II, Montpellier, France
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Genome-Wide Analysis of LRR-RLK Gene Family in Four Gossypium Species and Expression Analysis during Cotton Development and Stress Responses. Genes (Basel) 2018; 9:genes9120592. [PMID: 30501109 PMCID: PMC6316826 DOI: 10.3390/genes9120592] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 11/26/2018] [Accepted: 11/26/2018] [Indexed: 11/26/2022] Open
Abstract
Leucine-rich repeat receptor-like kinases (LRR-RLKs) have been reported to play important roles in plant growth, development, and stress responses. However, no comprehensive analysis of this family has been performed in cotton (Gossypium spp.), which is an important economic crop that suffers various stresses in growth and development. Here we conducted a comprehensive analysis of LRR-RLK family in four Gossypium species (Gossypium arboreum, Gossypium barbadense, Gossypium hirsutum, and Gossypium raimondii). A total of 1641 LRR-RLK genes were identified in the four Gossypium species involved in our study. The maximum-likelihood phylogenetic tree revealed that all the LRR-RLK genes were divided into 21 subgroups. Exon-intron organization structure of LRR-RLK genes kept relatively conserved within subfamilies and between Arabidopsis and Gossypium genomes. Notably, subfamilies XI and XII were found dramatically expanded in Gossypium species. Tandem duplication acted as an important mechanism in expansion of the Gossypium LRR-RLK gene family. Functional analysis suggested that GossypiumLRR-RLK genes were enriched for plant hormone signaling and plant-pathogen interaction pathways. Promoter analysis revealed that GossypiumLRR-RLK genes were extensively regulated by transcription factors (TFs), phytohormonal, and various environmental stimuli. Expression profiling showed that GossypiumLRR-RLK genes were widely involved in stress defense and diverse developmental processes including cotton fiber development and provides insight into potential functional divergence within and among subfamilies. Our study provided valuable information for further functional study of GossypiumLRR-RLK genes.
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Song H, Guo Z, Chen T, Sun J, Yang G. Genome-wide identification of LRR-containing sequences and the response of these sequences to nematode infection in Arachis duranensis. BMC PLANT BIOLOGY 2018; 18:279. [PMID: 30424729 PMCID: PMC6234637 DOI: 10.1186/s12870-018-1508-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 10/29/2018] [Indexed: 05/25/2023]
Abstract
BACKGROUND Leucine-rich repeat (LRR)-containing genes are involved in responses to various diseases. Recently, RNA-seq data from A. duranensis after nematode (Meloidogyne arenaria) infection were released. However, the number of LRR-containing genes present in A. duranensis and the response of LRR-containing genes to nematode infection are poorly understood. RESULTS In this study, we found 509 amino acid sequences containing nine types of LRR domains in A. duranensis. The inferred phylogenetic relationships revealed that the nine types of LRR domains had two originations. The inferred selective pressure was mainly consistent with LRR domains undergoing purifying selection. Twenty-one LRR-containing genes were associated with possible resistance to nematode infection after 3, 6, and 9 days. Among them, Aradu.T5WNW, Aradu.JM17V, and Aradu.MKP1A were up-regulate at these three time points, while Aradu.QD5DS and Aradu.M0ENQ were up-regulated 6 and 9 days after nematode infection. The expression of the above mentioned five genes was significantly and negatively correlated with the number of LRR8 domain, indicating that fewer LRR8 domains are associated with the promotion of LRR-containing genes that resist nematode infection. Patterns of co-expression and cis-acting elements indicated that WRKY possibly regulate the responses of LRR-containing genes to nematode infection and that expansin genes may work together with LRR-containing genes in response to nematode infection. CONCLUSIONS We identified the number and type of LRR-containing genes in A. duranensis. The LRR-containing genes that were found appear to be involved in responses to nematode infection. The number of LRR8 domains was negatively correlated with expression after nematode infection. The WRKY transcription factor may regulate resistance to nematode infection based on LRR-containing genes. Our results could improve the understanding of resistance to nematodes and molecular breeding in peanuts.
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Affiliation(s)
- Hui Song
- Grassland Agri-husbandry Research Center, Qingdao Agricultural University, Qingdao, 266109 China
| | - Zhonglong Guo
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Life Sciences and School of Advanced Agricultural Sciences, Peking University, Beijing, 100871 China
| | - Tao Chen
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000 China
| | - Juan Sun
- Grassland Agri-husbandry Research Center, Qingdao Agricultural University, Qingdao, 266109 China
| | - Guofeng Yang
- Grassland Agri-husbandry Research Center, Qingdao Agricultural University, Qingdao, 266109 China
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Zhu K, Liu H, Chen X, Cheng Q, Cheng ZM(M. The kinome of pineapple: catalog and insights into functions in crassulacean acid metabolism plants. BMC PLANT BIOLOGY 2018; 18:199. [PMID: 30227850 PMCID: PMC6145126 DOI: 10.1186/s12870-018-1389-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 08/14/2018] [Indexed: 05/04/2023]
Abstract
BACKGROUND Crassulacean acid metabolism (CAM) plants use water 20-80% more efficiently by shifting stomata opening and primary CO2 uptake and fixation to the nighttime. Protein kinases (PKs) play pivotal roles in this biological process. However, few PKs have been functionally analyzed precisely due to their abundance and potential functional redundancy (caused by numerous gene duplications). RESULTS In this study, we systematically identified a total of 758 predicted PK genes in the genome of a CAM plant, pineapple (Ananas comosus). The pineapple kinome was classified into 20 groups and 116 families based on the kinase domain sequences. The RLK was the largest group, containing 480 members, and over half of them were predicted to locate at the plasma membrane. Both segmental and tandem duplications make important contributions to the expansion of pineapple kinome based on the synteny analysis. Ka/Ks ratios showed all of the duplication events were under purifying selection. The global expression analysis revealed that pineapple PKs exhibit different tissue-specific and diurnal expression patterns. Forty PK genes in a cluster performed higher expression levels in green leaf tip than in white leaf base, and fourteen of them had strong differential expression patterns between the photosynthetic green leaf tip and the non-photosynthetic white leaf base tissues. CONCLUSIONS Our findings provide insights into the evolution and biological function of pineapple PKs and a foundation for further functional analysis of PKs in CAM plants. The gene duplication, expression, and coexpression analysis helped us to rapidly identify the key candidates in pineapple kinome, which may play roles in the carbon fixation process in pineapple and help engineering CAM pathway into C3 crops for improved drought tolerance.
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Affiliation(s)
- Kaikai Zhu
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 Jiangsu China
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996 USA
| | - Hui Liu
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 Jiangsu China
| | - Xinlu Chen
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996 USA
| | - Qunkang Cheng
- Department of Botany and Plant Pathology, Central Oregon Agricultural Research Center, Oregon State University, Madras, OR 97741 USA
| | - Zong-Ming (Max) Cheng
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 Jiangsu China
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996 USA
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Jamieson PA, Shan L, He P. Plant cell surface molecular cypher: Receptor-like proteins and their roles in immunity and development. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 274:242-251. [PMID: 30080610 PMCID: PMC6297115 DOI: 10.1016/j.plantsci.2018.05.030] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 05/03/2018] [Accepted: 05/26/2018] [Indexed: 05/21/2023]
Abstract
Plant receptor-like proteins (RLPs) are a family of transmembrane receptors which are distinguished from receptor-like kinases (RLKs) by their lack of a cytoplasmic kinase domain. RLPs continue to be implicated in a broad range of plant immunological and developmental processes as critical sensors or participants in receptor complexes on the plasma membrane. RLPs often associate with RLKs to activate or attenuate signal perception and relay. Some RLPs also physically cluster with RLKs and bear similar expression patterns. Here, we discuss the characteristics, function, and expression of characterized RLPs in the context of their associated RLKs in plant immunity and development.
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Affiliation(s)
- Pierce A Jamieson
- Department of Plant Pathology and Microbiology, and Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX 77843, USA
| | - Libo Shan
- Department of Plant Pathology and Microbiology, and Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX 77843, USA
| | - Ping He
- Department of Biochemistry and Biophysics, and Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX 77843, USA.
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Plomion C, Aury JM, Amselem J, Leroy T, Murat F, Duplessis S, Faye S, Francillonne N, Labadie K, Le Provost G, Lesur I, Bartholomé J, Faivre-Rampant P, Kohler A, Leplé JC, Chantret N, Chen J, Diévart A, Alaeitabar T, Barbe V, Belser C, Bergès H, Bodénès C, Bogeat-Triboulot MB, Bouffaud ML, Brachi B, Chancerel E, Cohen D, Couloux A, Da Silva C, Dossat C, Ehrenmann F, Gaspin C, Grima-Pettenati J, Guichoux E, Hecker A, Herrmann S, Hugueney P, Hummel I, Klopp C, Lalanne C, Lascoux M, Lasserre E, Lemainque A, Desprez-Loustau ML, Luyten I, Madoui MA, Mangenot S, Marchal C, Maumus F, Mercier J, Michotey C, Panaud O, Picault N, Rouhier N, Rué O, Rustenholz C, Salin F, Soler M, Tarkka M, Velt A, Zanne AE, Martin F, Wincker P, Quesneville H, Kremer A, Salse J. Oak genome reveals facets of long lifespan. NATURE PLANTS 2018; 4:440-452. [PMID: 29915331 PMCID: PMC6086335 DOI: 10.1038/s41477-018-0172-3] [Citation(s) in RCA: 194] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Accepted: 05/08/2018] [Indexed: 05/18/2023]
Abstract
Oaks are an important part of our natural and cultural heritage. Not only are they ubiquitous in our most common landscapes1 but they have also supplied human societies with invaluable services, including food and shelter, since prehistoric times2. With 450 species spread throughout Asia, Europe and America3, oaks constitute a critical global renewable resource. The longevity of oaks (several hundred years) probably underlies their emblematic cultural and historical importance. Such long-lived sessile organisms must persist in the face of a wide range of abiotic and biotic threats over their lifespans. We investigated the genomic features associated with such a long lifespan by sequencing, assembling and annotating the oak genome. We then used the growing number of whole-genome sequences for plants (including tree and herbaceous species) to investigate the parallel evolution of genomic characteristics potentially underpinning tree longevity. A further consequence of the long lifespan of trees is their accumulation of somatic mutations during mitotic divisions of stem cells present in the shoot apical meristems. Empirical4 and modelling5 approaches have shown that intra-organismal genetic heterogeneity can be selected for6 and provides direct fitness benefits in the arms race with short-lived pests and pathogens through a patchwork of intra-organismal phenotypes7. However, there is no clear proof that large-statured trees consist of a genetic mosaic of clonally distinct cell lineages within and between branches. Through this case study of oak, we demonstrate the accumulation and transmission of somatic mutations and the expansion of disease-resistance gene families in trees.
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Affiliation(s)
| | - Jean-Marc Aury
- Commissariat à l'Energie Atomique (CEA), Genoscope, Institut de Biologie François-Jacob, Evry, France
| | | | | | | | | | - Sébastien Faye
- Commissariat à l'Energie Atomique (CEA), Genoscope, Institut de Biologie François-Jacob, Evry, France
| | | | - Karine Labadie
- Commissariat à l'Energie Atomique (CEA), Genoscope, Institut de Biologie François-Jacob, Evry, France
| | | | - Isabelle Lesur
- BIOGECO, INRA, Université de Bordeaux, Cestas, France
- HelixVenture, Mérignac, France
| | | | | | | | | | - Nathalie Chantret
- AGAP, Université de Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Jun Chen
- Department of Ecology and Genetics, Evolutionary Biology Centre, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Anne Diévart
- CIRAD, UMR AGAP, Montpellier, France
- Université de Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | | | - Valérie Barbe
- Commissariat à l'Energie Atomique (CEA), Genoscope, Institut de Biologie François-Jacob, Evry, France
| | - Caroline Belser
- Commissariat à l'Energie Atomique (CEA), Genoscope, Institut de Biologie François-Jacob, Evry, France
| | | | | | | | - Marie-Lara Bouffaud
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Halle/Saale, Germany
| | | | | | - David Cohen
- UMR Silva, INRA, Université de Lorraine, AgroPariTech, Nancy, France
| | - Arnaud Couloux
- Commissariat à l'Energie Atomique (CEA), Genoscope, Institut de Biologie François-Jacob, Evry, France
| | - Corinne Da Silva
- Commissariat à l'Energie Atomique (CEA), Genoscope, Institut de Biologie François-Jacob, Evry, France
| | - Carole Dossat
- Commissariat à l'Energie Atomique (CEA), Genoscope, Institut de Biologie François-Jacob, Evry, France
| | | | - Christine Gaspin
- Plateforme bioinformatique Toulouse Midi-Pyrénées, INRA, Auzeville Castanet-Tolosan, France
| | | | | | - Arnaud Hecker
- IAM, INRA, Université de Lorraine, Champenoux, France
| | - Sylvie Herrmann
- German Centre for Integrative Research (iDiv), Halle-Jena-Leipzig, Leipzig, Germany
| | | | - Irène Hummel
- UMR Silva, INRA, Université de Lorraine, AgroPariTech, Nancy, France
| | - Christophe Klopp
- Plateforme bioinformatique Toulouse Midi-Pyrénées, INRA, Auzeville Castanet-Tolosan, France
| | | | - Martin Lascoux
- Department of Ecology and Genetics, Evolutionary Biology Centre, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Eric Lasserre
- Université de Perpignan, UMR 5096, Perpignan, France
| | - Arnaud Lemainque
- Commissariat à l'Energie Atomique (CEA), Genoscope, Institut de Biologie François-Jacob, Evry, France
| | | | | | - Mohammed-Amin Madoui
- Commissariat à l'Energie Atomique (CEA), Genoscope, Institut de Biologie François-Jacob, Evry, France
| | - Sophie Mangenot
- Commissariat à l'Energie Atomique (CEA), Genoscope, Institut de Biologie François-Jacob, Evry, France
| | | | | | - Jonathan Mercier
- Commissariat à l'Energie Atomique (CEA), Genoscope, Institut de Biologie François-Jacob, Evry, France
| | | | | | | | | | - Olivier Rué
- Plateforme bioinformatique Toulouse Midi-Pyrénées, INRA, Auzeville Castanet-Tolosan, France
| | | | - Franck Salin
- BIOGECO, INRA, Université de Bordeaux, Cestas, France
| | - Marçal Soler
- Université de Toulouse, CNRS, UMR 5546, LRSV, Castanet-Tolosan, France
- Laboratori del Suro, University of Girona, Girona, Spain
| | - Mika Tarkka
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Halle/Saale, Germany
| | - Amandine Velt
- SVQV, Université de Strasbourg, INRA, Colmar, France
| | - Amy E Zanne
- Department of Biological Sciences, George Washington University, Washington, DC, USA
| | | | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut de Biologie François-Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Université d'Evry, Université Paris-Saclay, Evry, France
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Yan J, Li G, Guo X, Li Y, Cao X. Genome-wide classification, evolutionary analysis and gene expression patterns of the kinome in Gossypium. PLoS One 2018; 13:e0197392. [PMID: 29768506 PMCID: PMC5955557 DOI: 10.1371/journal.pone.0197392] [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: 01/06/2018] [Accepted: 05/01/2018] [Indexed: 11/18/2022] Open
Abstract
The protein kinase (PK, kinome) family is one of the largest families in plants and regulates almost all aspects of plant processes, including plant development and stress responses. Despite their important functions, comprehensive functional classification, evolutionary analysis and expression patterns of the cotton PK gene family has yet to be performed on PK genes. In this study, we identified the cotton kinomes in the Gossypium raimondii, Gossypium arboretum, Gossypium hirsutum and Gossypium barbadense genomes and classified them into 7 groups and 122-24 subfamilies using software HMMER v3.0 scanning and neighbor-joining (NJ) phylogenetic analysis. Some conserved exon-intron structures were identified not only in cotton species but also in primitive plants, ferns and moss, suggesting the significant function and ancient origination of these PK genes. Collinearity analysis revealed that 16.6 million years ago (Mya) cotton-specific whole genome duplication (WGD) events may have played a partial role in the expansion of the cotton kinomes, whereas tandem duplication (TD) events mainly contributed to the expansion of the cotton RLK group. Synteny analysis revealed that tetraploidization of G. hirsutum and G. barbadense contributed to the expansion of G. hirsutum and G. barbadense PKs. Global expression analysis of cotton PKs revealed stress-specific and fiber development-related expression patterns, suggesting that many cotton PKs might be involved in the regulation of the stress response and fiber development processes. This study provides foundational information for further studies on the evolution and molecular function of cotton PKs.
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Affiliation(s)
- Jun Yan
- College of Information Science and Engineering, Shandong Agricultural University, Tai’an, Shandong, PR China
- College of Life Sciences, Shandong Agricultural University, Tai’an, Shandong, PR China
| | - Guilin Li
- College of Life Sciences, Shandong Agricultural University, Tai’an, Shandong, PR China
| | - Xingqi Guo
- College of Life Sciences, Shandong Agricultural University, Tai’an, Shandong, PR China
| | - Yang Li
- College of Information Science and Engineering, Shandong Agricultural University, Tai’an, Shandong, PR China
| | - Xuecheng Cao
- College of Information Science and Engineering, Shandong Agricultural University, Tai’an, Shandong, PR China
- * E-mail:
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Liu PL, Huang Y, Shi PH, Yu M, Xie JB, Xie L. Duplication and diversification of lectin receptor-like kinases (LecRLK) genes in soybean. Sci Rep 2018; 8:5861. [PMID: 29651041 PMCID: PMC5897391 DOI: 10.1038/s41598-018-24266-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 03/29/2018] [Indexed: 01/12/2023] Open
Abstract
Lectin receptor-like kinases (LecRLKs) play important roles in plant development and stress responses. Although genome-wide studies of LecRLKs have been performed in several species, a comprehensive analysis including evolutionary, structural and functional analysis has not been carried out in soybean (Glycine max). In this study, we identified 185 putative LecRLK genes in the soybean genome, including 123 G-type, 60 L-type and 2 C-type LecRLK genes. Tandem duplication and segmental duplication appear to be the main mechanisms of gene expansion in the soybean LecRLK (GmLecRLK) gene family. According to our phylogenetic analysis, G-type and L-type GmLecRLK genes can be organized into fourteen and eight subfamilies, respectively. The subfamilies within the G-type GmLecRLKs differ from each other in gene structure and/or protein domains and motifs, which indicates that the subfamilies have diverged. The evolution of L-type GmLecRLKs has been more conservative: most genes retain the same gene structures and nearly the same protein domain and motif architectures. Furthermore, the expression profiles of G-type and L-type GmLecRLK genes show evidence of functional redundancy and divergence within each group. Our results contribute to a better understanding of the evolution and function of soybean LecRLKs and provide a framework for further functional investigation of them.
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Affiliation(s)
- Ping-Li Liu
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Yuan Huang
- Institute of Hutchison Whampoa Guangzhou Baiyunshan Chinese Medicine Co., Ltd, Guangzhou, 510515, China
| | - Peng-Hao Shi
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Meng Yu
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Jian-Bo Xie
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China.
| | - LuLu Xie
- Department of Chinese Cabbage, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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Wang Y, Xu Y, Sun Y, Wang H, Qi J, Wan B, Ye W, Lin Y, Shao Y, Dong S, Tyler BM, Wang Y. Leucine-rich repeat receptor-like gene screen reveals that Nicotiana RXEG1 regulates glycoside hydrolase 12 MAMP detection. Nat Commun 2018; 9:594. [PMID: 29426870 PMCID: PMC5807360 DOI: 10.1038/s41467-018-03010-8] [Citation(s) in RCA: 107] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2017] [Accepted: 01/12/2018] [Indexed: 12/30/2022] Open
Abstract
Activation of innate immunity by membrane-localized receptors is conserved across eukaryotes. Plant genomes contain hundreds of such receptor-like genes and those encoding proteins with an extracellular leucine-rich repeat (LRR) domain represent the largest family. Here, we develop a high-throughput approach to study LRR receptor-like genes on a genome-wide scale. In total, 257 tobacco rattle virus-based constructs are generated to target 386 of the 403 identified LRR receptor-like genes in Nicotiana benthamiana for silencing. Using this toolkit, we identify the LRR receptor-like protein Response to XEG1 (RXEG1) that specifically recognizes the glycoside hydrolase 12 protein XEG1. RXEG1 associates with XEG1 via the LRR domain in the apoplast and forms a complex with the LRR receptor-like kinases BAK1 and SOBIR1 to transduce the XEG1-induced defense signal. Thus, this genome-wide silencing assay is demonstrated to be an efficient toolkit to pinpoint new immune receptors, which will contribute to developing durable disease resistance.
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Affiliation(s)
- Yan Wang
- Department of Plant Pathology, Nanjing Agricultural University, 210095, Nanjing, China
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), 210095, Nanjing, China
| | - Yuanpeng Xu
- Department of Plant Pathology, Nanjing Agricultural University, 210095, Nanjing, China
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), 210095, Nanjing, China
| | - Yujing Sun
- Department of Plant Pathology, Nanjing Agricultural University, 210095, Nanjing, China
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), 210095, Nanjing, China
| | - Huibin Wang
- Department of Plant Pathology, Nanjing Agricultural University, 210095, Nanjing, China
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), 210095, Nanjing, China
| | - Jiaming Qi
- Department of Plant Pathology, Nanjing Agricultural University, 210095, Nanjing, China
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), 210095, Nanjing, China
| | - Bowen Wan
- Department of Plant Pathology, Nanjing Agricultural University, 210095, Nanjing, China
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), 210095, Nanjing, China
| | - Wenwu Ye
- Department of Plant Pathology, Nanjing Agricultural University, 210095, Nanjing, China
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), 210095, Nanjing, China
| | - Yachun Lin
- Department of Plant Pathology, Nanjing Agricultural University, 210095, Nanjing, China
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), 210095, Nanjing, China
| | - Yuanyuan Shao
- Department of Plant Pathology, Nanjing Agricultural University, 210095, Nanjing, China
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), 210095, Nanjing, China
| | - Suomeng Dong
- Department of Plant Pathology, Nanjing Agricultural University, 210095, Nanjing, China
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), 210095, Nanjing, China
| | - Brett M Tyler
- Center for Genome Research and Biocomputing and Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
| | - Yuanchao Wang
- Department of Plant Pathology, Nanjing Agricultural University, 210095, Nanjing, China.
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), 210095, Nanjing, China.
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Thapa G, Gunupuru LR, Hehir JG, Kahla A, Mullins E, Doohan FM. A Pathogen-Responsive Leucine Rich Receptor Like Kinase Contributes to Fusarium Resistance in Cereals. FRONTIERS IN PLANT SCIENCE 2018; 9:867. [PMID: 29997638 PMCID: PMC6029142 DOI: 10.3389/fpls.2018.00867] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 06/04/2018] [Indexed: 05/19/2023]
Abstract
Receptor-like kinases form the largest family of receptors in plants and play an important role in recognizing pathogen-associated molecular patterns and modulating the plant immune responses to invasive fungi, including cereal defenses against fungal diseases. But hitherto, none have been shown to modulate the wheat response to the economically important Fusarium head blight (FHB) disease of small-grain cereals. Homologous genes were identified on barley chromosome 6H (HvLRRK-6H) and wheat chromosome 6DL (TaLRRK-6D), which encode the characteristic domains of surface-localized receptor like kinases. Gene expression studies validated that the wheat TaLRRK-6D is highly induced in heads as an early response to both the causal pathogen of FHB disease, Fusarium graminearum, and its' mycotoxic virulence factor deoxynivalenol. The transcription of other wheat homeologs of this gene, located on chromosomes 6A and 6B, was also up-regulated in response to F. graminearum. Virus-induced gene silencing (VIGS) of the barley HvLRRK-6H compromised leaf defense against F. graminearum. VIGS of TaLRRK-6D in two wheat cultivars, CM82036 (resistant to FHB disease) and cv. Remus (susceptible to FHB), confirmed that TaLRRK-6D contributes to basal resistance to FHB disease in both genotypes. Although the effect of VIGS did not generally reduce grain losses due to FHB, this experiment did reveal that TaLRRK-6D positively contributes to grain development. Further gene expression studies in wheat cv. Remus indicated that VIGS of TaLRRK-6D suppressed the expression of genes involved in salicylic acid signaling, which is a key hormonal pathway involved in defense. Thus, this study provides the first evidence of receptor like kinases as an important component of cereal defense against Fusarium and highlights this gene as a target for enhancing cereal resistance to FHB disease.
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Affiliation(s)
- Ganesh Thapa
- UCD School of Biology and Environmental Science, UCD Earth Institute and UCD Institute of Food and Health, University College of Dublin, Belfield, Ireland
| | - Lokanadha R. Gunupuru
- UCD School of Biology and Environmental Science, UCD Earth Institute and UCD Institute of Food and Health, University College of Dublin, Belfield, Ireland
| | - James G. Hehir
- Crop Science Department, Oak Park Crops Research Centre, Teagasc, Carlow, Ireland
| | - Amal Kahla
- UCD School of Biology and Environmental Science, UCD Earth Institute and UCD Institute of Food and Health, University College of Dublin, Belfield, Ireland
| | - Ewen Mullins
- Crop Science Department, Oak Park Crops Research Centre, Teagasc, Carlow, Ireland
| | - Fiona M. Doohan
- UCD School of Biology and Environmental Science, UCD Earth Institute and UCD Institute of Food and Health, University College of Dublin, Belfield, Ireland
- *Correspondence: Fiona M. Doohan,
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Sun J, Li L, Wang P, Zhang S, Wu J. Genome-wide characterization, evolution, and expression analysis of the leucine-rich repeat receptor-like protein kinase (LRR-RLK) gene family in Rosaceae genomes. BMC Genomics 2017; 18:763. [PMID: 29017442 PMCID: PMC5635495 DOI: 10.1186/s12864-017-4155-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 10/02/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Leucine-rich repeat receptor-like protein kinase (LRR-RLK) is the largest gene family of receptor-like protein kinases (RLKs) and actively participates in regulating the growth, development, signal transduction, immunity, and stress responses of plants. However, the patterns of LRR-RLK gene family evolution in the five main Rosaceae species for which genome sequences are available have not yet been reported. In this study, we performed a comprehensive analysis of LRR-RLK genes for five Rosaceae species: Fragaria vesca (strawberry), Malus domestica (apple), Pyrus bretschneideri (Chinese white pear), Prunus mume (mei), and Prunus persica (peach), which contained 201, 244, 427, 267, and 258 LRR-RLK genes, respectively. RESULTS All LRR-RLK genes were further grouped into 23 subfamilies based on the hidden Markov models approach. RLK-Pelle_LRR-XII-1, RLK-Pelle_LRR-XI-1, and RLK-Pelle_LRR-III were the three largest subfamilies. Synteny analysis indicated that there were 236 tandem duplicated genes in the five Rosaceae species, among which subfamilies XII-1 (82 genes) and XI-1 (80 genes) comprised 68.6%. CONCLUSIONS Our results indicate that tandem duplication made a large contribution to the expansion of the subfamilies. The gene expression, tissue-specific expression, and subcellular localization data revealed that LRR-RLK genes were differentially expressed in various organs and tissues, and the largest subfamily XI-1 was highly expressed in all five Rosaceae species, suggesting that LRR-RLKs play important roles in each stage of plant growth and development. Taken together, our results provide an overview of the LRR-RLK family in Rosaceae genomes and the basis for further functional studies.
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Affiliation(s)
- Jiangmei Sun
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Leiting Li
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Peng Wang
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shaoling Zhang
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Juyou Wu
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.
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Bettembourg M, Dardou A, Audebert A, Thomas E, Frouin J, Guiderdoni E, Ahmadi N, Perin C, Dievart A, Courtois B. Genome-wide association mapping for root cone angle in rice. RICE (NEW YORK, N.Y.) 2017; 10:45. [PMID: 28971382 PMCID: PMC5624858 DOI: 10.1186/s12284-017-0184-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 09/19/2017] [Indexed: 05/24/2023]
Abstract
BACKGROUND Plant root systems play a major role in anchoring and in water and nutrient uptake from the soil. The root cone angle is an important parameter of the root system architecture because, combined with root depth, it helps to determine the volume of soil explored by the plant. Two genes, DRO1 and SOR1, and several QTLs for root cone angle have been discovered in the last 5 years. RESULTS To find other QTLs linked to root cone angle, a genome-wide association mapping study was conducted on two panels of 162 indica and 169 japonica rice accessions genotyped with two sets of SNP markers (genotyping-by-sequencing set with approximately 16,000 markers and high-density-rice-array set with approximately 300,000 markers). The root cone angle of all accessions was measured using a screen protractor on images taken after 1 month of plant growth in the Rhizoscope phenotyping system. The distribution of the root cone angle in the indica panel was Gaussian, but several accessions of the japonica panel (all the bulus from Indonesia and three temperate japonicas from Nepal or India) appeared as outliers with a very wide root cone angle. The data were submitted to association mapping using a mixed model with control of structure and kinship. A total of 15 QTLs for the indica panel and 40 QTLs for the japonica panel were detected. Genes underlying these QTLs (+/-50 kb from the significant markers) were analyzed. We focused our analysis on auxin-related genes, kinases, and genes involved in root developmental processes and identified 8 particularly interesting genes. CONCLUSIONS The present study identifies new sources of wide root cone angle in rice, proposes ways to bypass some drawbacks of association mapping to further understand the genetics of the trait and identifies candidate genes deserving further investigation.
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Affiliation(s)
| | | | - Alain Audebert
- Cirad, UMR AGAP, F34398 Montpellier Cedex 5, France
- Cirad / ISRA-Ceraas, BP 3320 Thies, Senegal
| | | | | | | | | | | | - Anne Dievart
- Cirad, UMR AGAP, F34398 Montpellier Cedex 5, France
- Shanghai Jiao Tong University (SJTU), School of Life Sciences and Biotechnology, Shanghai, 200240 China
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Plant signalling in symbiosis and immunity. Nature 2017; 543:328-336. [PMID: 28300100 DOI: 10.1038/nature22009] [Citation(s) in RCA: 395] [Impact Index Per Article: 56.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 01/13/2017] [Indexed: 12/12/2022]
Abstract
Plants encounter a myriad of microorganisms, particularly at the root-soil interface, that can invade with detrimental or beneficial outcomes. Prevalent beneficial associations between plants and microorganisms include those that promote plant growth by facilitating the acquisition of limiting nutrients such as nitrogen and phosphorus. But while promoting such symbiotic relationships, plants must restrict the formation of pathogenic associations. Achieving this balance requires the perception of potential invading microorganisms through the signals that they produce, followed by the activation of either symbiotic responses that promote microbial colonization or immune responses that limit it.
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Expression of Plant Receptor Kinases in E. coli. Methods Mol Biol 2017. [PMID: 28567638 DOI: 10.1007/978-1-4939-7063-6_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Plant receptor kinases play diverse signaling roles in disease resistance and plant development. They represent a large plant gene family with over 600 members in Arabidopsis thaliana. While the functions of several members of the receptor kinase family have now been elucidated, a great proportion still remains uncharacterized. The structural and functional characterization of such plant receptor kinases may entail biochemical approaches that require access to purified protein, which can be made possible through heterologous protein expression. This chapter describes a strategy for expressing plant receptor kinases in E. coli, a bacterial host that has successfully been used to express and purify certain plant receptor kinase domains, some of which were subsequently used for biochemical assays. As full-length receptor-like kinases may be difficult to express, it is suggested to clone and express domains separately, after having identified domain borders using bioinformatics tools. A detailed cloning protocol is provided, as well as advice for testing expression efficiency and handling of expressed protein ending up in inclusion bodies.
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Liu PL, Du L, Huang Y, Gao SM, Yu M. Origin and diversification of leucine-rich repeat receptor-like protein kinase (LRR-RLK) genes in plants. BMC Evol Biol 2017; 17:47. [PMID: 28173747 PMCID: PMC5296948 DOI: 10.1186/s12862-017-0891-5] [Citation(s) in RCA: 117] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 01/26/2017] [Indexed: 02/05/2023] Open
Abstract
Background Leucine-rich repeat receptor-like protein kinases (LRR-RLKs) are the largest group of receptor-like kinases in plants and play crucial roles in development and stress responses. The evolutionary relationships among LRR-RLK genes have been investigated in flowering plants; however, no comprehensive studies have been performed for these genes in more ancestral groups. The subfamily classification of LRR-RLK genes in plants, the evolutionary history and driving force for the evolution of each LRR-RLK subfamily remain to be understood. Results We identified 119 LRR-RLK genes in the Physcomitrella patens moss genome, 67 LRR-RLK genes in the Selaginella moellendorffii lycophyte genome, and no LRR-RLK genes in five green algae genomes. Furthermore, these LRR-RLK sequences, along with previously reported LRR-RLK sequences from Arabidopsis thaliana and Oryza sativa, were subjected to evolutionary analyses. Phylogenetic analyses revealed that plant LRR-RLKs belong to 19 subfamilies, eighteen of which were established in early land plants, and one of which evolved in flowering plants. More importantly, we found that the basic structures of LRR-RLK genes for most subfamilies are established in early land plants and conserved within subfamilies and across different plant lineages, but divergent among subfamilies. In addition, most members of the same subfamily had common protein motif compositions, whereas members of different subfamilies showed variations in protein motif compositions. The unique gene structure and protein motif compositions of each subfamily differentiate the subfamily classifications and, more importantly, provide evidence for functional divergence among LRR-RLK subfamilies. Maximum likelihood analyses showed that some sites within four subfamilies were under positive selection. Conclusions Much of the diversity of plant LRR-RLK genes was established in early land plants. Positive selection contributed to the evolution of a few LRR-RLK subfamilies. Electronic supplementary material The online version of this article (doi:10.1186/s12862-017-0891-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ping-Li Liu
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China.
| | - Liang Du
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Yuan Huang
- College of Life Sciences, Peking University, Beijing, 100871, China
| | - Shu-Min Gao
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Meng Yu
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
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Dufayard JF, Bettembourg M, Fischer I, Droc G, Guiderdoni E, Périn C, Chantret N, Diévart A. New Insights on Leucine-Rich Repeats Receptor-Like Kinase Orthologous Relationships in Angiosperms. FRONTIERS IN PLANT SCIENCE 2017; 8:381. [PMID: 28424707 PMCID: PMC5380761 DOI: 10.3389/fpls.2017.00381] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 03/06/2017] [Indexed: 05/18/2023]
Abstract
Leucine-Rich Repeats Receptor-Like Kinase (LRR-RLK) genes represent a large and complex gene family in plants, mainly involved in development and stress responses. These receptors are composed of an LRR-containing extracellular domain (ECD), a transmembrane domain (TM) and an intracellular kinase domain (KD). To provide new perspectives on functional analyses of these genes in model and non-model plant species, we performed a phylogenetic analysis on 8,360 LRR-RLK receptors in 31 angiosperm genomes (8 monocots and 23 dicots). We identified 101 orthologous groups (OGs) of genes being conserved among almost all monocot and dicot species analyzed. We observed that more than 10% of these OGs are absent in the Brassicaceae species studied. We show that the ECD structural features are not always conserved among orthologs, suggesting that functions may have diverged in some OG sets. Moreover, we looked at targets of positive selection footprints in 12 pairs of OGs and noticed that depending on the subgroups, positive selection occurred more frequently either in the ECDs or in the KDs.
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Affiliation(s)
| | | | | | | | | | | | - Nathalie Chantret
- INRA, UMR AGAPMontpellier, France
- *Correspondence: Anne Diévart, Nathalie Chantret,
| | - Anne Diévart
- CIRAD, UMR AGAPMontpellier, France
- *Correspondence: Anne Diévart, Nathalie Chantret,
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73
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Shumayla, Sharma S, Kumar R, Mendu V, Singh K, Upadhyay SK. Genomic Dissection and Expression Profiling Revealed Functional Divergence in Triticum aestivum Leucine Rich Repeat Receptor Like Kinases (TaLRRKs). FRONTIERS IN PLANT SCIENCE 2016; 7:1374. [PMID: 27713749 PMCID: PMC5031697 DOI: 10.3389/fpls.2016.01374] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 08/29/2016] [Indexed: 09/01/2023]
Abstract
The leucine rich repeat receptor like kinases (LRRK) constitute the largest subfamily of receptor like kinases (RLK), which play critical roles in plant development and stress responses. Herein, we identified 531 TaLRRK genes in Triticum aestivum (bread wheat), which were distributed throughout the A, B, and D sub-genomes and chromosomes. These were clustered into 233 homologous groups, which were mostly located on either homeologous chromosomes from various sub-genomes or in proximity on the same chromosome. A total of 255 paralogous genes were predicted which depicted the role of duplication events in expansion of this gene family. Majority of TaLRRKs consisted of trans-membrane region and localized on plasma-membrane. The TaLRRKs were further categorized into eight phylogenetic groups with numerous subgroups on the basis of sequence homology. The gene and protein structure in terms of exon/intron ratio, domains, and motifs organization were found to be variably conserved across the different phylogenetic groups/subgroups, which indicated a potential divergence and neofunctionalization during evolution. High-throughput transcriptome data and quantitative real time PCR analyses in various developmental stages, and biotic and abiotic (heat, drought, and salt) stresses provided insight into modus operandi of TaLRRKs during these conditions. Distinct expression of majority of stress responsive TaLRRKs homologous genes suggested their specified role in a particular condition. These results provided a comprehensive analysis of various characteristic features including functional divergence, which may provide the way for future functional characterization of this important gene family in bread wheat.
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Affiliation(s)
- Shumayla
- Deparment of Botany, Panjab UniversityChandigarh, India
- Deparment of Biotechnology, Panjab UniversityChandigarh, India
| | | | - Rohit Kumar
- Deparment of Biotechnology, Panjab UniversityChandigarh, India
| | - Venugopal Mendu
- Department of Plant and Soil Science, Fiber and Biopolymer Research Institute, Texas Tech UniversityLubbock, TX, USA
| | - Kashmir Singh
- Deparment of Biotechnology, Panjab UniversityChandigarh, India
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74
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Magalhães DM, Scholte LLS, Silva NV, Oliveira GC, Zipfel C, Takita MA, De Souza AA. LRR-RLK family from two Citrus species: genome-wide identification and evolutionary aspects. BMC Genomics 2016; 17:623. [PMID: 27515968 PMCID: PMC4982124 DOI: 10.1186/s12864-016-2930-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 07/12/2016] [Indexed: 11/17/2022] Open
Abstract
Background Leucine-rich repeat receptor-like kinases (LRR-RLKs) represent the largest subfamily of plant RLKs. The functions of most LRR-RLKs have remained undiscovered, and a few that have been experimentally characterized have been shown to have important roles in growth and development as well as in defense responses. Although RLK subfamilies have been previously studied in many plants, no comprehensive study has been performed on this gene family in Citrus species, which have high economic importance and are frequent targets for emerging pathogens. In this study, we performed in silico analysis to identify and classify LRR-RLK homologues in the predicted proteomes of Citrus clementina (clementine) and Citrus sinensis (sweet orange). In addition, we used large-scale phylogenetic approaches to elucidate the evolutionary relationships of the LRR-RLKs and further narrowed the analysis to the LRR-XII group, which contains several previously described cell surface immune receptors. Results We built integrative protein signature databases for Citrus clementina and Citrus sinensis using all predicted protein sequences obtained from whole genomes. A total of 300 and 297 proteins were identified as LRR-RLKs in C. clementina and C. sinensis, respectively. Maximum-likelihood phylogenetic trees were estimated using Arabidopsis LRR-RLK as a template and they allowed us to classify Citrus LRR-RLKs into 16 groups. The LRR-XII group showed a remarkable expansion, containing approximately 150 paralogs encoded in each Citrus genome. Phylogenetic analysis also demonstrated the existence of two distinct LRR-XII clades, each one constituted mainly by RD and non-RD kinases. We identified 68 orthologous pairs from the C. clementina and C. sinensis LRR-XII genes. In addition, among the paralogs, we identified a subset of 78 and 62 clustered genes probably derived from tandem duplication events in the genomes of C. clementina and C. sinensis, respectively. Conclusions This work provided the first comprehensive evolutionary analysis of the LRR-RLKs in Citrus. A large expansion of LRR-XII in Citrus genomes suggests that it might play a key role in adaptive responses in host-pathogen co-evolution, related to the perennial life cycle and domestication of the citrus crop species. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2930-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Diogo M Magalhães
- Instituto Agronômico, Centro de Citricultura Sylvio Moreira, Cordeirópolis, São Paulo, Brazil.,Departamento de Genética e Biologia Molecular, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
| | - Larissa L S Scholte
- Instituto Nacional de Ciência e Tecnologia em Doenças Tropicais, Grupo de Genômica e Biologia Computacional, Centro de Pesquisas René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Minas Gerais, Brazil
| | - Nicholas V Silva
- Instituto Agronômico, Centro de Citricultura Sylvio Moreira, Cordeirópolis, São Paulo, Brazil
| | - Guilherme C Oliveira
- Instituto Nacional de Ciência e Tecnologia em Doenças Tropicais, Grupo de Genômica e Biologia Computacional, Centro de Pesquisas René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Minas Gerais, Brazil.,Instituto Tecnológico Vale - ITV, Belém, Pará, Brazil
| | - Cyril Zipfel
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Marco A Takita
- Instituto Agronômico, Centro de Citricultura Sylvio Moreira, Cordeirópolis, São Paulo, Brazil
| | - Alessandra A De Souza
- Instituto Agronômico, Centro de Citricultura Sylvio Moreira, Cordeirópolis, São Paulo, Brazil.
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75
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Liu PL, Xie LL, Li PW, Mao JF, Liu H, Gao SM, Shi PH, Gong JQ. Duplication and Divergence of Leucine-Rich Repeat Receptor-Like Protein Kinase ( LRR-RLK) Genes in Basal Angiosperm Amborella trichopoda. FRONTIERS IN PLANT SCIENCE 2016; 7:1952. [PMID: 28066499 PMCID: PMC5179525 DOI: 10.3389/fpls.2016.01952] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 12/08/2016] [Indexed: 05/22/2023]
Abstract
Leucine-rich repeat receptor-like protein kinases (LRR-RLKs) are the largest group of receptor-like kinases, which are one of the largest protein superfamilies in plants, and play crucial roles in development and stress responses. Although the evolution of LRR-RLK families has been investigated in some eudicot and monocot plants, no comprehensive evolutionary studies have been performed for these genes in basal angiosperms like Amborella trichopoda. In this study, we identified 94 LRR-RLK genes in the genome of A. trichopoda. The number of LRR-RLK genes in the genome of A. trichopoda is only 17-50% of that of several eudicot and monocot species. Tandem duplication and whole-genome duplication have made limited contributions to the expansion of LRR-RLK genes in A. trichopoda. According to the phylogenetic analysis, all A. trichopoda LRR-RLK genes can be organized into 18 subfamilies, which roughly correspond to the LRR-RLK subfamilies defined in Arabidopsis thaliana. Most LRR-RLK subfamilies are characterized by highly conserved protein structures, motif compositions, and gene structures. The unique gene structure, protein structures, and protein motif compositions of each subfamily provide evidence for functional divergence among LRR-RLK subfamilies. Moreover, the expression data of LRR-RLK genes provided further evidence for the functional diversification of them. In addition, selection analyses showed that most LRR-RLK protein sites are subject to purifying selection. Our results contribute to a better understanding of the evolution of LRR-RLK gene family in angiosperm and provide a framework for further functional investigation on A. trichopoda LRR-RLKs.
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Affiliation(s)
- Ping-Li Liu
- College of Biological Sciences and Biotechnology, Beijing Forestry UniversityBeijing, China
- *Correspondence: Ping-Li Liu
| | - Lu-Lu Xie
- Department of Chinese Cabbage, Institute of Vegetables and Flowers, Chinese Academy of Agricultural SciencesBeijing, China
| | - Peng-Wei Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of SciencesBeijing, China
| | - Jian-Feng Mao
- College of Biological Sciences and Biotechnology, Beijing Forestry UniversityBeijing, China
| | - Hui Liu
- College of Biological Sciences and Biotechnology, Beijing Forestry UniversityBeijing, China
| | - Shu-Min Gao
- College of Biological Sciences and Biotechnology, Beijing Forestry UniversityBeijing, China
| | - Peng-Hao Shi
- College of Biological Sciences and Biotechnology, Beijing Forestry UniversityBeijing, China
| | - Jun-Qing Gong
- College of Biological Sciences and Biotechnology, Beijing Forestry UniversityBeijing, China
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