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Cantila AY, Chen S, Siddique KHM, Cowling WA. Heat shock responsive genes in Brassicaceae: genome-wide identification, phylogeny, and evolutionary associations within and between genera. Genome 2024; 67:464-481. [PMID: 39412080 DOI: 10.1139/gen-2024-0061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2024]
Abstract
Heat stress affects the growth and development of Brassicaceae crops. Plant breeders aim to mitigate the effects of heat stress by selecting for heat stress tolerance, but the genes responsible for heat stress in Brassicaceae remain largely unknown. During heat stress, heat shock proteins (HSPs) function as molecular chaperones to aid in protein folding, and heat shock transcription factors (HSFs) serve as transcriptional regulators of HSP expression. We identified 5002 heat shock related genes, including HSPs and HSFs, across 32 genomes in Brassicaceae. Among these, 3347 genes were duplicated, with segmented duplication primarily contributing to their expansion. We identified 466 physical gene clusters, including 240 homogenous clusters and 226 heterogeneous clusters, shedding light on the organization of heat shock related genes. Notably, 37 genes were co-located with published thermotolerance quantitative trait loci, which supports their functional role in conferring heat stress tolerance. This study provides a comprehensive resource for the identification of functional Brassicaceae heat shock related genes, elucidates their clustering and duplication patterns and establishes the genomic foundation for future heat tolerance research. We hypothesise that genetic variants in HSP and HSF genes in certain species have potential for improving heat stress tolerance in Brassicaceae crops.
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Affiliation(s)
- Aldrin Y Cantila
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6000, Australia
| | - Sheng Chen
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6000, Australia
| | - Kadambot H M Siddique
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6000, Australia
| | - Wallace A Cowling
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6000, Australia
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Beauchet A, Bollier N, Grison M, Rofidal V, Gévaudant F, Bayer E, Gonzalez N, Chevalier C. The CELL NUMBER REGULATOR FW2.2 protein regulates cell-to-cell communication in tomato by modulating callose deposition at plasmodesmata. PLANT PHYSIOLOGY 2024; 196:883-901. [PMID: 38588030 PMCID: PMC11444278 DOI: 10.1093/plphys/kiae198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 02/28/2024] [Accepted: 02/28/2024] [Indexed: 04/10/2024]
Abstract
FW2.2 (standing for FRUIT WEIGHT 2.2), the founding member of the CELL NUMBER REGULATOR (CNR) gene family, was the first cloned gene underlying a quantitative trait locus (QTL) governing fruit size and weight in tomato (Solanum lycopersicum). However, despite this discovery over 20 yr ago, the molecular mechanisms by which FW2.2 negatively regulates cell division during fruit growth remain undeciphered. In the present study, we confirmed that FW2.2 is a membrane-anchored protein whose N- and C-terminal ends face the apoplast. We unexpectedly found that FW2.2 is located at plasmodesmata (PD). FW2.2 participates in the spatiotemporal regulation of callose deposition at PD and belongs to a protein complex which encompasses callose synthases. These results suggest that FW2.2 has a regulatory role in cell-to-cell communication by modulating PD transport capacity and trafficking of signaling molecules during fruit development.
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Affiliation(s)
- Arthur Beauchet
- INRAE, UMR1332 Biologie du Fruit et Pathologie, Université Bordeaux, Villenave d'Ornon F-33140, France
| | - Norbert Bollier
- INRAE, UMR1332 Biologie du Fruit et Pathologie, Université Bordeaux, Villenave d'Ornon F-33140, France
| | - Magali Grison
- CNRS, UMR5200 Laboratoire de Biogenèse Membranaire, Université Bordeaux, Villenave d'Ornon F-33140, France
| | - Valérie Rofidal
- IPSiM, CNRS, INRAE, Institut Sup Agro, Université Montpellier, Montpellier F-34060, France
| | - Frédéric Gévaudant
- INRAE, UMR1332 Biologie du Fruit et Pathologie, Université Bordeaux, Villenave d'Ornon F-33140, France
| | - Emmanuelle Bayer
- CNRS, UMR5200 Laboratoire de Biogenèse Membranaire, Université Bordeaux, Villenave d'Ornon F-33140, France
| | - Nathalie Gonzalez
- INRAE, UMR1332 Biologie du Fruit et Pathologie, Université Bordeaux, Villenave d'Ornon F-33140, France
| | - Christian Chevalier
- INRAE, UMR1332 Biologie du Fruit et Pathologie, Université Bordeaux, Villenave d'Ornon F-33140, France
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Ding H, Feng X, Yuan Y, Wang B, Wang Y, Zhang J. Genomic investigation of duplication, functional conservation, and divergence in the LRR-RLK Family of Saccharum. BMC Genomics 2024; 25:165. [PMID: 38336615 PMCID: PMC10854099 DOI: 10.1186/s12864-024-10073-z] [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: 08/29/2023] [Accepted: 02/01/2024] [Indexed: 02/12/2024] Open
Abstract
BACKGROUND Sugarcane (Saccharum spp.) holds exceptional global significance as a vital crop, serving as a primary source of sucrose, bioenergy, and various by-products. The optimization of sugarcane breeding by fine-tuning essential traits has become crucial for enhancing crop productivity and stress resilience. Leucine-rich repeat receptor-like kinases (LRR-RLK) genes present promising targets for this purpose, as they are involved in various aspects of plant development and defense processes. RESULTS Here, we present a detailed overview of phylogeny and expression of 288 (495 alleles) and 312 (1365 alleles) LRR-RLK genes from two founding Saccharum species, respectively. Phylogenetic analysis categorized these genes into 15 subfamilies, revealing considerable expansion or reduction in certain LRR-type subfamilies. Compared to other plant species, both Saccharum species had more significant LRR-RLK genes. Examination of cis-acting elements demonstrated that SsLRR-RLK and SoLRR-RLK genes exhibited no significant difference in the types of elements included, primarily involved in four physiological processes. This suggests a broad conservation of LRR-RLK gene function during Saccharum evolution. Synteny analysis indicated that all LRR-RLK genes in both Saccharum species underwent gene duplication, primarily through whole-genome duplication (WGD) or segmental duplication. We identified 28 LRR-RLK genes exhibiting novel expression patterns in response to different tissues, gradient development leaves, and circadian rhythm in the two Saccharum species. Additionally, SoLRR-RLK104, SoLRR-RLK7, SoLRR-RLK113, and SsLRR-RLK134 were identified as candidate genes for sugarcane disease defense response regulators through transcriptome data analysis of two disease stresses. This suggests LRR-RLK genes of sugarcane involvement in regulating various biological processes, including leaf development, plant morphology, photosynthesis, maintenance of circadian rhythm stability, and defense against sugarcane diseases. CONCLUSIONS This investigation into gene duplication, functional conservation, and divergence of LRR-RLK genes in two founding Saccharum species lays the groundwork for a comprehensive genomic analysis of the entire LRR-RLK gene family in Saccharum. The results reveal LRR-RLK gene played a critical role in Saccharum adaptation to diverse conditions, offering valuable insights for targeted breeding and precise phenotypic adjustments.
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Affiliation(s)
- Hongyan Ding
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources and Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, 530004, China
| | - Xiaoxi Feng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources and Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, 530004, China
| | - Yuan Yuan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources and Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, 530004, China
| | - Baiyu Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources and Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, 530004, China
| | - Yuhao Wang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Sugarcane Biology and Genetic Breeding, National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jisen Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources and Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, 530004, China.
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Wang Q, Zhao X, Sun Q, Mou Y, Wang J, Yan C, Yuan C, Li C, Shan S. Genome-wide identification of the LRR-RLK gene family in peanut and functional characterization of AhLRR-RLK265 in salt and drought stresses. Int J Biol Macromol 2024; 254:127829. [PMID: 37926304 DOI: 10.1016/j.ijbiomac.2023.127829] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 10/22/2023] [Accepted: 10/26/2023] [Indexed: 11/07/2023]
Abstract
Leucine-rich repeat receptor-like kinases (LRR-RLKs) play important roles in plant developmental regulations and various stress responses. Peanut (Arachis hypogaea L.) is a worldwide important oil crop; however, no systematic identification or analysis of the peanut LRR-RLK gene family has been reported. In present study, 495 LRR-RLK genes in peanut were identified and analyzed. The 495 AhLRR-RLK genes were classed into 14 groups and 10 subgroups together with their Arabidopsis homologs according to phylogenetic analyses, and 491 of 495 AhLRR-RLK genes unequally located on 20 chromosomes. Analyses of gene structure and protein motif organization revealed similarity in exon/intron and motif organization among members of the same subgroup, further supporting the phylogenetic results. Gene duplication events were found in peanut LRR-RLK gene family via syntenic analysis, which were important in LRR-RLK gene family expansion in peanut. We found that the expression of AhLRR-RLK genes was detected in different tissues using RNA-seq data, implying that AhLRR-RLK genes may differ in function. In addition, Arabidopsis plants overexpressing stress-induced AhLRR-RLK265 displayed lower seed germination rates and root lengths compared to wild-type under exogenous ABA treatment. Notably, overexpression of AhLRR-RLK265 enhanced tolerance to salt and drought stresses in transgenic Arabidopsis. Moreover, the AhLRR-RLK265-OE lines were found to have higher activities of superoxide dismutase (SOD), catalase (CAT), and peroxidase (POD) under salt and drought stress treatments. We believe these results may provide valuable information about the function of peanut LRR-RLK genes for further analysis.
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Affiliation(s)
- Qi Wang
- Shandong Peanut Research Institute, Qingdao, Shandong 266100, China.
| | - Xiaobo Zhao
- Shandong Peanut Research Institute, Qingdao, Shandong 266100, China
| | - Quanxi Sun
- Shandong Peanut Research Institute, Qingdao, Shandong 266100, China
| | - Yifei Mou
- Shandong Peanut Research Institute, Qingdao, Shandong 266100, China
| | - Juan Wang
- Shandong Peanut Research Institute, Qingdao, Shandong 266100, China
| | - Caixia Yan
- Shandong Peanut Research Institute, Qingdao, Shandong 266100, China
| | - Cuiling Yuan
- Shandong Peanut Research Institute, Qingdao, Shandong 266100, China
| | - Chunjuan Li
- Shandong Peanut Research Institute, Qingdao, Shandong 266100, China
| | - Shihua Shan
- Shandong Peanut Research Institute, Qingdao, Shandong 266100, China.
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Wang Q, Li X, Guo C, Wen L, Deng Z, Zhang Z, Li W, Liu T, Guo Y. Senescence-related receptor kinase 1 functions downstream of WRKY53 in regulating leaf senescence in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:5140-5152. [PMID: 37351601 DOI: 10.1093/jxb/erad240] [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: 09/28/2022] [Accepted: 06/22/2023] [Indexed: 06/24/2023]
Abstract
Receptor-like kinases (RLKs) are the most important class of cell surface receptors, and play crucial roles in plant development and stress responses. However, few studies have been reported about the biofunctions of RLKs in leaf senescence. Here, we characterized a novel Arabidopsis RLK-encoding gene, SENESCENCE-RELATED RECEPTOR KINASE 1 (SENRK1), which was significantly down-regulated during leaf senescence. Notably, the loss-of-function senrk1 mutants displayed an early leaf senescence phenotype, while overexpression of SENRK1 significantly delayed leaf senescence, indicating that SENRK1 negatively regulates age-dependent leaf senescence in Arabidopsis. Furthermore, the senescence-promoting transcription factor WRKY53 repressed the expression of SENRK1. While the wrky53 mutant showed a delayed senescence phenotype as previously reported, the wrky53 senrk1-1 double mutant exhibited precocious leaf senescence, suggesting that SENRK1 functions downstream of WRKY53 in regulating age-dependent leaf senescence in Arabidopsis.
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Affiliation(s)
- Qi Wang
- Shandong Peanut Research Institute, Qingdao, China
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Xiaoxu Li
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
- Technology Center, China Tobacco Hunan Industrial Co., Ltd., Changsha, China
| | - Cun Guo
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Lichao Wen
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Zhichao Deng
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Zenglin Zhang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Wei Li
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Tao Liu
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Yongfeng Guo
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
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da Silva Dambroz CM, Aono AH, de Andrade Silva EM, Pereira WA. Genome-wide analysis and characterization of the LRR-RLK gene family provides insights into anthracnose resistance in common bean. Sci Rep 2023; 13:13455. [PMID: 37596307 PMCID: PMC10439169 DOI: 10.1038/s41598-023-40054-3] [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: 10/04/2022] [Accepted: 08/03/2023] [Indexed: 08/20/2023] Open
Abstract
Anthracnose, caused by the hemibiotrophic fungus Colletotrichum lindemuthianum, is a damaging disease of common beans that can drastically reduce crop yield. The most effective strategy to manage anthracnose is the use of resistant cultivars. There are many resistance loci that have been identified, mapped and associated with markers in common bean chromosomes. The Leucine-rich repeat kinase receptor protein (LRR-RLK) family is a diverse group of transmembrane receptors, which potentially recognizes pathogen-associated molecular patterns and activates an immune response. In this study, we performed in silico analyses to identify, classify, and characterize common bean LRR-RLKs, also evaluating their expression profile in response to the infection by C. lindemuthianum. By analyzing the entire genome of Phaseolus vulgaris, we could identify and classify 230 LRR-RLKs into 15 different subfamilies. The analyses of gene structures, conserved domains and motifs suggest that LRR-RLKs from the same subfamily are consistent in their exon/intron organization and composition. LRR-RLK genes were found along the 11 chromosomes of the species, including regions of proximity with anthracnose resistance markers. By investigating the duplication events within the LRR-RLK family, we associated the importance of such a family with an expansion resulting from a strong stabilizing selection. Promoter analysis was also performed, highlighting cis-elements associated with the plant response to biotic stress. With regard to the expression pattern of LRR-RLKs in response to the infection by C. lindemuthianum, we could point out several differentially expressed genes in this subfamily, which were associated to specific molecular patterns of LRR-RLKs. Our work provides a broad analysis of the LRR-RLK family in P. vulgaris, allowing an in-depth structural and functional characterization of genes and proteins of this family. From specific expression patterns related to anthracnose response, we could infer a direct participation of RLK-LRR genes in the mechanisms of resistance to anthracnose, highlighting important subfamilies for further investigations.
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Affiliation(s)
| | - Alexandre Hild Aono
- Molecular Biology and Genetic Engineering Center (CBMEG), University of Campinas (UNICAMP), Campinas, SP, Brazil
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Prajapati MR, Singh J, Kumar P, Dixit R. De novo transcriptome analysis and identification of defensive genes in garlic (Allium sativum L.) using high-throughput sequencing. J Genet Eng Biotechnol 2023; 21:56. [PMID: 37162611 PMCID: PMC10172436 DOI: 10.1186/s43141-023-00499-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 04/20/2023] [Indexed: 05/11/2023]
Abstract
BACKGROUND Garlic (Allium sativum L.) is the second most widely cultivated Allium which is mainly grown in temperate regions and used as a flavoring agent in a wide variety of foods. Garlic contains various bioactive compounds whose metabolic pathways, plant-pathogen interactions, defensive genes, identify interaction networks, and functional genomics were not previously predicted in the garlic at the genomic level. To address this issue, we constructed two garlic Illumina 2000 libraries from tissues of garlic clove and leaf. RESULTS Approximately 43 million 125 bp paired-end reads were obtained in the two libraries. A total of 239,973 contigs were generated by de novo assembly of both samples and were compared with the sequences in the NCBI non-redundant protein database (Nr). In total, 42% of contigs were matched to known proteins in public databases including Nr, Gene Ontology (GO), and Cluster Orthologous Gene Database (COG), and then, contigs were mapped to 138 via functional annotation against the Kyoto Encyclopedia of Genes and Genomes pathway database (KEGG). In addition, a number of regulatory genes including the CCHC (Zn) family, followed by WD40, bromodomain, bZIP, AP2-EREBP, BED-type (Zn) proteins, and defense response proteins related to different conserved domains, such as RGA3, NBS-LRR, TIR-NBS-LRR, LRR, NBS-ARC, and CC-NBS-LRR were discovered based on the transcriptome dataset. We compared the ortholog gene family of the A. sativum transcriptome to A. thaliana, O. sativa, and Z. mays and found that 12,077 orthologous gene families are specific to A. sativum L. Furthermore, we identified genes involved in plant defense mechanisms, their protein-protein interaction network, and plant-pathogen interaction pathways. CONCLUSIONS Our study contains an extensive sequencing and functional gene-annotation analysis of A. sativum L. The findings provide insights into the molecular basis of TFs, defensive genes, and a reference for future studies on the genetics and breeding of A. sativum L.
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Affiliation(s)
- Malyaj R Prajapati
- Division of Microbial and Environmental Biotechnology, College of Biotechnology, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut, Uttar Pradesh, 250110, India
| | - Jitender Singh
- Department of Microbiology, Chaudhary Charan Singh University, Meerut, Uttar Pradesh, 250004, India.
| | - Pankaj Kumar
- Division of Microbial and Environmental Biotechnology, College of Biotechnology, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut, Uttar Pradesh, 250110, India.
| | - Rekha Dixit
- Division of Microbial and Environmental Biotechnology, College of Biotechnology, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut, Uttar Pradesh, 250110, India
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Liu S, Lei J, Zhang J, Liu H, Ye Z, Yang J, Lu Q, Liu P, Chen J, Yang J. Genome-wide identification and analysis of wheat LRR-RLK family genes following Chinese wheat mosaic virus infection. FRONTIERS IN PLANT SCIENCE 2023; 13:1109845. [PMID: 36733595 PMCID: PMC9887201 DOI: 10.3389/fpls.2022.1109845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 12/28/2022] [Indexed: 06/18/2023]
Abstract
BACKGROUND As the largest plant receptor-like protein kinase (RLK) superfamily, the 21 leucine-rich repeat receptor-like kinases (LRR-RLKs) family are involved in plant 22 growth, development, and stress responses. However, the functions of LRR-RLKs in 23 wheat immunity remain unknown. RESULTS In the current study, 929 LRR-RLKs were identified in Triticum aestivum 25 genome database using the BLAST and hidden Markov models (HMM) approach and 26 divided into 14 clades. Chromosomal localization and synteny analysis revealed that 27 TaLRR-RLKs were randomly distributed on all chromosomes with 921 collinear 28 events. Through the cis-acting elements analysis, we observed that TaLRR-RLKs 29 participated in hormone response, light response, development, metabolism, and 30 response to environmental stress. The transcript level of 14 random selected 31 TaLRR-RLKs from each subfamily was regulated by plant hormone treatment and 32 Chinese wheat mosaic virus (CWMV) infection. The function of TaLRR-RLKs in 33 wheat resistance to CWMV infection was further investigated by virus-induced gene 34 silencing assay. Additionally, the accumulation of MeJA response genes, as well as 35 CWMV RNA were not changed in the TaLRR-RLK silencing plants under MeJA 36 treatment. CONCLUSIONS Our results demonstrated that TaLRR-RLKs play an important role in 38 wheat resistance to viral infection via hormone signals and lay the groundwork for the 39 functional study of TaLRR-RLKs in wheat.
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Affiliation(s)
- Shuang Liu
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Jiajia Lei
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Juan Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Hanhong Liu
- Junan County Bureau of Agriculture and Country, Linyi, China
| | - Zhuangxin Ye
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Jin Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Qiseng Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Peng Liu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Jianping Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Jian Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
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Cao Y, Fan T, Zhang B, Li Y. Dissection of leucine-rich repeat receptor-like protein kinases: insight into resistance to Fusarium wilt in tung tree. PeerJ 2022; 10:e14416. [PMID: 36590451 PMCID: PMC9798904 DOI: 10.7717/peerj.14416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 10/28/2022] [Indexed: 11/21/2022] Open
Abstract
The tung tree is a woody oil plant native to China and widely distributed in the subtropics. The three main species commonly known as Vernicia are V. fordii, V. montana, and V. cordata. The growth and development of V. fordii are affected by a large number of plant pathogens, such as Fusarium wilt caused by Fusarium sp. In contrast, V. montana shows significant resistance to Fusarium wilt. The leucine-rich repeat receptor-like protein kinase (LRR-RLK) is the largest class of receptor-like kinases associated with plant resistance to Fusarium wilt. Here, we identified 239 VmLRR-RLKs in V. montana, and found that there were characteristic domains of resistance to Fusarium wilt in them. Phylogenetic analysis suggested that the VmLRR-RLKs are divided into 14 subfamilies, indicating that homologous genes in the same group may have similar functions. Chromosomal localization analysis showed that VmLRR-RLKs were unevenly distributed on chromosomes, and segment duplications were the main reason for the expansion of VmLRR-RLK family members. The transcriptome data showed that six orthologous pairs were up-regulated in V. montana in response to Fusarium wilt, while the corresponding orthologous genes showed low or no expression in V. fordii in resistance Fusarium wilt, further indicating the important role of LRR-RLKs in V. montana's resistance to infection by Fusarium spp. Our study provides important reference genes for the future use of molecular breeding to improve oil yield and control of Fusarium wilt in tung tree.
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Affiliation(s)
- Yunpeng Cao
- School of Health and Nursing, Wuchang University of Technology, Wuhan, China,School of Forestry, Central South University of Forestry and Technology, Changsha, China,Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Tingting Fan
- School of Forestry, Central South University of Forestry and Technology, Changsha, China
| | - Bo Zhang
- School of Forestry, Central South University of Forestry and Technology, Changsha, China
| | - Yanli Li
- School of Forestry, Central South University of Forestry and Technology, Changsha, China
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Cantila AY, Thomas WJW, Bayer PE, Edwards D, Batley J. Predicting Cloned Disease Resistance Gene Homologs (CDRHs) in Radish, Underutilised Oilseeds, and Wild Brassicaceae Species. PLANTS (BASEL, SWITZERLAND) 2022; 11:3010. [PMID: 36432742 PMCID: PMC9693284 DOI: 10.3390/plants11223010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/01/2022] [Accepted: 11/02/2022] [Indexed: 06/16/2023]
Abstract
Brassicaceae crops, including Brassica, Camelina and Raphanus species, are among the most economically important crops globally; however, their production is affected by several diseases. To predict cloned disease resistance (R) gene homologs (CDRHs), we used the protein sequences of 49 cloned R genes against fungal and bacterial diseases in Brassicaceae species. In this study, using 20 Brassicaceae genomes (17 wild and 3 domesticated species), 3172 resistance gene analogs (RGAs) (2062 nucleotide binding-site leucine-rich repeats (NLRs), 497 receptor-like protein kinases (RLKs) and 613 receptor-like proteins (RLPs)) were identified. CDRH clusters were also observed in Arabis alpina, Camelina sativa and Cardamine hirsuta with assigned chromosomes, consisting of 62 homogeneous (38 NLR, 17 RLK and 7 RLP clusters) and 10 heterogeneous RGA clusters. This study highlights the prevalence of CDRHs in the wild relatives of the Brassicaceae family, which may lay the foundation for rapid identification of functional genes and genomics-assisted breeding to develop improved disease-resistant Brassicaceae crop cultivars.
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Liu D, Shen Z, Zhuang K, Qiu Z, Deng H, Ke Q, Liu H, Han H. Systematic Annotation Reveals CEP Function in Tomato Root Development and Abiotic Stress Response. Cells 2022; 11:2935. [PMID: 36230896 PMCID: PMC9562649 DOI: 10.3390/cells11192935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 09/11/2022] [Accepted: 09/16/2022] [Indexed: 11/25/2022] Open
Abstract
Tomato (Solanum lycopersicum) is one of the most important vegetable crops worldwide; however, environmental stressors severely restrict tomato growth and yield. Therefore, it is of great interest to discover novel regulators to improve tomato growth and environmental stress adaptions. Here, we applied a comprehensive bioinformatics approach to identify putative tomato C-TERMINALLY ENCODED PEPTIDE (CEP) genes and to explore their potential physiological function in tomato root development and abiotic stress responses. A total of 17 tomato CEP genes were identified and grouped into two subgroups based on the similarity of CEP motifs. The public RNA-Seq data revealed that tomato CEP genes displayed a diverse expression pattern in tomato tissues. Additionally, CEP genes expression was differentially regulated by nitrate or ammonium status in roots and shoots, respectively. The differences in expression levels of CEP genes induced by nitrogen indicate a potential involvement of CEPs in tomato nitrogen acquisition. The synthetic CEP peptides promoted tomato primary root growth, which requires nitric oxide (NO) and calcium signaling. Furthermore, we also revealed that CEP peptides improved tomato root resistance to salinity. Overall, our work will contribute to provide novel genetic breeding strategies for tomato cultivation under adverse environments.
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Affiliation(s)
| | | | | | | | | | | | | | - Huibin Han
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China
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12
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Mining of Cloned Disease Resistance Gene Homologs (CDRHs) in Brassica Species and Arabidopsis thaliana. BIOLOGY 2022; 11:biology11060821. [PMID: 35741342 PMCID: PMC9220128 DOI: 10.3390/biology11060821] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Revised: 05/15/2022] [Accepted: 05/24/2022] [Indexed: 01/23/2023]
Abstract
Simple Summary Developing cultivars with resistance genes (R genes) is an effective strategy to support high yield and quality in Brassica crops. The availability of clone R gene and genomic sequences in Brassica species and Arabidopsis thaliana provide the opportunity to compare genomic regions and survey R genes across genomic databases. In this paper, we aim to identify genes related to cloned genes through sequence identity, providing a repertoire of species-wide related R genes in Brassica crops. The comprehensive list of candidate R genes can be used as a reference for functional analysis. Abstract Various diseases severely affect Brassica crops, leading to significant global yield losses and a reduction in crop quality. In this study, we used the complete protein sequences of 49 cloned resistance genes (R genes) that confer resistance to fungal and bacterial diseases known to impact species in the Brassicaceae family. Homology searches were carried out across Brassica napus, B. rapa, B. oleracea, B. nigra, B. juncea, B. carinata and Arabidopsis thaliana genomes. In total, 660 cloned disease R gene homologs (CDRHs) were identified across the seven species, including 431 resistance gene analogs (RGAs) (248 nucleotide binding site-leucine rich repeats (NLRs), 150 receptor-like protein kinases (RLKs) and 33 receptor-like proteins (RLPs)) and 229 non-RGAs. Based on the position and distribution of specific homologs in each of the species, we observed a total of 87 CDRH clusters composed of 36 NLR, 16 RLK and 3 RLP homogeneous clusters and 32 heterogeneous clusters. The CDRHs detected consistently across the seven species are candidates that can be investigated for broad-spectrum resistance, potentially providing resistance to multiple pathogens. The R genes identified in this study provide a novel resource for the future functional analysis and gene cloning of Brassicaceae R genes towards crop improvement.
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Su Y, Peng X, Shen S. Identification of leucine-rich repeat receptor-like protein kinase (LRR-RLK) genes in paper mulberry and their potential roles in response to cold stress. Comput Biol Chem 2022; 97:107622. [DOI: 10.1016/j.compbiolchem.2022.107622] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 01/02/2022] [Accepted: 01/04/2022] [Indexed: 11/03/2022]
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Ma Q, Hu Z, Mao Z, Mei Y, Feng S, Shi K. A novel leucine-rich repeat receptor-like kinase MRK1 regulates resistance to multiple stresses in tomato. HORTICULTURE RESEARCH 2022; 9:uhab088. [PMID: 35048129 PMCID: PMC9123237 DOI: 10.1093/hr/uhab088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 12/13/2021] [Indexed: 06/14/2023]
Abstract
Leucine-rich repeat receptor-like kinases (LRR-RLKs) are ubiquitous in higher plants, which act as receptors of extracellular signals to trigger multiple physiological processes. However, the functions of the majority of LRR-RLKs remain largely unknown, especially in tomato (Solanum lycopersicum L.). Here, we found that MRK1 (Multiple resistance-associated kinase 1), encoding a novel tomato LRR-RLK, was significantly induced either by temperature stresses or bacterial pathogen attacks. Knocking out MRK1 impaired the tolerance to both cold and heat stress, accompanied with the decrease in transcripts of master regulators C-repeat binding factor 1 (CBF1) and Heat shock transcription factor a-1a (HsfA1a), respectively. Additionally, mrk1 mutants were hypersensitive to Pseudomonas syringae pv. tomato DC3000 and Ralstonia solanacearum and compromised pattern-triggered immunity (PTI) responses as evidenced by decreased reactive oxygen species production and reduced upregulation of the PTI marker genes. Moreover, bimolecular fluorescence complementation, split-luciferase assay and coimmunoprecipitation supported the existence of complex formation between the MRK1, FLS2 and Somatic embryogenesis receptor kinase (SERK3A/SERK3B) in a ligand-independent manner. This work demonstrates that tomato MRK1 as a novel positive regulator of multiple stresses, which might be a potential breeding target to improve crop stress resistance.
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Affiliation(s)
- Qiaomei Ma
- Department of Horticulture, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China
| | - Zhangjian Hu
- Department of Horticulture, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China
| | - Zhuo Mao
- Department of Horticulture, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China
| | - Yuyang Mei
- Department of Horticulture, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China
| | - Shuxian Feng
- Department of Horticulture, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China
| | - Kai Shi
- Department of Horticulture, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China
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15
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Liu Z, Ren Z, Yan L, Li F. DeepLRR: An Online Webserver for Leucine-Rich-Repeat Containing Protein Characterization Based on Deep Learning. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11010136. [PMID: 35009139 PMCID: PMC8796025 DOI: 10.3390/plants11010136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/31/2021] [Accepted: 01/01/2022] [Indexed: 05/26/2023]
Abstract
Members of the leucine-rich repeat (LRR) superfamily play critical roles in multiple biological processes. As the LRR unit sequence is highly variable, accurately predicting the number and location of LRR units in proteins is a highly challenging task in the field of bioinformatics. Existing methods still need to be improved, especially when it comes to similarity-based methods. We introduce our DeepLRR method based on a convolutional neural network (CNN) model and LRR features to predict the number and location of LRR units in proteins. We compared DeepLRR with six existing methods using a dataset containing 572 LRR proteins and it outperformed all of them when it comes to overall F1 score. In addition, DeepLRR has integrated identifying plant disease-resistance proteins (NLR, LRR-RLK, LRR-RLP) and non-canonical domains. With DeepLRR, 223, 191 and 183 LRR-RLK genes in Arabidopsis (Arabidopsis thaliana), rice (Oryza sativa ssp. Japonica) and tomato (Solanum lycopersicum) genomes were re-annotated, respectively. Chromosome mapping and gene cluster analysis revealed that 24.2% (54/223), 29.8% (57/191) and 16.9% (31/183) of LRR-RLK genes formed gene cluster structures in Arabidopsis, rice and tomato, respectively. Finally, we explored the evolutionary relationship and domain composition of LRR-RLK genes in each plant and distributions of known receptor and co-receptor pairs. This provides a new perspective for the identification of potential receptors and co-receptors.
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Affiliation(s)
- Zhenya Liu
- Key Lab of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Zirui Ren
- College of Informatics, Huazhong Agricultural University, Wuhan 430070, China; (Z.R.); (L.Y.)
| | - Lunyi Yan
- College of Informatics, Huazhong Agricultural University, Wuhan 430070, China; (Z.R.); (L.Y.)
| | - Feng Li
- Key Lab of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
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16
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Song M, Linghu B, Huang S, Li F, An R, Xie C, Zhu Y, Hu S, Mu J, Zhang Y. Genome-Wide Survey of Leucine-Rich Repeat Receptor-Like Protein Kinase Genes and CRISPR/Cas9-Targeted Mutagenesis BnBRI1 in Brassica napus. FRONTIERS IN PLANT SCIENCE 2022; 13:865132. [PMID: 35498707 PMCID: PMC9039726 DOI: 10.3389/fpls.2022.865132] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 03/14/2022] [Indexed: 05/19/2023]
Abstract
The leucine-rich repeat receptor-like protein kinase (LRR-RLK) family represents the largest group of RLKs in plants and plays vital roles in plant growth, development and the responses to environmental stress. Although LRR-RLK families have been identified in many species, they have not yet been reported in B. napus. In this study, a total of 444 BnLRR-RLK genes were identified in the genome of Brassica napus cultivar "Zhongshuang 11" (ZS11), and classified into 22 subfamilies based on phylogenetic relationships and genome-wide analyses. Conserved motifs and gene structures were shared within but not between subfamilies. The 444 BnLRR-RLK genes were asymmetrically distributed on 19 chromosomes and exhibited specific expression profiles in different tissues and in response to stress. We identified six BnBRI1 homologs and obtained partial knockouts via CRISPR/Cas9 technology, generating semi-dwarf lines without decreased yield compared with controls. This study provides comprehensive insight of the LRR-RLK family in B. napus. Additionally, the semi-dwarf lines expand the "ideotype" germplasm resources and accelerate the breeding process for B. napus.
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Affiliation(s)
- Min Song
- Hybrid Rapeseed Research Center of Shaanxi Province, Yangling, China
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, China
| | - Bin Linghu
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, China
| | - Shuhua Huang
- Hybrid Rapeseed Research Center of Shaanxi Province, Yangling, China
| | - Fang Li
- Hybrid Rapeseed Research Center of Shaanxi Province, Yangling, China
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, China
| | - Ran An
- Hybrid Rapeseed Research Center of Shaanxi Province, Yangling, China
| | - Changgen Xie
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, China
| | - Yantao Zhu
- Hybrid Rapeseed Research Center of Shaanxi Province, Yangling, China
| | - Shengwu Hu
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, China
| | - Jianxin Mu
- Hybrid Rapeseed Research Center of Shaanxi Province, Yangling, China
- *Correspondence: Jianxin Mu,
| | - Yanfeng Zhang
- Hybrid Rapeseed Research Center of Shaanxi Province, Yangling, China
- Yanfeng Zhang,
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Genome-Wide Identification of LRR-RLK Family in Saccharum and Expression Analysis in Response to Biotic and Abiotic Stress. Curr Issues Mol Biol 2021; 43:1632-1651. [PMID: 34698114 PMCID: PMC8929030 DOI: 10.3390/cimb43030116] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 10/05/2021] [Accepted: 10/07/2021] [Indexed: 12/17/2022] Open
Abstract
The leucine-rich repeat receptor-like protein kinase (LRR-RLK) gene family is the largest family of the receptor-like protein kinases (RLKs) superfamily in higher plants, which is involved in regulating the plant growth and development, stress responses, signal transduction and so on. However, no comprehensive analyses of LRR-RLKs have been reported in sugarcane. Here, we performed a comprehensive analysis of the LRR-RLK gene family in sugarcane ancestor species Saccharum spontaneum. A total of 437 LRR-RLK genes were identified and categorized into 14 groups based on a maximum likelihood phylogenetic tree. The chromosome location showed an uneven distribution on all 32 chromosomes in sugarcane. Subsequently, the exon-intron organization structure and conserved motif arrangement were relatively conserved among the same groups or subgroups and between Arabidopsis and S. spontaneum genomes. Furthermore, the promoter sequences analyses showed that sugarcane LRR-RLK genes (SsLRR-RLKs) were strongly regulated by various environmental stimuli, phytohormonal factors and transcription factors (TFs). Eventually, the expression profiles of SsLRR-RLK genes at different stresses were analyzed based on RNA-seq data, suggesting their potential roles in the regulation of sugarcane responses to diverse abiotic and biotic stress. Overall, the findings provide insight into the potential functional roles and lay the foundation for further functional study.
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18
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Mou S, Meng Q, Gao F, Zhang T, He W, Guan D, He S. A cysteine-rich receptor-like protein kinase CaCKR5 modulates immune response against Ralstonia solanacearum infection in pepper. BMC PLANT BIOLOGY 2021; 21:382. [PMID: 34412592 PMCID: PMC8375189 DOI: 10.1186/s12870-021-03150-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 07/28/2021] [Indexed: 05/12/2023]
Abstract
BACKGROUND Cysteine-rich receptor-like kinases (CRKs) represent a large subfamily of receptor-like kinases and play vital roles in diverse physiological processes in regulating plant growth and development. RESULTS CaCRK5 transcripts were induced in pepper upon the infection of Ralstonia solanacearum and treatment with salicylic acid. The fusions between CaCRK5 and green fluorescence protein were targeted to the plasma membrane. Suppression of CaCRK5 via virus-induced gene silencing (VIGS) made pepper plants significantly susceptible to R. solanacearum infection, which was accompanied with decreased expression of defense related genes CaPR1, CaSAR8.2, CaDEF1 and CaACO1. Overexpression of CaCRK5 increased resistance against R. solanacearum in Nicotiana benthamiana. Furthermore, electrophoretic mobility shift assay and chromatin immunoprecipitation coupled with quantitative real-time PCR analysis revealed that a homeodomain zipper I protein CaHDZ27 can active the expression of CaCRK5 through directly binding to its promoter. Yeast two-hybrid and bimolecular fluorescence complementation (BiFC) analyses suggested that CaCRK5 heterodimerized with the homologous member CaCRK6 on the plasma membrane. CONCLUSIONS Our data revealed that CaCRK5 played a positive role in regulating immune responses against R. solanacearum infection in pepper.
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Affiliation(s)
- Shaoliang Mou
- College of Life Science, Fujian Agriculture and Forestry University, Fujian, 350002, Fuzhou, People's Republic of China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fujian, 350002, Fuzhou, People's Republic of China
- Key Laboratory of Plant Genetic Improvement, National Education Minister, Comprehensive Utilization Fujian Agriculture and Forestry University, Fujian, 350002, Fuzhou, People's Republic of China
| | - Qianqian Meng
- College of Life Science, Fujian Agriculture and Forestry University, Fujian, 350002, Fuzhou, People's Republic of China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fujian, 350002, Fuzhou, People's Republic of China
- Key Laboratory of Plant Genetic Improvement, National Education Minister, Comprehensive Utilization Fujian Agriculture and Forestry University, Fujian, 350002, Fuzhou, People's Republic of China
| | - Feng Gao
- College of Life Science, Fujian Agriculture and Forestry University, Fujian, 350002, Fuzhou, People's Republic of China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fujian, 350002, Fuzhou, People's Republic of China
- Key Laboratory of Plant Genetic Improvement, National Education Minister, Comprehensive Utilization Fujian Agriculture and Forestry University, Fujian, 350002, Fuzhou, People's Republic of China
| | - Tingting Zhang
- College of Life Science, Fujian Agriculture and Forestry University, Fujian, 350002, Fuzhou, People's Republic of China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fujian, 350002, Fuzhou, People's Republic of China
- Key Laboratory of Plant Genetic Improvement, National Education Minister, Comprehensive Utilization Fujian Agriculture and Forestry University, Fujian, 350002, Fuzhou, People's Republic of China
| | - Weihong He
- College of Life Science, Fujian Agriculture and Forestry University, Fujian, 350002, Fuzhou, People's Republic of China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fujian, 350002, Fuzhou, People's Republic of China
- Key Laboratory of Plant Genetic Improvement, National Education Minister, Comprehensive Utilization Fujian Agriculture and Forestry University, Fujian, 350002, Fuzhou, People's Republic of China
| | - Deyi Guan
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fujian, 350002, Fuzhou, People's Republic of China
- Key Laboratory of Plant Genetic Improvement, National Education Minister, Comprehensive Utilization Fujian Agriculture and Forestry University, Fujian, 350002, Fuzhou, People's Republic of China
- College of Agriculture Science, Fujian Agriculture and Forestry University, Fujian, 350002, Fuzhou, People's Republic of China
| | - Shuilin He
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fujian, 350002, Fuzhou, People's Republic of China.
- Key Laboratory of Plant Genetic Improvement, National Education Minister, Comprehensive Utilization Fujian Agriculture and Forestry University, Fujian, 350002, Fuzhou, People's Republic of China.
- College of Agriculture Science, Fujian Agriculture and Forestry University, Fujian, 350002, Fuzhou, People's Republic of China.
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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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20
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Haider MS, De Britto S, Nagaraj G, Gurulingaiah B, Shekhar R, Ito SI, Jogaiah S. Genome-Wide Identification, Diversification, and Expression Analysis of Lectin Receptor-Like Kinase (LecRLK) Gene Family in Cucumber under Biotic Stress. Int J Mol Sci 2021; 22:6585. [PMID: 34205396 PMCID: PMC8234520 DOI: 10.3390/ijms22126585] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 06/16/2021] [Accepted: 06/16/2021] [Indexed: 12/27/2022] Open
Abstract
Members of the lectin receptor-like kinase (LecRLKs) family play a vital role in innate plant immunity. Few members of the LecRLKs family have been characterized in rice and Arabidopsis, respectively. However, little literature is available about LecRLKs and their role against fungal infection in cucumber. In this study, 60 putative cucumber LecRLK (CsLecRLK) proteins were identified using genome-wide analysis and further characterized into L-type LecRLKs (24) and G-type LecRLKs (36) based on domain composition and phylogenetic analysis. These proteins were allocated to seven cucumber chromosomes and found to be involved in the expansion of the CsLecRLK gene family. Subcellular localization of CsaLecRLK9 and CsaLecRLK12 showed green fluorescence signals in the plasma membrane of leaves. The transcriptional profiling of CsLecRLK genes showed that L-type LecRLKs exhibited functional redundancy as compared to G-type LecRLKs. The qRT-PCR results indicated that both L- and G-type LecRLKs showed significant response against plant growth-promoting fungi (PGPF-Trichoderma harzianum Rifai), powdery mildew pathogen (PPM-Golovinomyces orontii (Castagne) V.P. Heluta), and combined (PGPF+PPM) treatments. The findings of this study contribute to a better understanding of the role of cucumber CsLecRLK genes in response to PGPF, PPM, and PGPF+PPM treatments and lay the basis for the characterization of this important functional gene family.
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Affiliation(s)
- Muhammad Salman Haider
- Key Laboratory of Genetics and Fruit Development, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China;
| | - Savitha De Britto
- Laboratory of Plant Healthcare and Diagnostics, P.G. Department of Biotechnology and Microbiology, Karnatak University, Dharwad 580003, India;
- Division of Biological Sciences, School of Science and Technology, University of Goroka, Goroka 441, Papua New Guinea
| | - Geetha Nagaraj
- Nanobiotechnology Laboratory, Department of Studies in Biotechnology, University of Mysore, Manasagangotri, Mysuru 570006, India; (G.N.); (B.G.); (R.S.)
| | - Bhavya Gurulingaiah
- Nanobiotechnology Laboratory, Department of Studies in Biotechnology, University of Mysore, Manasagangotri, Mysuru 570006, India; (G.N.); (B.G.); (R.S.)
| | - Ravikant Shekhar
- Nanobiotechnology Laboratory, Department of Studies in Biotechnology, University of Mysore, Manasagangotri, Mysuru 570006, India; (G.N.); (B.G.); (R.S.)
| | - Shin-ichi Ito
- Laboratory of Molecular Plant Pathology, Department of Biological and Environmental Sciences, Graduate School of Sciences and Technology for Innovation, Yamaguchi University, Yamaguchi 753-8515, Japan
- Research Center for Thermotolerant Microbial Resources (RCTMR), Yamaguchi University, Yamaguchi 753-8515, Japan
| | - Sudisha Jogaiah
- Laboratory of Plant Healthcare and Diagnostics, P.G. Department of Biotechnology and Microbiology, Karnatak University, Dharwad 580003, India;
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Yang H, Bayer PE, Tirnaz S, Edwards D, Batley J. Genome-Wide Identification and Evolution of Receptor-Like Kinases (RLKs) and Receptor like Proteins (RLPs) in Brassica juncea. BIOLOGY 2020; 10:biology10010017. [PMID: 33396674 PMCID: PMC7823396 DOI: 10.3390/biology10010017] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 12/21/2020] [Accepted: 12/21/2020] [Indexed: 12/19/2022]
Abstract
Brassica juncea, an allotetraploid species, is an important germplasm resource for canola improvement, due to its many beneficial agronomic traits, such as heat and drought tolerance and blackleg resistance. Receptor-like kinase (RLK) and receptor-like protein (RLP) genes are two types of resistance gene analogues (RGA) that play important roles in plant innate immunity, stress response and various development processes. In this study, genome wide analysis of RLKs and RLPs is performed in B. juncea. In total, 493 RLKs (LysM-RLKs and LRR-RLKs) and 228 RLPs (LysM-RLPs and LRR-RLPs) are identified in the genome of B. juncea, using RGAugury. Only 13.54% RLKs and 11.79% RLPs are observed to be grouped within gene clusters. The majority of RLKs (90.17%) and RLPs (52.83%) are identified as duplicates, indicating that gene duplications significantly contribute to the expansion of RLK and RLP families. Comparative analysis between B. juncea and its progenitor species, B. rapa and B. nigra, indicate that 83.62% RLKs and 41.98% RLPs are conserved in B. juncea, and RLPs are likely to have a faster evolution than RLKs. This study provides a valuable resource for the identification and characterisation of candidate RLK and RLP genes.
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Affiliation(s)
- Hua Yang
- School of Biological Sciences, University of Western Australia, Crawley, WA 6009, Australia; (H.Y.); (P.E.B.); (S.T.); (D.E.)
- School of Agriculture and Food Sciences, University of Queensland, St Lucia, QLD 4067, Australia
| | - Philipp E. Bayer
- School of Biological Sciences, University of Western Australia, Crawley, WA 6009, Australia; (H.Y.); (P.E.B.); (S.T.); (D.E.)
| | - Soodeh Tirnaz
- School of Biological Sciences, University of Western Australia, Crawley, WA 6009, Australia; (H.Y.); (P.E.B.); (S.T.); (D.E.)
| | - David Edwards
- School of Biological Sciences, University of Western Australia, Crawley, WA 6009, Australia; (H.Y.); (P.E.B.); (S.T.); (D.E.)
| | - Jacqueline Batley
- School of Biological Sciences, University of Western Australia, Crawley, WA 6009, Australia; (H.Y.); (P.E.B.); (S.T.); (D.E.)
- Correspondence: ; Tel.: +61-8-6488-5929
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Meng X, Cai J, Deng L, Li G, Sun J, Han Y, Dong T, Liu Y, Xu T, Liu S, Li Z, Zhu M. SlSTE1 promotes abscisic acid-dependent salt stress-responsive pathways via improving ion homeostasis and reactive oxygen species scavenging in tomato. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2020; 62:1942-1966. [PMID: 32618097 DOI: 10.1111/jipb.12987] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 06/29/2020] [Indexed: 06/11/2023]
Abstract
High salinity is one of the major limiting factors that reduces crop productivity and quality. Herein, we report that small SALT TOLERANCE ENHANCER1 (STE1) protein without any known conserved domains is required for tomato salt tolerance. Overexpression (OE) of SlSTE1 enhanced the tolerance to multiple chloride salts (NaCl, KCl, and LiCl) and oxidative stress, along with elevated antioxidant enzyme activities, increased abscisic acid (ABA) and chlorophyll contents, and reduced malondialdehyde (MDA) and reactive oxygen species (ROS) accumulations compared to that of wild-type (WT) plants. Moreover, decreased K+ efflux and increased H+ efflux were detected in the OE plants, which induced a higher K+ /Na+ ratio. In contrast, SlSTE1-RNAi plants displayed decreased tolerance to salt stress. RNA-seq data revealed 1 330 differentially expressed genes in the OE plants versus WT plants under salt stress, and the transcription of numerous and diverse genes encoding transcription factors, stress-related proteins, secondary metabolisms, kinases, and hormone synthesis/signaling-related proteins (notably ABA and 1-aminocyclopropane-1-carboxylate) was greatly elevated. Furthermore, SlSTE1-OE plants showed increased sensitivity to ABA, and the results suggest that SlSTE1 promotes ABA-dependent salt stress-responsive pathways by interacting with SlPYLs and SlSnRK2s. Collectively, our findings reveal that the small SlSTE1 protein confers salt tolerance via ABA signaling and ROS scavenging and improves ion homeostasis in tomato.
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Affiliation(s)
- Xiaoqing Meng
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China
- Jiangsu Key laboratory of Phylogenomics & Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China
| | - Jing Cai
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China
- Jiangsu Key laboratory of Phylogenomics & Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China
| | - Lei Deng
- State Key Laboratory of Plant Genomics, National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, the Chinese Academy of Sciences, Beijing, 100101, China
| | - Ge Li
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China
- Jiangsu Key laboratory of Phylogenomics & Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China
| | - Jian Sun
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China
- Jiangsu Key laboratory of Phylogenomics & Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China
| | - Yonghua Han
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China
- Jiangsu Key laboratory of Phylogenomics & Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China
| | - Tingting Dong
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China
- Jiangsu Key laboratory of Phylogenomics & Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China
| | - Yang Liu
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China
- Jiangsu Key laboratory of Phylogenomics & Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China
| | - Tao Xu
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China
- Jiangsu Key laboratory of Phylogenomics & Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China
| | - Siyuan Liu
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China
- Jiangsu Key laboratory of Phylogenomics & Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China
| | - Zongyun Li
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China
- Jiangsu Key laboratory of Phylogenomics & Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China
| | - Mingku Zhu
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China
- Jiangsu Key laboratory of Phylogenomics & Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China
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Genome-Wide Characterization, Evolution, and Expression Analysis of the Leucine-Rich Repeat Receptor-Like Protein Kinase (LRR-RLK) Gene Family in Medicago truncatula. Life (Basel) 2020; 10:life10090176. [PMID: 32899802 PMCID: PMC7555646 DOI: 10.3390/life10090176] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 08/28/2020] [Accepted: 09/02/2020] [Indexed: 11/23/2022] Open
Abstract
Leucine-rich repeat receptor-like kinases (LRR-RLKs) constitute the largest subfamily of receptor-like kinases (RLKs) in plants. They play roles in plant growth and developmental and physiological processes, but less is known about the functions of LRR-RLKs in Medicago truncatula. Our genome-wide analysis revealed 329 LRR-RLK genes in the M.truncatula genome. Phylogenetic and classification analysis suggested that these genes could be classified into 15 groups and 24 subgroups. A total of 321 genes were mapped onto all chromosomes, and 23 tandem duplications (TDs) involving 56 genes were distributed on each chromosome except 4. Twenty-seven M.truncatula LRR-RLK segmental duplication gene pairs were colinearly related. The exon/intron organization, motif composition and arrangements were relatively conserved among members of the same groups or subgroups. Using publicly available RNAseq data and quantitative real-time polymerase chain reaction (qRT-PCR), expression profiling suggested that LRR-RLKs were differentially expressed among different tissues, while some were expressed specifically in the roots and nodules. The expression of LRR-RLKs in A17 and 4 nodule mutants under rhizobial infection showed that 36 LRR-RKLs were highly upregulated in the sickle (skl) mutant [an ethylene (ET)-insensitive, Nod factor-hypersensitive mutant] after 12 h of rhizobium inoculation. Among these LRR-RLKs, six genes were also expressed specifically in the roots and nodules, which might be specific to the Nod factor and involved in autoregulation of the nodulation signal. Our results provide information on the LRR-RLK gene family in M. truncatula and serve as a guide for functional research of the LRR-RLKs.
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Hosseini S, Schmidt EDL, Bakker FT. Leucine-rich repeat receptor-like kinase II phylogenetics reveals five main clades throughout the plant kingdom. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:547-560. [PMID: 32175641 PMCID: PMC7496461 DOI: 10.1111/tpj.14749] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 01/17/2020] [Accepted: 02/27/2020] [Indexed: 05/22/2023]
Abstract
Receptor-like kinases (RLKs) represent the largest group of cell surface receptors in plants. The monophyletic leucine-rich repeat (LRR)-RLK subfamily II is considered to contain the somatic embryogenesis receptor kinases (SERKs) and NSP-interacting kinases known to be involved in developmental processes and cellular immunity in plants. There are only a few published studies on the phylogenetics of LRR-RLKII; unfortunately these suffer from poor taxon/gene sampling. Hence, it is not clear how many and what main clades this family contains, let alone what structure-function relationships exist. We used 1342 protein sequences annotated as 'SERK' and 'SERK-like' plus related sequences in order to estimate phylogeny within the LRR-RLKII clade, using the nematode protein kinase Pelle as an outgroup. We reconstruct five main clades (LRR-RLKII 1-5), in each of which the main pattern of land plant relationships re-occurs, confirming previous hypotheses that duplication events happened in this gene subfamily prior to divergence among land plant lineages. We show that domain structures and intron-exon boundaries within the five clades are well conserved in evolution. Furthermore, phylogenetic patterns based on the separate LRR and kinase parts of LRR-RLKs are incongruent: whereas the LRR part supports a LRR-RLKII 2/3 sister group relationship, the kinase part supports clades 1/2. We infer that the kinase part includes few 'radical' amino acid changes compared with the LRR part. Finally, our results confirm that amino acids involved in each LRR-RLKII-receptor complex interaction are located at N-capping residues, and that the short amino acid motifs of this interaction domain are highly conserved throughout evolution within the five LRR-RLKII clades.
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Affiliation(s)
- Samin Hosseini
- Biosystematics GroupWageningen UniversityRadix Building 107, Droevendaalsesteeg 16708 PB WageningenThe Netherlands
| | - Ed D. L. Schmidt
- Biosystematics GroupWageningen UniversityRadix Building 107, Droevendaalsesteeg 16708 PB WageningenThe Netherlands
| | - Freek T. Bakker
- Biosystematics GroupWageningen UniversityRadix Building 107, Droevendaalsesteeg 16708 PB WageningenThe Netherlands
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Wang Y, Xu Y, Gupta S, Zhou Y, Wallwork H, Zhou G, Broughton S, Zhang XQ, Tan C, Westcott S, Moody D, Sun D, Loughman R, Zhang W, Li C. Fine mapping QSc.VR4, an effective and stable scald resistance locus in barley (Hordeum vulgare L.), to a 0.38-Mb region enriched with LRR-RLK and GLP genes. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:2307-2321. [PMID: 32405768 DOI: 10.1007/s00122-020-03599-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 05/01/2020] [Indexed: 06/11/2023]
Abstract
An effective and stable quantitative resistance locus, QSc.VR4, was fine mapped, characterized and physically anchored to the short arm of 4H, conferring adult plant resistance to the fungus Rhynchosporium commune in barley. Scald caused by Rhynchosporium commune is one of the most destructive barley diseases worldwide. Accumulation of adult plant resistance (APR) governed by multiple resistance alleles is predicted to be effective and long-lasting against a broad spectrum of pathotypes. However, the molecular mechanisms that control APR remain poorly understood. Here, quantitative trait loci (QTL) analysis of APR and fine mapping were performed on five barley populations derived from a common parent Vlamingh, which expresses APR to scald. Two QTLs, designated QSc.VR4 and QSc.BR7, were detected from a cross between Vlamingh and Buloke. Our data confirmed that QSc.VR4 is an effective and stable APR locus, residing on the short arm of chromosome 4H, and QSc.BR7 derived from Buloke may be an allele of reported Rrs2. High-resolution fine mapping revealed that QSc.VR4 is located in a 0.38 Mb genomic region between InDel markers 4H2282169 and 4H2665106. The gene annotation analysis and sequence comparison suggested that a gene cluster containing two adjacent multigene families encoding leucine-rich repeat receptor kinase-like proteins (LRR-RLKs) and germin-like proteins (GLPs), respectively, is likely contributing to scald resistance. Adult plant resistance (APR) governed by QSc.VR4 may confer partial levels of resistance to the fungus Rhynchosporium commune and, furthermore, be an important resource for gene pyramiding that may contribute broad-based and more durable resistance.
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Affiliation(s)
- Yonggang Wang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Western Barley Genetics Alliance, Western Australian State Agricultural Biotechnology Centre, School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA, Australia
| | - Yanhao Xu
- Western Barley Genetics Alliance, Western Australian State Agricultural Biotechnology Centre, School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA, Australia
- Hubei Collaborative Innovation Centre for Grain Industry, Yangtze University, Jingzhou, Hubei, China
| | - Sanjiv Gupta
- Western Barley Genetics Alliance, Western Australian State Agricultural Biotechnology Centre, School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA, Australia
| | - Yi Zhou
- Western Barley Genetics Alliance, Western Australian State Agricultural Biotechnology Centre, School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA, Australia
- Hubei Collaborative Innovation Centre for Grain Industry, Yangtze University, Jingzhou, Hubei, China
| | - Hugh Wallwork
- South Australian Research and Development Institute, Hartley Grove, Urrbrae, SA, Australia
| | - Gaofeng Zhou
- Western Barley Genetics Alliance, Western Australian State Agricultural Biotechnology Centre, School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA, Australia
- Agriculture and Food, Department of Primary Industries and Regional Development, South Perth, WA, Australia
| | - Sue Broughton
- Agriculture and Food, Department of Primary Industries and Regional Development, South Perth, WA, Australia
| | - Xiao-Qi Zhang
- Western Barley Genetics Alliance, Western Australian State Agricultural Biotechnology Centre, School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA, Australia
| | - Cong Tan
- Western Barley Genetics Alliance, Western Australian State Agricultural Biotechnology Centre, School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA, Australia
| | - Sharon Westcott
- Western Barley Genetics Alliance, Western Australian State Agricultural Biotechnology Centre, School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA, Australia
- Agriculture and Food, Department of Primary Industries and Regional Development, South Perth, WA, Australia
| | - David Moody
- InterGrain Pty Ltd, South Perth, WA, Australia
| | - Dongfa Sun
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Hubei Collaborative Innovation Centre for Grain Industry, Yangtze University, Jingzhou, Hubei, China
| | - Robert Loughman
- Agriculture and Food, Department of Primary Industries and Regional Development, South Perth, WA, Australia
| | - Wenying Zhang
- Hubei Collaborative Innovation Centre for Grain Industry, Yangtze University, Jingzhou, Hubei, China.
| | - Chengdao Li
- Western Barley Genetics Alliance, Western Australian State Agricultural Biotechnology Centre, School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA, Australia.
- Hubei Collaborative Innovation Centre for Grain Industry, Yangtze University, Jingzhou, Hubei, China.
- Agriculture and Food, Department of Primary Industries and Regional Development, South Perth, WA, Australia.
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Sun M, Voorrips RE, van’t Westende W, van Kaauwen M, Visser RGF, Vosman B. Aphid resistance in Capsicum maps to a locus containing LRR-RLK gene analogues. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:227-237. [PMID: 31595336 PMCID: PMC6952328 DOI: 10.1007/s00122-019-03453-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 09/28/2019] [Indexed: 05/15/2023]
Abstract
A QTL for aphid resistance on pepper chromosome 2 was identified and validated. This QTL affects aphid survival and reproduction, and was fine mapped to a locus containing LRR-RLK analogues. Myzus persicae is one of the most threatening insect pests that adversely affects pepper (Capsicum) cultivation. Resistance to aphids was previously identified in Capsicum baccatum. This study aimed at elucidating the genetics of aphid resistance in C. baccatum. A QTL analysis was carried out for M. persicae resistance in an F2 population derived from an intraspecific cross between a highly resistant plant and a susceptible plant. Survival and reproduction were used as resistance parameters. Interval mapping detected two QTLs affecting aphid survival (Rmpas-1) and reproduction (Rmprp-1), respectively, both localized in the same area and sharing the same top marker on chromosome 2. Use of this marker as co-factor in multiple-QTL mapping analysis revealed a second, minor QTL (Rmprp-2) only affecting aphid reproduction, on chromosome 4. Fine mapping confirmed the effects of Rmpas-1 and Rmprp-1 and narrowed the major QTL Rmprp-1 down to a genomic region of 96 kb which is predicted to encode four analogues of resistance genes of the receptor-like kinase family containing a leucine-rich repeat domain (LRR-RLKs). This work provides not only initial information for breeding aphid-resistant pepper varieties, but also forms the basis for future molecular analysis of gene(s) involved in aphid resistance.
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Affiliation(s)
- Mengjing Sun
- Plant Breeding, Wageningen University and Research, P.O. Box 386, 6700 AJ Wageningen, The Netherlands
| | - Roeland E. Voorrips
- Plant Breeding, Wageningen University and Research, P.O. Box 386, 6700 AJ Wageningen, The Netherlands
| | - Wendy van’t Westende
- Plant Breeding, Wageningen University and Research, P.O. Box 386, 6700 AJ Wageningen, The Netherlands
| | - Martijn van Kaauwen
- Plant Breeding, Wageningen University and Research, P.O. Box 386, 6700 AJ Wageningen, The Netherlands
| | - Richard G. F. Visser
- Plant Breeding, Wageningen University and Research, P.O. Box 386, 6700 AJ Wageningen, The Netherlands
| | - Ben Vosman
- Plant Breeding, Wageningen University and Research, P.O. Box 386, 6700 AJ Wageningen, The Netherlands
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Ahmad S, Guo Y. Signal Transduction in Leaf Senescence: Progress and Perspective. PLANTS 2019; 8:plants8100405. [PMID: 31658600 PMCID: PMC6843215 DOI: 10.3390/plants8100405] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 10/08/2019] [Accepted: 10/08/2019] [Indexed: 02/07/2023]
Abstract
Leaf senescence is a degenerative process that is genetically controlled and involves nutrient remobilization prior to the death of leaf tissues. Age is a key developmental determinant of the process along with other senescence inducing factors. At the cellular level, different hormones, signaling molecules, and transcription factors contribute to the regulation of senescence. This review summarizes the recent progress in understanding the complexity of the senescence process with primary focuses on perception and transduction of senescence signals as well as downstream regulatory events. Future directions in this field and potential applications of related techniques in crop improvement will be discussed.
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Affiliation(s)
- Salman Ahmad
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
- Plant Breeding & Genetics Division, Nuclear Institute for Food & Agriculture, Tarnab, Peshawar P.O. Box 446, Pakistan.
| | - Yongfeng Guo
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
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Xiao L, Li T, Jiang G, Jiang Y, Duan X. Cell wall proteome analysis of banana fruit softening using iTRAQ technology. J Proteomics 2019; 209:103506. [DOI: 10.1016/j.jprot.2019.103506] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 06/22/2019] [Accepted: 08/19/2019] [Indexed: 10/26/2022]
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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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He X, Feng T, Zhang D, Zhuo R, Liu M. Identification and comprehensive analysis of the characteristics and roles of leucine-rich repeat receptor-like protein kinase (LRR-RLK) genes in Sedum alfredii Hance responding to cadmium stress. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 167:95-106. [PMID: 30312890 DOI: 10.1016/j.ecoenv.2018.09.122] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 09/13/2018] [Accepted: 09/28/2018] [Indexed: 05/27/2023]
Abstract
Sedum alfredii Hance is a Zn/Cd co-hyperaccumulator and its underlying molecular mechanism of Cd tolerance is worthy to be elucidated. Although numerous studies have reported the uptake, sequestration and detoxification of Cd in S. alfredii Hance, how it senses Cd-stress stimuli and transfers signals within tissues remains unclear. Leucine-rich repeat receptor-like protein kinases (LRR-RLKs) are vital for plant growth, development, immunity and signal transduction. Till now, there is lack of comprehensive studies addressing their functions in S. alfredii Hance responding to Cd stress. In the present study, we identified 60 LRR-RLK genes in S. alfredii Hance based on transcriptome analysis under Cd stress. They were categorized into 11 subfamilies and most of them had highly conserved protein structures and motif compositions. The inter-family diversity provided evidence for their functional divergence, supported by their expression level and profile in tissues under Cd stress. Co-expression network analysis revealed that the most highly connected hubs, Sa0F.522, Sa0F.1036, Sa28F.115 and Sa1F.472, were closely related with other genes involved in metal transport, stimulus response and transcription regulations. Of the ten hub genes exhibiting differential expression dynamics under the short-term Cd stress (Sa0F.522, Sa0F.1036 and Sa28F.115) were dramatically induced in the whole plant. Among them, Sa0F.522 gene was heterologously expressed in a Cd-sensitive yeast cell line and its function in Cd signal perception was confirmed. For the first time, our findings performed a comprehensive analysis of LRR-RLKs in S. alfredii Hance, mapped their expression patterns under Cd stress, and identified the key roles of Sa0F.522, Sa0F.1036 and Sa28F.115 in Cd signal transduction.
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Affiliation(s)
- Xuelian He
- State Key Laboratory of Forest Genetics and Breeding, Xiangshan Road, Beijing 100091, P.R. China; Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical of Forestry, Chinese Academy of Forestry, Hangzhou 311400, P.R. China.
| | - Tongyu Feng
- State Key Laboratory of Forest Genetics and Breeding, Xiangshan Road, Beijing 100091, P.R. China; Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical of Forestry, Chinese Academy of Forestry, Hangzhou 311400, P.R. China.
| | - Dayi Zhang
- School of Environment, Tsinghua University, Beijing 100084, P.R. China.
| | - Renying Zhuo
- State Key Laboratory of Forest Genetics and Breeding, Xiangshan Road, Beijing 100091, P.R. China; Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical of Forestry, Chinese Academy of Forestry, Hangzhou 311400, P.R. China.
| | - Mingying Liu
- State Key Laboratory of Forest Genetics and Breeding, Xiangshan Road, Beijing 100091, P.R. China; Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical of Forestry, Chinese Academy of Forestry, Hangzhou 311400, P.R. China.
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Li X, Ahmad S, Ali A, Guo C, Li H, Yu J, Zhang Y, Gao X, Guo Y. Characterization of Somatic Embryogenesis Receptor-Like Kinase 4 as a Negative Regulator of Leaf Senescence in Arabidopsis. Cells 2019; 8:cells8010050. [PMID: 30646631 PMCID: PMC6356292 DOI: 10.3390/cells8010050] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 01/10/2019] [Accepted: 01/10/2019] [Indexed: 11/16/2022] Open
Abstract
Leaf senescence is a genetically controlled process that involves the perception of extracellular signals and signal transduction. The receptor-like protein kinases (RLKs) are known to act as an important class of cell surface receptors and are involved in multiple biological processes such as development and stress responses. The functions of a number of RLK members have been characterized in Arabidopsis and other plant species, but only a limited number of RLK proteins have been reported to be associated with leaf senescence. In the present study, we have characterized the role of the somatic embryogenesis receptor kinase 4 (SERK4) gene in leaf senescence. The expression of SERK4 was up-regulated during leaf senescence and by several abiotic stress treatments in Arabidopsis. The serk4-1 knockout mutant was found to display a significant early leaf senescence phenotype. Furthermore, the results of overexpression analysis and complementary analysis supported the idea that SERK4 acts as a negative regulator in the process of leaf senescence.
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Affiliation(s)
- Xiaoxu Li
- Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
- Graduate School of Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Salman Ahmad
- Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
- Graduate School of Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Akhtar Ali
- Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
| | - Cun Guo
- Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
- Graduate School of Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Hong Li
- Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
| | - Jing Yu
- Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
| | - Yan Zhang
- Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
- Graduate School of Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Xiaoming Gao
- Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
- Graduate School of Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Yongfeng Guo
- Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
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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: 15] [Impact Index Per Article: 2.5] [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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Li X, Salman A, Guo C, Yu J, Cao S, Gao X, Li W, Li H, Guo Y. Identification and Characterization of LRR-RLK Family Genes in Potato Reveal Their Involvement in Peptide Signaling of Cell Fate Decisions and Biotic/Abiotic Stress Responses. Cells 2018; 7:cells7090120. [PMID: 30150583 PMCID: PMC6162732 DOI: 10.3390/cells7090120] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 08/25/2018] [Accepted: 08/25/2018] [Indexed: 12/22/2022] Open
Abstract
Leucine-rich repeat receptor-like kinases (LRR-RLKs) represent the largest subfamily of receptor-like kinases (RLKs) and play important roles in regulating growth, development, and stress responses in plants. In this study, 246 LRR-RLK genes were identified in the potato (Solanum tuberosum) genome, which were further classified into 14 subfamilies. Gene structure analysis revealed that genes within the same subgroup shared similar exon/intron structures. A signature small peptide recognition motif (RxR) was found to be largely conserved within members of subfamily IX, suggesting that these members may recognize peptide signals as ligands. 26 of the 246 StLRR-RLK genes were found to have arisen from tandem or segmental duplication events. Expression profiling revealed that StLRR-RLK genes were differentially expressed in various organs/tissues, and several genes were found to be responsive to different stress treatments. Furthermore, StLRR-RLK117 was found to be able to form homodimers and heterodimers with StLRR-RLK042 and StLRR-RLK052. Notably, the overlapping expression region of StLRR-RLK117 with Solanum tuberosumWUSCHEL (StWUS) suggested that the CLV3–CLV1/BAM–WUS feedback loop may be conserved in potato to maintain stem cell homeostasis within the shoot apical meristem.
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Affiliation(s)
- Xiaoxu Li
- Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
| | - Ahmad Salman
- Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
| | - Cun Guo
- Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
| | - Jing Yu
- Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
| | - Songxiao Cao
- Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
| | - Xiaoming Gao
- Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
| | - Wei Li
- Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
| | - Hong Li
- Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
| | - Yongfeng Guo
- Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
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Wang C, Reid JB, Foo E. The Art of Self-Control - Autoregulation of Plant-Microbe Symbioses. FRONTIERS IN PLANT SCIENCE 2018; 9:988. [PMID: 30042780 PMCID: PMC6048281 DOI: 10.3389/fpls.2018.00988] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 06/19/2018] [Indexed: 05/07/2023]
Abstract
Plants interact with diverse microbes including those that result in nutrient-acquiring symbioses. In order to balance the energy cost with the benefit gained, plants employ a systemic negative feedback loop to control the formation of these symbioses. This is particularly well-understood in nodulation, the symbiosis between legumes and nitrogen-fixing rhizobia, and is known as autoregulation of nodulation (AON). However, much less is understood about the autoregulation of the ancient arbuscular mycorrhizal symbioses that form between Glomeromycota fungi and the majority of land plants. Elegant physiological studies in legumes have indicated there is at least some overlap in the genes and signals that regulate these two symbioses but there are major gaps in our understanding. In this paper we examine the hypothesis that the autoregulation of mycorrhizae (AOM) pathway shares some elements with AON but that there are also some important differences. By reviewing the current knowledge of the AON pathway, we have identified important directions for future AOM studies. We also provide the first genetic evidence that CLV2 (an important element of the AON pathway) influences mycorrhizal development in a non-legume, tomato and review the interaction of the autoregulation pathway with plant hormones and nutrient status. Finally, we discuss whether autoregulation may play a role in the relationships plants form with other microbes.
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Affiliation(s)
| | | | - Eloise Foo
- School of Natural Sciences, University of Tasmania, Hobart, TAS, Australia
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Prihatna C, Barbetti MJ, Barker SJ. A Novel Tomato Fusarium Wilt Tolerance Gene. Front Microbiol 2018; 9:1226. [PMID: 29937759 PMCID: PMC6003170 DOI: 10.3389/fmicb.2018.01226] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 05/22/2018] [Indexed: 01/07/2023] Open
Abstract
The reduced mycorrhizal colonization (rmc) tomato mutant is unable to form mycorrhiza and is more susceptible to Fusarium wilt compared with its wild-type isogenic line 76R. The rmc mutant has a chromosomal deletion affecting five genes, one of which is similar to CYCLOPS. Loss of this gene is responsible for non-mycorrhizality in rmc but not enhanced Fusarium wilt susceptibility. Here, we describe assessment of a second gene in the rmc deletion, designated Solyc08g075770 that is expressed in roots. Sequence analyses show that Solyc08g075770 encodes a small transmembrane protein with putative phosphorylation and glycosylation sites. It is predicted to be localized in the plasma membrane and may function in transmembrane ion transport and/or as a cell surface receptor. Complementation and knock-out strategies were used to test its function. Some putative CRISPR/Cas-9 knock-out transgenic events exhibited Fusarium wilt susceptibility like rmc and some putative complementation lines were 76R-like, suggesting that the tomato Solyc08g075770 functions in Fusarium wilt tolerance. This is the first study to demonstrate that Solyc08g075770 is the contributor to the Tfw locus, conferring tolerance to Fusarium wilt in 76R which was lost in rmc.
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Affiliation(s)
- Cahya Prihatna
- School of Agriculture and Environment, Faculty of Science, The University of Western Australia, Crawley, WA, Australia
- Research and Development for Biotechnology, PT Wilmar Benih Indonesia, Bekasi, Indonesia
| | - Martin J. Barbetti
- School of Agriculture and Environment, Faculty of Science, The University of Western Australia, Crawley, WA, Australia
- The UWA Institute of Agriculture, Faculty of Science, The University of Western Australia, Crawley, WA, Australia
| | - Susan J. Barker
- School of Agriculture and Environment, Faculty of Science, The University of Western Australia, Crawley, WA, Australia
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36
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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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Ezura K, Ji-Seong K, Mori K, Suzuki Y, Kuhara S, Ariizumi T, Ezura H. Genome-wide identification of pistil-specific genes expressed during fruit set initiation in tomato (Solanum lycopersicum). PLoS One 2017; 12:e0180003. [PMID: 28683065 PMCID: PMC5500324 DOI: 10.1371/journal.pone.0180003] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Accepted: 06/07/2017] [Indexed: 11/19/2022] Open
Abstract
Fruit set involves the developmental transition of an unfertilized quiescent ovary in the pistil into a fruit. While fruit set is known to involve the activation of signals (including various plant hormones) in the ovary, many biological aspects of this process remain elusive. To further expand our understanding of this process, we identified genes that are specifically expressed in tomato (Solanum lycopersicum L.) pistils during fruit set through comprehensive RNA-seq-based transcriptome analysis using 17 different tissues including pistils at six different developmental stages. First, we identified 532 candidate genes that are preferentially expressed in the pistil based on their tissue-specific expression profiles. Next, we compared our RNA-seq data with publically available transcriptome data, further refining the candidate genes that are specifically expressed within the pistil. As a result, 108 pistil-specific genes were identified, including several transcription factor genes that function in reproductive development. We also identified genes encoding hormone-like peptides with a secretion signal and cysteine-rich residues that are conserved among some Solanaceae species, suggesting that peptide hormones may function as signaling molecules during fruit set initiation. This study provides important information about pistil-specific genes, which may play specific roles in regulating pistil development in relation to fruit set.
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Affiliation(s)
- Kentaro Ezura
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Kim Ji-Seong
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Kazuki Mori
- Faculty of Agriculture, Kyushu University, Higashi-ku, Fukuoka, Japan
| | - Yutaka Suzuki
- Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Satoru Kuhara
- Faculty of Agriculture, Kyushu University, Higashi-ku, Fukuoka, Japan
| | - Tohru Ariizumi
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Hiroshi Ezura
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
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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: 120] [Impact Index Per Article: 17.1] [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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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: 41] [Impact Index Per Article: 5.1] [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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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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41
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Genome-Wide Identification and Characterization of the LRR-RLK Gene Family in Two Vernicia Species. Int J Genomics 2015; 2015:823427. [PMID: 26783513 PMCID: PMC4691485 DOI: 10.1155/2015/823427] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 11/17/2015] [Indexed: 11/17/2022] Open
Abstract
Leucine-rich repeat receptor-like kinases (LRR-RLKs) make up the largest group of RLKs in plants and play important roles in many key biological processes such as pathogen response and signal transduction. To date, most studies on LRR-RLKs have been conducted on model plants. Here, we identified 236 and 230 LRR-RLKs in two industrial oil-producing trees: Vernicia fordii and Vernicia montana, respectively. Sequence alignment analyses showed that the homology of the RLK domain (23.81%) was greater than that of the LRR domain (9.51%) among the Vf/VmLRR-RLKs. The conserved motif of the LRR domain in Vf/VmLRR-RLKs matched well the known plant LRR consensus sequence but differed at the third last amino acid (W or L). Phylogenetic analysis revealed that Vf/VmLRR-RLKs were grouped into 16 subclades. We characterized the expression profiles of Vf/VmLRR-RLKs in various tissue types including root, leaf, petal, and kernel. Further investigation revealed that Vf/VmLRR-RLK orthologous genes mainly showed similar expression patterns in response to tree wilt disease, except 4 pairs of Vf/VmLRR-RLKs that showed opposite expression trends. These results represent an extensive evaluation of LRR-RLKs in two industrial oil trees and will be useful for further functional studies on these proteins.
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