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Ahmed FF, Dola FS, Islam MSU, Zohra FT, Akter N, Rahman SM, Rauf Sarkar MA. Genome-Wide Comprehensive Identification and In Silico Characterization of Lectin Receptor-Like Kinase Gene Family in Barley ( Hordeum vulgare L.). Genet Res (Camb) 2024; 2024:2924953. [PMID: 38444770 PMCID: PMC10914435 DOI: 10.1155/2024/2924953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 01/27/2024] [Accepted: 02/16/2024] [Indexed: 03/07/2024] Open
Abstract
Lectin receptor-like kinases (LecRLKs) are a significant subgroup of the receptor-like kinases (RLKs) protein family. They play crucial roles in plant growth, development, immune responses, signal transduction, and stress tolerance. However, the genome-wide identification and characterization of LecRLK genes and their regulatory elements have not been explored in a major cereal crop, barley (Hordeum vulgare L.). Therefore, in this study, integrated bioinformatics tools were used to identify and characterize the LecRLK gene family in barley. Based on the phylogenetic tree and domain organization, a total of 113 LecRLK genes were identified in the barley genome (referred to as HvlecRLK) corresponding to the LecRLK genes of Arabidopsis thaliana. These putative HvlecRLK genes were classified into three groups: 62 G-type LecRLKs, 1 C-type LecRLK, and 50 L-type LecRLKs. They were unevenly distributed across eight chromosomes, including one unknown chromosome, and were predominantly located in the plasma membrane (G-type HvlecRLK (96.8%), C-type HvlecRLK (100%), and L-type HvlecRLK (98%)). An analysis of motif composition and exon-intron configuration revealed remarkable homogeneity with the members of AtlecRLK. Notably, most of the HvlecRLKs (27 G-type, 43 L-type) have no intron, suggesting their rapid functionality. The Ka/Ks and syntenic analysis demonstrated that HvlecRLK gene pairs evolved through purifying selection and gene duplication was the major factor for the expansion of the HvlecRLK gene family. Exploration of gene ontology (GO) enrichment indicated that the identified HvlecRLK genes are associated with various cellular processes, metabolic pathways, defense mechanisms, kinase activity, catalytic activity, ion binding, and other essential pathways. The regulatory network analysis identified 29 transcription factor families (TFFs), with seven major TFFs including bZIP, C2H2, ERF, MIKC_MADS, MYB, NAC, and WRKY participating in the regulation of HvlecRLK gene functions. Most notably, eight TFFs were found to be linked to the promoter region of both L-type HvleckRLK64 and HvleckRLK86. The promoter cis-acting regulatory element (CARE) analysis of barley identified a total of 75 CARE motifs responsive to light responsiveness (LR), tissue-specific (TS), hormone responsiveness (HR), and stress responsiveness (SR). The maximum number of CAREs was identified in HvleckRLK11 (25 for LR), HvleckRLK69 (17 for TS), and HvleckRLK80 (12 for HR). Additionally, HvleckRLK14, HvleckRLK16, HvleckRLK33, HvleckRLK50, HvleckRLK52, HvleckRLK56, and HvleckRLK110 were predicted to exhibit higher responses in stress conditions. In addition, 46 putative miRNAs were predicted to target 81 HvlecRLK genes and HvlecRLK13 was the most targeted gene by 8 different miRNAs. Protein-protein interaction analysis demonstrated higher functional similarities of 63 HvlecRLKs with 7 Arabidopsis STRING proteins. Our overall findings provide valuable information on the LecRLK gene family which might pave the way to advanced research on the functional mechanism of the candidate genes as well as to develop new barley cultivars in breeding programs.
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Affiliation(s)
- Fee Faysal Ahmed
- Department of Mathematics, Faculty of Science, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - Farah Sumaiya Dola
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - Md Shohel Ul Islam
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - Fatema Tuz Zohra
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Nasrin Akter
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - Shaikh Mizanur Rahman
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - Md. Abdur Rauf Sarkar
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore 7408, Bangladesh
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Bao Y, Li Y, Chang Q, Chen R, Wang W, Zhang Q, Chen S, Xu G, Wang X, Cui F, Dou D, Liang X. A pair of G-type lectin receptor-like kinases modulates nlp20-mediated immune responses by coupling to the RLP23 receptor complex. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:1312-1327. [PMID: 36633200 DOI: 10.1111/jipb.13449] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 01/05/2023] [Indexed: 05/13/2023]
Abstract
Plant cells recognize microbial patterns with the plasma-membrane-localized pattern-recognition receptors consisting mainly of receptor kinases (RKs) and receptor-like proteins (RLPs). RKs, such as bacterial flagellin receptor FLS2, and their downstream signaling components have been studied extensively. However, newly discovered regulatory components of RLP-mediated immune signaling, such as the nlp20 receptor RLP23, await identification. Unlike RKs, RLPs lack a cytoplasmic kinase domain, instead recruiting the receptor-like kinases (RLKs) BAK1 and SOBIR1. SOBIR1 specifically works as an adapter for RLP-mediated immunity. To identify new regulators of RLP-mediated signaling, we looked for SOBIR1-binding proteins (SBPs) in Arabidopsis thaliana using protein immunoprecipitation and mass spectrometry, identifying two G-type lectin RLKs, SBP1 and SBP2, that physically interacted with SOBIR1. SBP1 and SBP2 showed high sequence similarity, were tandemly repeated on chromosome 4, and also interacted with both RLP23 and BAK1. sbp1 sbp2 double mutants obtained via CRISPR-Cas9 gene editing showed severely impaired nlp20-induced reactive oxygen species burst, mitogen-activated protein kinase (MAPK) activation, and defense gene expression, but normal flg22-induced immune responses. We showed that SBP1 regulated nlp20-induced immunity in a kinase activity-independent manner. Furthermore, the nlp20-induced the RLP23-BAK1 interaction, although not the flg22-induced FLS2-BAK1 interaction, was significantly reduced in sbp1 sbp2. This study identified SBPs as new regulatory components in RLP23 receptor complex that may specifically modulate RLP23-mediated immunity by positively regulating the interaction between the RLP23 receptor and the BAK1 co-receptor.
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Affiliation(s)
- Yazhou Bao
- MOA Key Laboratory of Pest Monitoring and Green Management, Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, 100193, China
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yixin Li
- MOA Key Laboratory of Pest Monitoring and Green Management, Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Qin Chang
- MOA Key Laboratory of Pest Monitoring and Green Management, Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Rubin Chen
- MOA Key Laboratory of Pest Monitoring and Green Management, Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Weijie Wang
- MOA Key Laboratory of Pest Monitoring and Green Management, Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Qian Zhang
- MOA Key Laboratory of Pest Monitoring and Green Management, Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Shuxian Chen
- MOA Key Laboratory of Pest Monitoring and Green Management, Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Guangyuan Xu
- MOA Key Laboratory of Pest Monitoring and Green Management, Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Xiaodan Wang
- MOA Key Laboratory of Pest Monitoring and Green Management, Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Fuhao Cui
- MOA Key Laboratory of Pest Monitoring and Green Management, Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Daolong Dou
- MOA Key Laboratory of Pest Monitoring and Green Management, Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, 100193, China
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiangxiu Liang
- MOA Key Laboratory of Pest Monitoring and Green Management, Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, 100193, China
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
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Nanda S, Rout P, Ullah I, Nag SR, Reddy VV, Kumar G, Kumar R, He S, Wu H. Genome-wide identification and molecular characterization of CRK gene family in cucumber (Cucumis sativus L.) under cold stress and sclerotium rolfsii infection. BMC Genomics 2023; 24:219. [PMID: 37101152 PMCID: PMC10131431 DOI: 10.1186/s12864-023-09319-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 04/17/2023] [Indexed: 04/28/2023] Open
Abstract
BACKGROUND The plant cysteine-rich receptor-like kinases (CRKs) are a large family having multiple roles, including defense responses under both biotic and abiotic stress. However, the CRK family in cucumbers (Cucumis sativus L.) has been explored to a limited extent. In this study, a genome-wide characterization of the CRK family has been performed to investigate the structural and functional attributes of the cucumber CRKs under cold and fungal pathogen stress. RESULTS A total of 15 C. sativus CRKs (CsCRKs) have been characterized in the cucumber genome. Chromosome mapping of the CsCRKs revealed that 15 genes are distributed in cucumber chromosomes. Additionally, the gene duplication analysis of the CsCRKs yielded information on their divergence and expansion in cucumbers. Phylogenetic analysis divided the CsCRKs into two clades along with other plant CRKs. Functional predictions of the CsCRKs suggested their role in signaling and defense response in cucumbers. The expression analysis of the CsCRKs by using transcriptome data and via qRT-PCR indicated their involvement in both biotic and abiotic stress responses. Under the cucumber neck rot pathogen, Sclerotium rolfsii infection, multiple CsCRKs exhibited induced expressions at early, late, and both stages. Finally, the protein interaction network prediction results identified some key possible interacting partners of the CsCRKs in regulating cucumber physiological processes. CONCLUSIONS The results of this study identified and characterized the CRK gene family in cucumbers. Functional predictions and validation via expression analysis confirmed the involvement of the CsCRKs in cucumber defense response, especially against S. rolfsii. Moreover, current findings provide better insights into the cucumber CRKs and their involvement in defense responses.
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Affiliation(s)
- Satyabrata Nanda
- MS Swaminathan School of Agriculture, Centurion University of Technology and Management, Paralakhemundi, 761211, India
| | - Priyadarshini Rout
- MS Swaminathan School of Agriculture, Centurion University of Technology and Management, Paralakhemundi, 761211, India
| | - Ikram Ullah
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, 650201, China
| | - Swapna Rani Nag
- MS Swaminathan School of Agriculture, Centurion University of Technology and Management, Paralakhemundi, 761211, India
| | - Velagala Veerraghava Reddy
- MS Swaminathan School of Agriculture, Centurion University of Technology and Management, Paralakhemundi, 761211, India
| | - Gagan Kumar
- Krishi Vigyan Kendra, Narkatiaganj, Dr. Rajendra Prasad Central Agricultural University, Pusa Samastipur, Bihar, 848125, India
| | - Ritesh Kumar
- MS Swaminathan School of Agriculture, Centurion University of Technology and Management, Paralakhemundi, 761211, India
| | - Shuilian He
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, 650201, China
| | - Hongzhi Wu
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, 650201, China.
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Zhu Q, Feng Y, Xue J, Chen P, Zhang A, Yu Y. Advances in Receptor-like Protein Kinases in Balancing Plant Growth and Stress Responses. PLANTS (BASEL, SWITZERLAND) 2023; 12:427. [PMID: 36771514 PMCID: PMC9919196 DOI: 10.3390/plants12030427] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/07/2023] [Accepted: 01/10/2023] [Indexed: 06/18/2023]
Abstract
Accompanying the process of growth and development, plants are exposed to ever-changing environments, which consequently trigger abiotic or biotic stress responses. The large protein family known as receptor-like protein kinases (RLKs) is involved in the regulation of plant growth and development, as well as in the response to various stresses. Understanding the biological function and molecular mechanism of RLKs is helpful for crop breeding. Research on the role and mechanism of RLKs has recently received considerable attention regarding the balance between plant growth and environmental adaptability. In this paper, we systematically review the classification of RLKs, the regulatory roles of RLKs in plant development (meristem activity, leaf morphology and reproduction) and in stress responses (disease resistance and environmental adaptation). This review focuses on recent findings revealing that RLKs simultaneously regulate plant growth and stress adaptation, which may pave the way for the better understanding of their function in crop improvement. Although the exact crosstalk between growth constraint and plant adaptation remains elusive, a profound study on the adaptive mechanisms for decoupling the developmental processes would be a promising direction for the future research.
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Dhillon MK, Jaba J, Mishra P, Iquebal MA, Jaiswal S, Tanwar AK, Bharat N, Arora N, Mishra SP, Gogineni SP, Hasan F, Rai A, Kumar D, Sharma HC. Whole genome sequencing of spotted stem borer, Chilo partellus, reveals multiple genes encoding enzymes for detoxification of insecticides. Funct Integr Genomics 2022; 22:611-624. [PMID: 35426546 DOI: 10.1007/s10142-022-00852-w] [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: 11/24/2021] [Revised: 03/20/2022] [Accepted: 03/22/2022] [Indexed: 11/24/2022]
Abstract
Spotted stem borer, Chilo partellus, is the most important constraint for increasing the production and productivity of maize and sorghum, the two major coarse cereals in Asia and Africa. The levels of resistance to this pest in the cultivated germplasm are low to moderate, and hence, farmers have to use insecticides for effective control of this pest. However, there is no information on the detoxification mechanisms in C. partellus, which is one of the constraints for deployment of appropriate insecticides to control this pest. The ability to detoxify insecticides varies across insect populations, and hence, we sequenced different populations of C. partellus to identify and understand detoxification mechanisms to devise appropriate strategies for deployment of different insecticides for controlling this pest. Larval samples were sequenced from three different cohorts of C. partellus using the Illumina HiSeq 2500 platform. The data were subjected to identify putative genes that are involved in detoxification on insecticides in our cohort insect species. These studies resulted in identification of 64 cytochrome P450 genes (CYP450s), and 36 glutathione S-transferases genes (GSTs) encoding metabolic detoxification enzymes, primarily responsible for xenobiotic metabolism in insects. A total of 183 circadian genes with > 80% homolog and 11 olfactory receptor genes that mediate chemical cues were found in the C. partellus genome. Also, target receptors related to insecticide action, 4 acetylcholinesterase (AChE), 14 γ-aminobutyric acid (GABA), and 15 nicotinic acetylcholine (nAChR) receptors were detected. This is the first report of whole genome sequencing of C. partellus useful for understanding mode of action of different insecticides, and mechanisms of detoxification and designing target-specific insecticides to develop appropriate strategies to control C. partellus for sustainable crop production.
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Affiliation(s)
- Mukesh K Dhillon
- Division of Entomology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Jagdish Jaba
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Hyderabad, 502324, Telangana, India
| | - Pallavi Mishra
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India
| | - Mir Asif Iquebal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India
| | - Sarika Jaiswal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India
| | - Aditya K Tanwar
- Division of Entomology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Nareshkumar Bharat
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Hyderabad, 502324, Telangana, India
| | - Naveen Arora
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Hyderabad, 502324, Telangana, India
| | - Suraj Prasad Mishra
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Hyderabad, 502324, Telangana, India
| | - Shyam Prasad Gogineni
- ICAR-Indian Institute of Millets Research, Rajendranagar, Hyderabad, 500030, Telangana, India
| | - Fazil Hasan
- Division of Entomology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Anil Rai
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India
| | - Dinesh Kumar
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India. .,Department of Biotechnology, School of Interdisciplinary and Applied Sciences, Central University of Haryana, Mahendergarh, 123031, Haryana, India.
| | - Hari C Sharma
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Hyderabad, 502324, Telangana, India
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Liu Y, Zuo T, Qiu Z, Zhuang K, Hu S, Han H. Genome-wide identification reveals the function of CEP peptide in cucumber root development. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 169:119-126. [PMID: 34775178 DOI: 10.1016/j.plaphy.2021.11.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 10/28/2021] [Accepted: 11/06/2021] [Indexed: 06/13/2023]
Abstract
C-Terminally Encoded (CEP) peptides are crucial plant growth regulators. Nevertheless, their physiological roles in cucumber (Cucumis sativus L.), an essential worldwide economical vegetable, remains untapped. In this study, 6 cucumber CEP (CsCEP) genes were identified. A comprehensive analysis showed that the CsCEP proteins displayed conserved characteristics to the identified CEP protein members in other species. CsCEP genes expression levels were variant in cucumber tissues, and were also differentially induced by several environmental factors, suggesting distinct and overlapping roles of CsCEPs in various cucumber developmental processes. We further revealed that synthetic CsCEP4 peptide promoted cucumber primary root growth in a reactive oxygen species (ROS) dependent manner. Overall, our work will provide fundamental insights into the crucial physiological roles of small bioactive peptides during cucumber root development.
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Affiliation(s)
- Yiting Liu
- Research Center of Plant Functional Genes and Tissue Culture Technology, College of Bioscience and Bioengineering, Jiangxi Agricultural University, 330045, Nanchang, China
| | - Tingting Zuo
- Research Center of Plant Functional Genes and Tissue Culture Technology, College of Bioscience and Bioengineering, Jiangxi Agricultural University, 330045, Nanchang, China
| | - Ziwen Qiu
- Research Center of Plant Functional Genes and Tissue Culture Technology, College of Bioscience and Bioengineering, Jiangxi Agricultural University, 330045, Nanchang, China
| | - Keqing Zhuang
- Research Center of Plant Functional Genes and Tissue Culture Technology, College of Bioscience and Bioengineering, Jiangxi Agricultural University, 330045, Nanchang, China
| | - Songping Hu
- Research Center of Plant Functional Genes and Tissue Culture Technology, College of Bioscience and Bioengineering, Jiangxi Agricultural University, 330045, Nanchang, China; Key Laboratory of Ministry of Education for Crop Physiology, Ecology and Genetics and Breeding of Jiangxi Agricultural University, 330045 Nanchang, China.
| | - Huibin Han
- Research Center of Plant Functional Genes and Tissue Culture Technology, College of Bioscience and Bioengineering, Jiangxi Agricultural University, 330045, Nanchang, China.
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