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Sullivan KA, Miller JI, Townsend A, Morgan M, Lane M, Pavicic M, Shah M, Cashman M, Jacobson DA. MENTOR: Multiplex Embedding of Networks for Team-Based Omics Research. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.17.603821. [PMID: 39091782 PMCID: PMC11291001 DOI: 10.1101/2024.07.17.603821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
While the proliferation of data-driven omics technologies has continued to accelerate, methods of identifying relationships among large-scale changes from omics experiments have stagnated. It is therefore imperative to develop methods that can identify key mechanisms among one or more omics experiments in order to advance biological discovery. To solve this problem, here we describe the network-based algorithm MENTOR - Multiplex Embedding of Networks for Team-Based Omics Research. We demonstrate MENTOR's utility as a supervised learning approach to successfully partition a gene set containing multiple ontological functions into their respective functions. Subsequently, we used MENTOR as an unsupervised learning approach to identify important biological functions pertaining to the host genetic architectures in Populus trichocarpa associated with microbial abundance of multiple taxa. Moreover, as open source software designed with scientific teams in mind, we demonstrate the ability to use the output of MENTOR to facilitate distributed interpretation of omics experiments.
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Zhang J, Sun L, Wang Y, Li B, Li X, Ye Z, Zhang J. A Calcium-Dependent Protein Kinase Regulates the Defense Response in Citrus sinensis. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2024; 37:459-466. [PMID: 38597923 DOI: 10.1094/mpmi-12-23-0208-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
Citrus Huanglongbing (HLB), which is caused by 'Candidatus Liberibacter asiaticus' (CLas), is one of the most destructive citrus diseases worldwide, and defense-related Citrus sinensis gene resources remain largely unexplored. Calcium signaling plays an important role in diverse biological processes. In plants, a few calcium-dependent protein kinases (CDPKs/CPKs) have been shown to contribute to defense against pathogenic microbes. The genome of C. sinensis encodes dozens of CPKs. In this study, the role of C. sinensis calcium-dependent protein kinases (CsCPKs) in C. sinensis defense was investigated. Silencing of CsCPK6 compromised the induction of defense-related genes in C. sinensis. Expression of a constitutively active form of CsCPK6 (CsCPK6CA) triggered the activation of defense-related genes in C. sinensis. Complementation of CsCPK6 rescued the defense-related gene induction in an Arabidopsis thaliana cpk4/11 mutant, indicating that CsCPK6 carries CPK activity and is capable of functioning as a CPK in Arabidopsis. Moreover, an effector derived from CLas inhibits defense induced by the expression of CsCPK6CA and autophosphorylation of CsCPK6, which suggests the involvement of CsCPK6 and calcium signaling in defense. These results support a positive role for CsCPK6 in C. sinensis defense against CLas, and the autoinhibitory regulation of CsCPK6 provides a potential genome-editing target for improving C. sinensis defense. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Jinghan Zhang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- School of Life Sciences, Hebei University, Baoding, Hebei 071002, China
| | - Lifan Sun
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yu Wang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Baiyang Li
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiangguo Li
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- College of Agronomy, Shanxi Agricultural University, Taigu 030801, China
| | - Ziqin Ye
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jie Zhang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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Liu Y, Lin Y, Wei F, Lv Y, Xie F, Chen D, Lin H, Li Y. G-type receptor-like kinase AsNIP43 interacts with rhizobia effector nodulation outer protein P and is required for symbiosis. PLANT PHYSIOLOGY 2023; 193:1527-1546. [PMID: 37432453 PMCID: PMC10517198 DOI: 10.1093/plphys/kiad318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 04/27/2023] [Indexed: 07/12/2023]
Abstract
In the Rhizobium-Legume symbiosis, the nodulation outer protein P (NopP) effector is one of the key regulators for rhizobial infection and nodule organogenesis. However, the molecular mechanism through which host legume plants sense NopP remains largely unknown. Here, we constructed an nopP deletion mutant of Mesorhizobium huakuii and found that nopP negatively regulates nodulation on Chinese milk vetch (Astragalus sinicus). Screening for NopP interacting proteins in host plants using the yeast 2-hybrid system identified NopP interacting protein 43 (AsNIP43), which encodes a G-type receptor-like kinase (LecRLK). The B-lectin domain at the N terminus of AsNIP43 was essential in mediating its interaction with NopP, which was confirmed in vitro and in vivo. Subcellular localization, co-localization, and gene expression analyses showed that AsNIP43 and NopP function tightly associated with earlier infection events. RNA interference (RNAi) knockdown of AsNIP43 expression by hairy root transformation led to decreased nodule formation. AsNIP43 plays a positive role in symbiosis, which was further verified in the model legume Medicago truncatula. Transcriptome analysis indicated that MtRLK (a homolog of AsNIP43 in M. truncatula) may function to affect defense gene expression and thus to regulate early nodulation. Taken together, we show that LecRLK AsNIP43 is a legume host target that interacts with rhizobia effector NopP is essential for rhizobial infection and nodulation.
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Affiliation(s)
- Yuan Liu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei Province, China
| | - Ye Lin
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei Province, China
| | - Feng Wei
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei Province, China
| | - Yanfei Lv
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei Province, China
| | - Fuli Xie
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei Province, China
| | - Dasong Chen
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei Province, China
| | - Hui Lin
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei Province, China
| | - Youguo Li
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei Province, China
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Jin Y, Zhang W, Cong S, Zhuang QG, Gu YL, Ma YN, Filiatrault MJ, Li JZ, Wei HL. Pseudomonas syringae Type III Secretion Protein HrpP Manipulates Plant Immunity To Promote Infection. Microbiol Spectr 2023; 11:e0514822. [PMID: 37067445 PMCID: PMC10269811 DOI: 10.1128/spectrum.05148-22] [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] [Received: 12/14/2022] [Accepted: 03/22/2023] [Indexed: 04/18/2023] Open
Abstract
The bacterial plant pathogen Pseudomonas syringae deploys a type III secretion system (T3SS) to deliver effector proteins into plant cells to facilitate infection, for which many effectors have been characterized for their interactions. However, few T3SS Hrp (hypersensitive response and pathogenicity) proteins from the T3SS secretion apparatus have been studied for their direct interactions with plants. Here, we show that the P. syringae pv. tomato DC3000 T3SS protein HrpP induces host cell death, suppresses pattern-triggered immunity (PTI), and restores the effector translocation ability of the hrpP mutant. The hrpP-transgenic Arabidopsis lines exhibited decreased PTI responses to flg22 and elf18 and enhanced disease susceptibility to P. syringae pv. tomato DC3000. Transcriptome analysis reveals that HrpP sensing activates salicylic acid (SA) signaling while suppressing jasmonic acid (JA) signaling, which correlates with increased SA accumulation and decreased JA biosynthesis. Both yeast two-hybrid and bimolecular fluorescence complementation assays show that HrpP interacts with mitogen-activated protein kinase kinase 2 (MKK2) on the plant membrane and in the nucleus. The HrpP truncation HrpP1-119, rather than HrpP1-101, retains the ability to interact with MKK2 and suppress PTI in plants. In contrast, HrpP1-101 continues to cause cell death and electrolyte leakage. MKK2 silencing compromises SA signaling but has no effect on cell death caused by HrpP. Overall, our work highlights that the P. syringae T3SS protein HrpP facilitates effector translocation and manipulates plant immunity to facilitate bacterial infection. IMPORTANCE The T3SS is required for the virulence of many Gram-negative bacterial pathogens of plants and animals. This study focuses on the sensing and function of the T3SS protein HrpP during plant interactions. Our findings show that HrpP and its N-terminal truncation HrpP1-119 can interact with MKK2, promote effector translocation, and manipulate plant immunity to facilitate bacterial infection, highlighting the P. syringae T3SS component involved in the fine-tuning of plant immunity.
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Affiliation(s)
- Ya Jin
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wei Zhang
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, New York, USA
| | - Shen Cong
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qi-Guo Zhuang
- China-New Zealand Belt and Road Joint Laboratory on Kiwifruit, Kiwifruit Breeding and Utilization Key Laboratory of Sichuan Province, Sichuan Provincial Academy of Natural Resource Sciences, Chengdu, China
| | - Yi-Lin Gu
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yi-Nan Ma
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Melanie J. Filiatrault
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, New York, USA
- Emerging Pests and Pathogens Research Unit, Agricultural Research Service, United States Department of Agriculture, Robert W. Holley Center for Agriculture and Health, Ithaca, New York, USA
| | - Jun-Zhou Li
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hai-Lei Wei
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
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Liu L, Liu J, Xu N. Ligand recognition and signal transduction by lectin receptor-like kinases in plant immunity. FRONTIERS IN PLANT SCIENCE 2023; 14:1201805. [PMID: 37396638 PMCID: PMC10311507 DOI: 10.3389/fpls.2023.1201805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 05/31/2023] [Indexed: 07/04/2023]
Abstract
Lectin receptor-like kinases (LecRKs) locate on the cell membrane and play diverse roles in perceiving environmental factors in higher plants. Studies have demonstrated that LecRKs are involved in plant development and response to abiotic and biotic stresses. In this review, we summarize the identified ligands of LecRKs in Arabidopsis, including extracellular purine (eATP), extracellular pyridine (eNAD+), extracellular NAD+ phosphate (eNADP+) and extracellular fatty acids (such as 3-hydroxydecanoic acid). We also discussed the posttranslational modification of these receptors in plant innate immunity and the perspectives of future research on plant LecRKs.
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Yan J, Su P, Meng X, Liu P. Phylogeny of the plant receptor-like kinase (RLK) gene family and expression analysis of wheat RLK genes in response to biotic and abiotic stresses. BMC Genomics 2023; 24:224. [PMID: 37127571 PMCID: PMC10152718 DOI: 10.1186/s12864-023-09303-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 04/10/2023] [Indexed: 05/03/2023] Open
Abstract
BACKGROUND The receptor-like kinase (RLK) gene families in plants contains a large number of members. They are membrane proteins with an extracellular receptor domain and participate in biotic and abiotic stress responses. RESULTS In this study, we identified RLKs in 15 representative plant genomes, including wheat, and classified them into 64 subfamilies by using four types of phylogenetic trees and HMM models. Conserved exon‒intron structures with conserved exon phases in the kinase domain were found in many RLK subfamilies from Physcomitrella patens to Triticum aestivum. Domain distributions of RLKs were also diagrammed. Collinearity events and tandem gene clusters suggested that polyploidization and tandem duplication events contributed to the member expansions of T. aestivum RLKs. Global expression pattern analysis was performed by using public transcriptome data. These analyses were involved in T. aestivum, Aegilops tauschii and Brachypodium distachyon RLKs under biotic and abiotic stresses. We also selected 9 RLKs to validate the transcriptome prediction by using qRT‒PCR under drought treatment and with Fusarium graminearum infection. The expression trends of these 9 wheat RLKs from public transcriptome data were consistent with the results of qRT‒PCR, indicating that they might be stress response genes under drought or F. graminearum treatments. CONCLUSION In this study, we identified, classified, evolved, and expressed RLKs in wheat and related plants. Thus, our results will provide insights into the evolutionary history and molecular mechanisms of wheat RLKs.
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Affiliation(s)
- Jun Yan
- Key Laboratory of Huang-Huai-Hai Smart Agricultural Technology of the Ministry of Agriculture and Rural Affairs, College of Information Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, 271018, People's Republic of China.
| | - Peisen Su
- College of Agronomy, Liaocheng University, Liaocheng, 252059, People's Republic of China.
| | - Xianyong Meng
- Key Laboratory of Huang-Huai-Hai Smart Agricultural Technology of the Ministry of Agriculture and Rural Affairs, College of Information Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, 271018, People's Republic of China
| | - Pingzeng Liu
- Key Laboratory of Huang-Huai-Hai Smart Agricultural Technology of the Ministry of Agriculture and Rural Affairs, College of Information Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, 271018, People's Republic of China.
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Han P, Li R, Yue Q, Li F, Nie J, Yin Z, Xu M, Guan Q, Huang L. The Apple Receptor-Like Kinase MdSRLK3 Positively Regulates Resistance Against Pathogenic Fungus Valsa mali by Affecting the Ca 2+ Signaling Pathway. PHYTOPATHOLOGY 2022; 112:2187-2197. [PMID: 35509209 DOI: 10.1094/phyto-11-21-0471-r] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Valsa mali is the main pathogenic fungus that causes the apple Valsa canker, a destructive disease severely threatening apple production in the world. However, the underlying key components involved in resistance against V. mali in apple trees remain largely unexplored. Here, we isolated and functionally characterized a G-type lectin S-receptor-like protein kinase MdSRLK3 from the cultivar Royal Gala derivative line GL-3. qRT-PCR showed that the relative expression of MdSRLK3 in apple branches reached its highest level at 24 h post V. mali inoculation, which was 13.42 times higher than without inoculation. Transient overexpression of MdSRLK3 enhanced apple resistance against V. mali, while transient silencing of MdSRLK3 reduced its resistance against the pathogen. More importantly, stable silencing of MdSRLK3 resulted in reduced resistance against this fungus. Furthermore, we demonstrated that MdSRLK3 positively regulated apple resistance by affecting the Ca2+ signaling pathway, and the regulation was also related to the H2O2 and callose signaling pathways. Overall, our data reveal that MdSRLK3 is a positive regulator of apple immunity.
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Affiliation(s)
- Pengliang Han
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, China
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Rui Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, China
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Qianyu Yue
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, China
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Fudong Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, China
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jiajun Nie
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, China
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhiyuan Yin
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, China
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Ming Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, China
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Qingmei Guan
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, China
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Lili Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, China
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
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Zuo R, Xie M, Gao F, Liu J, Tang M, Cheng X, Liu Y, Bai Z, Liu S. Genome-wide identification and functional exploration of the legume lectin genes in Brassica napus and their roles in Sclerotinia disease resistance. FRONTIERS IN PLANT SCIENCE 2022; 13:963263. [PMID: 35968144 PMCID: PMC9374194 DOI: 10.3389/fpls.2022.963263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 06/28/2022] [Indexed: 06/15/2023]
Abstract
As one of the largest classes of lectins, legume lectins have a variety of desirable features such as antibacterial and insecticidal activities as well as anti-abiotic stress ability. The Sclerotinia disease (SD) caused by the soil-borne fungus Sclerotinia sclerotiorum is a devastating disease affecting most oil crops such as Brassica napus. Here, we identified 130 legume lectin (LegLu) genes in B. napus, which could be phylogenetically classified into seven clusters. The BnLegLu gene family has been significantly expanded since the whole-genome duplication (WGD) or segmental duplication. Gene structure and conserved motif analysis suggested that the BnLegLu genes were well conserved in each cluster. Moreover, relative to those genes only containing the legume lectin domain in cluster VI-VII, the genes in cluster I-V harbored a transmembrane domain and a kinase domain linked to the legume lectin domain in the C terminus. The expression of most BnLegLu genes was relatively low in various tissues. Thirty-five BnLegLu genes were responsive to abiotic stress, and 40 BnLegLu genes were strongly induced by S. sclerotiorum, with a most significant up-regulation of 715-fold, indicating their functional roles in SD resistance. Four BnLegLu genes were located in the candidate regions of genome-wide association analysis (GWAS) results which resulted from a worldwide rapeseed population consisting of 324 accessions associated with SD. Among them, the positive role of BnLegLus-16 in SD resistance was validated by transient expression in tobacco leaves. This study provides important information on BnLegLu genes, particularly about their roles in SD resistance, which may help targeted functional research and genetic improvement in the breeding of B. napus.
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Affiliation(s)
- Rong Zuo
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs of PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Meili Xie
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs of PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Feng Gao
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs of PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Jie Liu
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs of PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | | | - Xiaohui Cheng
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs of PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Yueying Liu
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs of PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Zetao Bai
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs of PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Shengyi Liu
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs of PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
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9
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Sanguankiattichai N, Buscaill P, Preston GM. How bacteria overcome flagellin pattern recognition in plants. CURRENT OPINION IN PLANT BIOLOGY 2022; 67:102224. [PMID: 35533494 DOI: 10.1016/j.pbi.2022.102224] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 03/03/2022] [Accepted: 03/29/2022] [Indexed: 06/14/2023]
Abstract
Efficient plant immune responses depend on the ability to recognise an invading microbe. The 22-amino acids in the N-terminal domain and the 28-amino acids in the central region of the bacterial flagellin, called flg22 and flgII-28, respectively, are important elicitors of plant immunity. Plant immunity is activated after flg22 or flgII-28 recognition by the plant transmembrane receptors FLS2 or FLS3, respectively. There is strong selective pressure on many plant pathogenic and endophytic bacteria to overcome flagellin-triggered immunity. Here we provide an overview of recent developments in our understanding of the evasion and suppression of flagellin pattern recognition by plant-associated bacteria.
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Affiliation(s)
| | - Pierre Buscaill
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Gail M Preston
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK.
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10
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Romero-Hernandez G, Martinez M. Plant Kinases in the Perception and Signaling Networks Associated With Arthropod Herbivory. FRONTIERS IN PLANT SCIENCE 2022; 13:824422. [PMID: 35599859 PMCID: PMC9116192 DOI: 10.3389/fpls.2022.824422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 04/14/2022] [Indexed: 06/15/2023]
Abstract
The success in the response of plants to environmental stressors depends on the regulatory networks that connect plant perception and plant response. In these networks, phosphorylation is a key mechanism to activate or deactivate the proteins involved. Protein kinases are responsible for phosphorylations and play a very relevant role in transmitting the signals. Here, we review the present knowledge on the contribution of protein kinases to herbivore-triggered responses in plants, with a focus on the information related to the regulated kinases accompanying herbivory in Arabidopsis. A meta-analysis of transcriptomic responses revealed the importance of several kinase groups directly involved in the perception of the attacker or typically associated with the transmission of stress-related signals. To highlight the importance of these protein kinase families in the response to arthropod herbivores, a compilation of previous knowledge on their members is offered. When available, this information is compared with previous findings on their role against pathogens. Besides, knowledge of their homologous counterparts in other plant-herbivore interactions is provided. Altogether, these observations resemble the complexity of the kinase-related mechanisms involved in the plant response. Understanding how kinase-based pathways coordinate in response to a specific threat remains a major challenge for future research.
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Affiliation(s)
- Gara Romero-Hernandez
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid – Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Madrid, Spain
| | - Manuel Martinez
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid – Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
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11
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Ubiquitination of Receptorsomes, Frontline of Plant Immunity. Int J Mol Sci 2022; 23:ijms23062937. [PMID: 35328358 PMCID: PMC8948693 DOI: 10.3390/ijms23062937] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/13/2022] [Accepted: 02/18/2022] [Indexed: 12/14/2022] Open
Abstract
Sessile plants are constantly exposed to myriads of unfavorable invading organisms with different lifestyles. To survive, plants have evolved plasma membrane-resident pattern recognition receptors (PRRs) and intracellular nucleotide-binding domain leucine-rich repeat receptors (NLRs) to initiate sophisticated downstream immune responses. Ubiquitination serves as one of the most important and prevalent posttranslational modifications (PTMs) to fine-tune plant immune responses. Over the last decade, remarkable progress has been made in delineating the critical roles of ubiquitination in plant immunity. In this review, we highlight recent advances in the understanding of ubiquitination in the modulation of plant immunity, with a particular focus on ubiquitination in the regulation of receptorsomes, and discuss how ubiquitination and other PTMs act in concert to ensure rapid, proper, and robust immune responses.
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12
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Yang L, Zhao M, Sha G, Sun Q, Gong Q, Yang Q, Xie K, Yuan M, Mortimer JC, Xie W, Wei T, Kang Z, Li G. The genome of the rice variety LTH provides insight into its universal susceptibility mechanism to worldwide rice blast fungal strains. Comput Struct Biotechnol J 2022; 20:1012-1026. [PMID: 35242291 PMCID: PMC8866493 DOI: 10.1016/j.csbj.2022.01.030] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 01/30/2022] [Accepted: 01/30/2022] [Indexed: 12/13/2022] Open
Abstract
The widely used rice variety Lijiangxintuanheigu (LTH) shows a universal susceptibility to thousands of Magnaporthe oryzae isolates, the causal agent of devastating rice blast, making LTH an ideal line in resistance (R) gene cloning. However, the underlying genetic mechanism of the universal susceptibility has not been fully revealed because of the lack of a high-quality genome. Here, we took a genomic approach together with experimental assays to investigate LTH’s universal susceptibility to rice blast. Using Nanopore long reads, we assembled a chromosome-level genome. Millions of genomic variants were detected by comparing LTH with 10 other rice varieties, of which large-effect variants could affect plant immunity. Gene family analyses show that the number of R genes and leucine-rich repeat receptor-like protein kinase (LRR-RLK)-encoding genes decrease significantly in LTH. Rice blast resistance genes called Pi genes are either absent or disrupted by genomic variations. Additionally, residual R genes of LTH are likely under weak pathogen selection pressure, and other plant defense-related genes are weakly induced by rice blast. In contrast, the pattern-triggered immunity (PTI) of LTH is normal, as demonstrated by experimental assays. Therefore, we conclude that weak effector-trigger immunity (ETI)-mediated primarily by Pi genes but not PTI results in the universal susceptibility of LTH to rice blast. The attenuated ETI of LTH may be also associated with reduced numbers of R genes and LRR-RLKs, and minimally functional residual defense-related genes. Finally, we demonstrate the use of the LTH genome by rapid cloning of the Pi gene Piak from a resistant variety.
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Affiliation(s)
- Lei Yang
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, the Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Mengfei Zhao
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, the Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Gan Sha
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, the Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Qiping Sun
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, the Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Qiuwen Gong
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, the Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Qun Yang
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, the Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Kabin Xie
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Meng Yuan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Jenny C. Mortimer
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, SA, Australia
| | - Weibo Xie
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Tong Wei
- Department of Plant Pathology and the Genome Center, University of California, Davis, CA 95616, USA
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Guotian Li
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, the Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan 430070, China
- Corresponding author at: State Key Laboratory of Agricultural Microbiology, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan 430070, China.
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Zeng M, Wan B, Wang L, Chen Z, Lin Y, Ye W, Wang Y, Wang Y. Identification and characterization of L-type lectin receptor-like kinases involved in Glycine max-Phytophthora sojae interaction. PLANTA 2021; 254:128. [PMID: 34812941 DOI: 10.1007/s00425-021-03789-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 11/15/2021] [Indexed: 06/13/2023]
Abstract
MAIN CONCLUSION Soybean contains a group of 64 L-type lectin receptor-like kinases. Three LecRKs were involved in the interactions with Phytophthora sojae and Bradyrhizobium diazoefficiens. L-type lectin receptor-like kinases (LecRKs) comprise an important class of membrane-localized receptor-like kinases that are involved in plant adaptation. In this study, we performed an inventory analysis of LecRKs in Glycine max (soybean). In total, 64 GmLecRKs containing the canonical LecRK feature were identified. Phylogenetic analysis revealed that 48 GmLecRKs have close orthologs in Arabidopsis or Solanum lycopersicum, while 16 are likely present only in the leguminous plant species. Transcriptome analyses revealed that expressions of multiple GmLecRK genes are either induced or suppressed during infection by the soybean root rot pathogen Phytophthora sojae. In addition, overexpression of the three LecRKs (Glyma.17G085000, Glyma.05G041300 or Glyma.17G224600) in the soybean hairy roots enhanced resistance to P. sojae. Upon inoculation with Bradyrhizobium diazoefficiens, overexpression of Glyma.17G085000 in the soybean hairy roots does not significantly influence the nodulation, while overexpression of Glyma.05G041300 or Glyma.17G224600 slightly reduced the number and dry weight of nodules. This study highlights the importance of LecRKs in regulating plant-microbe interactions and provides new knowledge on the deployment of LecRKs to increase resistance in soybean.
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Affiliation(s)
- Mengzhu Zeng
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu, China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Bowen Wan
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu, China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Lei Wang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu, China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Zhiyuan Chen
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu, China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Yachun Lin
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu, China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Wenwu Ye
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu, China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, Jiangsu, China
- The Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Nanjing, Jiangsu, China
| | - Yan Wang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu, China.
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, Jiangsu, China.
- The Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Nanjing, Jiangsu, China.
| | - Yuanchao Wang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu, China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, Jiangsu, China
- The Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Nanjing, Jiangsu, China
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14
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Xiao W, Hu S, Zou X, Cai R, Liao R, Lin X, Yao R, Guo X. Lectin receptor-like kinase LecRK-VIII.2 is a missing link in MAPK signaling-mediated yield control. PLANT PHYSIOLOGY 2021; 187:303-320. [PMID: 34618128 PMCID: PMC8418426 DOI: 10.1093/plphys/kiab241] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 05/01/2021] [Indexed: 05/13/2023]
Abstract
The energy allocation for vegetative and reproductive growth is regulated by developmental signals and environmental cues, which subsequently affects seed output. However, the molecular mechanism underlying how plants coordinate yield-related traits to control yield in changing source-sink relationships remains largely unknown. Here, we discovered the lectin receptor-like kinase LecRK-VIII.2 as a specific receptor-like kinase that coordinates silique number, seed size, and seed number to determine seed yield in Arabidopsis (Arabidopsis thaliana). The lecrk-VIII.2 mutants develop smaller seeds, but more siliques and seeds, leading to increased yield. In contrast, the plants overexpressing LecRK-VIII.2 form bigger seeds, but less siliques and seeds, which results in similar yield to that of wild-type plants. Interestingly, LecRK-VIII.2 promotes the growth of the rosette, root, and stem by coordinating the source-sink relationship. Additionally, LecRK-VIII.2 positively regulates cell expansion and proliferation in the seed coat, and maternally controls seed size. The genetic and biochemical analyses demonstrated that LecRK-VIII.2 acts upstream of the mitogen-activated protein kinase (MAPK) gene MPK6 to regulate silique number, seed size, and seed number. Collectively, these findings uncover LecRK-VIII.2 as an upstream component of the MAPK signaling pathway to control yield-related traits and suggest its potential for crop improvement aimed at developing plants with stable yield, a robust root system, and improved lodging resistance.
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Affiliation(s)
- Wenjun Xiao
- College of Biology, Hunan University, Changsha 410082, China
| | - Shuai Hu
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xiaoxiao Zou
- College of Biology, Hunan University, Changsha 410082, China
| | - Ruqiong Cai
- College of Biology, Hunan University, Changsha 410082, China
| | - Rui Liao
- College of Biology, Hunan University, Changsha 410082, China
| | - Xiaoxia Lin
- College of Biology, Hunan University, Changsha 410082, China
| | - Ruifeng Yao
- College of Biology, Hunan University, Changsha 410082, China
| | - Xinhong Guo
- College of Biology, Hunan University, Changsha 410082, China
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15
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Han H, Mu X, Wang P, Wang Z, Fu H, Gao YG, Du J. Identification of LecRLK gene family in Cerasus humilis through genomic-transcriptomic data mining and expression analyses. PLoS One 2021; 16:e0254535. [PMID: 34252163 PMCID: PMC8274838 DOI: 10.1371/journal.pone.0254535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 06/29/2021] [Indexed: 11/18/2022] Open
Abstract
Lectin receptor-like protein kinases (LecRLKs) have been shown to be involved in plants’ responses to various biotic and abiotic stresse factors. Cerasus humilis is an important fruit species widely planted for soil and water conservation in northern China due to its strong tolerance to drought and salinity stresses. In this study, a total of 170 LecRLK family genes (125 G-types, 43 L-types and 2 C-types) were identified in the newly released whole-genome sequences of C. humilis. Furthermore, nine representative LecRLK genes in young plants of C. humilis under varying drought and salinity stresses were selected for qRT-PCR analysis. Our systematic comparative analyses revealed the active participation of these nine LecRLK genes in the salt and drought stress responses of C. humilis. The results from our study have provided a solid foundation for future functional verification of these LecRLK family genes and will likely help facilitate the more rapid and effective development of new stress resistant Cerasus humilis cultivars.
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Affiliation(s)
- Hongyan Han
- College of Horticulture, Shanxi Agricultural University, Taigu, Shanxi, P. R. China
- Department of Biological Science and Technology, Jinzhong University, Jinzhong, Yuci, Shanxi, P. R. China
| | - Xiaopeng Mu
- College of Horticulture, Shanxi Agricultural University, Taigu, Shanxi, P. R. China
| | - Pengfei Wang
- College of Horticulture, Shanxi Agricultural University, Taigu, Shanxi, P. R. China
| | - Zewen Wang
- College of Horticulture, Shanxi Agricultural University, Taigu, Shanxi, P. R. China
| | - Hongbo Fu
- College of Horticulture, Shanxi Agricultural University, Taigu, Shanxi, P. R. China
| | - Yu Gary Gao
- OSU South Centers, The Ohio State University, Piketon, Ohio, United States of America
- Department of Extension, The Ohio State University, Columbus, Ohio, United States of America
| | - Junjie Du
- College of Horticulture, Shanxi Agricultural University, Taigu, Shanxi, P. R. China
- Shanxi Key Laboratory of Germplasm Improvement and Utilization in Pomology, Taigu, Shanxi, P. R. China
- * E-mail:
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16
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Schreiber KJ, Chau-Ly IJ, Lewis JD. What the Wild Things Do: Mechanisms of Plant Host Manipulation by Bacterial Type III-Secreted Effector Proteins. Microorganisms 2021; 9:1029. [PMID: 34064647 PMCID: PMC8150971 DOI: 10.3390/microorganisms9051029] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/03/2021] [Accepted: 05/04/2021] [Indexed: 01/05/2023] Open
Abstract
Phytopathogenic bacteria possess an arsenal of effector proteins that enable them to subvert host recognition and manipulate the host to promote pathogen fitness. The type III secretion system (T3SS) delivers type III-secreted effector proteins (T3SEs) from bacterial pathogens such as Pseudomonas syringae, Ralstonia solanacearum, and various Xanthomonas species. These T3SEs interact with and modify a range of intracellular host targets to alter their activity and thereby attenuate host immune signaling. Pathogens have evolved T3SEs with diverse biochemical activities, which can be difficult to predict in the absence of structural data. Interestingly, several T3SEs are activated following injection into the host cell. Here, we review T3SEs with documented enzymatic activities, as well as T3SEs that facilitate virulence-promoting processes either indirectly or through non-enzymatic mechanisms. We discuss the mechanisms by which T3SEs are activated in the cell, as well as how T3SEs modify host targets to promote virulence or trigger immunity. These mechanisms may suggest common enzymatic activities and convergent targets that could be manipulated to protect crop plants from infection.
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Affiliation(s)
- Karl J. Schreiber
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94710, USA; (K.J.S.); (I.J.C.-L.)
| | - Ilea J. Chau-Ly
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94710, USA; (K.J.S.); (I.J.C.-L.)
| | - Jennifer D. Lewis
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94710, USA; (K.J.S.); (I.J.C.-L.)
- Plant Gene Expression Center, United States Department of Agriculture, University of California, Berkeley, CA 94710, USA
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