1
|
Lalun VO, Breiden M, Galindo-Trigo S, Smakowska-Luzan E, Simon RGW, Butenko MA. A dual function of the IDA peptide in regulating cell separation and modulating plant immunity at the molecular level. eLife 2024; 12:RP87912. [PMID: 38896460 PMCID: PMC11186634 DOI: 10.7554/elife.87912] [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] [Indexed: 06/21/2024] Open
Abstract
The abscission of floral organs and emergence of lateral roots in Arabidopsis is regulated by the peptide ligand inflorescence deficient in abscission (IDA) and the receptor protein kinases HAESA (HAE) and HAESA-like 2 (HSL2). During these cell separation processes, the plant induces defense-associated genes to protect against pathogen invasion. However, the molecular coordination between abscission and immunity has not been thoroughly explored. Here, we show that IDA induces a release of cytosolic calcium ions (Ca2+) and apoplastic production of reactive oxygen species, which are signatures of early defense responses. In addition, we find that IDA promotes late defense responses by the transcriptional upregulation of genes known to be involved in immunity. When comparing the IDA induced early immune responses to known immune responses, such as those elicited by flagellin22 treatment, we observe both similarities and differences. We propose a molecular mechanism by which IDA promotes signatures of an immune response in cells destined for separation to guard them from pathogen attack.
Collapse
Affiliation(s)
- Vilde Olsson Lalun
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of OsloOsloNorway
| | - Maike Breiden
- Institute for Developmental Genetics and Cluster of Excellence on Plant Sciences, Heinrich Heine UniversityDüsseldorfGermany
| | - Sergio Galindo-Trigo
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of OsloOsloNorway
| | - Elwira Smakowska-Luzan
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC)ViennaAustria
| | - Rüdiger GW Simon
- Institute for Developmental Genetics and Cluster of Excellence on Plant Sciences, Heinrich Heine UniversityDüsseldorfGermany
| | - Melinka A Butenko
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of OsloOsloNorway
| |
Collapse
|
2
|
Jiang L, Dai C, Wei Y, Zhao B, Li Q, Wu Z, Zou L, Ye Z, Yang Z, Huang L, Shi Y. Identification of LRRC46 as a novel candidate gene for high myopia. SCIENCE CHINA. LIFE SCIENCES 2024:10.1007/s11427-024-2583-6. [PMID: 38874710 DOI: 10.1007/s11427-024-2583-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 03/19/2024] [Indexed: 06/15/2024]
Abstract
High myopia (HM) is the primary cause of blindness, with the microstructural organization and composition of collagenous fibers in the cornea and sclera playing a crucial role in the biomechanical behavior of these tissues. In a previously reported myopic linkage region, MYP5 (17q21-22), a potential candidate gene, LRRC46 (c.C235T, p.Q79X), was identified in a large Han Chinese pedigree. LRRC46 is expressed in various eye tissues in humans and mice, including the retina, cornea, and sclera. In subsequent cell experiments, the mutation (c.C235T) decreased the expression of LRRC46 protein in human corneal epithelial cells (HCE-T). Further investigation revealed that Lrrc46-/- mice (KO) exhibited a classical myopia phenotype. The thickness of the cornea and sclera in KO mice became thinner and more pronounced with age, the activity of limbal stem cells decreased, and microstructural changes were observed in the fibroblasts of the sclera and cornea. We performed RNA-seq on scleral and corneal tissues of KO and normal control wild-type (WT) mice, which indicated a significant downregulation of the collagen synthesis-related pathway (extracellular matrix, ECM) in KO mice. Subsequent in vitro studies further indicated that LRRC46, a member of the important LRR protein family, primarily affected the formation of collagens. This study suggested that LRRC46 is a novel candidate gene for HM, influencing collagen protein VIII (Col8a1) formation in the eye and gradually altering the biomechanical structure of the cornea and sclera, thereby promoting the occurrence and development of HM.
Collapse
Affiliation(s)
- Lingxi Jiang
- Sichuan Provincial Key Laboratory for Human Disease Gene Study and the Center for Medical Genetics, Department of Laboratory Medicine, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 610072, China
| | - Chao Dai
- Sichuan Provincial Key Laboratory for Human Disease Gene Study and the Center for Medical Genetics, Department of Laboratory Medicine, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 610072, China
| | - Yao Wei
- Sichuan Provincial Key Laboratory for Human Disease Gene Study and the Center for Medical Genetics, Department of Laboratory Medicine, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 610072, China
| | - Bo Zhao
- Sichuan Provincial Key Laboratory for Human Disease Gene Study and the Center for Medical Genetics, Department of Laboratory Medicine, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 610072, China
- Department of Ophthalmology, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 610072, China
| | - Qi Li
- Sichuan Provincial Key Laboratory for Human Disease Gene Study and the Center for Medical Genetics, Department of Laboratory Medicine, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 610072, China
| | - Zhengzheng Wu
- Sichuan Provincial Key Laboratory for Human Disease Gene Study and the Center for Medical Genetics, Department of Laboratory Medicine, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 610072, China
- Department of Ophthalmology, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 610072, China
| | - Liang Zou
- School of Food and Bioengineering, Chengdu University, Chengdu, 610106, China
| | - Zimeng Ye
- Sichuan Provincial Key Laboratory for Human Disease Gene Study and the Center for Medical Genetics, Department of Laboratory Medicine, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 610072, China
- School of Medicine, University of Sydney, Sydney, 2050, Australia
| | - Zhenglin Yang
- Sichuan Provincial Key Laboratory for Human Disease Gene Study and the Center for Medical Genetics, Department of Laboratory Medicine, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 610072, China.
- Department of Ophthalmology, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 610072, China.
- Research Unit for Blindness Prevention of Chinese Academy of Medical Sciences (2019RU026), Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, 610072, China.
- Jinfeng Laboratory, Chongging, 40000, China.
| | - Lulin Huang
- Sichuan Provincial Key Laboratory for Human Disease Gene Study and the Center for Medical Genetics, Department of Laboratory Medicine, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 610072, China.
- Research Unit for Blindness Prevention of Chinese Academy of Medical Sciences (2019RU026), Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, 610072, China.
| | - Yi Shi
- Sichuan Provincial Key Laboratory for Human Disease Gene Study and the Center for Medical Genetics, Department of Laboratory Medicine, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 610072, China.
- Department of Ophthalmology, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 610072, China.
- Research Unit for Blindness Prevention of Chinese Academy of Medical Sciences (2019RU026), Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, 610072, China.
| |
Collapse
|
3
|
Chauveau C, Roby D. Molecular complexity of quantitative immunity in plants: from QTL mapping to functional and systems biology. C R Biol 2024; 347:35-44. [PMID: 38771313 DOI: 10.5802/crbiol.153] [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: 02/16/2024] [Revised: 03/20/2024] [Accepted: 03/28/2024] [Indexed: 05/22/2024]
Abstract
In nature, plants defend themselves against pathogen attack by activating an arsenal of defense mechanisms. During the last decades, work mainly focused on the understanding of qualitative disease resistance mediated by a few genes conferring an almost complete resistance, while quantitative disease resistance (QDR) remains poorly understood despite the fact that it represents the predominant and more durable form of resistance in natural populations and crops. Here, we review our past and present work on the dissection of the complex mechanisms underlying QDR in Arabidopsis thaliana. The strategies, main steps and challenges of our studies related to one atypical QDR gene, RKS1 (Resistance related KinaSe 1), are presented. First, from genetic analyses by QTL (Quantitative Trait Locus) mapping and GWAs (Genome Wide Association studies), the identification, cloning and functional analysis of this gene have been used as a starting point for the exploration of the multiple and coordinated pathways acting together to mount the QDR response dependent on RKS1. Identification of RKS1 protein interactors and complexes was a first step, systems biology and reconstruction of protein networks were then used to decipher the molecular roadmap to the immune responses controlled by RKS1. Finally, exploration of the potential impact of key components of the RKS1-dependent gene network on leaf microbiota offers interesting and challenging perspectives to decipher how the plant immune systems interact with the microbial communities' systems.
Collapse
|
4
|
Wang H. Endogenous and environmental signals in regulating vascular development and secondary growth. FRONTIERS IN PLANT SCIENCE 2024; 15:1369241. [PMID: 38628366 PMCID: PMC11018896 DOI: 10.3389/fpls.2024.1369241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 03/18/2024] [Indexed: 04/19/2024]
Affiliation(s)
- Huanzhong Wang
- Department of Plant Science & Landscape Architecture, University of Connecticut, Storrs, CT, United States
- Institute for System Genomics, University of Connecticut, Storrs, CT, United States
| |
Collapse
|
5
|
Yin Y, Jia J, He H, Zhao W, Guo Z, Chen K, Li H, He J, Ding Y, Chen W, Li J, Li Y, Zhang H, Li Z, Raboanatahiry N, Fu C, Zhang L, Yu L, Li M. BnSTINet: An experimentally-based transcription factor interaction network in seeds of Brassica napus. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:799-801. [PMID: 38217300 PMCID: PMC10955481 DOI: 10.1111/pbi.14277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 11/20/2023] [Accepted: 12/14/2023] [Indexed: 01/15/2024]
Affiliation(s)
- Yongtai Yin
- Department of Biotechnology, College of Life Science and TechnologyHuazhong University of Science and TechnologyWuhanChina
- Institute of Resource Biology and Biotechnology, College of Life Science and Technology, Huazhong University of Science and TechnologyWuhanChina
| | - Jia Jia
- Department of Biotechnology, College of Life Science and TechnologyHuazhong University of Science and TechnologyWuhanChina
- Institute of Resource Biology and Biotechnology, College of Life Science and Technology, Huazhong University of Science and TechnologyWuhanChina
| | - Hongsheng He
- Department of Biotechnology, College of Life Science and TechnologyHuazhong University of Science and TechnologyWuhanChina
- Institute of Resource Biology and Biotechnology, College of Life Science and Technology, Huazhong University of Science and TechnologyWuhanChina
| | - Weiguo Zhao
- Department of Biotechnology, College of Life Science and TechnologyHuazhong University of Science and TechnologyWuhanChina
- Institute of Resource Biology and Biotechnology, College of Life Science and Technology, Huazhong University of Science and TechnologyWuhanChina
- School of Modern Agriculture & BiotechnologyAnkang UniversityAnkangChina
| | - Zhenyi Guo
- Department of Biotechnology, College of Life Science and TechnologyHuazhong University of Science and TechnologyWuhanChina
- Institute of Resource Biology and Biotechnology, College of Life Science and Technology, Huazhong University of Science and TechnologyWuhanChina
| | - Kang Chen
- Department of Biotechnology, College of Life Science and TechnologyHuazhong University of Science and TechnologyWuhanChina
- Institute of Resource Biology and Biotechnology, College of Life Science and Technology, Huazhong University of Science and TechnologyWuhanChina
| | - Huaixin Li
- Department of Biotechnology, College of Life Science and TechnologyHuazhong University of Science and TechnologyWuhanChina
- Institute of Resource Biology and Biotechnology, College of Life Science and Technology, Huazhong University of Science and TechnologyWuhanChina
| | - Jianjie He
- Department of Biotechnology, College of Life Science and TechnologyHuazhong University of Science and TechnologyWuhanChina
- Institute of Resource Biology and Biotechnology, College of Life Science and Technology, Huazhong University of Science and TechnologyWuhanChina
| | - Yiran Ding
- Department of Biotechnology, College of Life Science and TechnologyHuazhong University of Science and TechnologyWuhanChina
- Institute of Resource Biology and Biotechnology, College of Life Science and Technology, Huazhong University of Science and TechnologyWuhanChina
| | - Wang Chen
- Department of Biotechnology, College of Life Science and TechnologyHuazhong University of Science and TechnologyWuhanChina
- Institute of Resource Biology and Biotechnology, College of Life Science and Technology, Huazhong University of Science and TechnologyWuhanChina
| | - Jingrong Li
- Department of Biotechnology, College of Life Science and TechnologyHuazhong University of Science and TechnologyWuhanChina
| | - Yujiao Li
- Department of Biotechnology, College of Life Science and TechnologyHuazhong University of Science and TechnologyWuhanChina
| | - Haikun Zhang
- Department of Biotechnology, College of Life Science and TechnologyHuazhong University of Science and TechnologyWuhanChina
| | - Zilong Li
- Department of Biotechnology, College of Life Science and TechnologyHuazhong University of Science and TechnologyWuhanChina
| | - Nadia Raboanatahiry
- Department of Biotechnology, College of Life Science and TechnologyHuazhong University of Science and TechnologyWuhanChina
- Institute of Resource Biology and Biotechnology, College of Life Science and Technology, Huazhong University of Science and TechnologyWuhanChina
| | - Chunhua Fu
- Department of Biotechnology, College of Life Science and TechnologyHuazhong University of Science and TechnologyWuhanChina
- Institute of Resource Biology and Biotechnology, College of Life Science and Technology, Huazhong University of Science and TechnologyWuhanChina
| | - Libin Zhang
- Department of Biotechnology, College of Life Science and TechnologyHuazhong University of Science and TechnologyWuhanChina
| | - Longjiang Yu
- Department of Biotechnology, College of Life Science and TechnologyHuazhong University of Science and TechnologyWuhanChina
- Institute of Resource Biology and Biotechnology, College of Life Science and Technology, Huazhong University of Science and TechnologyWuhanChina
| | - Maoteng Li
- Department of Biotechnology, College of Life Science and TechnologyHuazhong University of Science and TechnologyWuhanChina
- Institute of Resource Biology and Biotechnology, College of Life Science and Technology, Huazhong University of Science and TechnologyWuhanChina
| |
Collapse
|
6
|
Liu Q, Fu Q, Yan Y, Jiang Q, Mao L, Wang L, Yu F, Zheng H. Curation, nomenclature, and topological classification of receptor-like kinases from 528 plant species for novel domain discovery and functional inference. MOLECULAR PLANT 2024; 17:658-671. [PMID: 38384130 DOI: 10.1016/j.molp.2024.02.015] [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: 11/19/2023] [Revised: 01/25/2024] [Accepted: 02/19/2024] [Indexed: 02/23/2024]
Abstract
Receptor-like kinases (RLKs) are the most numerous signal transduction components in plants and play important roles in determining how different plants adapt to their ecological environments. Research on RLKs has focused mainly on a small number of typical RLK members in a few model plants. There is an urgent need to study the composition, distribution, and evolution of RLKs at the holistic level to increase our understanding of how RLKs assist in the ecological adaptations of different plant species. In this study, we collected the genome assemblies of 528 plant species and constructed an RLK dataset. Using this dataset, we identified and characterized 524 948 RLK family members. Each member underwent systematic topological classification and was assigned a gene ID based on a unified nomenclature system. Furthermore, we identified two novel extracellular domains in some RLKs, designated Xiao and Xiang. Evolutionary analysis of the RLK family revealed that the RLCK-XVII and RLCK-XII-2 classes were present exclusively in dicots, suggesting that diversification of RLKs between monocots and dicots may have led to differences in downstream cytoplasmic responses. We also used an interaction proteome to help empower data mining for inference of new RLK functions from a global perspective, with the ultimate goal of understanding how RLKs shape the adaptation of different plants to the environments/ecosystems. The assembled RLK dataset, together with annotations and analytical tools, forms an integrated foundation of multiomics data that is publicly accessible via the metaRLK web portal (http://metaRLK.biocloud.top).
Collapse
Affiliation(s)
- Qian Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University College of Biology, Changsha, Hunan 410082, China
| | - Qiong Fu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University College of Biology, Changsha, Hunan 410082, China
| | - Yujie Yan
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University College of Biology, Changsha, Hunan 410082, China
| | - Qian Jiang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University College of Biology, Changsha, Hunan 410082, China
| | - Longfei Mao
- Bioinformatics Center, Hunan University College of Biology, Changsha, Hunan 410082, China
| | - Long Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University College of Biology, Changsha, Hunan 410082, China
| | - Feng Yu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University College of Biology, Changsha, Hunan 410082, China.
| | - Heping Zheng
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University College of Biology, Changsha, Hunan 410082, China; Bioinformatics Center, Hunan University College of Biology, Changsha, Hunan 410082, China.
| |
Collapse
|
7
|
Tanarsuwongkul S, Fisher KW, Mullis BT, Negi H, Roberts J, Tomlin F, Wang Q, Stratmann JW. Green leaf volatiles co-opt proteins involved in molecular pattern signalling in plant cells. PLANT, CELL & ENVIRONMENT 2024; 47:928-946. [PMID: 38164082 DOI: 10.1111/pce.14795] [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: 07/18/2023] [Revised: 11/27/2023] [Accepted: 12/13/2023] [Indexed: 01/03/2024]
Abstract
The green leaf volatiles (GLVs) Z-3-hexen-1-ol (Z3-HOL) and Z-3-hexenyl acetate (Z3-HAC) are airborne infochemicals released from damaged plant tissues that induce defenses and developmental responses in receiver plants, but little is known about their mechanism of action. We found that Z3-HOL and Z3-HAC induce similar but distinctive physiological and signaling responses in tomato seedlings and cell cultures. In seedlings, Z3-HAC showed a stronger root growth inhibition effect than Z3-HOL. In cell cultures, the two GLVs induced distinct changes in MAP kinase (MAPK) activity and proton fluxes as well as rapid and massive changes in the phosphorylation status of proteins within 5 min. Many of these phosphoproteins are involved in reprogramming the proteome from cellular homoeostasis to stress and include pattern recognition receptors, a receptor-like cytoplasmic kinase, MAPK cascade components, calcium signaling proteins and transcriptional regulators. These are well-known components of damage-associated molecular pattern (DAMP) signaling pathways. These rapid changes in the phosphoproteome may underly the activation of defense and developmental responses to GLVs. Our data provide further evidence that GLVs function like DAMPs and indicate that GLVs coopt DAMP signaling pathways.
Collapse
Affiliation(s)
| | - Kirsten W Fisher
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina, USA
| | - B Todd Mullis
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina, USA
- IMCS, Irmo, South Carolina, USA
| | - Harshita Negi
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina, USA
| | - Jamie Roberts
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina, USA
| | - Fallon Tomlin
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina, USA
| | - Qiang Wang
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina, USA
| | - Johannes W Stratmann
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina, USA
| |
Collapse
|
8
|
Liang J, Lu L, Zhou H, Fang J, Zhao Y, Hou H, Chen L, Cao C, Yang D, Diao Z, Tang D, Li S. Receptor-like kinases OsRLK902-1 and OsRLK902-2 form immune complexes with OsRLCK185 to regulate rice blast resistance. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:1565-1579. [PMID: 37976240 DOI: 10.1093/jxb/erad460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 11/16/2023] [Indexed: 11/19/2023]
Abstract
Receptor-like kinases (RLKs) are major regulators of the plant immune response and play important roles in the perception and transmission of immune signals. RECEPTOR LIKE KINASE 902 (RLK902) is at the key node in leucine-rich repeat receptor-like kinase interaction networks and positively regulates resistance to the bacterial pathogen Pseudomonas syringae in Arabidopsis. However, the function of RLK902 in fungal disease resistance remains obscure. In this study, we found that the expression levels of OsRLK902-1 and OsRLK902-2, encoding two orthologues of RLK902 in rice, were induced by Magnaporthe oryzae, chitin, and flg22 treatment. osrlk902-1 and osrlk902-2 knockout mutants displayed enhanced susceptibility to M. oryzae. Interestingly, the osrlk902-1 rlk902-2 double mutant exhibited similar disease susceptibility, hydrogen peroxide production, and callose deposition to the two single mutants. Further investigation showed that OsRLK902-1 interacts with and stabilizes OsRLK902-2. The two OsRLKs form a complex with OsRLCK185, a key regulator in chitin-triggered immunity, and stabilize it. Taken together, our data demonstrate that OsRLK902-1 and OsRLK902-2, as well as OsRLCK185 function together in regulating disease resistance to M. oryzae in rice.
Collapse
Affiliation(s)
- Jiahui Liang
- State Key Laboratory of Ecological Control of Fujian-Taiwan Crop Pests, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Plant Immunity Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ling Lu
- State Key Laboratory of Ecological Control of Fujian-Taiwan Crop Pests, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Plant Immunity Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Houli Zhou
- State Key Laboratory of Ecological Control of Fujian-Taiwan Crop Pests, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Plant Immunity Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jianbo Fang
- State Key Laboratory of Ecological Control of Fujian-Taiwan Crop Pests, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Plant Immunity Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yaofei Zhao
- College of Agriculture, Shanxi Agricultural University, Taigu, Shanxi 030801, China
| | - Hongna Hou
- State Key Laboratory of Ecological Control of Fujian-Taiwan Crop Pests, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Plant Immunity Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Lizhe Chen
- State Key Laboratory of Ecological Control of Fujian-Taiwan Crop Pests, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Plant Immunity Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Chang Cao
- State Key Laboratory of Ecological Control of Fujian-Taiwan Crop Pests, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Plant Immunity Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Dewei Yang
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, 350019, China
| | - Zhijuan Diao
- State Key Laboratory of Ecological Control of Fujian-Taiwan Crop Pests, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Plant Immunity Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Dingzhong Tang
- State Key Laboratory of Ecological Control of Fujian-Taiwan Crop Pests, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Plant Immunity Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shengping Li
- State Key Laboratory of Ecological Control of Fujian-Taiwan Crop Pests, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Plant Immunity Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, China
| |
Collapse
|
9
|
Sistenich AJ, Fürtauer L, Scheele F, Conrath U. Marker and readout genes for defense priming in Pseudomonas cannabina pv. alisalensis interaction aid understanding systemic immunity in Arabidopsis. Sci Rep 2024; 14:3489. [PMID: 38347062 PMCID: PMC10861594 DOI: 10.1038/s41598-024-53982-5] [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: 09/29/2023] [Accepted: 02/07/2024] [Indexed: 02/15/2024] Open
Abstract
Following localized infection, the entire plant foliage becomes primed for enhanced defense. However, specific genes induced during defense priming (priming-marker genes) and those showing increased expression in defense-primed plants upon rechallenge (priming-readout genes) remain largely unknown. In our Arabidopsis thaliana study, genes AT1G76960 (function unknown), CAX3 (encoding a vacuolar Ca2+/H+ antiporter), and CRK4 (encoding a cysteine-rich receptor-like protein kinase) were strongly expressed during Pseudomonas cannabina pv. alisalensis-induced defense priming, uniquely marking the primed state for enhanced defense. Conversely, PR1 (encoding a pathogenesis-related protein), RLP23 and RLP41 (both encoding receptor-like proteins) were similarly activated in defense-primed plants before and after rechallenge, suggesting they are additional marker genes for defense priming. In contrast, CASPL4D1 (encoding Casparian strip domain-like protein 4D1), FRK1 (encoding flg22-induced receptor-like kinase), and AT3G28510 (encoding a P loop-containing nucleoside triphosphate hydrolases superfamily protein) showed minimal activation in uninfected, defense-primed, or rechallenged plants, but intensified in defense-primed plants after rechallenge. Notably, mutation in only priming-readout gene NHL25 (encoding NDR1/HIN1-like protein 25) impaired both defense priming and systemic acquired resistance, highlighting its previously undiscovered pivotal role in systemic plant immunity.
Collapse
Affiliation(s)
- Andrea J Sistenich
- Plant Biochemistry and Molecular Biology Group, Department of Plant Physiology, RWTH Aachen University, 52062, Aachen, Germany
| | - Lisa Fürtauer
- Plant Molecular Systems Biology Group, Department of Plant Physiology, RWTH Aachen University, 52062, Aachen, Germany
| | - Franziska Scheele
- Plant Biochemistry and Molecular Biology Group, Department of Plant Physiology, RWTH Aachen University, 52062, Aachen, Germany
| | - Uwe Conrath
- Plant Biochemistry and Molecular Biology Group, Department of Plant Physiology, RWTH Aachen University, 52062, Aachen, Germany.
| |
Collapse
|
10
|
Watkins JM, Montes C, Clark NM, Song G, Oliveira CC, Mishra B, Brachova L, Seifert CM, Mitchell MS, Yang J, Braga Dos Reis PA, Urano D, Muktar MS, Walley JW, Jones AM. Phosphorylation Dynamics in a flg22-Induced, G Protein-Dependent Network Reveals the AtRGS1 Phosphatase. Mol Cell Proteomics 2024; 23:100705. [PMID: 38135118 PMCID: PMC10837098 DOI: 10.1016/j.mcpro.2023.100705] [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: 04/03/2023] [Revised: 11/22/2023] [Accepted: 12/19/2023] [Indexed: 12/24/2023] Open
Abstract
The microbe-associated molecular pattern flg22 is recognized in a flagellin-sensitive 2-dependent manner in root tip cells. Here, we show a rapid and massive change in protein abundance and phosphorylation state of the Arabidopsis root cell proteome in WT and a mutant deficient in heterotrimeric G-protein-coupled signaling. flg22-induced changes fall on proteins comprising a subset of this proteome, the heterotrimeric G protein interactome, and on highly-populated hubs of the immunity network. Approximately 95% of the phosphorylation changes in the heterotrimeric G-protein interactome depend, at least partially, on a functional G protein complex. One member of this interactome is ATBα, a substrate-recognition subunit of a protein phosphatase 2A complex and an interactor to Arabidopsis thaliana Regulator of G Signaling 1 protein (AtRGS1), a flg22-phosphorylated, 7-transmembrane spanning modulator of the nucleotide-binding state of the core G-protein complex. A null mutation of ATBα strongly increases basal endocytosis of AtRGS1. AtRGS1 steady-state protein level is lower in the atbα mutant in a proteasome-dependent manner. We propose that phosphorylation-dependent endocytosis of AtRGS1 is part of the mechanism to degrade AtRGS1, thus sustaining activation of the heterotrimeric G protein complex required for the regulation of system dynamics in innate immunity. The PP2A(ATBα) complex is a critical regulator of this signaling pathway.
Collapse
Affiliation(s)
- Justin M Watkins
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Christian Montes
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa, USA
| | - Natalie M Clark
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa, USA
| | - Gaoyuan Song
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa, USA
| | - Celio Cabral Oliveira
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; Department of Biochemistry and Molecular Biology/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Bharat Mishra
- Department of Biology, University of Alabama-Birmingham, Birmingham, Alabama, USA
| | - Libuse Brachova
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, USA
| | - Clara M Seifert
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Malek S Mitchell
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jing Yang
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | | | - Daisuke Urano
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - M Shahid Muktar
- Department of Biology, University of Alabama-Birmingham, Birmingham, Alabama, USA
| | - Justin W Walley
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa, USA.
| | - Alan M Jones
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
| |
Collapse
|
11
|
Fontes EPB. SERKs and NIKs: Coreceptors or signaling hubs in a complex crosstalk between growth and defense? CURRENT OPINION IN PLANT BIOLOGY 2024; 77:102447. [PMID: 37690927 DOI: 10.1016/j.pbi.2023.102447] [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: 06/12/2023] [Revised: 08/01/2023] [Accepted: 08/14/2023] [Indexed: 09/12/2023]
Abstract
SOMATIC EMBRYOGENESIS RECEPTOR-LIKE KINASES (SERKs) and NUCLEAR SHUTTLE PROTEIN-INTERACTING KINASES (NIKs) belong to superfamily II of leucine-rich repeat receptor-like kinases, which share cytosolic kinase conservation and a similar ectodomain configuration. SERKs have been extensively demonstrated to function as coreceptors of receptor-like kinases, which sense biotic or developmental signals to initiate specific responses. NIKs, on the other hand, have emerged as downstream components in signaling cascades, not functioning as coreceptors but rather serving as hubs that converge information from both biotic and abiotic signals, resulting in a unified response. Like SERKs, NIKs play a crucial role as information spreaders in plant cells, forming hubs of high centrality. However, unlike SERKs, which function as coreceptors and assemble paired receptor-specific responses, NIKs employ a shared signaling circuit to transduce diverse biotic and abiotic signals into the same physiological response. Therefore, this review highlights the concept of signaling hubs that differ from coreceptors in signaling pathways.
Collapse
Affiliation(s)
- Elizabeth P B Fontes
- Biochemistry and Molecular Biology Department, Bioagro, Universidade Federal de Viçosa, 36570.000, Viçosa, MG, Brazil.
| |
Collapse
|
12
|
Liu J, Li W, Wu G, Ali K. An update on evolutionary, structural, and functional studies of receptor-like kinases in plants. FRONTIERS IN PLANT SCIENCE 2024; 15:1305599. [PMID: 38362444 PMCID: PMC10868138 DOI: 10.3389/fpls.2024.1305599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 01/03/2024] [Indexed: 02/17/2024]
Abstract
All living organisms must develop mechanisms to cope with and adapt to new environments. The transition of plants from aquatic to terrestrial environment provided new opportunities for them to exploit additional resources but made them vulnerable to harsh and ever-changing conditions. As such, the transmembrane receptor-like kinases (RLKs) have been extensively duplicated and expanded in land plants, increasing the number of RLKs in the advanced angiosperms, thus becoming one of the largest protein families in eukaryotes. The basic structure of the RLKs consists of a variable extracellular domain (ECD), a transmembrane domain (TM), and a conserved kinase domain (KD). Their variable ECDs can perceive various kinds of ligands that activate the conserved KD through a series of auto- and trans-phosphorylation events, allowing the KDs to keep the conserved kinase activities as a molecular switch that stabilizes their intracellular signaling cascades, possibly maintaining cellular homeostasis as their advantages in different environmental conditions. The RLK signaling mechanisms may require a coreceptor and other interactors, which ultimately leads to the control of various functions of growth and development, fertilization, and immunity. Therefore, the identification of new signaling mechanisms might offer a unique insight into the regulatory mechanism of RLKs in plant development and adaptations. Here, we give an overview update of recent advances in RLKs and their signaling mechanisms.
Collapse
Affiliation(s)
| | | | - Guang Wu
- College of Life Sciences, Shaanxi Normal University, Xi’an, China
| | - Khawar Ali
- College of Life Sciences, Shaanxi Normal University, Xi’an, China
| |
Collapse
|
13
|
Abukhalaf M, Proksch C, Thieme D, Ziegler J, Hoehenwarter W. Changing turn-over rates regulate abundance of tryptophan, GS biosynthesis, IAA transport and photosynthesis proteins in Arabidopsis growth defense transitions. BMC Biol 2023; 21:249. [PMID: 37940940 PMCID: PMC10634109 DOI: 10.1186/s12915-023-01739-3] [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: 06/29/2023] [Accepted: 10/16/2023] [Indexed: 11/10/2023] Open
Abstract
BACKGROUND Shifts in dynamic equilibria of the abundance of cellular molecules in plant-pathogen interactions need further exploration. We induced PTI in optimally growing Arabidopsis thaliana seedlings for 16 h, returning them to growth conditions for another 16 h. METHODS Turn-over and abundance of 99 flg22 responding proteins were measured chronologically using a stable heavy nitrogen isotope partial labeling strategy and targeted liquid chromatography coupled to mass spectrometry (PRM LC-MS). These experiments were complemented by measurements of mRNA and phytohormone levels. RESULTS Changes in synthesis and degradation rate constants (Ks and Kd) regulated tryptophane and glucosinolate, IAA transport, and photosynthesis-associated protein (PAP) homeostasis in growth/PTI transitions independently of mRNA levels. Ks values increased after elicitation while protein and mRNA levels became uncorrelated. mRNA returned to pre-elicitation levels, yet protein abundance remained at PTI levels even 16 h after media exchange, indicating protein levels were robust and unresponsive to transition back to growth. The abundance of 23 PAPs including FERREDOXIN-NADP( +)-OXIDOREDUCTASE (FNR1) decreased 16 h after PAMP exposure, their depletion was nearly abolished in the myc234 mutant. FNR1 Kd increased as mRNA levels decreased early in PTI, its Ks decreased in prolonged PTI. FNR1 Kd was lower in myc234, mRNA levels decreased as in wild type. CONCLUSIONS Protein Kd and Ks values change in response to flg22 exposure and constitute an additional layer of protein abundance regulation in growth defense transitions next to changes in mRNA levels. Our results suggest photosystem remodeling in PTI to direct electron flow away from the photosynthetic carbon reaction towards ROS production as an active defense mechanism controlled post-transcriptionally and by MYC2 and homologs. Target proteins accumulated later and PAP and auxin/IAA depletion was repressed in myc234 indicating a positive effect of the transcription factors in the establishment of PTI.
Collapse
Affiliation(s)
- Mohammad Abukhalaf
- Present address: Institute for Experimental Medicine, Christian-Albrechts University Kiel, Niemannsweg 11, 24105, Kiel, Germany
- Department Biochemistry of Plant Interactions, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06122, Halle (Saale), Germany
| | - Carsten Proksch
- Department Biochemistry of Plant Interactions, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06122, Halle (Saale), Germany
| | - Domenika Thieme
- Department Biochemistry of Plant Interactions, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06122, Halle (Saale), Germany
| | - Jörg Ziegler
- Department Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06122, Halle (Saale), Germany
| | - Wolfgang Hoehenwarter
- Department Biochemistry of Plant Interactions, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06122, Halle (Saale), Germany.
| |
Collapse
|
14
|
Arnaiz A, Romero-Puertas MC, Santamaria ME, Rosa-Diaz I, Arbona V, Muñoz A, Grbic V, González-Melendi P, Mar Castellano M, Sandalio LM, Martinez M, Diaz I. The Arabidopsis thioredoxin TRXh5regulates the S-nitrosylation pattern of the TIRK receptor being both proteins essential in the modulation of defences to Tetranychus urticae. Redox Biol 2023; 67:102902. [PMID: 37797370 PMCID: PMC10622877 DOI: 10.1016/j.redox.2023.102902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 09/08/2023] [Accepted: 09/21/2023] [Indexed: 10/07/2023] Open
Abstract
The interaction between plants and phytophagous arthropods encompasses a complex network of molecules, signals, and pathways to overcome defences generated by each interacting organism. Although most of the elements and modulators involved in this interplay are still unidentified, plant redox homeostasis and signalling are essential for the establishment of defence responses. Here, focusing on the response of Arabidopsis thaliana to the spider mite Tetranychus urticae, we demonstrate the involvement in plant defence of the thioredoxin TRXh5, a small redox protein whose expression is induced by mite infestation. TRXh5 is localized in the cell membrane system and cytoplasm and is associated with alterations in the content of reactive oxygen and nitrogen species. Protein S-nitrosylation signal in TRXh5 over-expression lines is decreased and alteration in TRXh5 level produces changes in the JA/SA hormonal crosstalk of infested plants. Moreover, TRXh5 interacts and likely regulates the redox state of an uncharacterized receptor-like kinase, named THIOREDOXIN INTERACTING RECEPTOR KINASE (TIRK), also induced by mite herbivory. Feeding bioassays performed withTRXh5 over-expression plants result in lower leaf damage and reduced egg accumulation after T. urticae infestation than in wild-type (WT) plants. In contrast, mites cause a more severe injury in trxh5 mutant lines where a greater number of eggs accumulates. Likewise, analysis of TIRK-gain and -loss-of-function lines demonstrate the defence role of this receptor in Arabidopsis against T. urticae. Altogether, our findings demonstrate the interaction between TRXh5 and TIRK and highlight the importance of TRXh5 and TIRK in the establishment of effective Arabidopsis defences against spider mite herbivory.
Collapse
Affiliation(s)
- Ana Arnaiz
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria/CSIC, Campus de Montegancedo, 20223, Madrid, Spain.
| | - Maria C Romero-Puertas
- Department of Biochemistry and Molecular and Cellular Biology of Plants, Estación Experimental del Zaidín, CSIC, Granada, Spain.
| | - M Estrella Santamaria
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria/CSIC, Campus de Montegancedo, 20223, Madrid, Spain.
| | - Irene Rosa-Diaz
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria/CSIC, Campus de Montegancedo, 20223, Madrid, Spain.
| | - Vicent Arbona
- Departament de Biologia, Bioquímica i Ciències Naturals, Universitat Jaume I, E-12071, Castelló de la Plana, Spain.
| | - Alfonso Muñoz
- Departamento de Sistemas y Recursos Naturales. Escuela Técnica Superior de Ingeniería de Montes, Forestal y del Medio Natural, UPM, Madrid, Spain.
| | - Vojislava Grbic
- Department of Biology, University of Western Ontario, N6A 5BT, London, Ontario, Canada.
| | - Pablo González-Melendi
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria/CSIC, Campus de Montegancedo, 20223, Madrid, Spain; Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, UPM, Madrid, Spain.
| | - M Mar Castellano
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria/CSIC, Campus de Montegancedo, 20223, Madrid, Spain.
| | - Luisa Maria Sandalio
- Department of Biochemistry and Molecular and Cellular Biology of Plants, Estación Experimental del Zaidín, CSIC, Granada, Spain.
| | - Manuel Martinez
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria/CSIC, Campus de Montegancedo, 20223, Madrid, Spain; Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, UPM, Madrid, Spain.
| | - Isabel Diaz
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria/CSIC, Campus de Montegancedo, 20223, Madrid, Spain; Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, UPM, Madrid, Spain.
| |
Collapse
|
15
|
Zhou D, Chen X, Chen X, Xia Y, Liu J, Zhou G. Plant immune receptors interact with hemibiotrophic pathogens to activate plant immunity. Front Microbiol 2023; 14:1252039. [PMID: 37876778 PMCID: PMC10591190 DOI: 10.3389/fmicb.2023.1252039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 09/20/2023] [Indexed: 10/26/2023] Open
Abstract
Phytopathogens pose a devastating threat to the productivity and yield of crops by causing destructive plant diseases in natural and agricultural environments. Hemibiotrophic pathogens have a variable-length biotrophic phase before turning to necrosis and are among the most invasive plant pathogens. Plant resistance to hemibiotrophic pathogens relies mainly on the activation of innate immune responses. These responses are typically initiated after the plant plasma membrane and various plant immune receptors detect immunogenic signals associated with pathogen infection. Hemibiotrophic pathogens evade pathogen-triggered immunity by masking themselves in an arms race while also enhancing or manipulating other receptors to promote virulence. However, our understanding of plant immune defenses against hemibiotrophic pathogens is highly limited due to the intricate infection mechanisms. In this review, we summarize the strategies that different hemibiotrophic pathogens interact with host immune receptors to activate plant immunity. We also discuss the significant role of the plasma membrane in plant immune responses, as well as the current obstacles and potential future research directions in this field. This will enable a more comprehensive understanding of the pathogenicity of hemibiotrophic pathogens and how distinct plant immune receptors oppose them, delivering valuable data for the prevention and management of plant diseases.
Collapse
Affiliation(s)
- Diao Zhou
- Key Laboratory of National Forestry and Grassland Administration on Control of Artificial Forest Diseases and Pests in South China, Central South University of Forestry and Technology, Changsha, China
- Hunan Provincial Key Laboratory for Control of Forest Diseases and Pests, Central South University of Forestry and Technology, Changsha, China
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, China
| | - Xingzhou Chen
- Key Laboratory of National Forestry and Grassland Administration on Control of Artificial Forest Diseases and Pests in South China, Central South University of Forestry and Technology, Changsha, China
- Hunan Provincial Key Laboratory for Control of Forest Diseases and Pests, Central South University of Forestry and Technology, Changsha, China
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, China
| | - Xinggang Chen
- Key Laboratory of National Forestry and Grassland Administration on Control of Artificial Forest Diseases and Pests in South China, Central South University of Forestry and Technology, Changsha, China
- Hunan Provincial Key Laboratory for Control of Forest Diseases and Pests, Central South University of Forestry and Technology, Changsha, China
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, China
| | - Yandong Xia
- Key Laboratory of National Forestry and Grassland Administration on Control of Artificial Forest Diseases and Pests in South China, Central South University of Forestry and Technology, Changsha, China
- Hunan Provincial Key Laboratory for Control of Forest Diseases and Pests, Central South University of Forestry and Technology, Changsha, China
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, China
| | - Junang Liu
- Key Laboratory of National Forestry and Grassland Administration on Control of Artificial Forest Diseases and Pests in South China, Central South University of Forestry and Technology, Changsha, China
- Hunan Provincial Key Laboratory for Control of Forest Diseases and Pests, Central South University of Forestry and Technology, Changsha, China
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, China
| | - Guoying Zhou
- Key Laboratory of National Forestry and Grassland Administration on Control of Artificial Forest Diseases and Pests in South China, Central South University of Forestry and Technology, Changsha, China
- Hunan Provincial Key Laboratory for Control of Forest Diseases and Pests, Central South University of Forestry and Technology, Changsha, China
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, China
| |
Collapse
|
16
|
Contreras MP, Lüdke D, Pai H, Toghani A, Kamoun S. NLR receptors in plant immunity: making sense of the alphabet soup. EMBO Rep 2023; 24:e57495. [PMID: 37602936 PMCID: PMC10561179 DOI: 10.15252/embr.202357495] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 07/22/2023] [Accepted: 08/03/2023] [Indexed: 08/22/2023] Open
Abstract
Plants coordinately use cell-surface and intracellular immune receptors to perceive pathogens and mount an immune response. Intracellular events of pathogen recognition are largely mediated by immune receptors of the nucleotide binding and leucine rich-repeat (NLR) classes. Upon pathogen perception, NLRs trigger a potent broad-spectrum immune reaction, usually accompanied by a form of programmed cell death termed the hypersensitive response. Some plant NLRs act as multifunctional singleton receptors which combine pathogen detection and immune signaling. However, NLRs can also function in higher order pairs and networks of functionally specialized interconnected receptors. In this article, we cover the basic aspects of plant NLR biology with an emphasis on NLR networks. We highlight some of the recent advances in NLR structure, function, and activation and discuss emerging topics such as modulator NLRs, pathogen suppression of NLRs, and NLR bioengineering. Multi-disciplinary approaches are required to disentangle how these NLR immune receptor pairs and networks function and evolve. Answering these questions holds the potential to deepen our understanding of the plant immune system and unlock a new era of disease resistance breeding.
Collapse
Affiliation(s)
| | - Daniel Lüdke
- The Sainsbury LaboratoryUniversity of East AngliaNorwichUK
| | - Hsuan Pai
- The Sainsbury LaboratoryUniversity of East AngliaNorwichUK
| | | | - Sophien Kamoun
- The Sainsbury LaboratoryUniversity of East AngliaNorwichUK
| |
Collapse
|
17
|
Demirjian C, Razavi N, Yu G, Mayjonade B, Zhang L, Lonjon F, Chardon F, Carrere S, Gouzy J, Genin S, Macho AP, Roux F, Berthomé R, Vailleau F. An atypical NLR gene confers bacterial wilt susceptibility in Arabidopsis. PLANT COMMUNICATIONS 2023; 4:100607. [PMID: 37098653 PMCID: PMC10504594 DOI: 10.1016/j.xplc.2023.100607] [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: 07/29/2022] [Revised: 01/19/2023] [Accepted: 04/20/2023] [Indexed: 06/12/2023]
Abstract
Quantitative disease resistance (QDR) remains the most prevalent form of plant resistance in crop fields and wild habitats. Genome-wide association studies (GWAS) have proved to be successful in deciphering the quantitative genetic basis of complex traits such as QDR. To unravel the genetics of QDR to the devastating worldwide bacterial pathogen Ralstonia solanacearum, we performed a GWAS by challenging a highly polymorphic local mapping population of Arabidopsis thaliana with four R. solanacearum type III effector (T3E) mutants, identified as key pathogenicity determinants after a first screen on an A. thaliana core collection of 25 accessions. Although most quantitative trait loci (QTLs) were highly specific to the identity of the T3E mutant (ripAC, ripAG, ripAQ, and ripU), we finely mapped a common QTL located on a cluster of nucleotide-binding domain and leucine-rich repeat (NLR) genes that exhibited structural variation. We functionally validated one of these NLRs as a susceptibility factor in response to R. solanacearum, named it Bacterial Wilt Susceptibility 1 (BWS1), and cloned two alleles that conferred contrasting levels of QDR. Further characterization indicated that expression of BWS1 leads to suppression of immunity triggered by different R. solanacearum effectors. In addition, we showed a direct interaction between BWS1 and RipAC T3E, and BWS1 and SUPPRESSOR OF G2 ALLELE OF skp1 (SGT1b), the latter interaction being suppressed by RipAC. Together, our results highlight a putative role for BWS1 as a quantitative susceptibility factor directly targeted by the T3E RipAC, mediating negative regulation of the SGT1-dependent immune response.
Collapse
Affiliation(s)
- Choghag Demirjian
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Narjes Razavi
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Gang Yu
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | | | - Lu Zhang
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Fabien Lonjon
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Fabien Chardon
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France
| | - Sébastien Carrere
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Jérome Gouzy
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Stéphane Genin
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Alberto P Macho
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Fabrice Roux
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Richard Berthomé
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Fabienne Vailleau
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France.
| |
Collapse
|
18
|
Liu F, Zeng M, Sun Y, Chen Z, Chen Z, Wang L, Cui JR, Zhang F, Lv D, Chen X, Xu Y, Duan KX, Wang Y, Wang Y. BAK1 protects the receptor-like kinase BIR2 from SNIPER2a/b-mediated degradation to promote pattern-triggered immunity in Nicotiana benthamiana. THE PLANT CELL 2023; 35:3566-3584. [PMID: 37378590 PMCID: PMC10473216 DOI: 10.1093/plcell/koad187] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 05/16/2023] [Accepted: 06/01/2023] [Indexed: 06/29/2023]
Abstract
The detection of microbial infections by plants induces the rapid formation of immune receptor complexes at the plasma membrane. However, how this process is controlled to ensure proper immune signaling remains largely unknown. Here, we found that the Nicotiana benthamiana membrane-localized leucine-rich repeat receptor-like kinase BAK1-INTERACTING RLK 2 (NbBIR2) constitutively associates with BRI1-ASSOCIATED RECEPTOR KINASE 1 (NbBAK1) in vivo and in vitro and promotes complex formation with pattern recognition receptors. In addition, NbBIR2 is targeted by 2 RING-type ubiquitin E3 ligases, SNC1-INFLUENCING PLANT E3 LIGASE REVERSE 2a (NbSNIPER2a) and NbSNIPER2b, for ubiquitination and subsequent degradation in planta. NbSNIPER2a and NbSNIPER2b interact with NbBIR2 in vivo and in vitro and are released from NbBIR2 upon treatment with different microbial patterns. Furthermore, accumulation of NbBIR2 in response to microbial patterns is tightly associated with NbBAK1 abundance in N. benthamiana. NbBAK1 acts as a modular protein that stabilizes NbBIR2 by competing with NbSNIPER2a or NbSNIPER2b for association with NbBIR2. Similar to NbBAK1, NbBIR2 positively regulates pattern-triggered immunity and resistance to bacterial and oomycete pathogens in N. benthamiana, whereas NbSNIPER2a and NbSNIPER2b have the opposite effect. Together, these results reveal a feedback regulatory mechanism employed by plants to tailor pattern-triggered immune signaling.
Collapse
Affiliation(s)
- Fan Liu
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs), Nanjing Agricultural University, Nanjing 210095, China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing 210095, China
| | - Mengzhu Zeng
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs), Nanjing Agricultural University, Nanjing 210095, China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing 210095, China
| | - Yujing Sun
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs), Nanjing Agricultural University, Nanjing 210095, China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhiyuan Chen
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs), Nanjing Agricultural University, Nanjing 210095, China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhaodan Chen
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs), Nanjing Agricultural University, Nanjing 210095, China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing 210095, China
| | - Lei Wang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs), Nanjing Agricultural University, Nanjing 210095, China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing 210095, China
| | - Jia-Rong Cui
- Department of Entomology, Nanjing Agricultural University, Nanjing 210095, China
| | - Fushuang Zhang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs), Nanjing Agricultural University, Nanjing 210095, China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing 210095, China
| | - Di Lv
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs), Nanjing Agricultural University, Nanjing 210095, China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing 210095, China
| | - Xue Chen
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs), Nanjing Agricultural University, Nanjing 210095, China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing 210095, China
| | - Yuanpeng Xu
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs), Nanjing Agricultural University, Nanjing 210095, China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing 210095, China
| | - Kai-Xuan Duan
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs), Nanjing Agricultural University, Nanjing 210095, China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing 210095, China
| | - Yan Wang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs), Nanjing Agricultural University, Nanjing 210095, China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing 210095, China
| | - Yuanchao Wang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs), Nanjing Agricultural University, Nanjing 210095, China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing 210095, China
| |
Collapse
|
19
|
Laflamme B. Functional divergence of an immune receptor complex in Nicotiana benthamiana. THE PLANT CELL 2023; 35:3394-3395. [PMID: 37382479 PMCID: PMC10473192 DOI: 10.1093/plcell/koad186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 06/20/2023] [Indexed: 06/30/2023]
Affiliation(s)
- Bradley Laflamme
- Assistant Features Editor, The Plant Cell, American Society of Plant Biologists, USA
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| |
Collapse
|
20
|
Pei Y, Ji P, Si J, Zhao H, Zhang S, Xu R, Qiao H, Duan W, Shen D, Yin Z, Dou D. A Phytophthora receptor-like kinase regulates oospore development and can activate pattern-triggered plant immunity. Nat Commun 2023; 14:4593. [PMID: 37524729 PMCID: PMC10390575 DOI: 10.1038/s41467-023-40171-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 07/05/2023] [Indexed: 08/02/2023] Open
Abstract
Plant cell-surface leucine-rich repeat receptor-like kinases (LRR-RLKs) and receptor-like proteins (LRR-RLPs) form dynamic complexes to receive a variety of extracellular signals. LRR-RLKs are also widespread in oomycete pathogens, whereas it remains enigmatic whether plant and oomycete LRR-RLKs could mediate cell-to-cell communications between pathogen and host. Here, we report that an LRR-RLK from the soybean root and stem rot pathogen Phytophthora sojae, PsRLK6, can activate typical pattern-triggered immunity in host soybean and nonhost tomato and Nicotiana benthamiana plants. PsRLK6 homologs are conserved in oomycetes and also exhibit immunity-inducing activity. A small region (LRR5-6) in the extracellular domain of PsRLK6 is sufficient to activate BAK1- and SOBIR1-dependent immune responses, suggesting that PsRLK6 is likely recognized by a plant LRR-RLP. Moreover, PsRLK6 is shown to be up-regulated during oospore maturation and essential for the oospore development of P. sojae. Our data provide a novel type of microbe-associated molecular pattern that functions in the sexual reproduction of oomycete, and a scenario in which a pathogen LRR-RLK could be sensed by a plant LRR-RLP to mount plant immunity.
Collapse
Affiliation(s)
- Yong Pei
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Peiyun Ji
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jierui Si
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hanqing Zhao
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Sicong Zhang
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ruofei Xu
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Huijun Qiao
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Weiwei Duan
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Danyu Shen
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhiyuan Yin
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Daolong Dou
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China.
- Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, 210095, China.
| |
Collapse
|
21
|
Lecona AM, Nanjareddy K, Blanco L, Piazza V, Vera-Núñez JA, Lara M, Arthikala MK. CRK12: A Key Player in Regulating the Phaseolus vulgaris- Rhizobium tropici Symbiotic Interaction. Int J Mol Sci 2023; 24:11720. [PMID: 37511479 PMCID: PMC10380779 DOI: 10.3390/ijms241411720] [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: 06/16/2023] [Revised: 07/16/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023] Open
Abstract
Cysteine-rich receptor-like kinases (CRKs) are a type of receptor-like kinases (RLKs) that are important for pathogen resistance, extracellular reactive oxygen species (ROS) signaling, and programmed cell death in plants. In a previous study, we identified 46 CRK family members in the Phaseolus vulgaris genome and found that CRK12 was highly upregulated under root nodule symbiotic conditions. To better understand the role of CRK12 in the Phaseolus-Rhizobia symbiotic interaction, we functionally characterized this gene by overexpressing (CRK12-OE) and silencing (CRK12-RNAi) it in a P. vulgaris hairy root system. We found that the constitutive expression of CRK12 led to an increase in root hair length and the expression of root hair regulatory genes, while silencing the gene had the opposite effect. During symbiosis, CRK12-RNAi resulted in a significant reduction in nodule numbers, while CRK12-OE roots showed a dramatic increase in rhizobial infection threads and the number of nodules. Nodule cross sections revealed that silenced nodules had very few infected cells, while CRK12-OE nodules had enlarged infected cells, whose numbers had increased compared to controls. As expected, CRK12-RNAi negatively affected nitrogen fixation, while CRK12-OE nodules fixed 1.5 times more nitrogen than controls. Expression levels of genes involved in symbiosis and ROS signaling, as well as nitrogen export genes, supported the nodule phenotypes. Moreover, nodule senescence was prolonged in CRK12-overexpressing roots. Subcellular localization assays showed that the PvCRK12 protein localized to the plasma membrane, and the spatiotemporal expression patterns of the CRK12-promoter::GUS-GFP analysis revealed a symbiosis-specific expression of CRK12 during the early stages of rhizobial infection and in the development of nodules. Our findings suggest that CRK12, a membrane RLK, is a novel regulator of Phaseolus vulgaris-Rhizobium tropici symbiosis.
Collapse
Affiliation(s)
- Antonino M Lecona
- Ciencias Agrogenómicas, Escuela Nacional de Estudios Superiores Unidad León, Universidad Nacional Autónoma de México (UNAM), León 37689, GTO, Mexico
| | - Kalpana Nanjareddy
- Ciencias Agrogenómicas, Escuela Nacional de Estudios Superiores Unidad León, Universidad Nacional Autónoma de México (UNAM), León 37689, GTO, Mexico
| | - Lourdes Blanco
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Cuernavaca 62210, MOR, Mexico
| | - Valeria Piazza
- Centro de Investigaciones en Óptica A. C., Loma del Bosque 115, León 37150, GTO, Mexico
| | - José Antonio Vera-Núñez
- Departamento Biotecnología, Centro de Investigación y de Estudios Avanzados, Unidad Irapuato, Irapuato 36821, GTO, Mexico
| | - Miguel Lara
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Cuernavaca 62210, MOR, Mexico
| | - Manoj-Kumar Arthikala
- Ciencias Agrogenómicas, Escuela Nacional de Estudios Superiores Unidad León, Universidad Nacional Autónoma de México (UNAM), León 37689, GTO, Mexico
| |
Collapse
|
22
|
Bender KW, Zipfel C. Paradigms of receptor kinase signaling in plants. Biochem J 2023; 480:835-854. [PMID: 37326386 PMCID: PMC10317173 DOI: 10.1042/bcj20220372] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 06/02/2023] [Accepted: 06/05/2023] [Indexed: 06/17/2023]
Abstract
Plant receptor kinases (RKs) function as key plasma-membrane localized receptors in the perception of molecular ligands regulating development and environmental response. Through the perception of diverse ligands, RKs regulate various aspects throughout the plant life cycle from fertilization to seed set. Thirty years of research on plant RKs has generated a wealth of knowledge on how RKs perceive ligands and activate downstream signaling. In the present review, we synthesize this body of knowledge into five central paradigms of plant RK signaling: (1) RKs are encoded by expanded gene families, largely conserved throughout land plant evolution; (2) RKs perceive many different kinds of ligands through a range of ectodomain architectures; (3) RK complexes are typically activated by co-receptor recruitment; (4) post-translational modifications fulfill central roles in both the activation and attenuation of RK-mediated signaling; and, (5) RKs activate a common set of downstream signaling processes through receptor-like cytoplasmic kinases (RLCKs). For each of these paradigms, we discuss key illustrative examples and also highlight known exceptions. We conclude by presenting five critical gaps in our understanding of RK function.
Collapse
Affiliation(s)
- Kyle W. Bender
- Institute of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, 8008 Zürich, Switzerland
| | - Cyril Zipfel
- Institute of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, 8008 Zürich, Switzerland
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, NR4 7UH Norwich, U.K
| |
Collapse
|
23
|
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: 0] [Impact Index Per Article: 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.
Collapse
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.
| |
Collapse
|
24
|
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.
Collapse
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
| |
Collapse
|
25
|
Lu G, Wang Z, Pan YB, Wu Q, Cheng W, Xu F, Dai S, Li B, Que Y, Xu L. Identification of QTLs and critical genes related to sugarcane mosaic disease resistance. FRONTIERS IN PLANT SCIENCE 2023; 14:1107314. [PMID: 36818882 PMCID: PMC9932707 DOI: 10.3389/fpls.2023.1107314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 01/23/2023] [Indexed: 06/18/2023]
Abstract
Mosaic viral diseases affect sugarcane productivity worldwide. Mining disease resistance-associated molecular markers or genes is a key component of disease resistance breeding programs. In the present study, 285 F1 progeny were produced from a cross between Yuetang 93-159, a moderately resistant variety, and ROC22, a highly susceptible variety. The mosaic disease symptoms of these progenies, with ROC22 as the control, were surveyed by natural infection under 11 different environmental conditions in the field and by artificial infections with a mixed sugarcane mosaic virus (SCMV) and sorghum mosaic virus (SrMV) inoculum. Analysis of consolidated survey data enabled the identification of 29 immune, 55 highly resistant, 70 moderately resistant, 62 susceptible, and 40 highly susceptible progenies. The disease response data and a high-quality SNP genetic map were used in quantitative trait locus (QTL) mapping. The results showed that the correlation coefficients (0.26~0.91) between mosaic disease resistance and test environments were significant (p< 0.001), and that mosaic disease resistance was a highly heritable quantitative trait (H2 = 0.85). Seven mosaic resistance QTLs were located to the SNP genetic map, each QTL accounted for 3.57% ~ 17.10% of the phenotypic variation explained (PVE). Furthermore, 110 pathogen response genes and 69 transcription factors were identified in the QTLs interval. The expression levels of nine genes (Soffic.07G0015370-1P, Soffic.09G0015410-2T, Soffic.09G0016460-1T, Soffic.09G0016460-1P, Soffic.09G0017080-3C, Soffic.09G0018730-3P, Soffic.09G0018730-3C, Soffic.09G0019920-3C and Soffic.03G0019710-2C) were significantly different between resistant and susceptible progenies, indicating their key roles in sugarcane resistance to SCMV and SrMV infection. The seven QTLs and nine genes can provide a certain scientific reference to help sugarcane breeders develop varieties resistant to mosaic diseases.
Collapse
Affiliation(s)
- Guilong Lu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou, China
- Institute of Vegetables, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Zhoutao Wang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yong-Bao Pan
- USDA-ARS, Sugarcane Research Unit, Houma, LA, United States
| | - Qibin Wu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wei Cheng
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Fu Xu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shunbin Dai
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Boyu Li
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Youxiong Que
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Liping Xu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou, China
| |
Collapse
|
26
|
Martín-Dacal M, Fernández-Calvo P, Jiménez-Sandoval P, López G, Garrido-Arandía M, Rebaque D, Del Hierro I, Berlanga DJ, Torres MÁ, Kumar V, Mélida H, Pacios LF, Santiago J, Molina A. Arabidopsis immune responses triggered by cellulose- and mixed-linked glucan-derived oligosaccharides require a group of leucine-rich repeat malectin receptor kinases. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 113:833-850. [PMID: 36582174 DOI: 10.1111/tpj.16088] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/15/2022] [Accepted: 12/21/2022] [Indexed: 05/20/2023]
Abstract
The plant immune system perceives a diversity of carbohydrate ligands from plant and microbial cell walls through the extracellular ectodomains (ECDs) of pattern recognition receptors (PRRs), which activate pattern-triggered immunity (PTI). Among these ligands are oligosaccharides derived from mixed-linked β-1,3/β-1,4-glucans (MLGs; e.g. β-1,4-D-(Glc)2 -β-1,3-D-Glc, MLG43) and cellulose (e.g. β-1,4-D-(Glc)3 , CEL3). The mechanisms behind carbohydrate perception in plants are poorly characterized except for fungal chitin oligosaccharides (e.g. β-1,4-d-(GlcNAc)6 , CHI6), which involve several receptor kinase proteins (RKs) with LysM-ECDs. Here, we describe the isolation and characterization of Arabidopsis thaliana mutants impaired in glycan perception (igp) that are defective in PTI activation mediated by MLG43 and CEL3, but not by CHI6. igp1-igp4 are altered in three RKs - AT1G56145 (IGP1), AT1G56130 (IGP2/IGP3) and AT1G56140 (IGP4) - with leucine-rich-repeat (LRR) and malectin (MAL) domains in their ECDs. igp1 harbors point mutation E906K and igp2 and igp3 harbor point mutation G773E in their kinase domains, whereas igp4 is a T-DNA insertional loss-of-function mutant. Notably, isothermal titration calorimetry (ITC) assays with purified ECD-RKs of IGP1 and IGP3 showed that IGP1 binds with high affinity to CEL3 (with dissociation constant KD = 1.19 ± 0.03 μm) and cellopentaose (KD = 1.40 ± 0.01 μM), but not to MLG43, supporting its function as a plant PRR for cellulose-derived oligosaccharides. Our data suggest that these LRR-MAL RKs are components of a recognition mechanism for both cellulose- and MLG-derived oligosaccharide perception and downstream PTI activation in Arabidopsis.
Collapse
Affiliation(s)
- Marina Martín-Dacal
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Campus de Montegancedo UPM, 28223, Pozuelo de Alarcón, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, UPM, 28040, Madrid, Spain
| | - Patricia Fernández-Calvo
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Campus de Montegancedo UPM, 28223, Pozuelo de Alarcón, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, UPM, 28040, Madrid, Spain
| | - Pedro Jiménez-Sandoval
- University of Lausanne (UNIL), Biophore Building, Départament de Biologie Moléculaire Végétale (DBMV), UNIL Sorge, CH-1015, Lausanne, Switzerland
| | - Gemma López
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Campus de Montegancedo UPM, 28223, Pozuelo de Alarcón, Spain
| | - María Garrido-Arandía
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Campus de Montegancedo UPM, 28223, Pozuelo de Alarcón, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, UPM, 28040, Madrid, Spain
| | - Diego Rebaque
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Campus de Montegancedo UPM, 28223, Pozuelo de Alarcón, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, UPM, 28040, Madrid, Spain
| | - Irene Del Hierro
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Campus de Montegancedo UPM, 28223, Pozuelo de Alarcón, Spain
| | - Diego José Berlanga
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Campus de Montegancedo UPM, 28223, Pozuelo de Alarcón, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, UPM, 28040, Madrid, Spain
| | - Miguel Ángel Torres
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Campus de Montegancedo UPM, 28223, Pozuelo de Alarcón, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, UPM, 28040, Madrid, Spain
| | - Varun Kumar
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Campus de Montegancedo UPM, 28223, Pozuelo de Alarcón, Spain
| | - Hugo Mélida
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Campus de Montegancedo UPM, 28223, Pozuelo de Alarcón, Spain
| | - Luis F Pacios
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Campus de Montegancedo UPM, 28223, Pozuelo de Alarcón, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, UPM, 28040, Madrid, Spain
| | - Julia Santiago
- University of Lausanne (UNIL), Biophore Building, Départament de Biologie Moléculaire Végétale (DBMV), UNIL Sorge, CH-1015, Lausanne, Switzerland
| | - Antonio Molina
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Campus de Montegancedo UPM, 28223, Pozuelo de Alarcón, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, UPM, 28040, Madrid, Spain
| |
Collapse
|
27
|
Zhang Y, Yin Z, Pi L, Wang N, Wang J, Peng H, Dou D. A Nicotiana benthamiana receptor-like kinase regulates Phytophthora resistance by coupling with BAK1 to enhance elicitin-triggered immunity. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023. [PMID: 36661038 DOI: 10.1111/jipb.13458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 01/19/2023] [Indexed: 06/17/2023]
Abstract
Cell-surface-localized leucine-rich-repeat receptor-like kinases (LRR-RLKs) are crucial for plant immunity. Most LRR-RLKs that act as receptors directly recognize ligands via a large extracellular domain (ECD), whereas LRR-RLK that serve as regulators are relatively small and contain fewer LRRs. Here, we identified LRR-RLK regulators using high-throughput tobacco rattle virus (TRV)-based gene silencing in the model plant Nicotiana benthamiana. We used the cell-death phenotype caused by INF1, an oomycete elicitin that induces pattern-triggered immunity, as an indicator. By screening 33 small LRR-RLKs (≤6 LRRs) of unknown function, we identified ELICITIN INSENSITIVE RLK 1 (NbEIR1) as a positive regulator of INF1-induced immunity and oomycete resistance. Nicotiana benthamiana mutants of eir1 generated by CRISPR/Cas9-editing showed significantly compromised immune responses to INF1 and were more vulnerable to the oomycete pathogen Phytophthora capsici. NbEIR1 associates with BRI1-ASSOCIATED RECEPTOR KINASE 1 (NbBAK1) and a downstream component, BRASSINOSTEROID-SIGNALING KINASE 1 (NbBSK1). NbBSK1 also contributes to INF1-induced defense and P. capsici resistance. Upon INF1 treatment, NbEIR1 was released from NbBAK1 and NbBSK1 in vivo. Moreover, the silencing of NbBSK1 compromised the association of NbEIR1 with NbBAK1. We also showed that NbEIR1 regulates flg22-induced immunity and associates with its receptor, FLAGELLIN SENSING 2 (NbFLS2). Collectively, our results suggest that NbEIR1 is a novel regulatory element for BAK1-dependent immunity. NbBSK1-NbEIR1 association is required for maintaining the NbEIR1/NbBAK1 complex in the resting state.
Collapse
Affiliation(s)
- Yifan Zhang
- College of Plant Protection, China Agricultural University, Beijing, 100094, China
| | - Zhiyuan Yin
- College of Plant Protection, China Agricultural University, Beijing, 100094, China
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Lei Pi
- College of Plant Protection, China Agricultural University, Beijing, 100094, China
| | - Nan Wang
- College of Plant Protection, China Agricultural University, Beijing, 100094, China
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Jinghao Wang
- College of Plant Protection, China Agricultural University, Beijing, 100094, China
| | - Hao Peng
- Department of Plant Pathology, Washington State University, Pullman, Washington, 99164, USA
| | - Daolong Dou
- College of Plant Protection, China Agricultural University, Beijing, 100094, China
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| |
Collapse
|
28
|
Clasen SJ, Bell MEW, Borbón A, Lee DH, Henseler ZM, de la Cuesta-Zuluaga J, Parys K, Zou J, Wang Y, Altmannova V, Youngblut ND, Weir JR, Gewirtz AT, Belkhadir Y, Ley RE. Silent recognition of flagellins from human gut commensal bacteria by Toll-like receptor 5. Sci Immunol 2023; 8:eabq7001. [PMID: 36608151 DOI: 10.1126/sciimmunol.abq7001] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Flagellin, the protein subunit of the bacterial flagellum, stimulates the innate immune receptor Toll-like receptor 5 (TLR5) after pattern recognition or evades TLR5 through lack of recognition. This binary response fails to explain the weak agonism of flagellins from commensal bacteria, raising the question of how TLR5 response is tuned. Here, we screened abundant flagellins present in metagenomes from human gut for both TLR5 recognition and activation and uncovered a class of flagellin-TLR5 interaction termed silent recognition. Silent flagellins were weak TLR5 agonists despite pattern recognition. Receptor activity was tuned by a TLR5-flagellin interaction distal to the site of pattern recognition that was present in Salmonella flagellin but absent in silent flagellins. This interaction enabled flagellin binding to preformed TLR5 dimers and increased TLR5 signaling by several orders of magnitude. Silent recognition by TLR5 occurred in human organoids and mice, and silent flagellin proteins were present in human stool. These flagellins were produced primarily by the abundant gut bacteria Lachnospiraceae and were enriched in nonindustrialized populations. Our findings provide a mechanism for the innate immune system to tolerate commensal-derived flagellins while remaining vigilant to the presence of flagellins produced by pathogens.
Collapse
Affiliation(s)
- Sara J Clasen
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen 72076, Germany
| | - Michael E W Bell
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen 72076, Germany
| | - Andrea Borbón
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen 72076, Germany
| | - Du-Hwa Lee
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, Vienna, Austria
| | - Zachariah M Henseler
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen 72076, Germany
| | | | - Katarzyna Parys
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, Vienna, Austria
| | - Jun Zou
- Center for Inflammation, Immunity and Infection, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA
| | - Yanling Wang
- Center for Inflammation, Immunity and Infection, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA
| | - Veronika Altmannova
- Friedrich Miescher Laboratory of the Max Planck Society, Max-Planck-Ring 9, Tübingen 72076, Germany
| | - Nicholas D Youngblut
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen 72076, Germany
| | - John R Weir
- Friedrich Miescher Laboratory of the Max Planck Society, Max-Planck-Ring 9, Tübingen 72076, Germany
| | - Andrew T Gewirtz
- Center for Inflammation, Immunity and Infection, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA
| | - Youssef Belkhadir
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, Vienna, Austria
| | - Ruth E Ley
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen 72076, Germany.,Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
| |
Collapse
|
29
|
Mohan B, Thingujam D, Pajerowska-Mukhtar KM. Cytotrap: An Innovative Approach for Protein-Protein Interaction Studies for Cytoplasmic Proteins. Methods Mol Biol 2023; 2690:9-22. [PMID: 37450133 DOI: 10.1007/978-1-0716-3327-4_2] [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: 07/18/2023]
Abstract
Protein-protein interaction mapping has gained immense importance in understanding protein functions in diverse biological pathways. There are various in vivo and in vitro techniques associated with the protein-protein interaction studies but generally, the focus is confined to understanding the protein interaction in the nucleus of the cell, and thus it limits the availability to explore protein interactions that are happening in the cytoplasm of the cell. Since posttranslational modification is a crucial step in signaling pathways and cellular protein interactions harnessing the cytoplasmic protein and evaluating the interaction in the cytoplasm, this protocol will provide more information about studying these types of protein interactions. Cytotrap is a type of yeast-two-hybrid system that differs in its ability to anchor along the membrane, thus directing the protein of interest to anchor along the membrane through the myristoylation signaling unit. The vector containing the target protein contains the myristoylation unit, called the prey, and the bait unit contains the protein of interest as a fusion with the hSos protein. In an event of interaction between the target and the protein of interest, the hSos protein unit will be localized to the membrane and the GDP/GTP exchange unit will trigger the activation of the Ras pathway that leads to the survival of the temperature-sensitive yeast strain at a higher temperature.
Collapse
Affiliation(s)
- Binoop Mohan
- Department of Biology, University of Alabama, Birmingham, AL, USA
| | - Doni Thingujam
- Department of Biology, University of Alabama, Birmingham, AL, USA
| | | |
Collapse
|
30
|
Fakhar AZ, Liu J, Pajerowska-Mukhtar KM. Dynamic Enrichment for Evaluation of Protein Networks (DEEPN): A High Throughput Yeast Two-Hybrid (Y2H) Protocol to Evaluate Networks. Methods Mol Biol 2023; 2690:179-192. [PMID: 37450148 DOI: 10.1007/978-1-0716-3327-4_17] [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: 07/18/2023]
Abstract
Proteins are the building blocks of life, and a vast array of cellular processes is handled by protein-protein interactions (PPIs). The protein complexes formed via PPIs lead to tangled networks that, with their continuous remodeling, build up systematic functional units. Over the years, PPIs have become an area of interest for many researchers, leading to the development of multiple in vitro and in vivo methods to reveal these interactions. The yeast-two-hybrid (Y2H) system is a potent genetic way to map PPIs in both a micro- and high-throughput manner. Y2H is a technique that involves using modified yeast cells to identify protein-protein interactions. For Y2H, the yeast cells are engineered only to grow when there is a significant interaction between a specific protein with its interacting partner. PPIs are identified in the Y2H system by stimulating reporter genes in response to a restored transcription factor. However, Y2H results may be constrained by stringency requirements, as the limited number of colony screenings through this technique could result in the possible elimination of numerous genuine interactions. Therefore, DEEPN (dynamic enrichment for evaluation of protein networks) can be used, offering the potential to study the multiple static and transient protein interactions in a single Y2H experiment. DEEPN utilizes next-generation DNA sequencing (NGS) data in a high-throughput manner and subsequently applies computational analysis and statistical modeling to identify interacting partners. This protocol describes customized reagents and protocols through which DEEPN analysis can be utilized efficiently and cost-effectively.
Collapse
Affiliation(s)
| | - Jinbao Liu
- Department of Biology at University of Alabama, Birmingham, AL, USA
| | | |
Collapse
|
31
|
Hussain A, Farooq M, Naqvi RZ, Aslam MQ, Siddiqui HA, Amin I, Liu C, Liu X, Scheffler J, Asif M, Mansoor S. Whole-Genome Resequencing Deciphers New Insight Into Genetic Diversity and Signatures of Resistance in Cultivated Cotton Gossypium hirsutum. Mol Biotechnol 2023; 65:34-51. [PMID: 35778659 DOI: 10.1007/s12033-022-00527-8] [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: 03/26/2022] [Accepted: 06/07/2022] [Indexed: 01/11/2023]
Abstract
Cotton is an important crop that produces fiber and cottonseed oil for the textile and oil industry. However, cotton leaf curl virus disease (CLCuD) stress is limiting its yield in several Asian countries. In this study, we have sequenced Mac7 accession, a Gossypium hirsutum resistance source against several biotic stresses. By aligning with the Gossypium hirsutum (AD1) 'TM-1' genome, a total of 4.7 and 1.2 million SNPs and InDels were identified in the Mac7 genome. The gene ontology and metabolic pathway enrichment indicated SNPs and InDels role in nucleotide bindings, secondary metabolite synthesis, and plant-pathogen interaction pathways. Furthermore, the RNA-seq data in different tissues and qPCR expression profiling under CLCuD provided individual gene roles in resistant and susceptible accessions. Interestingly, the differential NLR genes demonstrated higher expression in resistant plants rather than in susceptible plants expression. The current resequencing results may provide primary data to identify DNA resistance markers which will be helpful in marker-assisted breeding for development of Mac7-derived resistance lines.
Collapse
Affiliation(s)
- Athar Hussain
- National Institute for Biotechnology and Genetic Engineering (NIBGE), College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Muhammad Farooq
- National Institute for Biotechnology and Genetic Engineering (NIBGE), College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan.,Bioinformatics Group, Wageningen University & Research (WUR), Wageningen, Netherlands
| | - Rubab Zahra Naqvi
- National Institute for Biotechnology and Genetic Engineering (NIBGE), College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Muhammad Qasim Aslam
- National Institute for Biotechnology and Genetic Engineering (NIBGE), College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Hamid Anees Siddiqui
- National Institute for Biotechnology and Genetic Engineering (NIBGE), College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Imran Amin
- National Institute for Biotechnology and Genetic Engineering (NIBGE), College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | | | - Xin Liu
- Beijing Genomics Institute (BGI), Shenzhen, China
| | - Jodi Scheffler
- Genomics and Bioinformatics Research Unit, United States Department of Agriculture-Agricultural Research Service, USDA-ARS), 141 Experimental Station Road, Stoneville, MS, USA
| | - Muhammad Asif
- National Institute for Biotechnology and Genetic Engineering (NIBGE), College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Shahid Mansoor
- National Institute for Biotechnology and Genetic Engineering (NIBGE), College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan.
| |
Collapse
|
32
|
Abstract
As the protein-protein interaction (PPI) data increase exponentially, the development and usage of computational methods to analyze these datasets have become a new research horizon in systems biology. The PPI network analysis and visualization can help identify functional modules of the network, pathway genes involved in common cellular functions, and functional annotations of novel genes. Currently, a variety of tools are available for network graph visualization and analysis. Cytoscape, an open-source software tool, is one of them. It provides an interactive visualization interface along with other core features to import, navigate, filter, cluster, search, and export networks. It comes with hundreds of in-built Apps in App Manager to resolve research questions related to network visualization and integration. This chapter aims to illustrate the Cytoscape application to visualize and analyze the PPI network using Arabidopsis interactome-1 main (AI-1MAIN) PPI network dataset from Plant Interactome Database.
Collapse
Affiliation(s)
- Aqsa Majeed
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Shahid Mukhtar
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, USA.
| |
Collapse
|
33
|
Kumar N, Mukhtar S. Building Protein-Protein Interaction Graph Database Using Neo4j. Methods Mol Biol 2023; 2690:469-479. [PMID: 37450167 DOI: 10.1007/978-1-0716-3327-4_36] [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: 07/18/2023]
Abstract
A cell's various components interact with each other in a coordinated manner to respond to environmental cues and intracellular signals. Compared to the other biological networks, the protein-protein interaction (PPI) is mostly responsible for maintaining signaling pathways. Increasing numbers of experimentally verified and predicted PPIs in plants demand a scalable platform to deal with large and complex datasets. Network/graph data can be organized and analyzed using different tools. This chapter uses Neo4j, a graph database management system, to store and analyze plant PPI networks. To make the graph database and analyze network centrality, we used Arabidopsis interactome-1 main (AI-1MAIN) PPI network.
Collapse
Affiliation(s)
- Nilesh Kumar
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Shahid Mukhtar
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, USA.
| |
Collapse
|
34
|
Hasan M, Kumar N, Majeed A, Ahmad A, Mukhtar S. Protein-Protein Interaction Network Analysis Using NetworkX. Methods Mol Biol 2023; 2690:457-467. [PMID: 37450166 DOI: 10.1007/978-1-0716-3327-4_35] [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: 07/18/2023]
Abstract
In recent years, extracting information from biological data has become a particularly valuable way of gaining knowledge. Molecular interaction networks provide a framework for visualizing cellular processes, but their complexity frequently makes their interpretation difficult. Proteins are one of the primary determinants of biological function. Indeed, most biological activities in the living cells are functionally regulated by protein-protein interactions (PPIs). Thus, studying protein interactions is critical for understanding their roles within the cell. Exploring the PPI networks can open new avenues for future experimental studies and offer interspecies predictions for effective interaction mapping. In this chapter we will demonstrate how to construct, visualize, and analyze a protein-protein interaction network using NetworkX.
Collapse
Affiliation(s)
- Mehadi Hasan
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Nilesh Kumar
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Aqsa Majeed
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Aftab Ahmad
- Department of Anesthesiology and Perioperative Medicine, Birmingham, AL, USA
| | - Shahid Mukhtar
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, USA.
| |
Collapse
|
35
|
Stouthamer J, Martin-Ramirez S, Smakowska-Luzan E. An Interactome Assay for Detecting Interactions between Extracellular Domains of Receptor Kinases. Methods Mol Biol 2023; 2690:193-204. [PMID: 37450149 DOI: 10.1007/978-1-0716-3327-4_18] [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: 07/18/2023]
Abstract
Interactions between extracellular domains (ECDs) are crucial for many physiological processes in the cell, most importantly perception of its environment. However, studying these often-transient interactions can be challenging. Here we describe a method that allows for in vitro detection of extracellular domain interactions through an oligomerization-based cell surface interaction (CSI) assay. In a CSI, bait- and prey-tagged proteins are produced and secreted by Drosophila S2 cells to ensure proper folding and post-translational modifications. Subsequently, Bait (FC fragment) and Prey (pentamer domain and alkaline phosphatase) tags allow the detection of interactions in protein A-coated 96 wells plates through a colorimetric readout. Due to the easy detection of interactions this approach can be used for high-throughput screening and mapping of extracellular interaction networks.
Collapse
Affiliation(s)
- Jente Stouthamer
- Wageningen University & Research Laboratory of Biochemistry, Wageningen, The Netherlands
| | - Sergio Martin-Ramirez
- Wageningen University & Research Laboratory of Biochemistry, Wageningen, The Netherlands
| | - Elwira Smakowska-Luzan
- Wageningen University & Research Laboratory of Biochemistry, Wageningen, The Netherlands.
| |
Collapse
|
36
|
Diwan D, Pajerowska-Mukhtar KM. Preparation and Utilization of a Versatile GFP-Protein Trap-Like System for Protein Complex Immunoprecipitation in Plants. Methods Mol Biol 2023; 2690:59-68. [PMID: 37450136 DOI: 10.1007/978-1-0716-3327-4_5] [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: 07/18/2023]
Abstract
Protein complex immunoprecipitation (co-IP) is an in vitro technique used to study protein-protein interaction between two or more proteins. This method relies on affinity purification of recombinant epitope-tagged proteins followed by western blotting detection using tag-specific antibodies for the confirmation of positive interaction. The traditional co-IP method relies on the use of porous beaded support with immobilized antibodies to precipitate protein complexes. However, this method is time-consuming, labor-intensive, and provides lower reproducibility and yield of protein complexes. Here, we describe the implementation of magnetic beads and high-affinity anti-green fluorescent protein (GFP) antibodies to develop an in vitro GFP-protein trap-like system. This highly reproducible system utilizes a combination of small sample size, versatile lysis buffer, and lower amounts of magnetic beads to obtain protein complexes and aggregates that are compatible with functional assays, Western blotting, and mass spectrometry. In addition to protein-protein interactions, this versatile method can be employed to study protein-nucleic acid interactions. This protocol also highlights troubleshooting and includes recommendations to optimize its application.
Collapse
Affiliation(s)
- Danish Diwan
- Department of Biology, University of Alabama, Birmingham, AL, USA
| | | |
Collapse
|
37
|
Xie W, Xu X, Qiu W, Lai X, Liu M, Zhang F. Expression of PmACRE1 in Arabidopsis thaliana enables host defence against Bursaphelenchus xylophilus infection. BMC PLANT BIOLOGY 2022; 22:541. [PMID: 36418942 PMCID: PMC9682698 DOI: 10.1186/s12870-022-03929-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Accepted: 11/07/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Pine wilt disease (PWD) is a destructive disease that endangers pine trees, resulting in the wilting, with yellowing and browning of the needles, and eventually the death of the trees. Previous studies showed that the Avr9/Cf-9 rapidly elicited (PmACRE1) gene was downregulated by Bursaphelenchus xylophilus infection, suggesting a correlation between PmACRE1 expression and pine tolerance. Here, we used the expression of PmACRE1 in Arabidopsis thaliana to evaluate the role of PmACRE1 in the regulation of host defence against B. xylophilus infection. RESULTS Our results showed that the transformation of PmACRE1 into A. thaliana enhanced plant resistance to the pine wood nematode (PWN); that is, the leaves of the transgenic line remained healthy for a longer period than those of the blank vector group. Ascorbate peroxidase (APX) activity and total phenolic acid and total flavonoid contents were higher in the transgenic line than in the control line. Widely targeted metabolomics analysis of the global secondary metabolites in the transgenic line and the vector control line showed that the contents of 30 compounds were significantly different between these two lines; specifically, the levels of crotaline, neohesperidin, nobiletin, vestitol, and 11 other compounds were significantly increased in the transgenic line. The studies also showed that the ACRE1 protein interacted with serine hydroxymethyltransferase, catalase domain-containing protein, myrosinase, dihydrolipoyl dehydrogenase, ketol-acid reductoisomerase, geranylgeranyl diphosphate reductase, S-adenosylmethionine synthase, glutamine synthetase, and others to comprehensively regulate plant resistance. CONCLUSIONS Taken together, these results indicate that PmACRE1 has a potential role in the regulation of plant defence against PWNs.
Collapse
Affiliation(s)
- Wanfeng Xie
- Jinshan College, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China
- Key Laboratory of Integrated Pest Management in Ecological Forests, Fujian Province University, Fujian Agriculture and Forestry University, Fuzhou, 350000, People's Republic of China
| | - Xiaomei Xu
- Key Laboratory of Integrated Pest Management in Ecological Forests, Fujian Province University, Fujian Agriculture and Forestry University, Fuzhou, 350000, People's Republic of China
- Forestry College, Fujian Agriculture and Forestry University, Fuzhou, 350000, People's Republic of China
| | - Wenjing Qiu
- Key Laboratory of Integrated Pest Management in Ecological Forests, Fujian Province University, Fujian Agriculture and Forestry University, Fuzhou, 350000, People's Republic of China
- Forestry College, Fujian Agriculture and Forestry University, Fuzhou, 350000, People's Republic of China
| | - Xiaolin Lai
- Key Laboratory of Integrated Pest Management in Ecological Forests, Fujian Province University, Fujian Agriculture and Forestry University, Fuzhou, 350000, People's Republic of China
- Forestry College, Fujian Agriculture and Forestry University, Fuzhou, 350000, People's Republic of China
| | - Mengxia Liu
- Key Laboratory of Integrated Pest Management in Ecological Forests, Fujian Province University, Fujian Agriculture and Forestry University, Fuzhou, 350000, People's Republic of China
- Forestry College, Fujian Agriculture and Forestry University, Fuzhou, 350000, People's Republic of China
| | - Feiping Zhang
- Key Laboratory of Integrated Pest Management in Ecological Forests, Fujian Province University, Fujian Agriculture and Forestry University, Fuzhou, 350000, People's Republic of China.
- Forestry College, Fujian Agriculture and Forestry University, Fuzhou, 350000, People's Republic of China.
| |
Collapse
|
38
|
Transcriptome Profiling of the Resistance Response of Musa acuminata subsp. burmannicoides, var. Calcutta 4 to Pseudocercospora musae. Int J Mol Sci 2022; 23:ijms232113589. [DOI: 10.3390/ijms232113589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 10/26/2022] [Accepted: 10/31/2022] [Indexed: 11/09/2022] Open
Abstract
Banana (Musa spp.), which is one of the world’s most popular and most traded fruits, is highly susceptible to pests and diseases. Pseudocercospora musae, responsible for Sigatoka leaf spot disease, is a principal fungal pathogen of Musa spp., resulting in serious economic damage to cultivars in the Cavendish subgroup. The aim of this study was to characterize genetic components of the early immune response to P. musae in Musa acuminata subsp. burmannicoides, var. Calcutta 4, a resistant wild diploid. Leaf RNA samples were extracted from Calcutta 4 three days after inoculation with fungal conidiospores, with paired-end sequencing conducted in inoculated and non-inoculated controls using lllumina HiSeq 4000 technology. Following mapping to the reference M. acuminata ssp. malaccensis var. Pahang genome, differentially expressed genes (DEGs) were identified and expression representation analyzed on the basis of gene ontology enrichment, Kyoto Encyclopedia of Genes and Genomes orthology and MapMan pathway analysis. Sequence data mapped to 29,757 gene transcript models in the reference Musa genome. A total of 1073 DEGs were identified in pathogen-inoculated cDNA libraries, in comparison to non-inoculated controls, with 32% overexpressed. GO enrichment analysis revealed common assignment to terms that included chitin binding, chitinase activity, pattern binding, oxidoreductase activity and transcription factor (TF) activity. Allocation to KEGG pathways revealed DEGs associated with environmental information processing, signaling, biosynthesis of secondary metabolites, and metabolism of terpenoids and polyketides. With 144 up-regulated DEGs potentially involved in biotic stress response pathways, including genes involved in cell wall reinforcement, PTI responses, TF regulation, phytohormone signaling and secondary metabolism, data demonstrated diverse early-stage defense responses to P. musae. With increased understanding of the defense responses occurring during the incompatible interaction in resistant Calcutta 4, these data are appropriate for the development of effective disease management approaches based on genetic improvement through introgression of candidate genes in superior cultivars.
Collapse
|
39
|
Macquet J, Mounichetty S, Raffaele S. Genetic co-option into plant-filamentous pathogen interactions. TRENDS IN PLANT SCIENCE 2022; 27:1144-1158. [PMID: 35909010 DOI: 10.1016/j.tplants.2022.06.011] [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: 02/23/2022] [Revised: 06/16/2022] [Accepted: 06/30/2022] [Indexed: 06/15/2023]
Abstract
Plants are engaged in a coevolutionary arms race with their pathogens that drives rapid diversification and specialization of genes involved in resistance and virulence. However, some major innovations in plant-pathogen interactions, such as molecular decoys, trans-kingdom RNA interference, two-speed genomes, and receptor networks, evolved through the expansion of the functional landscape of genes. This is a typical outcome of genetic co-option, the evolutionary process by which available genes are recruited into new biological functions. Co-option into plant-pathogen interactions emerges generally from (i) cis-regulatory variation, (ii) horizontal gene transfer (HGT), (iii) mutations altering molecular promiscuity, and (iv) rewiring of gene networks and protein complexes. Understanding these molecular mechanisms is key for the functional and predictive biology of plant-pathogen interactions.
Collapse
Affiliation(s)
- Joris Macquet
- Laboratoire des Interactions Plante-Microbe-Environnement (LIPME), Université de Toulouse, Institut National de Recherche pour l'Agriculture, l'Alimentation, et l'Environnement (INRAE), Centre National de la Recherche Scientifique (CNRS), Castanet Tolosan, France
| | - Shantala Mounichetty
- Laboratoire des Interactions Plante-Microbe-Environnement (LIPME), Université de Toulouse, Institut National de Recherche pour l'Agriculture, l'Alimentation, et l'Environnement (INRAE), Centre National de la Recherche Scientifique (CNRS), Castanet Tolosan, France
| | - Sylvain Raffaele
- Laboratoire des Interactions Plante-Microbe-Environnement (LIPME), Université de Toulouse, Institut National de Recherche pour l'Agriculture, l'Alimentation, et l'Environnement (INRAE), Centre National de la Recherche Scientifique (CNRS), Castanet Tolosan, France.
| |
Collapse
|
40
|
Xu C, Ma D, Ding Q, Zhou Y, Zheng H. PlantPhoneDB: A manually curated pan-plant database of ligand-receptor pairs infers cell-cell communication. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:2123-2134. [PMID: 35842742 PMCID: PMC9616517 DOI: 10.1111/pbi.13893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 07/10/2022] [Accepted: 07/13/2022] [Indexed: 06/15/2023]
Abstract
Ligand-receptor pairs play important roles in cell-cell communication for multicellular organisms in response to environmental cues. Recently, the emergence of single-cell RNA-sequencing (scRNA-seq) provides unprecedented opportunities to investigate cellular communication based on ligand-receptor expression. However, so far, no reliable ligand-receptor interaction database is available for plant species. In this study, we developed PlantPhoneDB (https://jasonxu.shinyapps.io/PlantPhoneDB/), a pan-plant database comprising a large number of high-confidence ligand-receptor pairs manually curated from seven resources. Also, we developed a PlantPhoneDB R package, which not only provided optional four scoring approaches that calculate interaction scores of ligand-receptor pairs between cell types but also provided visualization functions to present analysis results. At the PlantPhoneDB web interface, the processed datasets and results can be searched, browsed, and downloaded. To uncover novel cell-cell communication events in plants, we applied the PlantPhoneDB R package on GSE121619 dataset to infer significant cell-cell interactions of heat-shocked root cells in Arabidopsis thaliana. As a result, the PlantPhoneDB predicted the actively communicating AT1G28290-AT2G14890 ligand-receptor pair in atrichoblast-cortex cell pair in Arabidopsis thaliana. Importantly, the downstream target genes of this ligand-receptor pair were significantly enriched in the ribosome pathway, which facilitated plants adapting to environmental changes. In conclusion, PlantPhoneDB provided researchers with integrated resources to infer cell-cell communication from scRNA-seq datasets.
Collapse
Affiliation(s)
- Chaoqun Xu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and EcologyXiamen UniversityXiamenChina
| | - Dongna Ma
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and EcologyXiamen UniversityXiamenChina
| | - Qiansu Ding
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and EcologyXiamen UniversityXiamenChina
| | - Ying Zhou
- National Institute for Data Science in Health and Medicine, School of MedicineXiamen UniversityXiamenChina
| | - Hai‐Lei Zheng
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and EcologyXiamen UniversityXiamenChina
| |
Collapse
|
41
|
Soltabayeva A, Dauletova N, Serik S, Sandybek M, Omondi JO, Kurmanbayeva A, Srivastava S. Receptor-like Kinases (LRR-RLKs) in Response of Plants to Biotic and Abiotic Stresses. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11192660. [PMID: 36235526 PMCID: PMC9572924 DOI: 10.3390/plants11192660] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 09/30/2022] [Accepted: 10/01/2022] [Indexed: 05/14/2023]
Abstract
Plants live under different biotic and abiotic stress conditions, and, to cope with the adversity and severity, plants have well-developed resistance mechanisms. The mechanism starts with perception of the stimuli followed by molecular, biochemical, and physiological adaptive measures. The family of LRR-RLKs (leucine-rich repeat receptor-like kinases) is one such group that perceives biotic and abiotic stimuli and also plays important roles in different biological processes of development. This has been mostly studied in the model plant, Arabidopsis thaliana, and to some extent in other plants, such as Solanum lycopersicum, Nicotiana benthamiana, Brassica napus, Oryza sativa, Triticum aestivum, Hordeum vulgare, Brachypodium distachyon, Medicago truncatula, Gossypium barbadense, Phaseolus vulgaris, Solanum tuberosum, and Malus robusta. Most LRR-RLKs tend to form different combinations of LRR-RLKs-complexes (dimer, trimer, and tetramers), and some of them were observed as important receptors in immune responses, cell death, and plant development processes. However, less is known about the function(s) of LRR-RLKs in response to abiotic and biotic stresses. Here, we give recent updates about LRR-RLK receptors, specifically focusing on their involvement in biotic and abiotic stresses in the model plant, A. thaliana. Furthermore, the recent studies on LRR-RLKs that are homologous in other plants is also reviewed in relation to their role in triggering stress response processes against biotic and abiotic stimuli and/or in exploring their additional function(s). Furthermore, we present the interactions and combinations among LRR-RLK receptors that have been confirmed through experiments. Moreover, based on GENEINVESTIGATOR microarray database analysis, we predict some potential LRR-RLK genes involved in certain biotic and abiotic stresses whose function and mechanism may be explored.
Collapse
Affiliation(s)
- Aigerim Soltabayeva
- Biology Department, School of Science and Humanities, Nazarbayev University, Astana 010000, Kazakhstan
- Correspondence:
| | - Nurbanu Dauletova
- Biology Department, School of Science and Humanities, Nazarbayev University, Astana 010000, Kazakhstan
| | - Symbat Serik
- Biology Department, School of Science and Humanities, Nazarbayev University, Astana 010000, Kazakhstan
| | - Margulan Sandybek
- Biology Department, School of Science and Humanities, Nazarbayev University, Astana 010000, Kazakhstan
| | - John Okoth Omondi
- International Institute of Tropical Agriculture, Lilongwe P.O. Box 30258, Malawi
| | - Assylay Kurmanbayeva
- Department of Biotechnology and Microbiology, L.N. Gumilyov Eurasian National University, Astana 010000, Kazakhstan
| | - Sudhakar Srivastava
- NCS-TCP, National Institute of Plant Genome Research, New Delhi 110067, India
| |
Collapse
|
42
|
Ren J, Guo P, Zhang H, Shi X, Ai X, Wang J, Jiang C, Zhao X, Liu X, Yu H. Comparative physiological and coexpression network analyses reveal the potential drought tolerance mechanism of peanut. BMC PLANT BIOLOGY 2022; 22:460. [PMID: 36162997 PMCID: PMC9511739 DOI: 10.1186/s12870-022-03848-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 09/19/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Drought stress has negative effects on plant growth and productivity. In this study, a comprehensive analysis of physiological responses and gene expression was performed. The responses and expressions were compared between drought-tolerant (DT) and drought-sensitive (DS) peanut varieties to investigate the regulatory mechanisms and hub genes involved in the impact of drought stress on culture. RESULTS The drought-tolerant variety had robust antioxidative capacities with higher total antioxidant capacity and flavonoid contents, and it enhanced osmotic adjustment substance accumulation to adapt to drought conditions. KEGG analysis of differentially expressed genes demonstrated that photosynthesis was strongly affected by drought stress, especially in the drought-sensitive variety, which was consistent with the more severe suppression of photosynthesis. The hub genes in the key modules related to the drought response, including genes encoding protein kinase, E3 ubiquitin-protein ligase, potassium transporter, pentatricopeptide repeat-containing protein, and aspartic proteinase, were identified through a comprehensive combined analysis of genes and physiological traits using weighted gene co-expression network analysis. There were notably differentially expressed genes between the two varieties, suggesting the positive roles of these genes in peanut drought tolerance. CONCLUSION A comprehensive analysis of physiological traits and relevant genes was conducted on peanuts with different drought tolerances. The findings revealed diverse drought-response mechanisms and identified candidate genes for further research.
Collapse
Affiliation(s)
- Jingyao Ren
- College of Agronomy, Shenyang Agricultural University, Shenyang, China
| | - Pei Guo
- College of Agronomy, Shenyang Agricultural University, Shenyang, China
| | - He Zhang
- College of Agronomy, Shenyang Agricultural University, Shenyang, China
| | - Xiaolong Shi
- College of Agronomy, Shenyang Agricultural University, Shenyang, China
| | - Xin Ai
- College of Agronomy, Shenyang Agricultural University, Shenyang, China
| | - Jing Wang
- College of Agronomy, Shenyang Agricultural University, Shenyang, China
| | - Chunji Jiang
- College of Agronomy, Shenyang Agricultural University, Shenyang, China
| | - Xinhua Zhao
- College of Agronomy, Shenyang Agricultural University, Shenyang, China
| | - Xibo Liu
- College of Agronomy, Shenyang Agricultural University, Shenyang, China.
| | - Haiqiu Yu
- College of Agronomy, Shenyang Agricultural University, Shenyang, China.
| |
Collapse
|
43
|
Breit-McNally C, Laflamme B, Singh RA, Desveaux D, Guttman DS. ZAR1: Guardian of plant kinases. FRONTIERS IN PLANT SCIENCE 2022; 13:981684. [PMID: 36212348 PMCID: PMC9539561 DOI: 10.3389/fpls.2022.981684] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 09/07/2022] [Indexed: 05/25/2023]
Abstract
A key facet of innate immunity in plants entails the recognition of pathogen "effector" virulence proteins by host Nucleotide-Binding Leucine-Rich Repeat Receptors (NLRs). Among characterized NLRs, the broadly conserved ZAR1 NLR is particularly remarkable due to its capacity to recognize at least six distinct families of effectors from at least two bacterial genera. This expanded recognition spectrum is conferred through interactions between ZAR1 and a dynamic network of two families of Receptor-Like Cytoplasmic Kinases (RLCKs): ZED1-Related Kinases (ZRKs) and PBS1-Like Kinases (PBLs). In this review, we survey the history of functional studies on ZAR1, with an emphasis on how the ZAR1-RLCK network functions to trap diverse effectors. We discuss 1) the dynamics of the ZAR1-associated RLCK network; 2) the specificity between ZRKs and PBLs; and 3) the specificity between effectors and the RLCK network. We posit that the shared protein fold of kinases and the switch-like properties of their interactions make them ideal effector sensors, enabling ZAR1 to act as a broad spectrum guardian of host kinases.
Collapse
Affiliation(s)
- Clare Breit-McNally
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Bradley Laflamme
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Racquel A. Singh
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Darrell Desveaux
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
- Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, ON, Canada
| | - David S. Guttman
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
- Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, ON, Canada
| |
Collapse
|
44
|
Wang J, Ye H, Zhou H, Chen P, Liu H, Xi R, Wang G, Hou N, Zhao P. Genome-wide association analysis of 101 accessions dissects the genetic basis of shell thickness for genetic improvement in Persian walnut (Juglans regia L.). BMC PLANT BIOLOGY 2022; 22:436. [PMID: 36096735 PMCID: PMC9469530 DOI: 10.1186/s12870-022-03824-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 09/02/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Understanding the underlying genetic mechanisms that drive phenotypic variations is essential for enhancing the efficacy of crop improvement. Persian walnut (Juglans regia L.), which is grown extensively worldwide, is an important economic tree fruit due to its horticultural, medicinal, and material value. The quality of the walnut fruit is related to the selection of traits such as thinner shells, larger filling rates, and better taste, which is very important for breeding in China. The complex quantitative fruit-related traits are influenced by a variety of physiological and environmental factors, which can vary widely between walnut genotypes. RESULTS For this study, a set of 101 Persian walnut accessions were re-sequenced, which generated a total of 906.2 Gb of Illumina sequence data with an average read depth of 13.8× for each accession. We performed the genome-wide association study (GWAS) using 10.9 Mb of high-quality single-nucleotide polymorphisms (SNPs) and 10 agronomic traits to explore the underlying genetic basis of the walnut fruit. Several candidate genes are proposed to be involved in walnut characteristics, including JrPXC1, JrWAKL8, JrGAMYB, and JrFRK1. Specifically, the JrPXC1 gene was confirmed to participate in the regulation of secondary wall cellulose thickening in the walnut shell. CONCLUSION In addition to providing considerable available genetic resources for walnut trees, this study revealed the underlying genetic basis involved in important walnut agronomic traits, particularly shell thickness, as well as providing clues for the improvement of genetic breeding and domestication in other perennial economic crops.
Collapse
Affiliation(s)
- Jiangtao Wang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, 710069, Shaanxi, China
| | - Hang Ye
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, 710069, Shaanxi, China
| | - Huijuan Zhou
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, 710069, Shaanxi, China
- College of Forestry, Northwest A&F University, Yangling, 712100, China
| | - Pengpeng Chen
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, 710069, Shaanxi, China
| | - Hengzhao Liu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, 710069, Shaanxi, China
| | - Ruimin Xi
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, 710069, Shaanxi, China
| | - Gang Wang
- Guizhou Academy of Forestry, Guiyang, 550005, Guizhou, China
| | - Na Hou
- Guizhou Academy of Forestry, Guiyang, 550005, Guizhou, China.
| | - Peng Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, 710069, Shaanxi, China.
| |
Collapse
|
45
|
ABP1-TMK auxin perception for global phosphorylation and auxin canalization. Nature 2022; 609:575-581. [PMID: 36071161 DOI: 10.1038/s41586-022-05187-x] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 08/03/2022] [Indexed: 12/22/2022]
Abstract
The phytohormone auxin triggers transcriptional reprogramming through a well-characterized perception machinery in the nucleus. By contrast, mechanisms that underlie fast effects of auxin, such as the regulation of ion fluxes, rapid phosphorylation of proteins or auxin feedback on its transport, remain unclear1-3. Whether auxin-binding protein 1 (ABP1) is an auxin receptor has been a source of debate for decades1,4. Here we show that a fraction of Arabidopsis thaliana ABP1 is secreted and binds auxin specifically at an acidic pH that is typical of the apoplast. ABP1 and its plasma-membrane-localized partner, transmembrane kinase 1 (TMK1), are required for the auxin-induced ultrafast global phospho-response and for downstream processes that include the activation of H+-ATPase and accelerated cytoplasmic streaming. abp1 and tmk mutants cannot establish auxin-transporting channels and show defective auxin-induced vasculature formation and regeneration. An ABP1(M2X) variant that lacks the capacity to bind auxin is unable to complement these defects in abp1 mutants. These data indicate that ABP1 is the auxin receptor for TMK1-based cell-surface signalling, which mediates the global phospho-response and auxin canalization.
Collapse
|
46
|
Ma Y, Stafford L, Ratcliffe J, Bacic A, Johnson KL. WAKL8 Regulates Arabidopsis Stem Secondary Wall Development. PLANTS (BASEL, SWITZERLAND) 2022; 11:2297. [PMID: 36079678 PMCID: PMC9460275 DOI: 10.3390/plants11172297] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/24/2022] [Accepted: 08/30/2022] [Indexed: 06/15/2023]
Abstract
Wall-associated kinases/kinase-likes (WAKs/WAKLs) are plant cell surface sensors. A variety of studies have revealed the important functions of WAKs/WAKLs in regulating cell expansion and defense in cells with primary cell walls. Less is known about their roles during the development of the secondary cell walls (SCWs) that are present in xylem vessel (XV) and interfascicular fiber (IF) cells. In this study, we used RNA-seq data to screen Arabidopsis thaliana WAKs/WAKLs members that may be involved in SCW development and identified WAKL8 as a candidate. We obtained T-DNA insertion mutants wakl8-1 (inserted at the promoter region) and wakl8-2 (inserted at the first exon) and compared the phenotypes to wild-type (WT) plants. Decreased WAKL8 transcript levels in stems were found in the wakl8-2 mutant plants, and the phenotypes observed included reduced stem length and thinner walls in XV and IFs compared with those in the WT plants. Cell wall analysis showed no significant changes in the crystalline cellulose or lignin content in mutant stems compared with those in the WT. We found that WAKL8 had alternative spliced versions predicted to have only extracellular regions, which may interfere with the function of the full-length version of WAKL8. Our results suggest WAKL8 can regulate SCW thickening in Arabidopsis stems.
Collapse
Affiliation(s)
- Yingxuan Ma
- School of BioSciences, University of Melbourne, Parkville, VIC 3052, Australia
- La Trobe Institute for Agriculture & Food, Department of Animal, Plant and Soil Science, AgriBio Building, La Trobe University, Bundoora, VIC 3086, Australia
| | - Luke Stafford
- La Trobe Institute for Agriculture & Food, Department of Animal, Plant and Soil Science, AgriBio Building, La Trobe University, Bundoora, VIC 3086, Australia
| | - Julian Ratcliffe
- La Trobe Institute for Agriculture & Food, Department of Animal, Plant and Soil Science, AgriBio Building, La Trobe University, Bundoora, VIC 3086, Australia
| | - Antony Bacic
- La Trobe Institute for Agriculture & Food, Department of Animal, Plant and Soil Science, AgriBio Building, La Trobe University, Bundoora, VIC 3086, Australia
- Sino-Australia Plant Cell Wall Research Centre, College of Forestry and Biotechnology, Zhejiang Agriculture and Forestry University, Lin’an, Hangzhou 311300, China
| | - Kim L. Johnson
- La Trobe Institute for Agriculture & Food, Department of Animal, Plant and Soil Science, AgriBio Building, La Trobe University, Bundoora, VIC 3086, Australia
- Sino-Australia Plant Cell Wall Research Centre, College of Forestry and Biotechnology, Zhejiang Agriculture and Forestry University, Lin’an, Hangzhou 311300, China
| |
Collapse
|
47
|
Kumar N, Mishra B, Mukhtar MS. A pipeline of integrating transcriptome and interactome to elucidate central nodes in host-pathogens interactions. STAR Protoc 2022; 3:101608. [PMID: 35990739 PMCID: PMC9386103 DOI: 10.1016/j.xpro.2022.101608] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Investigating the complexity of host-pathogen interactions is challenging. Here, we outline a pipeline to identify important proteins and signaling molecules in human-viral interactomes. Firstly, we curate a comprehensive human interactome. Subsequently, we infer viral targets and transcriptome-specific human interactomes (VTTSHI) for papillomavirus and herpes viruses by integrating viral targets and transcriptome data. Finally, we reveal the common and shared nodes and pathways in viral pathogenesis following network topology and pathway enrichment analyses. For complete details on the use and execution of this protocol, please refer to Kumar et al. (2020). Protocol for integrative analysis of transcriptome and proteome network data Network subgroup enrichment of two host-pathogen interaction networks Preprocessing of data and heterogeneous network integration
Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.
Collapse
Affiliation(s)
- Nilesh Kumar
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
| | - Bharat Mishra
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - M Shahid Mukhtar
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
| |
Collapse
|
48
|
Chen R, Sun P, Zhong G, Wang W, Tang D. The RECEPTOR-LIKE PROTEIN53 immune complex associates with LLG1 to positively regulate plant immunity. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:1833-1846. [PMID: 35796320 DOI: 10.1111/jipb.13327] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 07/06/2022] [Indexed: 06/15/2023]
Abstract
Pattern recognition receptors (PRRs) sense ligands in pattern-triggered immunity (PTI). Plant PRRs include numerous receptor-like proteins (RLPs), but many RLPs remain functionally uncharacterized. Here, we examine an Arabidopsis thaliana RLP, RLP53, which positively regulates immune signaling. Our forward genetic screen for suppressors of enhanced disease resistance1 (edr1) identified a point mutation in RLP53 that fully suppresses disease resistance and mildew-induced cell death in edr1 mutants. The rlp53 mutants showed enhanced susceptibility to virulent pathogens, including fungi, oomycetes, and bacteria, indicating that RLP53 is important for plant immunity. The ectodomain of RLP53 contains leucine-rich repeat (LRR) motifs. RLP53 constitutively associates with the LRR receptor-like kinase SUPPRESSOR OF BRASSINOSTEROID INSENSITIVE1-ASSOCIATED KINASE (BAK1)-INTERACTING RECEPTOR KINASE1 (SOBIR1) and interacts with the co-receptor BAK1 in a pathogen-induced manner. The double mutation sobir1-12 bak1-5 suppresses edr1-mediated disease resistance, suggesting that EDR1 negatively regulates PTI modulated by the RLP53-SOBIR1-BAK1 complex. Moreover, the glycosylphosphatidylinositol (GPI)-anchored protein LORELEI-LIKE GPI-ANCHORED PROTEIN1 (LLG1) interacts with RLP53 and mediates RLP53 accumulation in the plasma membrane. We thus uncovered the role of a novel RLP and its associated immune complex in plant defense responses and revealed a potential new mechanism underlying regulation of RLP immune function by a GPI-anchored protein.
Collapse
Affiliation(s)
- Renjie Chen
- State Key Laboratory of Ecological Control of Fujian-Taiwan Crop Pests, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Plant Immunity Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Pengwei Sun
- Institute of Genetics and Developmental Biology, the Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Guitao Zhong
- State Key Laboratory of Ecological Control of Fujian-Taiwan Crop Pests, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Plant Immunity Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Wei Wang
- State Key Laboratory of Ecological Control of Fujian-Taiwan Crop Pests, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Plant Immunity Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Dingzhong Tang
- State Key Laboratory of Ecological Control of Fujian-Taiwan Crop Pests, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Plant Immunity Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| |
Collapse
|
49
|
Invernizzi M, Hanemian M, Keller J, Libourel C, Roby D. PERKing up our understanding of the proline-rich extensin-like receptor kinases, a forgotten plant receptor kinase family. THE NEW PHYTOLOGIST 2022; 235:875-884. [PMID: 35451507 DOI: 10.1111/nph.18166] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 04/12/2022] [Indexed: 06/14/2023]
Abstract
Proline-rich extensin-like receptor kinases (PERKs) are an important class of receptor-like kinases (RLKs) containing an extracellular proline-rich domain. While they are thought to be putative sensors of the cell wall integrity, there are very few reports on their biological functions in the plant, as compared with other RLKs. Several studies support a role for PERKs in plant growth and development, but their effect on the cell wall composition to regulate cell expansion is still lacking. Gene expression data suggest that they may intervene in response to environmental changes, in agreement with their subcellular localization. And there is growing evidence for PERKs as novel sensors of environmental stresses such as insects and viruses. However, little is known about their precise role in plant immunity and in the extracellular network of RLKs, as no PERK-interacting RLK or any coreceptor has been identified as yet. Similarly, their signaling activities and downstream signaling components are just beginning to be deciphered, including Ca2+ fluxes, reactive oxygen species accumulation and phosphorylation events. Here we outline emerging roles for PERKs as novel sensors of environmental stresses, and we discuss how to better understand this overlooked class of receptor kinases via several avenues of research.
Collapse
Affiliation(s)
- Marie Invernizzi
- Laboratoire des Interactions Plantes-Microbes-Environnement, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, CNRS, Université de Toulouse, 31326, Castanet-Tolosan, France
| | - Mathieu Hanemian
- Laboratoire des Interactions Plantes-Microbes-Environnement, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, CNRS, Université de Toulouse, 31326, Castanet-Tolosan, France
| | - Jean Keller
- Laboratoire de Recherche en Sciences Végétales (LRSV), CNRS, UPS, INP Toulouse, Université de Toulouse, 31326, Castanet-Tolosan, France
| | - Cyril Libourel
- Laboratoire de Recherche en Sciences Végétales (LRSV), CNRS, UPS, INP Toulouse, Université de Toulouse, 31326, Castanet-Tolosan, France
| | - Dominique Roby
- Laboratoire des Interactions Plantes-Microbes-Environnement, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, CNRS, Université de Toulouse, 31326, Castanet-Tolosan, France
| |
Collapse
|
50
|
Peng Y, Zuo W, Zhou H, Miao F, Zhang Y, Qin Y, Liu Y, Long Y, Ma S. EXPLICIT-Kinase: A gene expression predictor for dissecting the functions of the Arabidopsis kinome. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:1374-1393. [PMID: 35446465 DOI: 10.1111/jipb.13267] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 04/19/2022] [Indexed: 06/14/2023]
Abstract
Protein kinases regulate virtually all cellular processes, but it remains challenging to determine the functions of all protein kinases, collectively called the "kinome", in any species. We developed a computational approach called EXPLICIT-Kinase to predict the functions of the Arabidopsis kinome. Because the activities of many kinases can be regulated transcriptionally, their gene expression patterns provide clues to their functions. A universal gene expression predictor for Arabidopsis was constructed to predict the expression of 30,172 non-kinase genes based on the expression of 994 kinases. The model reconstituted highly accurate transcriptomes for diverse Arabidopsis samples. It identified the significant kinases as predictor kinases for predicting the expression of Arabidopsis genes and pathways. Strikingly, these predictor kinases were often regulators of related pathways, as exemplified by those involved in cytokinesis, tissue development, and stress responses. Comparative analyses revealed that portions of these predictor kinases are shared and conserved between Arabidopsis and maize. As an example, we identified a conserved predictor kinase, RAF6, from a stomatal movement module. We verified that RAF6 regulates stomatal closure. It can directly interact with SLAC1, a key anion channel for stomatal closure, and modulate its channel activity. Our approach enables a systematic dissection of the functions of the Arabidopsis kinome.
Collapse
Affiliation(s)
- Yuming Peng
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, School of Life Sciences, University of Science and Technology of China, Innovation Academy for Seed Design, Chinese Academy of Sciences, Hefei, 230027, China
| | - Wanzhu Zuo
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, School of Life Sciences, University of Science and Technology of China, Innovation Academy for Seed Design, Chinese Academy of Sciences, Hefei, 230027, China
| | - Hui Zhou
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475001, China
| | - Fenfen Miao
- State Key Laboratory for Plant Molecular Genetics, Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Yu Zhang
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, School of Life Sciences, University of Science and Technology of China, Innovation Academy for Seed Design, Chinese Academy of Sciences, Hefei, 230027, China
| | - Yue Qin
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, School of Life Sciences, University of Science and Technology of China, Innovation Academy for Seed Design, Chinese Academy of Sciences, Hefei, 230027, China
| | - Yi Liu
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, School of Life Sciences, University of Science and Technology of China, Innovation Academy for Seed Design, Chinese Academy of Sciences, Hefei, 230027, China
| | - Yu Long
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475001, China
| | - Shisong Ma
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, School of Life Sciences, University of Science and Technology of China, Innovation Academy for Seed Design, Chinese Academy of Sciences, Hefei, 230027, China
- School of Data Science, University of Science and Technology of China, Hefei, 230027, China
| |
Collapse
|