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Ellur V, Wei W, Ghogare R, Solanki S, Vandemark G, Brueggeman R, Chen W. Unraveling the genomic reorganization of polygalacturonase-inhibiting proteins in chickpea. Front Genet 2023; 14:1189329. [PMID: 37342773 PMCID: PMC10278945 DOI: 10.3389/fgene.2023.1189329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Accepted: 05/26/2023] [Indexed: 06/23/2023] Open
Abstract
Polygalacturonase-inhibiting proteins (PGIPs) are cell wall proteins that inhibit pathogen polygalacturonases (PGs). PGIPs, like other defense-related proteins, contain extracellular leucine-rich repeats (eLRRs), which are required for pathogen PG recognition. The importance of these PGIPs in plant defense has been well documented. This study focuses on chickpea (Cicer arietinum) PGIPs (CaPGIPs) owing to the limited information available on this important crop. This study identified two novel CaPGIPs (CaPGIP3 and CaPGIP4) and computationally characterized all four CaPGIPs in the gene family, including the previously reported CaPGIP1 and CaPGIP2. The findings suggest that CaPGIP1, CaPGIP3, and CaPGIP4 proteins possess N-terminal signal peptides, ten LRRs, theoretical molecular mass, and isoelectric points comparable to other legume PGIPs. Phylogenetic analysis and multiple sequence alignment revealed that the CaPGIP1, CaPGIP3, and CaPGIP4 amino acid sequences are similar to the other PGIPs reported in legumes. In addition, several cis-acting elements that are typical of pathogen response, tissue-specific activity, hormone response, and abiotic stress-related are present in the promoters of CaPGIP1, CaPGIP3, and CaPGIP4 genes. Localization experiments showed that CaPGIP1, CaPGIP3, and CaPGIP4 are located in the cell wall or membrane. Transcript levels of CaPGIP1, CaPGIP3, and CaPGIP4 genes analyzed at untreated conditions show varied expression patterns analogous to other defense-related gene families. Interestingly, CaPGIP2 lacked a signal peptide, more than half of the LRRs, and other characteristics of a typical PGIP and subcellular localization indicated it is not located in the cell wall or membrane. The study's findings demonstrate CaPGIP1, CaPGIP3, and CaPGIP4's similarity to other legume PGIPs and suggest they might possess the potential to combat chickpea pathogens.
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Affiliation(s)
- Vishnutej Ellur
- Molecular Plant Science, Washington State University, Pullman, WA, United States
| | - Wei Wei
- Department of Plant Pathology, Washington State University, Pullman, WA, United States
| | - Rishikesh Ghogare
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, United States
| | - Shyam Solanki
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD, United States
| | - George Vandemark
- Grain Legume Genetics Physiology Research, Pullman, WA, United States
| | - Robert Brueggeman
- Department of Crop and Soil Science, Washington State University, Pullman, WA, United States
| | - Weidong Chen
- Grain Legume Genetics Physiology Research, Pullman, WA, United States
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Zhu G, Liang E, Lan X, Li Q, Qian J, Tao H, Zhang M, Xiao N, Zuo S, Chen J, Gao Y. ZmPGIP3 Gene Encodes a Polygalacturonase-Inhibiting Protein that Enhances Resistance to Sheath Blight in Rice. Phytopathology 2019; 109:1732-1740. [PMID: 31479403 DOI: 10.1094/phyto-01-19-0008-r] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Plant polygalacturonase-inhibiting protein (PGIP) is a structural protein that can specifically recognize and bind to fungal polygalacturonase (PG). PGIP plays an important role in plant antifungal activity. In this study, a maize PGIP gene, namely ZmPGIP3, was cloned and characterized. Agarose diffusion assay suggested that ZmPGIP3 could inhibit the activity of PG. ZmPGIP3 expression was significantly induced by wounding, Rhizoctonia solani infection, jasmonate, and salicylic acid. ZmPGIP3 might be related to disease resistance. The gene encoding ZmPGIP3 was posed under the control of the ubiquitin promoter and constitutively expressed in transgenic rice. In an R. solani infection assay, ZmPGIP3 transgenic rice was more resistant to sheath blight than the wild-type rice regardless of the inoculated plant part (leaves or sheaths). Digital gene expression analysis indicated that the expression of some rice PGIP genes significantly increased in ZmPGIP3 transgenic rice, suggesting that ZmPGIP3 might activate the expression of some rice PGIP genes to resist sheath blight. Our investigation of the agronomic traits of ZmPGIP3 transgenic rice showed that ZmPGIP3 overexpression in rice did not show any detrimental phenotypic or agronomic effect. ZmPGIP3 is a promising candidate gene in the transgenic breeding for sheath blight resistance and crop improvement.
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Affiliation(s)
- Guang Zhu
- Jiangsu Key Laboratories of Crop Genetics and Physiology and Plant Functional Genomics of the Ministry of Education, Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province, Yangzhou University, Yangzhou 225009, China
| | - Enxing Liang
- Jiangsu Key Laboratories of Crop Genetics and Physiology and Plant Functional Genomics of the Ministry of Education, Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province, Yangzhou University, Yangzhou 225009, China
| | - Xiang Lan
- Jiangsu Key Laboratories of Crop Genetics and Physiology and Plant Functional Genomics of the Ministry of Education, Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province, Yangzhou University, Yangzhou 225009, China
| | - Qian Li
- Jiangsu Key Laboratories of Crop Genetics and Physiology and Plant Functional Genomics of the Ministry of Education, Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province, Yangzhou University, Yangzhou 225009, China
| | - Jingjie Qian
- Jiangsu Key Laboratories of Crop Genetics and Physiology and Plant Functional Genomics of the Ministry of Education, Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province, Yangzhou University, Yangzhou 225009, China
| | - Haixia Tao
- Jiangsu Key Laboratories of Crop Genetics and Physiology and Plant Functional Genomics of the Ministry of Education, Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province, Yangzhou University, Yangzhou 225009, China
| | - Mengjiao Zhang
- Jiangsu Key Laboratories of Crop Genetics and Physiology and Plant Functional Genomics of the Ministry of Education, Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province, Yangzhou University, Yangzhou 225009, China
| | - Ning Xiao
- Lixiahe Region Agricultural Scientific Research Institute of Jiangsu, Yangzhou 225009, Jiangsu, China
| | - Shimin Zuo
- Jiangsu Key Laboratories of Crop Genetics and Physiology and Plant Functional Genomics of the Ministry of Education, Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province, Yangzhou University, Yangzhou 225009, China
| | - Jianmin Chen
- Jiangsu Key Laboratories of Crop Genetics and Physiology and Plant Functional Genomics of the Ministry of Education, Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province, Yangzhou University, Yangzhou 225009, China
| | - Yong Gao
- Jiangsu Key Laboratories of Crop Genetics and Physiology and Plant Functional Genomics of the Ministry of Education, Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province, Yangzhou University, Yangzhou 225009, China
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Hu H, Wang C, Li X, Tang Y, Wang Y, Chen S, Yan S. RNA-Seq identification of candidate defense genes targeted by endophytic Bacillus cereus-mediated induced systemic resistance against Meloidogyne incognita in tomato. Pest Manag Sci 2018; 74:2793-2805. [PMID: 29737595 DOI: 10.1002/ps.5066] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 04/25/2018] [Accepted: 05/03/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND The endophytic bacteria Bacillus cereus BCM2 has shown great potential as a defense against the parasitic nematode Meloidogyne incognita. Here, we studied endophytic bacteria-mediated plant defense against M. incognita and searched for defense-related candidate genes using RNA-Seq. RESULTS The induced systemic resistance of BCM2 against M. incognita was tested using the split-root method. Pre-inoculated BCM2 on the inducer side was associated with a dramatic reduction in galls and egg masses on the responder side, but inoculated BCM2 alone did not produce the same effect. In order to investigate which plant defense-related genes are specifically activated by BCM2, four RNA samples from tomato roots were sequenced, and four high-quality total clean bases were obtained, ranging from 6.64 to 6.75 Gb, with an average of 21 558 total genes. The 34 candidate defense-related genes were identified by pair-wise comparison among libraries, representing the targets for BCM2 priming resistance against M. incognita. Functional characterization revealed that the plant-pathogen interaction pathway (ID: ko04626) was significantly enriched for BCM2-mediated M. incognita resistance. CONCLUSION This study demonstrates that B. cereus BCM2 maintains a harmonious host-microbe relationship with tomato, but appeared to prime the plant, resulting in more vigorous defense response toward the infection nematode. © 2018 Society of Chemical Industry.
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Affiliation(s)
- Haijing Hu
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, China
- School of Life Sciences, Nanjing University, Nanjing, China
| | - Cong Wang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xia Li
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Yunyun Tang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Yufang Wang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Shuanglin Chen
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Shuzhen Yan
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, China
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Cao Z, Deng Z. De Novo Assembly, Annotation, and Characterization of Root Transcriptomes of Three Caladium Cultivars with a Focus on Necrotrophic Pathogen Resistance/ Defense-Related Genes. Int J Mol Sci 2017; 18:E712. [PMID: 28346370 DOI: 10.3390/ijms18040712] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 03/21/2017] [Accepted: 03/24/2017] [Indexed: 01/11/2023] Open
Abstract
Roots are vital to plant survival and crop yield, yet few efforts have been made to characterize the expressed genes in the roots of non-model plants (root transcriptomes). This study was conducted to sequence, assemble, annotate, and characterize the root transcriptomes of three caladium cultivars (Caladium × hortulanum) using RNA-Seq. The caladium cultivars used in this study have different levels of resistance to Pythiummyriotylum, the most damaging necrotrophic pathogen to caladium roots. Forty-six to 61 million clean reads were obtained for each caladium root transcriptome. De novo assembly of the reads resulted in approximately 130,000 unigenes. Based on bioinformatic analysis, 71,825 (52.3%) caladium unigenes were annotated for putative functions, 48,417 (67.4%) and 31,417 (72.7%) were assigned to Gene Ontology (GO) and Clusters of Orthologous Groups (COG), respectively, and 46,406 (64.6%) unigenes were assigned to 128 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. A total of 4518 distinct unigenes were observed only in Pythium-resistant "Candidum" roots, of which 98 seemed to be involved in disease resistance and defense responses. In addition, 28,837 simple sequence repeat sites and 44,628 single nucleotide polymorphism sites were identified among the three caladium cultivars. These root transcriptome data will be valuable for further genetic improvement of caladium and related aroids.
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Liu B, Li JF, Ao Y, Li Z, Liu J, Feng D, Qi K, He Y, Zeng L, Wang J, Wang HB. OsLYP4 and OsLYP6 play critical roles in rice defense signal transduction. Plant Signal Behav 2013; 8:e22980. [PMID: 23299421 PMCID: PMC3656994 DOI: 10.4161/psb.22980] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Plant innate immunity relies on successful detection of trespassing pathogens through recognizing their microbe-associated molecular patterns (MAMPs) by pattern recognition receptors (PRRs) at the cell surface. We recently reported two rice lysin motif (LysM)-containing proteins, OsLYP4 and OsLYP6, as dual functional PRRs sensing bacterial peptidoglycan (PGN) and fungal chitin. Here we further demonstrated the important roles of OsLYP4 and OsLYP6 in rice defense signaling, as silencing of either LYP impaired the defense marker gene activation induced by either bacterial pathogen Xanthomonas oryzaecola or fungal pathogen Magnaporthe oryzae. Moreover, we found that OsLYP4 and OsLYP6 could form homo- and hetero-dimers, and could interact with CEBiP, suggesting an unexpected complexity of chitin perception in rice.
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Affiliation(s)
- Bing Liu
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources; School of Life Sciences; Sun Yat-sen University; P.R. China
| | - Jian-Feng Li
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources; School of Life Sciences; Sun Yat-sen University; P.R. China
| | - Ying Ao
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources; School of Life Sciences; Sun Yat-sen University; P.R. China
| | - Zhangqun Li
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources; School of Life Sciences; Sun Yat-sen University; P.R. China
| | - Jun Liu
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources; School of Life Sciences; Sun Yat-sen University; P.R. China
| | - Dongru Feng
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources; School of Life Sciences; Sun Yat-sen University; P.R. China
| | - Kangbiao Qi
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources; School of Life Sciences; Sun Yat-sen University; P.R. China
| | - Yanming He
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources; School of Life Sciences; Sun Yat-sen University; P.R. China
| | - Liexian Zeng
- The Plant Protection Research Institute; Guangdong Academy of Agricultural Sciences; P.R. China
| | - Jinfa Wang
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources; School of Life Sciences; Sun Yat-sen University; P.R. China
| | - Hong-Bin Wang
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources; School of Life Sciences; Sun Yat-sen University; P.R. China
- Correspondence to: Hong-Bin Wang,
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