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Hu H, Yuan X, Saini DK, Yang T, Wu X, Wu R, Liu Z, Jan F, Mir RR, Liu L, Miao J, Liu N, Xu P. A panomics-driven framework for the improvement of major food legume crops: advances, challenges, and future prospects. HORTICULTURE RESEARCH 2025; 12:uhaf091. [PMID: 40352287 PMCID: PMC12064956 DOI: 10.1093/hr/uhaf091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2025] [Accepted: 03/13/2025] [Indexed: 05/14/2025]
Abstract
Food legume crops, including common bean, faba bean, mungbean, cowpea, chickpea, and pea, have long served as vital sources of energy, protein, and minerals worldwide, both as grains and vegetables. Advancements in high-throughput phenotyping, next-generation sequencing, transcriptomics, proteomics, and metabolomics have significantly expanded genomic resources for food legumes, ushering research into the panomics era. Despite their nutritional and agronomic importance, food legumes still face constraints in yield potential and genetic improvement due to limited genomic resources, complex inheritance patterns, and insufficient exploration of key traits, such as quality and stress resistance. This highlights the need for continued efforts to comprehensively dissect the phenome, genome, and regulome of these crops. This review summarizes recent advances in technological innovations and multi-omics applications in food legumes research and improvement. Given the critical role of germplasm resources and the challenges in applying phenomics to food legumes-such as complex trait architecture and limited standardized methodologies-we first address these foundational areas. We then discuss recent gene discoveries associated with yield stability, seed composition, and stress tolerance and their potential as breeding targets. Considering the growing role of genetic engineering, we provide an update on gene-editing applications in legumes, particularly CRISPR-based approaches for trait enhancement. We advocate for integrating chemical and biochemical signatures of cells ('molecular phenomics') with genetic mapping to accelerate gene discovery. We anticipate that combining panomics approaches with advanced breeding technologies will accelerate genetic gains in food legumes, enhancing their productivity, resilience, and contribution to sustainable global food security.
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Affiliation(s)
- Hongliang Hu
- Zhejiang-Israel Joint Laboratory for Plant Metrology and Equipment Innovation, College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Xingxing Yuan
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Dinesh Kumar Saini
- Department of Plant and Soil Science, Texas Tech University, Lubbock, TX 79409, USA
| | - Tao Yang
- State Key Laboratory of Crop Gene Resources and Breeding/ Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Haidian District, Beijing 100081, China
| | - Xinyi Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Ranran Wu
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Zehao Liu
- State Key Laboratory of Crop Gene Resources and Breeding/ Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Haidian District, Beijing 100081, China
| | - Farkhandah Jan
- Division of Genetics & Plant Breeding, Faculty of Agriculture, SKUAST-Kashmir, Wadura Campus, Sopore, Jammu and Kashmir 193201, India
| | - Reyazul Rouf Mir
- Centre for Crop and Food Innovation, WA State Agricultural Biotechnology Centre, Murdoch University, Murdoch WA 6150, Australia
| | - Liu Liu
- Zhejiang Xianghu Laboratory, Hangzhou, China
| | | | - Na Liu
- Zhejiang Xianghu Laboratory, Hangzhou, China
- State Key Laboratory for Quality and Safety of Agro-products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Pei Xu
- Zhejiang-Israel Joint Laboratory for Plant Metrology and Equipment Innovation, College of Life Sciences, China Jiliang University, Hangzhou 310018, China
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Muhammad M, Basit A, Ali K, Ahmad H, Li WJ, Khan A, Mohamed HI. A review on endophytic fungi: a potent reservoir of bioactive metabolites with special emphasis on blight disease management. Arch Microbiol 2024; 206:129. [PMID: 38416214 DOI: 10.1007/s00203-023-03828-x] [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: 11/15/2023] [Accepted: 12/30/2023] [Indexed: 02/29/2024]
Abstract
Phytopathogenic microorganisms have caused blight diseases that present significant challenges to global agriculture. These diseases result in substantial crop losses and have a significant economic impact. Due to the limitations of conventional chemical treatments in effectively and sustainably managing these diseases, there is an increasing interest in exploring alternative and environmentally friendly approaches for disease control. Using endophytic fungi as biocontrol agents has become a promising strategy in recent years. Endophytic fungi live inside plant tissues, forming mutually beneficial relationships, and have been discovered to produce a wide range of bioactive metabolites. These metabolites demonstrate significant potential for fighting blight diseases and provide a plentiful source of new biopesticides. In this review, we delve into the potential of endophytic fungi as a means of biocontrol against blight diseases. We specifically highlight their significance as a source of biologically active compounds. The review explores different mechanisms used by endophytic fungi to suppress phytopathogens. These mechanisms include competing for nutrients, producing antifungal compounds, and triggering plant defense responses. Furthermore, this review discusses the challenges of using endophytic fungi as biocontrol agents in commercial applications. It emphasizes the importance of conducting thorough research to enhance their effectiveness and stability in real-world environments. Therefore, bioactive metabolites from endophytic fungi have considerable potential for sustainable and eco-friendly blight disease control. Additional research on endophytes and their metabolites will promote biotechnology solutions.
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Affiliation(s)
- Murad Muhammad
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Abdul Basit
- Department of Horticultural Science, Kyungpook National University, Daegu, 41566, Korea
| | - Kashif Ali
- Center of Biotechnology and Microbiology, University of Peshawar, Peshawar, 25120, Pakistan
| | - Haris Ahmad
- Center of Biotechnology and Microbiology, University of Peshawar, Peshawar, 25120, Pakistan
| | - Wen-Jun Li
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Ayesha Khan
- Department of Horticulture, Faculty of Crop Production Sciences, The University of Agriculture, Peshawar, 25120, Pakistan
| | - Heba I Mohamed
- Biological and Geological Sciences Department, Faculty of Education, Ain Shams University, Cairo, 11341, Egypt.
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Aono AH, Pimenta RJG, Dambroz CMDS, Costa FCL, Kuroshu RM, de Souza AP, Pereira WA. Genome-wide characterization of the common bean kinome: Catalog and insights into expression patterns and genetic organization. Gene 2023; 855:147127. [PMID: 36563714 DOI: 10.1016/j.gene.2022.147127] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 12/06/2022] [Accepted: 12/16/2022] [Indexed: 12/25/2022]
Abstract
The protein kinase (PK) superfamily is one of the largest superfamilies in plants and is the core regulator of cellular signaling. Even considering this substantial importance, the kinome of common bean (Phaseolus vulgaris) has not been profiled yet. Here, we identified and characterised the complete set of kinases of common bean, performing an in-depth investigation with phylogenetic analyses and measurements of gene distribution, structural organization, protein properties, and expression patterns over a large set of RNA-Sequencing data. Being composed of 1,203 PKs distributed across all P. vulgaris chromosomes, this set represents 3.25% of all predicted proteins for the species. These PKs could be classified into 20 groups and 119 subfamilies, with a more pronounced abundance of subfamilies belonging to the receptor-like kinase (RLK)-Pelle group. In addition to provide a vast and rich reservoir of data, our study supplied insights into the compositional similarities between PK subfamilies, their evolutionary divergences, highly variable functional profile, structural diversity, and expression patterns, modeled with coexpression networks for investigating putative interactions associated with stress response.
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Affiliation(s)
- Alexandre Hild Aono
- Molecular Biology and Genetic Engineering Center (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil.
| | | | | | | | - Reginaldo Massanobu Kuroshu
- Instituto de Ciência e Tecnologia, Universidade Federal de São Paulo (UNIFESP), São José dos Campos, Brazil.
| | - Anete Pereira de Souza
- Molecular Biology and Genetic Engineering Center (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil; Department of Plant Biology, Biology Institute, University of Campinas (UNICAMP), Campinas, Brazil.
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Khoshru B, Mitra D, Joshi K, Adhikari P, Rion MSI, Fadiji AE, Alizadeh M, Priyadarshini A, Senapati A, Sarikhani MR, Panneerselvam P, Mohapatra PKD, Sushkova S, Minkina T, Keswani C. Decrypting the multi-functional biological activators and inducers of defense responses against biotic stresses in plants. Heliyon 2023; 9:e13825. [PMID: 36873502 PMCID: PMC9981932 DOI: 10.1016/j.heliyon.2023.e13825] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 01/31/2023] [Accepted: 02/14/2023] [Indexed: 02/19/2023] Open
Abstract
Plant diseases are still the main problem for the reduction in crop yield and a threat to global food security. Additionally, excessive usage of chemical inputs such as pesticides and fungicides to control plant diseases have created another serious problem for human and environmental health. In view of this, the application of plant growth-promoting rhizobacteria (PGPR) for controlling plant disease incidences has been identified as an eco-friendly approach for coping with the food security issue. In this review, we have identified different ways by which PGPRs are capable of reducing phytopathogenic infestations and enhancing crop yield. PGPR suppresses plant diseases, both directly and indirectly, mediated by microbial metabolites and signaling components. Microbial synthesized anti-pathogenic metabolites such as siderophores, antibiotics, lytic enzymes, hydrogen cyanide, and several others act directly on phytopathogens. The indirect mechanisms of reducing plant disease infestation are caused by the stimulation of plant immune responses known as initiation of systemic resistance (ISR) which is mediated by triggering plant immune responses elicited through pathogen-associated molecular patterns (PAMPs). The ISR triggered in the infected region of the plant leads to the development of systemic acquired resistance (SAR) throughout the plant making the plant resistant to a wide range of pathogens. A number of PGPRs including Pseudomonas and Bacillus genera have proven their ability to stimulate ISR. However, there are still some challenges in the large-scale application and acceptance of PGPR for pest and disease management. Further, we discuss the newly formulated PGPR inoculants possessing both plant growth-promoting activities and plant disease suppression ability for a holistic approach to sustaining plant health and enhancing crop productivity.
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Affiliation(s)
- Bahman Khoshru
- Department of Soil Science, Faculty of Agriculture, University of Tabriz, Tabriz, Iran
| | - Debasis Mitra
- Department of Microbiology, Raiganj University, Raiganj - 733 134, West Bengal, India
| | - Kuldeep Joshi
- G.B. Pant National Institute of Himalayan Environment, Kosi-Katarmal, Almora-263643, Uttarakhand, India
| | - Priyanka Adhikari
- Centre for Excellence on GMP Extraction Facility (DBT, Govt. of India), National Institute of Pharmaceutical Education and Research. Guwahati-781101, Assam, India
| | | | - Ayomide Emmanuel Fadiji
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho 2735, South Africa
| | - Mehrdad Alizadeh
- Department of Plant Pathology, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
| | - Ankita Priyadarshini
- Crop Production Division, ICAR – National Rice Research Institute, Cuttack, 753006, Odisha, India
| | - Ansuman Senapati
- Crop Production Division, ICAR – National Rice Research Institute, Cuttack, 753006, Odisha, India
| | | | - Periyasamy Panneerselvam
- Crop Production Division, ICAR – National Rice Research Institute, Cuttack, 753006, Odisha, India
| | | | - Svetlana Sushkova
- Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don 344090, Russia
| | - Tatiana Minkina
- Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don 344090, Russia
| | - Chetan Keswani
- Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don 344090, Russia
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Rahmanzadeh A, Khahani B, Taghavi SM, Khojasteh M, Osdaghi E. Genome-wide meta-QTL analyses provide novel insight into disease resistance repertoires in common bean. BMC Genomics 2022; 23:680. [PMID: 36192697 PMCID: PMC9531352 DOI: 10.1186/s12864-022-08914-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Accepted: 09/27/2022] [Indexed: 11/02/2023] Open
Abstract
BACKGROUND Common bean (Phaseolus vulgaris) is considered a staple food in a number of developing countries. Several diseases attack the crop leading to substantial economic losses around the globe. However, the crop has rarely been investigated for multiple disease resistance traits using Meta-analysis approach. RESULTS AND CONCLUSIONS In this study, in order to identify the most reliable and stable quantitative trait loci (QTL) conveying disease resistance in common bean, we carried out a meta-QTL (MQTL) analysis using 152 QTLs belonging to 44 populations reported in 33 publications within the past 20 years. These QTLs were decreased into nine MQTLs and the average of confidence interval (CI) was reduced by 2.64 folds with an average of 5.12 cM in MQTLs. Uneven distribution of MQTLs across common bean genome was noted where sub-telomeric regions carry most of the corresponding genes and MQTLs. One MQTL was identified to be specifically associated with resistance to halo blight disease caused by the bacterial pathogen Pseudomonas savastanoi pv. phaseolicola, while three and one MQTLs were specifically associated with resistance to white mold and anthracnose caused by the fungal pathogens Sclerotinia sclerotiorum and Colletotrichum lindemuthianum, respectively. Furthermore, two MQTLs were detected governing resistance to halo blight and anthracnose, while two MQTLs were detected for resistance against anthracnose and white mold, suggesting putative genes governing resistance against these diseases at a shared locus. Comparative genomics and synteny analyses provide a valuable strategy to identify a number of well‑known functionally described genes as well as numerous putative novels candidate genes in common bean, Arabidopsis and soybean genomes.
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Affiliation(s)
- Asma Rahmanzadeh
- Department of Plant Protection, School of Agriculture, Shiraz University, Shiraz, 71441-65186, Iran
| | - Bahman Khahani
- Department of Plant Genetics and Production, College of Agriculture, Shiraz University, Shiraz, Iran
| | - S Mohsen Taghavi
- Department of Plant Protection, School of Agriculture, Shiraz University, Shiraz, 71441-65186, Iran
| | - Moein Khojasteh
- Department of Plant Protection, School of Agriculture, Shiraz University, Shiraz, 71441-65186, Iran.
| | - Ebrahim Osdaghi
- Department of Plant Protection, College of Agriculture, University of Tehran, Karaj, 31587-77871, Iran.
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Cooper B. The Detriment of Salicylic Acid to the Pseudomonas savastanoi pv. phaseolicola Proteome. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2022; 35:814-824. [PMID: 35612310 DOI: 10.1094/mpmi-05-22-0104-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Salicylic acid (SA), a natural product, is the major hormonal regulator of the plant immune system. SA also has antibacterial activity that is not completely elucidated. To gain a better understanding of this, Pseudomonas savastanoi pv. phaseolicola, a bacterial pathogen of beans, was exposed to sub-inhibitory amounts of SA and was then examined using quantitative mass spectrometry. Among the 2,185 proteins quantified, there were pronounced increases in p-hydroxybenzoic acid efflux pumps and multidrug efflux pumps. By contrast there were significant decreases in porin proteins, high-osmolarity response proteins, and protein components of the type VI secretion system. In addition, there were alterations in enzymes likely affecting the production of alginate, which is needed for infection. Furthermore, there was a decrease in an enzyme needed to detoxify methylglyoxal. Assays confirmed a reduction in alginate production and an increase in cellular methylglyoxal concentrations after SA treatment. Culture assays demonstrated that SA altered bacterial growth curves more so than other hydroxylated benzoic acid isomers. These data reveal that SA is antibiotic and that P. savastanoi pv. phaseolicola significantly alters its proteome in response to SA in vitro. Similar alterations to the bacterial proteome occur in beans during an immune reaction when SA increases at the site of infection. Thus, in beans, SA likely deters bacterial infection by adversely altering the bacterial proteome. [Formula: see text] The author(s) have dedicated the work to the public domain under the Creative Commons CC0 "No Rights Reserved" license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law, 2022.
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Affiliation(s)
- Bret Cooper
- Soybean Genomics and Improvement Laboratory, USDA-ARS, Beltsville, MD, 20705, U.S.A
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Cooper B, Campbell KB, Garrett WM. Salicylic Acid and Phytoalexin Induction by a Bacterium that Causes Halo Blight in Beans. PHYTOPATHOLOGY 2022; 112:1766-1775. [PMID: 35147446 DOI: 10.1094/phyto-12-21-0496-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Pseudomonas savastanoi pv. phaseolicola is a bacterium that causes halo blight in beans. Different varieties of beans have hypersensitive resistance to specific races of P. savastanoi pv. phaseolicola. During hypersensitive resistance, also known as effector-triggered immunity (ETI), beans produce hormones that signal molecular processes to produce phytoalexins that are presumed to be antibiotic to bacteria. To shed light on hormone and phytoalexin production during immunity, we inoculated beans with virulent and avirulent races of P. savastanoi pv. phaseolicola. We then used mass spectrometry to measure the accumulation of salicylic acid (SA), the primary hormone that controls immunity in plants, and other hormones including jasmonate, methyljasmonate, indole-3-acetic acid, abscisic acid, cytokinin, gibberellic acid, and 1-aminocyclopropane-1-carboxylic acid. SA, but no other examined hormone, consistently increased at sites of infection to greater levels in resistant beans compared with susceptible beans at 4 days after inoculation. We then monitored 10 candidate bean phytoalexins. Daidzein, genistein, kievitone, phaseollin, phaseollidin, coumestrol, and resveratrol substantially increased alongside SA in resistant beans but not in susceptible beans. In vitro culture assays revealed that SA, daidzein, genistein, coumestrol, and resveratrol inhibited P. savastanoi pv. phaseolicola race 5 culture growth. These results demonstrate that these phytoalexins may be regulated by SA and work with SA during ETI to restrict bacterial replication. This is the first report of antibiotic activity for daidzein, genistein, and resveratrol to P. savastanoi pv. phaseolicola. These results improve our understanding of the mechanistic output of ETI toward this bacterial pathogen of beans.
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Affiliation(s)
- Bret Cooper
- U.S. Department of Agriculture, Agricultural Research Service, Soybean Genomics and Improvement Laboratory, Beltsville, MD 20705
| | - Kimberly B Campbell
- U.S. Department of Agriculture, Agricultural Research Service, Soybean Genomics and Improvement Laboratory, Beltsville, MD 20705
| | - Wesley M Garrett
- U.S. Department of Agriculture, Agricultural Research Service, Animal Biosciences and Biotechnology Laboratory, Beltsville, MD 20705
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De la Rubia AG, Centeno ML, Moreno-González V, De Castro M, García-Angulo P. Perception and First Defense Responses Against Pseudomonas syringae pv. phaseolicola in Phaseolus vulgaris: Identification of Wall-Associated Kinase Receptors. PHYTOPATHOLOGY 2021; 111:2332-2342. [PMID: 33944603 DOI: 10.1094/phyto-10-20-0449-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Common bean (Phaseolus vulgaris) is attacked by several pathogens such as the biotrophic gamma-proteobacterium Pseudomonas syringae pv. phaseolicola. To study the P. syringae pv. phaseolicola-bean interaction during the first stages of infection, leaf discs of a susceptible bean cultivar Riñón were infected with pathogenic P. syringae pv. phaseolicola. Using this experimental system, we tested six new putative wall-associated kinase (WAK) receptors, previously identified in silico. These six P. vulgaris WAKs (PvWAKs) showed high protein sequence homology to the well-described Arabidopsis thaliana WAK1 (AtWAK1) receptor and, by phylogenetic analysis, clustered together with AtWAKs. The expression of PvWAK1 increased at very early stages after the P. syringae pv. phaseolicola infection. Time course experiments were performed to evaluate the accumulation of apoplastic H2O2, Ca2+ influx, total H2O2, antioxidant enzymatic activities, lipid peroxidation, and the concentrations of abscisic acid and salicylic acid (SA), as well as the expression of six defense-related genes: MEKK-1, MAPKK, WRKY33, RIN4, PR1, and NPR1. The results showed that overexpression of PR1 occurred 2 h after P. syringae pv. phaseolicola infection without a concomitant increase in SA levels. Although apoplastic H2O2 increased after infection, the oxidative burst was neither intense nor rapid, and an efficient antioxidant response did not occur, suggesting that the observed cellular damage was caused by the initial increase in total H2O2 early after infection. In conclusion, Riñón can perceive the presence of P. syringae pv. phaseolicola, but this recognition results in only a modest and slow activation of host defenses, leading to high susceptibility to P. syringae pv. phaseolicola.
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Affiliation(s)
- Alfonso Gonzalo De la Rubia
- Área de Fisiología Vegetal, Departamento de Ingeniería y Ciencias Agrarias, Universidad de León, E-24071, León, Spain
| | - María Luz Centeno
- Área de Fisiología Vegetal, Departamento de Ingeniería y Ciencias Agrarias, Universidad de León, E-24071, León, Spain
| | - Victor Moreno-González
- Área de Zoología, Departamento de Biodiversidad y Gestión Ambiental, Universidad de León, E-24071, León, Spain
| | - María De Castro
- Departamento de Biotecnología Vegetal, Laboratorios Analíticos Agrovet, Mansilla Mayor, 24217, León, España
| | - Penélope García-Angulo
- Área de Fisiología Vegetal, Departamento de Ingeniería y Ciencias Agrarias, Universidad de León, E-24071, León, Spain
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Cooper B, Beard HS, Yang R, Garrett WM, Campbell KB. Bacterial Immobilization and Toxicity Induced by a Bean Plant Immune System. J Proteome Res 2021; 20:3664-3677. [PMID: 34097416 DOI: 10.1021/acs.jproteome.1c00232] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Pseudomonas savastanoi pv. phaseolicola causes halo blight disease in the common bean Phaseolus vulgaris. The bacterium invades the leaf apoplast and uses a type III secretion system to inject effector proteins into a bean cell to interfere with the bean immune system. Beans counter with resistance proteins that can detect effectors and coordinate effector-triggered immunity responses transduced by salicylic acid, the primary defense hormone. Effector-triggered immunity halts bacterial spread, but its direct effect on the bacterium is not known. In this study, mass spectrometry of bacterial infections from immune and susceptible beans revealed that immune beans inhibited the accumulation of bacterial proteins required for virulence, secretion, motility, chemotaxis, quorum sensing, and alginate production. Sets of genes encoding these proteins appeared to function in operons, which implies that immunity altered the coregulated genes in the bacterium. Immunity also reduced amounts of bacterial methylglyoxal detoxification enzymes and their transcripts. Treatment of bacteria with salicylic acid, the plant hormone produced during immunity, reduced bacterial growth, decreased gene expression for methylglyoxal detoxification enzymes, and increased bacterial methylglyoxal concentrations in vitro. Increased methylglyoxal concentrations reduced bacterial reproduction. These findings support the hypothesis that plant immunity involves the chemical induction of adverse changes to the bacterial proteome to reduce pathogenicity and to cause bacterial self-toxicity.
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Affiliation(s)
- Bret Cooper
- Soybean Genomics and Improvement Laboratory, USDA-ARS, Beltsville 20705, Maryland, United States
| | - Hunter S Beard
- Soybean Genomics and Improvement Laboratory, USDA-ARS, Beltsville 20705, Maryland, United States
| | - Ronghui Yang
- Soybean Genomics and Improvement Laboratory, USDA-ARS, Beltsville 20705, Maryland, United States
| | - Wesley M Garrett
- Animal Biosciences and Biotechnology Laboratory, USDA-ARS, Beltsville 20705, Maryland, United States
| | - Kimberly B Campbell
- Soybean Genomics and Improvement Laboratory, USDA-ARS, Beltsville 20705, Maryland, United States
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10
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Cooper B, Yang R. Genomic Resources for Pseudomonas savastanoi pv. phaseolicola Races 5 and 8. PHYTOPATHOLOGY 2021; 111:893-895. [PMID: 33315475 DOI: 10.1094/phyto-10-20-0462-a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Pseudomonas savastanoi pv. phaseolicola causes halo blight disease on Phaseolus vulgaris. Using a long-read DNA sequencing platform, we assembled the genome sequences for P. savastanoi pv. phaseolicola races 5 and 8 that have distinguishable avirulent and virulent phenotypes on Phaseolus vulgaris PI G19833, a common bean with an annotated genome sequence. The 12 race 5 assemblies comprise two major 4.5 and 1.4 Mb chromosome-like contigs and 10 smaller contigs. The four race 8 assemblies comprise a major 6.1 Mb chromosome and three smaller contigs. Annotation yielded 5,890 genes for race 5 and 5,919 genes for race 8. These data will enable the discovery of the genetic and proteomic differences between these two races and allow comparisons to other races for which genomic information already exists.
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Affiliation(s)
- Bret Cooper
- Soybean Genomics and Improvement Laboratory, U.S. Department of Agriculture-Agriculture Research Service, Beltsville, MD
| | - Ronghui Yang
- Soybean Genomics and Improvement Laboratory, U.S. Department of Agriculture-Agriculture Research Service, Beltsville, MD
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11
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Klein A, Husselmann LHH, Williams A, Bell L, Cooper B, Ragar B, Tabb DL. Proteomic Identification and Meta-Analysis in Salvia hispanica RNA-Seq de novo Assemblies. PLANTS (BASEL, SWITZERLAND) 2021; 10:765. [PMID: 33919777 PMCID: PMC8070742 DOI: 10.3390/plants10040765] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 03/26/2021] [Accepted: 03/28/2021] [Indexed: 11/24/2022]
Abstract
While proteomics has demonstrated its value for model organisms and for organisms with mature genome sequence annotations, proteomics has been of less value in nonmodel organisms that are unaccompanied by genome sequence annotations. This project sought to determine the value of RNA-Seq experiments as a basis for establishing a set of protein sequences to represent a nonmodel organism, in this case, the pseudocereal chia. Assembling four publicly available chia RNA-Seq datasets produced transcript sequence sets with a high BUSCO completeness, though the number of transcript sequences and Trinity "genes" varied considerably among them. After six-frame translation, ProteinOrtho detected substantial numbers of orthologs among other species within the taxonomic order Lamiales. These protein sequence databases demonstrated a good identification efficiency for three different LC-MS/MS proteomics experiments, though a seed proteome showed considerable variability in the identification of peptides based on seed protein sequence inclusion. If a proteomics experiment emphasizes a particular tissue, an RNA-Seq experiment incorporating that same tissue is more likely to support a database search identification of that proteome.
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Affiliation(s)
- Ashwil Klein
- Department of Biotechnology, University of the Western Cape, Bellville 7535, South Africa; (A.K.); (L.H.H.H.); (A.W.)
| | - Lizex H. H. Husselmann
- Department of Biotechnology, University of the Western Cape, Bellville 7535, South Africa; (A.K.); (L.H.H.H.); (A.W.)
| | - Achmat Williams
- Department of Biotechnology, University of the Western Cape, Bellville 7535, South Africa; (A.K.); (L.H.H.H.); (A.W.)
| | - Liam Bell
- Centre for Proteomic and Genomic Research, Cape Town 7925, South Africa;
| | - Bret Cooper
- USDA Agricultural Research Service, Beltsville, MD 20705, USA;
| | - Brent Ragar
- Departments of Internal Medicine and Pediatrics, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02150, USA;
| | - David L. Tabb
- Department of Biotechnology, University of the Western Cape, Bellville 7535, South Africa; (A.K.); (L.H.H.H.); (A.W.)
- Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7500, South Africa
- Centre for Bioinformatics and Computational Biology, Stellenbosch University, Stellenbosch 7602, South Africa
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