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Rocher F, Dou S, Philippe G, Martin ML, Label P, Langin T, Bonhomme L. Integrative systems biology of wheat susceptibility to Fusarium graminearum uncovers a conserved gene regulatory network and identifies master regulators targeted by fungal core effectors. BMC Biol 2024; 22:53. [PMID: 38443953 PMCID: PMC10916188 DOI: 10.1186/s12915-024-01852-x] [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: 10/11/2023] [Accepted: 02/21/2024] [Indexed: 03/07/2024] Open
Abstract
BACKGROUND Plant diseases are driven by an intricate set of defense mechanisms counterbalanced by the expression of host susceptibility factors promoted through the action of pathogen effectors. In spite of their central role in the establishment of the pathology, the primary components of plant susceptibility are still poorly understood and challenging to trace especially in plant-fungal interactions such as in Fusarium head blight (FHB) of bread wheat. Designing a system-level transcriptomics approach, we leveraged the analysis of wheat responses from a susceptible cultivar facing Fusarium graminearum strains of different aggressiveness and examined their constancy in four other wheat cultivars also developing FHB. RESULTS In this study, we describe unexpected differential expression of a conserved set of transcription factors and an original subset of master regulators were evidenced using a regulation network approach. The dual-integration with the expression data of pathogen effector genes combined with database mining, demonstrated robust connections with the plant molecular regulators and identified relevant candidate genes involved in plant susceptibility, mostly able to suppress plant defense mechanisms. Furthermore, taking advantage of wheat cultivars of contrasting susceptibility levels, a refined list of 142 conserved susceptibility gene candidates was proposed to be necessary host's determinants for the establishment of a compatible interaction. CONCLUSIONS Our findings emphasized major FHB determinants potentially controlling a set of conserved responses associated with susceptibility in bread wheat. They provide new clues for improving FHB control in wheat and also could conceivably leverage further original researches dealing with a broader spectrum of plant pathogens.
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Affiliation(s)
- Florian Rocher
- UMR 1095 Génétique Diversité Ecophysiologie Des Céréales, Université Clermont Auvergne, INRAE, Clermont-Ferrand, France
| | - Samir Dou
- UMR 1095 Génétique Diversité Ecophysiologie Des Céréales, Université Clermont Auvergne, INRAE, Clermont-Ferrand, France
| | - Géraldine Philippe
- UMR 1095 Génétique Diversité Ecophysiologie Des Céréales, Université Clermont Auvergne, INRAE, Clermont-Ferrand, France
| | - Marie-Laure Martin
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Gif Sur Yvette, 91190, France
- Université de Paris, Institute of Plant Sciences Paris-Saclay (IPS2), Gif Sur Yvette, 91190, France
- UMR MIA Paris-Saclay, AgroParisTech, INRAE, Université Paris-Saclay, Gif Sur Yvette, France
| | - Philippe Label
- Physique Et Physiologie Intégratives de L'Arbre en Environnement Fluctuant, Université Clermont Auvergne, INRAE, UMR 547, Aubière, Cedex, France
| | - Thierry Langin
- UMR 1095 Génétique Diversité Ecophysiologie Des Céréales, Université Clermont Auvergne, INRAE, Clermont-Ferrand, France
| | - Ludovic Bonhomme
- UMR 1095 Génétique Diversité Ecophysiologie Des Céréales, Université Clermont Auvergne, INRAE, Clermont-Ferrand, France.
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2
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Zhang Z, Luo W, Chen G, Chen J, Lin S, Ren T, Lin Z, Zhao C, Wen H, Nie Q, Meng X, Zhang X. Chicken muscle antibody array reveals the regulations of LDHA on myoblast differentiation through energy metabolism. Int J Biol Macromol 2024; 254:127629. [PMID: 37890747 DOI: 10.1016/j.ijbiomac.2023.127629] [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: 08/08/2023] [Revised: 10/20/2023] [Accepted: 10/21/2023] [Indexed: 10/29/2023]
Abstract
Myoblast proliferation and differentiation are highly dynamic and regulated processes in skeletal muscle development. Given that proteins serve as the executors for the majority of biological processes, exploring key regulatory factors and mechanisms at the protein level offers substantial opportunities for understanding the skeletal muscle development. In this study, a total of 607 differentially expressed proteins between proliferation and differentiation in myoblasts were screened out using our chicken muscle antibody array. Biological function analysis revealed the importance of energy production processes and compound metabolic processes in myogenesis. Our antibody array specifically identified an upregulation of LDHA during differentiation, which was associated with the energy metabolism. Subsequent investigation demonstrated that LDHA promoted the glycolysis and TCA cycle, thereby enhancing myoblasts differentiation. Mechanistically, LDHA promotes the glycolysis and TCA cycle but inhibits the ETC oxidative phosphorylation through enhancing the NADH cycle, providing the intermediate metabolites that improve the myoblasts differentiation. Additionally, increased glycolytic ATP by LDHA induces Akt phosphorylation and activate the PI3K-Akt pathway, which might also contribute to the promotion of myoblasts differentiation. Our studies not only present a powerful tool for exploring myogenic regulatory factors in chicken muscle, but also identify a novel role for LDHA in modulating myoblast differentiation through its regulation of cellular NAD+ levels and subsequent downstream effects on mitochondrial function.
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Affiliation(s)
- Zihao Zhang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou 510642, China; State Key Laboratory of Livestock and Poultry Breeding, South China Agricultural University, Guangzhou 510642, China; College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China
| | - Wen Luo
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou 510642, China; State Key Laboratory of Livestock and Poultry Breeding, South China Agricultural University, Guangzhou 510642, China; Lingnan Guangdong Laboratory of Agriculture, South China Agricultural University, Guangzhou 510642, China; Department of Orthaepedics and Traumatology, The Chinese University of Hong Kong, Hong Kong 999077, China
| | - Genghua Chen
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou 510642, China; State Key Laboratory of Livestock and Poultry Breeding, South China Agricultural University, Guangzhou 510642, China
| | - Jiahui Chen
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou 510642, China; State Key Laboratory of Livestock and Poultry Breeding, South China Agricultural University, Guangzhou 510642, China
| | - Shudai Lin
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China
| | - Tuanhui Ren
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou 510642, China; State Key Laboratory of Livestock and Poultry Breeding, South China Agricultural University, Guangzhou 510642, China
| | - Zetong Lin
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou 510642, China; State Key Laboratory of Livestock and Poultry Breeding, South China Agricultural University, Guangzhou 510642, China
| | - Changbin Zhao
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou 510642, China; State Key Laboratory of Livestock and Poultry Breeding, South China Agricultural University, Guangzhou 510642, China
| | - Huaqiang Wen
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou 510642, China; State Key Laboratory of Livestock and Poultry Breeding, South China Agricultural University, Guangzhou 510642, China
| | - Qinghua Nie
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou 510642, China; State Key Laboratory of Livestock and Poultry Breeding, South China Agricultural University, Guangzhou 510642, China; Lingnan Guangdong Laboratory of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Xun Meng
- School of Life Sciences, Northwest University, Xi'an 710069, China; Abmart, 333 Guiping Road, Shanghai 200033, China.
| | - Xiquan Zhang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou 510642, China; State Key Laboratory of Livestock and Poultry Breeding, South China Agricultural University, Guangzhou 510642, China; Lingnan Guangdong Laboratory of Agriculture, South China Agricultural University, Guangzhou 510642, China.
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Liu B, Stevens-Green R, Johal D, Buchanan R, Geddes-McAlister J. Fungal pathogens of cereal crops: Proteomic insights into fungal pathogenesis, host defense, and resistance. JOURNAL OF PLANT PHYSIOLOGY 2022; 269:153593. [PMID: 34915227 DOI: 10.1016/j.jplph.2021.153593] [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: 08/31/2021] [Revised: 11/28/2021] [Accepted: 12/10/2021] [Indexed: 06/14/2023]
Abstract
Fungal infections of cereal crops pose a significant risk to global food security through reduced grain production and quality, as well as contamination of animal feed and human products for consumption. To combat fungal disease, we need to understand how the pathogen adapts and survives within the hostile environment of the host and how the host's defense response can be modulated for protection from disease. Such investigations offer insight into fungal pathogenesis, host immunity, the development of resistance, and mechanisms of action for currently-used control strategies. Mass spectrometry-based proteomics provides a technologically-advanced platform to define differences among fungal pathogens and their hosts at the protein level, supporting the discovery of proteins critical for disease, and uncovering novel host responses driving susceptibly or resistance of the host. In this Review, we explore the role of mass spectrometry-based proteomics in defining the intricate relationship between a pathogen and host during fungal disease of cereal crops with a focus on recent discoveries derived from the globally-devastating diseases of Fusarium head blight, Rice blast, and Powdery mildew. We highlight advances made for each of these diseases and discuss opportunities to extrapolate findings to further our fight against fungal pathogens on a global scale.
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Affiliation(s)
- B Liu
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - R Stevens-Green
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - D Johal
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - R Buchanan
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - J Geddes-McAlister
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada; Canadian Proteomics and Artificial Intelligence Research and Training Consortium, Canada.
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Yang M, Wang X, Dong J, Zhao W, Alam T, Thomashow LS, Weller DM, Gao X, Rustgi S, Wen S. Proteomics Reveals the Changes that Contribute to Fusarium Head Blight Resistance in Wheat. PHYTOPATHOLOGY 2021; 111:386-397. [PMID: 32706317 DOI: 10.1094/phyto-05-20-0171-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: 05/20/2023]
Abstract
Fusarium head blight (FHB) is a devastating disease of wheat, causing yield losses and quality reduction as a result of mycotoxin production. In this study, iTRAQ (isobaric tags for relative and absolute quantification)-labeling-based mass spectrometry was employed to characterize the proteome in wheat cultivars Xinong 538 and Zhoumai 18 with contrasting levels of FHB resistance as a means to elucidate the molecular mechanisms contributing to FHB resistance. A total of 13,669 proteins were identified in the two cultivars 48 h after Fusarium graminearum inoculation. Among these, 2,505 unique proteins exclusively accumulated in Xinong 538 (resistant) and 887 proteins in Zhoumai 18 (susceptible). Gene Ontology enrichment analysis showed that most differentially accumulated proteins (DAPs) from both cultivars were assigned to the following categories: metabolic process, single-organism process, cellular process, and response to stimulus. Kyoto Encyclopedia of Genes and Genomes analysis showed that a greater number of proteins belonging to different metabolic pathways were identified in Xinong 538 compared with Zhoumai 18. Specifically, DAPs from the FHB-resistant cultivar Xinong 538 populated categories of metabolic pathways related to plant-pathogen interaction. These DAPs might play a critical role in defense responses exhibited by Xinong 538. DAPs from both genotypes were assigned to all wheat chromosomes except chromosome 6B, with approximately 30% mapping to wheat chromosomes 2B, 3B, 5B, and 5D. Twenty single nucleotide polymorphism markers, flanking DAPs on chromosomes 1B, 3B, 5B, and 6A, overlapped with the location of earlier mapped FHB-resistance quantitative trait loci. The data provide evidence for the involvement of several DAPs in the early stages of the FHB-resistance response in wheat; however, further functional characterization of candidate proteins is warranted.
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Affiliation(s)
- Mingming Yang
- College of Agronomy, Northwest A&F University, Yangling 712100, People's Republic of China
- Wheat Engineering Research Center of Shaanxi Province, Yangling 712100, People's Republic of China
| | - Xianguo Wang
- College of Agronomy, Northwest A&F University, Yangling 712100, People's Republic of China
| | - Jian Dong
- College of Agronomy, Northwest A&F University, Yangling 712100, People's Republic of China
- Wheat Engineering Research Center of Shaanxi Province, Yangling 712100, People's Republic of China
| | - Wanchun Zhao
- College of Agronomy, Northwest A&F University, Yangling 712100, People's Republic of China
- Wheat Engineering Research Center of Shaanxi Province, Yangling 712100, People's Republic of China
| | - Tariq Alam
- Department of Plant and Environmental Sciences, Clemson University Pee Dee Research and Education Center, Florence, SC 29506, U.S.A
| | - Linda S Thomashow
- Wheat Health, Genetics, and Quality Research Unit, U.S. Department of Agriculture-Agricultural Research Service, Pullman, WA 99164-6430, U.S.A
| | - David M Weller
- Wheat Health, Genetics, and Quality Research Unit, U.S. Department of Agriculture-Agricultural Research Service, Pullman, WA 99164-6430, U.S.A
| | - Xiang Gao
- College of Agronomy, Northwest A&F University, Yangling 712100, People's Republic of China
- Wheat Engineering Research Center of Shaanxi Province, Yangling 712100, People's Republic of China
| | - Sachin Rustgi
- Department of Plant and Environmental Sciences, Clemson University Pee Dee Research and Education Center, Florence, SC 29506, U.S.A
| | - Shanshan Wen
- College of Agronomy, Northwest A&F University, Yangling 712100, People's Republic of China
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Fabre F, Urbach S, Roche S, Langin T, Bonhomme L. Proteomics-Based Data Integration of Wheat Cultivars Facing Fusarium graminearum Strains Revealed a Core-Responsive Pattern Controlling Fusarium Head Blight. FRONTIERS IN PLANT SCIENCE 2021; 12:644810. [PMID: 34135919 PMCID: PMC8201412 DOI: 10.3389/fpls.2021.644810] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 04/07/2021] [Indexed: 05/03/2023]
Abstract
Fusarium head blight (FHB), mainly occurring upon Fusarium graminearum infection in a wide variety of small-grain cereals, is supposed to be controlled by a range of processes diverted by the fungal pathogen, the so-called susceptibility factors. As a mean to provide relevant information about the molecular events involved in FHB susceptibility in bread wheat, we studied an extensive proteome of more than 7,900 identified wheat proteins in three cultivars of contrasting susceptibilities during their interaction with three F. graminearum strains of different aggressiveness. No cultivar-specific proteins discriminated the three wheat genotypes, demonstrating the establishment of a core proteome regardless of unequivocal FHB susceptibility differences. Quantitative protein analysis revealed that most of the FHB-induced molecular adjustments were shared by wheat cultivars and occurred independently of the F. graminearum strain aggressiveness. Although subtle abundance changes evidenced genotype-dependent responses to FHB, cultivar distinction was found to be mainly due to basal abundance differences, especially regarding the chloroplast functions. Integrating these data with previous proteome mapping of the three F. graminearum strains facing the three same wheat cultivars, we demonstrated strong correlations between the wheat protein abundance changes and the adjustments of fungal proteins supposed to interfere with host molecular functions. Together, these results provide a resourceful dataset that expands our understanding of the specific molecular events taking place during the wheat-F. graminearum interaction.
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Affiliation(s)
- Francis Fabre
- Université Clermont Auvergne, INRAE, UMR 1095 Génétique Diversité Ecophysiologie des Céréales, Clermont-Ferrand, France
| | - Serge Urbach
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, Montpellier, France
| | - Sylvie Roche
- INRAE, Unité Experimentale 1375, Phénotypage au Champ des Céréales (PHACC), Clermont-Ferrand, France
| | - Thierry Langin
- Université Clermont Auvergne, INRAE, UMR 1095 Génétique Diversité Ecophysiologie des Céréales, Clermont-Ferrand, France
| | - Ludovic Bonhomme
- Université Clermont Auvergne, INRAE, UMR 1095 Génétique Diversité Ecophysiologie des Céréales, Clermont-Ferrand, France
- *Correspondence: Ludovic Bonhomme,
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