1
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Lee GH, Min CW, Jang JW, Wang Y, Jeon JS, Gupta R, Kim ST. Analysis of post-translational modification dynamics unveiled novel insights into Rice responses to MSP1. J Proteomics 2023; 287:104970. [PMID: 37467888 DOI: 10.1016/j.jprot.2023.104970] [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: 05/03/2023] [Revised: 07/04/2023] [Accepted: 07/09/2023] [Indexed: 07/21/2023]
Abstract
Magnaporthe oryzae snodprot1 homologous protein (MSP1) is known to function as a pathogen-associated molecular pattern (PAMP) and trigger PAMP-triggered immunity (PTI) in rice including induction of programmed cell death and expression of defense-related genes. The involvement of several post-translational modifications (PTMs) in the regulation of plant immune response, especially PTI, is well established, however, the information on the regulatory roles of these PTMs in response to MSP1-induced signaling is currently elusive. Here, we report the phosphoproteome, ubiquitinome, and acetylproteome to investigate the MSP1-induced PTMs alterations in MSP1 overexpressed and wild-type rice. Our analysis identified a total of 4666 PTMs-modified sites in rice leaves including 4292 phosphosites, 189 ubiquitin sites, and 185 acetylation sites. Among these, the PTM status of 437 phosphorylated, 53 ubiquitinated, and 68 acetylated peptides was significantly changed by MSP1. Functional annotation of MSP1 modulated peptides by MapMan analysis revealed that these were majorly associated with cellular immune responses including signaling, transcription factors, DNA and RNA regulation, and protein metabolism, among others. Taken together, our study provides novel insights into post-translational mediated regulation of rice proteins in response to M. oryzae secreted PAMP which help in understanding the molecular mechanism of MSP1-induced signaling in rice in greater detail. SIGNIFICANCE: The research investigates the effect of overexpression of MSP1 protein in rice leaves on the phosphoproteome, acetylome, and ubiquitinome. The study found that MSP1 is involved in rice protein phosphorylation, particularly in signaling pathways, and identified a key component, PTAC16, in MSP1-induced signaling. The analysis also revealed MSP1's role in protein degradation and modification by inducing ubiquitination of the target rice proteins. The research identified potential kinases involved in the phosphorylation of rice proteins, including casein kinase II, 14-3-3 domain binding motif, β-adrenergic receptor kinase, ERK1,2 kinase substrate motif, and casein kinase I motifs. Overall, the findings provide insights into the molecular mechanisms underlying of MSP1 induced signaling in rice which may have implications for improving crop yield and quality.
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Affiliation(s)
- Gi Hyun Lee
- Department of Plant Bioscience, Pusan National University, Miryang 50463, South Korea
| | - Cheol Woo Min
- Department of Plant Bioscience, Pusan National University, Miryang 50463, South Korea
| | - Jeong Woo Jang
- Department of Plant Bioscience, Pusan National University, Miryang 50463, South Korea
| | - Yiming Wang
- Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education, Department of Plant Pathology, Nanjing Agricultural University, 210095 Nanjing, China
| | - Jong-Seong Jeon
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Ravi Gupta
- College of General Education, Kookmin University, Seoul 02707, South Korea.
| | - Sun Tae Kim
- Department of Plant Bioscience, Pusan National University, Miryang 50463, South Korea.
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2
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Ducker C, Ratnam M, Shaw PE, Layfield R. Comparative analysis of protein expression systems and PTM landscape in the study of transcription factor ELK-1. Protein Expr Purif 2023; 203:106216. [PMID: 36528218 DOI: 10.1016/j.pep.2022.106216] [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: 10/11/2022] [Revised: 12/06/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022]
Abstract
Post-translational modifications (PTMs) are important for protein folding and activity, and the ability to recreate physiologically relevant PTM profiles on recombinantly-expressed proteins is vital for meaningful functional analysis. The ETS transcription factor ELK-1 serves as a paradigm for cellular responses to mitogens and can synergise with androgen receptor to promote prostate cancer progression, although in vitro protein function analyses to date have largely overlooked its complex PTM landscapes. We expressed and purified human ELK-1 using mammalian (HEK293T), insect (Sf9) and bacterial (E. coli) systems in parallel and compared PTMs imparted upon purified proteins, along with their performance in DNA and protein interaction assays. Phosphorylation of ELK-1 within its transactivation domain, known to promote DNA binding, was most apparent in protein isolated from human cells and accordingly conferred the strongest DNA binding in vitro, while protein expressed in insect cells bound most efficiently to the androgen receptor. We observed lysine acetylation, a hitherto unreported PTM of ELK-1, which appeared highest in insect cell-derived ELK-1 but was also present in HEK293T-derived ELK-1. Acetylation of ELK-1 was enhanced in HEK293T cells following starvation and mitogen stimulation, and modified lysines showed overlap with previously identified regulatory SUMOylation and ubiquitination sites. Our data demonstrate that the choice of recombinant expression system can be tailored to suit biochemical application rather than to maximise soluble protein production and suggest the potential for crosstalk and antagonism between different PTMs of ELK-1.
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Affiliation(s)
- Charles Ducker
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom.
| | - Manohar Ratnam
- Department of Oncology, Wayne State University School of Medicine and Barbara Ann Karmanos Cancer Institute, Detroit, MI, USA
| | - Peter E Shaw
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom
| | - Robert Layfield
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom
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3
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Song N, Lin J, Liu X, Liu Z, Liu D, Chu W, Li J, Chen Y, Chang S, Yang Q, Liu X, Guo W, Xin M, Yao Y, Peng H, Ni Z, Xie C, Sun Q, Hu Z. Histone acetyltransferase TaHAG1 interacts with TaPLATZ5 to activate TaPAD4 expression and positively contributes to powdery mildew resistance in wheat. THE NEW PHYTOLOGIST 2022; 236:590-607. [PMID: 35832009 PMCID: PMC9795918 DOI: 10.1111/nph.18372] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 07/06/2022] [Indexed: 05/24/2023]
Abstract
Plants have evolved a two-branched innate immune system to detect and cope with pathogen attack, which are initiated by cell-surface and intracellular immune receptors leading to pattern-triggered immunity (PTI) and effector-triggered immunity (ETI), respectively. A core transducer including PAD4-EDS1 node is proposed as the convergence point for a two-tiered immune system in conferring pathogen immunity. However, the transcriptional regulatory mechanisms controlling expression of these key transducers remain largely unknown. Here, we identified histone acetyltransferase TaHAG1 as a positive regulator of powdery mildew resistance in wheat. TaHAG1 regulates expression of key transducer gene TaPAD4 and promotes SA and reactive oxygen species accumulation to accomplish resistance to Bgt infection. Moreover, overexpression and CRISPR-mediated knockout of TaPAD4 validate its role in wheat powdery mildew resistance. Furthermore, TaHAG1 physically interacts with TaPLATZ5, a plant-specific zinc-binding protein. TaPLATZ5 directly binds to promoter of TaPAD4 and together with TaHAG1 to potentiate the expression of TaPAD4 by increasing the levels of H3 acetylation. Our study revealed a key transcription regulatory node in which TaHAG1 acts as an epigenetic modulator and interacts with TaPLATZ5 that confers powdery mildew resistance in wheat through activating a convergence point gene between PTI and ETI, which could be effective for genetic improvement of disease resistance in wheat and other crops.
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Affiliation(s)
- Na Song
- Frontiers Science Center for Molecular Design Breeding/State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijing100193China
| | - Jingchen Lin
- Frontiers Science Center for Molecular Design Breeding/State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijing100193China
| | - Xingbei Liu
- Frontiers Science Center for Molecular Design Breeding/State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijing100193China
| | - Zehui Liu
- Frontiers Science Center for Molecular Design Breeding/State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijing100193China
| | - Debiao Liu
- Frontiers Science Center for Molecular Design Breeding/State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijing100193China
| | - Wei Chu
- Frontiers Science Center for Molecular Design Breeding/State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijing100193China
| | - Jinpeng Li
- Frontiers Science Center for Molecular Design Breeding/State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijing100193China
| | - Yongming Chen
- Frontiers Science Center for Molecular Design Breeding/State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijing100193China
| | - Shumin Chang
- Frontiers Science Center for Molecular Design Breeding/State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijing100193China
| | - Qun Yang
- Frontiers Science Center for Molecular Design Breeding/State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijing100193China
| | - Xiaoyu Liu
- Frontiers Science Center for Molecular Design Breeding/State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijing100193China
| | - Weilong Guo
- Frontiers Science Center for Molecular Design Breeding/State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijing100193China
| | - Mingming Xin
- Frontiers Science Center for Molecular Design Breeding/State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijing100193China
| | - Yingyin Yao
- Frontiers Science Center for Molecular Design Breeding/State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijing100193China
| | - Huiru Peng
- Frontiers Science Center for Molecular Design Breeding/State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijing100193China
| | - Zhongfu Ni
- Frontiers Science Center for Molecular Design Breeding/State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijing100193China
| | - Chaojie Xie
- Frontiers Science Center for Molecular Design Breeding/State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijing100193China
| | - Qixin Sun
- Frontiers Science Center for Molecular Design Breeding/State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijing100193China
| | - Zhaorong Hu
- Frontiers Science Center for Molecular Design Breeding/State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijing100193China
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4
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Applications of cell- and tissue-specific 'omics to improve plant productivity. Emerg Top Life Sci 2022; 6:163-173. [PMID: 35293572 PMCID: PMC9023014 DOI: 10.1042/etls20210286] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Revised: 02/21/2022] [Accepted: 02/25/2022] [Indexed: 01/05/2023]
Abstract
The individual tissues and cell types of plants each have characteristic properties that contribute to the function of the plant as a whole. These are reflected by unique patterns of gene expression, protein and metabolite content, which enable cell-type-specific patterns of growth, development and physiology. Gene regulatory networks act within the cell types to govern the production and activity of these components. For the broader organism to grow and reproduce successfully, cell-type-specific activity must also function within the context of surrounding cell types, which is achieved by coordination of signalling pathways. We can investigate how gene regulatory networks are constructed and function using integrative ‘omics technologies. Historically such experiments in plant biological research have been performed at the bulk tissue level, to organ resolution at best. In this review, we describe recent advances in cell- and tissue-specific ‘omics technologies that allow investigation at much improved resolution. We discuss the advantages of these approaches for fundamental and translational plant biology, illustrated through the examples of specialised metabolism in medicinal plants and seed germination. We also discuss the challenges that must be overcome for such approaches to be adopted widely by the community.
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5
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Clark NM, Elmore JM, Walley JW. To the proteome and beyond: advances in single-cell omics profiling for plant systems. PLANT PHYSIOLOGY 2022; 188:726-737. [PMID: 35235661 PMCID: PMC8825333 DOI: 10.1093/plphys/kiab429] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 08/16/2021] [Indexed: 05/19/2023]
Abstract
Recent advances in single-cell proteomics for animal systems could be adapted for plants to increase our understanding of plant development, response to stimuli, and cell-to-cell signaling.
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Affiliation(s)
- Natalie M Clark
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011, USA
| | - James Mitch Elmore
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011, USA
| | - Justin W Walley
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011, USA
- Author for communication:
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Xia L, Kong X, Song H, Han Q, Zhang S. Advances in proteome-wide analysis of plant lysine acetylation. PLANT COMMUNICATIONS 2022; 3:100266. [PMID: 35059632 PMCID: PMC8760137 DOI: 10.1016/j.xplc.2021.100266] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 10/21/2021] [Accepted: 11/22/2021] [Indexed: 06/14/2023]
Abstract
Lysine acetylation (LysAc) is a conserved and important post-translational modification (PTM) that plays a key role in plant physiological and metabolic processes. Based on advances in Lys-acetylated protein immunoenrichment and mass-spectrometric technology, LysAc proteomics studies have been performed in many species. Such studies have made substantial contributions to our understanding of plant LysAc, revealing that Lys-acetylated histones and nonhistones are involved in a broad spectrum of plant cellular processes. Here, we present an extensive overview of recent research on plant Lys-acetylproteomes. We provide in-depth insights into the characteristics of plant LysAc modifications and the mechanisms by which LysAc participates in cellular processes and regulates metabolism and physiology during plant growth and development. First, we summarize the characteristics of LysAc, including the properties of Lys-acetylated sites, the motifs that flank Lys-acetylated lysines, and the dynamic alterations in LysAc among different tissues and developmental stages. We also outline a map of Lys-acetylated proteins in the Calvin-Benson cycle and central carbon metabolism-related pathways. We then introduce some examples of the regulation of plant growth, development, and biotic and abiotic stress responses by LysAc. We discuss the interaction between LysAc and Nα-terminal acetylation and the crosstalk between LysAc and other PTMs, including phosphorylation and succinylation. Finally, we propose recommendations for future studies in the field. We conclude that LysAc of proteins plays an important role in the regulation of the plant life cycle.
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7
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Guo J, Chai X, Mei Y, Du J, Du H, Shi H, Zhu JK, Zhang H. Acetylproteomics analyses reveal critical features of lysine-ε-acetylation in Arabidopsis and a role of 14-3-3 protein acetylation in alkaline response. STRESS BIOLOGY 2022; 2:1. [PMID: 37676343 PMCID: PMC10442023 DOI: 10.1007/s44154-021-00024-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 12/07/2021] [Indexed: 09/08/2023]
Abstract
Lysine-ε-acetylation (Kac) is a post-translational modification (PTM) that is critical for metabolic regulation and cell signaling in mammals. However, its prevalence and importance in plants remain to be determined. Employing high-resolution tandem mass spectrometry, we analyzed protein lysine acetylation in five representative Arabidopsis organs with 2 ~ 3 biological replicates per organ. A total of 2887 Kac proteins and 5929 Kac sites were identified. This comprehensive catalog allows us to analyze proteome-wide features of lysine acetylation. We found that Kac proteins tend to be more uniformly expressed in different organs, and the acetylation status exhibits little correlation with the gene expression level, indicating that acetylation is unlikely caused by stochastic processes. Kac preferentially targets evolutionarily conserved proteins and lysine residues, but only a small percentage of Kac proteins are orthologous between rat and Arabidopsis. A large portion of Kac proteins overlap with proteins modified by other PTMs including ubiquitination, SUMOylation and phosphorylation. Although acetylation, ubiquitination and SUMOylation all modify lysine residues, our analyses show that they rarely target the same sites. In addition, we found that "reader" proteins for acetylation and phosphorylation, i.e., bromodomain-containing proteins and GRF (General Regulatory Factor)/14-3-3 proteins, are intensively modified by the two PTMs, suggesting that they are main crosstalk nodes between acetylation and phosphorylation signaling. Analyses of GRF6/14-3-3λ reveal that the Kac level of GRF6 is decreased under alkaline stress, suggesting that acetylation represses plant alkaline response. Indeed, K56ac of GRF6 inhibits its binding to and subsequent activation of the plasma membrane H+-ATPase AHA2, leading to hypersensitivity to alkaline stress. These results provide valuable resources for protein acetylation studies in plants and reveal that protein acetylation suppresses phosphorylation output by acetylating GRF/14-3-3 proteins.
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Affiliation(s)
- Jianfei Guo
- State Key Laboratory of Plant Molecular Genetics, Shanghai Center for Plant Stress Biology, Center for Excellence in Plant Molecular Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoqiang Chai
- State Key Laboratory of Plant Molecular Genetics, Shanghai Center for Plant Stress Biology, Center for Excellence in Plant Molecular Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
| | - Yuchao Mei
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Jiamu Du
- Department of Biology, Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen, 518055, Guangdong, China
| | - Haining Du
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Huazhong Shi
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Jian-Kang Zhu
- State Key Laboratory of Plant Molecular Genetics, Shanghai Center for Plant Stress Biology, Center for Excellence in Plant Molecular Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
| | - Heng Zhang
- State Key Laboratory of Plant Molecular Genetics, Shanghai Center for Plant Stress Biology, Center for Excellence in Plant Molecular Sciences, Chinese Academy of Sciences, Shanghai, 201602, China.
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8
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Li W, Xiong Y, Lai LB, Zhang K, Li Z, Kang H, Dai L, Gopalan V, Wang G, Liu W. The rice RNase P protein subunit Rpp30 confers broad-spectrum resistance to fungal and bacterial pathogens. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:1988-1999. [PMID: 33932077 PMCID: PMC8486239 DOI: 10.1111/pbi.13612] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 03/25/2021] [Accepted: 04/25/2021] [Indexed: 05/23/2023]
Abstract
RNase P functions either as a catalytic ribonucleoprotein (RNP) or as an RNA-free polypeptide to catalyse RNA processing, primarily tRNA 5' maturation. To the growing evidence of non-canonical roles for RNase P RNP subunits including regulation of chromatin structure and function, we add here a role for the rice RNase P Rpp30 in innate immunity. This protein (encoded by LOC_Os11g01074) was uncovered as the top hit in yeast two-hybrid assays performed with the rice histone deacetylase HDT701 as bait. We showed that HDT701 and OsRpp30 are localized to the rice nucleus, OsRpp30 expression increased post-infection by Pyricularia oryzae (syn. Magnaporthe oryzae), and OsRpp30 deacetylation coincided with HDT701 overexpression in vivo. Overexpression of OsRpp30 in transgenic rice increased expression of defence genes and generation of reactive oxygen species after pathogen-associated molecular pattern elicitor treatment, outcomes that culminated in resistance to a fungal (P. oryzae) and a bacterial (Xanthomonas oryzae pv. oryzae) pathogen. Knockout of OsRpp30 yielded the opposite phenotypes. Moreover, HA-tagged OsRpp30 co-purified with RNase P pre-tRNA cleavage activity. Interestingly, OsRpp30 is conserved in grass crops, including a near-identical C-terminal tail that is essential for HDT701 binding and defence regulation. Overall, our results suggest that OsRpp30 plays an important role in rice immune response to pathogens and provides a new approach to generate broad-spectrum disease-resistant rice cultivars.
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Affiliation(s)
- Wei Li
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant ProtectionChinese Academy of Agricultural SciencesBeijingChina
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests and College of Plant ProtectionHunan Agricultural UniversityChangshaHunanChina
- Department of Plant PathologyThe Ohio State UniversityColumbusOHUSA
| | - Yehui Xiong
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant ProtectionChinese Academy of Agricultural SciencesBeijingChina
| | - Lien B. Lai
- Department of Chemistry and BiochemistryCenter for RNA BiologyThe Ohio State UniversityColumbusOhioUSA
| | - Kai Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant ProtectionChinese Academy of Agricultural SciencesBeijingChina
| | - Zhiqiang Li
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant ProtectionChinese Academy of Agricultural SciencesBeijingChina
| | - Houxiang Kang
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant ProtectionChinese Academy of Agricultural SciencesBeijingChina
| | - Liangying Dai
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests and College of Plant ProtectionHunan Agricultural UniversityChangshaHunanChina
| | - Venkat Gopalan
- Department of Chemistry and BiochemistryCenter for RNA BiologyThe Ohio State UniversityColumbusOhioUSA
| | - Guo‐Liang Wang
- Department of Plant PathologyThe Ohio State UniversityColumbusOHUSA
| | - Wende Liu
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant ProtectionChinese Academy of Agricultural SciencesBeijingChina
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9
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Gough C, Sadanandom A. Understanding and Exploiting Post-Translational Modifications for Plant Disease Resistance. Biomolecules 2021; 11:1122. [PMID: 34439788 PMCID: PMC8392720 DOI: 10.3390/biom11081122] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 07/23/2021] [Accepted: 07/26/2021] [Indexed: 12/27/2022] Open
Abstract
Plants are constantly threatened by pathogens, so have evolved complex defence signalling networks to overcome pathogen attacks. Post-translational modifications (PTMs) are fundamental to plant immunity, allowing rapid and dynamic responses at the appropriate time. PTM regulation is essential; pathogen effectors often disrupt PTMs in an attempt to evade immune responses. Here, we cover the mechanisms of disease resistance to pathogens, and how growth is balanced with defence, with a focus on the essential roles of PTMs. Alteration of defence-related PTMs has the potential to fine-tune molecular interactions to produce disease-resistant crops, without trade-offs in growth and fitness.
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Affiliation(s)
| | - Ari Sadanandom
- Department of Biosciences, Durham University, Stockton Road, Durham DH1 3LE, UK;
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10
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Mani SD, Pandey S, Govindan M, Muthamilarasan M, Nagarathnam R. Transcriptome dynamics underlying elicitor-induced defense responses against Septoria leaf spot disease of tomato ( Solanum lycopersicum L.). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:873-888. [PMID: 33967469 PMCID: PMC8055812 DOI: 10.1007/s12298-021-00970-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 03/03/2021] [Accepted: 03/07/2021] [Indexed: 06/12/2023]
Abstract
UNLABELLED Elicitor-induced defense response against potential plant pathogens has been widely reported in several crop plants; however, transcriptome dynamics underlying such defense response remains elusive. Our previous study identified and characterized a novel elicitor, κ-carrageenan, from Kappaphycus alvarezii, a marine red seaweed. Our preliminary studies have shown that the elicitor-treatment enhances the tolerance of a susceptible tomato cultivar to Septoria lycopersici (causative agent of leaf spot disease). To gain further insights into the genes regulated during elicitor treatment followed by pathogen infection, we have performed RNA-Seq experiments under different treatments, namely, control (untreated and uninfected), elicitor treatment, pathogen infection alone, and elicitor treatment followed by pathogen infection. To validate the results, forty-three genes belonging to five different classes, namely, ROS activating and detoxifying enzyme encoding genes, DEAD-box RNA helicase genes, autophagy-related genes, cysteine proteases, and pathogenesis-related genes, were chosen. Expression profiling of each gene was performed using qRT-PCR, and the data was correlated with the RNA-seq data. Altogether, the study has pinpointed a repertoire of genes that could be potential candidates for further functional characterization to provide insights into novel elicitor-induced fungal defense and develop transgenic lines resistant to foliar diseases. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-00970-y.
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Affiliation(s)
- Sumithra Devi Mani
- Unit of Plant Pathology, Center for Advanced Studies in Botany, University of Madras, Tamil Nadu, Guindy Campus, Chennai, 600 025 India
| | - Saurabh Pandey
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110 067 India
| | - Muthukumar Govindan
- Unit of Plant Pathology, Center for Advanced Studies in Botany, University of Madras, Tamil Nadu, Guindy Campus, Chennai, 600 025 India
| | - Mehanathan Muthamilarasan
- Repository of Tomato Genomics Resources, Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, 500 046 Telangana India
| | - Radhakrishnan Nagarathnam
- Unit of Plant Pathology, Center for Advanced Studies in Botany, University of Madras, Tamil Nadu, Guindy Campus, Chennai, 600 025 India
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11
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Xu M, Luo J, Li Y, Shen L, Zhang X, Yu J, Guo Z, Wu J, Chi Y, Yang J. First comprehensive proteomics analysis of lysine crotonylation in leaves of peanut (Arachis hypogaea L.). Proteomics 2021; 21:e2000156. [PMID: 33480167 DOI: 10.1002/pmic.202000156] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 12/21/2020] [Accepted: 01/05/2021] [Indexed: 12/16/2022]
Abstract
Lysine crotonylation is an important post-translational modification process. Most research in this area has been carried out on mammals and yeast, but there has been little research on it in plants. In the current study, large-scale lysine crotonylome analysis was performed by a combination of affinity enrichment and high-resolution LC-MS/MS analysis. Altogether, 6051 lysine crotonylation sites were identified in 2508 protein groups. Bioinformatics analysis showed that lysine-crotonylated proteins were involved in many biological processes, such as carbon fixation in photosynthetic organisms, biosynthesis of amino acids, ribosomes structure and function. In particular, subcellular localization analysis showed that 43% of the crotonylated proteins were located in the chloroplast. Twenty-nine crotonylation proteins were associated with photosynthesis and functional enrichment that these proteins were associated with the reaction center, photosynthetic electron transport, and ATP synthesis. Based on these results, further studies to expand on the lysine crotonylome analysis were suggested.
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Affiliation(s)
- Manlin Xu
- Shandong Peanut Research Institute, Qingdao, Shandong, China
| | - Jianda Luo
- Tobacco Research Institute of CAAS, Qingdao, Shandong, China
| | - Ying Li
- Tobacco Research Institute of CAAS, Qingdao, Shandong, China
| | - Lili Shen
- Tobacco Research Institute of CAAS, Qingdao, Shandong, China
| | - Xia Zhang
- Shandong Peanut Research Institute, Qingdao, Shandong, China
| | - Jing Yu
- Shandong Peanut Research Institute, Qingdao, Shandong, China
| | - Zhiqing Guo
- Shandong Peanut Research Institute, Qingdao, Shandong, China
| | - Juxiang Wu
- Shandong Peanut Research Institute, Qingdao, Shandong, China
| | - Yucheng Chi
- Shandong Peanut Research Institute, Qingdao, Shandong, China
| | - Jinguang Yang
- Tobacco Research Institute of CAAS, Qingdao, Shandong, China
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12
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Zhi P, Chang C. Exploiting Epigenetic Variations for Crop Disease Resistance Improvement. FRONTIERS IN PLANT SCIENCE 2021; 12:692328. [PMID: 34149790 PMCID: PMC8212930 DOI: 10.3389/fpls.2021.692328] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 04/27/2021] [Indexed: 05/07/2023]
Abstract
Pathogen infections seriously threaten plant health and global crop production. Epigenetic processes such as DNA methylation, histone post-translational modifications, chromatin assembly and remodeling play important roles in transcriptional regulation of plant defense responses and could provide a new direction to drive breeding strategies for crop disease resistance improvement. Although past decades have seen unprecedented proceedings in understanding the epigenetic mechanism of plant defense response, most of these advances were derived from studies in model plants like Arabidopsis. In this review, we highlighted the recent epigenetic studies on crop-pathogen interactions and discussed the potentials, challenges, and strategies in exploiting epigenetic variations for crop disease resistance improvement.
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13
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Mucha J, Pawłowski TA, Klupczyńska EA, Guzicka M, Zadworny M. The Effect of Hydroxamic Siderophores Structure on Acetylation of Histone H3 and Alpha Tubulin in Pinus sylvestris Root Cells. Int J Mol Sci 2019; 20:E6099. [PMID: 31816938 PMCID: PMC6928989 DOI: 10.3390/ijms20236099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 11/18/2019] [Accepted: 11/30/2019] [Indexed: 12/03/2022] Open
Abstract
Protein acetylation affects gene expression, as well as other processes in cells, and it might be dependent on the availability of the metals. However, whether iron chelating compounds (siderophores) can have an effect on the acetylation process in plant roots is largely unknown. In the present study, western blotting and confocal microscopy was used to examine the degree of acetylation of histone H3 and alpha tubulin in Pinus sylvestris root cells in the presence of structurally different siderophores. The effect of metabolites that were produced by pathogenic and mycorrhizal fungi was also assessed. No effect was observed on histone acetylation. By contrast, the metabolites of the pathogenic fungus were able to decrease the level of microtubule acetylation, whereas treatment with iron-free ferrioxamine (DFO) was able to increase it. This latter was not observed when ferrioxamine-iron complexes were used. The pathogen metabolites induced important modifications of cytoskeleton organization. Siderophores also induced changes in the tubulin skeleton and these changes were iron-dependent. The effect of siderophores on the microtubule network was dependent on the presence of iron. More root cells with a depolymerized cytoskeleton were observed when the roots were exposed to iron-free siderophores and the metabolites of pathogenic fungi; whereas, the metabolites from mycorrhizal fungi and iron-enriched forms of siderophores slightly altered the cytoskeleton network of root cells. Collectively, these data indicated that the metabolites of pathogenic fungi mirror siderophore action, and iron limitation can lead to enhanced alternations in cell structure and physiology.
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Affiliation(s)
- Joanna Mucha
- Institute of Dendrology, Polish Academy of Sciences, Parkowa 5, 62-035 Kórnik, Poland; (T.A.P.); (E.A.K.); (M.G.); (M.Z.)
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14
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Galvin HD, Husain M. Influenza A virus-induced host caspase and viral PA-X antagonize the antiviral host factor, histone deacetylase 4. J Biol Chem 2019; 294:20207-20221. [PMID: 31757810 DOI: 10.1074/jbc.ra119.010650] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 11/05/2019] [Indexed: 12/22/2022] Open
Abstract
Influenza A virus (IAV) effectively manipulates host machinery to replicate. There is a growing evidence that an optimal acetylation environment in the host cell is favorable to IAV proliferation and vice versa. The histone deacetylases (HDACs), a family of 18 host enzymes classified into four classes, are central to negatively regulating the acetylation level, hence the HDACs would not be favorable to IAV. Indeed, by using the RNAi and overexpression strategies, we found that human HDAC4, a class II member, possesses anti-IAV properties and is a component of host innate antiviral response. We discovered that IAV multiplication was augmented in HDAC4-depleted cells and abated in HDAC4-supplemented cells. Likewise, the expression of IFITM3, ISG15, and viperin, some of the critical markers of host anti-IAV response was abated in HDAC4-depleted cells and augmented in HDAC4-supplemented cells. In turn, IAV strongly antagonizes the HDAC4, by down-regulating its expression both at the mRNA level via viral RNA endonuclease PA-X and at the polypeptide level by inducing its cleavage via host caspase 3 in infected cells. Such HDAC4 polypeptide cleavage resulted in a ∼30 kDa fragment that is also observed in some heterologous systems and may have a significant role in IAV replication.
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Affiliation(s)
- Henry D Galvin
- Department of Microbiology and Immunology, University of Otago, Dunedin 9054, New Zealand
| | - Matloob Husain
- Department of Microbiology and Immunology, University of Otago, Dunedin 9054, New Zealand
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15
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Sun J, Shi Q, Chen X, Liu R. Decoding the similarities and specific differences between latent and active tuberculosis infections based on consistently differential expression networks. Brief Bioinform 2019; 21:2084-2098. [PMID: 31724702 DOI: 10.1093/bib/bbz127] [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: 06/22/2019] [Revised: 08/21/2019] [Accepted: 09/06/2019] [Indexed: 11/14/2022] Open
Abstract
Although intensive efforts have been devoted to investigating latent tuberculosis (LTB) and active tuberculosis (PTB) infections, the similarities and differences in the host responses to these two closely associated stages remain elusive, probably due to the difficulty in identifying informative genes related to LTB using traditional methods. Herein, we developed a framework known as the consistently differential expression network to identify tuberculosis (TB)-related gene pairs by combining microarray profiles and protein-protein interactions. We thus obtained 774 and 693 pairs corresponding to the PTB and LTB stages, respectively. The PTB-specific genes showed higher expression values and fold-changes than the LTB-specific genes. Furthermore, the PTB-related pairs generally had higher expression correlations and would be more activated compared to their LTB-related counterparts. The module analysis implied that the detected gene pairs tended to cluster in the topological and functional modules. Functional analysis indicated that the LTB- and PTB-specific genes were enriched in different pathways and had remarkably different locations in the NF-κB signaling pathway. Finally, we showed that the identified genes and gene pairs had the potential to distinguish TB patients in different disease stages and could be considered as drug targets for the specific treatment of patients with LTB or PTB.
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Affiliation(s)
- Jun Sun
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Qianqian Shi
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Xi Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Rong Liu
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
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16
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Santamaría L, Reverón I, Plaza-Vinuesa L, Oliveros JC, de Las Rivas B, Muñoz R, López de Felipe F. Oleuropein Transcriptionally Primes Lactobacillus plantarum to Interact With Plant Hosts. Front Microbiol 2019; 10:2177. [PMID: 31620115 PMCID: PMC6759512 DOI: 10.3389/fmicb.2019.02177] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 09/05/2019] [Indexed: 12/14/2022] Open
Abstract
Oleuropein (OLE) is a secoiridoid unique to Oleaceae known to play a role in the plant–herbivore interaction. However, it is not clear how this molecule is induced to mediate plant responses to microbes and how microbes, in turn, withstand with OLE. To better understand how OLE affects the plant–microbe interaction, the contribution of differential gene expression in the adaptation to OLE was characterized by whole genome transcriptional profiling in Lactobacillus plantarum, a bacterium associated to the olive. OLE downregulated functions associated to rapid growth, remodeled membrane phospholipid biosynthesis pathways and markedly repressed the expression of several ABC transporters from L. plantarum. Genes encoding the plantaricin and lamABDCA quorum-sensing (QS) systems were down-regulated indicating the potential of OLE as a QS-antagonist. Notably, OLE diminished the expression of a set of genes encoding inmunomodulatory components and reoriented metabolic pathways to increase protein acetylation, probably to attenuate plant immunity. Responses were also triggered to repress the transport of acetoin and to buffer reactive oxygen species accumulation, two signals involved in plant development. The results suggest that OLE could act as a signaling molecule in the plant–microbe interaction and facilitate the accommodation of beneficial microbes such as L. plantarum by the plant host, via controlled expression of bacterial molecular players involved in this reciprocal interplay.
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Affiliation(s)
- Laura Santamaría
- Laboratorio de Biotecnología Bacteriana, Instituto de Ciencia y Tecnología de los Alimentos y Nutrición (ICTAN-CSIC), Madrid, Spain
| | - Inés Reverón
- Laboratorio de Biotecnología Bacteriana, Instituto de Ciencia y Tecnología de los Alimentos y Nutrición (ICTAN-CSIC), Madrid, Spain
| | - Laura Plaza-Vinuesa
- Laboratorio de Biotecnología Bacteriana, Instituto de Ciencia y Tecnología de los Alimentos y Nutrición (ICTAN-CSIC), Madrid, Spain
| | | | - Blanca de Las Rivas
- Laboratorio de Biotecnología Bacteriana, Instituto de Ciencia y Tecnología de los Alimentos y Nutrición (ICTAN-CSIC), Madrid, Spain
| | - Rosario Muñoz
- Laboratorio de Biotecnología Bacteriana, Instituto de Ciencia y Tecnología de los Alimentos y Nutrición (ICTAN-CSIC), Madrid, Spain
| | - Félix López de Felipe
- Laboratorio de Biotecnología Bacteriana, Instituto de Ciencia y Tecnología de los Alimentos y Nutrición (ICTAN-CSIC), Madrid, Spain
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17
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Sandalio LM, Gotor C, Romero LC, Romero-Puertas MC. Multilevel Regulation of Peroxisomal Proteome by Post-Translational Modifications. Int J Mol Sci 2019; 20:E4881. [PMID: 31581473 PMCID: PMC6801620 DOI: 10.3390/ijms20194881] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Revised: 09/24/2019] [Accepted: 09/26/2019] [Indexed: 01/10/2023] Open
Abstract
Peroxisomes, which are ubiquitous organelles in all eukaryotes, are highly dynamic organelles that are essential for development and stress responses. Plant peroxisomes are involved in major metabolic pathways, such as fatty acid β-oxidation, photorespiration, ureide and polyamine metabolism, in the biosynthesis of jasmonic, indolacetic, and salicylic acid hormones, as well as in signaling molecules such as reactive oxygen and nitrogen species (ROS/RNS). Peroxisomes are involved in the perception of environmental changes, which is a complex process involving the regulation of gene expression and protein functionality by protein post-translational modifications (PTMs). Although there has been a growing interest in individual PTMs in peroxisomes over the last ten years, their role and cross-talk in the whole peroxisomal proteome remain unclear. This review provides up-to-date information on the function and crosstalk of the main peroxisomal PTMs. Analysis of whole peroxisomal proteomes shows that a very large number of peroxisomal proteins are targeted by multiple PTMs, which affect redox balance, photorespiration, the glyoxylate cycle, and lipid metabolism. This multilevel PTM regulation could boost the plasticity of peroxisomes and their capacity to regulate metabolism in response to environmental changes.
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Affiliation(s)
- Luisa M Sandalio
- Department of Biochemistry and Cellular and Molecular Biology of Plants, Estación Experimental del Zaidín, CSIC, 18008 Granada, Spain.
| | - Cecilia Gotor
- Institute of Plant Biochemistry and Photosynthesis, CSIC and the University of Seville, 41092 Seville, Spain.
| | - Luis C Romero
- Institute of Plant Biochemistry and Photosynthesis, CSIC and the University of Seville, 41092 Seville, Spain.
| | - Maria C Romero-Puertas
- Department of Biochemistry and Cellular and Molecular Biology of Plants, Estación Experimental del Zaidín, CSIC, 18008 Granada, Spain.
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18
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Cao Y, Fan G, Wang Z, Gu Z. Phytoplasma-induced Changes in the Acetylome and Succinylome of Paulownia tomentosa Provide Evidence for Involvement of Acetylated Proteins in Witches' Broom Disease. Mol Cell Proteomics 2019; 18:1210-1226. [PMID: 30936209 PMCID: PMC6553929 DOI: 10.1074/mcp.ra118.001104] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 02/20/2019] [Indexed: 12/16/2022] Open
Abstract
Lysine acetylation and succinylation are post-translational modifications of proteins that have been shown to play roles in plants response to pathogen infection. Phytoplasma infection can directly alter multiple metabolic processes in the deciduous plant Paulownia and lead to Paulownia witches' broom (PaWB) disease, the major cause of Paulownia mortality worldwide. However, the extent and function of lysine aceylation and succinylation during phytoplasma infection have yet to be explored. Here, we investigated the changes in the proteome, acetylome, and succinylome of phytoplasma-infected Paulownia tomentosa seedlings using quantitative mass spectrometry. In total, we identified 8963 proteins, 2893 acetylated proteins (5558 acetylation sites), and 1271 succinylated proteins (1970 succinylation sites), with 425 (533 sites) simultaneously acetylated and succinylated. Comparative analysis revealed that 276 proteins, 546 acetylated proteins (741 acetylation sites) and 5 succinylated proteins (5 succinylation sites) were regulated in response to phytoplasma infection, suggesting that acetylation may be more important than succinylation in PaWB. Enzymatic assays showed that acetylation of specific sites in protochlorophyllide reductase and RuBisCO, key enzymes in chlorophyll and starch biosynthesis, respectively, modifies their activity in phytoplasma-infected seedlings. On the basis of these results, we propose a model to elucidate the molecular mechanism of responses to PaWB and offer a resource for functional studies on the effects of acetylation on protein function.
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Affiliation(s)
| | - Guoqiang Fan
- From the ‡Institute of Paulownia and
- §College of Forestry, Henan Agricultural University, Zhengzhou, Henan, 450002, P. R. China
| | - Zhe Wang
- From the ‡Institute of Paulownia and
| | - Zhibin Gu
- From the ‡Institute of Paulownia and
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19
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Christensen DG, Baumgartner JT, Xie X, Jew KM, Basisty N, Schilling B, Kuhn ML, Wolfe AJ. Mechanisms, Detection, and Relevance of Protein Acetylation in Prokaryotes. mBio 2019; 10:e02708-18. [PMID: 30967470 PMCID: PMC6456759 DOI: 10.1128/mbio.02708-18] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Posttranslational modification of a protein, either alone or in combination with other modifications, can control properties of that protein, such as enzymatic activity, localization, stability, or interactions with other molecules. N-ε-Lysine acetylation is one such modification that has gained attention in recent years, with a prevalence and significance that rival those of phosphorylation. This review will discuss the current state of the field in bacteria and some of the work in archaea, focusing on both mechanisms of N-ε-lysine acetylation and methods to identify, quantify, and characterize specific acetyllysines. Bacterial N-ε-lysine acetylation depends on both enzymatic and nonenzymatic mechanisms of acetylation, and recent work has shed light into the regulation of both mechanisms. Technological advances in mass spectrometry have allowed researchers to gain insight with greater biological context by both (i) analyzing samples either with stable isotope labeling workflows or using label-free protocols and (ii) determining the true extent of acetylation on a protein population through stoichiometry measurements. Identification of acetylated lysines through these methods has led to studies that probe the biological significance of acetylation. General and diverse approaches used to determine the effect of acetylation on a specific lysine will be covered.
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Affiliation(s)
- D G Christensen
- Department of Microbiology and Immunology, Loyola University Chicago, Health Sciences Division, Stritch School of Medicine, Maywood, Illinois, USA
| | - J T Baumgartner
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, California, USA
| | - X Xie
- Buck Institute for Research on Aging, Novato, California, USA
| | - K M Jew
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, California, USA
| | - N Basisty
- Buck Institute for Research on Aging, Novato, California, USA
| | - B Schilling
- Buck Institute for Research on Aging, Novato, California, USA
| | - M L Kuhn
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, California, USA
| | - A J Wolfe
- Department of Microbiology and Immunology, Loyola University Chicago, Health Sciences Division, Stritch School of Medicine, Maywood, Illinois, USA
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20
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Nutsford AN, Galvin HD, Ahmed F, Husain M. The Class IV human deacetylase, HDAC11, exhibits anti-influenza A virus properties via its involvement in host innate antiviral response. Cell Microbiol 2018; 21:e12989. [PMID: 30511515 DOI: 10.1111/cmi.12989] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 11/06/2018] [Accepted: 11/22/2018] [Indexed: 01/01/2023]
Abstract
Histone deacetylase 11 (HDAC11) is most recently discovered deacetylase. Here, we demonstrate that human HDAC11 exhibits anti-influenza A virus (IAV) properties. We found that knockdown of HDAC11 expression augments IAV growth kinetics in human lung epithelial cells A549 by up to 1 log. One of the ways HDAC11 exerts its anti-IAV function is by being a part of IAV-induced host antiviral response. We found that the kinetics of both IAV- and interferon-induced innate antiviral response is significantly delayed in HDAC11-depleted cells. Further, in the absence of HDAC11 expression, there was a significant decrease in the expression of interferon-stimulated genes-IFITM3, ISG15, and viperin-previously implicated in anti-IAV function. One of the ways IAV antagonises HDAC11 is by downregulating its expression in host cells. We found that there was up to 93% reduction in HDAC11 transcript levels in A549 cells in response to IAV infection. HDAC11 is the smallest HDAC with majority of its polypeptide assigned to catalytic domain. Evolutionarily, it seems to be the least evolved and most closely related to common ancestral HDAC gene(s). Furthermore, HDAC11 has also been described as a deacylase. Therefore, our findings present exciting prospects for further investigations into significance of HDAC11 in virus infections.
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Affiliation(s)
- Ashley N Nutsford
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Henry D Galvin
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Farjana Ahmed
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Matloob Husain
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
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21
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Filippova A, Lyapina I, Kirov I, Zgoda V, Belogurov A, Kudriaeva A, Ivanov V, Fesenko I. Salicylic acid influences the protease activity and posttranslation modifications of the secreted peptides in the moss Physcomitrella patens. J Pept Sci 2018; 25:e3138. [PMID: 30575224 DOI: 10.1002/psc.3138] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 11/18/2018] [Accepted: 11/20/2018] [Indexed: 02/06/2023]
Abstract
Plant secretome comprises dozens of secreted proteins. However, little is known about the composition of the whole secreted peptide pools and the proteases responsible for the generation of the peptide pools. The majority of studies focus on target detection and characterization of specific plant peptide hormones. In this study, we performed a comprehensive analysis of the whole extracellular peptidome, using moss Physcomitrella patens as a model. Hundreds of modified and unmodified endogenous peptides that originated from functional and nonfunctional protein precursors were identified. The plant proteases responsible for shaping the pool of endogenous peptides were predicted. Salicylic acid (SA) influenced peptide production in the secretome. The proteasome activity was altered upon SA treatment, thereby influencing the composition of the peptide pools. These results shed more light on the role of proteases and posttranslational modification in the "active management" of the extracellular peptide pool in response to stress conditions. It also identifies a list of potential peptide hormones in the moss secretome for further analysis.
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Affiliation(s)
- Anna Filippova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Irina Lyapina
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Ilya Kirov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Victor Zgoda
- V.N. Orekhovich Research Institute of Biomedical Chemistry, Department of Proteomic Research and Mass Spectrometry, Moscow, Russian Federation
| | - Alexey Belogurov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Anna Kudriaeva
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Vadim Ivanov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Igor Fesenko
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
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22
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Arsova B, Watt M, Usadel B. Monitoring of Plant Protein Post-translational Modifications Using Targeted Proteomics. FRONTIERS IN PLANT SCIENCE 2018; 9:1168. [PMID: 30174677 PMCID: PMC6107839 DOI: 10.3389/fpls.2018.01168] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 07/23/2018] [Indexed: 05/19/2023]
Abstract
Protein post-translational modifications (PTMs) are among the fastest and earliest of plant responses to changes in the environment, making the mechanisms and dynamics of PTMs an important area of plant science. One of the most studied PTMs is protein phosphorylation. This review summarizes the use of targeted proteomics for the elucidation of the biological functioning of plant PTMs, and focuses primarily on phosphorylation. Since phosphorylated peptides have a low abundance, usually complex enrichment protocols are required for their research. Initial identification is usually performed with discovery phosphoproteomics, using high sensitivity mass spectrometers, where as many phosphopeptides are measured as possible. Once a PTM site is identified, biological characterization can be addressed with targeted proteomics. In targeted proteomics, Selected/Multiple Reaction Monitoring (S/MRM) is traditionally coupled to simple, standard protein digestion protocols, often omitting the enrichment step, and relying on triple-quadruple mass spectrometer. The use of synthetic peptides as internal standards allows accurate identification, avoiding cross-reactivity typical for some antibody based approaches. Importantly, internal standards allow absolute peptide quantitation, reported down to 0.1 femtomoles, also useful for determination of phospho-site occupancy. S/MRM is advantageous in situations where monitoring and diagnostics of peptide PTM status is needed for many samples, as it has faster sample processing times, higher throughput than other approaches, and excellent quantitation and reproducibility. Furthermore, the number of publicly available data-bases with plant PTM discovery data is growing, facilitating selection of modified peptides and design of targeted proteomics workflows. Recent instrument developments result in faster scanning times, inclusion of ion-trap instruments leading to parallel reaction monitoring- which further facilitates S/MRM experimental design. Finally, recent combination of data independent and data dependent spectra acquisition means that in addition to anticipated targeted data, spectra can now be queried for unanticipated information. The potential for future applications in plant biology is outlined.
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Affiliation(s)
- Borjana Arsova
- Institut für Bio- und Geowissenschaften, IBG-2–Plant Sciences, Forschungszentrum Jülich, Jülich, Germany
| | - Michelle Watt
- Institut für Bio- und Geowissenschaften, IBG-2–Plant Sciences, Forschungszentrum Jülich, Jülich, Germany
| | - Björn Usadel
- Institut für Bio- und Geowissenschaften, IBG-2–Plant Sciences, Forschungszentrum Jülich, Jülich, Germany
- IBMG: Institute for Biology I, RWTH Aachen University, Aachen, Germany
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23
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Ruiz‐May E, Segura‐Cabrera A, Elizalde‐Contreras JM, Shannon LM, Loyola‐Vargas VM. A recent advance in the intracellular and extracellular redox post‐translational modification of proteins in plants. J Mol Recognit 2018; 32:e2754. [DOI: 10.1002/jmr.2754] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 06/08/2018] [Accepted: 06/14/2018] [Indexed: 02/01/2023]
Affiliation(s)
- Eliel Ruiz‐May
- Red de Estudios Moleculares AvanzadosInstituto de Ecología A. C., Cluster BioMimic® Xalapa Veracruz Mexico
| | - Aldo Segura‐Cabrera
- European Molecular Biology LaboratoryEuropean Bioinformatics Institute, Wellcome Genome Campus Hinxton Cambridgeshire UK
| | - Jose M. Elizalde‐Contreras
- Red de Estudios Moleculares AvanzadosInstituto de Ecología A. C., Cluster BioMimic® Xalapa Veracruz Mexico
| | - Laura M. Shannon
- Department of Horticultural ScienceUniversity of Minnesota Saint Paul MN USA
| | - Víctor M. Loyola‐Vargas
- Unidad de Bioquímica y Biología Molecular de PlantasCentro de Investigación Científica de Yucatán Mérida Yucatán Mexico
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24
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Abstract
Lysine acetylation is a key posttranslational modification that regulates diverse proteins involved in a range of biological processes. The role of histone acetylation in plant defense is well established, and it is known that pathogen effector proteins encoding acetyltransferases can directly acetylate host proteins to alter immunity. However, it is unclear whether endogenous plant enzymes can modulate protein acetylation during an immune response. Here, we investigate how the effector molecule HC-toxin (HCT), a histone deacetylase inhibitor produced by the fungal pathogen Cochliobolus carbonum race 1, promotes virulence in maize through altering protein acetylation. Using mass spectrometry, we globally quantified the abundance of 3,636 proteins and the levels of acetylation at 2,791 sites in maize plants treated with HCT as well as HCT-deficient or HCT-producing strains of C. carbonum Analyses of these data demonstrate that acetylation is a widespread posttranslational modification impacting proteins encoded by many intensively studied maize genes. Furthermore, the application of exogenous HCT enabled us to show that the activity of plant-encoded enzymes (histone deacetylases) can be modulated to alter acetylation of nonhistone proteins during an immune response. Collectively, these results provide a resource for further mechanistic studies examining the regulation of protein function by reversible acetylation and offer insight into the complex immune response triggered by virulent C. carbonum.
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He Z, Huang T, Ao K, Yan X, Huang Y. Sumoylation, Phosphorylation, and Acetylation Fine-Tune the Turnover of Plant Immunity Components Mediated by Ubiquitination. FRONTIERS IN PLANT SCIENCE 2017; 8:1682. [PMID: 29067028 PMCID: PMC5641357 DOI: 10.3389/fpls.2017.01682] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 09/13/2017] [Indexed: 05/20/2023]
Abstract
Ubiquitination-mediated protein degradation plays a crucial role in the turnover of immune proteins through rapid alteration of protein levels. Specifically, the over-accumulation of immune proteins and consequent activation of immune responses in uninfected cells is prevented through degradation. Protein post-translational modifications can influence and affect ubiquitination. There is accumulating evidence that suggests sumoylation, phosphorylation, and acetylation differentially affect the stability of immune-related proteins, so that control over the accumulation or degradation of proteins is fine-tuned. In this paper, we review the function and mechanism of sumoylation, phosphorylation, acetylation, and ubiquitination in plant disease resistance responses, focusing on how ubiquitination reacts with sumoylation, phosphorylation, and acetylation to regulate plant disease resistance signaling pathways. Future research directions are suggested in order to provide ideas for signaling pathway studies, and to advance the implementation of disease resistance proteins in economically important crops.
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Affiliation(s)
- Zhouqing He
- College of Life Sciences, Sichuan Agricultural University, Ya’an, China
| | - Tingting Huang
- College of Life Sciences, Sichuan Agricultural University, Ya’an, China
| | - Kevin Ao
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Xiaofang Yan
- College of Life Sciences, Sichuan Agricultural University, Ya’an, China
| | - Yan Huang
- College of Life Sciences, Sichuan Agricultural University, Ya’an, China
- *Correspondence: Yan Huang,
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