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Williams J, Regedanz E, Lucinda N, Nava Fereira AR, Lacatus G, Berger M, O’Connell N, Coursey T, Ruan J, Bisaro DM, Sunter G. Mutation of the conserved late element in geminivirus CP promoters abolishes Arabidopsis TCP24 transcription factor binding and decreases H3K27me3 levels on viral chromatin. PLoS Pathog 2024; 20:e1012399. [PMID: 39024402 PMCID: PMC11288445 DOI: 10.1371/journal.ppat.1012399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 07/30/2024] [Accepted: 07/07/2024] [Indexed: 07/20/2024] Open
Abstract
In geminiviruses belonging to the genus Begomovirus, coat protein (CP) expression depends on viral AL2 protein, which derepresses and activates the CP promoter through sequence elements that lie within the viral intergenic region (IR). However, AL2 does not exhibit sequence-specific DNA binding activity but is instead directed to responsive promoters through interactions with host factors, most likely transcriptional activators and/or repressors. In this study, we describe a repressive plant-specific transcription factor, Arabidopsis thaliana TCP24 (AtTCP24), that interacts with AL2 and recognizes a class II TCP binding site in the CP promoter (GTGGTCCC). This motif corresponds to the previously identified conserved late element (CLE). We also report that histone 3 lysine 27 trimethylation (H3K27me3), an epigenetic mark associated with facultative repression, is enriched over the viral IR. H3K27me3 is deposited by Polycomb Repressive Complex 2 (PRC2), a critical regulator of gene expression and development in plants and animals. Remarkably, mutation of the TCP24 binding site (the CLE) in tomato golden mosaic virus (TGMV) and cabbage leaf curl virus (CaLCuV) CP promoters greatly diminishes H3K27me3 levels on viral chromatin and causes a dramatic delay and attenuation of disease symptoms in infected Arabidopsis and Nicotiana benthamiana plants. Symptom remission is accompanied by decreased viral DNA levels in systemically infected tissue. Nevertheless, in transient replication assays CLE mutation delays but does not limit the accumulation of viral double-stranded DNA, although single-stranded DNA and CP mRNA levels are decreased. These findings suggest that TCP24 binding to the CLE leads to CP promoter repression and H3K27me3 deposition, while TCP24-AL2 interaction may recruit AL2 to derepress and activate the promoter. Thus, a repressive host transcription factor may be repurposed to target a viral factor essential for promoter activity. The presence of the CLE in many begomoviruses suggests a common scheme for late promoter regulation.
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Affiliation(s)
- Jacqueline Williams
- Department of Biology, The University of Texas at San Antonio, San Antonio, Texas, United States of America
| | - Elizabeth Regedanz
- Department of Molecular Genetics, Center for Applied Plant Sciences, Center for RNA Biology, and Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, United States of America
| | - Natalia Lucinda
- Department of Biological Sciences, Northern Illinois University, DeKalb, Illinois, United States of America
| | - Alba Ruth Nava Fereira
- Department of Biological Sciences, Northern Illinois University, DeKalb, Illinois, United States of America
| | - Gabriela Lacatus
- Department of Biology, The University of Texas at San Antonio, San Antonio, Texas, United States of America
| | - Mary Berger
- Department of Biology, The University of Texas at San Antonio, San Antonio, Texas, United States of America
| | - Nels O’Connell
- Department of Molecular Genetics, Center for Applied Plant Sciences, Center for RNA Biology, and Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, United States of America
| | - Tami Coursey
- Department of Molecular Genetics, Center for Applied Plant Sciences, Center for RNA Biology, and Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, United States of America
| | - Jianhua Ruan
- Department of Computer Science, The University of Texas at San Antonio, San Antonio, Texas, United States of America
| | - David M. Bisaro
- Department of Molecular Genetics, Center for Applied Plant Sciences, Center for RNA Biology, and Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, United States of America
| | - Garry Sunter
- Department of Biology, The University of Texas at San Antonio, San Antonio, Texas, United States of America
- Department of Biological Sciences, Northern Illinois University, DeKalb, Illinois, United States of America
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Zeng Z, Chen L, Luo H, Xiao H, Gao S, Zeng Y. Progress on H2B as a multifunctional protein related to pathogens. Life Sci 2024; 347:122654. [PMID: 38657835 DOI: 10.1016/j.lfs.2024.122654] [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: 01/03/2024] [Revised: 04/06/2024] [Accepted: 04/21/2024] [Indexed: 04/26/2024]
Abstract
Histone H2B is a member of the core histones, which together with other histones form the nucleosome, the basic structural unit of chromosomes. As scientists delve deeper into histones, researchers gradually realize that histone H2B is not only an important part of nucleosomes, but also plays a momentous role in regulating gene transcription, acting as a receptor and antimicrobial action outside the nucleus. There are a variety of epigenetically modified sites in the H2B tail rich in arginine and lysine, which can occur in ubiquitination, phosphorylation, methylation, acetylation, etc. When stimulated by foreign factors such as bacteria, viruses or parasites, histone H2B can act as a receptor for the recognition of these pathogens, and induce an intrinsic immune response to enhance host defense. In addition, the extrachromosomal histone H2B is also an important anti-microorganism agent, which may be the key to the development of antibiotics in the future. This review aims to summarize the interaction between histone H2B and etiological agents and explore the role of H2B in epigenetic modifications, receptors and antimicrobial activity.
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Affiliation(s)
- Zhuo Zeng
- Institute of Pathogenic Biology, Basic Medicine School, Hengyang Medical College, University of South China, Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Hengyang City, Hunan Province 421001, PR China
| | - Li Chen
- Institute of Pathogenic Biology, Basic Medicine School, Hengyang Medical College, University of South China, Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Hengyang City, Hunan Province 421001, PR China
| | - Haodang Luo
- Institute of Pathogenic Biology, Basic Medicine School, Hengyang Medical College, University of South China, Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Hengyang City, Hunan Province 421001, PR China; The Laboratory Department, The affiliated Nanhua Hospital, University of South China, Hengyang City, Hunan Province 421001, PR China.
| | - Hua Xiao
- Institute of Pathogenic Biology, Basic Medicine School, Hengyang Medical College, University of South China, Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Hengyang City, Hunan Province 421001, PR China
| | - Siqi Gao
- Institute of Pathogenic Biology, Basic Medicine School, Hengyang Medical College, University of South China, Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Hengyang City, Hunan Province 421001, PR China
| | - Yanhua Zeng
- Institute of Pathogenic Biology, Basic Medicine School, Hengyang Medical College, University of South China, Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Hengyang City, Hunan Province 421001, PR China.
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Prasad A, Sharma S, Prasad M. Post translational modifications at the verge of plant-geminivirus interaction. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194983. [PMID: 37717937 DOI: 10.1016/j.bbagrm.2023.194983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 09/10/2023] [Accepted: 09/12/2023] [Indexed: 09/19/2023]
Abstract
Plant-virus interaction is a complex phenomenon and involves the communication between plant and viral factors. Viruses have very limited coding ability yet, they are able to cause infection which results in huge agro-economic losses throughout the globe each year. Post-translational modifications (PTMs) are covalent modifications of proteins that have a drastic effect on their conformation, stability and function. Like the host proteins, geminiviral proteins are also subject to PTMs and these modifications greatly expand the diversity of their functions. Additionally, these viral proteins can also interact with the components of PTM pathways and modulate them. Several studies have highlighted the importance of PTMs such as phosphorylation, ubiquitination, SUMOylation, myristoylation, S-acylation, acetylation and methylation in plant-geminivirus interaction. PTMs also regulate epigenetic modifications during geminivirus infection which determines viral gene expression. In this review, we have summarized the role of PTMs in regulating geminiviral protein function, influence of PTMs on viral gene expression and how geminiviral proteins interact with the components of PTM pathways to modulate their function.
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Affiliation(s)
- Ashish Prasad
- Department of Botany, Kurukshetra University, Kurukshetra, India.
| | | | - Manoj Prasad
- National Institute of Plant Genome Research, New Delhi, India; Department of Plant Sciences, University of Hyderabad, Hyderabad, India.
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4
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Wang Z, Castillo-González CM, Zhao C, Tong CY, Li C, Zhong S, Liu Z, Xie K, Zhu J, Wu Z, Peng X, Jacob Y, Michaels SD, Jacobsen SE, Zhang X. H3.1K27me1 loss confers Arabidopsis resistance to Geminivirus by sequestering DNA repair proteins onto host genome. Nat Commun 2023; 14:7484. [PMID: 37980416 PMCID: PMC10657422 DOI: 10.1038/s41467-023-43311-1] [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: 10/05/2022] [Accepted: 11/06/2023] [Indexed: 11/20/2023] Open
Abstract
The H3 methyltransferases ATXR5 and ATXR6 deposit H3.1K27me1 to heterochromatin to prevent genomic instability and transposon re-activation. Here, we report that atxr5 atxr6 mutants display robust resistance to Geminivirus. The viral resistance is correlated with activation of DNA repair pathways, but not with transposon re-activation or heterochromatin amplification. We identify RAD51 and RPA1A as partners of virus-encoded Rep protein. The two DNA repair proteins show increased binding to heterochromatic regions and defense-related genes in atxr5 atxr6 vs wild-type plants. Consequently, the proteins have reduced binding to viral DNA in the mutant, thus hampering viral amplification. Additionally, RAD51 recruitment to the host genome arise via BRCA1, HOP2, and CYCB1;1, and this recruitment is essential for viral resistance in atxr5 atxr6. Thus, Geminiviruses adapt to healthy plants by hijacking DNA repair pathways, whereas the unstable genome, triggered by reduced H3.1K27me1, could retain DNA repairing proteins to suppress viral amplification in atxr5 atxr6.
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Affiliation(s)
- Zhen Wang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
- Molecular and Environmental Plant Sciences, Texas A&M University, College Station, TX, 77843, USA
| | | | - Changjiang Zhao
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Chun-Yip Tong
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Changhao Li
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Songxiao Zhong
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Zhiyang Liu
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Kaili Xie
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Jiaying Zhu
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Zhongshou Wu
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Xu Peng
- Department of Molecular Physiology, College of Medicine, Texas A&M University, College Station, TX, 77843, USA
| | - Yannick Jacob
- Department of Molecular, Cellular & Developmental Biology, Yale University, New Haven, CT, 06511, USA
| | - Scott D Michaels
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA
| | - Steven E Jacobsen
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Xiuren Zhang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA.
- Molecular and Environmental Plant Sciences, Texas A&M University, College Station, TX, 77843, USA.
- Department of Biology, Texas A&M University, College Station, TX, 77843, USA.
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5
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Zhang J, Ma M, Liu Y, Ismayil A. Plant Defense and Viral Counter-Defense during Plant-Geminivirus Interactions. Viruses 2023; 15:v15020510. [PMID: 36851725 PMCID: PMC9964946 DOI: 10.3390/v15020510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 02/09/2023] [Accepted: 02/10/2023] [Indexed: 02/17/2023] Open
Abstract
Geminiviruses are the largest family of plant viruses that cause severe diseases and devastating yield losses of economically important crops worldwide. In response to geminivirus infection, plants have evolved ingenious defense mechanisms to diminish or eliminate invading viral pathogens. However, increasing evidence shows that geminiviruses can interfere with plant defense response and create a suitable cell environment by hijacking host plant machinery to achieve successful infections. In this review, we discuss recent findings about plant defense and viral counter-defense during plant-geminivirus interactions.
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Affiliation(s)
- Jianhang Zhang
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, College of Life Sciences, Shihezi University, Shihezi 832003, China
| | - Mengyuan Ma
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, College of Life Sciences, Shihezi University, Shihezi 832003, China
| | - Yule Liu
- MOE Key Laboratory of Bioinformatics, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Asigul Ismayil
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, College of Life Sciences, Shihezi University, Shihezi 832003, China
- Correspondence:
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6
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Lu X, Xin DE, Du JK, Zou QC, Wu Q, Zhang YS, Deng W, Yue J, Fan XS, Zeng Y, Cheng X, Li X, Hou Z, Mohan M, Zhao TC, Lu X, Chang Z, Xu L, Sun Y, Zu X, Zhang Y, Chinn YE. Loss of LOXL2 Promotes Uterine Hypertrophy and Tumor Progression by Enhancing H3K36ac-Dependent Gene Expression. Cancer Res 2022; 82:4400-4413. [PMID: 36197797 DOI: 10.1158/0008-5472.can-22-0848] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 06/23/2022] [Accepted: 09/30/2022] [Indexed: 02/05/2023]
Abstract
UNLABELLED Lysyl oxidase-like 2 (LOXL2) is a member of the scavenger receptor cysteine-rich (SRCR) repeat carrying LOX family. Although LOXL2 is suspected to be involved in histone association and chromatin modification, the role of LOXL2 in epigenetic regulation during tumorigenesis and cancer progression remains unclear. Here, we report that nuclear LOXL2 associates with histone H3 and catalyzes H3K36ac deacetylation and deacetylimination. Both the N-terminal SRCR repeats and the C-terminal catalytic domain of LOXL2 carry redundant deacetylase catalytic activity. Overexpression of LOXL2 markedly reduced H3K36 acetylation and blocked H3K36ac-dependent transcription of genes, including c-MYC, CCND1, HIF1A, and CD44. Consequently, LOXL2 overexpression reduced cancer cell proliferation in vitro and inhibited xenograft tumor growth in vivo. In contrast, LOXL2 deficiency resulted in increased H3K36 acetylation and aberrant expression of H3K36ac-dependent genes involved in multiple oncogenic signaling pathways. Female LOXL2-deficient mice spontaneously developed uterine hypertrophy and uterine carcinoma. Moreover, silencing LOXL2 in cancer cells enhanced tumor progression and reduced the efficacy of cisplatin and anti-programmed cell death 1 (PD-1) combination therapy. Clinically, low nuclear LOXL2 expression and high H3K36ac levels corresponded to poor prognosis in uterine endometrial carcinoma patients. These results suggest that nuclear LOXL2 restricts cancer development in the female reproductive system via the regulation of H3K36ac deacetylation. SIGNIFICANCE LOXL2 loss reprograms the epigenetic landscape to promote uterine cancer initiation and progression and repress the efficacy of anti-PD-1 immunotherapy, indicating that LOXL2 is a tumor suppressor.
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Affiliation(s)
- Xufeng Lu
- Clinical Medicine Research Institute, Zhejiang Provincial People's Hospital, Hangzhou Medical College, Zhejiang; Research Center of Basic Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Zhejiang, China
| | - Dazhuan E Xin
- Clinical Medicine Research Institute, Zhejiang Provincial People's Hospital, Hangzhou Medical College, Zhejiang
- Research Center of Basic Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Zhejiang, China
- Institutes of Biology and Medical Sciences, Soochow University Medical College, Jiangsu, China
| | - Juanjuan K Du
- Clinical Medicine Research Institute, Zhejiang Provincial People's Hospital, Hangzhou Medical College, Zhejiang
- Research Center of Basic Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Zhejiang, China
- Institutes of Biology and Medical Sciences, Soochow University Medical College, Jiangsu, China
| | - Quanli C Zou
- Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Qian Wu
- Clinical Medicine Research Institute, Zhejiang Provincial People's Hospital, Hangzhou Medical College, Zhejiang; Research Center of Basic Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Zhejiang, China
| | - Yanan S Zhang
- Clinical Medicine Research Institute, Zhejiang Provincial People's Hospital, Hangzhou Medical College, Zhejiang; Research Center of Basic Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Zhejiang, China
- Institutes of Biology and Medical Sciences, Soochow University Medical College, Jiangsu, China
| | - Wenhai Deng
- Clinical Medicine Research Institute, Zhejiang Provincial People's Hospital, Hangzhou Medical College, Zhejiang; Research Center of Basic Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Zhejiang, China
| | - Jicheng Yue
- Institutes of Biology and Medical Sciences, Soochow University Medical College, Jiangsu, China
| | - Xing S Fan
- Institutes of Biology and Medical Sciences, Soochow University Medical College, Jiangsu, China
- Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yuanyuan Zeng
- Institutes of Biology and Medical Sciences, Soochow University Medical College, Jiangsu, China
| | - Xiaju Cheng
- Institutes of Biology and Medical Sciences, Soochow University Medical College, Jiangsu, China
| | - Xue Li
- Clinical Medicine Research Institute, Zhejiang Provincial People's Hospital, Hangzhou Medical College, Zhejiang; Research Center of Basic Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Zhejiang, China
| | - Zhaoyuan Hou
- Department of Biochemistry and Molecular Cell Biology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Man Mohan
- Department of Biochemistry and Molecular Cell Biology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ting C Zhao
- Departments of Surgery and Medicine, Brown University School of Medicine-Rhode Island Hospital, Providence, Rhode Island
| | - Xiaomei Lu
- Cancer Hospital of Xinjiang Medical University, Urumqi, Xinjiang, China
| | - Zhijie Chang
- State Key Laboratory of Membrane Biology, Tsinghua University School of Medicine, Beijing, China
| | - Liyan Xu
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Institute of Oncologic Pathology, Cancer Research Center, Shantou University Medical College, Shantou, Guangdong, China
| | - Yu Sun
- Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xiongbing Zu
- Departments of Urology and Obstetrics and Gynecology, Xiangya Hospital, Central South University, Hunan, China
| | - Yu Zhang
- Departments of Urology and Obstetrics and Gynecology, Xiangya Hospital, Central South University, Hunan, China
| | - Y Eugene Chinn
- Clinical Medicine Research Institute, Zhejiang Provincial People's Hospital, Hangzhou Medical College, Zhejiang
- Research Center of Basic Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Zhejiang, China
- Institutes of Biology and Medical Sciences, Soochow University Medical College, Jiangsu, China
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7
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Chan J, Kumar A, Kono H. RNAPII driven post-translational modifications of nucleosomal histones. Trends Genet 2022; 38:1076-1095. [PMID: 35618507 DOI: 10.1016/j.tig.2022.04.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Revised: 04/08/2022] [Accepted: 04/22/2022] [Indexed: 12/12/2022]
Abstract
The current understanding of how specific distributions of histone post-translational modifications (PTMs) are achieved throughout the chromatin remains incomplete. This review focuses on the role of RNA polymerase II (RNAPII) in establishing H2BK120/K123 ubiquitination and H3K4/K36 methylation distribution. The rate of RNAPII transcription is mainly a function of the RNAPII elongation and recruitment rates. Two major mechanisms link RNAPII's transcription rate to the distribution of PTMs. First, the phosphorylation patterns of Ser2P/Ser5P in the C-terminal domain of RNAPII change as a function of time, since the start of elongation, linking them to the elongation rate. Ser2P/Ser5P recruits specific histone PTM enzymes/activators to the nucleosome. Second, multiple rounds of binding and catalysis by the enzymes are required to establish higher methylations (H3K4/36me3). Thus, methylation states are determined by the transcription rate. In summary, the first mechanism determines the location of methylations in the gene, while the second mechanism determines the methylation state.
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Affiliation(s)
- Justin Chan
- Molecular Modelling and Simulation (MMS) Team, Institute for Quantum Life Science (iQLS), National Institutes for Quantum Science and Technology (QST), 8-1-7 Umemidai, Kizugawa, Kyoto 619-0215, Japan
| | - Amarjeet Kumar
- Molecular Modelling and Simulation (MMS) Team, Institute for Quantum Life Science (iQLS), National Institutes for Quantum Science and Technology (QST), 8-1-7 Umemidai, Kizugawa, Kyoto 619-0215, Japan
| | - Hidetoshi Kono
- Molecular Modelling and Simulation (MMS) Team, Institute for Quantum Life Science (iQLS), National Institutes for Quantum Science and Technology (QST), 8-1-7 Umemidai, Kizugawa, Kyoto 619-0215, Japan.
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Abstract
The NIa protease of potyviruses is a chymotrypsin-like cysteine protease related to the picornavirus 3C protease. It is also a multifunctional protein known to play multiple roles during virus infection. Picornavirus 3C proteases cleave hundreds of host proteins to facilitate virus infection. However, whether or not potyvirus NIa proteases cleave plant proteins has so far not been tested. Regular expression search using the cleavage site consensus sequence [EQN]xVxH[QE]/[SGTA] for the plum pox virus (PPV) protease identified 90 to 94 putative cleavage events in the proteomes of Prunus persica (a crop severely affected by PPV), Arabidopsis thaliana, and Nicotiana benthamiana (two experimental hosts). In vitro processing assays confirmed cleavage of six A. thaliana and five P. persica proteins by the PPV protease. These proteins were also cleaved in vitro by the protease of turnip mosaic virus (TuMV), which has a similar specificity. We confirmed in vivo cleavage of a transiently expressed tagged version of AtEML2, an EMSY-like protein belonging to a family of nuclear histone readers known to be involved in pathogen resistance. Cleavage of AtEML2 was efficient and was observed in plants that coexpressed the PPV or TuMV NIa proteases or in plants that were infected with TuMV. We also showed partial in vivo cleavage of AtDUF707, a membrane protein annotated as lysine ketoglutarate reductase trans-splicing protein. Although cleavage of the corresponding endogenous plant proteins remains to be confirmed, the results show that a plant virus protease can cleave host proteins during virus infection and highlight a new layer of plant-virus interactions. IMPORTANCE Viruses are highly adaptive and use multiple molecular mechanisms to highjack or modify the cellular resources to their advantage. They must also counteract or evade host defense responses. One well-characterized mechanism used by vertebrate viruses is the proteolytic cleavage of host proteins to inhibit the activities of these proteins and/or to produce cleaved protein fragments that are beneficial to the virus infection cycle. Even though almost half of the known plant viruses encode at least one protease, it was not known whether plant viruses employ this strategy. Using an in silico prediction approach and the well-characterized specificity of potyvirus NIa proteases, we were able to identify hundreds of putative cleavage sites in plant proteins, several of which were validated by downstream experiments. It can be anticipated that many other plant virus proteases also cleave host proteins and that the identification of these cleavage events will lead to novel antiviral strategies.
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9
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Wang Z, Wang M, Yang C, Zhao L, Qin G, Peng L, Zheng Q, Nie W, Song CP, Shi H, Zhu JK, Zhao C. SWO1 modulates cell wall integrity under salt stress by interacting with importin ɑ in Arabidopsis. STRESS BIOLOGY 2021; 1:9. [PMID: 37676567 PMCID: PMC10442049 DOI: 10.1007/s44154-021-00010-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 08/24/2021] [Indexed: 09/08/2023]
Abstract
Maintenance of cell wall integrity is of great importance not only for plant growth and development, but also for the adaptation of plants to adverse environments. However, how the cell wall integrity is modulated under salt stress is still poorly understood. Here, we report that a nuclear-localized Agenet domain-containing protein SWO1 (SWOLLEN 1) is required for the maintenance of cell wall integrity in Arabidopsis under salt stress. Mutation in SWO1 gene results in swollen root tips, disordered root cell morphology, and root elongation inhibition under salt stress. The swo1 mutant accumulates less cellulose and pectin but more lignin under high salinity. RNA-seq and ChIP-seq assays reveal that SWO1 binds to the promoter of several cell wall-related genes and regulates their expression under saline conditions. Further study indicates that SWO1 interacts with importin ɑ IMPA1 and IMPA2, which are required for the import of nuclear-localized proteins. The impa1 impa2 double mutant also exhibits root growth inhibition under salt stress and mutations of these two genes aggravate the salt-hypersensitive phenotype of the swo1 mutant. Taken together, our data suggest that SWO1 functions together with importin ɑ to regulate the expression of cell wall-related genes, which enables plants to maintain cell wall integrity under high salinity.
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Affiliation(s)
- Zhidan Wang
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Mugui Wang
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Changhong Yang
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lun Zhao
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Guochen Qin
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Li Peng
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Qijie Zheng
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Wenfeng Nie
- Department of Horticulture, College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, China
| | - Chun-Peng Song
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, 475001, China
| | - Huazhong Shi
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, 79409, USA
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China.
| | - Chunzhao Zhao
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China.
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, 475001, China.
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Gupta N, Reddy K, Bhattacharyya D, Chakraborty✉ S. Plant responses to geminivirus infection: guardians of the plant immunity. Virol J 2021; 18:143. [PMID: 34243802 PMCID: PMC8268416 DOI: 10.1186/s12985-021-01612-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 06/29/2021] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Geminiviruses are circular, single-stranded viruses responsible for enormous crop loss worldwide. Rapid expansion of geminivirus diversity outweighs the continuous effort to control its spread. Geminiviruses channelize the host cell machinery in their favour by manipulating the gene expression, cell signalling, protein turnover, and metabolic reprogramming of plants. As a response to viral infection, plants have evolved to deploy various strategies to subvert the virus invasion and reinstate cellular homeostasis. MAIN BODY Numerous reports exploring various aspects of plant-geminivirus interaction portray the subtlety and flexibility of the host-pathogen dynamics. To leverage this pool of knowledge towards raising antiviral resistance in host plants, a comprehensive account of plant's defence response against geminiviruses is required. This review discusses the current knowledge of plant's antiviral responses exerted to geminivirus in the light of resistance mechanisms and the innate genetic factors contributing to the defence. We have revisited the defence pathways involving transcriptional and post-transcriptional gene silencing, ubiquitin-proteasomal degradation pathway, protein kinase signalling cascades, autophagy, and hypersensitive responses. In addition, geminivirus-induced phytohormonal fluctuations, the subsequent alterations in primary and secondary metabolites, and their impact on pathogenesis along with the recent advancements of CRISPR-Cas9 technique in generating the geminivirus resistance in plants have been discussed. CONCLUSIONS Considering the rapid development in the field of plant-virus interaction, this review provides a timely and comprehensive account of molecular nuances that define the course of geminivirus infection and can be exploited in generating virus-resistant plants to control global agricultural damage.
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Affiliation(s)
- Neha Gupta
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067 India
| | - Kishorekumar Reddy
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067 India
| | - Dhriti Bhattacharyya
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067 India
| | - Supriya Chakraborty✉
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067 India
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11
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Scheid R, Chen J, Zhong X. Biological role and mechanism of chromatin readers in plants. CURRENT OPINION IN PLANT BIOLOGY 2021; 61:102008. [PMID: 33581373 PMCID: PMC8222062 DOI: 10.1016/j.pbi.2021.102008] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 01/12/2021] [Accepted: 01/13/2021] [Indexed: 05/05/2023]
Abstract
Epigenetic modifications are important gene regulatory mechanisms conserved in plants, animals, and fungi. Chromatin reader domains are protein-protein/DNA interaction modules acting within the chromatin-modifying complex to function as molecular interpreters of the epigenetic code. Understanding how reader proteins recognize specific epigenetic modifications and mediate downstream chromatin and transcriptional events is fundamental to many biological processes. Recent studies have uncovered a number of novel reader proteins with diverse functions and mechanisms in plants. Here, we provide an overview of the recent progress on reader-mark recognition modes, the mechanisms by which reader proteins influence chromatin dynamics, and how reader-chromatin interactions regulate biological function. Because of space limitations, this review focuses on reader domains in plants that specifically bind histone methylation, histone acetylation, and DNA methylation.
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Affiliation(s)
- Ray Scheid
- Laboratory of Genetics & Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jiani Chen
- Laboratory of Genetics & Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Xuehua Zhong
- Laboratory of Genetics & Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53706, USA.
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12
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Liu X, Huang W, Zhai Z, Ye T, Yang C, Lai J. Protein modification: A critical modulator in the interaction between geminiviruses and host plants. PLANT, CELL & ENVIRONMENT 2021; 44:1707-1715. [PMID: 33506956 DOI: 10.1111/pce.14008] [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] [Received: 11/16/2020] [Revised: 01/06/2021] [Accepted: 01/18/2021] [Indexed: 06/12/2023]
Abstract
Geminiviruses are a large group of single-stranded DNA viruses that infect plants and cause severe agricultural losses worldwide. Given geminiviruses only have small genomes that encode a few proteins, viral factors have to interact with host components to establish an environment suitable for virus infection, whilst the host immunity system recognizes and targets these viral components during infection. Post-translational protein modifications, such as phosphorylation, lipidation, ubiquitination, SUMOylation, acetylation and methylation, have been reported to be critical during the interplay between host plants and geminiviruses. Here we summarize the research progress, including phosphorylation and lipidation which usually control the activity and localization of viral factors; as well as ubiquitination and histone modification which are predominantly interfered with by viral components. We also discuss the dynamic competition on protein modifications between host defence and geminivirus efficient infection, as well as potential applications of protein modifications in geminivirus resistance. The summary and perspective of this topic will improve our understanding on the mechanism of geminivirus-plant interaction and contribute to further protection of plants from virus infection.
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Affiliation(s)
- Xiaoshi Liu
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou, China
| | - Wei Huang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou, China
| | - Zhenqian Zhai
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou, China
| | - Tushu Ye
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou, China
| | - Chengwei Yang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou, China
| | - Jianbin Lai
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou, China
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13
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Zarreen F, Chakraborty S. Epigenetic regulation of geminivirus pathogenesis: a case of relentless recalibration of defence responses in plants. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:6890-6906. [PMID: 32869846 DOI: 10.1093/jxb/eraa406] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 08/27/2020] [Indexed: 06/11/2023]
Abstract
Geminiviruses constitute one of the largest families of plant viruses and they infect many economically important crops. The proteins encoded by the single-stranded DNA genome of these viruses interact with a wide range of host proteins to cause global dysregulation of cellular processes and help establish infection in the host. Geminiviruses have evolved numerous mechanisms to exploit host epigenetic processes to ensure the replication and survival of the viral genome. Here, we review our current knowledge of diverse epigenetic processes that have been implicated in the regulation of geminivirus pathogenesis, including DNA methylation, histone post-transcriptional modification, chromatin remodelling, and nucleosome repositioning. In addition, we discuss the currently limited evidence of host epigenetic defence responses that are aimed at counteracting geminivirus infection, and the potential for exploiting these responses for the generation of resistance against geminiviruses in crop species.
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Affiliation(s)
- Fauzia Zarreen
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Supriya Chakraborty
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
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14
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Milutinovic M, Lindsey BE, Wijeratne A, Hernandez JM, Grotewold N, Fernández V, Grotewold E, Brkljacic J. Arabidopsis EMSY-like (EML) histone readers are necessary for post-fertilization seed development, but prevent fertilization-independent seed formation. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 285:99-109. [PMID: 31203898 DOI: 10.1016/j.plantsci.2019.04.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 04/07/2019] [Accepted: 04/09/2019] [Indexed: 06/09/2023]
Abstract
Seed development is a complex regulatory process that includes a transition from gametophytic to sporophytic program. The synchronized development of different seed compartments (seed coat, endosperm and embryo) depends on a balance in parental genome contributions. In the most severe cases, the disruption of the balance leads to seed abortion. This represents one of the main obstacles for the engineering of asexual reproduction through seeds (apomixis), and for generating new interspecies hybrids. The repression of auxin synthesis by the Polycomb Repressive Complex 2 (PRC2) is a major mechanism contributing to sensing genome balance. However, current efforts focusing on decreasing PRC2 or elevating auxin levels have not yet resulted in the production of apomictic seed. Here, we show that EMSY-Like Tudor/Agenet H3K36me3 histone readers EML1 and EML3 are necessary for early stages of seed development to proceed at a normal rate in Arabidopsis. We further demonstrate that both EML1 and EML3 are required to prevent the initiation of seed development in the absence of fertilization. Based on the whole genome expression analysis, we identify auxin transport and signaling genes as the most enriched downstream targets of EML1 and EML3. We hypothesize that EML1 and EML3 function to repress and soften paternal gene expression by fine-tuning auxin responses. Discovery of this pathway may contribute to the engineering of apomixis and interspecies hybrids.
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Affiliation(s)
- Milica Milutinovic
- Arabidopsis Biological Resource Center, The Ohio State University, Columbus, OH, 43210, USA
| | - Benson E Lindsey
- Arabidopsis Biological Resource Center, The Ohio State University, Columbus, OH, 43210, USA
| | - Asela Wijeratne
- Department of Molecular Genetics, Center for Applied Plant Sciences, The Ohio State University, Columbus, OH, 43210, USA
| | - J Marcela Hernandez
- Department of Molecular Genetics, Center for Applied Plant Sciences, The Ohio State University, Columbus, OH, 43210, USA
| | - Nikolas Grotewold
- Arabidopsis Biological Resource Center, The Ohio State University, Columbus, OH, 43210, USA
| | - Virginia Fernández
- Arabidopsis Biological Resource Center, The Ohio State University, Columbus, OH, 43210, USA
| | - Erich Grotewold
- Department of Molecular Genetics, Center for Applied Plant Sciences, The Ohio State University, Columbus, OH, 43210, USA.
| | - Jelena Brkljacic
- Arabidopsis Biological Resource Center, The Ohio State University, Columbus, OH, 43210, USA.
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15
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Kumar RV. Plant Antiviral Immunity Against Geminiviruses and Viral Counter-Defense for Survival. Front Microbiol 2019; 10:1460. [PMID: 31297106 PMCID: PMC6607972 DOI: 10.3389/fmicb.2019.01460] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 06/11/2019] [Indexed: 12/27/2022] Open
Abstract
The family Geminiviridae includes plant-infecting viruses whose genomes are composed of one or two circular non-enveloped ssDNAs(+) of about 2.5-5.2 kb each in size. These insect-transmissible geminiviruses cause significant crop losses across continents and pose a serious threat to food security. Under the control of promoters generally located within the intergenic region, their genomes encode five to eight ORFs from overlapping viral transcripts. Most proteins encoded by geminiviruses perform multiple functions, such as suppressing defense responses, hijacking ubiquitin-proteasomal pathways, altering hormonal responses, manipulating cell cycle regulation, and exploiting protein-signaling cascades. Geminiviruses establish complex but coordinated interactions with several host elements to spread and facilitate successful infection cycles. Consequently, plants have evolved several multilayered defense strategies against geminivirus infection and distribution. Recent studies on the evasion of host-mediated resistance factors by various geminivirus proteins through novel mechanisms have provided new insights into the development of antiviral strategies against geminiviruses. This review summarizes the current knowledge concerning virus movement within and between cells, as well as the recent advances in our understanding of the biological roles of virus-encoded proteins in manipulating host-mediated responses and insect transmission. This review also highlights unexplored areas that may increase our understanding of the biology of geminiviruses and how to combat these important plant pathogens.
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Affiliation(s)
- R. Vinoth Kumar
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, India
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16
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Bruns AN, Li S, Mohannath G, Bisaro DM. Phosphorylation of Arabidopsis eIF4E and eIFiso4E by SnRK1 inhibits translation. FEBS J 2019; 286:3778-3796. [PMID: 31120171 DOI: 10.1111/febs.14935] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 03/28/2019] [Accepted: 05/21/2019] [Indexed: 01/01/2023]
Abstract
Regulation of protein synthesis is critical for maintaining cellular homeostasis. In mammalian systems, translational regulatory networks have been elucidated in considerable detail. In plants, however, regulation occurs through different mechanisms that remain largely elusive. In this study, we present evidence that the Arabidopsis thaliana energy sensing kinase SnRK1, a homologue of mammalian AMP-activated kinase and yeast sucrose non-fermenting 1 (SNF1), inhibits translation by phosphorylating the cap binding proteins eIF4E and eIFiso4E. We establish that eIF4E and eIFiso4E contain two deeply conserved SnRK1 consensus target sites and that both interact with SnRK1 in vivo. We then demonstrate that SnRK1 phosphorylation inhibits the ability of Arabidopsis eIF4E and eIFiso4E to complement a yeast strain lacking endogenous eIF4E, and that inhibition correlates with repression of polysome formation. Finally, we show that SnRK1 over-expression in Nicotiana benthamiana plants reduces polysome formation, and that this effect can be counteracted by transient expression of eIF4E or mutant eIF4E containing non-phosphorylatable SnRK1 target residues, but not by a phosphomimic eIF4E. Together, these studies elucidate a novel and direct pathway for translational control in plant cells. In light of previous findings that SnRK1 conditions an innate antiviral defense and is inhibited by geminivirus pathogenicity factors, we speculate that phosphorylation of cap binding proteins may be a component of the resistance mechanism.
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Affiliation(s)
- Aaron N Bruns
- Department of Molecular Genetics, Center for Applied Plant Sciences, Center for RNA Biology, and Infectious Diseases Institute, The Ohio State University, Columbus, OH, USA.,Ohio State Biochemistry Program, The Ohio State University, Columbus, OH, USA
| | - Sizhun Li
- Department of Molecular Genetics, Center for Applied Plant Sciences, Center for RNA Biology, and Infectious Diseases Institute, The Ohio State University, Columbus, OH, USA
| | - Gireesha Mohannath
- Department of Molecular Genetics, Center for Applied Plant Sciences, Center for RNA Biology, and Infectious Diseases Institute, The Ohio State University, Columbus, OH, USA
| | - David M Bisaro
- Department of Molecular Genetics, Center for Applied Plant Sciences, Center for RNA Biology, and Infectious Diseases Institute, The Ohio State University, Columbus, OH, USA.,Ohio State Biochemistry Program, The Ohio State University, Columbus, OH, USA
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