1
|
Singh A, Verma S, Modak SB, Chaturvedi MM, Purohit JS. Extra-nuclear histones: origin, significance and perspectives. Mol Cell Biochem 2022; 477:507-524. [PMID: 34796445 DOI: 10.1007/s11010-021-04300-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 11/08/2021] [Indexed: 12/15/2022]
Abstract
Histones are classically known to organize the eukaryotic DNA into chromatin. They are one of the key players in regulating transcriptionally permissive and non-permissive states of the chromatin. Nevertheless, their context-dependent appearance within the cytoplasm and systemic circulation has also been observed. The past decade has also witnessed few scientific communications on the existence of vesicle-associated histones. Diverse groups have attempted to determine the significance of these extra-nuclear histones so far, with many of those studies still underway. Of note amongst these are interactions of extra-nuclear or free histones with cellular membranes, mediated by mutual cationic and anionic natures, respectively. It is here aimed to consolidate the mechanism of formation of extra-nuclear histones; implications of histone-induced membrane destabilization and explore the mechanisms of their association/release with extracellular vesicles, along with the functional aspects of these extra-nuclear histones in cell and systemic physiology.
Collapse
Affiliation(s)
- Abhilasha Singh
- Department of Zoology, University of Delhi, Delhi, 110007, India
| | - Sudhir Verma
- Department of Zoology, Deen Dayal Upadhyaya College, University of Delhi, Delhi, 110078, India
| | | | | | - Jogeswar S Purohit
- Department of Zoology, University of Delhi, Delhi, 110007, India.
- Molecular and Systems Biology Lab, Cluster Innovation Centre, University of Delhi, North Campus, DREAM Building, Delhi, 110007, India.
| |
Collapse
|
2
|
Zheng Z, Li R, Aweya JJ, Yao D, Wang F, Li S, Tuan TN, Zhang Y. The PirB toxin protein from Vibrio parahaemolyticus induces apoptosis in hemocytes of Penaeus vannamei. Virulence 2021; 12:481-492. [PMID: 33487106 PMCID: PMC7834086 DOI: 10.1080/21505594.2021.1872171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Acute hepatopancreatic necrosis disease (AHPND) is a major debilitating disease that causes massive shrimp death resulting in substantial economic losses in shrimp aquaculture. The Pir toxin proteins secreted by a unique strain of Vibrio parahaemolyticus play an essential role in the pathogenesis of AHPND. At present, most studies on the effects of Pir toxin proteins in shrimp focus on digestive tissues or organs such as hepatopancreas, stomach, etc., with none on the immune organs. In the present study, two recombinant Pir toxin proteins (rPirA and rPirB) of V. parahaemolyticus were expressed with rPirB shown to enter shrimp hemocytes. Employing pull-down and LC-MS/MS analysis, GST-rPirB was found to interact with 13 proteins in hemocytes, including histone H3 and histone H4 and among which histone H4 had the highest protein score. Further analysis using GST pull-down and Far-Western blot analysis revealed that rPirB could interact with histone H4. In addition, using the purified nucleosome protein from Drosophila S2 cells, it was found that PirB protein could specifically bind to histones. When flow cytometry was applied, it was observed that the interaction between PirB and histones in shrimp hemocytes induces apoptosis, which results in the dephosphorylation of Serine 10 in histone H3. Collectively, the current study shows that in addition to its effect on the digestive tract of shrimp, the PirB toxin protein interacts with histones to affect the phosphorylation of histone H3-S10, thereby inducing apoptosis.
Collapse
Affiliation(s)
- Zhou Zheng
- Department of Biology and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University , Shantou, China.,STU-UMT Joint Shellfish Research Laboratory, Shantou University , Shantou, China
| | - Ruiwei Li
- Department of Biology and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University , Shantou, China.,STU-UMT Joint Shellfish Research Laboratory, Shantou University , Shantou, China
| | - Jude Juventus Aweya
- Department of Biology and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University , Shantou, China.,STU-UMT Joint Shellfish Research Laboratory, Shantou University , Shantou, China
| | - Defu Yao
- Department of Biology and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University , Shantou, China.,STU-UMT Joint Shellfish Research Laboratory, Shantou University , Shantou, China
| | - Fan Wang
- Department of Biology and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University , Shantou, China.,STU-UMT Joint Shellfish Research Laboratory, Shantou University , Shantou, China
| | - Shengkang Li
- Department of Biology and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University , Shantou, China.,STU-UMT Joint Shellfish Research Laboratory, Shantou University , Shantou, China
| | - Tran Ngoc Tuan
- Department of Biology and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University , Shantou, China.,STU-UMT Joint Shellfish Research Laboratory, Shantou University , Shantou, China
| | - Yueling Zhang
- Department of Biology and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University , Shantou, China.,STU-UMT Joint Shellfish Research Laboratory, Shantou University , Shantou, China.,Southern Marine Science and Engineering Guangdong Laboratory , Guangzhou, China
| |
Collapse
|
3
|
Wiese M, Bannister AJ. Two genomes, one cell: Mitochondrial-nuclear coordination via epigenetic pathways. Mol Metab 2020; 38:100942. [PMID: 32217072 PMCID: PMC7300384 DOI: 10.1016/j.molmet.2020.01.006] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 01/06/2020] [Accepted: 01/07/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Virtually all eukaryotic cells contain spatially distinct genomes, a single nuclear genome that harbours the vast majority of genes and much smaller genomes found in mitochondria present at thousands of copies per cell. To generate a coordinated gene response to various environmental cues, the genomes must communicate with each another. Much of this bi-directional crosstalk relies on epigenetic processes, including DNA, RNA, and histone modification pathways. Crucially, these pathways, in turn depend on many metabolites generated in specific pools throughout the cell, including the mitochondria. They also involve the transport of metabolites as well as the enzymes that catalyse these modifications between nuclear and mitochondrial genomes. SCOPE OF REVIEW This study examines some of the molecular mechanisms by which metabolites influence the activity of epigenetic enzymes, ultimately affecting gene regulation in response to metabolic cues. We particularly focus on the subcellular localisation of metabolite pools and the crosstalk between mitochondrial and nuclear proteins and RNAs. We consider aspects of mitochondrial-nuclear communication involving histone proteins, and potentially their epigenetic marks, and discuss how nuclear-encoded enzymes regulate mitochondrial function through epitranscriptomic pathways involving various classes of RNA molecules within mitochondria. MAJOR CONCLUSIONS Epigenetic communication between nuclear and mitochondrial genomes occurs at multiple levels, ultimately ensuring a coordinated gene expression response between different genetic environments. Metabolic changes stimulated, for example, by environmental factors, such as diet or physical activity, alter the relative abundances of various metabolites, thereby directly affecting the epigenetic machinery. These pathways, coupled to regulated protein and RNA transport mechanisms, underpin the coordinated gene expression response. Their overall importance to the fitness of a cell is highlighted by the identification of many mutations in the pathways we discuss that have been linked to human disease including cancer.
Collapse
Affiliation(s)
- Meike Wiese
- Max-Planck-Institute for Immunobiology und Epigenetics, Department of Chromatin Regulation, Stübeweg 51, 79108, Freiburg im Breisgau, Germany
| | - Andrew J Bannister
- Gurdon Institute and Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK.
| |
Collapse
|
4
|
Monteonofrio L, Valente D, Rinaldo C, Soddu S. Extrachromosomal Histone H2B Contributes to the Formation of the Abscission Site for Cell Division. Cells 2019; 8:cells8111391. [PMID: 31694230 PMCID: PMC6912571 DOI: 10.3390/cells8111391] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 10/25/2019] [Accepted: 10/31/2019] [Indexed: 12/13/2022] Open
Abstract
Histones are constitutive components of nucleosomes and key regulators of chromatin structure. We previously observed that an extrachromosomal histone H2B (ecH2B) localizes at the intercellular bridge (ICB) connecting the two daughter cells during cytokinesis independently of DNA and RNA. Here, we show that ecH2B binds and colocalizes with CHMP4B, a key component of the ESCRT-III machinery responsible for abscission, the final step of cell division. Abscission requires the formation of an abscission site at the ICB where the ESCRT-III complex organizes into narrowing cortical helices that drive the physical separation of sibling cells. ecH2B depletion does not prevent membrane cleavage rather results in abscission delay and accumulation of abnormally long and thin ICBs. In the absence of ecH2B, CHMP4B and other components of the fission machinery, such as IST1 and Spastin, are recruited to the ICB and localize at the midbody. However, in the late stage of abscission, these fission factors fail to re-localize at the periphery of the midbody and the abscission site fails to form. These results show that extrachromosomal activity of histone H2B is required in the formation of the abscission site and the proper localization of the fission machinery.
Collapse
Affiliation(s)
- Laura Monteonofrio
- Unit of Cellular Networks and Molecular Therapeutic Targets, IRCCS-Regina Elena National Cancer Institute, 00144 Rome, Italy; (D.V.); (C.R.)
- Correspondence: (L.M.); (S.S.); Tel.: +1-(443)-410-9571 (L.M.); +39-065266-2492 (S.S.)
| | - Davide Valente
- Unit of Cellular Networks and Molecular Therapeutic Targets, IRCCS-Regina Elena National Cancer Institute, 00144 Rome, Italy; (D.V.); (C.R.)
| | - Cinzia Rinaldo
- Unit of Cellular Networks and Molecular Therapeutic Targets, IRCCS-Regina Elena National Cancer Institute, 00144 Rome, Italy; (D.V.); (C.R.)
- Institutes of Molecular Biology and Pathology (IBPM), National Research Council (CNR), c/o Sapienza University, 00185 Rome, Italy
| | - Silvia Soddu
- Unit of Cellular Networks and Molecular Therapeutic Targets, IRCCS-Regina Elena National Cancer Institute, 00144 Rome, Italy; (D.V.); (C.R.)
- Correspondence: (L.M.); (S.S.); Tel.: +1-(443)-410-9571 (L.M.); +39-065266-2492 (S.S.)
| |
Collapse
|
5
|
Meng X, Peng H, Ding Y, Zhang L, Yang J, Han X. A transcriptomic regulatory network among miRNAs, piRNAs, circRNAs, lncRNAs and mRNAs regulates microcystin-leucine arginine (MC-LR)-induced male reproductive toxicity. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 667:563-577. [PMID: 30833255 DOI: 10.1016/j.scitotenv.2019.02.393] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 02/19/2019] [Accepted: 02/25/2019] [Indexed: 06/09/2023]
Abstract
Microcystin-leucine arginine (MC-LR) which is produced by cyanobacteria is a potent toxin for the reproductive system. Our previous work has demonstrated that both acute and chronic reproductive toxicity engendered by MC-LR can result in the decline of sperm quality and damage of testicular structures in male mice. The present study was designed to investigate the impact of chronic low-dose exposure to MC-LR on the regulation of RNA networks including mRNA, microRNA (miRNA), piwi-associated RNA (piRNA), covalently closed circular RNA (circRNA) and long non-coding RNA (lncRNA) in testicular tissues. By high-throughput sequencing analysis, 1091 mRNAs, 21 miRNAs, 644 piRNAs, 278 circRNAs and 324 lncRNAs were identified to be significantly altered in testicular tissues treated with MC-LR. We performed gene ontology (GO) analysis to ascertain the biological functions of differentially expressed genes. Among the altered 21 miRNAs and 644 piRNAs, the miRNA chr13_8977, which is a newly discovered species, and the piRNA mmu_piR_027558 were dramatically down-regulated after exposure to MC-LR. Consistently, both mRNA levels and protein expression levels of their predicted targets were increased significantly when chr13_8977 and mmu_piR_027558 were each down-regulated. Testicular structures, germ cell apoptosis and sperm quality were also affected by the altered expression of chr13_8977 and mmu_piR_027558 severally. We further investigated the differential expression of circRNAs and lncRNAs and their biological functions in testicular tissues following treatment with chronic low-dose exposure to MC-LR. We also constructed a competing endogenous RNA (ceRNA) network to predict the functions of the altered expressed RNAs using MiRanda. Our study suggested a crucial role for the potential network regulation of miRNAs, piRNAs, circRNAs, lncRNAs and mRNAs impacting the cytotoxicity of MC-LR in testicular tissues, which provides new perspectives in the development of diagnosis and treatment strategies for MC-LR-induced male reproductive toxicity.
Collapse
Affiliation(s)
- Xiannan Meng
- Immunology and Reproduction Biology Laboratory & State Key Laboratory of Analytical Chemistry for Life Science, Medical School, Nanjing University, Nanjing, Jiangsu 210093, China; Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing, Jiangsu 210093, China
| | - Haoran Peng
- Immunology and Reproduction Biology Laboratory & State Key Laboratory of Analytical Chemistry for Life Science, Medical School, Nanjing University, Nanjing, Jiangsu 210093, China; Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing, Jiangsu 210093, China
| | - Yuanzhen Ding
- Immunology and Reproduction Biology Laboratory & State Key Laboratory of Analytical Chemistry for Life Science, Medical School, Nanjing University, Nanjing, Jiangsu 210093, China; Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing, Jiangsu 210093, China
| | - Ling Zhang
- Immunology and Reproduction Biology Laboratory & State Key Laboratory of Analytical Chemistry for Life Science, Medical School, Nanjing University, Nanjing, Jiangsu 210093, China; Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing, Jiangsu 210093, China
| | - Jingping Yang
- Immunology and Reproduction Biology Laboratory & State Key Laboratory of Analytical Chemistry for Life Science, Medical School, Nanjing University, Nanjing, Jiangsu 210093, China; Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing, Jiangsu 210093, China.
| | - Xiaodong Han
- Immunology and Reproduction Biology Laboratory & State Key Laboratory of Analytical Chemistry for Life Science, Medical School, Nanjing University, Nanjing, Jiangsu 210093, China; Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing, Jiangsu 210093, China.
| |
Collapse
|