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Du Q, Peng F, Xiong Q, Xu K, Yang KY, Wang M, Wu Z, Li S, Cheng X, Rao X, Wang Y, Tsui SKW, Zeng X. Genomic Analysis of Amphioxus Reveals a Wide Range of Fragments Homologous to Viral Sequences. Viruses 2023; 15:v15040909. [PMID: 37112889 PMCID: PMC10145014 DOI: 10.3390/v15040909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 03/11/2023] [Accepted: 03/28/2023] [Indexed: 04/05/2023] Open
Abstract
Amphioxus species are considered living fossils and are important in the evolutionary study of chordates and vertebrates. To explore viral homologous sequences, a high-quality annotated genome of the Beihai amphioxus (Branchiostoma belcheri beihai) was examined using virus sequence queries. In this study, 347 homologous fragments (HFs) of viruses were identified in the genome of B. belcheri beihai, of which most were observed on 21 genome assembly scaffolds. HFs were preferentially located within protein-coding genes, particularly in their CDS regions and promoters. A range of amphioxus genes with a high frequency of HFs is proposed, including histone-related genes that are homologous to the Histone H4 or Histone H2B domains of viruses. Together, this comprehensive analysis of viral HFs provides insights into the neglected role of viral integration in the evolution of amphioxus.
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Affiliation(s)
- Qiao Du
- Agricultural Bioinformatics Key Laboratory of Hubei Province and 3D Genomics Research Centre, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Fang Peng
- Agricultural Bioinformatics Key Laboratory of Hubei Province and 3D Genomics Research Centre, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Qing Xiong
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong, China
| | - Kejin Xu
- Agricultural Bioinformatics Key Laboratory of Hubei Province and 3D Genomics Research Centre, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Kevin Yi Yang
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong, China
| | - Mingqiang Wang
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Zhitian Wu
- Agricultural Bioinformatics Key Laboratory of Hubei Province and 3D Genomics Research Centre, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Shanying Li
- Agricultural Bioinformatics Key Laboratory of Hubei Province and 3D Genomics Research Centre, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaorui Cheng
- Agricultural Bioinformatics Key Laboratory of Hubei Province and 3D Genomics Research Centre, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Xinjie Rao
- Agricultural Bioinformatics Key Laboratory of Hubei Province and 3D Genomics Research Centre, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Yuyouye Wang
- Agricultural Bioinformatics Key Laboratory of Hubei Province and 3D Genomics Research Centre, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Stephen Kwok-Wing Tsui
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong, China
| | - Xi Zeng
- Agricultural Bioinformatics Key Laboratory of Hubei Province and 3D Genomics Research Centre, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
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Talbert PB, Armache KJ, Henikoff S. Viral histones: pickpocket's prize or primordial progenitor? Epigenetics Chromatin 2022; 15:21. [PMID: 35624484 PMCID: PMC9145170 DOI: 10.1186/s13072-022-00454-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 04/19/2022] [Indexed: 12/12/2022] Open
Abstract
The common histones H2A, H2B, H3, and H4 are the characteristic components of eukaryotic nucleosomes, which function to wrap DNA and compact the genome as well as to regulate access to DNA for transcription and replication in all eukaryotes. In the past two decades, histones have also been found to be encoded in some DNA viruses, where their functions and properties are largely unknown, though recently histones from two related viruses have been shown to form nucleosome-like structures in vitro. Viral histones can be highly similar to eukaryotic histones in primary sequence, suggesting they have been recently picked up from eukaryotic hosts, or they can be radically divergent in primary sequence and may occur as conjoined histone doublets, triplets, or quadruplets, suggesting ancient origins prior to the divergence of modern eukaryotes. Here, we review what is known of viral histones and discuss their possible origins and functions. We consider how the viral life cycle may affect their properties and histories, and reflect on the possible roles of viruses in the origin of the nucleus of modern eukaryotic cells.
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Affiliation(s)
- Paul B Talbert
- Howard Hughes Medical Institute and Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA, 98109, USA
| | - Karim-Jean Armache
- Skirball Institute of Biomolecular Medicine, Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, 550 First Ave, New York, NY, 10016, USA
| | - Steven Henikoff
- Howard Hughes Medical Institute and Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA, 98109, USA.
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Villagra C, Frías-Lasserre D. Epigenetic Molecular Mechanisms in Insects. NEOTROPICAL ENTOMOLOGY 2020; 49:615-642. [PMID: 32514997 DOI: 10.1007/s13744-020-00777-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 04/06/2020] [Indexed: 06/11/2023]
Abstract
Insects are the largest animal group on Earth both in biomass and diversity. Their outstanding success has inspired genetics and developmental research, allowing the discovery of dynamic process explaining extreme phenotypic plasticity and canalization. Epigenetic molecular mechanisms (EMMs) are vital for several housekeeping functions in multicellular organisms, regulating developmental, ontogenetic trajectories and environmental adaptations. In Insecta, EMMs are involved in the development of extreme phenotypic divergences such as polyphenisms and eusocial castes. Here, we review the history of this research field and how the main EMMs found in insects help to understand their biological processes and diversity. EMMs in insects confer them rapid response capacity allowing insect either to change with plastic divergence or to keep constant when facing different stressors or stimuli. EMMs function both at intra as well as transgenerational scales, playing important roles in insect ecology and evolution. We discuss on how EMMs pervasive influences in Insecta require not only the control of gene expression but also the dynamic interplay of EMMs with further regulatory levels, including genetic, physiological, behavioral, and environmental among others, as was earlier proposed by the Probabilistic Epigenesis model and Developmental System Theory.
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Affiliation(s)
- C Villagra
- Instituto de Entomología, Univ Metropolitana de Ciencias de la Educación, Santiago, Chile.
| | - D Frías-Lasserre
- Instituto de Entomología, Univ Metropolitana de Ciencias de la Educación, Santiago, Chile
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Abeywickrama-Samarakoon N, Cortay JC, Sureau C, Müller S, Alfaiate D, Guerrieri F, Chaikuad A, Schröder M, Merle P, Levrero M, Dény P. Hepatitis Delta Virus histone mimicry drives the recruitment of chromatin remodelers for viral RNA replication. Nat Commun 2020; 11:419. [PMID: 31964889 PMCID: PMC6972770 DOI: 10.1038/s41467-020-14299-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 12/21/2019] [Indexed: 12/26/2022] Open
Abstract
Hepatitis Delta virus (HDV) is a satellite of Hepatitis B virus with a single-stranded circular RNA genome. HDV RNA genome synthesis is carried out in infected cells by cellular RNA polymerases with the assistance of the small hepatitis delta antigen (S-HDAg). Here we show that S-HDAg binds the bromodomain (BRD) adjacent to zinc finger domain 2B (BAZ2B) protein, a regulatory subunit of BAZ2B-associated remodeling factor (BRF) ISWI chromatin remodeling complexes. shRNA-mediated silencing of BAZ2B or its inactivation with the BAZ2B BRD inhibitor GSK2801 impairs HDV replication in HDV-infected human hepatocytes. S-HDAg contains a short linear interacting motif (SLiM) KacXXR, similar to the one recognized by BAZ2B BRD in histone H3. We found that the integrity of the S-HDAg SLiM sequence is required for S-HDAg interaction with BAZ2B BRD and for HDV RNA replication. Our results suggest that S-HDAg uses a histone mimicry strategy to co-activate the RNA polymerase II-dependent synthesis of HDV RNA and sustain HDV replication. Histone mimicry of viral components is a strategy to subvert host factors for virus replication. Here, the authors show that an acetylated histone-like motif of the small Hepatitis Delta Antigen (S-HDAg) interacts with the chromatin remodeler BAZ2B to recruit the DNA-dependent RNA polymerase II for HDV RNA replication.
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Affiliation(s)
| | - Jean-Claude Cortay
- INSERM, U1052 UMR CNRS 5286, Cancer Research Center of Lyon (CRCL), 151 cours Albert Thomas, 69424, Lyon, France
| | - Camille Sureau
- Laboratoire de Virologie Moléculaire, INSERM U1134, Institut National de la Transfusion Sanguine, 6 rue Alexandre Cabanel, 75739, Paris, France
| | - Susanne Müller
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse 15, D-60438, Frankfurt am Main, Germany
| | - Dulce Alfaiate
- INSERM, U1052 UMR CNRS 5286, Cancer Research Center of Lyon (CRCL), 151 cours Albert Thomas, 69424, Lyon, France.,Département de Pathologie et Immunologie, Université de Genève, avenue de Champel 41, 1206, Genève, Switzerland.,Department of Infectious and Tropical Diseases, Hôpital de la Croix Rousse, Hospices Civils de Lyon and Université Lyon I, 103 Grande Rue de la Croix-Rousse, 69004, Lyon, France
| | - Francesca Guerrieri
- INSERM, U1052 UMR CNRS 5286, Cancer Research Center of Lyon (CRCL), 151 cours Albert Thomas, 69424, Lyon, France.,Italian Institute of Technology (IIT) - Center for Life Nanoscience (CLNS), Sapienza University, Viale Regina Elena, 291, 00161, Rome, Italy
| | - Apirat Chaikuad
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse 15, D-60438, Frankfurt am Main, Germany
| | - Martin Schröder
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse 15, D-60438, Frankfurt am Main, Germany
| | - Philippe Merle
- INSERM, U1052 UMR CNRS 5286, Cancer Research Center of Lyon (CRCL), 151 cours Albert Thomas, 69424, Lyon, France.,Department of Hepatology, Hôpital de la Croix Rousse, Hospices Civils de Lyon and Université Lyon I, 103 Grande Rue de la Croix-Rousse, 69004, Lyon, France
| | - Massimo Levrero
- INSERM, U1052 UMR CNRS 5286, Cancer Research Center of Lyon (CRCL), 151 cours Albert Thomas, 69424, Lyon, France. .,Italian Institute of Technology (IIT) - Center for Life Nanoscience (CLNS), Sapienza University, Viale Regina Elena, 291, 00161, Rome, Italy. .,Department of Hepatology, Hôpital de la Croix Rousse, Hospices Civils de Lyon and Université Lyon I, 103 Grande Rue de la Croix-Rousse, 69004, Lyon, France.
| | - Paul Dény
- INSERM, U1052 UMR CNRS 5286, Cancer Research Center of Lyon (CRCL), 151 cours Albert Thomas, 69424, Lyon, France. .,Laboratoire de Microbiologie Clinique, Groupe des Hôpitaux Universitaires de Paris - Seine Saint Denis, UFR Santé Médecine, Biologie Humaine, Université Paris 13, 125 Rue de Stalingrad, 93009, Bobigny, France.
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Encinas-García T, Loreto-Quiroz DL, Mendoza-Cano F, Peña-Rodriguez A, Fimbres-Olivarria D, Re-Vega ED, Sánchez-Paz A. White spot syndrome virus down-regulates expression of histones H2A and H4 of Penaeus vannamei to promote viral replication. DISEASES OF AQUATIC ORGANISMS 2019; 137:73-79. [PMID: 31802744 DOI: 10.3354/dao03428] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The white spot syndrome virus (WSSV) is a highly lethal and contagious pathogen to most cultivated shrimp species. The WSSV genome contains the ICP11 gene and its encoded protein acts as a multifunctinal DNA mimic protein that disrupts the nucleosome assembly by binding to the histone proteins H2A and H3. In addition, WSSV provokes severe nuclear hypertrophy and DNA damage. However, little is known about the influence of WSSV on the expression of the host's genes encoding for histones. Therefore, we investigated the effect of WSSV infection on the expression of the genes encoding histones in shrimp Penaeus vannamei. An RT-qPCR assay was performed to evaluate the temporal expression of H2A and H4 transcripts in the shrimp. Significant changes were observed in the expression of these genes, which coincided with the dynamics of replication of the virus. H2A reached its maximum expression levels at 12 hpi. Thus, it may be suggested that this is a viral strategy to evade the host's immune response in order to promote viral replication.
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Affiliation(s)
- Trinidad Encinas-García
- Laboratorio de Análisis, Referencia y Diagnóstico en Sanidad Acuícola, Centro de Investigaciones Biológicas del Noroeste (CIBNOR), Calle Hermosa 101, Col. Los Ángeles, Hermosillo, Sonora 83106, México
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Kim Y, Kumar S. Persistent expression of Cotesia plutellae bracovirus genes in parasitized host, Plutella xylostella. PLoS One 2018; 13:e0200663. [PMID: 30011308 PMCID: PMC6047808 DOI: 10.1371/journal.pone.0200663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 06/30/2018] [Indexed: 12/02/2022] Open
Abstract
Cotesia plutellae (= vestalis) bracovirus (CpBV) is symbiotic to an endoparasitoid wasp, C. plutellae, and plays crucial roles in parasitism against the diamondback moth, Plutella xylostella. CpBV virion genome consists of 35 circular DNAs encoding 157 putative open reading frames (ORFs). This study re-annotated 157 ORFs with update genome database and analyzed their gene expressions at early and late parasitic stages. Re-annotation has established 15 different viral gene families, to which 83 ORFs are assigned with remaining 74 hypothetical genes. Among 157 ORFs, 147 genes were expressed at early or late parasitic stages, among which 141 genes were expressed in both parasitic stages, indicating persistent nature of gene expression. Relative frequencies of different viral circles present in the ovarian lumen did not explain the expression variation of the viral ORFs. Furthermore, expression level of each viral gene was varied during parasitism along with host development. Highly up-regulated CpBV genes at early parasitic stage included BEN (BANP, E5R and NAC1), ELP (EP1-like protein), IkB (inhibitor kB), P494 (protein 494 kDa) family genes, while those at late stage were mostly hypothetical genes. Along with the viral gene expression, 362 host genes exhibited more than two fold changes in expression levels at early parasitic stage compared to nonparasitized host. At late stage, more number (1,858) of host genes was regulated. These results suggest that persistent expression of most CpBV genes may be necessary to regulate host physiological processes during C. plutellae parasitism.
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Affiliation(s)
- Yonggyun Kim
- Department of Plant Medicals, Andong National University, Andong, Korea
- * E-mail:
| | - Sunil Kumar
- Department of Plant Medicals, Andong National University, Andong, Korea
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Tarakhovsky A, Prinjha RK. Drawing on disorder: How viruses use histone mimicry to their advantage. J Exp Med 2018; 215:1777-1787. [PMID: 29934321 PMCID: PMC6028506 DOI: 10.1084/jem.20180099] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 04/24/2018] [Accepted: 06/07/2018] [Indexed: 12/16/2022] Open
Abstract
Humans carry trillions of viruses that thrive because of their ability to exploit the host. In this exploitation, viruses promote their own replication by suppressing the host antiviral response and by inducing changes in host biosynthetic processes, often with extremely small genomes of their own. In the review, we discuss the phenomenon of histone mimicry by viral proteins and how this mimicry allows the virus to dial in to the cell's transcriptional processes and establish a cell state that promotes infection. We suggest that histone mimicry is part of a broader viral strategy to use intrinsic protein disorder as a means to overcome the size limitations of its own genome and to maximize its impact on host protein networks. In particular, we discuss how intrinsic protein disorder may enable viral proteins to interfere with phase-separated host protein condensates, including those that contribute to chromatin-mediated control of gene expression.
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Affiliation(s)
- Alexander Tarakhovsky
- Laboratory of the Immune Cell Epigenetics and Signaling, The Rockefeller University, New York, NY
| | - Rab K Prinjha
- Epigenetics DPU, Oncology and Immuno-inflammation TA Units, GlaxoSmithKline Medicines Research Centre, Stevenage, England, UK
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8
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Ye XQ, Shi M, Huang JH, Chen XX. Parasitoid polydnaviruses and immune interaction with secondary hosts. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2018; 83:124-129. [PMID: 29352983 DOI: 10.1016/j.dci.2018.01.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 01/02/2018] [Accepted: 01/12/2018] [Indexed: 05/26/2023]
Abstract
Polydnaviruses (PDVs) are obligatory symbionts with parasitoid wasps. The PDV virions are produced solely in wasp (the primary host) calyx cells. They are injected into caterpillar hosts (the secondary host) during parasitoid oviposition, where they express irreplaceable actions to ensure survival and development of wasp larvae. Some of PDV gene products suppress host immune responses while others alter host growth, metabolism or endocrine system. Here, we treat new findings on PDV gene products and their action on immunity within secondary hosts.
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Affiliation(s)
- Xi-Qian Ye
- State Key Lab of Rice Biology and Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China
| | - Min Shi
- State Key Lab of Rice Biology and Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China
| | - Jian-Hua Huang
- State Key Lab of Rice Biology and Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China
| | - Xue-Xin Chen
- State Key Lab of Rice Biology and Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China.
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Characterization of joining sites of a viral histone H4 on host insect chromosomes. PLoS One 2017; 12:e0177066. [PMID: 28486493 PMCID: PMC5423620 DOI: 10.1371/journal.pone.0177066] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 04/22/2017] [Indexed: 12/28/2022] Open
Abstract
A viral histone H4 (CpBV-H4) is encoded in a polydnavirus, Cotesia plutellae bracovirus (CpBV). It plays a crucial role in parasitism of an endoparasitoid wasp, C. plutellae, against diamondback moth, Plutella xylostella, by altering host gene expression in an epigenetic mode by its N-terminal tail after joining host nucleosomes. Comparative transcriptomic analysis between parasitized and nonparasitized P. xylostella by RNA-Seq indicated that 1,858 genes were altered at more than two folds in expression levels at late parasitic stage, including 877 up-regulated genes and 981 down-regulated genes. Among parasitic factors altering host gene expression, CpBV-H4 alone explained 16.3% of these expressional changes. To characterize the joining sites of CpBV-H4 on host chromosomes, ChIP-Seq (chromatin immunoprecipitation followed by deep sequencing) was applied to chromatins extracted from parasitized larvae. It identified specific 538 ChIP targets. Joining sites were rich (60.2%) in AT sequence. Almost 40% of ChIP targets included short nucleotide repeat sequences presumably recognizable by transcriptional factors and chromatin remodeling factors. To further validate these CpBV-H4 targets, CpBV-H4 was transiently expressed in nonparasitized host at late larval stage and subjected to ChIP-Seq. Two kinds of ChIP-Seqs shared 51 core joining sites. Common targets were close (within 1 kb) to genes regulated at expression levels by CpBV-H4. However, other host genes not close to CpBV-H4 joining sites were also regulated by CpBV-H4. These results indicate that CpBV-H4 joins specific chromatin regions of P. xylostella and controls about one sixth of the total host genes that were regulated by C. plutellae parasitism in an epigenetic mode.
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Lusi EA, Maloney D, Caicci F, Guarascio P. Questions on unusual Mimivirus-like structures observed in human cells. F1000Res 2017; 6:262. [PMID: 28663783 PMCID: PMC5473404 DOI: 10.12688/f1000research.11007.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/13/2017] [Indexed: 12/15/2022] Open
Abstract
Background: Mimiviruses or giant viruses that infect amoebas have the ability to retain the Gram stain, which is usually used to colour bacteria. There is some evidence suggesting that Mimiviruses can also infect human cells. Guided by these premises, we performed a routine Gram stain on a variety of human specimens to see if we could detect the same Gram positive blue granules that identify Mimiviruses in the amoebas.
Methods: We analysed 24 different human specimens (liver, brain, kidney, lymph node and ovary) using Gram stain histochemistry, electron microscopy immunogold, high resolution mass spectrometry and protein identification.
Results: We detected in the human cells Gram positive granules that were distinct from bacteria. The fine blue granules displayed the same pattern of the Gram positive granules that diagnose Mimiviruses in the cytoplasm of the amoebas. Electron microscopy confirmed the presence of human Mimiviruses-like structures and mass spectrometry identified histone H4 peptides, which had the same footprints as giant viruses. However, some differences were noted: the Mimivirus-like structures identified in the human cells were ubiquitous and manifested a distinct mammalian retroviral antigenicity.
Conclusions: Our main hypotheses are that the structures could be either giant viruses having a retroviral antigenicity or ancestral cellular components having a viral origin. However, other possible alternatives have been proposed to explain the nature and function of the newly identified structures.
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Affiliation(s)
- Elena Angela Lusi
- St Vincent Health Care Group, University College of Dublin, Dublin 4, Ireland
| | - Dan Maloney
- Bioinformatics Solutions Inc., Waterloo, ON, N2L 6J2, Canada
| | - Federico Caicci
- Department of Biology, University of Padua, Padua, 35121, Italy
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An endoparasitoid wasp influences host DNA methylation. Sci Rep 2017; 7:43287. [PMID: 28230192 PMCID: PMC5322367 DOI: 10.1038/srep43287] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 09/30/2016] [Indexed: 12/24/2022] Open
Abstract
Parasitism by endoparasitoid wasps changes the expression of various host genes, and alters host immune and developmental processes. However, it is not clearly understood how parasitism changes host gene expression in a whole genome scale. This study focused on an epigenetic control of Cotesia plutellae, an endoparasitoid wasp, against its host, Plutella xylostella. Two DNA methyltransferases (DNMT-1 and DNMT-2) are encoded in the genome of P. xylostella. In addition, methyl-binding domain proteins (MBDs) and DNA demethylation factor, ten-eleven translation protein (TET) are encoded. DNA methylation of P. xylostella genomic DNA was confirmed by restriction digestion with Gla I specific to 5-methylcytosine. DNA methylation intensity in parasitized (P) larvae was decreased compared to that in nonparasitized (NP) larvae, especially at late parasitic stage, at which expression levels of both DNMT-1 and DNMT-2 were also decreased. DNA demethylation of P. xylostella was confirmed in both NP and P larvae by restriction digestion with PvuRts1I recognizing 5-hydroxymethyl cytosine. Parasitism also suppressed expression levels of TET and MBDs. Treatment of 5-aza-2′-deoxycytidine (AZA) reduced DNA methylation intensity of NP larvae, causing suppression of hemocyte-spreading behavior and delay of immature development. RNA interference of DNMT-1 or DNMT-2 mimicked the adverse effects of AZA.
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12
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Kumar S, Gu X, Kim Y. A viral histone H4 suppresses insect insulin signal and delays host development. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2016; 63:66-77. [PMID: 27216029 DOI: 10.1016/j.dci.2016.05.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2016] [Revised: 05/18/2016] [Accepted: 05/18/2016] [Indexed: 06/05/2023]
Abstract
Parasitization by an endoparasitoid wasp, Cotesia plutellae, alters host development of Plutella xylostella by extending larval period and preventing metamorphosis. Insulin signal plays a crucial role in mediating insect development and controlling blood sugar level in insects. In this study, three insulin-like peptide genes (PxILP1-3) were predicted from the genome of P. xylostella. However, only PxILP1 was confirmed to be expressed in P. xylostella. Starvation suppressed the expression level of PxILP1 and up-regulated plasma trehalose level. RNA interference against PxILP1 mimicked starvation effect and extended the larval period of P. xylostella. Parasitized larvae exhibited significantly lower levels of PxILP1 expression compared to nonparasitized larvae. Injection of wasp-symbiotic polydnavirus C. plutellae bracovirus (CpBV) also suppressed PxILP1 expression and extended the larval period. Injection of a viral segment (CpBV-S30) containing a viral histone H4 (CpBV-H4) also suppressed PxILP1 expression. Co-injection of CpBV-S30 and double-stranded RNA (dsCpBV-H4) specific to CpBV-H4 rescued the suppression of PxILP1 expression. Injection of CpBV-S30 significantly extended larval development. Co-injection of CpBV-S30 with dsCpBV-H4 rescued the delay of larval development. Injection of a bovine insulin to parasitized larvae prevented parasitoid development. These results indicate that parasitism of C. plutellae can down-regulate host insulin signaling with the help of parasitic factor CpBV-H4.
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Affiliation(s)
- Sunil Kumar
- Department of Bioresource Sciences, Andong National University, Andong 36729, South Korea
| | - Xiaojun Gu
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yonggyun Kim
- Department of Bioresource Sciences, Andong National University, Andong 36729, South Korea.
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King CR, Tessier TM, Mymryk JS. Color Me Infected: Painting Cellular Chromatin with a Viral Histone Mimic. Trends Microbiol 2016; 24:774-776. [PMID: 27592243 DOI: 10.1016/j.tim.2016.08.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 08/16/2016] [Indexed: 10/21/2022]
Abstract
Viruses manipulate cellular chromatin to create a favourable milieu for infection. In several cases, virally-encoded proteins structurally mimic cellular histones to molecularly rewire the host cell. A recent study identified a novel mechanism whereby adenovirus protein VII, a viral histone, binds and manipulates host cell chromatin to suppress inflammatory signalling.
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Affiliation(s)
- Cason R King
- Department of Microbiology & Immunology, University of Western Ontario, London, Ontario, Canada
| | - Tanner M Tessier
- Department of Microbiology & Immunology, University of Western Ontario, London, Ontario, Canada
| | - Joe S Mymryk
- Department of Microbiology & Immunology, University of Western Ontario, London, Ontario, Canada; Departments of Oncology and Otolaryngology, University of Western Ontario, London, Ontario, Canada; London Regional Cancer Program and Lawson Health Research Institute, London, Ontario, Canada.
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14
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Kumar S, Venkata P, Kim Y. Suppressive activity of a viral histone H4 against two host chromatin remodelling factors: lysine demethylase and SWI/SNF. J Gen Virol 2016; 97:2780-2796. [PMID: 27443988 DOI: 10.1099/jgv.0.000560] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Histone H4, a nucleosome subunit in eukaryotes, plays crucial roles in DNA package and regulation of gene expression through covalent modification. A viral histone H4 encoded in Cotesia plutellae bracovirus (CpBV), a polydnavirus, is called CpBV-H4. It is highly homologous to other histone H4 proteins excepting 38 extra amino acid residues in the N terminus. CpBV-H4 can form octamer with other histone subunits and alter host gene expression. In this study, CpBV-H4 was transiently expressed in a natural host (Plutella xylostella) and its suppressive activity on host gene expression was evaluated by the suppressive subtractive hybridization (SSH) technique. The SSH targets down-regulated by CpBV-H4 were read with the 454 pyrosequencing platform and annotated using the genome of P. xylostella. The down-regulated genes (610 contigs) were annotated in most functional categories based on gene ontology. Among these SSH targets, 115 genes were functionally distinct, including two chromatin remodelling factors: a lysine-specific demethylase (Px-KDM) and a chromatin remodelling complex [Px-SWI/SNF (SWItch/Sucrose Non-Fermentable)]. Px-KDM was highly expressed in all tested tissues during the entire larval period. Suppression of Px-KDM expression by specific RNA interference (RNAi) significantly (P<0.05) reduced haemocyte nodule formation in response to immune challenge and impaired both larval and pupal development. Px-SWI/SNF was expressed in all developmental stages. Suppression of Px-SWI/SNF expression by RNAi reduced cellular immune response and interfered with adult metamorphosis. These results suggest that CpBV-H4 can alter host gene expression by interfering with chromatin modification and remodelling factors in addition to its direct epigenetic control activity.
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Affiliation(s)
- Sunil Kumar
- Department of Bioresource Sciences, Andong National University, Andong 36729, Republic of Korea
| | - Prasad Venkata
- Department of Bioresource Sciences, Andong National University, Andong 36729, Republic of Korea
| | - Yonggyun Kim
- Department of Bioresource Sciences, Andong National University, Andong 36729, Republic of Korea
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15
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The evolutionary landscape of intergenic trans-splicing events in insects. Nat Commun 2015; 6:8734. [PMID: 26521696 PMCID: PMC4667647 DOI: 10.1038/ncomms9734] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 09/24/2015] [Indexed: 01/29/2023] Open
Abstract
To explore the landscape of intergenic trans-splicing events and characterize their functions and evolutionary dynamics, we conduct a mega-data study of a phylogeny containing eight species across five orders of class Insecta, a model system spanning 400 million years of evolution. A total of 1,627 trans-splicing events involving 2,199 genes are identified, accounting for 1.58% of the total genes. Homology analysis reveals that mod(mdg4)-like trans-splicing is the only conserved event that is consistently observed in multiple species across two orders, which represents a unique case of functional diversification involving trans-splicing. Thus, evolutionarily its potential for generating proteins with novel function is not broadly utilized by insects. Furthermore, 146 non-mod trans-spliced transcripts are found to resemble canonical genes from different species. Trans-splicing preserving the function of 'breakup' genes may serve as a general mechanism for relaxing the constraints on gene structure, with profound implications for the evolution of genes and genomes.
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16
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Manivannan SN, Lai LB, Gopalan V, Simcox A. Transcriptional control of an essential ribozyme in Drosophila reveals an ancient evolutionary divide in animals. PLoS Genet 2015; 11:e1004893. [PMID: 25569672 PMCID: PMC4287351 DOI: 10.1371/journal.pgen.1004893] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Accepted: 11/13/2014] [Indexed: 11/19/2022] Open
Abstract
Ribonuclease P (RNase P) is an essential enzyme required for 5'-maturation of tRNA. While an RNA-free, protein-based form of RNase P exists in eukaryotes, the ribonucleoprotein (RNP) form is found in all domains of life. The catalytic component of the RNP is an RNA known as RNase P RNA (RPR). Eukaryotic RPR genes are typically transcribed by RNA polymerase III (pol III). Here we showed that the RPR gene in Drosophila, which is annotated in the intron of a pol II-transcribed protein-coding gene, lacks signals for transcription by pol III. Using reporter gene constructs that include the RPR-coding intron from Drosophila, we found that the intron contains all the sequences necessary for production of mature RPR but is dependent on the promoter of the recipient gene for expression. We also demonstrated that the intron-coded RPR copurifies with RNase P and is required for its activity. Analysis of RPR genes in various animal genomes revealed a striking divide in the animal kingdom that separates insects and crustaceans into a single group in which RPR genes lack signals for independent transcription and are embedded in different protein-coding genes. Our findings provide evidence for a genetic event that occurred approximately 500 million years ago in the arthropod lineage, which switched the control of the transcription of RPR from pol III to pol II.
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Affiliation(s)
- Sathiya N. Manivannan
- Molecular Cellular Developmental Biology Program, Ohio State University, Columbus, Ohio, United States of America
- Department of Molecular Genetics, Ohio State University, Columbus, Ohio, United States of America
| | - Lien B. Lai
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, Ohio, United States of America
- Center for RNA Biology, Ohio State University, Columbus, Ohio, United States of America
| | - Venkat Gopalan
- Molecular Cellular Developmental Biology Program, Ohio State University, Columbus, Ohio, United States of America
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, Ohio, United States of America
- Center for RNA Biology, Ohio State University, Columbus, Ohio, United States of America
- * E-mail: (VG); (AS)
| | - Amanda Simcox
- Molecular Cellular Developmental Biology Program, Ohio State University, Columbus, Ohio, United States of America
- Department of Molecular Genetics, Ohio State University, Columbus, Ohio, United States of America
- * E-mail: (VG); (AS)
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17
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Talbert PB, Henikoff S. Environmental responses mediated by histone variants. Trends Cell Biol 2014; 24:642-50. [PMID: 25150594 DOI: 10.1016/j.tcb.2014.07.006] [Citation(s) in RCA: 97] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Revised: 07/22/2014] [Accepted: 07/24/2014] [Indexed: 01/19/2023]
Abstract
Fluctuations in the ambient environment can trigger chromatin disruptions, involving replacement of nucleosomes or exchange of their histone subunits. Unlike canonical histones, which are available only during S-phase, replication-independent histone variants are present throughout the cell cycle and are adapted for chromatin repair. The H2A.Z variant mediates responses to environmental perturbations including fluctuations in temperature and seasonal variation. Phosphorylation of histone H2A.X rapidly marks double-strand DNA breaks for chromatin repair, which is mediated by both H2A and H3 histone variants. Other histones are used as weapons in conflicts between parasites and their hosts, which suggests broad involvement of histone variants in environmental responses beyond chromatin repair.
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Affiliation(s)
- Paul B Talbert
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Howard Hughes Medical Institute, Seattle, WA 98109, USA
| | - Steven Henikoff
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Howard Hughes Medical Institute, Seattle, WA 98109, USA.
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