1
|
Blinov VM, Zverev VV, Krasnov GS, Filatov FP, Shargunov AV. Viral component of the human genome. Mol Biol 2017; 51:205-215. [PMID: 32214476 PMCID: PMC7089383 DOI: 10.1134/s0026893317020066] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2015] [Revised: 04/27/2016] [Indexed: 12/17/2022]
Abstract
Relationships between viruses and their human host are traditionally described from the point of view taking into consideration hosts as victims of viral aggression, which results in infectious diseases. However, these relations are in fact two-sided and involve modifications of both the virus and host genomes. Mutations that accumulate in the populations of viruses and hosts may provide them advantages such as the ability to overcome defense barriers of host cells or to create more efficient barriers to deal with the attack of the viral agent. One of the most common ways of reinforcing anti-viral barriers is the horizontal transfer of viral genes into the host genome. Within the host genome, these genes may be modified and extensively expressed to compete with viral copies and inhibit the synthesis of their products or modulate their functions in other ways. This review summarizes the available data on the horizontal gene transfer between viral and human genomes and discusses related problems.
Collapse
Affiliation(s)
- V M Blinov
- 1Mechnikov Research Institute of Vaccines and Sera, Moscow, 105064 Russia
| | - V V Zverev
- 1Mechnikov Research Institute of Vaccines and Sera, Moscow, 105064 Russia
| | - G S Krasnov
- 1Mechnikov Research Institute of Vaccines and Sera, Moscow, 105064 Russia.,2Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 111911 Russia.,3Orekhovich Research Institute of Biomedical Chemistry, Moscow, 119121 Russia
| | - F P Filatov
- 1Mechnikov Research Institute of Vaccines and Sera, Moscow, 105064 Russia.,Gamaleya Research Center of Epidemiology and Microbiology, Moscow, 123098 Russia
| | - A V Shargunov
- 1Mechnikov Research Institute of Vaccines and Sera, Moscow, 105064 Russia
| |
Collapse
|
2
|
Gupta P, Saksena NK. miRNAs: small molecules with a big impact on HIV infection and pathogenesis. Future Virol 2013. [DOI: 10.2217/fvl.13.59] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
miRNAs belong to a class of small noncoding RNAs that regulate gene expression at the post-transcriptional level. These are approximately 22-nt long sequences and control expression of 30–60% of all human genes, which has considerable significance in HIV infection, especially the way in which host–virus interaction occurs in vivo. Over the course of human evolution, viruses too have evolved, but there is still controversy surrounding the presence of miRNAs encoded by HIV. Considering the wide involvement of miRNAs in host gene regulation during infection and their association with HIV, this review provides insights into miRNAs encoded by the host and their role in host–virus interactions in addition to controlling host gene expression.
Collapse
Affiliation(s)
- Priyanka Gupta
- Retroviral Genetics Division, Centre for Virus Research, Westmead Millennium Institute, Westmead Hospital, University of Sydney, Westmead, NSW 2145, Sydney, Australia
| | - Nitin K Saksena
- Retroviral Genetics Division, Centre for Virus Research, Westmead Millennium Institute, Westmead Hospital, University of Sydney, Westmead, NSW 2145, Sydney, Australia.
| |
Collapse
|
3
|
Narayanan A, Iordanskiy S, Das R, Van Duyne R, Santos S, Jaworski E, Guendel I, Sampey G, Dalby E, Iglesias-Ussel M, Popratiloff A, Hakami R, Kehn-Hall K, Young M, Subra C, Gilbert C, Bailey C, Romerio F, Kashanchi F. Exosomes derived from HIV-1-infected cells contain trans-activation response element RNA. J Biol Chem 2013; 288:20014-33. [PMID: 23661700 PMCID: PMC3707700 DOI: 10.1074/jbc.m112.438895] [Citation(s) in RCA: 222] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2012] [Revised: 05/03/2013] [Indexed: 12/20/2022] Open
Abstract
Exosomes are nano-sized vesicles produced by healthy and virus-infected cells. Exosomes derived from infected cells have been shown to contain viral microRNAs (miRNAs). HIV-1 encodes its own miRNAs that regulate viral and host gene expression. The most abundant HIV-1-derived miRNA, first reported by us and later by others using deep sequencing, is the trans-activation response element (TAR) miRNA. In this study, we demonstrate the presence of TAR RNA in exosomes from cell culture supernatants of HIV-1-infected cells and patient sera. TAR miRNA was not in Ago2 complexes outside the exosomes but enclosed within the exosomes. We detected the host miRNA machinery proteins Dicer and Drosha in exosomes from infected cells. We report that transport of TAR RNA from the nucleus into exosomes is a CRM1 (chromosome region maintenance 1)-dependent active process. Prior exposure of naive cells to exosomes from infected cells increased susceptibility of the recipient cells to HIV-1 infection. Exosomal TAR RNA down-regulated apoptosis by lowering Bim and Cdk9 proteins in recipient cells. We found 10(4)-10(6) copies/ml TAR RNA in exosomes derived from infected culture supernatants and 10(3) copies/ml TAR RNA in the serum exosomes of highly active antiretroviral therapy-treated patients or long term nonprogressors. Taken together, our experiments demonstrated that HIV-1-infected cells produced exosomes that are uniquely characterized by their proteomic and RNA profiles that may contribute to disease pathology in AIDS.
Collapse
Affiliation(s)
- Aarthi Narayanan
- From the National Center for Biodefense and Infectious Diseases, George Mason University, Manassas, Virginia 20110
| | - Sergey Iordanskiy
- From the National Center for Biodefense and Infectious Diseases, George Mason University, Manassas, Virginia 20110
- the Department of Microbiology, Immunology and Tropical Medicine, George Washington University, Washington D. C. 20037
| | - Ravi Das
- From the National Center for Biodefense and Infectious Diseases, George Mason University, Manassas, Virginia 20110
| | - Rachel Van Duyne
- From the National Center for Biodefense and Infectious Diseases, George Mason University, Manassas, Virginia 20110
- the Department of Microbiology, Immunology and Tropical Medicine, George Washington University, Washington D. C. 20037
| | - Steven Santos
- the Department of Microbiology, Immunology and Tropical Medicine, George Washington University, Washington D. C. 20037
| | - Elizabeth Jaworski
- From the National Center for Biodefense and Infectious Diseases, George Mason University, Manassas, Virginia 20110
| | - Irene Guendel
- From the National Center for Biodefense and Infectious Diseases, George Mason University, Manassas, Virginia 20110
| | - Gavin Sampey
- From the National Center for Biodefense and Infectious Diseases, George Mason University, Manassas, Virginia 20110
| | - Elizabeth Dalby
- From the National Center for Biodefense and Infectious Diseases, George Mason University, Manassas, Virginia 20110
| | - Maria Iglesias-Ussel
- the Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland 21201
| | - Anastas Popratiloff
- the Department of Microbiology, Immunology and Tropical Medicine, George Washington University, Washington D. C. 20037
| | - Ramin Hakami
- From the National Center for Biodefense and Infectious Diseases, George Mason University, Manassas, Virginia 20110
| | - Kylene Kehn-Hall
- From the National Center for Biodefense and Infectious Diseases, George Mason University, Manassas, Virginia 20110
| | - Mary Young
- the Washington Metropolitan Women's Interagency HIV Study, Division of Infectious Diseases, Georgetown University Medical Center, Washington, D. C. 20007, and
| | - Caroline Subra
- the Department of Microbiology, Infectiology, and Immunology, Medicine Faculty, Laval University Center Hospitalier Universitaire de Quebec Research Center, City of Quebec, Quebec G1R2J6, Canada
| | - Caroline Gilbert
- the Department of Microbiology, Infectiology, and Immunology, Medicine Faculty, Laval University Center Hospitalier Universitaire de Quebec Research Center, City of Quebec, Quebec G1R2J6, Canada
| | - Charles Bailey
- From the National Center for Biodefense and Infectious Diseases, George Mason University, Manassas, Virginia 20110
| | - Fabio Romerio
- the Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland 21201
| | - Fatah Kashanchi
- From the National Center for Biodefense and Infectious Diseases, George Mason University, Manassas, Virginia 20110
| |
Collapse
|
4
|
Xu X, Yang X, Xing C, Zhang S, Cao J. miRNA: The nemesis of gastric cancer (Review). Oncol Lett 2013; 6:631-641. [PMID: 24137382 PMCID: PMC3789097 DOI: 10.3892/ol.2013.1428] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Accepted: 06/13/2013] [Indexed: 12/31/2022] Open
Abstract
microRNAs (miRNAs) are a group of small non-coding RNAs that are ~22 (18 to 25) nucleotides (nt) long and have been associated with a variety of diseases, including cancer. Increasing evidence indicates that miRNAs are essential in the development, diagnosis, treatment and prognosis of a variety of tumors. The utility of miRNAs as biomarkers for diagnosis and of target molecules for the treatment of cancers is increasingly being recognized. With the discovery of circulating miRNAs, a non-invasive approach for the diagnosis and treatment of cancer has been identified. This review summarizes the role of miRNAs in the development of different tumors, as well as a variety of other biological events. Moreover, this review focuses on analyzing the function and mechanism of gastric cancer-related miRNAs and investigates the importance of circulating miRNAs in gastric cancer, as well as their origin. Finally, this review lists a number of the problems that must be solved prior to miRNAs being used as reliable non-invasive tools for the diagnosis, treatment and prognosis of gastric cancer.
Collapse
Affiliation(s)
- Xiaohui Xu
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, Suzhou 215004, P.R. China
| | | | | | | | | |
Collapse
|
5
|
Klase ZA, Sampey GC, Kashanchi F. Retrovirus infected cells contain viral microRNAs. Retrovirology 2013; 10:15. [PMID: 23391025 PMCID: PMC3571942 DOI: 10.1186/1742-4690-10-15] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2012] [Accepted: 02/01/2013] [Indexed: 11/17/2022] Open
Abstract
The encoding of microRNAs in retroviral genomes has remained a controversial hypothesis despite significant supporting evidence in recent years. A recent publication demonstrating the production of functional miRNAs from the retrovirus bovine leukemia virus adds further credence to the fact that retroviruses do indeed encode their own miRNAs. Here we comment on the importance of this paper to the field, as well as examine the other known examples of miRNAs encoded by RNA viruses.
Collapse
Affiliation(s)
- Zachary A Klase
- Molecular Virology Section, Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, 9000 Rockville Pike, Bethesda, MD 20810, USA
| | | | | |
Collapse
|
6
|
Zheng YH, Jeang KT, Tokunaga K. Host restriction factors in retroviral infection: promises in virus-host interaction. Retrovirology 2012; 9:112. [PMID: 23254112 PMCID: PMC3549941 DOI: 10.1186/1742-4690-9-112] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Accepted: 12/09/2012] [Indexed: 01/19/2023] Open
Abstract
Retroviruses have an intricate life cycle. There is much to be learned from studying retrovirus-host interactions. Among retroviruses, the primate lentiviruses have one of the more complex genome structures with three categories of viral genes: structural, regulatory, and accessory genes. Over time, we have gained increasing understanding of the lentivirus life cycle from studying host factors that support virus replication. Similarly, studies on host restriction factors that inhibit viral replication have also made significant contributions to our knowledge. Here, we review recent progress on the rapidly growing field of restriction factors, focusing on the antiretroviral activities of APOBEC3G, TRIM5, tetherin, SAMHD1, MOV10, and cellular microRNAs (miRNAs), and the counter-activities of Vif, Vpu, Vpr, Vpx, and Nef.
Collapse
Affiliation(s)
- Yong-Hui Zheng
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | | | - Kenzo Tokunaga
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| |
Collapse
|
7
|
Liu X, Houzet L, Jeang KT. Tombusvirus P19 RNA silencing suppressor (RSS) activity in mammalian cells correlates with charged amino acids that contribute to direct RNA-binding. Cell Biosci 2012; 2:41. [PMID: 23216864 PMCID: PMC3533911 DOI: 10.1186/2045-3701-2-41] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Accepted: 11/21/2012] [Indexed: 12/31/2022] Open
Abstract
Background Tombusvirus P19 is a protein encoded by tomato bushy stunt virus and related tombusviruses. Earlier studies have demonstrated that P19 is an RNA silencing suppressor (RSS) in plant cells. However, it has not been systematically investigated how P19 suppresses RNA interference in various mammalian cell settings. Results We have studied the RSS effect of P19 in mammalian cells, HEK293T, HeLa, and mouse embryonic fibroblasts. We have individually mutated 18 positively charged residues in P19 and found that 6 of these charged residues in P19 reduce its ability to suppress RNA interference. In each case, the reduction of silencing of RNA interference correlated with the reduced ability by these P19 mutants to bind siRNAs (small interfering RNAs). Conclusions Our findings characterize a class of RNA-binding proteins that function as RSS moieties. We find a tight correlation between positively charged residues in P19 accounting for siRNA-binding and their RSS activity. Because P19’s activity is conserved in plant and animal cells, we conclude that its RSS function unlikely requires cell type-specific co-factors and likely arises from direct RNA-binding.
Collapse
Affiliation(s)
- Xiang Liu
- Molecular Virology Section, Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
| | | | | |
Collapse
|
8
|
Houzet L, Klase Z, Yeung ML, Wu A, Le SY, Quiñones M, Jeang KT. The extent of sequence complementarity correlates with the potency of cellular miRNA-mediated restriction of HIV-1. Nucleic Acids Res 2012; 40:11684-96. [PMID: 23042677 PMCID: PMC3526334 DOI: 10.1093/nar/gks912] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
MicroRNAs (miRNAs) are 22-nt non-coding RNAs involved in the regulation of cellular gene
expression and potential cellular defense against viral infection. Using in
silico analyses, we predicted target sites for 22 human miRNAs in the HIV
genome. Transfection experiments using synthetic miRNAs showed that five of these miRNAs
capably decreased HIV replication. Using one of these five miRNAs, human miR-326 as an
example, we demonstrated that the degree of complementarity between the predicted viral
sequence and cellular miR-326 correlates, in a Dicer-dependent manner, with the potency of
miRNA-mediated restriction of viral replication. Antagomirs to miR-326 that knocked down
this cell endogenous miRNA increased HIV-1 replication in cells, suggesting that miR-326
is physiologically functional in moderating HIV-1 replication in human cells.
Collapse
Affiliation(s)
- Laurent Houzet
- Molecular Virology Section, Laboratory of Molecular Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892-0460, USA
| | | | | | | | | | | | | |
Collapse
|
9
|
Jeang KT. RNAi in the regulation of mammalian viral infections. BMC Biol 2012; 10:58. [PMID: 22734679 PMCID: PMC3383472 DOI: 10.1186/1741-7007-10-58] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Accepted: 06/22/2012] [Indexed: 12/28/2022] Open
Abstract
Although RNA interference (RNAi) is known to play an important part in defense against viruses of invertebrates, its contribution to mammalian anti-viral defense has been a matter of dispute. This is surprising because all components of the RNAi machinery necessary for robust RNAi-mediated restriction of viruses are conserved in mammals, and the introduction of synthetic small interfering RNAs (siRNAs) into cells efficiently silences the replication of viruses that contain siRNA complementary sequences in those cells. Here, I discuss the reasons for the dispute, and review the evidence that RNAi is a part of the physiological defense of mammalian cells against viral infections.
Collapse
Affiliation(s)
- Kuan-Teh Jeang
- The National Institutes of Health, Bethesda, MD 20892-0460, USA.
| |
Collapse
|
10
|
Althaus CF, Vongrad V, Niederöst B, Joos B, Di Giallonardo F, Rieder P, Pavlovic J, Trkola A, Günthard HF, Metzner KJ, Fischer M. Tailored enrichment strategy detects low abundant small noncoding RNAs in HIV-1 infected cells. Retrovirology 2012; 9:27. [PMID: 22458358 PMCID: PMC3341194 DOI: 10.1186/1742-4690-9-27] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2011] [Accepted: 03/29/2012] [Indexed: 12/27/2022] Open
Abstract
Background The various classes of small noncoding RNAs (sncRNAs) are important regulators of gene expression across divergent types of organisms. While a rapidly increasing number of sncRNAs has been identified over recent years, the isolation of sncRNAs of low abundance remains challenging. Virally encoded sncRNAs, particularly those of RNA viruses, can be expressed at very low levels. This is best illustrated by HIV-1 where virus encoded sncRNAs represent approximately 0.1-1.0% of all sncRNAs in HIV-1 infected cells or were found to be undetected. Thus, we applied a novel, sequence targeted enrichment strategy to capture HIV-1 derived sncRNAs in HIV-1 infected primary CD4+ T-lymphocytes and macrophages that allows a greater than 100-fold enrichment of low abundant sncRNAs. Results Eight hundred and ninety-two individual HIV-1 sncRNAs were cloned and sequenced from nine different sncRNA libraries derived from five independent experiments. These clones represent up to 90% of all sncRNA clones in the generated libraries. Two hundred and sixteen HIV-1 sncRNAs were distinguishable as unique clones. They are spread throughout the HIV-1 genome, however, forming certain clusters, and almost 10% show an antisense orientation. The length of HIV-1 sncRNAs varies between 16 and 89 nucleotides with an unexpected peak at 31 to 50 nucleotides, thus, longer than cellular microRNAs or short-interfering RNAs (siRNAs). Exemplary HIV-1 sncRNAs were also generated in cells infected with different primary HIV-1 isolates and can inhibit HIV-1 replication. Conclusions HIV-1 infected cells generate virally encoded sncRNAs, which might play a role in the HIV-1 life cycle. Furthermore, the enormous capacity to enrich low abundance sncRNAs in a sequence specific manner highly recommends our selection strategy for any type of investigation where origin or target sequences of the sought-after sncRNAs are known.
Collapse
Affiliation(s)
- Claudia F Althaus
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Rämistrasse 100, CH-8091 Zurich, Switzerland
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|