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Koga A, Ahmad SF, Panthum T, Singchat W, Srikulnath K. Characterization of the marsupial endogenous retrovirus walb with a focus on satellite DNA formation. Virology 2023; 588:109911. [PMID: 37918186 DOI: 10.1016/j.virol.2023.109911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/06/2023] [Accepted: 10/10/2023] [Indexed: 11/04/2023]
Abstract
The walbRep megasatellite DNA found in the red-necked wallaby was formed from the walb endogenous retrovirus. Our previous PCR experiments suggested the presence of walb and absence of walbRep in the genome of the tammar wallaby, which diverged from the red-necked wallaby 2-3 Mya. The results failed to exclude the possibility that certain walbRep sequences might have remained undetected owing to variation in the primer-annealing regions; therefore, the aforementioned suggestion was not confirmed. To obtain conclusive evidence, we analyzed the structure of walb sequences drawn from the tammar wallaby genome database recently updated to a chromosome-level assembly. All walb copies existed as separate DNA segments, not constituting tandem repeats. We concluded that walbRep was formed in the red-necked wallaby lineage after its divergence from the tammar wallaby. We also confirm the presence of a walb copy with an anomalistic, complex structure and propose a simple model for its generation mechanism.
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Affiliation(s)
- Akihiko Koga
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Syed Farhan Ahmad
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Thitipong Panthum
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Worapong Singchat
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand; Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Kornsorn Srikulnath
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand; Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand.
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Horváth KB, Boros Á, Kálmán E, Pankovics P, Delwart E, Reuter G. Characterization of an integrated, endogenous mouse mammary tumor virus-like (MMTV) betaretrovirus genome in a black Syrian hamster (Mesocricetus auratus). Infect Genet Evol 2019; 75:103995. [PMID: 31404669 DOI: 10.1016/j.meegid.2019.103995] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 08/02/2019] [Accepted: 08/05/2019] [Indexed: 11/28/2022]
Abstract
Retroviruses (family Retroviridae) are important agents of humans and animals. This study reports the detection and complete genome characterization of a novel endogenous retrovirus from the black Syrian hamster (Mesocricetus auratus) with a squamous cell skin tumor. The proviral genome, tentatively named black Syrian hamster retrovirus (BSHRV/2013/HUN, MK304634), was 8784 nucleotide in length with typical full-length betaretrovirus genome organization of 5'LTR-gag-pro-pol-env-3'LTR and with a characteristic mouse mammary tumor virus-like (MMTV) betaretrovirus dUTPase domain but without a sag gene. The BSHRV gag (534aa), pro/pol (~1099aa) and env (672aa) proteins had 56%/63%/50% aa identity to the corresponding proteins of MMTV (AF228552). The proviral DNA is detectable in tumor as well as in tumor-free cells by conventional PCR and qPCR but only visible in the tumor cells by in situ hybridization. Low level retroviral RNA expression was found only in the DNase-treated RNA tumor samples using RT/nested PCR. BSHRV/2013/HUN-like betaretrovirus DNA was also identified from a faecal and tissue samples from 1 of the further 3 tested individuals by nested-PCR and qPCR. Further research is needed to investigate the distribution, activity and etiological role of this novel MMTV-like betaretrovirus species in hamster.
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Affiliation(s)
- Katalin B Horváth
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Pécs, Hungary; Regional Laboratory of Virology, National Reference Laboratory of Gastroenteric Viruses, ÁNTSZ Regional Institute of State Public Health Service, Pécs, Hungary
| | - Ákos Boros
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Pécs, Hungary; Regional Laboratory of Virology, National Reference Laboratory of Gastroenteric Viruses, ÁNTSZ Regional Institute of State Public Health Service, Pécs, Hungary
| | - Endre Kálmán
- Department of Pathology, Medical School, University of Pécs, Pécs, Hungary
| | - Péter Pankovics
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Pécs, Hungary; Regional Laboratory of Virology, National Reference Laboratory of Gastroenteric Viruses, ÁNTSZ Regional Institute of State Public Health Service, Pécs, Hungary
| | - Eric Delwart
- Blood Systems Research Institute, San Francisco, CA, USA; University of California, San Francisco, CA, USA
| | - Gábor Reuter
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Pécs, Hungary; Regional Laboratory of Virology, National Reference Laboratory of Gastroenteric Viruses, ÁNTSZ Regional Institute of State Public Health Service, Pécs, Hungary.
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Abstract
Integration of the reverse-transcribed viral cDNA into the host's genome is a critical step in the lifecycle of all retroviruses. Retrovirus integration is carried out by integrase (IN), a virus-encoded enzyme that forms an oligomeric 'intasome' complex with both ends of the linear viral DNA to catalyze their concerted insertions into the backbones of the host's DNA. IN also forms a complex with host proteins, which guides the intasome to the host's chromosome. Recent structural studies have revealed remarkable diversity as well as conserved features among the architectures of the intasome assembly from different genera of retroviruses. This chapter will review how IN oligomerizes to achieve its function, with particular focus on alpharetrovirus including the avian retrovirus Rous sarcoma virus. Another chapter (Craigie) will focus on the structure and function of IN from HIV-1.
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Affiliation(s)
- Duane P Grandgenett
- Saint Louis University Health Sciences Center, Department of Microbiology and Immunology, Institute for Molecular Virology, Doisy Research Center, St. Louis, MO, USA
| | - Hideki Aihara
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA.
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He Y, Zhang Q, Wang J, Zhou M, Fu M, Xu X. Full-length genome sequence analysis of enzootic nasal tumor virus isolated from goats in China. Virol J 2017; 14:141. [PMID: 28747230 PMCID: PMC5530571 DOI: 10.1186/s12985-017-0795-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 07/03/2017] [Indexed: 11/10/2022] Open
Abstract
Background Enzootic nasal tumor virus (ENTV) is a betaretrovirus of sheep (ENTV-1) and goats (ENTV-2) associated with neoplastic transformation of epithelial cells of the ethmoid turbinate. Confirmation of the role of ENTV in the pathogenesis of enzootic nasal adenocarcinoma (ENA) has yet to be resolved due to the inability to culture the virus. Very little is known about the prevalence of this disease, particularly in China. Methods To evaluate the genetic diversity of ENTV-2 from Shaanxi province of China, the complete genome sequence of four isolates from Shaanxi province was determined by RT-PCR. These sequences were analyzed to evaluate their genetic relatedness with other small ruminant betaretroviruses. Phylogenetic analyses based on the gag gene and env gene were performed. Results The ENTV-2-Shaanxi1 genome shared 97.0% sequence identity with ENTV-2-SC (accession number HM104174.1), and 89.6% sequence identity with the ENTV-2 sequences (accession number AY197548.1). ENTV-2 is closely related to the ENTV-1 and jaagsiekte retrovirus (JSRV). The main sequence differences between these viruses reside in LTR, two small regions of Gag, Orf-x, and the transmembrane (TM) region of Env. A stretch of 6 consecutive proline residues exists in VR1 of the ENTV-2-Shaanxi1 ~ 4 isolates. All the ENTV-2-Shaanxi isolates have the YXXM motif in the cytoplasmic tail of the Env. Phylogenetic analysis by nucleotide sequences showed that ENTV-2-Shaanxi1 ~ 4 isolates were closest related to two ENTV-2 isolates published in NCBI, especially with ENTV-2-SC strain. Conclusions This finding indicates that ENA most likely was introduced to Shaanxi province by the movement of contaminated goats from other areas in China. This study adds to understand the circulation, variation and distribution of ENTV-2, and may prove beneficial in future control or eradication programmes.
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Affiliation(s)
- Yapeng He
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Qi Zhang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Jing Wang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Man Zhou
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Mingzhe Fu
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China.
| | - Xingang Xu
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China.
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Kramer P, Lausch V, Volkwein A, Hanke K, Hohn O, Bannert N. The human endogenous retrovirus K(HML-2) has a broad envelope-mediated cellular tropism and is prone to inhibition at a post-entry, pre-integration step. Virology 2015; 487:121-8. [PMID: 26517399 DOI: 10.1016/j.virol.2015.10.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 10/09/2015] [Accepted: 10/14/2015] [Indexed: 11/28/2022]
Abstract
The HERV-K(HML-2) family is the most recent addition to the collection of human endogenous retroviruses. It comprises proviruses that encode functional proteins that can assemble into replication defective particles carrying the envelope protein. Using a reconstituted HERV-K113 envelope sequence, we have analyzed its ability to mediate entry into a set of 33 cell lines from 10 species. Of these, 30 were permissive, demonstrating an amphotropism consistent with a broad expression of receptor protein(s). In an initial effort to identify a receptor for HERV-K(HML-2) we investigated whether transferrin receptor 1 and hyaluronidase 2, known cellular receptors of the closely related betaretroviruses mouse mammary tumor virus (MMTV) and Jaagsiekte sheep retrovirus (JSRV), could facilitate HERV-K(HML-2) entry. However, neither of these proteins could serve as a receptor for HERV-K(HML-2). Moreover, during attempts to further characterize the tropism of HERV-K(HML-2), we identified a cellular activity that inhibits infection at a post-entry, pre-integration step.
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Affiliation(s)
- Philipp Kramer
- Robert Koch Institute, Division for HIV and Other Retroviruses, Nordufer 20, 13353 Berlin, Germany
| | - Veronika Lausch
- Robert Koch Institute, Division for HIV and Other Retroviruses, Nordufer 20, 13353 Berlin, Germany
| | - Alexander Volkwein
- Robert Koch Institute, Division for HIV and Other Retroviruses, Nordufer 20, 13353 Berlin, Germany
| | - Kirsten Hanke
- Robert Koch Institute, Division for HIV and Other Retroviruses, Nordufer 20, 13353 Berlin, Germany
| | - Oliver Hohn
- Robert Koch Institute, Division for HIV and Other Retroviruses, Nordufer 20, 13353 Berlin, Germany
| | - Norbert Bannert
- Robert Koch Institute, Division for HIV and Other Retroviruses, Nordufer 20, 13353 Berlin, Germany.
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