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A novel endogenous betaretrovirus group characterized from polar bears (Ursus maritimus) and giant pandas (Ailuropoda melanoleuca)

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A novel endogenous betaretrovirus group characterized from polar bears (Ursus maritimus) and giant pandas (Ailuropoda melanoleuca)
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  A novel endogenous betaretrovirus group characterized from polarbears ( Ursus maritimus ) and giant pandas (  Ailuropoda melanoleuca)  Jens Mayer a,1 , Kyriakos Tsangaras b,1 , Felix Heeger c , María Ávila-Arcos d ,Mark D. Stenglein e , Wei Chen f  , Wei Sun f  , Camila J. Mazzoni c ,Nikolaus Osterrieder g , Alex D. Greenwood b, n a Department of Human Genetics, Center of Human and Molecular Biology, Medical Faculty, University of Saarland, 66421 Homburg, Germany b Leibniz-Institute for Zoo and Wildlife Research Berlin, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany c Berlin Center for Genomics in Biodiversity Research (BeGenDiv), Königin-Luise-Straße 6-8, 14195 Berlin, Germany d GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Østervoldgade 5-7, DK 1350 Copenhagen, Denmark e Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA f  The Berlin Institute for Medical Systems Biology (BIMSB), Genomics, Berlin, Germany g Institut für Virologie, Freie Universität Berlin, Philippstr. 13, Haus 18, 10115 Berlin, Germany a r t i c l e i n f o  Article history: Received 13 February 2013Returned to author for revisions25 March 2013Accepted 3 May 2013Available online 29 May 2013 Keywords: Polar bearGiant pandaEndogenous retrovirusGenomics a b s t r a c t Transcriptome analysis of polar bears ( Ursus maritimus ) yielded sequences with highest similarity to thehuman endogenous retrovirus group HERV-K(HML-2). Further analysis of the polar bear draft genomeidenti fi ed an endogenous betaretrovirus group comprising 26 proviral copies and 231 solo LTRs.Molecular dating indicates the group srcinated before the divergence of bears from a common ancestorbut is not present in all carnivores. Closely related sequences were identi fi ed in the giant panda(  Ailuropoda melanoleuca ) and characterized from its genome. We have designated the polar bear andgiant panda sequences  U. maritimus  endogenous retrovirus (UmaERV) and  A. melanoleuca  endogenousretrovirus (AmeERV), respectively. Phylogenetic analysis demonstrated that the bear virus group isnested within the HERV-K supergroup among bovine and bat endogenous retroviruses suggesting acomplex evolutionary history within the HERV-K group. All individual remnants of proviral sequencescontain numerous frameshifts and stop codons and thus, the virus is likely non-infectious. &  2013 Elsevier Inc. All rights reserved. Endogenous retroviruses are a complex and large (up to 10%)part of the genome of vertebrates. They represent the successfulcolonization of the genome by exogenous retroviruses upon infec-tion of the germline or hybridizationwith a species or population inwhich endogenization has occurred (Gifford and Tristem, 2003). The classi fi cation of retroviruses as endogenous or exogenous is notalways clearly delineated as some may exist in both states and thusspread by both Mendelian transmission and by infection. Forexample, the mouse mammary tumor viruses (MMTV) are bothtransmitted to offspring as Mendelian traits and by infection frommaternal breast milk. Exogenous and endogenous betaretrovirusesare associated with mammary tumors in mice. Though de fi nitiveproof is not available, ERVs have been associated with variousdiseases such as cancer, neurodegenerative diseases and autoimmunediseases (Denner et al.,1995; Greenwood et al., 2011; Sugimoto et al., 2001). Betaretroviruses, in particular HERV-K (HML-2), several loci of which encode functional proteins, have been implicated in varioushuman tumor diseases (Ruprecht et al., 2008). A betaretrovirus in sheep, endogenous Jaagsiekte sheep retrovirus (enJSRV), the exogen-ous counterpart of which is strongly supported as the causative agentof a transmissible lung cancer in sheep, protects against exJSRV infection and is required for sheep placental development (Varelaet al., 2009). The diversity of tumor types associated with betare-troviruses contrasts somewhat with gammaretroviruses, anotherretroviral group speci fi cally associated with oncogenesis. Gammare-troviruses are typically associated with leukemia such as murineleukemia viruses (MLV) or koala retrovirus (KoRV) (Avila-Arcos et al.,2012; Tarlinton et al., 2005). Most exogenous retrovirus groups identi fi ed to date haveendogenous counterparts. However, not all groups have endogen-ous counterparts in all species, for example, endogenous retro-viruses closely related to lentiviruses have only been identi fi ed inlemurs, rabbits, weasels and ferrets to date (Cui and Holmes, 2012;Gilbert et al., 2009; Han and Worobey, 2012; Katzourakis et al., 2007). Endogenous counterparts of delta retroviruses andHIV/SIV have not been identi fi ed to date. Gammaretroviruses,foamy retroviruses, and betaretroviruses have been discovered inContents lists available at SciVerse ScienceDirect journal homepage: www.elsevier.com/locate/yviro Virology 0042-6822/$-see front matter  &  2013 Elsevier Inc. All rights reserved.http://dx.doi.org/10.1016/j.virol.2013.05.008 n Corresponding author. E-mail address:  greenwood@izw-berlin.de (A.D. Greenwood). 1 Authors contributed equally.Virology 443 (2013) 1  –  10  Fig. 1.  Consensus sequence of UmaERV provirus. The consensus provirus sequence of UmaERV is displayed in A. ORFs for proviral  gag  ,  pro ,  pol  and  env  genes, resultingprotein sequences and protein domains, the latter as predicted by NCBI Conserved Domain Search (Marchler-Bauer et al., 2013) and Retrotector (Sperber et al., 2007, 2009), are indicated. Starts and ends of ORF are further highlighted by colored arrows and lines ending in diamonds respectively. The generated consensus sequence did not resultin complete ORFs for  pol  and  env  gene regions, and frameshifts are indicated. Proviral 5 ′  and 3 ′  LTRs are highlighted in light green. Note that the PBS predicted by Retrotector(Sperber et al., 2007) overlaps with the 5 ′ LTR 3 ′  end by 5 nt. The Pustell matrix diagram in Fig. 2 and the comparative alignment in Fig. S1 demonstrates the near identity of  the consensus sequences of UmaERV and AmeERV.  J. Mayer et al. / Virology 443 (2013) 1 – 10 2  a greater number of species. For example, it was recently proposedthat betaretroviruses have been evolving within the genomes of murid rodents for at least the last 20 million years and wereoccasionally transmitted to non-rodent species in the course of theglobal spread of murids (Baillie et al., 2004). However, knowledge about distribution and diversity of ERVs is limited by lack of  Fig. 1.  Continued.  J. Mayer et al. / Virology 443 (2013) 1 – 10  3  characterization of genomes as opposed to their absence or lack of diversity.As more genomes become available, the opportunity to character-ize novel retroviruses is increasing. Both the polar bear ( Ursusmaritimus ) and the giant panda (  Ailuropoda melanoleuca ) haverecently been sequenced to the draft genome level (Li et al., 2011;Li et al., 2010). Endogenous retroviruses have not been described inbears. As part of a study to identify novel viral and bacterial microbesfrom two polar bears, brain and liver cDNA were deep sequenced togenerate transcriptomes and microbial sequences were characterizedfrom the sequence reads. While the majority of sequences identi fi edby shotgun sequencing were of polar bear origin, a subset of transcribed viral sequences identi fi ed were most similar to HERV-K(HML-2) as determined by genetic database searches. A number of corresponding endogenous retroviral loci were found in variousscaffold sequences of a recently generated polar bear draft genomesequence (Li et al., 2011). We characterized this newly discoveredendogenous betaretrovirus group regarding species distribution, evo-lutionary age and phylogenetic relationship with other retroviruses,and established a limited tissue transcription pro fi le. We documenthere the full-length consensus polar bear ERV that we designated  U.maritimus  endogenous retrovirus (UmaERV) and its close relative ingiant pandas,  A. melanoleuca  endogenous retrovirus (AmeERV). Results Identi  fi cation of UmaERV from polar tissues RNA was extracted from brain and liver from two polar bears(Knut of the Berlin Zoological Garden and Jerka of the WuppertalZoological Garden) both of whom died as a result of viralencephalitis. Approximately 260 million 100 nt sequences weregenerated by Illumina shotgun sequencing of ribosome-subtractedlibraries (74, 63, 58, and 65 million each from liver and brain fromKnut and Jerka, respectively). These datasets were searched forpossible pathogen-derived sequences, and the results of thesesearches will be described elsewhere. The searches also revealedthe presence of apparent endogenous retrovirus-like sequences,including HERV-K(HML-2)  gag   and  pol  sequences. Primers weredesigned in both  gag   and  pol  to amplify a larger portion of thegenome from the bear cDNAs and a PCR product was ampli fi edfrom all four polar bear tissues from which the sequence readswere derived. Direct sequencing of the products and blastnsearches again revealed highest similarity to HERV-K(HML-2). Identi  fi cation of UmaERV integration sites in polar bear and in pandabear genomes PCR product sequences identi fi ed a subregion within the polarbear draft genome scaffold000030 sequence. A  “ seed ”  UmaERV ( U. maritimus  endogenous retrovirus) locus was identi fi ed in thatscaffold subregion using RetroTector (Sperber et al., 2009; Sperber et al., 2007) and Repeatmasker (Tempel, 2012). A BLASTn search of  all the 72,214 polar bear scaffold sequences, using the proviral bodysequence of the seed UmaERV as probe, identi fi ed 26 UmaERV lociin the polar bear draft genome. Another BLASTn search with theseed UmaERV LTR sequence as probe identi fi ed 261 UmaERV locus-associated and solitary LTRs. Multiple alignments of identi fi edproviral and LTR sequences were generated, and majority rule-based consensus sequences were generated. Characteristics of theUmaERV consensus provirus are shown in Fig. 1 (and Fig. S1  –  S2 inthe supplementary data). Further sequence analysis of consensusprotein sequences employing RetroTector and NCBI CD Searchidenti fi ed typical retroviral motifs and also a dUTPase domainwithin the protease coding sequence. The UmaERV LTR was mostsimilar to an LTR sequence annotated in the giant panda asLTR1_AMe, and UmaERV like sequences were found in the giantpanda by PCR. The giant panda genome draft assembly (BGI-Shenzhen AilMel 1.0 Dec. 2009), as provided by the UCSC GenomeBrowser, was therefore BLAT-searched with UmaERV LTR and bodyconsensus sequences as probe. We detected ca. 20 loci similar to theUmaERV body sequence and about 145 loci similar to the UmaERV LTR sequence in the giant panda draft assembly. We propose toname the UmaERV-similar sequences in the panda  A. melanoleuca Endogenous Retrovirus (AmeERV). Characteristics of the AmeERV sequence can be found in Fig. S3. Characteristics of UmaERV andAmeERV sequences astheyare found inthe respective draftgenomesequences are provided as supplementary data (Tables S1  –  S6) andthe relative similarity of the UmaERV and AmeERV consensussequences is shown in Fig. 2. The respective consensus sequencesare also provided in a supplementary text  fi le.Most UmaERV loci were severely mutated and 5 ′  or 3 ′  orinternal proviral regions were often missing (Fig. S2). Similarresults were obtained for AmeERV (Fig. 2 and S3). Although retroviral  gag  ,  pro ,  pol  or  env  gene regions were often presentwithin the proviruses, none of them appeared capable of encodingretroviral proteins of signi fi cant length. Thus, it is unlikely that anysingle UmaERV locus could produce retroviral proteins, let aloneinfectious virus. The state of the UmaERV loci in the polar beargenome thus suggests that UmaERV is exclusively endogenous.A comparison of the consensus sequence of UmaERV and AmeERV demonstrate their overall high similarity (Fig. S1).  Age estimates of UmaERV and distribution in bears As the data suggested UmaERV is an ERV, the age of the ERV group was estimated using two different approaches. First, Fig. 2.  High sequence similarity between UmaERV and AmeERV proviralsequences. Shown is a Pustell matrix comparison of UmaERV and AmeERV proviralconsensus sequences (window size ¼ 30; min% score ¼ 90; jump ¼ 1). Note that theLTR1_Ame sequence, as provided by Repbase v17.08, in the AmeERV provirussequence displays some sequence differences to the actual majority rule consensussequence for AmeERV-associated LTRs, the latter of which is very similar to theconsensus sequence of UmaERV-associated LTRs. A pairwise sequence comparisonof both proviral sequences is shown in Fig. S1.  J. Mayer et al. / Virology 443 (2013) 1 – 10 4  Fig. 3.  Phylogenetic relationship of UmaERV and AmeERV within the Retroviridae. Bayesian phylogenetic trees are shown for the GAG, PRO, POL and ENV proteins. Posteriorprobabilities 4 50% are shown. All sequences from taxa represented in the trees are described in the Materials and Methods. The overall topology with respect to UmaERV and AMeERV was consistent regardless of the protein analyzed except for PRO where HML-6 was not basal to UmaERV and AMeERV.  J. Mayer et al. / Virology 443 (2013) 1 – 10  5
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