A mobile genetic element with unknown function found in distantly related viruses

Virology Journal

Christine Monceyron Jonassen¹  Tsvetan R Bachvaroff²  Anja Bråthen Kristoffersen¹  Torstein Tengs¹ 

[1] National Veterinary Institute, P.O. Box 750 Sentrum, 0106, Oslo, Norway;Institute for Marine and Environmental Technology, 701 E. Pratt St, Baltimore, MD 21202, USA

关键词: s2m;    Mobile genetic element;    Coronaviruses;    Picornaviruses;    Caliciviruses;    Astroviruses;   

Others  :  1150617
DOI  :  10.1186/1743-422X-10-132

 received in 2012-12-12, accepted in 2013-04-18,  发布年份 2013

【 摘 要 】

Background

The genetic element s2m seems to represent one of very few examples of mobile genetic elements in viruses. The function remains obscure and a scattered taxonomical distribution has been reported by numerous groups.

Methods

We have searched GenBank in order to identify all viral accessions that have s2m(−like) sequence motifs. Rigorous phylogenetic analyses and constrained tree topology testing were also performed in order to investigate the apparently mobile nature of s2m.

Results

The stem-loop s2m structure can be found in four families of + ssRNA viruses; Astroviridae, Caliciviridae, Picornaviridae and Coronaviridae. In all of these virus families, with the possible exception of Caliciviridae, multiple gains and/or losses of s2m would have to be postulated in order to explain the distribution of this character.

Conclusions

s2m appears to be a mobile genetic element with a unique evolutionary history in all of the four virus families where it can be found. Based on our findings and a review of the current literature on s2m, a hypothesis implying an RNAi-like function for the s2m element is also outlined.

【 授权许可】

   
2013 Tengs et al.; licensee BioMed Central Ltd.

【 图 表 】

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【 参考文献 】

• [1]Monceyron C, Grinde B, Jonassen TO: Molecular characterisation of the 3′-end of the astrovirus genome. Arch Virol 1997, 142:699-706.
• [2]Jonassen CM, Jonassen TO, Grinde B: A common RNA motif in the 3′ end of the genomes of astroviruses, avian infectious bronchitis virus and an equine rhinovirus. J Gen Virol 1998, 79(Pt 4):715-718.
• [3]Kofstad T, Jonassen CM: Screening of feral and wood pigeons for viruses harbouring a conserved mobile viral element: characterization of novel Astroviruses and Picornaviruses. PLoS One 2011, 6:e25964.
• [4]Robertson MP, Igel H, Baertsch R, Haussler D, Ares M Jr, Scott WG: The structure of a rigorously conserved RNA element within the SARS virus genome. PLoS Biol 2005, 3:e5.
• [5]Jonassen CM: Detection and sequence characterization of the 3′-end of coronavirus genomes harboring the highly conserved RNA motif s2m. Methods Mol Biol 2008, 454:27-34.
• [6]Zuker M: Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 2003, 31:3406-3415.
• [7]Leplae R, Hebrant A, Wodak SJ, Toussaint A: ACLAME: a CLAssification of mobile genetic elements. Nucleic Acids Res 2004, 32:D45-D49.
• [8]Leplae R, Lima-Mendez G, Toussaint A: ACLAME: a CLAssification of mobile genetic elements, update 2010. Nucleic Acids Res 2010, 38:D57-D61.
• [9]Chare ER, Holmes EC: A phylogenetic survey of recombination frequency in plant RNA viruses. Arch Virol 2006, 151:933-946.
• [10]Hatfull GF, Hendrix RW: Bacteriophages and their genomes. Current Opinion Virol 2011, 1:298-303.
• [11]Liu H, Fu Y, Xie J, Cheng J, Ghabrial SA, Li G, Peng Y, Yi X, Jiang D: Evolutionary genomics of mycovirus-related dsRNA viruses reveals cross-family horizontal gene transfer and evolution of diverse viral lineages. BMC Evol Biol 2012, 12:91. BioMed Central Full Text
• [12]Woo PC, Lau SK, Huang Y, Lam CS, Poon RW, Tsoi HW, Lee P, Tse H, Chan AS, Luk G: Comparative analysis of six genome sequences of three novel picornaviruses, turdiviruses 1, 2 and 3, in dead wild birds, and proposal of two novel genera, orthoturdivirus and paraturdivirus, in the family picornaviridae. J Gen Virol 2010, 91:2433-2448.
• [13]Lau SK, Woo PC, Lai KK, Huang Y, Yip CC, Shek CT, Lee P, Lam CS, Chan KH, Yuen KY: Complete genome analysis of three novel picornaviruses from diverse bat species. J Virol 2011, 85:8819-8828.
• [14]Woo PC, Lau SK, Lam CS, Lau CC, Tsang AK, Lau JH, Bai R, Teng JL, Tsang CC, Wang M: Discovery of seven novel mammalian and avian coronaviruses in the genus deltacoronavirus supports bat coronaviruses as the gene source of alphacoronavirus and betacoronavirus and avian coronaviruses as the gene source of gammacoronavirus and deltacoronavirus. J Virol 2012, 86:3995-4008.
• [15]Goebel SJ, Taylor J, Masters PS: The 3′ cis-acting genomic replication element of the severe acute respiratory syndrome coronavirus can function in the murine coronavirus genome. J Virol 2004, 78:7846-7851.
• [16]Tse H, Chan WM, Li KS, Lau SK, Woo PC, Yuen KY: Discovery and genomic characterization of a novel bat sapovirus with unusual genomic features and phylogenetic position. PLoS One 2012, 7:e34987.
• [17]Calisher CH, Childs JE, Field HE, Holmes KV, Schountz T: Bats: important reservoir hosts of emerging viruses. Clin Microbiol Rev 2006, 19:531-545.
• [18]Domingo E: Mechanisms of viral emergence. Vet Res 2010, 41:38.
• [19]Shapiro JS, Langlois RA, Pham AM, Tenoever BR: Evidence for a cytoplasmic microprocessor of pri-miRNAs. RNA 2012, 18:1338-1346.
• [20]Thompson JD, Higgins DG, Gibson TJ: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994, 22:4673-4680.
• [21]Hall TA: BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 1999, 41:95-98.
• [22]Stamatakis A: RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 2006, 22:2688-2690.
• [23]Shimodaira H, Hasegawa M: CONSEL: for assessing the confidence of phylogenetic tree selection. Bioinformatics 2001, 17:1246-1247.