Sequence analysis of an Archaeal virus isolated from a hypersaline lake in Inner Mongolia, China

BMC Genomics

Volumn 8, Issue , 2007, Pages

  Pagaling, Eulyn ^a   Haigh, Richard D ^a   Grant, William D ^a   Cowan, Don A ^b   Jones, Brian E ^c   Ma, Yanhe ^d   Ventosa, Antonio ^e   Heaphy, Shaun ^a  

^a UNIVERSITY OF LEICESTER   (United Kingdom)

^b UNIVERSITY OF THE WESTERN CAPE   (South Africa)

^c Genencor International BV   (Netherlands)

^d INSTITUTE OF MICROBIOLOGY   (China)

^e UNIVERSITY OF SEVILLE   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

CAPSID PROTEIN; DOUBLE STRANDED DNA; HELICASE; INTEGRASE; LAKE WATER; RNA 16S; TRANSFER RNA; VIRUS RNA; FRESH WATER; SODIUM CHLORIDE; VIRUS DNA;

ARCHAEAL VIRUS; ARTICLE; BJI VIRUS; CHINA; DNA CONTENT; GENE SEQUENCE; GENETIC CODE; GENETIC DATABASE; GENETIC VARIABILITY; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; POXVIRUS; PROTEIN ANALYSIS; SALINITY; SEQUENCE ANALYSIS; VIRUS DNA CELL DNA INTERACTION; VIRUS IDENTIFICATION; VIRUS ISOLATION; VIRUS MORPHOLOGY; VIRUS STRAIN; ARCHAEBACTERIUM; CHEMISTRY; GENETICS; ISOLATION AND PURIFICATION; MICROBIOLOGY; VIROLOGY; VIRUS; VIRUS GENOME;

ARCHAEA; HALOBACTERIA; HALORUBRUM SACCHAROVORUM; MIRIDAE;

ARCHAEA; BASE SEQUENCE; CHINA; DNA, VIRAL; FRESH WATER; GENOME, VIRAL; OPEN READING FRAMES; SODIUM CHLORIDE; VIRUSES; WATER MICROBIOLOGY;

EID: 38049107794     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-8-410     Document Type: Article

References (46)

1. Wheelis ML Kandler O Woese CR On the nature of global classification Proc Natl Acad Sci USA 1992, 89:2930-2934. 48777 11537862 10.1073/ pnas.89.7.2930
2. Angly FE Felts B Breitbart M Salamon P Edwards RA Carlson C Chan AM Haynes M Kelley S Liu H Mahaffy JM Mueller JE Nulton J Olson R Parsons R Rayhawk S Suttle CA Rohwer F The marine viromes of four oceanic regions PLoS Biol 2006, 4:e368. 1634881 17090214 10.1371/journal.pbio.0040368
3. Breitbart M Hewson I Felts B Mahaffy JM Nulton J Salamon P Rohwer F Metagenomic analyses of an uncultured viral community from human feces J Bacteriol 2003, 185:6220-6223. 225035 14526037 10.1128/ JB.185.20.6220-6223.2003
4. Breitbart M Salamon P Andresen B Mahaffy JM Segall AM Mead D Azam F Rohwer F Genomic analysis of uncultured marine viral communities Proc Natl Acad Sci USA 2002, 99:14250-14255. 137870 12384570 10.1073/ pnas.202488399
5. Cann AJ Fandrich SE Heaphy S Analysis of the virus population present in equine faeces indicates the presence of hundreds of uncharacterized virus genomes Virus Genes 2005, 30:151-156. 10.1007/s11262-004-5624-3 15744573
6. Edwards R Rohwer F Viral metagenomics Nat Rev Microbiol 2005, 3:504-510. 10.1038/nrmicro1163 15886693
7. Virus Taxonomy: Classification and Nomenclature of Viruses Elsevier, Amsterdam Fauquet CM, Mayo MA, Maniloff J, Desselberger U, Ball LA 2005
8. Ackermann HW 5500 Phages examined in the electron microscope Arch Virol 2007, 152:227-243. 10.1007/s00705-006-0849-1 17051420
9. Prangishvili D Forterre P Garrett RA Viruses of the Archaea: A unifying view Nat Rev Microbiol 2006, 4:837-848. 10.1038/nrmicro1527 17041631
10. Barns SM Delwiche CF Palmer JD Pace NR Perspectives on archaeal diversity, thermophily and monophyly from environmental rRNA sequences Proc Natl Acad Sci USA 1996, 93:9188-9193. 38617 8799176 10.1073/ pnas.93.17.9188
11. Huber H Hohn MJ Rachel R Fuchs T Wimmer VC Stetter KO A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont Nature 2002, 417:63-7. 10.1038/417063a 11986665
12. Dyall-Smith M Tang SL Bath C Haloarchaeal viruses: How diverse are they? Res Microbiol 2003, 154:309-313. 10.1016/S0923-2508(03)00076-7 12798237
13. Klein R Baranyi U Rossler N Greineder B Scholz H Witte A Natrialba magadii virus φCh1: First complete nucleotide sequence and functional organization of a virus infecting a haloalkaliphilic archaeon Mol Microbiol 2002, 45:851-863. 10.1046/j.1365-2958.2002.03064.x 12139629
14. Tang SL Nuttall S Dyall-Smith M Haloviruses HF1 and HF2: Evidence for a recent and large recombination event J Bacteriol 2004, 186:2810-2817. 387818 15090523 10.1128/JB.186.9.2810-2817.2004
15. Tang SL Nuttall S Ngui K Fisher C Lopez P Dyall-Smith M HF2: A double-stranded DNA tailed haloarchaeal virus with a mosaic genome Mol Microbiol 2002, 44:283-296. 10.1046/j.1365-2958.2002.02890.x 11967086
16. Bath C Cukalac T Porter K Dyall-Smith M His1 and His2 are distantly related, spindle-shaped haloviruses belonging to the novel virus group, Salterprovirus Virology 2006, 350:228-239. 10.1016/j.virol.2006.02.005 16530800
17. Bamford DH Ravantti JJ Ronnholm G Laurinavicius S Kukkaro P Dyall-Smith M Somerharju P Kalkkinen N Bamford JK Constituents of SH1, a novel lipid-containing virus infecting the halophilic euryarchaeon Haloarcula hispanica J Virol 2005, 79:9097-9107. 1168735 15994804 10.1128/ JVI.79.14.9097-9107.2005
18. Porter K Kukkaro P Bamford JK Bath C Kivela HM Dyall-Smith ML Bamford DH SH1: A novel, spherical halovirus isolated from an Australian hypersaline lake Virology 2005, 335:22-33. 10.1016/j.virol.2005.01.043 15823603
19. McGenity TJ Grant WD Genus Halorubrum Bergey's Manual of Systematic Bacteriology Springer Boone DR, Castenholz RW 2 2001, 1:320-324.
20. Cui HL Tohty D Zhou PJ Liu SJ Halorubrum lipolyticum sp. nov. and Halorubrum aidingense sp. nov., isolated from two salt lakes in Xin-Jiang, China Int J Syst Evol Microbiol 2006, 56:1631-1634. 10.1099/ ijs.0.64305-0 16825640
21. Grigoriev A Strand-specific compositional asymmetries in double-stranded DNA viruses Virus Res 1999, 60:1-19 10.1016/S0168-1702(98)00139-7 10225270
22. Bell SD Jackson SP Transcription and translation in Archaea: A mosaic of eukaryal and bacterial features Trends Microbiol 1998, 6:222-228. 10.1016/S0966-842X(98)01281-5 9675798
23. Sartorius-Neef S Pfeifer F In vivo studies on putative Shine-Dalgarno sequences of the halophilic archaeon Halobacterium salinarum Mol Microbiol 2004, 51:579-588. 10.1046/j.1365-2958.2003.03858.x 14756795
24. Tolstrup N Sensen CW Garrett RA Clausen IG Two different and highly organized mechanisms of translation initiation in the archaeon Sulfolobus solfataricus Extremophiles 2000, 4:175-179. 10.1007/ s007920070032 10879562
25. Mongodin EF Nelson KE Daugherty S Deboy RT Wister J Khouri H Weidman J Walsh DA Papke RT Sanchez Perez G Sharma AK Nesbo CL MacLeod D Bapteste E Doolittle WF Charlebois RL Legault B Rodriguez-Valera F The genome of Salinibacter ruber: Convergence and gene exchange among hyperhalophilic bacteria and archaea Proc Natl Acad Sci USA 2005, 102:18147-18152. 1312414 16330755 10.1073/pnas.0509073102
26. Bickle TA Krüger DH Biology of DNA restriction Microbiol Rev 1993, 57:434-450. 372918 8336674
27. Holmes ML Nuttall SD Construction and use of halobacterial shuttle vectors and further studies on Haloferax DNA gyrase J Bacteriol 1991, 173:3807-3813. 208012 1711028
28. Allers T Mevarech M Archaeal genetics - the third way Nature Rev Genet 2005, 6:58-73. 10.1038/nrg1504
29. Zillig W Prangishvilli D Schleper C Elferink M Holz I Albers S Janekovic D Gotz D Viruses, plasmids and other genetic elements of thermophilic and hyperthermophilic Archaea FEMS Microbiol Rev 1996, 18:225-236. 10.1111/j.1574-6976.1996.tb00239.x 8639330
30. Stolt P Zillig W Transcription of the halophage phi H repressor gene is abolished by transcription from an inversely oriented lytic promoter FEBS Lett 1994, 344:125-128. 10.1016/0014-5793(94)00347-5 8187870
31. Purdy KJ Cresswell-Maynard TD Nedwell DB McGenity TJ Grant WD Timmis KN Embley TM Isolation of haloarchaea that grow at low salinities Environ Microbiol 2004, 6:591-595. 10.1111/j.1462-2920.2004.00592.x 15142247
32. Rees HC Grant WD Jones BE Heaphy S Diversity of Kenyan soda lake alkaliphiles assessed by molecular methods Extremophiles 2004, 8:63-71. 10.1007/s00792-003-0361-4 15064991
33. Weisburg WG Barns SM Pelletier DA Lane DJ 16S ribosomal DNA amplification for phylogenetic study J Bacteriol 1991, 173:697-703. 207061 1987160
34. Altschul SF Gish W Miller W Myers EW Lipman DJ Basic local alignment search tool J Mol Biol 1990, 215:403-410. 2231712
35. Kumar S Tamura K Nei M MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment Brief Bioinform 2004, 5:150-163. 10.1093/bib/5.2.150 15260895
36. Upgrade http://rsb.info.nih.gov/ij/upgrade/index.html
37. de Lorenzo V Herrero M Jakubzik U Timmis KN Mini-Tn5 transposon derivatives for insertion mutagenesis, promoter probing, and chromosomal insertion of cloned DNA in Gram-negative eubacteria J Bacteriol 1990 172 6568 6572 526846 2172217
38. Softberry http://www.softberry.com
39. GeneMark http://opal.biology.gatech.edu/GeneMark/index.html
40. tRNAscan-SE Search Server http://lowelab.ucsc.edu/tRNAscan-SE/
41. ProtParam tool http://www.expasy.ch/tools/protparam.html
42. DNA base composition analysis tool http://molbiol-tools.ca/Jie_Zheng
43. NCBI/BLAST home http://www.ncbi.nlm.nih.gov/BLAST/
44. emboss einverted http://bioweb.pasteur.fr/docs/EMBOSS/einverted.html
45. PALINDROME http://bioweb.pasteur.fr/seqanal/interfaces/palindrome.html
46. PROTEOME ALLIANCE http://tp12.pzr.uni-rostock.de/~moeller/palim/ index.html