A new example of viral intein in Mimivirus

Virology Journal

Volumn 2, Issue , 2005, Pages

  Ogata, Hiroyuki ^a   Raoult, Didier ^b   Claverie, Jean Michel ^a  

^a CNRS and Aix Marseille University   (France)

^b AIX MARSEILLE UNIVERSITY   (France)

Author keywords

[No Author keywords available]

Indexed keywords

DNA POLYMERASE; INTEIN;

ARTICLE; BACTERIVORY; BIOINFORMATICS; DNA VIRUS; GENE IDENTIFICATION; GENE LOCATION; GENETIC ASSOCIATION; INTRON; MIMIVIRUS; MOLECULAR PHYLOGENY; NUCLEOTIDE SEQUENCE; PROTEIN MOTIF; SEQUENCE ANALYSIS; VIRUS GENE;

AMINO ACID SEQUENCE; AMOEBA; ANIMALS; DNA VIRUSES; DNA-DIRECTED DNA POLYMERASE; GENE EXPRESSION REGULATION, VIRAL; INTEINS; MOLECULAR SEQUENCE DATA; PHYLOGENY; VIRAL PROTEINS;

EID: 15544379710     PISSN: 1743422X     EISSN: 1743422X     Source Type: Journal    
DOI: 10.1186/1743-422X-2-8     Document Type: Article

References (30)

1. La Scola B, Audic S, Robert C, Jungang L, de Lamballerie X, Drancourt M, Birtles R, Claverie JM, Raoult D: A giant virus in amoebae. Science 2003, 299:2033.
2. Raoult D, Audic S, Robert C, Abergel C, Renesto P, Ogata H, La Scola B, Suzan M, Claverie JM: The 1.2-megabase genome sequence of Mimivirus. Science 2004, 306:1344-1350.
3. Pietrokovski S: Identification of a virus intein and a possible variation in the protein-splicing reaction. Curr Biol 1998, 8:R634-5.
4. Hirata R, Ohsumk Y, Nakano A, Kawasaki H, Suzuki K, Anraku Y: Molecular structure of a gene, VMA1, encoding the catalytic subunit of H(+)-translocating adenosine triphosphatase from vacuolar membranes of Saccharomyces cerevisiae. J Biol Chem 1990, 265:6726-6733.
5. Kane PM, Yamashiro CT, Wolczyk DF, Neff N, Goebl M, Stevens TH: Protein splicing converts the yeast TFP1 gene product to the 69-kD subunit of the vacuolar H(+)-adenosine triphosphatase. Science 1990, 250:651-657.
6. Hendrickson EL, Kaul R, Zhou Y, Bovee D, Chapman P, Chung J, Conway de Macario E, Dodsworth JA, Gillett W, Graham DE, Hackett M, Haydock AK, Kang A, Land ML, Levy R, Lie TJ, Major TA, Moore BC, Porat I, Palmeiri A, Rouse G, Saenphimmachak C, Soll D, Van Dien S, Wang T, Whitman WB, Xia Q, Zhang Y, Larimer FW, Olson MV, Leigh JA: Complete genome sequence of the genetically tractable hydrogenotrophic methanogen Methanococcus maripaludis. J Bacteriol 2004, 186:6956-6969.
7. van der Wilk F, Dullemans AM, Verbeek M, van den Heuvel JF: Isolation and characterization of APSE-1, a bacteriophage infecting the secondary endosymbiont of Acyrthosiphon pisum. Virology 1999, 262:104-113.
8. Lazarevic V: Ribonucleotide reductase genes of Bacillus prophages: a refuge to introns and intein coding sequences. Nucleic Acids Res 2001, 29:3212-3218.
9. Pedulla ML, Ford ME, Houtz JM, Karthikeyan T, Wadsworth C, Lewis JA, Jacobs-Sera D, Falbo J, Gross J, Pannunzio NR, Brucker W, Kumar V, Kandasamy J, Keenan L, Bardarov S, Kriakov J, Lawrence JG, Jacobs WRJ, Hendrix RW, Hatfull GF: Origins of highly mosaic mycobacteriophage genomes. Cell 2003, 113:171-182.
10. Ward N, Larsen O, Sakwa J, Bruseth L, Khouri H, Durkin AS, Dimitrov G, Jiang L, Scanlan D, Kang KH, Lewis M, Nelson KE, Methe B, Wu M, Heidelberg JF, Paulsen IT, Fouts D, Ravel J, Tettelin H, Ren Q, Read T, Deboy RT, Seshadri R, Salzberg SL, Jensen HB, Birkeland NK, Nelson WC, Dodson RJ, Grindhaug SH, Holt I, Eidhammer I, Jonasen I, Vanaken S, Utterback T, Feldblyum TV, Fraser CM, Lillehaug JR, Eisen JA: Genomic Insights into Methanotrophy: The Complete Genome Sequence of Methylococcus capsulatus (Bath). PLoS Biol 2004, 2:e303.
11. Hashimoto H, Nishioka M, Fujiwara S, Takagi M, Imanaka T, Inoue T, Kai Y: Crystal structure of DNA polymerase from hyperthermophilic archaeon Pyrococcus kodakaraensis KOD1. J Mol Biol 2001, 306:469-477.
12. Doublie S, Tabor S, Long AM, Richardson CC, Ellenberger T: Crystal structure of a bacteriophage T7 DNA replication complex at 2.2 A resolution. Nature 1998, 391:251-258.
13. Villarreal LP, DeFilippis VR: A hypothesis for DNA viruses as the origin of eukaryotic replication proteins. J Virol 2000, 74:7079-7084.
14. Pietrokovski S: Modular organization of inteins and C-terminal autocatalytic domains. Protein Sci 1998, 7:64-71.
15. Amitai G, Dassa B, Pietrokovski S: Protein splicing of inteins with atypical glutamine and aspartate C-terminal residues. J Biol Chem 2004, 279:3121-3131.
16. Perler FB: InBase: the Intein Database. Nucleic Acids Res 2002, 30:383-384.
17. Waters E, Hohn MJ, Ahel I, Graham DE, Adams MD, Barnstead M, Beeson KY, Bibbs L, Bolanos R, Keller M, Kretz K, Lin X, Mathur E, Ni J, Podar M, Richardson T, Sutton GG, Simon M, Soll D, Stetter KO, Short JM, Noordewier M: The genome of Nanoarchaeum equitans: insights into early archaeal evolution and derived parasitism. Proc Natl Acad Sci U S A 2003, 100:12984-8. Epub 2003 Oct 17..
18. Perler FB, Olsen GJ, Adam E: Compilation and analysis of intein sequences. Nucleic Acids Res 1997, 25:1087-1093.
19. Belfort M, Roberts RJ: Homing endonucleases: keeping the house in order. Nucleic Acids Res 1997, 25:3379-3388.
20. Liu XQ, Hu Z: A DnaB intein in Rhodothermus marinus: indication of recent intein homing across remotely related organisms. Proc Natl Acad Sci U S A 1997, 94:7851-7856.
21. Tajima K, Nagamine T, Matsui H, Nakamura M, Aminov RI: Phylogenetic analysis of archaeal 16S rRNA libraries from the rumen suggests the existence of a novel group of archaea not associated with known methanogens. FEMS Microbiol Lett 2001, 200:67-72.
22. Whitford MF, Teather RM, Forster RJ: Phylogenetic analysis of methanogens from the bovine rumen. BMC Microbiol 2001, 1:5. Epub 2001 May 16..
23. Kulik EM, Sandmeier H, Hinni K, Meyer J: Identification of archaeal rDNA from subgingival dental plaque by PCR amplification and sequence analysis. FEMS Microbiol Lett 2001, 196:129-133.
24. Nagasaki K, Shirai Y, Tomaru Y, Nishida K, Pietrokovski S: Algal viruses with distinct intraspecies host specificities include identical intein elements. Appl Environ Microbiol 2005, (in press):.
25. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25:3389-3402.
26. Boeckmann B, Bairoch A, Apweiler R, Blatter MC, Estreicher A, Gasteiger E, Martin MJ, Michoud K, O'Donovan C, Phan I, Pilbout S, Schneider M: The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res 2003, 31:365-370.
27. Bateman A, Birney E, Cerruti L, Durbin R, Etwiller L, Eddy SR, Griffiths-Jones S, Howe KL, Marshall M, Sonnhammer EL: The Pfam protein families database. Nucleic Acids Res 2002, 30:276-280.
28. Notredame C, Higgins DG, Heringa J: T-Coffee: A novel method for fast and accurate multiple sequence alignment. J Mol Biol 2000, 302:205-217.
29. Kumar S, Tamura K, Jakobsen IB, Nei M: MEGA2: molecular evolutionary genetics analysis software. Bioinformatics 2001, 17:1244-1245.
30. Gu X, Zhang J: A simple method for estimating the parameter of substitution rate variation among sites. Mol Biol Evol 1997, 14:1106-1113.