Housekeeping recA gene interrupted by group II intron in the thermophilic Geobacillus kaustophilus

Gene

Volumn 363, Issue 1-2, 2005, Pages 211-220

  Chee, Gab Joo ^a   Takami, Hideto ^a  

^a JAPAN AGENCY FOR MARINE EARTH SCIENCE AND TECHNOLOGY   (Japan)

Author keywords

Geobacillus kaustophilus; Group II intron; Housekeeping gene; recA gene; Self splicing

Indexed keywords

RECA PROTEIN;

ARTICLE; BACTERIAL GENOME; CONTROLLED STUDY; GENE FUNCTION; GEOBACILLUS; GEOBACILLUS KAUSTOPHILUS; HOUSEKEEPING GENE; INTRON; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROKARYOTE; THERMOPHILIC BACTERIUM;

AMINO ACID SEQUENCE; BACILLUS; BASE SEQUENCE; DNA PRIMERS; GENES, BACTERIAL; INTRONS; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; OPEN READING FRAMES; REC A RECOMBINASES; RNA SPLICING; RNA, BACTERIAL; SEQUENCE HOMOLOGY, AMINO ACID;

BACTERIA (MICROORGANISMS); EUKARYOTA; GEOBACILLUS; GEOBACILLUS KAUSTOPHILUS; PROKARYOTA;

EID: 28044472289     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.gene.2005.08.017     Document Type: Article

References (39)

1. C. Adamidi, O. Fedorova, and A.M. Pyle A group II intron inserted into a bacterial heat-shock operon shows autocatalytic activity and unusual thermostability Biochemistry 42 2003 3409 3418
2. D.L. Cheo, K.W. Bayles, and R.E. Yasbin Cloning and characterization of DNA damage-inducible promoter regions from Bacillus subtilis J. Bacteriol. 173 1991 1696 1703
3. D.L. Cheo, K.W. Bayles, and R.E. Yasbin Elucidation of regulatory elements that control damage induction and competence induction of the Bacillus subtilis SOS system J. Bacteriol. 175 1993 5907 5915
4. L. Dai, and S. Zimmerly Compilation and analysis of group II intron insertions in bacterial genomes: evidence for retroelement behavior Nucleic Acids Res. 30 2002 1091 1102
5. L. Dai, and S. Zimmerly ORF-less and reverse-transcriptase-encoding group II introns in archaebacteria, with a pattern of homing into related group II intron ORFs RNA 9 2003 14 19
6. J. Felsenstein PHYLIP: Phylogenetic Inference Package 1995 University of Washington Seattle, WA Version 3.57c
7. J.L. Ferat, M. Le Gouar, and F. Michel A group II intron has invaded the genus Azotobacter and is inserted within the termination codon of the essential groEL gene Mol. Microbiol. 49 2003 1407 1423
8. M.M. Igo, and R. Losick Regulation of a promoter that is utilized by minor forms of RNA polymerase holoenzyme in Bacillus subtilis J. Mol. Biol. 191 1986 615 624
9. S. Karlin, and L. Brocchieri Evolutionary conservation of recA genes in relation to protein structure and function J. Bacteriol. 178 1996 1881 1894
10. R.D. Knight, S.J. Freeland, and L.F. Landweber A simple model based on mutation and selection explains trends in codon and amino-acid usage and GC composition within and across genomes Genome Biol. 2 2001 (RESEARCH0010)
11. M. Ko, H. Choi, and C. Park Group I self-splicing intron in the recA gene of Bacillus anthracis J. Bacteriol. 184 2002 3917 3922
12. S.C. Kowalczykowski, and A.K. Eggleston Homologous pairing and DNA strand-exchange protein Annu. Rev. Biochem. 63 1994 991 1043
13. J.G. Lawrence, and H. Ochman Amelioration of bacterial genomes: rates of change and exchange J. Mol. Evol. 44 1997 383 397
14. J.G. Lawrence, and H. Ochman Molecular archaeology of the Escherichia coli genome Proc. Natl. Acad. Sci. U. S. A. 95 1998 9413 9417
15. J. Lazowska, B. Meunier, and C. Macadre Homing of a group II intron in yeast mitochondrial DNA is accompanied by unidirectional co-conversion of upstream-located markers EMBO J. 13 1994 4963 4972
16. K. Lehmann, and U. Schmidt Group II introns: structure and catalytic versatility of large natural ribozymes Crit. Rev. Biochem. Mol. Biol. 38 2003 249 303
17. F. Martinez-Abarca, and N. Toro Group II introns in the bacterial world Mol. Microbiol. 38 2000 917 926
18. F. Michel, K. Umesono, and H. Ozeki Comparative and functional anatomy of group II catalytic introns-a review Gene 82 1989 5 30
19. D.A. Mills, L.L. McKay, and G.M. Dunny Splicing of a group II intron involved in the conjugative transfer of pRS01 in lactococci J. Bacteriol. 178 1996 3531 3538
20. G. Mohr, P.S. Perlman, and A.M. Lambowitz Evolutionary relationships among group II intron-encoded proteins and identification of a conserved domain that may be related to maturase function Nucleic Acids Res. 21 1993 4991 4997
21. J.D. Pata, B.R. King, and T.A. Steitz Assembly, purification and crystallization of an active HIV-1 reverse transcriptase initiation complex Nucleic Acids Res. 30 2002 4855 4863
22. C.L. Peebles A self-splicing RNA excises an intron lariat Cell 44 1986 213 223
23. D.A. Rasko The genome sequence of Bacillus cereus ATCC 10987 reveals metabolic adaptations and a large plasmid related to Bacillus anthracis pXO1 Nucleic Acids Res. 32 2004 977 988
24. T.D. Read The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria Nature 423 2003 81 86
25. A.R. Robart, N.K. Montgomery, K.L. Smith, and S. Zimmerly Principles of 3' splice site selection and alternative splicing for an unusual group II intron from Bacillus anthracis RNA 10 2004 854 862
26. A.I. Roca, and M.M. Cox The recA protein: structure and function Crit. Rev. Biochem. Mol. Biol. 25 1990 415 456
27. N. Saitou, and M. Nei The neighbor-joining method: a new method for reconstructing phylogenetic trees Mol. Bio. Evol. 4 1987 406 425
28. P.M. Sharp, and W.H. Li An evolutionary perspective on synonymous codon usage in unicellular organisms J. Mol. Evol. 24 1986 28 38
29. D.A. Shub, H. Goodrich-Blair, and S.R. Eddy Amino acid sequence motif of group I intron endonucleases is conserved in open reading frames of group II introns Trends Biochem. Sci. 19 1994 402 404
30. H. Takami, A. Inoue, F. Fuji, and K. Horikoshi Microbial flora in the deepest sea mud of the Mariana Trench FEMS Microbiol. Lett. 152 1997 279 285
31. H. Takami Complete genome sequence of the alkaliphilic bacterium Bacillus halodurans and genomic sequence comparison with Bacillus subtilis Nucleic Acids Res. 28 2000 4317 4331
32. H. Takami, Y. Takaki, and I. Uchiyama Genome sequence of Oceanobacillus iheyensis isolated from the Iheya Ridge and its unexpected adaptive capabilities to extreme environments Nucleic Acids Res. 30 2002 3927 3935
33. H. Takami, S. Nishi, J. Lu, S. Shimamura, and Y. Takaki Genomic characterization of thermophilic Geobacillus species isolated from the deepest sea mud of the Mariana Trench Extremophilies 8 2004 351 356
34. H. Takami Thermoadaptation trait revealed by the genome sequence of thermophilic Geobacillus kaustophilus Nucleic Acids Res. 32 2004 6292 6303
35. J.D. Thompson, D.G. Higgins, and T.J. Gibson CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice Nucleic Acids Res. 22 1994 4673 4680
36. N. Toor, G. Hausner, and S. Zimmerly Coevolution of group II intron RNA structures with their intron-encoded reverse transcriptases RNA 7 2001 1142 1152
37. N. Toro Bacteria and Archaea Group II introns: additional mobile genetic elements in the environment Environ. Microbiol. 5 2003 143 151
38. K.W. Winterling, A.S. Levine, R.E. Yasbin, and R. Woodgate Characterization of DinR, the Bacillus subtilis SOS repressor J. Bacteriol. 179 1997 1698 1703
39. Y. Xiong, and T.H. Eickbush Origin and evolution of retroelements based upon their reverse transcriptase sequences EMBO J. 9 1990 3353 3362