Analysis of the 3′ ends of tRNA as the cause of insertion sites of foreign DNA in Prochlorococcus

Journal of Zhejiang University: Science B

Volumn 11, Issue 9, 2010, Pages 708-718

  Liu, Hai Lan ^a,b   Zhu, Jun ^a  

^a ZHEJIANG UNIVERSITY   (China)

^b SICHUAN AGRICULTURAL UNIVERSITY   (China)

Author keywords

Codon usage; Genomic islands; Palindromic structure; Prochlorococcus; Transfer RNA (tRNA)

Indexed keywords

PALINDROMIC DNA; TRANSFER RNA;

ARTICLE; CODON; GENE IDENTIFICATION; GENE INSERTION; GENE ORDER; GENETIC ANALYSIS; GENETIC ASSOCIATION; MONTE CARLO METHOD; NONHUMAN; PRIORITY JOURNAL; PROCHLOROCOCCUS; SITE DIRECTED MUTAGENESIS; BACTERIAL GENOME; COMPUTER PROGRAM; CONFORMATION; GENETIC RECOMBINATION; GENETICS; GENOMIC ISLAND; NUCLEOTIDE SEQUENCE; PHYLOGENY; SEQUENCE ALIGNMENT;

PROCHLOROCOCCUS; PROCHLOROCOCCUS MARINUS;

BASE SEQUENCE; GENOME, BACTERIAL; GENOMIC ISLANDS; NUCLEIC ACID CONFORMATION; PHYLOGENY; PROCHLOROCOCCUS; RECOMBINATION, GENETIC; RNA, TRANSFER; SEQUENCE ALIGNMENT; SOFTWARE;

EID: 77958017772     PISSN: 16731581     EISSN: 18621783     Source Type: Journal    
DOI: 10.1631/jzus.B0900417     Document Type: Article

References (35)

1. S.F. Altschul T.L. Madden A.A. Schaffer J. Zhang Z. Zhang W. Miller D.J. Lipman 1997 Gapped BLAST and PSI-BLAST: a new generation of protein database search programs Nucleic Acids Res. 25 17 3389 3402 1:CAS:528:DyaK2sXlvFyhu7w%3D 10.1093/nar/25.17.3389 9254694
2. C. Baar M. Eppinger G. Raddatz J. Simon C. Lanz O. Klimmer R. Nandakumar R. Cross A. Rosinus H. Keller, et al. 2003 Complete genome sequence and analysis of Wolinella succinogenes PNAS 100 20 11690 11695 1:CAS:528: DC%2BD3sXotFKmtb4%3D 10.1073/pnas.1932838100 14500908
3. L. Boto 2010 Horizontal gene transfer in evolution: facts and challenges Proc. R. Soc. B 277 1683 819 827 10.1098/rspb.2009.1679 19864285
4. B.F. Cheetham M.E. Katz 1995 A role for bacteriophages in the evolution and transfer of bacterial virulence determinants Mol. Microbiol. 18 2 201 208 1:CAS:528:DyaK2MXpslynsLg%3D 10.1111/j.1365-2958.1995.mmi-18020201.x 8709840
5. I.G. Choi S.H. Kim 2007 Global extent of horizontal gene transfer PNAS 104 11 4489 4494 1:CAS:528:DC%2BD2sXjsFKmsbc%3D 10.1073/pnas.0611557104 17360551
6. M.L. Coleman M.B. Sullivan A.C. Martiny C. Steglich K. Barry E.F. Delong S.W. Chisholm 2006 Genomic islands and the ecology and evolution of Prochlorococcus Science 311 5768 1768 1770 1:CAS:528:DC%2BD28Xis1eqtbg%3D 10.1126/science.1122050 16556843
7. J. Elhai A. Taton J.P. Massar J.K. Myers M. Travers J. Casey M. Slupesky J. Shrager 2009 BioBIKE: a Web-based, programmable, integrated biological knowledge base Nucleic Acids Res. 37 webserver W28 W32 1:CAS:528: DC%2BD1MXosFSrs7s%3D 10.1093/nar/gkp354 19433511
8. V.S. Garcia-Vallvé A. Romeu J. Palau 2000 Horizontal gene transfer in bacterial and archaeal complete genomes Genome Res. 10 11 1719 1725 10.1101/gr.130000 11076857
9. J. Hacker E. Carniel 2001 Ecological fitness, genomic islands and bacterial pathogenicity EMBO Rep. 2 5 376 381 1:CAS:528:DC%2BD3MXks1akurY%3D 11375927
10. W.R. Hess G. Rocap C.S. Ting F. Larimer S. Stilwagen J. Lamerdin S.W. Chisholm 2001 The photosynthetic apparatus of Prochlorococcus: insights through comparative genomics Photosynth. Res. 70 1 53 71 1:CAS:528:DC%2BD38Xht1Wgt7w%3D 10.1023/A:1013835924610 16228362
11. Y.M. Hou 1999 Transfer RNAs and pathogenicity islands Trends Biochem. Sci. 24 8 295 298 1:CAS:528:DC%2BD3cXjtVKruw%3D%3D 10.1016/S0968-0004(99)01428-0 10431171
12. W. Hsiao I. Wan S.J. Jones F.S.L. Brinkman 2003 IslandPath: aiding detection of genomic islands in prokaryotes Bioinformatics 19 3 418 420 1:CAS:528:DC%2BD3sXit1ygtLc%3D 10.1093/bioinformatics/btg004 12584130
13. G.C. Kettler A.C. Martiny K. Huang J. Zuker M.L. Coleman S. Rodrigue F. Chen A. Lapidus S. Ferriera J. Johnson, et al. 2007 Patterns and implications of gene gain and loss in the evolution of Prochlorococcus PLoS Genet. 3 12 e231 10.1371/journal.pgen.0030231 18159947
14. E.V. Koonin 2009 Darwinian evolution in the light of genomics Nucleic Acids Res. 37 4 1011 1034 1:CAS:528:DC%2BD1MXivFSgtro%3D 10.1093/nar/gkp089 19213802
15. E.V. Koonin K.S. Makarova L. Aravind 2001 Horizontal gene transfer in prokaryotes: quantification and classification Annu. Rev. Microbiol. 55 1 709 742 1:CAS:528:DC%2BD3MXnslKjtbw%3D 10.1146/annurev.micro.55.1.709 11544372
16. H.L. Liu J. Zhu 2010 Identification of genomic islands in the genomes of five Prochlorococcus strains by multiple genomic comparison J. Zhejiang Univ. (Agric. & Life Sci.) 36 5 473 484
17. Y. Nakamura T. Itoh H. Matsuda T. Gojobori 2004 Biased biological functions of horizontally transferred genes in prokaryotic genomes Nat. Genet. 36 7 760 766 1:CAS:528:DC%2BD2cXlt1Cku7s%3D 10.1038/ng1381 15208628
18. K.E. Nelson R.A. Clayton S.R. Gill M.L. Gwinn R.J. Dodson D.H. Haft E.K. Hickey J.D. Peterson W.C. Nelson K.A. Ketchum, et al. 1999 Evidence for lateral gene transfer between archaea and bacteria from genome sequence of Thermotoga maritime Nature 399 6734 323 329 1:CAS:528:DyaK1MXjs1WnsLo%3D 10.1038/20601 10360571
19. V.R. Parreira C.L. Gyles 2003 A novel pathogenicity island integrated adjacent to the thrW tRNA gene of avian pathogenic Escherichia coli encodes a vacuolating autotransporter toxin Infect. Immun. 71 9 5087 5096 1:CAS:528:DC%2BD3sXntFOqs7c%3D 10.1128/IAI.71.9.5087-5096.2003 12933851
20. F. Partensky W.R. Hess D. Vaulot 1999 Prochlorococcus, a marine photosynthetic prokaryote of global significance Microbiol. Mol. Biol. Rev. 63 1 106 127 1:CAS:528:DyaK1MXitVert78%3D 10066832
21. W.D. Reiter P. Palm S. Yeats 1989 Transfer RNA genes frequently serve as integration sites for prokaryotic genetic elements Nucleic Acids Res. 17 5 1907 1914 1:CAS:528:DyaL1MXhvVKqsLw%3D 10.1093/nar/17.5.1907 2467253
22. A. Ritter G. Blum L. Emody M. Kerenyi A. Bock B. Neuhieri W. Rabsch F. Scheutz J. Hacker 1995 tRNA genes and pathogenicity islands: influence on virulence and metabolic properties of uropathogenic Escherichia coli Mol. Microbiol. l7 1 109 121 10.1111/j.1365-2958.1995.mmi-17010109.x
23. G. Rocap F.W. Larimer J. Lamerdin S. Malfatti P. Chain N.A. Ahlgren A. Arellano M. Coleman L. Hauser W.R. Hess, et al. 2003 Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation Nature 424 6952 1042 1047 1:CAS:528:DC%2BD3sXmslSjt70%3D 10.1038/nature01947 12917642
24. S. Semsey B. Blaha K. Koles L. Orosz P.P. Papp 2002 Site-specific integrative elements of rhizobiophage 16-3 can integrate into proline tRNA (CGG) genes in different bacterial genera J. Bacteriol. 184 1 177 182 1:CAS:528:DC%2BD3MXpt1CmtLg%3D 10.1128/JB.184.1.177-182.2002 11741858
25. M. Syvanen 1994 Horizontal gene transfer: evidence and possible consequences Annu. Rev. Genet. 28 1 237 261 1:CAS:528:DyaK2MXislWmu7w%3D 7893125
26. K. Tamura J. Dudley M. Nei S. Kumar 2007 MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0 Mol. Biol. Evol. 24 8 1596 1599 1:CAS:528:DC%2BD2sXpsVGrsL8%3D 10.1093/molbev/msm092 17488738
27. Y.J. Tian H. Yang X.J. Wu D.T. Li 2005 Molecular analysis of microbial community in a groundwater sample polluted by landfill leachate and seawater J. Zhejiang Univ.-Sci. B 6 3 165 170 10.1631/jzus.2005.B0165 15682499
28. A. Tuanyok B.R. Leadem R.K. Auerbach S.M. Beckstrom-Sternberg J.S. Beckstrom-Sternberg M. Mayo V. Wuthiekanum T.S. Brettin W.C. Nierman S.J. Peacock, et al. 2008 Genomic islands from five strains of Burkholderia pseudomallei BMC Genomics 9 1 566 10.1186/1471-2164-9-566 19038032
29. J.J. van Aartsen 2008 The Klebsiella pheV tRNA locus: a hotspot for integration of alien genomic islands Biosci. Horiz. 1 1 51 60 10.1093/biohorizons/hzn006
30. X.S. Wang J. Zhu L. Mansueto R. Bruskiewich 2005 Identification of candidate genes for drought strees tolerance in rice by the integration of a genetic (QTL) map with the rice genome physical map J. Zhejiang Univ.-Sci. B 6 5 382 388 10.1631/jzus.2005.B0382 15822152
31. K.P. Williams 2002 Integration sites for genetic elements in prokaryotic tRNA and tmRNA genes: sublocation preference of integrase subfamilies Nucleic. Acids Res. 30 4 866 875 1:CAS:528:DC%2BD38Xhs1Cjtb0%3D 10.1093/nar/30.4.866 11842097
32. X.Z. Xu Q.B. Liu L.J. Fan X.F. Cui X.P. Zhou 2008 Analysis of synonymous codon usage and evolution of begomoviruses J. Zhejiang Univ.-Sci. B 9 9 667 674 1:CAS:528:DC%2BD1cXht1Gntr%2FN 10.1631/jzus.B0820005 18763298
33. O. Zhaxybayeva J.P. Gogarten R.L. Charlebois W.F. Doolittle R.T. Papke 2006 Phylogenetic analyses of cyanobacterial genomes: quantification of horizontal gene transfer events Genome Res. 16 9 1099 1108 1:CAS:528: DC%2BD28XpsFelsrs%3D 10.1101/gr.5322306 16899658
34. E.R. Zinser Z.I. Johnson A. Coe E. Karaca D. Veneziano S.W. Chisholm 2007 Influence of light and temperature on Prochlorococcus ecotype distributions in the Atlantic Ocean Limnol. Oceanogr. 52 5 2205 2220
35. M. Zuker 2003 Mfold web server for nucleic acid folding and hybridization prediction Nucleic. Acids Res. 31 13 3406 3415 1:CAS:528:DC%2BD3sXltVWisr8%3D 10.1093/nar/gkg595 12824337