Horizontal gene transfer of zinc and non-zinc forms of bacterial ribosomal protein S4

BMC Evolutionary Biology

Volumn 9, Issue 1, 2009, Pages

  Chen, Ke ^a   Roberts, Elijah ^a   Luthey Schulten, Zaida ^a  

^a UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; PROTEIN S 4; UNCLASSIFIED DRUG; ZINC; ZINC BINDING PROTEIN; RIBOSOME PROTEIN;

ACTINOBACTERIA; ARTICLE; BACTERIAL GENOME; BINDING SITE; CLOSTRIDIA; GENE CLUSTER; GENE SEQUENCE; GENETIC VARIABILITY; HORIZONTAL GENE TRANSFER; MAXIMUM LIKELIHOOD METHOD; MOLECULAR EVOLUTION; NONHUMAN; PHYLOGENETIC TREE; PHYLOGENY; PROTEIN BINDING; SEQUENCE ALIGNMENT; AMINO ACID SEQUENCE; BACTERIAL GENE; BACTERIUM; CLASSIFICATION; GENETICS; MOLECULAR GENETICS;

BACTERIA (MICROORGANISMS); CLOSTRIDIA;

AMINO ACID SEQUENCE; BACTERIA; BACTERIAL PROTEINS; EVOLUTION, MOLECULAR; GENE TRANSFER, HORIZONTAL; GENES, BACTERIAL; GENOME, BACTERIAL; MOLECULAR SEQUENCE DATA; PHYLOGENY; RIBOSOMAL PROTEINS; SEQUENCE ALIGNMENT; ZINC;

EID: 69549122181     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-9-179     Document Type: Article

References (46)

1. Towards a natural system of organisms: Proposal for the domains Archaea, Bacteria, and Eucarya. C Woese O Kandler M Wheelis, Proc Natl Acad Sci USA 1990 87 12 4576 4579 2112744 10.1073/pnas.87.12.4576 (Pubitemid 20204145)
2. Molecular signatures of ribosomal evolution. E Roberts A Sethi J Montoya CR Woese Z Luthey-Schulten, Proc Natl Acad Sci USA 2008 105 37 13953 13958 18768810 10.1073/pnas.0804861105
3. The universal ancestor. C Woese, Proc Natl Acad Sci USA 1998 95 12 6854 6859 9618502 10.1073/pnas.95.12.6854 (Pubitemid 28278070)
4. On the evolution of cells. C Woese, Proc Natl Acad Sci USA 2002 99 13 8742 12077305 10.1073/pnas.132266999 (Pubitemid 34693630)
5. Phylogenetic classification and the universal tree. W Doolittle, Science 1999 284 5423 2124 10.1126/science.284.5423.2124 10381871 (Pubitemid 29297466)
6. Reverse gyrase from hyperthermophiles: probable transfer of a thermoadaptation trait from Archaea to Bacteria. P Forterre C Bouthier de la Tour H Philippe M Duguet, 2000 16 4 152 154 10729828
7. Horizontal gene transfer in prokaryotes: Quantification and classification. E Koonin K Makarova L Aravind, Annu Rev Microbiol 2001 55 709 742 10.1146/annurev.micro.55.1.709 11544372 (Pubitemid 32978121)
8. Prokaryotic evolution in light of gene transfer. J Gogarten W Doolittle J Lawrence, Mol Biol Evol 2002 19 12 2226 2238 12446813
9. Genomes in flux: The evolution of archaeal and proteobacterial gene content. B Snel P Bork M Huynen, Genome Res 2002 12 17 25 10.1101/gr.176501 11779827 (Pubitemid 34065586)
10. Ancient horizontal gene transfer. J Brown, Nat Rev Genet 2003 4 2 121 132 10.1038/nrg1000 12560809 (Pubitemid 36150684)
11. Lateral gene transfer and the nature of bacterial innovation. H Ochman J Lawrence E Groisman, Nature 2000 405 6784 299 304 10.1038/35012500 10830951 (Pubitemid 30337055)
12. The evolutionary history of ribosomal protein RpS14: Horizontal gene transfer at the heart of the ribosome. C Brochier H Philippe D Moreira, Trends Genet 2000 16 12 529 533 10.1016/S0168-9525(00)02142-9 11102698 (Pubitemid 30843823)
13. Horizontal gene transfer among genomes: The complexity hypothesis. R Jain M Rivera J Lake, Proc Natl Acad Sci USA 1999 96 7 3801 3806 10097118 10.1073/pnas.96.7.3801 (Pubitemid 29168991)
14. Two C or not two C: recurrent disruption of Zn-ribbons, gene duplication, lineage-specific gene loss, and horizontal gene transfer in evolution of bacterial ribosomal proteins. K Makarova V Ponomarev E Koonin, Genome Biol 2001 2 9 0033 10.1186/gb-2001-2-9-research0033
15. Comparative genomics of bacterial zinc regulons: Enhanced ion transport, pathogenesis, and rearrangement of ribosomal proteins. E Panina A Mironov M Gelfand, Proc Natl Acad Sci USA 2003 100 17 9912 9917 12904577 10.1073/pnas.1733691100 (Pubitemid 37087042)
16. Zinc is a key factor in controlling alternation of two types of L31 protein in the Bacillus subtilis ribosome. H Nanamiya G Akanuma Y Natori R Murayama S Kosono T Kudo K Kobayashi N Ogasawara S Park K Ochi F Kawamura, Mol Microbiol 2004 52 273 283 10.1111/j.1365-2958.2003.03972.x 15049826 (Pubitemid 38519637)
17. A fail-safe system for the ribosome under zinc-limiting conditions in Bacillus subtilis. Y Natori H Nanamiya G Akanuma S Kosono T Kudo K Ochi F Kawamura, Mol Microbiol 2007 63 294 307 10.1111/j.1365-2958.2006.05513.x 17163968 (Pubitemid 44968126)
18. R. G Owen B Pascoe D Kallifidas M Paget, J Bacteriol 2007 189 11 4078 4086 17400736 10.1128/JB.01901-06 (Pubitemid 46847355)
19. Global analysis of the Mycobacterium tuberculosis Zur (FurB) regulon. A Maciag E Dainese G Rodriguez A Milano R Provvedi M Pasca I Smith G Pal G Riccardi M R, J Bacteriol 2007 189 3 730 740 17098899 10.1128/JB.01190-06 (Pubitemid 46183847)
20. The use of hydroxylamine cleavage to produce a fragment of ribosomal protein S4 which retains the capacity to specifically bind 16S ribosomal RNA. L Changchien G Craven, Nucl Acids Res 1986 14 5 1957 1966 3515315 10.1093/nar/14.5.1957
21. Messenger RNA recognition by fragments of ribosomal protein S4. A Baker D Draper, J Biol Chem 1995 270 39 22939 22945 10.1074/jbc.270.39.22939 7559430
22. Novel predicted RNA-binding domains associated with the translation machinery. L Aravind E Koonin, J Mol Evol 1999 48 3 291 302 10.1007/PL00006472 10093218
23. Structural preordering in the N-terminal region of ribosomal protein S4 revealed by heteronuclear NMR spectroscopy. E Sayers R Gerstner D Draper D Torchia, Biochemistry (Washington) 2000 39 44 13602 13613 10.1021/bi0013391 (Pubitemid 30819847)
24. Structure of the 30S ribosomal subunit. B Wimberly D Brodersen W Clemons Jr R Morgan-Warren A Carter C Vonrhein T Hartsch V Ramakrishnan, Nature 2000 407 327 339 10.1038/35030006 11014182 (Pubitemid 30736003)
25. Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world. E Koonin Y Wolf, Nucl Acids Res 2008 36 21 6688 6719 18948295 10.1093/nar/gkn668
26. Widespread distribution of archaeal reverse gyrase in thermophilic bacteria suggests a complex history of vertical inheritance and lateral gene transfers. C Brochier-Armanet P Forterre, Archaea 2007 2 2 83 17350929 10.1155/2006/582916
27. Organisation of the S10, spc and alpha ribosomal protein gene clusters in prokaryotic genomes. T Coenye P Vandamme, FEMS Microbiol Lett 2005 242 117 126 10.1016/j.femsle.2004.10.050 15621428 (Pubitemid 40038428)
28. Phylogenetic diversity and ecology of environmental Archaea. C Robertson J Harris J Spear N Pace, Curr Opin Microbiol 2005 8 6 638 642 10.1016/j.mib.2005.10.003 16236543 (Pubitemid 41643031)
29. Genome of Methylobacillus flagellatus, molecular basis for obligate methylotrophy, and polyphyletic origin of methylotrophy. L Chistoserdova A Lapidus C Han L Goodwin L Saunders T Brettin R Tapia P Gilna S Lucas P Richardson, J Bacteriol 2007 189 11 4020 7 17416667 10.1128/JB.00045-07 (Pubitemid 46847348)
30. Transcriptional program of early sporulation and stationary-phase events in Clostridium acetobutylicum. K Alsaker E Papoutsakis, J Bacteriol 2005 187 20 7103 7118 16199581 10.1128/JB.187.20.7103-7118.2005 (Pubitemid 41428887)
31. The genome and transcriptomes of the anti-tumor agent Clostridium novyi-NT. C Bettegowda X Huang J Lin I Cheong M Kohli S Szabo X Zhang L Diaz Jr V Velculescu G Parmigiani, Nat Biotechnol 2006 24 12 1573 1580 10.1038/nbt1256 17115055 (Pubitemid 44967483)
32. Evolution of mosaic operons by horizontal gene transfer and gene displacement in situ. M Omelchenko K Makarova Y Wolf I Rogozin E Koonin, Genome Biol 2003 4 9 R55 12952534 10.1186/gb-2003-4-9-r55
33. Signature proteins that are distinctive of alpha proteobacteria. P Kainth R Gupta, BMC Genom 2005 6 94 1471 2164 10.1186/1471-2164-6-94 15960851 (Pubitemid 41378925)
34. Evidence for autotrophy via the reverse tricarboxylic acid cycle in the marine magnetotactic coccus strain MC-1. T Williams C Zhang J Scott D Bazylinski, Appl Environ Microbiol 2006 72 2 1322 1329 16461683 10.1128/AEM.72.2.1322-1329.2006 (Pubitemid 43271243)
35. Toward automatic reconstruction of a highly resolved tree of life. F Ciccarelli T Doerks C von Mering C Creevey B Snel P Bork, Science 2006 311 5765 1283 1287 10.1126/science.1123061 16513982 (Pubitemid 43334717)
36. Alternative methods for concatenation of core genes indicate a lack of resolution in deep nodes of the prokaryotic phylogeny. E Bapteste E Susko J Leigh I Ruiz-Trillo J Bucknam W Doolittle, Mol Biol Evol 2008 25 83 10.1093/molbev/msm229 17940208
37. The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata. K Liolios K Mavromatis N Tavernarakis N Kyrpides, Nucl Acids Res 2007 36 475 479 10.1093/nar/gkm884
38. Evolutionary profiles from the QR factorization of multiple sequence alignments. A Sethi P O'Donoghue Z Luthey-Schulten, Proc Natl Acad Sci USA 2005 102 11 4045 4050 15741270 10.1073/pnas.0409715102 (Pubitemid 40388552)
39. The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. B Boeckmann A Bairoch R Apweiler M Blatter A Estreicher E Gasteiger M Martin K Michoud C O'Donovan I Phan, Nucl Acids Res 2003 31 365 370 12520024 10.1093/nar/gkg095 (Pubitemid 36157284)
40. Basic local alignment search tool. S Altschul W Gish W Miller E Myers D Lipman, J Mol Biol 1990 215 3 403 410 2231712
41. CLUSTALW: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. J Thompson D Higgins G TJ, Nucl Acids Res 1994 22 22 4673 4680 7984417 10.1093/nar/22.22.4673
42. MultiSeq: unifying sequence and structure data for evolutionary analysis. E Roberts J Eargle D Wright Z Luthey-Schulten, BMC Bioinformatics 2006 7 382 16914055 10.1186/1471-2105-7-382 (Pubitemid 44508914)
43. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. A Stamatakis, Bioinformatics 2006 22 21 2688 10.1093/bioinformatics/btl446 16928733 (Pubitemid 44642609)
44. A new approach to protein fold recognition. D Jones W Taylort J Thornton, Nature 1992 358 6381 86 89 10.1038/358086a0 1614539
45. A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. S Whelan N Goldman, Mol Biol Evol 2001 18 5 691 699 11319253
46. Combining evidence using p-values: application to sequence homology searches. T Bailey M Gribskov, Bioinformatics 1998 14 48 54 10.1093/ bioinformatics/14.1.48 9520501