Phylogenetic classification of diverse LysR-Type transcriptional regulators of a model prokaryote Geobacter sulfurreducens

Journal of Molecular Evolution

Volumn 74, Issue 3-4, 2012, Pages 187-205

  Krushkal, Julia ^a   Qu, Yanhua ^a   Lovley, Derek R ^b   Adkins, Ronald M ^a  

^a UNIVERSITY OF TENNESSEE HEALTH SCIENCE CENTER   (United States)

^b UNIVERSITY OF MASSACHUSETTS   (United States)

Author keywords

Geobacter sulfurreducens; LTTR; LysR; Operon; Phylogenetic tree; Transcriptional regulation

Indexed keywords

BACTERIAL PROTEIN; LYSR PROTEIN, BACTERIA; TRANSCRIPTION FACTOR;

ARTICLE; DNA SEQUENCE; GENETICS; GEOBACTER; MOLECULAR GENETICS; MULTIGENE FAMILY; NUCLEOTIDE MOTIF; NUCLEOTIDE SEQUENCE; PHYLOGENY;

BACTERIAL PROTEINS; BASE SEQUENCE; GEOBACTER; MOLECULAR SEQUENCE DATA; MULTIGENE FAMILY; NUCLEOTIDE MOTIFS; PHYLOGENY; SEQUENCE ANALYSIS, DNA; TRANSCRIPTION FACTORS;

GEOBACTER SULFURREDUCENS; GEOBACTERACEAE; PROKARYOTA;

EID: 84861888620     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-012-9498-z     Document Type: Article

References (62)

1. M Aklujkar J Krushkal G DiBartolo A Lapidus ML Land DR Lovley 2009 The genome sequence of Geobacter metallireducens: features of metabolism, physiology and regulation common and dissimilar to Geobacter sulfurreducens BMC Microbiol 9 109 19473543 10.1186/1471-2180-9-109
2. M Aklujkar ND Young D Holmes M Chavan C Risso HE Kiss CS Han ML Land DR Lovley 2010 The genome of Geobacter bemidjiensis, exemplar for the subsurface clade of Geobacter species that predominate in Fe(III)-reducing subsurface environments BMC Genomics 11 490 20828392 10.1186/1471-2164-11-490
3. 2 acquisition by the CBB cycle J Exp Bot 59 1525 18245799 10.1093/jxb/erm297 1:CAS:528: DC%2BD1cXmtleltL8%3D
4. FR Blattner G Plunkett III CA Bloch NT Perna V Burland M Riley J Collado-Vides JD Glasner CK Rode GF Mayhew J Gregor NW Davis HA Kirkpatrick MA Goeden DJ Rose B Mau Y Shao 1997 The complete genome sequence of Escherichia coli K-12 Science 277 1453 9278503 10.1126/science.277.5331.1453 1:CAS:528:DyaK2sXlvVGnu78%3D
5. JE Butler ND Young DR Lovley 2009 Evolution from a respiratory ancestor to fill syntrophic and fermentative niches: comparative genomics of six Geobacteraceae species BMC Genomics 10 103 19284579 10.1186/1471-2164-10-103
6. JE Butler ND Young DR Lovley 2010 Evolution of electron transfer out of the cell: comparative genomics of six Geobacter genomes BMC Genomics 11 40 20078895 10.1186/1471-2164-11-40
7. FJ Caccavo DJ Lonergan DR Lovley M Davis JF Stolz MJ McInerney 1994 Geobacter sulfurreducens sp. nov., a hydrogen- and acetate-oxidizing dissimilatory metal-reducing microorganism Appl Environ Microbiol 60 3752 7527204 1:CAS:528:DyaK2cXmt1KgsL4%3D
8. MV Coppi C Leang SJ Sandler DR Lovley 2001 Development of a genetic system for Geobacter sulfurreducens Appl Environ Microbiol 67 3180 11425739 10.1128/AEM.67.7.3180-3187.2001 1:CAS:528:DC%2BD3MXkvFSnu7g%3D
9. L Cummings L Riley L Black A Souvorov S Resenchuk I Dondoshansky T Tatusova 2002 Genomic BLAST: custom-defined virtual databases for complete and unfinished genomes FEMS Microbiol Lett 216 133 12435493 10.1111/j.1574-6968. 2002.tb11426.x 1:CAS:528:DC%2BD38XosFCmtbk%3D
10. E Diaz A Ferrandez JL Garcia 1998 Characterization of the hca cluster encoding the dioxygenolytic pathway for initial catabolism of 3-phenylpropionic acid in Escherichia coli K-12 J Bacteriol 180 2915 9603882 1:CAS:528: DyaK1cXjsVCjtrY%3D
11. YH Ding KK Hixson CS Giometti A Stanley A Esteve-Núñez T Khare SL Tollaksen W Zhu JN Adkins MS Lipton RD Smith T Mester DR Lovley 2006 The proteome of dissimilatory metal-reducing microorganism Geobacter sulfurreducens under various growth conditions Biochim Biophys Acta 1764 1198 16797259 1:CAS:528:DC%2BD28Xnt1ymtrs%3D
12. YH Ding KK Hixson MA Aklujkar MS Lipton RD Smith DR Lovley T Mester 2008 Proteome of Geobacter sulfurreducens grown with Fe(III) oxide or Fe(III) citrate as the electron acceptor Biochim Biophys Acta 1784 1935 18638577 1:CAS:528:DC%2BD1cXhtlaqtb7L
13. U Gerischer 2002 Specific and global regulation of genes associated with the degradation of aromatic compounds in bacteria J Mol Microbiol Biotechnol 4 111 11873906 1:CAS:528:DC%2BD38XitVSmtLw%3D
14. DH Huson DC Richter C Rausch T Dezulian M Franz R Rupp 2007 Dendroscope: an interactive viewer for large phylogenetic trees BMC Bioinform 8 460 10.1186/1471-2105-8-460
15. GS Joshi CE Bobst FR Tabita 2011 Unravelling the regulatory twist-regulation of CO(2) fixation in Rhodopseudomonas palustris CGA010 mediated by atypical response regulator(s) Mol Microbiol 80 756 21362064 10.1111/j.1365-2958.2011.07606.x 1:CAS:528:DC%2BC3MXmvFeisr8%3D
16. K Juárez BC Kim K Nevin L Olvera G Reguera DR Lovley BA Methe 2009 PilR, a transcriptional regulator for pilin and other genes required for Fe(III) reduction in Geobacter sulfurreducens J Mol Microbiol Biotechnol 16 146 18253022 10.1159/000115849
17. GS Knapp JC Hu 2010 Specificity of the E. coli LysR-type transcriptional regulators PLoS ONE 5 e15189 21187915 10.1371/journal.pone.0015189 1:CAS:528:DC%2BC3MXntlyq
18. Gsu mutant of Geobacter sulfurreducens Funct Integr Genomics 7 229 17406915 10.1007/s10142-007-0048-5 1:CAS:528:DC%2BD2sXls1SitL4%3D
19. Krushkal J, Puljic M, Yan B, Barbe JF, Mahadevan R, Postier B, O'Neil RA, Reguera G, Leang C, DiDonato LN, Núñez C, Methé BA, Adkins RM, Lovley DR (2008) Genome regions involved in multiple regulatory pathways identified from GSEL, a genome-wide database of regulatory sequence elements of Geobacter sulfurreducens BMEI2008. Biomedical engineering and informatics: new developments and the future. Proceedings the First International Conference on Biomedical Engineering and Informatics. IEEE Computer Society, Las Alamitos, CA, Sanya, China 1:424-431
20. S Kumar K Tamura IB Jakobsen M Nei 2001 MEGA2: molecular evolutionary genetics analysis software Bioinformatics 17 1244 11751241 10.1093/ bioinformatics/17.12.1244 1:CAS:528:DC%2BD38XmtVCktQ%3D%3D
21. MA Larkin G Blackshields NP Brown R Chenna PA McGettigan H McWilliam F Valentin IM Wallace A Wilm R Lopez JD Thompson TJ Gibson DG Higgins 2007 Clustal W and Clustal X version 2.0 Bioinformatics 23 2947 17846036 10.1093/bioinformatics/btm404 1:CAS:528:DC%2BD2sXhtlaqsL%2FM
22. C Leang D Lovley 2005 Differential transcriptional regulation and function of two highly similar genes, omcB and omcC, in a 10-kb chromosomal duplication in Geobacter sulfurreducens Microbiology 151 1761 15941985 10.1099/mic.0.27870-0 1:CAS:528:DC%2BD2MXlslertLo%3D
23. C Leang J Krushkal T Ueki M Puljic J Sun K Juarez C Nunez G Reguera R Di Donato B Postier RM Adkins DR Lovley 2009 Genome-wide analysis of the RpoN regulon in Geobacter sulfurreducens BMC Genomics 10 331 19624843 10.1186/1471-2164-10-331
24. K Liu S Raghavan S Nelesen CR Linder T Warnow 2009 Rapid and accurate large-scale coestimation of sequence alignments and phylogenetic trees Science 324 1561 19541996 10.1126/science.1171243 1:CAS:528:DC%2BD1MXnsFOrs7w%3D
25. DR Lovley 2008 The microbe electric: conversion of organic matter to electricity Curr Opin Biotechnol 19 564 19000760 10.1016/j.copbio.2008.10.005 1:CAS:528:DC%2BD1cXhsVKrtLjP
26. DR Lovley DE Holmes KP Nevin 2004 Dissimilatory Fe(III) and Mn(IV) reduction Adv Microb Physiol 49 219 15518832 10.1016/S0065-2911(04)49005-5 1:CAS:528:DC%2BD2cXhtVaksrrE
27. SE Maddocks PC Oyston 2008 Structure and function of the LysR-type transcriptional regulator (LTTR) family proteins Microbiology 154 3609 19047729 10.1099/mic.0.2008/022772-0 1:CAS:528:DC%2BD1MXhsVCjsg%3D%3D
28. R Mahadevan DR Bond JE Butler A Esteve-Núñez MV Coppi BO Palsson CH Schilling DR Lovley 2006 Characterization of metabolism in the Fe(III)-reducing organism Geobacter sulfurreducens by constraint-based modeling Appl Environ Microbiol 72 1558 16461711 10.1128/AEM.72.2.1558-1568.2006 1:CAS:528:DC%2BD28Xhs1Ghurs%3D
29. R Mahadevan B Yan B Postier K Nevin T Woodard R O'Neil M Coppi B Methé J Krushkal 2008 Characterizing regulation of metabolism in Geobacter sulfurreducens through genome-wide expression data and sequence analysis OMICS 12 1 10.1089/omi.2007.0043
30. R Mahadevan B∅ Palsson DR Lovley 2011 In situ to in silico and back: elucidating the physiology and ecology of Geobacter spp. using genome-scale modelling Nat Rev Microbiol 9 39 21132020 10.1038/nrmicro2456 1:CAS:528:DC%2BC3cXhsFajur7E
31. BA Methé KE Nelson JA Eisen IT Paulsen W Nelson JF Heidelberg D Wu M Wu N Ward MJ Beanan RJ Dodson R Madupu LM Brinkac SC Daugherty RT DeBoy AS Durkin M Gwinn JF Kolonay SA Sullivan DH Haft J Selengut TM Davidsen N Zafar O White B Tran C Romero HA Forberger J Weidman H Khouri TV Feldblyum TR Utterback SE Van Aken DR Lovley CM Fraser 2003 The genome of Geobacter sulfurreducens: insights into metal reduction in subsurface environments Science 302 1967 14671304 10.1126/science.1088727
32. BA Methé J Webster K Nevin J Butler DR Lovley 2005 DNA microarray analysis of nitrogen fixation and Fe(III) reduction in Geobacter sulfurreducens Appl Environ Microbiol 71 2530 15870343 10.1128/AEM.71.5.2530-2538.2005
33. J Mrázek S Xie 2006 Pattern locator: a new tool for finding local sequence patterns in genomic DNA sequences Bioinformatics 22 3099 17095514 10.1093/bioinformatics/btl551
34. KM Nelson GM Young VL Miller 2001 Identification of a locus involved in systemic dissemination of Yersinia enterocolitica Infect Immun 69 6201 11553561 10.1128/IAI.69.10.6201-6208.2001 1:CAS:528:DC%2BD3MXntFCjsb0%3D
35. C Núñez A Esteve-Núñez C Giometti W Lin B Methé DR Lovley 2006 DNA-microarray and proteomics analysis of the RpoS regulon in Geobacter sulfurreducens J Bacteriol 188 2792 16585740 10.1128/JB.188.8.2792-2800.2006
36. GC Paoli F Soyer J Shively FR Tabita 1998 Rhodobacter capsulatus genes encoding form I ribulose-1,5-bisphosphate carboxylase/oxygenase (cbbLS) and neighbouring genes were acquired by a horizontal gene transfer Microbiology 144 Pt 1 219 9467914 10.1099/00221287-144-1-219 1:CAS:528:DyaK1cXnsVeksQ%3D%3D
37. G Parmentier D Trystram J Zola 2006 Large scale multiple sequence alignment with simultaneous phylogeny inference J Parallel Distrib Comput 66 1534 10.1016/j.jpdc.2006.03.003
38. R Powney TH Smits T Sawbridge B Frey J Blom JE Frey KM Plummer SV Beer J Luck B Duffy B Rodoni 2011 Genome sequence of an Erwinia amylovora strain with pathogenicity restricted to Rubus plants J Bacteriol 193 785 21131493 10.1128/JB.01352-10 1:CAS:528:DC%2BC3MXisFOqtLc%3D
39. Y Qiu B-K Cho YS Park D Lovley B∅ Palsson K Zengler 2010 Structural and operational complexity of the Geobacter sulfurreducens genome Genome Res 20 1304 20592237 10.1101/gr.107540.110 1:CAS:528:DC%2BC3cXhtFeru7jN
40. Y Qu P Brown JF Barbe M Puljic E Merino RM Adkins DR Lovley J Krushkal 2009 GSEL v. 2, a genome-wide query system of operon organization and regulatory sequence elements of Geobacter sulfurreducens OMICS 413 439 10.1089/omi.2009.0081
41. H Rediers PB Rainey J Vanderleyden R De Mot 2005 Unraveling the secret lives of bacteria: use of in vivo expression technology and differential fluorescence induction promoter traps as tools for exploring niche-specific gene expression Microbiol Mol Biol Rev 69 217 15944455 10.1128/MMBR.69.2.217-261. 2005 1:CAS:528:DC%2BD2MXmtFartr4%3D
42. C Risso J Sun K Zhuang R Mahadevan R DeBoy W Ismail S Shrivastava H Huot S Kothari S Daugherty O Bui CH Schilling DR Lovley BA Methe 2009 Genome-scale comparison and constraint-based metabolic reconstruction of the facultative anaerobic Fe(III)-reducer Rhodoferax ferrireducens BMC Genomics 10 447 19772637 10.1186/1471-2164-10-447
43. K Robison AM McGuire GM Church 1998 A comprehensive library of DNA-binding site matrices for 55 proteins applied to the complete Escherichia coli K-12 genome J Mol Biol 284 241 9813115 10.1006/jmbi.1998.2160 1:CAS:528:DyaK1cXnvVeqtbY%3D
44. DA Rodionov I Dubchak A Arkin E Alm MS Gelfand 2004 Reconstruction of regulatory and metabolic pathways in metal-reducing δ-proteobacteria Genome Biol 5 R90 15535866 10.1186/gb-2004-5-11-r90
45. N Saitou M Nei 1987 The neighbor-joining method: a new method for reconstructing phylogenetic trees Mol Biol Evol 4 406 3447015 1:STN:280:DyaL1c7ovFSjsA%3D%3D
46. MA Schell 1993 Molecular biology of the LysR family of transcriptional regulators Annu Rev Microbiol 47 597 8257110 10.1146/annurev.mi.47.100193.003121 1:CAS:528:DyaK3sXms1emsb8%3D
47. HR Schlaman RJ Okker BJ Lugtenberg 1992 Regulation of nodulation gene expression by NodD in rhizobia J Bacteriol 174 5177 1644745 1:CAS:528: DyaK38Xls1Cru78%3D
48. D Segura R Mahadevan K Juarez DR Lovley 2008 Computational and experimental analysis of redundancy in the central metabolism of Geobacter sulfurreducens PLoS Comput Biol 4 e36 18266464 10.1371/journal.pcbi.0040036
49. TH Smits F Rezzonico T Kamber A Goesmann CA Ishimaru VO Stockwell JE Frey B Duffy 2010 Genome sequence of the biocontrol agent Pantoea vagans strain C9-1 J Bacteriol 192 6486 20952567 10.1128/JB.01122-10 1:CAS:528: DC%2BC3MXhvFGmtL8%3D
50. 54- dependent transcriptional activators J Bacteriol 185 1757 12618438 10.1128/JB.185.6.1757-1767.2003 1:CAS:528:DC%2BD3sXitFWktr8%3D
51. YC Sung JA Fuchs 1992 The Escherichia coli K-12 cyn operon is positively regulated by a member of the lysR family J Bacteriol 174 3645 1592818 1:CAS:528:DyaK3sXitVKksLs%3D
52. JD Thompson TJ Gibson F Plewniak F Jeanmougin DG Higgins 1997 The CLUSTAL-X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools Nucleic Acids Res 25 4876 9396791 10.1093/nar/25.24.4876 1:CAS:528:DyaK1cXntFyntQ%3D%3D
53. HT Tran J Krushkal FM Antommattei DR Lovley RM Weis 2008 Comparative genomics of Geobacter chemotaxis genes reveals diverse signaling function BMC Genomics 9 471 18844997 10.1186/1471-2164-9-471
54. D Tropel JR van der Meer 2004 Bacterial transcriptional regulators for degradation pathways of aromatic compounds Microbiol Mol Biol Rev 68 474 15353566 10.1128/MMBR.68.3.474-500.2004 1:CAS:528:DC%2BD2cXosVyhtLY%3D
55. E Turlin M Perrotte-piquemal A Danchin F Biville 2001 Regulation of the early steps of 3-phenylpropionate catabolism in Escherichia coli J Mol Microbiol Biotechnol 3 127 11200225 1:CAS:528:DC%2BD3MXhslKnsL8%3D
56. E Turlin O Sismeiro JP Le Caer V Labas A Danchin F Biville 2005 3-Phenylpropionate catabolism and the Escherichia coli oxidative stress response Res Microbiol 156 312 15808934 10.1016/j.resmic.2004.10.012 1:CAS:528:DC%2BD2MXjtlWjt7w%3D
57. T Ueki DR Lovley 2007 Heat-shock sigma factor RpoH from Geobacter sulfurreducens Microbiology 384 73
58. T Ueki DR Lovley 2010 Genome-wide gene regulation of biosynthesis and energy generation by a novel transcriptional repressor in Geobacter species Nucleic Acids Res 38 810 19939938 10.1093/nar/gkp1085 1:CAS:528: DC%2BC3cXitVSltrY%3D
59. T Ueki DR Lovley 2010 Novel regulatory cascades controlling expression of nitrogen-fixation genes in Geobacter sulfurreducens Nucleic Acids Res 38 7485 20660485 10.1093/nar/gkq652 1:CAS:528:DC%2BC3cXhsFamtb7J
60. AM Waterhouse JB Procter DM Martin M Clamp GJ Barton 2009 Jalview Version 2-a multiple sequence alignment editor and analysis workbench Bioinformatics 25 1189 19151095 10.1093/bioinformatics/btp033 1:CAS:528:DC%2BD1MXltFWis7Y%3D
61. B Yan C Núñez T Ueki A Esteve-Núñez M Puljic RM Adkins BA Methé DR Lovley J Krushkal 2006 Computational prediction of RpoS and RpoD regulatory sites in Geobacter sulfurreducens using sequence and gene expression information Gene 384 73 17014972 10.1016/j.gene.2006.06.025 1:CAS:528:DC%2BD28Xht1Wms7%2FI
62. B Yan DR Lovley J Krushkal 2007 Genome-wide similarity search for transcription factors and their binding sites in a metal-reducing prokaryote Geobacter sulfurreducens BioSystems 90 421 17184904 10.1016/j.biosystems.2006. 10.006 1:CAS:528:DC%2BD2sXhtVWmsLfK