Journal of Molecular Evolution

, Volume 74, Issue 3–4, pp 187–205 | Cite as

Phylogenetic Classification of Diverse LysR-Type Transcriptional Regulators of a Model Prokaryote Geobacter sulfurreducens

  • Julia Krushkal
  • Yanhua Qu
  • Derek R. Lovley
  • Ronald M. Adkins


The protein family of LysR-type transcriptional regulators (LTTRs) is highly abundant among prokaryotes. We analyzed 10,145 non-redundant microbial sequences with homology to eight LysR family regulators of a model prokaryote, Geobacter sulfurreducens, and employed phylogenetic tree inference for LTTR classification. We also analyzed the arrangement of genome clusters containing G. sulfurreducens LTTR genes and searched for LTTR regulatory motifs, suggesting likely regulatory targets of G. sulfurreducens LTTRs. This is the first study to date providing a detailed classification of LTTRs in the deltaproteobacterial family Geobacteraceae.


Geobacter sulfurreducens LysR LTTR Phylogenetic tree Operon Transcriptional regulation 



This research was supported by the Office of Science (BER), U.S. Department of Energy, Cooperative Agreement No. DEFC02-02ER63446. Additional support for this study was provided by the Office of Research at the University of Tennessee Health Science Center. We thank Dr. M. Aklujkar (University of Massachusetts) for access to the functional annotation of the G. sulfurreducens genome and for helpful discussions about functional roles of genes and operons. We also thank Dr. P. Brown (University of Massachusetts) for development and computational support of the Geobacter Project web site, which was used to search for the functional roles of the G. sulfurreducens LTTRs. We thank Dr. K. Zengler (University of California, San Diego) for sharing information on experimentally derived operon organization of G. sulfurreducens and RpoN-dependent regulation. We are grateful to J. Peeples (The University of Tennessee Health Science Center) for editorial assistance.

Supplementary material

239_2012_9498_MOESM1_ESM.nwk (1.1 mb)
Supplementary Figure 1. The neighbor-joining tree NJ-10145 inferred from 10,145 LTTRs with ≥90% coverage of the length of the G. sulfurreducens query sequences. The tree was inferred using Poisson correction for multiple hits and uniform distribution of substitution rates among sites. A. A text file containing the entire tree in the Newick format. (NWK 1172 kb)
239_2012_9498_MOESM2_ESM.pdf (138 kb)
Supplementary Figure 1. The neighbor-joining tree NJ-10145 inferred from 10,145 LTTRs with ≥90% coverage of the length of the G. sulfurreducens query sequences. The tree was inferred using Poisson correction for multiple hits and uniform distribution of substitution rates among sites. A. A text file containing the entire tree in the Newick format. B. A graphical overview of the tree NJ-10145, presented using the Dendroscope software as an unrooted radial phylogram. Due to a very large number of sequences in the tree, only selected representative sequence names are shown for groups of closely related lineages. Five names of sequences of G. sulfurreducens LTTRs representing the five phylogenetic clusters containing all eight LTTRs of G. sulfurreducens are shown in red color. (PDF 137 kb)
239_2012_9498_MOESM3_ESM.pdf (2.4 mb)
Supplementary Figure 2. Protein sequence alignment of 591 LTTRs containing eight G. sulfurreducens LTTRs and their close homologs, which were included in phylogenetic inference of the tree NJ-591. This alignment was generated by Clustal X and further manually edited and visually presented using Jalview (JV2) multiple sequence analysis software. (PDF 2445 kb)
239_2012_9498_MOESM4_ESM.pdf (130 kb)
Supplementary Figure 3. Detailed view of the phylogenetic tree NJ-591, inferred from 591 LTTRs family regulators, presented using the MEGA software. The tree was inferred using the neighbor-joining method, with Poisson correction for multiple hits and uniform distribution of substitution rates among sites. The tree was midpoint rooted. Numbers show bootstrap support (%) for individual tree nodes, computed using 500 bootstrap replications. (PDF 129 kb)


  1. Aklujkar M, Krushkal J, DiBartolo G, Lapidus A, Land ML, Lovley DR (2009) The genome sequence of Geobacter metallireducens: features of metabolism, physiology and regulation common and dissimilar to Geobacter sulfurreducens. BMC Microbiol 9:109PubMedCrossRefGoogle Scholar
  2. Aklujkar M, Young ND, Holmes D, Chavan M, Risso C, Kiss HE, Han CS, Land ML, Lovley DR (2010) The genome of Geobacter bemidjiensis, exemplar for the subsurface clade of Geobacter species that predominate in Fe(III)-reducing subsurface environments. BMC Genomics 11:490PubMedCrossRefGoogle Scholar
  3. Badger MR, Bek EJ (2008) Multiple Rubisco forms in proteobacteria: their functional significance in relation to CO2 acquisition by the CBB cycle. J Exp Bot 59:1525PubMedCrossRefGoogle Scholar
  4. Blattner FR, Plunkett G III, Bloch CA, Perna NT, Burland V, Riley M, Collado-Vides J, Glasner JD, Rode CK, Mayhew GF, Gregor J, Davis NW, Kirkpatrick HA, Goeden MA, Rose DJ, Mau B, Shao Y (1997) The complete genome sequence of Escherichia coli K-12. Science 277:1453PubMedCrossRefGoogle Scholar
  5. Butler JE, Young ND, Lovley DR (2009) Evolution from a respiratory ancestor to fill syntrophic and fermentative niches: comparative genomics of six Geobacteraceae species. BMC Genomics 10:103PubMedCrossRefGoogle Scholar
  6. Butler JE, Young ND, Lovley DR (2010) Evolution of electron transfer out of the cell: comparative genomics of six Geobacter genomes. BMC Genomics 11:40PubMedCrossRefGoogle Scholar
  7. Caccavo FJ, Lonergan DJ, Lovley DR, Davis M, Stolz JF, McInerney MJ (1994) Geobacter sulfurreducens sp. nov., a hydrogen- and acetate-oxidizing dissimilatory metal-reducing microorganism. Appl Environ Microbiol 60:3752PubMedGoogle Scholar
  8. Coppi MV, Leang C, Sandler SJ, Lovley DR (2001) Development of a genetic system for Geobacter sulfurreducens. Appl Environ Microbiol 67:3180PubMedCrossRefGoogle Scholar
  9. Cummings L, Riley L, Black L, Souvorov A, Resenchuk S, Dondoshansky I, Tatusova T (2002) Genomic BLAST: custom-defined virtual databases for complete and unfinished genomes. FEMS Microbiol Lett 216:133PubMedCrossRefGoogle Scholar
  10. Diaz E, Ferrandez A, Garcia JL (1998) Characterization of the hca cluster encoding the dioxygenolytic pathway for initial catabolism of 3-phenylpropionic acid in Escherichia coli K-12. J Bacteriol 180:2915PubMedGoogle Scholar
  11. Ding YH, Hixson KK, Giometti CS, Stanley A, Esteve-Núñez A, Khare T, Tollaksen SL, Zhu W, Adkins JN, Lipton MS, Smith RD, Mester T, Lovley DR (2006) The proteome of dissimilatory metal-reducing microorganism Geobacter sulfurreducens under various growth conditions. Biochim Biophys Acta 1764:1198PubMedGoogle Scholar
  12. Ding YH, Hixson KK, Aklujkar MA, Lipton MS, Smith RD, Lovley DR, Mester T (2008) Proteome of Geobacter sulfurreducens grown with Fe(III) oxide or Fe(III) citrate as the electron acceptor. Biochim Biophys Acta 1784:1935PubMedGoogle Scholar
  13. Gerischer U (2002) Specific and global regulation of genes associated with the degradation of aromatic compounds in bacteria. J Mol Microbiol Biotechnol 4:111PubMedGoogle Scholar
  14. Huson DH, Richter DC, Rausch C, Dezulian T, Franz M, Rupp R (2007) Dendroscope: an interactive viewer for large phylogenetic trees. BMC Bioinform 8:460CrossRefGoogle Scholar
  15. Joshi GS, Bobst CE, Tabita FR (2011) Unravelling the regulatory twist-regulation of CO(2) fixation in Rhodopseudomonas palustris CGA010 mediated by atypical response regulator(s). Mol Microbiol 80:756PubMedCrossRefGoogle Scholar
  16. Juárez K, Kim BC, Nevin K, Olvera L, Reguera G, Lovley DR, Methe BA (2009) PilR, a transcriptional regulator for pilin and other genes required for Fe(III) reduction in Geobacter sulfurreducens. J Mol Microbiol Biotechnol 16:146PubMedCrossRefGoogle Scholar
  17. Knapp GS, Hu JC (2010) Specificity of the E. coli LysR-type transcriptional regulators. PLoS ONE 5:e15189PubMedCrossRefGoogle Scholar
  18. Krushkal J, Yan B, Di Donato LN, Puljic M, Nevin KP, Woodard TL, Adkins RM, Methé BA, Lovley DR (2007) Identification of Fur and RpoS transcription regulatory sites using genome-wide expression profiling in a rel Gsu mutant of Geobacter sulfurreducens. Funct Integr Genomics 7:229PubMedCrossRefGoogle Scholar
  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 1:424–431Google Scholar
  20. Kumar S, Tamura K, Jakobsen IB, Nei M (2001) MEGA2: molecular evolutionary genetics analysis software. Bioinformatics 17:1244PubMedCrossRefGoogle Scholar
  21. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23:2947PubMedCrossRefGoogle Scholar
  22. Leang C, Lovley D (2005) Differential transcriptional regulation and function of two highly similar genes, omcB and omcC, in a 10-kb chromosomal duplication in Geobacter sulfurreducens. Microbiology 151:1761PubMedCrossRefGoogle Scholar
  23. Leang C, Krushkal J, Ueki T, Puljic M, Sun J, Juarez K, Nunez C, Reguera G, Di Donato R, Postier B, Adkins RM, Lovley DR (2009) Genome-wide analysis of the RpoN regulon in Geobacter sulfurreducens. BMC Genomics 10:331PubMedCrossRefGoogle Scholar
  24. Liu K, Raghavan S, Nelesen S, Linder CR, Warnow T (2009) Rapid and accurate large-scale coestimation of sequence alignments and phylogenetic trees. Science 324:1561PubMedCrossRefGoogle Scholar
  25. Lovley DR (2008) The microbe electric: conversion of organic matter to electricity. Curr Opin Biotechnol 19:564PubMedCrossRefGoogle Scholar
  26. Lovley DR, Holmes DE, Nevin KP (2004) Dissimilatory Fe(III) and Mn(IV) reduction. Adv Microb Physiol 49:219PubMedCrossRefGoogle Scholar
  27. Maddocks SE, Oyston PC (2008) Structure and function of the LysR-type transcriptional regulator (LTTR) family proteins. Microbiology 154:3609PubMedCrossRefGoogle Scholar
  28. Mahadevan R, Bond DR, Butler JE, Esteve-Núñez A, Coppi MV, Palsson BO, Schilling CH, Lovley DR (2006) Characterization of metabolism in the Fe(III)-reducing organism Geobacter sulfurreducens by constraint-based modeling. Appl Environ Microbiol 72:1558PubMedCrossRefGoogle Scholar
  29. Mahadevan R, Yan B, Postier B, Nevin K, Woodard T, O’Neil R, Coppi M, Methé B, Krushkal J (2008) Characterizing regulation of metabolism in Geobacter sulfurreducens through genome-wide expression data and sequence analysis. OMICS 12:1CrossRefGoogle Scholar
  30. Mahadevan R, Palsson BØ, Lovley DR (2011) In situ to in silico and back: elucidating the physiology and ecology of Geobacter spp. using genome-scale modelling. Nat Rev Microbiol 9:39PubMedCrossRefGoogle Scholar
  31. Methé BA, Nelson KE, Eisen JA, Paulsen IT, Nelson W, Heidelberg JF, Wu D, Wu M, Ward N, Beanan MJ, Dodson RJ, Madupu R, Brinkac LM, Daugherty SC, DeBoy RT, Durkin AS, Gwinn M, Kolonay JF, Sullivan SA, Haft DH, Selengut J, Davidsen TM, Zafar N, White O, Tran B, Romero C, Forberger HA, Weidman J, Khouri H, Feldblyum TV, Utterback TR, Van Aken SE, Lovley DR, Fraser CM (2003) The genome of Geobacter sulfurreducens: insights into metal reduction in subsurface environments. Science 302:1967PubMedCrossRefGoogle Scholar
  32. Methé BA, Webster J, Nevin K, Butler J, Lovley DR (2005) DNA microarray analysis of nitrogen fixation and Fe(III) reduction in Geobacter sulfurreducens. Appl Environ Microbiol 71:2530PubMedCrossRefGoogle Scholar
  33. Mrázek J, Xie S (2006) Pattern locator: a new tool for finding local sequence patterns in genomic DNA sequences. Bioinformatics 22:3099PubMedCrossRefGoogle Scholar
  34. Nelson KM, Young GM, Miller VL (2001) Identification of a locus involved in systemic dissemination of Yersinia enterocolitica. Infect Immun 69:6201PubMedCrossRefGoogle Scholar
  35. Núñez C, Esteve-Núñez A, Giometti C, Lin W, Methé B, Lovley DR (2006) DNA-microarray and proteomics analysis of the RpoS regulon in Geobacter sulfurreducens. J Bacteriol 188:2792PubMedCrossRefGoogle Scholar
  36. Paoli GC, Soyer F, Shively J, Tabita FR (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):219PubMedCrossRefGoogle Scholar
  37. Parmentier G, Trystram D, Zola J (2006) Large scale multiple sequence alignment with simultaneous phylogeny inference. J Parallel Distrib Comput 66:1534CrossRefGoogle Scholar
  38. Powney R, Smits TH, Sawbridge T, Frey B, Blom J, Frey JE, Plummer KM, Beer SV, Luck J, Duffy B, Rodoni B (2011) Genome sequence of an Erwinia amylovora strain with pathogenicity restricted to Rubus plants. J Bacteriol 193:785PubMedCrossRefGoogle Scholar
  39. Qiu Y, Cho B-K, Park YS, Lovley D, Palsson BØ, Zengler K (2010) Structural and operational complexity of the Geobacter sulfurreducens genome. Genome Res 20:1304PubMedCrossRefGoogle Scholar
  40. Qu Y, Brown P, Barbe JF, Puljic M, Merino E, Adkins RM, Lovley DR, Krushkal J (2009) GSEL v. 2, a genome-wide query system of operon organization and regulatory sequence elements of Geobacter sulfurreducens. OMICS 413:439CrossRefGoogle Scholar
  41. Rediers H, Rainey PB, Vanderleyden J, De Mot R (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 69:217PubMedCrossRefGoogle Scholar
  42. Risso C, Sun J, Zhuang K, Mahadevan R, DeBoy R, Ismail W, Shrivastava S, Huot H, Kothari S, Daugherty S, Bui O, Schilling CH, Lovley DR, Methe BA (2009) Genome-scale comparison and constraint-based metabolic reconstruction of the facultative anaerobic Fe(III)-reducer Rhodoferax ferrireducens. BMC Genomics 10:447PubMedCrossRefGoogle Scholar
  43. Robison K, McGuire AM, Church GM (1998) A comprehensive library of DNA-binding site matrices for 55 proteins applied to the complete Escherichia coli K-12 genome. J Mol Biol 284:241PubMedCrossRefGoogle Scholar
  44. Rodionov DA, Dubchak I, Arkin A, Alm E, Gelfand MS (2004) Reconstruction of regulatory and metabolic pathways in metal-reducing δ-proteobacteria. Genome Biol 5:R90PubMedCrossRefGoogle Scholar
  45. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406PubMedGoogle Scholar
  46. Schell MA (1993) Molecular biology of the LysR family of transcriptional regulators. Annu Rev Microbiol 47:597PubMedCrossRefGoogle Scholar
  47. Schlaman HR, Okker RJ, Lugtenberg BJ (1992) Regulation of nodulation gene expression by NodD in rhizobia. J Bacteriol 174:5177PubMedGoogle Scholar
  48. Segura D, Mahadevan R, Juarez K, Lovley DR (2008) Computational and experimental analysis of redundancy in the central metabolism of Geobacter sulfurreducens. PLoS Comput Biol 4:e36PubMedCrossRefGoogle Scholar
  49. Smits TH, Rezzonico F, Kamber T, Goesmann A, Ishimaru CA, Stockwell VO, Frey JE, Duffy B (2010) Genome sequence of the biocontrol agent Pantoea vagans strain C9-1. J Bacteriol 192:6486PubMedCrossRefGoogle Scholar
  50. Studholme DJ, Dixon R (2003) Domain architectures of σ54-dependent transcriptional activators. J Bacteriol 185:1757PubMedCrossRefGoogle Scholar
  51. Sung YC, Fuchs JA (1992) The Escherichia coli K-12 cyn operon is positively regulated by a member of the lysR family. J Bacteriol 174:3645PubMedGoogle Scholar
  52. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876PubMedCrossRefGoogle Scholar
  53. Tran HT, Krushkal J, Antommattei FM, Lovley DR, Weis RM (2008) Comparative genomics of Geobacter chemotaxis genes reveals diverse signaling function. BMC Genomics 9:471PubMedCrossRefGoogle Scholar
  54. Tropel D, van der Meer JR (2004) Bacterial transcriptional regulators for degradation pathways of aromatic compounds. Microbiol Mol Biol Rev 68:474PubMedCrossRefGoogle Scholar
  55. Turlin E, Perrotte-piquemal M, Danchin A, Biville F (2001) Regulation of the early steps of 3-phenylpropionate catabolism in Escherichia coli. J Mol Microbiol Biotechnol 3:127PubMedGoogle Scholar
  56. Turlin E, Sismeiro O, Le Caer JP, Labas V, Danchin A, Biville F (2005) 3-Phenylpropionate catabolism and the Escherichia coli oxidative stress response. Res Microbiol 156:312PubMedCrossRefGoogle Scholar
  57. Ueki T, Lovley DR (2007) Heat-shock sigma factor RpoH from Geobacter sulfurreducens. Microbiology 384:73Google Scholar
  58. Ueki T, Lovley DR (2010a) Genome-wide gene regulation of biosynthesis and energy generation by a novel transcriptional repressor in Geobacter species. Nucleic Acids Res 38:810PubMedCrossRefGoogle Scholar
  59. Ueki T, Lovley DR (2010b) Novel regulatory cascades controlling expression of nitrogen-fixation genes in Geobacter sulfurreducens. Nucleic Acids Res 38:7485PubMedCrossRefGoogle Scholar
  60. Waterhouse AM, Procter JB, Martin DM, Clamp M, Barton GJ (2009) Jalview Version 2—a multiple sequence alignment editor and analysis workbench. Bioinformatics 25:1189PubMedCrossRefGoogle Scholar
  61. Yan B, Núñez C, Ueki T, Esteve-Núñez A, Puljic M, Adkins RM, Methé BA, Lovley DR, Krushkal J (2006) Computational prediction of RpoS and RpoD regulatory sites in Geobacter sulfurreducens using sequence and gene expression information. Gene 384:73PubMedCrossRefGoogle Scholar
  62. Yan B, Lovley DR, Krushkal J (2007) Genome-wide similarity search for transcription factors and their binding sites in a metal-reducing prokaryote Geobacter sulfurreducens. BioSystems 90:421PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  • Julia Krushkal
    • 1
  • Yanhua Qu
    • 1
  • Derek R. Lovley
    • 2
  • Ronald M. Adkins
    • 3
  1. 1.Department of Preventive MedicineThe University of Tennessee Health Science CenterMemphisUSA
  2. 2.Department of MicrobiologyThe University of MassachusettsAmherstUSA
  3. 3.Department of PediatricsThe University of Tennessee Health Science CenterMemphisUSA

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