Phylogenetic Classification of Diverse LysR-Type Transcriptional Regulators of a Model Prokaryote Geobacter sulfurreducens
- 382 Downloads
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.
KeywordsGeobacter 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.
- 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
- 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
- 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
- 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
- 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
- Ueki T, Lovley DR (2007) Heat-shock sigma factor RpoH from Geobacter sulfurreducens. Microbiology 384:73Google Scholar