Diversity of promoter elements in a Geobacter sulfurreducens mutant adapted to disruption in electron transfer
- 289 Downloads
The delta-proteobacterium, Geobacter sulfurreducens, can obtain energy by coupling the oxidation of organic matter to the reduction of insoluble Fe(III) or the anode of a microbial fuel cell. Because Fe(III) oxide or the anode surface, in contrast to oxygen, nitrate, or sulfate, is not soluble nor can it be reduced readily, Geobacter species have developed mechanisms which allow electrons to be delivered across outer membrane to the cell surface. OmcB is an outer-membrane c-type cytochrome important for G. sulfurreducens Fe(III) respiration. In the absence of OmcB, cells lost the ability to reduce soluble or insoluble Fe(III). However, the omcB deletion mutant can slowly adapt to growth on soluble Fe(III) over prolonged incubation in the medium with acetate as the electron donor. We discuss available information about predicted or experimentally validated promoters and transcription regulatory sites identified upstream of operons with transcriptional expression significantly changed in the adapted omcB mutant. DNA sequences of upstream regions of coregulated operons in the adapted mutant are divergent, suggesting the presence of recognition sites for different transcriptional regulators and indicating that adaptation of the omcB mutant to growth on soluble Fe(III) has shifted the relevant expression networks involved to a more diverse molecular basis.
KeywordsGeobacter sulfurreducens Promoter c-type cytochrome Transcription
We are grateful to E. Anderson (University of Virginia) and J. Peeples (University of Tennessee, Memphis) for editorial assistance. We are also grateful to R. O’Neil and M. Coppi (University of Massachusetts, Amherst) for providing gene expression data on Fur-dependent regulation of G. sulfurreducens, to T. Ueki for sharing his results of primer extension analysis of RpoD-dependent promoters, and to K. Nevin and B.-C. Kim for information about the OmcZ cytochrome. We also thank B. Methé (JCVI) for microarray data submission to the GEO database and B. Palsson (UCSD) for helpful discussions about sigma-factor-dependent regulation.
This research was supported by the Office of Science (BER), US Department of Energy, Cooperative Agreement No. DE-FC02-02ER63446.
- Krushkal J, Yan B, DiDonato 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 7:229–255PubMedCrossRefGoogle 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 of the First International Conference on Biomedical Engineering and Informatics. IEEE Computer Society, Las Alamitos, CA Sanya, China, pp. 424–431Google Scholar
- Liu X, Brutlag DL, Liu JS (2001) BioProspector: discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes. Pac Symp Biocomput 6:127–138Google Scholar
- Lovley DR, Mahadevan R, Nevin K (2008) Systems biology approach to bioremediation with extracellular electron transfer. In: Díaz E (ed) Microbial bioremediation: genomics and molecular biology. Caister Academic, Norfolk, pp 71–96Google 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 302:1967–1969PubMedCrossRefGoogle Scholar
- Ueki T, Lovley DR (2007) Heat-shock sigma factor RpoH from Geobacter sulfurreducens. Microbiology 384:73–95Google Scholar