Abstract
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.
Similar content being viewed by others
Notes
GenBank accession number AE017180
Descriptions of the microarray experiments, quantitation data, and array design are available from the Gene Expression Omnibus (GEO) database (http://www.ncbi.nlm.nih.gov/geo/); accession number GSE8983
References
Afkar E, Reguera G, Schiffer M, Lovley DR (2005) A novel Geobacteraceae-specific outer membrane protein J (OmpJ) is essential for electron transport to Fe(III) and Mn(IV) oxides in Geobacter sulfurreducens. BMC Microbiol 5:41
Anderson RT, Lovley DR (1999) Naphthalene and benzene degradation under Fe(III)-reducing conditions in petroleum-contaminated aquifers. Bioremediation J 3:121–135
Andrews SC, Robinson AK, Rodriguez-Quinones F (2003) Bacterial iron homeostasis. FEMS Microbiol Rev 27:215–237
Barrios H, Valderrama B, Morett E (1999) Compilation and analysis of s54-dependent promoter sequences. Nucleic Acids Res 27:4305–4313
Bond DR, Lovley DR (2003) Electricity production by Geobacter sulfurreducens attached to electrodes. Appl Environ Microbiol 69:1548–1555
Butler JE, Kaufmann F, Coppi MV, Nunez C, Lovley DR (2004) MacA, a diheme c-type cytochrome involved in Fe(III) reduction by Geobacter sulfurreducens. J Bacteriol 186:4042–4045
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 60:3752–3759
Coppi MV, Leang C, Sandler SJ, Lovley DR (2001) Development of a genetic system for Geobacter sulfurreducens. Appl Environ Microbiol 67:3180–3187
DiDonato LN, Sullivan SA, Nevin K, Methé BA, England R, Lovley DR (2006) Role of Rel Gsu in stress response and Fe(III) reduction in Geobacter sulfurreducens. J Bacteriol 24:8469–8478
Giometti CS (2006) Tale of two metal reducers: comparative proteome analysis of Geobacter sulfurreducens PCA and Shewanella oneidensis MR-1. Methods Biochem Anal 49:97–111
Griggs DW, Konisky J (1989) Mechanism for iron-regulated transcription of the Escherichia coli cir gene: metal-dependent binding of fur protein to the promoters. J Bacteriol 171:1048–1054
Gruber TM, Gross CA (2003) Multiple sigma subunits and the partitioning of bacterial transcription space. Annu Rev Microbiol 57:441–466
Guillier M, Gottesman S, Storz G (2006) Modulating the outer membrane with small RNAs. Genes Dev 20:2338–2348
Harvie DR, Vilchez S, Steggles JR, Ellar DJ (2005) Bacillus cereus Fur regulates iron metabolism and is required for full virulence. Microbiology 151:569–577
Hengge-Aronis R (2002a) Signal transduction and regulatory mechanisms involved in control of the sigma(S) (RpoS) subunit of RNA polymerase. Microbiol Mol Biol Rev 66:373–395
Hengge-Aronis R (2002b) Recent insights into the general stress response regulatory network in Escherichia coli. J Mol Microbiol Biotechnol 4:341–346
Holmes DE, Finneran KT, O’Neil RA, Lovley DR (2002) Enrichment of members of the family Geobacteraceae associated with stimulation of dissimilatory metal reduction in uranium-contaminated aquifer sediments. Appl Environ Microbiol 68:2300–2306
Holmes DE, Bond DR, O’Neil RA, Reimers CE, Tender LR, Lovley DR (2004) Microbial communities associated with electrodes harvesting electricity from a variety of aquatic sediments. Microb Ecol 48:178–190
Holmes DE, Chaudhuri SK, Nevin KP, Mehta T, Methe BA, Liu A, Ward JE, Woodard TL, Webster J, Lovley DR (2006) Microarray and genetic analysis of electron transfer to electrodes in Geobacter sulfurreducens. Environ Microbiol 8:1805–1815
Huerta AM, Francino MP, Morett E, Collado-Vides J (2006) Selection for unequal densities of s70 promoter-like signals in different regions of large bacterial genomes. PLoS Genet 2:e185
Jackson EN, Yanofsky C (1973) Thr region between the operator and first structural gene of the tryptophan operon of Escherichia coli may have a regulatory function. J Mol Biol 76:89–101
Jensen ST, Liu JS (2004) BioOptimizer: a Bayesian scoring function approach to motif discovery. Bioinformatics 20:1557–1564
Kim BC, Leang C, Ding YH, Glaven RH, Coppi MV, Lovley DR (2005) OmcF, a putative c-type monoheme outer membrane cytochrome required for the expression of other outer membrane cytochromes in Geobacter sulfurreducens. J Bacteriol 187:4505–4513
Kim BC, Qian X, Leang C, Coppi MV, Lovley DR (2006) Two putative c-type multiheme cytochromes required for the expression of OmcB, an outer membrane protein essential for optimal Fe(III) reduction in Geobacter sulfurreducens. J Bacteriol 188:3138–3142
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 7:229–255
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. 424–431
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 151:1761–1767
Leang C, Coppi MV, Lovley DR (2003) OmcB, a c-type polyheme cytochrome, involved in Fe(III) reduction in Geobacter sulfurreducens. J Bacteriol 185:2096–2103
Leang C, Adams LA, Chin KJ, Nevin KP, Methe BA, Webster J, Sharma ML, Lovley DR (2005) Adaptation to disruption of the electron transfer pathway for Fe(III) reduction in Geobacter sulfurreducens. J Bacteriol 187:5918–5926
Liu X, Brutlag DL, Liu JS (2001) BioProspector: discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes. Pac Symp Biocomput 6:127–138
Lloyd JR, Leang C, Hodges Myerson AL, Coppi MV, Cuifo S, Methe B, Sandler SJ, Lovley DR (2003) Biochemical and genetic characterization of PpcA, a periplasmic c-type cytochrome in Geobacter sulfurreducens. Biochem J 369:153–161
Lovley DR (2006a) Bug juice: harvesting electricity with microorganisms. Nat Rev Microbiol 4:497–508
Lovley DR (2006b) Microbial fuel cells: novel microbial physiologies and engineering approaches. Curr Opin Biotechnol 17:327–332
Lovley DR, Holmes DE, Nevin KP (2004) Dissimilatory Fe(III) and Mn(IV) reduction. Adv Microb Physiol 49:219–286
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 71–96
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 12:1–27
Mehta T, Coppi MV, Childers SE, Lovley DR (2005) Outer membrane c-type cytochromes required for Fe(III) and Mn(IV) oxide reduction in Geobacter sulfurreducens. Appl Environ Microbiol 71:8634–8641
Mehta T, Childers SE, Glaven R, Lovley DR, Mester T (2006) A putative multicopper protein secreted by an atypical type II secretion system involved in the reduction of insoluble electron acceptors in Geobacter sulfurreducens. Microbiology 152:2257–2264
Merino E, Yanofsky C (2005) Transcription attenuation: a highly conserved regulatory strategy used by bacteria. Trends Genet 21:260–264
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 302:1967–1969
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 71:2530–2538
Núñez C, Adams L, Childers S, Lovley DR (2004) The RpoS sigma factor in the dissimilatory Fe(III)-reducing bacterium Geobacter sulfurreducens. J Bacteriol 186:5543–5546
Núñez C, Esteve-Nunez A, Giometti C, Lin W, Methé B, Lovley DR (2006) DNA-microarray and proteomics analysis of the RpoS regulon in Geobacter sulfurreducens. J Bacteriol 188:2792–2800
Ortiz-Bernad I, Anderson RT, Vrionis HA, Lovley DR (2004) Vanadium respiration by Geobacter metallireducens: novel strategy for in situ removal of vanadium from groundwater. Appl Environ Microbiol 70:3091–3095
Qian X, Reguera G, Mester T, Lovley D (2007) Evidence that OmcB and OmpB of Geobacter sulfurreducens are outer membrane surface proteins. FEMS Microbiol Lett 277:21–27
Reguera G, McCarthy KD, Mehta T, Nicoll JS, Tuominen MT, Lovley DR (2005) Extracellular electron transfer via microbial nanowires. Nature 435:1098–1101
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 284:241–254
Rodionov DA, Dubchak I, Arkin A, Alm E, Gelfand MS (2004) Reconstruction of regulatory and metabolic pathways in metal-reducing d-proteobacteria. Genome Biol 5:R90 doi:10.1186/gb-2004-1185-1111-r1190
Roling WF, van Breukelen BM, Braster M, Lin B, van Verseveld HW (2001) Relationships between microbial community structure and hydrochemistry in a landfill leachate-polluted aquifer. Appl Environ Microbiol 67:4619–4629
Rooney-Varga JN, Anderson RT, Fraga JL, Ringelberg D, Lovley DR (1999) Microbial communities associated with anaerobic benzene degradation in a petroleum-contaminated aquifer. Appl Environ Microbiol 65:3056–3063
Roth FP, Hughes JD, Estep PW, Church GM (1998) Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation. Nat Biotechnol 16:939–945
Shelobolina ES, Coppi MV, Korenevsky AA, DiDonato LN, Sullivan SA, Konishi H, Xu H, Leang C, Butler JE, Kim BC, Lovley DR (2007) Importance of c-type cytochromes for U(VI) reduction by Geobacter sulfurreducens. BMC Microbiol 7:16
Shi L, Squier TC, Zachara JM, Fredrickson JK (2007) Respiration of metal (hydr)oxides by Shewanella and Geobacter: a key role for multihaem c-type cytochromes. Mol Microbiol 65:12–20
Studholme DJ, Buck M, Nixon T (2000) Identification of potential sN-dependent promoters in bacterial genomes. Microbiology 146(Pt 12):3021–3023
Sung Y, Fletcher KE, Ritalahti KM, Apkarian RP, Ramos-Hernandez N, Sanford RA, Mesbah NM, Loffler FE (2006) Geobacter lovleyi sp. nov. strain SZ, a novel metal-reducing and tetrachloroethene-dechlorinating bacterium. Appl Environ Microbiol 72:2775–2782
Tatusov RL, Koonin EV, Lipman DJ (1997) A genomic perspective on protein families. Science 278:631–637
Tatusov RL, Natale DA, Garkavtsev IV, Tatusova TA, Shankavaram UT, Rao BS, Kiryutin B, Galperin MY, Fedorova ND, Koonin EV (2001) The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucl Acids Res 29:22–28
Ueki T, Lovley DR (2007) Heat-shock sigma factor RpoH from Geobacter sulfurreducens. Microbiology 384:73–95
Vitreschak AG, Rodionov DA, Mironov AA, Gelfand MS (2004) Riboswitches: the oldest mechanism for the regulation of gene expression? Trends Genet 20:44–50
Wade JT, Roa DC, Grainger DC, Hurd D, Busby SJ, Struhl K, Nudler E (2006) Extensive functional overlap between sigma factors in Escherichia coli. Nat Struct Mol Biol 13:806–814
Wang L, Gralla JD (1998) Multiple in vivo roles for the -12-region elements of sigma 54 promoters. J Bacteriol 180:5626–5631
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 384:73–95
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 90:421–441
Yanofsky C (1981) Attenuation in the control of expression of bacterial operons. Nature 289:751–758
Yanofsky C (1988) Transcription attenuation. J Biol Chem 263:609–612
Yanofsky C (2000) Transcription attenuation: once viewed as a novel regulatory strategy. J Bacteriol 182:1–8
Acknowledgements
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.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Krushkal, J., Leang, C., Barbe, J.F. et al. Diversity of promoter elements in a Geobacter sulfurreducens mutant adapted to disruption in electron transfer. Funct Integr Genomics 9, 15–25 (2009). https://doi.org/10.1007/s10142-008-0094-7
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10142-008-0094-7