@article {422,
	title = {Genome diversity of the TetR family of transcriptional regulators in a metal-reducing bacterial family Geobacteraceae and other microbial species.},
	journal = {OMICS},
	volume = {15},
	year = {2011},
	month = {2011 Jul-Aug},
	pages = {495-506},
	abstract = {Members of the TetR family of bacterial transcriptional regulators affect expression of genes whose products are involved in a variety of important functions, including osmotic stress, catabolic pathways, homeostasis, biosynthesis of antibiotics, expression of efflux pumps, multidrug resistance, and virulence of pathogenic bacteria. We used genome sequence information to carry out phylogenetic classification of 864 TetR family members with a special focus on TetR regulators in Geobacteraceae, an environmentally important family of delta-Proteobacteria. The genome of Geobacter sulfurreducens, a model representative of Geobacteraceae, contains nine genes from the tetR family. Several of these genes are located immediately upstream of operons encoding functionally important c-type cytochromes. Computational analyses identified the presence of conserved promoters and other regulatory binding sites upstream of several G. sulfurreducens tetR genes. This suggests the possibility of an intermediary role of TetR family proteins in Geobacteraceae in regulatory cascades involving a variety of sigma factors. In order to understand the role of the TetR regulatory family in Geobacteraceae, we have inferred phylogenetic relationships among the Geobacteraceae TetR proteins and their homologs in other microbial species.},
	keywords = {Bacterial Proteins, Binding Sites, Gram-Negative Bacteria, Metals, Oxidation-Reduction, Phylogeny, Promoter Regions, Genetic, Sigma Factor},
	issn = {1557-8100},
	doi = {10.1089/omi.2010.0117},
	author = {Krushkal, Julia and Sontineni, Sreedhar and Leang, Ching and Qu, Yanhua and Adkins, Ronald M and Lovley, Derek R}
}
@article {473,
	title = {Diversity of promoter elements in a Geobacter sulfurreducens mutant adapted to disruption in electron transfer.},
	journal = {Funct Integr Genomics},
	volume = {9},
	year = {2009},
	month = {2009 Feb},
	pages = {15-25},
	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.},
	keywords = {Adaptation, Physiological, Electron Transport, Genetic Variation, Geobacter, Mutation, Promoter Regions, Genetic},
	issn = {1438-7948},
	doi = {10.1007/s10142-008-0094-7},
	author = {Krushkal, Julia and Leang, Ching and Barbe, Jose F and Qu, Yanhua and Yan, Bin and Puljic, Marko and Adkins, Ronald M and Lovley, Derek R}
}
@article {458,
	title = {Genome-wide analysis of the RpoN regulon in Geobacter sulfurreducens.},
	journal = {BMC Genomics},
	volume = {10},
	year = {2009},
	month = {2009},
	pages = {331},
	abstract = {BACKGROUND: The role of the RNA polymerase sigma factor RpoN in regulation of gene expression in Geobacter sulfurreducens was investigated to better understand transcriptional regulatory networks as part of an effort to develop regulatory modules for genome-scale in silico models, which can predict the physiological responses of Geobacter species during groundwater bioremediation or electricity production.

RESULTS: An rpoN deletion mutant could not be obtained under all conditions tested. In order to investigate the regulon of the G. sulfurreducens RpoN, an RpoN over-expression strain was made in which an extra copy of the rpoN gene was under the control of a taclac promoter. Combining both the microarray transcriptome analysis and the computational prediction revealed that the G. sulfurreducens RpoN controls genes involved in a wide range of cellular functions. Most importantly, RpoN controls the expression of the dcuB gene encoding the fumarate/succinate exchanger, which is essential for cell growth with fumarate as the terminal electron acceptor in G. sulfurreducens. RpoN also controls genes, which encode enzymes for both pathways of ammonia assimilation that is predicted to be essential under all growth conditions in G. sulfurreducens. Other genes that were identified as part of the RpoN regulon using either the computational prediction or the microarray transcriptome analysis included genes involved in flagella biosynthesis, pili biosynthesis and genes involved in central metabolism enzymes and cytochromes involved in extracellular electron transfer to Fe(III), which are known to be important for growth in subsurface environment or electricity production in microbial fuel cells. The consensus sequence for the predicted RpoN-regulated promoter elements is TTGGCACGGTTTTTGCT.

CONCLUSION: The G. sulfurreducens RpoN is an essential sigma factor and a global regulator involved in a complex transcriptional network controlling a variety of cellular processes.},
	keywords = {Bacterial Proteins, DNA, Bacterial, Gene Expression Profiling, Gene Expression Regulation, Bacterial, Genome-Wide Association Study, Geobacter, Multigene Family, Oligonucleotide Array Sequence Analysis, Promoter Regions, Genetic, Regulon, RNA Polymerase Sigma 54},
	issn = {1471-2164},
	doi = {10.1186/1471-2164-10-331},
	author = {Leang, Ching and Krushkal, Julia and Ueki, Toshiyuki and Puljic, Marko and Sun, Jun and Ju{\'a}rez, Katy and N{\'u}{\~n}ez, Cinthia and Reguera, Gemma and DiDonato, Raymond and Postier, Bradley and Adkins, Ronald M and Lovley, Derek R}
}
@article {537,
	title = {Regulation of two highly similar genes, omcB and omcC, in a 10 kb chromosomal duplication in Geobacter sulfurreducens.},
	journal = {Microbiology},
	volume = {151},
	year = {2005},
	month = {2005 Jun},
	pages = {1761-7},
	abstract = {The Fe(III)-reducing micro-organism Geobacter sulfurreducens requires an outer-membrane c-type cytochrome, OmcB, for Fe(III) reduction, but a related cytochrome, OmcC, which is 73 \% identical to OmcB, is not required. The omcB and omcC genes are part of a tandem chromosomal duplication consisting of two repeated clusters of four genes. The 2.7 kb sequences preceding omcB and omcC are identical with the exception of a single base pair change. Studies that combined genetic, Northern blotting and primer extension analyses demonstrated that both omcB and omcC are transcribed as monocistronic and polycistronic (orf1-orf2-omcB/omcC) transcripts. All of the promoters for the various transcripts were found to be located within the 2.7 kb identical region upstream of omcB and omcC. The sequences of the promoter regions for the two monocistronic transcripts are identical and equidistant from the omcB or omcC start codons. The promoters for the two polycistronic transcripts, in contrast, are distinct. One is specific for transcription of orf1-orf2-omcB and the other is associated with transcription of orf1-orf2-omcC. Studies with an RpoS-deficient mutant suggested that transcription from all four promoters is RpoS dependent under one or more growth conditions. Deletion of orfR, a gene immediately upstream of orf1-orf2-omcB that encodes a putative transcriptional regulator, significantly lowered the omcB transcription when Fe(III) was the electron acceptor and partially inhibited Fe(III) reduction. In contrast, levels of omcC transcripts were unaffected in the orfR mutant. These results indicate that omcB and omcC operons represent a rare instance in which duplicated operons, located in tandem on the chromosome, have different transcriptional regulation.},
	keywords = {Bacterial Outer Membrane Proteins, Bacterial Proteins, Blotting, Northern, DNA, Bacterial, Gene Deletion, Gene Expression Regulation, Bacterial, Geobacter, Molecular Sequence Data, Operon, Promoter Regions, Genetic, RNA, Bacterial, RNA, Messenger, Sequence Analysis, DNA, Sigma Factor, Transcription, Genetic},
	issn = {1350-0872},
	doi = {10.1099/mic.0.27870-0},
	author = {Leang, Ching and Lovley, Derek R}
}
