@article {3149, title = {The genome of Pelobacter carbinolicus reveals surprising metabolic capabilities and physiological features.}, journal = {BMC Genomics}, volume = {13}, year = {2012}, month = {2012 Dec 10}, pages = {690}, abstract = {

BACKGROUND: The bacterium Pelobacter carbinolicus is able to grow by fermentation, syntrophic hydrogen/formate transfer, or electron transfer to sulfur from short-chain alcohols, hydrogen or formate; it does not oxidize acetate and is not known to ferment any sugars or grow autotrophically. The genome of P. carbinolicus was sequenced in order to understand its metabolic capabilities and physiological features in comparison with its relatives, acetate-oxidizing Geobacter species.

RESULTS: Pathways were predicted for catabolism of known substrates: 2,3-butanediol, acetoin, glycerol, 1,2-ethanediol, ethanolamine, choline and ethanol. Multiple isozymes of 2,3-butanediol dehydrogenase, ATP synthase and [FeFe]-hydrogenase were differentiated and assigned roles according to their structural properties and genomic contexts. The absence of asparagine synthetase and the presence of a mutant tRNA for asparagine encoded among RNA-active enzymes suggest that P. carbinolicus may make asparaginyl-tRNA in a novel way. Catabolic glutamate dehydrogenases were discovered, implying that the tricarboxylic acid (TCA) cycle can function catabolically. A phosphotransferase system for uptake of sugars was discovered, along with enzymes that function in 2,3-butanediol production. Pyruvate:ferredoxin/flavodoxin oxidoreductase was identified as a potential bottleneck in both the supply of oxaloacetate for oxidation of acetate by the TCA cycle and the connection of glycolysis to production of ethanol. The P. carbinolicus genome was found to encode autotransporters and various appendages, including three proteins with similarity to the geopilin of electroconductive nanowires.

CONCLUSIONS: Several surprising metabolic capabilities and physiological features were predicted from the genome of P. carbinolicus, suggesting that it is more versatile than anticipated.

}, keywords = {Base Pairing, Base Sequence, Butylene Glycols, Choline, Deltaproteobacteria, Ethanolamine, Ethylene Glycol, Genome, Bacterial, Glycerol, Metabolic Networks and Pathways, Molecular Sequence Annotation, Molecular Sequence Data, Mutation, Oxidation-Reduction, Oxidoreductases, Propylene Glycols, RNA, Transfer, Asn, Sequence Analysis, DNA}, issn = {1471-2164}, doi = {10.1186/1471-2164-13-690}, author = {Aklujkar, Muktak and Haveman, Shelley A and DiDonato, Raymond and Chertkov, Olga and Han, Cliff S and Land, Miriam L and Brown, Peter and Lovley, Derek R} } @article {455, title = {GSEL version 2, an online genome-wide query system of operon organization and regulatory sequence elements of Geobacter sulfurreducens.}, journal = {OMICS}, volume = {13}, year = {2009}, month = {2009 Oct}, pages = {439-49}, abstract = {Geobacter sulfurreducens is a model organism within the delta-Proteobacterial family Geobacteraceae, members of which can participate in environmental bioremediation of metal and organic waste contaminants and in production of bioenergy. In this report, we describe a new, significantly expanded and updated, version 2 of the GSEL (Geobacter Sequence Elements) database ( http://geobacter.org/research/gsel2/ and http://geobacter.org/refs/gsel2/ ) and its accompanying online query system, which compiles information on operon organization and regulatory sequence elements in the genome of G. sulfurreducens. It incorporates a new online graphical browser, provides novel search capabilities, and includes updated operon predictions along with new information on predicted and experimentally validated genome regulatory sites. The GSEL database and online search system provides a unique and comprehensive tool cataloging information about gene regulation in G. sulfurreducens, aiding in investigation of mechanisms that regulate its ability to generate electric power, bioremediate environmental waste, and adapt to environmental changes.}, keywords = {Base Sequence, Databases, Genetic, Gene Expression Regulation, Bacterial, Genome, Bacterial, Geobacter, Humans, Internet, Online Systems, Operon, Regulatory Sequences, Nucleic Acid, Software, User-Computer Interface}, issn = {1557-8100}, doi = {10.1089/omi.2009.0081}, author = {Qu, Yanhua and Brown, Peter and Barbe, Jose F and Puljic, Marko and Merino, Enrique and Adkins, Ronald M and Lovley, Derek R and Krushkal, Julia} }