Open Access Research article

The genome of Pelobacter carbinolicus reveals surprising metabolic capabilities and physiological features

Muktak Aklujkar1*, Shelley A Haveman1, Raymond DiDonato1, Olga Chertkov2, Cliff S Han2, Miriam L Land3, Peter Brown1 and Derek R Lovley1

Author Affiliations

1 University of Massachusetts Amherst, Amherst, MA, 01003, USA

2 Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA

3 Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA

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BMC Genomics 2012, 13:690  doi:10.1186/1471-2164-13-690

Published: 10 December 2012

Additional files

Additional file 1:

Table S1. Locations of multicopy nucleotide sequences in the P.carbinolicus genome. For exact coordinates and sequence alignments, see Additional file 2: Figure S1.

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Additional file 2:

Figure S1. Alignments of multicopy nucleotide sequences of the P.carbinolicus genome. For the locus tags and functional annotations of adjacent genes, see Additional file 1: Table S1.

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Additional file 3:

Table S2. Gene sets of P.carbinolicus for the catabolism of acetoin/2,3-butanediol, glycerol, 1,3-propanediol, 1,2-ethanediol, ethanolamine and choline, for proton/sodium pumping, hydrogen/formate production and electron transport.

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Additional file 4:

Table S3. Thiamin and cobalamin biosynthesis genes of P.carbinolicus.

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Additional file 5:

Table S4. Cytochrome c proteins and biogenesis factors, TonB-dependent transport systems, tetrapyrrole methyltransferases, and outer surface features of P.carbinolicus: genes for biogenesis of geopilin pili, Msh pili, Pih pili, type II secretion systems, Flp pili, sigma-fimbriae, flagella, autotransporters, and the type VI secretion system.

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Additional file 6:

Figure S2. Alignments of ferredoxin and flavodoxin-like protein sequences of P.carbinolicus and its relatives. Ferredoxins of D. africanus, for which rates of electron transfer are known, and flavodoxins of E. coli and D. africanus are shown for comparison. Only double-4Fe4S-cluster ferredoxins have been detected in the partial genome sequence of D. acetoxidans, the closest relative of P. carbinolicus, which is able to operate a catabolic TCA cycle, but one of them has serine and aspartate in lieu of cysteine as two of the predicted ligands to iron atoms, and the other has two additional cysteine residues, which could affect their electron transfer properties. The existence of single-4Fe4S-cluster ferredoxins in D. acetoxidans cannot be ruled out.

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