Pelobacter carbinolicus

aA Microbial Biorealm page on the genus Pelobacter carbinolicus

Classification

Higher order taxa

Bacteria, Proteobacteria, Deltaproteobacteria, Desulfuromonadales, Pelobacteraceae, Pelobacter, Carbinolicus, DSM 2380

Species

NCBI: Taxonomy

Genus: Pelobacter

Species: Carbinolicus

Description and significance

Pelobacter carbinolicus is a rod shaped bacteria that moves by flagella and is mesophillic and its ecotype is aquatic. It is a Iron- and sulfur-reducing anaerobic organism and a gram-negative delta-proteobacterium from the Geobacteraceae family. It is commonly isolated from marine and freshwater debri, and sewage sludge. This organism can make up a large portion of the anaerobic microbial community in these environments. Pelobacter carbinolicus can ferment ethanol in the presence of hydrogen-utilizing bacteria using interspecies hydrogen transfer. Using hydrogen reduces the hydrogen partial pressure allowing ethanol fermentation of Pelobacter carbinolicus to be energetically favorable. Pelobacter carbinolicus is also able to grow using iron and sulfur as terminal electron acceptors. This organism is closely related to the sulfur-reducing Desulfuromonas spp. and iron-reducing Geobacter spp.. Further studies of the organism will be beneficial in comparative genomics.

Although Pelobacter species are phylogenetically related to Geobacter and Desulfuromonas species in this family, the Pelobacter lacks many common physiological characteristics of the Geobacter and Desulfuromonas species. For example, Pelobacter species are unable to completely oxidize organic electron donors to carbon dioxide. In addition, the abundant c-type cytochromes found in other Geobacteraceae are lacking in this species . Pelobacter species were initially recognized for their ability to grow fermentatively with novel substrates and as syntrophic organisms, generating hydrogen for consumption by methanogens. However, further studies revealed that, like other members of the Geobacteraceae , these organisms can grow through respiration with S° or Fe(III) serving as the electron acceptor. Functional analysis of the genome of P. carbinolicus offers important insights into the evolution of the Geobacteraceae , the predominant dissimilatory metal-reducing microorganisms in a diversity of sedimentary environments, as well as aid in elucidating the mechanisms for electron transfer to metals in Geobacteraceae and their syntrophic interactions.

This organism grows by fermentation of butanediol, acetoin, and ethylene glycol to ethanol and acetate. It was isolated from marine mud. P. carbinolicus can also grow by oxidizing ethanol and other alcohols in co-culture with H2-oxidizing methanogens or acetogens with Fe(III) as an electron acceptor. From anaerobic enrichments with 2,3-butanediol as the only substrate pure cultures of new Gram-negative, strictly anaerobic, non-spore forming bacteria were isolated.

It is important to sequence the genome because the functional analysis of the genome of P.carbinolicus is expected to provide important insights into the evolution of the Geobacteraceae, the metal-reducing microorganisms in a diversity of sedimentary environments, as well as aid in elucidating the mechanisms for electron transfer to metals in Geobacteraceae and their syntrophic interactions.

Genome structure

The genome is circular and is 3662252 nucleotides. It is 22.3% A, 22.4% T, 27.4%C, 27.6% G and 44.7% AT and 55% GC content. There are 2448 TIGR assigned genes, and 2578 TIGR genes assigned a role category and 3145 sequencing center assigned genes. There are 3353 protein genes and 63 RNA genes.

Cell structure and metabolism

P.carbinolicus is a gram negative bacteria and has 2 cell walls. P. carbinolicus appears to be capable of conserving energy to support growth from Fe(III) respiration as it also grew with Hydrogen or formate as the electron donor and Fe(III) as the electron acceptor. If it is adapted to Fe(III) reduction, P. carbinolicus can also grow on ethanol or H2 using S0 as the electron acceptor. P. carbinolicus did not contain significant concentrations of c-type cytochromes that other studies have suggested are involved in electron transport to Fe(III) in other organisms that conserve energy to support growth from Fe(III) reduction.

Pathology

This organism is non-pathogenic and does not cause disease.

Application to Biotechnology

Analysis of the recently completed genome sequence of Pelobacter carbinolicus showed 14 open reading frames that may encode for c-type cytochromes. Transcripts for all but one of the open reading frames were detected in acetoin-fermenting and/or Fe(III)-reducing cells. It was found that three putative c-type cytochrome genes were expressed during Fe(III) reduction, which suggests that the encoded proteins may play a role in electron transfer to Fe(III).

Current Research

1. Previous studies have not detected c-type cytochromes in Pelobacter species even though its other close relatives in the Geobacteraceae family, such as Geobacter and Desulfuromonas species, have many c-type cytochromes. Analysis of the recently completed genome sequence of Pelobacter carbinolicus showed 14 open reading frames that may encode for c-type cytochromes. Transcripts for all but one of the open reading frames were detected in acetoin-fermenting and/or Fe(III)-reducing cells. It was found that three putative c-type cytochrome genes were expressed during Fe(III) reduction, which suggests that the encoded proteins may play a role in electron transfer to Fe(III). One of these proteins was a periplasmic triheme cytochrome which was very similar to PpcA, which has a role in Fe(III) reduction in Geobacter sulfurreducens. Genes for heme biosynthesis and system II cytochrome c biogenesis were also identified in the genome and expressed. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis gels of protein extracted from acetoin-fermenting P. carbinolicus cells showed three heme-staining bands. These results were confirmed with mass spectrometry to be among the 14 predicted c-type cytochromes. The number of cytochrome genes, the predicted amount of heme c per protein, and the ratio of heme-stained protein to total protein were much smaller in Pelobacter. carbinolicus than in G. sulfurreducens. Furthermore, many of the c-type cytochromes that genetic studies have indicated are required for optimal Fe(III) reduction in G. sulfurreducens were not present in the P. carbinolicus genome. These results suggest that further studies of the functions of c-type cytochromes in the Geobacteraceae is needed and will be beneficial for further development of the specific roles of these cytochrome genes.

2. A recent study indicated that Bacillus subtilis catabolizes acetoin by enzymes encoded by the acu gene cluster that are completely different from the ones in the multicomponent acetoin dehydrogenase enzyme system which are encoded by aco gene clusters found before in all other bacteria capable of utilizing acetoin as the sole carbon source for growth. By hybridization with a DNA probe covering acoA and acoB of the AoDH ES from Clostridium magnum, genomic fragments from B. subtilis harboring acoA, acoB, acoC, acoL, and acoR homologous genes were identified, and some of them were functionally expressed in E. coli. Detailed knowledge about the catabolism of acetoin was obtained from studies on a diversity of acetoin-utilizing bacteria: Pelobacter carbinolicus

3. In this study, a set of three closely located genes, DVU2103, DVU2104, and DVU2108 of D. vulgaris, was found to be up-regulated 2- to 4-fold following the lifestyle shift from syntroph to sulfate reducer. None of the genes in this gene set were differentially regulated when comparing gene expression from various pure culture experiments. Although exact function of this gene set is unknown, the results suggest that it may play roles related to the lifestyle change of D. vulgaris from syntroph to sulfate reducer. In addition, this is supported by phylogenomic analyses showing that there were few homologies present in several groups of bacteria, most of which are restricted to a syntrophic lifestyle, such as Pelobacter carbinolicus. Phylogenetic analysis showed that all three genes in the gene set are usually clustered with their homologies from archaea genera, and they were branched off of the archaeal species in the phylogenetic trees. This suggests to scientists that they were horizontally transferred from archaeal methanogens. Also, no significant difference in codon and amino acid usages was detected between these genes and the rest of the D. vulgaris genome which lends support to the fact that the gene transfer probably occurred early in the evolutionary history so that enough time has passed for adaptation to the codon and amino acid usages of D. vulgaris. This study provides new insights into the origin and evolution of bacterial genes linked to the lifestyle change of D. vulgaris from a syntrophic to a sulfate-reducing lifestyle.

4. By use of oligonucleotide probes based on the N-terminal sequences of the alpha and beta subunits of E1 which were purified recently and of E2-E3, structural genes acoA (encoding E1 alpha), acoB (encoding E1 beta), acoC (encoding E2), and acoL (encoding E3) were identified on a single ClaI restriction fragment and expressed in Escherichia coli. The nucleotide sequences of acoA (978 bp), acoB (999 bp), acoC (1,332 bp), and acoL (1,734 bp), as well as those of acoX (996 bp) and acoR (1,956 bp), were determined. The amino acid sequences deduced from acoA, acoB, acoC, and acoL for E1 alpha (M(r), 35,532), E1 beta (M(r), 35,541), E2 (M(r), 48,149), and E3 (M(r), 61,255) exhibited huge similarities to the amino acid sequences of the corresponding components of the Pelobacter carbinolicus acetoin dehydrogenase enzyme system and the Alcaligenes eutrophus acetoin-cleaving system, respectively. Significant homologies to the enzyme components of various 2-oxo acid dehydrogenase complexes were also found, indicating a close relationship between the two enzyme systems.

References

1. http://genome.jgi-psf.org/finished_microbes/pelca/pelca.home.html, Schink, B. Lovley, DR, Phillips, EJP, Lonergan, DJ, Widman, PK, Lonergan DJ, Jenter HL, Coates JD, Phillips EJP, Schmidt TM, Lovley DR, “The Genus Pelobacter”

2. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=13337. “Pelobacter carbinolicus DSM 2380 project at DOE Joint Genome Institute” Entrez Genome project

3. http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=93865. Min Huang, Fred Bernd Oppermann-Sanio, and Alexander Steinbüchel “Biochemical and Molecular Characterization of the Bacillus subtilis Acetoin Catabolic Pathway” Journal of Bacteriology, v.181(12); Jun 1999

4. http://genamics.com/cgi-bin/genamics/genomes/genomesearch.cgi?field=ID&query=1258. Scholten JC, Culley DE, Brockman FJ, Wu G, Zhang W. “Evolution of the syntrophic interaction between Desulfovibrio vulgaris and Methanosarcina barkeri: Involvement of an ancient horizontal gene transfer.”

5. http://expasy.org/sprot/hamap/PELCD.html. Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C., Glavina T., Hammon N., Israni S., Pitluck S., Chertkov O., Schmutz J., Larimer F., Land M., Kyrpides N., Ivanova N., Richardson P. ; "Complete sequence of Pelobacter carbinolicus DSM 2380.";

6. http://biocyc.org/PCAR338963/organism-summary?object=PCAR338963. Karp02: Karp PD, Paley SM, Romero P (2002). "The Pathway Tools Software." Bioinformatics 18:S225-32. PMID: 12169551 http://cmr.tigr.org/tigr-scripts/CMR/GenomePage.cgi?org=ntpc01. “Pelobacter carbinolicus DSM 2380 Genome Page” September 27, 2006

7.http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=8206840&query_hl=1&itool=pubmed_docsum. Kruger N, Oppermann FB, Lorenzl H, Steinbuchel A. “Biochemical and molecular characterization of the Clostridium magnum acetoin dehydrogenase enzyme system.” 1994 Jun

Edited by student of [mailto:ralarsen@ucsd.edu Rachel