Pelobacter carbinolicus

A 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 mesophillic bacteria that utilizes flagella for movement and its ecotype is aquatic. Since it is mesophillic, it means that this organism lives in moderate temperature, not too hot and not to cold, usually between 25 and 40 °C. This organism is both an 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,sewage sludge and can make up a large population of the anaerobic microbial community. Pelobacter carbinolicus can ferment ethanol with hydrogen using bacteria by using hydrogen transfer amongst its own species. The use of hydrogen reduces the hydrogen partial pressure and allows ethanol fermentation of Pelobacter carbinolicus to be energetically favorable. Pelobacter carbinolicus can also grow by using iron and sulfur as electron acceptors. Further studies of the organism show a promising future in the field of comparative genomics.

This organism is very similarly related to the sulfur-reducing species of Desulfuromonas and the iron-reducing species of Geobactes. However, even though Pelobacter species are linealy and phylogenetically related to Geobacters and Desulfuromonas species, Pelobacter carbinolicus is missing many of the usual physiological characteristics that are present in Geobacter and Desulfuromonas species. One of the differences is that Pelobacter species can not oxidize organic electron donors completely into carbon dioxide. Also, this species is also missing the abundant c-type cytochromes found in other Geobacteraceae species. Pelobacter species were originally found for being able to grow fermentatively using unusual substrates and also for being syntrophic organisms which means it uses methanogens to generate hydrogens for use. However, further research have found that like other members of the Geobacteraceae , these organisms can grow using sulfur or iron as the electron acceptors during the process of respiration. By studying the functional analysis of the genome of Pelobacter carbinolicus we will be able to further understand the evolution of the Geobacteraceae , which is themost common different metal-reducing microorganisms that have been found in many different sedimentary environments. In addition, it will help us understand the complicated mechanisms involved during the process of metal electron trasfer in Geobacteracae.

This organism grows by fermentating butanediol, acetoin, and ethylene glycol into ethanol and acetate. Pelobacter carbinolicus can also grow by oxidizing ethanol and other types of alcohols in the presence of methanogens that use hydrogens or acetogens using iron as an electron acceptor. New Gram-negative, specifically anaerobic, non-spore forming bacteria were found in naerobic enrichments with 2,3-butanediol as the substrate.

Research and sequencing of the genome of this species is important because the functional analysis of Pelobacter carbinolicus is expected to provide new and exicitng developments of the evolution of the Geobacteraceae. This will help us understand metal-reducing microorganisms in a diversity of sedimentary environments and help elucidate the mechanisms in metal electron processes in Geobacteraceae.

This is a schematic of a Pelobacter Carbinolicus bacterium

Genome structure

The genome of Pelobacter carbinolicus is circular and contains 3,662,252 nucleotides. The genome consists of 22.3% Adenine, 22.4% Thymine, 27.4% Cytosine, 27.6% Guanine and it base pair percentages are 44.7% AT and 55% GC content. There are 2,448 TIGR assigned genes in the genome and 2,578 TIGR genes assigned a role category and 3145 sequencing center assigned genes. It's entire genome consists of 3,353 protein genes and 63 RNA genes: 54 tRNA genes and 6 rRNA genes.

Pelobacter carbinolicus contains 2380 chromosomes.Analysis of genome sequence of Pelobacter carbinolicus showed 14 open reading frames that possibly encode for c-type cytochromes. Transcripts for almost all open reading frames were found in acetoin-fermenting and iron reducing cells. During iron reduction, three c-type cytochrome genes were expressed which suggests that these proteins may possible play a role in electron transfer to iron in Pelobacter carbinolicus. One of these specific proteins was found to be a periplasmic tri-heme cytochrome which has is involved in iron reduction in the orgnamism Geobacter sulfurreducens. In addition, genes for the biosynthesis of heme and for system II cytochrome c biogenesis were found and expressed in the genome of this species.

Cell structure and metabolism

Pelobacter carbinolicus is a Gram negative bacteria and has 2 cell walls. This organism seems to be able to conserve energy and aid in growth with iron respiration as well as growth with hydrogen or formate as the electron donor and uron as the electron acceptor. If it is adapted or changed to iron reduction, Pelobacter carbinolicus can also grow using ethanol or hydrogen. Pelobacter carbinolicus do not contain high concentrations of c-type cytochromes that previous studies have tried to prove. They are involved in electron transport to iron in other organisms that conserve energy to support growth from iron reduction.

Pelobacter species have been considered to have a fermentative metabolism. It is able to grow by fermentation of 2,3-butanediol with Fe(III), the iron being reduced. It was found that there was less buildup of ethanol and more production of acetate when iron is present. Pelobacter carbinolicus grows with ethanol as the only electron donor and iron as the only electron acceptor. Ethanol is then metabolized to acetate. Growth was also found when Fe(III)oxidizes propanol into propionate or butanol into butyrate when acetate was provided as a carbon source. Pelobacter carbinolicus seems to capable of conserving energy to provide optimal growth conditions by using Fe(III) respiration. It is also able to grow using hydrgen or formate as the electron donor and iron as the electron acceptor.

Gram Negative Pelobacter carbinolicus

Ecology

Pelobacter carbinolicus' ecotype is aquatic and it is commonly found in marine and freshwater debri, and sewage sludge. It was first isolated in marine mud. This organism can make up a large populatiion of the anaerobic microbial community in these kinds of aquatic environments. Pelobacter carbinolicus can ferment ethanol in the presence of bacteria that use hydrogen by using interspecies hydrogen transfer.

It was found that Pelobacter related species was also observed in the analysis of Deep Sea water sludge. Mn-reducing bacteria found in sediments with Mn oxide concentrations greater than approximately 10 micromol cm(-3) shows that bacteria specialized in Mn reduction, are and important part of this kind of environment.

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 Rachel Larsen