Difference between revisions of "Pelobacter carbinolicus"

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<i>Pelobacter carbinolicus</i> contains 2380 chromosomes and has 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, c-type cytochrome genes are expressed which means that these proteins may possible play a role in electron transfer to iron in this particular organism. One of these specific proteins was found to be a periplasmic tri-heme cytochrome which is involved in iron reduction. In addition, genes for the biosynthesis of heme and for system II cytochrome c biogenesis were found and expressed in the genome of <i>Pelobacter carbinolicus</i>
 
<i>Pelobacter carbinolicus</i> contains 2380 chromosomes and has 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, c-type cytochrome genes are expressed which means that these proteins may possible play a role in electron transfer to iron in this particular organism. One of these specific proteins was found to be a periplasmic tri-heme cytochrome which is involved in iron reduction. In addition, genes for the biosynthesis of heme and for system II cytochrome c biogenesis were found and expressed in the genome of <i>Pelobacter carbinolicus</i>
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==Cell structure and metabolism==
 
==Cell structure and metabolism==

Revision as of 06:28, 5 June 2007

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 uses 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 an iron and sulfur-reducing anaerobic organism which means it lives in the absence of air or free oxygen. Pelobacter carbinolicus is a Gram-negative delta-proteobacterium from the Geobacteraceae family. It is very commonly found in marine and freshwater debri, sewage sludge and can make up an extensive population of the anaerobic microbial community. Pelobacter carbinolicus can ferment ethanol in the presence of bacteria that utilize hydrogen by a hydrogen transfer reaction between its own species. The use of hydrogen decreases 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.

This organism is 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 other Geobacter and Desulfuromonas species have. 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. C-type cytochromes are proteins that are needed for life of almost all organisms. They usually contain heme that is covalently bonded through thioether bonds to two cysteines in a protein. Pelobacter species were originally found for being able to grow fermentatively using unusual substrates and also for being syntrophic organisms which means that it uses methanogens to generate hydrogens for use. However, further research has found that these organisms can grow using sulfur or iron as the electron acceptors during the process of respiration. By studying the genome of Pelobacter carbinolicus, we will be able to further understand the evolution of the Geobacteraceae , which is the most common metal-reducing microorganisms that has been found in a variety of sedimentary environments. Also, research 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 that use hydrogens or acetogens using iron as an electron acceptor. New Gram-negative, anaerobic, non-spore forming bacteria were found in anaerobic 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 better and clear up the mechanisms in metal electron processes in Geobacteraceae. Further studies of the organism show a promising future in the field of comparative genomics.


File.jpg

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 its base pair percentages are 44.7% AT and 55% GC content. There are 2,448 assigned genes in the genome and 2,578 genes assigned to 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. THere are 3,145 protein encoding genes. The entire size of the DNA molecule is 3662252 base pairs.

Pelobacter carbinolicus contains 2380 chromosomes and has 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, c-type cytochrome genes are expressed which means that these proteins may possible play a role in electron transfer to iron in this particular organism. One of these specific proteins was found to be a periplasmic tri-heme cytochrome which is involved in iron reduction. In addition, genes for the biosynthesis of heme and for system II cytochrome c biogenesis were found and expressed in the genome of Pelobacter carbinolicus


File:File3.jpg

Cell structure and metabolism

Pelobacter carbinolicus is a Gram negative bacteria which means it has 2 cell walls. There is no interaction with other similar organisms. This organism seems to be able to conserve energy and aid in iron respiration as well as growth using hydrogen or formate as the electron donor and iron 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.


File1.jpg

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.

A multilevel sampler (MLS) was emplaced in a borehole straddling anaerobic, sulfate-rich Cretaceous-era shale and sandstone rock formations approximately 200 m below ground surface at Cerro Negro, New Mexico. Sterile quartzite sand contained in chambers in the sampler allowed in situ colonization and recovery of nucleic acids for molecular analyses. Denaturing gradient gel electrophoresis and 16S rRNA gene cloning results indicated a homogeneously distributed bacterial community across the shale-sandstone interface. delta-Proteobacteria sequences were common at all depths, and were dominated by members of the Geobacteraceae family (Pelobacter, Desulphuromonas and Geobacter). Other members of this group are capable of dissimilatory Fe(III) and/or S degrees reduction, but not sulfate reduction. RNA hybridization data also suggested that Fe(III)-/S degrees -reducing bacteria were predominant. These findings are striking considering the lack of significant concentrations of these electron acceptors in this environment. The next most abundant bacterial group indicated was the sulfate reducers, including Desulfobacterium, Desulfocapsa and Desulfobulbus. Sequences related to fermenters, denitrifiers and acetogens were also recovered. The presence of a phylogenetically and functionally diverse microbial community in this deep subsurface environment likely reflects the complex nature of the primary energy and carbon sources, kerogen associated with the shale.

Pathology

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

Application to Biotechnology

Pelobacter carbinolicus is a microbes that can transfer electrons to extracellular electron acceptors, such as iron iron oxides. They are not only important in organic matter degradation but also nutrient cycling in sediments. Conducting-probe atomic force microscopy has shown that pili are highly conductive but Pelobacter carbinolicus don't have pili. Pelobacter carbinolicus electron conducting abilities may be able to serve important roles in biological nanowires by transferring electrons from the cell surface to the surface of iron oxides. Electron transfer ndicates possibilities for other new cell−cell interactions, and may be used for bioengineering of conductive materials.


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Experimental research results: voltage applied to cell surface of electron conducting microbes


The application of molecular biological methods to investigate the occurrence and distribution of bacteria in the environment has the advantage of providing direct information on community structure. Not only do culture-based methods recover merely a fraction of the natural population, but for sulfate-reducing bacteria (SRB), the isolation of axenic cultures from environmental samples is not straightforward. 16S rRNA-targeted oligonucleotide probes have been designed to detect groups of SRB (Devereux et al., 1992Down ) and used successfully to demonstrate the presence of SRB in such diverse habitats as anaerobic biofilms

Landfill sites are essentially bioreactors in which anaerobic bacterial communities mediate the mineralization and stabilization of organic matter (Barlaz, 1997Down ). They have long been overlooked as important habitats for SRB due to the fact that methanogenesis predominates as the key terminal process of carbon mineralization in the absence of significant concentrations of sulfate. Our knowledge of the occurrence and distribution of SRB in landfill is therefore extremely limited. The SRB are a diverse group of anaerobic bacteria that have the ability to use sulfate as a terminal electron acceptor in the consumption of organic matter, with the concomitant production of H2S. They are ubiquitous in the environment and have pivotal roles in the biogeochemical cycling of carbon and sulfur. Sulfate reduction could be responsible for up to 50% of organic matter degradation in high-sulfate environments such as estuarine and marine sediments (Jorgensen, 1982Down ); however, active sulfate reduction has also been reported in low-sulfate environments such as soils and freshwater sediments

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

8.http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=16343329&ordinalpos=7&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Kovacik WP, Takai K, Mormile MR, McKinley JP, Brockman FJ, Fredrickson JK, Holben WE. "Molecular analysis of deep subsurface Cretaceous rock indicates abundant Fe(III)- and S(zero)-reducing bacteria in a sulfate-rich environment." Jan 8, 2006

9.http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=15683401&ordinalpos=8&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Mussmann M, Ishii K, Rabus R, Amann R. "Diversity and vertical distribution of cultured and uncultured Deltaproteobacteria in an intertidal mud flat of the Wadden Sea." march 7, 2005

10.http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=10877783&ordinalpos=14&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Thamdrup B, Rosselló-Mora R, Amann R. "Microbial manganese and sulfate reduction in Black Sea shelf sediments." July 2000


Edited by Jennifer Chang, student of Rachel Larsen UCSD