Difference between revisions of "Pelobacter carbinolicus"

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2. “Pelobacter carbinolicus DSM 2380 project at DOE Joint Genome Institute” Entrez Genome project http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=13337.  
 
2. “Pelobacter carbinolicus DSM 2380 project at DOE Joint Genome Institute” Entrez Genome project http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=13337.  
  
3.  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 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=93865.
+
3.  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
 +
http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=93865.
  
4. 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. http://genamics.com/cgi-bin/genamics/genomes/genomesearch.cgi?field=ID&query=1258.  
+
4. 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.
 +
http://genamics.com/cgi-bin/genamics/genomes/genomesearch.cgi?field=ID&query=1258.  
  
 
5. 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. ;
 
5. 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. ;

Revision as of 08:03, 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


File3.JPG

complete genome of Pelobacter carbinolicus

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 found when analyzing of Deep Sea water sludge. Mn-reducing bacteria found in sediments with Mn oxide concentrations greater than approximately 10 micromol cm suggests that bacteria specialized in Mn reduction are an important part of this kind of environment.

By studying anaerobic, sulfate-rich Cretaceous-era rock formations about 200 m below ground surface at Cerro Negro, New Mexico, it was found that there were bacterial communities all across the surface of the shale-sandstone. Delta-Proteobacteria were found at all depths, especially from the Geobacteraceae family such as Pelobacters. This is especially interesting because usually electron acceptors are not commonly found in these environments.

Pathology

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

Application to Biotechnology

Pelobacter carbinolicus is a microbe that can transfer electrons to extracellular electron acceptors, such as iron oxides. They are not only important in organic matter degradation but also in 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 indicates possibilities for other new cell−cell interactions, and may be used for bioengineering of conductive materials.


File2.jpg

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


The application of molecular biology to study bacteria in the environment has helped to provide important information on community structure and sulfur reducing bacteria were isolated in diverse habitats such as anaerobic biofilms.

Landfill sites previously have been underestimated as essential habitats for sulfur reducing bacteria such as Pelobacter carbinolicus. Landfills are able to serve as bioreactors for anarobic bacteria and mediate mineralization of organic matter. Because methanogenesis is the key terminal process of carbon mineralization when sulfate is absent, it is hard to study these environments. Sulfur reducing bacteria are anaerobic bacteria that use sulfate as a electron acceptor in the consumption of organic matter. They are very common in the environment and important for cycling of carbon and sulfur.

Current Research

One research study found that in the past, c-type cytochromes in Pelobacter species had not been detected even though close relatives in the Geobacteraceae family have many c-type cytochromes present. Careful study of the entire completed genome sequence of Pelobacter carbinolicus found 14 open reading frames that encode for c-type cytochromes. It was found that three c-type cytochrome genes were expressed during iron reduction, which suggests that these particular proteins may play a role in electron transfer to iron. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis gels of acetoin-fermenting Pelobacter carbinolicus protein cells showed three heme-staining bands. In addition, many of the c-type cytochromes that genetic studies have realized are required for optimal iron reduction in G. sulfurreducens were not present in the P. carbinolicus genome. These results from this study suggest more in depth studies of the functions of c-type cytochromes may possibly be beneficial for further development of the specific roles of these cytochromes.

Another recent study found that the organism Bacillus subtilis catabolized acetoin using the acu gene cluster enzymes that are completely different from the ones in the multicomponent acetoin dehydrogenase enzyme system which are normally encoded by aco gene clusters found in all the other bacteria able to utilize acetoin as the only carbon source for growth. Using a DNA probe for hybridization, genomic fragments from Bacillus subtilis were located, and some of them were expressed in E. coli. This study was made possible from using detailed knowledge about the catabolism of acetoin that had been obtained from the acetoin-utilizing bacteria Pelobacter carbinolicus. Research in Pelobacter carbinolicus will help us to further understand the mechanisms of other types of acetoin system bacterial microorganisms.

In another study, a set of three closely located genes, DVU2103, DVU2104, and DVU2108 of D. vulgaris, was found to be up-regulated after a transition from being a syntroph to becoming a sulfate reducer. Although the researchers did not know the exact function of this gene set, the results provide some explanations that suggest these genes may play roles related to the lifestyle change. In addition, this is supported by phylogenomic analyses which show that there were few homologies present in several groups of bacteria, most of which are only allowed to be syntrophic, such as organisms Pelobacter carbinolicus. Phylogenetic analysis showed that all three genes in the gene set are usually grouped with other organsims from the archaea genera, and they were branched off of the archaeal species in the phylogenetic trees. This suggests to scientists that these genes were probably horizontally transferred from archaeal methanogens. Also, the study found that there were no important differences in codon and amino acid usages between these genes and the rest of the genome. This helps us come to the conclusion that gene transfer probably happened early in the evolutionary history, so that enough time has passed for adaptation to the codon and amino acid usages. This study helps to rovide new and important insights about the origin and evolution of bacterial genes linked to the syntrophic and sulfate reducing capabilities.

In another study, researchers were able to use oligonucleotide probes based on the N-terminal sequences of the alpha and beta subunits acoA and expressed in Escherichia coli. The nucleotide sequences were determined and amino acid sequences deduced showed very important similarities to the amino acid sequences of Pelobacter carbinolicus acetoin dehydrogenase enzyme system. Important homologies to the enzyme components of other dehydrogenase complexes were also found,showing a close relationship between the two enzyme systems.

References

1. 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” http://genome.jgi-psf.org/finished_microbes/pelca/pelca.home.html,

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

3. 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 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=93865.

4. 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. http://genamics.com/cgi-bin/genamics/genomes/genomesearch.cgi?field=ID&query=1258.

5. 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." http://expasy.org/sprot/hamap/PELCD.html.

6. Karp02: Karp PD, Paley SM, Romero P (2002).“Pelobacter carbinolicus DSM 2380 Genome Page” September 27, 2006 http://biocyc.org/PCAR338963/organism-summary?object=PCAR338963.

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

8.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 http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=16343329&ordinalpos=7&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum


9.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 http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=15683401&ordinalpos=8&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum


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


Edited by Jennifer Chang, student of Rachel Larsen UCSD