Pelobacter carbinolicus: Difference between revisions

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Genus: Pelobacter  
Genus: Pelobacter  


Species: Carbinolicus
Species: carbinolicus


==Description and significance==
==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.
<i>Pelobacter carbinolicus</i> 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 too 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. <i>Pelobacter carbinolicus</i> is a Gram-negative delta-proteobacterium from the Geobacteraceae family. It is very commonly found in marine and freshwater debris, sewage sludge and can make up an extensive population of the anaerobic microbial community. <i>Pelobacter carbinolicus</i> 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. <i>Pelobacter carbinolicus</i> 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 <i>Pelobacter</i> species are linealy and phylogenetically related to Geobacters and Desulfuromonas species, <i>Pelobacter carbinolicus</i> 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. <i>Pelobacter</i> 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 hydrogen 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 <i>Pelobacter carbinolicus</i>, we will be able to further understand the evolution of the Geobacteraceae , which is the most common metal-reducing microorganism 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 transfer in Geobacteracae.


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 fermenting butanediol, acetoin, and ethylene glycol into ethanol and acetate. <i>Pelobacter carbinolicus</i> 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.


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 <i>Pelobacter carbinolicus</i> is expected to provide new and excitng 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.


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.


==Genome structure==


[[Image:File.jpg]]


This is a schematic of a Pelobacter Carbinolicus bacterium
The genome of <i>Pelobacter carbinolicus</i> 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.
Its entire genome consists of 3,353 protein genes and 63 RNA genes: 54 tRNA genes and 6 rRNA genes.


==Genome structure==
<i>Pelobacter carbinolicus</i> 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>




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.
[[Image:File3.JPG]]
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.
complete genome of <i>Pelobacter carbinolicus</i>


==Cell structure and metabolism==
==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.
<i>Pelobacter carbinolicus</i> 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, <i>Pelobacter carbinolicus</i> can also grow using ethanol or hydrogen. <i>Pelobacter carbinolicus</i> 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.
 


[[Image:File1.jpg]]
<i>Pelobacter</i> 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. <i>Pelobacter carbinolicus</i> 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. <i>Pelobacter carbinolicus</i> seems to capable of conserving energy to provide optimal growth conditions by using Fe(III) respiration. It is also able to grow using hydrogen or formate as the electron donor and iron as the electron acceptor.


Gram Negative Pelobacter carbinolicus


==Ecology==
==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.
<i>Pelobacter carbinolicus</i>' ecotype is aquatic and it is commonly found in marine and freshwater debris, and sewage sludge. It was first isolated in marine mud. This organism can make up a large population of the anaerobic microbial community in these kinds of aquatic environments. <i>Pelobacter carbinolicus</i> can ferment ethanol in the presence of bacteria that use hydrogen by using interspecies hydrogen transfer.
 
<i>Pelobacter</i> related species were 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.
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.
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 <i>Pelobacters</i>. This is especially interesting because usually electron acceptors are not commonly found in these environments.
 
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==
==Pathology==
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==Application to Biotechnology==
==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.
<i>Pelobacter carbinolicus</i> 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 <i>Pelobacter carbinolicus</i> don't have pili. <i>Pelobacter carbinolicus</i> 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.
 




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.


[[Image:File2.jpg]]
Landfill sites previously have been underestimated as essential habitats for sulfur reducing bacteria such as <i>Pelobacter carbinolicus</i>. Landfills are able to serve as bioreactors for anaerobic 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==


Experimental research results: voltage applied to cell surface of electron conducting microbes
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 <i>Pelobacter carbinolicus</i> 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 <i>Pelobacter carbinolicus</i> 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. The 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 <i>Bacillus subtilis</i> catabolized acetoin using the acu gene cluster enzymes that are completely different from the ones in the multicomponent acetoin dehydrogenase enzyme system normally encoded by aco gene clusters found in all the other bacteria able to use acetoin as the only carbon source for growth. Using a DNA probe for  hybridization, genomic fragments from <i>Bacillus subtilis</i> 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 <i>Pelobacter carbinolicus</i>. Research in <i>Pelobacter carbinolicus</i> will help us to further understand the mechanisms of other types of acetoin system bacterial microorganisms.


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
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 <i>Pelobacter carbinolicus</i>. Phylogenetic analysis showed that all three genes in the gene set are usually grouped with other organisms 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 provides new and important insights about the origin and evolution of bacterial genes linked to the syntrophic and sulfate reducing capabilities.


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
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 <i>Pelobacter carbinolicus</i> 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.


==Current Research==
==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,


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. “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. 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.  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. 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. 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. 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.
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.  


==References==
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.
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
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.  


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
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


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.”
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


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. ;
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
"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 Jennifer Chang, student of [mailto:ralarsen@ucsd.edu Rachel Larsen] UCSD


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

Latest revision as of 15:27, 7 July 2011

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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 too 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 debris, 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 hydrogen 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 microorganism 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 transfer in Geobacteracae.


This organism grows by fermenting 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 excitng 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.


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. Its entire genome consists of 3,353 protein genes and 63 RNA genes: 54 tRNA genes and 6 rRNA genes.

Pelobacter carbinolicus 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 hydrogen or formate as the electron donor and iron as the electron acceptor.


Ecology

Pelobacter carbinolicus' ecotype is aquatic and it is commonly found in marine and freshwater debris, and sewage sludge. It was first isolated in marine mud. This organism can make up a large population 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. Pelobacter related species were 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.


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 anaerobic 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. The 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 normally encoded by aco gene clusters found in all the other bacteria able to use 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 organisms 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 provides 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

KMG

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