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Genome sequence of Desulfitobacterium hafniense DCB-2, a Gram-positive anaerobe capable of dehalogenation and metal reduction.

Kim SH, Harzman C, Davis JK, Hutcheson R, Broderick JB, Marsh TL, Tiedje JM - BMC Microbiol. (2012)

Bottom Line: In addition, it contained genes for 53 molybdopterin-binding oxidoreductases, 19 flavoprotein paralogs of the fumarate reductase, and many other FAD/FMN-binding oxidoreductases, proving the cell's versatility in both adaptive and reductive capacities.Together with the ability to form spores, the presence of the CO2-fixing Wood-Ljungdahl pathway and the genes associated with oxygen tolerance add flexibility to the cell's options for survival under stress.D. hafniense DCB-2's genome contains genes consistent with its abilities for dehalogenation, metal reduction, N2 and CO2 fixation, anaerobic respiration, oxygen tolerance, spore formation, and biofilm formation which make this organism a potential candidate for bioremediation at contaminated sites.

View Article: PubMed Central - HTML - PubMed

Affiliation: Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA. kimsang8@msu.edu

ABSTRACT

Background: The genome of the Gram-positive, metal-reducing, dehalorespiring Desulfitobacterium hafniense DCB-2 was sequenced in order to gain insights into its metabolic capacities, adaptive physiology, and regulatory machineries, and to compare with that of Desulfitobacterium hafniense Y51, the phylogenetically closest strain among the species with a sequenced genome.

Results: The genome of Desulfitobacterium hafniense DCB-2 is composed of a 5,279,134-bp circular chromosome with 5,042 predicted genes. Genome content and parallel physiological studies support the cell's ability to fix N2 and CO2, form spores and biofilms, reduce metals, and use a variety of electron acceptors in respiration, including halogenated organic compounds. The genome contained seven reductive dehalogenase genes and four nitrogenase gene homologs but lacked the Nar respiratory nitrate reductase system. The D. hafniense DCB-2 genome contained genes for 43 RNA polymerase sigma factors including 27 sigma-24 subunits, 59 two-component signal transduction systems, and about 730 transporter proteins. In addition, it contained genes for 53 molybdopterin-binding oxidoreductases, 19 flavoprotein paralogs of the fumarate reductase, and many other FAD/FMN-binding oxidoreductases, proving the cell's versatility in both adaptive and reductive capacities. Together with the ability to form spores, the presence of the CO2-fixing Wood-Ljungdahl pathway and the genes associated with oxygen tolerance add flexibility to the cell's options for survival under stress.

Conclusions: D. hafniense DCB-2's genome contains genes consistent with its abilities for dehalogenation, metal reduction, N2 and CO2 fixation, anaerobic respiration, oxygen tolerance, spore formation, and biofilm formation which make this organism a potential candidate for bioremediation at contaminated sites.

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Putative diagram of sporulation and germination events in D. hafniense DCB-2. The proposed genes are based on known developmental and genetic processes of sporulation and germination in Bacillus and Clostridium species. A brief description for each developmental stage and the genes encoding stage-specific enzymes or structural proteins are depicted. Compartment-specific sigma factors are also indicated. Gene homologs in D. hafniense DCB-2 were identified by using BLASTP with cutoff values of 1e-2 (E-value) and 30% identity in amino acid sequence.
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Figure 8: Putative diagram of sporulation and germination events in D. hafniense DCB-2. The proposed genes are based on known developmental and genetic processes of sporulation and germination in Bacillus and Clostridium species. A brief description for each developmental stage and the genes encoding stage-specific enzymes or structural proteins are depicted. Compartment-specific sigma factors are also indicated. Gene homologs in D. hafniense DCB-2 were identified by using BLASTP with cutoff values of 1e-2 (E-value) and 30% identity in amino acid sequence.

Mentions: Of the 12 Desulfitobacterium strains that have been examined, seven strains including D. hafniense DCB-2 were observed to sporulate [1]. Sporulation of Clostridium and Bacillus involves a cascade gene expression triggered by stage- and compartment-specific sigma factors [66,67]. The genes for the key σ factors (σH, σF, σE, σG, and σK) and the master regulator SpoOA were identified in the genome of DCB-2, and homologs for most of the sporulation genes were identified. Although less conserved, the earliest sporulation genes of sensory histidine kinases could not be positively assigned among 59 histidine kinase genes in the genome (Figure 8). A gene homolog for SpoIIGA, a pro-σE processing protease, was not identified in either D. hafniense DCB-2 or Y51 strains, nor in four other spore-formers of Peptococcaceae listed in IMG. However, a homolog for spoIIR was identified in all six strains, the product of which could interact with SpoIIGA for the processing of pro-σE into active σE, a sigma factor responsible for the expression of ~250 genes in the mother cell of Bacillus subtilis [68]. Both genes are also present in Clostridium spore-formers. Notable Bacillus sporulation genes that are missing in D. hafniense DCB-2 as well as in Clostridium are the genes encoding SpoIVFB, a pro-σK processing enzyme, SpoIVFA, an inhibitor of SpoIVFB, and NucB, a sporulation-specific extracellular nuclease (Figure 8). This suggests that although sporulation in Bacillus and D. hafniense DCB-2 have much in common, there are differences in the regulatory mechanism or in the enzyme system for the initiation of sporulation stages.


Genome sequence of Desulfitobacterium hafniense DCB-2, a Gram-positive anaerobe capable of dehalogenation and metal reduction.

Kim SH, Harzman C, Davis JK, Hutcheson R, Broderick JB, Marsh TL, Tiedje JM - BMC Microbiol. (2012)

Putative diagram of sporulation and germination events in D. hafniense DCB-2. The proposed genes are based on known developmental and genetic processes of sporulation and germination in Bacillus and Clostridium species. A brief description for each developmental stage and the genes encoding stage-specific enzymes or structural proteins are depicted. Compartment-specific sigma factors are also indicated. Gene homologs in D. hafniense DCB-2 were identified by using BLASTP with cutoff values of 1e-2 (E-value) and 30% identity in amino acid sequence.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3306737&req=5

Figure 8: Putative diagram of sporulation and germination events in D. hafniense DCB-2. The proposed genes are based on known developmental and genetic processes of sporulation and germination in Bacillus and Clostridium species. A brief description for each developmental stage and the genes encoding stage-specific enzymes or structural proteins are depicted. Compartment-specific sigma factors are also indicated. Gene homologs in D. hafniense DCB-2 were identified by using BLASTP with cutoff values of 1e-2 (E-value) and 30% identity in amino acid sequence.
Mentions: Of the 12 Desulfitobacterium strains that have been examined, seven strains including D. hafniense DCB-2 were observed to sporulate [1]. Sporulation of Clostridium and Bacillus involves a cascade gene expression triggered by stage- and compartment-specific sigma factors [66,67]. The genes for the key σ factors (σH, σF, σE, σG, and σK) and the master regulator SpoOA were identified in the genome of DCB-2, and homologs for most of the sporulation genes were identified. Although less conserved, the earliest sporulation genes of sensory histidine kinases could not be positively assigned among 59 histidine kinase genes in the genome (Figure 8). A gene homolog for SpoIIGA, a pro-σE processing protease, was not identified in either D. hafniense DCB-2 or Y51 strains, nor in four other spore-formers of Peptococcaceae listed in IMG. However, a homolog for spoIIR was identified in all six strains, the product of which could interact with SpoIIGA for the processing of pro-σE into active σE, a sigma factor responsible for the expression of ~250 genes in the mother cell of Bacillus subtilis [68]. Both genes are also present in Clostridium spore-formers. Notable Bacillus sporulation genes that are missing in D. hafniense DCB-2 as well as in Clostridium are the genes encoding SpoIVFB, a pro-σK processing enzyme, SpoIVFA, an inhibitor of SpoIVFB, and NucB, a sporulation-specific extracellular nuclease (Figure 8). This suggests that although sporulation in Bacillus and D. hafniense DCB-2 have much in common, there are differences in the regulatory mechanism or in the enzyme system for the initiation of sporulation stages.

Bottom Line: In addition, it contained genes for 53 molybdopterin-binding oxidoreductases, 19 flavoprotein paralogs of the fumarate reductase, and many other FAD/FMN-binding oxidoreductases, proving the cell's versatility in both adaptive and reductive capacities.Together with the ability to form spores, the presence of the CO2-fixing Wood-Ljungdahl pathway and the genes associated with oxygen tolerance add flexibility to the cell's options for survival under stress.D. hafniense DCB-2's genome contains genes consistent with its abilities for dehalogenation, metal reduction, N2 and CO2 fixation, anaerobic respiration, oxygen tolerance, spore formation, and biofilm formation which make this organism a potential candidate for bioremediation at contaminated sites.

View Article: PubMed Central - HTML - PubMed

Affiliation: Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA. kimsang8@msu.edu

ABSTRACT

Background: The genome of the Gram-positive, metal-reducing, dehalorespiring Desulfitobacterium hafniense DCB-2 was sequenced in order to gain insights into its metabolic capacities, adaptive physiology, and regulatory machineries, and to compare with that of Desulfitobacterium hafniense Y51, the phylogenetically closest strain among the species with a sequenced genome.

Results: The genome of Desulfitobacterium hafniense DCB-2 is composed of a 5,279,134-bp circular chromosome with 5,042 predicted genes. Genome content and parallel physiological studies support the cell's ability to fix N2 and CO2, form spores and biofilms, reduce metals, and use a variety of electron acceptors in respiration, including halogenated organic compounds. The genome contained seven reductive dehalogenase genes and four nitrogenase gene homologs but lacked the Nar respiratory nitrate reductase system. The D. hafniense DCB-2 genome contained genes for 43 RNA polymerase sigma factors including 27 sigma-24 subunits, 59 two-component signal transduction systems, and about 730 transporter proteins. In addition, it contained genes for 53 molybdopterin-binding oxidoreductases, 19 flavoprotein paralogs of the fumarate reductase, and many other FAD/FMN-binding oxidoreductases, proving the cell's versatility in both adaptive and reductive capacities. Together with the ability to form spores, the presence of the CO2-fixing Wood-Ljungdahl pathway and the genes associated with oxygen tolerance add flexibility to the cell's options for survival under stress.

Conclusions: D. hafniense DCB-2's genome contains genes consistent with its abilities for dehalogenation, metal reduction, N2 and CO2 fixation, anaerobic respiration, oxygen tolerance, spore formation, and biofilm formation which make this organism a potential candidate for bioremediation at contaminated sites.

Show MeSH
Related in: MedlinePlus