Limits...
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.

Show MeSH

Related in: MedlinePlus

Phylogenetic tree derived from 53 molybdenum-binding oxidoreductases. The tree was constructed by using MEGA 4.1 neighbor-joining method with 500 bootstrap replicates. Genes annotated by IMG are color-coded; blue for TMAO reductase, purple for pyrogallol hydroxytransferase, red for DMSO reductase, green for nitrate reductase, and yellow for formate dehydrogenase. Genes that were newly assigned in this study for their potential protein function are indicated with arrows. Bootstrap values are shown for each node, and the scale indicates the number of amino acid substitutions per site.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3306737&req=5

Figure 4: Phylogenetic tree derived from 53 molybdenum-binding oxidoreductases. The tree was constructed by using MEGA 4.1 neighbor-joining method with 500 bootstrap replicates. Genes annotated by IMG are color-coded; blue for TMAO reductase, purple for pyrogallol hydroxytransferase, red for DMSO reductase, green for nitrate reductase, and yellow for formate dehydrogenase. Genes that were newly assigned in this study for their potential protein function are indicated with arrows. Bootstrap values are shown for each node, and the scale indicates the number of amino acid substitutions per site.

Mentions: Of completed genomes thus far, D. hafniense DCB-2 and Y51 have the largest number of molybdopterin oxidoreductase genes (pfam01568), with 53 and 57 genes, respectively. Next in rank are Eggerthella lenta DSM 2243 (34 genes), and Slackia heliotrinireducens DSM 20476 (25 genes). Members of the molybdopterin oxidoreductase family include formate dehydrogenase, nitrate reductase, DMSO reductase, TMAO reductase, pyrogallol hydroxytransferase, and arsenate reductase. A phylogenetic tree with the 53 molybdopterin sequences reveals seven relatively well-defined groups (Figure 4). BLAST analysis of two outliers reveals that Dhaf_4785 and Dhaf_1197 both code for tetrathionate reductase subunit A of the TtrABC complex that catalyzes reduction of tetrathionate to thiosulfate [29]:


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)

Phylogenetic tree derived from 53 molybdenum-binding oxidoreductases. The tree was constructed by using MEGA 4.1 neighbor-joining method with 500 bootstrap replicates. Genes annotated by IMG are color-coded; blue for TMAO reductase, purple for pyrogallol hydroxytransferase, red for DMSO reductase, green for nitrate reductase, and yellow for formate dehydrogenase. Genes that were newly assigned in this study for their potential protein function are indicated with arrows. Bootstrap values are shown for each node, and the scale indicates the number of amino acid substitutions per site.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 4: Phylogenetic tree derived from 53 molybdenum-binding oxidoreductases. The tree was constructed by using MEGA 4.1 neighbor-joining method with 500 bootstrap replicates. Genes annotated by IMG are color-coded; blue for TMAO reductase, purple for pyrogallol hydroxytransferase, red for DMSO reductase, green for nitrate reductase, and yellow for formate dehydrogenase. Genes that were newly assigned in this study for their potential protein function are indicated with arrows. Bootstrap values are shown for each node, and the scale indicates the number of amino acid substitutions per site.
Mentions: Of completed genomes thus far, D. hafniense DCB-2 and Y51 have the largest number of molybdopterin oxidoreductase genes (pfam01568), with 53 and 57 genes, respectively. Next in rank are Eggerthella lenta DSM 2243 (34 genes), and Slackia heliotrinireducens DSM 20476 (25 genes). Members of the molybdopterin oxidoreductase family include formate dehydrogenase, nitrate reductase, DMSO reductase, TMAO reductase, pyrogallol hydroxytransferase, and arsenate reductase. A phylogenetic tree with the 53 molybdopterin sequences reveals seven relatively well-defined groups (Figure 4). BLAST analysis of two outliers reveals that Dhaf_4785 and Dhaf_1197 both code for tetrathionate reductase subunit A of the TtrABC complex that catalyzes reduction of tetrathionate to thiosulfate [29]:

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