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

Carbon metabolic pathways of D. hafniense DCB-2. The pathways were constructed based on the presence or absence of key metabolic genes in D. hafniense DCB-2. The acetyl-CoA degradation and related genes are shown in more detail (boxed). Enzymes for the numbered reactions in figure are listed below with their potential genes; 1. pyruvate kinase; Dhaf_2755. 2. phosphoenolpyruvate synthase; Dhaf_1117, Dhaf_1622, Dhaf_3294. 3. pyruvate, phosphate dikinase; Dhaf_1046, Dhaf_4240, Dhaf_4251. 4. D-lactate dehydrogenase (cytochrome); Dhaf_3228, Dhaf_4382. 5. L-lactate dehydrogenase; Dhaf_1965. 6. PEP carboxykinase; Dhaf_1134. 7. malate dehydrogenase (NADP+); Dhaf_0902, Dhaf_3085. 8. pyruvate carboxyltransferase; Dhaf_1012, Dhaf_1059. 9. pyruvate formate-lyase; Dhaf_0366, Dhaf_1246, Dhaf_4905. 10. pyruvate flavodoxin/ferredoxin oxidoreductase; Dhaf_0054, Dhaf_4766. 11a. acetate-CoA ligase; Dhaf_0467. 11b. acetyl-CoA hydrolase/transferase; Dhaf_0603, Dhaf_2858, Dhaf_4529. 12. aldehyde dehydrogenase (NAD+); Dhaf_2181. 13. acetaldehyde dehydrogenase (acetylating); Dhaf_2180. 14. malate dehydrogenase; Dhaf_1799, Dhaf_4412. 15. citrate lyase; Dhaf_4206. 16. succinate-CoA ligase (ADP-forming); Dhaf_0192, Dhaf_2066. 17. alcohol dehydrogenase; Dhaf_2180, Dhaf_0588. 18. succinate dehydrogenase; Dhaf_0743-0745. 19. fumarase; Dhaf_4397. 20. citrate synthase; Dhaf_0903. 21. isocitrate dehydrogenase (NADP+); Dhaf_1523. 22. hydrogen:quinone oxidoreductase; Dhaf_2742. 23. hydrogenase (ferredoxin); Dhaf_0805, Dhaf_3270, Dhaf_3368. 24. formate dehydrogenase; Dhaf_1398, Dhaf_1509, Dhaf_4271. 25. aconitase; Dhaf_1133. 26. tryptophanase; Dhaf_1324, Dhaf_2460.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 2: Carbon metabolic pathways of D. hafniense DCB-2. The pathways were constructed based on the presence or absence of key metabolic genes in D. hafniense DCB-2. The acetyl-CoA degradation and related genes are shown in more detail (boxed). Enzymes for the numbered reactions in figure are listed below with their potential genes; 1. pyruvate kinase; Dhaf_2755. 2. phosphoenolpyruvate synthase; Dhaf_1117, Dhaf_1622, Dhaf_3294. 3. pyruvate, phosphate dikinase; Dhaf_1046, Dhaf_4240, Dhaf_4251. 4. D-lactate dehydrogenase (cytochrome); Dhaf_3228, Dhaf_4382. 5. L-lactate dehydrogenase; Dhaf_1965. 6. PEP carboxykinase; Dhaf_1134. 7. malate dehydrogenase (NADP+); Dhaf_0902, Dhaf_3085. 8. pyruvate carboxyltransferase; Dhaf_1012, Dhaf_1059. 9. pyruvate formate-lyase; Dhaf_0366, Dhaf_1246, Dhaf_4905. 10. pyruvate flavodoxin/ferredoxin oxidoreductase; Dhaf_0054, Dhaf_4766. 11a. acetate-CoA ligase; Dhaf_0467. 11b. acetyl-CoA hydrolase/transferase; Dhaf_0603, Dhaf_2858, Dhaf_4529. 12. aldehyde dehydrogenase (NAD+); Dhaf_2181. 13. acetaldehyde dehydrogenase (acetylating); Dhaf_2180. 14. malate dehydrogenase; Dhaf_1799, Dhaf_4412. 15. citrate lyase; Dhaf_4206. 16. succinate-CoA ligase (ADP-forming); Dhaf_0192, Dhaf_2066. 17. alcohol dehydrogenase; Dhaf_2180, Dhaf_0588. 18. succinate dehydrogenase; Dhaf_0743-0745. 19. fumarase; Dhaf_4397. 20. citrate synthase; Dhaf_0903. 21. isocitrate dehydrogenase (NADP+); Dhaf_1523. 22. hydrogen:quinone oxidoreductase; Dhaf_2742. 23. hydrogenase (ferredoxin); Dhaf_0805, Dhaf_3270, Dhaf_3368. 24. formate dehydrogenase; Dhaf_1398, Dhaf_1509, Dhaf_4271. 25. aconitase; Dhaf_1133. 26. tryptophanase; Dhaf_1324, Dhaf_2460.

Mentions: The tricarboxylic acid cycle (TCA) of D. hafniense DCB-2 and Y51 appears incomplete since they lack the gene coding for 2-oxoglutarate dehydrogenase, and the cycle lacks the anaplerotic glyoxylate bypass (Figure 2). In most autotrophic bacteria and anaerobic Archaea, the TCA cycle operates in a reductive, biosynthetic direction [13]. In line with this observation, DCB-2 and Y51 are apparently capable of performing the reductive TCA cycle due to the possession of additional enzymes such as fumarate reductase and citrate lyase to potentially bypass the unidirectional steps of the conventional oxidative TCA cycle [14] (Figure 2). However, the reconstruction of the TCA cycle based solely on genome sequence should be carefully addressed, as observed in Clostridium acetobutylicum where both functional oxidative and reductive TCA cycles were confirmed experimentally in contrast to the previous genomic interpretation [15].


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)

Carbon metabolic pathways of D. hafniense DCB-2. The pathways were constructed based on the presence or absence of key metabolic genes in D. hafniense DCB-2. The acetyl-CoA degradation and related genes are shown in more detail (boxed). Enzymes for the numbered reactions in figure are listed below with their potential genes; 1. pyruvate kinase; Dhaf_2755. 2. phosphoenolpyruvate synthase; Dhaf_1117, Dhaf_1622, Dhaf_3294. 3. pyruvate, phosphate dikinase; Dhaf_1046, Dhaf_4240, Dhaf_4251. 4. D-lactate dehydrogenase (cytochrome); Dhaf_3228, Dhaf_4382. 5. L-lactate dehydrogenase; Dhaf_1965. 6. PEP carboxykinase; Dhaf_1134. 7. malate dehydrogenase (NADP+); Dhaf_0902, Dhaf_3085. 8. pyruvate carboxyltransferase; Dhaf_1012, Dhaf_1059. 9. pyruvate formate-lyase; Dhaf_0366, Dhaf_1246, Dhaf_4905. 10. pyruvate flavodoxin/ferredoxin oxidoreductase; Dhaf_0054, Dhaf_4766. 11a. acetate-CoA ligase; Dhaf_0467. 11b. acetyl-CoA hydrolase/transferase; Dhaf_0603, Dhaf_2858, Dhaf_4529. 12. aldehyde dehydrogenase (NAD+); Dhaf_2181. 13. acetaldehyde dehydrogenase (acetylating); Dhaf_2180. 14. malate dehydrogenase; Dhaf_1799, Dhaf_4412. 15. citrate lyase; Dhaf_4206. 16. succinate-CoA ligase (ADP-forming); Dhaf_0192, Dhaf_2066. 17. alcohol dehydrogenase; Dhaf_2180, Dhaf_0588. 18. succinate dehydrogenase; Dhaf_0743-0745. 19. fumarase; Dhaf_4397. 20. citrate synthase; Dhaf_0903. 21. isocitrate dehydrogenase (NADP+); Dhaf_1523. 22. hydrogen:quinone oxidoreductase; Dhaf_2742. 23. hydrogenase (ferredoxin); Dhaf_0805, Dhaf_3270, Dhaf_3368. 24. formate dehydrogenase; Dhaf_1398, Dhaf_1509, Dhaf_4271. 25. aconitase; Dhaf_1133. 26. tryptophanase; Dhaf_1324, Dhaf_2460.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 2: Carbon metabolic pathways of D. hafniense DCB-2. The pathways were constructed based on the presence or absence of key metabolic genes in D. hafniense DCB-2. The acetyl-CoA degradation and related genes are shown in more detail (boxed). Enzymes for the numbered reactions in figure are listed below with their potential genes; 1. pyruvate kinase; Dhaf_2755. 2. phosphoenolpyruvate synthase; Dhaf_1117, Dhaf_1622, Dhaf_3294. 3. pyruvate, phosphate dikinase; Dhaf_1046, Dhaf_4240, Dhaf_4251. 4. D-lactate dehydrogenase (cytochrome); Dhaf_3228, Dhaf_4382. 5. L-lactate dehydrogenase; Dhaf_1965. 6. PEP carboxykinase; Dhaf_1134. 7. malate dehydrogenase (NADP+); Dhaf_0902, Dhaf_3085. 8. pyruvate carboxyltransferase; Dhaf_1012, Dhaf_1059. 9. pyruvate formate-lyase; Dhaf_0366, Dhaf_1246, Dhaf_4905. 10. pyruvate flavodoxin/ferredoxin oxidoreductase; Dhaf_0054, Dhaf_4766. 11a. acetate-CoA ligase; Dhaf_0467. 11b. acetyl-CoA hydrolase/transferase; Dhaf_0603, Dhaf_2858, Dhaf_4529. 12. aldehyde dehydrogenase (NAD+); Dhaf_2181. 13. acetaldehyde dehydrogenase (acetylating); Dhaf_2180. 14. malate dehydrogenase; Dhaf_1799, Dhaf_4412. 15. citrate lyase; Dhaf_4206. 16. succinate-CoA ligase (ADP-forming); Dhaf_0192, Dhaf_2066. 17. alcohol dehydrogenase; Dhaf_2180, Dhaf_0588. 18. succinate dehydrogenase; Dhaf_0743-0745. 19. fumarase; Dhaf_4397. 20. citrate synthase; Dhaf_0903. 21. isocitrate dehydrogenase (NADP+); Dhaf_1523. 22. hydrogen:quinone oxidoreductase; Dhaf_2742. 23. hydrogenase (ferredoxin); Dhaf_0805, Dhaf_3270, Dhaf_3368. 24. formate dehydrogenase; Dhaf_1398, Dhaf_1509, Dhaf_4271. 25. aconitase; Dhaf_1133. 26. tryptophanase; Dhaf_1324, Dhaf_2460.
Mentions: The tricarboxylic acid cycle (TCA) of D. hafniense DCB-2 and Y51 appears incomplete since they lack the gene coding for 2-oxoglutarate dehydrogenase, and the cycle lacks the anaplerotic glyoxylate bypass (Figure 2). In most autotrophic bacteria and anaerobic Archaea, the TCA cycle operates in a reductive, biosynthetic direction [13]. In line with this observation, DCB-2 and Y51 are apparently capable of performing the reductive TCA cycle due to the possession of additional enzymes such as fumarate reductase and citrate lyase to potentially bypass the unidirectional steps of the conventional oxidative TCA cycle [14] (Figure 2). However, the reconstruction of the TCA cycle based solely on genome sequence should be carefully addressed, as observed in Clostridium acetobutylicum where both functional oxidative and reductive TCA cycles were confirmed experimentally in contrast to the previous genomic interpretation [15].

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