publication . Article . 2012

The Purine-Utilizing Bacterium Clostridium acidurici 9a: A Genome-Guided Metabolic Reconsideration

Katrin Hartwich; Anja Poehlein; Rolf Daniel;
Open Access English
  • Published: 11 Dec 2012 Journal: PLoS ONE, volume 7, issue 12 (issn: 1932-6203, eissn: 1932-6203, Copyright policy)
  • Publisher: Public Library of Science
Abstract
Clostridium acidurici is an anaerobic, homoacetogenic bacterium, which is able to use purines such as uric acid as sole carbon, nitrogen, and energy source. Together with the two other known purinolytic clostridia C. cylindrosporum and C. purinilyticum, C. acidurici serves as a model organism for investigation of purine fermentation. Here, we present the first complete sequence and analysis of a genome derived from a purinolytic Clostridium. The genome of C. acidurici 9a consists of one chromosome (3,105,335 bp) and one small circular plasmid (2,913 bp). The lack of candidate genes encoding glycine reductase indicates that C. acidurici 9a uses the...
Subjects
free text keywords: Research Article, Biology, Microbial Metabolism, Bacterial Physiology, Microbiology, Medicine, Functional Genomics, Genome Expression Analysis, Purine-Utilizing; Bacterium; Clostridium acidurici 9a; Metabolic Reconsideration, Comparative Genomics, Q, R, Bacteriology, Bacterial Biochemistry, Microbial Physiology, Science, Genomics, Genome Sequencing
63 references, page 1 of 5

1 Gupta RS, Gao B (2009) Phylogenomic analyses of clostridia and identification of novel protein signatures that are specific to the genus Clostridium sensu stricto (cluster I). Int J Syst Evol Microbiol 59: 285–294.19196767 [PubMed]

2 Stickland LH (1934) Studies in the metabolism of the strict anaerobes (genus Clostridium): The chemical reactions by which Cl. sporogenes obtains its energy. Biochem J 28: 1746–1759.16745572 [OpenAIRE] [PubMed]

3 Barker HA (1981) Amino acid degradation by anaerobic bacteria. Annu Rev Biochem 50: 23–40.6791576 [PubMed]

4 Dürre P, Andreesen JR (1983) Purine and glycine metabolism by purinolytic clostridia. J Bacteriol 154: 192–199.6833177 [OpenAIRE] [PubMed]

5 Dürre P, Andreesen JR (1982) Selenium-dependent growth and glycine fermentation by Clostridium purinolyticum . J Gen Microbiol 128: 1457–1466.7119740 [PubMed]

6 Barker HA, Beck JV (1941) The fermentative decomposition of purines by Clostridium acidi-urici and Clostridium cylindrosporum . J Biol Chem 141: 3–27.

7 Barker HA, Beck JV (1942) Clostridium acidi-uridi and Clostridium cylindrosporum, organisms fermenting uric acid and some other purines. J Bacteriol 43: 291–304.16560499 [OpenAIRE] [PubMed]

8 Waber LJ, Wood HG (1979) Mechanism of acetate synthesis from CO 2 by Clostridium acidiurici . J Bacteriol 140: 468–478.500560 [OpenAIRE] [PubMed]

9 Andreesen JR (1994) Glycine metabolism in anaerobes. Antonie Van Leeuwenhoek 66: 223–237.7747933 [PubMed]

10 Dürre P, Andersch W, Andreesen JR (1981) Isolation and characterization of an adenine-utilizing, anaerobic sporeformer, Clostridium purinolyticum sp. nov. Int J Syst Bacteriol. 184–194.

11 Dürre P, Andreesen JR (1982) Pathway of carbon dioxide reduction to acetate without a net energy requirement in Clostridium purinolyticum . FEMS Microbiol Lett 15: 51–56.

12 Rabinowitz JC (1963) Intermedites in purine breakdown. In: SP C, NO K, editors. Methods in Enzymology. New York: Academic Press. 703–713.

13 Staden R, Beal KF, Bonfield JK (2000) The Staden package, 1998. Methods Mol Biol 132: 115–130.10547834 [PubMed]

14 Hu i EK, Wang PC, Lo SJ (1998) Strategies for cloning unknown cellular flanking DNA sequences from foreign integrants. Cell Mol Life Sci 54: 1403–1411.9893713 [PubMed]

15 Tettelin H, Radune D, Kasif S, Khouri H, Salzberg SL (1999) Optimized multiplex PCR: efficiently closing a whole-genome shotgun sequencing project. Genomics 62: 500–507.10644449 [PubMed]

63 references, page 1 of 5
Abstract
Clostridium acidurici is an anaerobic, homoacetogenic bacterium, which is able to use purines such as uric acid as sole carbon, nitrogen, and energy source. Together with the two other known purinolytic clostridia C. cylindrosporum and C. purinilyticum, C. acidurici serves as a model organism for investigation of purine fermentation. Here, we present the first complete sequence and analysis of a genome derived from a purinolytic Clostridium. The genome of C. acidurici 9a consists of one chromosome (3,105,335 bp) and one small circular plasmid (2,913 bp). The lack of candidate genes encoding glycine reductase indicates that C. acidurici 9a uses the...
Subjects
free text keywords: Research Article, Biology, Microbial Metabolism, Bacterial Physiology, Microbiology, Medicine, Functional Genomics, Genome Expression Analysis, Purine-Utilizing; Bacterium; Clostridium acidurici 9a; Metabolic Reconsideration, Comparative Genomics, Q, R, Bacteriology, Bacterial Biochemistry, Microbial Physiology, Science, Genomics, Genome Sequencing
63 references, page 1 of 5

1 Gupta RS, Gao B (2009) Phylogenomic analyses of clostridia and identification of novel protein signatures that are specific to the genus Clostridium sensu stricto (cluster I). Int J Syst Evol Microbiol 59: 285–294.19196767 [PubMed]

2 Stickland LH (1934) Studies in the metabolism of the strict anaerobes (genus Clostridium): The chemical reactions by which Cl. sporogenes obtains its energy. Biochem J 28: 1746–1759.16745572 [OpenAIRE] [PubMed]

3 Barker HA (1981) Amino acid degradation by anaerobic bacteria. Annu Rev Biochem 50: 23–40.6791576 [PubMed]

4 Dürre P, Andreesen JR (1983) Purine and glycine metabolism by purinolytic clostridia. J Bacteriol 154: 192–199.6833177 [OpenAIRE] [PubMed]

5 Dürre P, Andreesen JR (1982) Selenium-dependent growth and glycine fermentation by Clostridium purinolyticum . J Gen Microbiol 128: 1457–1466.7119740 [PubMed]

6 Barker HA, Beck JV (1941) The fermentative decomposition of purines by Clostridium acidi-urici and Clostridium cylindrosporum . J Biol Chem 141: 3–27.

7 Barker HA, Beck JV (1942) Clostridium acidi-uridi and Clostridium cylindrosporum, organisms fermenting uric acid and some other purines. J Bacteriol 43: 291–304.16560499 [OpenAIRE] [PubMed]

8 Waber LJ, Wood HG (1979) Mechanism of acetate synthesis from CO 2 by Clostridium acidiurici . J Bacteriol 140: 468–478.500560 [OpenAIRE] [PubMed]

9 Andreesen JR (1994) Glycine metabolism in anaerobes. Antonie Van Leeuwenhoek 66: 223–237.7747933 [PubMed]

10 Dürre P, Andersch W, Andreesen JR (1981) Isolation and characterization of an adenine-utilizing, anaerobic sporeformer, Clostridium purinolyticum sp. nov. Int J Syst Bacteriol. 184–194.

11 Dürre P, Andreesen JR (1982) Pathway of carbon dioxide reduction to acetate without a net energy requirement in Clostridium purinolyticum . FEMS Microbiol Lett 15: 51–56.

12 Rabinowitz JC (1963) Intermedites in purine breakdown. In: SP C, NO K, editors. Methods in Enzymology. New York: Academic Press. 703–713.

13 Staden R, Beal KF, Bonfield JK (2000) The Staden package, 1998. Methods Mol Biol 132: 115–130.10547834 [PubMed]

14 Hu i EK, Wang PC, Lo SJ (1998) Strategies for cloning unknown cellular flanking DNA sequences from foreign integrants. Cell Mol Life Sci 54: 1403–1411.9893713 [PubMed]

15 Tettelin H, Radune D, Kasif S, Khouri H, Salzberg SL (1999) Optimized multiplex PCR: efficiently closing a whole-genome shotgun sequencing project. Genomics 62: 500–507.10644449 [PubMed]

63 references, page 1 of 5
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publication . Article . 2012

The Purine-Utilizing Bacterium Clostridium acidurici 9a: A Genome-Guided Metabolic Reconsideration

Katrin Hartwich; Anja Poehlein; Rolf Daniel;