Open Access Research article

Clostridium sticklandii, a specialist in amino acid degradation:revisiting its metabolism through its genome sequence

Nuria Fonknechten123, Sébastien Chaussonnerie123, Sabine Tricot123, Aurélie Lajus123, Jan R Andreesen5, Nadia Perchat123, Eric Pelletier123, Michel Gouyvenoux123, Valérie Barbe123, Marcel Salanoubat123, Denis Le Paslier123, Jean Weissenbach123, Georges N Cohen4 and Annett Kreimeyer123*

Author Affiliations

1 CEA, DSV, Institut de Génomique, Genoscope, 2 rue Gaston Crémieux, F-91057 Evry, France

2 CNRS-UMR 8030 F-91057 Evry, France

3 UEVE, Université d'Evry, F-91057 Evry, France

4 Institut Pasteur, 28 rue du Dr. Roux, F-75724 Paris cedex 15, France

5 Institute of Biology/Microbiology, University of Halle, Kurt-Mothes-Str. 3, D-06120 Halle, Germany

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BMC Genomics 2010, 11:555  doi:10.1186/1471-2164-11-555

Published: 11 October 2010

Additional files

Additional file 1:

Genomic and metabolic features of C. sticklandii compared with other clostridia. All data are extracted from the MaGe annotations except those of Clostridium sporogenes, which are from the NCBI database. C.stick: Clostridium sticklandii DSM 519; C.acet: Clostridium acetobutylicum ATCC 824; C.beij: Clostridium beijerinckii NCIMB 8052; C.botu: Clostridium botulinum A Hall; C.diff: Clostridium difficile 630; C.kluv: Clostridium kluyveri DSM 555; C.novy: Clostridium novyi NT; C.perf: Clostridium perfringens ATCC 13124; C.phyt: Clostridium phytofermentans ISDg; C.teta: Clostridium tetani E88; C.ther: C. thermocellum ATCC 27405; C.spor: C. sporogenes ATCC 1557; A.meta: Alkaliphilus metalliredigens QYMF; A.orem: Alkaliphilus oremlandii OhILAs; M.ther: Moorella thermoacetica ATCC 39073. *2-ketoacid ferredoxin oxidoreductases.

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Additional file 2:

C. sticklandii synteny conservation and Bidirectional Best Hit percentages with the most closely related clostrial species. Synteny conservation is given by the percentage of CDS in synteny between C. sticklandii and the complete sequenced genomes.

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Additional file 3:

Characteristic gene products of C. sticklandii, their protein symbols and their corresponding labels. This is a listing of all genes/proteins that are discussed in the text.

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Additional file 4:

Comparative analysis of amino acid degradation pathways in several clostridial species. Blast searches (criteria: 30% identity over at least 80% of the length of the reference protein) were performed to determine the presence of the key enzymes in the microorganisms. All protein sequences were taken from C. sticklandii with two exceptions: the sequence of methylaspartate mutase was from Clostridium cochlearium, and that of 2-hydroxyglutaryl-CoA dehydratase from Acidaminococcus fermentans. C.stick: Clostridium sticklandii DSM 519; C.acet: Clostridium acetobutylicum ATCC 824; C.beij: Clostridium beijerinckii NCIMB 8052; C.botu: Clostridium botulinum A Hall; C.diff: Clostridium difficile 630; C.kluv: Clostridium kluyveri DSM 555; C.novy: Clostridium novyi NT; C.perf: Clostridium perfringens ATCC 13124; C.phyt: Clostridium phytofermentans ISDg; C.teta: Clostridium tetani E88; C.ther: C. thermocellum ATCC 27405; C.spor: C. sporogenes ATCC 15579; A.meta: Alkaliphilus metalliredigens QYMF; A.orem: Alkaliphilus oremlandii OhILAs; M.ther: Moorella thermoacetica ATCC 39073; C.coch: Clostridium cochlearium; A.ferm: Acidaminococcus fermentans DSM 20731. The genome of Clostridium cochlearium is not yet sequenced.

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Additional file 5:

LC-MS analyses of amino acid utilization during growth. For each amino acid, its presence in the medium was checked at different growth phases (colour graphs). The growth kinetic is represented by a yellow graph. Citrulline, ornithine, alanine and aspartate (indicated by a black frame) were not added to the medium. They appeared as intermediates or products of metabolism from other amino acids. Since the utilization of methionine was not discussed in the article, the graph for this amino acid is not shown.

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Additional file 6:

Cell growth of C. sticklandii in three types of media with different amino acid composition. Graph 1: medium containing amino acids that are catabolized in the exponential phase (Pro, Asn, Thr, Ser, Arg, Cys); Graph 2: medium containing amino acids that are catabolized in the exponential and stationary phase (Pro, Asn, Thr, Ser, Arg, Cys, Leu, Iso, Met, Gln, His, Lys); Graph 3: the amino acid combination of this medium is equivalent to the second medium, complemented with amino acids apparently not metabolized (Pro, Asn, Thr, Ser, Arg, Cys, Leu, Iso, Met, Gln, His, Lys, Trp, Val, Phe, Glu). Tyrosine was added to each medium.

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Additional file 7:

Comparison of the D-proline reductase gene cluster from different clostridial species. White arrows indicate hypothetical proteins or those presumed not to be involved in the D-proline reductase reaction. The letter "U" indicates the presence of selenocysteine. In Clostridium botulinum A Hall, a part of the cluster is duplicated.

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Additional file 8:

Presence of characteristic enzymes of the glycine synthase (Gcv proteins)/glycine reductase (Grd proteins) and Wood-Ljungdahl (CODH proteins) pathway in microbial genomes. Complete and WGS microbial genomes (as of May 6th, 2010) were scanned for some selected characteristic orthologous genes coding for carbon monoxide dehydrogenase/acetyl-CoA synthetase (Wood-Ljungdahl pathway), glycine reductase (Stickland reaction), and the glycine synthase (gcv-system) using a blastx search with stringent criteria (40% of positive residues over at least 80% of the length of the reference protein). For each target genome, the presence/absence of each protein was summarized in a 1/0 vector. Those WGS microbial genomes which do not contain all genes of both pathways are omitted.

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