Clostridium sticklandii, a specialist in amino acid degradation:revisiting its metabolism through its genome sequence - PubMed (original) (raw)

doi: 10.1186/1471-2164-11-555.

Sébastien Chaussonnerie, Sabine Tricot, Aurélie Lajus, Jan R Andreesen, Nadia Perchat, Eric Pelletier, Michel Gouyvenoux, Valérie Barbe, Marcel Salanoubat, Denis Le Paslier, Jean Weissenbach, Georges N Cohen, Annett Kreimeyer

Affiliations

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

Nuria Fonknechten et al. BMC Genomics. 2010.

Abstract

Background: Clostridium sticklandii belongs to a cluster of non-pathogenic proteolytic clostridia which utilize amino acids as carbon and energy sources. Isolated by T.C. Stadtman in 1954, it has been generally regarded as a "gold mine" for novel biochemical reactions and is used as a model organism for studying metabolic aspects such as the Stickland reaction, coenzyme-B12- and selenium-dependent reactions of amino acids. With the goal of revisiting its carbon, nitrogen, and energy metabolism, and comparing studies with other clostridia, its genome has been sequenced and analyzed.

Results: C. sticklandii is one of the best biochemically studied proteolytic clostridial species. Useful additional information has been obtained from the sequencing and annotation of its genome, which is presented in this paper. Besides, experimental procedures reveal that C. sticklandii degrades amino acids in a preferential and sequential way. The organism prefers threonine, arginine, serine, cysteine, proline, and glycine, whereas glutamate, aspartate and alanine are excreted. Energy conservation is primarily obtained by substrate-level phosphorylation in fermentative pathways. The reactions catalyzed by different ferredoxin oxidoreductases and the exergonic NADH-dependent reduction of crotonyl-CoA point to a possible chemiosmotic energy conservation via the Rnf complex. C. sticklandii possesses both the F-type and V-type ATPases. The discovery of an as yet unrecognized selenoprotein in the D-proline reductase operon suggests a more detailed mechanism for NADH-dependent D-proline reduction. A rather unusual metabolic feature is the presence of genes for all the enzymes involved in two different CO2-fixation pathways: C. sticklandii harbours both the glycine synthase/glycine reductase and the Wood-Ljungdahl pathways. This unusual pathway combination has retrospectively been observed in only four other sequenced microorganisms.

Conclusions: Analysis of the C. sticklandii genome and additional experimental procedures have improved our understanding of anaerobic amino acid degradation. Several specific metabolic features have been detected, some of which are very unusual for anaerobic fermenting bacteria. Comparative genomics has provided the opportunity to study the lifestyle of pathogenic and non-pathogenic clostridial species as well as to elucidate the difference in metabolic features between clostridia and other anaerobes.

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Figures

Figure 1

Figure 1

Presentation of relevant metabolic features and amino acid utilization. (A) Genome-based model of amino acid metabolism and energy conservation processes of C. sticklandii. (B) LC-MS analyses of amino acid utilization. The presence of each amino acid in the medium was checked at different phases of growth (colour graphs). The growth kinetic is represented by a yellow graph. Only the curves for rapidly used amino acids are shown.

Figure 2

Figure 2

Multiple sequence alignments of the C-terminal sequence of PrdC of several Clostridiales. Conserved residues are highlighted. The red arrows show the position of the selenocysteine (U). The redox centre is boxed in red.

Figure 3

Figure 3

Proposed mechanism of D-proline reductase (adapted from Kabisch [45]). PrdA is shown after the hydrolytic processing of the proprotein to form a pyruvoyl group that binds D-proline [46].

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