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

Abstract

BackgroundClostridium 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.ResultsC. 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.ConclusionsAnalysis 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.

Erratum: Divergent functional isoforms drive niche specialisation for nutrient acquisition and use in rumen microbiome

“…This supports reports that species of Clostridium may utilise histidine as part of a strategy to overcome nutrient limitation during the stationary growth phase (Fonknechten et al, 2010). Finally, the class of glycosylases to which the cellulosome enzymes from Clostridium species belong (EC 3.2; Ravachol et al, 2014), was more functionally divergent in Clostridium than in Prevotella.…”

“…Interestingly, some Clostridium species from the rumen have been characterised as having a preferential utilisation for serine, threonine, cysteine, proline and glycine in their exponential growth phase (Flythe and Kagan, 2010;Fonknechten et al, 2010). Our results suggest that this may be a specific niche specialisation by these species in the rumen.…”

Diversity and Evolution in the Genome of Clostridium difficile

“…This is also true for C. difficile, with a genome up to 42% larger than those of other closely related clostridial species such as C. bifermentans and C. sticklandii and larger than those of most other Firmicutes (62,63). This large, complex genome reflects the ability of the bacterium to survive, often for long periods of time, within a diverse range of human, animal, and abiotic environments.…”

A comparison of bee bread made by Africanized and European honey bees (Apis mellifera) and its effects on hemolymph protein titers

“…The reduction could be due to the presence of indole bacteria previously reported by Chevtchik (1950) (cited in Gilliam 1979a) that use tryptophan as an energy source. Similarly, proline concentrations were lower in EBB than in the pollen or in ABB, and this could be due to bacteria with specific pathways to degrade amino acids (Collins et al 1994;Fonknechten et al 2010). Free amino acids also can be incorporated into proteins and this too would reduce their concentrations.…”