Metabolism the Difficile Way: The Key to the Success of the Pathogen Clostridioides difficile

Abstract

Strains of Clostridioides difficile cause detrimental diarrheas with thousands of deaths worldwide. The infection process by the Gram-positive, strictly anaerobic gut bacterium is directly related to its unique metabolism, using multiple Stickland-type amino acid fermentation reactions coupled to Rnf complex-mediated sodium/proton gradient formation for ATP generation. Major pathways utilize phenylalanine, leucine, glycine and proline with the formation of 3-phenylproprionate, isocaproate, butyrate, 5-methylcaproate, valerate and 5-aminovalerate. In parallel a versatile sugar catabolism including pyruvate formate-lyase as a central enzyme and an incomplete tricarboxylic acid cycle to prevent unnecessary NADH formation completes the picture. However, a complex gene regulatory network that carefully mediates the continuous adaptation of this metabolism to changing environmental conditions is only partially elucidated. It involves the pleiotropic regulators CodY and SigH, the known carbon metabolism regulator CcpA, the proline regulator PrdR, the iron regulator Fur, the small regulatory RNA CsrA and potentially the NADH-responsive regulator Rex. Here, we describe the current knowledge of the metabolic principles of energy generation by C. difficile and the underlying gene regulatory scenarios.

A High-Fat/High-Protein, Atkins-Type Diet Exacerbates Clostridioides ( Clostridium ) difficile Infection in Mice, whereas a High-Carbohydrate Diet Protects

“…Effects of protein on CDI could be direct and/or indirect. C. difficile can use many different amino acids as Stickland donors, and both proline and glycine can be used as Stickland acceptors (9). And yet the C. difficile proline reductase (PrdA) was expressed only in humanized mice inoculated with dysbiotic microbiomes (11), suggesting that C. difficile may not compete well for proteins or amino acids with healthy microflora.…”

In vivocommensal control ofClostridioides difficilevirulence

“…Monoclonization with CSAR or with CBI markedly changed the luminal environment prior to C. difficile's introduction. CSAR-monocolonization enriched multiple amine-containing carbon sources (Fig 2A, top), including Stickland donor amino acids (SDF_2.24), additional fermentable amino acids (SDF_2.11) including cysteine, glutamate and asparate, which C. difficile can ferment in non-Stickland reactions (11), g-glutamyl-amino acids (SDF_2.8), which originate from microbial metabolism and host amino acid transport (29), and di-and polyamines (SDF_2.3). Among these sources, branched chain amino acids increased >2-3-fold (Fig.…”

“…difficile-monoclonization produced acetate ( Fig. 2G), which arises from carbohydrate fermentation, Stickland glycine and alanine fermentation, Wood-Ljungdahl metabolism, and other cellular processes (11), and the Stickland branched-SCFA metabolites isobutyrate, isovalerate, 2-methylbutyrate and isocaproate ( Fig. 2G).…”

“…tcdR encodes a sigma factor specific for the toxin gene promoters, and the tcdC gene a TcdR anti-sigma factor (8-10). Multiple metabolic regulators influence PaLoc expression (11,12). In particular, C. difficile elaborates toxin under starvation conditions to extract nutrients from the host and promote the shedding of spores.C.…”

“…In addition to carbohydrate fermentation, the pathogen uses Stickland fermentations, and Stickland-independent fermentations of other amino acids including threonine and cysteine (13), to extract energy from amino acids. The pathogen can ferment ethanolamine, extract electrons from primary bile salts, and undergo carbon fixation through the Wood-Ljungdhal pathway to generate acetate for metabolism or biosynthetic pathways (11,14). Metabolic regulators within C. difficile, including CodY, CcpA, PrdR, and Rex sense intracellular levels of GTP, branched-chain amino acids, fructose 1,6 bis-phosphate, and proline -the dominant Stickland acceptor amino acid, or NAD + /NADH pools respectively (12, 15).…”