Flexible cobamide metabolism in Clostridioides (Clostridium) difficile 630 Δerm

Abstract

11Clostridioides (Clostridium) difficile is an opportunistic pathogen known for its ability to 12 colonize the human gut under conditions of dysbiosis. Several aspects of its carbon and amino 13 acid metabolism have been investigated, but its cobamide (vitamin B 12 and related cofactors) 14 metabolism remains largely unexplored. C. difficile has seven predicted cobamide-dependent 15 metabolisms encoded in its genome in addition to a nearly complete cobamide biosynthesis 16 pathway and a cobamide uptake system. To address the importance of cobamides to C. difficile, 17we studied C. difficile 630 ∆erm and mutant derivatives under cobamide-dependent conditions in 18 vitro. Our results show that C. difficile can use a surprisingly diverse array of cobamides for 19 methionine and deoxyribonucleotide synthesis, and can use alternative metabolites or enzymes, 20 respectively, to bypass these cobamide-dependent processes. C. difficile 630 ∆erm produces the 21 cobamide pseudocobalamin when provided the early precursor 5-aminolevulinc acid or the late 22 metabolic pathways that are predicted to require cobamide-dependent enzymes. Here, we show 34 that C. difficile cobamide metabolism is versatile, as it can use a surprisingly wide variety of 35 cobamides and has alternative functions that can bypass some of its cobamide requirements. 36 Furthermore, C. difficile does not synthesize cobamides de novo, but produces them when given 37 cobamide precursors. Better understanding of C. difficile cobamide metabolism may lead to new 38 strategies to treat and prevent C. difficile-associated disease. 383This work was supported by grants NIH DP2AI117984 and R01GM114535 to M.E.T. 384 385We thank Aimee Shen for her extensive advice and protocols for working with C. difficile, Craig

Comparative Analysis of Corrinoid Profiles across Host-Associated and Environmental Samples

“…This structural variability is key to understanding the specificity and evolution of cobamide-dependent enzymes and RNAs in bacteria. Different bacteria have distinct cobamide preferences that impact their growth and metabolism, ,− in part because the lower ligand differentially impacts both enzyme–cofactor interactions and the reactivity of the cobalt–carbon reactive center . Because cobamides other than cobalamin are not commercially available, research on cobamides requires extraction and purification of various cobamides from bacterial cultures …”

Cobalamin riboswitches are broadly sensitive to corrinoid cofactors to enable an efficient gene regulatory strategy

“…In regard to gene regulatory strategies, it seems sensible that Cbl-riboswitches are not highly effector-specific because bacteria are often flexible in their corrinoid usage. A variety of corrinoids have been shown to support growth of C. difficile, S. ovata, and Ensifer meliloti despite each of these organisms displaying highly specific corrinoid production (Mok and Taga, 2013; Shelton et al, 2020; Sokolovskaya et al, 2019). Furthermore, since corrinoid auxotrophy is prevalent among corrinoid-dependent bacteria, many organisms may need to take advantage of the wide range of corrinoids that may be available in their environment (Shelton et al, 2019).…”

A contemporary review of Clostridioides difficile infections in patients with haematologic diseases

“…Intrinsic factor and bacterial cells have similar affinity for cobalamin [74]. Cobamides in vitro support robust C. difficile growth [78]. C. difficile has multiple cobamide-dependent pathways in its genome [76] and may use many cobamides and cobamide precursors to support its growth and metabolism [78].…”

“…Cobamides in vitro support robust C. difficile growth [78]. C. difficile has multiple cobamide‐dependent pathways in its genome [76] and may use many cobamides and cobamide precursors to support its growth and metabolism [78]. Since deficiency of intrinsic factor in PA increases the availability of intestinal cobalamin, it favours dysbiosis and growth and proliferation of C. difficile .…”