Auxotrophy from bioenergetic demand: the case of proline addiction in Clostridioides difficile.

Abstract

Many microbial growth requirements are interpreted as auxotrophy arising from loss of biosynthetic capacity. Clostridioides difficile is widely considered to be proline auxotrophic because it fails to grow in defined media lacking proline, yet it harbors proline biosynthesis genes. Because C. difficile preferentially uses proline as an electron acceptor via D-proline reductase (Prd), we argue that this phenotype arises from a bioenergetic constraint rather than an inability to make proline. Consistent with this view, mutants lacking Prd gain the ability to grow without proline. Moreover, conditions that adapt the organism to Prd-independent redox metabolism, such as Wood-Ljungdahl-linked acetobutyrogenesis, also enable proline-independent growth. We propose a model for "proline addiction" in which sustained Prd flux depletes the intracellular proline pool faster than biosynthesis can replenish it, making growth dependent on environmental proline. This bioenergetic addiction model may help explain cryptic auxotrophies that genome-based cultivation approaches would otherwise miss.