Evolutionary Trajectories of Methionine Metabolism in Mycobacterium and Its Application to Engineer a Vitamin B12 Whole-Cell Ribosensor

Abstract

Vitamin B12 metabolism differs among members of the Mycobacterium genus. While non-tuberculous mycobacterial species are B12 producers, tuberculous mycobacteria lack endogenous production and rely on the host supply of this vitamin. Here, we hypothesise that this discrepant phenotype might impact the function of B12-dependent enzymes. We specifically focused on methionine synthases MetH and MetE. Both enzymes showed genetic differences in the Mycobacterium genus, resulting in a clear divergence between tuberculous and non-tuberculous species. Unexpectedly, the dependency of MetH on B12 was indistinguishable between M. tuberculosis and M. smegmatis, assayed as representative members of tuberculous and non-tuberculous species, respectively. However, MetE showed robust phenotypic differences between these species, displaying a finely tuned B12 regulation in M. tuberculosis, in contrast to a more permissive regulation in M. smegmatis. Both orthologs differ in the vitamin isoform specifically recognised, and the B12 threshold level required for MetE regulation. Since the B12 regulatory element in the metE gene is an RNA riboswitch, we analysed the polymorphisms in this region, with a special focus on loss-of-function mutations identified after in vitro selection. We used this information to engineer a whole-cell B12 biosensor in the genetically fastidious Mycobacterium genus, being able to detect vitamin B12 concentration in the range of micrograms per millilitre.