Functional dissection and modulation of the BirA protein for improved autotrophic growth of gas‐fermenting Clostridium ljungdahlii

Summary Gas‐fermenting Clostridium species can convert one‐carbon gases (CO2/CO) into a variety of chemicals and fuels, showing excellent application prospects in green biological manufacturing. The discovery of crucial genes and proteins with novel functions is important for understanding and further optimization of these autotrophic bacteria. Here, we report that the Clostridium ljungdahlii BirA protein (ClBirA) plays a pleiotropic regulator role, which, together with its biotin protein ligase (BPL) activity, enables an effective control of autotrophic growth of C. ljungdahlii. The structural modulation of ClBirA, combined with the in vivo and in vitro analyses, further reveals the action mechanism of ClBirA’s dual roles as well as their interaction in C. ljungdahlii. Importantly, an atypical, flexible architecture of the binding site was found to be employed by ClBirA in the regulation of a lot of essential pathway genes, thereby expanding BirA’s target genes to a broader range in clostridia. Based on these findings, molecular modification of ClBirA was performed, and an improved cellular performance of C. ljungdahlii was achieved in gas fermentation. This work reveals a previously unknown potent role of BirA in gas‐fermenting clostridia, providing new perspective for understanding and engineering these autotrophic bacteria. The discovery of regulators as new resources for functional studies and strain modifications are promising strategies in industrially important microorganisms, which, however, still remains poorly explored. Here, we identified the ClBirA protein as a determinant regulator controlling the autotrophic growth of C. ljungdahlii, a representative gas‐fermenting Clostridium species, and performed a detailed functional analysis. We revealed the pleiotropic regulatory function of ClBirA as well as the underlying mechanisms, which would contribute to deeper understanding and optimization of this bifunctional protein in C. ljungdahlii.