Halothiobacillus neapolitanus c2 RB-TnSeq for CCM genes and essential genes

Bacterial autotrophs often rely on CO2 concentrating mechanisms (CCMs) to assimilate carbon. Although many CCM proteins have been identified, a systematic screen of CCM components has not been carried out. Here, we performed a genome-wide barcoded transposon screen to identify essential and CCM-related genes in the ɣ-proteobacterium H. neapolitanus. Screening revealed that the CCM comprises about 25 genes mostly encoded in 3 operons. Two of these operons contain a two-gene locus encoding a domain of unknown function (PFAM:PF10070) and a putative cation transporter (PFAM:PF00361). Physiological and biochemical assays demonstrate that these proteins, which we name DabA and DabB for “DABs accumulate bicarbonate,” assemble into a heterodimeric complex, contain a putative β-carbonic anhydrase-like active site, and function as an energy-coupled inorganic carbon (Ci) pump. Surprisingly, DabAB operons are found in diverse bacteria and archaea. We demonstrate that functional DABs are present in the human pathogens B. anthracis and V. cholerae. Based on these results, we propose that DABs constitute a new class of energized Ci pump and play a critical role in Ci metabolism throughout prokaryotic phyla.