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9.A.2 The Putative Dissolved Inorganic Carbon Concentrating Transporter (DIC-CT) Family 

Many autotrophic microorganisms adapt to scarcity in dissolved inorganic carbon (DIC; = CO2 + HCO3- + CO32-) with CO2 concentrating mechanisms (CCM) which actively transport DIC across the cell membrane to facilitate carbon fixation. The deep-sea vent γ-proteobacterial chemolithoautotroph, Thiomicrospira crunogena, has a low-DIC inducible CCM. Proteins encoded by Tcr_0854 and the adjacent Tcr_0853 genes, required elevated DIC for growth (Mangiapia et al. 2017). Strains carrying mutated copies of Tcr_0853 and Tcr_0854 overexpressed carboxysomes and had diminished ability to accumulate intracellular DIC. Tcr_0853 and Tcr_0854 are cotranscribed and upregulated under low-DIC conditions. The Tcr_0853 protein has 13 - 15 TMSs and is homologous to NADH dehydrogenase subunits (TC#3.D.1). Tcr_0853 and Tcr_0854 may encode a two-subunit DIC transporter. These proteins are widespread among autotrophs from multiple phyla of Bacteria and Archaea. Homologues are present in 14 phyla in Bacteria and in one phylum of Archaea, the Euryarchaeota. Many organisms carrying these homologs are autotrophs, suggesting a role in facilitating dissolved inorganic carbon (Mangiapia et al. 2017).

DabB2/DabA2 comprises a putative CO2 concentrating transporter, where DabB2 is a possible inorganic ion (H+ or Na+) transporter, homologous to integral membrane NADH dehydrogenase subunites, while   DabA2 is homologous to carbonic anhydrases.  Bacterial autotrophs often rely on CO2 concentrating mechanisms (CCMs) to assimilate carbon. Desmarais et al. 2019 performed a genome-wide barcoded transposon screen to identify essential and CCM-related genes in the γ-proteobacterium Halothiobacillus neapolitanus. Screening revealed that the CCM comprises at least 17 and probably no more than 25 genes, most of which are encoded in 3 operons. Two of these operons (DAB1 and DAB2) contain a two-gene locus that encodes a domain of unknown function (Pfam: PF10070) and a putative cation transporter (Pfam: PF00361). Physiological and biochemical assays demonstrated that these proteins (DabA and DabB), for DABs accumulate bicarbonate - assemble into a heterodimeric complex, which contains a putative β-carbonic anhydrase-like active site and functions as an energy-coupled inorganic carbon (Ci) pump. DAB operons are found in a diverse range of bacteria and archaea. Desmarais et al. 2019 demonstrated that functional DABs are present in the human pathogens Bacillus anthracis and Vibrio cholerae. Possibly DABs constitute a class of energized Ci pumps and play a critical role in the metabolism of Ci throughout prokaryotic phyla.

References associated with 9.A.2 family:

Desmarais, J.J., A.I. Flamholz, C. Blikstad, E.J. Dugan, T.G. Laughlin, L.M. Oltrogge, A.W. Chen, K. Wetmore, S. Diamond, J.Y. Wang, and D.F. Savage. (2019). DABs are inorganic carbon pumps found throughout prokaryotic phyla. Nat Microbiol 4: 2204-2215. 31406332
Fan, S.H., R.A. Proctor, S.C. Ersoy, A.C. Manna, A.L. Cheung, F. Götz, H.F. Chambers, and A.S. Bayer. (2023). Role of the NaHCO Transporter MpsABC in the NaHCO-β-Lactam-Responsive Phenotype in Methicillin-Resistant Staphylococcus aureus. Microbiol Spectr e0014123. [Epub: Ahead of Print] 37102972
Mangiapia, M., , T.W. Brown, D. Chaput, E. Haller, T.L. Harmer, Z. Hashemy, R. Keeley, J. Leonard, P. Mancera, D. Nicholson, S. Stevens, P. Wanjugi, T. Zabinski, C. Pan, and K.M. Scott. (2017). Proteomic and mutant analysis of the CO2 concentrating mechanism of hydrothermal vent chemolithoautotroph Thiomicrospira crunogena. J. Bacteriol. [Epub: Ahead of Print] 28115547
Menning, K.J., B.B. Menon, G. Fox, , and K.M. Scott. (2016). Dissolved inorganic carbon uptake in Thiomicrospira crunogena XCL-2 is Δp- and ATP-sensitive and enhances RubisCO-mediated carbon fixation. Arch. Microbiol. 198: 149-159. 26581415