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Background  Reef-building corals regularly experience changes in intra- and extracellular H +  concentrations ([H + ]) due to physiological and environmental processes. Stringent control of [H + ] is required to maintain the homeostatic acid-base balance in coral cells and is achieved through the regulation of intracellular pH (pH i ). This task is especially challenging for reef-building corals that share an endosymbiotic relationship with photosynthetic dinoflagellates (family Symbiodinaceae), which significantly affect the pH i  of coral cells. Despite their importance, the pH regulatory proteins involved in the homeostatic acid-base balance have been scarcely investigated in corals. Here, we report in the coral  Stylophora pistillata  a full characterization of the genomic structure, domain topology and phylogeny of three major H +  transporter families that are known to play a role in the intracellular pH regulation of animal cells; we investigated their tissue-specific expression patterns and assessed the effect of seawater acidification on their expression levels.    Results  We identified members of the Na + /H +  exchanger (SLC9), vacuolar-type electrogenic H + -ATP hydrolase (V-ATPase) and voltage-gated proton channel (H v CN) families in the genome and transcriptome of  S. pistillata . In addition, we identified a novel member of the H v CN gene family in the cnidarian subclass Hexacorallia that has not been previously described in any species. We also identified key residues that contribute to H +  transporter substrate specificity, protein function and regulation. Last, we demonstrated that some of these proteins have different tissue expression patterns, and most are unaffected by exposure to seawater acidification.    Conclusions  In this study, we provide the first characterization of H +  transporters that might contribute to the homeostatic acid-base balance in coral cells. This work will enrich the knowledge of the basic aspects of coral biology and has important implications for our understanding of how corals regulate their intracellular environment.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12860-021-00353-x.

Intracellular pH regulation: characterization and functional investigation of H+ transporters in Stylophora pistillata