Identifying the Alkaline Tolerance-Related Genes Through Transcriptome Analysis of Halomonas alkalicola CICC 11012 s

Halomonas alkalicola CICC 11012 s is the strongest alkaliphile in the genus Halomonas. So far, studies have focused on the genome level and functional validation of a single gene, providing an overview and partial analysis of the adaptive mechanisms. As such, the comprehensive adaptations of alkaliphiles to extremely alkaline stress remain largely unclear. Therefore, in this study, the transcriptome profiling of H. alkalicola under neutral and alkaline conditions was compared to explore its global adaptation mechanisms towards pH homeostasis. In addition, the different up-regulated genes of this strain grown at pH 11.0 were compared with those grown at pH 7.0. The results revealed that the up-regulated genes were mainly distributed in six categories, including glycosyl transferase, fimbrial assembly protein, TonB-dependent transport system, C₄-dicarboxylate TRAP transport system, transposase, and toxin-antitoxin system. This result indicated that H. alkalicola developed various adaptive strategies to survive under extremely alkaline pressure, from modifying their cell wall structure to enhancing their membrane transport activities and intracellular metabolism homeostasis. Furthermore, the function of the gene cluster tonB-exbB-exbB2-exbD under extreme alkaline stress was verified by the CRISPR-Cas9 gene-editing system, indicating that the TonB-dependent transport system significantly affected the growth of the strain under extreme alkaline stresses.