Abstract

Extreme acidophiles from the Acidithiobacillia class thrive in highly acidic environments where they rely on diverse regulatory mechanisms for adaptation. These mechanisms include sigma factors, transcription factors (TFs), and transcription factor binding sites (TFBS), which control essential pathways. Comparative genomics and bioinformatics analyses identified sigma factors and TFs in Acidithiobacillia, showing similarities but key differences from reference neutrophiles. This study highlights sigma54-dependent one- and two-component systems that are crucial for survival in energy acquisition from sulfur compounds and hydrogen as well as nutrient assimilation. Furthermore, the data suggested evolutionary divergence in regulatory elements distinguishes S-oxidizing from Fe-S-oxidizing members of Acidithiobacillia. Conservation of gene clusters, synteny, and phylogenetic analyses supported the expected phenotypes in each species. Notable examples include HupR’s role in hydrogenase-2 oxidation in Fe-S-oxidizers, TspR/TspS regulation of the sulfur oxidation complex, and FleR/FleS control of flagellar motility in S-oxidizers. These regulatory mechanisms act as master controllers of bacterial activity, reflecting adaptation to distinct metabolic needs within Acidithiobacillia. © 2025 by the authors.