Comparative Genomics of Sigma Factors in Acidithiobacillia Sheds Light into the Transcriptional Regulatory Networks Involved in Biogeochemical Dynamics in Extreme Acidic Environments

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.

Keywords: Acidithiobacillia; RpoN; enhancer-binding proteins; hydrogen; motility; nitrogen metabolism; sigma-factors; sulfur metabolism.

Figure 1

Phylogenetic distribution of Acidithiobacillia sigma factors. (A) Protein domain architecture of sigma54 and sigma70 proteins and (B) heatmap indicating presence/absence of known and potential SFs, based on protein orthology analysis. Acidithiobacillia representatives are phylogenetically arranged as represented by the dendrogram. Orthologous SFs counts are colored by the number (0–2) and rearranged in clusters according to Euclidean distance (left side dendrogram).

Figure 2

Phylogenetic relationships between sigma70 family proteins in Acidithiobacillia. Maximum-likelihood phylogenetic tree based on the sigma70 proteins identified in Acidithiobacillia. Groups of SFs were colored by species. Model E. coli, and B. subtilis representative SFs are shown in black.

Figure 3

Phylogeny of Acidithiobacillia sigma54 orthologs. Maximum-likelihood phylogenetic tree based on Acidithiobacillia sigma54 (RpoN) representatives. Sigma54s are colored by phenotype, represented by outer layout color, and species lineages are represented by inner sub-clade colors (colored tree branches). Model species outgroups (E. coli and B. subtilis) are highlighted in gray.

Figure 4

Sigma54-dependent two-component systems repertoire in Acidithiobacillia. (A) Protein domain architecture of sigma54-dependent TCSs separated by response regulator bEBP component and histidine kinase sensor component. AAA⁺, ATPase associated with cellular activities; REC, phosphoacceptor receiver domain; HTH, helix–turn–helix domain; PAS, Per–Arnt–Sim domain; HisKa, Signal transduction histidine kinase; HATPase_c, histidine kinase/HSP90-like ATPase. A dashed frame denotes that the HTH_8 domain was not detected in GlrR with the applied parameters, but its presence is inferred from its identification in the GlrR_2 group. (B) Protein ortholog groups in Acidithiobacillia representatives with TCSs grouped in a bracket with the histidine kinase sensor first, followed by the transcription factor.

Figure 5

Transcriptional regulatory circuits of bacterial enhancer binding proteins in Acidithiobacillia. (A) RpoN binding site and (B) bEBP binding sites and regulatory activity retrieved for known and de novo inferences. The number of binding sites that build the logos graph are given in parentheses. Transcriptional units are represented by referential species, where bEBP binding sites are depicted in color circles in the promoter regions. Genes encoding metabolic pathways of hydrogen in cyan, nitrogen in green, sulfur in orange, and additional genes in white; res, response regulator protein. (C) Transcriptional regulatory network representation of sigma factors and bEBPs.