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

Sepúlveda-Rebolledo, Pedro; González-Rosales, Carolina; Dopson, Mark; Pérez-Rueda, Ernesto; Holmes, David S.; Valdés, Jorge H.

doi:10.3390/microorganisms13061199

This is an early access version, the complete PDF, HTML, and XML versions will be available soon.

Open AccessArticle

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

by

Pedro Sepúlveda-Rebolledo

^1,2,

Carolina González-Rosales

³

,

Mark Dopson

³

,

Ernesto Pérez-Rueda

⁴

,

David S. Holmes

^5,6,*

and

Jorge H. Valdés

^2,*

¹

Microbial Ecophysiology Laboratory, CCTE Ciencia y Vida, Fundación Ciencia y Vida, Huechuraba 8580704, Chile

²

Centro de Bioinformática y Biología Integrativa, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago 8370146, Chile

³

Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, SE-391 82 Kalmar, Sweden

⁴

Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Unidad Académica del Estado de Yucatán, Universidad Nacional Autónoma de México, Mérida, Yucatán, 97302, Mexico

⁵

Center for Bioinformatics and Genome Biology, CCTE Ciencia y Vida, Santiago 7780272, Chile

⁶

Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago 7510156, Chile

^*

Authors to whom correspondence should be addressed.

Microorganisms 2025, 13(6), 1199; https://doi.org/10.3390/microorganisms13061199

Submission received: 17 April 2025 / Revised: 16 May 2025 / Accepted: 17 May 2025 / Published: 24 May 2025

(This article belongs to the Special Issue Bioinformatics and Omic Data Analysis in Microbial Research)

Download Versions Notes

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

Share and Cite

MDPI and ACS Style

Sepúlveda-Rebolledo, P.; González-Rosales, C.; Dopson, M.; Pérez-Rueda, E.; Holmes, D.S.; Valdés, J.H. Comparative Genomics of Sigma Factors in Acidithiobacillia Sheds Light into the Transcriptional Regulatory Networks Involved in Biogeochemical Dynamics in Extreme Acidic Environments. Microorganisms 2025, 13, 1199. https://doi.org/10.3390/microorganisms13061199

AMA Style

Sepúlveda-Rebolledo P, González-Rosales C, Dopson M, Pérez-Rueda E, Holmes DS, Valdés JH. Comparative Genomics of Sigma Factors in Acidithiobacillia Sheds Light into the Transcriptional Regulatory Networks Involved in Biogeochemical Dynamics in Extreme Acidic Environments. Microorganisms. 2025; 13(6):1199. https://doi.org/10.3390/microorganisms13061199

Chicago/Turabian Style

Sepúlveda-Rebolledo, Pedro, Carolina González-Rosales, Mark Dopson, Ernesto Pérez-Rueda, David S. Holmes, and Jorge H. Valdés. 2025. "Comparative Genomics of Sigma Factors in Acidithiobacillia Sheds Light into the Transcriptional Regulatory Networks Involved in Biogeochemical Dynamics in Extreme Acidic Environments" Microorganisms 13, no. 6: 1199. https://doi.org/10.3390/microorganisms13061199

APA Style

Sepúlveda-Rebolledo, P., González-Rosales, C., Dopson, M., Pérez-Rueda, E., Holmes, D. S., & Valdés, J. H. (2025). Comparative Genomics of Sigma Factors in Acidithiobacillia Sheds Light into the Transcriptional Regulatory Networks Involved in Biogeochemical Dynamics in Extreme Acidic Environments. Microorganisms, 13(6), 1199. https://doi.org/10.3390/microorganisms13061199

Note that from the first issue of 2016, this journal uses article numbers instead of page numbers. See further details here.

Article Menu

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

Abstract

Share and Cite

Article Metrics

Article Access Statistics

Further Information

Guidelines

MDPI Initiatives

Follow MDPI