Acidithiobacillus thiooxidans is one of the most studied biomining species, highlighting its ability to oxidize reduced inorganic sulfur compounds, coupled with its elevated capacity to live under an elevated concentration of heavy metals. In this work, using an in silico semi-automatic genome scale approach, two biological networks for A. thiooxidans Licanantay were generated: (i) An affinity transcriptional regulatory network composed of 42 regulatory family genes and 1,501 operons (57% genome coverage) linked through 2,646 putative DNA binding sites (arcs), (ii) A metabolic network reconstruction made of 523 genes and 1,203 reactions (22 pathways related to biomining processes). Through the identification of confident connections between both networks (V-shapes), it was possible to identify a sub-network of transcriptional factor (34 regulators) regulating genes (61 operons) encoding for proteins involved in biomining-related pathways. Network analysis suggested that transcriptional regulation of biomining genes is organized into different modules. The topological parameters showed a high hierarchical organization by levels inside this network (14 layers), highlighting transcription factors CysB, LysR, and IHF as complex modules with high degree and number of controlled pathways. In addition, it was possible to identify transcription factor modules named primary regulators (not controlled by other regulators in the sub-network). Inside this group, CysB was the main module involved in gene regulation of several bioleaching processes. In particular, metabolic processes related to energy metabolism (such as sulfur metabolism) showed a complex integrated regulation, where different primary regulators controlled several genes. In contrast, pathways involved in iron homeostasis and oxidative stress damage are mainly regulated by unique primary regulators, conferring Licanantay an efficient, and specific metal resistance response. This work shows new evidence in terms of transcriptional regulation at a systems level and broadens the study of bioleaching in A. thiooxidans species.
Keywords: Acidithiobacillus thiooxidans; bioleaching; biological networks; biotechnology; co-regulation.
Copyright © 2020 Cortés, Acuña, Travisany, Siegel, Maass and Latorre.
A new genome of Acidithiobacillus thiooxidans provides insights into adaptation to a bioleaching environment.Res Microbiol. 2014 Nov;165(9):743-52. doi: 10.1016/j.resmic.2014.08.004. Epub 2014 Aug 19. Res Microbiol. 2014. PMID: 25148779
The bioleaching potential of a bacterial consortium.Bioresour Technol. 2016 Oct;218:659-66. doi: 10.1016/j.biortech.2016.07.012. Epub 2016 Jul 6. Bioresour Technol. 2016. PMID: 27416516
Metabolomic study of Chilean biomining bacteria Acidithiobacillus ferrooxidans strain Wenelen and Acidithiobacillus thiooxidans strain Licanantay.Metabolomics. 2013 Feb;9(1):247-257. doi: 10.1007/s11306-012-0443-3. Epub 2012 Jul 21. Metabolomics. 2013. PMID: 23335869 Free PMC article.
Acidithiobacillus thiooxidans and its potential application.Appl Microbiol Biotechnol. 2019 Oct;103(19):7819-7833. doi: 10.1007/s00253-019-10098-5. Epub 2019 Aug 28. Appl Microbiol Biotechnol. 2019. PMID: 31463545 Review.
Genomic insights into the iron uptake mechanisms of the biomining microorganism Acidithiobacillus ferrooxidans.J Ind Microbiol Biotechnol. 2005 Dec;32(11-12):606-14. doi: 10.1007/s10295-005-0233-2. Epub 2005 May 14. J Ind Microbiol Biotechnol. 2005. PMID: 15895264 Review.