Integration of biological networks for Acidithiobacillus thiooxidans Describes a modular gene regulatory organization of bioleaching pathways
Author
dc.contributor.author
Cortés Burgos, María Paz
Author
dc.contributor.author
Acuña Aguayo, Vicente
Author
dc.contributor.author
Travisany Flores, Dante
Author
dc.contributor.author
Siegel, Anne
Author
dc.contributor.author
Maass Sepúlveda, Alejandro
Author
dc.contributor.author
Latorre, Mauricio
Admission date
dc.date.accessioned
2020-10-26T18:29:38Z
Available date
dc.date.available
2020-10-26T18:29:38Z
Publication date
dc.date.issued
2020
Cita de ítem
dc.identifier.citation
Front. Mol. Biosci. 6:155
es_ES
Identifier
dc.identifier.other
10.3389/fmolb.2019.00155
Identifier
dc.identifier.uri
https://repositorio.uchile.cl/handle/2250/177362
Abstract
dc.description.abstract
Acidithiobacillus thiooxidansis 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 anin silicosemi-automatic genome scale approach, two biological networks forA. thiooxidansLicanantay 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 inA. thiooxidansspecies.
es_ES
Patrocinador
dc.description.sponsorship
National Laboratory of High Performance Computing NLHPC
PIA ECM-02