Identification and Unusual Properties of the Master Regulator FNR in the Extreme Acidophile Acidithiobacillus ferrooxidans

Abstract

The ability to conserve energy in the presence or absence of oxygen provides a metabolic versatility that confers an advantage in natural ecosystems. The switch between alternative electron transport systems is controlled by the fumarate nitrate reduction transcription factor (FNR) that senses oxygen via an oxygen-sensitive [4Fe-4S] 2+ iron-sulfur cluster. Under O 2 limiting conditions, FNR plays a key role in allowing bacteria to transition from aerobic to anaerobic lifestyles. This is thought to occur via transcriptional activation of genes involved in anaerobic respiratory pathways and by repression of genes involved in aerobic energy production. The Proteobacterium Acidithiobacillus ferrooxidans is a model species for extremely acidophilic microorganisms that are capable of aerobic and anaerobic growth on elemental sulfur coupled to oxygen and ferric iron reduction, respectively. In this study, an FNR-like protein (FNR AF ) was discovered in At. ferrooxidans that exhibits a primary amino acid sequence and major motifs and domains characteristic of the FNR family of proteins, including an effector binding domain with at least three of the four cysteines known to coordinate an [4Fe-4S] 2+ center, a dimerization domain, and a DNA binding domain. Western blotting with antibodies against Escherichia coli FNR (FNR EC ) recognized FNR AF . FNR AF was able to drive expression from the FNR-responsive E. coli promoter P narG , suggesting that it is functionally active as an FNR-like protein. Upon air exposure, FNR AF demonstrated an unusual lack of sensitivity to oxygen compared to the archetypal FNR EC . Comparison of the primary amino acid sequence of FNR AF with that of other natural and mutated FNRs, including FNR EC , coupled with an analysis of the predicted tertiary structure of FNR AF using the crystal structure of the related FNR from Aliivibrio fisheri as a template revealed a number of amino acid changes that could potentially stabilize FNR AF in the presence of oxygen. These include a truncated N terminus and amino acid changes both around the putative Fe-S cluster coordinating cysteines and also in the dimer interface. Increased O 2 stability could allow At. ferrooxidans to survive in environments with fluctuating O 2 concentrations, providing an evolutionary advantage in natural, and engineered environments where oxygen gradients shape the bacterial community.

Genomic Variation and Arsenic Tolerance Emerged as Niche Specific Adaptations by Different Exiguobacterium Strains Isolated From the Extreme Salar de Huasco Environment in Chilean – Altiplano

“…Also, this molecule is a co-factor for ArxA too (Zargar et al, 2010). Besides, the presence of the transcriptional fumarate and nitrate reductase regulator fnr in this genetic cluster could be evidence of an anoxic related response (Osorio et al, 2019). Finally, as most of our studied markers are part of the core genome compartment, we would imply that differences in regulation and expression levels among the strains could be the source of their variable arsenic tolerance levels.…”

A Large-Scale Genome-Based Survey of Acidophilic Bacteria Suggests That Genome Streamlining Is an Adaption for Life at Low pH

“…The abundancy of signal transduction mechanisms generally declines with decreasing genome size, as it has been found that the number of one- and two-component signal transduction systems is proportional to the square of the genome size ( Konstantinidis and Tiedje, 2004 ; Galperin, 2005 ; Ulrich et al, 2005 ). Extensive research has been conducted on the different signal pathways and regulatory networks of acidophiles ( Rzhepishevska et al, 2007 ; Shmaryahu et al, 2009 ; Moinier et al, 2017 ; Díaz et al, 2018 ; Osorio et al, 2019 ). However, additional research is needed to uncover what signal pathways are not present in these organisms.…”

Multiple sensors provide spatiotemporal oxygen regulation of gene expression in a Rhizobium-legume symbiosis

“…This would create pressure for strains to rapidly demonstrate their effectiveness to their legume host. Past work has suggested that one of the benefits of FnrN compared to FixLJ-FixK is that it is more responsive to O 2 concentration, providing more flexible regulation [ 86 , 87 , 128 ]. By enabling more fine-tuned control, integrated multi-sensor O 2 regulatory pathways may speed up the symbiotic transition, providing a competitive advantage.…”