This mini-review describes the current status of recent genome sequencing projects of extremely acidophilic microorganisms and highlights the most current scientific advances emerging from their analysis. There are now at least 56 draft or completely sequenced genomes of acidophiles including 30 bacteria and 26 archaea. There are also complete sequences for 38 plasmids, 29 viruses, and additional DNA sequence information of acidic environments is available from eight metagenomic projects. A special focus is provided on the genomics of acidophiles from industrial bioleaching operations. It is shown how this initial information provides a rich intellectual resource for microbiologists that has potential to open innovative and efficient research avenues. Examples presented illustrate the use of genomic information to construct preliminary models of metabolism of individual microorganisms. Most importantly, access to multiple genomes allows the prediction of metabolic and genetic interactions between members of the bioleaching microbial community (ecophysiology) and the investigation of major evolutionary trends that shape genome architecture and evolution. Despite these promising beginnings, a major conclusion is that the genome projects help focus attention on the tremendous effort still required to understand the biological principles that support life in extremely acidic environments, including those that might allow engineers to take appropriate action designed to improve the efficiency and rate of bioleaching and to protect the environment.
We wish to understand how membrane proteins function in extremely acid conditions (<pH1 - pH3) using, as initial models, a predicted aquaporin and a potassium (K+) channel from the acidophile, Acidithiobacillus ferrooxidans ATCC 23270. A fundamental question is how these proteins function when confronted by a proton concentration difference of 6 orders of magnitude across the membrane. Similarity alignments were used to find the most similar three dimensional structure for each protein from crystallized orthologs deposited in the protein database PDB and these were used as templates for molecular simulations. Proteins from A. ferrooxidans were submitted to a molecular modeling strategy and their structural and dynamic properties were determined using molecular dynamics (MD) simulations (20 ns). Aquaporins are a large family of transmembrane channel proteins that allow the passive but selective movement of water, glycerol or CO2 across cell membranes. MD calculations computed key biophysical features related to permeation parameters. K+ channels are membrane proteins that allow voltage-driven potassium flux across cellular membranes. A structural analysis of the A. ferrooxidans K+ channel predicts that it does not expose ionizable amino acids to the external surface. This would reduce protonation of residues at pH 1, permitting tertiary structure to be maintained.
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