Acidophile (organisms)

Acidophilic organisms are those that thrive under highly acidic conditions (usually at pH 2.0 or below) . These organisms can be found in different branches of the tree of life, including Archaea, Bacteria, and Fungus. A partial list of these organisms will include:

Archaea

• Sulfolobales, an order in the Crenarchaeota branch of Archaea
• Thermoplasmatales, an order in the Euryarchaeota branch of Archaea
• Acidianus brierleyi, A. infernus, facultatively anaerobic thermoacidophilic archaebacteria
• Metallosphaera sedula, thermoacidophilic

Bacteria

• Acidobacteriuma phylum of the Bacteria
• Acidithiobacillales, an order of Proteobacteria
• Thiobacillus ferrooxidans, T. thiooxidans, T. prosperus, T. acidophilus, T. organovorus, T. cuprinus
• Acetobacter aceti, a bacterium that produces acetic acid (vinegar) from the oxidation of ethanol.

Mechanisms of adaptation to acidic environments

Most acidophilic organism have evolved extremely efficient mechanisms to pump protons out of the intracellular space in order to keep the cytoplasm at or near neutral pH. Therefore, intracellular proteins do not need to develop acid stability through evolution. However, other acidophiles, such as Acetobacter aceti, have an acidified cytoplasm which forces nearly all proteins in the genome to evolve acid stability. For this reason, Acetobacter aceti has become a valuable resource for understanding the mechanisms by which proteins can attain acid stability.

Studies of proteins adapted to low pH have revealed a few general mechanisms by which proteins can achieve acid stability. In most acid stable proteins (such as pepsin and the soxF protein from Sulfolobus acidocaldarius), there is an overabundance of acidic residues which minimizes low pH destabilization induced by a buildup of positive charge. Other mechanisms include minimization of solvent accessibility of acidic residues or binding of metal cofactors. In a specialized case of acid stability, the NAPase protein from Nocardiopsis alba was shown to have relocated acid-sensitive salt bridges to regions that play an important role in the unfolding process. In this case of kinetic acid stability, protein longevity is accomplished across a wide range of pH.

References

• Cooper, J. B. (1990). "X-ray analyses of aspartic proteinases. II. Three-dimensional structure of the hexagonal crystal form of porcine pepsin at 2.3 A resolution". J Mol Biol. 214 (1): 199–222. PMID 2115088.
• Bonisch, H., (2002). "The structure of the soluble domain of an archaeal Rieske iron-sulfur protein at 1.1 A resolution". J Mol Biol. 319 (3): 791–805. PMID 12054871. CS1 maint: Multiple names: authors list (link)
• Schafer, K. (2004). "X-ray structures of the maltose-maltodextrin-binding protein of the thermoacidophilic bacterium Alicyclobacillus acidocaldarius provide insight into acid stability of proteins". J Mol Biol. 335 (1): 261-74. PMID 14659755.
• Walter, R. L. (1996). "Multiple wavelength anomalous diffraction (MAD) crystal structure of rusticyanin: a highly oxidizing cupredoxin with extreme acid stability". J Mol Biol. 263 (5): 730-51.
• Botuyan, M. V. (1996). "NMR solution structure of Cu(I) rusticyanin from Thiobacillus ferrooxidans: structural basis for the extreme acid stability and redox potential". J Mol Biol. 263: 752-67.
• Kelch, B. A. (2007). "Structural and Mechanistic Exploration of Acid Resistance: Kinetic Stability Facilitates Evolution of Extremophilic Behavior". J Mol Biol. 368 (3): 870–883. doi:10.1016/j.jmb.2007.02.032.