Acidophile

Acidophiles or acidophilic organisms are those that thrive under highly acidic conditions (usually at pH 5.0 or below^[1]). These organisms can be found in different branches of the tree of life, including Archaea, Bacteria,^[2] and Eukarya.

Examples

A list of these organisms includes:

Archaea

Sulfolobales, an order in the Thermoproteota branch^[3] of Archaea
Thermoplasmatales, an order in the Euryarchaeota branch^[3] of Archaea
ARMAN, in the Euryarchaeota branch^[3] of Archaea
Acidianus brierleyi, A. infernus, facultatively anaerobic thermoacidophilic archaebacteria
Halarchaeum acidiphilum, acidophilic member of the Halobacteriacaeae^[4]
Metallosphaera sedula, thermoacidophilic

Bacteria

Acidobacteriota,^[5] a phylum of Bacteria
Acidithiobacillales, an order of Pseudomonadota e.g. A. ferrooxidans, A. thiooxidans
Thiobacillus prosperus, T. acidophilus, T. organovorus, T. cuprinus
Acetobacter aceti, a bacterium that produces acetic acid (vinegar) from the oxidation of ethanol.
Alicyclobacillus, a genus of bacteria that can contaminate fruit juices.^[6]

Eukarya

Mucor racemosus^[7]
Urotricha^[7]
Dunaliella acidophila^[7]
Members of the algal class Cyanidiophyceae, including Cyanidioschyzon merolae

Mechanisms of adaptation to acidic environments

Most acidophile organisms 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.^[8] 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 away from 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, both acidic and basic.

References

^ Jin, Qusheng; Kirk, Matthew F. (2018-05-01). "pH as a Primary Control in Environmental Microbiology: 1. Thermodynamic Perspective". Frontiers in Environmental Science. 6: 21. doi:10.3389/fenvs.2018.00021. ISSN 2296-665X.
^ Becker, A., Types of Bacteria Living in Acidic pH". Retrieved 10 May 2017.
^ ^a ^b ^c Dworkin M, Falkow S (2006). The Prokaryotes: A handbook on the biology of bacteria.
^ Singh OV (2012). Extremophiles: Sustainable Resources and Biotechnological Implications. John Wiley & Sons. pp. 76–79. ISBN 978-1-118-10300-5.
^ Quaiser, Achim; Ochsenreiter, Torsten; Lanz, Christa; Schuster, Stephan C.; Treusch, Alexander H.; Eck, Jürgen; Schleper, Christa (27 August 2003). "Acidobacteria form a coherent but highly diverse group within the bacterial domain: evidence from environmental genomics". Molecular Microbiology. 50 (2): 563–575. doi:10.1046/j.1365-2958.2003.03707.x. PMID 14617179. S2CID 25162803.
^ Pettipher GL; Osmundson ME; Murphy JM (March 1997). "Methods for the detection and enumeration of Alicyclobacillus acidoterrestris and investigation of growth and production of taint in fruit juice and fruit juice-containing drinks". Letters in Applied Microbiology. 24 (3): 185–189. doi:10.1046/j.1472-765X.1997.00373.x. PMID 9080697. S2CID 6976998.
^ ^a ^b ^c Rawlings, Douglas; Johnson, D. Barrie. "Eukaryotic Acidophiles". Encyclopedia of Life Support System (EOLSS). Eolss Publishers. Archived from the original on 2014-10-13. Retrieved 3 February 2014.
^ Menzel, U.; Gottschalk, G. (1985). "The internal pH of Acetobacterium wieringae and Acetobacter aceti during growth and production of acetic acid". Arch Microbiol. 143 (1): 47–51. Bibcode:1985ArMic.143...47M. doi:10.1007/BF00414767. S2CID 6477488.

Cooper, J. B.; Khan, G.; Taylor, G.; Tickle, I. J.; Blundell, T. L. (July 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. doi:10.1016/0022-2836(90)90156-G. PMID 2115088.
Bonisch, H.; Schmidt, C. L.; Schafer, G.; Ladenstein, R. (June 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. doi:10.1016/S0022-2836(02)00323-6. PMID 12054871.
Schafer, K; Magnusson, U; Scheffel, F; Schiefner, A; Sandgren, MO; Diederichs, K; Welte, W; Hülsmann, A; Schneider, E; Mowbray, SL (January 2004). "X-ray structures of the maltose-maltodextrin-binding protein of the thermoacidophilic bacterium Alicyclobacillus acidocaldarius provide insight into acid stability of proteins". Journal of Molecular Biology. 335 (1): 261–74. doi:10.1016/j.jmb.2003.10.042. PMID 14659755.
Walter, R. L.; Ealick, S. E.; Friedman, A. M.; Blake, R. C. 2nd; Proctor, P.; Shoham, M. (November 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. doi:10.1006/jmbi.1996.0612. PMID 8947572.{{cite journal}}: CS1 maint: numeric names: authors list (link)
Botuyan, M. V.; Toy-Palmer, A.; Chung, J.; Blake, R. C. 2nd; Beroza, P.; Case, D. A.; Dyson, H. J. (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 (5): 752–67. doi:10.1006/jmbi.1996.0613. PMID 8947573.{{cite journal}}: CS1 maint: numeric names: authors list (link)
Kelch, B. A.; Eagen, K. P.; Erciyas, F. P.; Humphris, E. L.; Thomason, A. R.; Mitsuiki, S.; Agard, D. A. (May 2007). "Structural and mechanistic exploration of acid resistance: kinetic stability facilitates evolution of extremophilic behavior". J Mol Biol. 368 (3): 870–883. CiteSeerX 10.1.1.79.3711. doi:10.1016/j.jmb.2007.02.032. PMID 17382344.

[1] Jin, Qusheng; Kirk, Matthew F. (2018-05-01). "pH as a Primary Control in Environmental Microbiology: 1. Thermodynamic Perspective". Frontiers in Environmental Science. 6: 21. doi:10.3389/fenvs.2018.00021. ISSN 2296-665X.

[bacteria-2] Becker, A., Types of Bacteria Living in Acidic pH". Retrieved 10 May 2017.

[autogenerated1-3] Dworkin M, Falkow S (2006). The Prokaryotes: A handbook on the biology of bacteria.

[Singh-4] Singh OV (2012). Extremophiles: Sustainable Resources and Biotechnological Implications. John Wiley & Sons. pp. 76–79. ISBN 978-1-118-10300-5.

[5] Quaiser, Achim; Ochsenreiter, Torsten; Lanz, Christa; Schuster, Stephan C.; Treusch, Alexander H.; Eck, Jürgen; Schleper, Christa (27 August 2003). "Acidobacteria form a coherent but highly diverse group within the bacterial domain: evidence from environmental genomics". Molecular Microbiology. 50 (2): 563–575. doi:10.1046/j.1365-2958.2003.03707.x. PMID 14617179. S2CID 25162803.

[6] Pettipher GL; Osmundson ME; Murphy JM (March 1997). "Methods for the detection and enumeration of Alicyclobacillus acidoterrestris and investigation of growth and production of taint in fruit juice and fruit juice-containing drinks". Letters in Applied Microbiology. 24 (3): 185–189. doi:10.1046/j.1472-765X.1997.00373.x. PMID 9080697. S2CID 6976998.

[eolss-7] Rawlings, Douglas; Johnson, D. Barrie. "Eukaryotic Acidophiles". Encyclopedia of Life Support System (EOLSS). Eolss Publishers. Archived from the original on 2014-10-13. Retrieved 3 February 2014.

[8] Menzel, U.; Gottschalk, G. (1985). "The internal pH of Acetobacterium wieringae and Acetobacter aceti during growth and production of acetic acid". Arch Microbiol. 143 (1): 47–51. Bibcode:1985ArMic.143...47M. doi:10.1007/BF00414767. S2CID 6477488.

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