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Extremophile Protein Database
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Acidophiles

Acidophiles are the microorganism that can have unusual growing ability at pH 3 or below. These organisms generally maintain a cytoplasmic pH relatively close to neutrality. Acidophilic stability is the intersecting branch as alkaliphilic and barophilic stability of main branches of extreme adaptations (thermophilic, psychrophilic and halophilic stability) (Reed et al. 2013). Some acidophiles can grow at high temperatures, they are called as Thermoacidophiles. Some thermoacidophilic Archaea thrive at low pH up to very high temperatures. Sulfolobus and Acidanus spp. grow up to 96° C at pH 1-5; Picrophilus oshimae tolerates pH < 0 and grows up to 65° C. The activities of the same types of organisms that cause acid mine drainage are exploited industrially for the bioleaching of copper and other metals from ores (Oren 2010).

Factors responsible for Acidostability

Genomic adaptations

A lesser number of repertoire of acidophilic organisms have been identified. Search for genomes with the key words "acidophilic" in NCBI genome search results in a total of only 29 hits for acidophiles. The genome size of acidophiles is smaller than that of neutrophiles. For example, the smallest genome belongs to thermoacidophilic Thermoplasmatales (< 2 Mb) (Tyson et al. 2004). Acidophilic genomes possess genes for organic acid degradation pathway (Angelov and Liebl, 2006); DNA and protein repair genes (e.g., chaperones) (Baker-Austin and Dopson 2007); and higher proportion of secondary transporters and membrane biosynthesis proteins (Tyson et al. 2004). These genes give a clue about their mechanism of acid homeostasis (Baker-Austin and Dopson 2007). For acidophiles, pyrimidine-rich codons are preferred, which are less susceptible to acid hydrolysis for protection from acid stress (Baker-Austin and Dopson, 2007; Paul et al., 2008). Thus, the genomes of thermoacidophiles such as Picrophilus torridus have evolved by lowering the purine-containing codons in long open reading frames (Baker-Austin and Dopson 2007).

Proteomic adaptations

On the proteome level, acidophiles differ markedly from neutrophiles by synthesizing organic acid degrading proteins and higher proportion of secondary membrane transporters which lead to maintaining the mechanism of neutral pH homeostasis at low pH. The chaperones are involved in protein refolding and they are expressed strongly in acidophiles (Baker-Austin and Dopson 2007).

The molecular adaptations of acidostable proteins are not yet completely clear. The variability in the protein stability and adaptations under acidic condition is very fuzzy and case specific as few changes in the protein can lead to adaptations in a range of conditions (Reed et al. 2013; Vieille and Zeikus 2001). Corresponding to thermoacidophilic organisms, their proteins are showing both the thermophilic as well as acidophilic stability. For example acidophilic proteins can also be thermophilic (Sharma et al. 2012); acidophilic thermostable endo-1,4-β-mannanase of Penicillium oxalicum GZ-2, is highly stable at 60 ° C and pH 4.0 (Liao et al. 2014).

To the ground of low pH, acidostable proteins are observed to be rich in acidic residues, which also show low solvent exposure. Stability is also obtained by replacement of charged amino acids by neutral polar amino acids in proteins which reduce the electrostatic repulsion that occur between charged groups at low pH (Norris et al. 2000). Adaptation of proteins at low pH seem to be attributed to the prevalence of acidic (negatively charged at a neutral pH) amino acids (Asp and Glu) whereas adaptation of proteins at basic pH seem to be attributed to the prevalence of basic amino acids (Lys, Arg and His) on the surface of these enzymes and proteins (Suplatov et al. 2014). An increase in the isoleucine content of the proteins in acidophiles is another observed trend, which is assumed to contribute to acidostability (Baker-Austin and Dopson 2007).

Further Reading

Baker-Austin C, Dopson M (2007) Life in acid: pH homeostasis in acidophiles Trends in microbiology 15:165-171.

Liao H et al. (2014) A new acidophilic thermostable endo-1, 4-β-mannanase from Penicillium oxalicum GZ-2: cloning, characterization and functional expression in Pichia pastoris BMC biotechnology 14:1.

Norris PR, Burton NP, Foulis NA (2000) Acidophiles in bioreactor mineral processing Extremophiles 4:71-76.

Oren A (2010) Acidophiles eLS.

Reed CJ, Lewis H, Trejo E, Winston V, Evilia C (2013) Protein adaptations in archaeal extremophiles Archaea 2013.

Sharma A, Kawarabayasi Y, Satyanarayana T (2012) Acidophilic bacteria and archaea: acid stable biocatalysts and their potential applications Extremophiles 16:1-19.

Suplatov D, Panin N, Kirilin E, Shcherbakova T, Kudryavtsev P, Svedas V (2014) Computational design of a pH stable enzyme: understanding molecular mechanism of penicillin acylase's adaptation to alkaline conditions PloS one 9:e100643.

Tyson GW et al. (2004) Community structure and metabolism through reconstruction of microbial genomes from the environment Nature 428:37-43.

Vieille C, Zeikus GJ (2001) Hyperthermophilic enzymes: sources, uses, and molecular mechanisms for thermostability Microbiology and Molecular Biology Reviews 65:1-43.