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Extremophile Protein Database
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Barophiles



Barophilic microorganisms thrive in extremely high pressure environments, often exceeding upto 150 MPa (Zeng et al. 2009). For example, Pyrococcus yayanosii is the most pressure resistant microorganism which can survive up to 150 MPa. The habitats of such organisms are marine trenches, deep sea sediments, hydrothermal vents, ocean floors and rocks deep under the Earth (Kato et al. 1998; Rothschild and Mancinelli 2001). Most barophilic organisms can also face other environmental extremities in addition to high pressure, such as extremes of temperature, pH, high salt concentration and scarcity of nutrients (Kumar et al. 2018). This indicates that barophiles can also be mixotrophic in nature harboring properties of thermophiles, psychrophiles, halophiles, alkaliphiles and acidophiles (Chakravorty et al. 2017).

Barostability can be defined by proteins to remain kinetically and thermodynamically stable at elevated pressures exceeding from 30 MPa to 130 MPa. Such proteins are of high industrial priority as they are useful in high pressure bioreactors for food processing and antibiotic production.

Factors responsible for Barostability

Genomic adaptations

To the best of our knowledge less work on genomes from barophilic micro-organisms has been reported. Reports on barophilic adaptations can be found in the work of Di Giulio (2005) who initiated his studies by comparison of homologous genomic sequences of barophilic Pyrococcus abyssi and non-barophilic Pyrococcus furiosus. He reported that barophilic genomes are poor in GC-content and also showed that GC-rich codons were insignificant in barophiles ( Di Giulio 2013; Di Giulio 2005). It has also been reported that in order to survive in such environments, barophilic microorganisms require robust DNA repair systems since high pressure can damage DNA and proteins, so survival necessitates avoidance of damage or high repair rates (Rothschild and Mancinelli 2001). Additionally, pressure-regulated operons (ompH) have evolved in barophilic genomes which are responsible for high-pressure adaptations in barophiles (Kato et al. 1997; Kato et al. 1995).

Proteomic adaptations

The molecular basis of proteomic adaptations of thermophilic, psychrophilic, halophilic, acidophilic and alkalophilic proteins are well-known but the barophilic adaptation is still unclear. The extreme pressure adaptation of proteome was also explored for the first time by Di Giulio (2005) that reported the barophilic P. abyssi tends to substitute arginine (Arg) for all other amino acids in sequences homologous to non-barophilic P. furiosus (Di Giulio 2005). He considered Arg to be the "barophilic amino acid" (Di Giulio 2005). Yafremava et al. 2013 also shown that Arg is preferred in barophilic proteins when compared to non-barophilic proteins (Yafremava et al. 2013). Another example of adaptation in piezophile P. abyssi, having an increase in small amino acids (Gly, Ala, Ser, Thr, Pro, Asp and Asn) across its proteome when compared to that of the related non-piezophile, P. furiosus have been found ( Yafremava et al. 2013; Di Giulio 2005).

The physical factor like pressure is also involved in the stabilization of proteins. Like, hyperthermophiles survive under high-temperature environments and also survive under high-pressure environments. Because of these environments, hyperthermophiles cannot avoid pressure and temperature (such as Thermococcus barophilus). All their macromolecular cell components have to be adapted to high pressures (Michels and Clark 1997). In such microorganisms, the enzymes are stabilized and activated by high pressures (e.g., M. jannaschii protease and hydrogenase). The three-dimensional structure of these enzymes is stabilized mainly by the three types of biophysical interactions: hydrogen bond, electrostatic interactions and hydrophobic interactions. Michels and Clark (1997) reported that the pressure favors the smallest volume and high percentage of hydrophobic interactions in the enzyme structure is the main rationale behind the protein stabilization under high pressure (Michels and Clark 1997). Since pressure played an important role in stabilization of enzymes, it has great potential benefits for activation in biocatalysis. They also found that increase in pressure upto 500 atm resulted in 3.4-fold and 2.7-fold increase in activity and thermostability, of M. jannaschii protease and hydrogenase, respectively (Michels and Clark 1997). The barophilic and thermophilic behavior of the enzyme is consistent with the barophilic growth of M. jannaschii observed previously (Miller et al. 1988).

Further Reading

Chakravorty D, Khan MF, Patra S (2017b) Multifactorial level of extremostability of proteins: can they be exploited for protein engineering? Extremophiles, 21:419-444.

Di Giulio M (2005) Comparison of proteins from Pyrococcus furiosus and Pyrococcus abyssi: barophily in the physicochemical properties of amino acids and in the genetic code. Gene 346:1-6.

Di Giulio M (2013) The origin of the genetic code in the ocean abysses: new comparisons confirm old observations. J Theor Biol 333:109-16.

Kato C, Bartlett DH (1997) The molecular biology of barophilic bacteria Extremophiles 1:111-116

Kato C, Li L, Tamaoka J, Horikoshi K (1997) Molecular analyses of the sediment of the 11000-m deep Mariana Trench Extremophiles 1:117-123.

Kato C, Sato T, Horikoshi K (1995) Isolation and properties of barophilic and barotolerant bacteria from deep-sea mud samples Biodiversity & Conservation 4:1-9.

Kumar A, Alam A, Tripathi D, Rani M, Khatoon H, Pandey S, Ehtesham NZ, Hasnain SE (2018) Protein adaptations in extremophiles: An insight into extremophilic connection of mycobacterial proteome. InSeminars in cell & developmental biology. Academic Press.

Michels PC, Clark DS (1997) Pressure-enhanced activity and stability of a hyperthermophilic protease from a deep-sea methanogen Applied and environmental microbiology 63:3985-3991.

Miller JF, Almond EL, Shah NN, Ludlow JM, Zollweg JA, Streett WB, Zinder SH, Clark DS (1988) High-pressure-temperature bioreactor for studying pressure-temperature relationships in bacterial growth and productivity. Biotechnol Bioeng 31:407-13.

Rothschild LJ, Mancinelli RL (2001) Life in extreme environments Nature 409:1092-1101.

Yafremava LS, Di Giulio M, Caetano-Anolles G (2013) Comparative analysis of barophily-related amino acid content in protein domains of Pyrococcus abyssi and Pyrococcus furiosus Archaea 2013.

Zeng X, Birrien JL, Fouquet Y et al (2009) Pyrococcus CH1, an obligate piezophilic hyperthermophile: extending the upper pressure-temperature limits for life. ISME J 3:873-876.