title: Insights into the molecular basis of piezophilic adaptation: Extraction of piezophilic signatures.
abstract: Piezophiles are the organisms which can successfully survive at extreme pressure conditions. However, the molecular basis of piezophilic adaptation is still poorly understood. Analysis of the protein sequence adjustments that had taken place during evolution can help to reveal the sequence adaptation parameters responsible for protein functional and structural adaptation at such high pressure conditions. In this current work we have used SVM classifier for filtering strong instances and generated human interpretable rules from these strong instances by using the PART algorithm. These generated rules were analyzed for getting insights into the molecular signature patterns present in the piezophilic proteins. The experiments were performed on three different temperature ranges piezophilic groups, namely psychrophilic-piezophilic, mesophilic-piezophilic, and thermophilic-piezophilic for the detailed comparative study. The best classification results were obtained as we move up the temperature range from psychrophilic-piezophilic to thermophilic-piezophilic. Based on the physicochemical classification of amino acids and using feature ranking algorithms, hydrophilic and polar amino acid groups have higher discriminative ability for psychrophilic-piezophilic and mesophilic-piezophilic groups along with hydrophobic and nonpolar amino acids for the thermophilic-piezophilic groups. We also observed an overrepresentation of polar, hydrophilic and small amino acid groups in the discriminatory rules of all the three temperature range piezophiles along with aliphatic, nonpolar and hydrophobic groups in the mesophilic-piezophilic and thermophilic-piezophilic groups.
authors.affiliation: Department of Computer Science, Banaras Hindu University, India. Electronic address: abhigyannath01@gmail.com.
authors.forename: Abhigyan
authors.initials: A
authors.lastname: Nath
authors.affiliation: Department of Computer Science, Banaras Hindu University, India. Electronic address: karthinikita@gmail.com.
authors.forename: Karthikeyan
authors.initials: K
authors.lastname: Subbiah
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics*; D000465:Algorithms; D000596:Amino Acids / Q000737:chemistry / Q000235:genetics; D001105:Archaea / Q000145:classification / Q000235:genetics / Q000254:growth & development; D019843:Archaeal Proteins / Q000235:genetics*; D001419:Bacteria / Q000145:classification / Q000235:genetics / Q000254:growth & development; D001426:Bacterial Proteins / Q000235:genetics*; D019295:Computational Biology / Q000379:methods; D057927:Hydrophobic and Hydrophilic Interactions; D008957:Models, Genetic; D011312:Pressure; D013696:Temperature
chemical_list: D000596:Amino Acids; D019843:Archaeal Proteins; D001426:Bacterial Proteins
keywords: Amino acid composition; Molecular signature; PART; Piezophiles; SVM