Haloadaptation: insights from comparative modeling studies between halotolerant and non-halotolerant dehalogenases


Edbeib M. F., Aksoy H. M., Kaya Y., Wahabe R. A., Huyop F.

JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, vol.38, no.12, pp.3452-3461, 2020 (SCI-Expanded) identifier identifier identifier

  • Publication Type: Article / Article
  • Volume: 38 Issue: 12
  • Publication Date: 2020
  • Doi Number: 10.1080/07391102.2019.1657498
  • Journal Name: JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
  • Journal Indexes: Science Citation Index Expanded (SCI-EXPANDED), Scopus, BIOSIS, Chemical Abstracts Core, EMBASE, MEDLINE
  • Page Numbers: pp.3452-3461
  • Keywords: Haloadaptation, structure prediction, comparative analysis, molecular dynamics, dehalogenase, HALOPHILIC ADAPTATION, MALATE-DEHYDROGENASE, STRUCTURAL FEATURES, CRYSTAL-STRUCTURE, RHIZOBIUM SP, PROTEIN, SALT, PURIFICATION, CONFORMATION, ENVIRONMENT
  • Ondokuz Mayıs University Affiliated: Yes

Abstract

Halophiles are extremophilic microorganisms that grow optimally at high salt concentrations by producing a myriad of equally halotolerant enzymes. Structural haloadaptation of these enzymes adept to thriving under high-salt environments, though are not fully understood. Herein, the study attempts an in silico investigation to identify and comprehend the evolutionary structural adaptation of a halotolerant dehalogenase, DehHX (GenBank accession number: KR297065) of the halotolerant Pseudomonas halophila, over its non-halotolerant counterpart, DehMX1 (GenBank accession number KY129692) produced by Pseudomonas aeruginosa. GC content of the halotolerant DehHX DNA sequence was distinctively higher (58.9%) than the non-halotolerant dehalogenases (55% average GC). Its acidic residues, Asp and Glu were 8.27% and 12.06%, respectively, compared to an average 5.5% Asp and 7% Glu, in the latter; but lower contents of basic and hydrophobic residues in the DehHX. The secondary structure of DehHX interestingly revealed a lower incidence of alpha-helix forming regions (29%) and a higher percentage of coils (57%), compared to 49% and 29% in the non-halotolerant homologues, respectively. Simulation models showed the DehHX is stable under a highly saline environment (25% w/v) by adopting a highly negative-charged surface with a concomitant weakly interacting hydrophobic core. The study thus, established that a halotolerant dehalogenase undergoes notable evolutionary structural changes related to GC content over its non-halotolerant counterpart, in order to adapt and thrive under highly saline environments. Communicated by Ramaswamy H. Sarma