Gene isolation and prediction of the corresponding three-dimensional structure of subtilisin from the psychrophilic yeast, Glaciozyma antarctica PI12

Siti Mardhiah Mustafha, Shazilah Kamaruddin, Nor Muhammad Mahadi, Abdul Munir Abd. Murad, Farah Diba Abu Bakar

Research output: Contribution to journalArticle

Abstract

Aims: Subtilisin, a serine protease, is a key player in many industrial applications especially in the detergent industry. Most reported subtilisins originate from mesophilic and thermophilic microorganisms. Only scarce information about cold-active subtilisins from psychrophilic microbes is available. Here we describe the isolation, cloning and in silico characterisation of a gene encoding subtilisin in the obligate psychrophilic yeast, Glaciozyma antarctica PI12. Methodology and results: A full-length cDNA from Glaciozyma antarctica encoding subtilisin (GaSUB) was isolated through Reverse-Transcription-Polymerase Chain Reaction (RT-PCR) techniques. The open reading frame of GaSUB comprised 1,125 nucleotides encoding 375 amino acids. The GaSUB amino acid sequence had 49% sequence identity with a subtilisin from the yeast, Puccinia striiformis. Bioinformatic analyses revealed that the GaSUB protein contains a domain that represents the S8 domain of the largest protease family. The predicted model of GaSUB protein using MODELLER and Pymol software revealed that this enzyme has longer loops and less intramolecular interactions between amino acid residues as compared to its mesophilic and thermophilic counterparts. These characteristics are known to help in protein flexibility and stability in cold-active enzymes. Conclusion, significance and impact of study: Bioinformatics characterisations suggested that this enzyme is uniquely adapted to cold environments. Further work using amplified cDNA will be conducted to confirm the catalytic function of this enzyme.

Original languageEnglish
Pages (from-to)452-461
Number of pages10
JournalMalaysian Journal of Microbiology
Volume14
Issue numberSpecialissue6
DOIs
Publication statusPublished - 1 Jan 2018

Fingerprint

Subtilisin
Yeasts
Genes
Subtilisins
Enzymes
Computational Biology
Complementary DNA
Amino Acids
Protein Stability
Serine Proteases
Detergents
Computer Simulation
Open Reading Frames
Reverse Transcription
Organism Cloning
Amino Acid Sequence
Industry
Proteins
Peptide Hydrolases
Software

Keywords

  • Cold-active enzyme
  • Protein homology modelling
  • S8 protease family

ASJC Scopus subject areas

  • Microbiology (medical)
  • Infectious Diseases

Cite this

Gene isolation and prediction of the corresponding three-dimensional structure of subtilisin from the psychrophilic yeast, Glaciozyma antarctica PI12. / Mustafha, Siti Mardhiah; Kamaruddin, Shazilah; Mahadi, Nor Muhammad; Abd. Murad, Abdul Munir; Abu Bakar, Farah Diba.

In: Malaysian Journal of Microbiology, Vol. 14, No. Specialissue6, 01.01.2018, p. 452-461.

Research output: Contribution to journalArticle

@article{0b98c7831bdb44f89accdd729adf1d7c,
title = "Gene isolation and prediction of the corresponding three-dimensional structure of subtilisin from the psychrophilic yeast, Glaciozyma antarctica PI12",
abstract = "Aims: Subtilisin, a serine protease, is a key player in many industrial applications especially in the detergent industry. Most reported subtilisins originate from mesophilic and thermophilic microorganisms. Only scarce information about cold-active subtilisins from psychrophilic microbes is available. Here we describe the isolation, cloning and in silico characterisation of a gene encoding subtilisin in the obligate psychrophilic yeast, Glaciozyma antarctica PI12. Methodology and results: A full-length cDNA from Glaciozyma antarctica encoding subtilisin (GaSUB) was isolated through Reverse-Transcription-Polymerase Chain Reaction (RT-PCR) techniques. The open reading frame of GaSUB comprised 1,125 nucleotides encoding 375 amino acids. The GaSUB amino acid sequence had 49{\%} sequence identity with a subtilisin from the yeast, Puccinia striiformis. Bioinformatic analyses revealed that the GaSUB protein contains a domain that represents the S8 domain of the largest protease family. The predicted model of GaSUB protein using MODELLER and Pymol software revealed that this enzyme has longer loops and less intramolecular interactions between amino acid residues as compared to its mesophilic and thermophilic counterparts. These characteristics are known to help in protein flexibility and stability in cold-active enzymes. Conclusion, significance and impact of study: Bioinformatics characterisations suggested that this enzyme is uniquely adapted to cold environments. Further work using amplified cDNA will be conducted to confirm the catalytic function of this enzyme.",
keywords = "Cold-active enzyme, Protein homology modelling, S8 protease family",
author = "Mustafha, {Siti Mardhiah} and Shazilah Kamaruddin and Mahadi, {Nor Muhammad} and {Abd. Murad}, {Abdul Munir} and {Abu Bakar}, {Farah Diba}",
year = "2018",
month = "1",
day = "1",
doi = "10.21161/mjm.1461802",
language = "English",
volume = "14",
pages = "452--461",
journal = "Malaysian Journal of Microbiology",
issn = "1823-8262",
publisher = "Malaysian Society for Microbiology",
number = "Specialissue6",

}

TY - JOUR

T1 - Gene isolation and prediction of the corresponding three-dimensional structure of subtilisin from the psychrophilic yeast, Glaciozyma antarctica PI12

AU - Mustafha, Siti Mardhiah

AU - Kamaruddin, Shazilah

AU - Mahadi, Nor Muhammad

AU - Abd. Murad, Abdul Munir

AU - Abu Bakar, Farah Diba

PY - 2018/1/1

Y1 - 2018/1/1

N2 - Aims: Subtilisin, a serine protease, is a key player in many industrial applications especially in the detergent industry. Most reported subtilisins originate from mesophilic and thermophilic microorganisms. Only scarce information about cold-active subtilisins from psychrophilic microbes is available. Here we describe the isolation, cloning and in silico characterisation of a gene encoding subtilisin in the obligate psychrophilic yeast, Glaciozyma antarctica PI12. Methodology and results: A full-length cDNA from Glaciozyma antarctica encoding subtilisin (GaSUB) was isolated through Reverse-Transcription-Polymerase Chain Reaction (RT-PCR) techniques. The open reading frame of GaSUB comprised 1,125 nucleotides encoding 375 amino acids. The GaSUB amino acid sequence had 49% sequence identity with a subtilisin from the yeast, Puccinia striiformis. Bioinformatic analyses revealed that the GaSUB protein contains a domain that represents the S8 domain of the largest protease family. The predicted model of GaSUB protein using MODELLER and Pymol software revealed that this enzyme has longer loops and less intramolecular interactions between amino acid residues as compared to its mesophilic and thermophilic counterparts. These characteristics are known to help in protein flexibility and stability in cold-active enzymes. Conclusion, significance and impact of study: Bioinformatics characterisations suggested that this enzyme is uniquely adapted to cold environments. Further work using amplified cDNA will be conducted to confirm the catalytic function of this enzyme.

AB - Aims: Subtilisin, a serine protease, is a key player in many industrial applications especially in the detergent industry. Most reported subtilisins originate from mesophilic and thermophilic microorganisms. Only scarce information about cold-active subtilisins from psychrophilic microbes is available. Here we describe the isolation, cloning and in silico characterisation of a gene encoding subtilisin in the obligate psychrophilic yeast, Glaciozyma antarctica PI12. Methodology and results: A full-length cDNA from Glaciozyma antarctica encoding subtilisin (GaSUB) was isolated through Reverse-Transcription-Polymerase Chain Reaction (RT-PCR) techniques. The open reading frame of GaSUB comprised 1,125 nucleotides encoding 375 amino acids. The GaSUB amino acid sequence had 49% sequence identity with a subtilisin from the yeast, Puccinia striiformis. Bioinformatic analyses revealed that the GaSUB protein contains a domain that represents the S8 domain of the largest protease family. The predicted model of GaSUB protein using MODELLER and Pymol software revealed that this enzyme has longer loops and less intramolecular interactions between amino acid residues as compared to its mesophilic and thermophilic counterparts. These characteristics are known to help in protein flexibility and stability in cold-active enzymes. Conclusion, significance and impact of study: Bioinformatics characterisations suggested that this enzyme is uniquely adapted to cold environments. Further work using amplified cDNA will be conducted to confirm the catalytic function of this enzyme.

KW - Cold-active enzyme

KW - Protein homology modelling

KW - S8 protease family

UR - http://www.scopus.com/inward/record.url?scp=85061395932&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85061395932&partnerID=8YFLogxK

U2 - 10.21161/mjm.1461802

DO - 10.21161/mjm.1461802

M3 - Article

VL - 14

SP - 452

EP - 461

JO - Malaysian Journal of Microbiology

JF - Malaysian Journal of Microbiology

SN - 1823-8262

IS - Specialissue6

ER -