Sains Malaysiana 53(9)(2024): 3031-3044

http://doi.org/10.17576/jsm-2024-5309-10

Exploring the Protease Diversity of Psychrophilic Yeast, Glaciozyma antarctica through Genome Mining Analysis

(Meneroka Kepelbagaian Protease Yis Psikrofili, Glaciozyma antarctica melalui Analisis Perlombongan Genom)

NORFARHAN MOHD-ASSAAD¹, ROHAIZA AHMAD REDZUAN² MOHD FAIZAL ABU BAKAR³, NOR MUHAMMAD MAHADI², ABDUL MUNIR ABDUL MURAD², ROSLI MD. ILLIAS⁴, DORIS QUAY HUAI XIA¹, IZWAN BHARUDIN², FARAH DIBA ABU BAKAR² & SHAZILAH KAMARUDDIN^2,*

¹Department of Applied Physics, Faculty of Science & Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia

²Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia

³Malaysia Genome & Vaccine Institute, Jalan Bangi Lama, 43000 Kajang, Selangor, Malaysia

⁴Department of Bioprocess Engineering, Faculty of Chemical and Energy Engineering, Universiti Teknologi Malaysia, 81310 Skudai, Johor, Malaysia

Received: 20 February 2024/Accepted: 17 July 2024

Abstract

Proteases are one of the most significant classes of enzymes, holding immense physiological relevance and extensive industrial applications. The genome of Glaciozyma antarctica was fully sequenced, showing 7,857 open reading frames that offer an intriguing opportunity to investigate its proteolytic repertoire. This study aims to unveil the protease landscape of G. antarctica, a psychrophilic yeast that produces cold-active enzymes that offer remarkable benefits, particularly in the food and pharmaceutical industries. In this work, we performed a comprehensive analysis to identify the diverse families of proteases encoded within the G. antarctica genome and compare them with proteases from other mesophilic and thermophilic fungi in the MEROPS database. The sequence similarity searches resulted in the identification of 195 open reading frames predicted to encode for proteases in G. antarctica with a high number of intracellular proteases. These findings suggest an evolved system for protein quality control and turnover, essential for cell viability and adaptation to environmental stressors. The MEROPS classification analysis showed an abundance of metalloproteases, constituting 38% of the total protease genes, a proportion surpassing that found in other yeast and fungal genomes studied. This reflects the vital role of metalloproteases in the cold adaptation of microbes in the Antarctic region. This unique profile not only sheds light on the adaptive mechanisms of psychrophilic organisms but also presents a rich reservoir of potential cold-active proteases for various applications. The findings of this study provide a foundation for targeted enzyme discovery and engineering, unlocking new frontiers in industrial biotechnology and extremophile biology.

Keywords: Cold active enzyme; cold adaptation; comparative genomics; peptidase; polar microbiology

Abstrak

Protease adalah salah satu kelas enzim penting yang mempunyai peranan fisiologi yang besar dan aplikasi industri yang luas. Genom G. antarctica telah dijujuk sepenuhnya dan memaparkan sejumlah 7,857 rangka bacaan terbuka yang membuka peluang menarik untuk kajian himpunan enzim proteolitiknya. Kajian ini mendedahkan landskap protease Glaciozyma antarctica, yis psikofilik yang menghasilkan enzim aktif sejuk yang menawarkan manfaat yang luas terutamanya dalam industri makanan dan farmaseutik. Dalam kajian ini, satu analisis komprehensif telah dijalankan untuk mengenal pasti kepelbagaian keluarga protease yang dikodkan dalam genom G. antarctica dan melakukan analisis perbandingan dengan protease daripada kulat mesofil dan termofil dalam pangkalan data MEROPS. Analisis carian persamaan jujukan molekul telah mengenal pasti sebanyak 195 bingkai bacaan terbuka yang diramalkan sebagai gen mengekod protease dalam genom G. antarctica dengan bilangan gen mengekod protease intrasel adalah yang tertinggi. Penemuan ini mencadangkan satu evolusi dalam sistem kawalan kualiti dan kadar pusing ganti protein yang penting untuk kelangsungan hidup G. antarcticadan penyesuaian kepada tekanan alam sekitar. Analisis pengelasan MEROPS G. antarctica menunjukkan yis ini mempunyai bilangan gen mengekod metaloprotease yang tinggi iaitu kira-kira 38% daripada gen mengekod protease keseluruhan di dalam genom. Peratusan ini adalah yang tertinggi jika dibandingkan dengan genom yis dan kulat yang telah dikaji. Ini mencerminkan peranan penting metaloprotease dalam penyesuaian mikrob sejuk di rantau Antartika. Profil protease yang unik ini bukan sahaja memberikan gambaran mekanisme penyesuaian organisme psikofil tetapi juga menyediakan reservoir genom yang kaya dengan protease aktif sejuk yang berpotensi untuk aplikasi yang pelbagai. Hasil kajian ini menyediakan asas untuk penemuan dan kejuruteraan enzim secara bersasar serta penerokaan sempadan ilmu baharu dalam bioteknologi industri dan biologi ekstremofil.

Kata kunci: Adaptasi sejuk; enzim aktif sejuk; genom perbandingan; mikrobiologi kutub; peptidase

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*Corresponding author; email: shazilah@ukm.edu.my