Sains Malaysiana 52(7)(2023): 1955-1966

http://doi.org/10.17576/jsm-2023-5207-05

Genomic Analysis of a Novel Antarctic Bacterium, Cryobacterium sp. SO2 Provides Insights into its Genomic Potential for Production of Antimicrobial Compounds

(Analisis Genom Bakteria Antartika Baharu, Cryobacterium sp. SO2 Memberi Cerapan tentang Potensi Genomnya untuk Pengeluaran Sebatian Antimikrob)

TEOH, C.P.¹, LAVIN, P.², GONZÁLEZ-ARAVENA, M.³ & WONG, C.M.V.L.¹*

¹Biotechnology Research Institute, Universiti Malaysia Sabah, 88400 Kota Kinabalu, Sabah, Malaysia

²Departamento de Biotecnologia, Facultad de Ciencias del Mar y Recursos Biologicos, Universidad de Antofagasta, 601 Avenida Angamos, Antofagasta 1270300, Chile

³Instituto Antártico Chileno, Plaza Muñoz Gamero 1055, Punta Arenas, Chile

Received: 17 February 2023/Accepted: 19 June 2023

Abstract

A novel strain of Cryobacterium designated as SO2, was isolated from the Antarctic. Hence, this study was undertaken to gain further insight into the antimicrobial compounds and secondary metabolites produced by Cryobacterium sp. SO2. It was found that strain SO2 is a Gram-positive that exhibits an irregular rod shape, which formed yellow to orange pigmented colonies on semi-solid media. Strain SO2 grows at temperatures ranging from 4 to 25 ºC. It has a complete genomic size of 4.097 Mb. SO2 has a DNA G+C content of 68.43%, and genomic annotation showed that the genome contained 3,862 CDS, 10 rRNA, 55 tRNA and 1 tm-RNA. Phylogenetic and OrthoANI analysis suggested Cryobacterium sp. strains SO1, N22, TMB1-8, LW097, TMN39-1, C. zongtaiiTMN-42, C. arcticumPAMC27867 and C. soli GCJ02 as its closest phylogenetic neighbour. Genome annotation shows that strain SO2 confers β-lactamase class A, cephalosporin-C deacetylases, and 27 drug-resistance encoding genes, and allows resistance to ceftazidime. Functional annotation identifies 28.74% of predicted genes are of unknown functions. Genome mining indicates that there are six putative secondary metabolite gene clusters in strain SO2. They are made up of RRE-containing, terpene, beta-lactone, T3PKS, NAPAA, and 2dos. This finding shows strain SO2 harbours genes that may be involved in the production of compounds with antibacterial and antioxidant activities.

Keywords: Complete genome; Cryobacterium sp.; drug-resistant; psychrotolerant; secondary metabolite gene cluster

Abstrak

Strain baharu Cryobacterium yang ditetapkan sebagai SO2 telah dipencilkan dari Antartika. Oleh itu, kajian ini dijalankan untuk mendapatkan pemahaman yang lebih mendalam mengenai sebatian antimikrob dan penghasilan metabolit sekunder oleh Cryobacterium sp. SO2. Didapati bahawa strain SO2 adalah Gram-positif yang mempamerkan bentuk rod yang tidak teratur, yang membentuk koloni berpigmen kuning hingga oren pada media separa pepejal. Strain SO2 tumbuh pada suhu antara 4 hingga 25 ºC. Saiz genomnya yang lengkap adalah 4.097 Mb. Strain SO2 mempunyai kandungan G+C DNA sebanyak 68.43% dan anotasi genom menunjukkan terdapatnya 3,862 CDS, 10 rRNA, 55 tRNA dan 1 tm-RNA. Analisis filogenetik dan OrthoANI mencadangkan Cryobacterium sp strain SO1, N22, TMB1-8, LW097, TMN39-1, C. zongtaii TMN-42, C. arcticum PAMC27867 dan C. soli GCJ02 merupakan jiran filogenetik terdekat. Anotasi genom menunjukkan bahawa strain SO2 mengandungi β-laktamase kelas A, cephalosporin-C deacetylases dan 27 gen kerintangan dadah dan menyebabkan kerintangan strain SO2 terhadap ceftazidime. Anotasi kefungsian mengenal pasti 28.74% gen yang diramalkan mempunyai fungsi yang tidak diketahui. Perlombongan genom strain SO2 menunjukkan terdapatnya enam kluster gen metabolit sekunder. Merekaterdiri daripada RRE, terpena, beta-lakton, T3PKS, NAPAA dan 2dos. Penemuan ini menunjukkan strain SO2 mengandungi gen yang mungkin terlibat dalam aktiviti antibakteria dan antioksidan.

Kata kunci: Cryobacterium sp.; genom lengkap; kerintangan dadah; kluster gen metabolit sekunder; psikrotoleran

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*Corresponding author; email: michaelw@ums.edu.my