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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
Diserahkan: 17 Februari
2023/Diterima: 19 Jun 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. zongtaii TMN-42, C. arcticum PAMC27867
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
Strai baaruCryobacterium 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. Mereka terdiri 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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*Pengarang untuk surat-menyurat; email:
michaelw@ums.edu.my
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