Genome Report | Genome Report
Microbiol. Biotechnol. Lett. 2023; 51(4): 562-565
https://doi.org/10.48022/mbl.2311.11017
Su-Hyeon Kim and Mi-Kyung Park*
School of Food Science and Biotechnology, and Food and Bio-industry Research Institute, Kyungpook National University, Daegu 41566, Republic of Korea
Correspondence to :
Mi-Kyung Park, parkmik@knu.ac.kr
Escherichia coli-specific phage, KFS-EC1, was isolated and purified from a slaughterhouse. The complete genome of the phage was obtained using Illumina MiSeq platforms. Its assembled genome consisted of a single chromosome of 164,715 bp with a GC content of 40.5%. The phage genome contained 170 hypothetical and 101 functional ORFs, and exhibited orthologous average nucleotide identity values of >95% with other E. coli phages belonging to the family Straboviridae. Additionally, phylogenetic analysis revealed that KFS-EC1 was finally classified into the family Straboviridae of the genus Caudoviricetes. The genome has been deposited in GenBank under the accession number NC_055757.1.
Keywords: Bacteriophage, Straboviridae, Escherichia coli, whole genome sequencing
Bacteriophages (phages) have garnered interest as potent biocontrol agents against
KFS-EC1 was isolated and purified from slaughterhouse wastewater in Daegu, Korea [4]. For phage isolation, 1% (v/v) host culture of
The genomic DNA of KFS-EC1 was extracted using a Phage DNA Isolation Kit (Norgen Biotek Co., Canada) according to the manufacturer’s instructions. Quantification of the DNA was carried out using a Qubit 3.0 fluorometer (Thermo Fisher Scientific, USA). Subsequently, whole genome sequencing of the phage was performed using the Illumina Miseq platform with paired-end reads of 2 × 150 bp size. Error correction of the generated raw reads was conducted by quality filtering of the Illumina raw reads. The reads that had Phred-score of Q30 and above were collected and assembled using the SPAdes genome assembler (Illumina Inc., USA). The complete genome of KFS-EC1 was annotated using the Rapid Annotations Systems Technology (RAST) server [5] and BLASTP, and the genes linked to lysogenic properties were confirmed using the PHASTER’s database (https://phaster.ca/). After categorizing of the annotated open reading frames (ORFs), a genome map of KFS-EC1 was generated using Geneious software (v. 11.1.5, Biomatters Ltd., New Zealand). In addition, the genome of KFS-EC1 was compared with that of similar
The genetic characteristics of KFS-EC1 are shown in Table 1. The genome of KFS-EC1 consisted of one contig with a genome size of 164,715 bp and a GC content of 40.5%. In addition, its genome was predicted to comprise 170 hypothetical ORFs and 101 functional ORFs, and no tRNA was detected. Although some lytic phages have tRNAs for supporting protein synthesis, but their presence is not universal across all phages. This is because tRNA belongs to the accessory genome that is not an essential component [8]. Furthermore, the functional ORFs were categorized into four groups, including nucleotide metabolism, phage structure and packaging, host lysis, and additional functions (Fig. 1). Expressly, 42 genes related to nucleotide metabolism were confirmed, such as nucleotide replication, DNA repair, and its regulation, which encoded RNA polymerase, DNA polymerase, DNA ligase, DNA helicase, endonuclease, etc. Furthermore, 38 genes involved in the phage structure and packaging were found, such as capsid protein, baseplate and wedge proteins, phage tail, tail fibers, phage neck, phage prohead assembly and capsid scaffolding proteins, and phage tail assembly and scaffolding protein. The main components associated with host lysis (marked as pink arrows, Fig. 1) were also predicted to encode endolysin (9,050 bp−10,849 bp), phage spanin (73,706 bp−74,029 bp), holin (99,392−100,018), and peptidoglycan hydrolase (162,495 bp−162,884 bp). Endolysins degrade the peptidoglycan layer of the cell wall, whereas holins and spanins disrupt the inner membrane and outer membrane of the host, respectively [9], facilitating effective lysis of the host during phages’ lytic cycle. In addition, phage-encoded depolymerases, including hydrolases and lyases, can support the control of the host and its biofilm by cleaving the O-glycosidic bonds of bacterial polysaccharides and then degrading polymers [10]. More importantly, KFS-EC1 did not contain genes associated with prophages compared to the PHASTER’s database (20 December 2023). Overall, these genetic analyses confirmed that KFS-EC1 can control
Table 1 . Comparison of genetic characteristics between KFS-EC1 and other similar
Phage | Genome size (bp) | GC content (%) | tRNA | Predicted ORF | Query coverage (%) | Identity (%) | ANI (%) | Accession number |
---|---|---|---|---|---|---|---|---|
KFS-EC1 | 164,715 | 40.5 | ND | 271 | This study | This study | This study | NC_055757.1 |
vB_Eco_TB34 | 165,220 | 40.5 | ND | 289 | 95.0 | 98.6 | 96.6 | OX_001802.1 |
JEP8 | 165,295 | 40.5 | ND | 272 | 95.0 | 98.1 | 95.7 | MT_764208.1 |
W115 | 163,997 | 40.5 | ND | 268 | 94.0 | 98.4 | 96.5 | ON_286974.1 |
vB_EcoM-pEE20 | 166,422 | 40.4 | ND | 273 | 95.0 | 97.0 | 96.7 | OP_114734.1 |
vB_EcoM_PHB13 | 165,641 | 40.4 | ND | 274 | 95.0 | 94.5 | 96.3 | MK_573636.1 |
ORF, open reading frame; ANI, average nucleotide identity; ND, not detected.
Among
This research was supported by Cooperative Research Program for Agriculture Science and Technology Development (Project No. PJ01572601) funded by Rural Development Administration, Korea.
The authors have no financial conflicts of interest to declare.
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