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Complete Genome Sequence of Proteus mirabilis Phage pPM_01 Isolated from Raw Sewage
Ira Aryani Wirjon1, Nyok-Sean Lau, Yahya Mat Arip
1School of Biological Sciences, University Sains Malaysia, Sains@USM, Bayan Lepas, Penang, Malaysia.
Objectives:
Phage pPM_01 was previously isolated from a raw sewage treatment facility located in Batu Maung, Penang, Malaysia, and it was highly lytic against Proteus mirabilis, which causes urinary tract infections in humans. In this paper, we characterize the biology and complete genome sequence of the phage.
Methods And Results:
Transmission electron microscopy revealed phage pPM_01 to be a siphovirus (the first reported virus to infect P. mirabilis), with its complete genome sequence successfully determined. The genome was sequenced using Illumina technology and the reads obtained were assembled using CLC Genomic Workbench v.7.0.3. The whole genome contains a total of 58,546 bp of linear double-stranded DNA with a G+C content of 46.9%. Seventy putative genes were identified and annotated using various bioinformatics tools including RAST, Geneious v.R7, National Center for Biotechnology Information (NCBI) BLAST, and tRNAscan-SE-v1.3 Search. Functional clusters of related potential genes were defined (structural, lytic, packaging, replication, modification, and modulatory). The whole genome sequence showed a low similarity to known phages (i.e., Enterobacter phage Enc34 and Enterobacteria phage Chi). Host range determination and SDS-PAGE analysis were also performed.
Conclusions:
The inability to lysogenize a host, the absence of endotoxin genes in the annotated genome, and the lytic behavior suggest phage pPM_01 as a possible safe biological candidate to control P. mirabilis infection.
Insights
Phage pPM_01, a novel siphovirus, effectively targets Proteus mirabilis, a common cause of urinary tract infections. Its genome characterization reveals potential as a safe biological agent for controlling bacterial infections.
Area of Science:
- Microbiology
- Virology
- Genomics
Background:
- Proteus mirabilis is a significant human pathogen, frequently causing urinary tract infections.
- Bacteriophages offer a promising alternative for combating bacterial infections.
- Phage pPM_01 was previously isolated for its high lytic activity against P. mirabilis.
Purpose of the Study:
- To characterize the biological properties of phage pPM_01.
- To determine and analyze the complete genome sequence of phage pPM_01.
- To evaluate the potential of phage pPM_01 as a therapeutic agent.
Main Methods:
- Transmission electron microscopy was used for morphological analysis.
- Whole genome sequencing was performed using Illumina technology.
- Bioinformatic tools (RAST, Geneious, BLAST) were employed for gene annotation and analysis.
Main Results:
- Phage pPM_01 was identified as a siphovirus, the first reported to infect P. mirabilis.
- The complete genome is 58,546 bp of double-stranded DNA with 70 putative genes.
- The phage genome exhibited low similarity to known phages and lacked endotoxin genes.
Conclusions:
- Phage pPM_01 demonstrates lytic behavior and an inability to lysogenize.
- The absence of endotoxin genes supports its safety profile.
- Phage pPM_01 is a potential candidate for biological control of P. mirabilis infections.