Genomic Sequencing and Biological Characteristics of a Novel Escherichia Coli Bacteriophage 9g, a Putative Representative of a New Siphoviridae Genus

Abstract

Bacteriophage 9g was isolated from horse feces using Escherichia coli C600 as a host strain. Phage 9g has a slightly elongated capsid 62 × 76 nm in diameter and a non-contractile tail about 185 nm long. The complete genome sequence of this bacteriophage consists of 56,703 bp encoding 70 predicted open reading frames. The closest relative of phage 9g is phage PhiJL001 infecting marine alpha-proteobacterium associated with Ircinia strobilina sponge, sharing with phage 9g 51% of amino acid identity in the main capsid protein sequence. The DNA of 9g is resistant to most restriction endonucleases tested, indicating the presence of hypermodified bases. The gene cluster encoding a biosynthesis pathway similar to biosynthesis of the unusual nucleoside queuosine was detected in the phage 9g genome. The genomic map organization is somewhat similar to the typical temperate phage gene layout but no integrase gene was detected. Phage 9g efficiently forms stable associations with its host that continues to produce the phage over multiple passages, but the phage can be easily eliminated via viricide treatment indicating that no true lysogens are formed. Since the sequence, genomic organization and biological properties of bacteriophage 9g are clearly distinct from other known Enterobacteriaceae phages, we propose to consider it as the representative of a novel genus of the Siphoviridae family.

Identification of the minimal bacterial 2′‐deoxy‐7‐amido‐7‐deazaguanine synthesis machinery

“…[Note that the standard nomenclature uses ‘Q’ to represent the ribonucleoside, ‘preQ 0’ and ‘ADG’ to represent the corresponding base, ‘dPreQ 0 ’ and ‘dADG’ to represent the corresponding 2′‐deoxyribonucleosides.] In phages such as the Escherichia coli phage 9g, the presence of dG + confers resistance to many restriction enzymes (Kulikov et al ., ; Tsai et al ., ). The 11‐gene deazapurine‐in‐DNA ( dpd ) cluster of Salmonella enterica serovar Montevideo ATCC BAA‐710 ( S .…”

Novel genomic island modifies DNA with 7-deazaguanine derivatives

“…R-M systems and genomic islands are often transferred through phage transduction. Several examples of phage-encoded tgt-like genes and preQ 0 genes have already been reported in the literature, including Mycobacteriophage Rosebush (36), Streptococcus phage Dp-1 (37), and the E. coli phage 9g (38) (Fig. 6A and SI Appendix, Fig.…”

“…Another role for this modification could be to provide resistance to restriction systems, essentially acting as an antirestriction system (47). The phage 9g DNA is resistant to most restriction enzymes tested (38), suggesting the presence of modified bases inhibits recognition or cleavage by these enzymes.…”

“…S12). In the characterization of phage 9g, Kulikov et al (38) speculated that the restriction endonuclease-resistant nature of the phage DNA suggested it was heavily modified, and they proposed that tgt and preQ 0 synthesis genes were involved in inserting Q into the DNA. To evaluate the prevalence of tgt paralogs and PreQ 0 synthesis genes in phages, a similarity-based search was performed on all available phage genomes in the National Center for Biotechnology Information database.…”

Bacteriophage Genome Sequencing: A New Alternative to Understand Biochemical Interactions between Prokaryotic Cells and Phages

“…Ten families of bacteriophages have been already reported, according to the International committee on taxonomy of viruses (ICTV), phage classification in families and genera are based on capsid morphology, conserved genomic synteny and homology in amino acid sequences of phage genetic material encoded proteins [9]. There are basically four types of genetic material comprising bacteriophages genome, single-stranded and double-stranded DNA and RNA (ssDNA, dsDNA, ssRNA, dsRNA) [10,11].…”