From Orphan Phage to a Proposed New Family–The Diversity of N4-Like Viruses

Abstract

Escherichia phage N4 was isolated in 1966 in Italy and has remained a genomic orphan for a long time. It encodes an extremely large virion-associated RNA polymerase unique for bacterial viruses that became characteristic for this group. In recent years, due to new and relatively inexpensive sequencing techniques the number of publicly available phage genome sequences expanded rapidly. This revealed new members of the N4-like phage group, from 33 members in 2015 to 115 N4-like viruses in 2020. Using new technologies and methods for classification, the Bacterial and Archaeal Viruses Subcommittee of the International Committee on Taxonomy of Viruses (ICTV) has moved the classification and taxonomy of bacterial viruses from mere morphological approaches to genomic and proteomic methods. The analysis of 115 N4-like genomes resulted in a huge reassessment of this group and the proposal of a new family “Schitoviridae”, including eight subfamilies and numerous new genera.

A Roadmap for Genome-Based Phage Taxonomy

“…While this is a situation that is unsustainable in the long term, in the short term, little taxonomically important information will be lost. For example, the genera Lederbergvirus and Myxoctovirus are both assigned to the family Podoviridae, but their members share no orthologues (verified by CoreGenes 5.0 (coregenes.ngrok.io, accessed on 5 February 2021) as in [ 40 ](CoreGenes 3.5 [ 41 ]). Therefore, their position as floating genera in the class Caudoviricetes , is a better representation of their genomic relatedness than grouping them together in the family Podoviridae .…”

Prophage Genomics and Ecology in the Family Rhodobacteraceae

“…Two cultivated phages (SIO1 and P12053L) and six metagenome-assembled phages form a genus-level phylogenetic clade with the Cobaviruses according to their amino acid sequence similarity [ 44 ]. N4-like phages are another recently described group of roseophages initially classified as Podoviridae and likely to be placed in their own family, Schitoviridae [ 45 , 46 , 47 , 48 ]. N4-like phage genomes contain a set of 14 core genes with functions in DNA replication and transcription, including RNA polymerases [ 46 , 47 , 49 ].…”

Systematic exploration ofEscherichia coliphage-host interactions with the BASEL phage collection

“…Besides these 66 Table), we included a panel of ten classical model phages in our genomic and phenotypic characterization and view them as an accessory part of the BASEL collection. Beyond the T phages (without T1 that is a notorious laboratory contaminant [32]), we included well-studied podovirus N4 and obligately lytic mutants of the three most commonly studied temperate phages lambda, P1, and P2 [5,7,33,34] (Fig 2; see also S5 Table).…”

“…Consequently, we find that phages T7 and JacobBurckhardt, but not closely related Teseptimavirus JeanTingely (Bas62), encode a distinct variant of dGTPase Gp1.2 that likely causes their sensitivity to PifA (Fig 10D). Bacteriophage N4 is the archetype of Enquatrovirus phages that are hallmarked by using a large, virion-encapsidated RNA polymerase for the transcription of their early genes [33], and our new Enquatrovirus isolate AlfredRasser (Bas67) is a very close relative of N4 ( Fig 10E). Based primarily on genetic evidence, phage N4 is thought to initiate infections by contacting the host's ECA with its lateral tail fibers [73,85,86] (Fig 10A).…”

“…In addition to the 66 newly isolated bacteriophages, ten classical model phages were included for genomic and phenotypic characterization, and we view these phages as an accessory part of the BASEL collection. These ten phages were six of the seven T phages (excluding T1 because it is a notorious laboratory contaminant [32]), phage N4, and obligately lytic mutants of the three well-studied temperate phages lambda, P1, and P2 [5,7,33,34] (Fig 2; see also S5 Table ). To generate the T3(K12) chimera, the 3' end of gp17 lateral tail fiber gene of phage T7 was cloned into lowcopy plasmid pUA139 with flanking regions exhibiting high sequence similarity to the phage T3 genome (generating pUA139_T7(gp17), see S4 Table ).…”