Prophage genomics reveals patterns in phage genome organization and replication

Abstract

Temperate phage genomes are highly variable mosaic collections of genes that infect a bacterial host, integrate into the host's genome or replicate as low copy number plasmids, and are regulated to switch from the lysogenic to lytic cycles to generate new virions and escape their host. Genomes from most Bacterial phyla contain at least one or more prophages. We updated our PhiSpy algorithm to improve detection of prophages and to provide a web-based framework for PhiSpy. We have used this algorithm to identify 36,488 prophage regions from 11,941 bacterial genomes, including almost 600 prophages with no known homology to any proteins. Transfer RNA genes were abundant in the prophages, many of which alleviate the limits of translation efficiency due to host codon bias and presumably enable phages to surpass the normal capacity of the hosts' translation machinery. We identified integrase genes in 15,765 prophages (43% of the prophages). The integrase was routinely located at either end of the integrated phage genome, and was used to orient and align prophage genomes to reveal their underlying organization. The conserved genome alignments of phages recapitulate early, middle, and late gene order in transcriptional control of phage genes, and demonstrate that gene order, presumably selected by transcription timing and/or coordination among functional modules has been stably conserved throughout phage evolution. ConclusionsHere we presented an analysis of over 11,000 bacterial genomes from which we identified 36,488 prophages. Many phages appear to be limited by initiation of translation by the host's machinery, and may increase translation rates by carrying their own tRNA genes, effectively increasing the availability of both tRNAs loaded with methionine and of peptide deformylase. We have also demonstrated that phages maintain a highly conserved gene order that suggests phage genome mosaicism is limited to clusters of conserved genes rather than individual genes.

Comparative genomics groups phages of Negativicutes and classical Firmicutes despite different Gram-staining properties

“…This figure was only slightly higher, namely 1.9, when calculated for completely sequenced and assembled Negativicute genomes. A typical bacterial genome contains around 3 prophages based on in silico prediction (Kang et al, 2017), similar to our estimate of 3-4 prophages per genome for Clostridium and 135 Bacillus ( Table S2) Virome screening for Negativicute phages confirms prophage 145 predictions To circumvent this difficulty of a deficit of annotated phage proteins, we used viral-like particle (VLP) ("virome") data to confirm that we did not miss obvious prophage predictions. We screened 183 samples of virome sequences from human stool for matches to four completely sequenced strains of Negativicute that are residents of the 150 human gut.…”

“…However, conservation of aspects of phage genome organization (i.e. gene order) was observed between phages infecting distantly related hosts, for example across lambdoid phages from Proteobacteria, Firmicutes and viruses infecting Archaea (Lucchini et al, 1998;Pfister et al, 1998;Desiere et al, 1999;Lucchini et al, 55 1999; Desiere et al, 2000;Brüssow and Desiere, 2001;Casjens and Hendrix, 2015;Kang et al, 2017;Mahmoudabadi and Phillips, 2018). Structural biologists even detected relatedness between the protein folds of capsid components from phages and animal viruses (Bamford et al, 2005).…”

PhANNs, a fast and accurate tool and web server to classify phage structural proteins

“…Via transduction and/or lysogeny, they mediate horizontal transfer of genetic material such as virulence factors (2), metabolic auxiliary genes (3), photosystems and other genes to enhance photosynthesis (4), and phage production in general, by providing the host with immunity from killing by other phages. Temperate phages can become part of the host genome as prophages; most bacterial genomes contain at least one, and often multiple, prophages (5,6) . Phage structures (virions) are composed of proteins that encapsulate and protect their genomes.…”

Comparative genomics groups phages of Negativicutes and classical Firmicutes despite different Gram‐staining properties

“…Phages of a given type share substantial sequence homology when infecting the same bacterial species or genera, but for increasingly distant bacterial hosts, the ability to identify homology gradually decreases until the phage sequences can no longer be aligned. However, conservation of aspects of phage genome organization (i.e., gene order) was observed between phages infecting distantly related hosts, for example across lambdoid phages from Proteobacteria, Firmicutes and viruses infecting Archaea (Lucchini et al, 1998Pfister et al, 1998;Desiere et al, 1999;Desiere et al, 2000;Brüssow and Desiere, 2001;Casjens, 2003;Hatfull, 2008;Casjens and Hendrix, 2015;Kang et al, 2017;Mahmoudabadi and Phillips, 2018). Structural biologists even detected relatedness between the protein folds of capsid components from phages and animal viruses (Bamford et al, 2005;Prangishvili et al, 2017).…”