First crAss-Like Phage Genome Encoding the Diversity-Generating Retroelement (DGR)

Abstract

A new crAss-like genome encoding diversity-generating retroelement (DGR) was found in the fecal virome of a healthy volunteer. The genome of the phage referred to as the crAssphage LMMB, belonged to the candidate genus I of the AlphacrAssvirinae subfamily. The DGR-cassette of the crAssphage LMMB contained all the essential elements: the gene encoding reverse transcriptase (RT), the target gene (TG) encoding the tail-collar fiber protein, and variable and template repeats (VR and TR) with IMH (initiation of mutagenic homing) and IMH* sequences at the 3′-end of the VR and TR, respectively. Architecture of the DGR-cassette was TG-VR(IMH)-TR(IMH*)-RT and an accessory variable determinant (avd) was absent from the cassette. Analysis of 91 genomes and genome fragments from genus I of the AlphacrAssvirinae showed that 15 (16%) of the genomes had DGRs with the same architecture as the crAssphage LMMB, while 66 of the genomes contained incomplete DGR-cassettes or some elements of the DGR.

A Previously Undescribed Highly Prevalent Phage Identified in a Danish Enteric Virome Catalog

“…Typical of a crAssphage, PG2 was subdivided into two regions with opposite gene orientation, one region encoding proteins predicted to be involved in host interaction and phage structure and the other region encoding proteins predicted to be involved in DNA replication, recombination, and nucleotide metabolism. Downstream of the tail collar fiber protein we observed a reverse transcriptase—indicative of a diversity-generating retroelement previously described in crAssphages ( 57 ). No gene was annotated as RNA polymerase; however, we suspect that one of the large unknown genes may encode a divergent RNA polymerase subunit, as large unannotated proteins in crAss-like phages often contain an amino acid motif typical for RNA polymerases ( 58 ).…”

Isolation and characterisation of ΦcrAss002, a crAss-like phage from the human gut that infects Bacteroides xylanisolvens

“…This is particularly true for the most abundant representatives of this viral community, the crAss-like phages. With the exception of ΦcrAss001 and two close relatives of this phage, DAC15 and DAC17, all other crAss-like genomes described to date are the result of composite assemblies and have never been propagated in pure culture in a laboratory [ 4 , 6 , 17 – 20 , 23 , 36 – 40 ]. Biological characterisation of ΦcrAss001 revealed several intriguing traits.…”

“…CrAss-like phages also form part of the personal persistent virome (PPV), a consistently present, individual-specific core of mostly virulent phages in the viromes of healthy individuals [ 4 , 13 ]. In addition, crAss-like phages have been demonstrated to engraft and persist in the microbiome of faecal microbiota transplantation recipients and can undergo vertical transmission between mother and infant [ 36 , 38 , 40 ]. This suggests that ecological models yet to be characterised are at play in the human gut that allow this persistence.…”

A previously undescribed highly prevalent phage identified in a Danish enteric virome catalogue

“…Typical of a crAssphage, PG2 was clearly subdivided into two regions with opposite gene orientation, with one region encoding structural proteins and proteins involved in host interaction, and the other region encoding proteins involved in DNA replication, recombination and nucleotide metabolism. Downstream of the tail collar ber protein we observed a reverse transcriptase -indicative of a diversity-generating retroelement previously described in crAssphages [91]. No gene was annotated as RNA polymerase, however, we suspect that one of the large unknown genes of PG2 may encode a divergent RNA polymerase subunit, as large unannotated proteins in crAss-like phages often contain an amino acid motif typical for RNA polymerases [92].…”