Systematic analysis of prophage elements in actinobacterial genomes reveals a remarkable phylogenetic diversity

Abstract

Actinobacteria represent one of the largest bacterial phyla harboring many species of high medical, biotechnological and ecological relevance. Prophage elements are major contributors to bacterial genome diversity and were shown to significantly shape bacterial fitness and host-microbe interactions. In this study, we performed a systematic analysis of prophage elements in 2406 complete actinobacterial genomes. Overall, 2106 prophage elements were predicted to be present in about 50% (1172/2406) of the analyzed datasets. Interestingly, these identified sequences compose a high prevalence of cryptic prophage elements, indicating genetic decay and domestication. Analysis of the sequence relationship of predicted prophages with known actinobacteriophage genomes revealed an exceptional high phylogenetic diversity of prophage elements. As a trend, we observed a higher prevalence of prophage elements in vicinity to the terminus. Analysis of the prophage-encoded gene functions revealed that prophage sequences significantly contribute to the bacterial antiviral immune system, but no biosynthetic gene clusters involved in the synthesis of known antiphage molecules were identified in prophage genomes. Overall, the current study highlights the remarkable diversity of prophages in actinobacterial genomes, with highly divergent prophages in actinobacterial genomes and thus provides an important basis for further investigation of phage-host interactions in this important bacterial phylum.

Genomic and taxonomic evaluation of 38 Treponema prophage sequences

“…[ 40 , 41 ]. Six prophages (27087P2, 27087P3, KS1P4, KS1P5, B43P4 and B43P5) include an integrase, a terminase and several structural conserved protein domains in the correct order (terminase – portal – protease – scaffold – major head shell (coat) protein – head/tail joining proteins – tail shaft protein – tape measure protein – tail tip/baseplate proteins – tail fibre) and so have the potential be intact [ 9 , 42 ]. However, CheckV results indicated only 27087P3, B43P4 and B43P5 as high quality, at 91% complete and 73kb in length, while prophages 27087P2, KS1P4 and KS1P5 are shorter (66-67kb) and were considered medium quality.…”