Prophage-Derived Regions in Curtobacterium Genomes: Good Things, Small Packages

Abstract

Curtobacterium is a genus of Gram-positive bacteria within the order Actinomycetales. Some Curtobacterium species (C. flaccumfaciens, C. plantarum) are harmful pathogens of agricultural crops such as soybean, dry beans, peas, sugar beet and beetroot, which occur throughout the world. Bacteriophages (bacterial viruses) are considered to be potential curative agents to control the spread of harmful bacteria. Temperate bacteriophages integrate their genomes into bacterial chromosomes (prophages), sometimes substantially influencing bacterial lifestyle and pathogenicity. About 200 publicly available genomes of Curtobacterium species, including environmental metagenomic sequences, were inspected for the presence of sequences of possible prophage origin using bioinformatic methods. The comparison of the search results with several ubiquitous bacterial groups showed the relatively low level of the presence of prophage traces in Curtobacterium genomes. Genomic and phylogenetic analyses were undertaken for the evaluation of the evolutionary and taxonomic positioning of predicted prophages. The analyses indicated the relatedness of Curtobacterium prophage-derived sequences with temperate actinophages of siphoviral morphology. In most cases, the predicted prophages can represent novel phage taxa not described previously. One of the predicted temperate phages was induced from the Curtobacterium genome. Bioinformatic analysis of the modelled proteins encoded in prophage-derived regions led to the discovery of some 100 putative glycopolymer-degrading enzymes that contained enzymatic domains with predicted cell-wall- and cell-envelope-degrading activity; these included glycosidases and peptidases. These proteins can be considered for the experimental design of new antibacterials against Curtobacterium phytopathogens.

Using AlphaFold Predictions in Viral Research

“…The analysis of the structural features of phage RBPs and lysins can use modern deep-learning techniques, including AlphaFold. Together with experimental studies, AlphaFold predictions can be used to elucidate the domain organisation of TFP, TSP and cell-wall degrading enzymes, to reveal the sites of phage particle binding and enzymatic domains ( Figure 4 ) [ 45 , 46 , 47 , 52 ].…”

Tychonema sp. BBK16 Characterisation: Lifestyle, Phylogeny and Related Phages

“…However, some information about phage–host interactions can be recovered using the analysis of genomic CRISPR arrays [ 30 , 31 , 32 ]. Moreover, temperate phages that insert their genome into the host chromosome can leave traces of phage infection [ 33 , 34 , 35 , 36 ].…”