Prophage-Derived Regions in Curtobacterium Genomes: Good Things, Small Packages.
Peter V EvseevAnna A LukianovaRashit I TarakanovAnna D TokmakovaAnastasiya V PopovaEugene E KulikovMikhail ShneiderAlexander N IgnatovKonstantin A MiroshnikovPublished in: International journal of molecular sciences (2023)
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.
Keyphrases
- cell wall
- genetic diversity
- cardiovascular disease
- metabolic syndrome
- gram negative
- genome wide
- single cell
- small molecule
- climate change
- human health
- high throughput
- stem cells
- type diabetes
- nitric oxide
- multidrug resistant
- heavy metals
- high glucose
- dna methylation
- bone marrow
- endothelial cells
- staphylococcus aureus
- rectal cancer
- prognostic factors
- antibiotic resistance genes