Genome sequencing of Escherichia coli phage UFJF_EcSW4 reveals a novel lytic Kayfunavirus species

Abstract

The Escherichia coli phage UFJF_EcSW4 was isolated from polluted stream water and showed clear lysis plaques on the host, measuring 0.67 ± 0.43 mm, with a titer of 9.57 ± 0.23 log PFU/ml. It demonstrated a very narrow host range, infecting only its host. Additionally, it has a short latent period of 9 min, a burst size of 49 PFU/infected cell, and stability over a wide range of pH, temperature, and free residual chlorine. The phage has a double-stranded DNA genome spanning 40,299 bp, with a GC content of 49.87% and short-direct terminal repeats (DTR) sequences of 286 bp. The UFJF_EcSW4 genome contains 55 genes, organized into functional modules with a unidirectional arrangement, regulated by 22 promoters (three from the phage and 19 from the host) and three Rho-independent terminators. Comparative analysis revealed that the UFJF_EcSW4 genome shares an average genomic similarity of 77.82% with the genome sequences of phages from the Kayfunavirus genus but does not surpass the 95% threshold necessary for species classification. Therefore, the UFJF_EcSW4 is a novel Kayfunavirus UFJF_EcSW4 species belonging to the Studiervirinae subfamily.

Supplementary information: The online version contains supplementary material available at 10.1007/s13205-024-04172-7.

Keywords: Bacteriophage; Escherichia coli; Genome; Kayfunavirus; Virus.

Fig. 1

Schematic representation of the E. coli phage UFJF_EcSW4 genome compared to Kayfunavirus Vec13. The genome of the UFJF_EcSW4 phage (shown below) features a unidirectional organization with 55 genes, represented by arrows and organized into three functional modules: DNA replication and metabolism, structural proteins, and DNA packaging and host lysis, depicted by colored bars in the background. Each arrow represents an individual gene, with the numbers below corresponding to genes encoding proteins with predicted functions, detailed in the annotation list beneath the genome map. Arrow colors and connecting lines between genes indicate putative homologous genes shared by both genomes, with encoded proteins showing more than 40% sequence identity. The genome of Kayfunavirus Vec13 is displayed above as the reference, chosen for its high similarity to the UFJF_EcSW4 genome. For a detailed summary of the sequence identities and similarities, refer to Table S5

Fig. 2

Taxonomic assignment of E. coli phage UFJF_EcSW4. The viral proteomic tree (above) includes the genomes of Escherichia coli phage UFJF_EcSW4 and 146 species of the Studiervirinae subfamily (taxonomy ID 2731653) available in the NCBI Reference Sequence (RefSeq) database. The highlighted clade represents the Kayfunavirus genus. The pairwise matrix summarizes the genomic similarity scores calculated by VIRIDIC (lower triangle) and ViPtree (upper triangle), expressed as percentage values. A genomic similarity score of 95% is the threshold for species assignment and 70% for genus assignment. The genome of Caractorivirus CR8 is included as an outgroup of the Kayfunavirus genus. Refer to Figure S1 for the complete viral proteomic tree in detail