Journal Article

Characterization and genomic analysis of Sharanji: a jumbo bacteriophage of Escherichia coli

Singari, Ranjith Kumar, Parmar, Anjali, Sen, Debmitra, Barath, Sivaraj, Nagarajan, T., Govindarajan, Sutharsan, Magar, Sharayu

2025

Overview

Background Bacteriophages are the most genetically diverse biological entities in nature. Our current understanding of phage biology primarily stems from studies on a limited number of model bacteriophages. Jumbo phages, characterized by their exceptionally large genomes, are less frequently isolated and studied. Some jumbo phages exhibit remarkable genetic diversity, unique infection mechanisms, and therapeutic potential. Methods In this study, we describe the isolation of Sharanji, a novel Escherichia coli jumbo phage, isolated from chicken feces. The phage genome was sequenced and analyzed extensively through gene annotation and phylogenetic analysis. The jumbo phage was phenotypically characterized through electron microscopy, host range analysis, and survival at different pH and temperatures, and one-step growth curve assay. Finally, Sharanji mediated infection of E. coli is studied through fluorescence microscopy, to analyze its mechanism of infection compared to well-studied nucleus-forming jumbo phages. Results Whole genome sequencing reveals that Sharanji has a genome size of 350,079 bp and is a phage encompassing 593 ORFs. Genomic analysis indicates that the phage belongs to the Asteriusvirus genus and is related to E. coli jumbo phages PBECO4 and 121Q. Phenotypic analysis of isolated phage Sharanji, indicates that the phage size is 245.3 nm, and it is a narrow-spectrum phage infecting E. coli K12 strains, but not other bacteria including avian pathogenic E. coli . Infection analysis using microscopy shows that Sharanji infection causes cell filamentation. Furthermore, intracellular phage nucleus-like structures were not observed in Sharanji-infected cells, in contrast to infection by ΦKZ-like jumbo phages. Conclusions Our study reports the isolation and characterization of Sharanji, one of the large E. coli jumbo phages. Both genotypic and phenotypic analyses suggest that Sharanji serves as a unique model system for studying phage-bacteria interactions, particularly within the context of non-nucleus-forming jumbo phages. Further exploration of jumbo phages holds promise for uncovering new paradigms in the study of microbial viruses.

• Publisher: BioMed Central,BioMed Central Ltd,BMC
• Subject: Animals / Bacteriophage genomics / Bacteriophages / Bacteriophages - classification / Bacteriophages - genetics / Bacteriophages - isolation & purification / Bacteriophages - ultrastructure / Biomedical and Life Sciences / Biomedicine / Chickens / Coliphages - classification / Coliphages - genetics / Coliphages - isolation & purification / Coliphages - ultrastructure / Control / E. coli / electron microscopy / Escherichia coli / Escherichia coli - virology / Escherichia coli K12 / feces / Feces - virology / fluorescence microscopy / genes / Genetic aspects / genetic variation / Genome, Viral / Genomics / genus / growth curves / host range / Host Specificity / Jumbo phage / phenotype / Phylogeny / Physiological aspects / therapeutics / Virology / Virus research / Whole Genome Sequencing