Search bioRxiv⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.1101/2025.04.29.651204

Characterization and Genomic Analysis of vB_CoeS_P1, the First Vibrio hepatarius Phage, and Definition of the New Family Estovirdae

PK, S.·Ammini, P.·Angia Sriram, P. R.
View original source ↗Export metadata ↓

Abstract

A novel bacteriophage vB_CoeS_P1, isolated in the surface waters of the Cochin estuary of Kerala, India, was identified as the first phage known to infect Vibrio hepatarius. Transmission electron microscopy analysis revealed that the phage had a myovirus morphotype with an icosahedral head and a long contractile tail. Characterization experiments show that the phage was stable across a temperature range of 4{degrees}C to 60{degrees}C, a pH of 4 to 12, and a salinity range of 0.5 % to 16%. One-step growth curve analysis revealed a burst size of 30 PFU/Cell and a latent period of 20 minutes. The phage contains a double-stranded DNA with 136,927 bp and 34.93% GC content. The NCBI Blastn analysis reveals that vB_CoeS_P1 exhibits very low sequence similarity (1% query coverage and 77.82% identity) with Vb_VpaM_R16F (OP793884.1). It has 265 predicted ORFs, among them 57 have putative functions with no tRNA, antibiotic encoding genes, and resistance encoding genes. Three putative auxiliary metabolic genes were identified, encoding pyrophosphohydrolase enzyme (ORF 75), PhoH-like phosphate starvation-inducible (ORF 34), and Endonuclease V N-glycosylase UV repair enzyme (ORF 248). Phylogenetic analysis of conversed genes revealed that vB_CoeS_P1 is clustered with Vb_VpaM_R16F but diverged into a distinct clade. Further whole genome proteomic tree analysis, comparative genome analysis using average nucleotide identity (ANI), and network analysis confirmed that vB_CoeS_P1 contains a unique genetic and evolutionary architecture. These findings support the proposal of a new bacteriophage family Estovirdae, within the Caudoviricetes class.

Explore related subjects

genomicsPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

PK, S., Ammini, P., Angia Sriram, P. R.. 2025-05-01. Characterization and Genomic Analysis of vB_CoeS_P1, the First Vibrio hepatarius Phage, and Definition of the New Family Estovirdae. https://doi.org/10.1101/2025.04.29.651204

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Integrative Nanopore and Illumina sequencing reveals age-associated tRNA modification and CCA-tail dynamics in yeast

Aging is characterized by a progressive loss of proteostasis. Transfer RNAs (tRNAs) are essential regulators of translation, yet their dynamics during aging remain poorly understood due to challenges in sequencing highly modified RNAs. Here we present a benchmarked Nanopore direct RNA sequencing (RNA004 chemistry) resource that profiles the Saccharomyces cerevisiae tRNAome during replicative aging at single-molecule resolution. Using in vitro transcribed tRNA controls, we establish modification detection thresholds and validate key findings with orthogonal Illumina sequencing. While overall tRNA abundance remains largely stable, our resource reveals age-associated terminal A cleavage at the 3' CCA tail of mature tRNAs, targeted T-loop and anticodon modification changes, and single-molecule evidence of modification co-occurrence. This dataset provides a resource for exploring tRNA regulation, translation fidelity, and longevity.

genomics↗
bioRxiv2026

A hydrogen-producing mitochondrion in an anaerobic eukaryotrophic rhizarian

Diverse eukaryotes thrive under low oxygen conditions, in part through highly modified mitochondrion-related organelles (MROs) that use alternate metabolic pathways to support ATP production and cofactor recycling. Anaerobic lifestyles have evolved repeatedly across the eukaryotic tree of life, each providing an independent opportunity to understand how eukaryotes adapt to life in low oxygen conditions. Here, we use single-cell transcriptomics to reconstruct the MRO metabolism of PCE SSF, a benthic eukaryotrophic flagellate and the first cultivated representative of Novel Clade 12 (NC12; Rhizaria), an independently anaerobic rhizarian lineage. PCE SSF possesses an anaerobic hydrogen-producing mitochondrion capable of hydrogenosome-type substrate-level phosphorylation. It also retains a nearly complete but likely branched tricarboxylic acid pathway that lacks citrate synthase and malate dehydrogenase. The function of citrate synthase may instead be fulfilled by the typically cytosolic ATP citrate lyase, previously reported in this context only in the anaerobic cercozoan, Brevimastigomonas motovehiculus. Unlike B. motovehiculus, however, PCE SSF retains only Complex II and the NuoE/NuoF subunits of the electron transport chain and lacks a mitochondrial genome. Together, these features indicate an atypical and reduced mitochondrial metabolism, highlighting the diversity of evolutionary solutions to anaerobic energy metabolism in eukaryotes.

genomics↗
bioRxiv2026

Targeted CRISPRi screening reveals unexpected resilience across the RNA polymerase III transcriptome

Increased RNA polymerase III (Pol III) activity and tRNA abundance are widely linked to cancer cell growth, yet the functional requirement for individual Pol III genes and core components remains unclear, in part due to the difficulty of achieving gene-specific perturbation of highly conserved loci. Here, we developed an inducible CRISPR interference platform and a custom single-guide RNA (sgRNA) library enabling gene-specific targeting of Pol III-transcribed genes and Pol III machinery. Genome-wide screening identified several Pol III dependencies in diploid fibroblasts and HEK293T cells, including multiple initiator methionine tRNA genes among the strongest fitness dependencies. Unexpectedly, glioblastoma models remained largely insensitive to repression of both individual Pol III genes and core Pol III components, despite efficient target repression. These findings establish a general strategy for gene-specific interrogation of conserved Pol III genes and indicate that glioblastoma models tolerate extensive perturbation of Pol III genes and machinery.

genomics↗