Assembly and Annotation of the Complete Genome Sequence of T4-Like Bacteriophage 132.
Ontology highlight
ABSTRACT:
SUBMITTER: Roush C
PROVIDER: S-EPMC8483715 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:Phage T4 is among the best-characterized biological systems (S. Kanamaru and F. Arisaka, Seikagaku 74:131-135, 2002; E. S. Miller et al., Microbiol. Mol. Biol. Rev. 67:86-156, 2003; W. B. Wood and H. R. Revel, Bacteriol. Rev. 40:847-868, 1976). To date, several genomes of T4-like bacteriophages are available in public databases but without any APEC bacteriophages (H. Jiang et al., Arch. Virol. 156:1489-1492, 2011; L. Kaliniene, V. Klausa, A. Zajanckauskaite, R. Nivinskas, and L. Truncaite, Arch. Virol. 156:1913-1916, 2011; J. H. Kim et al., Vet. Microbiol. 157:164-171, 2012; W. C. Liao et al., J. Virol. 85:6567-6578, 2011). We isolated a bacteriophage from a duck factory, named HX01, that infects avian pathogenic Escherichia coli (APEC). Sequence and morphological analyses revealed that phage HX01 is a T4-like bacteriophage and belongs to the family Myoviridae. Here, we announce the complete genome sequence of phage HX01 and report the results of our analysis.
| S-EPMC3503030 | biostudies-literature
Project description:We present the annotated genome sequence of Escherichia coli bacteriophage 107, a T4-like bacteriophage. Phage 107 has a genome length of 167,509 bp and 287 predicted genes.
| S-EPMC10281100 | biostudies-literature
Project description:Phage T4 has provided countless contributions to the paradigms of genetics and biochemistry. Its complete genome sequence of 168,903 bp encodes about 300 gene products. T4 biology and its genomic sequence provide the best-understood model for modern functional genomics and proteomics. Variations on gene expression, including overlapping genes, internal translation initiation, spliced genes, translational bypassing, and RNA processing, alert us to the caveats of purely computational methods. The T4 transcriptional pattern reflects its dependence on the host RNA polymerase and the use of phage-encoded proteins that sequentially modify RNA polymerase; transcriptional activator proteins, a phage sigma factor, anti-sigma, and sigma decoy proteins also act to specify early, middle, and late promoter recognition. Posttranscriptional controls by T4 provide excellent systems for the study of RNA-dependent processes, particularly at the structural level. The redundancy of DNA replication and recombination systems of T4 reveals how phage and other genomes are stably replicated and repaired in different environments, providing insight into genome evolution and adaptations to new hosts and growth environments. Moreover, genomic sequence analysis has provided new insights into tail fiber variation, lysis, gene duplications, and membrane localization of proteins, while high-resolution structural determination of the "cell-puncturing device," combined with the three-dimensional image reconstruction of the baseplate, has revealed the mechanism of penetration during infection. Despite these advances, nearly 130 potential T4 genes remain uncharacterized. Current phage-sequencing initiatives are now revealing the similarities and differences among members of the T4 family, including those that infect bacteria other than Escherichia coli. T4 functional genomics will aid in the interpretation of these newly sequenced T4-related genomes and in broadening our understanding of the complex evolution and ecology of phages-the most abundant and among the most ancient biological entities on Earth.
| S-EPMC150520 | biostudies-literature
Project description:The complete genome sequence of the T4-like, broad-host-range vibriophage KVP40 has been determined. The genome sequence is 244,835 bp, with an overall G+C content of 42.6%. It encodes 386 putative protein-encoding open reading frames (CDSs), 30 tRNAs, 33 T4-like late promoters, and 57 potential rho-independent terminators. Overall, 92.1% of the KVP40 genome is coding, with an average CDS size of 587 bp. While 65% of the CDSs were unique to KVP40 and had no known function, the genome sequence and organization show specific regions of extensive conservation with phage T4. At least 99 KVP40 CDSs have homologs in the T4 genome (Blast alignments of 45 to 68% amino acid similarity). The shared CDSs represent 36% of all T4 CDSs but only 26% of those from KVP40. There is extensive representation of the DNA replication, recombination, and repair enzymes as well as the viral capsid and tail structural genes. KVP40 lacks several T4 enzymes involved in host DNA degradation, appears not to synthesize the modified cytosine (hydroxymethyl glucose) present in T-even phages, and lacks group I introns. KVP40 likely utilizes the T4-type sigma-55 late transcription apparatus, but features of early- or middle-mode transcription were not identified. There are 26 CDSs that have no viral homolog, and many did not necessarily originate from Vibrio spp., suggesting an even broader host range for KVP40. From these latter CDSs, an NAD salvage pathway was inferred that appears to be unique among bacteriophages. Features of the KVP40 genome that distinguish it from T4 are presented, as well as those, such as the replication and virion gene clusters, that are substantially conserved.
| S-EPMC180978 | biostudies-literature
Project description:Myxococcus xanthus is a social Gram-negative soil bacterium and the best studied member of the order Myxococcales in the class Deltaproteobacteria, which was recently reclassified as the phylum Myxococcota. Here, we report complete genomes, obtained using Illumina and PacBio sequencing, of M. xanthus strains DK1050 and DK101 (GenBank accession numbers CP104804 and CP104803, respectively).
| S-EPMC10019317 | biostudies-literature
Project description:We present the structural and functional annotation of Escherichia coli bacteriophage 55, which has a genome length of 170,393 bp, with 219 predicted genes.
| S-EPMC10353447 | biostudies-literature
Project description:We previously isolated EFDG1, a lytic phage against enterococci for therapeutic use. Nevertheless, EFDG1-resistant bacterial strains (EFDG1(r)) have evolved. EFLK1, a new highly effective phage against EFDG1(r) strains, was isolated in this study. The genome of EFLK1 was fully sequenced, analyzed, and deposited in GenBank.
| S-EPMC4653778 | biostudies-literature
Project description:Salmonella bacteriophage SPN3US was isolated from a chicken fecal sample. It is a virulent phage belonging to the Myoviridae family and showing effective inhibition of Salmonella enterica and a few Escherichia coli O157:H7 strains. Here we announce the completely sequenced first genome of a Salmonella phage using flagella as receptors. It is the largest genome among Salmonella phages sequenced to date, and major findings from its annotation are described.
| S-EPMC3233126 | biostudies-literature
Project description:The Streptomyces bacteriophage Abt2graduatex2 is a double-stranded DNA (dsDNA) Siphoviridae isolated from soil collected in Baltimore, MD, and harvested using Streptomyces griseus subsp. griseus Abt2graduatex2, a cluster BG phage, encodes an HicA-like toxin.
| S-EPMC5773734 | biostudies-literature
Project description:We characterized the complete genome sequence of Siphoviridae bacteriophage Erla, an obligatory lytic subcluster EA1 bacteriophage infecting Microbacterium foliorum NRRL B-24224, with a capsid width of 65 nm and a tail length of 112 nm. The 41.5-kb genome, encompassing 62 predicted protein-coding genes, is highly similar (99.52% identity) to that of bacteriophage Calix.
| S-EPMC8407768 | biostudies-literature