AI Article Synopsis
- Enterobacteriophage Mu is a well-studied example of transposable phages, which are bacterial viruses that can move within genomes and have a complex life cycle involving lytic and lysogenic phases.
- Detailed annotation of Mu-encoded proteins is available in UniProtKB, linking them to specific biological functions.
- The research proposes reorganizing the Caudovirales virus family to include a new family called "Saltoviridae" and two subfamilies, "Myosaltovirinae" and "Siphosaltovirinae," suggesting a more structured classification based on their shared characteristics.
Article Abstract
Enterobacteriophage Mu is the best studied and paradigm member of the transposable phages. Mu-encoded proteins have been annotated in detail in UniProtKB and linked to a controlled vocabulary describing the various steps involved in the phage lytic and lysogenic cycles. Transposable phages are ubiquitous temperate bacterial viruses with a dsDNA linear genome. Twenty-six of them, that infect α, β and γ-proteobacteria, have been sequenced. Their conserved properties are described. Based on these characteristics, we propose a reorganization of the Caudovirales, to allow for the inclusion of a "Saltoviridae" family and two newly proposed subfamilies, the "Myosaltovirinae" and "Siphosaltovirinae". The latter could temporarily be included in the existing Myoviridae and Siphoviridae families.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1016/j.virol.2014.10.009 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
CRISPR in mobile genetic elements: counter-defense, inter-element competition and RNA-guided transposition.
BMC Biol
December 2024
Computational Biology Branch, Division of Intramural Research, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA.
CRISPR are adaptive immunity systems that protect bacteria and archaea from viruses and other mobile genetic elements (MGE) via an RNA-guided interference mechanism. However, in the course of the host-parasite co-evolution, CRISPR systems have been recruited by MGE themselves for counter-defense or other functions. Some bacteriophages encode fully functional CRISPR systems that target host defense systems, and many others recruited individual components of CRISPR systems, such as single repeat units that inhibit host CRISPR systems and CRISPR mini-arrays that target related viruses contributing to inter-virus competition.
View Article and Find Full Text PDFSequence modeling and design from molecular to genome scale with Evo.
Science
November 2024
Arc Institute, Palo Alto, CA, USA.
The genome is a sequence that encodes the DNA, RNA, and proteins that orchestrate an organism's function. We present Evo, a long-context genomic foundation model with a frontier architecture trained on millions of prokaryotic and phage genomes, and report scaling laws on DNA to complement observations in language and vision. Evo generalizes across DNA, RNA, and proteins, enabling zero-shot function prediction competitive with domain-specific language models and the generation of functional CRISPR-Cas and transposon systems, representing the first examples of protein-RNA and protein-DNA codesign with a language model.
View Article and Find Full Text PDFDiscovery of the first Tn630 member and the closest homolog of IS630 from viruses.
Sci Rep
November 2024
College of Life Sciences, Nankai University, Tianjin, 300071, People's Republic of China.
IS630/Tc1/mariner (ITm) represents the most widely distributed superfamily of DNA transposons in nature. Currently, bioinformatics research on ITm members primarily involves collecting data of existing and emerging members and organizing them into new groups or families. In the present study, our survey revealed that Tc1 and IS630 members have a broad host range, spanning across all six biological kingdoms (bacteria, fungi, plantae, animalia, archaea and protista) and viruses.
View Article and Find Full Text PDFGenomic and phenotypic characterization of a strain of the epidemic ST37 type from China.
Front Cell Infect Microbiol
November 2024
Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, United States.
Article Synopsis
- Strains of sequence type (ST) 37, especially PCR ribotype (RT) 017, are common in mainland China, prompting a study on their virulence factors.
- The study involved comparing an epidemic isolate (Xy06) from China to two reference strains (R20291 and CD630E) and another local strain (Xy07), noting key genomic features and virulence traits.
- Results indicated that Xy06 exhibited stronger virulence compared to Xy07 and CD630E and was on par with R20291, highlighting the potential threat posed by ST37 strains in the region.
Colanic acid and lipopolysaccharide in Pectobacterium carotovorum Pcc21 serve as receptors for the bacteriophage phiPccP-2.
Microbiol Res
January 2025
Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea; Plant Immunity Research Center, Seoul National University. Seoul 08826, Republic of Korea; Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea; Interdisciplinary Programs in Agricultural Genomics, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea; Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Republic of Korea. Electronic address:
Bacteriophages (phages) are viruses that specifically bind to and infect target bacteria. The phage phiPccP-2, belonging to the Myoviridae family, efficiently controls Pectobacterium spp. In the present study, we aimed to elucidate the mechanism of recognition of P.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!