ArticleBMC bioinformatics2011
The evolution of the tape measure protein: units, duplications and losses.
Article in BMC bioinformatics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- Amino acid homorepeats in tape measure proteins correlate with bacteriophage tail length.The Journal of general virology · 2026Article
- A novel phage satellite class induces prophage excision in Mycolicibacterium aichiense.Virology · 2026Article
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- Phage P2-71 against multi-drug resistantFrontiers in cellular and infection microbiology · 2024Article
- Vic9 mycobacteriophage: the first subcluster B2 phage isolated in Russia.Frontiers in microbiology · 2024Article
- Virus-like Particles fromInsects · 2023Article
- Variants of a putative baseplate wedge protein extend the host range of Pseudomonas phage K8.Microbiome · 2023Article
- vHULK, a New Tool for Bacteriophage Host Prediction Based on Annotated Genomic Features and Neural Networks.PHAGE (New Rochelle, N.Y.) · 2022Article
- Microbial Proteins in Stomach Biopsies Associated with Gastritis, Ulcer, and Gastric Cancer.Molecules (Basel, Switzerland) · 2022Article
- Characterization and Comparative Genomics Analysis of a New Bacteriophage BUCT610 againstInternational journal of molecular sciences · 2022Article
- Characterization of the Bacteriophage BUCT603 and Therapeutic Potential Evaluation Against Drug-ResistantFrontiers in microbiology · 2022Article
- Improved bactericidal efficacy and thermostability of Staphylococcus aureus-specific bacteriophage SA3821 by repeated sodium pyrophosphate challenges.Scientific reports · 2021Article
- NovelMicroorganisms · 2021Article
- Induction and Genome Analysis of HY01, a Newly Reported Prophage from an Emerging Shrimp PathogenMicroorganisms · 2021Article
- Structure and mechanism of DNA delivery of a gene transfer agent.Nature communications · 2020Article
- Characterization of Novel Broad-Host-Range Bacteriophage DLP3 Specific toFrontiers in microbiology · 2020Article
- Genomics of Clostridium taeniosporum, an organism which forms endospores with ribbon-like appendages.PloS one · 2018Article
- Molecular Analysis of Arthrobacter Myovirus vB_ArtM-ArV1: We Blame It on the Tail.Journal of virology · 2017Article
- Functional and structural dissection of the tape measure protein of lactococcal phage TP901-1.Scientific reports · 2016Article
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3 authors.
Funding
Abstract
backgroundA large family of viruses that infect bacteria, called phages, is characterized by long tails used to inject DNA into their victims' cells. The tape measure protein got its name because the length of the corresponding gene is proportional to the length of the phage's tail: a fact shown by actually copying or splicing out parts of DNA in exemplar species. A natural question is whether there exist units for these tape measures, and if different tape measures have different units and lengths. Such units would allow us to retrace the evolution of tape measure proteins using their duplication/loss history. The vast number of sequenced phages genomes allows us to attack this problem with a comparative genomics approach.
resultsHere we describe a subset of phages whose tape measure proteins contain variable numbers of an 11 amino acids sequence repeat, aligned with sequence similarity, structural properties, and simple arithmetics. This subset provides a unique opportunity for the combinatorial study of phage evolution, without the added uncertainties of multiple alignments, which are trivial in this case, or of protein functions, that are well established. We give a heuristic that reconstructs the duplication history of these sequences, using divergent strains to discriminate between mutations that occurred before and after speciation, or lineage divergence. The heuristic is based on an efficient algorithm that gives an exhaustive enumeration of all possible parsimonious reconstructions of the duplication/speciation history of a single nucleotide. Finally, we present a method that allows, when possible, to discriminate between duplication and loss events.
conclusionsEstablishing the evolutionary history of viruses is difficult, in part due to extensive recombinations and gene transfers, and high mutation rates that often erase detectable similarity between homologous genes. In this paper, we introduce new tools to address this problem.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.