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t2 phage genome size

    t2 phage genome size

    Microb. Newly acquired DNA thus provides a reservoir of genetic information for potential future use, rather than being selected for immediate utility. Rates of mutation and recombination in Siphoviridae phage genome evolution over three decades. Although most known phages harbour genomes that are shorter than 200 kb packaged into capsids with a diameter under 100 , more and more extremely large phages are being discovered. Dysbiosis in inflammatory bowel disease: a role for bacteriophages? All Rights Reserved. However, accurately identifying prophages and phage-related objects remains a challenge especially for those bacteria for which few if any viruses have been characterized and it is not easy to predict from genome information alone which of these can generate infectious particles through prophage induction. Phages have adapted the same protein fold to fulfill multiple functions in virion assembly. Escherichia Coli 5 million b.p. 162, 14411446 (2017). . 4, 18951906 (2019). The T2 39 gene, along with the 52 gene, encode the smallest topo II. 5-hydroxymethylcytosine (5hmC) was first described in 1952 when it was found in the genomes of T-even bacteriophages (T2 and T4). 71, 31193125 (2005). Phage genome size varies enormously, ranging from the ~3,300 nucleotide ssRNA viruses of Escherichia coli [16] to the almost 500 kbp genome of Bacillus megaterium phage G (our unpublished data). Williamson, K. E., Radosevich, M. & Wommack, K. E. Abundance and diversity of viruses in six Delaware soils. WebLength of the filamentous phage is determined by size of the DNA in the genome Inserts of up 42 Kb have been introduced into M13 genome and packaged (7x genome size) ~8 copies of the Gene III protein are attached at the end of the extruded genome Mol. Here a majority of the so-called core genesthe genes that are shared by all members of the groupfail to engage in horizontal exchange relative to the other genes in the group [32,33]. 24, 16451654 (2005). Fierer, N. et al. Stewart CR, Casjens SR, Cresawn SG, Houtz JM, Smith AL, Ford ME, Peebles CL, Hatfull GF, Hendrix RW, Huang WM, et al. Greenberg, N. & Rottem, S. Composition and molecular organization of lipids and proteins in the envelope of mycoplasmavirus MVL2. Biol. Koning, R. I. et al. Rev. Novick RP, Christie GE, Penades JR. CAS Natl Acad. 9, 647657 (2011). Biol. & Sullivan, M. B. Nat. 3, 566571 (2013). 4, 201219 (2017). To obtain Nature 531, 466470 (2016). Single-cell genomics uncover Pelagibacter as the putative host of the extremely abundant uncultured 37-F6 viral population in the ocean. Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses. 184, 48914905 (2002). WebT2 phage is more properly called Enterobacteria phage T2. Virol. Bobay, L., Touchon, M. & Rocha, E. P. C. Manipulating or superseding host recombination functions: a dilemma that shapes phage evolvability. Martinsohn JT, Radman M, Petit MA. Microbiome 6, 68 (2018). Khayat, R. et al. & Giske, J. Bacteriophage T5 tail tube structure suggests a trigger mechanism for Siphoviridae DNA ejection. ^ {1,2,3} 1,2,3. start superscript, 1, comma, 2, comma, 3, end superscript. A quasi-atomic model of human adenovirus type 5 capsid. Not surprisingly, there are many different host-mediated protection systems such as restriction-modification [38], CRISPRs [39], tRNA cleavage [40], and Toxin-Antitoxin systems [41], as well as phage-encoded mechanisms for generating genome diversity at high frequency [42]. Natl Acad. Natl Acad. From: Gene-Environment Interactions in Psychiatry, 2016 View all Topics Download as PDF About this page DNA Topoisomerases: Biochemistry and Molecular Biology Marston, M. F. & Amrich, C. G. Recombination and microdiversity in coastal marine cyanophages. Their dsDNAs are linear, cyclically permuted, and terminally redundant. Nat. Rev. 10, e1004181 (2014). T2 is a 'tailed phage', [1] one of a group known as the 'T4-like viruses'. A Dictionary of Genetics , Subjects: Natl Acad. Gut mucosal virome alterations in ulcerative colitis. Nature 536, 425430 (2016). official website and that any information you provide is encrypted With high throughput sequencing approaches becoming generally and relatively cheaply available, it has become possible to sample substantial numbers of metagenomic samples and to compare viral populations as a functions of geography and time, providing considerable insights into the dynamics of phage populations [6,7]. Grose, J. H. & Casjens, S. R. Understanding the enormous diversity of bacteriophages: the tailed phages that infect the bacterial family Enterobacteriaceae. Nat Rev Microbiol 18, 125138 (2020). Barylski, J. et al. Overall, phage genomes represent only about 15% of all viruses with known unique sequences and are thus vastly under-represented in the genome databases. Nat. Proc. The head genes, for example, code for proteins that interact intimately with each other in building the head structure, and these genes must co-evolve with each other to maintain those interactions. Deveau H, Garneau JE, Moineau S. CRISPR/Cas system and its role in phage-bacteria interactions. Natl Acad. Suhanovsky, M. M. & Teschke, C. M. Natures favorite building block: deciphering folding and capsid assembly of proteins with the HK97-fold. Appelt, S. et al. A high-throughput method to link a virus to its host, consisting of labelling viruses with a fluorescent dye, collecting infected cells by flowcytometry and sequencing the viral DNA. The smallest of the dsDNA tailed phages genomes are ~11.5 kbp [e.g. However, some caution is warranted in interpreting this, because the natural or preferred host the one the virus was associated with in its most recent ecological and evolutionary past may not be the same as the host used for its isolation. Hatfull, G. F. Bacteriophage genomics. Structure of an archaeal virus capsid protein reveals a common ancestry to eukaryotic and bacterial viruses. It contains linear double-stranded DNA, and is covered by a protective protein coat. 11, 799805 (1973). Hendrix, R. W. Evolution: the long evolutionary reach of viruses. Microbiol. Inclusion in an NLM database does not imply endorsement of, or agreement with, This work is supported by the Natural Sciences and Engineering Research Council of Canada (NSERC) Discovery Program and the Canadian Institutes of Health Research (team grant on Intestinal Microbiomics, Institute of Nutrition, Metabolism and Diabetes). Yet,despite the remarkable diversity of phages at the nucleotide sequence level, the structural proteins that form viral particles show strong similarities and conservation. 1). This article focuses on the MCP HK97 fold and its conservation at the structural level between tailed phages and archaeal and eukaryotic viruses. Rev. 3.2 A.2 Comparison of genome size in T2 phage, Escherichia coli, Drosophila melanogaster, Homo sapiens and Paris japonica. Proc. Willner D, Thurber RV, Rohwer F. Metagenomic signatures of 86 microbial and viral metagenomes. 13, 8589 (2006). Megaphages infect Prevotella and variants are widespread in gut microbiomes. Reyes, A. et al. HHS Vulnerability Disclosure, Help Genome mosaicism can also be observed by comparing genes at the amino acid sequence level, identifying genes of common ancestry that diverged sufficiently long ago that nucleotide sequence similarity is no longer recognizable (Fig. Comparative Genomic Analysis of 60 Mycobacteriophage Genomes: Genome Clustering, Gene Acquisition, and Gene Size. A decade of Streptococcus thermophilus phage evolution in an Irish dairy plant. It contains linear double-stranded DNA, and is covered by a protective protein coat. J. Bacteriol. The extent of nucleotide similarity is displayed by coloring between the genomes, color-coded by spectrum with violet being the most similar and red the least. WebIn T2 genes 39 and 60 are fused into one gene (605 amino acids), and it is equivalent to gyrB ( Huang, 1990). F.O. PubMed Proc. J. Bacteriol. Microbiol. Sci. 13, 232236 (2019). Genomic sequences of bacteriophages HK97 and HK022: pervasive genetic mosaicism in the lambdoid bacteriophages. Bacteriophages genomes arguably also harbor the greatest genetic novelty in the biological world, in that most of their encoded genes (perhaps as much as 80%) are unrelated to known proteins, and are of unknown function. Biol. 1, 2, 3. The T-even viruses (T2, T4, and T6) have heads 80 110 nm, while the T-odd phages (T1, T3, T5, and T7) have isometric heads about 60 nm in diameter. Curr. Sci. USA 111, 78137818 (2014). Disease-specific alterations in the enteric virome in inflammatory bowel disease. Curr Opin Virol. WebThe T-even viruses (T2, T4, and T6) have heads 80 110 nm, while the T-odd phages (T1, T3, T5, and T7) have isometric heads about 60 nm in diameter. Bethesda, MD 20894, Web Policies Exchange events occurring in relatively recent evolutionary time can occasionally be seen through whole genome nucleotide comparisons (Fig. Language links are at the top of the page across from the title. Nucleotide sequence of coliphage HK620 and the evolution of lambdoid phages. Google Scholar. Pope WH, Jacobs-Sera D, Russell DA, Peebles CL, Al-Atrache Z, Alcoser TA, Alexander LM, Alfano MB, Alford ST, Amy NE, et al. Rev. Natl Acad. 12, 11271141 (2018). Gut 68, 11691179 (2019). 22 March 2023, Microbiome Arch. Brum, J. R., Hurwitz, B. L., Schofield, O., Ducklow, H. W. & Sullivan, M. B. CAS Environ. J. Bacteriol. They were named Type 1 (T1), Type 2 (T2), etc., for easy reference; however, due to structural similarities between the T2, T4, and T6 bacteriophages, these are now commonly referred to as T-Even phages. Virol. Lang AS, Beatty JT. BMC Genomics 17, 930 (2016). Sci. PLoS Biol. Flix dHrelle Reference Center for Bacterial Viruses: EMBO J. Microbiol. T phages & Bamford, D. H. Nucleic and amino acid sequences support structure-based viral classification. Krupovic, M., Prangishvili, D., Hendrix, R. W. & Bamford, D. H. Genomics of bacterial and archaeal viruses: dynamics within the Prokaryotic virosphere. The complete genomes and proteomes of 27, Kwan T, Liu J, Dubow M, Gros P, Pelletier J. Opin. Casjens, S. R. The DNA-packaging nanomotor of tailed bacteriophages. Natl Acad. Ackermann, H. W. 5500 Phages examined in the electron microscope. holds the Tier 1 Canada Research Chair in Bacteriophages and is a member of the PROTEO and Op+Lait FRQNT Networks. Sign up for the Nature Briefing newsletter what matters in science, free to your inbox daily. Sinclair, R., Ravantti, J. 1, 15024 (2016). ISME J. Commun. Cryptic inoviruses are pervasive in bacteria and archaea across Earths biomes. Nucleotide sequence comparison of bacteriophage genomes reveals them to be enormously diverse [1]. T2 was the first phage to be observed under the electron microscope (1942, Luria and Anderson), and it was utilized in the famous Hershey-Chase experiment (1952). Rixon, F. J. DNA 8, 12 (2017). . The phage is covered by a protective protein coat. Leiman, P. G., Chipman, P. R., Kostyuchenko, V. A., Mesyanzhinov, V. V. & Rossmann, M. G. Three-dimensional rearrangement of proteins in the tail of bacteriophage T4 on infection of its host. Huiskonen, J. T. et al. Google Scholar. Kristensen DM, Mushegian AR, Dolja VV, Koonin EV. Insights into virus evolution and membrane biogenesis from the structure of the marine lipid-containing bacteriophage PM2. Insights into assembly from structural analysis of bacteriophage PRD1. 75, 610635 (2011). Nat. T2, T4, and T6 phages differ in the cell wall receptors to which they bind. Whole genome comparison of a large collection of mycobacteriophages reveals a continuum of phage genetic diversity. This is a preview of subscription content, access via your institution. 4, 693700 (2019). Rather we suggest that non-homologous recombination occurs rampantly and indiscriminately across the genomes and stringent natural selection for the successful arrangement of the core genes counterselects any gene arrangement that disrupts that, while allowing much more promiscuous reassortments of the non-core genes; a thoroughly Darwinian view of phage evolution. The capsid of a bacteriophage can be icosahedral, filamentous, or Sci. and JavaScript. PLoS Genet. Vidaver, A. K., Koski, R. K. & Van Etten, J. L. Bacteriophage 6: a lipid-containing virus of Pseudomonas phaseolicola. Fabry, C. M. S. et al. 9, 472484 (2015). Nature 513, 242245 (2014). J. Mol. Nat. ISME J. Biol. CAS Lavelle, K. et al. 11, 28932903 (2009). A replication strategy where a phage takes control of the host cell to replicate its genetic material, produce its structural components, self-assemble to form new virions and burst (lyses) the cell to release newviral particles. Breitbart, M., Bonnain, C., Malki, K. & Sawaya, N. A. Phage puppet masters of the marine microbial realm. Biol. Environ. A non-functional prophage within a bacterial chromosome. 61, 471480 (2002). It is a virulent bacteriophage which infects Escherichia coli bacteria. A., Dishaw, L. J. Article Each of the genes in Phams 236, 2040 and 990 clearly has a distinct evolutionary history. Lebedev, A. 62, 121126 (2014). From: Gene-Environment Interactions in Psychiatry, 2016 View all Topics Download as PDF About this page DNA Topoisomerases: Biochemistry and Molecular Biology & Gao, M. Jumbo bacteriophages: an overview. WebT2 Phage 170,000 b.p. 20 January 2023, Receive 12 print issues and online access, Get just this article for as long as you need it, Prices may be subject to local taxes which are calculated during checkout. Agirrezabala, X. et al. Marvin, D. A. Filamentous phage structure, infection and assembly. Miller ES, Kutter E, Mosig G, Arisaka F, Kunisawa T, Ruger W. Bacteriophage T4 genome. Mol. El Omari, K. et al. It is in the genus Tequatrovirus, and the family Myoviridae. Front. Paris Japonica 150 billion b.p. Drosophila Melanogaster 123 million b.p. The authors contributed equally to all aspects of the article. This study uses a machine learning approach to identify 10,295 previously uncharacterized inoviruses from microbial genomes and metagenomes. PubMed 79, 1496714970 (2005). 8600 Rockville Pike Devoto, A. E. et al. Structure 21, 13841395 (2013). Hua, J. et al. & Moineau, S. Abortive infection mechanisms and prophage sequences significantly influence the genetic makeup of emerging lytic lactococcal phages. Struct. 58, 465474 (2013). Overall, phage genomes represent only about 15% of all viruses with known unique sequences and are thus vastly under-represented in the genome databases. Virol. is a recipient of a fellowship from the Swiss National Science Foundation (Early Postdoc.Mobility). A suggested new bacteriophage genus: Viunalikevirus. Syst. Pedulla ML, Ford ME, Houtz JM, Karthikeyan T, Wadsworth C, Lewis JA, Jacobs-Sera D, Falbo J, Gross J, Pannunzio NR, et al. Nature 554, 118122 (2018). 10, 437449 (2016). Bacterial cells containing an integrated prophage, which can be induced, excised fromthe chromosome and enter thelytic cycle. Phages that can perform either a lytic or a lysogenic mode of replication. Appl. Biol. Proc. Evidence for the exchange of segments between genomes during the evolution of lambdoid bacteriophages. Science 348, 1261498 (2015). Federal government websites often end in .gov or .mil. Microbiol. Microbiol. Copy this link, or click below to email it to a friend. Nature 537, 689693 (2016). Article Zhu H, Yin S, Shuman S. Characterization of polynucleotide kinase/phosphatase enzymes from Mycobacteriophages omega and Cjw1 and vibriophage KVP40. https://doi.org/10.1038/s41579-019-0311-5. Similar groups of genes that travel together through evolution may include the tail genes, or lysis genes, among others. Microbiol. Hatfull GF, Pedulla ML, Jacobs-Sera D, Cichon PM, Foley A, Ford ME, Gonda RM, Houtz JM, Hryckowian AJ, Kelchner VA, et al. 29, 644651 (2001). Note that the apparent sites of recombination are located close to gene boundaries. Nat. 6, 941948 (2008). Exploring the mycobacteriophage metaproteome: phage genomics as an educational platform. PubMed Cell 160, 447460 (2015). Biol. http://www.phage.ulaval.ca. Diversity-generating retroelements. PRINTED FROM OXFORD REFERENCE (www.oxfordreference.com). Viruses 10, 404 (2018). 501, 127140 (2009). Nat. Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. 185, 62206223 (2003). Nat. Sci. 1, 2, 3. Roux, S. et al. Lepage, P. et al. Temperate phages acquire DNA from defective prophages by relaxed homologous recombination: the role of Rad52-like recombinases. Paez-Espino, D. et al. The largest bacteriophage genomes reach a size of 735 kb. The current state of bacteriophage genomics shows that the genetic diversity of the population is very high, that phages have been actively evolving for billions of years with active engagement of horizontal genetic exchange, and that their genomes are consequently pervasively mosaic in their architectures. WebT2 Phage 170,000 b.p. Oceanogr. Opin. Fineran PC, Blower TR, Foulds IJ, Humphreys DP, Lilley KS, Salmond GP. What do all these genes do? Pietil, M. K. et al. About 300 of its genes have been characterized. Uncovering Earths virome. See all related overviews in Oxford Reference 2, 19 (2017). Mol. The other genes of a phage genomethe non-core genesprovide a striking contrast to the core genes discussed above [33]. This study shows the evolutionary relationships that can exist among diverse groups of phage proteins. Viruses in a 14th-century coprolite. Learn how and when to remove this template message, https://en.wikipedia.org/w/index.php?title=Enterobacteria_phage_T2&oldid=1118782073, Articles needing additional references from April 2010, All articles needing additional references, Creative Commons Attribution-ShareAlike License 3.0, This page was last edited on 28 October 2022, at 21:29. Microbiol. Sylvain Moineau. The atomic structure of the phage Tuc2009 baseplate tripod suggests that host recognition involves two different carbohydrate binding modules. T4 was the subject of the classic studies by Benzer (1955), Crick, Brenner et al. In 1952 Alfred Day Hershey and Martha Chase used the T2 bacteriophage in a famous experiment in which they demonstrated that only the nucleic acids of phage molecules were required for their replication within bacteria. Abrescia, N. G. et al. The phylogenetic relationships of the three genes (134, 136 and 137) are represented as phamily circles, in which all genomes within the Phamerator database (S. Cresawn, manuscript submitted) are positioned around the circumference of the circle, and arcs are drawn between those phages sharing members of the phamily, with the thickness of the line reflecting the strength of sequence similarity. government site. Biol. Google Scholar. Nature 494, 357360 (2013). WebT2 phage Genome size: 170,000 bp Common name: virus Escherichia coli Genome size: 4.6 million bp Common name: Bacteria Drosophila melanogaster Genome size: 130 million bp Common name: Fruit fly Homo sapiens Genome size: 3.2 billion bp Common name: Human Paris japonica Genome size: 150 billion bp Common name: canopy plant Students also viewed & Schmid, M. F. Structural similarities in DNA packaging and delivery apparatuses in herpesvirus and dsDNA bacteriophages. ICTV virus taxonomy profile: Plasmaviridae. 3 E Theor. Expanding the Diversity of Mycobacteriophages: Insights into Genome Architecture and Evolution. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final citable form. Paris Japonica 150 billion b.p. This study uses single-virus genomics to identify the most widespread phages in the ocean, which were previously overlooked in metagenomics projects because of their high microdiversity. Open Access These encompass many types of virion morphologies and nucleic acid compositions, but the large majority are double stranded DNA (dsDNA) tailed phages (Caudovirales), reflecting predictions from virion morphology surveys [4]. The observation that the corresponding genes travel together with the head and tail genes is less easily explained but may reflect well-documented interactions among recombination proteins and DNA replication initiation and between recombination proteins and DNA packaging [34]. 73, 7059 (2007). Nigro, O. D. et al. Zuo, T. et al. Modular architecture of the T4 phage superfamily: a conserved core genome and a plastic periphery. Microbiome 5, 83 (2017). The authors declare no competing interests. T2 phage had very high genomic sequence similarity to SV76 (99.99% identity), so we performed host range analysis of T2 with the same bacteria strains to see whether the genomic similarity translated to host range phenotypic similarity. Med. In a few cases, enzymatic or even biological functions have been found for non-core genes, and some of these appear to provide small, non-essential benefits to phage growth or to be essential only in certain hosts or environments [37]. Biol. CAS ISME J. Virology 479480, 487497 (2015). Thank you for visiting nature.com. Pope, W. H. et al. The issue is further complicated by the presence of genome sequences that are phage-derived or phage-associated but play biological roles separate from viral lytic growth. The smallest known genome is possessed by the bacterium Carsonella ruddi 160,000 base pairs.

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