Biotechnol. et al. The largest known genome is possessed by the canopy plant Paris japonica 150 billion base pairs. Internet Explorer). In most cases the functions of the non-core genes are unknown, and in some well-studied phages like coliphage , they have been deleted without adverse effect on phage growth under laboratory conditions. Article Genes are drawn and annotated as in Figure 1; those that have no homologues among the collection of mycobacteriophage genomes are shown as white boxes. Lawrence, J. G., Hatfull, G. F. & Hendrix, R. W. Imbroglios of viral taxonomy: genetic exchange and failings of phenetic approaches. Commun. Viruses in a 14th-century coprolite. Arch. J. Bacteriol. T2 phage USA 113, 201601060 (2016).This study identifies 44 phage groups in the gut microbiota, nine of which are shared across more than one-half of individuals and are proposed to be part of a healthy gut phageome. T2, T4, and T6 phages differ in the cell wall receptors to which they bind. However, a ~1.8 kbp segment of Colbert is closely related to Rosebush (94% nucleotide identity) and was presumably acquired relatively recently from a Rosebush-like phage. WebThe phage T2 screen (Fig. Article See all related overviews in Oxford Reference Microbiol. 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. The site is secure. Biol. Physical co-localization in thegenome of genes with associated functions. 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. There are essentially three types of populations available for study. Receptor-binding protein of Lactococcus lactis phages: identification and characterization of the saccharide receptor-binding site. PubMed Central Google Scholar. Biol. The functions of most of these genes are not known but are predicted to be involved in tail assembly. 8, 15892 (2017). Their dsDNAs are linear, cyclically permuted, and terminally redundant. Phage Kim, M.-S. & Bae, J.-W. Lysogeny is prevalent and widely distributed in the murine gut microbiota. Bacteriophage Nat. These discoveries supported that DNA, rather than proteins, is the hereditary material. Microbial ecology provides a framework for considering this, in that constant infection of bacteria by bacteriophages provides a strong selection for phage resistance, coupled with the necessity to evolve phage variants that overcome resistance. The newly made phages are now free to attack more cells. A large variation in capsid size can be observed among members of the Caudovirales, with diameters ranging from 45 to 185 nm, which is usually linked to genome size 18. 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. 69, 110123 (2019). Moreover, viral ecologists calculate that there are about 1023 phage infections per second on a global scale, indicating that the population is not only large and old but also highly dynamic [3]. This study uses a machine learning approach to identify 10,295 previously uncharacterized inoviruses from microbial genomes and metagenomes. Comparative genomic analysis of 18. 22 March 2023, Microbiome Rising to the challenge: accelerated pace of discovery transforms marine virology. Overall, phage genomes represent only about 15% of all viruses with known unique sequences and are thus vastly under-represented in the genome databases. Biol. T2 phage Bacteriophage adhering to mucus provide a non-host-derived immunity. Virus taxonomy in the age of metagenomics. Biol. Susskind MM, Botstein D. Molecular genetics of bacteriophage P22. Virology 479480, 487497 (2015). PeerJ 5, e3243 (2017). Proc. Sci. PubMed eLife 4, 120 (2015). Imbroglios of viral taxonomy: genetic exchange and failings of phenetic approaches. Evol. 58, 465474 (2013). Phage Proc. Environ. Extensive DNA mimicry by the ArdA anti-restriction protein and its role in the spread of antibiotic resistance. Nat. The observation that different regions (genes and gene blocks) of the phage genomes have distinct evolutionary histories, owing to horizontal gene transfer events. 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. Web1 Introduction. Greenberg, N. & Rottem, S. Composition and molecular organization of lipids and proteins in the envelope of mycoplasmavirus MVL2. Single-virus genomics reveals hidden cosmopolitan and abundant viruses. While these relationships are clearly evident among the larger collections of phages of a common host, it seems likely that this is a general property of bacteriophage genomes. Article Lima-Mendez, G., Helden, J. 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 Thingstad, T. F., Vage, S., Storesund, J. E., Sandaa, R.-A. Cell 98, 825833 (1999). Comeau AM, Bertrand C, Letarov A, Tetart F, Krisch HM. Microbiol. Virol. Google Scholar. Structural framework for DNA translocation via the viral portal protein. Microbiol. ^ {1,2,3} 1,2,3. start superscript, 1, comma, 2, comma, 3, end superscript. Curr. Cryptic inoviruses are pervasive in bacteria and archaea across Earths biomes. Suttle, C. A. FOIA Breitbart, M. et al. Nature 437, 356361 (2005). The lambda red proteins promote efficient recombination between diverged sequences: implications for bacteriophage genome mosaicism. 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. It is notable that the GC% content of the large collection of mycobacteriophages varies between 55% and 70%, which is consistent with this consideration [20]. Gregory, A. C. et al. Copy this link, or click below to email it to a friend. The first phages that were studied in detail included seven that commonly infect E. coli. Proc. Its genome consists of linear double-stranded DNA, with repeats at either end. Spinelli, S. et al. Van, Toussaint, A. Phages that can perform either a lytic or a lysogenic mode of replication. Seasonal time bombs: dominant temperate viruses affect Southern Ocean microbial dynamics. Brum, J. R. et al. Lim, E. S. et al. . Marine DNA viral macro- and microdiversity from pole to pole. This article focuses on the MCP HK97 fold and its conservation at the structural level between tailed phages and archaeal and eukaryotic viruses. 5-hydroxymethylcytosine (5hmC) was first described in 1952 when it was found in the genomes of T-even bacteriophages (T2 and T4). Nature 432, 6874 (2004). Dutilh, B. E. et al. Genome Res. Cell 177, 115 (2019). 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. 1). genome size Nucleic Acids Res. Adriaenssens, E. M. et al. 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. 80, 26482655 (2014). & Myers, R. J. WebEnterobacteria phage T2 is a virus that infects and kills E. coli. A large variation in capsid size can be observed among members of the Caudovirales, with diameters ranging from 45 to 185 nm, which is usually linked to genome size 18. Nature 537, 689693 (2016). Natl Acad. Opin. 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. Ackermann HW. Get the most important science stories of the day, free in your inbox. USA 110, 10604 (2013). Mol. T2, T4, and T6 phages differ in the cell wall receptors to which they bind. Sci. PubMed Central USA 106, 41604165 (2009). PubMed Central Article Opin. Willner D, Thurber RV, Rohwer F. Metagenomic signatures of 86 microbial and viral metagenomes. Exploring the mycobacteriophage metaproteome: phage genomics as an educational platform. Highton, P. J., Chang, Y. We understand the evolutionary coherence of these groups of genes in terms of the biological functions of the proteins they encode. PLoS Genet. 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]. mBio 8, 115 (2017). The host range of the recombinant phages was identical to that of IP008. PLoS Biol. Jang, H. Bin et al. Koning, R. I. et al. Nat. 9, 19 (2013). J. Bacteriol. 1, 2, 3. A decade of Streptococcus thermophilus phage evolution in an Irish dairy plant. Deveau H, Garneau JE, Moineau S. CRISPR/Cas system and its role in phage-bacteria interactions. ISME J. Hatfull, G. F. Dark matter of the biosphere: the amazing world of bacteriophage diversity. Flix dHrelle Reference Center for Bacterial Viruses: The .gov means its official. Their dsDNAs are linear, cyclically permuted, and terminally redundant. Hatfull, G. F. Bacteriophage genomics. WebGenome size can vary greatly between organisms and is not a valid indicator of genetic complexity. USA 111, 78137818 (2014). CAS Open Access Diversity-generating retroelements. McKenna, R. et al. 7, 12524 (2016). USA 102, 1894418949 (2005). 13, 1927 (1997). Microbiol. J. Virol. The genes that travel together include head genes, tail genes, DNA replication genes, and nucleotide metabolism genes. PubMed Modular architecture of the T4 phage superfamily: a conserved core genome and a plastic periphery. Annu. From: Gene-Environment Interactions in Psychiatry, 2016 View all Topics Download as PDF About this page DNA Topoisomerases: Biochemistry and Molecular Biology 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. T2 is a 'tailed phage', [1] one of a group known as the 'T4-like viruses'. Coutinho, F. H. et al. Ecol. Life Sciences, View all related items in Oxford Reference , Search for: 'T phages' in Oxford Reference . You could not be signed in, please check and try again. 281, 1425614262 (2006). Additional plausible mechanisms are by transposition, site-specific recombination, and homing endonucleases and while all these contribute they are likely also minor components. 3.2 A.2 Comparison of genome size in T2 phage, Escherichia coli, Drosophila melanogaster, Homo sapiens and Paris japonica. WebEnterobacteria phage T2 is a virus that infects and kills E. coli. The chromosome is contained in a large capsule of protein, and it is injected into the host through a hollow, tubular tail. Virol. Web1 Introduction. Rev. Bull. Asymmetric cryo-EM reconstruction of phage MS2 reveals genome structure in situ. Non-core genes are found in all tailed phage genomes where there is enough information to define the core genes; they are often in small clusters of genes, with the clusters interspersed among the clusters of core genes. A notable advantage of this genome-by-genome approach, however, is that individual phages with sequenced genomes become available for further genetic, biochemical and structural dissection. Simmonds, P. et al. Curr. Extreme dimensions how big (or small) can tailed Proc. The DNA of the phage is injected into E. coli cells. T phages Environ. PubMed Pittsburgh Bacteriophage Institute and Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, 412 624 6975, The publisher's final edited version of this article is available at, Bacteriophage genomes are enormously diverse, Bacteriophage genomes are pervasively mosaic, Bacteriophage-host dynamics are strong drivers of their evolution. Overall, phage genomes represent only about 15% of all viruses with known unique sequences and are thus vastly under-represented in the genome databases. Lavelle, K. et al. J. Gen. Virol. 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. Recent advances in viral metagenomics have enabled the rapid discovery of an unprecedented catalogue of phages in numerous environments, from the human gut to the deep ocean. See Chronology, 1949, Hershey and Rotman; 1961, Rubinstein, Thomas, and Hershey; Genome Sizes and Gene Numbers; bacteriophages, cyclically permuted sequences, rII, triplet code T4 RNA ligase, T7 RNA polymerase, virus. Biol. Genomic differentiation among wild cyanophages despite widespread horizontal gene transfer. J. Virol. Paris Japonica 150 billion b.p. Its genome consists of linear double-stranded DNA, with repeats at either end. 79, 1496714970 (2005). Structure 6, 135145 (1998). Wigington, C. H. et al. Syst. Ackermann, H. W. Phage classification and characterization. genome size Characterization of virus-like particles associated with the human faecal and caecal microbiota. Nature 505, 432435 (2014). Viruses in the fecal microbiota of monozygotic twins and their mothers. Paris Japonica 150 billion b.p. Mol. Genome Size The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final citable form. Microbiol. Natl Acad. These are (by definition) not found in all members of a group of related phages, and often only one example of a particular gene of this sort is present in known phage genomes. J. Mol. Atomic structure of single-stranded DNA bacteriophage X174 and its functional implications. Manrique, P. et al. Genes are colored according to their phamily membership. J. Mol. Cell 160, 447460 (2015). B. H. Genomic diversification of marine cyanophages into stable ecotypes. Nature 345, 3641 (1990). government site. Rev. McMahon SA, Roberts GA, Johnson KA, Cooper LP, Liu H, White JH, Carter LG, Sanghvi B, Oke M, Walkinshaw MD, et al. . Mechanism of membranous tunnelling nanotube formation in viral genome delivery. Sequencing and analysis of the prolate-headed lactococcal bacteriophage c2 genome and identification of the structural genes. First, there are examples of short conserved sequences at gene boundaries that could serve to target homologous recombination to these positions [27,28]. sharing sensitive information, make sure youre on a federal J. Virol. Fierer, N. et al. Soil. WebT2 phage is more properly called Enterobacteria phage T2. Barylski, J. et al. 91, 113 (2017). J. Bacteriol. J. Bacteriol. Olia, A. S., Prevelige Jr., P. E., Johnson, J. E. & Cingolani, G. Three-dimensional structure of a viral genome-delivery portal vertex. It contains linear double-stranded DNA, and is covered by a protective protein coat. 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. Hershey, A. D. Curr. Biol. Mol. Adams, M. J. et al. 29, 644651 (2001). Duda, R. L. & Teschke, C. M. The amazing HK97 fold: versatile results of modest differences. Labrie, S. J. J. Mol. These include Gene Transfer Agents [12], pathogenicity islands [13], encapsuins [14] and large bacteriocins [15], among others. eLife 4, e06416 (2015). Drosophila Melanogaster 123 million b.p. T2, T4, and T6 phages differ in the cell wall receptors to which they bind. 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). Gut 68, 11691179 (2019). Environ. Environ. We do not suppose that this means recombination occurs more frequently in certain areas of the genome. J. WebIn T2 genes 39 and 60 are fused into one gene (605 amino acids), and it is equivalent to gyrB ( Huang, 1990). Szymczak, P., Janzen, T., Neves, R. & Kot, W. Novel variants of Streptococcus thermophilus bacteriophages are indicative of genetic recombination among phages from different bacterial species. Leplae R, Lima-Mendez G, Toussaint A. ACLAME: a CLAssification of Mobile genetic Elements, update 2010. Single-cell genomics uncover Pelagibacter as the putative host of the extremely abundant uncultured 37-F6 viral population in the ocean. 9, 914917 (1999). T4, with a genome of 166 kbp, is the best-known of all the T phages. Struct. (ed.) in The junctions between phage genome segments with distinct phylogenies often correspond to gene boundaries (Fig. Juhala, R. J. et al. Proc. Valegard, K., Liljas, L., Fridborg, K. & Unge, T. The three-dimensional structure of the bacterial virus MS2. WebThe T-even phages, T2, T4, and T6, were used as model systems for the study of virus multiplication. Microbiome 5, 83 (2017). PubMed USA 110, 1077110776 (2013). 18, 597603 (2011). Google Scholar. Web1 Introduction. Language links are at the top of the page across from the title. As a service to our customers we are providing this early version of the manuscript. 82, 132 (2012). 8, 112 (2017). Tu AH, Voelker LL, Shen X, Dybvig K. Complete nucleotide sequence of the mycoplasma virus P1 genome. 1). Genome Size Hatfull GF, Jacobs-Sera D, Lawrence JG, Pope WH, Russell DA, Ko CC, Weber RJ, Patel MC, Germane KL, Edgar RH, et al. While there are a number of advantages of these metagenomic approaches including the vast amounts of sequence data that are obtained the disadvantage is that the output is pure data, and no biological materials for further experimentation are recovered [8]. 26, 19841994 (2007). Overall, phage genomes represent only about 15% of all viruses with known unique sequences and are thus vastly under-represented in the genome databases. In many cases, the modules that are being exchanged correspond to single genes (Fig. About 70% of these sequenced phages correspond to only 12 different bacterial hosts, and this modest collection likely represents just a small portion of the overall diversity. Sci. EMBO J. Lang AS, Beatty JT. Payet, J. P. & Suttle, C. A. Appl. Viruses in the sea. Google Scholar. At the time of writing the total number of unique sequenced bacteriophage genomes is about 750. 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 Homo Sapiens 3.3 billion b.p. Its genome consists of linear double-stranded DNA, with repeats at either end. This study shows that phage evolutionary relationships are better represented with a reticulate network because mosaicism leads to phages belonging to multiple groups. is a recipient of graduate scholarships from the Fonds de Recherche du Qubec Nature et Technologies (FRQNT) as well as Sentinelle Nord, and is a recipient of the Goran-Enhorning Graduate Student Research Award from the Canadian Allergy, Asthma and Immunology Foundation. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. & Giske, J. Global morphological analysis of marine viruses shows minimal regional variation and dominance of non-tailed viruses. Homo Sapiens 3.3 billion b.p. Thank you for visiting nature.com. Sun, L. et al. Nat. Open Access Casjens S. Prophages and bacterial genomics: what have we learned so far? This is a preview of subscription content, access via your institution. Ecology and evolution of viruses infecting uncultivated SUP05 bacteria as revealed by single-cell- and meta-genomics. ISSN 1740-1526 (print). 4, 201219 (2017). The T2 phage can quickly turn an E. coli cell into a T2-producing factory that releases phages when the cell ruptures. Variability in shapes and sizes for phages. Importance of widespread gene transfer agent genes in alpha-proteobacteria. holds the Tier 1 Canada Research Chair in Bacteriophages and is a member of the PROTEO and Op+Lait FRQNT Networks. Origins of highly mosaic mycobacteriophage genomes. Breitbart, M. et al. Restriction enzymes in cells, not eppendorfs. WebEnterobacteria phage T2 is a virus that infects and kills E. coli. 84, 117 (2018). T2 phage Krupovic, M., Prangishvili, D., Hendrix, R. W. & Bamford, D. H. Genomics of bacterial and archaeal viruses: dynamics within the Prokaryotic virosphere. (1961), Brenner, Stretton, and Kaplan (1965), and Edgar and Wood (1966). 185, 62206223 (2003). Marston, M. F. & Martiny, J. But we have barely scratched the surface and the next years of phage genome exploration promise to be especially revealing. Kristensen DM, Mushegian AR, Dolja VV, Koonin EV. Candidate receptors fadL ::Tn ( A = 2.60) and ompF ::Tn ( A = 2.53) were identified ( Fig. Escherichia Coli 5 million b.p. A suggested new bacteriophage genus: Viunalikevirus. Nat. Anyone you share the following link with will be able to read this content: Sorry, a shareable link is not currently available for this article. Structure 14, 10391048 (2006). Plate tectonics of virus shell assembly and reorganization in phage 8, a distant relative of mammalian reoviruses. Campoy S, Aranda J, Alvarez G, Barbe J, Llagostera M. Isolation and sequencing of a temperate transducing phage for Pasteurella multocida. Roux, S. et al. All Rights Reserved. 162, 14411446 (2017). Inclusion in an NLM database does not imply endorsement of, or agreement with, Paris Japonica 150 billion b.p. Google Scholar. Adriaenssens, E. M. et al. Nilsson, A. S. & Haggrd-Ljungquist, E. Detection of homologous recombination among bacteriophage P2 relatives. WebThe T-even phages, T2, T4, and T6, were used as model systems for the study of virus multiplication. Microbiol. Nature 466, 334338 (2010). Evol. It is a virulent bacteriophage which infects Escherichia coli bacteria. PubMed Central In the phage genomes, 5hmC is further glycosylated to 5ghmC and provides protection against cleavage by bacterial restriction endonucleases [1]. 395, 754768 (2010). The smallest of the dsDNA tailed phages genomes are ~11.5 kbp [e.g. As a result, if recombination generates a hybrid by joining parts of head gene sets from two different phages, the recombinant would be non-functional and so lost from the population, even though each of the genes was fully functional in its original context. J. Biol. Proc. Duarte, C. M. Seafaring in the 21st century: the Malaspina 2010 Circumnavigation Expedition. Peabody, D. S. The RNA binding site of bacteriophage MS2 coat protein. IB Biology 3.2 chromosomes Kupczok, A. et al. Zhao, Y. et al. Drosophila Melanogaster 123 million b.p. Enterobacteria phage T2 Eur. Grose, J. H. & Casjens, S. R. Understanding the enormous diversity of bacteriophages: the tailed phages that infect the bacterial family Enterobacteriaceae. 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 megateriumphage G (our
?>