25, 762777 (2008). USA 116, 5493 (2019). Hatfull GF, Pedulla ML, Jacobs-Sera D, Cichon PM, Foley A, Ford ME, Gonda RM, Houtz JM, Hryckowian AJ, Kelchner VA, et al. Paris Japonica 150 billion b.p. T4, with a genome of 166 kbp, is the best-known of all the T phages. Medhekar B, Miller JF. Breitbart, M. et al. 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. Enterobacteria Phage T2 26, 19841994 (2007). 347, 895902 (2005). Nat. Gut 68, 11691179 (2019). Virol. We understand the evolutionary coherence of these groups of genes in terms of the biological functions of the proteins they encode. 29, 644651 (2001). Dysbiosis in inflammatory bowel disease: a role for bacteriophages? Nucleic Acids Res. 36, 916 (2019). Rohwer, F. & Edwards, R. The phage proteomic tree: a genome-based taxonomy for phage. Candidate receptors fadL ::Tn ( A = 2.60) and ompF ::Tn ( A = 2.53) were identified ( Fig. 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. Curr. First, individual phages can be isolated in the laboratory that infect a particular bacterial host used for their propagation. Sci. Nature 466, 334338 (2010). 5500 Phages examined in the electron microscope. WebT2 Phage 170,000 b.p. Hendrix, R. W., Hatfull, G. F. & Smith, M. C. M. Bacteriophages with tails: chasing their origins and 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. 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 Rising to the challenge: accelerated pace of discovery transforms marine virology. Friedman SD, Genthner FJ, Gentry J, Sobsey MD, Vinje J. Gene mapping and phylogenetic analysis of the complete genome from 30 single-stranded RNA male-specific coliphages (family Leviviridae). 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 437, 356361 (2005). Mol. To obtain Sequencing genomes of the viral fraction in a sample. Article Google Scholar. A 3D conformation termed after the capsid protein structure of phage HK97. Enterobacteria Phage T2 Open Access Biol. Martinsohn JT, Radman M, Petit MA. Microbiol. Science 348, 1261447 (2015). The authors contributed equally to all aspects of the article. Oceanogr. Life Sciences, View all related items in Oxford Reference , Search for: 'T phages' in Oxford Reference . 13, 1927 (1997). Structure 6, 135145 (1998). Benson, S. D., Bamford, J. K. H., Bamford, D. H. & Burnett, R. M. Does common architecture reveal a viral lineage spanning all three domains of life? Biol. Environ. The capsid of a bacteriophage can be icosahedral, filamentous, or A substantial portion of these contain at least one prophage and prophages can occupy up to 20% of the chromosomal content [911]; this prevalence of prophages is not unexpected given the finding that a large proportion of isolated bacteriophages are temperate. 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. Paez-Espino, D. et al. WebThe T-even phages, T2, T4, and T6, were used as model systems for the study of virus multiplication. Biol. It is in the genus Tequatrovirus, and the family Myoviridae. Portal protein functions akin to a DNA-sensor that couples genome-packaging to icosahedral capsid maturation. Provided by the Springer Nature SharedIt content-sharing initiative, Nature Reviews Microbiology (Nat Rev Microbiol) Curr. It contains linear double-stranded DNA, and is covered by a protective protein coat. Proc. Proc. Virol. J. Mol. Biol. Mechanism of membranous tunnelling nanotube formation in viral genome delivery. & Gao, M. Jumbo bacteriophages: an overview. Grose, J. H. & Casjens, S. R. Understanding the enormous diversity of bacteriophages: the tailed phages that infect the bacterial family Enterobacteriaceae. The phage is covered by a protective protein coat. Krupovi, M. & Bamford, D. H. Virus evolution: how far does the double -barrel viral lineage extend? Microbiol. Bacteriophages 69, 110123 (2019). This selection for genome size plays an important role in bacteriophage evolution, providing a mechanism for DNA gain and loss that is independent of gene function. Marine viruses major players in the global ecosystem. Microbiol. Comparative Genomic Analysis of 60 Mycobacteriophage Genomes: Genome Clustering, Gene Acquisition, and Gene Size. PLoS Genet. Breitbart, M., Bonnain, C., Malki, K. & Sawaya, N. A. Phage puppet masters of the marine microbial realm. The capsid of a bacteriophage can be icosahedral, filamentous, or Phage The DNA of the phage is injected into E. coli cells. Norman, J. M. et al. The functions of most of these genes are not known but are predicted to be involved in tail assembly. Cell 177, 115 (2019). 7, 12524 (2016). 5, 801812 (2007). The phage can attach to the surface of a bacterium using the proteins on its 'feet' (tail fibers), and inject its genetic material (either DNA or RNA). (c) Copyright Oxford University Press, 2023. Enterobacteria Phage T2 volume18,pages 125138 (2020)Cite this article. Natl Acad. 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. A., Dishaw, L. J. Mol. & Molineux, I. J. Kauffman, K. M. et al. 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]. Gogokhia, L. et al. A dodecamer forming a centralchannel involved inviralDNA packaging and injection, providing a docking site for attachment of the tailmachinery. T2 phage Accessibility WebPhage genomes can consist of either DNA or RNA, and can contain as few as four genes or as many as several hundred. Cell 31, 749761 (2008). 8, 14310 (2017). Drosophila Melanogaster 123 million b.p. Rev. 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. Yuan, Y. A theoretical analysis of how strain-specific viruses can control microbial species diversity. These prokaryotic phage proteins share significant homology with the bacterial gyrase and the ParE and ParC proteins. ISME J. Syst. Lima-Mendez, G., Helden, J. These prokaryotic phage proteins share significant homology with the bacterial gyrase and the ParE and ParC proteins. 3 E Commun. Effect of different long-term fertilization regimes on the viral community in an agricultural soil of southern China. Note that the apparent sites of recombination are located close to gene boundaries. Stewart CR, Casjens SR, Cresawn SG, Houtz JM, Smith AL, Ford ME, Peebles CL, Hatfull GF, Hendrix RW, Huang WM, et al. Because their genomes are relatively small, elucidating the genetic diversity of the phage population, deciphering their origins, and identifying the evolutionary mechanisms that shape the population would seem readily feasible. Clark AJ, Inwood W, Cloutier T, Dhillon TS. Amitsur M, Levitz R, Kaufmann G. Bacteriophage T4 anticodon nuclease, polynucleotide kinase and RNA ligase reprocess the host lysine tRNA. Article WebT2 Phage 170,000 b.p. Biol. 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 mBio 8, e01579-17 (2017). Expansion of bacteriophages is linked to aggravated intestinal inflammation and colitis. Natl Acad. 3 E Several types of recombination events are postulated to contribute to this. 9, 472484 (2015). A third approach is mining prophage and phage-related sequences embedded in sequenced bacterial genomes. Phages that can perform either a lytic or a lysogenic mode of replication. 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]. Khan Academy 12, 595600 (1993). Phage ICTV virus taxonomy profile: Plasmaviridae. J. Virol. WebT2 phage is more properly called Enterobacteria phage T2. Similar groups of genes that travel together through evolution may include the tail genes, or lysis genes, among others. Abundant SAR11 viruses in the ocean. The largest bacteriophage genomes reach a size of 735 kb. This is seen most strikingly in the head gene regions of most phages, where there is little or no evidence of horizontal swapping of genes within this group of genes, even though other parts of the genome may be flamboyantly mosaic. Chen, L. et al. Microbiol. Appl. Plate tectonics of virus shell assembly and reorganization in phage 8, a distant relative of mammalian reoviruses. This is a preview of subscription content, access via your institution. Appl. A likely major contributor is illegitimate recombination, or recombination between short conserved sequences (a few bases), coupled with functional selection of genes [30]. 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. Origins of highly mosaic mycobacteriophage genomes. Structure of the connector of bacteriophage T7 at 8A resolution: structural homologies of a basic component of a DNA translocating machinery. Leplae R, Lima-Mendez G, Toussaint A. ACLAME: a CLAssification of Mobile genetic Elements, update 2010. First, there are examples of short conserved sequences at gene boundaries that could serve to target homologous recombination to these positions [27,28]. Williamson, K. E., Radosevich, M. & Wommack, K. E. Abundance and diversity of viruses in six Delaware soils. Homo Sapiens 3.3 billion b.p. Sci. S.M. Soil. WebThe phage T2 screen (Fig. The smallest known genome is possessed by the bacterium Carsonella ruddi 160,000 base pairs. Natl Acad. Before Microbiol. 3, 566571 (2013). Nilsson, A. S. & Haggrd-Ljungquist, E. Detection of homologous recombination among bacteriophage P2 relatives. Creasy, A., Rosario, K., Leigh, B. Highton, P. J., Chang, Y. 5-hydroxymethylcytosine (5hmC) was first described in 1952 when it was found in the genomes of T-even bacteriophages (T2 and T4). T2, T4, and T6 phages differ in the cell wall receptors to which they bind. Structure 14, 10391048 (2006). Baker, M. L., Jiang, W., Rixon, F. J. Simmonds, P. et al. The atomic structure of the phage Tuc2009 baseplate tripod suggests that host recognition involves two different carbohydrate binding modules. NPJ Biofilms Microbiomes 2, 16010 (2016). It is in the genus Tequatrovirus, and the family Myoviridae. This article focuses on the MCP HK97 fold and its conservation at the structural level between tailed phages and archaeal and eukaryotic viruses. Proc. 3B) resulted in 143 significant hits, of which 86 (SI Appendix, Dataset S1) were positively enriched in the presence of phage T2. Enterobacteria phage T2 The T2 39 gene, along with the 52 gene, encode the smallest topo II. genome size Escherichia Coli 5 million b.p. Rev. 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 Candidate receptors fadL ::Tn ( A = 2.60) and ompF ::Tn ( A = 2.53) were identified ( Fig. An intriguing possibility, whether they are providing a selective benefit or not, is that these genes could serve as a gene nursery, where novel genetic functions could be built by recombination and mutation among genetic sequences that have no essential role in phage survival. Rixon, F. J. Rev. Biol. 9, 647657 (2011). Limnol. This study uses the largest collection of phages infecting the same host (M. smegmatis) to evaluate evolutionary relationships, genomic clusters and discreteness of these clusters. Open Access Evol. 18, 42404253 (2016). Because virion infectivity is influenced by the amount of DNA packaged within any given capsid either too little or too much leads to loss of virion stability there are evolutionary pressures to either gain or lose DNA to accommodate packaging and virion stability. Microbiol. Nat. It is in the genus Tequatrovirus, and the family Myoviridae. & Myers, R. J. Greenberg, N. & Rottem, S. Composition and molecular organization of lipids and proteins in the envelope of mycoplasmavirus MVL2. In general, these genomes are packaged at similar densities into their capsids and the size of the capsid varies as a function of genome size. Google Scholar. 84, 117 (2018). T2 phage The largest known genome is possessed by the canopy plant Paris japonica 150 billion base pairs. Science 348, 1261498 (2015). Gregory, A. C. et al. Ecol. Biol. Res. & Schmid, M. F. Structural similarities in DNA packaging and delivery apparatuses in herpesvirus and dsDNA bacteriophages. Nat. Marine DNA viral macro- and microdiversity from pole to pole. 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. Hendrix, R. W. Bacteriophages: evolution of the majority. Environ. Limnol. De Paepe, M. et al. Proc. Marston, M. F. & Amrich, C. G. Recombination and microdiversity in coastal marine cyanophages. Popul. Furthermore, there may be phages that cannot be recovered using standard laboratory approaches and are missed using this approach. 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. Direct 7, 114 (2012). Kwan T, Liu J, DuBow M, Gros P, Pelletier J. CAS Article 50 years of the International Committee on Taxonomy of Viruses: progress and prospects. eLife 4, 120 (2015). 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. Wang, C., Tu, J., Liu, J. Comparison of genome size of T2 phage, Escherichia coli, Drosophila melanogaster, Homo sapiens and, Genome size can vary greatly between organisms and is not a valid indicator of genetic complexity, Comparison of Genome Size in Different Organisms, Variation in Genome Sizes For Different Types of Organisms. Lang AS, Beatty JT. Virol. 80, 26482655 (2014). Publisher's Disclaimer: This is a PDF file of an unedited manuscript that has been accepted for publication. 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. Spinelli, S. et al. 9, 914917 (1999). The examples of genome and chromosome number have been selected to allow points of interest to be raised Paris japonica Largest Known Genome Bacteriophage B. H. Genomic diversification of marine cyanophages into stable ecotypes. Sci. and JavaScript. Commun. 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. Opin. Importance of widespread gene transfer agent genes in alpha-proteobacteria. 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. ^ {1,2,3} 1,2,3. start superscript, 1, comma, 2, comma, 3, end superscript. 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. Krupovic, M. & ICTV Report Consortium. 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 Variability in shapes and sizes for phages. Benson, S. D., Bamford, J. K., Bamford, D. H. & Burnett, R. M. Viral evolution revealed by bacteriophage PRD1 and human adenovirus coat protein structures. Article 61, 471480 (2002). Proc. This genetic material uses the host cell's ribosomes to replicate, and synthesize proteins for the capsid and tail of the phage. Nat. The description of core and non-core genes given here implies that the non-core genes are moving in and out of the phage genomes on a much faster time scale than the core genes. Lepage, P. et al. Evolutionary relationships among diverse bacteriophages and prophages: all the world's a phage. & Sullivan, M. B. Curr. Zhao, Y. et al. T2, T4, and T6 phages differ in the cell wall receptors to which they bind. Comparative genomic analysis of 18. [Genome size is the total length of DNA in an organism. Cardarelli, L. et al. 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. USA 110, 12798 (2013). Microbiol. But we have barely scratched the surface and the next years of phage genome exploration promise to be especially revealing. The phage is covered by a protective protein coat. & Giske, J. Enterobacteria Phage T2 The phage is covered by a protective protein coat. CAS Nakayama K, Takashima K, Ishihara H, Shinomiya T, Kageyama M, Kanaya S, Ohnishi M, Murata T, Mori H, Hayashi T. The R-type pyocin of Pseudomonas aeruginosa is related to P2 phage, and the F-type is related to lambda phage. This suggests that host preferences represent a significant barrier to genetic exchange, and although phages clearly have the capacity to switch hosts perhaps more easily the more closely related the hosts are by a variety of mechanisms, it is unclear at what rate this occurs in natural populations. Restriction enzymes in cells, not eppendorfs. Mol. Mol. The junctions between phage genome segments with distinct phylogenies often correspond to gene boundaries (Fig. Environ. Natl Acad. Lactococcus phage c2, [18]], and ~ 30 kbp [e.g. Internet Explorer). Characterization of virus-like particles associated with the human faecal and caecal microbiota. Paris Japonica 150 billion b.p. Gut mucosal virome alterations in ulcerative colitis. It is a virulent bacteriophage which infects Escherichia coli bacteria. Opin. 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. Casjens, S. R. The DNA-packaging nanomotor of tailed bacteriophages. It is a virulent bacteriophage which infects Escherichia coli bacteria. 13, 232236 (2019). Res. The phage abortive infection system, ToxIN, functions as a protein-RNA toxin-antitoxin pair. WebHowever, some DNA phages such as T4 may have large genomes with hundreds of genes; the size and shape of the capsid varies along with the size of the genome. Predicted genes are shown as boxes, with gene numbers in the boxes and the sequence phamilies [24] above, with the number of phamily members shown in brackets; phamilies correspond to groups of related genes [24]. USA 96, 21922197 (1999). The kinetic and thermodynamic aftermath of horizontal gene transfer governs evolutionary recovery. is a recipient of a fellowship from the Swiss National Science Foundation (Early Postdoc.Mobility). Res. Uncovering Earths virome. . Lubbers MW, Waterfield NR, Beresford TP, Le Page RW, Jarvis AW. Viral dark matter and virushost interactions resolved from publicly available microbial genomes. 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. 24, 16451654 (2005). Adriaenssens, E. & Brister, J. R. How to name and classify your phage: an informal guide. Your current browser may not support copying via this button. Eur. Biol. Nat. USA 110, 1245012455 (2013). Flix dHrelle Reference Center for Bacterial Viruses: USA 111, 78137818 (2014). Miller ES, Kutter E, Mosig G, Arisaka F, Kunisawa T, Ruger W. Bacteriophage T4 genome. Modular structure of the receptor binding proteins of Lactococcus lactis phages. Nat. Phage Colbert is a more distant relative sharing similar overall genome organization and many common genes but without a high level of nucleotide sequence similarity. Diversity-generating retroelements. Virulent viruses that attack Escherichia coli and other enterobacteria. Nat. Nat. 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. 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). Bacterial cells containing an integrated prophage, which can be induced, excised fromthe chromosome and enter thelytic cycle. Commun. Viruses in the sea. T2 is a 'tailed phage', [1] one of a group known as the 'T4-like viruses'. 2). eLife 3, e03125 (2014). Furthermore, the recombinant phage bacterial lytic Microbiome 6, 68 (2018). Microbiol. PubMed Central Huiskonen, J. T. et al. 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. ^ {1,2,3} 1,2,3. start superscript, 1, comma, 2, comma, 3, end superscript. Aquat. Evol. ISSN 1740-1526 (print). And yet the pace of phage genome characterization has slowed over the past three years, reflecting in part a need to transition from sequencing known and well-characterized bacteriophages to the isolation and comparative analysis of new isolates. WebEnterobacteria phage T2 is a virus that infects and kills E. coli. This study uses a machine learning approach to identify 10,295 previously uncharacterized inoviruses from microbial genomes and metagenomes. Bacteriophage Natl Acad. PubMed To kill or not to kill: the balance between lytic and lysogenic viral infection is driven by trophic status. 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. Re-examination of the relationship between marine virus and microbial cell abundances. Hatfull GF, Jacobs-Sera D, Lawrence JG, Pope WH, Russell DA, Ko CC, Weber RJ, Patel MC, Germane KL, Edgar RH, et al. New dimensions of the virus world discovered through metagenomics. Insights into assembly from structural analysis of bacteriophage PRD1. Hendrix RW, Lawrence JG, Hatfull GF, Casjens S. The origins and ongoing evolution of viruses. Pedulla ML, Ford ME, Houtz JM, Karthikeyan T, Wadsworth C, Lewis JA, Jacobs-Sera D, Falbo J, Gross J, Pannunzio NR, et al. 9, 19 (2013). Genome Size Kim, M.-S. & Bae, J.-W. Lysogeny is prevalent and widely distributed in the murine gut microbiota. PRINTED FROM OXFORD REFERENCE (www.oxfordreference.com). et al. The possibility that some of these small genes provide no selective benefit to the phage that carries them cannot be ruled out, but their generally orderly arrangement on the genome, with good translation start sequences argues against their being disorganized junk DNA. Pietil, M. K. et al. Hendrix RW, Smith MC, Burns RN, Ford ME, Hatfull GF. 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. PLoS One 8, 112 (2013). The phage-related chromosomal islands of Gram-positive bacteria. Lawrence, J. G., Hatfull, G. F. & Hendrix, R. W. Imbroglios of viral taxonomy: genetic exchange and failings of phenetic approaches. & Chiu, W. Common ancestry of herpesviruses and tailed DNA bacteriophages. J. Mol. Nat. Sci. T2 phage 4, 201219 (2017). Luo, E., Aylward, F. O., Mende, D. R. & DeLong, E. F. Bacteriophage distributions and temporal variability in the oceans interior. T2, T4, and T6 phages differ in the cell wall receptors to which they bind. Virol. Expanding the Diversity of Mycobacteriophages: Insights into Genome Architecture and Evolution.

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