Evol. [Genome size is the total length of DNA in an organism. Nat. Their dsDNAs are linear, cyclically permuted, and terminally redundant. Natl Acad. T4 and Related Phages: Structure and Development. Viral tagging reveals discrete populations in Synechococcus viral genome sequence space. Atomic structure of single-stranded DNA bacteriophage X174 and its functional implications. Cell Host Microbe 25, 285299.e8 (2019). 3.2 A.2 Comparison of genome size in T2 phage, Escherichia coli, Drosophila melanogaster, Homo sapiens and Paris japonica. Soil. Microbiome 6, 68 (2018). 13, 147159 (2015). Bobay, L., Touchon, M. & Rocha, E. P. C. Manipulating or superseding host recombination functions: a dilemma that shapes phage evolvability. Microbiol. Biol. A. Nilsson, A. S. & Haggrd-Ljungquist, E. Detection of homologous recombination among bacteriophage P2 relatives. PubMed 8, 14310 (2017). 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. 10, 437449 (2016). This study presents a large-scale bioinformatic analysis of evolutionary relationships and the rate of HGT in a dataset of more than 2,300 phages. 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. 99, 617618 (2018). This study shows the evolutionary relationships that can exist among diverse groups of phage proteins. The Bacteriophage Lambda (Cold Spring Harbor Laboratory Press 1971). 37, 632639 (2019). Twelve previously unknown phage genera are ubiquitous in global oceans. Proc. Nature Reviews Microbiology & Moineau, S. Abortive infection mechanisms and prophage sequences significantly influence the genetic makeup of emerging lytic lactococcal phages. At the time of writing the total number of unique sequenced bacteriophage genomes is about 750. The examples of genome and chromosome number have been selected to allow points of interest to be raised Paris japonica Largest Known Genome Proc. USA 102, 1894418949 (2005). USA 116, 5493 (2019). Roux, S. et al. Nature 340, 467468 (1989). 11, 28932903 (2009). J. Mol. Single-cell genomics uncover Pelagibacter as the putative host of the extremely abundant uncultured 37-F6 viral population in the ocean. Characterization of virus-like particles associated with the human faecal and caecal microbiota. 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]. 62, 121126 (2014). Commun. Lavelle, K. et al. Hendrix, R. W. Evolution: the long evolutionary reach of viruses. 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 . Res. It is in the genus Tequatrovirus, and the family Myoviridae. Ackermann HW. It contains linear double-stranded DNA, and is covered by a protective protein coat. Viruses 9, 70 (2017). A 3D conformation termed after the capsid protein structure of phage HK97. Microbiol. Proc. PLoS One 8, 112 (2013). ISSN 1740-1526 (print). Microbiol. Microbiol. B. H. Genomic diversification of marine cyanophages into stable ecotypes. Res. Perhaps the most striking feature emerging from phage genome comparative analyses is that they are pervasively mosaic with different segments having distinct evolutionary histories [23]. The host range of the recombinant phages was identical to that of IP008. Chem. Phages are uniquely interconnected from an evolutionary perspective and undergo multiple events of genetic exchange in response to the selective pressure of their hosts, which drives their diversity. Mol. eLife 4, e06416 (2015). Peabody, D. S. The RNA binding site of bacteriophage MS2 coat protein. Devoto, A. E. et al. (c) Copyright Oxford University Press, 2023. 35, 11471159 (2018). Microbiol. Barr, J. J. et al. Cryptic inoviruses are pervasive in bacteria and archaea across Earths biomes. 152, 227243 (2007). Brum, J. R., Schenck, R. O. Insights into assembly from structural analysis of bacteriophage PRD1. Front. Nat. Veterinary Research The RBP structure of the temperate phage TP901-1. PubMedGoogle Scholar. Global morphological analysis of marine viruses shows minimal regional variation and dominance of non-tailed viruses. USA 110, 12798 (2013). The functions of most of these genes are not known but are predicted to be involved in tail assembly. Variability in shapes and sizes for phages. Marine viruses--major players in the global ecosystem. Oceanogr. Sci. 2011 Oct 1; 1(4): 298303. 13, 232236 (2019). Plate tectonics of virus shell assembly and reorganization in phage 8, a distant relative of mammalian reoviruses. Chopin, A., Bolotin, A., Sorokin, A., Ehrlich, S. D. & Chopin, M.-C. Escherichia Coli 5 million b.p. Spinelli, S. et al. Effect of different long-term fertilization regimes on the viral community in an agricultural soil of southern China. 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. Kim, M.-S. & Bae, J.-W. Lysogeny is prevalent and widely distributed in the murine gut microbiota. Bacteriophage T5 tail tube structure suggests a trigger mechanism for Siphoviridae DNA ejection. PRINTED FROM OXFORD REFERENCE (www.oxfordreference.com). Natl Acad. PubMed Comparison of genome size of T2 phage, Genome size can vary greatly between organisms and is not a valid indicator of genetic complexity, The largest known genome is possessed by the canopy plant, The smallest known genome is possessed by the bacterium, Viruses and bacteria tend to have very small genomes, Prokaryotes typically have smaller genomes than eukaryotes, Sizes of plant genomes can vary dramatically due to the capacity for plant species to self-fertilise and become polyploid. 26, 19841994 (2007). Biol. The global virome: not as big as we thought? Breitbart, M., Bonnain, C., Malki, K. & Sawaya, N. A. Phage puppet masters of the marine microbial realm. and JavaScript. It contains linear double-stranded DNA, and is covered by a protective protein coat. 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. Candidate receptors fadL ::Tn ( A = 2.60) and ompF ::Tn ( A = 2.53) were identified ( Fig. Coutinho, F. H. et al. Rev. Kwan T, Liu J, DuBow M, Gros P, Pelletier J. the contents by NLM or the National Institutes of Health. 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 Annu. 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. Numerous different hosts have been employed and it seems reasonable that phages exist for the vast majority of bacterial species that can be propagated in the lab. Cell 177, 115 (2019). DNA 8, 12 (2017). 188, 24002410 (2006). 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 Adriaenssens, E. M. et al. A second general approach is viral metagenomics, in which the viral population is harvested en masse from an environmental source, concentrated, and large numbers of DNA segments sequenced at random [5,6]. CAS Breitbart, M. et al. The smallest known genome is possessed by the bacterium Carsonella ruddi 160,000 base pairs. Sci. Med. 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 Minot, S. & Bryson, A. 3 E Under the terms of the licence agreement, an individual user may print out a PDF of a single entry from a reference work in OR for personal use (for details see Privacy Policy and Legal Notice). It is a virulent bacteriophage which infects Escherichia coli bacteria. Microbiol. Fineran PC, Blower TR, Foulds IJ, Humphreys DP, Lilley KS, Salmond GP. Sci. Natl Acad. Roux, S. et al. The phage is covered by a protective protein coat. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final citable form. T2, T4, and T6 phages differ in the cell wall receptors to which they bind. This genetic material uses the host cell's ribosomes to replicate, and synthesize proteins for the capsid and tail of the phage. Tu AH, Voelker LL, Shen X, Dybvig K. Complete nucleotide sequence of the mycoplasma virus P1 genome. Bolduc, B. et al. Natl Acad. Curr. 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. First, there are examples of short conserved sequences at gene boundaries that could serve to target homologous recombination to these positions [27,28]. 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 474, 604608 (2011). Insights into virus evolution and membrane biogenesis from the structure of the marine lipid-containing bacteriophage PM2. 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 Natl Acad. 80, 26482655 (2014). Get the most important science stories of the day, free in your inbox. WebEnterobacteria Phage T2 As the T2 bacteriophage consists of only two components, they selectively labelled the DNA with radioactive 32P, and (in a separate batch) the proteins with 35S. 7, 17381751 (2013). Theor. Sci. Nat. USA 99, 1425014255 (2002). Natl Acad. PubMed Nat. Novick RP, Christie GE, Penades JR. EMBO J. Casjens S. Prophages and bacterial genomics: what have we learned so far? 5, 4498 (2014). Arch. 18, 597603 (2011). Diemer, G. S. & Stedman, K. M. A novel virus genome discovered in an extreme environment suggests recombination between unrelated groups of RNA and DNA viruses. 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. WebT2 phage is more properly called Enterobacteria phage T2. Mycoplasma phage P1 [17]], ~21kbp [e.g. National Library of Medicine 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]. Ocean plankton. The examples of genome and chromosome number have been selected to allow points of interest to be raised Paris japonica Largest Known Genome Virol. With a sufficiently large collection of diverse genome sequences, homologues can be identified that are present in otherwise far-distantly related phages and establish their phylogenetic relationships [24]. Single-virus genomics reveals hidden cosmopolitan and abundant viruses. Willner D, Thurber RV, Rohwer F. Metagenomic signatures of 86 microbial and viral metagenomes. Opin. Structure 14, 10391048 (2006). These prokaryotic phage proteins share significant homology with the bacterial gyrase and the ParE and ParC proteins. This study shows that phage evolutionary relationships are better represented with a reticulate network because mosaicism leads to phages belonging to multiple groups. 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. Extensive DNA mimicry by the ArdA anti-restriction protein and its role in the spread of antibiotic resistance. BMC Genomics 17, 930 (2016). Rising to the challenge: accelerated pace of discovery transforms marine virology. Nat. Susskind MM, Botstein D. Molecular genetics of bacteriophage P22. 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). Mol. 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. PeerJ 5, e3243 (2017). Bacteriophages offer a special perspective on the diversity, origins, and evolution of viruses, not only in their tremendous abundance there are more than 1031 phage particles in the biosphere but in their distant origins, likely more than three billion years ago [1,2]. New phages are assembled within the cell until the cellular membrane lyses (splits open). 8, 15892 (2017). J. Virol. 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. 2). The complete genomes and proteomes of 27, Kwan T, Liu J, Dubow M, Gros P, Pelletier J. 4, 13291340 (1990). Nature 437, 356361 (2005). 13, e1007018 (2017). Commun. This viral ecology study proposes an approach to quantitatively link phage populations and their genomes to their hosts. Natl Acad. ISME J. Nat. Rapid evolution of the human gut virome. Microbiol. Paris Japonica 150 billion b.p. 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. Environ. Google Scholar. Web1 Introduction. In the phage genomes, 5hmC is further glycosylated to 5ghmC and provides protection against cleavage by bacterial restriction endonucleases [1]. Google Scholar. 11, e1001667 (2013). Inclusion in an NLM database does not imply endorsement of, or agreement with, 3.2 A.2 Comparison of genome size in T2 phage, Escherichia coli, Drosophila melanogaster, Homo sapiens and Paris japonica. Environ. mBio 8, e01579-17 (2017). Paris Japonica 150 billion b.p. Overall, phage genomes represent only about 15% of all viruses with known unique sequences and are thus vastly under-represented in the genome databases. Lepage, P. et al. The DNA of the phage is injected into E. coli cells. 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. J. Virol. Comparative Genomic Analysis of 60 Mycobacteriophage Genomes: Genome Clustering, Gene Acquisition, and Gene Size. 32, 25712584 (2015). Kupczok, A. et al. The junctions between phage genome segments with distinct phylogenies often correspond to gene boundaries (Fig. Abundant SAR11 viruses in the ocean. Marine viruses major players in the global ecosystem. Hendrix, R. W., Smith, M. C. M., Burns, R. N., Ford, M. E. & Hatfull, G. F. Evolutionary relationships among diverse bacteriophages and prophages: all the worlds a phage. 11, 447453 (2008). Nat. Biol. Cell 160, 447460 (2015). Phages have adapted the same protein fold to fulfill multiple functions in virion assembly. Imbroglios of viral taxonomy: genetic exchange and failings of phenetic approaches. vConTACT: an iVirus tool to classify double-stranded DNA viruses that infect archaea and bacteria. The human gut virome: inter-individual variation and dynamic response to diet. & Leplae, R. Reticulate representation of evolutionary and functional relationships between phage genomes. WebGenome size can vary greatly between organisms and is not a valid indicator of genetic complexity. 9, 472484 (2015). Structure 21, 13841395 (2013). Ecol. The T2 39 gene, along with the 52 gene, encode the smallest topo II. NPJ Biofilms Microbiomes 2, 16010 (2016). 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. Google Scholar. 8, 150158 (1998). Nat. 25, 762777 (2008). A., Dishaw, L. J. What do all these genes do? A shape of the phage capsid, which consists of many polygonal faces and is most commonly found as an icosahedron (polyhedron with20 faces). Lubbers MW, Waterfield NR, Beresford TP, Le Page RW, Jarvis AW. Bacteriophages occupy a unique position in biology, representing an absolute majority of all organisms in the biosphere. Bull. Appl. New dimensions of the virus world discovered through metagenomics. Deng, L. et al. Minot, S. et al. Rev. Bergh, ., Brsheim, K. Y., Bratbak, G. & Heldal, M. High abundance of viruses found in aquatic environments. USA 106, 41604165 (2009). 1, 2, 3. 3 E 3.2 A.2 Comparison of genome size in T2 phage, Escherichia coli, Drosophila melanogaster, Homo sapiens and Paris japonica. J. Biol. 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. & Molineux, I. J. Evol. The DNA of the phage is injected into E. coli cells. Nat. 61, 471480 (2002). Khayat, R. et al. The T2 phage can quickly turn an E. coli cell into a T2-producing factory that releases phages when the cell ruptures. J. Bacteriol. 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. 395, 754768 (2010). Modular architecture of the T4 phage superfamily: a conserved core genome and a plastic periphery. and transmitted securely. T4 was the subject of the classic studies by Benzer (1955), Crick, Brenner et al. McKenna, R. et al. 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. Evol. This article reports the ability of RNA phages to adopt defined conformations that can be involved in genome packaging and virion assembly. Arch. Nucleotide sequence of coliphage HK620 and the evolution of lambdoid phages. Highton, P. J., Chang, Y. The T2 39 gene, along with the 52 gene, encode the smallest topo II. Marvin, D. A. Filamentous phage structure, infection and assembly. Adv. Proc. & Bamford, D. H. Nucleic and amino acid sequences support structure-based viral classification. Proc. 1, 15024 (2016). Wang, C., Tu, J., Liu, J. These prokaryotic phage proteins share significant homology with the bacterial gyrase and the ParE and ParC proteins. Each of the genes in Phams 236, 2040 and 990 clearly has a distinct evolutionary history. Mycobacteriophages Colbert, Rosebush and Qyrzula share similar overall genome architectures and many genes, but only Rosebush and Qyrzula have extensive nucleotide sequence similarity. Sci. Cell 98, 825833 (1999). Brum, J. R. et al. 9, 647657 (2011). 6, 941948 (2008). https://doi.org/10.1038/s41579-019-0311-5, DOI: https://doi.org/10.1038/s41579-019-0311-5. Biol. J. Bacteriol. 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. Edwards RA, Rohwer F. Viral metagenomics. It contains linear double-stranded DNA, and is covered by a protective protein coat. 4, 693700 (2019). 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. Tremblay, D. M. et al. Similar groups of genes that travel together through evolution may include the tail genes, or lysis genes, among others. The other genes of a phage genomethe non-core genesprovide a striking contrast to the core genes discussed above [33]. Paris Japonica 150 billion b.p. Virulent viruses that attack Escherichia coli and other enterobacteria. WebIn T2 genes 39 and 60 are fused into one gene (605 amino acids), and it is equivalent to gyrB ( Huang, 1990). WebThe phage T2 screen (Fig. Mol. Duarte, C. M. Seafaring in the 21st century: the Malaspina 2010 Circumnavigation Expedition. 13, 8589 (2006). Candidate receptors fadL ::Tn ( A = 2.60) and ompF ::Tn ( A = 2.53) were identified ( Fig. 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. Thank you for visiting nature.com. But we have barely scratched the surface and the next years of phage genome exploration promise to be especially revealing. Virus Res. Virol. In the T7 phage DNA replication involves a concatenation (q.v.) WebThe long tail fiber genes (genes 37 and 38) from the genome of T2 were replaced with those of the IP008 phage by homologous recombination. Science and technology 79, 1496714970 (2005). Suttle, C. A. Williamson, K. E., Radosevich, M. & Wommack, K. E. Abundance and diversity of viruses in six Delaware soils. WebT2 phage is more properly called Enterobacteria phage T2. Biol. Their dsDNAs are linear, cyclically permuted, and terminally redundant. These include Gene Transfer Agents [12], pathogenicity islands [13], encapsuins [14] and large bacteriocins [15], among others. Genome Res. PLoS Genet. Genes are colored according to their phamily membership. 4, 18951906 (2019). FOIA Dutilh, B. E. et al. 58, 465474 (2013). Zhao, Y. et al. Article Russel, M. & Model, P. A mutation downstream from the signal peptidase cleavage site affects cleavage but not membrane insertion of phage coat protein. Although these advances have expanded our understanding of phage genomic diversity, they also revealed that we have only scratched the surface in the discovery of novel viruses. Sun, L. et al. 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. Icosahedral bacteriophage X174 forms a tail for DNA transport during infection. The link was not copied. 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. Drosophila Melanogaster 123 million b.p. Article Labrie, S. J. In the meantime, to ensure continued support, we are displaying the site without styles 50 years of the International Committee on Taxonomy of Viruses: progress and prospects. 12, 595600 (1993). Jordan, T. C. et al. Virol. Environ. Krupovic, M. & ICTV Report Consortium. Sci. Arnaud, C.-A. Norman, J. M. et al. 91, 113 (2017). Appl. 501, 127140 (2009). Nature 536, 425430 (2016). Enterobacteria phage T2 is a virus that infects and kills E. coli. 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. Structure of the connector of bacteriophage T7 at 8A resolution: structural homologies of a basic component of a DNA translocating machinery. Nat. Adriaenssens, E. & Brister, J. R. How to name and classify your phage: an informal guide. Luo, E., Aylward, F. O., Mende, D. R. & DeLong, E. F. Bacteriophage distributions and temporal variability in the oceans interior. A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes. The lambda red proteins promote efficient recombination between diverged sequences: implications for bacteriophage genome mosaicism. holds the Tier 1 Canada Research Chair in Bacteriophages and is a member of the PROTEO and Op+Lait FRQNT Networks. Fabry, C. M. S. et al. The largest bacteriophage genomes reach a size of 735 kb. From: Gene-Environment Interactions in Psychiatry, 2016 View all Topics Download as PDF About this page DNA Topoisomerases: Biochemistry and Molecular Biology Lpez-Prez, M., Haro-Moreno, J. M., Gonzalez-Serrano, R., Parras-Molt, M. & Rodriguez-Valera, F. Genome diversity of marine phages recovered from Mediterranean metagenomes: size matters.

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