Editing Bacteriophage (section)

== Genome structure ==
Given the millions of different phages in the environment, phage genomes come in a variety of forms and sizes. RNA phages such as [[Bacteriophage MS2|MS2]] have the smallest genomes, with only a few kilobases. However, some DNA phages such as [[Enterobacteria phage T4|T4]] may have large genomes with hundreds of genes; the size and shape of the [[capsid]] varies along with the size of the genome.<ref>{{cite book| vauthors = Black LW, Thomas JA |title=Viral Molecular Machines |chapter=Condensed Genome Structure |date=2012 |volume=726 |pages=469–87|pmid=22297527|pmc=3559133|doi=10.1007/978-1-4614-0980-9_21|series=Advances in Experimental Medicine and Biology|publisher=Springer |isbn=978-1-4614-0979-3}}</ref> The largest bacteriophage genomes reach a size of 735 kb.<ref>{{cite journal | vauthors = Al-Shayeb B, Sachdeva R, Chen LX, Ward F, Munk P, Devoto A, Castelle CJ, Olm MR, Bouma-Gregson K, Amano Y, He C, Méheust R, Brooks B, Thomas A, Lavy A, Matheus-Carnevali P, Sun C, Goltsman DS, Borton MA, Sharrar A, Jaffe AL, Nelson TC, Kantor R, Keren R, Lane KR, Farag IF, Lei S, Finstad K, Amundson R, Anantharaman K, Zhou J, Probst AJ, Power ME, Tringe SG, Li WJ, Wrighton K, Harrison S, Morowitz M, Relman DA, Doudna JA, Lehours AC, Warren L, Cate JH, Santini JM, Banfield JF | title = Clades of huge phages from across Earth's ecosystems | journal = Nature | volume = 578 | issue = 7795 | pages = 425–431 | date = February 2020 | pmid = 32051592 | pmc = 7162821 | doi = 10.1038/s41586-020-2007-4 | doi-access = free | bibcode = 2020Natur.578..425A }}</ref>[[File:T7 phage genome.png|alt=Phage T7 genome (schematic)|thumb|797x797px|Schematic view of the 44 kb [[T7 phage]] genome. Each box is a gene. Numbers indicate genes (or rather open reading frames). The "early", "middle" (DNA replication), and "late" genes (virus structure), roughly represent the time course of gene expression.<ref>{{cite journal | vauthors = Häuser R, Blasche S, Dokland T, Haggård-Ljungquist E, von Brunn A, Salas M, Casjens S, Molineux I, Uetz P | title = Bacteriophage protein-protein interactions | journal = Advances in Virus Research | volume = 83 | pages = 219–298 | date = 2012 | pmid = 22748812 | pmc = 3461333 | doi = 10.1016/B978-0-12-394438-2.00006-2 | isbn = 978-0-12-394438-2 }}</ref>]]Bacteriophage genomes can be highly [[Mosaic (genetics)|mosaic]], i.e. the genome of many phage species appear to be composed of numerous individual modules. These modules may be found in other phage species in different arrangements. [[Mycobacteriophage]]s, bacteriophages with [[mycobacteria]]l hosts, have provided excellent examples of this mosaicism. In these mycobacteriophages, genetic assortment may be the result of repeated instances of [[site-specific recombination]] and [[illegitimate recombination]] (the result of phage genome acquisition of bacterial host genetic sequences).<ref name="pmid18178732">{{cite journal | vauthors = Morris P, Marinelli LJ, Jacobs-Sera D, Hendrix RW, Hatfull GF | title = Genomic characterization of mycobacteriophage Giles: evidence for phage acquisition of host DNA by illegitimate recombination | journal = Journal of Bacteriology | volume = 190 | issue = 6 | pages = 2172–2182 | date = March 2008 | pmid = 18178732 | pmc = 2258872 | doi = 10.1128/JB.01657-07 }}</ref> Evolutionary mechanisms shaping the genomes of bacterial viruses vary between different families and depend upon the type of the nucleic acid, characteristics of the virion structure, as well as the mode of the viral life cycle.<ref name="pmid22126996">{{cite journal | vauthors = Krupovic M, Prangishvili D, Hendrix RW, Bamford DH | title = Genomics of bacterial and archaeal viruses: dynamics within the prokaryotic virosphere | journal = Microbiology and Molecular Biology Reviews | volume = 75 | issue = 4 | pages = 610–635 | date = December 2011 | pmid = 22126996 | pmc = 3232739 | doi = 10.1128/MMBR.00011-11 }}</ref>
Some marine [[roseobacter]] phages, also known as [[roseophage]]s, contain [[deoxyuridine]] (dU) instead of [[Thymidine|deoxythymidine]] (dT) in their genomic DNA. There is some evidence that this unusual component is a mechanism to evade bacterial defense mechanisms such as [[Restriction enzyme|restriction endonucleases]] and [[CRISPR|CRISPR/Cas]] systems which evolved to recognize and cleave sequences within invading phages, thereby inactivating them. Other phages have long been known to use unusual nucleotides. In 1963, Takahashi and Marmur identified a ''[[Bacillus]]'' phage that has dU substituting dT in its genome,<ref>{{cite journal | vauthors = Takahashi I, Marmur J | title = Replacement of thymidylic acid by deoxyuridylic acid in the deoxyribonucleic acid of a transducing phage for Bacillus subtilis | journal = Nature | volume = 197 | issue = 4869 | pages = 794–795 | date = February 1963 | pmid = 13980287 | doi = 10.1038/197794a0 | s2cid = 4166988 | bibcode = 1963Natur.197..794T }}</ref> and in 1977, Kirnos et al. identified a [[cyanophage]] containing 2-aminoadenine (Z) instead of adenine (A).<ref>{{cite journal | vauthors = Kirnos MD, Khudyakov IY, Alexandrushkina NI, Vanyushin BF | title = 2-aminoadenine is an adenine substituting for a base in S-2L cyanophage DNA | journal = Nature | volume = 270 | issue = 5635 | pages = 369–370 | date = November 1977 | pmid = 413053 | doi = 10.1038/270369a0 | s2cid = 4177449 | bibcode = 1977Natur.270..369K }}</ref>