t2 phage genome size

Nat. Manrique, P. et al. Nature Reviews Microbiology Proc. 4, 18951906 (2019). ICTV virus taxonomy profile: Plasmaviridae. Commun. 1). Pietil, M. K. et al. Viruses in a 14th-century coprolite. Overall, phage genomes represent only about 15% of all viruses with known unique sequences and are thus vastly under-represented in the genome databases. Microbiome 5, 83 (2017). 36, 916 (2019). 162, 14411446 (2017). Sci. The crystal structure of bacteriophage HK97 gp6: defining a large family of headtail connector proteins. Jang, H. Bin et al. 5, 801812 (2007). Iranzo, J., Krupovic, M. & Koonin, E. V. The double-stranded DNA virosphere as a modular hierarchical network of gene sharing. PubMed Nature 536, 425430 (2016). 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. Overall, phage genomes represent only about 15% of all viruses with known unique sequences and are thus vastly under-represented in the genome databases. Virulent viruses that attack Escherichia coli and other enterobacteria. The human gut virome: inter-individual variation and dynamic response to diet. Structure 21, 13841395 (2013). Microbiol. Curr. Microbiol. Their average size is substantially less than that of core genes, often by nearly a factor of two, and it has been suggested that they may correspond to individual functional protein domains [35,36]. Suttle CA. Bacteriophage T5 tail tube structure suggests a trigger mechanism for Siphoviridae DNA ejection. Creasy, A., Rosario, K., Leigh, B. Mavrich, T. N. & Hatfull, G. F. Bacteriophage evolution differs by host, lifestyle and genome. 6, 941948 (2008). of multiple head-to-tail copies of the genome. The T2 phage can quickly turn an E. coli cell into a T2-producing factory that releases phages when the cell ruptures. Inclusion in an NLM database does not imply endorsement of, or agreement with, Sci. Grose, J. H. & Casjens, S. R. Understanding the enormous diversity of bacteriophages: the tailed phages that infect the bacterial family Enterobacteriaceae. Maps were generated using the program Phamerator (S. Cresawn, manuscript submitted). While these likely contribute to mosaicism, it is far from clear that this is a general mechanism, because most phage gene boundaries are not associated with conserved sequence segments sufficiently long to be recognized by the homologous recombination machinery [29]. Rising to the challenge: accelerated pace of discovery transforms marine virology. Microbiol. 8, 1953 (2017). 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]. A. et al. PubMed The phage-related chromosomal islands of Gram-positive bacteria. Clark AJ, Inwood W, Cloutier T, Dhillon TS. . 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. Marine viruses--major players in the global ecosystem. USA 106, 41604165 (2009). Microbiol. The lambda red proteins promote efficient recombination between diverged sequences: implications for bacteriophage genome mosaicism. The tendency for genes whose proteins function together to stay together reaches an extreme in the group of phages related to coliphage T4. PubMed Central These prokaryotic phage proteins share significant homology with the bacterial gyrase and the ParE and ParC proteins. T2, T4, and T6 phages differ in the cell wall receptors to which they bind. The .gov means its official. Proc. 13, 1927 (1997). A major lineage of non-tailed dsDNA viruses as unrecognized killers of marine bacteria. Marine viruses discovered via metagenomics shed light on viral strategies throughout the oceans. T2 is a 'tailed phage', [1] one of a group known as the 'T4-like viruses'. Proc. CAS Open Access Lokareddy, R. K. et al. Modular architecture of the T4 phage superfamily: a conserved core genome and a plastic periphery. Phage genomes are mosaic, but not all genes in a given genome participate in mosaicism to the same degree. Ackermann, H. W. Phage classification and characterization. Microbiol. Rev. Nature 474, 604608 (2011). We predict that many more phage genes participate in these dances for survival, but that answers to these questions will await further dissection of bacteriophages genomes and their biology. Breitbart, M., Bonnain, C., Malki, K. & Sawaya, N. A. Phage puppet masters of the marine microbial realm. 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. Structure of an archaeal virus capsid protein reveals a common ancestry to eukaryotic and bacterial viruses. Gogokhia, L. et al. Cell 118, 419429 (2004). This article reports the ability of RNA phages to adopt defined conformations that can be involved in genome packaging and virion assembly. T2, T4, and T6 phages differ in the cell wall receptors to which they bind. Biol. Nature 432, 6874 (2004). Martinez-Hernandez, F. et al. PubMed Central Candidate receptors fadL ::Tn ( A = 2.60) and ompF ::Tn ( A = 2.53) were identified ( Fig. Medhekar B, Miller JF. Genomic differentiation among wild cyanophages despite widespread horizontal gene transfer. It is therefore not surprising that phages sometimes encode their own restriction systems, toxin-antitoxin systems, and immunity systems stolen from other bacteriophages [20]. Barylski, J. et al. Microbiol. Nature 466, 334338 (2010). Breitbart, M. et al. These include Gene Transfer Agents [12], pathogenicity islands [13], encapsuins [14] and large bacteriocins [15], among others. Nucleotide sequence of coliphage HK620 and the evolution of lambdoid phages. Evolutionary relationships among diverse bacteriophages and prophages: all the world's a phage. WebGenome size can vary greatly between organisms and is not a valid indicator of genetic complexity. 8, 19 (2017). Experiments conducted in 1952 by Alfred Hershey and Martha Chase demonstrated how the DNA of viruses is injected into the bacterial cells, while most of the viral proteins remain outside. 184, 45294535 (2002). Google Scholar. A likely major contributor is illegitimate recombination, or recombination between short conserved sequences (a few bases), coupled with functional selection of genes [30]. Mosaicism is of course not confined to phage genomes as bacteria also acquire DNA by horizontal genetic transfer; but the extent appears to be much greater in bacteriophage evolution. (1961), Brenner, Stretton, and Kaplan (1965), and Edgar and Wood (1966). official website and that any information you provide is encrypted Simmonds, P. et al. Spinelli, S. et al. & Schmid, M. F. Structural similarities in DNA packaging and delivery apparatuses in herpesvirus and dsDNA bacteriophages. Biol. Arnaud, C.-A. Curr. Proc. 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. Atomic structure of single-stranded DNA bacteriophage X174 and its functional implications. eLife 4, e06416 (2015). Virol. 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. To obtain Expanding the Diversity of Mycobacteriophages: Insights into Genome Architecture and Evolution. Cardarelli, L. et al. Genomic analysis of uncultured marine viral communities. Overall, phage genomes represent only about 15% of all viruses with known unique sequences and are thus vastly under-represented in the genome databases. A. 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]. Cell 31, 749761 (2008). 15, 161168 (2017). Comparative genomic analysis of 18. Environ. Sci. J. Virol. Edwards RA, Rohwer F. Viral metagenomics. Appl. Phage infecting a common host can also exhibit substantial diversity suggesting that there are additional barriers to genetic exchange [2022]. Microbiol. mBio 8, e01579-17 (2017). Luo, E., Aylward, F. O., Mende, D. R. & DeLong, E. F. Bacteriophage distributions and temporal variability in the oceans interior. Re-examination of the relationship between marine virus and microbial cell abundances. 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. Google Scholar. 2, 19 (2017). mBio 8, 115 (2017). From: vConTACT: an iVirus tool to classify double-stranded DNA viruses that infect archaea and bacteria. 5-hydroxymethylcytosine (5hmC) was first described in 1952 when it was found in the genomes of T-even bacteriophages (T2 and T4). Minot, S. & Bryson, A. Lavelle, K. et al. Bacteriophage adhering to mucus provide a non-host-derived immunity. 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. Curr. mBio 5, 18 (2014). NPJ Biofilms Microbiomes 2, 16010 (2016). Roux, S., Hallam, S. J., Woyke, T. & Sullivan, M. B. PLoS One 8, 112 (2013). Its genome consists of linear double-stranded DNA, with repeats at either end. CAS Virus Res. & Bamford, D. H. Nucleic and amino acid sequences support structure-based viral classification. BMC Genomics 17, 930 (2016). (c) Copyright Oxford University Press, 2023. Proc. Annu. The DNA of the phage is injected into E. coli cells. Exploring the mycobacteriophage metaproteome: phage genomics as an educational platform. https://doi.org/10.1038/s41579-019-0311-5, DOI: https://doi.org/10.1038/s41579-019-0311-5. WebIn T2 genes 39 and 60 are fused into one gene (605 amino acids), and it is equivalent to gyrB ( Huang, 1990). Casjens, S. R. The DNA-packaging nanomotor of tailed bacteriophages. WebT2 phage is more properly called Enterobacteria phage T2. Natl Acad. Avrani, S., Wurtzel, O., Sharon, I., Sorek, R. & Lindell, D. Genomic island variability facilitates Prochlorococcusvirus coexistence. USA 111, 78137818 (2014). These prokaryotic phage proteins share significant homology with the bacterial gyrase and the ParE and ParC proteins. 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? Wigington, C. H. et al. 8, 14310 (2017). Open Access J. Bacteriol. 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. In the T7 phage DNA replication involves a concatenation (q.v.) The largest bacteriophage genomes reach a size of 735 kb. Paris Japonica 150 billion b.p. 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. . Minot, S. et al. It is in the genus Tequatrovirus, and the family Myoviridae. 26, 19841994 (2007). Virology 479480, 487497 (2015). Zuo, T. et al. Newly acquired DNA thus provides a reservoir of genetic information for potential future use, rather than being selected for immediate utility. The largest known genome is possessed by the canopy plant Paris japonica 150 billion base pairs. Careers, Unable to load your collection due to an error. PLoS Genet. 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. As a library, NLM provides access to scientific literature. 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. To kill or not to kill: the balance between lytic and lysogenic viral infection is driven by trophic status. Chem. A Dictionary of Genetics , Subjects: Healthy human gut phageome. Nature 494, 357360 (2013). Commun. 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. 21, 12281234 (2015). 1, 15024 (2016). 82, 132 (2012). Hershey, A. D. Canchaya C, Fournous G, Brussow H. The impact of prophages on bacterial chromosomes. Coutinho, F. H. et al. In: Calendar R, editor. Commun. At the time of writing the total number of unique sequenced bacteriophage genomes is about 750. 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 This viral ecology study proposes an approach to quantitatively link phage populations and their genomes to their hosts. 18, 597603 (2011). & Leplae, R. Reticulate representation of evolutionary and functional relationships between phage genomes. Curr. WebEnterobacteria phage T2 is a virus that infects and kills E. coli. Rev. Nat. Suttle, C. A. Miller ES, Kutter E, Mosig G, Arisaka F, Kunisawa T, Ruger W. Bacteriophage T4 genome. sharing sensitive information, make sure youre on a federal Structure of the bacteriophage 6 nucleocapsid suggests a mechanism for sequential RNA packaging. Oceanogr. CAS Furthermore, phage-encoded homologous recombinases have properties that are well-suited to facilitating this process [31]. Virology 468, 421443 (2014). Microbiol. Microbiol. Natl Acad. This process is known as the Lytic cycle. Homo Sapiens 3.3 billion b.p. Article Its genome consists of linear double-stranded DNA, with repeats at either end. EMBO J. Willner D, Thurber RV, Rohwer F. Metagenomic signatures of 86 microbial and viral metagenomes. 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 Sci. Microbiol. Peabody, D. S. The RNA binding site of bacteriophage MS2 coat protein. Characterization of virus-like particles associated with the human faecal and caecal microbiota. Silveira, C. B. CAS 10, e1004181 (2014). Portal protein functions akin to a DNA-sensor that couples genome-packaging to icosahedral capsid maturation. Environ. Microbiol. 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. 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). 10, 437449 (2016). The functions of most of these genes are not known but are predicted to be involved in tail assembly. Lactococcus phage c2, [18]], and ~ 30 kbp [e.g. Open Access articles citing this article. Legrand, P. et al. The DNA of the phage is injected into E. coli cells. Suttle, C. A. But we have barely scratched the surface and the next years of phage genome exploration promise to be especially revealing. 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. Seasonal time bombs: dominant temperate viruses affect Southern Ocean microbial dynamics. 185, 62206223 (2003). 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. Cell 160, 447460 (2015). et al. Microbiome 6, 68 (2018). 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. Viral dark matter and virushost interactions resolved from publicly available microbial genomes. ISSN 1740-1526 (print). 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. Nat. As a service to our customers we are providing this early version of the manuscript. Mycoplasma phage P1 [17]], ~21kbp [e.g. Sci. 69, 110123 (2019). Virol. Disease-specific alterations in the enteric virome in inflammatory bowel disease. the contents by NLM or the National Institutes of Health. Biol. Hurwitz, B. L., Brum, J. R. & Sullivan, M. B. Depth-stratified functional and taxonomic niche specialization in the core and flexible Pacific Ocean virome. Hua, J. et al. Web1 Introduction. 29, 644651 (2001). Brum, J. R. & Sullivan, M. B. Mechanism of membranous tunnelling nanotube formation in viral genome delivery. Pope WH, Jacobs-Sera D, Russell DA, Peebles CL, Al-Atrache Z, Alcoser TA, Alexander LM, Alfano MB, Alford ST, Amy NE, et al. Microbiol. EMBO J. The smallest of the dsDNA tailed phages genomes are ~11.5 kbp [e.g. 1, 2, 3. Google Scholar. Lubbers MW, Waterfield NR, Beresford TP, Le Page RW, Jarvis AW. Microbiol. Hatfull GF, Jacobs-Sera D, Lawrence JG, Pope WH, Russell DA, Ko CC, Weber RJ, Patel MC, Germane KL, Edgar RH, et al. Res. PLoS Genet. 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. 152, 227243 (2007). Their dsDNAs are linear, cyclically permuted, and terminally redundant. . Google Scholar. Dutilh, B. E. et al. Roux, S. et al. Natl Acad. 11, 447453 (2008). 2). Shkoporov, A. N. et al. 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 79, 1496714970 (2005). J. Mol. 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. The genome of. Cell 16, 673685 (2004). In the phage genomes, 5hmC is further glycosylated to 5ghmC and provides protection against cleavage by bacterial restriction endonucleases [1]. Ackermann, H. W. 5500 Phages examined in the electron microscope. Lima-Mendez G, Van Helden J, Toussaint A, Leplae R. Reticulate representation of evolutionary and functional relationships between phage genomes. Aquat. Google Scholar. ISME J. What do all these genes do? Environmental drivers of viral community composition in Antarctic soils identified by viromics. 8, 15892 (2017). Evol. Nat. 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. 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. Nat. Effect of phage vB_EcoM_FJ1 on the reduction of ETEC O9:H9 infection in a neonatal pig cell line, Rhizosphere phage communities drive soil suppressiveness to bacterial wilt disease, Genomic diversity and ecological distribution of marine Pseudoalteromonas phages, Abundant and cosmopolitan lineage of cyanopodoviruses lacking a DNA polymerase gene, Unexplored diversity and ecological functions of transposable phages, Characterization and genome analysis of a novel phage Kayfunavirus TM1. Phages that can strictly undergo a lytic mode of replication. Hendrix, R. W., Hatfull, G. F. & Smith, M. C. M. Bacteriophages with tails: chasing their origins and evolution. Arch. Viruses in the sea. 11, 28932903 (2009). & Moineau, S. Abortive infection mechanisms and prophage sequences significantly influence the genetic makeup of emerging lytic lactococcal phages. Vidaver, A. K., Koski, R. K. & Van Etten, J. L. Bacteriophage 6: a lipid-containing virus of Pseudomonas phaseolicola. The number of individual phages isolated is substantial [>5,000; [4]], but the complete genome sequences of only about 750 of these have been determined. 71, 31193125 (2005). Gut mucosal virome alterations in ulcerative colitis.

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