phage T4

T4ファージ

関

bacteriophage T2、bacteriophage T4、phage T2、T4 phage

WordNet

1. the 20th letter of the Roman alphabet (同)t

PrepTutorEJDIC

1. tritiumの化学記号
2. =bacteriophage

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出典(authority):フリー百科事典『ウィキペディア（Wikipedia）』「2016/03/01 20:06:00」(JST)

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Enterobacteria phage T4
Virus classification
Group:	Group I (dsDNA)
Order:	Caudovirales
Family:	Myoviridae
Genus:	T4likeviruses
Species:	Enterobacteria phage T4

Enterobacteria phage T4 is a bacteriophage that infects Escherichia coli bacteria. The T4 phage is a member of the T-even phages, a group including enterobacteriophages T2 and T6. T4 is capable of undergoing only a lytic lifecycle and not the lysogenic lifecycle.

Genome and structure

The T4 phage's double-stranded DNA genome is about 169 kbp long and encodes 289 proteins. The T4 genome is terminally redundant and is first replicated as a unit, then several genomic units are recombined end-to-end to form a concatemer. When packaged, the concatemer is cut at unspecific positions of the same length, leading to several genomes that represent circular permutations of the original. The T4 genome bears eukaryote-like intron sequences.

Translation

The Shine-Dalgarno sequence GAGG dominates in bacteriophage T4 early genes, whereas the sequence GGAG is a target for the T4 endonuclease RegB that initiates the early mRNA degradation.

Virus particle structure

T4 is a relatively large phage, at approximately 90 nm wide and 200 nm long (most phages range from 25 to 200 nm in length). The DNA genome is held in an icosahedral head, also known as a capsid. The T4’s tail is hollow so that it can pass its nucleic acid into the cell it is infecting after attachment. The tail attaches to a host cell with the help of tail fibres. The tail fibres are also important in recognizing host cell surface receptors, so they determine if a bacterium is within the phage's host range.

Infection process

The T4 phage initiates an E. coli infection by binding OmpC porin proteins and Lipopolysaccharide (LPS) on the surface of E. coli cells with its long tail fibers (LTF). A recognition signal is sent through the LTFs to the baseplate. This unravels the short tail fibers (STF) that bind irreversibly to the E. coli cell surface. The baseplate changes conformation and the tail sheath contracts, causing GP5 at the end of the tail tube to puncture the outer membrane of the cell. The lysozyme domain of GP5 is activated and degrades the periplasmic peptidoglycan layer. The remaining part of the membrane is degraded and then DNA from the head of the phage can travel through the tail tube and enter the E. coli cell.

Life cycle

The lytic lifecycle (from entering a bacterium to its destruction) takes approximately 30 minutes (at 37 °C) and consists of:

• Adsorption and penetration (starting immediately)
• Arrest of host gene expression (starting immediately)
• Enzyme synthesis (starting after 5 minutes)
• DNA replication (starting after 10 minutes)
• Formation of new virus particles (starting after 12 minutes)

After the life cycle is complete, the host cell bursts open and ejects the newly built viruses into the environment, destroying the host cell. T4 has a burst size of approximately 100-150 viral particles per infected host. Complementation, deletion, and recombination tests can be used to map out the rII gene locus by using T4. These bacteriophage infect a host cell with their information and then blow up the host cell, thereby propagating themselves.

Replication and packaging

The rate of DNA replication in a living cell was first measured as the rate of phage T4 DNA elongation in phage-infected E. coli. During the period of exponential DNA increase at 37 °C, the rate was 749 nucleotides per second. The mutation rate per base pair per replication during phage T4 DNA synthesis is 1.7 per 10⁸, a highly accurate DNA copying mechanism, with only 1 error in 300 copies. The phage also codes for unique DNA repair mechanisms. The T4 DNA packaging motor has been found to load DNA into phage capsids at a rate up to 2000 base pairs per second. The power involved, if scaled up in size, would be equivalent to that of an average automobile engine.

Multiplicity reactivation

Survival curves for phage T4 with DNA damaged by UV (top) or MMC (bottom) after single phage T4 infecting host cells (monocomplexes) or two or more phage T4 simultaneously infecting host cells (multicomplexes).

Multiplicity reactivation (MR) is the process by which two or more virus genomes, each containing inactivating genome damage, can interact within an infected cell to form a viable virus genome. Salvador Luria, while studying UV irradiated phage T4 in 1946, discovered MR and proposed that the observed reactivation of damaged phage occurs by a recombination mechanism.(see refs.) This preceded the confirmation of DNA as the genetic material in 1952 in related phage T2 by the Hershey–Chase experiment.

As remembered by Luria (1984, pg. 97) the discovery of reactivation of irradiated phage (referred to as "multiplicity reactivation") immediately started a flurry of activity in the study of repair of radiation damage within the early phage group (reviewed by Bernstein in 1981). It turned out later that the repair of damaged phage by mutual help that Luria had discovered was only one special case of DNA repair. Cells of all types, not just, bacteria and their viruses, but all organisms studied, including humans, are now known to have complex biochemical processes for repairing DNA damages (see DNA repair). DNA repair processes are also now recognized as playing critical roles in protecting against aging, cancer, and infertility.

MR is usually represented by "survival curves" where survival of plaque forming ability of multiply infected cells (multicomplexes) is plotted against dose of genome damaging agent. For comparison, the survival of phage plaque forming ability of singly infected cells (monocomplexes) is also plotted against dose of genome damaging agent. The top figure shows the survival curves for phage T4 multicomplexes and monocomplexes with increasing dose of UV light. Since survival is plotted on a log scale it is clear that survival of multicomplexes exceeds that of monocomplexes by very large factors (depending on dose). The UV inactivation curve for multicomplexes has an initial shoulder. Other phage T4 DNA damaging agents with shoulders in their multicomplex survival curves are X-rays and ethyl methane sulfonate (EMS). The presence of a shoulder has been interpreted to mean that two recombinational processes are used. The first one repairs DNA with high efficiency (in the "shoulder"), but is saturated in its ability as damage increases; the second pathway functions at all levels of damage. Surviving T4 phage released from multicomplexes show no increase in mutation, indicating that MR of UV irradiated phage is an accurate process.

The bottom figure shows the survival curves for inactivation of phage T4 by the DNA damaging agent mitomycin C (MMC). In this case the survival curve for multicomplexes has no initial shoulder, suggesting that only the second recombinational repair process described above is active. The efficiency of repair by this process is indicated by the observation that a dose of MMC that allows survival of only 1 in 1,000 monocomplexes allows survival of about 70% of multicomplexes. Similar multicomplex survival curves (without shoulders) were also obtained for the DNA damaging agents P32 decay, psoralen plus near-UV irradiation (PUVA), N-methyl-N'-nitro-N-nitrosoguanidine (MNNG), methyl methane sulfonate (MMS) and nitrous acid.

Several of the genes found to be necessary for MR in phage T4 proved to be orthologs for genes essential for recombination in prokaryotes, eukaryotes and archaea. This includes, for instance, T4 gene uvsX which specifies a protein that has three-dimensional structural homology to RecA from Escherichia coli and the homologous protein RAD51 in eukaryotes and RadA in archaea. It has been suggested that the efficient and accurate recombinational repair of DNA damages during MR may be analogous to the recombinational repair process that occurs during meiosis in eukaryotes.

History

The specific time and place of T4 phage isolation remains unclear, though they were likely found in sewage or fecal material. T4 and similar phages were described in a paper by Thomas F. Anderson, Max Delbrück, and Milislav Demerec in November 1944.

A number of Nobel Prize winners worked with phage T4 or T4-like phages including Max Delbrück, Salvador Luria, Alfred Hershey, James D. Watson, and Francis Crick. Other important scientists who worked with phage T4 include Michael Rossmann, Seymour Benzer, Bruce Alberts, Gisela Mosig, Richard Lenski, and James Bull.

See also

• T4 rII system

References

Further reading

• Leiman, P.G., Kanamaru, S., Mesyanzhinov, V.V., Arisaka, F., and Rossmann, M.G., "Structure and morphogenesis of bacteriophage T4."[1]
• Karam, J., Petrov, V., Nolan, J., Chin, D., Shatley, C., Krisch, H., and Letarov, A. The T4-like phages genome project. http://phage.bioc.tulane.edu/. (The T4-like phage full genomic sequence depository)
• Mosig, G., and F. Eiserling. 2006. T4 and related phages: structure and development, R. Calendar and S. T. Abedon (eds.), The Bacteriophages. Oxford University Press, Oxford. (Review of phage T4 biology) ISBN 0-19-514850-9
• Filee J. Tetart F., Suttle C.A., Krisch H.M. (2005). "Marine T4-type bacteriophages, a ubiquitous component of the dark matter of the biosphere". Proc. Natl. Acad. Sci. USA 102 (35): 12471–6. doi:10.1073/pnas.0503404102. PMC 1194919. PMID 16116082.  (Indication of prevalence and T4-like phages in the wild)
• Chibani-Chennoufi S., Canchaya C., Bruttin A., Brussow H. (2004). "Comparative genomics of the T4-Like Escherichia coli phage JS98: implications for the evolution of T4 phages". J. Bacteriol. 186 (24): 8276–86. doi:10.1128/JB.186.24.8276-8286.2004. PMC 532421. PMID 15576776.  (Characterization of a T4-like phage)
• Desplats C, Krisch HM (May 2003). "The diversity and evolution of the T4-type bacteriophages". Res. Microbiol. 154 (4): 259–67. doi:10.1016/S0923-2508(03)00069-X. PMID 12798230. 
• Miller, E.S., Kutter E., Mosig G., Arisaka F., Kunisawa T., Ruger W. (2003). "Bacteriophage T4 genome". Microbiol. Mol. Biol. Rev. 67 (1): 86–156. doi:10.1128/MMBR.67.1.86-156.2003. PMC 150520. PMID 12626685.  (Review of phage T4, from the perspective of its genome)
• Desplats C., Dez C., Tetart F., Eleaume H., Krisch H.M. (2002). "Snapshot of the genome of the pseudo-T-even bacteriophage RB49". J. Bacteriol. 184 (10): 2789–2804. doi:10.1128/JB.184.10.2789-2804.2002. PMC 135041. PMID 11976309.  (Overview of the RB49 genome, a T4-like phage)
• Malys N, Chang DY, Baumann RG, Xie D, Black LW (2002). "A bipartite bacteriophage T4 SOC and HOC randomized peptide display library: detection and analysis of phage T4 terminase (gp17) and late sigma factor (gp55) interaction". J Mol Biol 319 (2): 289–304. doi:10.1016/S0022-2836(02)00298-X. PMID 12051907.  (T4 phage application in biotechnology for studying protein interaction)
• Tétart F., Desplats C., Kutateladze M., Monod C., Ackermann H.-W., Krisch H.M. (2001). "Phylogeny of the major head and tail genes of the wide-ranging T4-type bacteriophages". J. Bacteriol. 183 (1): 358–366. doi:10.1128/JB.183.1.358-366.2001. PMC 94885. PMID 11114936.  (Indication of the prevalence of T4-type sequences in the wild)
• Abedon S.T. (2000). "The murky origin of Snow White and her T-even dwarfs". Genetics 155 (2): 481–6. PMC 1461100. PMID 10835374.  (Historical description of the isolation of the T4-like phages T2, T4, and T6)
• Ackermann HW, Krisch HM (1997). "A catalogue of T4-type bacteriophages". Arch. Virol. 142 (12): 2329–45. doi:10.1007/s007050050246. PMID 9672598.  (Nearly complete list of then-known T4-like phages)
• Monod C, Repoila F, Kutateladze M, Tétart F, Krisch HM (March 1997). "The genome of the pseudo T-even bacteriophages, a diverse group that resembles T4". J. Mol. Biol. 267 (2): 237–49. doi:10.1006/jmbi.1996.0867. PMID 9096222.  (Overview of various T4-like phages from the perspective of their genomes)
• Kutter E., Gachechiladze K., Poglazov A., Marusich E., Shneider M., Aronsson P., Napuli A., Porter D., Mesyanzhinov V. (1995). "Evolution of T4-related phages". Virus Genes 11 (2-3): 285–297. doi:10.1007/BF01728666. PMID 8828153.  (Comparison of the genomes of various T4-like phages)
• Karam, J. D. et al. 1994. Molecular Biology of Bacteriophage T4. ASM Press, Washington, DC. (The second T4 bible, go here, as well as Mosig and Eiserling, 2006, to begin to learn about the biology T4 phage) ISBN 1-55581-064-0
• Eddy, S. R. 1992. Introns in the T-Even Bacteriophages. Ph.D. thesis. University of Colorado at Boulder. (Chapter 3 provides overview of various T4-like phages as well as the isolation of then-new T4-like phages)
• Surdis, T.J "et al" Bacteriophage attachment methods specific to T4, analysis, Overview.
• Mathews, C. K., E. M. Kutter, G. Mosig, and P. B. Berget. 1983. Bacteriophage T4. American Society for Microbiology, Washington, DC. (The first T4 bible; not all information here is duplicated in Karam et al., 1994; see especially the introductory chapter by Doermann for a historical overview of the T4-like phages) ISBN 0-914826-56-5
• Russell, R. L. 1967. Speciation Among the T-Even Bacteriophages. Ph.D. thesis. California Institute of Technology. (Isolation of the RB series of T4-like phages)
• Malys N, Nivinskas R (2009). "Non-canonical RNA arrangement in T4-even phages: accommodated ribosome binding site at the gene 26-25 intercistronic junction". Mol Microbiol 73 (6): 1115–1127. doi:10.1111/j.1365-2958.2009.06840.x. PMID 19708923.  (rare type of translational regulation characterized in T4)
• Kay D., Fildes P. (1962). "Hydroxymethylcytosine-containing and tryptophan-dependent bacteriophages isolated from city effluents". J. Gen. Microbiol. 27: 143–6. doi:10.1099/00221287-27-1-143. PMID 14454648.  (T4-like phage isolation, including that of phage Ox2)

External links

• Viralzone: T4-like viruses
• T4 Bacteriophage Infection Process Animations

UpToDate Contents

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English Journal

• Massive programmed translational jumping in mitochondria.

• Lang BF1, Jakubkova M, Hegedusova E, Daoud R, Forget L, Brejova B, Vinar T, Kosa P, Fricova D, Nebohacova M, Griac P, Tomaska L, Burger G, Nosek J.Author information 1Robert Cedergren Centre for Bioinformatics and Genomics, Département de Biochimie, Université de Montréal, Montréal, QC, Canada H3T 1J4.AbstractProgrammed translational bypassing is a process whereby ribosomes "ignore" a substantial interval of mRNA sequence. Although discovered 25 y ago, the only experimentally confirmed example of this puzzling phenomenon is expression of the bacteriophage T4 gene 60. Bypassing requires translational blockage at a "takeoff codon" immediately upstream of a stop codon followed by a hairpin, which causes peptidyl-tRNA dissociation and reassociation with a matching "landing triplet" 50 nt downstream, where translation resumes. Here, we report 81 translational bypassing elements (byps) in mitochondria of the yeast Magnusiomyces capitatus and demonstrate in three cases, by transcript analysis and proteomics, that byps are retained in mitochondrial mRNAs but not translated. Although mitochondrial byps resemble the bypass sequence in the T4 gene 60, they utilize unused codons instead of stops for translational blockage and have relaxed matching rules for takeoff/landing sites. We detected byp-like sequences also in mtDNAs of several Saccharomycetales, indicating that byps are mobile genetic elements. These byp-like sequences lack bypassing activity and are tolerated when inserted in-frame in variable protein regions. We hypothesize that byp-like elements have the potential to contribute to evolutionary diversification of proteins by adding new domains that allow exploration of new structures and functions.
• Proceedings of the National Academy of Sciences of the United States of America.Proc Natl Acad Sci U S A.2014 Apr 22;111(16):5926-31. doi: 10.1073/pnas.1322190111. Epub 2014 Apr 7.
• Programmed translational bypassing is a process whereby ribosomes "ignore" a substantial interval of mRNA sequence. Although discovered 25 y ago, the only experimentally confirmed example of this puzzling phenomenon is expression of the bacteriophage T4 gene 60. Bypassing requires translational bloc
• PMID 24711422

• Populations of endemic bacteriophage differ between cattle shedding high and low numbers of Escherichia coli O157:H7 in feces.

• Hallewell J1, Niu YD, Munns K, McAllister TA, Johnson RP, Ackermann HW, Thomas JE, Stanford K.Author information 1Department of Biological Sciences, University of Lethbridge, Lethbridge, Alberta.AbstractThe objectives of this study were to identify endemic bacteriophages (phages) in the feedlot environment and determine relationships of these phages with E. coli O157:H7 from cattle shedding high and low numbers of naturally-occurring E. coli O157:H7. Angus crossbred steers were purchased from a southern Alberta feedlot where cattle excreting ≥ 104 CFU⋅g-1 of E. coli O157:H7 in feces at a single time point were identified as super-shedders (SS; n=6) and cattle excreting < 104 CFU⋅g-1 of feces were identified as low-shedders (LS; n=5). Fecal pats or fecal grabs were collected daily from individual cattle for 5 wk. E. coli O157:H7 in feces was detected by immunomagnetic separation and enumerated by direct plating and phages were isolated using short- and overnight- enrichment methods. The total prevalence of E. coli O157:H7 isolated from feces was 14.4% and did not differ between LS and SS (P = 0.972). The total prevalence of phages was higher in the LS group (20.9%) compared to the SS group (8.3%; P = 0.01). Based on genome size estimated by pulsed field gel electrophoresis and morphology determined by transmission electron microscopy, T4- and O1-like phages of Myoviridae and T1-like phage of Siphoviridae were isolated. Compared to T1- and O1-like phages, T4-like phages exhibited broader host range and stronger lytic capability when targeting E. coli O157:H7. Moreover, the T4-like phages were more frequently isolated from feces of LS than SS, suggesting endemic phages may impact shedding dynamics of E. coli O157:H7 in cattle.
• Applied and environmental microbiology.Appl Environ Microbiol.2014 Apr 18. [Epub ahead of print]
• The objectives of this study were to identify endemic bacteriophages (phages) in the feedlot environment and determine relationships of these phages with E. coli O157:H7 from cattle shedding high and low numbers of naturally-occurring E. coli O157:H7. Angus crossbred steers were purchased from a sou
• PMID 24747892

• Structural basis for recognition of the type VI spike protein VgrG3 by a cognate immunity protein.

• Zhang J1, Zhang H2, Gao Z3, Hu H4, Dong C5, Dong YH6.Author information 1Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, People's Republic of China; School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230027, People's Republic of China.2State Key Laboratory of Protein and Plant Gene Research, and Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, No. 5 Yiheyuan Road, Beijing 100871, People's Republic of China.3Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, People's Republic of China.4Key Laboratory of Molecular Virology and Immunology, Institute Pasteur of Shanghai, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People's Republic of China.5Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, People's Republic of China; State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, People's Republic of China. Electronic address: dongcheng@ihep.ac.cn.6Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, People's Republic of China. Electronic address: dongyh@ihep.ac.cn.AbstractThe bacterial type VI secretion system (T6SS) is used by donor cells to inject toxic effectors into receptor cells. The donor cells produce the corresponding immunity proteins to protect themselves against the effector proteins, thereby preventing their self-intoxication. Recently, the C-terminal domain of VgrG3 was identified as a T6SS effector. Information on the molecular mechanism of VgrG3 and its immunity protein TsaB has been lacking. Here, we determined the crystal structures of native TsaB and the VgrG3C-TsaB complex. VgrG3C adopts a canonical phage-T4-lysozyme-like fold. TsaB interacts with VgrG3C through molecular mimicry, and inserts into the VgrG3C pocket.
• FEBS letters.FEBS Lett.2014 Apr 18. pii: S0014-5793(14)00302-0. doi: 10.1016/j.febslet.2014.04.016. [Epub ahead of print]
• The bacterial type VI secretion system (T6SS) is used by donor cells to inject toxic effectors into receptor cells. The donor cells produce the corresponding immunity proteins to protect themselves against the effector proteins, thereby preventing their self-intoxication. Recently, the C-terminal do
• PMID 24751834

Japanese Journal

• AbpA and AbpB provide anti-phage activity in Escherichia coli

• , , , ,
• Genes & Genetic Systems 89(2), 51-60, 2014
• … Here, we describe a novel anti-phage mechanism in Escherichia coli. … Cells harboring a plasmid with the genes abpA and abpB, formerly yfjL and yfjK, blocked the propagation of bacteriophages belonging to three families: T4, T2, T7 and λ phages. … Both genes were necessary for the inhibition of phage propagation, and deletion of either chromosomal gene resulted in a 20% increase of progeny compared to wild-type cells. …
• NAID 130004687230

• 3P003 T4ファージgp34C末端側半分の結晶構造から得られたファージ尾繊維に共通の構造(01A.蛋白質:構造,ポスター,日本生物物理学会年会第51回(2013年度))

• Kanamaru Shuji,Namura Mikiyoshi,Arisaka Fumio
• 生物物理 53(SUPPLEMENT_1-2), S212, 2013-09-13
• NAID 110009819807

• Disinfection Using Pressurized Carbon Dioxide Microbubbles to Inactivate <I>Escherichia coli</I>, Bacteriophage MS2 and T4

• , , , , , , ,
• Journal of Water and Environment Technology 11(6), 497-505, 2013
• … against <I>Escherichia coli</I>, bacteriophage MS2 and T4 were examined at equal pressures (0.3 - 0.9 MPa) and temperatures. … was achieved, while over 3.0 log and nearly 4.0 log reductions were observed for phage MS2 and phage T4, respectively. …
• NAID 130003382727

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「T4ファージ」

　　[★]

英

bacteriophage T4、phage T4、T4 phage

関

バクテリオファージT4、バクテリオファージT2、ファージT2

「bacteriophage T2」

　　[★]

• バクテリオファージT2

関

bacteriophage T4、phage T2、phage T4、T4 phage

「T4 phage」

　　[★]

T4ファージ

関

bacteriophage T2、bacteriophage T4、phage T2、phage T4

「phage T2」

　　[★]

• ファージT2

関

bacteriophage T2、bacteriophage T4、phage T4、T4 phage

「bacteriophage T4」

　　[★]

バクテリオファージT4、T4ファージ

関

bacteriophage T2、phage T2、phage T4、T4 phage

「T4」

　　[★]

甲状腺ホルモン

• サイロキシン thyroxine

脊椎

同

第4胸椎、第４胸椎、第四胸椎

• 胸骨柄と第4胸椎下縁を結ぶ線が上縦隔と下縦隔の境界となる

「T」

　　[★]

• T波 T wave
• チミン thymine
• ツイスト数
• スレオニントレオニン threonine

　 　

「phage」

　　[★]

• ファージ

関

bacteriophage

　

「t4」

　　[★]

同

T4

関

Thyroxine