Journal articles: 'Lambda phage'

1

Hecht, Michael H., and Robert T. Sauer. "Phage lambda repressor revertants." Journal of Molecular Biology 186, no. 1 (November 1985): 53–63. http://dx.doi.org/10.1016/0022-2836(85)90256-6.

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2

Poteete, A. R., and A. C. Fenton. "Efficient double-strand break-stimulated recombination promoted by the general recombination systems of phages lambda and P22." Genetics 134, no. 4 (August 1, 1993): 1013–21. http://dx.doi.org/10.1093/genetics/134.4.1013.

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Abstract To examine bacteriophage recombination in vivo, independent of such other processes as replication and packaging, substituted lambda phages bearing restriction site polymorphisms were employed in a direct physical assay. Bacteria were infected with two phage variants; DNA was extracted from the infected cells and cut with a restriction endonuclease. The production of a unique recombinant fragment was measured by Southern blotting and hybridization with a substitution sequence-specific probe. High frequency recombination was observed under the following conditions: the substituted lambda phages infected a wild-type host cell bearing a lambda repressor-expressing plasmid designed to shut down phage transcription and inhibit phage DNA replication as well. The same plasmid expressed the lambda red and gam genes. In addition, the host cell bore a second plasmid which expressed the EcoRI restriction-modification system. Both phage chromosomes possessed a single EcoRI site in the middle of the marked substitution sequence; however, as the site was modified in one of the parent phages, only the other partner was cut. Recombination was found to be dependent upon (1) red, (2) recA, (3) inactivation of the host recBCD function, either by Gam protein or by mutation and (4) double-strand breaks. The homologous recombination system of phage P22 could substitute for that of lambda.

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3

Ghaemi, Amir, Alijan Tabaraei, Pooria Gill, Hoorieh Soleimanja, and Ali Gorji. "Lambda Phage Nanoparticles for Targetomics." Biotechnology(Faisalabad) 11, no. 2 (February 15, 2012): 95–99. http://dx.doi.org/10.3923/biotech.2012.95.99.

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4

Murray, Noreen E. "The impact of phage lambda: from restriction to recombineering." Biochemical Society Transactions 34, no. 2 (March 20, 2006): 203–7. http://dx.doi.org/10.1042/bst0340203.

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Experiments using phage lambda provided early insights into important molecular mechanisms, including genetic recombination and the control of gene expression. Before recombinant DNA technology, the use of lambda, most particularly lambda transducing phages, illustrated the importance of cloning bacterial genes, already providing some insight into how to use cloned genes to advantage. Subsequently, lambda made significant contributions to recombinant DNA technology, including the early generation of genomic and cDNA libraries. More recently, lambda genes associated with recombination have enabled techniques referred to as ‘recombineering’ to be developed. These techniques permit the refined manipulation, including mutation, of foreign genes in Escherichia coli and their subsequent return to the donor organism.

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5

Blasche, Sonja, Stefan Wuchty, Seesandra V. Rajagopala, and Peter Uetz. "The Protein Interaction Network of Bacteriophage Lambda with Its Host, Escherichia coli." Journal of Virology 87, no. 23 (September 18, 2013): 12745–55. http://dx.doi.org/10.1128/jvi.02495-13.

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Although most of the 73 open reading frames (ORFs) in bacteriophage λ have been investigated intensively, the function of many genes in host-phage interactions remains poorly understood. Using yeast two-hybrid screens of all lambda ORFs for interactions with its hostEscherichia coli, we determined a raw data set of 631 host-phage interactions resulting in a set of 62 high-confidence interactions after multiple rounds of retesting. These links suggest novel regulatory interactions between theE. colitranscriptional network and lambda proteins. Targeted host proteins and genes required for lambda infection are enriched among highly connected proteins, suggesting that bacteriophages resemble interaction patterns of human viruses. Lambda tail proteins interact with both bacterial fimbrial proteins andE. coliproteins homologous to other phage proteins. Lambda appears to dramatically differ from other phages, such as T7, because of its unusually large number of modified and processed proteins, which reduces the number of host-virus interactions detectable by yeast two-hybrid screens.

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6

Wu, W. F., S. Christiansen, and M. Feiss. "Domains for protein-protein interactions at the N and C termini of the large subunit of bacteriophage lambda terminase." Genetics 119, no. 3 (July 1, 1988): 477–84. http://dx.doi.org/10.1093/genetics/119.3.477.

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Abstract The large subunit of phage lambda terminase, gpA, the gene product of the phage A gene, interacts with the small subunit, gpNul, to form functional terminase. Terminase binds to lambda DNA at cosB to form a binary complex. The terminase:DNA complex binds a prohead to form a ternary complex. Ternary complex formation involves an interaction of the prohead with gpA. The amino terminus of gpA contains a functional domain for interaction with gpNul, and the carboxy-terminal 38 amino acids of gpA contain a functional domain for prohead binding. This information about the structure of gpA was obtained through the use of hybrid phages resulting from recombination between lambda and the related phage 21. lambda and 21 encode terminases that are analogous in structural organization and have ca. 60% sequence identity. In spite of these similarities, lambda and 21 terminases differ in specificity for DNA binding, subunit assembly, and prohead binding. A lambda-21 hybrid phage produces a terminase in which one of the subunits is chimeric and had recombinant specificities. In the work reported here; a new hybrid, lambda-21 hybrid 67, is characterized. lambda-21 hybrid 67 is the result of a crossover between lambda and 21 in the large subunit genes, such that the DNA from the left chromosome end is from 21, including cosB phi 21, the 1 gene, and the first 48 codons for the 2 gene. The rest of the hybrid 67 chromosome is lambda DNA, including 593 codons of the A gene. The chimeric gp2/A of hybrid 67 binds gp1 to form functional terminase.(ABSTRACT TRUNCATED AT 250 WORDS)

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7

Stahl, F. W., C. E. Shurvinton, L. C. Thomason, S. Hill, and M. M. Stahl. "On the clustered exchanges of the RecBCD pathway operating on phage lambda." Genetics 139, no. 3 (March 1, 1995): 1107–21. http://dx.doi.org/10.1093/genetics/139.3.1107.

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Abstract Lytic cycle crosses of Red- Gam- phage lambda were conducted in rec+ Escherichia coli carrying one or another plasmid with homology to lambda. Lambda x lambda recombinants and lambda x plasmid recombinants were formed by RecBCD-mediated recombination. We showed previously that the act of recombining with a plasmid alters the disposition of selected lambda x lambda exchanges. This work reports that the relationships between the lambda x plasmid and the lambda x lambda exchanges is unaltered by the removal from one lambda parent of the homology shared with the plasmid. This result supports our view that a reciprocal exchange, allowing for cointegrate formation, is associated with but mechanistically separable from a (presumably) nonreciprocal lambda x lambda exchange. The nature of this relationship is independent of lambda's Rap function, which is shown to alter the ratio of cointegrate formation (splices) to marker pick-up (patches) in lambda x plasmid recombination mediated by the RecBCD pathway.

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8

Wróbel, B., S. Srutkowska, and G. Wegrzyn. "Biochemical and genetic analysis of lambdaW, the newly isolated lambdoid phage." Acta Biochimica Polonica 45, no. 1 (March 31, 1998): 251–59. http://dx.doi.org/10.18388/abp.1998_4308.

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Otherwise isogenic Escherichia coli CP78 (relA+) and CP79 (relA-) strains are commonly used in studies on the stringent control, the bacterial response to amino acid starvation. We found that these strains are lysogenic for a phage which is spontaneously induced with a low frequency, producing virions able to infect other E. coli strains. Genetic studies, restriction analysis of the phage DNA genome, and electron microscopy revealed that this phage is very similar to, but not identical with, bacteriophage lambda. We called the newly isolated phage lambdaW, and found that most of CP78/CP79 ancestor strains are lysogenic for this phage.

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9

Bustamante, C., J. Marko, E. Siggia, and S. Smith. "Entropic elasticity of lambda-phage DNA." Science 265, no. 5178 (September 9, 1994): 1599–600. http://dx.doi.org/10.1126/science.8079175.

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10

Stahl, F. W., M. S. Fox, D. Faulds, and M. M. Stahl. "Break-join recombination in phage lambda." Genetics 125, no. 3 (July 1, 1990): 463–74. http://dx.doi.org/10.1093/genetics/125.3.463.

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Abstract In phage lambda, when DNA replication is blocked, recombination mediated by the Red pathway occurs only near the double-chain break site, cos, that defines the termini of the virion chromosome. The recombinants initiated by cos contain newly synthesized DNA near cos, in amount corresponding to a few percent of the length of lambda. A restriction enzyme cut delivered to one parent far from cos results in elevated recombination near the restriction site. Recombinants induced by this cut have a similarly small amount of DNA synthesis in these replication-blocked crosses. When restriction cuts are introduced in the presence of normal amounts of all of the DNA replication enzymes, many of the resulting recombinants still enjoy, at most, a small amount of DNA synthesis associated with the exchange event. Thus, these experiments fail to support the previously considered possibility that Red-mediated recombination in lambda proceeds largely through a break-copy pathway.

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11

Wegrzyn, G., A. Wegrzyn, I. Konieczny, K. Bielawski, G. Konopa, M. Obuchowski, D. R. Helinski, and K. Taylor. "Involvement of the host initiator function dnaA in the replication of coliphage lambda." Genetics 139, no. 4 (April 1, 1995): 1469–81. http://dx.doi.org/10.1093/genetics/139.4.1469.

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Abstract We demonstrate that the initiation of coliphage lambda DNA replication is dependent on the host initiator function dnaA, provided that the lambdoid prophage Rac is absent. Presence of Rac compensated the absence of dnaA function, causing initiation of replication. In dnaAts rac+ cells at 43 degrees, most of parental phage DNA molecules, after one round of theta replication, switched to a replication with features of the sigma mode and produced progeny at high yield. Initiation of replication of the lambda Pts1 mutant at 43 degrees was blocked by dnaA function; however, under dnaA-rac+ conditions all parental phage DNA molecules, after one round of theta replication, switched to the sigma mode and produced progeny at high yield. Taking into account our recent finding that transcriptional activation of ori lambda seems to be dnaA-regulated (to be published elsewhere), we suggest that the DnaA-lambda Pts1 incompatibility occurs at the insertion of the ori lambda-bound lambda O-lambda P-DnaB preprimosome between the complementary lambda DNA strands. The role of Rac and the mechanism of the switch from theta to sigma mode of lambda phage DNA replication are discussed.

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12

Maruyama, I. N., H. I. Maruyama, and S. Brenner. "Lambda foo: a lambda phage vector for the expression of foreign proteins." Proceedings of the National Academy of Sciences 91, no. 17 (August 16, 1994): 8273–77. http://dx.doi.org/10.1073/pnas.91.17.8273.

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13

Guzmán, P., and G. Guarneros. "Phage genetic sites involved in lambda growth inhibition by the Escherichia coli rap mutant." Genetics 121, no. 3 (March 1, 1989): 401–9. http://dx.doi.org/10.1093/genetics/121.3.401.

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Abstract The rap mutation of Escherichia coli prevents the growth of bacteriophage lambda. We have isolated phage mutants that compensate for the host deficiency. The mutations, named bar, were genetically located to three different loci of the lambda genome: barI in the attP site, barII in the cIII ea10 region, and barIII within or very near the imm434 region. The level of lambda leftward transcription correlates with rap exclusion. Phage lambda mutants partially defective in the pL promoter or in pL-transcript antitermination showed a Bar- phenotype. Conversely, mutants constitutive for transcription from the pI or pL promoters were excluded more stringently by rap bacteria. We conclude that rap exclusion depends on the magnitude of transcription through the wild type bar loci in the phage genome.

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14

Chang, Jenny R., Eun-Ho Song, Eri Nakatani-Webster, Lucas Monkkonen, Daniel M. Ratner, and Carlos E. Catalano. "Phage Lambda Capsids as Tunable Display Nanoparticles." Biomacromolecules 15, no. 12 (November 20, 2014): 4410–19. http://dx.doi.org/10.1021/bm5011646.

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15

Sun, Yuting Liang, Naresh Kumar Mani, Damien Baigl, Thomas Gisler, André Pierre Schröder, and Carlos Manuel Marques. "Photocontrol of end-grafted lambda-phage DNA." Soft Matter 7, no. 12 (2011): 5578. http://dx.doi.org/10.1039/c1sm05046j.

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16

Patterson, Thomas A., and Michael Dean. "Preparation of high titer lambda phage lysates." Nucleic Acids Research 15, no. 15 (1987): 6298. http://dx.doi.org/10.1093/nar/15.15.6298.

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17

Pearson, R. K., and M. S. Fox. "Effects of DNA heterologies on bacteriophage lambda packaging." Genetics 118, no. 1 (January 1, 1988): 5–12. http://dx.doi.org/10.1093/genetics/118.1.5.

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Abstract We have examined the impact of DNA heterologies on the packaging of lambda DNA in vitro. Heterology-containing DNA molecules were constructed by denaturing and reannealing a mixture of DNA from cI+ phage and DNA front phage carrying small insertion or deletion mutations in the cI gene. We found that molecules with heterologies of up to 19 base pairs (bp) can be packaged as viable heterozygous phage with approximately the same efficiency as molecules with a base pair mismatch. In contrast, with a heterology of 26-bp heterozygous plaque formers are rare. In principle, the absence of cI heterozygotes among packaged phage may be due either to a failure to encapsulate the DNA or a failure to inject the packaged DNA on infection. Southern blot analysis of DNA isolated from packaged phage indicates that DNA harboring a 26-bp heterology is almost completely absent in packaged phage. Thus, an upper limit has been established for the size of heterology that can be accommodated by the packaging apparatus The size of the connector portal could be the basis for this limit.

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18

Shimizu, H., H. Yamaguchi, and H. Ikeda. "Molecular analysis of lambda bio transducing phage produced by oxolinic acid-induced illegitimate recombination in vivo." Genetics 140, no. 3 (July 1, 1995): 889–96. http://dx.doi.org/10.1093/genetics/140.3.889.

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Abstract To study the mechanism of DNA gyrase-mediated illegitimate recombination in Escherichia coli, we examined the formation of lambda Spi- phage during prophage induction. The frequency of Spi- phage was two to three orders of magnitude higher in the presence of oxolinic acid, an inhibitor of DNA gyrase A subunit, than in the absence of the drug, while it was very low in nalAr bacteria with the drug. RecA function is not required for the formation of these phages, indicating that this enhancement is not caused by the expression of SOS-controlled genes. Analyses of att region and recombination junctions of Spi- phages revealed that they have essentially the same structures as lambda bio transducing phages but are classified into two groups with respect to recombination sites. In the majority class of the transducing phages, there were not more than 3-bp homologies between the parental E. coli bio and lambda recombination sites. In the minority class of the transducing phages, on the other hand, 9-10-bp homologies were found between the parental recombination sites. These results suggested that oxolinic acid-induced illegitimate recombination takes place by two variants of a DNA gyrase-dependent mechanism.

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19

MAHAFFY, J. "A genetic switch: Gene control and phage lambda." Bulletin of Mathematical Biology 49, no. 6 (1987): 763–64. http://dx.doi.org/10.1016/s0092-8240(87)90021-8.

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20

ROBERTS, J. "Phage lambda and the regulation of transcription termination." Cell 52, no. 1 (January 1988): 5–6. http://dx.doi.org/10.1016/0092-8674(88)90523-5.

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21

Bertram, H., and U. Hagen. "Radical Effects on Mutation Spectra in Lambda Phage." International Journal of Radiation Biology 62, no. 1 (January 1992): 3–8. http://dx.doi.org/10.1080/09553009214551771.

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22

Reisinger, Günter R., Arne Rietsch, Werner Lubitz, and Udo Bläsi. "Lambda Kil-Mediated Lysis Requires the Phage Context." Virology 193, no. 2 (April 1993): 1033–36. http://dx.doi.org/10.1006/viro.1993.1222.

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23

Murray, Noreen E., and Alexander Gann. "What has phage lambda ever done for us?" Current Biology 17, no. 9 (May 2007): R305—R312. http://dx.doi.org/10.1016/j.cub.2007.03.006.

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24

Strauch, Eckhard, Christoph Schaudinn, and Lothar Beutin. "First-Time Isolation and Characterization of a Bacteriophage Encoding the Shiga Toxin 2c Variant, Which Is Globally Spread in Strains of Escherichia coli O157." Infection and Immunity 72, no. 12 (December 2004): 7030–39. http://dx.doi.org/10.1128/iai.72.12.7030-7039.2004.

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ABSTRACT A bacteriophage encoding the Shiga toxin 2c variant (Stx2c) was isolated from the human Escherichia coli O157 strain CB2851 and shown to form lysogens on the E. coli K-12 laboratory strains C600 and MG1655. Production of Stx2c was found in the wild-type E. coli O157 strain and the K-12 lysogens and was inducible by growing bacteria in the presence of ciprofloxacin. Phage 2851 is the first reported viable bacteriophage which carries an stx 2c gene. Electron micrographs of phage 2851 showed particles with elongated hexagonal heads and long flexible tails resembling phage lambda. Sequence analysis of an 8.4-kb region flanking the stx 2c gene and other genetic elements revealed a mosaic gene structure, as found in other Stx phages. Phage 2851 showed lysis of E. coli K-12 strains lysogenic for Stx phages encoding Stx1 (H19), Stx2 (933W), Stx (7888), and Stx1c (6220) but showed superinfection immunity with phage lambda, presumably originating from the similarity of the cI repressor proteins of both phages. Apparently, phage 2851 integrates at a different chromosomal locus than Stx2 phage 933W and Stx1 phage H19 in E. coli, explaining why Stx2c is often found in combination with Stx1 or Stx2 in E. coli O157 strains. Diagnostic PCR was performed to determine gene sequences specific for phage 2851 in wild-type E. coli O157 strains producing Stx2c. The phage 2851 q and o genes were frequently detected in Stx2c-producing E. coli O157 strains, indicating that phages related to 2851 are associated with Stx2c production in strains of E. coli O157 that were isolated in different locations and time periods.

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25

Okayama, H., and P. Berg. "Bacteriophage lambda vector for transducing a cDNA clone library into mammalian cells." Molecular and Cellular Biology 5, no. 5 (May 1985): 1136–42. http://dx.doi.org/10.1128/mcb.5.5.1136.

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We have developed a bacteriophage lambda vector (lambda NMT) that permits efficient transduction of mammalian cells with a cDNA clone library constructed with the pcD expression vector (H. Okayama and P. Berg, Mol. Cell. Biol. 3:280-289, 1983). The phage vector contains a bacterial gene (neo) fused to the simian virus 40 early-region promoter and RNA processing signals, providing a dominant-acting selectable marker for mammalian transformation. The phage DNA can accommodate pcD-cDNA recombinants with cDNA of up to about 9 kilobases without impairing the ability of the phage DNA to be packaged in vitro and propagated in vivo. Transfecting cells with the lambda NMT-pcD-cDNA recombinant phage yielded G418-resistant clones at high frequency (approximately 10(-2]. Cells that also acquired a particular cDNA segment could be detected among the G418-resistant transformants by a second selection or by a variety of screening protocols. Reconstitution experiments indicated that the vector could transduce 1 in 10(6) cells for a particular phenotype if the corresponding cDNA was present as 1 functional cDNA clone per 10(5) clones in the cDNA library. This expectation was confirmed by obtaining two hypoxanthine-guanine phosphoribosyltransferase (HPRT)-positive transductants after transfecting 10(7) HPRT-deficient mouse L cells with a simian virus 40-transformed human fibroblast cDNA library incorporated into the lambda NMT phage vector. These transductants contained the human HPRT cDNA sequences and expressed active human HPRT.

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Okayama, H., and P. Berg. "Bacteriophage lambda vector for transducing a cDNA clone library into mammalian cells." Molecular and Cellular Biology 5, no. 5 (May 1985): 1136–42. http://dx.doi.org/10.1128/mcb.5.5.1136-1142.1985.

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We have developed a bacteriophage lambda vector (lambda NMT) that permits efficient transduction of mammalian cells with a cDNA clone library constructed with the pcD expression vector (H. Okayama and P. Berg, Mol. Cell. Biol. 3:280-289, 1983). The phage vector contains a bacterial gene (neo) fused to the simian virus 40 early-region promoter and RNA processing signals, providing a dominant-acting selectable marker for mammalian transformation. The phage DNA can accommodate pcD-cDNA recombinants with cDNA of up to about 9 kilobases without impairing the ability of the phage DNA to be packaged in vitro and propagated in vivo. Transfecting cells with the lambda NMT-pcD-cDNA recombinant phage yielded G418-resistant clones at high frequency (approximately 10(-2]. Cells that also acquired a particular cDNA segment could be detected among the G418-resistant transformants by a second selection or by a variety of screening protocols. Reconstitution experiments indicated that the vector could transduce 1 in 10(6) cells for a particular phenotype if the corresponding cDNA was present as 1 functional cDNA clone per 10(5) clones in the cDNA library. This expectation was confirmed by obtaining two hypoxanthine-guanine phosphoribosyltransferase (HPRT)-positive transductants after transfecting 10(7) HPRT-deficient mouse L cells with a simian virus 40-transformed human fibroblast cDNA library incorporated into the lambda NMT phage vector. These transductants contained the human HPRT cDNA sequences and expressed active human HPRT.

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27

Oviedo de Anda, Norma Angélica, Luis Kameyama, José Manuel Galindo, Gabriel Guarneros, and Javier Hernandez-Sanchez. "Evidence of bar Minigene Expression and tRNA2IleSequestration as Peptidyl-tRNA2Ileduring Lambda Bacteriophage Development." Journal of Bacteriology 186, no. 16 (August 15, 2004): 5533–37. http://dx.doi.org/10.1128/jb.186.16.5533-5537.2004.

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ABSTRACT Lambda bacteriophage development is impaired in Escherichia coli cells defective for peptidyl (pep)-tRNA hydrolase (Pth). Single-base-pair mutations (bar −) that affect translatable two-codon open reading frames named bar minigenes (barI or barII) in the lambda phage genome promote the development of this phage in Pth-defective cells (rap cells). When the barI minigene is cloned and overexpressed from a plasmid, it inhibits protein synthesis and cell growth in rap cells by sequestering \batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(\mathrm{tRNA}_{2}^{\mathrm{Ile}}\) \end{document} as \batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(\mathrm{pep}-\mathrm{tRNA}_{2}^{\mathrm{Ile}}\) \end{document} . Either \batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(\mathrm{tRNA}_{2}^{\mathrm{Ile}}\) \end{document} or Pth may reverse these effects. In this paper we present evidence that both barI and barII minigenes are translatable elements that sequester \batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(\mathrm{tRNA}_{2}^{\mathrm{Ile}}\) \end{document} as \batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(\mathrm{pep}-\mathrm{tRNA}_{2}^{\mathrm{Ile}}\) \end{document} . In addition, overexpression of the barI minigene impairs the development even of bar − phages in rap cells. Interestingly, tRNA or Pth may reestablish lambda phage development. These results suggest that lambda bar minigenes are expressed and \batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(\mathrm{tRNA}_{2}^{\mathrm{Ile}}\) \end{document} is sequestered as \batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(\mathrm{pep}-\mathrm{tRNA}_{2}^{\mathrm{Ile}}\) \end{document} during lambda phage development.

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28

Poteete, Anthony R., Hsinju R. Wang, and Patricia L. Foster. "Phage λ Red-Mediated Adaptive Mutation." Journal of Bacteriology 184, no. 13 (July 1, 2002): 3753–55. http://dx.doi.org/10.1128/jb.184.13.3753-3755.2002.

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ABSTRACT Replacement of the recBCD genes of Escherichia coli with the red recombination genes of bacteriophage lambda results in a strain in which adaptive mutation occurs at an elevated frequency. Like RecBCD-dependent adaptive mutation, Red-mediated adaptive mutation is dependent upon recA and ruvABC functions.

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29

Kulkarni, S. K., and F. W. Stahl. "Interaction between the sbcC gene of Escherichia coli and the gam gene of phage lambda." Genetics 123, no. 2 (October 1, 1989): 249–53. http://dx.doi.org/10.1093/genetics/123.2.249.

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Abstract gam mutants of phage lambda carrying long palindromes fail to form plaques on wild-type Escherichia coli but do grow on strains that are mutant in the sbcC gene. gam + lambda carrying the same palindrome grow on both hosts and on a host deleted for the recB, C and D genes. These results suggest that the Gam protein of lambda, known to interact also with E. coli's recBCD protein, can interact with the product of the sbcC gene.

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30

Pearson, R. K., and M. S. Fox. "Effects of DNA heterologies on bacteriophage lambda recombination." Genetics 118, no. 1 (January 1, 1988): 13–19. http://dx.doi.org/10.1093/genetics/118.1.13.

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Abstract Previous studies of bacteriophage lambda recombination have provided indirect evidence that substantial sequence nonhomologies, such as insertions and deletions, may be included in regions of heteroduplex DNA. However, the direct products of heterology-containing heteroduplex DNA--heterozygous progeny phage--have not been observed. We have constructed a series of small insertion and deletion mutations in the cI gene to examine the possibility that small heterologies might be accommodated in heterozygous progeny phage. Genetic crosses were carried out between lambda cI- Oam29 and lambda cI+ Pam80 under replication-restricted conditions. Recombinant O+P+ progeny were selected on mutL hosts and tested for cI heterozygosity. Heterozygous recombinants were readily observed with crosses involving insertions of 4 to 19 base pairs (bp) in the cI gene. Thus, nonhomologies of at least 19 bp can be accommodated in regions of heteroduplex DNA during lambda recombination. In contrast, when a cI insertion or deletion mutation of 26 bp was present, few of the selected recombinants were heterozygous for cI. Results using a substitution mutation, involving a 26-bp deletion with a 22-bp insertion, suggest that the low recovery of cI heterozygotes containing heterologies of 26 bp or more is due to a failure to encapsulate DNA containing heterologies of 26 bp or more into viable phage particles.

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31

Rydman, Pia S., and Dennis H. Bamford. "Identification and Mutational Analysis of Bacteriophage PRD1 Holin Protein P35." Journal of Bacteriology 185, no. 13 (July 1, 2003): 3795–803. http://dx.doi.org/10.1128/jb.185.13.3795-3803.2003.

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ABSTRACT Holin proteins are phage-induced integral membrane proteins which regulate the access of lytic enzymes to host cell peptidoglycan at the time of release of progeny viruses by host cell lysis. We describe the identification of the membrane-containing phage PRD1 holin gene (gene XXXV). The PRD1 holin protein (P35, 12.8 kDa) acts similarly to its functional counterpart from phage lambda (gene S), and the defect in PRD1 gene XXXV can be corrected by the presence of gene S of lambda. Several nonsense, missense, and insertion mutations in PRD1 gene XXXV were analyzed. These studies support the overall conclusion that the charged amino acids at the protein C terminus are involved in the timing of host cell lysis.

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32

Hagemann, A. T., and S. M. Rosenberg. "Chain bias in Chi-stimulated heteroduplex patches in the lambda ren gene is determined by the orientation of lambda cos." Genetics 129, no. 3 (November 1, 1991): 611–21. http://dx.doi.org/10.1093/genetics/129.3.611.

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Abstract Heteroduplex patch recombinants have received information in one DNA chain but have not recombined flanking markers. Evidence regarding which chain is exchanged bears on the structure of recombination intermediates. The direction of travel along DNA of RecBCD recombinase, the central enzyme in the Escherichia coli RecBCD pathway of homologous recombination, is determined in phage lambda by the orientation of the packaging origin, cos. cos is a double-chain cut site which serves as a preferred entry site for RecBCD. Using partially denaturing gels to resolve heteroduplex molecules, we have examined patch recombinants at the lambda ren gene. We report that the transferred information in Chi-stimulated patches at ren can occur on either chain, but is biased to the chain ending 5' at the right of the lambda map (the lambda r chain) in phage carrying cos in its normal orientation. The chain bias switches in favor of the chain that ends 3' at the right (the lambda l chain) when RecBCD travel direction is reversed by inverting cos. We entertain models that accommodate these and other results pertaining to the structure of RecBCD-mediated recombinants.

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33

Giladi, Hilla, Max Gottesman, and Amos B. Oppenheim. "Integration host factor stimulates the phage lambda pL promoter." Journal of Molecular Biology 213, no. 1 (May 1990): 109–21. http://dx.doi.org/10.1016/s0022-2836(05)80124-x.

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34

Xu, Ning, Xue Lei, Ping Ao, and Jun Zhang. "Bifurcation Analysis for Phage Lambda with Binding Energy Uncertainty." Computational Biology Journal 2014 (February 3, 2014): 1–11. http://dx.doi.org/10.1155/2014/465216.

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In a phage λ genetic switch model, bistable dynamical behavior can be destroyed due to the bifurcation caused by inappropriately chosen model parameters. Since the values of many parameters with biological significance often cannot be accurately acquired, it is thus of fundamental importance to analyze how and to which extent the system dynamics is influenced by model parameters, especially those parameters pertaining to binding energies. In this paper, we apply a Jacobian method to investigate the relation between bifurcation and parameter uncertainties on a phage λ OR model. By introducing bistable range as a measure of system robustness, we find that RNA polymerase binding energies have the minimum bistable ranges among all the binding energies, which implies that the uncertainties on these parameters tend to demolish the bistability more easily. Moreover, parameters describing mutual prohibition between proteins Cro and CI have finite bistable ranges, whereas those describing self-prohibition have infinity bistable ranges. Hence, the former are more sensitive to parameter uncertainties than the latter. These results help to understand the influence of parameter uncertainties on the bifurcation and thus bistability.

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35

Kent, Bethany N., and Seth R. Bordenstein. "Phage WO of Wolbachia: lambda of the endosymbiont world." Trends in Microbiology 18, no. 4 (April 2010): 173–81. http://dx.doi.org/10.1016/j.tim.2009.12.011.

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36

Weisberg, Robert A. "A Genetic Switch: Phage lambda and Higher Organisms.Mark Ptashne." Quarterly Review of Biology 69, no. 2 (June 1994): 267–68. http://dx.doi.org/10.1086/418570.

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37

Cicchini, Carla, Helenia Ansuini, Laura Amicone, Tonino Alonzi, Alfredo Nicosia, Riccardo Cortese, Marco Tripodi, and Alessandra Luzzago. "Searching for DNA–protein Interactions by Lambda Phage Display." Journal of Molecular Biology 322, no. 4 (September 2002): 697–706. http://dx.doi.org/10.1016/s0022-2836(02)00851-3.

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38

Gussin, Gary. "Book review:A Genetic Switch-Third Edition Phage Lambda Revisited." BioEssays 26, no. 11 (2004): 1254–55. http://dx.doi.org/10.1002/bies.20148.

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39

St-Pierre, F., and D. Endy. "Determination of cell fate selection during phage lambda infection." Proceedings of the National Academy of Sciences 105, no. 52 (December 19, 2008): 20705–10. http://dx.doi.org/10.1073/pnas.0808831105.

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40

McVey, Duncan, Mohammed Zuber, Damodar Ettyreddy, Douglas E. Brough, and Imre Kovesdi. "Rapid Construction of Adenoviral Vectors by Lambda Phage Genetics." Journal of Virology 76, no. 8 (April 15, 2002): 3670–77. http://dx.doi.org/10.1128/jvi.76.8.3670-3677.2002.

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ABSTRACT Continued improvements of adenoviral vectors require the investigation of novel genome configurations. Since adenovirus can be generated directly by transfecting packaging cell lines with viral genomes isolated from plasmid DNA, it is possible to separate genome construction from virus production. In this way failure to generate a virus is not associated with an inability to generate the desired genome. We have developed a novel lambda-based system that allows rapid modification of the viral genome by double homologous recombination in Escherichia coli. The recombination reaction and newly generated genome may reside in a recombination-deficient bacterial host for enhanced plasmid stability. Furthermore, the process is independent of any restriction endonucleases. The strategy relies on four main steps: (i) homologous recombination between an adenovirus cosmid and a donor plasmid (the donor plasmid carries the desired modification[s] and flanking regions of homology to direct its recombination into the viral genome); (ii) in vivo packaging of the recombinant adenoviral cosmids during a productive lambda infection; (iii) transducing a recombination-deficient E. coli lambda lysogen with the generated lysate (the lysogen inhibits the helper phage used to package the recombinant andenoviral cosmid from productively infecting and destroying the host bacteria); (iv) effectively selecting for the desired double-recombinant cosmid. Approximately 10,000 double-recombinant cosmids are recovered per reaction with essentially all of them being the correct double-recombinant molecule. This system was used to generate quickly and efficiently adenoviral genomes deficient in the E1/E3 and E1/E3/E4 regions. The basis of this technology allows any region of the viral genome to be readily modified for investigation of novel configurations.

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41

Murray, Noreen E. "The impact of phage lambda: from restriction to recombineering." Biochemical Society Transactions 34, no. 2 (April 1, 2006): 203. http://dx.doi.org/10.1042/bst20060203.

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42

SHIMADA, TOMOAKI, MASAMI HAGIYA, MASANORI ARITA, SHIN-YA NISHIZAKI, and CHEW LIM TAN. "KNOWLEDGE-BASED SIMULATION OF REGULATORY ACTION IN LAMBDA PHAGE." International Journal on Artificial Intelligence Tools 04, no. 04 (December 1995): 511–23. http://dx.doi.org/10.1142/s0218213095000267.

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We have developed a knowledge-based but partially analytic simulation system. This system simulates regulatory action in lambda phage, a virus which infects E. coli. Specifically, we simulated the decision between its two developmental pathways, lytic and lysogenic growth. Our model is composed of two levels: roughly abstracted level and precisely abstracted level. The former level is discrete-event and knowledge-based. It covers overall regulations inside lambda phage in qualitative representation. On the other hand, the latter is based on quantitative chemical equations describing the sensitive bifurcation within pathways. In this way, qualitatively clear overview of regulatory action is efficiently simulated using knowledge base, and only the unpredictable part is analytically simulated in detail. This system can output not only input knowledge but also precise prediction by computational analysis, data which help molecular biologists find new theories of regulatory actions.

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43

Rackwitz, H. R., G. Zehetner, H. Murialdo, H. Delius, J. H. Chai, A. Poustka, A. Frischauf, and H. Lehrach. "Analysis of cosmids using linearization by phage lambda terminase." Gene 40, no. 2-3 (January 1985): 259–66. http://dx.doi.org/10.1016/0378-1119(85)90048-4.

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44

Sternberg, Nat. "The production of generalized transducing phage by bacteriophage lambda." Gene 50, no. 1-3 (January 1986): 69–85. http://dx.doi.org/10.1016/0378-1119(86)90311-2.

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Kersulyte, Dangeruta, B. Rajendra Krishnan, and Douglas E. Berg. "Nonrandom orientation of transposon Tn5supF insertions in phage lambda." Gene 114, no. 1 (May 1992): 91–96. http://dx.doi.org/10.1016/0378-1119(92)90712-x.

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46

Boyd, Dana, David S. Weiss, Joseph C. Chen, and Jon Beckwith. "Towards Single-Copy Gene Expression Systems Making Gene Cloning Physiologically Relevant: Lambda InCh, a Simple Escherichia coli Plasmid-Chromosome Shuttle System." Journal of Bacteriology 182, no. 3 (February 1, 2000): 842–47. http://dx.doi.org/10.1128/jb.182.3.842-847.2000.

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ABSTRACT We describe a simple system for reversible, stable integration of plasmid-borne genes into the Escherichia coli chromosome. Most ordinary E. coli strains and a variety of pBR322-derived ampicillin-resistant plasmids can be used. A single genetic element, a lambda phage, is the only specialized vector required. The resultant strains have a single copy of the plasmid fragment inserted stably at the lambda attachment site on the chromosome, with nearly the entire lambda genome deleted.

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47

Cohen, P. T. W., and P. Cohen. "Discovery of a protein phosphatase activity encoded in the genome of bacteriophage λ. Probable identity with open reading frame 221." Biochemical Journal 260, no. 3 (June 15, 1989): 931–34. http://dx.doi.org/10.1042/bj2600931.

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Infection of Escherichia coli with phage lambda gt10 resulted in the appearance of a protein phosphatase with activity towards 32P-labelled casein. Activity reached a maximum near the point of cell lysis and declined thereafter. The phosphatase was stimulated 30-fold by Mn2+, while Mg2+ and Ca2+ were much less effective. Activity was unaffected by inhibitors 1 and 2, okadaic acid, calmodulin and trifluoperazine, distinguishing it from the major serine/threonine-specific protein phosphatases of eukaryotic cells. The lambda phosphatase was also capable of dephosphorylating other substrates in the presence of Mn2+, although activity towards 32P-labelled phosphorylase was 10-fold lower, and activity towards phosphorylase kinase and glycogen synthase 25 50-fold lower than with casein. No casein phosphatase activity was present in either uninfected cells, or in E. coli infected with phage lambda gt11. Since lambda gt11 lacks part of the open reading frame (orf) 221, previously shown to encode a protein with sequence similarity to protein phosphatase-1 and protein phosphatase-2A of mammalian cells [Cohen, Collins, Coulson, Berndt & da Cruz e Silva (1988) Gene 69, 131-134], the results indicate that ORF221 is the protein phosphatase detected in cells infected with lambda gt10. Comparison of the sequence of ORF221 with other mammalian protein phosphatases defines three highly conserved regions which are likely to be essential for function. The first of these is deleted in lambda gt11.

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48

Chattopadhyay, S., S. C. Hung, A. C. Stuart, A. G. Palmer, J. Garcia-Mena, A. Das, and M. E. Gottesman. "Interaction between the phage HK022 Nun protein and the nut RNA of phage lambda." Proceedings of the National Academy of Sciences 92, no. 26 (December 19, 1995): 12131–35. http://dx.doi.org/10.1073/pnas.92.26.12131.

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49

Black, Lindsay W. "In vitro packaging into phage T4 particles and specific recircularization of phage lambda DNAs." Gene 46, no. 1 (January 1986): 97–101. http://dx.doi.org/10.1016/0378-1119(86)90171-x.

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50

Huisman, Olivier, and Maurice S. Fox. "A GENETIC ANALYSIS OF PRIMARY PRODUCTS OF BACTERIOPHAGE LAMBDA RECOMBINATION." Genetics 112, no. 3 (March 1, 1986): 409–20. http://dx.doi.org/10.1093/genetics/112.3.409.

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ABSTRACT Primary products of bacteriophage lambda recombination that display heterozygosity as a consequence of the presence of regions of heteroduplex DNA are rare in standard λ crosses. Phage manifesting heterozygosity at a given allele are evident when recombinants, emerging from a cross, are selected for an exchange in a neighboring interval. We show that the abundance of such heterozygotes can be increased 10- to 20-fold by selection on an E. coli indicator that is defective in methyl-directed mismatch repair (mutL). Thus, the activity of the methyl-directed mismatch repair system is, at least in part, responsible for the low frequency of detectably heterozygous phage emerging from a standard cross. In a mutL indicator, many primary products of recombination are replicated without the intervention of mismatch repair.—The products of a six-factor phage cross have been plated on a mutL indicator allowing visual detection of those phage products heterozygous for one of the allelic pairs, cI. By genetic analysis, we show that the heteroduplex regions of these primary products of recombination are on the average about 4 kb in length and can include as much as half of the lambda genome.

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Journal articles on the topic 'Lambda phage'

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