SEARCH · PubMed Health

Results for “Bacteriophage lambda”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 415 records · Page 23Linked to original sources

PubMed1986

Repression of a mutant derivative of the pRE promoter of bacteriophage lambda by its activator, CII.

A 2-bp insertion between the -10 and -35 regions of the pRE promoter of bacteriophage lambda reverses the effect of the activator protein, CII, on transcription from pRE in vitro. The mutant promoter is weakly constitutive in the absence of cII protein and repressed in its presence. This is in sharp contrast to wild-type pRE which is inactive in the absence of cII protein and stimulated at least 1000-fold in its presence (Shih and Gussin, 1984a; McClure and Hoopes, 1985). These effects are explained by the creation of a new -35 region with weak homology to the -35 consensus sequence for Escherichia coli promoters, and by the altered spatial relationship between the -35 region and the CII-binding site. This interpretation was confirmed by analysis of double mutants containing known cy (pRE) mutations together with the 2-bp insertion. Insertion of 4 bp or deletion of 2 bp completely inactivates pRE in the presence or absence of cII protein, again indicating that activation is dependent upon proper spacing between the -35 region and the transcription start point.

Bacteriophage lambda↗

PubMed1992

Site-specific enthalpic regulation of DNA transcription at bacteriophage lambda OR.

Binding of cI repressor to DNA fragments containing the three specific binding sites of the right operator (OR) of bacteriophage lambda was studied in vitro over the temperature range 5-37 degrees C by quantitative footprint titration. The individual-site isotherms, obtained for binding repressor dimers to each site of wild-type OR and to appropriate mutant operator templates, were analyzed for the Gibbs energies of intrinsic binding and pairwise cooperative interactions. It is found that dimer affinity for each of the three sites varies inversely with temperature, i.e., the binding reactions are enthalpy driven, unlike many protein-DNA reactions. By contrast, the magnitude of the pairwise cooperativity terms describing interaction between adjacently site-bound repressor dimers is quite small. This result in combination with the recent finding that repressor monomer-dimer assembly is highly enthalpy driven (with delta H degrees = -16 kcal mol-1) [Koblan, K. S., & Ackers, G. K. (1991) Biochemistry 30, 7817-7821] indicates that the associative contacts between site-bound repressors that mediate cooperativity are unlikely to be the same as those responsible for dimerization. The intrinsic binding enthalpies for all three sites are negative (exothermic) and nearly temperature-invariant, indicating no heat capacity changes on the scale of those inferred in other protein-DNA systems. However, the three operator sites are affected differentially by temperature: the intrinsic binding free energies for sites OR1 and OR3 change in parallel over the entire range, delta H0OR1 = -23.3 +/- 4.0 kcal mol-1 and delta H0OR3 = -22.7 +/- 1.2 kcal mol-1.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗

PubMed1986

hflB, a new Escherichia coli locus regulating lysogeny and the level of bacteriophage lambda cII protein.

The level of the viral cII protein has been proposed to be the crucial determinant in the lysis-lysogeny decision of bacteriophage lambda. A new Escherichia coli locus (hflB) has been identified in which a mutation (hflB29) leads to high frequency of lysogeny by lambda. A double mutant defective in both hflB and the previously identified hflA gene displays a more severe Hfl- phenotype than either single mutant. The hflB locus is at 69 minutes on the E. coli map, 85% co-transducible with argG. The hflB29 mutation results in increased stability of the phage cII protein (increasing its half-life twofold) and is recessive to hflB+. We conclude that the hflB+ locus is a negative regulator of cII, perhaps coding for or regulating a protease that acts on cII. In addition, we observe that the can1 mutation, an alteration of the cII gene that results in enhanced lysogenization, leads to increased stability of cII protein. These observations reinforce the view that the level of cII is a key factor in the lysis-lysogeny decision of lambda.

Bacteriophage lambda↗

PubMed1982

A novel endonuclease specified by bacteriophage lambda. Purification and properties of the enzyme.

A DNA endonuclease whose expression is under the control of the b region of bacteriophage lambda has been partially purified from an induced lambda lysogen. In a reaction that requires single-stranded DNA, ATP, and Mg2+, the lambda-induced endonuclease makes one double strand break in pBR322 and other covalently closed circular DNA molecules, converting these substrates into unit-length linear forms. The double strand break in pBR322 DNA occurs at one of several preferred sites. Linear DNA appears not to be a good substrate for the enzyme.

Bacteriophage lambda↗

PubMed2001

Bacteriophage lambda cIII gene product has an additional function apart from inhibition of cII degradation.

For lysogenization of Escherichia coli cells by bacteriophage lambda, functions of three lambda genes called c are necessary. The cI gene codes for a repressor that blocks activities of lytic promoters. However, early after infection, expression of cI is dependent on the function of the cII gene, coding for a specific transcriptional activator. The cII protein is unstable in E. coli cells due to FtsH-mediated proteolysis. The cIII gene product is an inhibitor of the FtsH protease. Here we demonstrate that cIII may have another function apart from inhibition of cII degradation. We found that overexpression of the cII gene results in impaired lysogenization by phage lambda, however simultaneous overexpression of the cIII gene abolished this negative effect on lysogenization. Analysis of cII-mediated transcriptional activation of certain promoters at different levels of cII and cIII proteins in cells confirmed that observed effects cannot be explained assuming that the only role of cIII is inhibition of FtsH-mediated degradation of cII. We propose that cIII has an additional role apart from its well-known function in indirect stabilization of cII. Apparently, cIII influences not only cII level but also activity of this transcriptional stimulator, especially at its high concentrations.

Bacteriophage lambda↗

PubMed1980

[Transposition of the kanamycin resistance determinant (Tn601) from plasmid 5T to the genome of bacteriophage lambda and the expression of this gene after prophage induction].

Tn601, determinging kanamycin resistance of Escherichia coli, has been transposed into the bacteriophage lambda genome from R6 plasmid. After curing lambda gtc1857 (Tn601) lysogenes on the kanamycin containing medium, the clones with stable and unstable integrations of the Tn6-1 into the chromosome were obtained. After the lysogenization of these clones with the phage lambda att80c1857S7, the phages lambda att80c1857S7 (Tn601) were obtained. These phages contained the Tn601 from the sites of stable or unstable integrations. The frequency of the Tn601 transposition from the sites of unstable integration was 10(-7), that was two order of magnitude higher than the frequency of the Tn601 transpostion from the site of stable integration. Temperature induction of the lambda att80c1857 (Tn601) prophage resulted in 10--15 times increase of the yeild of aminoglycoside-3'-phosphotransferase I, the enzyme coded by the aphA gene of the Tn601.

Bacteriophage lambda↗

PubMed1984

Mutations that alter the DNA binding site for the bacteriophage lambda cII protein and affect the translation efficiency of the cII gene.

The efficiency of translation of the cII gene of bacteriophage lambda is greatly reduced by the cII3059 mutation, a GUU----GAU (Val----Asp) change in the second cII codon. Mutations in the third and fourth codons of the cII gene, called ctr mutations, reverse this translation deficiency. Lambda cII3059 ctr-1, which has a GCA----ACA (Ala----Thr) change in the fourth cII codon, produces about half the normal level of cII activity in liquid cultures, and lambda cII3059 ctr-2 and lambda cII3059 ctr-3, which have identical CGT----CGC changes in the third codon, produce normal levels of cII activity in liquid culture. Since the cII protein of ctr-3 has the same primary sequence as that of lambda cII3059, the cII- phenotype of lambda cII3059 can be explained entirely by the deficiency of translating cII mRNA. We propose that ctr mutations increase translation efficiency by destabilizing a stable stem structure which can be formed by cII mRNA. The ctr mutations lie in an overlapping regulatory region which contains, in addition to sequence elements that influence the rate of cII translation, a region to which cII protein binds to activate transcription from the PRE promoter. The ctr-1 mutation alters the cII recognition sequence from 5'-T-T-G-C-N6T-T-G-C-3' to 5'-T-T-G-C-N6T-T-G-T-3', but has no effect on PRE activity. Since a C----T change in the first (5'-proximal) T-T-G-C sequence (to yield 5'-T-T-G-T-N6T-T-G-C) greatly lowers cII binding affinity, cII protein must not recognize the two T-T-G-C sequences in an identical manner.

Bacteriophage lambda↗

PubMed1980

Molecular cloning of unintegrated Moloney mouse sarcoma virus DNA in bacteriophage lambda.

The covalently closed circular forms of unintegrated viral DNA obtained from cells infected with Moloney mouse sarcoma virus was cloned in bacteriophage lambda. The viral DNA was cleaved with restriction endonuclease HindIII and inserted in the unique HindIII site of lambda Charon 21A DNA. Recombinant clones containing virus-reactive DNA sequences were analyzed by restriction endonuclease mapping, R-loop formation, and infectivity assays. Two of eight genome-length recombinant clones characterized contained the large terminal repeat. Only the recombinant clones containing the large terminal repeat were able to induce focus formation in uninfected mouse fibroblasts.

Animals↗

PubMed1992

Deformation of DNA during site-specific recombination of bacteriophage lambda: replacement of IHF protein by HU protein or sequence-directed bends.

Escherichia coli IHF protein is a prominent component of bacteriophage lambda integration and excision that binds specifically to DNA. We find that the homologous protein HU, a nonspecific DNA binding protein, can substitute for IHF during excisive recombination of a plasmid containing the prophage attachment sites attL and attR but not during integrative recombination between attP and attB. We have examined whether IHF and HU function in excisive recombination is mediated through DNA bending. Our strategy has been to construct chimeric attachment sites in which IHF binding sites are replaced by an alternative source of DNA deformation. Previously, we demonstrated that properly phased bends can substitute for the binding of IHF at one site in attP. Although this result is highly suggestive of a critical role of IHF-promoted bending in lambda integration, its interpretation is obscured by the continued need for IHF binding to the remaining IHF sites of these constructs. In the present work, we engineered a population of sequence-directed bends in the vicinity of the two essential IHF sites found in attR and attL. Even in the absence of IHF or HU, pairs of these attachment sites with properly phased bends are active for both in vitro and in vivo excision. This success, although tempered by the limited efficiency of these systems, reinforces our interpretation that IHF functions primarily as an architectural element.

Attachment Sites, Microbiological↗

PubMed1991

Heat-inducible reactivation of UV-damaged bacteriophage lambda.

Induction of the SOS response in UV-irradiated bacteria leads to an increase in the survival of an infecting irradiated bacteriophage lambda (Weigle 1953). We report that a similar reactivation of irradiated phage lambda was induced by shifting the culture of recipient bacteria from 30 degrees to 47 degrees C. However, this repair process was nonmutagenic. The amplitude of the phenomenon was increased with the quantity of UV lesions in the phage DNA. It was present despite mutations affecting the SOS response or the heat shock response in the infected strains (recA, lexA, umuC or rpoH mutations respectively). In contrast, the heat-inducible repair process was abolished in uvrA derivatives. Also, pretreatment with chloramphenicol largely enhanced phage reactivation after heat shock. Therefore, it appears that the excision repair mechanism of UV lesions was stimulated both by temperature shift-up and blockage of protein synthesis.

Bacteriophage lambda↗

PubMed1994

A new procedure for the purification of the bacteriophage lambda terminase enzyme and its subunits. Properties of gene product A, the large subunit.

New methods for the purification of highly active bacteriophage lambda terminase holoenzyme, and its individual subunits, gene products (gp) A and gpNu1, have been developed. These methods are rapid, simple, reproducible, and give high yields of unaggregated protein from small volumes of culture. The procedures involve fractionation of extracts of Escherichia coli strains harboring plasmids engineered to overproduce the respective proteins. All purified proteins exist as monomers or dimers at moderate concentrations. At concentrations where holoenzyme efficiently promotes in vitro cosN-cleavage and lambda DNA packaging, gpA displays neither of these activities unless supplemented with gpNu1 and the E. coli protein integration host factor. At high protein concentrations, however, gpA can promote cos-cleavage by itself. Although gpNu1 itself cannot promote either cosN-cleavage or DNA packaging, it does modulate these activities of gpA. GpA is a DNA-stimulated ATPase whose catalytic parameters closely resemble those of the holoenzyme. Like the holoenzyme, gpA displays a DNA helicase activity which is able to melt the annealed cosN overhangs. Certain preparations of gpA appear to undergo a time-dependent amino-terminal clipping at discrete sites even in the presence of as many as four protease inhibitors and at low temperature.

Adenosine Triphosphatases↗

PubMed1987

Carcinoembryonic antigen family: expression in a mouse L-cell transfectant and characterization of a partial cDNA in bacteriophage lambda gt11.

Genomic DNA and mRNA from the adenocarcinoma cell line LoVo were used to generate L-cell transfectants and a bacteriophage lambda gt11 cDNA clone that express epitopes of carcinoembryonic antigen (CEA). Primary and secondary L-cell transfectants expressing CEA were selected with a fluorescence-activated cell sorter (FACS). These transfectants, including some clones that were selected for high-level CEA expression by multiple rounds of FACS sorting, express a surface protein of 150 kDa that reacts with all anti-CEA antibodies tested. In parallel, a cDNA library of LoVo poly(A)+ RNA was constructed in lambda gt11 and fusion proteins were screened with polyclonal antisera against CEA. One positive clone, lambda cLV7, was identified that hybridized specifically to transfectant DNA. The nucleic acid sequence of the cDNA insert (cLV7) contained two regions of extensive internal homology, with greater than 70% identity at the amino acid level. cLV7 hybridized to three mRNA species of LoVo cells and to a predominant mRNA of the CEA-expressing transfectants. Hybridization of cLV7 to restriction endonuclease-digested genomic DNA of colon carcinoma cells, normal human cells, and human-mouse somatic cell hybrids revealed the presence of multiple hybridizing bands, one of which was present in transfectant cells. These CEA-related sequences are not rearranged in tumors and, by somatic cell hybrid analysis, were mapped to human chromosome 19.

Amino Acid Sequence↗

PubMed2000

The terminase enzyme from bacteriophage lambda: a DNA-packaging machine.

This review focuses on the biochemical, biophysical, and catalytic properties of terminase, an enzyme involved in bacteriophage lambda genome packaging. The holoenzyme possesses ATPase, DNA strand-separation, and site-specific nuclease activities that work in concert to insert a viral genome into the confines of a performed capsid. Moreover, the terminase subunits are part of a series of nucleoprotein complexes involved in genome packaging, including remarkably stable intermediates that transition to a highly mobile DNA packaging 'machine.' Models for the assembly and interconversion of these complexes are presented. Interactions between the catalytic sites in the enzyme complex, and modulation of these catalytic activities as it relates to the assembly and relative stability of the packaging intermediates are discussed. This ordered progression of nucleoprotein intermediates is a common theme in biology as demonstrated by mechanistic similarities between viral DNA packaging, the initiation of chromosomal replication, and the initiation of transcription. Terminase is thus part of a growing number of examples of biological 'machines' or molecular 'motors.'

Adenosine Triphosphatases↗

PubMed1976

In vitro construction of bacteriophage lambda and plasmid DNA molecules containing DNA fragments from bacteriophage T4.

Restriction endonucleases EcoRI and HindIII generated fragments of T4 cytosine-containing DNA were inserted into bacteriophage vector lambdagtSuIII and plasmid vectors pMB9 and pBR313. Resulting clones were screened for hybridization with 32P labeled T4 tRNA. Recombinant bacteriophages and plasmids were isolated which contained a T4 fragment coding for T4 RNA species 1 and 2 and T4 tRNA Arg. Selected lambda-T4 hybrid bacteriophages were grown to high titer and their DNA analyzed by gel electrophoresis.

Coliphages↗

PubMed1980

The EcoRI restriction endonuclease with bacteriophage lambda DNA. Kinetic studies.

The kinetics of the reactions of the EcoRI restriction endonuclease at individual recognition sites on the DNA from bacteriophage lambda were found to differ markedly from site to site. Under certain conditions of pH and ionic strength, the rates for the cleavage of the DNA were the same at each recognition site. But under altered experimental conditions, different reaction rates were observed at each recognition site. These results are consistent with a mechanism in which the kinetic stability of the complex between the enzyme and the recognition site on the DNA differs among the sites, due to the effect of interactions between the enzyme and DNA sequences surrounding each recognition site upon the transition state of the reaction. Reactions at individual sites on a DNA molecule containing more than one recognition site were found to be independent of each other, thus excluding the possibility of a processive mechanism for the EcoRI enzyme. The consequences of these observations are discussed with regard to both DNA-protein interactions and to the application of restriction enzymes in the study of the structure of DNA molecules.

Bacteriophage lambda↗

PubMed1987

T lymphocyte response to bacteriophage lambda repressor cI protein. Recognition of the same peptide presented by Ia molecules of different haplotypes.

The murine T cell response to bacteriophage lambda cI repressor protein has been investigated. Isolation and characterization of class II-restricted T cell hybridomas from BALB/c and A/J mice undergoing a primary response has revealed that a single region of the protein, residues 12-26, is the immunodominant site. Fine specificity analysis using truncated peptides (P12-24 and P15-26) reveals a great deal of heterogeneity at the clonal level of I-Ad-restricted T cells. I-Ek-restricted T cells are less heterogeneous in their reactivity toward P12-24 and P15-26, but show diversity in their responses to peptide analogues with substitution at Tyr22. The specificity difference between T cell hybridomas of I-Ad-restriction and I-Ek-restriction and the inhibition effect of different inactive peptides suggest that the same peptide is presented in different configurations by different Ia molecules. Further, no cross-reactivity can be detected between T cells of these two haplotypes, Ia molecules and Ia bound-peptides.

Amino Acid Sequence↗

PubMed2000

Thermodynamic and functional characterization of protein W from bacteriophage lambda. The three C-terminal residues are critical for activity.

Gene product W (gpW), the head-tail joining protein from bacteriophage lambda, provides a fascinating model for studying protein interactions. Composed of only 68 residues, it must interact with at least two other proteins in the phage, and probably with DNA. To study the structural and functional properties of gpW, plasmids were constructed expressing gpW with hexahistidine tag sequences at either the N or C terminus. The purified wild type fusion proteins were found to be stably folded and biologically active. The protein is monomeric as judged by equilibrium ultracentrifugation, and appears to unfold by a cooperative two-state mechanism. Circular dichroism studies indicate that the protein is 47% helical, with a T(m) of 71.3 degrees C, and a DeltaG(u) of 3.01 kcal/mol at 25 degrees C. Mutagenesis of the three hydrophobic C-terminal residues of gpW showed that they are critical for activity, even though they do not contribute to the thermodynamic stability of the protein. Using secondary structure prediction as a guide, we also designed destabilized gpW mutants. The hydrophobic nature of the gpW C terminus caused these mutants to be degraded by the ClpP-containing proteases in Escherichia coli.

Amino Acid Sequence↗

PubMed1983

Specific mismatch correction in bacteriophage lambda crosses by very short patch repair.

In crosses under rec+, red+, gam+ conditions, mutation am6 in the cI (repressor) gene of bacteriophage lambda recombines with other cI mutations much more frequently than predicted by the physical distances involved. In four-factor crosses of am6 with mutations located 22-60 base pairs to the left, cI+ recombinants that are expected to require three crossovers (triple recombinants) are more frequent than recombinants that require only one crossover. However, when am6 is crossed with large insertions in cI, which may be expected to interfere with the formation of heteroduplexes by branch migration, the frequency of cI+ triple recombinants is very low. In addition, cI+ recombinants in crosses between am6 and adjacent mutations have a high probability of retaining the flanking markers of the am6 parent. These findings suggest that am6 is particularly susceptible to mismatch repair in heteroduplexes spanning cI. A large fraction of such heteroduplexes are presumed to be the result of branch migration from crossovers occurring at some distance from am6. The absence of co-repair when am6 is crossed with adjacent cI mutations indicates that most repair tracts extend no farther than about 20 bp to either side of the mismatch. The am6 mutation arose in the glutamine codon in a CCAGG sequence, in which the central cytosines are methylated in K12 strains. Their location in methylated sequences may make certain amber mutations susceptible to a specific very short patch (VSP) repair.

Bacteriophage lambda↗