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PubMed1993

A method for quantitative recovery of DNA from plate lysates of bacteriophage lambda-derived clones.

A method is described for the purification of DNA from recombinant clones in lambda vectors. Plate lysates are used as the starting material, with the phage suspension being either loaded directly onto mini-cesium chloride two-step gradients or first subjected to precipitation with polyethylene glycol-8000 before application to the gradients. A single centrifugation step is used and the DNA is isolated from the harvested bacteriophage by incubation at room temperature with formamide followed by ethanol precipitation. The small-volume gradients were effective in isolating phage particles in the range of 1.0 to 12.5 x 10(11) pfu with quantitative recovery of approximately 7 micrograms DNA/10(11) pfu. The method was tested with a cDNA clone in lambda gt10 (as an example of a lambda-derived vector which gives a plate lysate with a high titer) and rat genomic fragments cloned into EMBL3A (for which the plate lysates are of low titer). For both vectors, the purified DNA appeared free of inhibitory contaminants as assessed by restriction endonuclease digestion and subcloning of fragments.

Bacteriophage lambda↗

PubMed1982

The head protein D of bacterial virus lambda is related to eukaryotic chromosomal proteins.

Bacteriophage lambda structural head protein D has physiochemical properties in common with eukaryotic chromosomal proteins. It has a low affinity for hydroxylapatite, it is heat stable and acid soluble. Moreover, it cross-reacts immunologically with histones H2A and H2B. The deduced primary structure of the D protein shows striking homology to calf chromosomal high mobility group HMG-14 protein. There are two clusters of four ( LSAK , ASDE ) and one of three (APA) identical amino acid residues. Additionally the cluster ETK of protein D occurs three times in HMG-14 and 14 single identical residues are present. A mechanism for an alternative to a nucleosomal mode of nuclear DNA condensation and a possible function of HMG proteins are discussed.

Amino Acid Sequence↗

PubMed2001

Purification and crystallization of CII: an unstable transcription activator from phage lambda.

The CII protein of the temperate bacteriophage lambda is a transcriptional activator involved in the lysis-lysogeny switch of the phage. It is an unstable protein of 97 amino acids and is known to exist as a tetramer in the native state. The cII gene has been cloned and expressed in Escherichia coli using a T7 promoter based over-expression system. The recombinant CII protein has been purified to homogeneity by ammonium sulfate fractionation followed by two steps of ion-exchange chromatography. The purified protein crystallized at pH 8.2 in hanging-drop vapor diffusion method at 293 K. The crystals diffract to a resolution of 2.8 A and belong to the space group C222 with unit-cell parameters a = 64.10, b = 106.95 and c = 120.16 A.

Bacteriophage lambda↗

PubMed1986

Gene fusion in vivo using transductional cointegrates.

A method is described which allows the efficient construction of hybrids between homologous genes. The technique is based on the phenomenon of cointegrate transduction in which the homology between cloned sequences present on a bacteriophage lambda vector and a plasmid vector is exploited to allow the packaging of a plasmid-phage recombinant. The size of the cointegrate molecule can be far beyond the normal packaging limit of lambda and still allow the transduction of plasmid-borne drug-resistance markers. This method allows the exchange of the 5' and 3' ends of the participating genes as well as the exchange of sequences residing between the end-points of homology between the two genes. Hybrids of either type were constructed between a sea urchin and a Drosophila actin gene using the transductional cointegrate method in vivo. This approach does not require the use of specialized phage or plasmid vectors and can also be used to screen plasmid libraries with a bacteriophage lambda probe.

Actins↗

PubMed1987

Plasmid and bacteriophage vectors for excision of intact inserts.

Plasmid (pPolyIII) and bacteriophage lambda (EMBL301) vectors are described in which sites for the rare-cutting enzymes SfiI and NotI (8-bp, recognition sequences) flank the polylinker cloning region. Intact DNA inserts for introduction into cultured cells or into the early embryo are readily excised from the vectors. General-purpose miniplasmid cloning vectors pPolyI and pPolyII are also described, and the utility of the bacteriophage lambda vector is demonstrated in the construction of a bovine genomic library.

Animals↗

PubMed1999

Mutations in the substrate binding domain of the Escherichia coli 70 kDa molecular chaperone, DnaK, which alter substrate affinity or interdomain coupling.

In Escherichia coli, DnaK is essential for the replication of bacteriophage lambda DNA; this in vivo activity provides the basis of a screen for mutations affecting DnaK function. Mn PCR was used to introduce mutations into residues 405-468 of the C-terminal polypeptide-binding domain of DnaK. These mutant proteins were screened for the ability to propagate bacteriophage lambda in the background of a dnaK deficient cell line, BB1553. This initial screen identified several proteins which were mutant at multiple positions. The multiple mutants were further dissected into single mutants which remained negative for lambda propagation. Four of these single-site mutants were purified and assayed for biochemical functionality. Two single-site mutations, F426S and S427P, are localized in the peptide binding site and display weakened peptide binding affinity. This indicates that the crystallographically determined peptide binding site is also critical for in vivo lambda replication. Two other mutations, K414I and N451K, are located at the edge of the beta-sandwich domain near alpha-helix A. The K414I mutant binds peptide moderately well, yet displays defects in allosteric functions, including peptide-stimulated ATPase activity, ATP-induced changes in tryptophan fluorescence, ATP-induced peptide release, and elevated ATPase activity. The K414 position is close in tertiary structure to the linker region to the ATPase domain and reflects a specific area of the peptide-binding domain which is necessary for interdomain coupling. The mutant N451K displays defects in both peptide binding and allosteric interaction.

Adenosine Triphosphatases↗

PubMed1988

Structural bases of a long-stretched deletion: completing the lambda plac5 DNA primary structure.

In studying molecular mechanisms of specialised transduction, the lacI (E. coli)-Ea47 (lambda) DNA junction in transducing bacteriophage lambda plac 5 has been structurally elucidated, thus yielding the complete sequence of lambda plac 5 DNA including the lac5 substitution, a well-known segment of lambdoid vectors. The lambda plac5 DNA is shown to consist of 19368 bp (lambda left arm) + 3924 bp (lac5 substitution) + 25353 bp (lambda right arm), totally amounting to 48645 bp. The presence of the phage rho bL promoter near to the right end of the lac5 insert is shown. The lacI gene distal end in lambda plac5 proved to be much longer than it was postulated earlier, coding for 224 C-terminal amino acid residues of lac repressor. Both the recombination studied in this paper and the earlier studied abnormal prophage excision (2, 3) occur near to Chi-like structures (chi*lacI and chi*lom, respectively). On the basis of the data obtained, a key role of the E. coli RecBCD system and Chi-like sequences in the formation of deletions in bacterial cells is suggested.

Bacteriophage lambda↗

PubMed2001

Identification of a human immunodominant B-cell epitope within the GRA1 antigen of Toxoplasma gondii by phage display of cDNA libraries.

Excreted secreted antigens of the protozoan parasite Toxoplasma gondii play a key role in stimulating the host immune system during acute and chronic infection. With the aim of identifying the immunodominant epitopes of T. gondii antigens involved in the human B-cell response against the parasite, we employed a novel immunological approach. A library of cDNA fragments from T. gondii tachyzoites was displayed as fusion proteins to the amino-terminus of lambda bacteriophage capsid protein D. The lambda D-tachyzoite library was then affinity-selected by using a panel of sera of pregnant women, all infected with the parasite. Some of the clones identified through this procedure matched the sequence of the dense granule GRA1 protein (p24), allowing us to identify its antigenic regions. In particular, the analysis of human antibody response against the recombinant GRA1 antigen fragments revealed the existence of an immunodominant epitope (epi-24 peptide).

Amino Acid Sequence↗

PubMed1993

Atomic force microscopy of long DNA: imaging in air and under water.

We have obtained striking atomic force microscopy images of the intact lambda bacteriophage genome and of several lambda restriction fragments both in air and under water. The DNA is unstained and the images are stable under continuous scanning for up to 30 min. Measured contour lengths of fully imaged restriction fragments and intact lambda DNA are accurate to within a few percent. The key to this development is the use of a process for binding unmodified double-stranded DNA to chemically treated mica surfaces. This procedure leads to strong DNA attachment and yields high-quality images that are stable under repeated scanning, even with the sample submerged in water. This allows normal hydration conditions to be maintained during scanning and in addition leads to a general improvement of image quality. Both the lateral resolution and the contrast increase by a factor of approximately 3 under water.

Bacteriophage lambda↗

PubMed2003

Single-molecule kinetics of lambda exonuclease reveal base dependence and dynamic disorder.

We used a multiplexed approach based on flow-stretched DNA to monitor the enzymatic digestion of lambda-phage DNA by individual bacteriophage lambda exonuclease molecules. Statistical analyses of multiple single-molecule trajectories observed simultaneously reveal that the catalytic rate is dependent on the local base content of the substrate DNA. By relating single-molecule kinetics to the free energies of hydrogen bonding and base stacking, we establish that the melting of a base from the DNA is the rate-limiting step in the catalytic cycle. The catalytic rate also exhibits large fluctuations independent of the sequence, which we attribute to conformational changes of the enzyme-DNA complex.

Bacteriophage lambda↗

PubMed1973

Isolation of a specialized lambda transducing bacteriophage carrying the beta subunit gene for Escherichia coli ribonucleic acid polymerase.

A heat-inducible lysis-defective lambda prophage has been integrated directly into the E. coli chromosome at a site (bfe) very closely linked to the ribonucleic acid polymerase mutation rif(d), a dominant rifampin resistance allele. This unusual lysogen has facilitated the isolation of specialized transducing phages conferring rifampin resistance to sensitive cells, and carrying at least the beta subunit gene of RNA polymerase in intact form.

Alleles↗

PubMed1994

The complete nucleotide sequence of cosmid vector pTL5: location and origin of its genetic components.

The complete nucleotide sequence (5793 bp) of the cosmid vector pTL5 and the origin of its genetic components has been determined. Cosmid pTL5, a derivative of cosmid vector pHC79, is composed of genetic components from pBR322, bacteriophage lambda and the hybrid lambdoid bacteriophage Charon (Ch) 4A cohesive ends (cos) region. The Ch4A cos region contains genetic components from two bacteriophages, the lambda cos-left arm and the phi 80 cos-right arm regions. The Ch4A cos region has been used in the construction of many other cosmid-type vectors, some of which have been sequenced and entered into the GenBank database.

Base Sequence↗

PubMed1988

Color graphics representations of large sequences in the GEM environment.

The analytical and descriptive color graphics capabilities (the GEM environment) of the CAGE/GEM(a) software system are described using bacteriophage lambda (48,502 base pairs) and Epstein Barr virus (172,282 base pairs) as examples. Genetics and features, as graphic drawings, and the results of sequence analysis as pseudo-colored representations, are simultaneously displayed at all zooming levels. The present upper limit on sequence size is 5 x 10(5) bases. The overlay editor utility which provides the capability to structure complex sequence associated data and knowledge bases into a manageable color graphics format is also described. Holistic correlations that can be made by the display of bacteriophage lambda and Epstein Barr virus in the GEM environment are also discussed.

Bacteriophage lambda↗

PubMed2003

Genetic analysis of bacteriophage lambdaN-dependent antitermination suggests a possible role for the RNA polymerase alpha subunit in facilitating specific functions of NusA and NusE.

A role for the Escherichia coli RNA polymerase alpha subunit in transcription antitermination dependent on bacteriophage lambda N protein has been previously inferred from the isolation of rpoA mutants that alter the efficiency of this process. This report describes studies on the efficiency of N-dependent transcription antitermination in a strain containing the rpoA341 mutation, which interferes with this process. The effect of mutations in genes coding for different Nus factors and/or plasmids overexpressing nus genes on bacteriophage lambda development in an E. coli rpoA341 host was examined. In addition, the effect of overproduction of the N protein in these genetic backgrounds was assessed. Analogous bacterial strains were employed to measure the efficiency of the antitermination process using the lacZ reporter gene under control of the lambda p(R) promoter, and containing the phage nutR region and the t( R1) terminator between the promoter and lacZ. The experimental results suggest interactions between components of the N-antitermination complex, which have been established biochemically, as well as additional functional relationships within the complex. Furthermore, the results indicate that amino acid substitution in the alpha subunit C-terminal domain encoded by the rpoA341 mutation may specifically disrupt the function of the NusA and NusE proteins. During this analysis, it was also found that the E. coli nusA1 mutant exhibits a conditional lethal phenotype.

Bacterial Proteins↗

PubMed1980

The nucleotide sequences recognized by endonucleases AvaI and AvaII from Anabaena variabilis.

Determination of the 5'-terminal sequences flanking all the individual cleavage sites for endonuclease AvaI in bacteriophage-lambda DNA has shown that this enzyme recognizes the hexanucleotide sequences: (Formula: see text), This sequence is cut as shown by the arrows to give single-stranded 5'-tetranucleotide protrusions (cohesive ends). Endonucleases SmaI, XhoI and XmaI recognize different symmetrical subsets of this sequence and provide independent evidence for the occurrence of these subsets at particular endonuclease-AvaI cleavage sites in the bacteriophage-lambda genome. Further evidence for this structure came from the demonstration that DNA fragments generated by endonuclease AvaI can be ligated to form a discrete set of larger molecules and from nearest-neighbor analysis which showed that cytosine residues occurred at the 3'-side of cleavage points. The observation that endonuclease AvaII recognized a subset of the sites recognized by AsuI [Hughes, Bruce & Murray (1979) Biochem. J. 185, 59-63[ led to the deduction that AvaII recognize the pentanucleotide sequence: (Formula: see text), and breaks internucleotide bonds at the positions indicated by the arrows.

Bacteriophage lambda↗

PubMed1999

Altered biological properties of cell membranes in Escherichia coli dnaA and seqA mutants.

We present evidence that biological properties of cell membranes are altered in dnaA and seqA mutants of Escherichia coli relative to wild-type bacteria. We found that bacteriophage lambda forms extremely large plaques on the dnaA seqA double mutants. On the single mutants, dnaA and seqA, the plaques are also bigger than those formed on the wild-type host. However, no significant differences in intracellular phage lambda development were observed between wild-type and mutant hosts, indicating that differences in burst size do not account for the observed differences in plaque size. On the other hand, more efficient release of the phage lytic proteins and/or higher sensitivity of the cell membranes to these proteins may result in more efficient cell lysis. We found that the efficiency of adsorption of bacteriophage lambda to the dnaA seqA mutant cells is decreased at 0 degrees C , but not at 30 degrees C, relative to the wild-type strain. A considerable increase in the permeability of membranes of the mutant cells for beta-galactosidase is demonstrated. The dnaA and seqA mutants are more sensitive to ethanol (an organic solvent) than wild-type bacteria, and the seqA strain and the double mutant dnaA seqA are very sensitive to deoxycholate (a detergent). We conclude that lesions in the genes dnaA and seqA result in alterations in cell membranes, such that the permeability and possibly also other properties of the membranes are significantly altered relative to wild-type bacteria.

Bacterial Outer Membrane Proteins↗

PubMed1979

Identification of the C. coli dnaK (groPC756) gene product.

The E. coli dnaK (groPC756) gene product is essential for bacteriophage lambda DNA replication. Bacterial DNA segments carrying this gene have been cloned onto a bacteriophage lambda vector. The product of the dnaK gene has been identified on SDS polyacrylamide gels after infection of UV-irradiated E. coli cells. The dnaK gene codes for a polypeptide with an apparent molecular weight of 93,000-Mr. Transducing phages carrying amber mutations in the dnaK gene fail to induce the synthesis of the 93,000-Mr polypeptide chain upon infection of sup+ bacteria, but do so upon infection of supF bacteria. E coli carrying the dnaK756 mutation are, in addition, temperature sensitive for growth at 43 degrees C. It is shown that the dnaK756 mutation results in an overproduction of the dnaK gene product at that temperature.

Bacterial Proteins↗

PubMed2003

[Recombineering and its application].

Driven by the need of functional genomics, a homologous recombination-based, highly efficient genetic engineering system that termed "recombineering" has recently been developed. Recombineering has been defined as a genetic engineering with phage-encoded recombination function that utilizes short homologies, a convenient term to describe homologous-dependent, recombination-mediated, genetic engineering. The bacteriophage lambda Red recombination system has critical differences from standard E. coli RecA-dependent recombination pathway. The phage systems have unique advantage in that they can catalyze efficient recombination with very short regions of sequence homology (< 50 bp). Recombineering does not require construction of plasmid or phage DNA intermediates containing the appropriately pre-engineered homology segment. All that is required in vitro is the synthesis of standard oligonucleotides or construction of PCR products that provide the homology. Importantly, they function even in the absence of RecA. These approaches do not rely on the presence of suitable restriction site, and can be used to insert, delete, clone or substitute genomic DNA sequences at any desired position on a target molecule in Escherichia Coli. Recombineering also facilitates many kinds of genomic experiments difficult to be carried out. In this article, the bacteriophage lambda Red recombinase system, the progression and applications of this powerful new technique are reviewed according to the data published recently.

Bacteriophage lambda↗