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Construction from Mu d1 (lac Apr) lysogens of lambda bacteriophage bearing promoter-lac fusions: isolation of lambda ppheA-lac.

Bacteriophage Mu d1 (lac Aprr) was used to obtain strains of Escherichia coli K-12 in which the lac genes are expressed from the promoter of pheA, the structural gene for the enzyme chorismate mutase P-prephenate-dehydratase. A derivative of bacteriophage lambda which carries the pheA-lac fusion was prepared; the method used is generally applicable for the construction, from Mu dl lysogens, of specialized transducing lambda phage carrying the promoter-lac fusions. A restriction enzyme cleavage map of lambda ppheA-lac for the enzymes HindIII and PstI is presented.

Bacteriophage lambda↗

Assembly of biologically active proheads of bacteriophage lambda in vitro.

Bacteriophage lambda DNA can be packaged in vitro into preformed proheads to generate plaque-forming units. This complex set of reactions is initiated when lambda DNA is mixed with the product of the phage A gene, and proheads. Because proheads are an essential early reactant, the system has potential as an assay for the formation of biologically active proheads. When extracts of cells infected with certain lambda head mutants (for example, B--, C--, Nu3--, and E--) are used as the prohead donor, plaque-forming units are not produced. However, when extracts of E- - and Nu3- - infected cells are first reacted together the combination provides prohead-donor activity to the in vitro packaging system. In vitro assembled, biologically active proheads have the same sedimentation properties and electron micrsocopic appearance as "wild-type" proheads isolated from lambdaA-D- -infected cells. Centrifugation analysis shows that the Nu3- extract contributes gpE, the major capsid protein, to the reaction in the form of monomers or small polymers.

Coliphages↗

Control of bacteriophage lambda CII activity by bacteriophage and host functions.

We have studied the regulation of the lambda cII gene in vivo using cloned lambda fragments. Lambda N protein stimulated cII expression. Surprisingly, although very high cII protein levels were detected by gel electrophoresis, little cII protein activity, measured as stimulation of the lambda pI and pE promoters, was observed. The half-life of cII protein depended critically on its initial level. At low concentrations its half-life was as short as 1.5 min, whereas at high cII protein levels, it could be as long as 22 min. The Escherichia coli mutant ER437 directs lambda towards lysogeny; cII protein was more stable in this strain than in the wild type. On the other hand, although cyclic AMP is required for efficient lysogeny, it did not appear to influence the synthesis, stability, or activity of cII protein.

Bacteriophage lambda↗

Genetic heterozygosity in unreplicated bacteriophage lambda recombinants.

Bacteriophage crosses using density-labeled parents have been carried out under conditions restricting DNA synthesis. The parental material and genetic contributions to progeny manifesting recombination within a genetic interval sufficiently short to exhibit high negative interference have been examined. The unreplicated products of recombination isolated as phage particles appear to contain long continuous heteroduplex regions which are heterozygous for the closely linked markers. Recombination between closely linked markers seems to be the consequence of the removal of base-pair mismatches that are present within the heteroduplex regions. This localized reduction of heterozygosity within the heteroduplex regions that join the parental components of recombinant DNA molecules can account for high negative interference.

Coliphages↗

[Analysis of insertions of the determinant of drug resistance to kanamycin and chloramphenicol into bacteriophage lambda att80].

The insertion sites of elements Tn9 and Tn601 which determine chloramphenicol and kanamycin resistance have been detected restriction analysis. The functioning of transposons i.e. their stability or instability, has been found to influence the specificity of their insertions into the genome of lambda att80 bacteriophage. During transposition from stable integration sites both transposons are inserted into the regions of the lambda att80 bacteriophage genome, definite for each transposon. However, during transposition from the site of unstable integration both determinants of drug resistance are inserted into different regions of the phage genome.

Bacteriophage lambda↗

Biochemical characterization of bacteriophage lambda genome packaging in vitro.

Bacteriophage lambda has been extensively studied, and the abundance of genetic and biochemical information available makes this an ideal model system to study virus DNA packaging at the molecular level. Limited in vitro packaging efficiency has hampered progress toward this end, however. It has been suggested that limited packaging efficiency is related to poor activity of purified procapsids. We describe the construction of a vector that expresses lambda procapsids with a yield that is 40-fold greater than existing systems. Consistent with previous studies, packaging of a mature lambda genome is very inefficient in vitro, with only 4% of the input procapsids utilized. Concatemeric DNA is the preferred packaging substrate in vivo, and procapsids interact with a nucleoprotein complex known as complex I to initiate genome packaging. When complex I is used as a packaging substrate in vitro, capsid utilization is extremely efficient, and 40% of the input DNA is packaged. Finally, we provide evidence for a packaging-stimulated ATPase activity, and kinetically characterize this reaction quantifying the energetic cost of DNA packaging in bacteriophage lambda.

Adenosine Triphosphatases↗

Bacteriophage lambda replication proteins: formation of a mixed oligomer and binding to the origin of lambda DNA.

The purified bacteriophage lambda replication proteins O and P sediment separately in metrizamide gradients of low ionic strength as dimers. Together they interact with each other forming an oligomer, composed of two molecules of lambda O and one molecule of lambda P. The lambda O-P oligomer is active in the in vitro replication of ori lambda-containing DNA. Equilibrium sedimentation in preformed metrizamide density gradients under conditions that separate DNA-protein complexes from free proteins was employed in order to study possible interactions among the lambda replication proteins and ori lambda DNA. It was found that the lambda P protein binds specifically to ori lambda-containing plasmid DNA only in the presence of lambda O protein. About 100 molecules of lambda O and 10 molecules of lambda P form a complex with the ori lambda DNA. The lambda DNA-lambda O-lambda P complex was shown to be active in an in vitro replication system. Since the physical interactions between ori lambda and lambda O and between lambda P and the Escherichia coli dnaB replication protein are well documented, the evidence for a lambda O-P interaction presented in this paper provides the missing link in the molecular mechanism that enables lambda to direct the host replication machinery to the replication of its own DNA.

Bacteriophage lambda↗

Revisited gene regulation in bacteriophage lambda.

The contribution of bacteriophage lambda to gene control research is far from over. A revised model of the lambda genetic switch includes extra cooperativity through octamerization of the cI repressor protein, mediated by long-range DNA looping. Structural analysis reveals remarkably subtle transcriptional activation by cI. The action of cI, activation by cII, and aspects of antitermination by N and Q all confirm the utility and versatility of simple, weak adhesive interactions mediated by nucleic acid tethers. New genetic and quantitative analysis of the lambda gene network is challenging cherished ideas about how complex behaviours emerge from this regulatory system.

Bacteriophage lambda↗

Nucleotide sequence of the chi recombinational hot spot chi +D in bacteriophage lambda.

Chi sites in bacteriophage lambda stimulate recombination promoted by the RecBC pathway of Escherichia coli. Mutations which create these sites occur at four widely separated loci in lambda. We report here the nucleotide sequence surrounding the site of one of these loci, chi D, located near the S gene. The mutations creating the active Chi site, designated chi +D, are transversions from CG to AT. This mutation, like the chi +B and chi +C mutations previously analyzed, leads to a nucleotide sequence common to all three active chi sites.

Bacteriophage lambda↗

A bacterial protein requirement for the bacteriophage lambda terminase reaction.

The bacteriophage lambda terminase enzyme cleaves the cohesive-end sites of lambda DNA to yield the protruding 5'-termini of the mature molecule. In vitro, this endonucleolytic event requires a protein factor which has been isolated and purified from extracts of uninfected E. coli. The terminase host factor (THF) is a heat stable basic protein of M.W. approximately 22,000. The integration host factor (IHF) protein of E. coli can efficiently substitute for THF in the terminase reaction; however, THF can be demonstrated to be physically present in, and isolated with full biological activity from extracts of cells defective or deficient in IHF.

Bacterial Proteins↗

pHG276: a multiple cloning site pBR322 copy number vector expressing a functional lac alpha peptide from the bacteriophage lambda PR promoter.

The bacteriophage lambda early promoter PR has been used to direct the synthesis of lac alpha in a plasmid containing the multiple cloning site of pUC8. The copy number of the plasmid is controlled by the rop(rom) gene and the plasmid incorporates the cI857 gene for temperature regulation of lac alpha expression. Isolation of recombinant derivatives with DNA inserts in the multiple cloning region can be identified by insertional inactivation of lac alpha and consequently, a Lac- phenotype in a host carrying the M15 deletion of lac. The potential of pHG276 as a fully regulated expression vector is examined.

Bacteriophage lambda↗

Purified bacteriophage lambda O protein binds to four repeating sequences at the lambda replication origin.

The bacteriophage lambda O protein is needed for initiation of lambda DNA replication. Several lines of evidence suggest that initiation requires that this protein interacts with a specific sequence called ori (for origin) in lambda DNA. We have purified this protein to near homogeneity and studied the protection against nuclease cleavage of the origin DNA sequences. Our data demonstrate that the O protein binds within an interval of about 95 base pairs (bp), which contains four tandemly arranged 19bp repeating sequences, ATCCCTCAAAACGA (G)GG GAT(A). At a low concentration of O protein, the inner two repeats are primarily covered, while binding to the outer two repeats requires a high concentration of O protein. From the molecular size of O protein (32,000 daltons), and the internal symmetry in each 19bp repeat, we inferred that the O protein may bind in dimeric form, and that the 95bp region may be filled only when four such dimers have bound. This interaction is discussed in connection with the "activation" of the ori by O protein leading to initiation of DNA synthesis.

Bacteriophage lambda↗

RNaselll activation of bacteriophage lambda N synthesis.

The bacteriophage lambda N gene product is one of the first genes expressed during phage development. N protein allows the expression of other phage genes by altering the transcription elongation process so as to prevent transcription termination. We have found that N levels may be modulated soon after induction or infection. Using N-lacZ fusions, we determined that cells containing RNaselll have at least a fourfold greater expression than cells defective for RNaselll. This effect is exerted at the post-transcriptional level. RNaselll processes an RNA stem structure in the N-leader RNA. Removal of the stem structure by deletion increases N expression and prevents further stimulation by RNaselll. The base of this stable stem is adjacent to the N ribosome binding site. We present a model for control of N synthesis in which this stable stem inhibits ribosome access to the N mRNA.

Bacteriophage lambda↗

Efficient epitope mapping by bacteriophage lambda surface display.

A bacteriophage lambda surface expression system, lambda foo, was used for epitope mapping of human galectin-3. We constructed random epitope and peptide libraries and compared their efficiencies in the mapping. The galectin-3 cDNA was randomly digested by DNase 1 to make random epitope libraries. The libraries were screened by affinity selection using a microtiter plate coated with monoclonal antibodies. Direct DNA sequencing of the selected clones defined two distinct epitope sites consisting of nine and 11 amino-acid residues. Affinity selection of random peptide libraries recovered a number of sequences that were similar to each other but distinct from the galectin-3 sequence. These results demonstrate that a single affinity selection of epitope libraries with antibodies is able to define an epitope determinant as small as nine residues long and is more efficient in epitope mapping than random peptide libraries.

Amino Acid Sequence↗

Domain structure and DNA binding regions of beta protein from bacteriophage lambda.

beta protein from bacteriophage lambda promotes a single-strand annealing reaction that is central to Red-mediated recombination at double-strand DNA breaks and chromosomal ends. beta protein binds most tightly to an intermediate of annealing formed by the sequential addition of two complementary oligonucleotides. Here we have characterized the domain structure of beta protein in the presence and absence of DNA using limited proteolysis. Residues 1-130 form an N-terminal "core" domain that is resistant to proteases in the absence of DNA, residues 131-177 form a central region with enhanced resistance to proteases upon DNA complex formation, and the C-terminal residues 178-261 of beta protein are sensitive to proteases in both the presence and absence of DNA. We probed the DNA binding regions of beta protein further using biotinylation of lysine residues and mass spectrometry. Several lysine residues within the first 177 residues of beta protein are protected from biotinylation in the DNA complex, whereas none of the lysine residues in the C-terminal portion are protected. The results lead to a model for the domain structure and DNA binding of beta protein in which a stable N-terminal core and a more flexible central domain come together to bind DNA, whereas a C-terminal tail remains disordered. A fragment consisting of residues 1-177 of beta protein maintains normal binding to sequentially added complementary oligonucleotides and has significantly enhanced binding to single-strand DNA.

Alanine↗

Effect of multiplicity of infection on transcription in Escherichia coli cells infected by bacteriophage lambda.

The effect of multiplicity of infection (m.o.i.) on transcription was studied by infecting Escherichia coli with bacteriophage lambda cI47, lambda cI47O29P3 and lambda cI857cro27P3. DNA-RNA hybridization with lambda cI47 l-strand DNA, phi 80imm lambda r-strand DNA, and lambda imm80 r-strand DNA were used to measure mRNA transcription from the l-strand, the r-strand of the early x-P-Q region and the late A-J-b2 region of lambda bacteriophage respectively. In lambda cI47cro+O-P--infected cells, transcription from the l-strand, r-strand of the early x-P-Q region and the late A-J-b2 region all decreased with increasing m.o.i. The response in the x-P-Q region was less marked than in other regions, but the pattern looked similar to that described above. When phage DNA replication was permitted, as in the case of lambda cI47, the response was similar to that observed in lambda cI47cro+O-P--infected cells, but the level of transcription was increased two- or threefold. In lambda cI857cro-P--infected cells, the leftward transcription and the rightward transcription from the early x-P-Q region and the late A-J-b2 region all increased with increasing m.o.i., but the extent of change was less drastic than with lambda cro+. This result demonstrated clearly that the decrease in transcription from various regions at increasing m.o.i. of lambda cro+ was due to the inhibitory action of the cro gene product. The results obtained with cro- strongly support the view that gene dosage is a significant controlling factor for the extent of gene expression.

Bacteriophage lambda↗

Injection of DNA into liposomes by bacteriophage lambda.

Small unilamellar vesicles (75-100 nm diameter) and large liposomes (greater than 1 micron in diameter) were prepared containing the lamB protein, an outer membrane protein of Escherichia coli and Shigella which serves as the receptor for bacteriophage lambda. Bacteriophage were observed to bind to these liposomes and vesicles by their tails and in most cases the heads of the bound bacteriophage appeared empty or partially empty of DNA. The lambda DNA was usually only partially ejected from the bacteriophage head when small unilamellar liposomes were used, presumably because the vesicles are too small to contain all the DNA. The partially ejected DNA was not susceptible to DNase unless the vesicle bilayer was first disrupted suggesting that DNA injection of phage DNA into the vesicle had occurred. After disruption of these vesicles on electron microscope grids, the bacteriophage are seen to have partially empty heads and a small mass of DNA associated with their tails. Using larger liposomes prepared by the fusion of lamB bearing vesicles with polyethylene glycol and n-hexyl bromide, the heads of most of the bound bacteriophage appeared to be completely empty of DNA. Disruption of these preparations on electron microscope grids revealed circular arrays of empty-headed bacteriophage surrounding DNA which had apparently been contained within the intact liposomes. These results indicate that high molecular weight DNA can be entrapped within liposomes with high efficiency by ejection from bacteriophage lambda. The possible use of these DNA-containing liposomes to facilitate gene transfer in eukaryotic cells is discussed.

Bacteriophage lambda↗

Formation of oligomeric structures from plasmid DNA carrying cos lambda that is packaged into bacteriophage lambda heads.

Plasmids that carry cos lambda, the region necessary for lambda phage packaging and that are as small as four kilobases in size can be packaged into lambda phage heads in head-to-tail tandem oligomeric structures. Multimeric oligomers as large as undecamers have been detected. Oligomer formation depends upon the products of red and gam of lambda, and the general recombination occurs between different plasmids that share homologous DNA regions. The packaging efficiency of plasmids depends on its copy number in cells and its genome size. Upon injection into a cell, the DNA establishes itself as a plasmid in a tandem structure. When such a plasmid in a high oligomeric structure is used as the source of packaging DNA, the packaging efficiency of the plasmids is elevated. The oligomers are stable in recA cells, whereas they drift toward lower oligomers in recA+ cells.

Bacteriophage lambda↗