Mapping and functional analysis of y and CII mutants

Identification of the DNA binding domain of the phage lambda cII transcriptional activator and the direct correlation of cII protein stability with its oligomeric forms

The bacteriophage lambda transcriptional activator protein cII is a DNA-binding protein that coordinately regulates transcription from phage promoters important for lysogenic growth. We have genetically and structurally characterized more than 80 different single amino acid substitutions in this 97-amino-acid protein. A subset of 25 of these variant proteins was utilized for detailed biochemical analysis, which allows us to define specific domains critical for sequence-selective DNA recognition, nonspecific DNA binding, and protein oligomerization. The mutation studies also demonstrated the remarkable correlation of oligomeric structure of cII protein to its stability within the bacterial host. An Escherichia coli HtpR- strain has been identified that greatly stabilizes these highly unstable cII mutants.

Mutational analysis of a regulatory region in bacteriophage lambda that has overlapping signals for the initiation of transcription and translation

The positively regulated PRE promoter of phage lambda structurally overlaps with the ribosome-binding and NH2-terminal coding region of the regulatory protein (cII) that activates PRE transcription. We have isolated and characterized 27 different point mutations that occur within the 36-base-pair overlapping region. A comparison of genetic crossover data with nucleotide separations as determined by DNA sequence analysis reveals that recombination frequencies are greatly depressed at very short distances. Moreover, recombination frequency is critically dependent upon the precise nucleotide sequence of the crossover region for distances of five nucleotides or less. The mutations define precise positions and sequences that are important to (i) PRE promoter function, (ii) translation of the cII gene, and (iii) cII gene function. Mutational changes that affect the function of one element in this region concomitantly define phenotypically silent alterations in the other two elements. Mutations deficient in promoter function (P-RE or cy) are clustered in two regions that lie approximately equal to 10 and approximately equal to 35 nucleotides before the initial base of PRE mRNA, analogous to mutations in other promoters. P-RE mutations in the -10 region alter bases that are conserved in prokaryotic promoters, but P-RE mutations in the -35 region do not affect bases that are normally conserved in other promoters. Several mutations deficient in cII gene activity affect the initiation of cII protein synthesis, including an A leads to G change four bases outside the cII coding region, and AUG leads to GUG, AUG leads to ACG, and AUG leads to AUA mutations in the initiation codon. In the region of overlap between the PRE promoter and the NH2-terminal region of the cII gene, most amino acid substitutions in the cII protein do not result in a loss of cII function, indicating that this region of the gene does not contain essential information for cII function. We suggest that the overlap itself is an evolutionarily conserved structure and that it somehow coordinates the bidirectional transcriptional and translational events that occur in this region.

DNA sequence of regulatory region for integration gene of bacteriophage lambda

The cII and cIII proteins specified by bacteriophage lambda direct the lysogenic response to infection through the coordinate establishment of repression and integration of the viral DNA. The regulatory activity of cII/cIII involves positive regulation of two promoter sites: the p(E) promoter, turning on expression of the cI protein that maintains lysogeny, and the p(I) promoter, activating synthesis of the Int protein for integrative recombination. Regulation of the p(I) promoter provides for differential expression of the Int protein with respect to the excision-specific Xis protein from the closely linked int and xis genes. We have determined the DNA sequence of the p(I) promoter region for wild-type lambda DNA and for two classes of mutations: intc mutations, which result in a high rate of Int synthesis in the absence of cII, and deletion mutations, some of which eliminate cII-activated expression of the int gene. We find a sequence with considerable homology (11 of 15 bases) to a "typical" (computer-generated) promoter sequence, adjacent to a region with striking homology (11 of 14 bases) to part of the p(E) promoter region. This presumed p(I) sequence overlaps the start of the xis gene and includes the site of two intc point mutations. A cII-insensitive xis(+) deletion partially removes the proposed p(I) sequence; a deletion that leaves the p(I) sequence intact but terminates 21 bases upstream does not interfere with cII activation of the int gene. From our results and the analysis of the p(E) region, we suggest that cII acts in the promoter -35 recognition region to facilitate binding by RNA polymerase at the -10 interaction region. Differential expression of the int and xis genes results because the p(I) transcript lacks the initiation codon for Xis protein synthesis.

A comprehensive molecular map of bacteriophage lambda

Physical and genetic mapping of deletion mutations has been correlated with the available molecular sizes of the lambda gene products and the DNA base sequence to construct a comprehensive molecular map of the phage lambda genome. The physical length of the DNA making up the left arm from the cos site through gene J is not sufficient to account in a nonoverlapping manner for all the proteins of the sizes reported to be coded, especially in the Nu1--C region. In the right arm all the coding capacity has not been accounted for, and it appears to be oversaturated only in the gam-ral region. The positions of several IS and Tn elements, and of restriction endonuclease cleavage sites are specified.

Bacteriophage lambda mutants (lambdatp) that overproduce repressor

Lambda tp mutants, selected for their ability to form turbid plaques on lon hosts, overproduce repressor. The tp1 and tp2 mutations have been located within (or adjacent to) the cIII gene. The tp1 mutation reduced late gene expression, as measured by endolysin synthesis (in the absence of functional cI repressor) and progeny phage yield. The tp4 mutation was mapped in the cY-cII region, and complementation tests indicated that tp4 affects the diffusible product of the cII gene. The tp4 mutation also reduced progeny production, but did not markedly affect endolysin synthesis.

Nucleotide sequence of cro, cII and part of the O gene in phage lambda DNA

A nucleotide sequence comprising 960 base pairs of bacteriophage lambda DNA has been determined. The sequence includes the entire genes of the regulatory proteins cro and cII, and part of the O gene, together with control elements for their transcription and translation. The right-hand boundaries of the lambdaimm434 and lambdaimm21 substitutions and the cy42 mutation have been located.

Analysis of a temperature sensitive mutation in gene cII of bacteriophage lambda

The mutation cIIts612 was found to map outside the immunity region of phage lambdaimm21 hybrid. As expected of a cII mutation, lambdacIIts612 is unable to stimulate either cI repressor or Int synthesis during the establishment of lysogeny. These results indicate that part of the cII gene of lambda is homologous to that of lambdaimm21 phage.

Overproduction of phage lambda repressor under control of the lac promotor of Escherichia coli

The gene coding for bacteriophage Lambda repressor (cI gene) has been fused to the lac operon of Escherichia coli. In some of the fusions Lambda repressor synthesis can be controlled by the lac operator and promoter. Upon induction of the lac operon the amount of Lambda repressor is increased by a factor of 7 over that found in a single lysogen. In combination with the polarity suppressor suA the induction factor rises to 20. Transducing phages of one fusion were constructed. After thermal induction of this phage the final level of Lambda repressor was enhanced by a factor of 150.

LambdacI mutants: intragenic complementation and complementation with a cI promoter mutant

Complementation for the maintenance of lysogeny was studied by superinfecting lambdacIts lysogens at 34 degrees C. and then heating to 43 degrees C. With certain exceptions, ts mutants with defects in the left half of the repressor complemented ts mutants with defects in the right half to produce a less heat-labile repressor (Fig. 3). All cI amber mutants failed to complement cIts mutants. The cI mutant c50 complements all ts mutants. Mutations in Pre (cy) or genes cII and cIII do not significantly affect the expression of cI by a superinfecting lambda genome in an immune lysogen. Mutants with very heat-labile repressors failed to complement lambdacy42 for the establishment of lysogeny at elevated temperatures, while those with less heat-sensitive repressors apparently did complement cy. According to a suggested model, the left side of the cI product is concerned primarily with subunit aggregation, while operator binding is the function of the right side of the oligomer.

A pleiotropic regulatory mutation in lambda bacteriophage

Lambda bacteriophage mutants, lambdasar, were isolated. These mutants can form plaques on a non lysogenic lawn and are unable to grow on nonimmune (imm-), cro constitutive hosts. Analysis of the restriction of lambdasar by a set of defective lysogens suggested that both the cro and cII gene products participate in the inhibition. The sar mutations were mapped in the ori region between the genes cII and O. Complementation experiments showed that under the restrictive conditions lamdasar is defective in the expression of both the N and the O genes. Transcription analyses support these findings, as lambdasar is unable to serve as a template for transcription after infecting cro constitutive hosts. In addition lambdasar does not replicate under the restrictive conditions, although its DNA can bind to the host membrane to some extent. The Sar phenotype can be relieved by removing sites of action of cro either by a V2 mutation or by substituting the lambda immunity region by imm434 or imm21. Similarly introducing a cy mutation, which interferes with the action of the cII gene product, also eliminates the Sar effect. The sar mutation can suppress cy mutations as manifested in plaque morphology, lysogenization frequency, cI repressor synthesis and the expression of rex function. Suppression takes place only when the sar mutation is present in cis to cy and it requires the action of the cII and cIII gene products. It is suggested that the sar mutation suppresses cy by activating a new promoter for repressor synthesis, pro. The results also suggest that the cII and cIII gene products may act at a site other than y.

Bidirectional transcription and the regulation of Phage lambda repressor synthesis

There are two promoters for transcription of gene cI in phage lambda, the gene that codes for phage repressor. The promoters, called pre and prm, are located on the distal (pre) and proximal (prm) sides of gene cro, which itself is adjacent to cI. Since cI and cro are transcribed in opposite directions, cI transcription initiating at pre gives rise to an antisense transcript of cro, while cI transcription initiating at prm does not. Pre, active after infection of a sensitive cell, is stimulated by products of phage genes cII and cIII, and may be located at the site defined by the mutant cY. Prm is active in an established lysogen. These conclusions are based on measurements of the rates of synthesis of antisense cro RNA, cI RNA, and repressor protein in infected and lysogenic cells. To measure antisense RNA, an assay based on the formation of nuclease-resistant, double-stranded RNA, specific to the cro region, was developed. These results raise the possibility that bidirectional transcription of cro has a regulatory function in phage lambda.

Regulation of lambda rex expression after infection of Escherichia coli K by lambda bacteriophage

The ability of Escherichia coli K to support bacteriophage T4rII replication starts to decline at 3 to 6 min after infection by lambda. This inhibition appears to depend on expression of the lambdarex(+) gene, since little inhibition was observed following infection by a lambdarex mutant or by a hybrid bacteriophage lambdai(434) which lacks a functional rex gene. For promotion of the synthesis of rex product, cII(+) and N(+) genes are required and can act trans, whereas cY(+), also required, must be cis to a rex(+) gene. These genes presumably play a role in the transcription of the cI-rex operon because they are also known to be required for repressor (cI product) synthesis. Functional cIII, O, P genes are not necessary for ample rex product synthesis. We also observed full rex expression after infection by lambdasuscI mutants, suggesting that rex and repressor are separate gene products and that repressor is not required for inhibition of T4rII replication. We also report experiments with a rex mutant that is not leaky when in a lysogen but is sufficiently leaky shortly after infection to cause inhibition of T4rII replication.

Establishment of repression by lambdoid phage in catabolite activator protein and adenylate cyclase mutants of Escherichia coli

Lambdoid phages form clear plaques and show reduced ability to establish immunity in strains of Escherichia coli that lack adenylate cyclase or catabolite activator protein. The absence of the activator protein or cyclic AMP reduces the frequency of lysogenization, but does not prevent steady-state repressor synthesis of a lysogen. Lambda phage mutants able to form turbid plaques on strains that lack catabolite activator protein or adenylate cyclase have been isolated and analyzed.

Establishment and maintenance of repression by bacteriophage lambda: the role of the cI, cII, and c3 proteins

To define the events necessary for the establishment and maintenance of repression in a lambda-infected cell, we have studied the requirements for efficient synthesis of the cI protein ("lambda-repressor"). Three classes of lambda mutants defective in the establishment of repression are also defective in the appearance of cI protein activity at the normal time. Two of these mutational classes (cII(-) and cIII(-)) probably result from inactivation of lambda-specified proteins, but the third class (cy(-)) may involve a structural defect. We conclude that at least three regulatory elements are likely to be required for the normal turn-on of cI protein synthesis in an infected nonlysogenic cell: cII and cIII proteins and an "active" y-region of lambda DNA. From these and other results, the complete role of cII and cIII proteins in the establishment of repression may involve a bifunctional regulatory activity: positive regulation of the cI gene and negative regulation of late genes. A possible molecular model for cII and cIII action is discussed. Since the cII and cIII genes are repressed by the cI protein under conditions of stable lysogeny, a separate mechanism is required for the maintenance of cI protein synthesis. After infection of a lysogen by cII(-) phage, the rate of increase of cI protein activity is substantially greater than after infection of a nonlysogen. From these and other results, the cI protein may also have a bifunctional regulatory activity: positive regulation of the cI gene and negative regulation of early lytic genes.

Control of lambda repressor synthesis

Direct measurements of the intracellular level of lambda repressor have been made by a DNA-filter assay and a radioimmune assay. Transcription of cI, the structural gene for repressor, appears to initiate at two different promoters, prm and pre. Promoter pre is activated during the establishment of lysogeny by the action of cII and cIII proteins at the DNA site cY. Phage mutated in cII, cIII, or cY do not make a normal burst of repressor after infection and do not efficiently lysogenize the cell. Cro product stops repressor synthesis midway in the infective cycle. Promoter prm maintains the repressor level in established lysogens. Delection mapping places it very near the right operator (Or). Prm is activated by repressor bound to the right operator. In the absence of cII or cIII protein, repressor synthesis requires active repressor and only proceeds on genomes able to bind repressor at Or.