Mutations in the right operator of bacteriophage lambda: evidence for operator-promoter interpenetration

Evidence that the promoter can influence assembly of antitermination complexes at downstream RNA sites

The N protein of phage lambda acts with Escherichia coli Nus proteins at RNA sites, NUT, to modify RNA polymerase (RNAP) to a form that overrides transcription terminators. These interactions have been thought to be the primary determinants of the effectiveness of N-mediated antitermination. We present evidence that the associated promoter, in this case the lambda early P(R) promoter, can influence N-mediated modification of RNAP even though modification occurs at a site (NUTR) located downstream of the intervening cro gene. As predicted by genetic analysis and confirmed by in vivo transcription studies, a combination of two mutations in P(R), at positions -14 and -45 (yielding P(R-GA)), reduces effectiveness of N modification, while an additional mutation at position -30 (yielding P(R-GCA)) suppresses this effect. In vivo, the level of P(R-GA)-directed transcription was twice as great as the wild-type level, while transcription directed by P(R-GCA) was the same as that directed by the wild-type promoter. However, the rate of open complex formation at P(R-GA) in vitro was roughly one-third the rate for wild-type P(R). We ascribe this apparent discrepancy to an effect of the mutations in P(R-GCA) on promoter clearance. Based on the in vivo experiments, one plausible explanation for our results is that increased transcription can lead to a failure to form active antitermination complexes with NUT RNA, which, in turn, causes failure to read through downstream termination sites. By blocking antitermination and thus expression of late functions, the effect of increased transcription through nut sites could be physiologically important in maintaining proper regulation of gene expression early in phage development.

Interaction of mutant lambda repressors with operator and non-operator DNA

We have described a set of mutations that alter side-chains on the operator binding surface of lambda repressor. In this paper, we study the interactions of 12 purified mutant repressors with operator and non-operator DNA. The mutant proteins have operator affinities that are reduced from tenfold to greater than 10,000-fold compared to wild-type. Nine of the mutants have affinities for non-operator DNA that are similar to wild-type, two mutants show decreased non-specific binding, and one mutant has increased affinity for non-operator DNA. We discuss these findings in terms of the structural and energetic contributions of side-chain--DNA interactions, and show that certain contacts between the repressor and the operator backbone contribute both energy and specificity to the interaction.

Kinetic analysis of mutations affecting the cII activation site at the PRE promoter of bacteriophage lambda

Abortive initiation and run-off transcription assays were used to study the effects of cy mutations on activation of the phage lambda PRE promoter by cII gene product. Six point mutations in the repeated T-T-G-C sequences that flank the -35 consensus region of PRE decreased the apparent affinity of the promoter for cII protein by factors of 4-16 relative to the wild-type affinity. Kinetic analyses of transcription initiation in the presence and absence of cII protein demonstrated that five of the six mutations did not significantly affect the intrinsic interaction of RNA polymerase with PRE. Thus, these mutations differ from other cy mutations, including those in the -35 consensus region, which affect the formation of polymerase-PRE closed complexes or the isomerization of closed complexes to open complexes but do not affect the binding of cII protein. A sixth T-T-G-C mutation, cy3001, may affect intrinsic initiation by RNA polymerase as well as cII binding.

Mutants in the y region of bacteriophage lambda constitutive for repressor synthesis: their isolation and the characterization of the Hyp phenotype

Bacteriophage lambdahyp mutants have been isolated as survivors of Escherichia coli K-12 bacteria lysogenic for lambda Nam7am53cI857. The hyp mutants are characterized by (i) their localization in the y region very close to the imm lambda/imm434 boundary, (ii) polarity on O gene expression, (iii) immediate recovery of lambda immunity at 30 degrees C after prolonged growth of lambda Nam7am53cI857 hyp lysogens at 42 degrees C even in the presence of an active cro gene product, (iv) ability of phage lambda v2v3vs326 but not lambda v1v2v3 to propagate on lambda cI+hyp lysogens, (v) inability to express lambda exonuclease activity after prophage induction, and (vi) inviability at any temperature of phage carrying the hyp mutation. All these properties are referred to collectively as the Hyp phenotype. We show that the Hyp phenotype is due to cII-independent constitutive cI-gene-product synthesis originating in the y region, which results in the synthesis of anti-cro RNA species, and constitutive levels of cro gene product present even in lambda cI+hyp lysogens. A model is presented which is consistent with all the experimental observations.

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.

Mutational analysis of the operators of bacteriophage lambda

Oc mutations in the operators of bacteriophage lambda have been used to analyze the functional organization of the operators. In each operator, repressor binding sites 1 and 2, as identified biochemically, were found to be primarily responsible for the repressor affinity of the operators in vitro and for the repression of lytic functions in vivo. In addition, both sites were shown to be involved in the action of cro product at the operators. The data obtained have been used to estimate the repressor affinities of the individual binding sites. These affinities suggest that repressor bound at OR1 and OR2 interacts cooperatively. The results obtained support a model for repression of the early lambda operons where repressor bound at binding sites 1 and 2 interferes with RNA polymerase binding to the promotor sites.

Purification and properties of a DNA-binding protein with characteristics expected for the Cro protein of bacteriophage lambda, a repressor essential for lytic growth

The Cro protein specified by bacteriophage lambda is a repressor essential for normal lytic growth of the virus, thus having a physiological role distinct from that of cI, the repressor that maintains lysogeny. We have purified a lambda-specific DNA-binding protein with the requirements for synthesis and biochemical activities expected for Cro protein from studies in vivo. As isolated, the protein appears to be a dimer of molecular weight approximately 18,000 with DNA-binding properties that are very similar, but not identical, to those of the cI protein. We infer that bacteriophage lambda uses the same regulatory region of DNA for two different DNA-binding repressor proteins with subtle differences in binding activity specialized for different physiological roles.

Lambda repressor turns off transcription of its own gene

We report transcription in vitro of the lambda repressor gene, cI, using specific restriction endonuclease fragments as templates. This transcription is repressed by lambda repressor. Moreover, we report the sequence change caused by a cI promoter mutation. This change is located between two repressor binding sites in the rightward operator (OR). Transcription studies using mutant templates indicate that repressor bound to two sites in OR regulates transcription of gene tof, and repressor bound to the remaining site(s) controls transcription of cI.

Sequence of the OR operator of phage lambda

A sequence of 79 nucleotides from the lambda OR operator is obtained by primed transcription of repressor protected DNA fragments. The sequence contains the primary repressor binding site plus partial duplications which can be interpreted as secondary repressor binding sites.

Sequence of the PR promoter of phage lambda

The RNA polymerase binding site from the lambda PR promoter was isolated and sequenced. This DNA fragment contains the transcription initiation site and shares 25 nucleotides with OR. The sequence preceding the initiation site suggests that the promoter recognition site is not identical with the tight binding and initiation site.

Initiator constitutive mutation with an 'up-promoter' effect in Aspergillus nidulans

A mutation leading to strong constitutivity for a uric acid-xanthine permease in the lower eukaryote Aspergillus nidulans has been found to be tightly linked to the putative structural gene whose expression it controls in the cis configuration. In addition, it increases the maximal induced level of transport 2.5-fold. This is the first demonstration of an initiator or promoter mutation in an eukaryote.