Regulation of the int gene of bacteriophage lambda: activation by the cII and cIII gene products and the role of the Pi and Pl promoters

Hybrid Vigor: Importance of Hybrid λ Phages in Early Insights in Molecular Biology

Laboratory-generated hybrids between phage λ and related phages played a seminal role in establishment of the λ model system, which, in turn, served to develop many of the foundational concepts of molecular biology, including gene structure and control. Important λ hybrids with phages 21 and 434 were the earliest of such phages. To understand the biology of these hybrids in full detail, we determined the complete genome sequences of phages 21 and 434. Although both genomes are canonical members of the λ-like phage family, they both carry unsuspected bacterial virulence gene types not previously described in this group of phages. In addition, we determined the sequences of the hybrid phages λ imm21, λ imm434, and λ h434 imm21. These sequences show that the replacements of λ DNA by nonhomologous segments of 21 or 434 DNA occurred through homologous recombination in adjacent sequences that are nearly identical in the parental phages. These five genome sequences correct a number of errors in published sequence fragments of the 21 and 434 genomes, and they point out nine nucleotide differences from Sanger's original λ sequence that are likely present in most extant λ strains in laboratory use today. We discuss the historical importance of these hybrid phages in the development of fundamental tenets of molecular biology and in some of the earliest gene cloning vectors. The 434 and 21 genomes reinforce the conclusion that the genomes of essentially all natural λ-like phages are mosaics of sequence modules from a pool of exchangeable segments.

Transcription and initiation of ColE1 DNA replication in Escherichia coli K-12

By S1 nuclease protection mapping, we characterized RNA transcripts and nascent ColE1 DNA synthesized in wild-type Escherichia coli cells after infection with lambda-mini-ColE1 hybrid bacteriophages. Transcription of the RNA II region of ColE1 DNA in vivo starts mostly from the RNA II promoter, which was identified by in vitro experiments, and ends at or near the ori site. Synthesis of the leading strand of ColE1 DNA was found to start at the ori site. Nevertheless, the molar ratio of the nascent DNA to the synthesized transcripts ending at the ori site was less than 0.05. In bacterial rnh mutants whose RNase H activities were less than 0.06% of that of the wild type, transcription patterns, as well as nascent DNA synthesis, were still similar to those in rnh+ cells. However, in bacteria whose rnh gene was interrupted by insertion of a drug resistance gene, the number of transcripts ending at the ori site was much reduced and that of transcripts reading through the ori site was definitely increased relative to that observed in wild-type bacteria. These results suggested that cleavage of the RNA transcript at the ori site in vivo is dependent on RNase H activity, as demonstrated in the in vitro system, but most of the cleaved RNA is unable to prime initiation of ColE1 DNA synthesis efficiently.

Aberrant regulation of synthesis and degradation of viral proteins in coliphage lambda-infected UV-irradiated cells and in minicells

The patterns of bacteriophage lambda proteins synthesized in UV-irradiated Escherichia coli cells and in anucleate minicells are significantly different; both systems exhibit aberrations of regulation in lambda gene expression. In unirradiated cells or cells irradiated with low UV doses (less than 600 J/m2), regulation of lambda protein synthesis is controlled by the regulatory proteins CI, N, CII, CIII, Cro, and Q. As the UV dose increases, activation of transcription of the cI, rexA, and int genes by CII and CIII proteins fails to occur and early protein synthesis, normally inhibited by the action of Cro, continues. After high UV doses (greater than 2,000 J/m2), late lambda protein synthesis does not occur. Progression through the sequence of regulatory steps in lambda gene expression is slower in infected minicells. In minicells, there is no detectable cII- and cIII-dependent synthesis of CI, RexA, or Int proteins and inhibition of early protein synthesis by Cro activity is always incomplete. The synthesis of early b region proteins is not subject to control by CI, N, or Cro proteins, and evidence is presented suggesting that, in minicells, transcription of the early b region is initiated at a promoter(s) within the b region. Proteolytic cleavage of the regulatory proteins O and N and of the capsid proteins C, B, and Nu3 is much reduced in infected minicells. Exposure of minicells to very high UV doses before infection does not completely inhibit late lambda protein synthesis.

Removal of a terminator structure by RNA processing regulates int gene expression

The int gene of phage lambda encodes a protein involved in site-specific recombination. Its expression is regulated differentially during successive phases of the lambda infective cycle. The gene is transcribed early after infection from one promoter, pL, and later from a second promoter pI. Each transcription event requires different positive activation factors, lambda N and cII proteins, respectively. Transcription from the pI promoter, located adjacent to int, passes through int and terminates 277 nucleotides beyond int at tI. Polymerases initiating at pL transcribe through tI and into the b segment of lambda DNA. The read-through pL transcript is sensitive to cleavage by the endonuclease, RNase III, both in vivo and in vitro. Two specific cuts are made by RNase III in a double-stranded structure about 260 nucleotides beyond int in the location of the tI terminator. Functionally, the processed pL transcript is unable to synthesize the int gene product, whereas the terminated and unprocessed pI transcript expresses int. Interestingly, unprocessed pL transcripts made in hosts defective in RNase III (rnc-) can express int. Thus a correlation exists between processing and negative control of int expression. The place where processing occurs, some 260 nucleotides beyond int, is called sib, and the control of int expression from this site is called retroregulation. Retroregulation by sib is not restricted just to the int gene; we show that if the sib site is cloned beyond a bacterial gene, the gene is controlled by sib and RNase III. Specific models are discussed with respect to control of gene expression by RNase III from a site beyond the controlled gene.

Deletion analysis of the retroregulatory site for the lambda int gene

The lambda int gene product, integrase, recombines phage and bacterial DNA at a specific site during the integration step of lysogeny. Regulation of integrase synthesis is complex. (1) Transcription of the gene can occur from either of two promoters. lambda cII protein activates transcription initiation near int at pI. The lambda N protein allows transcription of int from pL. N protein acts by preventing transcription termination at several terminators between pL and int. (2) The expression of integrase is also subject to post-transcriptional regulation by a site, sib, which is located beyond int in the b region of lambda. Expression of int from pL is inhibited by sib, whereas that from pI is not. The negative control of int expression by sib is termed retroregulation. Retroregulation of int is caused, in part, by processing of the pL transcript at the sib site by RNase III of Escherichia coli. The exonuclease, Bal31, was used to generate a set of deletions to define the sib regulatory site. Both sib+ and sib- deletions were sequenced, and it was concluded from this and other work that a dyad symmetry present in the b region, 270 base-pairs from int, was necessary for retroregulation. The RNA structure of this segment is similar to other RNase III-sensitive sites found in E. coli and phage RNAs.

Retroregulation: control of integrase expression by the b2 region of bacteriophages lambda and 434

Genetic fusions constructed by a combination of in vivo and in vitro techniques have been used to investigate the cis-regulatory role of a 250-base-pair segment of b2 DNA in the expression of int transcripts originating from three different promoters PI, PL, and PTRP. It has been established that (a) the PI and PTRP transcripts, which produce functional int protein, are efficiently terminated by the b2 segment, (b) in the same test system, the PL transcript, which does not result in functional integrase, is not terminated by the b2 segment, (c) this b2 (sib) effect does not depend on genes lying between int and N on the phage genome, (d) the sib effect is also observed with the b2 DNA of phage 434, which resembles that of lambda between -197 and att but diverges radically from it to the left of base -197.

Posttranscriptional control of bacteriophage lambda gene expression from a site distal to the gene

The bacteriophage lambda int gene product, integrase, recombines the phage DNA with the host DNA at specific sites on each to accomplish lysogeny. The int gene is transcribed from two promoters, PL and PI, each regulated positively by lambda proteins. The expression of integrase is also controlled from a site, sib, in the b region of the phage genome. This is a unique regulatory site because it is located distal to the structural gene in relation to the promoters. The expression of int from the PL promoter is inhibited when sib is present. This effect appears to be specific for PL because sib does not cause inhibition of PI-dependent int synthesis. lambda mutants that contain alterations in the site have been isolated. Sequence analyses of the mutations reveal single base changes, spanning 37 base pairs (bp) in the b region, some 240 bp beyond the int gene. Another mutant, hef13, which has a phenotype similar to that of sib, introduces a nucleotide change within the same 37-bp region. The sib and hef mutations cluster within a region of dyad symmetry. Regulation of int synthesis by sib occurs after transcription of the int gene. There is no difference in the rate of PL-promoted int mRNA synthesis in either sib+ or sib- phage infections, yet int mRNA is less stable in the sib+ infection. Because RNase III host mutants are defective in sib regulation, processing of the PL mRNA at sib by this endoribonuclease may cause int mRNA decay and decrease int synthesis.

Kinetics of P22 early gene expression suggests a cro-like regulatory function

Analysis of phage-specified protein synthesis after phage infection of UV-irradiated cells shows a turn-off of early gene expression, a regulatory event that is independent of the known P22 regulatory functions. This supports the suggestion of a cro lambda-like function in P22. We have identified the products of genes 18 and int as contributing to the complex 40,000 dalton band in our SDS-polyacrylamide gels. Both gene products appear to be subject to regulation by the cro-like function of P22. Proteins of 33,000, 29,000, 27,000, 25,000, and 24,000 MW, specified by as yet unidentified P22 genes of the early leftward operon, are regulated by the same function. Our data suggest that the cro-like function is expressed from the early rightward operon.

Functional analysis of hybrid plasmids carrying genes for lambda site-specific recombination

A number of hybrid plasmids, carrying lambda genes involved in site-specific integrative recombination, have been constructed in vitro. Analysis of protein synthesis in Escherichia coli minicells has shown that Int protein is synthesized only when int gene is expressed constitutively. The plasmids RSF2124::lambda-CD, RSF2124::lambda-Cint-c57, and pInt lambda were able to integrate into the chromosome of E.coli at the attB. The integration of hybrid plasmids into the genome of bacteria has also been shown for polA1 strains restricting the autonomous replication of ColE1 type plasmids. Genetic markers of hybrid plasmids are maintained in polA1 bacteria for at least 50 generations under nonselective conditions. The Southern blotting experiments using [32P]pBR322 DNA and EcoRI fragments of E. coli polA1 chromosome carrying integrated plasmid pInt lambda demonstrated that in this strain hybrid plasmids can be observed only when integrated into the attB of the chromosome according to Campbell's model of integration. In the cells, where autonomous replication of plasmids is possible, they can be observed both in extrachromosomal and integrated states. The integration of the ColE1 replication origin into the chromosome of bacteria is not lethal for the cells. Only attP and the int gene of lambda are necessary for the integration of hybrid plasmids under conditions of effective int gene expression. If the level of Int protein synthesis is high enough, the prophage excision can be observed in the absence of Xis product. The six-fold decrease of Int protein concentration in the cell (in case of pInt lambda 2 as compared to pInt lambda 1) is critical both for integration and excision.