Mutants of bacteriophage lambda which do not requre the cIII gene for efficient lysogenization

In silico Evolution of Lysis-Lysogeny Strategies Reproduces Observed Lysogeny Propensities in Temperate Bacteriophages

Bacteriophages are the most abundant organisms on the planet and both lytic and temperate phages play key roles as shapers of ecosystems and drivers of bacterial evolution. Temperate phages can choose between (i) lysis: exploiting their bacterial hosts by producing multiple phage particles and releasing them by lysing the host cell, and (ii) lysogeny: establishing a potentially mutually beneficial relationship with the host by integrating their chromosome into the host cell's genome. Temperate phages exhibit lysogeny propensities in the curiously narrow range of 5–15%. For some temperate phages, the propensity is further regulated by the multiplicity of infection, such that single infections go predominantly lytic while multiple infections go predominantly lysogenic. We ask whether these observations can be explained by selection pressures in environments where multiple phage variants compete for the same host. Our models of pairwise competition, between phage variants that differ only in their propensity to lysogenize, predict the optimal lysogeny propensity to fall within the experimentally observed range. This prediction is robust to large variation in parameters such as the phage infection rate, burst size, decision rate, as well as bacterial growth rate, and initial phage to bacteria ratio. When we compete phage variants whose lysogeny strategies are allowed to depend upon multiplicity of infection, we find that the optimal strategy is one which switches from full lysis for single infections to full lysogeny for multiple infections. Previous attempts to explain lysogeny propensity have argued for bet-hedging that optimizes the response to fluctuating environmental conditions. Our results suggest that there is an additional selection pressure for lysogeny propensity within phage populations infecting a bacterial host, independent of environmental conditions.

Lysis-lysogeny coexistence: prophage integration during lytic development

The infection of Escherichia coli cells by bacteriophage lambda results in bifurcated means of propagation, where the phage decides between the lytic and lysogenic pathways. Although traditionally thought to be mutually exclusive, increasing evidence suggests that this lysis-lysogeny decision is more complex than once believed, but exploring its intricacies requires an improved resolution of study. Here, with a newly developed fluorescent reporter system labeling single phage and E. coli DNAs, these two distinct pathways can be visualized by following the DNA movements in vivo. Surprisingly, we frequently observed an interesting "lyso-lysis" phenomenon in lytic cells, where phage integrates its DNA into the host, a characteristic event of the lysogenic pathway, followed by cell lysis. Furthermore, the frequency of lyso-lysis increases with the number of infecting phages, and specifically, with CII activity. Moreover, in lytic cells, the integration site attB on the E. coli genome migrates toward the polar region over time, leading to more spatial overlap with the phage DNA and frequent colocalization/collision of attB and phage DNA, possibly contributing to a higher chance for DNA integration.

SeqA-mediated stimulation of a promoter activity by facilitating functions of a transcription activator

It was demonstrated recently that the SeqA protein, a main negative regulator of Escherichia coli chromosome replication initiation, is also a specific transcription factor. SeqA specifically activates the bacteriophage lambda pR promoter while revealing no significant effect on the activity of another lambda promoter, pL. Here, we demonstrate that lysogenization by bacteriophage lambda is impaired in E. coli seqA mutants. Genetic analysis demonstrated that CII-mediated activation of the phage pI and paQ promoters, which are required for efficient lysogenization, is less efficient in the absence of seqA function. This was confirmed in in vitro transcription assays. Interestingly, SeqA stimulated CII-dependent transcription from pI and paQ when it was added to the reaction mixture before CII, although having little effect if added after a preincubation of CII with the DNA template. This SeqA-mediated stimulation was absolutely dependent on DNA methylation, as no effects of this protein were observed when using unmethylated DNA templates. Also, no effects of SeqA on transcription from pI and paQ were observed in the absence of CII. Binding of SeqA to templates containing the tested promoters occurs at GATC sequences located downstream of promoters, as revealed by electron microscopic studies. In contrast to pI and paQ, the activity of the third CII-dependent promoter, pE, devoid of neighbouring downstream GATC sequences, was not affected by SeqA both in vivo and in vitro. We conclude that SeqA stimulates transcription from pI and paQ promoters in co-operation with CII by facilitating functions of this transcription activator, most probably by allowing more efficient binding of CII to the promoter region.

The phage lambda CII transcriptional activator carries a C-terminal domain signaling for rapid proteolysis

ATP-dependent proteases, like FtsH (HflB), recognize specific protein substrates. One of these is the lambda CII protein, which plays a key role in the phage lysis-lysogeny decision. Here we provide evidence that the conserved C-terminal end of CII acts as a necessary and sufficient cis-acting target for rapid proteolysis. Deletions of this conserved tag, or a mutation that confers two aspartic residues at its C terminus do not affect the structure or activity of CII. However, the mutations abrogate CII degradation by FtsH. We have established an in vitro assay for the lambda CIII protein and demonstrated that CIII directly inhibits proteolysis by FtsH to protect CII and CII mutants from degradation. Phage lambda carrying mutations in the C terminus of CII show increased frequency of lysogenization, which indicates that this segment of CII may itself be sensitive to regulation that affects the lysis-lysogeny development. In addition, the region coding for the C-terminal end of CII overlaps with a gene that encodes a small antisense RNA called OOP. We show that deletion of the end of the cII gene can prevent OOP RNA, supplied in trans, interfering with CII activity. These findings provide an example of a gene that carries a region that modulates stability at the level of mRNA and protein.

Polyadenylation of oop RNA in the regulation of bacteriophage lambda development

We have shown that Escherichia coli pcnB mutants are lysogenized by bacteriophage lambda with lower efficiency as compared to the pcnB+ strains. Our genetic analysis revealed that expression of the lambda cII gene is decreased in the pcnB mutants. However, using various lacZ fusions we demonstrated that neither activities of pL and pR promoters nor transcription termination at tR1 were significantly impaired in the pcnB- host. On the other hand, we found that oop RNA, an antisense RNA for cII expression, is involved in this regulation. Primer protection experiments revealed that oop RNA was polyadenylated and that this polyadenylation was impaired in the pcnB mutant. We found that the oop RNA was more abundant in the pcnB mutant than in the pcnB+ strain. Furthermore, we showed that activity of the pO promoter was not stimulated in the pcnB mutant. Such findings indicated that degradation of oop RNA in the pcnB strain was slower because of inefficient polyadenylation, which could lead to more effective inhibition of cII expression by the antisense oop RNA, resulting in less efficient lysogenization of the host. The oop RNA was found previously to play a role in phage lambda development only under conditions of overproduction of this transcript. Here we demonstrate for the first time, the physiological function of oop RNA in lambda development, confirming that this short transcript plays an important role in the negative regulation of cII gene expression during lambda infection. Moreover, polyadenylation of oop RNA is one of very few known examples of specific RNA polyadenylation by PAP I in prokaryotic cells and its role in gene expression regulation.

The Cro-like Apl repressor of coliphage 186 is required for prophage excision and binds near the phage attachment site

The Apl protein of the temperature coliphage 186 represses transcription of the immunity repressor gene and down-regulates lytic transcription. It is shown here that an apl- mutant is competent for lytic development and establishes lysogeny normally but is defective in excision of the prophage. The Apl protein binds between the lytic and lysogenic promoters and also near the phage attachment site, suggesting that its role in excision is direct. Apl thus appears to act as an excisionase as well as a repressor. The pattern of Apl-induced DNase I enhancements indicates that the DNA is bent by Apl. Potential Apl recognition sequences are identified; these sequences are directly repeated several times across each binding region and are spaced 10 or 11 bases apart, suggesting that Apl binds to one face of the DNA helix.

Cell growth and lambda phage development controlled by the same essential Escherichia coli gene, ftsH/hflB

The lambda phage choice between lysis and lysogeny is influenced by certain host functions in Escherichia coli. We found that the frequency of lambda lysogenization is markedly increased in the ftsH1 temperature-sensitive mutant. The ftsH gene, previously shown to code for an essential inner membrane protein with putative ATPase activity, is identical to hflB, a gene involved in the stability of the phage cII activator protein. The lysogenic decision controlled by FtsH/HflB is independent of that controlled by the protease HflA. Overproduction of FtsH/HflB suppresses the high frequency of lysogenization in an hflA null mutant. The FtsH/HflB protein, which stimulates cII degradation, may be a component of an HflA-independent proteolytic pathway, or it may act as a chaperone, maintaining cII in a conformation subject to proteolysis via such a pathway. Suppressor mutations of ftsH1 temperature-sensitive lethality, located in the fur gene (coding for the ferric uptake regulator), did not restore FtsH/HflB activity with respect to lambda lysogenization.

Isolation, characterization, and sequence of an Escherichia coli heat shock gene, htpX

We isolated and characterized a new Escherichia coli gene, htpX. The htpX gene has been localized at min 40.3 on the chromosome. We determined its transcription and translation start site. htpX expresses a 32-kDa protein from a monocistronic transcript; expression of this protein is induced by temperature upshift. htpX is expressed from a sigma 32-dependent promoter and is thus part of the heat shock regulon. Cells carrying a htpX gene disruption grow well at all temperatures and under all conditions tested and have no apparent phenotype. However, cells which overexpress a truncated form of the protein display a higher rate of degradation of puromycyl peptides.

Cleavage of the cII protein of phage lambda by purified HflA protease: control of the switch between lysis and lysogeny

The activity of the cII protein of phage lambda is probably the critical controlling factor in the choice of the lytic or lysogenic pathway by an infecting virus. Previous work has established that cII activity is regulated through the turnover of cII protein; the products of the hflA and hflB loci of Escherichia coli are needed for a degradative reaction, and lambda cIII functions in stabilizing cII. By using the cloned hflA locus, we have purified a cII-cleaving enzyme that we term HflA. Purified HflA contains three polypeptides; at least two of the subunits are products of the hflA region, and the third is probably a cleavage product of the larger of these two hflA-encoded polypeptides. The HflA protease activity cleaves cII to small fragments. We conclude that the switch between lambda developmental pathways involves regulated cleavage of cII by the specific protease HflA.

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.

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.

Identification of polypeptides encoded by an Escherichia coli locus (hflA) that governs the lysis-lysogeny decision of bacteriophage lambda

We report the cloning of the Escherichia coli hflA locus, which governs stability of phage lambda cII protein and which has been proposed to encode or regulate a cII-specific protease. The hflA locus was cloned on an 18-kilobase DNA fragment by selecting for plasmids that carry the neighboring purA gene. The boundaries of hflA were delimited by analysis of deletions and insertions constructed in vitro and by use of transposon Tn1000. Maxicell analysis of the proteins encoded by the hflA-containing fragment shows that hflA consists of at least two nonoverlapping genes, hflC and hflK, encoding polypeptides of 37,000 (C) and 46,000 (K) daltons. We observe that insertions into one gene eliminate the corresponding polypeptide and greatly reduce synthesis of the other. We suggest that these two polypeptides (K and C) interact to form a multimeric complex and that free subunits are unstable. We have constructed two types of fusions between hflA and lacZ. One is an hflC-lacZ protein fusion constructed in vitro; the other is an hfl-lacZ operon fusion in which a Mu dX(Apr lac) has inserted into the hflK gene. We have used the operon fusion to infer the direction of transcription of the hflK gene--toward hflC and in the same direction as hflC. Last, we describe evidence that hflA contains an additional gene, hflX, encoding a 50,000-dalton polypeptide.

hflB, a new Escherichia coli locus regulating lysogeny and the level of bacteriophage lambda cII protein

The level of the viral cII protein has been proposed to be the crucial determinant in the lysis-lysogeny decision of bacteriophage lambda. A new Escherichia coli locus (hflB) has been identified in which a mutation (hflB29) leads to high frequency of lysogeny by lambda. A double mutant defective in both hflB and the previously identified hflA gene displays a more severe Hfl- phenotype than either single mutant. The hflB locus is at 69 minutes on the E. coli map, 85% co-transducible with argG. The hflB29 mutation results in increased stability of the phage cII protein (increasing its half-life twofold) and is recessive to hflB+. We conclude that the hflB+ locus is a negative regulator of cII, perhaps coding for or regulating a protease that acts on cII. In addition, we observe that the can1 mutation, an alteration of the cII gene that results in enhanced lysogenization, leads to increased stability of cII protein. These observations reinforce the view that the level of cII is a key factor in the lysis-lysogeny decision of lambda.

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.

Studies on polylysogens containing lambda N-cI- prophages. II. Role of high multiplicities in lysogen formation by lambda N-cI- phage

Results of the experiments presented in this paper show that lambda N-cI- phage can lysogenize a nonpermissive host Escherichia coli when it infects at very high multiplicities (around 100), and lambda N-cI-cII- and lambda cIII-N-cI- lysogenize poorly at similar high multiplicities. The latter two phages lysogenize with appreciable frequency when either lambda N-cI- or lambda int-cN-cI-cII- is used as helper. The phages, lambda N-cI-, lambda N-cI-cII-, and lambda cIII-N-cI- can lysogenize also at relatively low m.o.i. of 20 in presence of the above lambda int-c helper, and the lambda int-cN-cI-cII- phage alone forms converted lysogens at an m.o.i. as low as 12. All these results suggest that the establishment of prophage integration by lambda N-cI- is positively regulated, like lambda N+cI+ phage, by the cII/cIII-promoted expression of the int gene of lambda, and under the N- condition, high multiplicities are needed to provide optimum levels of cII and cIII products, especially the latter.

Control of phage lambda development by stability and synthesis of cII protein: role of the viral cIII and host hflA, himA and himD genes

The cII protein of bacteriophage lambda has a decisive role in the regulatory switch between the lysogenic and lytic pathways of viral development. Recent work has indicated that cII may be the primary control function providing for the initial partition between the two pathways, with other host and viral regulatory genes acting to determine the levels of cII in an infected cell. We have studied the synthesis and stability of cII protein with two experimental systems, phage infection and a cII-producing plasmid. We have found that the stability of cII is controlled by the host hflA and viral cIII genes; hflA protein facilitates degradation of cII, whereas cIII protects cII. The synthesis of cII appears to be under the positive control of the host himA and himD genes. We conclude that posttranscriptional regulation of cII by host and viral genes is critical for the choice of a developmental pathway.

Probing cII and himA action at the integrase promoter pi of bacteriophage lambda

Plasmids were constructed to supply cII-coded protein for activation of the phage promoter pI. Using a fusion which expresses lacZ from pI. We can accurately follow activation of pI without having to assay int activity in vivo. A large excess of cII protein compared to a normal lytic infection stimulates lacZ expression about 10-fold over the basal level. The int-c226 constitutive allele of pI is not further activated by cII even though its level of lacZ expression is less than the maximal cII-activated expression from wild type pI. A himA-deleted strain also shows activation, demonstrating that there is no absolute requirement for the himA gene product for cII-stimulated transcription at pI.

Multilevel regulation of bacteriophage lambda lysogeny by the E. coli himA gene

Previous experiments have shown that the himA gene of E. coli specifies a protein that is required for bacteriophage lambda integration. lambda Forms clear plaques on himA mutants indicating a possible additional defect in the establishment of repression. We have tested the effects of a himA mutation on the establishment and maintenance of lambda repressor (cl) synthesis and on the synthesis of Int protein. The rate of synthesis of cl and Int after infection by lambda is severely reduced in a strain carrying a himA gene deletion. Synthesis of Int or repressor can occur in the himA- strain if the phage carry constitutive promoters for either the int gene or the cl gene. Maintenance of repression is unaffected by himA mutations as judged by repressor-stimulated transcription of PM fused to the lacZ gene. These results indicate that the himA gene participates in the regulation of the promoter sites specific of the establishment of lysogeny: PE for cl synthesis and PI, for Int production. Since the himA gene product is required also for lambda site-specific recombination, it appears that the himA gene regulates lambda lysogeny at several levels. I discuss the significance of this multilevel regulation to lambda development.

Promoter for the establishment of repressor synthesis in bacteriophage lambda

Transcription of the lambda repressor gene (cI) is positively regulated by the phage-encoded proteins cII and cIII. We have isolated and characterized the 5'-terminal region of this RNA and shown that it originates at a promoter (pE) located between genes cro and cII. The DNA sequence of this promoter shows little homology to other known promoters. Initiation of transcription from PE is abolished by the cis-dominant mutations cY; these mutations alter the "-10" and "-35" regions of the promoter. We propose that the "-35" region is the site of activation of PE, possibly via the direct interaction of protein cII.

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.