Role of the cro gene in bacteriophage lambda development

Bacteriophage λ RexA and RexB Functions Assist the Transition from Lysogeny to Lytic Growth

The CI and Cro repressors of bacteriophage λ create a bistable switch between lysogenic and lytic growth. In λ lysogens, CI repressor expressed from the P_RM promoter blocks expression of the lytic promoters P_L and P_R to allow stable maintenance of the lysogenic state. When lysogens are induced, CI repressor is inactivated and Cro repressor is expressed from the lytic P_R promoter. Cro repressor blocks P_RM transcription and CI repressor synthesis to ensure that the lytic state proceeds. RexA and RexB proteins, like CI, are expressed from the P_RM promoter in λ lysogens; RexB is also expressed from a second promoter, P_LIT , embedded in rexA. Here we show that RexA binds CI repressor and assists the transition from lysogenic to lytic growth, using both intact lysogens and defective prophages with reporter genes under control of the lytic P_L and P_R promoters. Once lytic growth begins, if the bistable switch does return to the immune state, RexA expression lessens the probability that it will remain there, thus stabilizing the lytic state and activation of the lytic P_L  and P_R  promoters. RexB modulates the effect of RexA and may also help establish phage DNA replication as lytic growth ensues.

Extreme divergence between one-to-one orthologs: the structure of N15 Cro bound to operator DNA and its relationship to the λ Cro complex

The gene cro promotes lytic growth of phages through binding of Cro protein dimers to regulatory DNA sites. Most Cro proteins are one-to-one orthologs, yet their sequence, structure and binding site sequences are quite divergent across lambdoid phages. We report the cocrystal structure of bacteriophage N15 Cro with a symmetric consensus site. We contrast this complex with an orthologous structure from phage λ, which has a dissimilar binding site sequence and a Cro protein that is highly divergent in sequence, dimerization interface and protein fold. The N15 Cro complex has less DNA bending and smaller DNA-induced changes in protein structure. N15 Cro makes fewer direct contacts and hydrogen bonds to bases, relying mostly on water-mediated and Van der Waals contacts to recognize the sequence. The recognition helices of N15 Cro and λ Cro make mostly nonhomologous and nonanalogous contacts. Interface alignment scores show that half-site binding geometries of N15 Cro and λ Cro are less similar to each other than to distantly related CI repressors. Despite this divergence, the Cro family shows several code-like protein–DNA sequence covariations. In some cases, orthologous genes can achieve a similar biological function using very different specific molecular interactions.

Multistep mutational transformation of a protein fold through structural intermediates

New protein folds may evolve from existing folds through metamorphic evolution involving a dramatic switch in structure. To mimic pathways by which amino acid sequence changes could induce a change in fold, we designed two folded hybrids of Xfaso 1 and Pfl 6, a pair of homologous Cro protein sequences with ~40% identity but different folds (all-α vs. α + β, respectively). Each hybrid, XPH1 or XPH2, is 85% identical in sequence to its parent, Xfaso 1 or Pfl 6, respectively; 55% identical to its noncognate parent; and ~70% identical to the other hybrid. XPH1 and XPH2 also feature a designed hybrid chameleon sequence corresponding to the C-terminal region, which switched from α-helical to β-sheet structure during Cro evolution. We report solution nuclear magnetic resonance (NMR) structures of XPH1 and XPH2 at 0.3 Å and 0.5 Å backbone root mean square deviation (RMSD), respectively. XPH1 retains a global fold generally similar to Xfaso 1, and XPH2 retains a fold similar to Pfl 6, as measured by TM-align scores (~0.7), DALI Z-scores (7-9), and backbone RMSD (2-3 Å RMSD for the most ordered regions). However, these scores also indicate significant deviations in structure. Most notably, XPH1 and XPH2 have different, and intermediate, secondary structure content relative to Xfaso 1 and Pfl 6. The multistep progression in sequence, from Xfaso 1 to XPH1 to XPH2 to Pfl 6, thus involves both abrupt and gradual changes in folding pattern. The plasticity of some protein folds may allow for "polymetamorphic" evolution through intermediate structures.

Role of the lytic repressor in prophage induction of phage lambda as analyzed by a module-replacement approach

Using a module exchange approach, we have tested a long-standing model for the role of Cro repressor in lambda prophage induction. This epigenetic switch from lysogeny to the lytic state occurs on activation of the host SOS system, which leads to specific cleavage of CI repressor. It has been proposed that Cro repressor, which operates during lytic growth and which we shall term the lytic repressor, is crucial to prophage induction. In this view, Cro binds to the O(R)3 operator, thereby repressing the cI gene and making the switch irreversible. Here we tested this model by replacing lambda Cro with a dimeric form of Lac repressor and adding several lac operators. This approach allowed us to regulate the function of the lytic repressor at will and to prevent it from repressing cI, because lac repressor could not repress P(RM) in our constructs. Repression of cI by the lytic repressor was not required for prophage induction to occur. However, our evidence suggests that this binding can make induction more efficient, particularly at intermediate levels of DNA damage that otherwise cause induction of only a fraction of the population. These results indicate that this strategy of module exchange will have broad applications for analysis of gene regulatory circuits.

Interactions between Escherichia coli RNA polymerase and lambda repressor. Mutations in PRM affect repression of PR

The rightward operator, OR, of bacteriophage lambda is part of a complex regulatory region that includes PRM, the promoter for repressor synthesis by a prophage, the rightward early promoter PR, and three repressor-binding sites, OR1, OR2 and OR3. By binding to OR2, repressor blocks transcription from PR and simultaneously stimulates the formation of open complexes between RNA polymerase and PRM. In this letter, we describe a test of the hypothesis that the interaction between RNA polymerase bound at PRM and repressor bound at OR2 increases the apparent affinity of repressor for OR. One implication of this hypothesis is that the amount of repressor required for repression of PR should be inversely correlated with PRM promoter strength. This is indeed the case. The amount of repressor required for 50% repression of PR is decreased by prmup-1, an "up" mutation of PRM, and is increased by prm- mutations. An unexpected finding is that in addition to their effect on the apparent affinity of repressor for OR, mutations in the -35 region of PRM alter the shape of repressor-titration curves. We propose that these mutations alter the interaction between RNA polymerase bound at PRM and repressor bound at OR2 in such a way that cooperativity in the binding of repressor to OR1 and OR2 is also disrupted.

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.

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.

Repression of ant synthesis early in the lytic cycle of phage P22

Using SDS-polyacrylamide gel electrophoresis to study the early expression of P22 genes we show that early expression of the ant-gene (imm I region) is turned off after 6-8 min, independent of the 'late' acting mnt-repressor. A semi-clear mutant called cir5 is defective for this early ant turn-off. The mutation cir5 maps in the imm I region of P22 between genes mnt and ant. P22 cir5 mutants are defective for a repressor which acts in trans to regulate early ant synthesis. There appears to be no absolute requirement of the cir5 allele for the establishment of lysogeny. The overproduction of ant in the P22 cir5 mutant leads to a marked increase in abortive infections, killing the infected cells. The cir5-phenotype can be suppressed by an ant- mutation.

The phage promoter responsible for the expression of the inserted beta-galactosidase gene in bacteriophage lambda plac5

The lac transducing phage, lambda plac5, carries a segment of the E. coli lac operon on the left side of the b2 region of the lambda phage. In the absence of additional cyclic AMP, beta-galactosidase can only be expressed from the phage promoter, and the expression of the inserted lac promoter is suppressed. This phage promoter responsible for beta-galactosidase synthesis is shown to be under the control of the cI and N gene products; however, the repressive action of the cro gene product at high multiplicity of infection is not observed although some turn off at very late time is detected. To pin down this phage promoter, results described in this communication and those described elsewhere can rule out the promoter PI, PR, P'R, and the promoter PL also looks rather unlikely. No firm identification of this phage promoter has been made, but the promoter(s) in the b2 region (the b2 promoter) is proposed. The phage promoter responsible for beta-galacrosidase synthesis is shown to be a weak promoter, requires the Q gene product or one (or more) of the late gene products for activation, and the time of expression is very late.

Nucleotide sequence of the operators of lambda ultravirulent mutants

The nucleotide sequence of the operators of ultravirulent mutants of lambda, able to grow on host cells with elevated repressor levels, was determined. It appears that ultravirulence in lambda requires multiple mutational events at the operator sequences. OL1, OL2, and OL3 operator sites are the target of mutational changes in ultravirulent phages indicating that these sites participate in vivo in repression of the PL promoter. No changes were found in the OR3 sequence, in contrast there is a mutation in OR2 and two mutations in OR1, in both lambda 668 and lambda 2668 phages. This mutated operator structure accounts for the constitutive expression of their PR promoter either in cells overproducing the lambda repressor or in cells overproducing the cro gene product. A model of the structure of the lambda operator site is proposed. The nucleotide sequence in each site can be divided into two functionally different subsets, one of which is recognized by the repressor while the other stabilizes the repressor-operator interaction.

In vitro insertion of the lambda attachment site into the plasmid RP4

The region of the phage lambda chromosome containing the attachment site (P.P') and the genes int and xis, excised by the action of endonuclease R.EcoRI, has been inserted into the unique site for that enzyme on the promiscuous conjugative plasmid, RP4, generating the recombinant plasmid RP4att lambda. Transformants containing the hybrid plasmid were recognised by their ability to allow efficient lysogenization by phage lambda b2 (Weil and Signer, 1968; Echols et al., 1968) containing the mutant attachment site delta. P'. The construction and properties of the hybrid plasmid RP4att lambda are described.

Introduction of bacteriophage lambda into cells of Klebsiella aerogenes

We have shown that a mutation in the cro gene of phage lambda greatly reduces zygotic induction. This observation has allowed us to move this phage on an episome into cells of Klebsiella aerogenes where it grows as well as in cells of Escherichia coli. This technique should allow the introduction of various derivatives of lambda into any organism which is able to receive deoxyribonucleic acid from E. coli.

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.

Anomalous behavior of bacteriophage lambda polypeptides in polyacrylamide gels: resolution, identification, and control of the lambda rex gene product

The resolution of lambia proteins was compared on the two types of sodium dodecyl sulfate-polyacrylamide gels commonly in use. The two kinds of gel differ essentially in the ratio of the cross-linker, N'-N-bismethylene-acrylamide (bisacrylamide), to acrylamide monomer. Several lambda proteins migrate relatively more slowly in gels with high bisacrylamide/acrylamide ratios (HB gels) than in gels with low ratios, although the two types of gel are of roughly equivalent porosity. This effect is illustrated by a change in relative position of both the Rex and Int proteins, with apparent increases in molecular weight of about 8 and 15%, respectively, in the HB gels. This work confirms that like repressor and Int, the 28.5-kilodalton protein, identified as Rex on HB gels, is postively regulated by the lambdacII and cIII products and negatively controlled Cro. An intact y site is required for Rex and repressor expression after infection, whereas their synthesis in a lysogen is dependent upon a functional maintenance promoter, Prm.

Repressor and int synthesis of bacteriophage lambda in the E. coli host mutant ER437

Analysis of lambda phage infection of the host mutant ER437 by SDS polyacrylamide gel electrophoresis and autoradiography has revealed altered expression of repressor and integration function (Int). We show that in this host Int as well as repressor synthesis is not dependent upon the lambdacIII gene product in the usual manner, nor is their synthesis turned off in the normal way.

A complex control circuit. Regulation of immunity in temperate bacteriophages

Temperate bacteriophages can display in a stable way two essentially different behaviours. In the immune state, a gene (cI) produces a repressor which prevents expression of all the other viral genes; in the non-immune state the typically viral functions are expressed. The choice between the two pathways and the establishment of one of them have much in common with cell determination and differentiation. This choice depends on a complex control system, in fact one of the most intricate nets of regulation known in some detail. Our paper provides a formal description and partial analysis of this regulatory net. It is shown that even for relatively simple known models, this kind of analysis uncovers predictions which had previously remained hidden. Some of these predictions were checked experimentally. The experimental part chiefly deals with the efficiency of lysogenization by thermoinducible lambda phage carrying mutations in one or more of the regulatory genes, N, cro and cII. Although N- mutations are widely known for preventing efficient integration, and both N- and cII mutations for preventing efficient establishment of immunity, it is shown that, as predicted by a simple model, both N- and cII- phage efficiently lysogenize at low temperature if they are in addition cro-. In contrast with lambda N- cro+, lambda N- cro- is not propagated as a plasmid at low temperature, precisely because it establishes immunity too efficiently. Genetic control circuits are described in terms of sets of logic equations, which relate the state of expression of genes or of chemical reactions (functions) to input (genetic and environmental) variables and to the presence of gene and reaction products (internal, or memorization varibles). From the set of equations, one derives a matrix which shows the stable stationary states (if any) of the system, and from which one can derive the pathways (temporal sequences of states) consistent with the model. This kind of analysis is complementary to the more widely used analysis based on differential equations; it allows one to analyze in less detail more complex systems. The language might be used as well, mutatis mutandis, in fields very different from genetics. The last part of the discussion deals with the role of positive feedback loops in our specific problem (establishment and maintenance of immunity in temperate bacteriophages) and in developmental genetics in general. As a generalization of an old idea, it is suggested that cell determination (for a given character) depends on a set of genes whose interaction constitutes a positive feedback loop. Such a system has two stable stationary states: which one is chosen will usually depend on additional controls grafted on the loop.

The use of specialised transducing phages in the amplification of enzyme production

Two types of lambdatrp phages have been used as model systems to investigate ways of optimising the expression of bacterial genes from transducing phage genomes. Excellent yields of trp enzymes were achieved by infecting a trpR- host with Q- or Q-S- derivatives of lambdatrpAM1, which expresses its trp genese exclusively from the trp promoter. The five trp geneproducts constituted more than 50% of the total soluble protein of infected cells under these conditions, and an even higher proportion of the protein synthesized after infection. In a trpR+ host, phage DNA replication was easily able to override tryptophan-mediated repression by titration of the trp promoter were equally productive, while having the advantage of being much simpler to construct and propagate. lambdatrp phages lacking the trp promoter were used to investigate ways of optimising gene expression initiated at the phage promoter, PL. Though very powerful, the latter promoter is more difficult to harness then the trp promoter. Derepression of transcription from PL by the use of cro- mutations is accompanied by poor replication of transducing phage DNA. Attempts to circumvent this difficulty using virulent of cro,cII double mutants have not been successful. Nevertheless, cells infected with a lambdatrp phage expressing its trp genes exclusively from PL made up to 16 per cent of their protein as trp gene-products.

Second-site mutations in capR (lon) strains of Escherichia coli K-12 that prevent radiation sensitivity and allow bacteriophage lambda to lysogenize

capR (lon) mutants of Escherichia coli K-12 are mucoid and sensitive to ultraviolet (UV) and X-ray radiation as well as to nitrofurantoin. The mutants form filaments after exposure to these agents. capR mutants are also conditionally lethal since they die when plated on complex medium even without UV treatment; this phenomenon is designated "complex medium-induced killing". Furthermore, capR mutants are poorly lysogenized by bacteriophage lambda. Second-site revertants were isolated by plating on media containing nitrofurantoin. All 17 of the independent revertants studied were still mucoid but resistant to UV radiation. Sixteen of the 17 revertants contained a mutation, sulA, that cotransduced with pyrD (21 min). A second locus, sulB, was also found that cotransduced with leu (2 min). Studies with partial diploids (F'pyrD+ sulA+/pyrD36 sulA17 capR9 (lon) demonstrated that sulA+ is dominant to sulA; thus the indicated partial diploid is UV sensitive, whereas the haploid parent is UV resistant. Furthermore, two other phenotypic traits of capR (lon) mutants were reversed by the sul mutation:complex medium-induced killing and the inability of lambda phage to efficiently lysogenize capR strains. On the basis of these and other results, the following model is suggested to explain capR (lon) and sul gene interactions. capR (lon) is a regulator gene for the structural genes sulA+ and sulB+. Depression of both sul operons results in UV sensitivity and decreased ability of lambda to lysogenize, whereas inactivation of either sul+ protein by mutation to sul prevents these phenomena.

Escape synthesis of D-serine deaminase in lambda dsdC integration lysogens

Heat shock of lysogens that contain lambda thermosensitive repressor mutants integrated into the dsdC gene results in escape synthesis of d-serine deaminase at a high differential rate.

Control of cI gene expression in bacteriophage lambda imm434, studied in an immunity/trp fusion made in vitro

The trp genes of a lambda imm434 trp-transducing phage have been fused to the immunity region by deletion, in vitro, of the DNA between two targets for the restriction enzyme R.EcoRI. The resulting phage has been used to study the control of expression of the cI gene in vivo. The constitutive rate of expression of the cI gene is between 2 and 5% of the maximally stimulated rate. The products of the cII and cIII genes enhance expression of cI on infection of a sensitive host. The requirement for the cII product is more stringent than that for the cIII protein. The phage 434 repressor present in a 434-immune cell stimulates the rate of cI expression from a superinfecting homoimmune phage about fifteen-fold. This result strongly suggests that repressor stimulates its own synthesis by a direct effect on transcription of the cI gene.

4S oop RNA is a leader sequence for the immunity-establishment transcription in coliphage lambda

oop RNA, which is initiated at the po promoter and is 81 nucleotides long, can function as a leader sequence for the lambda immunity establishment transcription, previously believed to originate at a special promoter pre located in the y region. Thus, oop RNA seems to have a dual role, either favouring the lytic cycle as a primer for the initiation of lambda DNA replication, or leading to the establishment of lysogeny when elongated into the imm transcript, which directs synthesis of the repressor.

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.

A bacterial RNA polymerase mutant that renders lambda growth independent of the N and cro functions at 42 degrees C

We describe a bacterial RNA polymerase mutation, rif 501, which confers rifampicin resistance and thermosensitivity to E. coli K 12. The purified RNA polymerase enzyme from rif 501 bacteria shows increased heatsensitivity in vitro at 51 degrees C. However, in vivo, at 42 degrees C the non-permissive temperature, mutant bacteria continue to grow and to synthesize RNA for 90 min. On a lawn of the mutant bacteria, at 40-41 degrees C, phage lambda forms clear plaques (LycA phenotype); this is probably due to an enhancement of cro function; we surmise that at 42 degrees C the transcription originating from the pR (but not from the pL) promoter on the lamdba genome becomes N-independent and less sensitive to the absence of the cro product. We discuss the possibility that both the N and cro proteins of phage lambda interact directly with the bacterial RNA polymerase. These observations indicate that the loss of viability of the rif 501 mutant at the restrictive temperature is not a consequence of an immediate inactivation of RNA polymerase; rather we feel it is due to a modification of the activity of RNA polymerase, leading to a disruption of the cellular regulation.

The depression of endolysin synthesis in bacteria infected with high multiplicities of phage lambda

The effect of multiplicity of infection was studied in Escherichia coli with lambda phage, using phage endolysin as an example of a late gene product. A very sensitive endolysin assay method was used so that the initiation time of endolysin synthesis could be more accurately determined. It was observed that high multiplicity of infection (1) increases the rate of lysogenization, (2) progressively delays lysis time, and (3) significantly delays and reduces the synthesis of endolysin in lamdacIII+ cII+ -infected cells. The extent of delay and reduction in endolysin synthesis increases with increasing multiplicity. In contrast, lamdacIII67cII68-infected cells show no delay in endolysin synthesis at high multiplicity of infection when compared with the lamdacIII+ cII+ -infected cells. The results suggest that (1) the expression of cIII and cII genes is multiplicity dependent, (2) high multiplicity of infection enhances the expression of the cIII and cII genes, and (3) the expression of the cIII and cII genes interferes with the expression of the late genes. A model to explain how the expression of the cIII and cII genes interferes with the expression of the late genes is proposed.

Role of the tof gene in the production and perpetuation of the lambdadv plasmid

A series of lambda derivatives carrying tof mutations were tested for their ability to give rise to plasmid lambda dv. Phages carrying tof mutations that distorted expression of the pRoR-tof-OP operon, were unable to produce lambda dv. Phages carrying an altered tof gene, having only a moderate effect on the same operon, produced unstable lambdadv's. On the other hand, those tof mutants were only the expression of the pLoL-N-exo operon, but not that of the pRoR-tof-OP operon was affected, produced stable lambdadv's.