DNA replication of phage T4 rII mutants without polynucleotide ligase (gene 30)

Study of Ren, RexA, and RexB Functions Provides Insight Into the Complex Interaction Between Bacteriophage λ and Its Host, Escherichia coli

The phage λ rexA and rexB genes are expressed from the P RM promoter in λ lysogens along with the cI repressor gene. RexB is also expressed from a second promoter, P LIT, embedded in rexA. The combined expression of rexA and rexB causes Escherichia coli to be more ultraviolet (UV) sensitive. Sensitivity is further increased when RexB levels are reduced by a defect in the P LIT promoter, thus the degree of sensitivity can be modulated by the ratio of RexA/RexB. Expression of the phage λ ren gene rescues this host UV sensitive phenotype; Ren also rescues an aberrant lysis phenotype caused by RexA and RexB. We screened an E. coli two-hybrid library to identify bacterial proteins with which each of these phage proteins physically interact. The results extend previous observations concerning λ Rex exclusion and show the importance of E. coli electron transport and sulfur assimilation pathways for the phage.

The roles of the bacteriophage T4 r genes in lysis inhibition and fine-structure genetics: a new perspective

Seldom has the study of a set of genes contributed more to our understanding of molecular genetics than has the characterization of the rapid-lysis genes of bacteriophage T4. For example, T4 rII mutants were used to define gene structure and mutagen effects at the molecular level and to help unravel the genetic code. The large-plaque morphology of these mutants reflects a block in expressing lysis inhibition (LIN), the ability to delay lysis for several hours in response to sensing external related phages attacking the cell, which is a unique and highly adaptive attribute of the T4 family of phages. However, surprisingly little is known about the mechanism of LIN, or how the various r genes affect its expression. Here, we review the extensive old literature about the r genes and the lysis process and try to sort out the major players affecting lysis inhibition. We confirm that superinfection can induce lysis inhibition even while infected cells are lysing, suggesting that the signal response is virtually instantaneous and thus probably the result of post-translational regulation. We identify the rI gene as ORF tk.-2, based on sequence analysis of canonical rI mutants. The rI gene encodes a peptide of 97 amino acids (Mr = 11.1 kD; pI = 4.8) that probably is secreted into the periplasmic space. This gene is widely conserved among T-even phage. We then present a model for LIN, postulating that rI is largely responsible for regulating the gpt holin protein in response to superinfection. The evidence suggests that the rIIA and B genes are not directly involved in lysis inhibition; rather, when they are absent, an alternate pathway for lysis develops which depends on the presence of genes from any of several possible prophages and is not sensitive to lysis inhibition.

Impaired expression of certain prereplicative bacteriophage T4 genes explains impaired T4 DNA synthesis in Escherichia coli rho (nusD) mutants

The Escherichia coli rho 026 mutation that alters the transcription termination protein Rho prevents growth of wild-type bacteriophage T4. Among the consequences of this mutation are delayed and reduced T4 DNA replication. We show that these defects can be explained by defective synthesis of certain T4 replication-recombination proteins. Expression of T4 gene 41 (DNA helicase/primase) is drastically reduced, and expression of T4 genes 43 (DNA polymerase), 30 (DNA ligase), 46 (recombination nuclease), and probably 44 (DNA polymerase-associated ATPase) is reduced to a lesser extent. The compensating T4 mutation goF1 partially restores the synthesis of these proteins and, concomitantly, the synthesis of T4 DNA in the E. coli rho mutant. From analyzing DNA synthesis in wild-type and various multiply mutant T4 strains, we infer that defective or reduced synthesis of these proteins in rho 026-infected cells has several major effects on DNA replication. It impairs lagging-strand synthesis during the primary mode of DNA replication; it delays and depresses recombination-dependent (secondary mode) initiation; and it inhibits the use of tertiary origins. All three T4 genes whose expression is reduced in rho 026 cells and whose upstream sequences are known have a palindrome containing a CUUCGG sequence between the promoter(s) and ribosome-binding site. We speculate that these palindromes might be important for factor-dependent transcription termination-antitermination during normal T4 development. Our results are consistent with previous proposals that the altered Rho factor of rho 026 may cause excessive termination because the transcription complex does not interact normally with a T4 antiterminator encoded by the wild-type goF gene and that the T4 goF1 mutation restores this interaction.

Sequences and studies of bacteriophage T4 rII mutants

We have sequenced more than 80 mutants of the bacteriophage T4 rIIA and rIIB genes. These include deletions about whose origin we have speculated, mutations affecting the rIIB promoters, various pseudo-revertants of the rII- phenotype, including mutations that bring about the reinitiation of translation following termination, mutations that affect regulation of rIIB translation by regA, the toxic minute plaquing mutants FC237 and FC238 and their detoxifiers, and many more of the classic frameshifts from the Cambridge collection. These mutants have been sequenced using dideoxy-mediated chain termination by either Escherichia coli DNA polymerase using single-stranded DNA as a template or by avian retroviral reverse transcriptase using mRNA or DNA as the template molecule. We list the sequence changes of the mutants with pertinent historic and phenotypic data. The mutants that facilitate translation reinitiation are discussed, and we discuss a model that could account for the generation of many of the mutations.

Bacteriophage T4 as a generalized DNA-cloning vehicle

We have designed a method for inserting foreign DNA segments into bacteriophage T4. A plasmid containing T4 DNA is opened within the T4 sequence and the foreign DNA is inserted in vitro. Recombination in vivo, between T4 and the doubly chimeric plasmid, results in insertion of the foreign DNA into the genome of viable T4 phage. We have demonstrated the method by inserting a 203-bp DNA fragment from the lactose operon of Escherichia coli, into the dispensable region of the rIIB gene of T4. With minor modifications, the method should make possible the cloning of very large DNAs into any one of a large number of sites on the T4 chromosome.

Analysis of expression of the rII gene function of bacteriophage T4

Temperature-sensitive (ts) mutants of the T4 phage rII gene were islated and used in temperature shift experiments that revelaed two different expressions for the normal rII (rII+) gene function in vivo: (i) an early expression (0 to 12 min postinfection at 30 C) that prevents restriction of T4 growth in Escherichia coli hosts lysogenic for gamma phage, and (ii) a later expression (12 to 18 min postinfection at 30 C) that results in restriction of T4 growth when the phage DNA ligase (gene 30) is missing. The earlier expression appeared to coincide with the period of synthesis of the protein product of the T4 rIIA cistron, whereas the later expression occurred after rIIA protein synthesis had stopped. The synthesis of the protein product of the rIIB cistron continues for several minutes after rIIA protein synthesis ceases (O'Farrell and Gold, 1973). The two rII+ gene expressions might require different molar ratios of the rIIA and rIIB proteins. It is possible that the separate expressions of rII+ gene function are manifestations of different associations between the two rII proteins and other T4-induced proteins that are synthesized or activated at different times after phage infection.

Mutants of T7 bacteriophage inhibited by lambda prophage

Mutants in gene 20, a new T7 gene, cannot grow on rex+ lambda lysogens. Gene 20-- mutants suppress in double mutants the phenotype of T7 ligase negative mutations, but not vice versa. Amber 20- mutants have been obtained. There are differences between these T7 mutations and the similar T4 rII mutations. There are host mutations which permit T7 20- mutants to grow on lambda+ lysogens. T7 DNA synthesis on normal lambda+ lysogens infected with 20- mutants is essentially normal, but the DNA is not packaged. The gene 20 protein is active in in vitro complementation and probably used late in infection for DNA packaging into phage heads.

Genetic evidence for an additional function of phage T4 gene 32 protein: interaction with ligase

Gene 32 of bacteriophage T4 is essential for DNA replication, recombination, and repair. In an attempt to clarify the role of the corresponding gene product, we have looked for mutations that specifically inactivate one but not all of its functions and for compensating suppressor mutations in other genes. Here we describe a gene 32 ts mutant that does not produce progeny, but in contrast to an am mutant investigated by others, is capable of some primary and secondary DNA replication and of forming "joint" recombinational intermediates after infection of Escherichia coli B at the restrictive temperature. However, parental and progeny DNA strands are not ligated to covalently linked "recombinant" molecules, and single strands of vegetative DNA do not exceed unit length. Progeny production as well as capacity for covalent linkage in this gene 32 ts mutant are partially restored by additional rII mutations. Suppression by rII depends on functioning host ligase [EC 6.5.1.2; poly(deoxyribonucleotide):poly(deoxyribonucleotide) ligase (AMP-forming, NMN-forming)]. This gene 32 ts mutation (unlike some others) in turn suppresses the characteristic plaque morphology of rII mutants. We conclude that gene 32 protein, in addition to its role in DNA replication and in the formation of "joint" recombinational intermediates, interacts with T4 ligase [EC 6.5.1.1; poly(deoxyribonucleotide):poly(deoxyribonucleotide) ligase (AMP-forming)] when recombining DNA strands are covalently linked. The protein of the mutant that we describe here is mainly defective in this interaction, thus inactivating T4 ligase in recombination. Suppressing rII mutations facilitate substitution of host ligase. There is suggestive evidence that these interactions occur at the membrane.

Point mutants in the D2a region of bacteriophage T4 fail to induce T4 endonuclease IV

We have studied the properties of presumptive point mutants in the D2a region of bacteriophage T4. Dominance tests showed that the D2a mutation was recessive to the wild-type allele. The mutations were shown to map in the D2a region by complementation against rII deletions. The D2a mutations were also located between gene 52 and rIIB by two- and three-factor crosses. The mutants are located at at least two distinct loci in the D2a region. The point mutants grow normally on all hosts tested and none of the mutants makes T4 endonuclease IV. We propose the name "denB" for the D2a locus.

Nonreplicated DNA and DNA fragments in T4 r- bacteriophage particles: phenotypic mixing of a phage protein

"Conservative phage" containing a genome derived from an infecting phage particle which has not undergone replication in the cell but nevertheless has become encapsulated and released in a normal phage particle, are found after infection of Escherichia coli with rII(-) or rI(-) mutants under conditions which result in rapid lysis. If such conservative phage are derived from a mixed infection with v(+) and v(1) phage, they display phenotypic mixing of the v gene product (an endonuclease carried in the phage particle). Populations of rI and rII mutant phage grown under conditions of rapid lysis include particles containing short DNA fragments. It is suggested that a "maturation defect", common to rI and rII mutants, but absent in rIII mutants, may account for the encapsulation of nonreplicated DNA as well as that of the DNA fragments.

R-factor-mediated nuclease activity involved in thymineless elimination

R-factor 1818 (R-1818) had no effect on the efficiency of plating of ligase-deficient phage T4 mutants on strains of Escherichia coli containing excess, normal, or defective ligase. However, if the R(+) bacterial strain that overproduced ligase was first starved of thymine, its ability to propagate ligase-deficient phage was reduced by as much as fivefold compared with the burst size on the thymine-starved R(-) strain. In contrast, it was found that after ultraviolet irradiation of the host the phage burst size was higher on the R(+) ligase overproducing strain than the R(-) derivative. The maximal level of R-factor elimination produced by thymine starvation was inversely related to the ligase level of the host. Ultraviolet irradiation did not cure the R factor from strains containing wild-type levels of ligase, but did cause elimination from strains with excess or defective ligase. The results suggest that R-1818 codes for a nuclease that is induced by thymine starvation and which, possibly in conjunction with host-mediated nucleases, is responsible for its elimination under these conditions.

Host-mediated repair of discontinuities in DNA from T4 bacteriophage

Discontinuities of T4 DNA which are caused by excision of UV-damaged areas, by decay of (32)P atoms, or which are present in DNA from rII(-)lig(am) (-) phage produced in a host nonpermissive for amber mutants are all repaired by bacterial enzymes after infection in the presence of chloramphenicol. Escherichia coli DNA polymerase I participates in the host-mediated repair, but an approximately 20-fold variation in the levels of host polynucleotide ligase does not affect either the kinetics or the extent of repair observed. Upon removal of chloramphenicol, host-repaired DNA from UV-irradiated phage undergoes a secondary cycle of breakage, which ultimately results in solubilization of most of the phage DNA. If the cells are co-infected with nonirradiated helper phage, the secondary breaks are repaired and the continuity of the polynucleotide chain is restored. The close coincidence in the extent of primary and secondary breakage suggests that phage-coded enzymes recognize and excise areas improperly repaired by the host. In contrast to host-mediated repair, repair mediated by rescuing phage probably restored functionality to the damaged DNA.

Ligase-defective bacteriophage T4. II. Physiological studies

The timing of the suppression of gene 30 (deoxyribonucleic acid ligase) mutations by rII mutations was studied by temperature shift-down experiments with a temperature-sensitive rII mutation. The rII function must remain inactivated for about 5 to 8 min at 37 C for suppression to occur, thus making suppression an early function. This result is in agreement with the timing of expression of other rII functions. A gene 30 defect can also be overcome by replacing the Na(+) cation in the growth medium with the Mg(2+) cation, a result similar to the relief of the lethality of rII mutations in lambda lysogens. Prior infection with bacteriophages T3 or T7, which produce their own deoxyribonucleic acid ligases, can also partially overcome the lethality of gene 30 mutations.

Ligase-defective bacteriophage T4. I. Effects on mutation rates

Temperature-sensitive mutations in bacteriophage T4 gene 30 (polynucleotide ligase) were examined for their effects on spontaneous and proflavine-induced frameshift mutagenesis in the rII and ac (acridine resistance) cistrons. Only small (fourfold or less) effects on mutation rates were observed, even when selection artifacts involving suppression of gene 30 mutations by rII mutations were taken into account. The deoxyribonucleic acid ligase gene of T4 therefore appears to be only a minor determinant of frameshift mutation rates. This result is consistent with the particular nature of frameshift mutagenesis in bacteriophage T4.

Stability of cytosine-containing deoxyribonucleic acid after infection by certain T4 rII-D deletion mutants

When T-even phage infect Escherichia coli, synthesis of host deoxyribonucleic acid (DNA) rapidly ceases. If the phage carry a mutation in a gene essential for phage DNA synthesis, then the infected bacteria should make no DNA, either host DNA or phage DNA. However, we have found that infection with certain T4 gene 56 (deoxycytidine triphosphatase)-rII double mutants leads to substantial DNA synthesis. Only rII deletion mutations which extend into the middle third of the adjacent, nonessential D region lead to the anomalous DNA synthesis, when combined with a gene 56 mutation; the requirement probably is that the deletion extend into the D2a transcriptional unit identified by Sederoff et al. Genetic evidence indicates that the observed anomalous DNA synthesis is synthesis of phage DNA. We suggest that the D2a region controls, directly or indirectly, a nuclease involved in the breakdown of cytosine-containing DNA. In the absence of the D2a product, the cytosine-containing phage DNA made by the gene 56 mutant is stabilized.

Occurrence of lysophosphatides in bacteriophage T4rII-infected Escherichia coli S-6

Hydrolysis of phospholipids was observed to start about 15 min after Escherichia coli S/6 cells were infected with T4rII bacteriophage mutants. Hydrolysis continued through the latent period and well past the time when cell lysis occurs. The hydrolytic products that accumulated were free fatty acids, 2-acyl lysophosphatidylethanolamine, and various lysocardiolipins. These products indicated the action of phospholipase A(1). From 15 to 22 min after infection, there were equivalent amounts of fatty acids and lysophosphatides in extracts of cellular lipids. Thereafter, free fatty acids were produced in excess. This suggests that lysophospholipase was active at the later time. We also observed a stoichiometric relation between loss of phosphatidylglycerol and increase of cardiolipin plus lysocardiolipins. This continued well past the normal lysis time (25 min). The appearance of lipase activities during the latent period seems to be specific to infection with rII mutants. Neither the wild-type bacteriophage nor rI mutants produced similar activities by 22 min after infection.

Partial suppression of bacteriophage T4 ligase mutations by T4 endonuclease II deficiency: role of host ligase

Endonuclease II-deficient, ligase-deficient double mutants of phage T4 induce considerably more deoxyribonucleic acid (DNA) synthesis after infection of Escherichia coli B than does the ligase-deficient single mutant. Furthermore, the double mutant can replicate 10 to 15% as well as wild-type T4, whereas the single mutant fails to replicate. When the E. coli host is also deficient in ligase, the double mutant resembles the single mutant. The results indicate that host ligase can substitute for phage ligase when the host DNA is not attacked by the phage-induced endonuclease II.

Properties of bacteriophage T4 mutants defective in gene 30 (deoxyribonucleic acid ligase) and the rII gene

In Escherichia coli K-12 strains infected with phage T4 which is defective in gene 30 [deoxyribonucleic acid (DNA) ligase] and in the rII gene (product unknown), near normal levels of DNA and viable phage were produced. Growth of such T4 ligase-rII double mutants was less efficient in E. coli B strains which show the "rapidlysis" phenotype of rII mutations. In pulse-chase experiments coupled with temperature shifts and with inhibition of DNA synthesis, it was observed that DNA synthesized by gene 30-defective phage is more susceptible to breakdown in vivo when the phage is carrying a wild-type rII gene. Breakdown was delayed or inhibited by continued DNA synthesis. Mutations of the rII gene decreased but did not completely abolish the breakdown. T4 ligase-rII double mutants had normal sensitivity to ultraviolet irradiation.

DNA ligase mutants of Escherichia coli

A procedure is described for the isolation of Escherichia coli mutants with either excess or deficient DNA ligase activity. A mutant that overproduces DNA ligase supports the growth of ligase-defective (gene 30 mutant) T4 phages. Even T4 rII-gene 30 double mutants, which are able to grow in normal E. coli, cannot grow in cells deficient in DNA ligase. A functional DNA ligase, supplied either by the phage or the host, thus seems to be required for T4 growth. An E. coli strain that makes a temperature-sensitive DNA ligase becomes radiation-sensitive at high temperature, but otherwise grows normally and shows no obvious defect in DNA replication.

Parent-to-progeny transfer and recombination of T4rII bacteriophage

Transfer of parental, light (not substituted with 5-bromodeoxyuridine) (32)P-deoxyribonucleic acid (DNA) from rII(-) mutants of T4 bacteriophage to heavy (5-bromodeoxyuridine-substituted) progeny in Escherichia coli B was less homogeneous than in wild phages. The net transfer was 5 to 20% of the value for wild T4 phage, and the parental contribution per progeny DNA molecule amounted to 7 to 100% of the genome. Three classes could be distinguished, based on the density distribution of parental label in CsCl analysis of the progeny phages. "Far recombined" phages contain parental material only in semiconservatively replicated subunits covalently attached to progeny DNA, amounting to 5 to 10% parental contribution per genome. "Intermediate recombinants" contain, aside from conventional recombinant DNA, parental DNA banding at the original, light density. This DNA may be unattached to heavy progeny DNA or attached by weak bonds which are very sensitive to shearing during the extraction procedure. The parental contribution is 10 to 50% per progeny DNA molecule in this class. "Conservative" phages band close to the parental, light density in CsCl; their DNA is purely light. When the parental phage is labeled with both (3)H-leucine (capsid) and (32)P (DNA), the specific activity of (3)H/(32)P in the "conservative progeny" is 10 to 40% of that in the parental, showing that at least some of the (32)P in this area belongs to phages with parental DNA as the sole DNA component inside an unlabeled capsid, i.e., parental DNA which has been injected into the host and matured in a new capsid without replication or recombination. This phenomenon occurs to about the same extent in both single and multiple infection.