Mechanics of frameshift mutagenesis in bacteriophage T4: role of chromosome tips

A species barrier between bacteriophages T2 and T4: exclusion, join-copy and join-cut-copy recombination and mutagenesis in the dCTPase genes

Bacteriophage T2 alleles are excluded in crosses between T2 and T4 because of genetic isolation between these two virus species. The severity of exclusion varies in different genes, with gene 56, encoding an essential dCT(D)Pase/dUT(D)Pase of these phages, being most strongly affected. To investigate reasons for such strong exclusion, we have (1) sequenced the T2 gene 56 and an adjacent region, (2) compared the sequence with the corresponding T4 DNA, (3) constructed chimeric phages in which T2 and T4 sequences of this region are recombined, and (4) tested complementation, recombination, and exclusion with gene 56 cloned in a plasmid and in the chimeric phages in Escherichia coli CR63, in which growth of wild-type T2 is not restricted by T4. Our results argue against a role of the dCTPase protein in this exclusion and implicate instead DNA sequence differences as major contributors to the apparent species barrier. This sequence divergence exhibits a remarkable pattern: a major heterologous sequence counter-clockwise from gene 56 (and downstream of the gene 56 transcripts) replaces in T2 DNA the T4 gene 69. Gene 56 base sequences bordering this substituted region are significantly different, whereas sequences of the dam genes, adjacent in the clockwise direction, are similar in T2 and in T4. The gene 56 sequence differences can best be explained by multiple compensating frameshifts and base substitutions, which result in T2 and T4 dCTPases whose amino acid sequences and functions remain similar. Based on these findings we propose a model for the evolution of multiple sequence differences concomitant with the substitution of an adjacent gene by foreign DNA: invasion by the single-stranded segments of foreign DNA, nucleated from a short DNA sequence that was complementary by chance, has triggered recombination-dependent replication by "join-copy" and "join-cut-copy" pathways that are known to operate in the T-even phages and are implicated in other organisms as well. This invasion, accompanied by heteroduplex formation between partially similar sequences, and perhaps subsequent partial heteroduplex repair, simultaneously substituted T4 gene 69 for foreign sequences and scrambled the sequence of the dCTPase gene 56. We suggest that similar mechanisms can mobilize DNA segments for horizontal transfer without necessarily requiring transposase or site-specific recombination functions.

Frameshift mutations produced by proflavin in bacteriophage T4: specificity within a hotspot

Frameshift mutations were induced by proflavin in the rIIB gene of bacteriophage T4. rIIB DNA from each of 48 independent frameshifts was inserted into M13mp8 and sequenced. Two-thirds of the frameshifts (33/48) lie contiguous to one another in 10 base pairs of the rIIB sequence. This hotspot differs markedly from previously characterized mutagen-induced frameshift hotspots. Distinctive features of the hotspot include the absence of locally repetitive sequences, particularly G X C runs, and the fact that many different sequence changes are induced within the hotspot sequence at appreciable frequencies. Among the 33 mutants at the hotspot, 8 distinguishable DNA sequence changes were seen. All of the mutations were deletions of a single base or duplications of one or more bases. Duplications were more frequent than deletions. The patterns of the base sequence changes suggest that two specific phosphodiester bonds within the hotspot sequence are sites at which proflavin-induced mutation is initiated.

Perspectives in molecular mutagenesis

The models and paradigms that underlie a vigorously developing science may tend to stifle progress or may serve to sharpen the knife edge of paradox. Working out mutagenic mechanisms is a conceptually and technologically demanding task, and we are accumulating an increasingly uncomfortable number of experimental and theoretical inconsistencies. First, there continue to be widespread difficulties in specifying the chemical nature of mutagenic DNA alterations, both because of the multitude of DNA reaction products induced by many mutagens and because of the intrinsic rarity of most mutational responses. For instance, alkylation of the 0(6) position of guanine to generate adducts of modest dimensions is widely believed to form the basis for the mutagenic and carcinogenic actions of numerous chemicals. However, while this scheme is supported by in vitro evidence, it has failed to explain why bacteriophages can be thus alkylated in vitro by N-methyl-N'-nitro-N-nitrosoguanidine without the production of mutations, or why microbial eukaryotes alkylated by ethyl methanesulfonate or N-methyl-N'-nitro-N-nitrosoguanidine display no mutagenic response when their "error-prone repair systems" are mutationally inactivated. Second, a base pair is typically mutated at vastly different rates, and with different directional specificities, when it resides at different positions within a gene; whereas very little of this variability is explained by current theories that aim to describe the determinants of fidelity in DNA replication. (Some sizable portion of this variation now appears to depend not only upon neighboring base-pair influences but also upon much more subtle and distant effects). Third, experimental modifications of enzymatic fidelity by means of amino acid substitutions, and perhaps also cation replacements, lead to such a diversity of modified mutation rates as to seriously challenge the ability of any simple theory to organize the experimental observations into a coherent and predictive network.

Mutagen-nucleic acid intercalative binding: structure of a 9-aminoacridine: 5-iodocytidylyl(3'-5')guanosine crystalline complex

9-Aminoacridine forms a crystalline complex with the dinucleoside monophosphate, 5-iodocytidylyl(3'-5')guanosine. We have solved the three-dimensional structure of this complex by x-ray crystallography and have observed two distinct intercalative binding modes by this drug to miniature Watson-Crick double helical structures. The first of these involves a pseudosymmetric stacking interaction between 9-aminoacridine molecules and guanine-cytosine base-pairs. This configuration may be used by 9-aminoacridine when intercalating into DNA. The second configuration is an asymmetric interaction, largely governed by stacking forces between acridine and guanine rings. This type of association may play an important role in the mechanism of frameshift mutagenesis.

9-Aminoacridine mutagenesis of bacteriophage T4 intracellular DNA

Most of the intracellular T4 DNA made in the presence of 9-aminoacridine is of lower molecular weight than mature T4 DNA and does not get packaged into phage particles. Using a T4 DNA transformation assay, we have examined this intracellular T4 DNA for its content of 9-aminoacridine-induced revertants of certain rII gene frameshift mutations. The proportion of acridine-induced revertants in the intracellular DNA population is close to that found in the phage progency made in the presence of 9-aminoacridine. Thus, the generation of low molecular weight T4 DNA in the presence of 9-aminoacridine is not, in itself, also a mutagenic process.

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.

Inactivation of bacteriophage T4 by ethyl methanesulfonate: influence of host and viral genotypes

Inactivation of bacteriophage T4 by ethyl methanesulfonate (EMS) is a complex process which depends critically upon the conditions of treatment and upon both the viral and the host genotypes. EMS-inactivated particles are capable of multiplicity and cross-reactivation, indicating the need for caution in using EMS in certain types of mutation studies. The pyrimidine dimer excision systems of the phage and the host do not affect the EMS sensitivity of T4, but the T4x(+)y(+) system does. Mutational defects in the deoxyribonucleic acid (DNA) ligase and the DNA polymerase systems both of the virus and of its host also affect viral EMS sensitivity.

Reversion of frameshift mutations stimulated by lesions in early function genes of bacteriophage T4

Temperature-sensitive (ts) mutants representative of a number of genes of phage T4 were crossed with rII mutants to allow isolation of ts, rII double-mutant recombinants. The rII mutations used were characterized as frameshift mutations primarily on the basis of their revertability by proflavine. For each ts, rII double mutant, the effect of the ts mutation on spontaneous reversion of the rII mutation was determined over a range of incubation temperatures. A strong enhancement in reversion of two different rII mutants was detected when they were combined with tsL56, a mutation in gene 43 [deoxyribonucleic acid (DNA) polymerase]. Three other mutants defective in gene 43 enhanced reversion about fourfold. Two mutations in gene 32, which specifies a protein necessary for DNA replication, enhanced reversion about 5-fold and 18-fold, respectively. Two additional mutations in gene 43 and two in gene 32 had no effect. Fivefold and threefold enhancements in reversion were also found with mutations in genes 44 (DNA synthesis) and 47 (deoxyribonuclease), respectively. No significant effect was found with mutations in seven additional genes. The results of other workers suggest that frameshift mutations arise from errors in strand alignment during repair synthesis occurring at chromosome tips. Our results show that such errors can be enhanced by mutations in the DNA polymerase, the gene 32 protein, and the enzymes specified by genes 44 and 47. This implies that these proteins are employed in the repair process occurring at chromosome tips and that mutational errors in these proteins can lead to loss of ability to recognize and reject strand misalignments.

The influence of neighboring base pairs upon base-pair substitution mutation rates

The 2-aminopurine-induced transition, A.T --> G.C, was studied at particular sites in bacteriophage T4 as a function of the nearby base-pair composition of the DNA. Changing a base pair changed the transition rate at the adjacent base pair up to 23-fold, and at the next base pair by a lesser amount. Destabilization was achieved by replacing an A.T base pair by a G.C base pair.