Chromosome structure in phage T4, II. Terminal redundancy and heterozygosis

The Doctor of Delayed Publications: The Remarkable Life of George Streisinger (1927-1984)

The history of science offers multiple examples of how the perseverance of a single visionary person could open the floodgates for a whole new area of research. Zebrafish research is one of these fields with an exciting founding story, as it was the dogged persistence of one man, George Streisinger, that ultimately lifted this little fish out of the obscurity of pet shops into the pantheon of genetic model organisms. The Hungarian born Streisinger was one of the most gifted geneticists of his era and his network of mentors and friends really reads like a who-is-who of 20th century genetics. And it was not only science where he excelled: the way he took his civic duties seriously and outspokenly fought social injustice wherever he met it offers an important lesson on integrity for today's scientists as well.

Islands of non-essential genes, including a DNA translocation operon, in the genome of bacteriophage 0305ϕ8-36

We investigate genes of lytic, Bacillus thuringiensis bacteriophage 0305ϕ8-36 that are non-essential for laboratory propagation, but might have a function in the wild. We isolate deletion mutants to identify these genes. The non-permutation of the genome (218.948 Kb, with a 6.479 Kb terminal repeat and 247 identified orfs) simplifies isolation of deletion mutants. We find two islands of non-essential genes. The first island (3.01% of the genomic DNA) has an informatically identified DNA translocation operon. Deletion causes no detectable growth defect during propagation in a dilute agarose overlay. Identification of the DNA translocation operon begins with a DNA relaxase and continues with a translocase and membrane-binding anchor proteins. The relaxase is in a family, first identified here, with homologs in other bacteriophages. The second deleted island (3.71% of the genome) has genes for two metallo-protein chaperonins and two tRNAs. Deletion causes a significant growth defect. In addition, (1) we find by "in situ" (in-plaque) single-particle fluorescence microscopy that adsorption to the host occurs at the tip of the 486 nm long tail, (2) we develop a procedure of 0305ϕ8-36 purification that does not cause tail contraction, and (3) we then find by electron microscopy that 0305ϕ8-36 undergoes tail tip-tail tip dimerization that potentially blocks adsorption to host cells, presumably with effectiveness that increases as the bacteriophage particle concentration increases. These observations provide an explanation of the previous observation that 0305ϕ8-36 does not lyse liquid cultures, even though 0305ϕ8-36 is genomically lytic.

Amber mutants of bacteriophage T4D: their isolation and genetic characterization

We have isolated a large number of mutants of bacteriophage T4D that are unable to form plaques on strain B of Escherichia coli, but are able to grow (nearly) normally on some other strains of E. coli, in particular strain CR63. These mutants, designated amber (am), have been characterized by complementation tests, by genetic crosses, and by their response to chemical mutagens. It is concluded that a particular subclass of base substitution mutations may give rise to amber mutants and that such mutants occur in many genes, which are widely distributed over the T4 genome.

Some features of base pair mismatch repair and its role in the formation of genetic recombinants

For the formation of recombinants involving closely linked markers, two distinct processes play a role. The recombinational interaction between homologous DNA molecules results in the presence of heteroduplex DNA joining the parental components of the recombinant. The presence of markers distinguishing the parents in the region of heteroduplex DNA can result in base pair mismatches. The post recombination repair of such mismatches can contribute to the separation of closely linked markers. The processes responsible for such repair also play roles in mutation avoidance. The specificities, functions and contribution to the formation of recombinants for closely linked markers of the processes in Escherichia coli are described.

Heteroduplex DNA formation is associated with replication and recombination in poxvirus-infected cells

Poxviruses are large DNA viruses that replicate in the cytoplasm of infected cells and recombine at high frequencies. Calcium phosphate precipitates were used to cotransfect Shope fibroma virus-infected cells with different DNA substrates and the recombinant products assayed by genetic and biochemical methods. We have shown previously that bacteriophage lambda DNAs can be used as substrates in these experiments and recombinants assayed on Escherichia coli following DNA recovery and in vitro packaging. Using this assay it was observed that 2-3% of the phage recovered from crosses between point mutants retained heteroduplex at at least one of the mutant sites. The reliability of this genetic analysis was confirmed using DNA substrates that permitted the direct detection of heteroduplex molecules by denaturant gel electrophoresis and Southern blotting. It was further noted that heteroduplex formation coincided with the onset of both replication and recombination suggesting that poxviruses, like certain bacteriophage, make no clear biochemical distinction between these three processes. The fraction of heteroduplex molecules peaked about 12-hr postinfection then declined later in the infection. This decline was probably due to DNA replication rather than mismatch repair because, while high levels of induced DNA polymerase persisted beyond the time of maximal heteroduplex recovery, we were unable to detect any type of mismatch repair activity in cytoplasmic extracts. These results suggest that, although heteroduplex molecules are formed during the progress of poxviral infection, gene conversion through mismatch repair probably does not produce most of the recombinants. The significance of these observations are discussed considering some of the unique properties of poxviral biology.

Selection against dam methylation sites in the genomes of DNA of enterobacteriophages

Postreplicative methylation of adenine in Escherichia coli DNA to produce G6m ATC (where 6mA is 6-methyladenine) has been associated with preferential daughter-strand repair and possibly regulation of replication. An analysis was undertaken to determine if these, or other, as yet unknown roles of GATC, have had an effect on the frequency of GATC in E. coli or bacteriophage DNA. It was first ascertained that the most accurate predictions of GATC frequency were based on the observed frequencies of GAT and ATC, which would be expected since these predictors take into account preferences in codon usage. The predicted frequencies were compared with observed GATC frequencies in all available bacterial and phage nucleotide sequences. The frequency of GATC was close to the predicted frequency in most genes of E. coli and its RNA bacteriophages and in the genes of nonenteric bacteria and their bacteriophages. However, for DNA enterobacteriophages the observed frequency of GATC was generally significantly lower than predicted when assessed by the chi square test. No elevation in the rate of mutation of 6mA in GATC relative to other bases was found when pairs of DNA sequences from closely related phages or pairs of homologous genes from enterobacteria were compared, nor was any preferred pathway for mutation of 6mA evident in the E. coli DNA bacteriophages. This situation contrasts with that of 5-methylcytosine, which is hypermutable, with a preferred pathway to thymine. Thus, the low level of GATC in enterobacteriophages is probably due not to 6mA hypermutability, but no selection against GATC in order to bypass a GATC-mediated host function.(ABSTRACT TRUNCATED AT 250 WORDS)

High negative interference and recombination in bacteriophage T5

The process of close recombinant formation in bacteriophage T5 crosses has been studied by examining the structure of internal heterozygotes (HETs), the immediate products of recombination events. The T5 system was chosen because it permits the study of internal heterozygotes exclusively, thus avoiding the ambiguities inherent in previous studies with T4. The heterozygotes were obtained by the nonselective screening of progeny phage in a prematurely lysed sample from an eight-factor cross. The molecular structure of each HET was inferred from the strand genotypes displayed among its progeny. This investigation presents unequivocal evidence that both overlap and insertion HETs are intermediates in recombinant formation and that insertion HETs are a significant source of close double recombinants. There is evidence suggesting that mismatch repair of overlap HETs could be the source of close triple exchanges. Thus, a significant part, and perhaps all, of the high negative interference for close-marker recombination observed in this system is a direct consequence of the fine structure of the recombinational intermediates. These findings are compatible with recombination models proposed by others, in which a single branched intermediate can give rise to HETs of both the overlap and insertion types.

Region-specific recombination in phage T4. II. Structure of the recombinants

In this paper, we present results of crosses designed to elucidate the structure of recombinants in the tail-fiber region of bacteriophage T4, in which a glucosylation-dependent recombinations mechanism is operative, and the cause of the "special" recombination in glycosylated crosses is discussed. We present evidence that, when phage are nonglycosylated, recombination in the tail-fiber region proceeds via long heteroduplex overlaps. Mismatched bases within such regions (in nonglycosylated phage) are repaired efficiently (as contrasted to those of glucosylated phage), but asymmetrically; that is, there may be an equal probability of resolving the mismatch to mutant or wild type.

Evidence that mismatched bases in heteroduplex T4 bacteriophage are recognized in vivo

T4 heteroduplex heterozygotes are lost selectively after prolonged incubation of phage-infected Escherichia coli cells under nonreplicating conditions. The loss of heterozygosity occurs for four out of six rII sites tested and is not dependent upon T4 v gene function. The results are interpreted to indicate the existence of a base-specific system for the recognition of mismatched bases in intracellular DNA.

Gamma-ray mutagenesis in bacteriophage T4

137Cs-gamma irradiation of bacteriophage T4 induces large deletions plus a variety of types of point mutations. All mutations arise with single-hit kinetics, and all by a misrepair process. The estimated point mutation rate is 1.5 X 10(-9) per locus per rad.

Terminal redundancy heterozygotes involving the first-step-transfer region of the bacteriophage T5 chromosome

Individual progeny of two-factor crosses between A1am and A2am T5 phages give rise to bursts containing more than one type of plaque. The simplest explanation for these mixed bursts is that the A1 and A2 genes are located within the terminally repeated portion of the T5 genome and that the mixed bursts are made by "terminal redundancy heterozygotes". The observation of genetic heterozygosity means that the A1 and A2 genes are repeated intact. This implies that the terminal segments of T5 are genetically interchangeable.

Novel rII duplications in bacteriophage T4

The properties of two rII complementation heterozygotes (D5B and D7A) of bacteriophage T4 are described. These strains are characterized by their stability, each forming less than 10-3 r segregants among their viable progeny, and by their segregation of only one of the two parental types. No increase in r progeny was found on crossing D7A or D5B with T4r+, indicating that the duplications in these strains are not separated by an essential region of the phage genome. Both D5B and D7A from h-2+/h-4+ heterozygotes at frequencies similar to T4r+, suggesting that the duplicated regions in these strains are short. The progeny of these h-2+/h-4+ heterozygotes retain heterozygosity for rII but not for h: therefore, D5B and D7A are not stabilized terminal redundancy complementation heterozygotes. We conclude that D5B and D7A contain very short tandem duplications and we present structures consistent with the observed characteristics of these phages.

Selective allele loss in mixed infections with T4 bacteriophage

Evidence is presented that when E. coli B is mixedly infected with T4D wild type and rII deletion mutants, the excess DNA of the wild type allele is lost. No loss is seen in mixed infections with rII point mutants and wild type. In similar experiments with lysozyme addition mutants, the mutant allele is lost. We believe these results demonstrate a repair system which removes "loops" in heteroduplex DNA molecules. A number of phage and host functions have been tested for involvement in the repair of the excess DNA, and T4 genes x and v have been implicated in this process.

Polynucleotide ligase in bacteriophage T4D recombination

Following infection of E. coli B with ligase-deficient rII bacteriophage T4D recombination between linked markers is increased 4.2 fold and heterozygote frequency increased 2.3 fold. In such infection recombination occurs at a rapid rate for an extended period. This is in contrast to the time course of recombination observed in wild-type, lysis-inhibited, or lysis-defective (gene t defective) infection. In all of these cases recombination under standard cross conditions occurs early in the vegetative cycle. The increased recombination in ligase-deficient rII infection is reduced in a bacterial strain which produces greater than normal levels of host ligase. These results indicate that ligase has a crucial role not only in the replication of DNA but also in recombination. The level of ligase may determine whether DNA replication occurs with or without concomitant recombination.

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

In contrast to observations in bacteria and fungi, frameshift mutations in bacteriophage T4 do not arise during genetic recombination. Nascent mutants, captured in the heterozygous condition, exhibit properties which indicate that the new lesions are located at the extreme tips of the chromosomes, and are segregated by a combination of recombination and replication.

The effect of homozygous deletions upon heterozygote formation in bacteriophage T4D

Experiments were designed to investigate the effect of homozygous deletions upon the frequency and the average length of heterozygous regions in bacteriophage T4D. A long deletion,rdf41, which covers at least the wholerII region, was found to increase the heterozygosity forr48, while no increase was observed when a short deletion was employed. The long deletion was found to increase the average length ofamber-HETs by a length approximately the size of therII region.

A drastic reduction in average HET length was found in FUDR crosses homozygous for the long deletionrdf41, indicating that the type of HET that does increase in FUDR is very short.

In the cross with no deletion in either parent, premature lysis HETs were found to be much longer than normal lysis HETs. Assuming that redundancy HETs are long compared to heteroduplex HETs this result indicates that redundancy HETs are made earlier in the latent period than heteroduplex HETs. A fluctuation in HET frequencies was found for different markers, especially in FUDR.

About half of all HETs, both in normal crosses and in FUDR crosses, was found to be parental for outside markers.

In non-FUDR crosses, polarized segregation was shown by 12 out of 27 multi-marker HETs after normal lysis and 5 out of 22 multi-marker HETs after premature lysis. In FUDR crosses, 24 out of 77 multi-marker HETs showed polarity.

Variations in genetic recombination due to amber mutations in T4D bacteriophage

Recombination experiments were performed to assess the affect of amber mutations in 12 genes of T4D bacteriophage on genetic recombination. Crosses were performed in various suppressor-containing bacterial hosts to permit the production of progeny phage. Amber mutations in genes 32, 46, and 47 caused decreased recombination, amber mutations in genes 30, 41, 42, 43, 56, 61, and 62 caused increased recombination, whereas mutations in genes 63 and 37 showed no demonstrable effect on recombination.

The extent of rII deletions in phage T4

The extent of certainrIIdeletions in phage T4 has been mapped by genetic means beyond the terminus of the B cistron. They extend to varying degrees, nearly to theacslocus. The phenotypes of these mutants indicate that there are two or three cistrons betweenrIIB andacs, and that the functions coded for by these cistrons are not essential for growth in any knownE. coliK12 strain orE. colilysogen.

Transformation of African green monkey kidney cells by irradiated adenovirus 7-simian virus 40 hybrid

The ability of adenovirus 7-simian virus 40 (SV40) hybrid (strain LL "E-46") to replicate decreased exponentially as a function of the amount of gamma-irradiation; the ability to induce SV40 and adenovirus 7 T antigen decreased at a much slower rate. Nevertheless, the virus was still able to transform African green monkey kidney cells at a radiation dosage that had completely destroyed its replication ability. All transformed colonies were positive for SV40 T antigen but were negative for adenovirus 7 T antigen. The adenovirus 7-SV40 hybrid transformed cells were superinfectible with SV40 virus. Two of the three transformed cell populations apparently did not sensitize hamsters against the appearance SV40 primary tumors, thus suggesting a deficiency in the SV40 transplantation antigen.

The arrangement of information in DNA molecules

The anatomy of DNA molecules isolated from mature bacteriophage is reviewed. These molecules are linear, duplex DNA consisting mainly of uninterrupted polynucleotide chains. Certain phage (T5 and PB) contain four specifically located interruptions. While the nucleotide sequence of most of these molecules is unique (T5, T3, T7, lambda), some are circular permutations of each other (T2, T4, P22). Partial degradation of these DNA molecules by exonuclease III predisposes some of them to form circles upon annealing, but indicating they are terminally redundant.

Heteroduplex heterozygotes in bacteriophage T4 involving mutations of various dimensions

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