Role of DNA Sequences in Genetic Recombination in the Iso-1-Cytochrome c Gene of Yeast. II. Comparison of Mutants Altered at the Same and Nearby Base Pairs

X-ray-induced mitotic recombination rates and spontaneous meiotic recombination rates have been determined in two-point crosses of various defined cyc1 mutants of the yeast Saccharomyces cerevisiae. All but one of the 17 cyc1 mutants chosen for this study contained either the addition, deletion or substitution of single base-pairs located within a defined segment of the gene that corresponds to the 11 amino acid residues at the amino terminus of iso-1-cytochrome c; approximately half of these mutants had alterations of the AUG initiation codon, some at the same base pair. Up to 66-fold differences in X-ray-induced recombination rates were observed when the same cyc1 mutant was crossed to cyc1 mutants having different alterations in the AUG initiation codon; over a ten-fold difference was observed in series of homologous crosses involving mutants with different changes at the same base-pair. Recombination rates that were associated with specific cyc1 mutants co-segregated with the particular alleles following meiosis, and comparable recombination patterns were also observed for independently isolated, identical mutations. With the mutants used in this study, the frequencies of meiotic recombination did not differ as markedly, suggesting a dissimilar dependence on specific DNA sequences for these two modes of recombination. These disproportionalities of recombination rates suggest that the nature of the mismatched bases influences the recombination process, but not in a way that can be simply interpreted.     

Recombination between temperature-sensitive and deletion mutants of reovirus.

In standard pairwise crosses there was no detectable recombination between defective reovirus lacking the largest genomic segment and prototypes of the seven known classes of ts mutants. However, in such crosses between R2A (201) and the various prototypes frequencies of ts+ recombinants between 2.6 and 6.1% were observed, as others have found (Fields, 1971; Fields and Joklik, 1969). An infectious center assay was devised to measure recombination in this system, and it was found that all mixedly infected cells gave rise to ts+ recombinants in crosses between prototype ts mutants, but no recombination was detectable when the defective virus was crossed with three different ts mutants. The ts mutation of mutant R2A (201) was efficiently rescued when crossed with UV-inactivated wild-type virus but not when crossed with UV-inactivated defective virus. It is concluded from these various experiments that if there is any recombination between these defective reovirions and any known class of ts mutants it is too low to be measured by methods presently available. The kinetics of recombination were measured in cells mixedly infected with R2A (201) and R2B (352) mutants. At the earliest time progeny virus could be found in the cells the frequency of ts+ recombinants was 4.5%, and this frequency remained unchanged despite a subsequent 1,000-fold increase in progeny virus.     

Deficiency of double mutant recombinants in crosses of phage T4

Summary Only 1.4% of the double mutant recombinants expected on the basis of wild-type recombination frequencies were observed in the combined data from two-factor crosses between a gene 37 amber mutant, amB280, and eighteen different temperature sensitive mutants which were also defective in gene 37. Similar, though less extreme, deficiencies of double mutant recombinants were observed by Doermann and Parma (1968) for mutants in several other genes. In our amB280xts crosses, frequencies of wild-type recombinants were in reasonably good agreement with those expected from the map positions of the mutants determined in crosses not involving amB280. Wild-type and double mutant recombinants were found at comparable frequencies when each of three other gene 37 amber mutants was crossed to a gene 37 temperature sensitive mutant.Experiments were performed to test whether the deficiency of double mutant recombinants in the amB280xts crosses could be explained by assuming that they occurred primarily in heterozygous particles, where their expression was masked. However, no evidence in support of this explanation was found. Other possible explanations, that the deficiency of double mutants was due to their inviability or the inability of double mutant chromosomes to replicate, were also inconsistent with our observations. The hypothesis considered to most plausibly explain our evidence is that the process by which double mutant recombinant chromosomes are formed is inhibited in the vicinity of a poorly suppressed am mutation.     

Gene conversion spectrum of 15 mutants giving post-meiotic segregation in the b2 locus of Ascobolus immersus

Summary The conversion spectrum of fifteen mutants giving post-meiotic segregations and located in the b2 locus of Ascobolus immersus was studied in 77 mutant x wild-type crosses. These mutants all yield aberrant 4:4 asci, mutants located in the right portion of the locus yielding more aberrant 4:4 than left mutants. The basic frequency of conversion is higher in the left portion. The frequency of hybrid DNA, its symmetrical or asymmetrical distribution and the frequency of correction of the mismatch in hybrid DNA were estimated. The left region shows a higher frequency of hybrid DNA formation than the right region. The fraction of hybrid DNA with a symmetrical distribution tends to increase from left to right in the locus. The frequencies of mismatch correction show considerable variation from one mutant to another and have no relationship to their location. The implications of these observations on the molecular models of genetic recombination are discussed.     

Differential Mismatch Repair Can Explain the Disproportionalities between Physical Distances and Recombination Frequencies of Cyc1 Mutations in Yeast

Recombination rates have been examined in two-point crosses of various defined cyc1 mutations that cause the loss or nonfunction of iso-1-cytochrome c in the yeast Saccharomyces cerevisiae. Recombinants arising by three different means were investigated, including X-ray induced mitotic recombination, spontaneous mitotic recombination, and meiotic recombination. Heteroallelic diploid strains were derived by crossing cyc1 mutants containing a series of alterations at or near the same site to cyc1 mutants containing alterations at various distances. Marked disproportionalities between physical distances and recombination frequencies were observed with certain cyc1 mutations, indicating that certain mismatched bases can significantly affect recombination. The marker effects were more pronounced when the two mutational sites of the heteroalleles were within about 20 base pairs, but separated by at least 4 base pairs. Two alleles, cyc1-163 and cyc1-166, which arose by G.C----C.G transversions at nucleotide positions 3 and 194, respectively, gave rise to especially high rates of recombination. Other mutations having different substitutions at the same nucleotide positions were not associated with abnormally high recombination frequencies. We suggest that these marker effects are due to the lack of repair of either G/G or C/C mismatched base pairs, while the other mismatched base pair of the heteroallele undergoes substantial repair. Furthermore, we suggest that diminished recombination frequencies are due to the concomitant repair of both mismatches within the same DNA tract.     

Genetic and physiological studies of bacteriophage t5 I. An expanded genetic map of t5

An expanded genetic map of bacteriophage T5 has been constructed by using a set of amber, rather than temperature-sensitive, mutants that represent 29 cistrons. The map consists of three small groups and one large group of genes; mutants defective in genes that are located in different groups exhibit maximal recombination when crossed with one another. However, it has been possible to establish tentative linkage among these groups by use of a particular mutant that appears to affect recombination. One of the small groups of genes is located in the first-step-transfer or FST segment; the other two small groups represent newly discovered genetic regions. The large group probably includes most or all of the previously published maps of T5. The apparent genetic discontinuities are discussed in relation to certain anatomical and physiological features that are unique to bacteriophage T5.     

Homologous recombination in a Chinese hamster X-ray-sensitive mutant

We have tested the mutant Chinese hamster cell line xrs-5, which is sensitive to ionizing radiation, for the ability to carry out homologous recombination. In an in vivo assay to detect recombination between two transfected plasmids carrying non-complementing mutants in the neomycin resistance gene, xrs-5 showed a 6-fold reduction in recombination frequency when compared to the parental cell line K1. Extracts prepared from nuclei of the mutant were also tested for their ability to catalyze homologous recombination between the same two plasmids in vitro. Extracts from xrs-5 were found to mediate recombination in this assay at frequencies not significantly different from those obtained with extracts from the parental cell line.     

Attachment site mutants of bacteriophage lambda

Insertion and excision of the chromosome of phage λ occurs by recombination at special regions of the phage and bacterial chromosomes known as attachment sites (alt's). We have isolated att mutants which display reduced recombination frequencies. The mutations are cis-dominant, trans-recessive, and can be crossed into a phage, bacterial or prophage att. These results suggest that the att's, although different over-all, include the same DNA sequence as part of their structure, and that the mutations reside in these sequences. Crosses between mutant and wild-type att's occasionally yield heterozygotes. This result suggests that recombination of the att's generates complementary single-strands via staggered nicks in these common sequences. Recombinant att's are then formed by the interannealing of single-strands of different att's followed by ligation.     

Deletion of Ku70, Ku80, or both causes early aging without substantially increased cancer

Ku70 forms a heterodimer with Ku80, called Ku, that is critical for repairing DNA double-stand breaks by nonhomologous end joining and for maintaining telomeres. Mice with either gene mutated exhibit similar phenotypes that include increased sensitivity to ionizing radiation and severe combined immunodeficiency. However, there are also differences in the reported phenotypes. For example, only Ku70 mutants are reported to exhibit a high incidence of thymic lymphomas while only Ku80 mutants are reported to exhibit early aging with very low cancer levels. There are two explanations for these differences. First, either Ku70 or Ku80 functions outside the Ku heterodimer such that deletion of one is not identical to deletion of the other. Second, divergent genetic backgrounds or environments influence the phenotype. To distinguish between these possibilities, the Ku70 and Ku80 mutations were crossed together to generate Ku70, Ku80, and double-mutant mice in the same genetic background raised in the same environment. We show that these three cohorts have similar phenotypes that most resemble the previous report for Ku80 mutant mice, i.e., early aging without substantially increased cancer levels. Thus, our observations suggest that the Ku heterodimer is important for longevity assurance in mice since divergent genetic backgrounds and/or environments likely account for these previously reported differences.     

Variability of allelic recombination frequencies

Summary Estimates of allelic recombination frequencies are shown to have coefficients of variation of between 20 and 40%. In Coprinus this is true of both high and low recombination frequencies and is also true when the alleles involved show marker effect. This variability is not confined to Coprinus but is a general feature of both meiotic and mitotic allelic recombination. Experimental errors do not make a major contribution to the observed variation althought it has the nature of a sampling variation. It is suggested that the variation arises from the diversity of ways in which the initial errors introduced by hybrid DNA formation can be resolved during the excision-repair stages of recombination. If the enzymes responsible for these processes are present in low concentrations then much latitude can be anticipated in the way the same errors are dealt with by separate, though isogenic, diploid or dikaryotic organisms. Each separate cross is thus interpreted as providing an estimate of the recombination frequency which is but a sample from a varied population of possible estimates of the same recombination frequency. Each pair of alleles exhibits a recombination frequency which, within the statistical boundaries of the general variation, is sufficiently reproducible to be described as a characteristic of them. Combinations of allelic recombination frequencies derived from pair-wise crosses fall into patterns that are sufficiently consistent for allele maps to be drawn; and, providing a sufficient number of replicate crosses have been analysed, the allele map can be shown to be statistically soundly based. Two marker effect situations are examined. One causes reduction of recombination frequency and is probably intrinsic to the mutant site itself, the other causes enhancement of recombination frequency and is due to a factor or factors distinct from the allelic mutant site in the strain in which it was first identified. When intercrossed the two effects counteract one another.     

Molecular basis for the spontaneous generation of colonization-defective mutants of Streptococcus mutans

Spontaneous mutants of Streptococcus mutans GS-5 defective in sucrose-dependent colonization of smooth surfaces are generated at frequencies above the spontaneous mutation rate. Southern blot analysis of such mutants suggested rearrangement of the genes coding for glucosyltransferase (GTF) activity. Two strain GS-5 homologous tandem genes, gtfB and gtfC, coding for GTF-I and GTF-S activities respectively, were demonstrated to undergo recombination when introduced into recombination-proficient Escherichia coli transformants. However, the two genes were quite stable when transformed on a single DNA fragment into a recA mutant of E. coli. The DNA fragment coding for GTF activity from one S. mutans colonization-defective mutant, SP2, was isolated and shown also to have undergone recombination between the gtfB and gtfC genes, resulting in reduced GTF activity. These results are discussed relative to the in vivo generation of colonization-defective mutants in cultures of S. mutans.     

Endonuclease VII is a key component of the mismatch repair mechanism in bacteriophage T4

In previous papers we described an extra recombination mechanism in T4 phage, which contributed to general recombination only when particular mutations were used as geneticmarkers (high recombination or HR markers), whereas it was practically inactive towards other rIIB mutations (low recombination or LR markers). This marker-dependent recombination pathway was identified as a repair of mismatches in recombination heteroduplexes. We suggested that the first step in this pathway, recognition and incision of the mismatch, is performed by endonuclease VII (endo VII) encoded by the T4 gene 49. In the present paper, we tested this hypothesis in vivo. We used an experimental model system that combines site-specific double-strand breaks with the famous advantages of the recombination analysis of bacteriophage T4 rII mutants. We compared recombination of homoallelic HR and LR markers in the S17 and S17 E727 background (amber mutations in the uvsX and in the uvsX and 49 genes, respectively). In S17-crosses, the HR and LR markers retain their respective high-recombination and low-recombination behavior. In S17 E727-crosses, however, the HR and LR markers show no difference in the recombination frequency and both behave as LR markers. We conclude that endo VII is the enzyme that recognizes mismatches in recombinational heteroduplexes and performs their incision. This role for endo VII was suggested previously from biochemical studies, but this is its first in vivo demonstration.     

Unstable ascospore color mutants of Ascobolus immersus

Summary New unstable mutants of Ascobolus immersus involving the color or size of ascospores were sought among spontaneous mutants. Among the 34 unstable mutants isolated, 31 had white spores, 2 had pink spores and 1 had a large sized spores. The unstable mutants involve 11 loci whose mutation leads to white spores and 2 loci whose mutations give pink spores, among the 19 loci known to be implicated in this character; 1 locus is defined by only one large spore mutant. All these genes are localized on at least 7 different chromosomes. Unstable mutants of the same locus may correspond to several different sites, but the number of these sites is very limited.The frequency of unstable mutations was estimated: among 36 mutants belonging to 8 different genes, 20 were stable and 16 were unstable. This high frequency of unstable mutants is undoubtedly underestimated. The moment of reversion of 23 of these new mutants was also sought: 15 of them revert as does mutant B, previously studied, in the very young mycelium, at high temperature and with a reversion frequency of 0.004 to 0.34, according to the mutant; 5 of them revert as mutant 301, also previously studied, during the development of the fruit-body and with a frequency of 0.009 to 0.035; two of these mutants revert very early in the ascospore as soon as the first mitoses or in the very young mycelium at 22° C, with a very high reversion frequency that may reach 1.0; finally, the last mutant studied reverts in the fruit-body with a frequency reaching 0.40, but with modalities different from mutant 301. The mutants of the same locus may revert with different modalities. The same modality may correspond to different sites of the same gene.In unstable double-mutant strains involving two different genes, the reversion of one is independent of the reversion of the other, whether or not the reversion modailities of each mutant are identical.Results indicate the existence of inducers common to several unstable mutants which present the same modalities of reversion.These data support the previously formulated hypothesis of transposable elements.     

Generation of nondefective Rous sarcoma virus by asymmetric recombination between deletion mutants.

A replication-defective deletion mutant of Prague Rous sarcoma virus (RSV), which lacks functional gag, pol, and env genes, was crossed with a transformation-defective deletion mutant derived from Schmidt-Ruppin RSV. Transformation- and replication-competent viruses were generated in the cross. Characterization of one of these rescued viruses indicated that it was a nondefective recombinant containing the src gene of the replication-defective mutant plus the replicative genes of the transformation-defective virus. These results indicate that, contrary to previous reports, asymmetric recombination between RSV deletion mutants can result in the formation of nondefective RSV.     

The transmission disadvantage of yeast mitochondrial intergenic mutants is eliminated in the mgt1 (cce1) background.

A trans-acting element, MGT1 (also called CCE1), has previously been shown to be required in Saccharomyces cerevisiae for the preferential transmission of petite mitochondrial DNA (mtDNA) molecules over wild-type mtDNA molecules. In the present study a possible role of this nuclear gene in the transmission of mtDNA from various respiration-competent mutants was studied. Several of these mutants, lacking one or the other of two biologically active mitochondrial intergenic sequences, were employed in genetic crosses. When these deletion mutants were crossed to the parental wild-type strain in the MGT1/CCE1 background, the progeny contained predominantly wild-type mtDNA molecules. When crosses were performed in the mgt1/cce1 background, the parental molecules interacted in zygotes and underwent homologous recombination but wild-type and intergenic-deletion alleles were transmitted with equal frequencies.     

Allele specificity of genetic recombination in T4 phage using the indicator crossing study method]

The diagrams of relative correction ability of eighteen rII mutants of T4 phage were constructed on the basis of two-factor crosses, which were grouped into indicator series. In each series a pair of closely linked compared markers was crossed against indicator ones, the latter being distant enough so as to avoid simultaneous correction with the compared marker. The differences between the frequencies of wild type recombinants in crosses of two compared markers with indicator ones remained constant within the series and can be used as a measure of the differences between the compared markers in their correction ability. Mutants of base substitution type have small but statistically significant differences in correction ability. Simultaneous substitution of two bases in one codon yields a mutant which shows higher correction ability when compared to the mutant obtained as a result of substitution of only one base in the same codon. Frame shift mutants show much wider range of correctibility: some of them are corrected more rarely and others more frequently than base substitution mutants are.     

Genetic Control of Chromosomal and Plasmid Recombination in STAPHYLOCOCCUS AUREUS

Recombination-deficient mutants of Staphylococcus aureus have been isolated and found to have properties similar to those of recombination-deficient Escherichia coli. In addition, one Rec(-) mutant was found to be defective in the restriction and modification of DNA. There is a marked reduction ( approximately 10(4)-fold) in recombination between penicillinase plasmids in the Rec(-) mutants suggesting that these elements do not encode an efficient recombination system. There is, however, a demonstrable residuum of interplasmid recombination; evidence is lacking on whether this residuum is a plasmid or host function. In the absence of the generalized host recombination system it has been possible to demonstrate that interplasmid recombination occurs during vegetative bacteriophage growth and is presumably mediated by a phage-determined recombination system.     

Analysis of intragenic recombination at wx in rice: correlation between the molecular and genetic maps within the locus.

In plant genomes as well as other eukaryotic genomes, meiotic recombination does not occur uniformly. At the level of the gene, high recombination frequencies are often observed within genetic loci in maize, but this feature of intragenic recombination is not seen at the csr1 locus in Arabidopsis. These observations suggest that meiotic recombination in plant genomes varies considerably among species. In the present study we investigated meiotic recombination at the wx locus in rice. The mutation sites of wx mutants induced by ethyl methanesulfonate (EMS) treatment or gamma-ray irradiation and a spontaneous wx mutant were physically characterized, and the genetic distances between those wx mutation sites were estimated by pollen analysis. Based on these results, the recombination frequency at the wx locus in rice was estimated as 27.3 kb/cM, which was about 10 times higher than the average for the genome, suggesting that there was a radically different rate of meiotic recombination for intra- and intergenic regions in the rice genome.     

Molecular rearrangements between two plasmids of the FII incompatibility group in different recombination—Deficient Escherichia Coli strains

The frequencies and types of plasmid molecular rearrangements generated in different recombinant mutants which carried two plasmids of the FII incompatibility group were studied. The wild-type cells generated molecular rearrangements mainly by interplasmidic recombination with a frequency of 2.4 x 10(-6) per cell per cell doubling. Cells in which RecF was the principal recombination pathway generated different types of molecular rearrangements that involved either both plasmids or one of the plasmids and the chromosome. The frequencies of molecular rearrangements for these cells were 50-fold greater than those of wild-type cells. The recA- cells, even when the RecE pathway was derepressed, generated rearrangements only between one of the plasmids and the chromosome, at very low frequencies (10(-9]. In wild-type cells and in RecF cells, interplasmidic recombination generated mainly cointegrates carrying DNA deletions. These cointegrates were stable in recA- or recA- RecE+ cells, but unstable in wild-type or RecF+ cells. In the latter, the cointegrates generated smaller plasmids with different molecular structures at relatively low frequencies.