Mechanism of gene conversion in Ascobolus immersus. II. The relationships between the genetic alterations in b 1 or b 2 mutants and their conversion spectrum

Restoration to the parental genotype of mismatches formed in recombinant DNA heteroduplex

Crosses were set up, using the b2 locus of Ascobolus immersus, to detect and measure the restoration of the parental genotype of a chromatid from hetero-duplex. From the results it can be concluded that: (1) restoration occurs, and its frequency is comparable to the frequency of conversion; (2) the relative frequency of conversion and restoration on the two homologous chromatids is that expected if the disparity in conversion to mutant and to wild-type of the marker is caused by the decision whether to excise the mutant or wild-type chain. This decision is the same on both chromatids. However, when all data are pooled, a slight, but significant, excess of conversion over restoration is found. The cause of this in discussed; (3) the absence of an excess of restoration over conversion is taken to imply that, in this system, the length of heteroduplex formed in an event is continuous; (4) these findings support the interpretation of tetrads where a crossover is separated from conversion, that they arise by independent correction giving both conversion and restoration in a heteroduplex tract continuous with the crossover.

Disparity of gene conversion in frameshift mutants located in locus b2 of Ascobolus immersus

The frequency of conversion and the disparity in the direction of conversion were studied for six frameshift mutants lying in locus b2 of Ascobolus immersus and giving more 2 wild type:6 mutant (2+6m) than 6 wild type:2 mutant (6+2m) aberrant asci (type B). The frequency of conversion decreased from left to right in the locus. The disparity steadily increased from left to right and then reached a plateau. Twenty-two frameshift mutants giving more 6+2m than 2+6m aberrant asci (type A) and closely linked to three type B mutants were also studied; they showed the same frequency of conversion and the same disparity (but in the opposite direction) as the type B mutant to which they are linked. The polar variation of both the frequency of conversion and the disparity as a function of position were expected on the basis of a previous study of 15 mutants giving postmeiotic segregations and located in locus b2. This variation is assumed to reflect the existence of a preferential region for the initiation of hybrid DNA (HDNA) during recombination and a duality in the distribution of this HDNA, with preponderant asymmetrical HDNA near the starting point and preponderant symmetrical HDNA farther from it.

The extent to which gene conversion can change allele frequencies in populations

The gene conversion parameters which affect allele frequencies in populations are defined, and their ranges and typical values are given for several genera of fungi, where meiotic octads and tetrads provide the best information on conversion. Both gene conversion and disparity in direction of conversion are common. Data from Ascobolus immersus show that conversion properties are largely stable with time, but can be changed environmentally and by genetic conversion control factors. Equations are given for the interactions of selection, mutation and gene conversion in determining equilibrium frequencies. Numerical examples, using typical values of conversion parameters from the fungal data, show that for alleles which are selectively neutral or have very low selection coefficients, conversion will often have very large effects on their equilibrium frequencies and may lead to fixation. Where selection coefficients are higher, conversion has major effects on the frequencies of deleterious recessive alleles, but lesser effects on deleterious dominant alleles: a critical comparison is that of s with 2y. The available estimates for conversion parameters (at least in fungi) are of a magnitude to make gene conversion an important factor in evolution.

Abuffspore colour mutant inSordaria brevicollisshowing high-frequency conversion

A mutant, YS17, at thebuffspore colour locus inSordaria brevicollis, when crossed with wild type, gives rise to aberrant asci with a frequency over 10 times that of otherbuffmutants. Over 98% of the aberrant asci have 6 wild type and 2 mutant spores. From tests with anotherbuffmutant it is concluded that loss of the mutant spore colour when YS17 shows conversion to wild type is associated with loss of the high frequency conversion, and that both characters are caused by the same mutation. A methionine-requiring mutant (met-1) has been obtained that maps 5 units to the left ofbuff, and this, together with the nicotinamide-requiring mutant (nic-1) 2 units to the right, has provided flanking markers forbuffthat can be scored with complete reliability. Crosses between YS17 and 28 otherbuffmutants have revealed close linkage to three of them which map to its right on the basis of flanking marker behaviour, all the others mapping to its left. The frequency of postmeiotic segregation at the sites ofbuffmutants near to the site of YS17 is greatly increased in the presence of YS17, and occurs in the chromatid showing conversion to wild type at YS17.

From these and other results, obtained largely by ascus analysis, the following conclusions have been drawn.

(1) The YS17 mutation is probably acting as a recognition site for an endonuclease that initiates recombination, with the result that the frequency of heteroduplex DNA within thebuffgene is much increased.

(2) The recombination initiated at YS17 is asymmetric (or at least pre-dominantly so), with the YS17 site acting as a recipient of a nucleotide chain from the other parent, not a donor to it.

(3) The frequency of crossing over associated with conversion at YS17 is variable: about 30% in crosses with most of thebuffmutants, about half this value in crosses with wild type, and almost zero in crosses with closely-linkedbuffmutants.

(4) In about one third of the crossover asci in crosses between YS17 and otherbuffmutants the crossover is not adjacent to the site of YS17 but separated from it by the site of the allele, which shows normal 4:4 segregation.

(5) It seems necessary to revive the idea of more than one recombination event in proximity, a non-crossover conversion event sometimes leading to a second event – a crossover – in the vicinity. It is tentatively suggested that both might be controlled by a single enzyme aggregate.

Mutagen specificity in conversion pattern inSordaria brevicollis

A total of 39 mutants at thegrey-3,grey-4andgrey-5spore colour loci inSordaria brevicollishave been investigated for conversion pattern by crossing them with wild type and counting aberrant asci. Twenty-one of the mutants were obtained with ICR170 and all showed postmeiotic segregation only rarely (0–8% of the aberrant asci); two showed conversion predominantly to wild type (class A) and the other 19 predominantly to mutant (class B). Six mutants were obtained with ethylmethane sulphonate and one with nitrosoguanidine, and they all showed postmeiotic segregation frequently (14–54% of the aberrant asci) and conversion usually about equally frequently in each direction, though with considerable diversity between mutants (class C). Eleven UV-induced mutants comprised one of class B and ten of class C. There was considerable variation in aberrant ascus frequency between alleles, but conversion pattern seemed to be independent of this frequency.

Parameters in gene conversion: An algebraic analysis of the hybrid DNA model at thegraylocus ofSordaria fimicola

We have extended previous algebraic analyses of aberrant segregation at thegraylocus ofSordaria fimicola(Whitehouse, 1965; Emerson, 1966; Fincham, Hill & Reeve, 1980) to the more complex situation where aberrant segregations are detected in three factor crosses involving two flanking markers. This algebra has been applied to sevengrayalleles which have been extensively characterized for their pattern of gene conversion and postmeiotic segregation by Kitani & Olive (1967). It is based on seven major types of aberrant segregation which can be distinguished in the presence of flanking markers spanning the converting site, and allows us to use up to six parameters to describe hDNA formation and mismatch repair. We present solutions which predict a spectrum of aberrant segregation fitting the experimental data at theP> 0·05 level for six of the seven alleles tested. They are consistent with the following properties of hDNA at thegraylocus: (1) the single stranded DNA transferred during hDNA formation has always the same chemical polarity. (2) hDNA is mostly, if not entirely, symmetric, and its probability of formation is constant over the whole gene. (3) Disparity in aberrant segregation is mostly, if not entirely due to disparity in mismatch repair.

Gene conversion disparity in yeast: its extent, multiple origins, and effects on allele frequencies

The extent of disparity in gene conversion direction in yeast (Saccharomyces cerevisiae) is important for recombination mechanisms and for effects of conversion on allele frequencies in populations. An analysis of published and unpublished data demonstrates that yeast frequently shows significant and extensive conversion disparity, contrary to many published statements. All types of mutation--base-substitutions, frameshifts and longer deletions and additions--can show significant 6:2/2:6 and/or 5:3/3:5 disparity. There was little correlation between the occurrence of 6:2/2:6 and 5:3/3:5 disparities; when both were significant, they were more often in opposite directions than in the same direction. Surprisingly, there was little correlation between a mutation's molecular nature and its disparity properties, which generally seem unpredictable. Disparity in yeast has multiple origins. From the equations discussed, all disparity types can be explained by one or more of: correction direction disparity, chromatid invasion disparity (including cases caused by different frequencies of double-strand breaks or gaps in nonsister homologous chromatids), strand invasion disparity, and different correction frequencies for the two types of mispair for a heterozygous mutation. Levels of overall disparity and of conversion frequency mean that conversion must often change allele frequencies in sexually reproducing yeast populations.

High-frequency gene conversion between repeated C mu sequences integrated at the chromosomal immunoglobulin mu locus in mouse hybridoma cells

The occurrence of mitotic recombination between repeated immunoglobulin mu gene constant (C mu) region sequences stably integrated at the haploid chromosomal immunoglobulin mu locus in murine hybridoma cells was investigated. Recombination events are detected as changes in hapten-specific immunoglobulin M production. Recombination occurs with high frequency (0.5 to 0.8%) by a mechanism consistent with gene conversion. A double-strand break repair-like mechanism is suggested by the finding that repair of a 2-bp deletion mutation and a 2-bp insertion mutation occurs with parity in a donor-directed manner. The results also suggest that the gene conversion process is directional in that the 5' C mu region sequence is preferentially converted.

Further evidence that aberrant segregation and crossing over in Sordaria brevicollis may be discrete, though associated, events

Crosses were made between buff spore colour mutants in Sordaria brevicollis in the presence of flanking markers. Recombinant asci with one or more wild-type spores were isolated and the spores germinated and scored for buff and flanking marker genotype. The buff genotype was determined by back-crossing to each parent and looking for recombinants. It was found that the majority of the recombinant asci had aberrant segregation at one or other mutant site but not both. It was inferred that in the recombinants hybrid DNA rarely extended to both sites. When the aberrant segregation was associated with crossing-over, the crossovers were situated at either end of the gene rather than between the allelic sites where the hybrid DNA was believed to terminate. Thus, some of the crossovers were separated from the site of the aberrant segregation by a site apparently not involved in hybrid DNA and none was in the position predicted by the Meselson-Radding model, that is, where the hybrid DNA terminates.

Aberrant segregation patterns and gene mappability inAscobolus immersus

Crosses between various types of mutant giving specific patterns of aberrant segregation were performed in theb2spore colour locus ofAscobolus immersus. The map of 41 mutations showing various patterns of aberrant segregation was established. The frequency of wild-type recombinants and the map additivity, map expansion and map contraction characteristics were shown to be strongly dependent upon the pattern of aberrant segregation of the mutations used. Mutations giving no postmeiotic segregation and an excess of conversion to wild type over conversion to mutant exhibit map expansion in small intervals and a strong map contraction in large intervals. Mutations giving postmeiotic segregations also exhibit map contraction in large intervals. Mutations giving no postmeiotic segregations and an excess of conversion to mutant over conversion to wild type show map additivity and thus provide a simple way for devising gene maps. The relationship between the mapping properties and the pattern of aberrant segregations is accounted for when considering parameters of gene conversion: frequency and distribution of hybrid DNA, frequency and direction of mismatch correction.

Characterization of genes which influence allelic recombination in Coprinus cinereus

Previous work has shown that recombination between alleles of the ftr cistron is disturbed by two "marker effects", one reduces the recombination frequency and the other increases it. These effects have been studied further. The results show that both enhancement and reduction are controlled by single genes which seem to be independent of one another. The genes are symbolized recE (for recombination enhancement) and recR (recombination reduction). Both genes are fully dominant, non-additive, and segregate readily from one another and from the ftr cistron. Recombination between any pair of ftr alleles is increased when recE is part of the genotype, but recE has no effect on recombination between alleles of the me-5 locus. On the other hand, the reduction of recombination caused by recR in the ftr cistron is polarised and alley-specific, but recR increases the frequency of recombination between me-5 alleles. The data are interpreted on the basis that the rec-gene products may be involved in chromatid pairing and that polymorphic variants of them cause differences in pairing which, by altering the opportunities for recombination, are observed as differences in allelic recombination frequency.

The recognition of mismatched base pairs in DNA by DNase I from Ustilago maydis

The activity of Ustilago maydis DNase I, an enzyme implicated in genetic recombination, on DNA substrates containing unpaired or mismatched bases, was examined. The enzyme nicked supercoiled PM-2 molecules, converting these to relaxed circular and linear molecules. Discrete double stranded linear fragments smaller than unit length were also observed after digestion at high enzyme concentration. Heteroduplex molecules were constructed using phi80 bacteriophage derivatives which contained single base substitutions within the E. coli tRNA1tyr gene. Single and double stranded nicking at or near the single mismatched site was observed with three out of the five pairs of heteroduplexes.

Biochemical analysis of genetic recombination in eukaryotes

Recent studies concerning molecular mechanisms of genetic recombination in eukaryotes are reviewed. Since many of these studies have focused on the testable predictions arising from the hybrid DNA theory of genetic recombination, this theory is summarised. Experiments to determine the time of meiotic crossing-over and the structure of the synaptonemal complex which facilitates meiotic crossing-over are described. Investigations of DNA nicking and repair events implicated in recombination are discussed. Properties of proteins which may facilitate hybrid DNA formation, and biochemical evidence for hybrid DNA formation are presented. Finally, a nuclease which has been implicated in gene conversion is described.

Mitochondrial genetics in Bakers' yeast: a molecular mechanism for recombinational polarity and suppressiveness

Recombinational polarity and suppressiveness are two well-known but puzzling cytoplasmic genetic phenomena in bakers' yeast, Saccharomyces cerevisiae. Little progress has been made in characterizing the underlying molecular mechanisms of these phenomena. In this paper we describe a molecular model for recombinational polarity that is compatible with the available genetic evidence. The model stresses the role of small deletions and excision/repair processes in otherwise canonical recombinational events. According to the model, both phenomena require recombination and may share mechanistic elements.