The Organization of Genetic Variation for Recombination in DROSOPHILA MELANOGASTER

The amount and form of natural genetic variation for recombination were studied in six lines for which second chromosomes were extracted from a natural population of Drosophila melanogaster. Multiply marked second, X and third chromosomes were used to score recombination. Recombination in the second chromosomes varied in both amount and distribution. These second chromosomes caused variation in the amount and distribution of crossing over in the X chromosome and also caused variation in the amount, but not the distribution, of crossing over in the third chromosome. The total amount of crossing over on a chromosome varied by 12-14%. One small region varied twofold; other regions varied by 16-38%. Lines with less crossing over on one chromosome generally had less crossing over on other chromosomes, the opposite of the standard interchromosomal effect. These results show that modifiers of recombination can affect more than one chromosome, and that the variation exists for fine-scale response to selection on recombination.     

Crossing over is rarely associated with mitotic intragenic recombination in Schizosaccharomyces pombe

Chromosomal rearrangements can result from crossing over during ectopic homologous recombination between dispersed repetitive DNA. We have previously shown that meiotic ectopic recombination between artificially dispersed ade6 heteroalleles in the fission yeast Schizosaccharomyces pombe frequently results in chromosomal rearrangements. The same recombination substrates have been studied in mitotic recombination. Ectopic recombination rates in haploids were approximately 1-4 x 10(-6) recombinants per cell generation, similar to allelic recombination rates in diploids. In contrast, ectopic recombination rates in heterozygous diploids were 2.5-70 times lower than allelic recombination or ectopic recombination in haploids. These results suggest that diploid-specific factors inhibit ectopic recombination. Very few crossovers occurred in ade6 mitotic recombination, either allelic or ectopic. Allelic intragenic recombination was associated with 2% crossing over, and ectopic recombination between multiple different pairing partners showed 1-7% crossing over. These results contrast sharply with the 35-65% crossovers associated with meiotic ade6 recombination and suggest either differential control of resolution of recombination intermediates or alternative pathways of recombination in mitosis and meiosis.     

Crossing over between regions of limited homology in Escherichia coli. RecA-dependent and RecA-independent pathways

We have developed an assay for intermolecular crossing over between circular plasmids carrying variable amounts of homology. Screens of Escherichia coli mutants demonstrated that known recombination functions can only partially account for the observed recombination. Recombination rates increased three to four orders of magnitude as homology rose from 25 to 411 bp. Loss of recA blocked most recombination; however, RecA-independent crossing over predominated at 25 bp and could be detected at all homology lengths. Products of recA-independent recombination were reciprocal in nature. This suggests that RecA-independent recombination may involve a true break-and-join mechanism, but the genetic basis for this mechanism remains unknown. RecA-dependent crossing over occurred primarily by the RecF pathway but considerable recombination occurred independent of both RecF and RecBCD. In many respects, the genetic dependence of RecA-dependent crossing over resembled that reported for single-strand gap repair. Surprisingly, ruvC mutants, in both recA(+) and recA mutant backgrounds, scored as hyperrecombinational. This may occur because RuvC preferentially resolves Holliday junction intermediates, critical to both RecA-dependent and RecA-independent mechanisms, to the noncrossover configuration. Levels of crossing over were increased by defects in DnaB helicase and by oxidative damage, showing that damaged DNA or stalled replication can initiate genetic recombination.     

THE OCCURRENCE OF INTERCALARY AND UNINTERRUPTED MERISTEMS IN THE INTERNODES OF TROPICAL MONOCOTYLEDONS

The distribution of percent of dividing nuclei, parenchyma cell length, total cell number per internode, and total internode length were determined for successive internodes in the apex and growing vegetative internodes of 23 tropical species in 17 families of monocotyledons. Basal intercalary meristems (IM) were found in representatives of Commelinaceae, Cyperaceae, Flagellariaceae, Poaceae, Restionaceae, and Marantaceae. Uninterrupted meristems (UM) which are confined progressively to the upper region of the internode and are not isolated meristematic regions were found in the Costaceae, Dioscoreaceae, Philesiaceae, Smilacaceae, Agavaceae, Araceae, Arecaceae, Liliaceae, Pandanaceae, and Zingiberaceae. Both IM and UM were found in different species of Orchidaceae. The only morphological trait correlated with meristem type was presence of sheathing leaf bases in all species with IM. Both IM and UM are interpreted as extensions of the primary elongating meristem; the IM is disjunct, and the UM is continuous with it. The phytomer growth unit and the presence of internodal IM's cannot be applied generally to the monocotyledons.     

The relationship between homology length and crossing over during the repair of a broken chromosome

Homologous recombination can result in the transfer of genetic information from one DNA molecule to another (gene conversion). These events are often accompanied by a reciprocal exchange between the interacting molecules (termed "crossing over"). This association suggests that the two types of events could be mechanistically related. We have analyzed the repair, by homologous recombination, of a broken chromosome in yeast. We show that gene conversion can be uncoupled from crossing over when the length of homology of the interacting substrates is below a certain threshold. In addition, a minimal length of homology on each broken chromosomal arm is needed for crossing over. We also show that the coupling between gene conversion and crossing over is affected by the mismatch repair system; mutations in the MSH2 or MSH6 genes cause an increase in the crossing over observed for short alleles. Our results provide a mechanism to explain how chromosomal recombinational repair can take place without altering the stability of the genome.     

Étude de l'action de l'aminoptérine sur la recombinaison génique chez Drosophila melanogaster

Study of the action of aminopterin on genic recombination in Drosophila melanogaster—A study was made of the action, during meiosis, of aminopterin, inhibitor of nucleotide metabolism. An increase of the rate of crossing over was observed. This increase was studied on two systems, by using highly linked markers, so as to minimize the amount of double crossing over: vg-su, on chromosome II and y-w ^a, on the X chromosome. It is shown that aminopterin induces a significant increase of recombination. The independence of the two systems makes plausible that aminopterin could act on the whole genome at a meiotic level.     

THE CONTRIBUTION OF NEW MUTATIONS TO GENOTYPE-ENVIRONMENT INTERACTION FOR FITNESS IN DROSOPHILA MELANOGASTER

Many studies have documented the existence of genotype-environment interaction (GEI) for traits closely related to fitness in natural populations. A type of GEI that is commonly observed is changes in the fitness ranking of genetic groups (families, clones, or inbred lines) in different environments. We refer to such changes in ranking as crossing of reaction norms for fitness. A common interpretation of crossing of reaction norms for fitness is that selection favors different alleles in the different environments (i.e., that “trade-offs” exist). If this is the case, selection could maintain genetic variation, and even lead to reproductive isolation between subpopulations using different environments. Even if the same alleles are favored in every environment, however, deleterious mutations that vary in the magnitude of their effect depending on environment could cause reaction norms for fitness to cross. If deleterious mutations with environment-dependent effects are responsible for maintaining much of the variation leading to crossing of reaction norms for fitness in natural populations, it should be possible to observe crossing of reaction norms for fitness among otherwise genetically identical lines bearing newly arisen spontaneous mutations. We examined the contribution of new mutations to GEI for fitness in Drosophila melanogaster. Eighteen lines were derived from a common, highly inbred base stock, and maintained at a population size of 10 pairs for over 200 generations, to allow them to accumulate spontaneous mutations. Because of the small population size of the lines, selection against mildly deleterious mutations should have been relatively ineffective. The lines were tested for productivity (number of surviving adult progeny from a standard number of parents) in five different environmental treatments, comprising different food media, temperatures, and levels of competition. The lines showed highly significant GEI for productivity, owing largely to considerable changes in ranking in the different environments. We conclude that mutations that are deleterious on average, but whose quantitative effects depend on environment, could be responsible for maintaining much of the variation leading to crossing of reaction norms for fitness that has been observed in samples of D. melanogaster from the wild.     

Leagues of their own: sexually dimorphic features of meiotic prophase I

Meiosis is a conserved cell division process that is used by sexually reproducing organisms to generate haploid gametes. Males and females produce different end products of meiosis: eggs (females) and sperm (males). In addition, these unique end products demonstrate sex-specific differences that occur throughout meiosis to produce the final genetic material that is packaged into distinct gametes with unique extracellular morphologies and nuclear sizes. These sexually dimorphic features of meiosis include the meiotic chromosome architecture, in which both the lengths of the chromosomes and the requirement for specific meiotic axis proteins being different between the sexes. Moreover, these changes likely cause sex-specific changes in the recombination landscape with the sex that has the longer chromosomes usually obtaining more crossovers. Additionally, epigenetic regulation of meiosis may contribute to sexually dimorphic recombination landscapes. Here we explore the sexually dimorphic features of both the chromosome axis and crossing over for each stage of meiotic prophase I in Mus musculus, Caenorhabditis elegans, and Arabidopsis thaliana. Furthermore, we consider how sex-specific changes in the meiotic chromosome axes and the epigenetic landscape may function together to regulate crossing over in each sex, indicating that the mechanisms controlling crossing over may be different in oogenesis and spermatogenesis.

     

Chromosome size-dependent control of meiotic reciprocal recombination in Saccharomyces cerevisiae: the role of crossover interference.

In the yeast Saccharomyces cerevisiae, small chromosomes undergo meiotic reciprocal recombination (crossing over) at rates (centimorgans per kilobases) greater than those of large chromosomes, and recombination rates respond directly to changes in the total size of a chromosomal DNA molecule. This phenomenon, termed chromosome size-dependent control of meiotic reciprocal recombination, has been suggested to be important for ensuring that homologous chromosomes cross over during meiosis. The mechanism of this regulation was investigated by analyzing recombination in identical genetic intervals present on different size chromosomes. The results indicate that chromosome size-dependent control is due to different amounts of crossover interference. Large chromosomes have high levels of interference while small chromosomes have much lower levels of interference. A model for how crossover interference directly responds to chromosome size is presented. In addition, chromosome size-dependent control was shown to lower the frequency of homologous chromosomes that failed to undergo crossovers, suggesting that this control is an integral part of the mechanism for ensuring meiotic crossing over between homologous chromosomes.     

The function of recombinations occurring in the process of DNA replication in Escherichia coli

In a number of works dealing with the relationship between replication and recombination in bacteria, it is assumed that recombinations permit the replication forks to resume moving after having stopped at the damage sites of the template DNA. As an evidence for recombination occurring during DNA replication, the involvement in this process of proteins RuvABC and RecG, providing processing of the Holliday junctions after recombination, is considered. However, it has been shown that these proteins are not essential for resuming DNA synthesis after an exposure of bacteria to UV light. These data cast doubt on the necessity of recombination for reactivation of replication initiated in the oriC region. Studying recombination in tandem duplications in Escherichia coli showed that during replication, unequal crossing over occurs between direct DNA repeats of sister chromosomes. In wild strains, this crossing over results in tandem duplications, thereby enhancing the expression of certain genes. Thus, recombination of two types occurs during DNA replication: unequal crossing over leading to duplications and homologous exchange, responsible for post-replication DNA repair. The unequal exchange constitutes a component of SOS response of the cell to deterioration of the environment.     

THE EFFECTS OF AUXINS AND KINETIN ON XYLEM DIFFERENTIATION IN THE PEA EPICOTYL

Sorokin , Helen P., S. N. Mathur , and Kenneth V. Thimann . (Harvard U., Cambridge, Mass.) The effects of auxins and kinetin on xylem differentiation in the pea epicotyl. Amer. Jour. Bot. 49(5): 444–454. Illus. 1962.—Treatment of isolated segments from the second internode of etiolated ‘Alaska’ pea epicotyls with indoleacetic acid or 2,4-D results in: (1) activation of fascicular cambium, and initiation of some interfascicular cambium, resulting in abundant production of secondary xylem, and in formation of hyperplastic tissue; (2) partial or even total occlusion of proto- and metaxylem. The secondary xylem formed consists of short vessel members with scalariformly reticulate or pitted walls, which often lack vertical connection with each other, being interrupted by unlignified cells. When IAA is used, the hyperplastic growth mainly takes the form of root primordia, whereas 2,4-D initiates the formation of callus, but not of root primordia. The growth of this callus causes a characteristic split at the base of the internode. Treatment with kinetin, alone or in combination with the auxin, changes the above structure markedly. It leads to the initiation, over the entire circumference of the core of the internode, of a still more active cambium, which forms several layers of secondary xylem; this consists mainly of long vessel members with pitted walls. Hyperplastic growth is completely absent, and the xylem does not become occluded. Thus the effect of kinetin is to make the xylem more normal and to alter the epicotyl structure from herbaceous to more-or-less woody.     

Control of crossing over

The Holliday junction is a central intermediate in homologous recombination. It consists of a four-way structure that can be resolved by cleavage to give either the crossover or noncrossover products observed. We show here that the formation of these products is controlled by the E. coli resolvasome (RuvABC) in such way that double-strand break repair (DSBR) leads to crossing over and single-strand gap repair (SSGR) does not lead to crossing over. We argue that the positioning of the RuvABC complex and its consequent direction of junction-cleavage is not random. In fact, the action of the RuvABC complex avoids crossing over in the most commonly predicted situations where Holliday junctions are encountered in DNA replication and repair. Our observations suggest that the positioning of the resolvasome may provide a general biochemical mechanism by which cells can control crossing over in recombination.     

Recombinations occurring in the process of DNA replication in Escherichia coli

In a number of works dealing with the relationship between replication and recombination in bacteria, it is assumed that recombinations permit the replication forks to resume moving after having stopped at the damage sites of the template DNA. As an evidence for recombination occurring during DNA replication, the involvement in this process of proteins RuvABC and RecG, providing processing of the Holliday junctions after recombination, is considered. However, it has been shown that these proteins are not essential for resuming DNA synthesis after an exposure of bacteria to UV light. These data cast doubt on the necessity of recombination for reactivation of replication initiated in the oriC region. Studying recombination in tandem duplications in Escherichia coli showed that during replication, unequal crossing over occurs between direct DNA repeats of sister chromosomes. In wild strains, this crossing over results in tandem duplications, thereby enhancing the expression of certain genes. Thus, recombination of two types occurs during DNA replication: unequal crossing over leading to duplications and homologous exchange, responsible for post-replication DNA repair. The unequal exchange constitutes a component of SOS response of the cell to deterioration of the environment.     

Studies on crossover-specific mutants and the distribution of crossing over in Drosophila females

In Drosophila females, the majority of recombination events do not become crossovers and those that do occur are nonrandomly distributed. Furthermore, a group of Drosophila mutants specifically reduce crossing over, suggesting that crossovers depend on different gene products than noncrossovers. In mei-218 mutants, crossing over is reduced by approximately 90% while noncrossovers and the initiation of recombination remain unchanged. Importantly, the residual crossovers have a more random distribution than wild-type. It has been proposed that mei-218 has a role in establishing the crossover distribution by determining which recombination sites become crossovers. Surprisingly, a diverse group of genes, including those required for double strand break (DSB) formation or repair, have an effect on crossover distribution. Not all of these mutants, however, have a crossover-specific defect like mei-218 and it is not understood why some crossover-defective mutants alter the distribution of crossovers. Intragenic recombination experiments suggest that mei-218 is required for a molecular transition of the recombination intermediate late in the DSB repair pathway. We propose that the changes in crossover distribution in some crossover-defective mutants are a secondary consequence of the crossover reductions. This may be the activation of a regulatory system that ensures at least one crossover per chromosome, and which compensates for an absence of crossovers by attempting to generate them at random locations.     

Effects of Mutagen-Sensitive Mus Mutations on Spontaneous Mitotic Recombination in Aspergillus

Methyl methane-sulfonate (MMS)-sensitive, radiation-induced mutants of Aspergillus were shown to define nine new DNA repair genes, musK to musS. To test mus mutations for effects on mitotic recombination, intergenic crossing over was assayed between color markers and their centromeres, and intragenic recombination between two distinguishable adE alleles. Of eight mutants analyzed, four showed significant deviations from mus+ controls in both tests. Two mutations, musK and musL, reduced recombination, while musN and musQ caused increases. In contrast, musO diploids produced significantly higher levels only for intragenic recombination. Effects were relatively small, but averages between hypo- and hyperrec mus differed 15-20-fold. In musL diploids, most of the rare color segregants resulted from mitotic malsegregation rather than intergenic crossing over. This indicates that the musL gene product is required for recombination and that DNA lesions lead to chromosome loss when it is deficient. In addition, analysis of the genotypes of intragenic (ad+) recombinants showed that the musL mutation specifically reduced single allele conversion but increased complex conversion types (especially recombinants homozygous for ad+). Similar analysis revealed differences between the effects of two hyperrec mutations; musN apparently caused high levels solely of mitotic crossing over, while musQ increased various conversion types but not reciprocal crossovers. These results suggest that mitotic gene conversion and crossing over, while generally associated, are affected differentially in some of the mus strains of Aspergillus nidulans.     

Use of fluorescent protein to analyse recombination at three loci in Neurospora crassa

We have inserted a histone H1-GFP fusion gene adjacent to three loci on different chromosomes of Neurospora crassa and made mating pairs in which a wild type version of GFP is crossed to one with a mutation in the 5' end of GFP. The loci are his-3, am and his-5, chosen because recombination mechanisms appear to differ between his-3 and am, and because crossing over adjacent to his-5, like his-3, is regulated by rec-2. At his-3, the frequencies of crossing over between GFP and the centromere and of conversion of 5'GFP to GFP(+) are comparable to those obtained by classical recombination assays, as is the effect of rec-2 on these frequencies, suggesting that our system does not alter the process of recombination. At each locus we have obtained sufficient data, on both gene conversion and crossing over, to be able to assess the effect of deletion of any gene involved in recombination. In addition, crosses between a GFP(+) strain and one with normal sequence at all three loci have been used to measure the interval to the centromere and to show that GFP experiences gene conversion with this system. Since any gene expressed in meiosis is silenced in Neurospora if hemizygous, any of our GFP(+) strains can be used as a quick screen to determine if a gene deleted by the Neurospora Genome Project is involved in crossing over or gene conversion.     

Genetic analysis of eight linked polymorphisms within the human immunoglobulin heavy-chain region.

Genetic analyses of multiple restriction fragment length polymorphisms, revealed by a single DNA probe containing the switch region of the immunoglobulin constant heavy-chain (IgCH) mu gene, are presented here in detail. Five of the polymorphic loci segregate in complete linkage with IgCH allotypic markers, while one appears to be located at more than 10 centimorgans from the IgCH region. A study of over 100 random haplotypes typed at eight linked loci, including the Ig switch polymorphisms and the classical Gm-Am allotypes, allowed us to construct an evolutionary tree by which each haplotypic variant can be derived one from the other either by single-step mutation or by recombination. A few of the recombinant haplotypes appeared to carry large DNA duplications that could be explained by unequal crossing over; others might postulate gene-conversion events. Linkage disequilibria observed between the IgCH-linked loci were compared with expected ones. A heterogeneous distribution of recombination rates is clearly documented, a "hot" region of recombination being present between the gamma 2 and switch alpha 2 loci.     

Function of crossing-over

The literature data are considered concerning the significance of genetic recombination and crossing over. An obvious result of recombination is production of the genotypically diverse offspring, but the main role of recombination consists of combining the genes from diverging subspecies and races, thus maintaining a rather wide ecological potential of a species. This effect of recombination substantiates the tendency for increasing complexity of organic forms in progressive evolution. Accordingly, evolution is considered as a chain of recombinational "syntheses". The literature data treating crossing over as a mechanism of DNA repair are discussed. This function of crossing over is interpreted, based on a notion implying, from the composition of genetic code, that a crystalline associate composed of bases as free molecules precedes the appearance of DNA in evolution. The stability of the crystalline associate of bases was due to "balanced" distribution of bases for their electrochemical properties. The degeneracy of genetic code seems to provide possibility of construction of the electrostatically "balanced" base sequences in highly expressed bacterial genes. Crossing over possibly recovers "balanced" distribution of bases for their electrochemical properties and thus "repairs" a high level of heterocatalytic DNA activity.     

The Effects of Insertions on Mammalian Intrachromosomal Recombination

We examined the effects of insertion mutations on intrachromosomal recombination. A series of mouse L cell lines carrying mutant herpes simplex virus thymidine kinase (tk) heteroalleles was generated; these lines differed in the nature of their insertion mutations. In direct repeat lines with different large insertions in each gene, there was a 20-fold drop in gene conversion rate and only a five-fold drop in crossover rate relative to the analogous rates in lines with small insertions in each gene. Surprisingly, in direct repeat lines carrying the same large insertion in each gene, there was a larger drop in both types of recombination. When intrachromosomal recombination between inverted repeat tk genes with different large insertions was examined, we found that the rate of gene conversion dropped five-fold relative to small insertions, while the rate of crossing over was unaffected. The differential effects on conversion and crossing over imply that gene conversion is more sensitive to insertion mutation size. Finally, the fraction of gene conversions associated with a crossover increased from 2% for inverted repeats with small insertions to 18% for inverted repeats with large insertions. One interpretation of this finding is that during intrachromosomal recombination in mouse cells long conversion tracts are more often associated with crossing over.     

Separation of roles of Zip1 in meiosis revealed in heterozygous mutants of <Emphasis Type="Italic">Saccharomyces cerevisiae</Emphasis>

Synapsis of homologs during meiotic prophase I is associated with a protein complex built along the bivalents—the synaptonemal complex (SC). Mutations in the SC-component gene ZIP1 diminish SC formation, leading to reduced recombination levels and low spore viability. Here we show that in SK1 strains heterozygous for a deletion of ZIP1 in certain regions meiotic interference are impaired with no decrease in recombination levels. The extent of synapsis is over all reduced and NDJ levels of a large endogenous chromosome and of artificial chromosomes (YACs) rise to twice the level of wild type strains. A substantial proportion of mis-segregating YACs had undergone crossing over. This demonstrates that different functions of Zip1 display differential sensitivities to changes in expression levels.