Effect of limited homology on gene conversion in a Saccharomyces cerevisiae plasmid recombination system.

Ahn, Bokyung; Dornfeld, Kenneth J.; Fagrelius, Thomas J.; Livingston, Dennis

doi:10.1128/mcb.8.6.2442

Cited by 65 publications

(41 citation statements)

References 31 publications

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“…The questions of how long the stretch of homology must be and how closely the sequences must match within this stretch have been approached with various experimental systems in bacteria (2)(3)(4)(5), yeast (6)(7)(8), and mammals (9)(10)(11)(12)(13)(14)(15). The general conclusion from these studies is that the recombination mechanisms are much more sensitive to degree of homology than would be predicted purely on the basis of DNA-duplex stability.…”

Section: Introductionmentioning

confidence: 86%

DNA homology requirements for mitotic gap repair in Drosophila.

Nassif

Engels

1993

Proc. Natl. Acad. Sci. U.S.A.

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We used P transposable-element mobilization to study the repair of double-strand DNA breaks in Drosophila melanogaster premeiotic germ cells. Distribution of conversion tracts was found to be largely unaffected by changes in the length of sequence homology between the broken ends and the template, suggesting that only a short match is required. However, the frequency of repair was highly sensitive to single-base mismatches within the homologous region, ranging from 19% reversion when there were no mismatches to 5% when 15 mismatches were present over a 3455-bp span.Efficient recombination between two stretches of DNA requires that the two sequences locate each other in the genome and form the stable recombinational intermediate complex. Some degree of homology between the two interacting sequences is needed for efficient recombination by most pathways (1).The questions of how long the stretch of homology must be and how closely the sequences must match within this stretch have been approached with various experimental systems in bacteria (2-5), yeast (6-8), and mammals (9-15). The general conclusion from these studies is that the recombination mechanisms are much more sensitive to degree of homology than would be predicted purely on the basis of DNA-duplex stability. In Escherichia coli, for example, a single-base mismatch in 53 bp resulted in a 4-fold reduction in recombination (4), and a 40-fold reduction was seen when the mismatch proportion was increased to 10% (3). The minimum length of homology required has been estimated at 20-50 bp for E. coli (2-4) and 63-89 bp for Saccharomyces cerevisiae (7). For mammalian cells, estimates range from 163 to 300 bp (9, 13), but some studies indicate efficient recombination with as little as 20 bp (9, 10). One suggestion (2, 5) is that the length and stringency of homology requirements reflect an evolutionary adaptation to prevent recombination between unrelated sites and are, thus, expected to depend on size and complexity of the genome.In this report we make use of the recently developed method of transposable-element-induced gap repair to address the question of homology requirements for recombinational DNA repair. P elements are DNA transposons that have been used for a variety oftechniques in Drosophila (16). Recent data (17-19) led to a model in which P element excision leaves behind a double-stranded DNA break. According to this interpretation, such breaks are often extended into various-sized gaps through exonuclease activity. Repair occurs when the ends of the gap invade a homologous DNA sequence from which to copy the missing genetic information. The result is unidirectional transfer of information from the template sequence to the excision site. The template can be the sister strand or an ectopic site located elsewhere in the genome or extrachromosomally (17,18,20).The system allows us to examine the length and stringency of homology requirements in Drosophila melanogaster. A further advantage of this approach is that recombination occurs between sequ...

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Section: Introductionmentioning

confidence: 86%

DNA homology requirements for mitotic gap repair in Drosophila.

Nassif

Engels

1993

Proc. Natl. Acad. Sci. U.S.A.

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“…Recent duplicates are more similar across their entire length, not in particular regions (Nei et al 1997). Gene conversion occurs within individuals and is more likely to happen between similar paralogs, as increased sequence similarity facilitates ectopic strand invasion (Ahn et al 1988;Elliott et al 1998). Therefore, orthology breaks down in converted regions, the opposite outcome of functional constraint.…”

Section: Distribution Of Gene Conversion Events In Mammalian and Zebrmentioning

confidence: 99%

“…Gene conversion has been detected in genes coding for other cell adhesion molecules (Gally and Edelman 1992;Gallin 1998). Gene conversion is also indicated by the fact that homogenization is occurring among closely related paralogs, which are more likely to participate in ectopic conversion events due to their increased sequence similarity (Ahn et al 1988;Elliott et al 1998). In zebrafish, homogenization is also occurring among paralogs in close physical proximity (Figs.…”

Section: Figurementioning

confidence: 99%

Gene Conversion and the Evolution of Protocadherin Gene Cluster Diversity

Noonan¹,

Grimwood²,

Schmutz³

et al. 2004

Genome Res.

102

125

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The synaptic cell adhesion molecules encoded by the protocadherin gene cluster are hypothesized to provide a molecular code involved in the generation of synaptic complexity in the developing brain. Variation in copy number and sequence content of protocadherin cluster genes among vertebrate species could reflect adaptive differences in protocadherin function. We have completed an analysis of zebrafish protocadherin cluster genes. Zebrafish have two unlinked protocadherin clusters, DrPcdh1 and DrPcdh2. Like mammalian protocadherin clusters, DrPcdh1 has both ␣ and ␥ variable and constant region exons. A consensus protocadherin promoter motif sequence identified in mammals is also conserved in zebrafish. Few orthologous relationships, however, are apparent between zebrafish and mammalian protocadherin proteins. Here we show that protocadherin cluster genes in human, mouse, rat, and zebrafish are subject to striking gene conversion events. These events are restricted to regions of the coding sequence, particularly the coding sequences of ectodomain 6 and the cytoplasmic domain. Diversity among paralogs is restricted to particular ectodomains that are excluded from conversion events. Conversion events are also strongly correlated with an increase in third-position GC content. We propose that the combination of lineage-specific duplication, restricted gene conversion, and adaptive variation in diversified ectodomains drives vertebrate protocadherin cluster evolution.

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“…Gene conversion is dependent on homology and sufficient sequence similarity (Ahn et al, 1988;Elliott et al, 1998), and can therefore also be expected to be active between paralogues arising through WGDs.…”

Section: Concerted Evolution By Gene Conversionmentioning

confidence: 99%

Whole-genome duplication in teleost fishes and its evolutionary consequences

2014

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Whole-genome duplication (WGD) events have shaped the history of many evolutionary lineages. One such duplication has been implicated in the evolution of teleost fishes, by far the most species-rich vertebrate clade. After initial controversy, there is now solid evidence that such event took place in the common ancestor of all extant teleosts. It is termed teleost-specific (TS) WGD. After WGD, duplicate genes have different fates. The most likely outcome is non-functionalization of one duplicate gene due to the lack of selective constraint on preserving both. Mechanisms that act on preservation of duplicates are subfunctionalization (partitioning of ancestral gene functions on the duplicates), neofunctionalization (assigning a novel function to one of the duplicates) and dosage selection (preserving genes to maintain dosage balance between interconnected components). Since the frequency of these mechanisms is influenced by the genes' properties, there are over-retained classes of genes, such as highly expressed ones and genes involved in neural function. The consequences of the TS-WGD, especially its impact on the massive radiation of teleosts, have been matter of controversial debate. It is evident that gene duplications are crucial for generating complexity and that WGDs provide large amounts of raw material for evolutionary adaptation and innovation. However, it is less clear whether the TS-WGD is directly linked to the evolutionary success of teleosts and their radiation. Recent studies let us conclude that TS-WGD has been important in generating teleost complexity, but that more recent ecological adaptations only marginally related to TS-WGD might have even contributed more to diversification. It is likely, however, that TS-WGD provided teleosts with diversification potential that can become effective much later, such as during phases of environmental change. AbstractWhole genome duplication (WGD) events have shaped the history of many evolutionary lineages. One such duplication has been implicated in the evolution of teleost fishes, the by far most species-rich vertebrate clade. After initial controversy, evidence is now solid that such an event took place in the common ancestor of all extant teleosts, the so-called teleostspecific (TS) WGD. After WGD, duplicate genes have different fates. The most likely outcome is non-functionalization of one duplicate gene due to the lack of selective constraint on preserving both copies of the gene. Mechanisms that act on preservation of duplicates are subfunctionalization (partitioning of ancestral gene functions on the duplicates), neofunctionalization (assigning a novel function to one of the duplicates) and dosageselection (preserving genes to maintain dosage-balance between interconnected components).Since the frequency of these mechanisms is influenced by the gene's properties, there are over-retained classes of genes, such as highly expressed ones and genes involved in neural function. The consequences of the TS-WGD, especially its impact on the massi...

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Effect of limited homology on gene conversion in a Saccharomyces cerevisiae plasmid recombination system.

Cited by 65 publications

References 31 publications

DNA homology requirements for mitotic gap repair in Drosophila.

DNA homology requirements for mitotic gap repair in Drosophila.

Gene Conversion and the Evolution of Protocadherin Gene Cluster Diversity

Whole-genome duplication in teleost fishes and its evolutionary consequences

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