Biology subjects

llorente, b.

Publications and source records attributed to llorente, b..

5 recordsLinked to original sources

bioRxiv2024

Recurrent loss of crossover interference punctuates the recombination landscape across yeast species

Meiotic recombination is essential for the accurate chromosome segregation and the generation of genetic diversity through crossover and gene conversion events. Although this process has been studied extensively in a few selected model species, understanding how its properties vary across species remains limited. In this context, we first characterized the meiotic recombination landscape and properties of the Kluyveromyces lactis budding yeast. We then conducted a comprehensive analysis of 28,897 recombination events spanning 567 meioses in five budding yeast species including Saccharomyces cerevisiae, Saccharomyces paradoxus, Lachancea kluyveri, Lachancea waltii and K. lactis. We observed variations in the recombination landscapes and properties across these species. The Saccharomyces yeasts displayed higher recombination rates compared to the non-Saccharomyces yeasts. In addition, bona fide crossover interference and associated crossover homeostasis were found in the Saccharomyces species only. The evolutionarily conserved ZMM pathway, essential for generating interference-dependent crossovers, has undergone multiple losses throughout evolution, suggesting variations in the regulation of crossover formation. Finally, recombination hotspots, although highly conserved within the Saccharomyces yeasts are not conserved beyond the Saccharomyces genus. Overall, these results highlight great variability and evolution in the recombination landscape between species.

genomics↗

bioRxiv2023

Xrs2 C-terminus mediates Tel1-dependent meiotic double-strand break interference

During meiosis, the programmed formation of DNA double-strand breaks (DSBs) by Spo11, a conserved topoisomerase II-like protein, initiates homologous recombination that leads to crossovers between homologous chromosomes, essential for accurate chromosome segregation and genome evolution. The DSB number, distribution and timing of formation are regulated during meiosis to ensure crossing over on all chromosomes and prevent genome instability. In S. cerevisiae, DSB interference suppresses the coincident formation of DSBs in neighboring hotspots through a Tel1/ATM dependent mechanism that remains unexplored. Here, we demonstrate that Tel1 is recruited to meiotic DSB hotspots and chromosomal axis sites in a DSB-dependent manner. This supports the tethered loop-axis complex (TLAC) model that postulates meiotic DSBs are formed within the chromosome axis environment. Tel1 recruitment to meiotic DSBs, DSB interference and the meiotic DNA damage checkpoint are all dependent on the C-terminal moiety of Xrs2, known to mediate Tel1-Xrs2 interaction in vegetative cells. However, mutation of the Xrs2 FxF/Y motif, known to stabilize Tel1 interaction with Xrs2, does not affect DSBs interference but abolishes the Tel1-dependent DNA damage checkpoint. Altogether, this work uncovers the dynamic association of Tel1 with meiotic chromosomes and highlights the critical role of its interaction with Xrs2 in fine-tuning both the meiotic DNA damage checkpoint and DSB interference. AUTHOR SUMMARYDuring meiosis, a special type of cell division that produces gametes, cells intentionally break their own DNA at preferred genomic sites (hotspots) to help shuffle genetic material between chromosomes. The repair process of those breaks, called homologous recombination, is crucial for genetic diversity and for ensuring chromosomes are distributed correctly to gametes. The number and location of DNA breaks are tightly controlled to prevent errors that could affect genetic stability. In the yeast model S. cerevisiae, a protein called Tel1 (the counterpart of ATM in mammals, a DNA damage sensor) helps limit the number of breaks per cell. Our research shows that Tel1 is recruited to DNA breaks and to specific chromosome structures (called axis), supporting the idea that DNA breaks happen within the axis environment. We also found that recruitment of Tel1 to DNA breaks depends on another protein, Xrs2. This interaction is crucial to limit further DNA breaks formation and to arrest cell cycle progression in response to DNA breaks. Overall, these findings shed light on Tel1 dynamics on meiotic chromosomes, and reveal how Tel1 and Xrs2 work together to maintain genetic stability during meiosis, a process essential for healthy reproduction and evolution.

molecular biology↗

bioRxiv2023

Absence of chromosome axis proteins recruitment prevents meiotic recombination chromosome-wide in the budding yeast Lachancea kluyveri

Meiotic recombination shows broad variations across species and along chromosomes, and is often suppressed at and around genomic regions determining sexual compatibility such as mating type loci in fungi. Here we show that the absence of Spo11-DSBs and meiotic recombination on Lakl0C-left, the chromosome arm containing the sex locus of the Lachancea kluyveri budding yeast, results from the absence of recruitment of the two chromosome axis proteins Red1 and Hop1, essential for proper Spo11-DSBs formation. Furthermore, cytological observation of spread pachytene meiotic chromosomes reveals that Lakl0C-left does not undergo synapsis. However, we show that the behavior of Lakl0C-left is independent of its particularly early replication timing and is not accompanied by any peculiar chromosome structure as detectable by Hi-C in this yet poorly studied yeast. Finally, we observed an accumulation of heterozygous mutations on Lakl0C-left and a sexual dimorphism of the haploid meiotic offspring, supporting a direct effect of this absence of meiotic recombination on L. kluyveri genome evolution and fitness. Because suppression of meiotic recombination on sex chromosomes is widely observed across eukaryotes, the novel mechanism for recombination suppression described here may apply to other species, with the potential to impact sex chromosome evolution.

genetics↗

bioRxiv2021

Lessons from the meiotic recombination landscape of the ZMM deficient budding yeast Lachancea waltii

Meiotic recombination has been deeply characterized in a few model species only, notably in the budding yeast Saccharomyces cerevisiae. Interestingly, most members of the ZMM pathway that implements meiotic crossover interference in S. cerevisiae have been lost in Lachancea yeast species after the divergence of Lachancea kluyveri from the rest of the clade. This suggests major differences in the control of crossover distribution. After investigating meiosis in L. kluyveri, we determined the meiotic recombination landscape of Lachancea waltii and identified several characteristics that should help understand better the underlying mechanisms. Such characteristics include systematic regions of loss of heterozygosity (LOH) in L. waltii hybrids, compatible with dysregulated Spo11-mediated DNA double strand breaks (DSB) independently of meiosis. They include a higher recombination rate in L. waltii than in L. kluyveri despite the lack of multiple ZMM pro-crossover factors. L. waltii exhibits an elevated frequency of zero-crossover bivalents as L. kluyveri but opposite to S. cerevisiae. L. waltii gene conversion tracts lengths are comparable to those observed in S. cerevisiae and shorter than in L. kluyveri despite the lack of Mlh2, a factor limiting conversion tracts size in S. cerevisiae. L. waltii recombination hotspots are not shared with either S. cerevisiae or L. kluyveri, showing that meiotic recombination hotspots can evolve at a rather limited evolutionary scale within budding yeasts. Finally, in line with the loss of several ZMM genes, we found only residual crossover interference in L. waltii likely coming from the modest interference existing between recombination precursors. Significance statementStudying non-model species is relevant to understand better biological processes by shedding light on their evolutionary variations. Here we chose the non-model budding yeast Lachancea waltii to study meiotic recombination. In sexually reproducing organisms, meiotic recombination shuffles parental genetic combinations notably by crossovers that cluster in hotspots at the population level. We found remarkable variations compared to both the canonical Saccharomyces cerevisiae model and another close relative Lachancea kluyveri. Such variations notably include the loss in L. waltii of a layer of regulation of crossover distribution that is otherwise conserved in budding yeasts and mammals. They also include the lack of conservation of crossover hotspots across the Lachancea species while crossover hotspots are remarkably stable across the Saccharomyces species. Highlights- Extensive LOH events in L. waltii intraspecific hybrids - No conservation of the recombination hotspots across the Lachancea genus - Reduced but not suppressed crossover interference in the absence of the ZMM pathway - Similar gene conversion tract lengths in L. waltii, S. cerevisiae, and L. kluyveri despite the lack of MLH2 in L. waltii

genetics↗

bioRxiv2021

The Pif1 helicase is actively inhibited during meiotic recombination which restrains gene conversion tract length

Meiotic recombination ensures proper chromosome segregation to form viable gametes and results in gene conversions events between homologs. Conversion tracts are shorter in meiosis than in mitotically dividing cells. This results at least in part from the binding of a complex, containing the Mer3 helicase and the MutL{beta} heterodimer, to meiotic recombination intermediates. The molecular actors inhibited by this complex are elusive. The Pif1 DNA helicase is known to stimulate DNA polymerase delta (Pol {delta}) -mediated DNA synthesis from D-loops, allowing long synthesis required for break-induced replication. We show that Pif1 is also recruited genome wide to meiotic DNA double-strand break (DSB) sites. We further show that Pif1, through its interaction with PCNA, is required for the long gene conversions observed in the absence of MutL{beta} recruitment to recombination sites. In vivo, Mer3 interacts with the PCNA clamp loader RFC, and in vitro, Mer3-MutL{beta} ensemble inhibits Pif1-stimulated D-loop extension by Pol {delta} and RFC-PCNA. Mechanistically, our results suggest that Mer3-MutL{beta} may compete with Pif1 for binding to RFC-PCNA. Taken together, our data show that Pif1s activity that promotes meiotic DNA repair synthesis is restrained by the Mer3-MutL{beta} ensemble which in turn prevents long gene conversion tracts and possibly associated mutagenesis.

molecular biology↗