Periodic Reporting for period 4 - RHEA (Rotifers Highlight the Evolution of Asexuals: the mechanisms of genome evolution in the absence of meiosis)
Okres sprawozdawczy: 2022-04-01 do 2023-09-30
While sexual reproduction is common to almost all eukaryotes, its ubiquity and complexity is often reported as the “queen of problem in evolutionary biology”. Very few organisms have renounced to their complete absence for reproduction suggesting strong evolutionary advantages to the maintenance of sexual reproduction in the long term. It has often been stated that recombination during sexual reproduction (meiosis) is critical to improve the response to selection. However, to study this we need a model system that evolves without sexual reproduction. Bdelloid rotifers are the most notorious asexual animal model system, having diversified into more than 400 species without males or sexual reproduction. Both its longevity as an asexual clade and its diversity contradicts the expectation that asexual lineages are evolutionary dead-ends. Understanding how these asexual lineages evolve can help elucidating the evolutionary forces that maintain recombination and sexual reproduction. The first objective of this ERC project RHEA is to identify in bdelloid rotifers the specific mechanisms that prevents genome deterioration in the absence of sexual reproduction. The answers obtained will be informative for the theories of sex and to provide a broader understanding of some genetic mechanisms related to DNA repair and meiotic recombination. In addition to their asexual evolution, bdelloid rotifers possess the unusual feature of extreme desiccation resistance at any stage of their life-cycle, being able to colonize semi-terrestrial environments. This desiccation resistance also confers bdelloid rotifers with an extreme radiation resistance. Both prolonged desiccation and radiation induce oxidative stress and DNA double strand breaks that bdelloid rotifers seem to handle well by protecting their proteins allowing an efficient repair of the broken DNA upon rehydration. The second main objective of this ERC is to explore the molecular mechanisms that make these animals unique in terms of hyper-resistance to genome breakage and desiccation, providing a new biological model system for understanding fundamental biological processes such as DNA repair and cell survival. This ERC project, by focusing on a unique study organism combining asexual reproductive features with unusual resistance traits, provides a unique opportunity to discover novel mechanisms in eukaryotes. Moreover, deciphering how rotifers handle potential DNA damage is of considerable interest, not only for understanding their evolutionary adaptations, but also for possible applications to medical fields where DNA integrity is of central importance, such as cancer and aging.
This ERC project is combining cytogenetic and developmental studies with genomic analyses, to unravel the exact reproductive system of bdelloid rotifers and their genome dynamics. Using state-of-the-art sequencing technologies and assembly methods, we assembled the twelve chromosomes of Adineta vaga from telomere to telomere. This new chromosome-scale assembly found six pairs of colinear homologous chromosomes, compatible with homologous chromosome pairing, a hallmark of meiosis. Discovering homologous chromosomes in the bdelloid rotifer A. vaga, the model species of this ERC project, challenges fundamental aspects of their biology and constitutes a paradigm shift in their notoriety as ancient asexual scandal. This new, high-quality, chromosome-scale assembly also provides a precious tool for this ERC project for all the ongoing comparative and population genomic studies, but also for the molecular and cellular characterization of their resistances.
Using this high-quality assembly of A. vaga, the heterozygosity along chromosomes could be compared between different A.vaga lineages. Large-scale homozygous regions were detected in most samples suggesting that recombination between homologous chromosomes can occur. The homologous chromosomes found in A. vaga, with signatures of recombination, suggest the possibility of a modified meiosis as has been observed in several other asexual metazoans. However, the old founding studies of Hsu (1956a, 1956b) established that oogenesis in bdelloids is reduced to two maturation divisions analogous to somatic mitosis. We challenged this view within this ERC with a series of cytogenetic observations that allowed us to propose a model of automictic parthenogenesis in A. vaga where homologous chromosomes interact during a non-reductional meiosis I. Such a model would explain how diploidy and heterozygosity are maintained in A. vaga in the absence of sexual reproduction, while creating genetic variability through homologous recombination. This important finding changes the status of bdelloid rotifers to successful ancient automictic clade.
In addition to its importance in evolutionary biology, A. vaga is the ultimate model organism to study extreme resistance to desiccation and ionizing radiation and the associated DNA repair mechanisms. It has indeed an exceptional ability to reconstruct its genome following massive breakage. By studying the dynamics of DNA repair in somatic and germline cells in A. vaga following radiation, we observed that somatic nuclei repaired immediately the broken DNA while there was a delay in the germline cells with no repair activity occurring until the oocyte started its maturation through its modified meiosis. Moreover, the genome in the progeny of irradiated individuals was fully reconstituted except for some signatures of homologous recombination. DSB repair by inter-homolog recombination is a hallmark event of meiosis and we hypothesize that, in bdelloid rotifers, it would not only participate to the resolution of accidental genomic lesions undergone by the germ line, but it would also contribute to an allelic shuffling in these parthenogenetic species.
Finally, through a proteomic approach we detected a unique, horizontally acquired protein in A. vaga, ligase E, highly expressed upon irradiation. Its ligation function was studied in vitro and through heterologous expression in human cells. The expression of this AvLigase E in human cells significantly increased their radiotolerance, which will be studied further.
Using this high-quality assembly of A. vaga, the heterozygosity along chromosomes could be compared between different A.vaga lineages. Large-scale homozygous regions were detected in most samples suggesting that recombination between homologous chromosomes can occur. The homologous chromosomes found in A. vaga, with signatures of recombination, suggest the possibility of a modified meiosis as has been observed in several other asexual metazoans. However, the old founding studies of Hsu (1956a, 1956b) established that oogenesis in bdelloids is reduced to two maturation divisions analogous to somatic mitosis. We challenged this view within this ERC with a series of cytogenetic observations that allowed us to propose a model of automictic parthenogenesis in A. vaga where homologous chromosomes interact during a non-reductional meiosis I. Such a model would explain how diploidy and heterozygosity are maintained in A. vaga in the absence of sexual reproduction, while creating genetic variability through homologous recombination. This important finding changes the status of bdelloid rotifers to successful ancient automictic clade.
In addition to its importance in evolutionary biology, A. vaga is the ultimate model organism to study extreme resistance to desiccation and ionizing radiation and the associated DNA repair mechanisms. It has indeed an exceptional ability to reconstruct its genome following massive breakage. By studying the dynamics of DNA repair in somatic and germline cells in A. vaga following radiation, we observed that somatic nuclei repaired immediately the broken DNA while there was a delay in the germline cells with no repair activity occurring until the oocyte started its maturation through its modified meiosis. Moreover, the genome in the progeny of irradiated individuals was fully reconstituted except for some signatures of homologous recombination. DSB repair by inter-homolog recombination is a hallmark event of meiosis and we hypothesize that, in bdelloid rotifers, it would not only participate to the resolution of accidental genomic lesions undergone by the germ line, but it would also contribute to an allelic shuffling in these parthenogenetic species.
Finally, through a proteomic approach we detected a unique, horizontally acquired protein in A. vaga, ligase E, highly expressed upon irradiation. Its ligation function was studied in vitro and through heterologous expression in human cells. The expression of this AvLigase E in human cells significantly increased their radiotolerance, which will be studied further.
Another important characteristic to resist complete desiccation and ionizing radiation, is to be able to protect the proteome against oxidative stress accumulating during these stressful conditions. Extremotolerant organisms, such as bdelloid rotifers, are therefore under selection to develop novel means of antioxidant defense (AOD). In a PhD project linked to this ERC, we study AOD system of our model species A. vaga. Through several in vitro assays, we follow the protein carbonylation in A. vaga following exposure to desiccation and ionizing radiation, and we also study through an in-gel superoxide scavenging assay the actors involved in superoxide elimination. This research on the antioxidant mechanism of A. vaga is done in comparison with radio-tolerant and radio-sensitive organisms. Moreover, by using new methodologies, we also focus upon identifying the small molecule antioxidants (non-enzymatic ones) present in A.vaga.
In the end, we aim to identify the key players involved in extreme stress resistance in the bdelloid rotifer species A. vaga. This is complementary to the European Space Agency project RISE (Rotifers in Space) in which Karine Van Doninck is the Principal Investigator.
In the end, we aim to identify the key players involved in extreme stress resistance in the bdelloid rotifer species A. vaga. This is complementary to the European Space Agency project RISE (Rotifers in Space) in which Karine Van Doninck is the Principal Investigator.