Recent advances in understanding the roles of whole genome duplications in evolution

Ancient whole-genome duplications (WGDs)—paleopolyploidy events—are key to solving Darwin’s ‘abominable mystery’ of how flowering plants evolved and radiated into a rich variety of species. The vertebrates also emerged from their invertebrate ancestors via two WGDs, and genomes of diverse gymnosperm trees, unicellular eukaryotes, invertebrates, fishes, amphibians and even a rodent carry evidence of lineage-specific WGDs. Modern polyploidy is common in eukaryotes, and it can be induced, enabling mechanisms and short-term cost-benefit assessments of polyploidy to be studied experimentally. However, the ancient WGDs can be reconstructed only by comparative genomics: these studies are difficult because the DNA duplicates have been through tens or hundreds of millions of years of gene losses, mutations, and chromosomal rearrangements that culminate in resolution of the polyploid genomes back into diploid ones (rediploidisation). Intriguing asymmetries in patterns of post-WGD gene loss and retention between duplicated sets of chromosomes have been discovered recently, and elaborations of signal transduction systems are lasting legacies from several WGDs. The data imply that simpler signalling pathways in the pre-WGD ancestors were converted via WGDs into multi-stranded parallelised networks. Genetic and biochemical studies in plants, yeasts and vertebrates suggest a paradigm in which different combinations of sister paralogues in the post-WGD regulatory networks are co-regulated under different conditions. In principle, such networks can respond to a wide array of environmental, sensory and hormonal stimuli and integrate them to generate phenotypic variety in cell types and behaviours. Patterns are also being discerned in how the post-WGD signalling networks are reconfigured in human cancers and neurological conditions. It is fascinating to unpick how ancient genomic events impact on complexity, variety and disease in modern life

Diversity and evolution of cytochrome P450s of Jacobaea vulgaris and Jacobaea aquatica

Plant science

Detecting Functional Divergence after Gene Duplication through Evolutionary Changes in Posttranslational Regulatory Sequences

<div><p>Gene duplication is an important evolutionary mechanism that can result in functional divergence in paralogs due to neo-functionalization or sub-functionalization. Consistent with functional divergence after gene duplication, recent studies have shown accelerated evolution in retained paralogs. However, little is known in general about the impact of this accelerated evolution on the molecular functions of retained paralogs. For example, do new functions typically involve changes in enzymatic activities, or changes in protein regulation? Here we study the evolution of posttranslational regulation by examining the evolution of important regulatory sequences (short linear motifs) in retained duplicates created by the whole-genome duplication in budding yeast. To do so, we identified short linear motifs whose evolutionary constraint has relaxed after gene duplication with a likelihood-ratio test that can account for heterogeneity in the evolutionary process by using a non-central chi-squared null distribution. We find that short linear motifs are more likely to show changes in evolutionary constraints in retained duplicates compared to single-copy genes. We examine changes in constraints on known regulatory sequences and show that for the Rck1/Rck2, Fkh1/Fkh2, Ace2/Swi5 paralogs, they are associated with previously characterized differences in posttranslational regulation. Finally, we experimentally confirm our prediction that for the Ace2/Swi5 paralogs, Cbk1 regulated localization was lost along the lineage leading to <i>SWI5</i> after gene duplication. Our analysis suggests that changes in posttranslational regulation mediated by short regulatory motifs systematically contribute to functional divergence after gene duplication.</p></div

Motif co-regulation and co-operativity are common mechanisms in transcriptional, post-transcriptional and post-translational regulation

A substantial portion of the regulatory interactions in the higher eukaryotic cell are mediated by simple sequence motifs in the regulatory segments of genes and (pre-)mRNAs, and in the intrinsically disordered regions of proteins. Although these regulatory modules are physicochemically distinct, they share an evolutionary plasticity that has facilitated a rapid growth of their use and resulted in their ubiquity in complex organisms. The ease of motif acquisition simplifies access to basal housekeeping functions, facilitates the co-regulation of multiple biomolecules allowing them to respond in a coordinated manner to changes in the cell state, and supports the integration of multiple signals for combinatorial decision-making. Consequently, motifs are indispensable for temporal, spatial, conditional and basal regulation at the transcriptional, post-transcriptional and post-translational level. In this review, we highlight that many of the key regulatory pathways of the cell are recruited by motifs and that the ease of motif acquisition has resulted in large networks of co-regulated biomolecules. We discuss how co-operativity allows simple static motifs to perform the conditional regulation that underlies decision-making in higher eukaryotic biological systems. We observe that each gene and its products have a unique set of DNA, RNA or protein motifs that encode a regulatory program to define the logical circuitry that guides the life cycle of these biomolecules, from transcription to degradation. Finally, we contrast the regulatory properties of protein motifs and the regulatory elements of DNA and (pre-)mRNAs, advocating that co-regulation, co-operativity, and motif-driven regulatory programs are common mechanisms that emerge from the use of simple, evolutionarily plastic regulatory modules

Analyse de l'espace de séquence des domaines SH3 paralogues par l'étude des séquences ancestrales

Un mécanisme évolutif très important pour l'acquisition de nouvelles fonctions protéiques est la duplication génique. Les protéines paralogues résultantes subissent une divergence fonctionnelle permettant à leur gène d'être retenus dans le génome. Les événements de duplication étant à l'origine de l'expansion de la famille des domaines SH3, une compréhension de la divergence des propriétés de liaison de ceux-ci sur les protéines paralogues est essentielle pour saisir leur implication dans diverses fonctions cellulaires. La liaison des domaines SH3 peut être très spécifique ou elle peut reconnaître des groupes canoniques de peptides riches en proline. Ainsi, l'objectif de ce projet de maîtrise est d'améliorer notre compréhension sur l'évolution des propriétés de liaison des domaines SH3 portés par des paralogues. En utilisant des données sur les interactions physiques entre les protéines in vivo, nous avons établi que les domaines SH3 des myosines de type I de Saccharomyces cerevisiae, un organisme modèle, montraient une divergence fonctionnelle. Puis, les domaines SH3 ont été échangés entre les paralogues et les domaines ancestraux pré-duplications ont été insérés dans les paralogues. Cette expérience a révélé que le domaine SH3 présent au moment de la duplication montre le même profil d'interaction que les SH3 existants, mais que les SH3 plus anciens perdent graduellement leurs interactions. Ensuite, l'arrimage moléculaire des SH3s avec leurs peptides de liaison prédits ainsi que la caractérisation des interactions des SH3s libres montrent que l'affinité ne diminue pas avec le domaine ancestral. Ces résultats sont confirmés par le patron de PPIs des domaines SH3 libre de contexte protéique. Cela a permis de déterminer que la propriété de liaison n'est pas le facteur principal qui influence sur les interactions des domaines SH3 présent sur des paralogues, mais que c'est leur protéine hôte. Nos résultats s'accordent avec la recherche récente qui suggère que les domaines protéiques ne sont pas des éléments isolés dans une protéine, contrairement à la croyance répandue.A very important evolutionary mechanism for the acquisition of new protein functions is gene duplication. The resulting paralogous proteins undergo functional divergence allowing them to be retained in the genome. Since duplication events are responsible for the expansion of the SH3 domain family, an understanding of the divergence of the binding properties of SH3 domains on paralogous proteins is essential to grasp their involvement in various cellular functions. The binding of SH3 domains can be very specific or it can recognize canonical groups of proline-rich peptides. The objective of this master project is to improve our understanding of the evolution of the binding properties of SH3 domains carried by paralogs. Using data on physical interactions between proteins in vivo, we established that the SH3 domains of the type I myosins from Saccharomyces cerevisiae, a model organism, show functional divergence. Then, the SH3 domains were exchanged between paralogs and the pre-duplication ancestral domains were inserted into the paralogs. This experiment showed that the SH3 domain at the time of duplication displays the same interaction profile as the extant SH3s, but, as the SH3s get older, they gradually lose their interactions. Next, molecular docking of the SH3s with their predicted binding peptides and characterization of the free SH3s PPIs shows that the affinity does not decrease with the ancestral domain. Those results are confirmed by the PPI network of the SH3 domains free of a protein context. These experiments determined that the host protein is the primary factor influencing paralogous SH3 domain interactions instead of the SH3 binding preferences. Our results are consistent with recent research suggesting that protein domains are not isolated elements in a protein, contrary to popular belief

Genetic reconstruction of parentage and kinship in semi-feral domestic dogs, and analysis of effects of dog breeding patterns on an immune system gene MARCH7

Whilst there has been considerable research focusing on the kinship of wolves, data on free-ranging dogs was sparse and there has been a long standing controversial debate over their ability to form packs. One of the aims of this project was to reconstruct kinship relationships in a population of free-ranging dogs, assessing the genetic variability and inbreeding level. For this purpose, I studied a population inhabiting a nature reserve at the outskirts of Rome in Italy. Analysis of twelve microsatellite loci revealed low number of alleles per locus, low levels of heterozygosity and difficulties in assigning parentage, possibly resulting from high levels of inbreeding in the population. Results from parentage analysis suggested multiple breeding individuals to be present in the social groups. One explanation for this is a result of the domestication process as free-ranging dogs no longer follow seasonal reproductive behaviour and have a plentiful supply of human waste to scavenge reducing competition. Although parentage analysis suggested multiple paternity for two litters, results had low statistical support and could be due to low genetic variability in the population. Recent research has found MARCH7 as a common candidate gene under diversifying selection between free-breeding dogs and either East Asia or European dog breeds, with a SNP labelled in the intronic region of the gene. MARCH7 belongs to the membrane-associated RING-CH (MARCH) family, a RING finger protein family of E3 ubiquitin ligases, consisting of 11 members in mammals. The second aim of this study was to test for the possible signals of diversifying selection between free-ranging dogs, pure-breed dogs and wolves in the MARCH7 gene. This was achieved through three main routes: Sanger sequencing of a targeted region previously identified as being under selection, evolutionary comparison through investigation of nonsynonymous and synonymous patterns and phylogenetic analysis of mammalian species and ab initio prediction of protein structure . Sequence analysis demonstrated the possibility of copy number variation and alternative splicing in MARCH7 but failed to show polymorphism at the previously identified intronic SNP. Comparative analysis demonstrated MARCH7 to have highly conserved regions, most notably the RING-CH domain, but also polymorphic regions, where a multitude of both synonymous and nonsynonymous mutations are present across mammalian species studied. Comparison of nonsynonymous and synonymous mutations demonstrated MARCH7 to be under purifying selection across mammalian species. Ab initio prediction of protein structure indicated a highly disordered structure across the majority of the gene, with the exception of the RING-CH domain

Gene dosage and the evolution of gene expression

The duplication and loss of genes, chromosomes and whole genomes has had a major impact on the evolution of most organisms. Changes in gene copy number, called gene dosage, may influence the resulting level of gene product through changes in gene expression. These gene expression changes can be detrimental, resulting in compensation and buffering mechanisms, or beneficial, when selection favours increased gene dosage. Understanding how changes in gene dose can influence the evolution of gene expression within and between species is an important task in evolutionary biology. This thesis combines studies of gene, protein domain, and genome duplications with gene expression data from a range of bird species to understand the evolutionary consequences of gene dosage changes. In addition to gene duplication and loss events, the genomic location of genes can subject loci to different evolutionary pressures. Genes present on sex chromosomes or the mitochondria are inherited unequally between males and females, potentially causing sexual conflict over expression. This thesis investigates if inter-genomic conflict could drive gene movement on and off the sex chromosomes using a comparative genomics approach