Multigene Family Evolution: Perspectives from Insect Chemoreceptors.

Understanding the birth and diversification of multigene families is a fundamental evolutionary problem. I argue for the insect chemoreceptor superfamily as an outstanding model. Although these receptors are currently the preserve of neuroscientists, putative homologous genes exist in diverse animal and plant genomes, implying an ancient origin. Moreover, functional studies suggest that they act as ligand-gated ion channels in both chemosensory and non-chemosensory processes. This family permits synergism of investigations into its structural and regulatory evolution with ecological studies of the selective pressures driving these changes. In addition, sequence divergence in these receptors can be exploited through co-evolutionary and comparative genomics analyses to help to elucidate their 3D structure and signaling mechanisms, and to reveal experimentally-accessible candidate loci to explore the genetic basis of adaptation.

Consequences of lineage-specific gene loss on functional evolution of surviving paralogs: ALDH1A and retinoic acid signaling in vertebrate genomes

Genome duplications increase genetic diversity and may facilitate the evolution of gene subfunctions. Little attention, however, has focused on the evolutionary impact of lineage-specific gene loss. Here, we show that identifying lineage-specific gene loss after genome duplication is important for understanding the evolution of gene subfunctions in surviving paralogs and for improving functional connectivity among human and model organism genomes. We examine the general principles of gene loss following duplication, coupled with expression analysis of the retinaldehyde dehydrogenase Aldh1a gene family during retinoic acid signaling in eye development as a case study. Humans have three ALDH1A genes, but teleosts have just one or two. We used comparative genomics and conserved syntenies to identify loss of ohnologs (paralogs derived from genome duplication) and to clarify uncertain phylogenies. Analysis showed that Aldh1a1 and Aldh1a2 form a clade that is sister to Aldh1a3-related genes. Genome comparisons showed secondarily loss of aldh1a1 in teleosts, revealing that Aldh1a1 is not a tetrapod innovation and that aldh1a3 was recently lost in medaka, making it the first known vertebrate with a single aldh1a gene. Interestingly, results revealed asymmetric distribution of surviving ohnologs between co-orthologous teleost chromosome segments, suggesting that local genome architecture can influence ohnolog survival. We propose a model that reconstructs the chromosomal history of the Aldh1a family in the ancestral vertebrate genome, coupled with the evolution of gene functions in surviving Aldh1a ohnologs after R1, R2, and R3 genome duplications. Results provide evidence for early subfunctionalization and late subfunction-partitioning and suggest a mechanistic model based on altered regulation leading to heterochronic gene expression to explain the acquisition or modification of subfunctions by surviving ohnologs that preserve unaltered ancestral developmental programs in the face of gene loss.

Predator or prey? Chlamydophila abortus infections of a free-living amoebae, Acanthamoeba castellani 9GU.

Limited evidence exists to suggest that the ability to invade and escape protozoan host cell bactericidal activity extends to members of the Chlamydiaceae, intracellular pathogens of humans and animals and evolutionary descendants of amoeba-resisting Chlamydia-like organisms. PCR and microscopic analyses of Chlamydophila abortus infections of Acanthamoeba castellani revealed uptake of this chlamydial pathogen but, unlike the well-described inhabitant of A. castellani, Parachlamydia acanthamoebae, Cp. abortus did not appear to propagate and is likely digested by its amoebal host. These data raise doubts about the ability of free-living amoebae to serve as hosts and vectors of pathogenic members of the Chlamydiaceae but reveal opportunities, via comparative genomics, to understand virulence mechanisms used by Chlamydia-like organisms to avoid amoebal digestion.

Erwinia amylovora Novel Plasmid pEI70: Complete Sequence, Biogeography, and Role in Aggressiveness in the Fire Blight Phytopathogen

Comparative genomics of several strains of Erwinia amylovora, a plant pathogenic bacterium causal agent of fire blight disease, revealed that its diversity is primarily attributable to the flexible genome comprised of plasmids. We recently identified and sequenced in full a novel 65.8 kb plasmid, called pEI70. Annotation revealed a lack of known virulence-related genes, but found evidence for a unique integrative conjugative element related to that of other plant and human pathogens. Comparative analyses using BLASTN showed that pEI70 is almost entirely included in plasmid pEB102 from E. billingiae, an epiphytic Erwinia of pome fruits, with sequence identities superior to 98%. A duplex PCR assay was developed to survey the prevalence of plasmid pEI70 and also that of pEA29, which had previously been described in several E. amylovora strains. Plasmid pEI70 was found widely dispersed across Europe with frequencies of 5–92%, but it was absent in E. amylovora analyzed populations from outside of Europe. Restriction analysis and hybridization demonstrated that this plasmid was identical in at least 13 strains. Curing E. amylovora strains of pEI70 reduced their aggressiveness on pear, and introducing pEI70 into low-aggressiveness strains lacking this plasmid increased symptoms development in this host. Discovery of this novel plasmid offers new insights into the biogeography, evolution and virulence determinants in E. amylovora

Statistical Methods for Conservation and Alignment Quality in Proteins

Construction of multiple sequence alignments is a fundamental task in Bioinformatics. Multiple sequence alignments are used as a prerequisite in many Bioinformatics methods, and subsequently the quality of such methods can be critically dependent on the quality of the alignment. However, automatic construction of a multiple sequence alignment for a set of remotely related sequences does not always provide biologically relevant alignments.Therefore, there is a need for an objective approach for evaluating the quality of automatically aligned sequences. The profile hidden Markov model is a powerful approach in comparative genomics. In the profile hidden Markov model, the symbol probabilities are estimated at each conserved alignment position. This can increase the dimension of parameter space and cause an overfitting problem. These two research problems are both related to conservation. We have developed statistical measures for quantifying the conservation of multiple sequence alignments. Two types of methods are considered, those identifying conserved residues in an alignment position, and those calculating positional conservation scores. The positional conservation score was exploited in a statistical prediction model for assessing the quality of multiple sequence alignments. The residue conservation score was used as part of the emission probability estimation method proposed for profile hidden Markov models. The results of the predicted alignment quality score highly correlated with the correct alignment quality scores, indicating that our method is reliable for assessing the quality of any multiple sequence alignment. The comparison of the emission probability estimation method with the maximum likelihood method showed that the number of estimated parameters in the model was dramatically decreased, while the same level of accuracy was maintained. To conclude, we have shown that conservation can be successfully used in the statistical model for alignment quality assessment and in the estimation of emission probabilities in the profile hidden Markov models.

HUMAN GENOME VARIATIONS AND EVOLUTION WITH A FOCUS ON THE ANALYSIS OF TRANSPOSABLE ELEMENTS

Genome sequence varies in numerous ways among individuals although the gross architecture is fixed for all humans. Retrotransposons create one of the most abundant structural variants in the human genome and are divided in many families, with certain members in some families, e.g., L1, Alu, SVA, and HERV-K, remaining active for transposition. Along with other types of genomic variants, retrotransponson-derived variants contribute to the whole spectrum of genome variants in humans. With the advancement of sequencing techniques, many human genomes are being sequenced at the individual level, fueling the comparative research on these variants among individuals. In this thesis, the evolution and functional impact of structural variations is examined primarily focusing on retrotransposons in the context of human evolution. The thesis comprises of three different studies on the topics that are presented in three data chapters. First, the recent evolution of all human specific AluYb members, representing the second most active subfamily of Alus, was tracked to identify their source/master copy using a novel approach. All human-specific AluYb elements from the reference genome were extracted, aligned with one another to construct clusters of similar copies and each cluster was analyzed to generate the evolutionary relationship between the members of the cluster. The approach resulted in identification of one major driver copy of all human specific Yb8 and the source copy of the Yb9 lineage. Three new subfamilies within the AluYb family – Yb8a1, Yb10 and Yb11 were also identified, with Yb11 being the youngest and most polymorphic. Second, an attempt to construct a relation between transposable elements (TEs) and tandem repeats (TRs) was made at a genome-wide scale for the first time. Upon sequence comparison, positional cross-checking and other relevant analyses, it was observed that over 20% of all TRs are derived from TEs. This result established the first connection between these two types of repetitive elements, and extends our appreciation for the impact of TEs on genomes. Furthermore, only 6% of these TE-derived TRs follow the already postulated initiation and expansion mechanisms, suggesting that the others are likely to follow a yet-unidentified mechanism. Third, by taking a combination of multiple computational approaches involving all types of genetic variations published so far including transposable elements, the first whole genome sequence of the most recent common ancestor of all modern human populations that diverged into different populations around 125,000-100,000 years ago was constructed. The study shows that the current reference genome sequence is 8.89 million base pairs larger than our common ancestor’s genome, contributed by a whole spectrum of genetic mechanisms. The use of this ancestral reference genome to facilitate the analysis of personal genomes was demonstrated using an example genome and more insightful recent evolutionary analyses involving the Neanderthal genome. The three data chapters presented in this thesis conclude that the tandem repeats and transposable elements are not two entirely distinctly isolated elements as over 20% TRs are actually derived from TEs. Certain subfamilies of TEs themselves are still evolving with the generation of newer subfamilies. The evolutionary analyses of all TEs along with other genomic variants helped to construct the genome sequence of the most recent common ancestor to all modern human populations which provides a better alternative to human reference genome and can be a useful resource for the study of personal genomics, population genetics, human and primate evolution.

Algorithmes pour la réconciliation d’un arbre de gènes avec un arbre d’espèces

Une réconciliation entre un arbre de gènes et un arbre d’espèces décrit une histoire d’évolution des gènes homologues en termes de duplications et pertes de gènes. Pour inférer une réconciliation pour un arbre de gènes et un arbre d’espèces, la parcimonie est généralement utilisée selon le nombre de duplications et/ou de pertes. Les modèles de réconciliation sont basés sur des critères probabilistes ou combinatoires. Le premier article définit un modèle combinatoire simple et général où les duplications et les pertes sont clairement identifiées et la réconciliation parcimonieuse n’est pas la seule considérée. Une architecture de toutes les réconciliations est définie et des algorithmes efficaces (soit de dénombrement, de génération aléatoire et d’exploration) sont développés pour étudier les propriétés combinatoires de l’espace de toutes les réconciliations ou seulement les plus parcimonieuses. Basée sur le processus classique nommé naissance-et-mort, un algorithme qui calcule la vraisemblance d’une réconciliation a récemment été proposé. Le deuxième article utilise cet algorithme avec les outils combinatoires décrits ci-haut pour calculer efficacement (soit approximativement ou exactement) les probabilités postérieures des réconciliations localisées dans le sous-espace considéré. Basé sur des taux réalistes (selon un modèle probabiliste) de duplication et de perte et sur des données réelles/simulées de familles de champignons, nos résultats suggèrent que la masse probabiliste de toute l’espace des réconciliations est principalement localisée autour des réconciliations parcimonieuses. Dans un contexte d’approximation de la probabilité d’une réconciliation, notre approche est une alternative intéressante face aux méthodes MCMC et peut être meilleure qu’une approche sophistiquée, efficace et exacte pour calculer la probabilité d’une réconciliation donnée. Le problème nommé Gene Tree Parsimony (GTP) est d’inférer un arbre d’espèces qui minimise le nombre de duplications et/ou de pertes pour un ensemble d’arbres de gènes. Basé sur une approche qui explore tout l’espace des arbres d’espèces pour les génomes considérés et un calcul efficace des coûts de réconciliation, le troisième article décrit un algorithme de Branch-and-Bound pour résoudre de façon exacte le problème GTP. Lorsque le nombre de taxa est trop grand, notre algorithme peut facilement considérer des relations prédéfinies entre ensembles de taxa. Nous avons testé notre algorithme sur des familles de gènes de 29 eucaryotes.

L'évolution du phagosome

La phagocytose est un processus cellulaire par lequel de larges particules sont internalisées dans une vésicule, le phagosome. Lorsque formé, le phagosome acquiert ses propriétés fonctionnelles à travers un processus complexe de maturation nommé la biogénèse du phagolysosome. Cette voie implique une série d’interactions rapides avec les organelles de l’appareil endocytaire permettant la transformation graduelle du phagosome nouvellement formé en phagolysosome à partir duquel la dégradation protéolytique s’effectue. Chez l’amibe Dictyostelium discoideum, la phagocytose est employée pour ingérer les bactéries de son environnement afin de se nourrir alors que les organismes multicellulaires utilisent la phagocytose dans un but immunitaire, où des cellules spécialisées nommées phagocytes internalisent, tuent et dégradent les pathogènes envahissant de l’organisme et constitue la base de l’immunité innée. Chez les vertébrés à mâchoire cependant, la transformation des mécanismes moléculaires du phagosome en une organelle perfectionnée pour l’apprêtement et la présentation de peptides antigéniques place cette organelle au centre de l’immunité innée et de l’immunité acquise. Malgré le rôle crucial auquel participe cette organelle dans la réponse immunitaire, il existe peu de détails sur la composition protéique et l’organisation fonctionnelles du phagosome. Afin d’approfondir notre compréhension des divers aspects qui relient l’immunité innée et l’immunité acquise, il devient essentiel d’élargir nos connaissances sur les fonctions moléculaire qui sont recrutées au phagosome. Le profilage par protéomique à haut débit de phagosomes isolés fut extrêmement utile dans la détermination de la composition moléculaire de cette organelle. Des études provenant de notre laboratoire ont révélé les premières listes protéiques identifiées à partir de phagosomes murins sans toutefois déterminer le ou les rôle(s) de ces protéines lors du processus de la phagocytose (Brunet et al, 2003; Garin et al, 2001). Au cours de la première étude de cette thèse (Stuart et al, 2007), nous avons entrepris la caractérisation fonctionnelle du protéome entier du phagosome de la drosophile en combinant diverses techniques d’analyses à haut débit (protéomique, réseaux d’intéractions protéique et ARN interférent). En utilisant cette stratégie, nous avons identifié 617 protéines phagosomales par spectrométrie de masse à partir desquelles nous avons accru cette liste en construisant des réseaux d’interactions protéine-protéine. La contribution de chaque protéine à l’internalisation de bactéries fut ensuite testée et validée par ARN interférent à haut débit et nous a amené à identifier un nouveau régulateur de la phagocytose, le complexe de l’exocyst. En appliquant ce modèle combinatoire de biologie systémique, nous démontrons la puissance et l’efficacité de cette approche dans l’étude de processus cellulaire complexe tout en créant un cadre à partir duquel il est possible d’approfondir nos connaissances sur les différents mécanismes de la phagocytose. Lors du 2e article de cette thèse (Boulais et al, 2010), nous avons entrepris la caractérisation moléculaire des étapes évolutives ayant contribué au remodelage des propriétés fonctionnelles de la phagocytose au cours de l’évolution. Pour ce faire, nous avons isolé des phagosomes à partir de trois organismes distants (l’amibe Dictyostelium discoideum, la mouche à fruit Drosophila melanogaster et la souris Mus musculus) qui utilisent la phagocytose à des fins différentes. En appliquant une approche protéomique à grande échelle pour identifier et comparer le protéome et phosphoprotéome des phagosomes de ces trois espèces, nous avons identifié un cœur protéique commun à partir duquel les fonctions immunitaires du phagosome se seraient développées. Au cours de ce développement fonctionnel, nos données indiquent que le protéome du phagosome fut largement remodelé lors de deux périodes de duplication de gènes coïncidant avec l’émergence de l’immunité innée et acquise. De plus, notre étude a aussi caractérisée en détail l’acquisition de nouvelles protéines ainsi que le remodelage significatif du phosphoprotéome du phagosome au niveau des constituants du cœur protéique ancien de cette organelle. Nous présentons donc la première étude approfondie des changements qui ont engendré la transformation d’un compartiment phagotrophe à une organelle entièrement apte pour la présentation antigénique.

Identification, characterization and antigenicity of the Plasmodium vivax rhoptry neck protein 1 (PvRON1)

Background: Plasmodium vivax malaria remains a major health problem in tropical and sub-tropical regions worldwide. Several rhoptry proteins which are important for interaction with and/or invasion of red blood cells, such as PfRONs, Pf92, Pf38, Pf12 and Pf34, have been described during the last few years and are being considered as potential anti-malarial vaccine candidates. This study describes the identification and characterization of the P. vivax rhoptry neck protein 1 (PvRON1) and examine its antigenicity in natural P. vivax infections. Methods: The PvRON1 encoding gene, which is homologous to that encoding the P. falciparum apical sushi protein (ASP) according to the plasmoDB database, was selected as our study target. The pvron1 gene transcription was evaluated by RT-PCR using RNA obtained from the P. vivax VCG-1 strain. Two peptides derived from the deduced P. vivax Sal-I PvRON1 sequence were synthesized and inoculated in rabbits for obtaining anti-PvRON1 antibodies which were used to confirm the protein expression in VCG-1 strain schizonts along with its association with detergent-resistant microdomains (DRMs) by Western blot, and its localization by immunofluorescence assays. The antigenicity of the PvRON1 protein was assessed using human sera from individuals previously exposed to P. vivax malaria by ELISA. Results: In the P. vivax VCG-1 strain, RON1 is a 764 amino acid-long protein. In silico analysis has revealed that PvRON1 shares essential characteristics with different antigens involved in invasion, such as the presence of a secretory signal, a GPI-anchor sequence and a putative sushi domain. The PvRON1 protein is expressed in parasite's schizont stage, localized in rhoptry necks and it is associated with DRMs. Recombinant protein recognition by human sera indicates that this antigen can trigger an immune response during a natural infection with P. vivax. Conclusions: This study shows the identification and characterization of the P. vivax rhoptry neck protein 1 in the VCG-1 strain. Taking into account that PvRON1 shares several important characteristics with other Plasmodium antigens that play a functional role during RBC invasion and, as shown here, it is antigenic, it could be considered as a good vaccine candidate. Further studies aimed at assessing its immunogenicity and protection-inducing ability in the Aotus monkey model are thus recommended.

Sequence analysis of the cupin gene family in Synechocystis PCC6803

The recently described cupin superfamily of proteins includes the germin and germinlike proteins, of which the cereal oxalate oxidase is the best characterized. This superfamily also includes seed storage proteins, in addition to several microbial enzymes and proteins with unknown function. All these proteins are characterized by the conservation of two central motifs, usually containing two or three histidine residues presumed to be involved with metal binding in the catalytic active site. The present study on the coding regions of Synechocystis PCC6803 identifies a previously unknown group of 12 related cupins, each containing the characteristic two-motif signature. This group comprises 11 single-domain proteins, ranging in length from 104 to 289 residues, and includes two phosphomannose isomerases and two epimerases involved in cell wall synthesis, a member of the pirin group of nuclear proteins, a possible transcriptional regulator, and a close relative-of a cytochrome c551 from Rhodococcus. Additionally, there is a duplicated, two-domain protein that has close similarity to an oxalate decarboxylase from the fungus Collybia velutipes and that is a putative progenitor of the storage proteins of land plants.

Cupins: the most functionally diverse protein superfamily?

The cupin superfamily of proteins, named on the basis of a conserved β-barrel fold (‘cupa’ is the Latin term for a small barrel), was originally discovered using a conserved motif found within germin and germin-like proteins from higher plants. Previous analysis of cupins had identified some 18 different functional classes that range from single-domain bacterial enzymes such as isomerases and epimerases involved in the modification of cell wall carbohydrates, through to two-domain bicupins such as the desiccation-tolerant seed storage globulins, and multidomain transcription factors including one linked to the nodulation response in legumes. Recent advances in comparative genomics, and the resolution of many more 3-D structures have now revealed that the largest subset of the cupin superfamily is the 2-oxyglutarate-Fe2+ dependent dioxygenases. The substrates for this subclass of enzyme are many and varied and in total amount to probably 50–100 different biochemical reactions, including several involved in plant growth and development. Although the majority of enzymatic cupins contain iron as an active site metal, other members contain either copper, zinc, cobalt, nickel or manganese ions as a cofactor, with each cofactor allowing a different type of chemistry to occur within the conserved tertiary structure. This review discusses the range of structures and functions found in this most diverse of superfamilies.

Population structure and associated phenotypes of Salmonella enterica serovars Derby and Mbandaka overlap with host range

BACKGROUND:The Salmonella enterica serovar Derby is frequently isolated from pigs and turkeys whereas serovar Mbandaka is frequently isolated from cattle, chickens and animal feed in the UK. Through comparative genomics, phenomics and mutant construction we previously suggested possible mechanistic reasons why these serovars demonstrate apparently distinct host ranges. Here, we investigate the genetic and phenotypic diversity of these two serovars in the UK. We produce a phylogenetic reconstruction and perform several biochemical assays on isolates of S. Derby and S. Mbandaka acquired from sites across the UK between the years 2000 and 2010. RESULTS:We show that UK isolates of S. Mbandaka comprise of one clonal lineage which is adapted to proficient utilisation of metabolites found in soya beans under ambient conditions. We also show that this clonal lineage forms a biofilm at 25 °C, suggesting that this serovar maybe well adapted to survival ex vivo, growing in animal feed. Conversely, we show that S. Derby is made of two distinct lineages, L1 and L2. These lineages differ genotypically and phenotypically, being divided by the presence and absence of SPI-23 and the ability to more proficiently invade porcine jejunum derived cell line IPEC-J2. CONCLUSION:The results of this study lend support to the hypothesis that the differences in host ranges of S. Derby and S. Mbandaka are adaptations to pathogenesis, environmental persistence, as well as utilisation of metabolites abundant in their respective host environments.

Functionally conserved cis-regulatory elements of COL18A1 identified through zebrafish transgenesis

Type XVIII collagen is a component of basement membranes, and expressed prominently in the eye, blood vessels, liver, and the central nervous system. Homozygous mutations in COL18A1 lead to Knobloch Syndrome, characterized by ocular defects and occipital encephalocele. However, relatively little has been described on the role of type XVIII collagen in development, and nothing is known about the regulation of its tissue-specific expression pattern. We have used zebrafish transgenesis to identify and characterize cis-regulatory sequences controlling expression of the human gene. Candidate enhancers were selected from non-coding sequence associated with COL18A1 based on sequence conservation among mammals. Although these displayed no overt conservation with orthologous zebrafish sequences, four regions nonetheless acted as tissue-specific transcriptional enhancers in the zebrafish embryo, and together recapitulated the major aspects of col18a1 expression. Additional post-hoc computational analysis on positive enhancer sequences revealed alignments between mammalian and teleost sequences, which we hypothesize predict the corresponding zebrafish enhancers; for one of these, we demonstrate functional overlap with the orthologous human enhancer sequence. Our results provide important insight into the biological function and regulation of COL18A1, and point to additional sequences that may contribute to complex diseases involving COL18A1. More generally, we show that combining functional data with targeted analyses for phylogenetic conservation can reveal conserved cis-regulatory elements in the large number of cases where computational alignment alone falls short. (C) 2009 Elsevier Inc. All rights reserved.

NAD Biosynthesis Evolution in Bacteria: Lateral Gene Transfer of Kynurenine Pathway in Xanthomonadales and Flavobacteriales

The biosynthesis of quinolinate, the de novo precursor of nicotinamide adenine dinucleotide (NAD), may be performed by two distinct pathways, namely, the bacterial aspartate (aspartate-to-quinolinate) and the eukaryotic kynurenine (tryptophan-to-quinolinate). Even though the separation into eukaryotic and bacterial routes is long established, recent genomic surveys have challenged this view, because certain bacterial species also carry the genes for the kynurenine pathway. In this work, both quinolinate biosynthetic pathways were investigated in the Bacteria clade and with special attention to Xanthomonadales and Bacteroidetes, from an evolutionary viewpoint. Genomic screening has revealed that a small number of bacterial species possess some of the genes for the kynurenine pathway, which is complete in the genus Xanthomonas and in the order Flavobacteriales, where the aspartate pathway is absent. The opposite pattern (presence of the aspartate pathway and absence of the kynurenine pathway) in close relatives (Xylella ssp. and the order Bacteroidales, respectively) points to the idea of a recent acquisition of the kynurenine pathway through lateral gene transfer in these bacterial groups. In fact, sequence similarity comparison and phylogenetic reconstruction both suggest that at least part of the genes of the kynurenine pathway in Xanthomonas and Flavobacteriales is shared by eukaryotes. These results reinforce the idea of the role that lateral gene transfer plays in the configuration of bacterial genomes, thereby providing alternative metabolic pathways, even with the replacement of primary and essential cell functions, as exemplified by NAD biosynthesis.

Mapeamento de um conjunto de genes no cromossomo 6 bubalino

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)