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1.
Nat Commun ; 11(1): 3454, 2020 07 10.
Artigo em Inglês | MEDLINE | ID: mdl-32651383

RESUMO

Biological rhythms are a fundamental property of life. The deep ocean covers 66% of our planet surface and is one of the largest biomes. The deep sea has long been considered as an arrhythmic environment because sunlight is totally absent below 1,000 m depth. In the present study, we have sequenced the temporal transcriptomes of a deep-sea species, the ecosystem-structuring vent mussel Bathymodiolus azoricus. We reveal that tidal cycles predominate in the transcriptome and physiology of mussels fixed directly at hydrothermal vents at 1,688 m depth at the Mid-Atlantic Ridge, whereas daily cycles prevail in mussels sampled after laboratory acclimation. We identify B. azoricus canonical circadian clock genes, and show that oscillations observed in deep-sea mussels could be either a direct response to environmental stimulus, or be driven endogenously by one or more biological clocks. This work generates in situ insights into temporal organisation in a deep-sea organism.


Assuntos
Mytilidae/fisiologia , Animais , Ecossistema , Fontes Hidrotermais , Biologia Marinha , Periodicidade
2.
iScience ; 23(2): 100849, 2020 Jan 17.
Artigo em Inglês | MEDLINE | ID: mdl-32058961

RESUMO

Inferring genome-scale metabolic networks in emerging model organisms is challenged by incomplete biochemical knowledge and partial conservation of biochemical pathways during evolution. Therefore, specific bioinformatic tools are necessary to infer biochemical reactions and metabolic structures that can be checked experimentally. Using an integrative approach combining genomic and metabolomic data in the red algal model Chondrus crispus, we show that, even metabolic pathways considered as conserved, like sterols or mycosporine-like amino acid synthesis pathways, undergo substantial turnover. This phenomenon, here formally defined as "metabolic pathway drift," is consistent with findings from other areas of evolutionary biology, indicating that a given phenotype can be conserved even if the underlying molecular mechanisms are changing. We present a proof of concept with a methodological approach to formalize the logical reasoning necessary to infer reactions and molecular structures, abstracting molecular transformations based on previous biochemical knowledge.

3.
Mar Genomics ; 52: 100740, 2020 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31937506

RESUMO

Brown algae are multicellular photosynthetic stramenopiles that colonize marine rocky shores worldwide. Ectocarpus sp. Ec32 has been established as a genomic model for brown algae. Here we present the genome and metabolic network of the closely related species, Ectocarpus subulatus Kützing, which is characterized by high abiotic stress tolerance. Since their separation, both strains show new traces of viral sequences and the activity of large retrotransposons, which may also be related to the expansion of a family of chlorophyll-binding proteins. Further features suspected to contribute to stress tolerance include an expanded family of heat shock proteins, the reduction of genes involved in the production of halogenated defence compounds, and the presence of fewer cell wall polysaccharide-modifying enzymes. Overall, E. subulatus has mainly lost members of gene families down-regulated in low salinities, and conserved those that were up-regulated in the same condition. However, 96% of genes that differed between the two examined Ectocarpus species, as well as all genes under positive selection, were found to encode proteins of unknown function. This underlines the uniqueness of brown algal stress tolerance mechanisms as well as the significance of establishing E. subulatus as a comparative model for future functional studies.


Assuntos
Genoma/genética , Feófitas/genética , Estresse Fisiológico/genética , Proteínas de Algas/genética , Redes e Vias Metabólicas/genética , Família Multigênica/genética , Vitória
4.
Antioxidants (Basel) ; 8(11)2019 Nov 16.
Artigo em Inglês | MEDLINE | ID: mdl-31744163

RESUMO

Understanding growth mechanisms in brown algae is a current scientific and economic challenge that can benefit from the modeling of their metabolic networks. The sequencing of the genomes of Saccharina japonica and Cladosiphon okamuranus has provided the necessary data for the reconstruction of Genome-Scale Metabolic Networks (GSMNs). The same in silico method deployed for the GSMN reconstruction of Ectocarpus siliculosus to investigate the metabolic capabilities of these two algae, was used. Integrating metabolic profiling data from the literature, we provided functional GSMNs composed of an average of 2230 metabolites and 3370 reactions. Based on these GSMNs and previously published work, we propose a model for the biosynthetic pathways of the main carotenoids in these two algae. We highlight, on the one hand, the reactions and enzymes that have been preserved through evolution and, on the other hand, the specificities related to brown algae. Our data further indicate that, if abscisic acid is produced by Saccharina japonica, its biosynthesis pathway seems to be different in its final steps from that described in land plants. Thus, our work illustrates the potential of GSMNs reconstructions for formalizing hypotheses that can be further tested using targeted biochemical approaches.

5.
Planta ; 249(3): 647-661, 2019 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-30341489

RESUMO

MAIN CONCLUSION: Comparative genomic analysis of cytochromes P450 revealed high diversification and dynamic changes in stramenopiles, associated with transcriptional responsiveness to various environmental stimuli. Comparative genomic and molecular evolution approaches were used to characterize cytochromes P450 (P450) diversity in stramenopiles. Phylogenetic analysis pointed to a high diversity of P450 in stramenopiles and identified three major clans. The CYP51 and CYP97 clans were present in brown algae, diatoms and Nannochloropsis gaditana, whereas the CYP5014 clan mainly includes oomycetes. Gene gain and loss patterns revealed that six CYP families-CYP51, CYP97, CYP5160, CYP5021, CYP5022, and CYP5165-predated the split of brown algae and diatoms. After they diverged, diatoms gained more CYP families, especially in the cold-adapted species Fragilariopsis cylindrus, in which eight new CYP families were found. Selection analysis revealed that the expanded CYP51 family in the brown alga Cladosiphon okamuranus exhibited a more relaxed selection constraint compared with those of other brown algae and diatoms. Our RNA-seq data further evidenced that most of P450s in Saccharina japonica are highly expressed in large sporophytes, which could potentially promote the large kelp formation in this developmental stage. A survey of Ectocarpus siliculosus and diatom transcriptomes showed that many P450s are responsive to stress, nutrient limitation or light quality, suggesting pivotal roles in detoxification or metabolic processes under adverse environmental conditions. The information provided in this study will be helpful in designing functional experiments and interpreting P450 roles in this particular lineage.


Assuntos
Sistema Enzimático do Citocromo P-450/genética , Evolução Molecular , Variação Genética/genética , Estramenópilas/genética , Genômica , Feófitas/enzimologia , Feófitas/genética , Filogenia , Alinhamento de Sequência , Estramenópilas/enzimologia , Transcriptoma
6.
Gen Comp Endocrinol ; 265: 41-45, 2018 09 01.
Artigo em Inglês | MEDLINE | ID: mdl-29908834

RESUMO

Hormonally active phytochemicals (HAPs) are signaling molecules produced by plants that alter hormonal signaling in animals, due to consumption or environmental exposure. To date, HAPs have been investigated mainly in terrestrial ecosystems. To gain a full understanding of the origin and evolution of plant-animal interactions, it is necessary also to study these interactions in the marine environment, where the major photosynthetic lineages are very distant from the terrestrial plants. Here we focus on chemicals from red and brown macroalgae and point out their potential role as modulators of the endocrine system of aquatic animals through nuclear hormone receptors. We show that, regarding steroids and oxylipins, there are already some candidates available for further functional investigations of ligand-receptor interactions. Furthermore, several carotenoids, produced by cyanobacteria provide candidates that could be investigated with respect to their presence in macroalgae. Finally, regarding halogenated compounds, it is not clear yet which molecules could bridge the gap to explain the transition from lipid sensing to thyroid hormone high affinity binding among nuclear receptors.


Assuntos
Organismos Aquáticos/metabolismo , Compostos Fitoquímicos/farmacologia , Receptores Citoplasmáticos e Nucleares/metabolismo , Alga Marinha/química , Animais , Organismos Aquáticos/efeitos dos fármacos , Ecossistema , Ligantes , Modelos Animais , Compostos Fitoquímicos/química
7.
J Steroid Biochem Mol Biol ; 184: 11-19, 2018 11.
Artigo em Inglês | MEDLINE | ID: mdl-29940311

RESUMO

Steroid hormone receptors are important regulators of development and physiology in bilaterian animals, but the role of steroid signaling in cnidarians has been contentious. Cnidarians produce steroids, including A-ring aromatic steroids with a side-chain, but these are probably made through pathways different than the one used by vertebrates to make their A-ring aromatic steroids. Here we present comparative genomic analyses indicating the presence of a previously undescribed nuclear receptor family within medusozoan cnidarians, that we propose to call NR3E. This family predates the diversification of ERR/ER/SR in bilaterians, indicating that the first NR3 evolved in the common ancestor of the placozoan and cnidarian-bilaterian with lineage-specific loss in the anthozoans, even though multiple species in this lineage have been shown to produce aromatic steroids, whose function remain unclear. We discovered serendipitously that a cytoplasmic factor within epidermal cells of transgenic Hydra vulgaris can trigger the nuclear translocation of heterologously expressed human ERα. This led us to hypothesize that aromatic steroids may also be present in the medusozoan cnidarian lineage, which includes Hydra, and may explain the translocation of human ERα. Docking experiments with paraestrol A, a cnidarian A-ring aromatic steroid, into the ligand-binding pocket of Hydra NR3E indicates that, if an aromatic steroid is indeed the true ligand, which remains to be demonstrated, it would bind to the pocket through a partially distinct mechanism from the manner in which estradiol binds to vertebrate ER.


Assuntos
Hydra/metabolismo , Receptores de Esteroides/metabolismo , Transdução de Sinais/fisiologia , Animais , Sítios de Ligação/genética , Sítios de Ligação/fisiologia , Receptor alfa de Estrogênio/genética , Evolução Molecular , Humanos , Ligantes , Simulação de Acoplamento Molecular
8.
PLoS Comput Biol ; 14(5): e1006146, 2018 05.
Artigo em Inglês | MEDLINE | ID: mdl-29791443

RESUMO

Genome-scale metabolic models have become the tool of choice for the global analysis of microorganism metabolism, and their reconstruction has attained high standards of quality and reliability. Improvements in this area have been accompanied by the development of some major platforms and databases, and an explosion of individual bioinformatics methods. Consequently, many recent models result from "à la carte" pipelines, combining the use of platforms, individual tools and biological expertise to enhance the quality of the reconstruction. Although very useful, introducing heterogeneous tools, that hardly interact with each other, causes loss of traceability and reproducibility in the reconstruction process. This represents a real obstacle, especially when considering less studied species whose metabolic reconstruction can greatly benefit from the comparison to good quality models of related organisms. This work proposes an adaptable workspace, AuReMe, for sustainable reconstructions or improvements of genome-scale metabolic models involving personalized pipelines. At each step, relevant information related to the modifications brought to the model by a method is stored. This ensures that the process is reproducible and documented regardless of the combination of tools used. Additionally, the workspace establishes a way to browse metabolic models and their metadata through the automatic generation of ad-hoc local wikis dedicated to monitoring and facilitating the process of reconstruction. AuReMe supports exploration and semantic query based on RDF databases. We illustrate how this workspace allowed handling, in an integrated way, the metabolic reconstructions of non-model organisms such as an extremophile bacterium or eukaryote algae. Among relevant applications, the latter reconstruction led to putative evolutionary insights of a metabolic pathway.


Assuntos
Bases de Dados Factuais , Genômica , Armazenamento e Recuperação da Informação , Internet , Redes e Vias Metabólicas/genética , Antioxidantes/metabolismo , Genômica/métodos , Genômica/normas , Armazenamento e Recuperação da Informação/métodos , Armazenamento e Recuperação da Informação/normas , Microalgas/genética , Microalgas/metabolismo , Modelos Teóricos , Reprodutibilidade dos Testes
9.
Cell Chem Biol ; 25(6): 787-796.e12, 2018 06 21.
Artigo em Inglês | MEDLINE | ID: mdl-29779955

RESUMO

In the nematodes Caenorhabditis elegans and Pristionchus pacificus, a modular library of small molecules control behavior, lifespan, and development. However, little is known about the final steps of their biosynthesis, in which diverse building blocks from primary metabolism are attached to glycosides of the dideoxysugar ascarylose, the ascarosides. We combine metabolomic analysis of natural isolates of P. pacificus with genome-wide association mapping to identify a putative carboxylesterase, Ppa-uar-1, that is required for attachment of a pyrimidine-derived moiety in the biosynthesis of ubas#1, a major dauer pheromone component. Comparative metabolomic analysis of wild-type and Ppa-uar-1 mutants showed that Ppa-uar-1 is required specifically for the biosynthesis of ubas#1 and related metabolites. Heterologous expression of Ppa-UAR-1 in C. elegans yielded a non-endogenous ascaroside, whose structure confirmed that Ppa-uar-1 is involved in modification of a specific position in ascarosides. Our study demonstrates the utility of natural variation-based approaches for uncovering biosynthetic pathways.


Assuntos
Genômica , Metabolômica , Nematoides/genética , Nematoides/metabolismo , Feromônios/biossíntese , Feromônios/genética , Animais , Hidrolases de Éster Carboxílico/genética , Hidrolases de Éster Carboxílico/metabolismo , Feromônios/química
10.
Curr Top Dev Biol ; 125: 1-38, 2017.
Artigo em Inglês | MEDLINE | ID: mdl-28527568

RESUMO

Nuclear receptors (NRs) are a family of ligand-regulated transcription factors that modulate a wide variety of physiological functions in a ligand-dependent manner. The first NRs were discovered as receptors of well-known hormones such as 17ß-estradiol, corticosteroids, or thyroid hormones. In these cases a direct activation of the receptor transcriptional activity by a very specific ligand, with nanomolar affinity, was demonstrated, providing a strong conceptual framework to understand the mechanism of action of these hormones. However, the discovery that some NRs are able to bind different ligands with micromolar affinity was a first sign that the univocal relationship between a specific receptor (e.g., TR) and a specific ligand (e.g., thyroid hormone) should not be generalized to the whole family. These discussions about the nature of NR ligands have been reinforced by the study of the hormone/receptor couple evolution. Indeed when the ligand is not a protein but a small molecule derived from a biochemical pathway, a simple coevolution mechanism between the ligand and the receptor cannot operate. We and others have recently shown that the ligands acting for a given NR early on during evolution were often different from the classical mammalian ligands. This suggests that the NR/ligand evolutionary relationship is more dynamic than anticipated and that the univocal relationship between a receptor and a specific molecule may be an oversimplification. Moreover, classical NRs can have different ligands acting in a tissue-specific fashion with significant impact on their function. This also suggests that we may have to reevaluate the pharmacology of the ligand/receptor couple.


Assuntos
Evolução Molecular , Receptores Citoplasmáticos e Nucleares/genética , Receptores Citoplasmáticos e Nucleares/metabolismo , Animais , Ligantes , Modelos Biológicos , Transdução de Sinais
11.
Sci Adv ; 3(3): e1601778, 2017 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-28435861

RESUMO

The origin of ancient ligand/receptor couples is often analyzed via reconstruction of ancient receptors and, when ligands are products of metabolic pathways, they are not supposed to evolve. However, because metabolic pathways are inherited by descent with modification, their structure can be compared using cladistic analysis. Using this approach, we studied the evolution of steroid hormones. We show that side-chain cleavage is common to most vertebrate steroids, whereas aromatization was co-opted for estrogen synthesis from a more ancient pathway. The ancestral products of aromatic activity were aromatized steroids with a side chain, which we named "paraestrols." We synthesized paraestrol A and show that it effectively binds and activates the ancestral steroid receptor. Our study opens the way to comparative studies of biologically active small molecules.


Assuntos
Estrogênios/genética , Evolução Molecular , Modelos Genéticos , Receptores Estrogênicos/genética , Animais
12.
Mol Biol Evol ; 34(7): 1644-1653, 2017 07 01.
Artigo em Inglês | MEDLINE | ID: mdl-28333289

RESUMO

Phenotypic plasticity is increasingly recognized to facilitate adaptive change in plants and animals, including insects, nematodes, and vertebrates. Plasticity can occur as continuous or discrete (polyphenisms) variation. In social insects, for example, in ants, some species have workers of distinct size classes while in other closely related species variation in size may be continuous. Despite the abundance of examples in nature, how discrete morphs are specified remains currently unknown. In theory, polyphenisms might require robustness, whereby the distribution of morphologies would be limited by the same mechanisms that execute buffering from stochastic perturbations, a function attributed to heat-shock proteins of the Hsp90 family. However, this possibility has never been directly tested because plasticity and robustness are considered to represent opposite evolutionary principles. Here, we used a polyphenism of feeding structures in the nematode Pristionchus pacificus to test the relationship between robustness and plasticity using geometric morphometrics of 20 mouth-form landmarks. We show that reducing heat-shock protein activity, which reduces developmental robustness, increases the range of mouth-form morphologies. Specifically, elevated temperature led to a shift within morphospace, pharmacological inhibition of all Hsp90 genes using radicicol treatment increased shape variability in both mouth-forms, and CRISPR/Cas9-induced Ppa-daf-21/Hsp90 knockout had a combined effect. Thus, Hsp90 canalizes the morphologies of plastic traits resulting in discrete polyphenism of mouth-forms.


Assuntos
Plasticidade Celular/fisiologia , Proteínas de Choque Térmico HSP90/fisiologia , Nematoides/fisiologia , Animais , Evolução Biológica , Proteínas de Ciclo Celular/genética , Proteínas de Ciclo Celular/metabolismo , Plasticidade Celular/genética , Meio Ambiente , Proteínas de Choque Térmico HSP90/genética , Proteínas de Choque Térmico/genética , Boca/metabolismo , Nematoides/genética , Fenótipo
13.
Curr Biol ; 26(16): 2174-9, 2016 08 22.
Artigo em Inglês | MEDLINE | ID: mdl-27451902

RESUMO

Developmental plasticity, the ability of one genotype to produce distinct phenotypes in different environments, has been suggested to facilitate phenotypic diversification, and several examples in plants and animals support its macroevolutionary potential [1-8]. However, little is known about associated molecular mechanisms, because environmental effects on development are difficult to study by laboratory approaches. One promising system is the mouth dimorphism of the nematode Pristionchus pacificus [9-12]. Following an irreversible decision in larval development, these nematodes form moveable teeth that occur in either of two discrete morphs. The "eurystomatous" (Eu) form has a wide mouth and two teeth, allowing predatory feeding on other nematodes. In contrast, the alternative ("stenostomatous"; St) form has diminutive mouthparts that largely constrain its diet to microbes. The sulfatase EUD-1 was previously discovered to execute a polyphenism switch based on dosage of functional alleles [13] and confirmed a prediction of evolutionary theory about how developmental switches control plasticity [1, 3]. However, the genetic context of this single gene, and hence the molecular complexity of switch mechanisms, was previously unknown. Here we use a suppressor screen to identify factors downstream of eud-1 in mouth-form regulation. We isolated three dominant, X-linked mutants in the nuclear hormone receptor gene nhr-40 that are haploinsufficient. Both eud-1 nhr-40 double and nhr-40 single mutants are all Eu, whereas transgenic overexpression of nhr-40 does not restore the wild-type phenotype but instead results in nearly all-St lines. Thus, NHR-40 is part of a developmental switch, suggesting that switch mechanisms controlling plasticity consist of multi-component hormonal signaling systems.


Assuntos
Receptores Citoplasmáticos e Nucleares/genética , Rabditídios/genética , Sulfatases/genética , Animais , Regulação da Expressão Gênica no Desenvolvimento , Organismos Hermafroditas/genética , Organismos Hermafroditas/crescimento & desenvolvimento , Larva/anatomia & histologia , Larva/genética , Larva/crescimento & desenvolvimento , Masculino , Boca/anatomia & histologia , Fenótipo , Receptores Citoplasmáticos e Nucleares/metabolismo , Rabditídios/anatomia & histologia , Rabditídios/crescimento & desenvolvimento , Sulfatases/metabolismo , Dente/anatomia & histologia
14.
Genome Biol Evol ; 8(7): 2093-105, 2016 07 12.
Artigo em Inglês | MEDLINE | ID: mdl-27289092

RESUMO

Beetles represent the largest insect order and they display extreme morphological, ecological and behavioral diversity, which makes them ideal models for evolutionary studies. Here, we present the draft genome of the scarab beetle Oryctes borbonicus, which has a more basal phylogenetic position than the two previously sequenced pest species Tribolium castaneum and Dendroctonus ponderosae providing the potential for sequence polarization. Oryctes borbonicus is endemic to La Réunion, an island located in the Indian Ocean, and is the host of the nematode Pristionchus pacificus, a well-established model organism for integrative evolutionary biology. At 518 Mb, the O. borbonicus genome is substantially larger and encodes more genes than T. castaneum and D. ponderosae We found that only 25% of the predicted genes of O. borbonicus are conserved as single copy genes across the nine investigated insect genomes, suggesting substantial gene turnover within insects. Even within beetles, up to 21% of genes are restricted to only one species, whereas most other genes have undergone lineage-specific duplications and losses. We illustrate lineage-specific duplications using detailed phylogenetic analysis of two gene families. This study serves as a reference point for insect/coleopteran genomics, although its original motivation was to find evidence for potential horizontal gene transfer (HGT) between O. borbonicus and P. pacificus The latter was previously shown to be the recipient of multiple horizontally transferred genes including some genes from insect donors. However, our study failed to provide any clear evidence for additional HGTs between the two species.


Assuntos
Besouros/genética , Evolução Molecular , Genoma de Inseto , Animais , Besouros/classificação , Transferência Genética Horizontal , Filogenia
15.
Mol Biol Evol ; 33(10): 2506-14, 2016 10.
Artigo em Inglês | MEDLINE | ID: mdl-27189572

RESUMO

Small-molecule signaling in nematode dauer formation has emerged as a major model to study chemical communication in development and evolution. Developmental arrest as nonfeeding and stress-resistant dauer larvae represents the major survival and dispersal strategy. Detailed studies in Caenorhabditis elegans and Pristionchus pacificus revealed that small-molecule communication changes rapidly in evolution resulting in extreme structural diversity of small-molecule compounds. In C. elegans, a blend of ascarosides constitutes the dauer pheromone, whereas the P. pacificus dauer pheromone includes additional paratosides and integrates building blocks from diverse primary metabolic pathways. Despite this complexity of small-molecule structures and functions, little is known about the biosynthesis of small molecules in nematodes outside C. elegans Here, we show that the genes encoding enzymes of the peroxisomal ß-oxidation pathway involved in small-molecule biosynthesis evolve rapidly, including gene duplications and domain switching. The thiolase daf-22, the most downstream factor in C. elegans peroxisomal ß-oxidation, has duplicated in P. pacificus, resulting in Ppa-daf-22.1, which still contains the sterol-carrier-protein (SCP) domain that was lost in C. elegans daf-22, and Ppa-daf-22.2. Using the CRISPR/Cas9 system, we induced mutations in both P. pacificus daf-22 genes and identified an unexpected complexity of functional conservation and divergence. Under well-fed conditions, ascaroside biosynthesis proceeds exclusively via Ppa-daf-22.1 In contrast, starvation conditions induce Ppa-daf-22.2 activity, resulting in the production of a specific subset of ascarosides. Gene expression studies indicate a reciprocal up-regulation of both Ppa-daf-22 genes, which is, however, independent of starvation. Thus, our study reveals an unexpected functional complexity of dauer development and evolution.


Assuntos
Caenorhabditis elegans/genética , Rabditídios/genética , Animais , Evolução Biológica , Caenorhabditis elegans/metabolismo , Proteínas de Caenorhabditis elegans/genética , Proteínas de Caenorhabditis elegans/metabolismo , Sequência Conservada , Evolução Molecular , Glicolipídeos/metabolismo , Larva/genética , Redes e Vias Metabólicas , Feromônios/metabolismo , Rabditídios/metabolismo , Transdução de Sinais , Especificidade da Espécie , Compostos de Sulfidrila/metabolismo
16.
BMC Evol Biol ; 15: 185, 2015 Sep 15.
Artigo em Inglês | MEDLINE | ID: mdl-26370559

RESUMO

BACKGROUND: The development of multicellular organisms is accompanied by gene expression changes in differentiating cells. Profiling stage-specific expression during development may reveal important insights into gene sets that contributed to the morphological diversity across the animal kingdom. RESULTS: We sequenced RNA-seq libraries throughout a developmental timecourse of the nematode Pristionchus pacificus. The transcriptomes reflect early larval stages, adult worms including late larvae, and growth-arrested dauer larvae and allowed the identification of developmentally regulated gene clusters. Our data reveals similar trends as previous transcriptome profiling of dauer worms and represents the first expression data for early larvae in P. pacificus. Gene expression clusters characterizing early larval stages show most significant enrichments of chaperones, while collagens are most significantly enriched in transcriptomes of late larvae and adult worms. By combining expression data with phylogenetic analysis, we found that developmentally regulated genes are found in paralogous clusters that have arisen through lineage-specific duplications after the split from the Caenorhabditis elegans branch. CONCLUSIONS: We propose that gene duplications of developmentally regulated genes represent a plausible evolutionary mechanism to increase the dosage of stage-specific expression. Consequently, this may contribute to the substantial divergence in expression profiles that has been observed across larger evolutionary time scales.


Assuntos
Duplicação Gênica , Nematoides/genética , Animais , Evolução Biológica , Caenorhabditis elegans/genética , Perfilação da Expressão Gênica , Regulação da Expressão Gênica no Desenvolvimento , Biblioteca Gênica , Larva/crescimento & desenvolvimento , Família Multigênica , Nematoides/crescimento & desenvolvimento , Filogenia
17.
J Mol Evol ; 80(1): 18-36, 2015 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-25323991

RESUMO

Homology is a fundamental concept in comparative biology and a crucial tool for the analysis of character distribution. Introduced by Owen in 1843 (Lectures on comparative anatomy and physiology of the invertebrate animals, Longman, Brown, Green and Longman, London) in a morphological context, homology can similarly be applied to protein-coding genes. However, in molecular biology the proper distinction between orthology and paralogy was long limited by the absence of whole-genome sequencing data. By now, genome-wide sequencing allows comprehensive analyses of the homology of genes and gene families at the level of an entire phylum. Here, we analyze a manually curated dataset of more than 2,000 proteins from the genomes of 11 nematode species of seven different genera, including free-living and animal and plant parasites to study the principles of homology assignments in gene families. Using all sequenced species as an extensive outgroup, we specifically focus on the two model species Caenorhabditis elegans and Pristionchus pacificus and compare enzymes involved in detoxification of xenobiotics and synthesis of fatty acids. We find that only a small proportion of genes in these families are one-to-one orthologs and that their history is shaped by massive duplication events. Of a total of 349 and 528 genes from C. elegans and P. pacificus, respectively, only 39 are one-to-one orthologs. Thus, frequent amplifications and losses are a widespread phenomenon in nematode lineages. We also report variation in birth and death rates depending on gene families and nematode lineages. Finally, we discuss the consequence of the near absence of one-to-one orthology in related organisms for the application of the homology concept to protein-coding genes in the era of whole-genome sequencing data.


Assuntos
Proteínas de Caenorhabditis elegans/genética , Caenorhabditis elegans/genética , Proteínas de Helminto/genética , Família Multigênica , Nematoides/genética , Homologia de Sequência de Aminoácidos , Animais , Proteínas de Caenorhabditis elegans/química , Evolução Molecular , Proteínas de Helminto/química , Filogenia
18.
Curr Biol ; 24(13): 1536-41, 2014 Jul 07.
Artigo em Inglês | MEDLINE | ID: mdl-24980503

RESUMO

Dauer formation, a major nematode survival strategy, represents a model for small-molecule regulation of metazoan development [1-10]. Free-living nematodes excrete dauer-inducing pheromones that have been assumed to target conspecifics of the same genotype [9, 11]. However, recent studies in Pristionchus pacificus revealed that the dauer pheromone of some strains affects conspecifics of other genotypes more strongly than individuals of the same genotype [12]. To elucidate the mechanistic basis for this intriguing cross-preference, we compared six P. pacificus wild isolates to determine the chemical composition of their dauer-inducing metabolomes and responses to individual pheromone components. We found that these isolates produce dauer pheromone blends of different composition and respond differently to individual pheromone components. Strikingly, there is no correlation between production of and dauer response to a specific compound in individual strains. Specifically, pheromone components that are abundantly produced by one genotype induce dauer formation in other genotypes, but not necessarily in the abundant producer. Furthermore, some genotypes respond to pheromone components they do not produce themselves. These results support a model of intraspecific competition in nematode dauer formation. Indeed, we observed intraspecific competition among sympatric strains in a novel experimental assay, suggesting a new role of small molecules in nematode ecology.


Assuntos
Adaptação Fisiológica/fisiologia , Comportamento Competitivo/fisiologia , Modelos Biológicos , Nematoides/fisiologia , Feromônios/metabolismo , Adaptação Fisiológica/efeitos dos fármacos , Animais , Larva/metabolismo , Larva/fisiologia , Estrutura Molecular , Nematoides/genética , Nematoides/metabolismo , Feromônios/química , Feromônios/farmacologia , Filogenia , Bibliotecas de Moléculas Pequenas
19.
PLoS One ; 9(1): e85104, 2014.
Artigo em Inglês | MEDLINE | ID: mdl-24465486

RESUMO

Though pluripotency is well characterized in mammals, many questions remain to be resolved regarding its evolutionary history. A necessary prerequisite for addressing this issue is to determine the phylogenetic distributions and orthology relationships of the transcription factor families sustaining or modulating this property. In mammals, the NANOG homeodomain transcription factor is one of the core players in the pluripotency network. However, its evolutionary history has not been thoroughly studied, hindering the interpretation of comparative studies. To date, the NANOG family was thought to be monogenic, with numerous pseudogenes described in mammals, including a tandem duplicate in Hominidae. By examining a wide-array of craniate genomes, we provide evidence that the NANOG family arose at the latest in the most recent common ancestor of osteichthyans and that NANOG genes are frequently found as tandem duplicates in sarcopterygians and as a single gene in actinopterygians. Their phylogenetic distribution is thus reminiscent of that recently shown for Class V POU paralogues, another key family of pluripotency-controlling factors. However, while a single ancestral duplication has been reported for the Class V POU family, we suggest that multiple independent duplication events took place during evolution of the NANOG family. These multiple duplications could have contributed to create a layer of complexity in the control of cell competence and pluripotency, which could explain the discrepancies relative to the functional evolution of this important gene family. Further, our analysis does not support the hypothesis that loss of NANOG and emergence of the preformation mode of primordial germ cell specification are causally linked. Our study therefore argues for the need of further functional comparisons between NANOG paralogues, notably regarding the novel duplicates identified in sauropsids and non-eutherian mammals.


Assuntos
Evolução Molecular , Proteínas de Homeodomínio/genética , Animais , Loci Gênicos , Humanos , Proteína Homeobox Nanog , Filogenia , Homologia de Sequência de Aminoácidos , Sintenia/genética
20.
Int J Evol Biol ; 2012: 490894, 2012.
Artigo em Inglês | MEDLINE | ID: mdl-22779028

RESUMO

One of the major aims of contemporary evolutionary biology is the understanding of the current pattern of biological diversity. This involves, first, the description of character distribution at various nodes of the phylogenetic tree of life and, second, the functional explanation of such changes. The analysis of character distribution is a powerful tool at both the morphological and molecular levels. Recent high-throughput sequencing approaches provide new opportunities to study the genetic architecture of organisms at the genome-wide level. In eukaryotes, one overarching finding is the absence of simple correlations of gene count and biological complexity. Instead, the domain architecture of proteins is becoming a central focus for large-scale evolutionary innovations. Here, we review examples of the evolution of novelty in conserved gene families in insects and nematodes. We highlight how in the absence of whole-genome duplications molecular novelty can arise, how members of gene families have diversified at distinct mechanistic levels, and how gene expression can be maintained in the context of multiple innovations in regulatory mechanisms.

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