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1.
RNA ; 2019 Sep 10.
Artigo em Inglês | MEDLINE | ID: mdl-31506380

RESUMO

The origin of the genetic code remains enigmatic five decades after it was elucidated, although there is growing evidence that the code co-evolved progressively with the ribosome. A number of primordial codes were proposed as ancestors of the modern genetic code, including comma-free codes such as the RRY, RNY or GNC codes (R = G or A, Y = C or T, N = any nucleotide), and the X circular code, an error-correcting code that also allows identification and maintenance of the reading frame. It was demonstrated previously that motifs of the X circular code are significantly enriched in the protein-coding genes of most organisms, from bacteria to eukaryotes. Here, we show that imprints of this code also exist in the ribosomal RNA (rRNA). In a large-scale study involving 133 organisms representative of the three domains of life, we identified 32 universal X motifs that are conserved in the rRNA of >90% of the organisms. Intriguingly, most of the universal X motifs are located in rRNA regions involved in important ribosome functions, notably in the peptidyl transferase center and the decoding center that form the original 'proto-ribosome'. Building on the existing accretion models for ribosome evolution, we propose that error-correcting circular codes represented an important step in the emergence of the modern genetic code. Thus, circular codes would have allowed the simultaneous coding of amino acids and synchronization of the reading frame in primitive translation systems, prior to the emergence of more sophisticated start codon recognition and translation initiation mechanisms.

2.
Hum Mutat ; 2019 Sep 24.
Artigo em Inglês | MEDLINE | ID: mdl-31549751

RESUMO

Polydactyly is one of the most frequent inherited defects of the limbs characterized by supernumerary digits and high-genetic heterogeneity. Among the many genes involved, either in isolated or syndromic forms, eight have been implicated in postaxial polydactyly (PAP). Among those, IQCE has been recently identified in a single consanguineous family. Using whole-exome sequencing in patients with uncharacterized ciliopathies, including PAP, we identified three families with biallelic pathogenic variations in IQCE. Interestingly, the c.895_904del (p.Val301Serfs*8) was found in all families without sharing a common haplotype, suggesting a recurrent mechanism. Moreover, in two families, the systemic phenotype could be explained by additional pathogenic variants in known genes (TULP1, ATP6V1B1). RNA expression analysis on patients' fibroblasts confirms that the dysfunction of IQCE leads to the dysregulation of genes associated with the hedgehog-signaling pathway, and zebrafish experiments demonstrate a full spectrum of phenotypes linked to defective cilia: Body curvature, kidney cysts, left-right asymmetry, misdirected cilia in the pronephric duct, and retinal defects. In conclusion, we identified three additional families confirming IQCE as a nonsyndromic PAP gene. Our data emphasize the importance of taking into account the complete set of variations of each individual, as each clinical presentation could finally be explained by multiple genes.

3.
Astrobiology ; 19(8): 1037-1052, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31314573

RESUMO

The search for organic molecules at the surface of Mars is a top priority of the Mars Science Laboratory (NASA) and ExoMars 2020 (ESA) space missions. Their main goal is to search for past and/or present molecular compounds related to a potential prebiotic chemistry and/or a biological activity on the Red Planet. A key step to interpret their data is to characterize the preservation or the evolution of organic matter in the martian environmental conditions. Several laboratory experiments have been developed especially concerning the influence of ultraviolet (UV) radiation. However, the experimental UV sources do not perfectly reproduce the solar UV radiation reaching the surface of Mars. For this reason, the International Space Station (ISS) can be advantageously used to expose the same samples studied in the laboratory to UV radiation representative of martian conditions. Those laboratory simulations can be completed by experiments in low Earth orbit (LEO) outside the ISS. Our study was part of the Photochemistry on the Space Station experiment on board the EXPOSE-R2 facility that was kept outside the ISS from October 2014 to February 2016. Chrysene, adenine, and glycine, pure or deposited on an iron-rich amorphous mineral phase, were exposed to solar UV. The total duration of exposure to UV radiation is estimated to be in the 1250-1420 h range. Each sample was characterized prior to and after the flight by Fourier transform infrared (FTIR) spectroscopy. These measurements showed that all exposed samples were partially degraded. Their quantum efficiencies of photodecomposition were calculated in the 200-250 nm wavelength range. They range from 10-4 to 10-6 molecules·photon-1 for pure organic samples and from 10-2 to 10-5 molecules·photon-1 for organic samples shielded by the mineral phase. These results highlight that none of the tested organics are stable under LEO solar UV radiation conditions. The presence of an iron-rich mineral phase increases their degradation.

4.
Clin Genet ; 95(3): 384-397, 2019 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-30614526

RESUMO

Bardet-Biedl syndrome (BBS) is an emblematic ciliopathy associated with retinal dystrophy, obesity, postaxial polydactyly, learning disabilities, hypogonadism and renal dysfunction. Before birth, enlarged/cystic kidneys as well as polydactyly are the hallmark signs of BBS to consider in absence of familial history. However, these findings are not specific to BBS, raising the problem of differential diagnoses and prognosis. Molecular diagnosis during pregnancies remains a timely challenge for this heterogeneous disease (22 known genes). We report here the largest cohort of BBS fetuses to better characterize the antenatal presentation. Prenatal ultrasound (US) and/or autopsy data from 74 fetuses with putative BBS diagnosis were collected out of which molecular diagnosis was established in 51 cases, mainly in BBS genes (45 cases) following the classical gene distribution, but also in other ciliopathy genes (6 cases). Based on this, an updated diagnostic decision tree is proposed. No genotype/phenotype correlation could be established but postaxial polydactyly (82%) and renal cysts (78%) were the most prevalent symptoms. However, autopsy revealed polydactyly that was missed by prenatal US in 55% of the cases. Polydactyly must be carefully looked for in pregnancies with apparently isolated renal anomalies in fetuses.

5.
Nucleic Acids Res ; 2018 Oct 31.
Artigo em Inglês | MEDLINE | ID: mdl-30380106

RESUMO

OrthoInspector is one of the leading software suites for orthology relations inference. In this paper, we describe a major redesign of the OrthoInspector online resource along with a significant increase in the number of species: 4753 organisms are now covered across the three domains of life, making OrthoInspector the most exhaustive orthology resource to date in terms of covered species (excluding viruses). The new website integrates original data exploration and visualization tools in an ergonomic interface. Distributions of protein orthologs are represented by heatmaps summarizing their evolutionary histories, and proteins with similar profiles can be directly accessed. Two novel tools have been implemented for comparative genomics: a phylogenetic profile search that can be used to find proteins with a specific presence-absence profile and investigate their functions and, inversely, a GO profiling tool aimed at deciphering evolutionary histories of molecular functions, processes or cell components. In addition to the re-designed website, the OrthoInspector resource now provides a REST interface for programmatic access. OrthoInspector 3.0 is available at http://lbgi.fr/orthoinspectorv3.

6.
Biosystems ; 2018 Oct 24.
Artigo em Inglês | MEDLINE | ID: mdl-30367916

RESUMO

A set X of 20 trinucleotides has been found to have the highest average occurrence in the reading frame, compared to the two shifted frames, of genes of bacteria, archaea, eukaryotes, plasmids and viruses (Michel, 2017, 2015; Arquès and Michel, 1996). This set X has an interesting mathematical property, since X is a maximal C3 self-complementary trinucleotide circular code (Arquès and Michel, 1996). Furthermore, any motif obtained from this circular code X has the capacity to retrieve, maintain and synchronize the reading frame in genes. In a recent study of the X motifs in the complete genome of the yeast, Saccharomyces cerevisiae, it was shown that they are significantly enriched in the reading frame of the genes (protein-coding regions) of the genome (Michel et al., 2017). It was suggested that these X motifs may be evolutionary relics of a primitive code originally used for gene translation. The aim of this paper is to address two questions: are X motifs conserved during evolution? and do they continue to play a functional role in the processes of genome decoding and protein production? In a large scale analysis involving complete genomes from four mammals and nine different yeast species, we highlight specific evolutionary pressures on the X motifs in the genes of all the genomes, and identify important new properties of X motif conservation at the level of the encoded amino acids. We then compare the occurrence of X motifs with existing experimental data concerning protein expression and protein production, and report a significant correlation between the number of X motifs in a gene and increased protein abundance. In a general way, this work suggests that motifs from circular codes, i.e. motifs having the property of reading frame retrieval, may represent functional elements located within the coding regions of extant genomes.

7.
Bioinformatics ; 34(19): 3390-3392, 2018 Oct 01.
Artigo em Inglês | MEDLINE | ID: mdl-29741582

RESUMO

Summary: Comparative studies of protein sequences are widely used in evolutionary and comparative genomics studies, but there is a lack of efficient tools to identify conserved regions ab initio within a protein multiple alignment. PROBE provides a fully automatic analysis of protein family conservation, to identify conserved regions, or 'blocks', that may correspond to structural/functional domains or motifs. Conserved blocks are identified at two different levels: (i) family level blocks indicate sites that are probably of central importance to the protein's structure or function, and (ii) sub-family level blocks highlight regions that may signify functional specialization, such as binding partners, etc. All conserved blocks are mapped onto a phylogenetic tree and can also be visualized in the context of the multiple sequence alignment. PROBE thus facilitates in-depth studies of sequence-structure-function-evolution relationships, and opens the way to block-level phylogenetic profiling. Availability and implementation: Freely available on the web at http://www.lbgi.fr/∼julie/probe/web.

8.
Life (Basel) ; 7(4)2017 Dec 03.
Artigo em Inglês | MEDLINE | ID: mdl-29207500

RESUMO

A set X of 20 trinucleotides has been found to have the highest average occurrence in the reading frame, compared to the two shifted frames, of genes of bacteria, archaea, eukaryotes, plasmids and viruses. This set X has an interesting mathematical property, since X is a maximal C3 self-complementary trinucleotide circular code. Furthermore, any motif obtained from this circular code X has the capacity to retrieve, maintain and synchronize the original (reading) frame. Since 1996, the theory of circular codes in genes has mainly been developed by analysing the properties of the 20 trinucleotides of X, using combinatorics and statistical approaches. For the first time, we test this theory by analysing the X motifs, i.e., motifs from the circular code X, in the complete genome of the yeast Saccharomyces cerevisiae. Several properties of X motifs are identified by basic statistics (at the frequency level), and evaluated by comparison to R motifs, i.e., random motifs generated from 30 different random codes R. We first show that the frequency of X motifs is significantly greater than that of R motifs in the genome of S. cerevisiae. We then verify that no significant difference is observed between the frequencies of X and R motifs in the non-coding regions of S. cerevisiae, but that the occurrence number of X motifs is significantly higher than R motifs in the genes (protein-coding regions). This property is true for all cardinalities of X motifs (from 4 to 20) and for all 16 chromosomes. We further investigate the distribution of X motifs in the three frames of S. cerevisiae genes and show that they occur more frequently in the reading frame, regardless of their cardinality or their length. Finally, the ratio of X genes, i.e., genes with at least one X motif, to non-X genes, in the set of verified genes is significantly different to that observed in the set of putative or dubious genes with no experimental evidence. These results, taken together, represent the first evidence for a significant enrichment of X motifs in the genes of an extant organism. They raise two hypotheses: the X motifs may be evolutionary relics of the primitive codes used for translation, or they may continue to play a functional role in the complex processes of genome decoding and protein synthesis.

9.
J Med Internet Res ; 19(6): e212, 2017 06 16.
Artigo em Inglês | MEDLINE | ID: mdl-28623182

RESUMO

BACKGROUND: The constant and massive increase of biological data offers unprecedented opportunities to decipher the function and evolution of genes and their roles in human diseases. However, the multiplicity of sources and flow of data mean that efficient access to useful information and knowledge production has become a major challenge. This challenge can be addressed by taking inspiration from Web 2.0 and particularly social networks, which are at the forefront of big data exploration and human-data interaction. OBJECTIVE: MyGeneFriends is a Web platform inspired by social networks, devoted to genetic disease analysis, and organized around three types of proactive agents: genes, humans, and genetic diseases. The aim of this study was to improve exploration and exploitation of biological, postgenomic era big data. METHODS: MyGeneFriends leverages conventions popularized by top social networks (Facebook, LinkedIn, etc), such as networks of friends, profile pages, friendship recommendations, affinity scores, news feeds, content recommendation, and data visualization. RESULTS: MyGeneFriends provides simple and intuitive interactions with data through evaluation and visualization of connections (friendships) between genes, humans, and diseases. The platform suggests new friends and publications and allows agents to follow the activity of their friends. It dynamically personalizes information depending on the user's specific interests and provides an efficient way to share information with collaborators. Furthermore, the user's behavior itself generates new information that constitutes an added value integrated in the network, which can be used to discover new connections between biological agents. CONCLUSIONS: We have developed MyGeneFriends, a Web platform leveraging conventions from popular social networks to redefine the relationship between humans and biological big data and improve human processing of biomedical data. MyGeneFriends is available at lbgi.fr/mygenefriends.


Assuntos
Doenças Genéticas Inatas/genética , Testes Genéticos/métodos , Rede Social , Telemedicina/estatística & dados numéricos , Amigos , Humanos , Pesquisadores
10.
Hum Mutat ; 38(10): 1316-1324, 2017 10.
Artigo em Inglês | MEDLINE | ID: mdl-28608363

RESUMO

Numerous mutations in each of the mitochondrial aminoacyl-tRNA synthetases (aaRSs) have been implicated in human diseases. The mutations are autosomal and recessive and lead mainly to neurological disorders, although with pleiotropic effects. The processes and interactions that drive the etiology of the disorders associated with mitochondrial aaRSs (mt-aaRSs) are far from understood. The complexity of the clinical, genetic, and structural data requires concerted, interdisciplinary efforts to understand the molecular biology of these disorders. Toward this goal, we designed MiSynPat, a comprehensive knowledge base together with an ergonomic Web server designed to organize and access all pertinent information (sequences, multiple sequence alignments, structures, disease descriptions, mutation characteristics, original literature) on the disease-linked human mt-aaRSs. With MiSynPat, a user can also evaluate the impact of a possible mutation on sequence-conservation-structure in order to foster the links between basic and clinical researchers and to facilitate future diagnosis. The proposed integrated view, coupled with research on disease-related mt-aaRSs, will help to reveal new functions for these enzymes and to open new vistas in the molecular biology of the cell. The purpose of MiSynPat, freely available at http://misynpat.org, is to constitute a reference and a converging resource for scientists and clinicians.


Assuntos
Aminoacil-tRNA Sintetases/genética , Bases de Dados Genéticas , Mitocôndrias/enzimologia , Mutação/genética , Sequência de Aminoácidos , Aminoacil-tRNA Sintetases/química , Evolução Molecular , Doenças Genéticas Inatas/genética , Humanos , Mitocôndrias/genética , Estrutura Molecular , Conformação Proteica
11.
Mol Biol Evol ; 34(8): 2016-2034, 2017 08 01.
Artigo em Inglês | MEDLINE | ID: mdl-28460059

RESUMO

Cilia (flagella) are important eukaryotic organelles, present in the Last Eukaryotic Common Ancestor, and are involved in cell motility and integration of extracellular signals. Ciliary dysfunction causes a class of genetic diseases, known as ciliopathies, however current knowledge of the underlying mechanisms is still limited and a better characterization of genes is needed. As cilia have been lost independently several times during evolution and they are subject to important functional variation between species, ciliary genes can be investigated through comparative genomics. We performed phylogenetic profiling by predicting orthologs of human protein-coding genes in 100 eukaryotic species. The analysis integrated three independent methods to predict a consensus set of 274 ciliary genes, including 87 new promising candidates. A fine-grained analysis of the phylogenetic profiles allowed a partitioning of ciliary genes into modules with distinct evolutionary histories and ciliary functions (assembly, movement, centriole, etc.) and thus propagation of potential annotations to previously undocumented genes. The cilia/basal body localization was experimentally confirmed for five of these previously unannotated proteins (LRRC23, LRRC34, TEX9, WDR27, and BIVM), validating the relevance of our approach. Furthermore, our multi-level analysis sheds light on the core gene sets retained in gamete-only flagellates or Ecdysozoa for instance. By combining gene-centric and species-oriented analyses, this work reveals new ciliary and ciliopathy gene candidates and provides clues about the evolution of ciliary processes in the eukaryotic domain. Additionally, the positive and negative reference gene sets and the phylogenetic profile of human genes constructed during this study can be exploited in future work.


Assuntos
Cílios/genética , Ciliopatias/genética , Animais , Movimento Celular/genética , Cílios/metabolismo , Ciliopatias/metabolismo , Bases de Dados de Ácidos Nucleicos , Eucariotos , Células Eucarióticas , Evolução Molecular , Flagelos/genética , Flagelos/metabolismo , Genômica , Humanos , Filogenia , Análise de Sequência de DNA/métodos
12.
Astrobiology ; 17(3): 231-252, 2017 03.
Artigo em Inglês | MEDLINE | ID: mdl-28282216

RESUMO

To detect signs of life by remote sensing on objects of our Solar System and on exoplanets, the characterization of light scattered by surface life material could complement possible clues given by the atmospheric composition. We reviewed the reflectance spectra of a broad selection of major biomolecules that constitute terrestrial carbon-based life from 0.4 to 2.4 µm, and we discuss their detectability through atmospheric spectral windows. Biomolecule features in the near-infrared (0.8-2.4 µm) will likely be obscured by water spectral features and some atmospheric gases. The visible range (0.4-0.8 µm), including the strong spectral features of pigments, is the most favorable. We investigated the detectability of a pigmented microorganism (Deinococcus radiodurans) when mixed with silica sand, liquid water, and water-ice particles representative of diverse surfaces of potentially habitable worlds. We measured the visible to near-infrared reflectance spectra (0.4-2.4 µm) and the visible phase curves (at 0.45 and 0.75 µm) of the mixtures to assess how the surface medium and the viewing geometry affect the detectability of the microorganisms. The results show that ice appears to be the most favorable medium for the detection of pigments. Water ice is bright and featureless from 0.4 to 0.8 µm, allowing the absorption of any pigment present in the ice to be well noticeable. We found that the visible phase curve of water ice is the most strongly affected by the presence of pigments, with variations of the spectral slope by more than a factor of 3 with phase angles. Finally, we show that the sublimation of the ice results in the concentration of the biological material onto the surface and the consequent increase of its signal. These results have applications to the search for life on icy worlds, such as Europa or Enceladus. Key Words: Remote sensing-Biosignatures-Reflectance spectroscopy-Exoplanets-Spectroscopic biosignatures-Pigments. Astrobiology 17, 231-252.


Assuntos
Bactérias/metabolismo , Exobiologia/métodos , Meio Ambiente Extraterreno , Planetas , Tecnologia de Sensoriamento Remoto/métodos , Atmosfera/química , Deinococcus/metabolismo , Gelo , Origem da Vida , Dióxido de Silício/química , Água/química
13.
Infect Immun ; 85(3)2017 03.
Artigo em Inglês | MEDLINE | ID: mdl-28069815

RESUMO

MicroRNAs (miRNAs) are short, noncoding RNAs involved in the regulation of several processes associated with inflammatory diseases and infection. Bacterial infection modulates miRNA expression to subvert any innate immune response. In this study we analyzed, using microarray analysis, the bacterial modulation of miRNAs in bone marrow-derived macrophages (BMMs) in which activity was induced by infection with Porphyromonas gingivalis The expression of several miRNAs was modulated 3 h postinfection (at a multiplicity of infection of 25). A bioinformatic analysis was performed to further identify pathways related to the innate immune host response under the influence of selected miRNAs. To assess the effects of the miRNAs identified on cytokine secretion (tumor necrosis factor alpha [TNF-α] and interleukin-10 [IL-10]), BMMs were transfected with selected miRNA mimics and inhibitors. Transfection with mmu-miR-155 and mmu-miR-2137 did not modify TNF-α secretion, while their inhibitors increased it. Inhibitors of mmu-miR-2137 and mmu-miR-7674 increased the secretion of the anti-inflammatory factor IL-10. In P. gingivalis-infected BMMs, mmu-miR-155-5p significantly decreased TNF-α secretion while inhibitor of mmu-miR-2137 increased IL-10 secretion. In vivo, in a mouse model of P. gingivalis-induced calvarial bone resorption, injection of mmu-miR-155-5p or anti-mmu-miR-2137 reduced the size of the lesion significantly. Furthermore, anti-mmu-miR-2137 significantly reduced inflammatory cell infiltration, osteoclast activity, and bone loss. Bioinformatic analysis demonstrated that pathways related to cytokine- and chemokine-related pathways but also osteoclast differentiation may be involved in the effects observed. This study contributes further to our understanding of P. gingivalis-induced modulation of miRNAs and their physiological effects. It highlights the potential therapeutic merits of targeting mmu-miR-155-5p and mmu-miR-2137 to control inflammation induced by P. gingivalis infection.


Assuntos
Infecções por Bacteroidaceae/genética , Infecções por Bacteroidaceae/microbiologia , Regulação da Expressão Gênica , Macrófagos/metabolismo , Macrófagos/microbiologia , MicroRNAs/genética , Porphyromonas gingivalis/fisiologia , Animais , Infecções por Bacteroidaceae/imunologia , Interações Hospedeiro-Patógeno/genética , Interações Hospedeiro-Patógeno/imunologia , Imunidade Inata , Interleucina-10/biossíntese , Macrófagos/imunologia , Camundongos , Interferência de RNA , RNA Mensageiro/genética , Fator de Necrose Tumoral alfa/biossíntese
14.
PLoS One ; 11(12): e0168271, 2016.
Artigo em Inglês | MEDLINE | ID: mdl-27977773

RESUMO

GNAT1, encoding the transducin subunit Gα, is an important element of the phototransduction cascade. Mutations in this gene have been associated with autosomal dominant and autosomal recessive congenital stationary night blindness. Recently, a homozygous truncating GNAT1 mutation was identified in a patient with late-onset rod-cone dystrophy. After exclusion of mutations in genes underlying progressive inherited retinal disorders, by targeted next generation sequencing, a 32 year-old male sporadic case with severe rod-cone dystrophy and his unaffected parents were investigated by whole exome sequencing. This led to the identification of a homozygous nonsense variant, c.963C>A p.(Cys321*) in GNAT1, which was confirmed by Sanger sequencing. The mother was heterozygous for this variant whereas the variant was absent in the father. c.963C>A p.(Cys321*) is predicted to produce a shorter protein that lacks critical sites for the phototransduction cascade. Our work confirms that the phenotype and the mode of inheritance associated with GNAT1 variants can vary from autosomal dominant, autosomal recessive congenital stationary night blindness to autosomal recessive rod-cone dystrophy.


Assuntos
Códon sem Sentido , Distrofias de Cones e Bastonetes/genética , Proteínas Heterotriméricas de Ligação ao GTP/genética , Adulto , Análise Mutacional de DNA , Sequenciamento de Nucleotídeos em Larga Escala , Homozigoto , Humanos , Masculino , Retinite Pigmentosa/genética
15.
BMC Bioinformatics ; 17(1): 271, 2016 Jul 07.
Artigo em Inglês | MEDLINE | ID: mdl-27387560

RESUMO

BACKGROUND: A standard procedure in many areas of bioinformatics is to use a multiple sequence alignment (MSA) as the basis for various types of homology-based inference. Applications include 3D structure modelling, protein functional annotation, prediction of molecular interactions, etc. These applications, however sophisticated, are generally highly sensitive to the alignment used, and neglecting non-homologous or uncertain regions in the alignment can lead to significant bias in the subsequent inferences. RESULTS: Here, we present a new method, LEON-BIS, which uses a robust Bayesian framework to estimate the homologous relations between sequences in a protein multiple alignment. Sequences are clustered into sub-families and relations are predicted at different levels, including 'core blocks', 'regions' and full-length proteins. The accuracy and reliability of the predictions are demonstrated in large-scale comparisons using well annotated alignment databases, where the homologous sequence segments are detected with very high sensitivity and specificity. CONCLUSIONS: LEON-BIS uses robust Bayesian statistics to distinguish the portions of multiple sequence alignments that are conserved either across the whole family or within subfamilies. LEON-BIS should thus be useful for automatic, high-throughput genome annotations, 2D/3D structure predictions, protein-protein interaction predictions etc.


Assuntos
Teorema de Bayes , Biologia Computacional/métodos , Proteínas/química , Alinhamento de Sequência/métodos , Sequência de Aminoácidos , Humanos , Proteínas/genética , Homologia de Sequência de Aminoácidos
16.
PLoS One ; 11(3): e0150758, 2016.
Artigo em Inglês | MEDLINE | ID: mdl-26985665

RESUMO

To investigate the complexity of alternative splicing in the retina, we sequenced and analyzed a total of 115,706 clones from normalized cDNA libraries from mouse neural retina (66,217) and rat retinal pigmented epithelium (49,489). Based upon clustering the cDNAs and mapping them with their respective genomes, the estimated numbers of genes were 9,134 for the mouse neural retina and 12,050 for the rat retinal pigmented epithelium libraries. This unique collection of retinal of messenger RNAs is maintained and accessible through a web-base server to the whole community of retinal biologists for further functional characterization. The analysis revealed 3,248 and 3,202 alternative splice events for mouse neural retina and rat retinal pigmented epithelium, respectively. We focused on transcription factors involved in vision. Among the six candidates suitable for functional analysis, we selected Otx2S, a novel variant of the Otx2 gene with a deletion within the homeodomain sequence. Otx2S is expressed in both the neural retina and retinal pigmented epithelium, and encodes a protein that is targeted to the nucleus. OTX2S exerts transdominant activity on the tyrosinase promoter when tested in the physiological environment of primary RPE cells. By overexpressing OTX2S in primary RPE cells using an adeno associated viral vector, we identified 10 genes whose expression is positively regulated by OTX2S. We find that OTX2S is able to bind to the chromatin at the promoter of the retinal dehydrogenase 10 (RDH10) gene.


Assuntos
Processamento Alternativo , Fatores de Transcrição Otx/genética , Retina/citologia , Epitélio Pigmentado da Retina/citologia , Oxirredutases do Álcool/genética , Sequência de Aminoácidos , Animais , Células Cultivadas , Cromatina/genética , Cromatina/metabolismo , DNA Complementar/genética , Biblioteca Gênica , Camundongos , Camundongos Endogâmicos C57BL , Dados de Sequência Molecular , Monofenol Mono-Oxigenase/genética , Fatores de Transcrição Otx/análise , Fatores de Transcrição Otx/metabolismo , Regiões Promotoras Genéticas , Isoformas de Proteínas/análise , Isoformas de Proteínas/genética , Isoformas de Proteínas/metabolismo , RNA Mensageiro/genética , Ratos , Retina/metabolismo , Epitélio Pigmentado da Retina/metabolismo
17.
Dev Cell ; 36(1): 63-78, 2016 Jan 11.
Artigo em Inglês | MEDLINE | ID: mdl-26766443

RESUMO

Mitosis ensures equal segregation of the genome and is controlled by a variety of ubiquitylation signals on substrate proteins. However, it remains unexplored how the versatile ubiquitin code is read out during mitotic progression. Here, we identify the ubiquitin receptor protein UBASH3B as an important regulator of mitosis. UBASH3B interacts with ubiquitylated Aurora B, one of the main kinases regulating chromosome segregation, and controls its subcellular localization but not protein levels. UBASH3B is a limiting factor in this pathway and is sufficient to localize Aurora B to microtubules prior to anaphase. Importantly, targeting Aurora B to microtubules by UBASH3B is necessary for the timing and fidelity of chromosome segregation in human cells. Our findings uncover an important mechanism defining how ubiquitin attachment to a substrate protein is decoded during mitosis.


Assuntos
Aurora Quinase B/metabolismo , Segregação de Cromossomos/genética , Microtúbulos/metabolismo , Mitose/fisiologia , Proteínas Tirosina Fosfatases/metabolismo , Ubiquitina/metabolismo , Anáfase/fisiologia , Linhagem Celular , Células HeLa , Humanos , Cinetocoros/metabolismo , Fosforilação , Ubiquitinação/fisiologia
18.
BMC Evol Biol ; 15: 222, 2015 Oct 12.
Artigo em Inglês | MEDLINE | ID: mdl-26459560

RESUMO

BACKGROUND: Transposable elements (TE) have attracted much attention since they shape the genome and contribute to species evolution. Organisms have evolved mechanisms to control TE activity. Testis expressed 19 (Tex19) represses TE expression in mouse testis and placenta. In the human and mouse genomes, Tex19 and Secreted and transmembrane 1 (Sectm1) are neighbors but are not homologs. Sectm1 is involved in immunity and its molecular phylogeny is unknown. METHODS: Using multiple alignments of complete protein sequences (MACS), we inferred Tex19 and Sectm1 molecular phylogenies. Protein conserved regions were identified and folds were predicted. Finally, expression patterns were studied across tissues and species using RNA-seq public data and RT-PCR. RESULTS: We present 2 high quality alignments of 58 Tex19 and 58 Sectm1 protein sequences from 48 organisms. First, both genes are eutherian-specific, i.e., exclusively present in mammals except monotremes (platypus) and marsupials. Second, Tex19 and Sectm1 have both duplicated in Sciurognathi and Bovidae while they have remained as single copy genes in all further placental mammals. Phylogenetic concordance between both genes was significant (p-value < 0.05) and supported co-evolution and functional relationship. At the protein level, Tex19 exhibits 3 conserved regions and 4 invariant cysteines. In particular, a CXXC motif is present in the N-terminal conserved region. Sectm1 exhibits 2 invariant cysteines and an Ig-like domain. Strikingly, Tex19 C-terminal conserved region was lost in Haplorrhini primates while a Sectm1 C-terminal extra domain was acquired. Finally, we have determined that Tex19 and Sectm1 expression levels anti-correlate across the testis of several primates (ρ = -0.72) which supports anti-regulation. CONCLUSIONS: Tex19 and Sectm1 co-evolution and anti-regulated expressions support a strong functional relationship between both genes. Since Tex19 operates a control on TE and Sectm1 plays a role in immunity, Tex19 might suppress an immune response directed against cells that show TE activity in eutherian reproductive tissues.


Assuntos
Evolução Molecular , Mamíferos/genética , Proteínas de Membrana/genética , Proteínas Nucleares/genética , Sequência de Aminoácidos , Animais , Feminino , Expressão Gênica , Humanos , Masculino , Mamíferos/classificação , Mamíferos/metabolismo , Proteínas de Membrana/química , Proteínas de Membrana/metabolismo , Camundongos , Dados de Sequência Molecular , Proteínas Nucleares/química , Proteínas Nucleares/metabolismo , Filogenia , Placenta/metabolismo , Gravidez , Ratos , Retroelementos , Testículo/metabolismo
19.
Astrobiology ; 15(3): 221-37, 2015 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-25734356

RESUMO

Most of the phyllosilicates detected at the surface of Mars today are probably remnants of ancient environments that sustained long-term bodies of liquid water at the surface or subsurface and were possibly favorable for the emergence of life. Consequently, phyllosilicates have become the main mineral target in the search for organics on Mars. But are phyllosilicates efficient at preserving organic molecules under current environmental conditions at the surface of Mars? We monitored the qualitative and quantitative evolutions of glycine, urea, and adenine in interaction with the Fe(3+)-smectite clay nontronite, one of the most abundant phyllosilicates present at the surface of Mars, under simulated martian surface ultraviolet light (190-400 nm), mean temperature (218 ± 2 K), and pressure (6 ± 1 mbar) in a laboratory simulation setup. We tested organic-rich samples that were representative of the evaporation of a small, warm pond of liquid water containing a high concentration of organics. For each molecule, we observed how the nontronite influences its quantum efficiency of photodecomposition and the nature of its solid evolution products. The results reveal a pronounced photoprotective effect of nontronite on the evolution of glycine and adenine; their efficiencies of photodecomposition were reduced by a factor of 5 when mixed at a concentration of 2.6 × 10(-2) mol of molecules per gram of nontronite. Moreover, when the amount of nontronite in the sample of glycine was increased by a factor of 2, the gain of photoprotection was multiplied by a factor of 5. This indicates that the photoprotection provided by the nontronite is not a purely mechanical shielding effect but is also due to stabilizing interactions. No new evolution product was firmly identified, but the results obtained with urea suggest a particular reactivity in the presence of nontronite, leading to an increase of its dissociation rate.


Assuntos
Evolução Química , Marte , Compostos Orgânicos/química , Silicatos/química , Raios Ultravioleta , Meio Ambiente Extraterreno/química
20.
PLoS One ; 10(2): e0118024, 2015.
Artigo em Inglês | MEDLINE | ID: mdl-25706271

RESUMO

An in situ hybridization (ISH) study was performed on 2000 murine genes representing around 10% of the protein-coding genes present in the mouse genome using data generated by the EURExpress consortium. This study was carried out in 25 tissues of late gestation embryos (E14.5), with a special emphasis on the developing ear and on five distinct developing sensory organs, including the cochlea, the vestibular receptors, the sensory retina, the olfactory organ, and the vibrissae follicles. The results obtained from an analysis of more than 11,000 micrographs have been integrated in a newly developed knowledgebase, called ImAnno. In addition to managing the multilevel micrograph annotations performed by human experts, ImAnno provides public access to various integrated databases and tools. Thus, it facilitates the analysis of complex ISH gene expression patterns, as well as functional annotation and interaction of gene sets. It also provides direct links to human pathways and diseases. Hierarchical clustering of expression patterns in the 25 tissues revealed three main branches corresponding to tissues with common functions and/or embryonic origins. To illustrate the integrative power of ImAnno, we explored the expression, function and disease traits of the sensory epithelia of the five presumptive sensory organs. The study identified 623 genes (out of 2000) concomitantly expressed in the five embryonic epithelia, among which many (∼12%) were involved in human disorders. Finally, various multilevel interaction networks were characterized, highlighting differential functional enrichments of directly or indirectly interacting genes. These analyses exemplify an under-represention of "sensory" functions in the sensory gene set suggests that E14.5 is a pivotal stage between the developmental stage and the functional phase that will be fully reached only after birth.


Assuntos
Biologia Computacional/métodos , Perfilação da Expressão Gênica/métodos , Regulação da Expressão Gênica no Desenvolvimento , Hibridização In Situ/métodos , Animais , Plexo Corióideo/embriologia , Plexo Corióideo/metabolismo , Bases de Dados Genéticas , Orelha Interna/embriologia , Orelha Interna/metabolismo , Desenvolvimento Fetal/genética , Ontologia Genética , Redes Reguladoras de Genes , Genômica/métodos , Humanos , Armazenamento e Recuperação da Informação/métodos , Camundongos , Mucosa Olfatória/embriologia , Mucosa Olfatória/metabolismo , Retina/embriologia , Retina/metabolismo , Células Receptoras Sensoriais/metabolismo , Vibrissas/embriologia , Vibrissas/metabolismo
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