RESUMO
Prediction of transcription factor binding sites (TFBS) is an example of application of Bioinformatics where DNA molecules are represented as sequences of A, C, G and T symbols. The most used model in this problem is Position Weight Matrix (PWM). Notwithstanding the advantage of being simple, PWMs cannot capture dependency between nucleotide positions, which may affect prediction performance. Acyclic Probabilistic Finite Automata (APFA) is an alternative model able to accommodate position dependencies. However, APFA is a more complex model, which means more parameters have to be learned. In this paper, we propose an innovative method to identify when position dependencies influence preference for PWMs or APFAs. This implied using position dependency features extracted from 1106 sets of TFBS to infer a decision tree able to predict which is the best model - PWM or APFA - for a given set of TFBSs. According to our results, as few as three pinpointed features are able to choose the best model, providing a balance of performance (average precision) and model simplicity.
RESUMO
Soil biota has a crucial impact on soil ecology, global climate changes, and effective crop management and studying the diverse ecological roles of dipteran larvae deepens the understanding of soil food webs. A multi-omics study of Pseudolycoriella hygida comb. nov. (Diptera: Sciaroidea: Sciaridae) aimed to characterize carbohydrate-active enzymes (CAZymes) for litter degradation in this species. Manual curation of 17,881 predicted proteins in the Psl. hygida genome identified 137 secreted CAZymes, of which 33 are present in the saliva proteome, and broadly confirmed by saliva CAZyme catalytic profiling against plant cell wall polysaccharides and pNP-glycosyl substrates. Comparisons with two other sciarid species and the outgroup Lucilia cuprina (Diptera: Calliphoridae) identified 42 CAZyme families defining a sciarid CAZyme profile. The litter-degrading potential of sciarids corroborates their significant role as decomposers, yields insights to the evolution of insect feeding habits, and highlights the importance of insects as a source of biotechnologically relevant enzymes.
RESUMO
Segments are repeated anatomical units forming the body of insects. In Drosophila, the specification of the body takes place during the blastoderm through the segmentation cascade. Pair-rule genes such as hairy (h), even-skipped (eve), runt (run), and fushi-tarazu (ftz) are of the intermediate level of the cascade and each pair-rule gene is expressed in seven transversal stripes along the antero-posterior axis of the embryo. Stripes are formed by independent cis-regulatory modules (CRMs) under the regulation of transcription factors of maternal source and of gap proteins of the first level of the cascade. The initial blastoderm of Drosophila is a syncytium and it also coincides with the mid-blastula transition when thousands of zygotic genes are transcribed and their products are able to diffuse in the cytoplasm. Thus, we anticipated a complex regulation of the CRMs of the pair-rule stripes. The CRMs of h 1, eve 1, run 1, ftz 1 are able to be activated by bicoid (bcd) throughout the anterior blastoderm and several lines of evidence indicate that they are repressed by the anterior gap genes slp1 (sloppy-paired 1), tll (tailless) and hkb (huckebein). The modest activity of these repressors led to the premise of a combinatorial mechanism regulating the expression of the CRMs of h 1, eve 1, run 1, ftz 1 in more anterior regions of the embryo. We tested this possibility by progressively removing the repression activities of slp1, tll and hkb. In doing so, we were able to expose a mechanism of additive repression limiting the anterior borders of stripes 1. Stripes 1 respond depending on their distance from the anterior end and repressors operating at different levels.
Assuntos
Blastoderma , Proteínas de Drosophila , Animais , Blastoderma/metabolismo , Drosophila/genética , Proteínas de Drosophila/genética , Proteínas de Homeodomínio/genética , Fatores de Transcrição/genéticaRESUMO
The fruit fly Drosophila melanogaster is a great model system in developmental biology studies and related disciplines. In a historical perspective, I focus on the formation of the Drosophila segmental body plan using a comparative approach. I highlight the evolutionary trend of increasing complexity of the molecular segmentation network in arthropods that resulted in an incredible degree of complexity at the gap gene level in derived Diptera. There is growing evidence that Drosophila is a highly derived insect, and we are still far from fully understanding the underlying evolutionary mechanisms that led to its complexity. In addition, recent data have altered how we view the transcriptional regulatory mechanisms that control segmentation in Drosophila. However, these observations are not all bad news for the field. Instead, they stimulate further study of segmentation in Drosophila and in other species as well. To me, these seemingly new Drosophila paradigms are very challenging ones.
Assuntos
Drosophila/genética , Animais , Evolução Biológica , Biologia do DesenvolvimentoRESUMO
The hierarchy of the segmentation cascade responsible for establishing the Drosophila body plan is composed by gap, pair-rule and segment polarity genes. However, no pair-rule stripes are formed in the anterior regions of the embryo. This lack of stripe formation, as well as other evidence from the literature that is further investigated here, led us to the hypothesis that anterior gap genes might be involved in a combinatorial mechanism responsible for repressing the cis-regulatory modules (CRMs) of hairy (h), even-skipped (eve), runt (run), and fushi-tarazu (ftz) anterior-most stripes. In this study, we investigated huckebein (hkb), which has a gap expression domain at the anterior tip of the embryo. Using genetic methods we were able to detect deviations from the wild-type patterns of the anterior-most pair-rule stripes in different genetic backgrounds, which were consistent with Hkb-mediated repression. Moreover, we developed an image processing tool that, for the most part, confirmed our assumptions. Using an hkb misexpression system, we further detected specific repression on anterior stripes. Furthermore, bioinformatics analysis predicted an increased significance of binding site clusters in the CRMs of h 1, eve 1, run 1 and ftz 1when Hkb was incorporated in the analysis, indicating that Hkb plays a direct role in these CRMs. We further discuss that Hkb and Slp1, which is the other previously identified common repressor of anterior stripes, might participate in a combinatorial repression mechanism controlling stripe CRMs in the anterior parts of the embryo and define the borders of these anterior stripes.
Assuntos
Blastoderma/metabolismo , Padronização Corporal/fisiologia , Proteínas de Ligação a DNA/metabolismo , Proteínas de Drosophila/metabolismo , Drosophila/embriologia , Proteínas Repressoras/metabolismo , Animais , Fatores de Transcrição Hélice-Alça-Hélice Básicos/metabolismo , Sítios de Ligação/genética , Blastoderma/embriologia , Biologia Computacional , Embrião não Mamífero/anatomia & histologia , Embrião não Mamífero/embriologia , Embrião não Mamífero/metabolismo , Fatores de Transcrição Fushi Tarazu/metabolismo , Proteínas de Homeodomínio/metabolismo , Processamento de Imagem Assistida por Computador , Hibridização In Situ , Proteínas Nucleares/metabolismo , Fatores de Transcrição/metabolismoRESUMO
Drosophila pair-rule genes are expressed in striped patterns with a precise order of overlap between stripes of different genes. We investigated the role of Giant (Gt) in the regulation of even-skipped, hairy, runt, and fushi tarazu stripes formed in the vicinity of Gt expression domains. In gt null embryos, specific stripes of eve, h, run, and ftz are disrupted. With an ectopic expression system, we verified that stripes affected in the mutant are also repressed. Simultaneously hybridizing gt misxpressing embryos with two pair-rule gene probes, we were able to distinguish differences in the repression of pairs of stripes that overlap extensively. Together, our results showed Gt repression roles in the regulation of two groups of partially overlapping stripes and that Gt morphogen activity is part of the mechanism responsible for the differential positioning of these stripes borders. We discuss the possibility that other factors regulate Gt stripe targets as well.
Assuntos
Proteínas de Drosophila/metabolismo , Proteínas Repressoras/metabolismo , Animais , Drosophila , Proteínas de Drosophila/genética , Embrião não Mamífero/metabolismo , Regulação da Expressão Gênica no Desenvolvimento/genética , Regulação da Expressão Gênica no Desenvolvimento/fisiologia , Imuno-Histoquímica , Hibridização In Situ , Proteínas Repressoras/genéticaRESUMO
DNA puffs are genomic regions of polytene chromosomes that undergo developmentally controlled DNA amplification and transcription in salivary glands of sciarid flies. Here, we tested the hypothesis that DNA puff genes code for salivary proteins in Trichosia pubescens. To do that, we generated antibodies against saliva and immunoscreened a cDNA library made from salivary glands. We isolated clones corresponding to DNA puff regions, including clone D-50 that contained the entire coding sequence of the previously isolated C4B1 gene from puff 4C. Indeed, we showed that puff 4C is a DNA puff region detecting its local transcription and its extra rounds of DNA incorporation compared to neighboring regions. We further confirmed D-50 clone identity in Western blots reacted with the anti-saliva anitiserum. We detected a recombinant protein expressed by this clone that had the expected size for a full-length product of the gene. We end with a discussion of the relationship between DNA puff genes and their products.
Assuntos
Dípteros/genética , Expressão Gênica/genética , Proteínas de Insetos/genética , Proteínas e Peptídeos Salivares/genética , Sequência de Aminoácidos , Animais , Anticorpos/metabolismo , Sequência de Bases , Western Blotting , Cromossomos/metabolismo , Cromossomos/ultraestrutura , Replicação do DNA/genética , DNA Complementar/química , Dípteros/metabolismo , Feminino , Biblioteca Gênica , Proteínas de Insetos/metabolismo , Masculino , Camundongos , Dados de Sequência Molecular , Proteínas Recombinantes/biossíntese , Proteínas Recombinantes/metabolismo , Proteínas e Peptídeos Salivares/metabolismo , Timidina/metabolismo , Fatores de Tempo , Trítio/análiseRESUMO
The treatment of cells with staurosporine results in inhibition and less frequently activation of protein kinases, in a cell-type specific manner. In the social amoeba Dictyostelium discoideum, staurosporine induces marked changes in cell morphology affecting growth and development. Here we describe that incubation of D. discoideum growing or starved cells with staurosporine results in a rapid and unexpected tyrosine phosphorylation on two polypeptides of approximately 64 and approximately 62 kDa. These proteins emerge as novel substrates for tyrosine phosphorylation opening up new perspectives for the study of cell signalling in D. discoideum.
Assuntos
Dictyostelium/efeitos dos fármacos , Dictyostelium/metabolismo , Fosfotirosina/metabolismo , Proteínas de Protozoários/metabolismo , Estaurosporina/farmacologia , Animais , Especificidade de Anticorpos/efeitos dos fármacos , Dictyostelium/citologia , Privação de Alimentos , Fosforilação/efeitos dos fármacos , Solubilidade/efeitos dos fármacosRESUMO
A serina/treonina fosfatase tipo 1 (PP1) é uma enzima importante para diversos processos celulares nos eucariotos. Apesar disso, a atividade enzimática da PP1 nunca foi detectada em extratos celulares de Dictyostelium discoideum, ao contrário da atividade da enzima PP2A, que é outra proteína fosfatase de ocorrência geral nos eucariotos. Nesse estudo repostamos a clonagem e o sequenciamento de um cDNA codificador para a subunidade catalílitica da PP1 de D. discoideum. Verificamos que esse cDNA tem origem a partir de um gene em cópia única, que expressa uma proteína ao longo de todo o ciclo de vida desse organismo. A dedução da seqüência da proteína a partir do cDNA revela uma identidade de 80 por cento em média com as seqüências de outras PP1, sendo a principal diferença observada a substituição da cisteína 269 por uma fenilalanina...