Browse
Submit Data
Databases
API
Help

Dataset Information

14 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Aedes aegypti Piwi4 Structural Features Are Necessary for RNA Binding and Nuclear Localization.

ABSTRACT: The PIWI-interacting RNA (piRNA) pathway provides an RNA interference (RNAi) mechanism known from Drosophila studies to maintain the integrity of the germline genome by silencing transposable elements (TE). Aedes aegypti mosquitoes, which are the key vectors of several arthropod-borne viruses, exhibit an expanded repertoire of Piwi proteins involved in the piRNA pathway, suggesting functional divergence. Here, we investigate RNA-binding dynamics and subcellular localization of A. aegypti Piwi4 (AePiwi4), a Piwi protein involved in antiviral immunity and embryonic development, to better understand its function. We found that AePiwi4 PAZ (Piwi/Argonaute/Zwille), the domain that binds the 3' ends of piRNAs, bound to mature (3' 2' O-methylated) and unmethylated RNAs with similar micromolar affinities (K_D = 1.7 ± 0.8 μM and K_D of 5.0 ± 2.2 μM, respectively; p = 0.05) in a sequence independent manner. Through site-directed mutagenesis studies, we identified highly conserved residues involved in RNA binding and found that subtle changes in the amino acids flanking the binding pocket across PAZ proteins have significant impacts on binding behaviors, likely by impacting the protein secondary structure. We also analyzed AePiwi4 subcellular localization in mosquito tissues. We found that the protein is both cytoplasmic and nuclear, and we identified an AePiwi4 nuclear localization signal (NLS) in the N-terminal region of the protein. Taken together, these studies provide insights on the dynamic role of AePiwi4 in RNAi and pave the way for future studies aimed at understanding Piwi interactions with diverse RNA populations.

SUBMITTER: Williams AE

PROVIDER: S-EPMC8657434 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Predicting Aedes aegypti infestation using landscape and thermal features.

Project description:Identifying Aedes aegypti breeding hotspots in urban areas is crucial for the design of effective vector control strategies. Remote sensing techniques offer valuable tools for mapping habitat suitability. In this study, we evaluated the association between urban landscape, thermal features, and mosquito infestations. Entomological surveys were conducted between 2016 and 2019 in Vila Toninho, a neighborhood of São José do Rio Preto, São Paulo, Brazil, in which the numbers of adult female Ae. aegypti were recorded monthly and grouped by season for three years. We used data from 2016 to 2018 to build the model and data from summer of 2019 to validate it. WorldView-3 satellite images were used to extract land cover classes, and land surface temperature data were obtained using the Landsat-8 Thermal Infrared Sensor (TIRS). A multilevel negative binomial model was fitted to the data, which showed that the winter season has the greatest influence on decreases in mosquito abundance. Green areas and pavements were negatively associated, and a higher cover of asbestos roofs and exposed soil was positively associated with the presence of adult females. These features are related to socio-economic factors but also provide favorable breeding conditions for mosquitos. The application of remote sensing technologies has significant potential for optimizing vector control strategies, future mosquito suppression, and outbreak prediction.

| S-EPMC7729962 | biostudies-literature

Aedes aegypti embryos

Project description:RNA-Seq was used for transcriptome sequencing of 0-12 hour embryos.

2011-12-16 | GSE34480 | GEO

RNA-binding residues prediction using structural features.

Project description:RNA-protein complexes play an essential role in many biological processes. To explore potential functions of RNA-protein complexes, it's important to identify RNA-binding residues in proteins.In this work, we propose a set of new structural features for RNA-binding residue prediction. A set of template patches are first extracted from RNA-binding interfaces. To construct structural features for a residue, we compare its surrounding patches with each template patch and use the accumulated distances as its structural features. These new features provide sufficient structural information of surrounding surface of a residue and they can be used to measure the structural similarity between the surface surrounding two residues. The new structural features, together with other sequence features, are used to predict RNA-binding residues using ensemble learning technique.The experimental results reveal the effectiveness of the proposed structural features. In addition, the clustering results on template patches exhibit distinct structural patterns of RNA-binding sites, although the sequences of template patches in the same cluster are not conserved. We speculate that RNAs may have structure preferences when binding with proteins.

| S-EPMC4529986 | biostudies-literature

Aedes aegypti embryos

Project description:RNA-Seq was used for transcriptome sequencing of 0-12 hour embryos. RNA was isolated from described samples for RNA-Seq. Samples fromfour embryonic time points from 0-12 hr. Raw data not provided.

2011-12-16 | E-GEOD-34480 | biostudies-arrayexpress

Structural Analysis of Inhibitor Binding to CAMKK1 Identifies Features Necessary for Design of Specific Inhibitors.

Project description:The calcium/calmodulin-dependent protein kinases (CAMKKs) are upstream activators of CAMK1 and CAMK4 signalling and have important functions in neural development, maintenance and signalling, as well as in other aspects of biology such as Ca2+ signalling in the cardiovascular system. To support the development of specific inhibitors of CAMKKs we have determined the crystal structure of CAMKK1 with two ATP-competitive inhibitors. The structures reveal small but exploitable differences between CAMKK1 and CAMKK2, despite the high sequence identity, which could be used in the generation of specific inhibitors. Screening of a kinase inhibitor library revealed molecules that bind potently to CAMKK1. Isothermal titration calorimetry revealed that the most potent inhibitors had binding energies largely dependent on favourable enthalpy. Together, the data provide a foundation for future inhibitor development activities.

| S-EPMC6172212 | biostudies-literature

The Sub-Nuclear Localization of RNA-Binding Proteins in KSHV-Infected Cells.

Project description:RNA-binding proteins, particularly splicing factors, localize to sub-nuclear domains termed nuclear speckles. During certain viral infections, as the nucleus fills up with replicating virus compartments, host cell chromatin distribution changes, ending up condensed at the nuclear periphery. In this study we wished to determine the fate of nucleoplasmic RNA-binding proteins and nuclear speckles during the lytic cycle of the Kaposi's sarcoma associated herpesvirus (KSHV). We found that nuclear speckles became fewer and dramatically larger, localizing at the nuclear periphery, adjacent to the marginalized chromatin. Enlarged nuclear speckles contained splicing factors, whereas other proteins were nucleoplasmically dispersed. Polyadenylated RNA, typically found in nuclear speckles under regular conditions, was also found in foci separated from nuclear speckles in infected cells. Poly(A) foci did not contain lncRNAs known to colocalize with nuclear speckles but contained the poly(A)-binding protein PABPN1. Examination of the localization of spliced viral RNAs revealed that some spliced transcripts could be detected within the nuclear speckles. Since splicing is required for the maturation of certain KSHV transcripts, we suggest that the infected cell does not dismantle nuclear speckles but rearranges their components at the nuclear periphery to possibly serve in splicing and transport of viral RNAs into the cytoplasm.

| S-EPMC7564026 | biostudies-literature

Aedes aegypti circadian expression profiling

Project description:Background. Aedes aegypti is arguably the most studied of all mosquito species in the laboratory and is the primary vector of both Dengue and Yellow Fever flaviviruses in the field. A large number of transcriptional studies have been made in the species and these usually report transcript quantities observed at a certain age or stage of development. However, circadian oscillation is an important characteristic of gene expression in many animals and plants, modulating both their physiology and behavior. Circadian gene expression in mosquito species has been previously reported but for only a few genes directly involved in the function of the molecular clock. Results. Herein we analyze the transcription profiles of 21,494 messenger RNAs using an Ae. aegypti Agilent® microarray. Transcripts were quantified in adult female heads at 24 hours and then again at 72 hours and eight subsequent time points spaced four hours apart. We document circadian rhythms in multiple molecular pathways essential for growth, development, immune response, detoxification/pesticide resistance. Circadian rhythms were also noted in ribosomal protein genes used for normalization in reverse transcribed PCR (RT-PCR) to determine transcript abundance. We report pervasive oscillations and intricate synchronization patterns relevant to all known biological pathways. Conclusion. These results argue strongly that transcriptional analyses either need to be made over time periods rather than confining analyses to a single time point or development stage or exceptional care needs to be made to synchronize all mosquitoes to be analyzed and compared among treatment groups.

2011-03-17 | GSE28010 | GEO

Proteomic identification of dengue virus binding proteins in Aedes aegypti mosquitoes and Aedes albopictus cells.

Project description:The main vector of dengue in America is the mosquito Aedes aegypti, which is infected by dengue virus (DENV) through receptors of midgut epithelial cells. The envelope protein (E) of dengue virus binds to receptors present on the host cells through its domain III that has been primarily recognized to bind cell receptors. In order to identify potential receptors, proteins from mosquito midgut tissue and C6/36 cells were purified by affinity using columns with the recombinant E protein domain III (rE-DIII) or DENV particles bound covalently to Sepharose 4B to compare and evaluate their performance to bind proteins including putative receptors from female mosquitoes of Ae. aegypti. To determine their identity mass spectrometric analysis of purified proteins separated by polyacrylamide gel electrophoresis was performed. Our results indicate that both viral particles and rE-DIII bound proteins with the same apparent molecular weights of 57 and 67?kDa. In addition, viral particles bound high molecular weight proteins. Purified proteins identified were enolase, beta-adrenergic receptor kinase (beta-ARK), translation elongation factor EF-1 alpha/Tu, and cadherin.

| S-EPMC3842078 | biostudies-literature