Biology subjects

Chapman, E. G.

Publications and source records attributed to Chapman, E. G..

4 recordsLinked to original sources

bioRxiv2024

Manipulating TDP43 Aggregation via RNA G-quadruplexes

The events that lead to protein misfolding diseases are not fully understood. Many proteins implicated in neurodegenerative diseases (e.g., TDP43) interact with nucleic acids, including RNA G-quadruplexes. In this work, we investigate whether RNA G-quadruplexes play a role in TDP43 condensation in biophysical and cellular models. We find that G-quadruplexes modulate TDP43 aggregation in vitro and condensation in multiple cell types, including yeast, HEK293T, and motor-neuron-like NSC-34 cells. In yeast cells, treatment with G-quadruplexes causes increased TDP43 accumulation in cells before cellular death. In HEK293T cells expressing TDP43, incubation with G-quadruplex-binding small molecules causes an increase in G4 stability that also stabilizes TDP43 and reduces TDP43 condensation induced by proteasomal or oxidative stress. Finally, in NSC-34 cells overexpressing exogenous TDP43, we show that G-quadruplexes co-localize with TDP43 condensates under stress conditions and treatment with G-quadruplex-binding small molecules decreases TDP43-mediated toxicity. Together, these findings suggest that a novel future approach to explore for treating protein misfolding diseases may be to target specific RNA structures such as G-quadruplexes.

molecular biology↗

bioRxiv2023

Drosophila FMRP recruits the miRISC to target mRNAs to repress translation

Fragile X syndrome (FXS) is the most common inherited form of intellectual disability and is caused by mutations in the gene encoding for the Fragile X messenger ribonucleoprotein (FMRP). FMRP is an evolutionarily conserved and neuronally enriched RNA binding protein (RBP) with functions in the control of processes including RNA editing, RNA transport, and protein translation. Specific target RNAs play critical roles in neurodevelopment including the regulation of neurite morphogenesis, synaptic plasticity, and cognitive function. The different biological functions of FMRP are modulated by its cooperative interaction with distinct sets of neuronal RNA and protein binding partners. Here, we focus on interactions between FMRP and components of the microRNA (miRNA) pathway. Using the Drosophila model system, we show that dFMRP can repress the translation of a reporter mRNA via a deadenylation-independent mechanism. This repression requires the activity of both AGO1 and GW182, conserved components of the miRNA-containing RISC (miRISC). Interestingly, we find that dFMRP can bind directly to a short stem loop structure in the reporter and that dFMRP binding is a prerequisite for repression by miR-958. Finally, we show that dFmr1 interacts genetically with GW182 to control neurite morphogenesis. Collectively, these data suggest the dFMRP can directly recruit the miRISC to nearby miRNA binding sites and then repress translation via the activity of the miRISC effector, GW182.

molecular biology↗

bioRxiv2020

Custom-Designed, Degradation-Resistant Messenger RNAs in Yeast

Virally-derived RNA structures provide useful tools for engineering messenger RNA (mRNA) transcripts with unique properties. Here we show that 5[->]3 exoribonuclease-resistant RNA structures (xrRNAs) from Flaviviruses can be used to protect heterologously-expressed messenger RNAs (mRNAs) from 5[->]3 degradation in Saccharomyces cerevisiae (budding yeast). Installation of xrRNAs ahead of a downstream internal ribosome entry site (IRES) leads to the accumulation of partially-degraded mRNAs designed to undergo cap-independent translation. In a yeast strain favoring cap-independent translation, this strategy led to a 30-fold increase in the enzymatic activity of lysates obtained from cells expressing degradation-resistant reporters. Overall, these finding demonstrate the possibility of coupling multiple viral RNA structures together to enhance protein expression.

biochemistry↗

bioRxiv2019

Endosymbiotic bacteria are prevalent and diverse in agricultural spiders

Maternally inherited bacterial endosymbionts are common in arthropods, but their distribution and prevalence is poorly characterized in many host taxa. For example, spiders (Araneae) have received little attention, but initial surveys suggest that vertically transmitted symbionts may be common. Here, we characterized endosymbiont infection in a community of agricultural spiders. Using a combination of diagnostic PCR and high-throughput sequencing of the bacterial microbiome, we evaluated symbiont infection in 267 individual spiders representing 14 species in 3 families. We found 27 Operational Taxonomic Units (OTUs) that are likely endosymbiotic, including several strains of Wolbachia, Rickettsia and Cardinium, all of which are vertically transmitted and frequently associated with reproductive manipulation of arthropod hosts. Seventy percent of spider species had individuals that tested positive for one or more endosymbiotic OTUs, and specimens frequently contained multiple symbiotic strain types. The most symbiont-rich species, Idionella rugosa, had eight endosymbiotic OTUs, with as many as five present in the same specimen. Individual specimens within infected spider species had a variety of symbiotypes, differing from one another in the presence or absence of symbiotic strains. Our sample included both starved and unstarved specimens, and dominant bacterial OTUs were consistent per host species, regardless of feeding status. We conclude that spiders contain a remarkably diverse symbiotic microbiota. Spiders would be an informative group for investigating endosymbiont population dynamics in time and space, and unstarved specimens collected for other purposes (e.g., food web studies) could be used, with caution, for such investigations.

microbiology↗