Types Of RNA Granules Research Articles

Assay to Study the Phase-transition Behavior of Edc3, a Conserved Processing Body (P-body) Marker Protein.

RNA granules are conserved, non-membranous, biphasic structures predominantly composed of RNA and RNA-binding proteins. RNA granules often assemble as a result of cellular responses to a variety of stresses, including infection. Two types of RNA granules are best characterized: stress granules (SGs) and processing bodies (P-bodies). The mechanism of RNA granule assembly and disassembly is still understudied because of its complex composition and dynamic behavior. The assembly of RNA granules is driven by a process known as phase separation of granule components. Edc3 is a conserved decapping activator and an essential P-body component in Saccharomyces cerevisiae. Phase separation of P-body proteins has been poorly explored. This protocol will enable the visualization of the phase transition behavior of Edc3, since it is tagged to mCherry. It further describes using small molecules and other proteins to study P-body dynamics. In addition to the assembly of Edc3, this assay also lays the foundation to study disassembly of phase-separated assemblies in vitro , which was not explored earlier. We have devised the assay to describe the use of one such protein that acts as a disassembly factor. Overall, this protocol is simple to perform and can potentially be combined with analyzing these assemblies using other approaches. Graphical abstract.

Interplay between potato virus X and RNA granules in Nicotiana benthamiana

Cytoplasmic RNA granules consist of microscopic agglomerates of mRNAs and proteins and occur when the translation is reversibly and temporally halted (stress granules, SGs) or mRNAs are targeted for decapping (processing bodies, PBs). The induction of RNA granules formation by virus infection is a common feature of mammalian cells. However, plant-virus systems still remain poorly characterized. In this work, the SG marker AtUBP1b was expressed in Nicotiana benthamiana plants to decipher how the virus infection of plant cells affects SG dynamics. We found that the hypoxia-induced SG assembly was substantially inhibited in Potato virus X (PVX)-infected cells. Furthermore, we determined that the expression of PVX movement protein TGBp1 by itself, mimics the inhibitory effect of PVX on SG formation under hypoxia. Importantly, overexpression of AtUBP1b showed inhibition of the PVX spreading, whereas the overexpression of the dominant negative AtUBP1brrm enhanced PVX spreding, indicating that AtUBP1b negatively affects PVX infection. Notably, PVX infection did not inhibit the formation of processing bodies (PBs), indicating PVX has distinct effects depending on the type of RNA granule. Our results suggest that SG inhibition could be part of the virus strategy to infect the plant.

Modeling Analysis of RNA Granule Formation and Selectivity Mediated by Multivalent Interactions

RNA granules serve as intermediates in RNA trafficking targeting RNAs encoding specific proteins to particular subcellular locations. RNA granules contain various components such as RNAs, RNA binding proteins, molecular motors, and components of the protein synthetic machinery. RNA have large valence for low affinity multivalent interactions, maintaining molecular connectivity during rapid remodeling of the granule. Therefore, the specific molecular composition and connectivity in a granule is fluid, sensitive to local intracellular environment. Modeling multivalent interactions in granules is challenging because of a combinatorial complexity in the number of potential molecular complexes and very rapid changes in structure. Recently we introduced a hybrid modeling approach (Falkenberg et. al, 2013) appropriate when the overall properties of the multi-molecular complex are of greater importance than the specific interactions of individual molecular components. One type of RNA granule is the A2RE granule, which contains multiple different RNA molecules, including those with A2 response elements (A2RE). Multiple RNAs are linked together in the same granule by a heptavalent scaffold TOG and a bivalent adaptor protein A2. Selectivity is defined as a preferential assembly of granules with A2RE RNAs. We perform modeling studies titrating the concentrations of various proteins, varying site pair affinities, and RNA valence. We hypothesize that there are key parameters that control granule formation, and conclude that there is an optimum concentration range for the adaptor molecule A2 that optimizes granule assembly and selectivity.

ALS-Linked Mutations Enlarge TDP-43-Enriched Neuronal RNA Granules in the Dendritic Arbor

Trans-activating response region (TAR) DNA-binding protein of 43 kDa (TDP-43) is an RNA-binding protein that is mutated in familial amyotrophic lateral sclerosis (ALS). Disease-linked mutations in TDP-43 increase the tendency of TDP-43 to aggregate, leading to a corresponding increase in formation of stress granules, cytoplasmic protein/RNA complexes that form in response to stress. Although the field has focused on stress granules, TDP-43 also forms other types of RNA granules. For example, TDP-43 is associated with RNA granules that are prevalent throughout the dendritic arbor in neurons. Because aggregation of TDP-43 is also important for the formation of these neuronal RNA granules, we hypothesized that disease-linked mutations might alter granule formation even in the absence of stress. We now report that ALS-linked mutations in TDP-43 (A315T and Q343R) increase the size of neuronal TDP-43 granules in the dendritic arbor of rat hippocampal neurons. The mutations correspondingly reduce the granule density, movement, and mobility of TDP-43 granules. Depolarization of rat hippocampal neurons with KCl stimulates TDP-43 granule migration into dendrites, but A315T and Q343R TDP-43 granules migrate shorter distances and into fewer dendrites than wild-type TDP-43. These findings highlight novel elements of TDP-43 biology that are affected by disease-linked mutations and suggest a neuronally selective mechanism through which TDP-43 mutations might elicit neuronal dysfunction.

RNA Processing Bodies, Peroxisomes, Golgi Bodies, Mitochondria, and Endoplasmic Reticulum Tubule Junctions Frequently Pause at Cortical Microtubules

Organelle motility, essential for cellular function, is driven by the cytoskeleton. In plants, actin filaments sustain the long-distance transport of many types of organelles, and microtubules typically fine-tune the motile behavior. In shoot epidermal cells of Arabidopsis thaliana seedlings, we show here that a type of RNA granule, the RNA processing body (P-body), is transported by actin filaments and pauses at cortical microtubules. Interestingly, removal of microtubules does not change the frequency of P-body pausing. Similarly, we show that Golgi bodies, peroxisomes, and mitochondria all pause at microtubules, and again the frequency of pauses is not appreciably changed after microtubules are depolymerized. To understand the basis for pausing, we examined the endoplasmic reticulum (ER), whose overall architecture depends on actin filaments. By the dual observation of ER and microtubules, we find that stable junctions of tubular ER occur mainly at microtubules. Removal of microtubules reduces the number of stable ER tubule junctions, but those remaining are maintained without microtubules. The results indicate that pausing on microtubules is a common attribute of motile organelles but that microtubules are not required for pausing. We suggest that pausing on microtubules facilitates interactions between the ER and otherwise translocating organelles in the cell cortex.