Biology subjects

Trcek, T.

Publications and source records attributed to Trcek, T..

6 recordsLinked to original sources

bioRxiv2026

Synergy of RNA Concentration, RNA Binding Proteins, and RNA Palindrome Drives clustering of oskar mRNA in vivo

Organization of mRNAs into clusters has been observed in many cellular contexts, yet the features that govern this process in vivo remain poorly understood. Using super-resolution microscopy, single-mRNA imaging, and genetic perturbations, we investigated how mRNA concentration, the double-stranded RNA-binding protein Staufen (Stau), and intermolecular base-pairing driven by an RNA palindrome influence clustering of oskar (osk) mRNA in Drosophila embryos. We find that these factors collectively optimize osk clustering by promoting its dimerization and subsequent oligomerization. Both processes depend on all three factors, although oligomerization is more sensitive to their perturbation, indicating that the driving force for osk oligomerization is partially distinct from that governing dimerization. Furthermore, expression of Stau nearly doubles the likelihood of osk dimerization whereas disruption of the palindrome reduces it fourfold indicating that the presence of Stau and the palindrome lowers the concentration threshold of osk mRNA required for dimerization. Notably, insertion of the osk palindrome into a reporter mRNA markedly increased its association with the endogenous osk, further supporting the conclusion that the palindrome potently drives intermolecular base pairing. Importantly, this experiment also identified the palindrome as the major contributor to heterotypic clustering between the endogenous osk and the reporter mRNA. Finally, computational analyses identified a subset of early embryonic mRNAs predicted to harbor palindromes similar to those found in osk. Among these, eIF3a mRNA emerged as a candidate whose clustering may likewise be driven by intermolecular base pairing. Together, our findings raise the possibility that mRNA clustering driven by palindrome-mediated intermolecular base pairing may be more widespread than previously appreciated and may represent an important mechanism for controlling mRNA spatial organization during early Drosophila development.

molecular biology↗

bioRxiv2025

Conserved RNA helicase Vasa regulates ribonucleoprotein condensates through protein interaction and mRNA recruitment

Germlines contain ribonucleoprotein condensates known as germ granules, which concentrate proteins and mRNAs essential for animal development. Vasa, a conserved DEAD-box RNA helicase, is a core and highly concentrated constituent of germ granules. However, its roles within these structures remain poorly understood. Here, we use Drosophila germ granules as a model system to address this question. Applying in vivo and human cell systems, we found that condensation of Oskar (Osk) protein, which nucleates germ granules, occurred independently of Vasa. However, in oocytes lacking detectable Vasa protein, Osk formed aggregated condensates regardless of the eGFP tag. Furthermore, Osk-eGFP showed minimal recovery as measured by fluorescence recovery after photobleaching (FRAP) indicating that its exchange between condensates and their surroundings was greatly reduced in the absence of Vasa. Supporting this result, co-expression of Vasa increased the FRAP recovery of Osk-eGFP condensates and reduced Osk-eGFP partitioning into them in cells. This effect required the interaction between Vasa and Osk, suggesting that by binding Osk, Vasa modulates Osks phase behavior and its condensate material properties. Super-resolution microscopy further revealed that Vasa is required for germ granule mRNA localization to Osk condensates in vivo. Co-expression of Vasa with Osk-eGFP is necessary and sufficient to recruit germ granule mRNAs to condensates in cells. Although this activity depends on Vasa-Osk interaction, the interaction itself is not sufficient. Notably, localization of a conserved germ granule mRNA nanos reduced the FRAP recovery of Osk-eGFP condensates in cells, partially counteracting Vasas effect. Collectively, our findings uncovered a novel function of the DEAD-box RNA helicase Vasa in regulating the material properties of Osk condensates through coordinated protein-protein and protein-mRNA interactions. Four highlightsO_LIVasa modulates the material properties of Oskar ribonucleoprotein condensates in fly oocytes and human cells. C_LIO_LIVasa modulates condensate material properties through its interaction with Oskar. C_LIO_LImRNA localization to Oskar condensates requires Vasa and Vasa-Oskar interaction. C_LIO_LInanos mRNA localization counteracts Vasas enhancement of Oskar exchange between condensates and their surroundings. C_LI

molecular biology↗

bioRxiv2025

Characterization of intermolecular base pairing using AMT crosslinking in mammalian cells during oxidative stress

Cellular stress induces global translational repression, leading to exposure of RNA sequences that could engage in intermolecular base pairing. However, characterization of these interactions in stressed cells remains limited. Here, we coupled RNA crosslinking with biotin pulldown to probe intermolecular base pairing in mammalian cells during oxidative stress. We found that oxidative stress downregulates intermolecular base pairing of a reporter mRNA engineered to enhance detection of such interactions. Consistently, crosslinking-dependent intermolecular base pairing was not readily detected among candidate mRNAs that accumulate in stress granules - RNA-rich condensates that form during stress. Furthermore, chemical probing of base accessibility revealed that while RNA regions within these transcripts remain structured during stress, they increase in structural diversity in a manner dependent on oxidative stress and the stress granule nucleating proteins G3BP1 and G3BP2. This enhanced structural heterogeneity may help reduce a sustained exposure of interaction-prone RNA sequences during stress such as those prone to crosslinking. We propose that the combined downregulation of intermolecular base pairing and increased RNA structural diversity provides a mechanism to preserve normal function of RNAs during stress, while simultaneously enabling the reversible assembly of stress granules.

molecular biology↗

bioRxiv2024

The Folding of Germ Granule mRNAs Controls Intermolecular Base Pairing in Germ Granules and Maintains Normal Fly Development

Drosophila germ granules enrich mRNAs critical for fly development. Within germ granules, mRNAs form multi-transcript clusters marked by increased mRNA concentration, creating an elevated potential for intermolecular base pairing. However, the type and abundance of intermolecular base pairing in mRNA clusters is poorly characterized. Using single-molecule super-resolution microscopy, chemical probing for base accessibility, phase separation assays, and simulations, we demonstrated that mRNAs remain well-folded upon localization to germ granules. While most base pairing is intramolecular, mRNAs still display the ability for intermolecular base pairing, facilitating clustering without high sequence complementarity or significant melting of secondary structure. This base pairing among mRNAs is driven by scattered and discontinuous stretches of bases appearing on the surface of folded RNAs, providing multivalency to clustering but exhibits low probability for sustained interactions. Notably, engineered germ granule mRNAs with exposed GC-rich complementary sequences (CSs) presented within stable stem loops induce sustained base pairing in vitro and enhanced intermolecular interactions in vivo. However, the presence of these stem loops alone disrupts fly development, and the addition of GC-rich CSs exacerbates this phenotype. Although germ granule mRNAs contain numerous GC-rich CSs capable of stable intermolecular base pairing, they are primarily embedded by RNA folding. This study emphasizes the role of RNA folding in controlling the type and abundance of intermolecular base pairing, thereby preserving the functional integrity of mRNAs within the germ granules.

molecular biology↗

bioRxiv2023

Intrinsically Disordered Regions Promote Protein Refoldability and Facilitate Retrieval from Biomolecular Condensates

Many eukaryotic proteins contain intrinsically disordered regions (IDRs) that intersperse globular folded domains, in contrast with bacterial proteins which are typically highly globular1, 2. Recent years have seen great progress in identifying biological functions associated with these elusive protein sequence: in specific cases, they mediate liquid liquid phase separation3, perform molecular recognition4, or act as sensors to changes in the environment5. Nevertheless, only a small number of IDRs have annotated functions6 despite their presence in 64% of yeast proteins,7 stimulating some to question what general purpose they may serve8, 9. Here, by interrogating the refoldability of two fungal proteomes (Saccharomyces cerevisiae and Neurosporra crassa), we show that IDRs render their host proteins more refoldable from the denatured state, allowing them to cohere more closely to Anfinsens thermodynamic hypothesis10, 11. The data provide an exceptionally clear picture of which biophysical and topological characteristics enable refoldability. Moreover, we find that almost all yeast proteins that partition into stress granules during heat shock are refoldable, a finding that holds for other condensates such as P-bodies and the nucleolus. Finally, we find that the Hsp104 unfoldase12 is the principal actor in mediating disassembly of heat stress granules and that the efficiency with which condensed proteins are returned to the soluble phase is also well explained by refoldability. Hence, these studies establish spontaneous refoldability as an adaptive trait that endows proteins with the capacity to reform their native soluble structures following their extraction from condensates. Altogether, our results provide an intuitive model for the function of IDRs in many multidomain proteins and clarifies their relationship to the phenomenon of biomolecular condensation.

biochemistry↗

bioRxiv2018

PHASE TRANSITIONED NUCLEAR OSKAR PROMOTES CELL DIVISION OF DROSOPHILA PRIMORDIAL GERM CELLS

Germ granules are non-membranous ribonucleoprotein granules deemed the hubs for post-transcriptional gene regulation and functionally linked to germ cell fate across species. Little is known about the physical properties of germ granules and how these relate to germ cell function. Here we study two types of germ granules in the Drosophila embryo: cytoplasmic germ granules that instruct primordial germ cells (PGCs) formation and nuclear germ granules within early PGCs with unknown function. We show that cytoplasmic and nuclear germ granules are phase transitioned condensates nucleated by Oskar protein that display liquid as well as hydrogel-like properties. Focusing on nuclear granules, we find that Oskar drives their formation in heterologous cell systems. Multiple, independent Oskar protein domains synergize to promote granule phase separation. Deletion of Oskars nuclear localization sequence specifically ablates nuclear granules in cell systems. In the embryo, nuclear germ granules promote germ cell divisions thereby increasing PGC number for the next generation.

cell biology↗