P-Bodies: Composition, Properties, and Functions

Biomolecular condensates-Prerequisites for anhydrobiosis?

It is often underappreciated that despite water being a requirement for life on Earth, organisms belonging to all taxonomic kingdoms have developed mechanisms to survive desiccation. These organisms, referred to as anhydrobiotes, accumulate specific biomolecules during or before drying that facilitate the survival of desiccation stress. Compounds utilized by a wide variety of anhydrobiotes during desiccation include metabolites such as sugars and amino acids, as well as proteins with extensive intrinsically disordered regions. Intrinsically disordered proteins that are constitutively expressed or upregulated during the onset or in preparation for desiccation include late embryogenesis abundant proteins, tardigrade disordered proteins, hydrophilins, some small heat shock proteins, and prion-like proteins. Some of these proteins form biomolecular condensates in the cellular environment. We hypothesize that phase transitions driven by anhydrobiosis-related intrinsically disordered proteins play a substantial role in enabling anhydrobiosis by (1) contributing to the downregulation of metabolic and developmental processes, (2) selectively sequestering desiccation-sensitive molecules into a "protective compartment" during drying, (3) interfering with programmed cell death signaling pathways to confer optimal time for the cell to repair after rehydration, (4) resisting intracellular volume changes to aid in membrane stabilization during desiccation, and (5) changing the biophysical properties of water to reduce desiccation-induced cellular damage. Biochemical strategies in anhydrobiotes are certainly multifaceted and may differ among systems. Nevertheless, a better understanding of the relevance of phase transitions in anhydrobiosis may allow us to get one step closer to unraveling the enigmatic phenomenon of life without water.

Diverse roles of stress-responsive RNP granules in oogenesis and infertility

Effectively responding to cellular stress (e.g., nutrient deprivation, oxidative stress) is essential for cell and organismal survival. A protective mechanism is especially critical in developing oocytes, where a prolonged quiescent state and the inability to divide render oocytes highly susceptible to accumulating stress that can result in cell death if unaddressed. Despite the common view that stress granules are the primary stress-responsive ribonucleoprotein granule, accumulating evidence shows that in ovaries, other ribonucleoprotein granules also uniquely mediate gene regulation in response to stress. Here, we review recent insights into ribonucleoprotein granule dynamics and ribonucleoprotein granule protein function during stress in the context of oogenesis among both invertebrates and vertebrates, with an emphasis on insights from Drosophila and mice. We also discuss roles for stress-responsive ribonucleoproteins in maintaining stem cell populations and complicating fertility treatments. By exploring how stress-induced ribonucleoprotein dynamics can impact oogenesis, both positively and negatively, we can better understand how stress contributes to reduced fecundity and infertility. We conclude by offering key research questions that can drive the next generation of insights.

Spatially Resolved Multibait Mapping of Stress Granule and Processing Body Transcriptome

Stress granules (SGs) are dynamic, membrane-less organelles that house complex RNA-protein networks. Although previous profiling methods have characterized SG RNAs as long, translation-repressed, and extensively epigenetically modified, it remains unclear whether these RNAs are evenly distributed within SGs. In this study, we genetically targeted the photocatalyst protein miniSOG to multiple SG core proteins, enabling the comprehensive CAP-seq profiling of SG-associated RNAs. Our results reveal that RNAs near different SG core proteins display heterogeneous distributions and distinct intrinsic features. We also employed CAP-seq to map RNAs associated with processing body (PB) marker protein DDX6 under both unstressed conditions and arsenite-induced stress. By comparing the transcriptomes proximal to SGs and PBs, our data suggest that m6A modification may promote RNA localization to SGs, whereas higher AU content may facilitate mRNA targeting to PBs. These findings point to potential regulatory mechanisms that determine the subcellular localization of mRNAs within membrane-less organelles.

RNA-binding proteins DND1 and NANOS3 cooperatively suppress the entry of germ cell lineage

Specification of primordial germ cells (PGCs) establishes germline development during early embryogenesis, yet the underlying mechanisms in humans remain largely unknown. Here, we reveal the functional roles of germline-specific RNA-binding protein (RBP) DND1 in human PGC (hPGC) specification. We discovered that DND1 forms a complex with another RBP, NANOS3, to restrict hPGC specification. Furthermore, by analyzing the mRNAs bound by DND1 and NANOS3, we found that DND1 facilitates the binding of NANOS3 to hPGC-like cells-related mRNAs. We identified SOX4 mRNAs as the key downstream factor for the DND1 and NANOS3 complex. Mechanistically, DND1 and NANOS3 function in processing bodies (P-bodies) to repress the translation of SOX4 mRNAs, with NANOS3 mediating the interaction between DND1 and the translational repressor 4E-T. Altogether, these findings identify the RBP complex formed by DND1 and NANOS3 functioning as a "braking system" to restrict the entry of germ cell fate in humans.

Programmable control of spatial transcriptome in live cells and neurons

Spatial RNA organization has a pivotal role in diverse cellular processes and diseases1-4. However, functional implications of the spatial transcriptome remain largely unexplored due to limited technologies for perturbing endogenous RNA within specific subcellular regions1,5. Here we present CRISPR-mediated transcriptome organization (CRISPR-TO), a system that harnesses RNA-guided, nuclease-dead dCas13 for programmable control of endogenous RNA localization in live cells. CRISPR-TO enables targeted localization of endogenous RNAs to diverse subcellular compartments, including the outer mitochondrial membrane, p-bodies, stress granules, telomeres and nuclear stress bodies, across various cell types. It allows for inducible and reversible bidirectional RNA transport along microtubules via motor proteins, facilitating real-time manipulation and monitoring of RNA localization dynamics in living cells. In primary cortical neurons, we demonstrate that repositioned mRNAs undergo local translation along neurites and at neurite tips, and co-transport with ribosomes, with β-actin mRNA localization enhancing the formation of dynamic filopodial protrusions and inhibiting axonal regeneration. CRISPR-TO-enabled screening in primary neurons identifies Stmn2 mRNA localization as a driver of neurite outgrowth. By enabling large-scale perturbation of the spatial transcriptome, CRISPR-TO bridges a critical gap left by sequencing and imaging technologies, offering a versatile platform for high-throughput functional interrogation of RNA localization in living cells and organisms.

Dissecting the stress granule RNA world: dynamics, strategies, and data

Stress granules (SGs) are cytoplasmic ribonucleoprotein granules that commonly nucleate from the interaction of translationally stalled mRNAs and RNA-binding proteins. SGs are involved in the cellular adaptation to stress conditions participating in the regulation of gene expression and cell signaling. While dysregulation of SG dynamics has been increasingly implicated in human disease, a comprehensive understanding of SG composition, particularly of the RNA component, across various conditions remains elusive. Here, we review the physiological and pathological aspects of SGs, discuss current and future experimental strategies to identify SG components, and provide insights into the SG RNA world through the meta-analysis of 26 human SG transcriptome data sets.

The Regulatory Roles of RNA-Binding Proteins in Plant Salt Stress Response

Salt stress is one of the most prominent abiotic stresses. Behind the intricate adaptive responses of plants to salt stress, the regulation of gene expression assumes a pivotal role. Complementing transcriptional mechanisms, post-transcriptional regulation performed by RNA-binding proteins provides an additional layer of control through sophisticated molecular machinery. RBPs interact with both RNA molecules and protein partners to coordinate RNA metabolism and, thus, fine-tune the expression of salt-responsive genes, enabling plants to rapidly adapt to ionic challenges. This review systematically evaluates the functional roles of RBPs localized in distinct subcellular compartments, including nuclear, cytoplasmic, chloroplastic, and mitochondrial systems, in mediating post-transcriptional regulatory networks under salinity challenges. Specific classes of RBPs are discussed in detail, including glycine-rich RNA-binding proteins (GR-RBPs), serine/arginine-rich splicing factors (SR proteins), zinc finger domain-containing proteins, DEAD-box RNA helicases (DBRHs), KH domain-containing proteins, Pumilio domain-containing proteins (PUMs), pentatricopeptide repeat proteins (PPRs), and RBPs involved in cytoplasmic RNA granule formation. By integrating their subcellular localization and current mechanistic insights, this review concludes by summarizing the current knowledge and highlighting potential future research directions, aiming to inspire further investigations into the complex network of RBPs in modulating plant responses to salt stress and facilitating the development of strategies to enhance plant salt tolerance.

Artificial Cells Capable of NO Generation with Light Controllable Membraneless Organelles for Melanoma Therapy

Membraneless organelles (MLOs) formed by liquid-liquid phase separation exhibit diverse important biofunctions in cells. The construction of artificial cells containing MLOs with enhanced complexity and functions is still challenging. Here a light-responsive protein, Cry2olig-IDRs, is designed and purified to form MLOs upon light (488 nm) irradiation. They are capable of rapidly recruiting positively charged inducible nitric oxide synthase (iNOS+) from surroundings to regulate its activity for NO production. NO-artificial cells are constructed by encapsulating Cry2olig-IDRs and iNOS+ into giant unilamellar vesicles, which are capable of rapid production of NO with high concentration due to the formation of MLOs upon light irradiation. NO-artificial cells are confirmed to possess the ability for melanoma tumor therapy in mice. These findings provide an efficient method for remotely regulating enzyme activity inside artificial cells, paving the path to build more sophisticated artificial cells for their biomedical applications.

Praja2 controls P-body assembly and translation in glioblastoma by non-proteolytic ubiquitylation of DDX6

Glioblastoma multiforme (GBM) is the most lethal form of malignant brain tumor in adults. Dysregulation of protein synthesis contributes to cancer cell plasticity, driving GBM cell heterogeneity, metastatic behavior, and drug resistance. Understanding the complex network and signaling pathways governing protein translation, is therefore an important goal for GBM treatment. Here we identify a novel signaling network centered on the E3 ubiquitin ligase praja2 that controls protein translation in GBM. Praja2 forms a multimeric complex with the RNA helicase DDX6, which inhibits translation of target RNAs within processing bodies (P-bodies). Stimulation of cAMP signaling through activation of G-protein-coupled receptors induces P-body assembly through praja2-mediated non-proteolytic polyubiquitylation of DDX6. Genetic inactivation of praja2 reshapes DDX6/mRNA complexes and translating polysomes and promotes cellular senescence and GBM growth arrest. Expression of an ubiquitylation-defective DDX6 mutant suppresses the assembly of P-bodies and sustains GBM growth. Taken together, our findings identify a cAMP-driven network that controls translation in P-bodies and GBM growth.

Epigenetic regulation in oogenesis and fetal development: insights into m6A modifications

The unique physiological structure of women has led to a variety of diseases that have attracted the attention of many people in recent years. Disturbances in the reproductive system microenvironment lead to the progression of various female tumours and pregnancy disorders. Numerous studies have shown that epigenetic modifications crucially influence both oogenesis and foetal development. m6A, a modification at the mRNA level, consists of three parts, namely, writers, erasers, and readers, which are involved in several biological functions, such as the nucleation and stabilisation of mRNAs, thereby regulating the development of reproductive system diseases. In this manuscript, we delineate the constituents of m6A, their biological roles, and advancements in understanding m6A within the maternal-foetal immunological context. In addition, we summarise the mechanism of m6A in gynaecological diseases and provide a new perspective for targeting m6A to delay the progression of reproductive system diseases in clinical practice.

Quitting Your Day Job in Response to Stress: Cell Survival and Cell Death Require Secondary Cytoplasmic Roles of Cyclin C and Med13

Following unfavorable environmental cues, cells reprogram pathways that govern transcription, translation, and protein degradation systems. This reprogramming is essential to restore homeostasis or commit to cell death. This review focuses on the secondary roles of two nuclear transcriptional regulators, cyclin C and Med13, which play key roles in this decision process. Both proteins are members of the Mediator kinase module (MKM) of the Mediator complex, which, under normal physiological conditions, positively and negatively regulates a subset of stress response genes. However, cyclin C and Med13 translocate to the cytoplasm following cell death or cell survival cues, interacting with a host of cell death and cell survival proteins, respectively. In the cytoplasm, cyclin C is required for stress-induced mitochondrial hyperfission and promotes regulated cell death pathways. Cytoplasmic Med13 stimulates the stress-induced assembly of processing bodies (P-bodies) and is required for the autophagic degradation of a subset of P-body assembly factors by cargo hitchhiking autophagy. This review focuses on these secondary, a.k.a. "night jobs" of cyclin C and Med13, outlining the importance of these secondary functions in maintaining cellular homeostasis following stress.

Phase separation as a key mechanism in plant development, environmental adaptation, and abiotic stress response

Liquid-liquid phase separation is a fundamental biophysical process in which biopolymers, such as proteins, nucleic acids, and their complexes, spontaneously demix into distinct coexisting phases. This phenomenon drives the formation of membraneless organelles-cellular subcompartments without a lipid bilayer that perform specialized functions. In plants, phase-separated biomolecular condensates play pivotal roles in regulating gene expression, from genome organization to transcriptional and post-transcriptional processes. In addition, phase separation governs plant-specific traits, such as flowering and photosynthesis. As sessile organisms, plants have evolved to leverage phase separation for rapid sensing and response to environmental fluctuations and stress conditions. Recent studies highlight the critical role of phase separation in plant adaptation, particularly in response to abiotic stress. This review compiles the latest research on biomolecular condensates in plant biology, providing examples of their diverse functions in development, environmental adaptation, and stress responses. We propose that phase separation represents a conserved and dynamic mechanism enabling plants to adapt efficiently to ever-changing environmental conditions. Deciphering the molecular mechanisms underlying phase separation in plant stress responses opens new avenues for biotechnological strategies aimed at engineering stress-resistant crops. These advancements have significant implications for agriculture, particularly in addressing crop productivity in the face of climate change.

Context-dependent Interactors Regulate TDP-43 Dysfunction in ALS/FTLD

TDP-43 mislocalization, aggregation, and loss of splicing function are neuropathological hallmarks in over 97% of Amyotrophic Lateral Sclerosis (ALS), 45% of Frontotemporal Lobar Degeneration (FTLD), and 60% of Alzheimer's Disease, which has been reclassified as LATE-NC. However, the mechanisms underlying TDP-43 dysfunction remain elusive. Here, we utilize APEX2-driven proximity labeling and mass spectrometry to characterize the context-dependent TDP-43 interactome in conditions of cytoplasmic mislocalization, impaired RNA-binding contributing to aggregation, and oxidative stress. We describe context-dependent interactors, including disrupted interactions with splicing-related proteins and altered biomolecular condensate (BMC) associations. By integrating ALS and FTLD snRNA-seq data, we uncover disease-relevant molecular alterations and validate our dataset through a functional screen that identifies key TDP- 43 regulators. We demonstrate that disrupting nuclear speckle integrity, particularly through the downregulation of the splicing factor SRRM2, promotes TDP-43 mislocalization and loss of function. Additionally, we identify NUFIP2 as an interactor associated with mislocalization that sequesters TDP-43 into cytoplasmic aggregates and co-localizes with TDP-43 pathology in patient tissue. We also highlight HNRNPC as a potent TDP-43 splicing regulator, where precise modulation of TDP-43 or HNRNPC can rescue cryptic exon splicing. These findings provide mechanistic insights and potential therapeutic targets for TDP-43 dysfunction.

Unveiling the role of microRNAs in nonhost resistance to Sclerotinia sclerotiorum: Rice-specific microRNAs attack the pathogen via cross-kingdom RNAi

The development of rapeseed with high resistance against the pathogen Sclerotinia sclerotiorum is impeded by the lack of effective resistance resources within host species. Unraveling the molecular basis of nonhost resistance (NHR) holds substantial value for resistance improvement in crops. In the present study, small RNA sequencing and transcriptome sequencing were carried out between rice (a nonhost species of S. sclerotiorum) and rapeseed during infection, revealing the involvement of rice miRNAs on translation-related processes in both rice and the pathogen. Specifically, rice-specific miRNAs with potential capability for cross-kingdom RNAi against S. sclerotiorum were explored, of which Os-miR169y was selected as a representative case to elucidate its role in resistance to S. sclerotiorum. The silence of Os-miR169y decreased the resistance level of rice to S. sclerotiorum, and heterologous expression of Os-miR169y in Arabidopsis and rapeseed significantly enhanced the host resistance. The dual-luciferase reporter assay indicates that Os-miR169y targets S. sclerotiorum 60S ribosomal protein L19 (SsRPL19). Overexpressing Os-miR169y (OEss-miR169y) and RNAi of SsRPL19 (RNAiss-RPL19) in S. sclerotiorum significantly impaired the growth and pathogenicity of the pathogen, while overexpressing SsRPL19 exhibited a contrast effect. Yeast-two-hybridization revealed an interlinking role of SsRPL19 with multiple large and small ribosomal subunits, indicating its important role in translation. Proteome sequencing detected a decreased amount of proteins in transformants OEss-miR169y and RNAiss-RPL19 and significant suppression on key metabolic pathways such as carbon and nitrogen metabolisms. Collectively, this study suggests that rice can secrete specific miRNAs to suppress genes essential for S. sclerotiorum, such as Os-miR169y, which targets and suppresses SsRPL19 and thus impairs protein synthesis in the pathogen. This study sheds light on the intrinsic mechanisms of rice NHR against S. sclerotiorum, and further demonstrates the potential of using nonhost-specific "pathogen-attacking" miRNAs in improving resistance in host species.

Live-cell imaging of circular and long noncoding RNAs associated with FUS pathological aggregates by Pepper fluorescent RNA

Lately, important advancements in visualizing RNAs in fixed and live cells have been achieved. Although mRNA imaging techniques are well-established, the development of effective methods for studying noncoding RNAs (ncRNAs) in living cells is still challenging but necessary, as they show a variety of functions and intracellular localizations, including participation in highly dynamic processes like phase transition, which is still poorly studied in vivo. Addressing this issue, we tagged two exemplary ncRNAs with the fluorescent RNA (fRNA) Pepper. Specifically, we showed that circ-HDGFRP3 interacts with p-bodies and is recruited in pathological FUS aggregates in a dynamic fashion, and we super-resolved its distribution in such condensates via structured illumination microscopy. Moreover, we tracked the long noncoding RNA (lncRNA) nHOTAIRM1, a motor neuron-specific constituent of stress granules, monitoring its behavior throughout the oxidative-stress response in physiological and pathological conditions. Overall, as fRNA development progresses, our work demonstrates an effective use of Pepper for monitoring complex processes, such as phase transition, in living cells through the visualization of circular RNAs (circRNAs) and lncRNAs with super-resolution power.

Role of Assemblysomes in Cellular Stress Responses

Assemblysomes are recently discovered intracellular RNA-protein complexes that play important roles in cellular stress response, regulation of gene expression, and also in co-translational protein assembly. In this review, a wide spectrum overview of assemblysomes is provided, including their discovery, mechanism of action, characteristics, and potential applications in several fields. Assemblysomes are distinct liquid-liquid phase-separated condensates; they have certain unique properties differentiating them from other cellular granules. They are composed of ribosome-nascent protein chain complexes and are resistant to cycloheximide and EDTA. The discovery and observation of intracellular condensates, like assemblysomes, have further expanded our knowledge of cellular stress response mechanisms, particularly in DNA repair processes and defense against proteotoxicity. Ribosome profiling experiments and next-generation sequencing of cDNA libraries extracted from EDTA-resistant pellets-of ultracentrifuged cell lysates-have shed light on the composition and dynamics of assemblysomes, revealing their role as repositories for pre-made stress-responsive ribosome-nascent chain complexes. This review gives an exploration of assemblysomes' potential clinical applications from multiple aspects, including their usefulness as diagnostic biomarkers for chemotherapy resistance and their implications in cancer therapy. In addition, in this overview, we raise some theoretical ideas of industrial and agricultural applications connected to these membraneless organelles. However, we see several challenges. On one hand, we need to understand the complexity of assemblysomes' multiple functions and regulations; on the other hand, it is essential to bridge the gap between fundamental research and practical applications. Overall, assemblysome research can be perceived as a promising upcomer in the improvement of biomedical settings as well as those connected to agricultural and industrial aspects.

The dark side of fluorescent protein tagging-the impact of protein tags on biomolecular condensation

Biomolecular condensation has emerged as an important mechanism to control various cellular processes through the formation of membraneless organelles. Fluorescent protein tags have been extensively used to study the formation and the properties of condensates in vitro and in vivo, but there is evidence that tags may perturb the condensation properties of proteins. In this study, we carefully assess the effects of protein tags on the yeast DEAD-box ATPase Dhh1, a central regulator of processing bodies (P-bodies), which are biomolecular condensates involved in mRNA metabolism. We show that fluorescent tags as well as a polyhistidine tag greatly affect Dhh1 condensation in vitro and lead to condensates with different dynamic properties. Tagging of Dhh1 with various fluorescent proteins in vivo alters the number of P-bodies upon glucose starvation and some tags even show constitutive P-bodies in nonstressed cells. These data raise concerns about the accuracy of tagged protein condensation experiments, highlighting the need for caution when interpreting the results.

Disruption of ER-mitochondria contact sites induces autophagy-dependent loss of P-bodies through the Ca2+-CaMKK2-AMPK pathway

P-bodies (PBs) and stress granules (SGs) are conserved, non-membranous cytoplasmic condensates of RNA-protein complexes. PBs are implicated in post-transcriptional regulation of gene expression through mRNA decay, translational repression and/or storage. Although much is known about the de novo formation of PBs and SGs involving liquid-liquid phase separation through multiple protein-protein and protein-RNA interactions, their subcellular localization and turnover mechanisms are less understood. Here, we report the presence of a subpopulation of PBs and SGs that are in proximity to ER-mitochondria contact sites (ERMCSs) in mammalian cells. Disruption of ERMCSs, achieved through depletion of ER-mitochondria tethering proteins, leads to the disappearance of PBs but not SGs. This effect can be reversed by inhibiting autophagy through both genetic and pharmacological means. Additionally, we find that the disruption of ERMCSs leads to cytosolic Ca2+-induced activation of CaMKK2 and AMP-activated protein kinase (AMPK), ultimately resulting in an autophagy-dependent decrease in PB abundance. Collectively, our findings unveil a mechanism wherein disturbances in ERMCSs induce autophagy-dependent loss of PBs via activation of the Ca2+-CaMKK2-AMPK pathway, thus potentially linking the dynamics and functions of ERMCS with post-transcriptional gene regulation.

The Seneca Valley virus 3C protease cleaves DCP1A to attenuate its antiviral effects

Seneca Valley virus (SVV), a new member of Picornaviridae, causes idiopathic vesicular symptoms in pregnant sows and acute death in neonatal piglets, considerably damaging the swine industry. The viral protease 3C (3Cpro) cleaves host immune-related molecules to create a favorable environment for viral replication. In this study, we found that mRNA decapping enzyme 1A (DCP1A) is a novel antiviral effector against SVV infection that targets 3D viral RNA-dependent RNA polymerase for OPTN-mediated autophagic degradation. To counteract this effect, SVV 3Cpro targets DCP1A for cleavage at glutamine 343 (Q343), resulting in the cleaved products DCP1A (1-343) and DCP1A (344-580), which lose the ability to restrict SVV replication. In contrast, the 3C cleavage-resistant DCP1A-Q343A mutant exhibited stronger antiviral effects than the wild-type DCP1A. Additionally, the degradation of the viral 3D protein targeted by DCP1A was abolished after its cleavage by SVV 3Cpro. In conclusion, our study demonstrated that SVV 3Cpro is a pivotal ISG antagonist that cleaves DCP1A. These results offer novel insight into how viruses evade host immunity.

COCOMO2: A Coarse-Grained Model for Interacting Folded and Disordered Proteins

Biomolecular interactions are essential in many biological processes, including complex formation and phase separation processes. Coarse-grained computational models are especially valuable for studying such processes via simulation. Here, we present COCOMO2, an updated residue-based coarse-grained model that extends its applicability from intrinsically disordered peptides to folded proteins. This is accomplished with the introduction of a surface exposure scaling factor, which adjusts interaction strengths based on solvent accessibility, to enable the more realistic modeling of interactions involving folded domains without additional computational costs. COCOMO2 was parametrized directly with solubility and phase separation data to improve its performance on predicting concentration-dependent phase separation for a broader range of biomolecular systems compared to the original version. COCOMO2 enables new applications including the study of condensates that involve IDPs together with folded domains and the study of complex assembly processes. COCOMO2 also provides an expanded foundation for the development of multiscale approaches for modeling biomolecular interactions that span from residue-level to atomistic resolution.

The zinc finger protein ZFP36L2 inhibits flavivirus infection via the 5'-3' XRN1-mediated RNA decay pathway in the replication complexes

BACKGROUND

The zinc finger protein 36-like (ZFP36L) family is a CCCH-type group consisting of RNA-binding proteins, i.e., ZFP36L1 and ZFP36L2, which regulate cellular mRNA through the RNA decay pathway. ZFP36L1 combats flavivirus infections through the 5'-3' XRN1 and 3'-5' RNA exosome decay pathways. The present study clarified the role of human ZFP36L2 in the defense response of the host against flavivirus infection.

METHODS

Cell lines with overexpression or knockdown of ZFP36L2 were established using lentiviral vectors carrying genes for overexpression and short-hairpin RNA targeting specific genes, respectively. A plaque assay was employed to determine the viral titer. Immunofluorescence and real-time quantitative polymerase chain reaction were used to measure the viral RNA levels. The in vitro-transcribed RNA transcript derived from a replication-dead Japanese encephalitis virus (JEV) replicon containing the renilla luciferase reporter gene (J-R2A-NS5mt) was used to assess the stability of the flavivirus RNA. An RNA immunoprecipitation assay was used to detect the protein-RNA binding ability. Confocal microscopic images were captured to analyze protein colocalization.

RESULTS

ZFP36L2 served as an innate host defender against JEV and dengue virus. ZFP36L2 inhibited flavivirus infection solely through the 5'-3' XRN1 RNA decay pathway, whereas ZFP36L1 inhibited JEV infection via the 5'-3' XRN1 and 3'-5' RNA exosome RNA decay pathways. The direct binding between viral RNA and ZFP36L2 via its CCCH-type zinc finger motifs facilitated the degradation of flavivirus RNA mediated by 5'-3' XRN1. Furthermore, ZFP36L2 was localized in processing bodies (PBs), which participate in the 5'-3' XRN1-mediated RNA decay pathway. Nonetheless, the disruption of PBs did not affect the antiviral activity of ZFP36L2, suggesting that its localization is not essential for the function of the protein. Interestingly, the colocalization of ZFP36L2 and XRN1 with viral RNA and NS3 revealed that the antiviral activity of ZFP36L2 occurred within the replication complexes (RCs).

CONCLUSIONS

In summary, ZFP36L2 bound to and degraded viral RNA through the XRN1-mediated RNA decay pathway in the RCs, thereby inhibiting flavivirus replication. These findings provide valuable insights into the diverse antiviral mechanisms of the ZFP36-like family of proteins in the innate immune response against flavivirus infection.

catGRANULE 2.0: accurate predictions of liquid-liquid phase separating proteins at single amino acid resolution

Liquid-liquid phase separation (LLPS) enables the formation of membraneless organelles, essential for cellular organization and implicated in diseases. We introduce catGRANULE 2.0 ROBOT, an algorithm integrating physicochemical properties and AlphaFold-derived structural features to predict LLPS at single-amino-acid resolution. The method achieves high performance and reliably evaluates mutation effects on LLPS propensity, providing detailed predictions of how specific mutations enhance or inhibit phase separation. Supported by experimental validations, including microscopy data, it predicts LLPS across diverse organisms and cellular compartments, offering valuable insights into LLPS mechanisms and mutational impacts. The tool is freely available at https://tools.tartaglialab.com/catgranule2 and https://doi.org/10.5281/zenodo.14205831 .

Human skeletal muscle fiber heterogeneity beyond myosin heavy chains

Skeletal muscle is a heterogenous tissue comprised primarily of myofibers, commonly classified into three fiber types in humans: one "slow" (type 1) and two "fast" (type 2A and type 2X). However, heterogeneity between and within traditional fiber types remains underexplored. We applied transcriptomic and proteomic workflows to 1050 and 1038 single myofibers from human vastus lateralis, respectively. Proteomics was conducted in males, while transcriptomics included ten males and two females. We identify metabolic, ribosomal, and cell junction proteins, in addition to myosin heavy chain isoforms, as sources of multi-dimensional variation between myofibers. Furthermore, whilst slow and fast fiber clusters are identified, our data suggests that type 2X fibers are not phenotypically distinct to other fast fibers. Moreover, myosin heavy chain-based classifications do not adequately describe the phenotype of myofibers in nemaline myopathy. Overall, our data indicates that myofiber heterogeneity is multi-dimensional with sources of variation beyond myosin heavy chain isoforms.

Antisense oligonucleotide-mediated TRA2β poison exon inclusion induces the expression of a lncRNA with anti-tumor effects

Upregulated expression of the oncogenic splicing factor TRA2β occurs in human tumors partly through decreased inclusion of its autoregulatory non-coding poison exon (PE). Here, we reveal that low TRA2β-PE inclusion negatively impacts patient survival across several tumor types. We demonstrate the ability of splice-switching antisense oligonucleotides (ASOs) to promote TRA2β-PE inclusion and lower TRA2β protein levels in pre-clinical cancer models. TRA2β-PE-targeting ASOs induce anti-cancer phenotypes and widespread transcriptomic alterations with functional impact on RNA processing, mTOR, and p53 signaling pathways. Surprisingly, the effect of TRA2β-PE-targeting ASOs on cell viability are not phenocopied by TRA2β knockdown. Mechanistically, we find that the ASO functions by both decreasing TRA2β protein and inducing the expression of TRA2β-PE-containing transcripts that act as long non-coding RNAs to sequester nuclear proteins. Finally, TRA2β-PE-targeting ASOs are toxic to preclinical 3D organoid and in vivo patient-derived xenograft models. Together, we demonstrate that TRA2β-PE acts both as a regulator of protein expression and a long-noncoding RNA to control cancer cell growth. Drugging oncogenic splicing factors using PE-targeting ASOs is a promising therapeutic strategy.

Stress sensing and response through biomolecular condensates in plants

Plants have developed intricate mechanisms for rapid and efficient stress perception and adaptation in response to environmental stressors. Recent research highlights the emerging role of biomolecular condensates in modulating plant stress perception and response. These condensates function through numerous mechanisms to regulate cellular processes such as transcription, translation, RNA metabolism, and signaling pathways under stress conditions. In this review, we provide an overview of current knowledge on stress-responsive biomolecular condensates in plants, including well-defined condensates such as stress granules, processing bodies, and the nucleolus, as well as more recently discovered plant-specific condensates. By briefly referring to findings from yeast and animal studies, we discuss mechanisms by which plant condensates perceive stress signals and elicit cellular responses. Finally, we provide insights for future investigations on stress-responsive condensates in plants. Understanding how condensates act as stress sensors and regulators will pave the way for potential applications in improving plant resilience through targeted genetic or biotechnological interventions.

HP-Bodies - Ancestral Condensates that Regulate RNA Turnover and Protein Translation in Bacteria

Uncovering what drives select biomolecules to form phase-separated condensates in vivo and identifying their physiological significance are topics of fundamental importance. Here we show that nitrogen-starved Escherichia coli produce long-chain polyphosphates, which scaffold the RNA chaperone Hfq into phase-separating high molecular weight complexes together with components of the RNA translation and processing machinery. The presence of polyphosphate within these condensates, which we termed HP-bodies, controls Hfq function by selectively stabilizing polyadenylated RNAs involved in transcription and protein translation, and promoting interactions with translation- and RNA-metabolism-associated proteins involved in de novo protein synthesis. Lack of polyphosphate prevents HP-body formation, which increases cell death and significantly hinders recovery from N-starvation. In functional analogy, we demonstrate that polyP contributes specifically to the formation of Processing (P)-bodies in human cell lines, revealing that a single, highly conserved and ancestral polyanion serves as the universal scaffold for functional phase-separated condensate formation across the tree of life.

Artificial Compartments Encapsulating Enzymatic Reactions: Towards the Construction of Artificial Organelles

Cells have used compartmentalization to implement complex biological processes involving thousands of enzyme cascade reactions. Enzymes are spatially organized into the cellular compartments to carry out specific and efficient reactions in a spatiotemporally controlled manner. These compartments are divided into membrane-bound and membraneless organelles. Mimicking such cellular compartment systems has been a challenge for years. A variety of artificial scaffolds, including liposomes, polymersomes, proteins, nucleic acids, or hybrid materials have been used to construct artificial membrane-bound or membraneless compartments. These artificial compartments may have great potential for applications in biosynthesis, drug delivery, diagnosis and therapeutics, among others. This review first summarizes the typical examples of cellular compartments. In particular, the recent studies on cellular membraneless organelles (biomolecular condensates) are reviewed. We then summarize the recent advances in the construction of artificial compartments using engineered platforms. Finally, we provide our insights into the construction of biomimetic systems and the applications of these systems. This review article provides a timely summary of the relevant perspectives for the future development of artificial compartments, the building blocks for the construction of artificial organelles or cells.

RNA in Stow, Leukemia on the Go: P-Bodies RNA Sequestration Drives Leukemogenesis

A novel mechanism of sequestering tumor suppressor mRNAs reveals new therapeutic vulnerabilities in leukemic cells.

Recent advances in the synthesis and application of biomolecular condensates

Biomolecular condensates (BMCs) represent a group of organized and programmed systems that participate in gene transcription, chromosome organization, cell division, tumorigenesis, and aging. However, the understanding of BMCs in terms of internal organizations and external regulations remains at an early stage. Recently, novel approaches such as synthetic biology have been used for de novo synthesis of BMCs. These synthesized BMCs (SBMCs) driven by phase separation adeptly resemble the self-assembly and dynamics of natural BMCs, offering vast potentials in basic and applied research. This review introduces recent progresses in phase separation-induced SBMCs, attempting to elaborate on the intrinsic principles and regulatory methodologies used to construct SBMCs. Furthermore, the scientific applications of SBMCs are illustrated, as indicated by the studies of chromosome structure, pathogenesis, biomanufacturing, artificial cell design, and drug delivery. The controllable SBMCs offer a powerful tool for understanding metabolic regulations, cellular organizations, and disease-associated protein aggregations, raising both opportunities and challenges in the future of biomaterial, biotechnology, and biomedicine.

TDP43 autoregulation gives rise to dominant negative isoforms that are tightly controlled by transcriptional and post-translational mechanisms

The nuclear RNA-binding protein TDP43 is integrally involved in the pathogenesis of amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). Previous studies uncovered N-terminal TDP43 isoforms that are predominantly cytosolic in localization, prone to aggregation, and enriched in susceptible spinal motor neurons. In healthy cells, however, these shortened (s)TDP43 isoforms are difficult to detect in comparison to full-length (fl)TDP43, raising questions regarding their origin and selective regulation. Here, we show that sTDP43 is created as a by-product of TDP43 autoregulation and cleared by nonsense-mediated RNA decay (NMD). sTDP43-encoding transcripts that escape NMD are rapidly degraded post-translationally via the proteasome and macroautophagy. Circumventing these regulatory mechanisms by overexpressing sTDP43 results in neurodegeneration via N-terminal oligomerization and impairment of flTDP43 splicing activity, in addition to RNA-binding-dependent gain-of-function toxicity. Collectively, these studies highlight endogenous mechanisms that tightly regulate sTDP43 expression and underscore the consequences of aberrant sTDP43 accumulation in disease.

Biomolecular condensates in immune cell fate

Fate decisions during immune cell development require temporally precise changes in gene expression. Evidence suggests that the dynamic modulation of these changes is associated with the formation of diverse, membrane-less nucleoprotein assemblies that are termed biomolecular condensates. These condensates are thought to orchestrate fate-determining transcriptional and post-transcriptional processes by locally and transiently concentrating DNA or RNA molecules alongside their regulatory proteins. Findings have established a link between condensate formation and the gene regulatory networks that ensure the proper development of immune cells. Conversely, condensate dysregulation has been linked to impaired immune cell fates, including ageing and malignant transformation. This Review explores the putative mechanistic links between condensate assembly and the gene regulatory frameworks that govern normal and pathological development in the immune system.

Cytoplasmic mRNA decay and quality control machineries in eukaryotes

mRNA degradation pathways have key regulatory roles in gene expression. The intrinsic stability of mRNAs in the cytoplasm of eukaryotic cells varies widely in a gene- and isoform-dependent manner and can be regulated by cellular cues, such as kinase signalling, to control mRNA levels and spatiotemporal dynamics of gene expression. Moreover, specialized quality control pathways exist to rid cells of non-functional mRNAs produced by errors in mRNA processing or mRNA damage that negatively impact translation. Recent advances in structural, single-molecule and genome-wide methods have provided new insights into the central machineries that carry out mRNA turnover, the mechanisms by which mRNAs are targeted for degradation and the general principles that govern mRNA stability at a global level. This improved understanding of mRNA degradation in the cytoplasm of eukaryotic cells is finding practical applications in the design of therapeutic mRNAs.

Tristetraprolin Family Members and Processing Bodies: A Complex Regulatory Network Involved in Fatty Liver Disease, Viral Hepatitis and Hepatocellular Carcinoma

Chronic liver diseases, such as those encountered with obesity, chronic/abusive alcohol consumption or viral infections, represent not only major public health concerns with limited therapeutic options but also important risk factors for the onset of hepatocellular carcinoma (HCC). Deciphering the molecular traits underlying these disorders is of high interest for designing new and effective treatments. The tristetraprolin (TTP) family members are of particular importance given their ability to control the expression of a wide range of genes involved in metabolism, inflammation and carcinogenesis at the post-transcriptional level. This regulation can occur within small cytoplasmic granules, namely, processing bodies (P-bodies), where the mRNA degradation occurs. Increasing evidence indicates that TTP family members and P-bodies are involved in the development of chronic liver diseases and cancers. In this review, we discuss the role of this regulatory mechanism in metabolic-dysfunction-associated steatotic liver disease (MASLD), alcohol-related liver disease (ALD), hepatic viral infections and HCC.

MARTRE family proteins negatively regulate CCR4-NOT activity to protect poly(A) tail length and promote translation of maternal mRNA

The mammalian early embryo development requires translation of maternal mRNA inherited from the oocyte. While poly(A) tail length influences mRNA translation efficiency during the oocyte-to-embryo transition (OET), molecular mechanisms regulating maternal RNA poly(A) tail length are not fully understood. In this study, we identified MARTRE, a previously uncharacterized protein family (MARTRE1-MARTRE6), as regulators expressed during mouse OET that modulate poly(A) tail length. MARTRE inhibits deadenylation through the direct interaction with the deadenylase CCR4-NOT, and ectopic expression of Martre stabilized mRNA by attenuating poly(A) tail shortening. Deletion of the Martre gene locus results in shortened poly(A) tails and decreased translation efficiency of actively translated mRNAs in mouse zygotes, but does not affect maternal mRNA decay. MARTRE proteins thus fine-tune maternal mRNA translation by negatively regulating the deadenylating activity of CCR4-NOT. Moreover, Martre knockout embryos show delayed 2-cell stage progression and compromised preimplantation development. Together, our findings highlight protection of long poly(A) tails from active deadenylation as an important mechanism to coordinate translation of maternal mRNA.

Structural, biological, and biomedical implications of mRNA interactions with the master regulator HuR

Human antigen R (HuR) is a ubiquitously expressed RNA-binding protein (RBP) that has been implicated in a vast range of biological processes including stress response, angiogenesis, cell proliferation, and differentiation. Dysregulation of HuR has been linked to a number of pathological disorders including vascular disease, inflammation, and cancers such as those of the breast and colon. Like many RBPs, HuR is composed of multiple RNA-recognition motif (RRM) domains; however, HuR and the three other members of the Hu family (HuB, HuC, and HuD) possess a unique structural composition with two RRMs separated from a third C-terminal RRM by a long, unstructured hinge region. While there has been extensive research on the role of HuR in cellular, molecular, and developmental biology, there are fewer structural and biochemical studies of HuR and many questions still remain about the molecular mechanisms of HuR. In this review, we endeavor to synthesize existing HuR research spanning the last three decades in order to define known mechanistic roles of each domain, highlight remaining uncertainties, and provide a backdrop for ongoing research into the chemistry and biology of HuR and similar multi-RRM containing proteins.

The role of ER exit sites in maintaining P-body organization and integrity during Drosophila melanogaster oogenesis

Processing bodies (P-bodies) are cytoplasmic membrane-less organelles which host multiple mRNA processing events. While the fundamental principles of P-body organization are beginning to be elucidated in vitro, a nuanced understanding of how their assembly is regulated in vivo remains elusive. Here, we investigate the potential link between ER exit sites and P-bodies in Drosophila melanogaster egg chambers. Employing a combination of live and super-resolution imaging, we find that P-bodies associated with ER exit sites are larger and less mobile than cytoplasmic P-bodies, indicating that they constitute a distinct class of P-bodies. Moreover, we demonstrate that altering the composition of ER exit sites has differential effects on core P-body proteins (Me31B, Cup, and Trailer Hitch), suggesting a potential role for ER exit sites in P-body organization. Furthermore, we show that in the absence of ER exit sites, P-body integrity is compromised and the stability and translational repression efficiency of the maternal mRNA, oskar, are reduced. Together, our data highlights the crucial role of ER exit sites in governing P-body organization.

DCP1A, a MEK substrate, regulates the self-renewal and differentiation of mouse embryonic stem cells

Mitogen-activated extracellular signal-regulated kinase (MEK) inhibitors are widely applied to maintain pluripotency, while prolonged MEK inhibition compromises the developmental potential of mouse embryonic stem cells (ESCs). To understand the mechanism of MEK in pluripotency maintenance, we first demonstrated that MEK regulates gene expression at post-transcriptional steps. Consistently, many of the 66 MEK substrates identified by quantitative phosphoproteomics analysis are involved in RNA processing. We further confirmed that MEK1 phosphorylates S563 of DCP1A, an mRNA decapping cofactor and processing body (P body) component. DCP1A, as well as two other P body components, EDC4 and DCP2, are required for the self-renewal and differentiation of ESCs, indicating the role of P bodies in ESCs. Dephosphorylation of DCP1A S563 facilitates both self-renewal and differentiation of ESCs through promoting P body formation and RNA storage. In summary, our study identified 66 MEK substrates supporting the extracellular signal-regulated kinase (ERK)-independent function of MEK and revealed that DCP1A, phosphorylated by MEK, regulates ESC self-renewal and differentiation through modulating P body formation.

m6A sites in the coding region trigger translation-dependent mRNA decay

N6-Methyladenosine (m6A) is the predominant internal RNA modification in eukaryotic messenger RNAs (mRNAs) and plays a crucial role in mRNA stability. Here, using human cells, we reveal that m6A sites in the coding sequence (CDS) trigger CDS-m6A decay (CMD), a pathway that is distinct from previously reported m6A-dependent degradation mechanisms. Importantly, CDS m6A sites act considerably faster and more efficiently than those in the 3' untranslated region, which to date have been considered the main effectors. Mechanistically, CMD depends on translation, whereby m6A deposition in the CDS triggers ribosome pausing and transcript destabilization. The subsequent decay involves the translocation of the CMD target transcripts to processing bodies (P-bodies) and recruitment of the m6A reader protein YT521-B homology domain family protein 2 (YTHDF2). Our findings highlight CMD as a previously unknown pathway, which is particularly important for controlling the expression of developmental regulators and retrogenes.

Translation regulation in response to stress

Cell stresses occur in a wide variety of settings: in disease, during industrial processes, and as part of normal day-to-day rhythms. Adaptation to these stresses requires cells to alter their proteome. Cells modify the proteins they synthesize to aid proteome adaptation. Changes in both mRNA transcription and translation contribute to altered protein synthesis. Here, we discuss the changes in translational mechanisms that occur following the onset of stress, and the impact these have on stress adaptation.

Unraveling the noncoding RNA landscape in glioblastoma: from pathogenesis to precision therapeutics

Glioblastoma (GBM) is an aggressive type IV brain tumor that originates from astrocytes and has a poor prognosis. Despite intensive research, survival rates have not significantly improved. Noncoding RNAs (ncRNAs) are emerging as critical regulators of carcinogenesis, progression, and increased treatment resistance in GBM cells. They influence angiogenesis, migration, epithelial-to-mesenchymal transition, and invasion in GBM cells. ncRNAs, such as long ncRNAs (lncRNAs), microRNAs (miRNAs), and circular RNAs (circRNAs), are commonly dysregulated in GBM. miRNAs, such as miR-21, miR-133a, and miR-27a-3p, are oncogenes that increase cell proliferation, metastasis, and migration by targeting TGFBR1 and BTG2. In contrast, lncRNAs, such as HOXD-AS2 and LINC00511, are oncogenes that increase the migration, invasion, and proliferation of cells. CircRNAs, such as circ0001730, circENTPD7, and circFOXO3, are oncogenes responsible for cell growth, angiogenesis, and viability. Developing novel therapeutic strategies targeting ncRNAs, cell migration, and angiogenesis is a promising approach for GBM. By targeting these dysregulated ncRNAs, we can potentially restore a healthy balance in gene expression and influence disease progression. ncRNAs abound within GBM, demonstrating significant roles in governing the growth and behavior of these tumors. They may also be useful as biomarkers or targets for therapy. The use of morpholino oligonucleotides (MOs) suppressing the oncogene expression of HOTAIR, BCYRN1, and cyrano, antisense oligonucleotides (ASOs) suppressing the expression of ncRNAs such as MALAT1 and miR-10b, locked nucleic acids (LNAs) suppressing miR-21, and peptide nucleic acids (PNAs) suppressing the expression of miR-155 inhibited the PI3K pathway, tumor growth, angiogenesis, proliferation, migration, and invasion. Targeting oncogenic ncRNAs with RNA-interfering strategies such as MOs, ASOs, LNAs, CRISPR-Cas9 gene editing, and PNA approaches may represent a promising therapeutic strategy for GBM. This review emphasizes the critical role of ncRNAs in GBM pathogenesis, as well as the potential for new therapeutic strategies targeting these pathways to improve the prognosis and quality of life for GBM patients.

Cytoplasmic nucleoporin assemblage: the cellular artwork in physiology and disease

Nucleoporins, essential proteins building the nuclear pore, are pivotal for ensuring nucleocytoplasmic transport. While traditionally confined to the nuclear envelope, emerging evidence indicates their presence in various cytoplasmic structures, suggesting potential non-transport-related roles. This review consolidates findings on cytoplasmic nucleoporin assemblies across different states, including normal physiological conditions, stress, and pathology, exploring their structural organization, formation dynamics, and functional implications. We summarize the current knowledge and the latest concepts on the regulation of nucleoporin homeostasis, aiming to enhance our understanding of their unexpected roles in physiological and pathological processes.

MicroRNA Nobel Prize: Timely Recognition and High Anticipation of Future Products-A Prospective Analysis

MicroRNAs (miRNAs) maintain cellular homeostasis by blocking mRNAs by binding with them to fine-tune the expression of genes across numerous biological pathways. The 2024 Nobel Prize in Medicine and Physiology for discovering miRNAs was long overdue. We anticipate a deluge of research work involving miRNAs to repeat the history of prizes awarded for research on other RNAs. Although miRNA therapies are included for several complex diseases, the realization that miRNAs regulate genes and their roles in addressing therapies for hundreds of diseases are expected; but with advancement in drug discovery tools, we anticipate even faster entry of new drugs. To promote this, we provide details of the current science, logic, intellectual property, formulations, and regulatory process with anticipation that many more researchers will introduce novel therapies based on the discussion and advice provided in this paper.

mRNA compartmentalization via multimodule DNA nanostructure assembly augments the immunogenicity and efficacy of cancer mRNA vaccine

Messenger RNA (mRNA) vaccine has fueled a great hope for cancer immunotherapy. However, low immunogenicity, caused by inefficient mRNA expression and weak immune stimulation, hampers the efficacy of mRNA vaccines. Here, we present an mRNA compartmentalization-based cancer vaccine, comprising a multimodule DNA nanostructure (MMDNS)-assembled compartment for efficient mRNA translation via in situ localizing mRNA concentration and relevant reaction molecules. The MMDNS is constructed via programmable DNA hybridization chain reaction (HCR)-based strategy, with integrating antigen-coded mRNA, CpG oligodeoxynucleotides (ODNs), acidic-responsive DNA sequence, and dendritic cells targeting aptamer. MMDNS undergoes in situ assembly in acidic lysosomes to form a micro-sized aggregate, inducing an enhanced CpG ODN adjuvant efficacy. Subsequently, the aggregates escape into cytoplasm, providing a moderate compartment which supports the efficient translation of spatially proximal mRNA transcripts via localizing relevant reaction molecules. The mRNA compartmentalization-based vaccine boosts a strong immune response and effectively inhibits tumor growth and metastasis, offering a robust strategy for cancer immunotherapy.

Post-transcriptional regulation of cyclin A and cyclin B mRNAs is mediated by Bruno 1 and Cup, and further fine-tuned within P-bodies

Cell cycle progression is tightly controlled by the regulated synthesis and degradation of Cyclins, such as Cyclin A and Cyclin B, which activate CDK1 to trigger mitosis. Mutations affecting Cyclin regulation are often linked to tumorigenesis, making the study of cyclin mRNA regulation critical for identifying new cancer therapies. In this study, we demonstrate via super-resolution microscopy that cyclin A and cyclin B mRNAs associate with Bruno 1 and Cup in nurse cells. The depletion of either protein leads to abnormal Cyclin A and Cyclin B protein expression and a reduction in mRNA levels for both Cyclins. We further reveal that both cyclin A and cyclin B mRNAs accumulate in P-bodies marked by Me31B. Interestingly, Me31B is not involved in regulating cyclin A mRNA, as no changes in cyclin A mRNA levels or repression are observed upon Me31B depletion. However, cyclin B mRNA shows stage-specific derepression and reduced levels when Me31B is absent. Notably, the association between cyclin B and Cup is strengthened in the absence of Me31B, indicating that this interaction occurs independently of P-bodies. These results highlight the nuanced, mRNA-specific roles of P-body condensates in post-transcriptional regulation, challenging the idea of a uniform, binary mechanism of mRNA repression in P-bodies.

Enzyme-Responsive DNA Condensates

Membrane-less compartments and organelles are widely acknowledged for their role in regulating cellular processes, and there is an urgent need to harness their full potential as both structural and functional elements of synthetic cells. Despite rapid progress, synthetically recapitulating the nonequilibrium, spatially distributed responses of natural membrane-less organelles remains elusive. Here, we demonstrate that the activity of nucleic-acid cleaving enzymes can be localized within DNA-based membrane-less compartments by sequestering the respective DNA or RNA substrates. Reaction-diffusion processes lead to complex nonequilibrium patterns, dependent on enzyme concentration. By arresting similar dynamic patterns, we spatially organize different substrates in concentric subcompartments, which can be then selectively addressed by different enzymes, demonstrating spatial distribution of enzymatic activity. Besides expanding our ability to engineer advanced biomimetic functions in synthetic membrane-less organelles, our results may facilitate the deployment of DNA-based condensates as microbioreactors or platforms for the detection and quantitation of enzymes and nucleic acids.

Membraneless organelles in health and disease: exploring the molecular basis, physiological roles and pathological implications

Once considered unconventional cellular structures, membraneless organelles (MLOs), cellular substructures involved in biological processes or pathways under physiological conditions, have emerged as central players in cellular dynamics and function. MLOs can be formed through liquid-liquid phase separation (LLPS), resulting in the creation of condensates. From neurodegenerative disorders, cardiovascular diseases, aging, and metabolism to cancer, the influence of MLOs on human health and disease extends widely. This review discusses the underlying mechanisms of LLPS, the biophysical properties that drive MLO formation, and their implications for cellular function. We highlight recent advances in understanding how the physicochemical environment, molecular interactions, and post-translational modifications regulate LLPS and MLO dynamics. This review offers an overview of the discovery and current understanding of MLOs and biomolecular condensate in physiological conditions and diseases. This article aims to deliver the latest insights on MLOs and LLPS by analyzing current research, highlighting their critical role in cellular organization. The discussion also covers the role of membrane-associated condensates in cell signaling, including those involving T-cell receptors, stress granules linked to lysosomes, and biomolecular condensates within the Golgi apparatus. Additionally, the potential of targeting LLPS in clinical settings is explored, highlighting promising avenues for future research and therapeutic interventions.

Modulation of stress granule dynamics by phosphorylation and ubiquitination in plants

The Arabidopsis tandem CCCH zinc finger 1 (TZF1) is an RNA-binding protein that plays a pivotal role in plant growth and stress response. In this report, we show that TZF1 contains two intrinsically disordered regions necessary for its localization to stress granules (SGs). TZF1 recruits mitogen-activated protein kinase (MAPK) signaling components and an E3 ubiquitin ligase KEEP-ON-GOING (KEG) to SGs. TZF1 is phosphorylated by MPKs and ubiquitinated by KEG. Using a high throughput Arabidopsis protoplasts transient expression system, mutant studies reveal that the phosphorylation of specific residues plays differential roles in enhancing or reducing TZF1 SG assembly and protein-protein interaction with mitogen-activated kinase kinase 5 in SGs. Ubiquitination appears to play a positive role in TZF1 SG assembly, because mutations cause a reduction of typical SGs, while enhancing the assembly of large SGs encompassing the nucleus. Together, our results demonstrate that plant SG assembly is distinctively regulated by phosphorylation and ubiquitination.

TIRR regulates mRNA export and association with P-bodies in response to DNA damage

To ensure the integrity of our genetic code, a coordinated network of signalling and repair proteins, known as the DNA damage response (DDR), detects and repairs DNA insults, the most toxic being double-strand breaks (DSBs). Tudor interacting repair regulator (TIRR) is a key factor in DSB repair, acting through its interaction with p53 binding protein 1 (53BP1). TIRR is also an RNA binding protein, yet its role in RNA regulation during the DDR remains elusive. Here, we show that TIRR selectively binds to a subset of messenger RNAs (mRNAs) in response to DNA damage. Upon DNA damage, TIRR interacts with the nuclear export protein Exportin-1 through a nuclear export signal. Furthermore, TIRR plays a crucial role in the modulation of RNA processing bodies (PBs). TIRR itself and TIRR-bound RNA co-localize with PBs, and TIRR depletion results in nuclear RNA retention and impaired PB formation. We also suggest a potential link between TIRR-regulated RNA export and efficient DDR. This work reveals intricate involvement of TIRR in orchestrating mRNA nuclear export and storage within PBs, emphasizing its significance in the regulation of RNA-mediated DDR.

Med13 is required for efficient P-body recruitment and autophagic degradation of Edc3 following nitrogen starvation

The Cdk8 kinase module (CKM), a conserved, detachable unit of the Mediator complex, plays a vital role in regulating transcription and communicating stress signals from the nucleus to other organelles. Here, we describe a new transcription-independent role for Med13, a CKM scaffold protein, following nitrogen starvation. In Saccharomyces cerevisiae, nitrogen starvation triggers Med13 to translocate to the cytoplasm. This stress also induces the assembly of conserved membraneless condensates called processing bodies (P-bodies) that dynamically sequester translationally inactive messenger ribonucleoprotein particles. Cytosolic Med13 colocalizes with P-bodies, where it helps recruit Edc3, a highly conserved decapping activator and P-body assembly factor, into these conserved ribonucleoprotein granules. Moreover, Med13 orchestrates the autophagic degradation of Edc3 through a selective cargo-hitchhiking autophagy pathway that utilizes Ksp1 as its autophagic receptor protein. In contrast, the autophagic degradation of Xrn1, another conserved P-body assembly factor, is Med13 independent. These results place Med13 as a new player in P-body assembly and regulation following nitrogen starvation. They support a model in which Med13 acts as a conduit between P-bodies and phagophores, two condensates that use liquid-liquid phase separation in their assembly.

COCOMO2: A coarse-grained model for interacting folded and disordered proteins

Biomolecular interactions are essential in many biological processes, including complex formation and phase separation processes. Coarse-grained computational models are especially valuable for studying such processes via simulation. Here, we present COCOMO2, an updated residue-based coarse-grained model that extends its applicability from intrinsically disordered peptides to folded proteins. This is accomplished with the introduction of a surface exposure scaling factor, which adjusts interaction strengths based on solvent accessibility, to enable the more realistic modeling of interactions involving folded domains without additional computational costs. COCOMO2 was parameterized directly with solubility and phase separation data to improve its performance on predicting concentration-dependent phase separation for a broader range of biomolecular systems compared to the original version. COCOMO2 enables new applications including the study of condensates that involve IDPs together with folded domains and the study of complex assembly processes. COCOMO2 also provides an expanded foundation for the development of multi-scale approaches for modeling biomolecular interactions that span from residue-level to atomistic resolution.