scholarly journals PETISCO is a novel protein complex required for 21U RNA biogenesis and embryonic viability

2018 ◽  
Author(s):  
Ricardo J. Cordeiro Rodrigues ◽  
António Miguel de Jesus Domingues ◽  
Svenja Hellmann ◽  
Sabrina Dietz ◽  
Bruno F. M. de Albuquerque ◽  
...  
Keyword(s):  
Protein Complex ◽  
Intrinsically Disordered Proteins ◽  
Rna Binding ◽  
Disordered Proteins ◽  
Sequence Motif ◽  
C Elegans ◽  
Conserved Sequence ◽  
Intrinsically Disordered ◽  
Rna Biogenesis ◽  
Novel Protein

AbstractPiwi proteins are important for germ cell development in almost all animals studied thus far. These proteins are guided to specific targets, such as transposable elements, by small guide RNAs, often referred to as piRNAs, or 21U RNAs in C. elegans. In this organism, even though genetic screens have uncovered a number of potential 21U RNA biogenesis factors, little is known about how these factors interact or what they do. Based on the previously identified 21U biogenesis factor PID-1, we here define a novel protein complex, PETISCO, that is required for 21U RNA biogenesis. PETISCO contains both potential 5’-cap and 5’-phosphate RNA binding domains, suggesting involvement in 5’ end processing. We define the interaction architecture of PETISCO and reveal a second function for PETISCO in embryonic development. This essential function of PETISCO is not mediated by PID-1, but by TOST-1. Vice versa, TOST-1 is not involved in 21U RNA biogenesis. Both PID-1 and TOST-1 are small, intrinsically disordered proteins that interact directly with the PETISCO protein ERH-2 (enhancer of rudimentary homolog 2) using a conserved sequence motif. Finally, our data suggest an important role for TOST-1:PETISCO in SL1 homeostasis in the early embryo. Our work describes the first molecular platform for 21U RNA production in C. elegans, and strengthens the view that 21U RNA biogenesis is built upon a much more widely used, snRNA-related pathway.

scholarly journals Interactions between the Intrinsically Disordered Regions of hnRNP-A2 and TDP-43 Accelerate TDP-43′s Conformational Transition

2020 ◽  
Vol 21 (16) ◽  
pp. 5930
Author(s):  
Wan-Chin Chiang ◽  
Ming-Hsuan Lee ◽  
Tsai-Chen Chen ◽  
Jie-rong Huang
Keyword(s):  
Intrinsically Disordered Proteins ◽  
Rna Binding ◽  
Conformational Transition ◽  
Rna Binding Proteins ◽  
Sequence Similarity ◽  
Disordered Proteins ◽  
General Mechanism ◽  
Intrinsically Disordered ◽  
Intrinsically Disordered Regions ◽  
Disordered Regions

Most biological functions involve protein–protein interactions. Our understanding of these interactions is based mainly on those of structured proteins, because encounters between intrinsically disordered proteins (IDPs) or proteins with intrinsically disordered regions (IDRs) are much less studied, regardless of the fact that more than half eukaryotic proteins contain IDRs. RNA-binding proteins (RBPs) are a large family whose members almost all have IDRs in addition to RNA binding domains. These IDRs, having low sequence similarity, interact, but structural details on these interactions are still lacking. Here, using the IDRs of two RBPs (hnRNA-A2 and TDP-43) as a model, we demonstrate that the rate at which TDP-43′s IDR undergoes the neurodegenerative disease related α-helix-to-β-sheet transition increases in relation to the amount of hnRNP-A2′s IDR that is present. There are more than 1500 RBPs in human cells and most of them have IDRs. RBPs often join the same complexes to regulate genes. In addition to the structured RNA-recognition motifs, our study demonstrates a general mechanism through which RBPs may regulate each other’s functions through their IDRs.

scholarly journals RNA Droplets

2020 ◽  
Vol 49 (1) ◽  
pp. 247-265 ◽  
Author(s):  
Kevin Rhine ◽  
Velinda Vidaurre ◽  
Sua Myong
Keyword(s):  
Phase Separation ◽  
Intrinsically Disordered Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Disordered Proteins ◽  
In Vivo Studies ◽  
Anionic Polymer ◽  
Temporal And Spatial Distribution ◽  
Intrinsically Disordered ◽  
Rnp Granules

Liquid–liquid phase separation is emerging as the universal mechanism by which membraneless cellular granules form. Despite many previous studies on condensation of intrinsically disordered proteins and low complexity domains, we lack understanding about the role of RNA, which is the essential component of all ribonucleoprotein (RNP) granules. RNA, as an anionic polymer, is inherently an excellent platform for achieving multivalency and can accommodate many RNA binding proteins. Recent findings have highlighted the diverse function of RNA in tuning phase-separation propensity up or down, altering viscoelastic properties and thereby driving immiscibility between different condensates. In addition to contributing to the biophysical properties of droplets, RNA is a functionally critical constituent that defines the identity of cellular condensates and controls the temporal and spatial distribution of specific RNP granules. In this review, we summarize what we have learned so far about such roles of RNA in the context of in vitro and in vivo studies.

scholarly journals Uncovering non-random sequence patterns within intrinsically disordered proteins

2021 ◽  
Author(s):  
Megan C. Cohan ◽  
Min Kyung Shinn ◽  
Jared M. Lalmansingh ◽  
Rohit V. Pappu
Keyword(s):  
Intrinsically Disordered Proteins ◽  
Random Sequence ◽  
Null Model ◽  
Computational Method ◽  
Disordered Proteins ◽  
Sequence Alignments ◽  
Conserved Sequence ◽  
Intrinsically Disordered ◽  
Sequence Patterns ◽  
Z Scores

AbstractIntrinsically disordered proteins / regions (IDPs / IDRs) pose unique challenges for deriving sequence-function relationships from multiple sequence alignments. These challenges arise from variations in sequence lengths, similarities, and identities across orthologs. Recent computational efforts have demonstrated the utility of comparing large numbers of distinct sequence features as a strategy to identify conserved sequence-function relationships in IDPs / IDRs. Inspired by these efforts, and by biophysical studies that have established the importance of binary patterning features in IDPs / IDRs, we present here a computational method, NARDINI (Non-random Arrangement of Residues in Disordered Regions Inferred using Numerical Intermixing), to uncover truly non-random binary patterns within disordered proteins / regions. Binary patterns refer to the linear clustering or dispersion of specific residues or residue types with respect to all other residues or specific types of residues. Our approach does not use, nor does it require sequence alignments. Instead for each IDR, we generate an ensemble of scrambled sequences and use this to set up expectations from a composition-specific null model for the patterning parameters of interest. We annotate each IDR in terms of pattern-specific z-score matrices by computing how specific patterns deviate from the null model. The z-scores help in identifying the non-random linear sequence patterns within an IDR. We tested the accuracy of NARDINI derived z-scores by assessing the ability to identify sequence patterns that have been identified as determinants of sequence-function relationships in specific IDPs / IDRs.

scholarly journals Cellular Chaperone Function of Intrinsically Disordered Dehydrin ERD14

2021 ◽  
Vol 22 (12) ◽  
pp. 6190
Author(s):  
Nikoletta Murvai ◽  
Lajos Kalmar ◽  
Beata Szabo ◽  
Eva Schad ◽  
András Micsonai ◽  
...  
Keyword(s):  
Intrinsically Disordered Proteins ◽  
Stress Protein ◽  
Early Response ◽  
Disordered Proteins ◽  
Proper Function ◽  
Sequence Motifs ◽  
Protective Function ◽  
Cellular Protection ◽  
Conserved Sequence ◽  
Intrinsically Disordered

Disordered plant chaperones play key roles in helping plants survive in harsh conditions, and they are indispensable for seeds to remain viable. Aside from well-known and thoroughly characterized globular chaperone proteins, there are a number of intrinsically disordered proteins (IDPs) that can also serve as highly effective protecting agents in the cells. One of the largest groups of disordered chaperones is the group of dehydrins, proteins that are expressed at high levels under different abiotic stress conditions, such as drought, high temperature, or osmotic stress. Dehydrins are characterized by the presence of different conserved sequence motifs that also serve as the basis for their categorization. Despite their accepted importance, the exact role and relevance of the conserved regions have not yet been formally addressed. Here, we explored the involvement of each conserved segment in the protective function of the intrinsically disordered stress protein (IDSP) A. thaliana’s Early Response to Dehydration (ERD14). We show that segments that are directly involved in partner binding, and others that are not, are equally necessary for proper function and that cellular protection emerges from the balanced interplay of different regions of ERD14.

scholarly journals The mutational landscape of a prion-like domain

2019 ◽  
Author(s):  
Benedetta Bolognesi ◽  
Andre J. Faure ◽  
Mireia Seuma ◽  
Jörn M. Schmiedel ◽  
Gian Gaetano Tartaglia ◽  
...  
Keyword(s):  
Intrinsically Disordered Proteins ◽  
Rna Binding ◽  
Genetic Interactions ◽  
Disordered Proteins ◽  
Insoluble Protein ◽  
Cellular Toxicity ◽  
Intrinsically Disordered ◽  
Powerful Approach ◽  
Lateral Sclerosis

AbstractSpecific insoluble protein aggregates are the hallmarks of many neurodegenerative diseases1–5. For example, cytoplasmic aggregates of the RNA-binding protein TDP-43 are observed in 97% of cases of Amyotrophic Lateral Sclerosis (ALS)6,7. However, it is still unclear for ALS and other diseases whether it is the insoluble aggregates or other forms of the mutated proteins that cause these diseases that are actually toxic to cells8–13. Here we address this question for TDP-43 by systematically mutating14the protein and quantifying the effects on cellular toxicity. We generated >50,000 mutations in the intrinsically disordered prion-like domain (PRD) and observed that changes in hydrophobicity and aggregation potential are highly predictive of changes in toxicity. Surprisingly, however, increased hydrophobicity and cytoplasmic aggregation actually reduce cellular toxicity. Mutations have their strongest effects in a central region of the PRD, with variants that increase toxicity promoting the formation of more dynamic liquid-like condensates. The genetic interactions in double mutants reveal that specific structures exist in this ‘unstructured’ regionin vivo. Our results demonstrate that deep mutagenesis is a powerful approach for probing the sequence-function relationships of intrinsically disordered proteins as well as theirin vivostructural conformations. Moreover, we show that aggregation of TDP-43 is not harmful but actually protects cells, most likely by titrating the protein away from a toxic liquid-like phase.

scholarly journals Sequence dependent co-phase separation of RNA-protein mixtures elucidated using molecular simulations

2020 ◽  
Author(s):  
Roshan Mammen Regy ◽  
Gregory L. Dignon ◽  
Wenwei Zheng ◽  
Young Chan Kim ◽  
Jeetain Mittal
Keyword(s):  
Phase Separation ◽  
Intrinsically Disordered Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Experimental Studies ◽  
Coarse Grained ◽  
Disordered Proteins ◽  
Sequence Specificity ◽  
Intrinsically Disordered ◽  
Modelling Framework

ABSTRACTRibonucleoprotein (RNP) granules are membraneless organelles (MLOs) which majorly consist of RNA and RNA-binding proteins and are formed via liquid-liquid phase separation (LLPS). Experimental studies investigating the drivers of LLPS have shown that intrinsically disordered proteins (IDPs) and nucleic acids like RNA play a key role in modulating protein phase separation. There is currently a dearth of modelling techniques which allow one to delve deeper into how RNA plays its role as a modulator/promoter of LLPS in cells using computational methods. Here we present a coarse-grained RNA model developed to fill this gap, which together with our recently developed HPS model for protein LLPS, allows us to capture the factors driving RNA-protein co-phase separation. We explore the capabilities of the modelling framework with the LAF-1 RGG/RNA system which has been well studied in experiments and also with the HPS model previously. Further taking advantage of the fact that the HPS model maintains sequence specificity we explore the role of charge patterning on controlling RNA incorporation into condensates. With increased charge patterning we observe formation of structured or patterned condensates which suggests the possible roles of RNA in not only shifting the phase boundaries but also introducing microscopic organization in MLOs.

scholarly journals The intrinsically disordered protein SPE-18 promotes localized assembly of the major sperm protein in C. elegans spermatocytes

2020 ◽  
Author(s):  
Kari L. Price ◽  
Marc Presler ◽  
Christopher M. Uyehara ◽  
Diane C. Shakes
Keyword(s):  
Intrinsically Disordered Proteins ◽  
Intrinsically Disordered Protein ◽  
Disordered Proteins ◽  
Major Sperm Protein ◽  
Sperm Protein ◽  
C Elegans ◽  
Intrinsically Disordered ◽  
Disordered Protein ◽  
Changing Patterns ◽  
Cytoskeletal Elements

ABSTRACTMany specialized cells use unconventional strategies of cytoskeletal control. Nematode spermatocytes discard their actin and tubulin following meiosis, and instead employ the regulated assembly/disassembly of the Major Sperm Protein (MSP) to drive sperm motility. However prior to the meiotic divisions, MSP is effectively sequestered as it exclusively assembles into paracrystalline structures called fibrous bodies (FBs). The accessory proteins that direct this sequestration process have remained mysterious. This study reveals SPE-18 as an intrinsically disordered protein that that is essential for MSP assembly within FBs. In spe-18 mutant spermatocytes, MSP remains cytosolic, and the cells arrest in meiosis. In wildtype spermatocytes, SPE-18 localizes to pre-FB complexes and functions with the kinase SPE-6 to recruit MSP. Changing patterns of SPE-18 localization revealed unappreciated complexities in FB maturation. Later, within newly individualized spermatids, SPE −18 is rapidly lost, yet SPE-18 loss alone is insufficient for MSP disassembly. Our findings reveal an alternative strategy for sequestering cytoskeletal elements, not as monomers but in localized, bundled polymers. Additionally, these studies provide an important example of disordered proteins promoting ordered cellular structures.Summary StatementIntrinsically disordered proteins are increasingly recognized as key regulators of localized cytoskeletal assembly. Expanding that paradigm, SPE-18 localizes MSP assembly within C. elegans spermatocytes.

scholarly journals Regulation of RNA granule dynamics by phosphorylation of serine-rich, intrinsically disordered proteins in C. elegans

eLife ◽  
2014 ◽  
Vol 3 ◽  
Author(s):  
Jennifer T Wang ◽  
Jarrett Smith ◽  
Bi-Chang Chen ◽  
Helen Schmidt ◽  
Dominique Rasoloson ◽  
...  
Keyword(s):  
Intrinsically Disordered Proteins ◽  
Light Sheet ◽  
Disordered Proteins ◽  
Liquid Droplets ◽  
P Granules ◽  
C Elegans ◽  
Rna Granules ◽  
Intrinsically Disordered ◽  
Light Sheet Microscopy

RNA granules have been likened to liquid droplets whose dynamics depend on the controlled dissolution and condensation of internal components. The molecules and reactions that drive these dynamics in vivo are not well understood. In this study, we present evidence that a group of intrinsically disordered, serine-rich proteins regulate the dynamics of P granules in C. elegans embryos. The MEG (maternal-effect germline defective) proteins are germ plasm components that are required redundantly for fertility. We demonstrate that MEG-1 and MEG-3 are substrates of the kinase MBK-2/DYRK and the phosphatase PP2APPTR−½. Phosphorylation of the MEGs promotes granule disassembly and dephosphorylation promotes granule assembly. Using lattice light sheet microscopy on live embryos, we show that GFP-tagged MEG-3 localizes to a dynamic domain that surrounds and penetrates each granule. We conclude that, despite their liquid-like behavior, P granules are non-homogeneous structures whose assembly in embryos is regulated by phosphorylation.

scholarly journals Germ Granules Coordinate RNA-based Epigenetic Inheritance Pathways

2019 ◽  
Author(s):  
Anne E. Dodson ◽  
Scott Kennedy
Keyword(s):  
Intrinsically Disordered Proteins ◽  
Epigenetic Inheritance ◽  
Disordered Proteins ◽  
Wild Type ◽  
Granule Formation ◽  
Phase Separations ◽  
C Elegans ◽  
Intrinsically Disordered ◽  
Germ Granules ◽  
Systemic Rnai

AbstractGerm granules are biomolecular condensates that promote germ cell totipotency in most, if not all, animals. In C. elegans, MEG-3 and MEG-4 are two intrinsically disordered proteins that are redundantly required for the phase separations that drive germ granule assembly in germline blastomeres. Here, we show that animals lacking MEG-3/4 exhibit defects in dsRNA-mediated gene silencing (RNAi) that are due, at least in part, to defects in systemic RNAi. Interestingly, these RNAi defects are transgenerationally disconnected from meg-3/4 genotype: RNAi defects do not arise until 5-9 generations after animals become mutant for meg-3/4, and RNAi defects persist for 9-11 generations after meg-3/4 genotype is restored to wild type. Similar non-Mendelian patterns of inheritance are associated with other mutations that disrupt germ granule formation, indicating that germ granule disruption is the likely cause of genotype/phenotype disconnects. Loss of germ granules is associated with the production of aberrant populations of endogenous siRNAs, which, remarkably, are propagated for ≅10 generations in wild-type descendants of animals that lacked germ granules. sid-1, which encodes a factor required for systemic RNAi in C. elegans, is inappropriately and heritably silenced by aberrantly expressed sid-1 endogenous siRNAs, suggesting that transgenerational silencing of sid-1 likely underlies the heritable defect in RNAi. We conclude that one function of germ granules is to organize RNA-based epigenetic inheritance pathways and that failure to assemble germ granules has consequences that persist across many generations.

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