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.

scholarly journals Recruitment of mRNAs to P granules by gelation with intrinsically-disordered proteins

2019 ◽  
Author(s):  
Chih-Yung S. Lee ◽  
Andrea Putnam ◽  
Tu Lu ◽  
Shuaixin He ◽  
John Paul T. Ouyang ◽  
...  
Keyword(s):  
Cell Fate ◽  
Intrinsically Disordered Proteins ◽  
Intrinsically Disordered Protein ◽  
Disordered Proteins ◽  
P Granules ◽  
C Elegans ◽  
Rna Granules ◽  
Intrinsically Disordered ◽  
Cytoplasmic Rna ◽  
Germ Granules

AbstractAnimals with germ plasm assemble cytoplasmic RNA granules (germ granules) that segregate with the embryonic germ lineage. How germ granules assemble and recruit RNA is not well understood. Here we characterize the assembly and RNA composition of the germ (P) granules of C. elegans. ∼500 maternal mRNAs are recruited into P granules by a sequence independent mechanism that favors mRNAs with low ribosome coverage. Translational activation correlates temporally with P granule exit for two mRNAs that code for germ cell fate regulators. mRNAs are recruited into the granules by MEG-3, an intrinsically disordered protein that condenses with RNA to form nanoscale gels. Our observations reveal parallels between germ granules and stress granules and suggest that cytoplasmic RNA granules are reversible super-assemblies of nanoscale RNA-protein gel condensates.

scholarly journals Intrinsically Disordered Proteins as Regulators of Transient Biological Processes and as Untapped Drug Targets

Molecules ◽  
2021 ◽  
Vol 26 (8) ◽  
pp. 2118
Author(s):  
Yusuke Hosoya ◽  
Junko Ohkanda
Keyword(s):  
Drug Targets ◽  
Intrinsically Disordered Proteins ◽  
Dynamic Control ◽  
Disordered Proteins ◽  
Biological Processes ◽  
Phase Separations ◽  
Cellular Processes ◽  
Intrinsically Disordered ◽  
New Drug ◽  
Liquid Phase Separations

Intrinsically disordered proteins (IDPs) are critical players in the dynamic control of diverse cellular processes, and provide potential new drug targets because their dysregulation is closely related to many diseases. This review focuses on several medicinal studies that have identified low-molecular-weight inhibitors of IDPs. In addition, clinically relevant liquid–liquid phase separations—which critically involve both intermolecular interactions between IDPs and their posttranslational modification—are analyzed to understand the potential of IDPs as new drug targets.

scholarly journals Intrinsically disordered caldesmon binds calmodulin via the “buttons on a string” mechanism

PeerJ ◽  
2015 ◽  
Vol 3 ◽  
pp. e1265 ◽  
Author(s):  
Sergei E. Permyakov ◽  
Eugene A. Permyakov ◽  
Vladimir N. Uversky
Keyword(s):  
Local Structure ◽  
Intrinsically Disordered Proteins ◽  
String Model ◽  
Electrostatic Attraction ◽  
Disordered Proteins ◽  
Wild Type ◽  
Intrinsically Disordered ◽  
Tryptophan Residues ◽  
Specific Packing ◽  
Oppositely Charged

We show here that chicken gizzard caldesmon (CaD) and its C-terminal domain (residues 636–771, CaD136) are intrinsically disordered proteins. The computational and experimental analyses of the wild type CaD136and series of its single tryptophan mutants (W674A, W707A, and W737A) and a double tryptophan mutant (W674A/W707A) suggested that although the interaction of CaD136with calmodulin (CaM) can be driven by the non-specific electrostatic attraction between these oppositely charged molecules, the specificity of CaD136-CaM binding is likely to be determined by the specific packing of important CaD136tryptophan residues at the CaD136-CaM interface. It is suggested that this interaction can be described as the “buttons on a charged string” model, where the electrostatic attraction between the intrinsically disordered CaD136and the CaM is solidified in a “snapping buttons” manner by specific packing of the CaD136“pliable buttons” (which are the short segments of fluctuating local structure condensed around the tryptophan residues) at the CaD136-CaM interface. Our data also show that all three “buttons” are important for binding, since mutation of any of the tryptophans affects CaD136-CaM binding and since CaD136remains CaM-buttoned even when two of the three tryptophans are mutated to alanines.

scholarly journals A Family of Small Intrinsically Disordered Proteins Involved in Flagellum-Dependent Motility inSalmonella enterica

2018 ◽  
Vol 201 (2) ◽  
Author(s):  
Tamiko Oguri ◽  
Youjeong Kwon ◽  
Jerry K. K. Woo ◽  
Gerd Prehna ◽  
Hyun Lee ◽  
...  
Keyword(s):  
Intrinsically Disordered Proteins ◽  
Expression Profiles ◽  
Functional Characterization ◽  
Disordered Proteins ◽  
Wild Type ◽  
Content Type ◽  
Cellular Pathway ◽  
Intrinsically Disordered ◽  
Small Proteins ◽  
Wide Range

ABSTRACTBy screening a collection ofSalmonellamutants deleted for genes encoding small proteins of ≤60 amino acids, we identified three paralogous small genes (ymdF,STM14_1829, andyciG) required for wild-type flagellum-dependent swimming and swarming motility. TheymdF,STM14_1829, andyciGgenes encode small proteins of 55, 60, and 60 amino acid residues, respectively. A bioinformatics analysis predicted that these small proteins are intrinsically disordered proteins, and circular dichroism analysis of purified recombinant proteins confirmed that all three proteins are unstructured in solution. A mutant deleted for STM14_1829 showed the most severe motility defect, indicating that among the three paralogs, STM14_1829 is a key protein required for wild-type motility. We determined that relative to the wild type, the expression of the flagellin protein FliC is lower in the ΔSTM14_1829mutant due to the downregulation of theflhDCoperon encoding the FlhDC master regulator. By comparing the gene expression profiles between the wild-type and ΔSTM14_1829strains via RNA sequencing, we found that the gene encoding the response regulator PhoP is upregulated in the ΔSTM14_1829mutant, suggesting the indirect repression of theflhDCoperon by the activated PhoP. Homologs of STM14_1829 are conserved in a wide range of bacteria, includingEscherichia coliandPseudomonas aeruginosa. We showed that the inactivation of STM14_1829 homologs inE. coliandP. aeruginosaalso alters motility, suggesting that this family of small intrinsically disordered proteins may play a role in the cellular pathway(s) that affects motility.IMPORTANCEThis study reports the identification of a novel family of small intrinsically disordered proteins that are conserved in a wide range of flagellated and nonflagellated bacteria. Although this study identifies the role of these small proteins in the scope of flagellum-dependent motility inSalmonella, they likely play larger roles in a more conserved cellular pathway(s) that indirectly affects flagellum expression in the case of motile bacteria. Small intrinsically disordered proteins have not been well characterized in prokaryotes, and the results of our study provide a basis for their detailed functional characterization.

scholarly journals Ion Mobility Mass Spectrometry Uncovers the Impact of the Patterning of Oppositely Charged Residues on the Conformational Distributions of Intrinsically Disordered Proteins

2018 ◽  
Author(s):  
Rebecca Beveridge ◽  
Lukasz Migas ◽  
Rahul Das ◽  
Rohit Pappu ◽  
Richard Kriwacki ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Ion Mobility ◽  
Intrinsically Disordered Proteins ◽  
Disordered Proteins ◽  
Ion Mobility Mass Spectrometry ◽  
Conformational Heterogeneity ◽  
Wild Type ◽  
Intrinsically Disordered ◽  
Charged Residues ◽  
Oppositely Charged

The global dimensions and amplitudes of conformational fluctuations of intrinsically disordered proteins are governed, in part, by the linear segregation versus clustering of oppositely charged residues within the primary sequence. Ion Mobility-Mass Spectrometry (IM-MS) affords unique advantages for probing the conformational consequences of the linear patterning of oppositely charged residues because it measures and separates proteins electrosprayed from solution on the basis of charge and shape. Here, we use IM-MS to measure the conformational consequences of charge patterning on the C-terminal intrinsically disordered region (p27 IDR) of the cell cycle inhibitory protein p27<sup>Kip1</sup>. We report the range of charge states and accompanying collisional cross section distributions for wild-type p27 IDR and two variants with identical amino acid compositions, k14 and k56, distinguished by the extent of linear mixing versus segregation of oppositely charged residues. Wild-type p27 IDR (k31) and k14 where the oppositely charged residues are more evenly distributed, exhibit a broad distribution of charge states. This is concordant with high degrees of conformational heterogeneity in solution. By contrast, k56 with linear segregation of oppositely charged residues, leads to limited conformational heterogeneity and a narrow distribution of charged states. Molecular dynamics simulations demonstrate that the interplay between chain solvation and intra-chain interactions (self-solvation) leads to conformational distributions that are modulated by salt concentration, with the wild-type sequence showing the most sensitivity to changes in salt concentration. These results suggest that the charge patterning within the wild-type p27 IDR may be optimized to sample both highly solvated and self-solvated conformational states.

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 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.

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