scholarly journals Multivalent weak interactions between assembly units drive synaptonemal complex formation

2020 ◽  
Vol 219 (5) ◽  
Author(s):  
Zhenguo Zhang ◽  
Songbo Xie ◽  
Ruoxi Wang ◽  
Shuqun Guo ◽  
Qiuchen Zhao ◽  
...  
Keyword(s):  
Synaptonemal Complex ◽  
Weak Interactions ◽  
Meiotic Chromosome ◽  
Expression Patterns ◽  
Dynamic Structure ◽  
Intrinsically Disordered ◽  
Intrinsically Disordered Regions ◽  
Synaptonemal Complex Formation ◽  
Regulatory Functions

The synaptonemal complex (SC) is an ordered but highly dynamic structure assembled between homologous chromosomes to control interhomologous crossover formation, ensuring accurate meiotic chromosome segregation. However, the mechanisms regulating SC assembly and dynamics remain unclear. Here, we identified two new SC components, SYP-5 and SYP-6, in Caenorhabditis elegans that have distinct expression patterns and form distinct SC assembly units with other SYPs through stable interactions. SYP-5 and SYP-6 exhibit diverse in vivo SC regulatory functions and distinct phase separation properties in cells. Charge-interacting elements (CIEs) are enriched in SC intrinsically disordered regions (IDRs), and IDR deletion or CIE removal confirmed a requirement for these elements in SC regulation. Our data support the theory that multivalent weak interactions between the SC units drive SC formation and that CIEs confer multivalency to the assembly units.

scholarly journals The arrested state of processing bodies supports mRNA regulation in early development

2021 ◽  
Author(s):  
M. Sankaranarayanan ◽  
Ryan J. Emenecker ◽  
Marcus Jahnel ◽  
Irmela R. E. A. Trussina ◽  
Matt Wayland ◽  
...  
Keyword(s):  
Physical Properties ◽  
Electrostatic Interactions ◽  
Processing Bodies ◽  
P Bodies ◽  
Intrinsically Disordered ◽  
Intrinsically Disordered Regions ◽  
Dead Box ◽  
Premature Release ◽  
Liquid Liquid Phase Separation

ABSTRACTBiomolecular condensates that form via liquid-liquid phase separation can exhibit diverse physical states. Despite considerable progress, the relevance of condensate physical states forin vivobiological function remains limited. Here, we investigated the physical properties ofin vivoprocessing bodies (P bodies) and their impact on mRNA storage in matureDrosophilaoocytes. We show that the conserved DEAD-box RNA helicase Me31B forms P body condensates which adopt a less dynamic, arrested physical state. We demonstrate that structurally distinct proteins and hydrophobic and electrostatic interactions, together with RNA and intrinsically disordered regions, regulate the physical properties of P bodies. Finally, using live imaging, we show that the arrested state of P bodies is required to prevent the premature release ofbicoid(bcd) mRNA, a body axis determinant, and that P body dissolution leads tobcdrelease. Together, this work establishes a role for arrested states of biomolecular condensates in regulating cellular function in a developing organism.

scholarly journals Handcuffing intrinsically disordered regions in Mlh1-Pms1 disrupts mismatch repair

2021 ◽  
Author(s):  
Christopher M. Furman ◽  
Ting-Yi Wang ◽  
Qiuye Zhao ◽  
Kumar Yugandhar ◽  
Haiyuan Yu ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Mismatch Repair ◽  
Cross Linking ◽  
Dna Mismatch ◽  
Intrinsically Disordered ◽  
Intrinsically Disordered Regions ◽  
On Demand ◽  
Transient Loss ◽  
Disordered Regions

AbstractThe DNA mismatch repair (MMR) factor Mlh1-Pms1 contains long intrinsically disordered regions (IDRs). While essential for MMR, their exact functions remain elusive. We performed cross-linking mass spectrometry to identify the major interactions within the Mlh1-Pms1 heterodimer and used this information to insert FRB and FKBP dimerization domains into the IDRs of Mlh1 and Pms1. Yeast bearing these constructs were grown with rapamycin to induce dimerization. Strains containing FRB and FKBP domains in the Mlh1 IDR displayed complete MMR defects when grown with rapamycin, but removing rapamycin restored MMR functions. Furthermore, linking the Mlh1 and Pms1 IDRs through FRB-FKBP dimerization disrupted Mlh1-Pms1 binding to DNA, inappropriately activated Mlh1-Pms1, and caused MMR defects in vivo. We conclude that dynamic and coordinated rearrangements of the MLH IDRs regulate how the complex clamps DNA to catalyze MMR. The application of the FRB-FKBP dimerization system to interrogate in vivo functions of a critical repair complex will be useful for probing IDRs in diverse enzymes and to probe transient loss of MMR on demand.

scholarly journals Single-embryo phosphoproteomics reveals the importance of intrinsic disorder in cell cycle dynamics

2021 ◽  
Author(s):  
Juan Manuel Valverde ◽  
Geronimo Dubra ◽  
Henk van den Toorn ◽  
Guido van Mierlo ◽  
Michiel Vermeulen ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Intrinsically Disordered Proteins ◽  
Protein Complexes ◽  
Disordered Proteins ◽  
Cell Cycles ◽  
Intrinsically Disordered ◽  
Intrinsically Disordered Regions ◽  
Egg Extracts ◽  
Cell Cycle Dynamics

Switch-like cyclin-dependent kinase (CDK)-1 activation is thought to underlie the abruptness of mitotic onset, but how CDKs can simultaneously phosphorylate many diverse substrates is unknown, and direct evidence for such phosphorylation dynamics in vivo is lacking. Here, we analysed protein phosphorylation states in single Xenopus embryos throughout synchronous cell cycles. Over a thousand phosphosites were dynamic in vivo, and assignment of cell cycle phases using egg extracts revealed hundreds of S-phase phosphorylations. Targeted phosphoproteomics in single embryos showed switch-like mitotic phosphorylation of diverse protein complexes. The majority of cell cycle-regulated phosphosites occurred in CDK consensus motifs, and 72% located to intrinsically disordered regions. Dynamically phosphorylated proteins, and documented substrates of cell cycle kinases, are significantly more disordered than phosphoproteins in general. Furthermore, 30-50% are components of membraneless organelles. Our results suggest that phosphorylation of intrinsically disordered proteins by cell cycle kinases, particularly CDKs, allows switch-like mitotic cellular reorganisation.

scholarly journals Proteome-wide signatures of function in highly diverged intrinsically disordered regions

2019 ◽  
Author(s):  
Taraneh Zarin ◽  
Bob Strome ◽  
Alex N Nguyen Ba ◽  
Simon Alberti ◽  
Julie D Forman-Kay ◽  
...  
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequences ◽  
Functional Annotations ◽  
Intrinsically Disordered ◽  
Intrinsically Disordered Regions ◽  
Molecular Features ◽  
Primary Amino ◽  
Function Relationship ◽  
Disordered Regions

AbstractIntrinsically disordered regions make up a large part of the proteome, but the sequence-to-function relationship in these regions is poorly understood, in part because the primary amino acid sequences of these regions are poorly conserved in alignments. Here we use an evolutionary approach to detect molecular features that are preserved in the amino acid sequences of orthologous intrinsically disordered regions. We find that most disordered regions contain multiple molecular features that are preserved, and we define these as “evolutionary signatures” of disordered regions. We demonstrate that intrinsically disordered regions with similar evolutionary signatures can rescue functionin vivo,and that groups of intrinsically disordered regions with similar evolutionary signatures are strongly enriched for functional annotations and phenotypes. We propose that evolutionary signatures can be used to predict function for many disordered regions from their amino acid sequences.

scholarly journals Coilin oligomerization and remodeling by Nopp140 reveals a hybrid assembly mechanism for Cajal bodies

2021 ◽  
Author(s):  
Edward Courchaine ◽  
Martin Machyna ◽  
Korinna Straube ◽  
Sarah Sauyet ◽  
Jade Enright ◽  
...  
Keyword(s):  
Mutational Analysis ◽  
Protein Complexes ◽  
Scaffolding Protein ◽  
Single Amino Acid ◽  
Cajal Bodies ◽  
Intrinsically Disordered ◽  
Intrinsically Disordered Regions ◽  
Assembly Mechanism ◽  
Functional Components

Cajal bodies (CBs) are ubiquitous nuclear membraneless organelles (MLOs) that promote efficient biogenesis of RNA-protein complexes. Depletion of the CB scaffolding protein coilin is lethal for vertebrate embryogenesis, making CBs a strong model for understanding the structure and function of MLOs. Although it is assumed that CBs form through biomolecular condensation, the biochemical and biophysical principles that govern CB dynamics have eluded study. Here, we identify features of the coilin protein that drive CB assembly and shape. Focusing on coilin's N-terminal domain (NTD), we discovered its unexpected capacity for oligomerization in vivo. Single amino acid mutational analysis of coilin revealed distinct molecular interactions required for oligomerization and binding to the Nopp140 ligand, which facilitates CB assembly. We demonstrate that the intrinsically disordered regions of Nopp140 have substantial condensation properties and suggest that Nopp140 binding thereby remodels stable coilin oligomers to form a particle that recruits other functional components.

Synaptonemal complex formation in male scorpions exhibiting achiasmate meiosis and structural heterozygosity

Genome ◽  
1990 ◽  
Vol 33 (6) ◽  
pp. 914-926 ◽  
Author(s):  
Catherine M. Shanahan ◽  
David L. Hayman
Keyword(s):  
Complex Formation ◽  
Synaptonemal Complex ◽  
Meiotic Chromosome ◽  
Male Meiosis ◽  
Late Prophase ◽  
Maintenance System ◽  
Structural Heterozygosity ◽  
Synaptonemal Complex Formation ◽  
And Inversion ◽  
Metaphase I

Synaptonemal complex (SC) formation was studied in testicular material from individuals of a number of species from two families of Australian scorpions; Buthidae and Scorpionidae. These scorpions exhibit unusual cytogenetic features including achiasmate male meiosis, interchange heterozygosity, and centromeric fusion–fission and inversion heterozygosity. The synaptic behaviour of chromosomes involved in these rearrangements was studied from zygotene to metaphase I, using both meiotic chromosome preparations and techniques for examination of the SCs. Multivalent associations present during the achiasmate meiosis of both buthid and scorpionid scorpions are retained from prophase to metaphase I, unlike those present in polyploid achiasmate Bombyx females. Further evidence suggests that synaptic adjustment does not occur generally in achiasmate scorpionid inversion heterozygotes. However, for some inversions, pairing is seen to become more heterosynaptic from late prophase to metaphase I and this may be related to the pairing maintenance system during achiasmate meiosis in these specialized organisms.Key words: synaptonemal complex, achiasmate meiosis, heterozygosity, interchange, inversion.

scholarly journals Molecular and Biochemical Techniques for Deciphering p53-MDM2 Regulatory Mechanisms

Biomolecules ◽  
2020 ◽  
Vol 11 (1) ◽  
pp. 36
Author(s):  
Konstantinos Karakostis ◽  
Ignacio López ◽  
Ana M. Peña-Balderas ◽  
Robin Fåhareus ◽  
Vanesa Olivares-Illana
Keyword(s):  
Protein Complexes ◽  
Post Translational Modifications ◽  
Intrinsically Disordered ◽  
Advantages And Disadvantages ◽  
Intrinsically Disordered Regions ◽  
Multiple Partners ◽  
Allosteric Interactions ◽  
Spatio Temporal

The p53 and Mouse double minute 2 (MDM2) proteins are hubs in extensive networks of interactions with multiple partners and functions. Intrinsically disordered regions help to adopt function-specific structural conformations in response to ligand binding and post-translational modifications. Different techniques have been used to dissect interactions of the p53-MDM2 pathway, in vitro, in vivo, and in situ each having its own advantages and disadvantages. This review uses the p53-MDM2 to show how different techniques can be employed, illustrating how a combination of in vitro and in vivo techniques is highly recommended to study the spatio-temporal location and dynamics of interactions, and to address their regulation mechanisms and functions. By using well-established techniques in combination with more recent advances, it is possible to rapidly decipher complex mechanisms, such as the p53 regulatory pathway, and to demonstrate how protein and nucleotide ligands in combination with post-translational modifications, result in inter-allosteric and intra-allosteric interactions that govern the activity of the protein complexes and their specific roles in oncogenesis. This promotes elegant therapeutic strategies that exploit protein dynamics to target specific interactions.

scholarly journals RNA inhibits dMi-2/CHD4 chromatin binding and nucleosome remodelling

2021 ◽  
Author(s):  
Ikram Ullah ◽  
Clemens Thoelken ◽  
Yichen Zhong ◽  
Mara John ◽  
Oliver Rossbach ◽  
...  
Keyword(s):  
Genome Integrity ◽  
Chromatin Binding ◽  
Human Homolog ◽  
Rna Molecules ◽  
Intrinsically Disordered ◽  
Intrinsically Disordered Regions ◽  
Repressive Chromatin ◽  
Rnase Digestion ◽  
Nucleotide Resolution

The ATP-dependent nucleosome remodeller Mi-2/CHD4 broadly modulates epigenetic landscapes to repress transcription and to maintain genome integrity. Here we use individual nucleotide resolution crosslinking and immunoprecipitation (iCLIP) to show that Drosophila Mi-2 associates with thousands of mRNA molecules in vivo. Biochemical data reveal that recombinant dMi-2 preferentially binds to G-rich RNA molecules using two intrinsically disordered regions of previously undefined function. Pharmacological inhibition of transcription and RNase digestion approaches establish that RNA inhibits the association of dMi-2 with chromatin. We also show that RNA inhibits dMi-2-mediated nucleosome mobilization by competing with the nucleosome substrate. Importantly, this activity is shared by CHD4, the human homolog of dMi-2, strongly suggesting that RNA-mediated regulation of remodeller activity is an evolutionary conserved mechanism. Our data support a model in which RNA serves to protect actively transcribed regions of the genome from dMi-2/CHD4mediated establishment of repressive chromatin structures.

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