scholarly journals Finding the Correct Partner: The Meiotic Courtship

Scientifica ◽  
2012 ◽  
Vol 2012 ◽  
pp. 1-14 ◽  
Author(s):  
Tomás Naranjo
Keyword(s):  
Conformational Changes ◽  
Protein Complex ◽  
Homology Search ◽  
Homology Detection ◽  
Homologous Chromosomes ◽  
Meiotic Process ◽  
Mismatch Correction ◽  
Non Coding Rna ◽  
Relevant Role ◽  
Chromosome Movements

Homologous chromosomes are usually separated at the entrance of meiosis; how they become paired is one of the outstanding mysteries of the meiotic process. Reduction of spacing between homologues makes possible the occurrence of chromosomal interactions leading to homology detection and the formation of bivalents. In many organisms, telomere-led chromosome movements are generated that bring homologues together. Additional movements produced by chromatin conformational changes at early meiosis may also facilitate homologous contacts. Organisms used in the study of meiosis show a surprising variety of strategies for homology detection. In dipterans, homologous chromosomes remain paired throughout most of development. Pairing seems to arise as a balance between promoter and suppressor pairing genes. Some fungi, plants and animals, use mechanisms based on recombinational interactions. Other mechanisms leading to homology search are recombination-independent and require specialized pairing sites. In the wormCaenorhabditis elegans, each chromosome carries a pairing center consisting of a chromosome-specific DNA-protein complex, and in the fission yeastSchizosaccharomyces pombe, thesme2locus encodes a meiosis-specific non-coding RNA that mediates on homologous recognition. In addition, mismatch correction plays a relevant role, especially in polyploids, which evolved genetic systems that suppress pairing between non-homologous related (homoeologus) chromosomes.

Protein Flexibility Catalyzes a Cell Signaling Reaction of the Ras-GAP Complex

2019 ◽  
Author(s):  
Keiei Kumon ◽  
Masahiro Higashi ◽  
Shinji Saito ◽  
Shigehiko Hayashi
Keyword(s):  
Cell Signaling ◽  
Conformational Changes ◽  
Catalytic Reaction ◽  
Protein Complex ◽  
Enzyme Mechanism ◽  
Activation Free Energy ◽  
Chemical Catalysis ◽  
Simple Chemical ◽  
A Cell ◽  
Enzyme Molecules

Many enzyme molecules exhibit characteristic global and slow dynamics which furnish them with allostery realizing remarkable molecular functionalities more than simple chemical catalysis. However, molecular mechanism of a catalytic reaction associated with the molecular flexibility of enzymes is not well-understood. Here we report a hybrid molecular simulation study on GTPase activity of a Ras-GAP protein complex for cell signaling termination. We unveiled that extensive conformational changes of the protein complex and exclusion of internal water molecules are induced upon the transition state (TS) formation in the catalytic reaction and significantly lower the reaction activation free energy. We also revealed that tumor-related mutations perturb those conformational changes upon the TS formation, leading to reduction of the catalytic activity. The findings of the remarkably dynamic protein conformation directly linking to the catalytic reaction have broad implications for understanding of enzyme mechanism and for developments of allosteric drugs and novel catalysts.

scholarly journals The Role of Extracellular Vesicles as Shuttles of RNA and Their Clinical Significance as Biomarkers in Hepatocellular Carcinoma

Genes ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 902
Author(s):  
Eva Costanzi ◽  
Carolina Simioni ◽  
Gabriele Varano ◽  
Cinzia Brenna ◽  
Ilaria Conti ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Extracellular Vesicles ◽  
Tumor Metastasis ◽  
Biological Processes ◽  
Rna Molecules ◽  
Expression Of Genes ◽  
Non Coding Rna ◽  
Donor Cells ◽  
Relevant Role

Extracellular vesicles (EVs) have attracted interest as mediators of intercellular communication following the discovery that EVs contain RNA molecules, including non-coding RNA (ncRNA). Growing evidence for the enrichment of peculiar RNA species in specific EV subtypes has been demonstrated. ncRNAs, transferred from donor cells to recipient cells, confer to EVs the feature to regulate the expression of genes involved in differentiation, proliferation, apoptosis, and other biological processes. These multiple actions require accuracy in the isolation of RNA content from EVs and the methodologies used play a relevant role. In liver, EVs play a crucial role in regulating cell–cell communications and several pathophysiological events in the heterogeneous liver class of cells via horizontal transfer of their cargo. This review aims to discuss the rising role of EVs and their ncRNAs content in regulating specific aspects of hepatocellular carcinoma development, including tumorigenesis, angiogenesis, and tumor metastasis. We analyze the progress in EV-ncRNAs’ potential clinical applications as important diagnostic and prognostic biomarkers for liver conditions.

scholarly journals Ndj1, a Telomere-Associated Protein, Promotes Meiotic Recombination in Budding Yeast

2006 ◽  
Vol 26 (10) ◽  
pp. 3683-3694 ◽  
Author(s):  
Hsin-Yen Wu ◽  
Sean M. Burgess
Keyword(s):  
Meiotic Recombination ◽  
Double Strand Breaks ◽  
Homology Search ◽  
Strand Breaks ◽  
Homologous Chromosomes ◽  
Synaptonemal Complex Formation ◽  
Strand Invasion ◽  
Double Holliday Junction ◽  
Meiosis I

ABSTRACT Dynamic telomere repositioning is a prominent feature of meiosis. Deletion of a telomere-associated protein, Ndj1, results in the failure of both attachment and clustering of telomeres at the nuclear envelope and delays several landmarks of meiosis I, such as pairing, synaptonemal complex formation, and timing of the meiosis I division. We explored the role of Ndj1 in meiotic recombination, which occurs through the formation and repair of programmed double-strand breaks. The ndj1Δ mutation allows for the formation of the first detectable strand invasion intermediate (i.e., single-end invasion) with wild-type kinetics; however, it confers a delay in the formation of the double-Holliday junction intermediate and both crossover and noncrossover products. These results challenge the widely held notion that clustering of telomeres in meiosis promotes the ability of homologous chromosomes to find one another in budding Saccharomyces cerevisiae. We propose that an Ndj1-dependent function is critical for stabilizing analogous strand invasion intermediates that exist in two separate branches of the bifurcated pathway, leading to either noncrossover or crossover formation. These findings provide a link between telomere dynamics and a distinct mechanistic step of meiotic recombination that follows the homology search.

scholarly journals Mechanistic insight into crossing over during mouse meiosis

2019 ◽  
Author(s):  
Shaun E. Peterson ◽  
Scott Keeney ◽  
Maria Jasin
Keyword(s):  
Inbred Strains ◽  
Strand Break ◽  
Crossing Over ◽  
Recombination Suppression ◽  
Heteroduplex Dna ◽  
Homologous Chromosomes ◽  
Mismatch Correction ◽  
D Loop ◽  
Loop Migration ◽  
Dna Ends

SUMMARYCharacteristics of heteroduplex DNA illuminate how strands exchange during homologous recombination, but mismatch correction can obscure them. To investigate recombination mechanisms, meiotic crossover products were analyzed at two hotspots in Msh2–/– mice containing homologous chromosomes derived from inbred strains. Recombination frequencies were unchanged in the mutant, implying that MSH2-dependent recombination suppression does not occur at this level of diversity. However, a substantial fraction of crossover products retained heteroduplex DNA in the absence of MSH2, and some also had multiple switches between parental markers suggestive of MSH2-independent correction. Recombinants appeared to reflect a biased orientation of crossover resolution, possibly stemming from asymmetry at DNA ends established in earlier intermediates. Many crossover products showed no evidence of heteroduplex DNA, suggesting dismantling by D-loop migration. Unlike the complexity of crossovers in yeast, these two modifications of the original double-strand break repair model may be sufficient to explain most meiotic crossing over in mice.

scholarly journals Metagenomic Noncoding RNA Profiling and Biomarker Discovery

2020 ◽  
Author(s):  
Ben Liu ◽  
Sirisha Thippabhotla ◽  
Jun Zhang ◽  
Cuncong Zhong
Keyword(s):  
Gut Microbiome ◽  
Noncoding Rna ◽  
Biomarker Discovery ◽  
Gene Expression Regulation ◽  
De Novo ◽  
Structural Information ◽  
Noncoding Rnas ◽  
Homology Search ◽  
Metagenomic Sequencing ◽  
Homology Detection

AbstractNoncoding RNA plays important regulatory and functional roles in microorganisms, such as gene expression regulation, signaling, protein synthesis, and RNA processing. Given its essential role in microbial physiology, it is natural to question whether we can use noncoding RNAs as biomarkers to distinguish among environments under different biological conditions, such as those between healthy versus disease status. The current metagenomic sequencing technology primarily generates short reads, which contain incomplete structural information that may complicate noncoding RNA homology detection. On the other hand, de novo assembly of the metagenomics sequencing data remains fragmentary and has a risk of missing low-abundant noncoding RNAs. To tackle these challenges, we have developed DRAGoM (Detection of RNA using Assembly Graph from Metagenomics data), a novel noncoding RNA homology search algorithm. DRAGoM operates on a metagenome assembly graph, rather than on unassembled reads or assembled contigs. Our benchmark experiments show DRAGoM’s improved performance and robustness over the traditional approaches. We have further demonstrated DRAGoM’s real-world applications in disease characterization via analyzing a real case-control gut microbiome dataset for Type-2 diabetes (T2D). DRAGoM revealed potential ncRNA biomarkers that can clearly separate the T2D gut microbiome from those of healthy controls. DRAGoM is freely available from https://github.com/benliu5085/DRAGoM.

scholarly journals Repurposing of Synaptonemal Complex Proteins for Kinetochores in Kinetoplastida

2021 ◽  
Author(s):  
Eelco C. Tromer ◽  
Thomas A. Wemyss ◽  
Ross F. Waller ◽  
Bungo Akiyoshi
Keyword(s):  
Gene Family ◽  
Synaptonemal Complex ◽  
Chromosome Segregation ◽  
Homology Detection ◽  
Homologous Chromosomes ◽  
Chromosome Synapsis ◽  
Core Set ◽  
History Of ◽  
Macromolecular Protein ◽  
Axial Element

AbstractChromosome segregation in eukaryotes is driven by a macromolecular protein complex called the kinetochore that connects centromeric DNA to microtubules of the spindle apparatus. Kinetochores in well-studied model eukaryotes consist of a core set of proteins that are broadly conserved among distant eukaryotic phyla. In contrast, unicellular flagellates of the class Kinetoplastida have a unique set of kinetochore components. The evolutionary origin and history of these kinetochores remains unknown. Here, we report evidence of homology between three kinetoplastid kinetochore proteins KKT16–18 and axial element components of the synaptonemal complex, such as the SYCP2:SYCP3 multimers found in vertebrates. The synaptonemal complex is a zipper-like structure that assembles between homologous chromosomes during meiosis to promote recombination. Using a sensitive homology detection protocol, we identify divergent orthologues of SYCP2:SYCP3 in most eukaryotic supergroups including other experimentally established axial element components, such as Red1 and Rec10 in budding and fission yeast, and the ASY3:ASY4 multimers in land plants. These searches also identify KKT16–18 as part of this rapidly evolving protein family. The widespread presence of the SYCP2-3 gene family in extant eukaryotes suggests that the synaptonemal complex was likely present in the last eukaryotic common ancestor. We found at least twelve independent duplications of the SYCP2-3 gene family throughout the eukaryotic tree of life, providing opportunities for new functional complexes to arise, including KKT16–18 in Trypanosoma brucei. We propose that kinetoplastids evolved their unique kinetochore system by repurposing meiotic components of the chromosome synapsis and homologous recombination machinery that were already present in early eukaryotes.

scholarly journals High-Speed AFM directly visualizes conformational dynamics of the HIV-Vif protein complex

2020 ◽  
Author(s):  
Yangang Pan ◽  
Luda S. Shlyakhtenko ◽  
Yuri L. Lyubchenko
Keyword(s):  
Conformational Changes ◽  
Protein Complex ◽  
High Speed ◽  
Conformational Dynamics ◽  
Md Simulations ◽  
Time Lapse ◽  
Hiv Treatment ◽  
X Ray Crystallography ◽  
Host Cell Proteins ◽  
Virus Survival

AbstractViral infectivity factor (Vif) is a protein that is essential for the replication of the HIV-1 virus. The key function of Vif is to disrupt the antiviral activity of APOBEC3 proteins, which mutate viral nucleic acids. Inside the cell, Vif binds to the host cell proteins Elongin-C, Elongin-B, and CBF-β, forming a four-protein complex called VCBC. The structure of VCBC in complex with the Cullin5 (Cul5) protein has been solved by X-ray crystallography, and recently, using molecular dynamic (MD) simulations, the dynamics of VCBC and VCBC-Cul5 complexes were characterized. Here, we applied time-lapse high-speed atomic force microscopy (HS-AFM) to visualize the conformational changes of the VCBC complex. We determined the three most favorable conformations of the VCBC complex, which we identified as triangle, dumbbell, and globular structures. In addition, we characterized the dynamics of each of these structures. While our data show a very dynamic behavior for all these structures, we found the triangle and dumbbell structures to be the most dynamic. These findings provide insight into the structure and dynamics of the VCBC complex and support further research into the improvement of HIV treatment, as Vif is essential for virus survival in the cell.

scholarly journals Comprehensive analysis of heterotrimeric G-protein complex diversity and their interactions with GPCRs in solution

2015 ◽  
Vol 112 (11) ◽  
pp. E1181-E1190 ◽  
Author(s):  
Matthias Hillenbrand ◽  
Christian Schori ◽  
Jendrik Schöppe ◽  
Andreas Plückthun
Keyword(s):  
G Protein ◽  
G Proteins ◽  
Conformational Changes ◽  
Protein Complex ◽  
Protein Complexes ◽  
Heterotrimeric G Proteins ◽  
Agonist Binding ◽  
Transient Nature ◽  
The Stability ◽  
Neurotensin Receptor 1

Agonist binding to G-protein–coupled receptors (GPCRs) triggers signal transduction cascades involving heterotrimeric G proteins as key players. A major obstacle for drug design is the limited knowledge of conformational changes upon agonist binding, the details of interaction with the different G proteins, and the transmission to movements within the G protein. Although a variety of different GPCR/G protein complex structures would be needed, the transient nature of this complex and the intrinsic instability against dissociation make this endeavor very challenging. We have previously evolved GPCR mutants that display higher stability and retain their interaction with G proteins. We aimed at finding all G-protein combinations that preferentially interact with neurotensin receptor 1 (NTR1) and our stabilized mutants. We first systematically analyzed by coimmunoprecipitation the capability of 120 different G-protein combinations consisting of αi1or αsLand all possible βγ-dimers to form a heterotrimeric complex. This analysis revealed a surprisingly unrestricted ability of the G-protein subunits to form heterotrimeric complexes, including βγ-dimers previously thought to be nonexistent, except for combinations containing β5. A second screen on coupling preference of all G-protein heterotrimers to NTR1 wild type and a stabilized mutant indicated a preference for those Gαi1βγ combinations containing γ1and γ11. Heterotrimeric G proteins, including combinations believed to be nonexistent, were purified, and complexes with the GPCR were prepared. Our results shed new light on the combinatorial diversity of G proteins and their coupling to GPCRs and open new approaches to improve the stability of GPCR/G-protein complexes.

scholarly journals Recombination-independent recognition of DNA homology for meiotic silencing in Neurospora crassa

2021 ◽  
Vol 118 (33) ◽  
pp. e2108664118
Author(s):  
Nicholas Rhoades ◽  
Tinh-Suong Nguyen ◽  
Guillaume Witz ◽  
Germano Cecere ◽  
Thomas Hammond ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Dna Homology ◽  
Meiotic Silencing ◽  
Base Pairs ◽  
Homologous Chromosomes ◽  
Sequence Identity ◽  
Experimental Systems ◽  
Double Stranded Dna ◽  
Dna Fragment ◽  
Homology Recognition

The pairing of homologous chromosomes represents a critical step of meiosis in nearly all sexually reproducing species. In many organisms, pairing involves chromosomes that remain apparently intact. The mechanistic nature of homology recognition at the basis of such pairing is unknown. Using “meiotic silencing by unpaired DNA” (MSUD) as a model process, we demonstrate the existence of a cardinally different approach to DNA homology recognition in meiosis. The main advantage of MSUD over other experimental systems lies in its ability to identify any relatively short DNA fragment lacking a homologous allelic partner. Here, we show that MSUD does not rely on the canonical mechanism of meiotic recombination, yet it is promoted by REC8, a conserved component of the meiotic cohesion complex. We also show that certain patterns of interspersed homology are recognized as pairable during MSUD. Such patterns need to be colinear and must contain short tracts of sequence identity spaced apart at 21 or 22 base pairs. By using these periodicity values as a guiding parameter in all-atom molecular modeling, we discover that homologous DNA molecules can pair by forming quadruplex-based contacts with an interval of 2.5 helical turns. This process requires right-handed plectonemic coiling and additional conformational changes in the intervening double-helical segments. Our results 1) reconcile genetic and biophysical evidence for the existence of direct homologous double-stranded DNA (dsDNA)–dsDNA pairing, 2) identify a role for this process in initiating RNA interference, and 3) suggest that chromosomes can be cross-matched by a precise mechanism that operates on intact dsDNA molecules.

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