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Wiley Interdisciplinary Reviews. RNA 2015Defects in RNA metabolic pathways are well-established causes for neurodegenerative disorders. Several mutations in genes involved in pre-messenger RNA (pre-mRNA) and... (Review)
Review
Defects in RNA metabolic pathways are well-established causes for neurodegenerative disorders. Several mutations in genes involved in pre-messenger RNA (pre-mRNA) and tRNA metabolism, RNA stability and protein translation have been linked to motor neuron diseases. Our study on a mouse carrying a catalytically inactive version of the RNA kinase CLP1, a component of the tRNA splicing endonuclease complex, revealed a neurological disorder characterized by progressive loss of lower spinal motor neurons. Surprisingly, mutant mice accumulate a novel class of tRNA-derived fragments. In addition, patients with homozygous missense mutations in CLP1 (R140H) were recently identified who suffer from severe motor-sensory defects, cortical dysgenesis and microcephaly, and exhibit alterations in transfer RNA (tRNA) splicing. Here, we review functions of CLP1 in different RNA pathways and provide hypotheses on the role of the tRNA splicing machinery in the generation of tRNA fragments and the molecular links to neurodegenerative disorders. We further immerse the biology of tRNA splicing into topics of (t)RNA metabolism and oxidative stress, putting forward the idea that defects in tRNA processing leading to tRNA fragment accumulation might trigger the development of neurodegenerative diseases.
Topics: Animals; Mice; Mutant Proteins; Neurodegenerative Diseases; Oxidative Stress; RNA Splicing; RNA, Transfer; RNA-Binding Proteins; Transcription Factors
PubMed: 25142875
DOI: 10.1002/wrna.1255 -
Scientific Reports Aug 2021Chitosanases can catalyze the release of chitooligosaccharides which have a number of medical applications. Therefore, Chitosanases are good candidates for large-scale...
Chitosanases can catalyze the release of chitooligosaccharides which have a number of medical applications. Therefore, Chitosanases are good candidates for large-scale enzymatic synthesis due to their favorable thermostability properties and high catalytic efficiency. To further improve the thermostability of a chitosanase from Bacillus sp. TS, which has a half-life of 5.32 min, we mutated specific serine residues that we identified as potentially relevant through structure comparison with thermophilic CelA from Clostridium thermocellum. Out of a total of 15 mutants, three, namely S265G, S276A, and S347G, show higher thermostability. Their half-lives at 60 °C were calculated as 34.57 min, 36.79 min and 7.2 min. The K values of S265G, S276A and S347G mutants show substrate binding ability comparable to that of the wild-type enzyme, while the S265G mutant displays a significant decrease of enzymatic activities. Additionally, we studied the synergistic effects of combined mutations, observing that all double mutants and the triple mutant are more stable than the wild-type enzyme and single mutants. Finally, we investigated the mechanisms which might give a reasonable explanation for the improved thermostability via comparative analysis of the resulting 3D structures.
Topics: Bacillus; Catalysis; Enzyme Stability; Glycoside Hydrolases; Hot Temperature; Kinetics; Models, Molecular; Mutant Proteins; Mutation; Protein Conformation
PubMed: 34349190
DOI: 10.1038/s41598-021-95369-w -
ELife Mar 2018Antiviral development is plagued by drug resistance and genetic barriers to resistance are needed. For HIV and hepatitis C virus (HCV), combination therapy has proved...
Antiviral development is plagued by drug resistance and genetic barriers to resistance are needed. For HIV and hepatitis C virus (HCV), combination therapy has proved life-saving. The targets of direct-acting antivirals for HCV infection are NS3/4A protease, NS5A phosphoprotein and NS5B polymerase. Differential visualization of drug-resistant and -susceptible RNA genomes within cells revealed that resistant variants of NS3/4A protease and NS5A phosphoprotein are -dominant, ensuring their direct selection from complex environments. Confocal microscopy revealed that RNA replication complexes are genome-specific, rationalizing the non-interaction of wild-type and variant products. No HCV antivirals yet display the dominance of drug susceptibility shown for capsid proteins of other viruses. However, effective inhibitors of HCV polymerase exact such high fitness costs for drug resistance that stable genome selection is not observed. Barriers to drug resistance vary with target biochemistry and detailed analysis of these barriers should lead to the use of fewer drugs.
Topics: Antiviral Agents; Drug Resistance, Viral; Genetic Fitness; Hepacivirus; Mutant Proteins; Selection, Genetic; Viral Nonstructural Proteins
PubMed: 29589830
DOI: 10.7554/eLife.32579 -
Current Drug Targets 2016In many conformational diseases caused by protein mutations, the intracellular traffic of the misfolded protein is compromised, leading to reduced or abolished function... (Review)
Review
In many conformational diseases caused by protein mutations, the intracellular traffic of the misfolded protein is compromised, leading to reduced or abolished function of the affected protein. Pharmacoperones (from "pharmacological chaperones") are compounds that enter cells and serve as a molecular scaffold to aid misfolded mutant proteins to fold properly and adopt a stable, low-energy native conformation compatible with proper intracellular trafficking. The use of pharmacoperones represents the most promising therapeutic approach to treat misfolding disorders. This class of drugs has succeeded, in vitro and in vivo, in rescuing function of mutant, misfolded proteins, including enzymes, membrane receptors and ion channels. Here we describe the strategies to rescue function of misfolded G protein-coupled receptors, mainly of the gonadotropin-releasing hormone receptor, which has served as a valuable model for the development of pharmacoperone drugs and to better understand how this class of particular compounds is sensed by the target protein to correct routing, expression and function.
Topics: Animals; Drug Design; Humans; Molecular Chaperones; Mutant Proteins; Mutation; Protein Folding; Proteins; Proteostasis Deficiencies
PubMed: 26953247
DOI: 10.2174/1389450117666160307143345 -
Nature Dec 2020Most proteins assemble into multisubunit complexes. The persistence of these complexes across evolutionary time is usually explained as the result of natural selection...
Most proteins assemble into multisubunit complexes. The persistence of these complexes across evolutionary time is usually explained as the result of natural selection for functional properties that depend on multimerization, such as intersubunit allostery or the capacity to do mechanical work. In many complexes, however, multimerization does not enable any known function. An alternative explanation is that multimers could become entrenched if substitutions accumulate that are neutral in multimers but deleterious in monomers; purifying selection would then prevent reversion to the unassembled form, even if assembly per se does not enhance biological function. Here we show that a hydrophobic mutational ratchet systematically entrenches molecular complexes. By applying ancestral protein reconstruction and biochemical assays to the evolution of steroid hormone receptors, we show that an ancient hydrophobic interface, conserved for hundreds of millions of years, is entrenched because exposure of this interface to solvent reduces protein stability and causes aggregation, even though the interface makes no detectable contribution to function. Using structural bioinformatics, we show that a universal mutational propensity drives sites that are buried in multimeric interfaces to accumulate hydrophobic substitutions to levels that are not tolerated in monomers. In a database of hundreds of families of multimers, most show signatures of long-term hydrophobic entrenchment. It is therefore likely that many protein complexes persist because a simple ratchet-like mechanism entrenches them across evolutionary time, even when they are functionally gratuitous.
Topics: Binding Sites; DNA; Evolution, Molecular; Humans; Hydrophobic and Hydrophilic Interactions; Ligands; Models, Molecular; Multiprotein Complexes; Mutant Proteins; Mutation; Protein Aggregates; Protein Domains; Protein Multimerization; Protein Stability; Receptors, Steroid; Solvents
PubMed: 33299178
DOI: 10.1038/s41586-020-3021-2 -
Human Genetics Dec 2021Missense variants located in the N-terminal region of WDR37 were recently identified to cause a multisystemic syndrome affecting neurological, ocular, gastrointestinal,...
Missense variants located in the N-terminal region of WDR37 were recently identified to cause a multisystemic syndrome affecting neurological, ocular, gastrointestinal, genitourinary, and cardiac development. WDR37 encodes a WD40 repeat-containing protein of unknown function. We identified three novel WDR37 variants, two likely pathogenic de novo alleles and one inherited variant of uncertain significance, in individuals with phenotypes overlapping those previously reported but clustering in a different region of the protein. The novel alleles are C-terminal to the prior variants and located either within the second WD40 motif (c.659A>G p.(Asp220Gly)) or in a disordered protein region connecting the second and third WD40 motifs (c.778G>A p.(Asp260Asn) and c.770C>A p.(Pro257His)). The three novel mutants showed normal cellular localization but lower expression levels in comparison to wild-type WDR37. To investigate the normal interactions of WDR37, we performed co-immunoprecipitation and yeast two-hybrid assays. This revealed the ability of WDR37 to form homodimers and to strongly bind PACS1 and PACS2 phosphofurin acidic cluster sorting proteins; immunocytochemistry confirmed colocalization of WDR37 with PACS1 and PACS2 in human cells. Next, we analyzed previously reported and novel mutants for their ability to dimerize with wild-type WDR37 and bind PACS proteins. Interaction with wild-type WDR37 was not affected for any variant; however, one novel mutant, p.(Asp220Gly), lost its ability to bind PACS1 and PACS2. In summary, this study presents a novel region of WDR37 involved in human disease, identifies PACS1 and PACS2 as major binding partners of WDR37 and provides insight into the functional effects of various WDR37 variants.
Topics: Abnormalities, Multiple; Adolescent; Animals; Cells, Cultured; Child; Child, Preschool; Cognitive Dysfunction; Female; Humans; Male; Mutant Proteins; Nuclear Proteins; Pedigree; Protein Binding; Syndrome; Two-Hybrid System Techniques; Vesicular Transport Proteins
PubMed: 34642815
DOI: 10.1007/s00439-021-02384-y -
Journal of Virology Aug 2014Kaposi's sarcoma-associated herpesvirus (KSHV) ORF6 is homologous to the herpes simplex virus 1 (HSV-1) ICP8 and Epstein-Barr virus (EBV) BALF2 proteins. Here, we...
UNLABELLED
Kaposi's sarcoma-associated herpesvirus (KSHV) ORF6 is homologous to the herpes simplex virus 1 (HSV-1) ICP8 and Epstein-Barr virus (EBV) BALF2 proteins. Here, we describe its single-stranded DNA (ssDNA) binding properties. Based on previous findings with ICP8 and BALF2, a 60-amino-acid C-terminal deletion mutant of Orf6 was generated, and the protein was purified to explore the function of the C terminus in ssDNA binding. We showed that full-length ORF6 binds cooperatively to M13 ssDNA, disrupting its secondary structure and extending it to a length equivalent to that of duplex M13 DNA. The width of the ORF6-ssDNA filament is 9 nm, and a 7.3-nm repeat can be distinguished along the filament axis. Fluorescence polarization analysis revealed that the wild-type and C-terminal mutant ORF6 proteins bind equally well to short ssDNA substrates, with dissociation constant (Kd) values of 2.2 × 10(-7)M and 1.5 × 10(-7)M, respectively. These values were confirmed by electrophoretic mobility shift assay (EMSA) analysis, which also suggested that binding by the full-length protein may involve both monomers and small multimers. While no significant difference in affinities of binding between full-length ORF6 and the C-terminal deletion mutant were observed with the short DNAs, binding of the C-terminal mutant protein to M13 ssDNA showed a clear lack of cooperativity as seen by electron microscopy (EM). Incubation of a duplex DNA containing a long single-stranded tail with double-helical ORF6 protein filaments revealed that the ssDNA segment can be enveloped within the protein filament without disrupting the filament structure.
IMPORTANCE
This work describes the biochemical characterization of the single-stranded DNA binding protein of KSHV, ORF6, central to viral DNA replication in infected cells. A C-terminal deletion mutant protein was generated to aid in understanding the role of the C terminus in DNA binding. Here we analyze the binding of the wild-type and mutant proteins to short oligomeric and longer genomic ssDNA substrates. Although it is capable of interacting with the short substrates, the inability of mutant ORF6 to form oligomers in solution hindered it from fully covering the long genomic substrates. We previously showed that ORF6 forms long filaments in solution, and we showed here that these can absorb ssDNA without disruption of the filament structure. This work will provide an important basis for future studies by us and/or others.
Topics: Bacteriophage M13; DNA, Single-Stranded; DNA, Viral; DNA-Binding Proteins; Electrophoretic Mobility Shift Assay; Herpesvirus 8, Human; Humans; Kinetics; Microscopy, Electron; Mutant Proteins; Sequence Deletion; Viral Proteins
PubMed: 24850743
DOI: 10.1128/JVI.03652-13 -
Proceedings of the National Academy of... Aug 2022Twinkle is the mammalian helicase vital for replication and integrity of mitochondrial DNA. Over 90 Twinkle helicase disease variants have been linked to progressive...
Twinkle is the mammalian helicase vital for replication and integrity of mitochondrial DNA. Over 90 Twinkle helicase disease variants have been linked to progressive external ophthalmoplegia and ataxia neuropathies among other mitochondrial diseases. Despite the biological and clinical importance, Twinkle represents the only remaining component of the human minimal mitochondrial replisome that has yet to be structurally characterized. Here, we present 3-dimensional structures of human Twinkle W315L. Employing cryo-electron microscopy (cryo-EM), we characterize the oligomeric assemblies of human full-length Twinkle W315L, define its multimeric interface, and map clinical variants associated with Twinkle in inherited mitochondrial disease. Cryo-EM, crosslinking-mass spectrometry, and molecular dynamics simulations provide insight into the dynamic movement and molecular consequences of the W315L clinical variant. Collectively, this ensemble of structures outlines a framework for studying Twinkle function in mitochondrial DNA replication and associated disease states.
Topics: Cryoelectron Microscopy; DNA Helicases; DNA Replication; DNA, Mitochondrial; Humans; Mass Spectrometry; Mitochondrial Diseases; Mitochondrial Proteins; Molecular Dynamics Simulation; Mutant Proteins; Protein Multimerization
PubMed: 35914129
DOI: 10.1073/pnas.2207459119 -
MBio Apr 2019The flagellar motor can spin in both counterclockwise (CCW) and clockwise (CW) directions. The flagellar motor consists of a rotor and multiple stator units, which act...
The flagellar motor can spin in both counterclockwise (CCW) and clockwise (CW) directions. The flagellar motor consists of a rotor and multiple stator units, which act as a proton channel. The rotor is composed of the transmembrane MS ring made of FliF and the cytoplasmic C ring consisting of FliG, FliM, and FliN. The C ring is directly involved in rotation and directional switching. The FliF-FliG deletion fusion motor missing 56 residues from the C terminus of FliF and 94 residues from the N terminus of FliG keeps a domain responsible for the interaction with the stator intact, but its motor function is reduced significantly. Here, we report the structure and function of the FliF-FliG deletion fusion motor. The FliF-FliG deletion fusion not only resulted in a strong CW switch bias but also affected rotor-stator interactions coupled with proton translocation through the proton channel of the stator unit. The energy coupling efficiency of the deletion fusion motor was the same as that of the wild-type motor. Extragenic suppressor mutations in FliG, FliM, or FliN not only relieved the strong CW switch bias but also increased the motor speed at low load. The FliF-FliG deletion fusion made intersubunit interactions between C ring proteins tighter compared to the wild-type motor, whereas the suppressor mutations affect such tighter intersubunit interactions. We propose that a change of intersubunit interactions between the C ring proteins may be required for high-speed motor rotation as well as direction switching. The bacterial flagellar motor is a bidirectional rotary motor for motility and chemotaxis, which often plays an important role in infection. The motor is a large transmembrane protein complex composed of a rotor and multiple stator units, which also act as a proton channel. Motor torque is generated through their cyclic association and dissociation coupled with proton translocation through the proton channel. A large cytoplasmic ring of the motor, called C ring, is responsible for rotation and switching by interacting with the stator, but the mechanism remains unknown. By analyzing the structure and function of the wild-type motor and a mutant motor missing part of the C ring connecting itself with the transmembrane rotor ring while keeping a stator-interacting domain for bidirectional torque generation intact, we found interesting clues to the change in the C ring conformation for the switching and rotation involving loose and tight intersubunit interactions.
Topics: Bacterial Proteins; Flagella; Membrane Proteins; Motion; Mutant Proteins; Protein Binding; Protein Conformation; Recombinant Fusion Proteins; Salmonella typhimurium; Suppression, Genetic
PubMed: 30940700
DOI: 10.1128/mBio.00079-19 -
International Journal of Molecular... Aug 2021Lynch syndrome (LS) is one of the most common hereditary cancer predisposition syndromes worldwide. Individuals with LS have a high risk of developing colorectal or... (Review)
Review
Lynch syndrome (LS) is one of the most common hereditary cancer predisposition syndromes worldwide. Individuals with LS have a high risk of developing colorectal or endometrial cancer, as well as several other cancers. LS is caused by autosomal dominant pathogenic variants in one of the DNA mismatch repair (MMR) genes , , or , and typically include truncating variants, such as frameshift, nonsense or splicing variants. However, a significant number of missense, intronic, or silent variants, or small in-frame insertions/deletions, are detected during genetic screening of the MMR genes. The clinical effects of these variants are often more difficult to predict, and a large fraction of these variants are classified as variants of uncertain significance (VUS). It is pivotal for the clinical management of LS patients to have a clear genetic diagnosis, since patients benefit widely from screening, preventive and personal therapeutic measures. Moreover, in families where a pathogenic variant is identified, testing can be offered to family members, where non-carriers can be spared frequent surveillance, while carriers can be included in cancer surveillance programs. It is therefore important to reclassify VUSs, and, in this regard, functional assays can provide insight into the effect of a variant on the protein or mRNA level. Here, we briefly describe the disorders that are related to MMR deficiency, as well as the structure and function of MSH6. Moreover, we review the functional assays that are used to examine VUS identified in MSH6 and discuss the results obtained in relation to the ACMG/AMP PS3/BS3 criterion. We also provide a compiled list of the MSH6 variants examined by these assays. Finally, we provide a future perspective on high-throughput functional analyses with specific emphasis on the MMR genes.
Topics: Animals; DNA-Binding Proteins; Genetic Techniques; Genetic Testing; Humans; Mutant Proteins; Protein Isoforms; RNA Splicing
PubMed: 34445333
DOI: 10.3390/ijms22168627