Mutations In Different Subunits Research Articles

An Influenza A virus can evolve to use human ANP32E through altering polymerase dimerization

Human ANP32A and ANP32B are essential but redundant host factors for influenza virus genome replication. While most influenza viruses cannot replicate in edited human cells lacking both ANP32A and ANP32B, some strains exhibit limited growth. Here, we experimentally evolve such an influenza A virus in these edited cells and unexpectedly, after 2 passages, we observe robust viral growth. We find two mutations in different subunits of the influenza polymerase that enable the mutant virus to use a novel host factor, ANP32E, an alternative family member, which is unable to support the wild type polymerase. Both mutations reside in the symmetric dimer interface between two polymerase complexes and reduce polymerase dimerization. These mutations have previously been identified as adapting influenza viruses to mice. Indeed, the evolved virus gains the ability to use suboptimal mouse ANP32 proteins and becomes more virulent in mice. We identify further mutations in the symmetric dimer interface which we predict allow influenza to adapt to use suboptimal ANP32 proteins through a similar mechanism. Overall, our results suggest a balance between asymmetric and symmetric dimers of influenza virus polymerase that is influenced by the interaction between polymerase and ANP32 host proteins.

Elongator and the role of its subcomplexes in human diseases.

The Elongator complex was initially identified in yeast, and a variety of distinct cellular functions have been assigned to the complex. In the last decade, several research groups focussed on dissecting its structure, tRNA modification activity and role in translation regulation. Recently, Elongator emerged as a crucial factor for various human diseases, and its involvement has triggered a strong interest in the complex from numerous clinical groups. The Elongator complex is highly conserved among eukaryotes, with all six subunits (Elp1-6) contributing to its stability and function. Yet, recent studies have shown that the two subcomplexes, namely the catalytic Elp123 and accessory Elp456, may have distinct roles in the development of different neuronal subtypes. This Commentary aims to provide a brief overview and new perspectives for more systematic efforts to explore the functions of the Elongator in health and disease.

Cytopathological Outcomes of Knocking down Expression of Mitochondrial Complex II Subunits in Dictyostelium discoideum.

Mitochondrial Complex II is composed of four core subunits and mutations to any of the subunits result in lowered Complex II activity. Surprisingly, although mutations in any of the subunits can yield similar clinical outcomes, there are distinct differences in the patterns of clinical disease most commonly associated with mutations in different subunits. Thus, mutations to the SdhA subunit most often result in mitochondrial disease phenotypes, whilst mutations to the other subunits SdhB-D more commonly result in tumour formation. The reason the clinical outcomes are so different is unknown. Here, we individually antisense-inhibited three of the Complex II subunits, SdhA, SdhB or SdhC, in the simple model organism Dictyostelium discoideum. Whilst SdhB and SdhC knockdown resulted in growth defects on bacterial lawns, antisense inhibition of SdhA expression resulted in a different pattern of phenotypic defects, including impairments of growth in liquid medium, enhanced intracellular proliferation of the bacterial pathogen Legionella pneumophila and phagocytosis. Knockdown of the individual subunits also produced different abnormalities in mitochondrial function with only SdhA knockdown resulting in broad mitochondrial dysfunction. Furthermore, these defects were shown to be mediated by the chronic activation of the cellular energy sensor AMP-activated protein kinase. Our results are in agreement with a role for loss of function of SdhA but not the other Complex II subunits in impairing mitochondrial oxidative phosphorylation and they suggest a role for AMP-activated protein kinase in mediating the cytopathological outcomes.

Treatment of slow-channel congenital myasthenic syndrome in a Thai family with fluoxetine

The slow-channel congenital myasthenic syndrome is an autosomal dominant neuromuscular disorder caused by mutations in different subunits of the acetylcholine receptor. Fluoxetine, a common antidepressant and long-lived open-channel blocker of acetylcholine receptor, has been reported to be beneficial in the slow-channel congenital myasthenic syndrome. Here we report a prospective open label study of fluoxetine treatment in some affected members of a Thai family with slow-channel congenital myasthenic syndrome caused by a novel p.Gly153Ala (c.518G > C) mutation in CHRNA1 in the AChR α subunit. These patients showed significant clinical improvement following fluoxetine treatment but their respiratory function responded variably.

Drosophila as a Model Organism to Understand the Effects during Development of TFIIH-Related Human Diseases.

Human mutations in the transcription and nucleotide excision repair (NER) factor TFIIH are linked with three human syndromes: xeroderma pigmentosum (XP), trichothiodystrophy (TTD) and Cockayne syndrome (CS). In particular, different mutations in the XPB, XPD and p8 subunits of TFIIH may cause one or a combination of these syndromes, and some of these mutations are also related to cancer. The participation of TFIIH in NER and transcription makes it difficult to interpret the different manifestations observed in patients, particularly since some of these phenotypes may be related to problems during development. TFIIH is present in all eukaryotic cells, and its functions in transcription and DNA repair are conserved. Therefore, Drosophila has been a useful model organism for the interpretation of different phenotypes during development as well as the understanding of the dynamics of this complex. Interestingly, phenotypes similar to those observed in humans caused by mutations in the TFIIH subunits are present in mutant flies, allowing the study of TFIIH in different developmental processes. Furthermore, studies performed in Drosophila of mutations in different subunits of TFIIH that have not been linked to any human diseases, probably because they are more deleterious, have revealed its roles in differentiation and cell death. In this review, different achievements made through studies in the fly to understand the functions of TFIIH during development and its relationship with human diseases are analysed and discussed.

Machine Learning Unveils Proteotypic Mimicry in Genetically Defined SCN Variants

Background Novel computational algorithms for multi-omics analysis bear great potential to highlight pathomechanisms of monogenic diseases. We recently defined the in-depth proteome of primary human neutrophil granulocytes (PMID 30630937). Here, we ask the question whether proteotypic patterns differ between defined genetic subtypes associated with severe congenital neutropenia (SCN). We focus on two novel genetic variants in constituents of the signal recognition particle (SRPRA and SRP19) and previously reported SCN genotypes SRP54, HAX1, and ELANE. Methods We analyzed proteomes of highly purified neutrophil granulocytes from a total of 26 SCN patients, including 5 with homozygous splice site mutations in SRP19, one patient with a de-novo heterozygous missense mutation in SRPRA (using 5 biological replicates collected months apart) as well as 6 patients with SRP54, 8 with HAX1 and 6 with ELANE mutations. Samples of 70 healthy donors (HD) served as controls. Whole cell proteome analysis was based on data-independent acquisition using a Thermo Fisher QExactive HF mass spectrometer. Data analysis was performed in R and Cytoscape, machine learning approaches included lasso regression and random forest. Results Differential expression analysis in comparison to HD showed in all genotypes overexpression of ribosomes, the translational apparatus, mitochondria, cell-substrate junctions and response to unfolded proteins. Underexpressed proteins showed genotype specific enrichment for granule subsets. Whereas ELANE showed deficiency of primary and secretory granules, HAX1 showed deficiency of specific, tertiary and secretory granules. All SRP genotypes showed markedly reduced abundance of proteins in all granule subsets. Principal component analysis showed clear separation of healthy and diseased proteotypes on the first component, whereas the separation of patient genotypes became clear only using five dimensions. We derived genotype specific proteome signatures by lasso regression, consisting of 26 (minimal specific set) to 128 (comprehensive signature) proteins, and a signature of 48 proteins when joining the SRP genotypes as one group. This signatures allow for perfect separation of the genotypes, demonstrating a clear genotype specific effect on protein abundance levels. We asked the question if the genotypes SRP19 and SRPRA show more similar proteomic profile to SRP54 than the other genotypes (ELANE, HAX1) by training a random forest model on proteome data from SRP54, HAX1, ELANE and HD and subsequently testing if the other SRP samples get classified as SRP54. We observe only few misclassifications using either all proteins (7/10) or using the lasso derived genotype defining proteins (8/10). This strongly supports our hypothesis that mutations in different subunits of the same complex lead to similar proteotype changes, a phenomenon we propose to call "proteotypic mimicry". For a systems biology perspective we selected proteins that were exclusively regulated in the SRP genotypes and restricted a network of interactions to these proteins together with their direct interactors (based on APID level 1). The resulting network contained 464 proteins and 3587 interactions. MCODE analysis identified 16 clusters that were consequently annotated using BINGO enrichment analysis. The SRP specific network shows features of the translational apparatus, the proteasome, the septin complex, splicing and cell-metabolic processes. Further studies to dissect specific pathomechanisms are under way. Conclusion Here we provide for the first time evidence for the correlation between SCN causing genotypes and their corresponding neutrophil proteotypes. In particular, we demonstrate significant overlap of all SRP related proteotypes, indicating a phenomenon we propose to be called "proteotypic mimicry". Studies on similarities and disparities of neutrophil proteotypes will help to raise new hypothesis on distinct cellular dysfunction in defined genetic defects of neutrophil granulocytes. Disclosures No relevant conflicts of interest to declare.

Deciphering mediator's function and structure in mammalian cells

Introduction/Objectives Mediator is a multi-subunit complex organized into four modules (head, middle, tail and kinase module). It is involved in several steps of PolII-dependent transcription and enhancer–promoter (E–P) interactions. Mutations in different subunits (SU) are associated with cancer and developmental diseases. Mediator's function and structure have been mainly studied in yeast. Earlier studies suggest significant differences with the mammalian complex in terms of composition and structure. Additionally, the chromatin architecture between both species is different, particularly E–P interactions. We aimed to comprehensively characterize the mammalian complex. Materials/Patients and methods We screened for cell essentiality of Mediator subunits, in a murine B-lymphoma cell line, CH12, in embryonic stem cells and in primary CD4T cells, using CRISPR-Cas9 technology. We generated knockout clones (KO) whenever possible in CH12 cells, and a degron-based conditional KO of the essential Mediator's backbone, Med14. We analyzed the impact on gene expression (RNAseq), on PolII and Mediator recruitment at promoters and enhancers (ChIPseq), on chromatin accessibility (ATACseq), on histone modifications (MNase ChIPseq), on chromatin architecture (in situ HiC) and on structure (cryo-EM). Results Depletion of non-essential SUs induces transcriptional deregulation of only a subset of genes, whereas depleting the essential Med14 induces global decrease in transcription associated with a decrease in PolII recruitment. Interestingly, the ablation of the whole tail module is viable. With this tailless model and the Med14-degron we do not observe an impact on chromatin architecture. Preliminary cryo-EM results show a conserved location of common SUs between yeast and mammalian cells. We are able to locate mammalian specific SUs and describe the interactions between the different SUs in the mammalian complex. Conclusions Our study provides new insights into mammalian Mediator structure and a comprehensive view on how Mediator and its tail module are involved in transcription and chromatin architecture. This data is essential for a better understanding of transcriptional regulation and Mediator related diseases.

The Role of the M3 Helix in AChR Gating and PAM Action

We are examining the M3 transmembrane helix of mouse muscle AChRs with regard to C↔O gating and the effects of positive allosteric modulators (PAMs). The relative ground and transition state gating energies were estimated from single-channel currents of AChRs having M3 mutations. Diliganded gating rate and equilibrium constants were measured for ∼100 mutations in 5 subunits (α, β, δ, e and γ; 20 mM choline or 500 μM ACh, −100 mV, HEK cells). In general: i) the effects of the mutations were small (≤1 kcal/mol), ii) the effects were similar among subunits, iii) the mutations in different subunits were independent, iv) the mutations have no effect on the energy from the agonist affinity change (≤∼0.3 kcal/mol) and v) most phi values were low (∼0.3). Crystal structures of AChR homologues in detergents suggest that the low phi positions in M3 are interaction sites for PAMs. We investigated the actions of PNU-120596 and IVM (1-1000nM). In WT AChRs (adult and fetal) these ligands increase substantially the frequency and lifetime of constitutive openings in a manner consistent with action at a low-phi position such as in M3. Such potentiation was also apparent at low [agonist] (<1μM ACh or choline), but at higher [agonist] gating kinetics became complex and the potentiation was less clear. The PAMs also increased substantially the frequency and lifetime of constitutive openings in some of the M3 mutants (to W).

Analysis and modeling of heat-labile enterotoxins of Escherichia coli suggests a novel space with insights into receptor preference

Features of heat-labile enterotoxins of Escherichia coli which make them fit to use as novel receptors for antidiarrheals are not completely explored. Data-set of 14 different serovars of enterotoxigenic Escherichia coli producing heat-labile toxins were taken from NCBI Genbank database and used in the study. Sequence analysis showed mutations in different subunits and also at their interface residues. As these toxins lack crystallography structures, homology modeling using Modeller 9.11 led to the structural approximation for the E. coli producing heat-labile toxins. Interaction of modeled toxin subunits with proanthocyanidin, an antidiarrheal showed several strong hydrogen bonding interactions at the cost of minimized energy. The hits were subsequently characterized by molecular dynamics simulation studies to monitor their binding stabilities. This study looks into novel space where the ligand can choose the receptor preference not as a whole but as an individual subunit. Mutation at interface residues and interaction among subunits along with the binding of ligand to individual subunits would help to design a non-toxic labile toxin and also to improve the therapeutics.

Chapter 5 - Mechanisms underlying epilepsies associated with sodium channel mutations

Voltage-gated sodium channels provide the molecular basis for the generation and propagation of action potentials. It is therefore not surprising that mutations in different subunits of this ion channel family are the most common cause of genetic epilepsies. Voltage-gated sodium channel mutations are associated with different seizure phenotypes including benign familial neonatal-infantile convulsions, genetic epilepsy with febrile seizures plus, and Dravet syndrome. Unraveling the pathomechanisms that underlie these genetic epilepsies is challenging, and the complex genotype-phenotype correlations are still not fully understood.

Deficiency of the Cog8 Subunit in Normal and CDG‐Derived Cells Impairs the Assembly of the COG and Golgi SNARE Complexes

Multiple mutations in different subunits of the tethering complex Conserved Oligomeric Golgi (COG) have been identified as a cause for Congenital Disorders of Glycosylation (CDG) in humans. Yet, the mechanisms by which COG mutations induce the pleiotropic CDG defects have not been fully defined. By detailed analysis of Cog8 deficiency in either HeLa cells or CDG-derived fibroblasts, we show that Cog8 is required for the assembly of both the COG complex and the Golgi Stx5-GS28-Ykt6-GS15 and Stx6-Stx16-Vti1a-VAMP4 SNARE complexes. The assembly of these SNARE complexes is also impaired in cells derived from a Cog7-deficient CDG patient. Likewise, the integrity of the COG complex is also impaired in Cog1-, Cog4- and Cog6-depleted cells. Significantly, deficiency of Cog1, Cog4, Cog6 or Cog8 distinctly influences the production of COG subcomplexes and their Golgi targeting. These results shed light on the structural organization of the COG complex and its subcellular localization, and suggest that its integrity is required for both tethering of transport vesicles to the Golgi apparatus and the assembly of Golgi SNARE complexes. We propose that these two key functions are generally and mechanistically impaired in COG-associated CDG patients, thereby exerting severe pleiotropic defects.

In Glycine and GABAA Channels, Different Subunits Contribute Asymmetrically to Channel Conductance via Residues in the Extracellular Domain

Single-channel conductance in Cys-loop channels is controlled by the nature of the amino acids in the narrowest parts of the ion conduction pathway, namely the second transmembrane domain (M2) and the intracellular helix. In cationic channels, such as Torpedo ACh nicotinic receptors, conductance is increased by negatively charged residues exposed to the extracellular vestibule. We now show that positively charged residues at the same loop 5 position boost also the conductance of anionic Cys-loop channels, such as glycine (α1 and α1β) and GABA(A) (α1β2γ2) receptors. Charge reversal mutations here produce a greater decrease on outward conductance, but their effect strongly depends on which subunit carries the mutation. In the glycine α1β receptor, replacing Lys with Glu in α1 reduces single-channel conductance by 41%, but has no effect in the β subunit. By expressing concatameric receptors with constrained stoichiometry, we show that this asymmetry is not explained by the subunit copy number. A similar pattern is observed in the α1β2γ2 GABA(A) receptor, where only mutations in α1 or β2 decreased conductance (to different extents). In both glycine and GABA receptors, the effect of mutations in different subunits does not sum linearly: mutations that had no detectable effect in isolation did enhance the effect of mutations carried by other subunits. As in the nicotinic receptor, charged residues in the extracellular vestibule of anionic Cys-loop channels influence elementary conductance. The size of this effect strongly depends on the direction of the ion flow and, unexpectedly, on the nature of the subunit that carries the residue.

Phenotypic heterogeneity in a large Thai slow-channel congenital myasthenic syndrome kinship

The slow-channel congenital myasthenic syndrome (SCCMS) is an autosomal dominant neuromuscular disorder caused by mutations in different subunits of the acetylcholine receptor (AChR). We here report our clinical findings in three generations of a large Thai kinship suffering from SCCMS and trace the disease to the p.Gly153Ser mutation in the AChR α subunit. The same mutation had previously been reported only in Caucasian but not in Asian patients. The clinical features include ptosis, ophthalmoparesis, and weakness of the cervical and finger extensor muscles as well as marked phenotypic heterogeneity.

Human Complex I Defects Can Be Resolved by Monoclonal Antibody Analysis into Distinct Subunit Assembly Patterns

Complex I defects are one of the most frequent causes of mitochondrial respiratory chain disorders. Therefore, it is important to find new approaches for detecting and characterizing Complex I deficiencies. In this paper, we introduce a new set of monoclonal antibodies that react with 39-, 30-, 20-, 18-, 15-, and 8-kDa subunits of Complex I. These antibodies are shown to aid in diagnosis of Complex I deficiencies and add understanding to the genotype-phenotype relationships of different mutations. A total of 11 different patients were examined. Four patients had undefined Complex I defects, whereas the other patients had defects in NDUFV1, NDUFS2 (two patients), NDUFS4 (two patients), NDUFS7, and NDUFS8. We show here that Western blotting with these antibodies, particularly when used in conjunction with sucrose gradient studies and enzymatic activity measurements, helps distinguish catalytic versus assembly defects and further distinguishes between mutations in different subunits. Furthermore, different mutations in the same gene are shown to give very similar subunit profiles, and we show that one of the patients is a good candidate for having a defect in a Complex I assembly factor.

JAB1/CSN5 and the COP9 signalosome

The Jun activating binding protein (JAB1) specifically stabilizes complexes of c-Jun or JunD with AP-1 sites, increasing the specificity of target gene activation by AP-1 proteins. JAB1 is also known as COP9 signalosome subunit 5 (CSN5), which is a component of the COP9 signalosome regulatory complex (CSN). Over the past year, JAB1/CSN5 has been implicated in numerous signaling pathways including those that regulate light signaling in plants, larval development in Drosophila, and integrin signaling, cell cycle control, and steroid hormone signaling in a number of systems. However, the general role of the CSN complex, and the specific role of JAB1/CSN5, still remain obscure. This review attempts to integrate the available data to help explain the role of JAB1/CSN5 and the COP9 signalosome in regulating multiple pathways (in this review, both JAB1 and CSN5 terminologies are used interchangeably, depending on the source material).

REVIEW ■ : Molecular Basis of Congenital Myasthenic Syndromes: Mutations in the Acetylcholine Receptor

The congenital myasthenic syndromes include end-plate (EP) acetylcholinesterase deficiency, presynaptic abnormalities affecting the evoked release or size of transmitter quanta, and acetylcholine (ACh) receptor (AChR) channelopathies stemming from a kinetic abnormality and/or deficiency of AChR. A kinetic abnor mality predicts, and AChR deficiency may predict, one or more mutations in an AChR subunit gene. These clues have led to the identification of 53 mutations in different subunits of AChR in 55 kinships of the congenital myasthenic syndromes. The mutations either increase or decrease the response to ACh, produce AChR deficiency, or both. In the slow-channel syndromes, prolonged opening episodes of AChR cause cationic overloading of the EP and an EP myopathy; the mutations occur in different subunits and different domains of the subunits and have dominant positive effects. The M1 and M2 mutations slow channel closure, increase apparent affinity for ACh, and variably enhance desensitization, and the extracellular αG153S enhances affinity for ACh, promoting reopening of the diliganded receptor. In the low-affinity fast-channel syndrome, εP121L reduces affinity for ACh and reopening of the diliganded receptor, resulting in a de creased response to ACh and shorter burst durations. Severe EP AChR deficiency results from heterozy gous or homozygous mutations that terminate translation prematurely; these are concentrated in the ε subunit, probably because substitution of the fetal γ for the adult ε subunit can rescue the phenotype from fatal null mutations in ε. Variable AChR deficiency and variable functional abnormalities stem from hetero allelic nonsense and missense mutations in AChR subunit genes. NEUROSCIENTIST 4:185-194, 1998

Congenital myasthenic syndromes caused by mutations in acetylcholine receptor genes

Article abstract-Congenital myasthenic syndromes (CMS) are heterogeneous disorders in which the safety margin of neuromuscular transmission is compromised by one or more specific mechanisms. According to the site of the primary defect, the CMS can be classified as presynaptic, synaptic, or postsynaptic. The postsynaptic CMS identified to date are characterized by a kinetic abnormality of the acetylcholine receptor (AChR) with or without AChR deficiency, or by AChR deficiency without a primary kinetic abnormality. We hypothesized and subsequently confirmed that a kinetic abnormality of the AChR at the single-channel level predicts a mutation in an AChR subunit gene, and that a severe deficiency of AChR can stem from nonsense mutations in AChR subunit genes. Seven dominant slow-channel mutations in different subunits and different domains of the subunits have been identified thus far. Mutations in the M2 and M1 transmembrane domains act predominantly by slowing channel closure, and mutations in M2 also allow spontaneous channel opening. Another slow-channel mutation in the extracellular domain of the alpha-subunit acts predominantly by enhancing the affinity of AChR for ACh, causing repeated channel reopenings during a prolonged ACh occupancy. The recently discovered low-affinity fast-channel syndrome is the physiologic opposite of the slow-channel syndrome. Here, a mutation in the extracellular domain of the epsilon-subunit reduces the affinity of AChR for ACh; this decreases the rate of channel opening, and results in briefer than normal bursts of openings. Finally, a number of homozygous or heterozygous nonsense mutations in an AChR subunit cause severe AChR deficiency. NEUROLOGY 1997;48(Suppl 5): S28-S35

Dissection of the effector-binding site and complementation studies of Escherichia coli phosphofructokinase using site-directed mutagenesis

A systematic study by site-directed mutagenesis has been conducted on the effector site of phosphofructokinase from Escherichia coli to delineate the role of side chains in binding the allosteric activator, GDP, and inhibitor, PEP, and to search for key residues in the allosteric transtion. Target residues were identified from the crystal structure of the enzyme-nucleoside diphosphate complex. It is found that both activator and inhibitor bind to the same set of amino acid side chains. Deletion of positively charged groups (Arg21, Arg25, Arg54, Arg154, and Lys213 mutated to alanine) weakens binding of both effectors by 2-3 kcal/mol, consistent with the disruption of charged hydrogen bonds. Residue Glu187, which is known from the crystal structure to bind the coordinated Mg2+ ion of GDP, is found to have a unique behavior on mutation and appears to be crucial in triggering the allosteric transition. All other residues mutated simply weaken binding of both PEP and GDP in a parallel manner. However, mutation of Glu----Ala187 reverses the roles of GDP and PEP, causing GDP to become an allosteric inhibitor and PEP an activator. Mutation of Glu----Gln187 has only a small effect on the binding of PEP, and both PEP and GDP are inhibitors. Studies are described in which mutations in different subunits of a tetrameric complex complement each other. The effector site is composed of residues from two subunits. In particular, Arg21 and Lys213 in each site are from different subunits. Mutations of either one of these residues abolishes activation by GDP of the homotetramer.(ABSTRACT TRUNCATED AT 250 WORDS)