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1.
Int J Mol Sci ; 25(13)2024 Jul 06.
Article in English | MEDLINE | ID: mdl-39000521

ABSTRACT

The Na,K-ATPase is an α-ß heterodimer. It is well known that the Na,K-ATPase ß subunit is required for the biosynthesis and trafficking of the α subunit to the plasma membrane. During investigation of properties of human ATP1A3 mutations in 293 cells, we observed a reciprocal loss of endogenous ATP1A1 when expressing ATP1A3. Scattered reports going back as far as 1991 have shown that experimental expression of one subunit can result in reduction in another, suggesting that the total amount is strictly limited. It seems logical that either α or ß subunit should be rate-limiting for assembly and functional expression. Here, we present evidence that neither α nor ß may be limiting and that there is another level of control that limits the amount of Na,K-ATPase to physiological levels. We propose that α subunits compete for something specific, like a private chaperone, required to finalize their biosynthesis or to prevent their degradation in the endoplasmic reticulum.


Subject(s)
Protein Subunits , Sodium-Potassium-Exchanging ATPase , Sodium-Potassium-Exchanging ATPase/metabolism , Sodium-Potassium-Exchanging ATPase/genetics , Humans , Protein Subunits/metabolism , Protein Subunits/genetics , HEK293 Cells , Mutation , Animals , Endoplasmic Reticulum/metabolism
2.
Mol Biol Rep ; 51(1): 817, 2024 Jul 16.
Article in English | MEDLINE | ID: mdl-39012451

ABSTRACT

BACKGROUND: Nitrile Hydratase (NHase) is one of the most important industrial enzyme widely used in the petroleum exploitation field. The enzyme, composed of two unrelated α- and ß-subunits, catalyzes the conversion of acrylonitrile to acrylamide, releasing a significant amount of heat and generating the organic solvent product, acrylamide. Both the heat and acrylamide solvent have an impact on the structural stability of NHase and its catalytic activity. Therefore, enhancing the stress resistance of NHase to toxic substances is meaningful for the petroleum industry. METHODS AND RESULTS: To improve the thermo-stability and acrylamide tolerance of NHase, the two subunits were fused in vivo using SpyTag and SpyCatcher, which were attached to the termini of each subunit in various combinations. Analysis of the engineered strains showed that the C-terminus of ß-NHase is a better fusion site than the N-terminus, while the C-terminus of α-NHase is the most suitable site for fusion with a larger protein. Fusion of SpyTag and SpyCatcher to the C-terminus of ß-NHase and α-NHase, respectively, led to improved acrylamide tolerance and a slight enhancement in the thermo-stability of one of the engineered strains, NBSt. CONCLUSION: These results indicate that in vivo ligation of different subunits using SpyTag/SpyCatcher is a valuable strategy for enhancing subunit interaction and improving stress tolerance.


Subject(s)
Hydro-Lyases , Rhodococcus , Rhodococcus/enzymology , Rhodococcus/genetics , Hydro-Lyases/metabolism , Hydro-Lyases/genetics , Hydro-Lyases/chemistry , Enzyme Stability , Stress, Physiological , Acrylamide/metabolism , Bacterial Proteins/metabolism , Bacterial Proteins/genetics , Bacterial Proteins/chemistry , Protein Subunits/metabolism , Protein Subunits/genetics
3.
Genes (Basel) ; 15(7)2024 Jun 27.
Article in English | MEDLINE | ID: mdl-39062625

ABSTRACT

The human louse (Pediculus humanus) is an obligatory blood feeding ectoparasite with two ecotypes: the human body louse (Pediculus humanus humanus), a competent vector of several bacterial pathogens, and the human head louse (Pediculus humanus capitis), responsible for pediculosis and affecting millions of people around the globe. GABA (γ-aminobutyric acid) receptors, members of the cys-loop ligand gated ion channel superfamily, are among the main pharmacological targets for insecticides. In insects, there are four subunits of GABA receptors: resistant-to-dieldrin (RDL), glycin-like receptor of drosophila (GRD), ligand-gated chloride channel homologue3 (LCCH3), and 8916 are well described and form distinct phylogenetic clades revealing orthologous relationships. Our previous studies in the human body louse confirmed that subunits Phh-RDL, Phh-GRD, and Phh-LCCH3 are well clustered in their corresponding clades. In the present work, we cloned and characterized a putative new GABA receptor subunit in the human body louse that we named HoCas, for Homologous to Cys-loop α like subunit. Extending our analysis to arthropods, HoCas was found to be conserved and clustered in a new (fifth) phylogenetic clade. Interestingly, the gene encoding this subunit is ancestral and has been lost in some insect orders. Compared to the other studied GABA receptor subunits, HoCas exhibited a relatively higher expression level in all development stages and in different tissues of human body louse. These findings improved our understanding of the complex nature of GABA receptors in Pediculus humanus and more generally in arthropods.


Subject(s)
Pediculus , Phylogeny , Receptors, GABA , Animals , Pediculus/genetics , Pediculus/metabolism , Receptors, GABA/genetics , Receptors, GABA/metabolism , Humans , Insect Proteins/genetics , Insect Proteins/metabolism , Protein Subunits/genetics , Protein Subunits/metabolism , Amino Acid Sequence
5.
PLoS One ; 19(6): e0291568, 2024.
Article in English | MEDLINE | ID: mdl-38848420

ABSTRACT

Polymeric IgMs are secreted from plasma cells abundantly despite their structural complexity and intricate multimerization steps. To gain insights into IgM's assembly mechanics that underwrite such high-level secretion, we characterized the biosynthetic process of a natural human IgM, SAM-6, using a heterologous HEK293(6E) cell platform that allowed the production of IgMs both in hexameric and pentameric forms in a controlled fashion. By creating a series of mutant subunits that differentially disrupt secretion, folding, and specific inter-chain disulfide bond formation, we assessed their effects on various aspects of IgM biosynthesis in 57 different subunit chain combinations, both in hexameric and pentameric formats. The mutations caused a spectrum of changes in steady-state subcellular subunit distribution, ER-associated inclusion body formation, intracellular subunit detergent solubility, covalent assembly, secreted IgM product quality, and secretion output. Some mutations produced differential effects on product quality depending on whether the mutation was introduced to hexameric IgM or pentameric IgM. Through this systematic combinatorial approach, we consolidate diverse overlapping knowledge on IgM biosynthesis for both hexamers and pentamers, while unexpectedly revealing that the loss of certain inter-chain disulfide bonds, including the one between µHC and λLC, is tolerated in polymeric IgM assembly and secretion. The findings highlight the differential roles of underlying non-covalent protein-protein interactions in hexamers and pentamers when orchestrating the initial subunit interactions and maintaining the polymeric IgM product integrity during ER quality control steps, secretory pathway trafficking, and secretion.


Subject(s)
Immunoglobulin M , Mutation , Humans , Immunoglobulin M/metabolism , Immunoglobulin M/genetics , HEK293 Cells , Protein Multimerization , Protein Subunits/metabolism , Protein Subunits/genetics , Endoplasmic Reticulum/metabolism
6.
Gene ; 926: 148637, 2024 Oct 30.
Article in English | MEDLINE | ID: mdl-38844270

ABSTRACT

The cytosolic T-complex protein-1 ring complex (TRiC), also referred as chaperonin containing TCP-1(CCT), comprising eight different subunits stacked in double toroidal rings, binds to around 10 % of newly synthesized polypeptides and facilitates their folding in ATP dependent manner. In Leishmania, among five subunits of TCP1 complex, identified either by transcriptome or by proteome analysis, only LdTCP1γ has been well characterized. It forms biologically active homo-oligomeric complex and plays role in protein folding and parasite survival. Lack of information regarding rest of the TCP1 subunits and its structural configuration laid down the necessity to study individual subunits and their role in parasite pathogenicity. The present study involves the cloning, expression and biochemical characterization of TCP1ε subunit (LdTCP1ε) of Leishmania donovani, the causative agent of visceral leishmaniasis. LdTCP1ε exhibited significant difference in primary structure as compared to LdTCP1γ and was evolutionary close to LdTCP1 zeta subunit. Recombinant protein (rLdTCP1ε) exhibited two major bands of 132 kDa and 240 kDa on native-PAGE that corresponds to the dimeric and tetrameric assembly of the epsilon subunit, which showed the chaperonin activity (ATPase and luciferase refolding activity). LdTCP1ε also displayed an increased expression upto 2.7- and 1.8-fold in the late log phase and stationary phase promastigotes and exhibited majorly vesicular localization. The study, thus for the first time, provides an insight for the presence of highly diverge but functionally active dimeric/tetrameric TCP1 epsilon subunit in Leishmania parasite.


Subject(s)
Chaperonin Containing TCP-1 , Leishmania donovani , Protozoan Proteins , Leishmania donovani/genetics , Leishmania donovani/metabolism , Chaperonin Containing TCP-1/metabolism , Chaperonin Containing TCP-1/genetics , Protozoan Proteins/metabolism , Protozoan Proteins/genetics , Protozoan Proteins/chemistry , Protein Multimerization , Recombinant Proteins/metabolism , Recombinant Proteins/genetics , Protein Subunits/metabolism , Protein Subunits/genetics , Cloning, Molecular , Amino Acid Sequence , Chaperonins/metabolism , Chaperonins/genetics , Protein Folding
7.
Sci Adv ; 10(23): eadn7191, 2024 Jun 07.
Article in English | MEDLINE | ID: mdl-38848361

ABSTRACT

Loss-of-function mutations in PTEN-induced kinase 1 (PINK1) are a frequent cause of early-onset Parkinson's disease (PD). Stabilization of PINK1 at the translocase of outer membrane (TOM) complex of damaged mitochondria is critical for its activation. The mechanism of how PINK1 is activated in the TOM complex is unclear. Here, we report that co-expression of human PINK1 and all seven TOM subunits in Saccharomyces cerevisiae is sufficient for PINK1 activation. We use this reconstitution system to systematically assess the role of each TOM subunit toward PINK1 activation. We unambiguously demonstrate that the TOM20 and TOM70 receptor subunits are required for optimal PINK1 activation and map their sites of interaction with PINK1 using AlphaFold structural modeling and mutagenesis. We also demonstrate an essential role of the pore-containing subunit TOM40 and its structurally associated subunits TOM7 and TOM22 for PINK1 activation. These findings will aid in the development of small-molecule activators of PINK1 as a therapeutic strategy for PD.


Subject(s)
Mitochondrial Membrane Transport Proteins , Mitochondrial Precursor Protein Import Complex Proteins , Protein Kinases , Saccharomyces cerevisiae , Protein Kinases/metabolism , Protein Kinases/genetics , Humans , Mitochondrial Precursor Protein Import Complex Proteins/metabolism , Mitochondrial Membrane Transport Proteins/metabolism , Mitochondrial Membrane Transport Proteins/genetics , Saccharomyces cerevisiae/metabolism , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae Proteins/metabolism , Saccharomyces cerevisiae Proteins/genetics , Mitochondria/metabolism , Protein Binding , Enzyme Activation , Models, Molecular , Protein Subunits/metabolism , Protein Subunits/genetics
8.
Nat Commun ; 15(1): 5335, 2024 Jun 24.
Article in English | MEDLINE | ID: mdl-38914563

ABSTRACT

The NuA3 complex is a major regulator of gene transcription and the cell cycle in yeast. Five core subunits are required for complex assembly and function, but it remains unclear how these subunits interact to form the complex. Here, we report that the Taf14 subunit of the NuA3 complex binds to two other subunits of the complex, Yng1 and Sas3, and describe the molecular mechanism by which the extra-terminal domain of Taf14 recognizes the conserved motif present in Yng1 and Sas3. Structural, biochemical, and mutational analyses show that two motifs are sandwiched between the two extra-terminal domains of Taf14. The head-to-toe dimeric complex enhances the DNA binding activity of Taf14, and the formation of the hetero-dimer involving the motifs of Yng1 and Sas3 is driven by sequence complementarity. In vivo assays in yeast demonstrate that the interactions of Taf14 with both Sas3 and Yng1 are required for proper function of the NuA3 complex in gene transcription and DNA repair. Our findings suggest a potential basis for the assembly of three core subunits of the NuA3 complex, Taf14, Yng1 and Sas3.


Subject(s)
Protein Binding , Saccharomyces cerevisiae Proteins , Saccharomyces cerevisiae , Saccharomyces cerevisiae Proteins/metabolism , Saccharomyces cerevisiae Proteins/genetics , Saccharomyces cerevisiae Proteins/chemistry , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae/metabolism , Transcription Factor TFIID/metabolism , Transcription Factor TFIID/genetics , Transcription Factor TFIID/chemistry , Protein Subunits/metabolism , Protein Subunits/genetics , TATA-Binding Protein Associated Factors/metabolism , TATA-Binding Protein Associated Factors/genetics , TATA-Binding Protein Associated Factors/chemistry , Histone Acetyltransferases/metabolism , Histone Acetyltransferases/genetics , Protein Multimerization , Models, Molecular , Transcription, Genetic , Amino Acid Sequence
9.
Genome Biol Evol ; 16(6)2024 06 04.
Article in English | MEDLINE | ID: mdl-38874416

ABSTRACT

In flowering plants, euchromatic transposons are transcriptionally silenced by RNA-directed DNA Methylation, a small RNA-guided de novo methylation pathway. RNA-directed DNA Methylation requires the activity of the RNA Polymerases IV and V, which produce small RNA precursors and noncoding targets of small RNAs, respectively. These polymerases are distinguished from Polymerase II by multiple plant-specific paralogous subunits. Most RNA-directed DNA Methylation components are present in all land plants, and some have been found in the charophytic green algae, a paraphyletic group that is sister to land plants. However, the evolutionary origin of key RNA-directed DNA Methylation components, including the two largest subunits of Polymerase IV and Polymerase V, remains unclear. Here, we show that multiple lineages of charophytic green algae encode a single-copy precursor of the largest subunits of Polymerase IV and Polymerase V, resolving the two presumed duplications in this gene family. We further demonstrate the presence of a Polymerase V-like C-terminal domain, suggesting that the earliest form of RNA-directed DNA Methylation utilized a single Polymerase V-like polymerase. Finally, we reveal that charophytic green algae encode a single CLSY/DRD1-type chromatin remodeling protein, further supporting the presence of a single specialized polymerase in charophytic green algae.


Subject(s)
DNA Methylation , DNA-Directed RNA Polymerases , Evolution, Molecular , DNA-Directed RNA Polymerases/genetics , DNA-Directed RNA Polymerases/metabolism , Phylogeny , Charophyceae/genetics , Charophyceae/enzymology , Plant Proteins/genetics , Plant Proteins/metabolism , Chlorophyta/genetics , Chlorophyta/enzymology , Protein Subunits/genetics
10.
Int J Mol Sci ; 25(10)2024 May 09.
Article in English | MEDLINE | ID: mdl-38791189

ABSTRACT

The membrane Fo factor of ATP synthase is highly sensitive to mutations in the proton half-channel leading to the functional blocking of the entire protein. To identify functionally important amino acids for the proton transport, we performed molecular dynamic simulations on the selected mutants of the membrane part of the bacterial FoF1-ATP synthase embedded in a native lipid bilayer: there were nine different mutations of a-subunit residues (aE219, aH245, aN214, aQ252) in the inlet half-channel. The structure proved to be stable to these mutations, although some of them (aH245Y and aQ252L) resulted in minor conformational changes. aH245 and aN214 were crucial for proton transport as they directly facilitated H+ transfer. The substitutions with nonpolar amino acids disrupted the transfer chain and water molecules or neighboring polar side chains could not replace them effectively. aE219 and aQ252 appeared not to be determinative for proton translocation, since an alternative pathway involving a chain of water molecules could compensate the ability of H+ transmembrane movement when they were substituted. Thus, mutations of conserved polar residues significantly affected hydration levels, leading to drastic changes in the occupancy and capacity of the structural water molecule clusters (W1-W3), up to their complete disappearance and consequently to the proton transfer chain disruption.


Subject(s)
Bacterial Proton-Translocating ATPases , Molecular Dynamics Simulation , Lipid Bilayers/chemistry , Lipid Bilayers/metabolism , Mutation , Protein Conformation , Protein Subunits/chemistry , Protein Subunits/genetics , Protein Subunits/metabolism , Bacterial Proton-Translocating ATPases/chemistry , Bacterial Proton-Translocating ATPases/genetics
11.
Cell Mol Life Sci ; 81(1): 235, 2024 May 25.
Article in English | MEDLINE | ID: mdl-38795169

ABSTRACT

N-methyl-D-aspartate receptors (NMDARs emerging from GRIN genes) are tetrameric receptors that form diverse channel compositions in neurons, typically consisting of two GluN1 subunits combined with two GluN2(A-D) subunits. During prenatal stages, the predominant channels are di-heteromers with two GluN1 and two GluN2B subunits due to the high abundance of GluN2B subunits. Postnatally, the expression of GluN2A subunits increases, giving rise to additional subtypes, including GluN2A-containing di-heteromers and tri-heteromers with GluN1, GluN2A, and GluN2B subunits. The latter  emerge as the major receptor subtype at mature synapses in the hippocampus. Despite extensive research on purely di-heteromeric receptors containing two identical GRIN variants, the impact of a single variant on the function of other channel forms, notably tri-heteromers, is lagging. In this study, we systematically investigated the effects of two de novo GRIN2B variants (G689C and G689S) in pure, mixed di- and tri-heteromers. Our findings reveal that incorporating a single variant in mixed di-heteromers or tri-heteromers exerts a dominant negative effect on glutamate potency, although 'mixed' channels show improved potency compared to pure variant-containing di-heteromers. We show that a single variant within a receptor complex does not impair the response of all receptor subtypes to the positive allosteric modulator pregnenolone-sulfate (PS), whereas spermine completely fails to potentiate tri-heteromers containing GluN2A and -2B-subunits. We examined PS on primary cultured hippocampal neurons transfected with the variants, and observed a positive impact over current amplitudes and synaptic activity. Together, our study supports previous observations showing that mixed di-heteromers exhibit improved glutamate potency and extend these findings towards the exploration of the effect of Loss-of-Function variants over tri-heteromers. Notably, we provide an initial and crucial demonstration of the beneficial effects of GRIN2B-relevant potentiators on tri-heteromers. Our results underscore the significance of studying how different variants affect distinct receptor subtypes, as these effects cannot be inferred solely from observations made on pure di-heteromers. Overall, this study contributes to ongoing efforts to understand the pathophysiology of GRINopathies and provides insights into potential treatment strategies.


Subject(s)
Pregnenolone , Receptors, N-Methyl-D-Aspartate , Receptors, N-Methyl-D-Aspartate/genetics , Receptors, N-Methyl-D-Aspartate/metabolism , Pregnenolone/pharmacology , Pregnenolone/metabolism , Humans , Animals , HEK293 Cells , Hippocampus/metabolism , Loss of Function Mutation , Protein Multimerization , Neurons/metabolism , Protein Subunits/metabolism , Protein Subunits/genetics
12.
Nat Genet ; 56(6): 1203-1212, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38816647

ABSTRACT

Catalytic activity of the imitation switch (ISWI) family of remodelers is critical for nucleosomal organization and DNA binding of certain transcription factors, including the insulator protein CTCF. Here we define the contribution of individual subcomplexes by deriving a panel of isogenic mouse stem cell lines, each lacking one of six ISWI accessory subunits. Individual deletions of subunits of either CERF, RSF, ACF, WICH or NoRC subcomplexes only moderately affect the chromatin landscape, while removal of the NURF-specific subunit BPTF leads to a strong reduction in chromatin accessibility and SNF2H ATPase localization around CTCF sites. This affects adjacent nucleosome occupancy and CTCF binding. At a group of sites with reduced chromatin accessibility, CTCF binding persists but cohesin occupancy is reduced, resulting in decreased insulation. These results suggest that CTCF binding can be separated from its function as an insulator in nuclear organization and identify a specific role for NURF in mediating SNF2H localization and chromatin opening at bound CTCF sites.


Subject(s)
Adenosine Triphosphatases , CCCTC-Binding Factor , Chromatin , Repressor Proteins , Transcription Factors , CCCTC-Binding Factor/metabolism , CCCTC-Binding Factor/genetics , Animals , Mice , Transcription Factors/metabolism , Transcription Factors/genetics , Repressor Proteins/metabolism , Repressor Proteins/genetics , Chromatin/metabolism , Chromatin/genetics , Adenosine Triphosphatases/metabolism , Adenosine Triphosphatases/genetics , Protein Binding , Cell Line , Chromosomal Proteins, Non-Histone/metabolism , Chromosomal Proteins, Non-Histone/genetics , Nucleosomes/metabolism , Nucleosomes/genetics , Protein Subunits/metabolism , Protein Subunits/genetics , Cell Cycle Proteins/metabolism , Cell Cycle Proteins/genetics , Binding Sites
13.
Biochem Biophys Res Commun ; 718: 150087, 2024 Jul 23.
Article in English | MEDLINE | ID: mdl-38735139

ABSTRACT

Flooding deprives plants of oxygen and thereby causes severe stress by interfering with energy production, leading to growth retardation. Enzymes and metabolites may help protect plants from waterlogging and hypoxic environmental conditions. Acetolactate synthase (ALS) is a key enzyme in the biosynthesis of branched-chain amino acids (BCAAs), providing the building blocks for proteins and various secondary metabolites. Additionally, under energy-poor conditions, free BCAAs can be used as an alternative energy source by mitochondria through a catabolic enzyme chain reaction. In this study, we characterized ALS-INTERACTING PROTEIN 1 (OsAIP1), which encodes the regulatory subunit of ALS in rice (Oryza sativa). This gene was expressed in all parts of the rice plant, and its expression level was significantly higher in submerged and low-oxygen environments. Rice transformants overexpressing OsAIP1 showed a higher survival rate under hypoxic stress than did non-transgenic control plants under the same conditions. The OsAIP1-overexpressing plants accumulated increased levels of BCAAs, demonstrating that OsAIP1 is an important factor in the hypoxia resistance mechanism. These results suggest that ALS proteins are part of a defense mechanism that improves the tolerance of plants to low-oxygen environments.


Subject(s)
Acetolactate Synthase , Gene Expression Regulation, Plant , Oryza , Plant Proteins , Oryza/genetics , Oryza/metabolism , Oryza/enzymology , Acetolactate Synthase/genetics , Acetolactate Synthase/metabolism , Plant Proteins/genetics , Plant Proteins/metabolism , Plants, Genetically Modified , Stress, Physiological/genetics , Amino Acids, Branched-Chain/metabolism , Oxygen/metabolism , Protein Subunits/metabolism , Protein Subunits/genetics
14.
Methods Mol Biol ; 2799: 55-77, 2024.
Article in English | MEDLINE | ID: mdl-38727903

ABSTRACT

NMDA-type ionotropic glutamate receptors are critically involved in many brain functions and are implicated in a variety of brain disorders. Seven NMDA receptor subunits exist (GluN1, GluN2A-D, and GluN3A-B) that assemble into tetrameric receptor subtypes with distinct functional properties and physiological roles. The majority NMDA receptors are composed of two GluN1 and two GluN2 subunits, which can assemble into four diheteromeric receptors subtypes composed of GluN1 and one type of GluN2 subunit (e.g., GluN1/2A), and presumably also six triheteromeric receptor subtypes composed of GluN1 and two different GluN2 subunits (e.g., GluN1/2A/2B). Furthermore, the GluN1 subunit exists as eight splice variants (e.g., GluN1-1a and GluN1-1b isoforms), and two different GluN1 isoforms can co-assemble to also form triheteromeric NMDA receptors (e.g., GluN1-1a/1b/2A). Here, we describe a method to faithfully express triheteromeric NMDA receptors in heterologous expression systems by controlling the identity of two of the four subunits. This method overcomes the problem that co-expression of three different NMDA receptor subunits generates two distinct diheteromeric receptor subtypes as well as one triheteromeric receptor subtype, thereby confounding studies that require a homogenous population of triheteromeric NMDA receptors. The method has been applied to selectively express recombinant triheteromeric GluN1/2A/2B, GluN1/2A/2C, GluN1/2B/2D, GluN1-1a/GluN1-1b/2A, GluN1-1a/GluN1-1b/2B receptors with negligible co-expression of the respective diheteromeric receptor subtypes. This method therefore enables quantitative evaluation of functional and pharmacological properties of triheteromeric NMDA receptors, some of which are abundant NMDA receptor subtypes in the adult brain.


Subject(s)
Protein Isoforms , Protein Subunits , Receptors, N-Methyl-D-Aspartate , Receptors, N-Methyl-D-Aspartate/metabolism , Receptors, N-Methyl-D-Aspartate/genetics , Humans , Protein Subunits/metabolism , Protein Subunits/genetics , Protein Isoforms/genetics , Protein Isoforms/metabolism , HEK293 Cells , Animals , Cell Membrane/metabolism , Gene Expression
15.
Methods Mol Biol ; 2799: 29-46, 2024.
Article in English | MEDLINE | ID: mdl-38727901

ABSTRACT

The expression and activity of ionotropic glutamate receptors control signal transduction at the excitatory synapses in the CNS. The NMDAR comprises two obligatory GluN1 subunits and two GluN2 or GluN3 subunits in different combinations. Each GluN subunit consists of four domains: the extracellular amino-terminal and agonist-binding domains, the transmembrane domain, and the intracellular C-terminal domain (CTD). The CTD interaction with various classes of intracellular proteins is critical for trafficking and synaptic localization of NMDARs. Amino acid mutations or the inclusion of premature stop codons in the CTD could contribute to the emergence of neurodevelopmental and neuropsychiatric disorders. Here, we describe the method of preparing primary hippocampal neurons and lentiviral particles expressing GluN subunits that can be used as a model to study cell surface expression and synaptic localization of NMDARs. We also show a simple method of fluorescence immunostaining of eGFP-tagged GluN2 subunits and subsequent microscopy technique and image analysis to study the effects of disease-associated mutations in the CTDs of GluN2A and GluN2B subunits.


Subject(s)
Hippocampus , Neurons , Receptors, N-Methyl-D-Aspartate , Receptors, N-Methyl-D-Aspartate/metabolism , Receptors, N-Methyl-D-Aspartate/genetics , Hippocampus/metabolism , Hippocampus/cytology , Neurons/metabolism , Animals , Protein Subunits/metabolism , Protein Subunits/genetics , Cells, Cultured , Rats , Humans , Lentivirus/genetics , Primary Cell Culture/methods , Gene Expression
16.
Biochim Biophys Acta Bioenerg ; 1865(3): 149046, 2024 Aug 01.
Article in English | MEDLINE | ID: mdl-38642871

ABSTRACT

The respiratory chain alternative enzymes (AEs) NDX and AOX from the tunicate Ciona intestinalis (Ascidiacea) have been xenotopically expressed and characterized in human cells in culture and in the model organisms Drosophila melanogaster and mouse, with the purpose of developing bypass therapies to combat mitochondrial diseases in human patients with defective complexes I and III/IV, respectively. The fact that the genes coding for NDX and AOX have been lost from genomes of evolutionarily successful animal groups, such as vertebrates and insects, led us to investigate if the composition of the respiratory chain of Ciona and other tunicates differs significantly from that of humans and Drosophila, to accommodate the natural presence of AEs. We have failed to identify in tunicate genomes fifteen orthologous genes that code for subunits of the respiratory chain complexes; all of these putatively missing subunits are peripheral to complexes I, III and IV in mammals, and many are important for complex-complex interaction in supercomplexes (SCs), such as NDUFA11, UQCR11 and COX7A. Modeling of all respiratory chain subunit polypeptides of Ciona indicates significant structural divergence that is consistent with the lack of these fifteen clear orthologous subunits. We also provide evidence using Ciona AOX expressed in Drosophila that this AE cannot access the coenzyme Q pool reduced by complex I, but it is readily available to oxidize coenzyme Q molecules reduced by glycerophosphate oxidase, a mitochondrial inner membrane-bound dehydrogenase that is not involved in SCs. Altogether, our results suggest that Ciona AEs might have evolved in a mitochondrial inner membrane environment much different from that of mammals and insects, possibly without SCs; this correlates with the preferential functional interaction between these AEs and non-SC dehydrogenases in heterologous mammalian and insect systems. We discuss the implications of these findings for the applicability of Ciona AEs in human bypass therapies and for our understanding of the evolution of animal respiratory chain.


Subject(s)
Ciona intestinalis , Mitochondrial Proteins , Oxidative Phosphorylation , Animals , Mitochondrial Proteins/genetics , Mitochondrial Proteins/metabolism , Ciona intestinalis/genetics , Ciona intestinalis/enzymology , Humans , Oxidoreductases/genetics , Oxidoreductases/metabolism , Protein Subunits/metabolism , Protein Subunits/genetics , Drosophila melanogaster/genetics , Drosophila melanogaster/enzymology , Urochordata/genetics , Urochordata/enzymology , Electron Transport , Electron Transport Complex I/metabolism , Electron Transport Complex I/genetics , Phylogeny , Plant Proteins
17.
MAbs ; 16(1): 2342243, 2024.
Article in English | MEDLINE | ID: mdl-38650451

ABSTRACT

The controlled expression of two or more proteins at a defined and stable ratio remains a substantial challenge, particularly in the bi- and multispecific antibody field. Achieving an optimal ratio of protein subunits can facilitate the assembly of multimeric proteins with high efficiency and minimize the production of by-products. In this study, we propose a solution based on alternative splicing, enabling the expression of a tunable and predefined ratio of two distinct polypeptide chains from the same pre-mRNA under the control of a single promoter. The pre-mRNA used in this study contains two open reading frames situated on separate exons. The first exon is flanked by two copies of the chicken troponin intron 4 (cTNT-I4) and is susceptible to excision from the pre-mRNA by means of alternative splicing. This specific design enables the modulation of the splice ratio by adjusting the strength of the splice acceptor. To illustrate this approach, we developed constructs expressing varying ratios of GFP and dsRED and extended their application to multimeric proteins such as monoclonal antibodies, achieving industrially relevant expression levels (>1 g/L) in a 14-day fed-batch process. The stability of the splice ratio was confirmed by droplet digital PCR in a stable pool cultivated over a 28-day period, while product quality was assessed via intact mass analysis, demonstrating absence of product-related impurities resulting from undesired splice events. Furthermore, we showcased the versatility of the construct by expressing two subunits of a bispecific antibody of the BEAT® type, which contains three distinct subunits in total.


Subject(s)
Alternative Splicing , Animals , Protein Subunits/genetics , Humans , Chickens , Antibodies, Bispecific/genetics , Antibodies, Bispecific/biosynthesis , CHO Cells , Exons/genetics , Cricetulus , Green Fluorescent Proteins/genetics , Antibodies, Monoclonal/genetics , Antibodies, Monoclonal/biosynthesis , RNA Precursors/genetics
18.
J Biol Chem ; 300(4): 107130, 2024 Apr.
Article in English | MEDLINE | ID: mdl-38432630

ABSTRACT

The actin cytoskeleton and reactive oxygen species (ROS) both play crucial roles in various cellular processes. Previous research indicated a direct interaction between two key components of these systems: the WAVE1 subunit of the WAVE regulatory complex (WRC), which promotes actin polymerization and the p47phox subunit of the NADPH oxidase 2 complex (NOX2), which produces ROS. Here, using carefully characterized recombinant proteins, we find that activated p47phox uses its dual Src homology 3 domains to bind to multiple regions within the WAVE1 and Abi2 subunits of the WRC, without altering WRC's activity in promoting Arp2/3-mediated actin polymerization. Notably, contrary to previous findings, p47phox uses the same binding pocket to interact with both the WRC and the p22phox subunit of NOX2, albeit in a mutually exclusive manner. This observation suggests that when activated, p47phox may separately participate in two distinct processes: assembling into NOX2 to promote ROS production and engaging with WRC to regulate the actin cytoskeleton.


Subject(s)
NADPH Oxidase 2 , Wiskott-Aldrich Syndrome Protein Family , Humans , Actin Cytoskeleton/genetics , Actin Cytoskeleton/metabolism , Actins/metabolism , NADPH Oxidase 2/metabolism , NADPH Oxidase 2/genetics , NADPH Oxidases/metabolism , NADPH Oxidases/genetics , Protein Binding , Reactive Oxygen Species/metabolism , Wiskott-Aldrich Syndrome Protein Family/metabolism , Wiskott-Aldrich Syndrome Protein Family/genetics , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , Protein Subunits/genetics , Protein Subunits/metabolism , Actin-Related Protein 2-3 Complex/metabolism , Binding Sites
19.
Mol Cancer Res ; 22(5): 423-439, 2024 May 02.
Article in English | MEDLINE | ID: mdl-38324016

ABSTRACT

NDC80 complex (NDC80C) is composed of four subunits (SPC24, SPC25, NDC80, and NUF2) and is vital for kinetochore-microtubule (KT-MT) attachment during mitosis. Paradoxically, NDC80C also functions in the activation of the spindle-assembly checkpoint (SAC). This raises an interesting question regarding how mitosis is regulated when NDC80C levels are compromised. Using a degron-mediated depletion system, we found that acute silencing of SPC24 triggered a transient mitotic arrest followed by mitotic slippage. SPC24-deficient cells were unable to sustain SAC activation despite the loss of KT-MT interaction. Intriguingly, our results revealed that other subunits of the NDC80C were co-downregulated with SPC24 at a posttranslational level. Silencing any individual subunit of NDC80C likewise reduced the expression of the entire complex. We found that the SPC24-SPC25 and NDC80-NUF2 subcomplexes could be individually stabilized using ectopically expressed subunits. The synergism of SPC24 downregulation with drugs that promote either mitotic arrest or mitotic slippage further underscored the dual roles of NDC80C in KT-MT interaction and SAC maintenance. The tight coordinated regulation of NDC80C subunits suggests that targeting individual subunits could disrupt mitotic progression and provide new avenues for therapeutic intervention. IMPLICATIONS: These results highlight the tight coordinated regulation of NDC80C subunits and their potential as targets for antimitotic therapies.


Subject(s)
Cell Cycle Proteins , Cytoskeletal Proteins , Mitosis , Nuclear Proteins , Humans , Nuclear Proteins/metabolism , Nuclear Proteins/genetics , Cell Cycle Proteins/metabolism , Cell Cycle Proteins/genetics , HeLa Cells , Cytoskeletal Proteins/metabolism , Cytoskeletal Proteins/genetics , Kinetochores/metabolism , M Phase Cell Cycle Checkpoints/genetics , Spindle Apparatus/metabolism , Protein Subunits/metabolism , Protein Subunits/genetics , Microtubule-Associated Proteins/metabolism , Microtubule-Associated Proteins/genetics
20.
J Biomol NMR ; 78(2): 109-117, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38421550

ABSTRACT

N-linked glycosylation is an essential and highly conserved co- and post-translational protein modification in all domains of life. In humans, genetic defects in N-linked glycosylation pathways result in metabolic diseases collectively called Congenital Disorders of Glycosylation. In this modification reaction, a mannose rich oligosaccharide is transferred from a lipid-linked donor substrate to a specific asparagine side-chain within the -N-X-T/S- sequence (where X ≠ Proline) of the nascent protein. Oligosaccharyltransferase (OST), a multi-subunit membrane embedded enzyme catalyzes this glycosylation reaction in eukaryotes. In yeast, Ost4 is the smallest of nine subunits and bridges the interaction of the catalytic subunit, Stt3, with Ost3 (or its homolog, Ost6). Mutations of any C-terminal hydrophobic residues in Ost4 to a charged residue destabilizes the enzyme and negatively impacts its function. Specifically, the V23D mutation results in a temperature-sensitive phenotype in yeast. Here, we report the reconstitution of both purified recombinant Ost4 and Ost4V23D each in a POPC/POPE lipid bilayer and their resonance assignments using heteronuclear 2D and 3D solid-state NMR with magic-angle spinning. The chemical shifts of Ost4 changed significantly upon the V23D mutation, suggesting a dramatic change in its chemical environment.


Subject(s)
Hexosyltransferases , Liposomes , Membrane Proteins , Nuclear Magnetic Resonance, Biomolecular , Hexosyltransferases/genetics , Hexosyltransferases/chemistry , Hexosyltransferases/metabolism , Nuclear Magnetic Resonance, Biomolecular/methods , Membrane Proteins/chemistry , Membrane Proteins/genetics , Membrane Proteins/metabolism , Liposomes/chemistry , Saccharomyces cerevisiae Proteins/chemistry , Saccharomyces cerevisiae Proteins/genetics , Saccharomyces cerevisiae Proteins/metabolism , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae/metabolism , Mutation , Glycosylation , Protein Subunits/chemistry , Protein Subunits/genetics
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