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The present study was focused to analyse and evaluate potential targets of NADPH Oxidase (NOX) at varying sub-units and co-relating their interactions with apocynin to identify appropreiate mechanism of inhibition for NOX by applying specific facets of computational biology . Active site molecular docking analysis was carried for apocynin against various subunits of NOX and comparatively analysise the binding affinity profiles which were obtained when apocynin was docked with p47phox complete subunit of NOX and all the other subunits.

In 2020 and 2021, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a novel coronavirus, caused a global pandemic. Vaccines are expected to reduce the pressure of prevention and control, and have become the most effective strategy to solve the pandemic crisis. SARS-CoV-2 infects the host by binding to the cellular receptor angiotensin converting enzyme 2 (ACE2) via the receptor-binding domain (RBD) of the surface spike (S) glycoprotein. In this study, a candidate vaccine based on a RBD recombinant subunit was prepared by means of a novel glycoengineered yeast Pichia pastoris expression system with characteristics of glycosylation modification similar to those of mammalian cells. The candidate vaccine effectively stimulated mice to produce high-titer anti-RBD specific antibody. Furthermore, the specific antibody titer and virus-neutralizing antibody (NAb) titer induced by the vaccine were increased significantly by the combination of the double adjuvants Al(OH)3 and CpG. Our results showed that the virus-NAb lasted for more than 6 months in mice. To summarize, we have obtained a SARS-CoV-2 vaccine based on the RBD of the S glycoprotein expressed in glycoengineered Pichia pastoris, which stimulates neutralizing and protective antibody responses. A technical route for fucose-free complex-type N-glycosylation modified recombinant subunit vaccine preparation has been established.

Transmembrane protein channels enable fast and highly sensitive electrical detection of single molecules. Nanopore sequencing of DNA was achieved using an engineered Mycobacterium smegmatis porin A (MspA) in combination with a motor enzyme. Due to its favorable channel geometry, the octameric MspA pore exhibits the highest current level as compared to other pore proteins. To date, MspA is the only protein nanopore with a published record of DNA sequencing. While widely used in commercial devices, nanopore sequencing of DNA suffers from significant base-calling errors due to stochastic events of the complex DNA-motor-pore combination and the contribution of up to five nucleotides to the signal at each position. Asymmetric mutations within subunits of the channel protein offer an enormous potential to improve nucleotide resolution and sequencing accuracy. However, random subunit assembly does not allow control of the channel composition of MspA and other oligomeric protein pores. In this study, we showed that it is feasible to convert octameric MspA into a single-chain pore by connecting eight subunits using peptide linkers. We constructed single-chain MspA trimers, pentamers, hexamers and heptamers to demonstrate that it is feasible to alter the subunit stoichiometry and the MspA pore diameter. All single-chain MspA proteins formed functional channels in lipid bilayer experiments. Importantly, we demonstrated that single-chain MspA discriminated all four nucleotides identical to MspA produced from monomers. Thus, single-chain MspA constitutes a new milestone in its development and adaptation as a biosensor for DNA sequencing and many other applications.STATEMENT OF SIGNFICANCENanopore sequencing of DNA is a fast and cheap technology that uniquely delivers multi-kilobase reads. It is currently used world-wide in many applications such as genome sequencing, epigenetics, and surveillance of viral and bacterial pathogens and has started to revolutionize human lives in medicine, agriculture and environmental studies. However, the high base-calling error rates prevent nanopore DNA sequencing from reaching its full potential. In this study, we converted octameric MspA into a single-chain pore enabling asymmetric mutations to fine-tune the pore geometry and chemistry and address the shortcomings of nanopores. Thus, single-chain MspA constitutes a new milestone in its development and adaptation as a biosensor for DNA sequencing and many other applications.

SummaryA biofilm inhibiting mechanism operates in the cyanobacterium Synechococcus elongatus. Here, we demonstrate that the glycosyltransferase homolog, Ogt, participates in the inhibitory process – inactivation of ogt results in robust biofilm formation. Furthermore, a mutational approach shows requirement of the glycosyltransferase activity for biofilm inhibition. This enzyme is necessary for glycosylation of the pilus subunit and for adequate pilus formation. In contrast to wild-type culture in which most cells exhibit several pili, only 25% of the mutant cells are piliated, half of which possess a single pilus. In spite of this poor piliation, natural DNA competence was similar to that of wild-type, therefore, we propose that the unglycosylated pili facilitate DNA transformation. Additionally, conditioned medium from wild-type culture, which contains a biofilm inhibiting substance(s), only partially blocks biofilm development by the ogt-mutant. Thus, we suggest that inactivation of ogt affects multiple processes including production or secretion of the inhibitor as well as the ability to sense or respond to it.Originality-Significance StatementThe molecular mechanisms that underlie biofilm development in cyanobacteria are just emerging. Using the cyanobacterium S. elongatus as a model, we demonstrate that glycosylation of the pilus subunit is crucial for the biofilm self-suppression mechanism, however, it is dispensable for DNA competence.

Numerous studies using a combination of confocal microscopic- and pharmacological-based approaches have demonstrated that the actin cytoskeleton dynamically responds to pathogen infection. Here, we observed that phalloidin treatment induced actin nucleation, resulting in enhanced resistance of wheat against the stripe rust pathogen Puccinia striiformis f. sp. tritici (Pst). To define the mechanism underpinning this process, we characterized a family of conserved actin-binding proteins, the actin related protein (ARP) family, which controls actin polymerization. Specifically, we identified and characterized a wheat ARPC gene (TaARPC5), which encodes a 136-amino acid protein containing a P16-Arc domain, the smallest subunit of the ARP2/3 complex. TaARPC5 mRNA accumulation was induced following the infection of plants with the avirulent Pst strain, and following the elicitation with flagellin (e.g., flg22) as well. Subcellular localization analysis revealed that TaARPC5 is primarily localized to the cortical actin cytoskeleton, and its precise cellular localizations suggest the proximity to processes correlated with the actin-organelle interface. Upon treatment with virulent Pst, TaARPC5-knockdown plants exhibited a significant reduction in the expression of PTI-specific mRNAs. Conversely, we observed enhanced induction of reactive oxygen species (ROS) accumulation and a decrease in TaCAT1 expression following infection with an incompatible Pst isolate. Together with yeast complementation assays, the current study demonstrates a role for TaARPC5 in resistance signaling in wheat against Pst infection by regulating the host actin cytoskeleton.

Aims: We aimed to explore the role of nicotinamide adenine dinucleotide phosphate oxidase subunit 4 (Nox4) in the regulation of hypercalciuria-induced renal oxidative damage and crystal depositions...

Tumor necrosis factor (TNF) α-induced nuclear translocation of the NF-κB subunit RELA has been implicated in several pathological conditions. Here we report the discovery of a spirocyclic dimer (SpiD7) that covalently modifies RELA to inhibit TNFα-induced nuclear translocation. This is a previously unexplored strategy to inhibit TNFα-induced NF-κB activation., Discovery of a spirocyclic dimer (SpiD7) that covalently modifies RELA to generate stable high molecular weight complexes. SpiD7 inhibits TNFα-induced nuclear translocation of RELA resulting in the blockade of NF-kB gene transcription, through a previously unexplored modality.

Stringent starvation protein A (SspA) involved in nucleotide metabolism, acid tolerance and virulence of bacteria has been demonstrated to function as a transcription factor to regulate σ70-dependent gene transcription through interacting with σ70 region 4 and the zinc binding domain (ZBD) of E. coli RNA polymerase (EcoRNAP) β′ subunit simultaneously. Despite extensive biochemical and structural analyses were reported recently, the interactions of SspA with RNAP are not comprehensively understood. Here, we reprocessed our previous cryo-EM dataset of EcoRNAP-promoter open complex with SspA (SspA-RPo) and obtained a significantly improved density map. Unexpectedly, the new map showed that SspA interacts with both N-terminal helix of β′ subunit (β′ΝΤΗ) and ω subunit, which contributes to stabilize the SspA-EcoRNAP σ70 holoenzyme complex. Sequence alignments and phylogenetic tree analyses of N-terminal sequences of β′ subunit from different classes of bacteria revealed that β′ΝΤΗ is highly conserved and exclusively found in low-GC-content Gram-negative bacteria that harbor SspA, implying a co-evolution of β′ΝΤΗ and SspA. The transcription assays of wild-type SspA and its mutants demonstrated the interaction between SspA and β′ΝΤΗ facilitates the transcription regulation of SspA. Together, our results provide a more comprehensive insight into the interactions between SspA and RNAP and their roles in bacterial transcription regulation.

The bacterial condensin MukB and the cellular chromosomal decatenase, topoisomerase IV interact and this interaction is required for proper condensation and topological ordering of the chromosome. Here, we show that Topo IV stimulates MukB DNA condensation by stabilizing loops in DNA: MukB alone can condense nicked plasmid DNA into a protein–DNA complex that has greater electrophoretic mobility than that of the DNA alone, but both MukB and Topo IV are required for a similar condensation of a linear DNA representing long stretches of the chromosome. Remarkably, we show that rather than MukB stimulating the decatenase activity of Topo IV, as has been argued previously, in stoichiometric complexes of the two enzymes each inhibits the activity of the other: the ParC subunit of Topo IV inhibits the MukF-stimulated ATPase activity of MukB and MukB inhibits both DNA crossover trapping and DNA cleavage by Topo IV. These observations suggest that when in complex on the DNA, Topo IV inhibits the motor function of MukB and the two proteins provide a stable scaffold for chromosomal DNA condensation.

Congenital disorders of glycosylation (CDGs) form a group of rare diseases characterized by hypoglycosylation. We here report the identification of 16 individuals from nine families who have either inherited or de novo heterozygous missense variants in STT3A, leading to an autosomal-dominant CDG. STT3A encodes the catalytic subunit of the STT3A-containing oligosaccharyltransferase (OST) complex, essential for protein N-glycosylation. Affected individuals presented with variable skeletal anomalies, short stature, macrocephaly, and dysmorphic features; half had intellectual disability. Additional features included increased muscle tone and muscle cramps. Modeling of the variants in the 3D structure of the OST complex indicated that all variants are located in the catalytic site of STT3A, suggesting a direct mechanistic link to the transfer of oligosaccharides onto nascent glycoproteins. Indeed, expression of STT3A at mRNA and steady-state protein level in fibroblasts was normal, while glycosylation was abnormal. In S. cerevisiae, expression of STT3 containing variants homologous to those in affected individuals induced defective glycosylation of carboxypeptidase Y in a wild-type yeast strain and expression of the same mutants in the STT3 hypomorphic stt3-7 yeast strain worsened the already observed glycosylation defect. These data support a dominant pathomechanism underlying the glycosylation defect. Recessive mutations in STT3A have previously been described to lead to a CDG. We present here a dominant form of STT3A-CDG that, because of the presence of abnormal transferrin glycoforms, is unusual among dominant type I CDGs. ispartof: AMERICAN JOURNAL OF HUMAN GENETICS vol:108 issue:11 pages:2130-2144 ispartof: location:United States status: published

Cereal grain-derived protein hydrolysates exert beneficial effects for human health, thus utilization of by-products with high protein content has drawn attention. In this study, hot water extraction of rice husk has been optimized to obtain protein hydrolysate with the highest anticancer activity. The optimum protein value was obtained as 2.40 g/L corresponding to 43.2 g protein/kg dried rice husk under the conditions of 60 degrees C, 2.0 mL/min flow rate and pH 10.0. The protein hydrolysate was encapsulated with chitosan, where the mean particle size of protein hydrolysate (0.3 %) loaded chitosan nanoparticles was 256.4 +/- 33. 4 nm with 89 % encapsulation efficiency and a 65% release at the end of 6 days. Cytotoxicity assays showed that the lowest cell viabilities have been achieved with A549 and MCF7 cells with IC50 values of 1.98 and 3.58 mu g/mL, respectively, whereas nuclear fragmentation and apoptotic bodies were observed through Hoechst 33342 staining. The cytotoxic effect might be associated with the wide variety of peptide/protein subunits ranging from 10 kDa to more than 180 kDa in the protein hydrolysate of rice husk. (C) 2021 The Korean Society of Industrial and Engineering Chemistry. Published by Elsevier B.V. All rights reserved., Kocaeli University [KOU-BAP-2016-081, KOU-BAP-2018-149], The research funds provided by Kocaeli University (KOU-BAP-2016-081 and KOU-BAP-2018-149) are highly appreciated. Special thanks to Mr. Ahmet Yilmaz who provided the rice husk from Ozserhat Gida Sanayi Tic. Ltd. Sti, Edirne, Turkey. We are grateful to Dilan Yerli for helping with SDS-PAGE, Prof. Dr. Kemal Sami Korkmaz for providing access to his lab at Ege University and Pelin Saglam-Metiner for her contributions to fluorescent staining assays.

Cancer cells release a variety of factors that contribute to the alteration of proximal and distal tissues to promote metastasis. Recent studies have demonstrated that aggressive cancer cells release extracellular vesicles with higher protein content and in excess than extracellular vesicles isolated from patients with less aggressive disease or healthy individuals. We found that melanoma tumor-derived extracellular vesicles (TEV) downregulate type I interferon receptor subunit 1 (IFNAR1), suppress expression of the interferon stimulated gene cholesterol 25-hydroxylase (CH25H). Loss of CH25H is observed in the leukocytes from melanoma patients, which correlated with metastasis and poor survival. Similarly, mice also exhibit loss of IFNAR1 following TEV administration. Moreover, loss of CH25H increased TEV uptake and TEV-induced pre metastatic niche and lung metastasis. Use of the anti-hypertensive drug, reserpine, mimicked the effects of the CH25H product 25-hydroxycholesterol to suppress TEV uptake and TEV-mediated tumor growth, pre-metastatic niche formation, and lung metastasis. These results suggest the importance of CH25H in suppressing TEV mediate cancer progression and importance of developing strategies to suppress TEV uptake and TEV-mediated disease progression.

In SARS-CoV-2 replication complex, the Non-structural protein 9 (Nsp9) is an important RNA binding subunit in the RNA-synthesizing machinery. The dimeric forms of coronavirus Nsp9 increase their nucleic acid binding affinity and the N-finger motif appears to play a critical role in dimerization. Here, we present a structural, lipophilic and energetic study about the Nsp9 dimer of SARS-CoV-2 through computational methods that complement hydrophobicity scales of amino acids with molecular dynamics simulations. Additionally, we presented a virtual N-finger mutation to investigate whether this motif contributes to dimer stability. The results reveal for the native dimer that the N-finger contributes favorably through hydrogen bond interactions and two amino acids bellowing to the hydrophobic region, Leu45 and Leu106, are crucial in the formation of the cavity for potential drug binding. On the other hand, Gly100 and Gly104, are responsible for stabilizing the α-helices and making the dimer interface remain stable in both, native and mutant (without N-finger motif) systems. Besides, clustering results for the native dimer showed accessible cavities to drugs. In addition, the energetic and lipophilic analysis reveal that the higher binding energy in the native dimer can be deduced since it is more lipophilic than the mutant one, increasing non-polar interactions, which is in line with the result of MM-GBSA and SIE approaches where the van der Waals energy term has the greatest weight in the stability of the native dimer. Overall, we provide a detailed study on the Nsp9 dimer of SARS-CoV-2 that may aid in the development of new strategies for the treatment and prevention of COVID-19.

Domain swapping is a mechanism of protein oligomerization by which two or more subunits exchange structural elements to generate an intertwined complex. Numerous studies support a diversity of swapping mechanisms in which structural elements can be exchanged at different stages of the folding pathway of a subunit. Here, we used single-molecule optical tweezers technique to analyze the swapping mechanism of the forkhead DNA-binding domain of human transcription factor FoxP1. FoxP1 populates folded monomers in equilibrium with a swapped dimer. We generated a fusion protein linking two FoxP1 domains in tandem to obtain repetitive mechanical folding and unfolding trajectories. Thus, by stretching the same molecule several times, we detected either the independent folding of each domain or the elusive swapping step between domains. We found that a swapped dimer can be formed directly from fully or mostly folded monomer. In this situation, the interaction between the monomers in route to the domain-swapped dimer is the rate-limiting step. This approach is a useful strategy to test the different proposed domain swapping mechanisms for proteins with relevant physiological functions.

The funny current, and the HCN channels that form it, are affected by the direct binding of cyclic nucleotides. Binding of these second messengers causes a depolarizing shift of the activation curve, which leads to greater availability of current at physiological membrane voltages. This review outlines a brief history on this regulation and provides some evidence that other cyclic nucleotides, especially cGMP, may be important for the regulation of the funny channel in the heart. Current understanding of the molecular mechanism of cyclic nucleotide regulation is also presented, which includes the notions that full and partial agonism occur as a consequence of negatively cooperative binding. Knowledge gaps, including a potential role of cyclic nucleotide-regulation of the funny current under pathophysiological conditions, are included. The work highlighted here is in dedication to Dario DiFrancesco on his retirement.

Nitric oxide (NO)-mediated vasodilatation is a fundamental response of vasculature, however, regulation of NO signaling pathway on resistance vessels in the older adult with hypertension is still unclear. The 16-week-spontaneously hypertensive rats (SHR), the 18-month-SHR (OldSHR), and the age-matched Wistar-Kyoto rats were used to study the changes of mesenteric resistance artery dilatation caused by sodium nitroprusside (SNP). After pre-vasoconstriction by norepinephrine (NE), the response of endothelium-denuded mesenteric artery ring to SNP was observed, and the changes in vascular response after pharmacological interventions of key nodes in the NO/sGC/cGMP/PKG1α signaling pathway were observed as well. RNA sequencing and functional enrichment analyses were used to provide information for conducting validation experiments. Vasodilation of NO in OldSHR was decreased, which significantly correlated with the reduction of PKG-mediated effect. Functional enrichment analysis of RNA sequencing showed that genes encoding important proteins such as sGC and MYPT1 (protein phosphatase 1 regulatory subunit 12A) were downregulated in OldSHR. Molecular biology validation results showed that mRNA expression of both α and β subunits of sGC were reduced, while mRNA and protein expression of PKG1α were reduced in OldSHR. More importantly, the expression of MYPT1 and pS668-MYPT1 was significantly reduced in OldSHR, even under the treatment of SNP. The experiment also revealed an enhanced cAMP system in vasodilation in hypertension, while this function was completely lost in the OldSHR. Therefore, an NO-mediated decrease in vascular smooth muscle relaxation was found in the OldSHR. The dysfunction in cGMP-PKG signaling, in particular, decreased pS668-MYPT1 was mechanistically involved.

The human liver fluke Opisthorchis viverrini (Ov), the primary risk factor for cholangiocarcinoma (CHCA), is a parasite endemic to southeast Asian countries. With no effective treatments for CHCA currently available, early diagnosis and treatment of Ov infection remains the only practical method for the prevention of CHCA. In this study, plasma phosphoproteomes of patients in the non-Ov infection, non-cholangiocarcinoma subject group (non-OVCCA), the asymptomatic Ov infected group (OV), and the CHCA group (CCA), were investigated to identify potential biomarkers for Ov infection and CHCA. The AKT signalling pathway was found to be up-regulated. Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit beta isoform (PIK3CB), an upstream signalling molecule, was selected as a potential biomarker and evaluated using indirect enzyme-linked immunosorbent assay (ELISA). Results demonstrated evidence that levels of PIK3CB in both the OV group and CCA group was statistically different compared to the non-OVCCA group (P < 0.01). However, the levels of PIK3CB between the OV group and the CCA group were found not to be statistically different. Sensitivity and specificity for OV using OD450 cut-off at >1.570 was 76 and 72%, respectively. For CCA, sensitivity and specificity using OD450 cut-off at >1.398 was 68 and 76%, respectively. Application of indirect ELISA detecting plasma PIK3CB will be of great benefit for screening of opisthorchiasis and CHCA.

Dithiaaza-17-crown-5 ethers containing piperidin-4-one subunit and dithiacrown ether fragment were synthesized in one-pot Petrenko–Kritschenko reaction from 2,2'-[ethane-1,2-diylbis(oxyethane-2,1-diylsulfanediyl)]dibenzaldehyde, methyl ethyl ketone or dibenzyl ketone, and ammonium acetate. Molecular structure of dithiaaza-17-crown-5 ethers were confirmed by NMR, HRMS, and single crystal X-ray diffraction.

We previously observed decreased expression of rice OsmiR159a.1 on infection with the bacterial blight‐causing pathogen Xanthomonas oryzae pv. oryzae (Xoo), and identified the OsLRR_RLK (leucine‐rich repeat_ receptor like kinase) gene as an authentic target of OsmiR159a.1. Here, we found that a Tos17 insertion mutant of LRR_RLK displayed increasing temporal resistance to Xoo, whereas the LRR_RLK overexpression lines were susceptible to the pathogen early on in the infection, indicating that LRR_RLK encodes a repressor of rice resistance to Xoo infection, and it was renamed as RIR1 (Rice Immunity Repressor 1). RIR1 overexpression plants were more susceptible to Xoo at late growth stage, suggesting that RIR1 mRNA levels are negatively correlated with the resistance of rice against Xoo. We discovered that OsmiR159a.1 repression in Xoo‐infected plants was largely dependent on the pathogen's type III secretion system. Co‐immunoprecipitation, bimolecular fluoresence complementation, and pull‐down assays indicated that RIR1 interacted with the NADH‐ubiquinone oxidoreductase (NUO) 51‐kDa subunit of the mitochondrial complex I through its kinase domain. Notably, impairment of RIR1 or overexpression of NUO resulted in reactive oxygen species accumulation and enhanced expression of pathogen‐resistance genes, including jasmonic acid pathway genes. We propose that pathogens may inhibit OsmiR159 to interfere with the RIR1–NUO interaction, and subsequently depression of rice immune signalling pathways. The resistance genes manipulated by Xoo can be a probe to explore the regulatory network during host–pathogen interactions., Xanthomonas oryzae may use type III effectors to inhibit OsmiR159 and release its target rice gene RIR1 expression, then promote RIR1–NUO interaction that leads to depression of rice immune signalling pathways.

Robust neural information transfer relies on a delicate molecular nano-architecture of chemical synapses. Neurotransmitter release is controlled by a specific arrangement of proteins within presynaptic active zones. How the specific presynaptic molecular architecture relates to postsynaptic organization and how synaptic nano-architecture is transsynaptically regulated to enable stable synaptic transmission remain enigmatic. Using time-gated stimulated emission-depletion microscopy at the Drosophila neuromuscular junction, we found that presynaptic nanorings formed by the active-zone scaffold Bruchpilot (Brp) align with postsynaptic glutamate receptor (GluR) rings. Individual rings harbor approximately four transsynaptically aligned Brp-GluR nanocolumns. Similar nanocolumn rings are formed by the presynaptic protein Unc13A and GluRs. Intriguingly, acute GluR impairment triggers transsynaptic nanocolumn formation on the minute timescale during homeostatic plasticity. We reveal distinct phases of structural transsynaptic homeostatic plasticity, with postsynaptic GluR reorganization preceding presynaptic Brp modulation. Finally, homeostatic control of transsynaptic nano-architecture and neurotransmitter release requires the auxiliary GluR subunit Neto. Thus, transsynaptic nanocolumn rings provide a substrate for rapid homeostatic stabilization of synaptic efficacy., Proceedings of the National Academy of Sciences of the United States of America, 119 (45), ISSN:0027-8424, ISSN:1091-6490

The ionotropic γ-aminobutyric acid (iGABA) receptor is commonly considered as a fast inhibitory channel and is an important insecticide target. Since 1990, RDL, LCCH3, and GRD have been successively isolated and found to be potential subunits of the insect iGABA receptor. More recently, one orphan gene named 8916 was found and considered to be another potential iGABA receptor subunit according to its amino acid sequence. However, little information about 8916 has been reported. Here, the 8916 subunit from Chilo suppressalis was studied to determine whether it can form part of a functional iGABA receptor by co-expressing this subunit with CsRDL1 or CsLCCH3 in the Xenopus oocyte system. Cs8916 or CsLCCH3 did not form functional ion channels when expressed alone. However, Cs8916 was able to form heteromeric ion channels when expressed with either CsLCCH3 or CsRDL1. The recombinant heteromeric Cs8916/LCCH3 channel was a cation-selective channel, which was sensitive to GABA or β-alanine. The current of the Cs8916/LCCH3 channel was inhibited by dieldrin, endosulfan, fipronil, or ethiprole. In contrast, fluralaner, broflanilide, and avermectin showed little effect on the Cs8916/LCCH3 channel (IC50s > 10 000 nM). The Cs8916/RDL1 channel was sensitive to GABA, but was significantly different in EC50 and Imax for GABA to those of homomeric CsRDL1. Fluralaner, fipronil, or dieldrin showed antagonistic actions on Cs8916/RDL1. In conclusion, Cs8916 is a potential iGABA receptor subunit, which can interact with CsLCCH3 to generate a cation-selective channel that is sensitive to several insecticides. Also, as Cs8916/RDL1 has a higher EC50 than homomeric CsRDL1, Cs8916 may affect the physiological functions of CsRDL1 and therefore play a role in fine-tuning GABAergic signaling.

BACKGROUND AND PURPOSE Glycine receptors composed of α1 and β subunits are primarily found in the spinal cord and brainstem and are potentiated by ethanol (10-100 mM). However, much less is known about the presence, composition and ethanol sensitivity of these receptors in higher CNS regions. Here, we examined two regions of the brain reward system, the ventral tegmental area (VTA) and the prefrontal cortex (PFC), to determine their glycine receptor subunit composition and sensitivity to ethanol. EXPERIMENTAL APPROACH We used Western blot, immunohistochemistry and electrophysiological techniques in three different models: wild-type C57BL/6, glycine receptor subunit α1 knock-in and glycine receptor subunit α2 knockout mice. KEY RESULTS Similar levels of α and β receptor subunits were detected in both brain regions, and electrophysiological recordings demonstrated the presence of glycine-activated currents in both areas. Sensitivity of glycine receptors to glycine was lower in the PFC compared with VTA. Picrotoxin only partly blocked the glycine-activated current in the PFC and VTA, indicating that both regions express heteromeric αβ receptors. Glycine receptors in VTA neurons, but not in PFC neurons, were potentiated by ethanol. CONCLUSION AND IMPLICATIONS Glycine receptors in VTA neurons from WT and α2 KO mice were potentiated by ethanol, but not in neurons from the α1 KI mice, supporting the conclusion that α1 glycine receptors are predominantly expressed in the VTA. By contrast, glycine receptors in PFC neurons were not potentiated in any of the mouse models studied, suggesting the presence of α2/α3/α4, rather than α1 glycine receptor subunits.

The anoxygenic phototrophic bacterium Heliobacterium modesticaldum contains a photochemical reaction center protein complex (called the HbRC) consisting of a homodimer of the PshA polypeptide and two copies of a newly discovered polypeptide called PshX, which is a single transmembrane helix that binds two bacteriochlorophyll g molecules. To assess the function of PshX, we produced a ∆pshX strain of Hbt. modesticaldum by leveraging the endogenous Hbt. modesticaldum Type I-A CRISPR-Cas system to aid in mutant selection. We optimized this system by separating the homologous recombination and CRISPR-based selection steps into two plasmid transformations, allowing for markerless gene replacement. Fluorescence and low-temperature absorbance of the purified HbRC from the wild-type and ∆pshX strains showed that the bacteriochlorophylls bound by PshX have the lowest site energies in the entire HbRC. This indicates that PshX acts as a low-energy antenna subunit, participating in entropy-assisted uphill energy transfer toward the P800 special bacteriochlorophyll g pair. We further discuss the role that PshX may play in stability of the HbRC, its conservation in other heliobacterial species, and the evolutionary pressure to produce and maintain single-TMH subunits in similar locations in other reaction centers.

Probiotics are microbes having tremendous potential to prevent gastrointestinal disorders. In current investigation, immunomodulatory action of probiotic Lacticaseibacillus rhamnosus MTCC-5897 was studied during exclusion, competition and displacement of Escherichia coli on intestinal epithelial (Caco-2) cells. The incubation of intestinal cells with Escherichia coli, enhanced downstream signalling and activated nuclear factor kappa B (NF-κB). This significantly increased (p

Abstract Bacterial chaperonin GroEL is a complex ring-shaped protein oligomer that promotes the folding of other proteins by encapsulating them in the cavity. There is very little structural information about the disordered C-terminal fragment of the GroEL subunits, which is involved in the folding of the substrate protein. A 3D reconstruction of the GroEL apo-form was obtained by cryo-electron microscopy (cryo-EM) with a resolution of 3.02 Å and supplemented by molecular dynamics (MD) calculations. The results of cryo-EM and MD are in good agreement and demonstrate a diverse mobility of the protein subunit domains. The MD results predict the dynamics and the network of intramolecular contacts of the C-terminal sections of the protein. These results are of great importance for the subsequent study of the mechanism of protein folding in the GroEL cavity.

Enzymes from extremophilic organisms are of great interest in biotechnology because they possess natural adaptation to extreme conditions often required in biotechnological processes. Lipases are a large class of hydrolytic enzymes, which catalyze the cleavage of ester bonds in triacylglycerols and have numerous biotechnological applications. The structure of a single-point mutant of esterase PMGL2 was studied. The gene encoding this enzyme was identified by the screening of a Siberian permafrost metagenomic DNA library. The structure of the mutant was determined at 1.5 A resolution and is compared with wild-type PMGL2 in relation to the structures of the subunit, the functional dimer, and the active site of the enzyme.

The mature HIV-1 envelope (Env) glycoprotein is composed of gp120, the exterior subunit, and gp41, the transmembrane subunit assembled as trimer by noncovalent interaction. There is a great body of literature to prove that gp120 binds to CD4 first, then to the coreceptor. Binding experiments and functional assays have demonstrated that CD4 binding induces conformational changes in gp120 that enable or enhance its interaction with a coreceptor. Previous studies provided different glycomic maps for the HIV-1 gp120. Here, we build on previous work to report that the use of LC-MS/MS, in conjunction with hydrophilic interaction liquid chromatography (HILIC) enrichment to glycosylation sites, associated with the assorted neutralizing or binding events of glycosylation targeted antibodies from different clades or strains. In this study, the microheterogeneity of the glycosylation from 4 different clades of gp120s is deeply investigated. Aberrant glycosylation patterns were detected on gp120 that originated from different clades, viral sequences, and host cells. The results of this study may help provide a better understanding of the mechanism of how the glycans participate in the antibody neutralizing process that targets glycosylation sites.

CRISPR–Cas systems are bacterial adaptive immune systems, and phages counteract these systems using many approaches such as producing anti-CRISPR (Acr) proteins. Here, we report the structures of both AcrIF14 and its complex with the crRNA-guided surveillance (Csy) complex. Our study demonstrates that apart from interacting with the Csy complex to block the hybridization of target DNA to the crRNA, AcrIF14 also endows the Csy complex with the ability to interact with non-sequence-specific dsDNA as AcrIF9 does. Further structural studies of the Csy–AcrIF14–dsDNA complex and biochemical studies uncover that the PAM recognition loop of the Cas8f subunit of the Csy complex and electropositive patches within the N-terminal domain of AcrIF14 are essential for the non-sequence-specific dsDNA binding to the Csy–AcrIF14 complex, which is different from the mechanism of AcrIF9. Our findings highlight the prevalence of Acr-induced non-specific DNA binding and shed light on future studies into the mechanisms of such Acr proteins.

Bacterial microcompartments are large supramolecular structures comprising an outer proteinaceous shell that encapsulates various enzymes in order to optimize metabolic processes. The outer shells of bacterial microcompartments are made of several thousand protein subunits, generally forming hexameric building blocks based on the canonical bacterial microcompartment (BMC) domain. Among the diverse metabolic types of bacterial microcompartments, the structures of those that use glycyl radical enzymes to metabolize choline have not been adequately characterized. Here, six structures of hexameric shell proteins from type I and type II choline-utilization microcompartments are reported. Sequence and structure analysis reveals electrostatic surface properties that are shared between the four types of shell proteins described here.

Voltage-gated Ca2+ (Cav) channels consist of a pore-forming Cavα1 subunit and auxiliary Cavα2-δ and Cavβ subunits. In fibroblasts, Cavβ3, independent of its role as a Cav subunit, reduces the sensitivity to low concentrations of inositol-1,4,5-trisphosphate (IP3). Similarly, Cavβ3 could affect cytosolic [Ca2+] in pancreatic β-cells. Here, we deleted the Cavβ3-encoding gene Cacnb3 in insulin-secreting rat β-(Ins-1) cells using CRISPR/Cas9. These cells were used as controls to investigate the role of Cavβ3 on Ca2+-signalling, glucose-induced insulin secretion (GIIS), Cav-channel activity and gene expression in wild-type cells in which Cavβ3 and the IP3-receptor were co-immunoprecipitated. Transcript and protein profiling revealed significantly increased levels of insulin transcription factor Mafa, CaMKIV, neuroendocrine convertase1 (Pcsk1) and nitric oxide synthase-1 (NOS-1) in Cavβ3-KO cells. In the absence of Cavβ3, Cav-currents were not altered. In contrast, CREB activity, the amount of MAFA protein and GIIS, the extent of IP3-dependent Ca2+ release and the frequency of Ca2+-oscillations were increased. These processes were decreased by the Cavβ3 protein in a concentration-dependent manner. Our study shows that Cavβ3 interacts with the IP3-receptor in isolated β-cells, controls IP3-dependent Ca2+-signalling independently of Cav channel functions, and thereby regulates insulin expression and its glucose-dependent release in a cell-autonomous manner.

The Rel proteins of the NF-κB complex comprise one of the most investigated transcription factor families, forming a variety of hetero- or homodimers. Nevertheless, very little is known about the fundamental kinetics of NF-κB complex assembly, or the inter-conversion potential of dimerised Rel subunits. Here, we examined an unexplored aspect of NF-κB dynamics, focusing on the dissociation and reassociation of the canonical p50 and p65 Rel subunits and their ability to form new hetero- or homodimers. We employed a soluble expression system to enable the facile production of NF-κB Rel subunits, and verified these proteins display canonical NF-κB nucleic acid binding properties. Using a combination of biophysical techniques, we demonstrated that, at physiological temperatures, homodimeric Rel complexes routinely exchange subunits with a half-life of less than 10 min. In contrast, we found a dramatic preference for the formation of the p50/p65 heterodimer, which demonstrated a kinetic stability of at least an order of magnitude greater than either homodimer. These results suggest that specific DNA targets of either the p50 or p65 homodimers can only be targeted when these subunits are expressed exclusively, or with the intervention of additional post-translational modifications. Together, this work implies a new model of how cells can modulate NF-κB activity by fine-tuning the relative proportions of the p50 and p65 proteins, as well as their time of expression. This work thus provides a new quantitative interpretation of Rel dimer distribution in the cell, particularly for those who are developing mathematical models of NF-κB activity.

Heparan sulfate (HS), a sulfated glycosaminoglycan (GAG), was reported to be a necessary host attachment factor that promotes SARS-CoV-2 infection. In this study, we developed GAG microarrays based on fluorescence detection for high-sensitivity screening of the GAG-binding specificity of proteins and applied it for the analysis of SARS-CoV-2 spike (S) protein. Among the 20 distinct GAGs, the S protein bound not only to heparin (HEP)/HS but also to chondroitin sulfate E (CSE) in a concentration-dependent manner. We then analyzed the specificity of each subunit of the S protein. While the S1 subunit showed exclusive binding to HEP, the S2 subunit also bound to CSE and HEP/HS. CSE might act as an alternative attachment factor for HS in SARS-CoV-2 infection.

Immersion vaccination of single-walled carbon nanotubes loaded with mannose-modified glycoprotein (SWCNTs-MG) vaccine has been proved to be effective in preventing spring viraemia of carp virus (SVCV). Immunization procedure has immense consequence on the immune effect of the immersion vaccine. However, immunization procedure optimization for SWCNTs-MG vaccine against SVCV has not been reported. In this study, accordingly, a full-factor experiment was designed to optimize the immunization procedure of SWCNTs-MG vaccine by three aspects of vaccine dose (30 mg/L, 40 mg/L and 50 mg/L), immunization density (8 fish L-1 , 24 fish L-1 and 48 fish L-1 ) and immunization time (6, 12 and 24 hr). Furthermore, we used the immunization group (A1B2C1, 30 mg/L, 24 fish L-1 and 6 hr) in the previous study as a positive control (PC) to evaluate the immunization effect optimized conditions from the expression of immune-related genes and relative percentage survival (RPS). At 28 days post-vaccination (DPV), common carps were intraperitoneal injected SVCV challenged test indicated that the A1B2C2 group (30 mg/L, 24 fish L-1 , 12 hr) displayed superiority of protective efficacy compare with other groups and the RPS with 77.9%, which was 15.6% higher than the PC group of RPS with 62.3%. Moreover, the expression of immune-related genes such as IL-10, CD4 and MHC-II was also significantly higher than PC group. The specific experimental flow chart is shown in Figure 1. Conclusively, these results demonstrated that vaccine dose, immunization density and immunization time are 30 mg/L, 24 fish L-1 and 12 hr, which is the more appropriate immunization programme with juvenile carp for SWCNTs-MG vaccine. This study provides a profitable reference for improving the immune efficiency of aquatic immersion vaccine. [Figure: see text].

Proteins perform their functions by interacting with other biomolecules. For these interactions, proteins often form homo- or hetero-oligomers as well. Thus, oligomer protein structures provide important clues regarding the biological roles of proteins. To this end, computational prediction of oligomer structures may be a useful tool in the absence of experimentally resolved structures. Here, we describe our server and human-expert methods used to predict oligomer structures in the CASP14 experiment. Examples are provided for cases in which manual domain-splitting led to improved oligomeric domain structures by ab initio docking, automated oligomer structure refinement led to improved subunit orientation and terminal structure, and manual oligomer modeling utilizing literature information generated a reasonable oligomer model. We also discussed the results of post-prediction docking calculations with AlphaFold2 monomers as input in comparison to our blind prediction results. Overall, ab initio docking of AlphaFold2 models did not lead to better oligomer structure prediction, which may be attributed to the interfacial structural difference between the AlphaFold2 monomer structures and the crystal oligomer structures. This result poses a next-stage challenge in oligomer structure prediction after the success of AlphaFold2. For successful protein assembly structure prediction, a different approach that exploits further evolutionary information on the interface and/or flexible docking taking the interfacial conformational flexibilities of subunit structures into account is needed.

During RNA elongation, the influenza A viral (IAV) RNA-dependent RNA polymerase (RdRp) residues in the active site interact with the triphosphate moiety of nucleoside triphosphate (NTP) for catalysis. The molecular mechanisms by which they control the rate and fidelity of NTP incorporation remain elusive. Here, we demonstrated through enzymology, virology and computational approaches that the R239 and K235 in the PB1 subunit of RdRp are critical to controlling the activity and fidelity of transcription. Contrary to common beliefs that high-fidelity RdRp variants exert a slower incorporation rate, we discovered a first-of-its-kind, single lysine-to-arginine mutation on K235 exhibited enhanced fidelity and activity compared with wild-type. In particular, we employed a single-turnover NTP incorporation assay for the first time on IAV RdRp to show that K235R mutant RdRp possessed a 1.9-fold increase in the transcription activity of the cognate NTP and a 4.6-fold increase in fidelity compared to wild-type. Our all-atom molecular dynamics simulations further elucidated that the higher activity is attributed to the shorter distance between K235R and the triphosphate moiety of NTP compared with wild-type. These results provide novel insights into NTP incorporation and fidelity control mechanisms, which lay the foundation for the rational design of IAV vaccine and antiviral targets.

The catalytic subunit of SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) contains two active sites that catalyze nucleotidyl-monophosphate transfer (NMPylation). Mechanistic studies and drug discovery have focused on RNA synthesis by the highly conserved RdRp. The second active site, which resides in a Nidovirus RdRp-Associated Nucleotidyl transferase (NiRAN) domain, is poorly characterized, but both catalytic reactions are essential for viral replication. One study showed that NiRAN transfers NMP to the first residue of RNA-binding protein nsp9; another reported a structure of nsp9 containing two additional N-terminal residues bound to the NiRAN active site but observed NMP transfer to RNA instead. We show that SARS-CoV-2 RdRp NMPylates the native but not the extended nsp9. Substitutions of the invariant NiRAN residues abolish NMPylation, whereas substitution of a catalytic RdRp Asp residue does not. NMPylation can utilize diverse nucleotide triphosphates, including remdesivir triphosphate, is reversible in the presence of pyrophosphate, and is inhibited by nucleotide analogs and bisphosphonates, suggesting a path for rational design of NiRAN inhibitors. We reconcile these and existing findings using a new model in which nsp9 remodels both active sites to alternately support initiation of RNA synthesis by RdRp or subsequent capping of the product RNA by the NiRAN domain., Graphical Abstract Graphical AbstractCoronaviral RNA polymerase uses nucleoside triphosphates to make RNA and modify proteins, fueling viral replication. Acting as direct inhibitors or alternative substrates, nucleotide analogs can thwart SARS-CoV-2 and other viruses.

PB1 is a bromodomain-containing protein hypothesized to act as the nucleosome-recognition subunit of the PBAF complex. Although PB1 is a key component of the PBAF chromatin remodeling complex, its exact role has not been elucidated due to the lack of potent and selective inhibitors. Chemical probes that target specific bromodomains within the complex would constitute highly valuable tools to characterize the function and therapeutic pertinence of PB1 and of each of its bromodomains. Here, we report the design and synthesis of lead compound LM146, which displays strong stabilization of the second and fifth bromodomains of PB1 as shown by DSF. LM146 does not interact with bromodomains outside of sub-family VIII and binds to PB1(2), PB1(5), and SMARCA2B with K D values of 110, 61, and 2100 nM, respectively, providing a ∼34-fold selectivity profile for PB1(5) over SMARCA2.

CO2 responsive CCT protein (CRCT) is a positive regulator of starch synthesis related genes such as ADP-glucose pyrophosphorylase large subunit 1 and starch branching enzyme I particularly in the leaf sheath of rice (Oryza sativa L.). The promoter GUS analysis revealed that CRCT expressed exclusively in the vascular bundle, whereas starch synthesis related genes were expressed in different sites such as mesophyll cell and starch storage parenchyma cell. However, the chromatin immunoprecipitation (ChIP) using a FLAG-CRCT overexpression line and subsequent qPCR analyses showed that the 5’-flanking regions of these starch synthesis-related genes tended to be enriched by ChIP, suggesting that CRCT can bind to the promoter regions of these genes. The monomer of CRCT is 34.2 kDa, however CRCT was detected at 270 kDa via gel filtration chromatography, suggesting that CRCT forms a complex in vivo. Immunoprecipitation and subsequent MS analysis pulled down several 14-3-3-like proteins. A yeast two-hybrid analysis and bimolecular fluorescence complementation assays confirmed the interaction between CRCT and 14-3-3-like proteins. Although there is an inconsistency in the place of expression, this study provide important findings regarding the molecular function of CRCT to control the expression of key starch synthesis-related genes.

Recent studies have shown the involvement of GluN2A subunit‐containing NMDA receptors in various neurological and pathological disorders. In the X‐ray crystal structure, TCN‐201 (1) and analogous pyrazine derivatives 2 and 3 adopt a U‐shape (hairpin) conformation within the binding site formed by the ligand binding domains of the GluN1 and GluN2A subunits. In order to mimic the resulting π/π‐interactions of two aromatic rings in the binding site, a [2.2]paracyclophane system was designed to lock these aromatic rings in a parallel orientation. Acylation of [2.2]paracyclophane (5) with oxalyl chloride and chloroacetyl chloride and subsequent transformations led to the oxalamide 7, triazole 10 and benzamides 12. The GluN2A inhibitory activities of the paracyclophane derivatives were tested with two‐electrode voltage clamp electrophysiology using Xenopus laevis oocytes expressing selectively functional NMDA receptors with GluN2A subunit. The o‐iodobenzamide 12 b with the highest similarity to TCN‐201 showed the highest GuN2A inhibitory activity of this series of compounds. At a concentration of 10 μM, 12 b reached 36 % of the inhibitory activity of TCN‐201 (1). This result indicates that the [2.2]paracyclophane system is well accepted by the TCN‐201 binding site., In the binding pocket of crystallized GluN1/GluN2A ligand binding domain, the prototypical antagonist TCN‐201 and analogs adopt a U‐shaped conformation. [2.2]Paracyclophane‐based GluN2A antagonists were designed to mimic the U‐shaped conformation of TCN‐201 in the binding pocket. The synthesized benzamide shown here possesses 36 % of the GluN2A inhibitory activity of TCN‐201, confirming that compounds with the [2.2]paracyclophane system are well accepted by GluN2A‐NMDA receptors.

Nanomotors in nanotechnology may be as important as cars in daily life. Biomotors are nanoscale machines ubiquitous in living systems to carry out ATP-driven activities such as walking, breathing, blinking, mitosis, replication, transcription, and trafficking. The sequential action in an asymmetrical hexamer by a revolving mechanism has been confirmed in dsDNA packaging motors of phi29, herpesviruses, bacterial dsDNA translocase FtsK, and Streptomyces TraB for conjugative dsDNA transfer. These elaborate, delicate, and exquisite ring structures have inspired scientists to design biomimetics in nanotechnology. Many multisubunit ATPase rings generate force via sequential action of multiple modules, such as the Walker A, Walker B, P-loop, arginine finger, sensors, and lid. The chemical to mechanical energy conversion usually takes place in sequential order. It is commonly believed that ATP binding triggers such conversion, but how the multimodule motor starts the sequential process has not been explicitly investigated. Identification of the starter is of great significance for biomimetic motor fabrication. Here, we report that the arginine finger is the starter of the motor. Only one amino acid residue change in the arginine finger led to the impediment and elimination of all following steps. Without the arginine finger, the motor failed to assemble, bind ATP, recruit DNA, or hydrolyze ATP and was eventually unable to package DNA. However, the loss of ATPase activity due to an inactive arginine finger can be rescued by an arginine finger from the adjacent subunit of Walker A mutant through trans-complementation. Taken together, we demonstrate that the formation of dimers triggered by the arginine finger initiates the motor action rather than the general belief of initiation by ATP binding.

The post-translational acetylation of lysine residues is found in many nonhistone proteins and is involved in a wide range of biological processes. Recently, we showed that the nucleoprotein of the influenza A virus is acetylated by histone acetyltransferases (HATs), a phenomenon that affects viral transcription. Here, we report that the PA subunit of influenza A virus RNA-dependent RNA polymerase is acetylated by the HATs, P300/CREB-binding protein-associated factor (PCAF), and general control nonderepressible 5 (GCN5), resulting in accelerated endonuclease activity. Specifically, the full-length PA subunit expressed in cultured 293T cells was found to be strongly acetylated. Moreover, the partial recombinant protein of the PA N-terminal region containing the endonuclease domain was also acetylated by PCAF and GCN5 in vitro, which facilitated its endonuclease activity. Mass spectrometry analyses identified K19 as a candidate acetylation target in the PA N-terminal region. Notably, the substitution of the lysine residue at position 19 with glutamine, a mimic of the acetyl-lysine residue, enhanced its endonuclease activity in vitro; this point mutation also accelerated influenza A virus RNA-dependent RNA polymerase activity in the cell. Our findings suggest that PA acetylation is important for the regulation of the endonuclease and RNA polymerase activities of the influenza A virus.

Mind your metals Iron–sulfur clusters are important cofactors for proteins involved in metabolism and electron transfer but are also sometimes found in enzymes involved in transcription and replication of DNA. In vitro expression of such enzymes can result in faulty cluster assembly and confusion about the composition of the functional enzyme. Using a careful anoxic purification scheme, Maio et al. found that the severe acute respiratory syndrome coronavirus 2 RNA–dependent RNA polymerase contains two iron–sulfur clusters at two sites previously observed to bind zinc ions. Mutation of the ligating cysteine residues resulted in loss of polymerase activity. A less severe loss of activity was seen in the zinc-containing enzyme. Treatment with the nitroxide drug TEMPOL resulted in degradation of the clusters, enzyme inhibition, and inhibition of viral replication in cell culture. Science , abi5224, this issue p. 236

MLRQ is a subunit of nicotinamide adenine dinucleotide hydride (NADH)-ubiquinone reductase complex 1, the largest complex of the respiratory chain in the mitochondria. In this study, the PgMLRQ gene from pearl millet Pennisetum glaucum subsp. monodii (Maire) Brunken was sequenced and characterized to examine its expression under stress and during germination. The sequenced cDNA for PgMLRQ was 493 bp, containing an open reading frame of 282 bp. The translated protein is 94 amino acids length and contained a B12D domain from 5 to 73 amino acids. Transmembrane helix prediction revealed the deduced PgMLRQ protein accommodates transmembrane helix spanning from 14 to 30 amino acids embedded in the mitochondrion membrane. Transmembrane topology indicated that the hydrophobic N-terminal of the PgMLRQ protein was found outside the membrane while the C-terminal was inside the membrane. Quantitative real-time PCR revealed high expression of PgMLRQ in flowers during heading, whereas the expression in shoots, roots, and seeds of 5-day-old seedlings and spikes before ripening was low. Moreover, the expression of PgMLRQ in seedlings root under salt and short exposure to cold was substantially higher than shoots and seeds. However, exposure to drought during germination resulted in expression in roots lower than in shoots and seeds. The results of this study help to uncover of the role of the MLRQ in response to stress during P. glaucum growth.

Mitochondrial dysfunction and ubiquitin-proteasome system (UPS) failure contribute significantly to the development of Parkinson's disease (PD). The proteasome subunit Rpn13 located on the regulatory (19S) subparticle play an important role in the delivery of proteins, subjected to degradation, to the proteolytic (20S) part of proteasome. We have previously found several brain mitochondrial proteins specifically bound to Rpn13 (Buneeva et al. (2020) Biochemistry (Moscow), Supplement Series B: Biomedical Chemistry, 14, 297-305). In this study we have investigated the effect of the neurotoxin 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) and the neuroprotector isatin on the mitochondrial subproteome of Rpn13-binding proteins of the mouse brain. Administration of MPTP (30 mg/kg) to animals caused movement disorders typical of PD, while pretreatment with isatin (100 mg/kg, 30 min before MPTP) reduced their severity. At the same time, the injection of MPTP, isatin, or their combination (isatin + MPTP) had a significant impact on the total number and the composition of Rpn13-binding proteins. The injection of MPTP decreased the total number of Rpn13-binding proteins in comparison with control, and the injection of isatin prior to MPTP or without MPTP caused an essential increase in the number of Rpn13-binding proteins, mainly of the functional group of proteins participating in the protein metabolism regulation, gene expression, and differentiation. Selected biosensor validation confirmed the interaction of Rpn13 subunit of proteasome with some proteins (glyceraldehyde-3-phosphate dehydrogenase, pyruvate kinase, histones H2A and H2B) revealed while proteomic profiling. The results obtained testify that under the conditions of experimental MPTP-induced parkinsonism the neuroprotective effect of isatin may be aimed at the interaction of mitochondria with the components of UPS.Mitokhondrial'naia disfunktsiia i sboĭ v rabote ubikvitin-proteasomnoĭ sistemy (UPS) vnosiat sushchestvennyĭ vklad v razvitie bolezni Parkinsona (BP). Sub"edinitsa proteasomy Rpn13, raspolozhennaia na reguliatornoĭ subchastitse (19S), igraet vazhnuiu rol' v dostavke belkov, podlezhashchikh degradatsii, v proteoliticheskuiu chast' (20S) proteasomy. Ranee nami obnaruzhen riad mitokhondrial'nykh belkov mozga, spetsificheski sviazyvaiushchikhsia s Rpn13 (Buneeva i dr., Biomeditsinskaia khimiia, 2020, 66(2), 138-144). V dannoĭ rabote izucheno vliianie neĭrotoksina 1-metil-4-fenil-1,2,3,6-tetragidropiridina (MFTP) i neĭroprotektora izatina na mitokhondrial'nyĭ subproteom Rpn13-sviazyvaiushchikh belkov mozga myshi. Vvedenie MFTP (30 mg/kg) zhivotnym vyzyvalo razvitie dvigatel'nykh narusheniĭ, svoĭstvennykh dlia BP, a predvaritel'noe vvedenie izatina (100 mg/kg) oslablialo ikh vyrazhennost'. Pri étom vvedenie MFTP, izatina ili ikh kombinatsii (izatin + MFTP) privodilo k izmeneniiu obshchego chisla i sostava Rpn13-sviazyvaiushchikh belkov. Vvedenie MFTP snizhalo obshchee chislo Rpn13-sviazyvaiushchikh belkov po sravneniiu s kontrolem, a vvedenie izatina pered vvedeniem MFTP ili bez MFTP privodilo k sushchestvennomu uvelicheniiu chisla Rpn13-sviazyvaiushchikh belkov preimushchestvenno iz funktsional'noĭ gruppy belkov, uchastvuiushchikh v reguliatsii metabolizma belkov, a takzhe ékspressii genov, kletochnogo deleniia i differentsirovki. Vyborochnaia biosensornaia validatsiia podtverdila vzaimodeĭstvie riada belkov (glitseral'degid-3-fosfatdegidrogenaza, piruvatkinaza, gistony N2A i N2V), vyiavlennykh v khode proteomnogo profilirovaniia, s sub"edinitseĭ proteasomy Rpn13. Poluchennye rezul'taty svidetel'stvuiut o tom, chto v usloviiakh éksperimental'nogo MFTP-indutsirovannogo parkinsonizma neĭroprotektornoe deĭstvie izatina mozhet byt' napravleno na vzaimodeĭstvie mitokhondriĭ s komponentami UPS.

DNA-dependent protein kinase catalytic subunit DNA-PKcs/PRKDC is the largest serine/threonine protein kinase of the phosphatidyl inositol 3-kinase-like protein kinase (PIKK) family and is the most highly expressed PIKK in human cells. With its DNA-binding partner Ku70/80, DNA-PKcs is required for regulated and efficient repair of ionizing radiation-induced DNA double-strand breaks via the non-homologous end joining (NHEJ) pathway. Loss of DNA-PKcs or other NHEJ factors leads to radiation sensitivity and unrepaired DNA double-strand breaks (DSBs), as well as defects in V(D)J recombination and immune defects. In this review, we highlight the contributions of the late Dr. Carl W. Anderson to the discovery and early characterization of DNA-PK. We furthermore build upon his foundational work to provide recent insights into the structure of NHEJ synaptic complexes, an evolutionarily conserved and functionally important YRPD motif, and the role of DNA-PKcs and its phosphorylation in NHEJ. The combined results identify DNA-PKcs as a master regulator that is activated by its detection of two double-strand DNA ends for a cascade of phosphorylation events that provide specificity and efficiency in assembling the synaptic complex for NHEJ.

Transcription initiation is the first step in gene expression, and is therefore strongly regulated in all domains of life. The RNA polymerase (RNAP) first associates with the initiation factorσto form a holoenzyme, which binds, bends and opens the promoter in a succession of reversible states. These states are critical for transcription regulation, but remain poorly understood. Here, we addressed the mechanism of open complex formation by monitoring its assembly/disassembly kinetics on individual consensuslacUV5promoters using high-throughput single-molecule magnetic tweezers. We probed the key protein–DNA interactions governing the open-complex formation and dissociation pathway by modulating the dynamics at different concentrations of monovalent salts and varying temperatures. Consistent with ensemble studies, we observed that RPOis a stable, slowly reversible state that is preceded by a kinetically significant open intermediate (RPI), from which the holoenzyme dissociates. A strong anion concentration and type dependence indicates that the RPOstabilization may involve sequence-independent interactions between the DNA and the holoenzyme, driven by a non-Coulombic effect consistent with the non-template DNA strand interacting withσand the RNAPβsubunit. The temperature dependence provides the energy scale of open-complex formation and further supports the existence of additional intermediates.

Введение. Геронтология - это наука о причинах биологического старения организма. Ее составной частью является гериатрия - наука о болезнях и факторах, вызывающих старение. Полагаем, что митохондриальные мутации, затрагивающие гены белковых субъединиц дыхательной цепи, а также транспортных и рибосомальных РНК, могут являться одним из факторов старения индивидов. При этом, согласно данным литературы, проблема связи мутаций митохондриального генома со старением индивидов изучена недостаточно. Цель исследования - анализ ассоциации уровня гетероплазмии мутаций мтДНК с возрастом индивидов. Методика. Объектом исследования была выборка жителей Московского региона состоящая из 712 участников. ДНК выделяли из образцов лейкоцитов крови участников исследования с помощью метода фенол-хлороформной экстракции. Была проведена ПЦР фрагментов ДНК, содержащих область исследованных мутаций. Полученные амплификаты были пиросеквенированы. Анализ уровня гетероплазмии данных мутаций был проведен с помощью количественного метода, разработанного авторами статьи. Для подсчета уровня гетероплазмии мутаций по данным пирограммы использовалась ранее разработанная авторами формула. Результаты. Показано, что с возрастом индивидов положительно коррелируют однонуклеотидные замены митохондриального генома m.12315G>A, m.14459G>A и m.15059G>A (p≤0,05) и отрицательно - m.1555A>G и m.14846G>A (p≤0,05). Мутации m.652insG и m.13513G>A отрицательно коррелируют с возрастом на уровне значимости p≤0,1. Заключение. Обнаружены 3 однонуклеотидные замены m.14459G>A, m.15059G>A и m.12315G>A генов MT-ND6, MT-CYTB и MT-TL2 (соответственно) ассоциированные со старением организма человека. Данные мутации могут быть использованы для создания молекулярно-клеточных моделей старения. В то же время, выявлены мутации m.1555A>G, m.652insG (ген MT-RNR1), m.14846G>A (ген CYTB) и m.13513G>A (ген MT-ND5), отрицательно коррелирующие с возрастом индивидов. Данные мутации могут быть использованы при генотерапии для замедления старения людей. Introduction. Gerontology is a branch of science that focuses on the causes of biological aging. Its clinical component is geriatrics, a branch of medical science that focuses on diseases and factors causing aging. We hypothesize that mitochondrial mutations that affect genes of protein subunits of the respiratory chain, and, also, transport and ribosomal RNAs may be factors of aging. Meanwhile, according to the literature, the connection of mitochondrial genome mutations with aging has not been adequately studied. Aim. To analyze the association of heteroplasmy level in mtDNA mutations with the age of individuals. Methods. A sample of inhabitants of the Moscow region, composed of 712 study participants, was enrolled in the study. DNA was isolated from blood leukocytes by phenol chloroform extraction, and PCR of DNA fragments, containing the region of the studied mutations was performed. The obtained amplificates were pyrosequenced. These mutations were analyzed for the heteroplasmy level using a quantitative method developed by the authors. To determine the heteroplasmy level of mutations from the pyrogram data, a formula was used that had earlier been developed by the authors. The results were statistically analyzed with the software package, IBM SPSS Statistics, version 27.0 (SPSS Inc., USA). Results. Analysis of mutations showed that single nucleotide substitutions of the mitochondrial genomes m.12315G>A, m.14459G>A and m.15059G>A correlated positively with subject age (p≤0.05) whereas m.1555A>G and m.14846G>A correlated negatively (p≤0.05). Mutations m.652insG and m.13513G>A tended to correlate negatively with aging (p≤0.1). Conclusion. Three single nucleotide substitutions were found: m.14459G>A, m.15059G>A, and m.12315G>A of genes MT-ND6, MT-CYTB, and MT-TL2, respectively, that are associated with human aging. Thus, these mutations may be used for creating molecular cellular models of aging. At the same time, mutations m.1555A>G, m.652insG (gene MT-RNR1), m.14846G>A (gene CYTB), and m.13513G>A (gene MT-ND5) were detected, which correlate with aging negatively. These mutations may be used in gene therapy to slow aging.

BACKGROUND AND PURPOSE: Nitric oxide (NO) activates soluble guanylyl cyclase (sGC) for cGMP production, but in disease, sGC becomes insensitive towards NO activation. What changes occur to sGC during its inactivation in cells is not clear. EXPERIMENTAL APPROACH: We utilized HEK293 cells expressing sGC proteins to study the changes that occur regarding its haem content, heterodimer status and sGCβ protein partners when the cells were given the oxidant ODQ or the NO donor NOC12 to inactivate sGC. Haem content of sGCβ was monitored in live cells through use of a fluorescent-labelled sGCβ construct, whereas sGC heterodimer status and protein interactions were studied by Western blot analysis. Experiments with purified proteins were also performed. KEY RESULTS: ODQ- or NOC12-driven inactivation of sGC in HEK293 cells was associated with haem oxidation (by ODQ), S-nitrosation of the sGCβ subunit (by NOC12), sGC heterodimer breakup and association of the freed sGCβ subunit with cell chaperone Hsp90. These changes occurred without detectable loss of haem from the sGCβ reporter construct. Treating a purified ferrous haem-containing sGCβ with ODQ or NOC12 caused it to bind with Hsp90 without showing any haem loss. CONCLUSION AND IMPLICATIONS: Oxidative (ODQ) or nitrosative (NOC12) inactivation of cell sGC involves sGC heterodimer dissociation and rearrangement of the sGCβ protein partners without any haem loss from sGCβ. Clarifying what changes do and do not occur to sGC during its inactivation in cells may direct strategies to preserve or recover NO-dependent cGMP signalling in health and disease. LINKED ARTICLES: This article is part of a themed issue on cGMP Signalling in Cell Growth and Survival. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v179.11/issuetoc

The eukaryotic chaperonin TRiC/CCT is a large ATP-dependent complex essential for cellular protein folding. Its subunit arrangement into two stacked eight-membered hetero-oligomeric rings is conserved from yeast to man. A recent breakthrough enables production of functional human TRiC (hTRiC) from insect cells. Here, we apply a suite of mass spectrometry techniques to characterize recombinant hTRiC. We find all subunits CCT1-8 are N-terminally processed by combinations of methionine excision and acetylation observed in native human TRiC. Dissociation by organic solvents yields primarily monomeric subunits with a small population of CCT dimers. Notably, some dimers feature non-canonical inter-subunit contacts absent in the initial hTRiC. This indicates individual CCT monomers can promiscuously re-assemble into dimers, and lack the information to assume the specific interface pairings in the holocomplex. CCT5 is consistently the most stable subunit and engages in the greatest number of non-canonical dimer pairings. These findings confirm physiologically relevant post-translational processing and function of recombinant hTRiC and offer quantitative insight into the relative stabilities of TRiC subunits and interfaces, a key step toward reconstructing its assembly mechanism. Our results also highlight the importance of assigning contacts identified by native mass spectrometry after solution dissociation as canonical or non-canonical when investigating multimeric assemblies.