Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), a novel evolutionary divergent RNA virus, is responsible for the present devastating COVID-19 pandemic. To explore the genomic ...signatures, we comprehensively analyzed 2,492 complete and/or near-complete genome sequences of SARS-CoV-2 strains reported from across the globe to the GISAID database up to 30 March 2020. Genome-wide annotations revealed 1,516 nucleotide-level variations at different positions throughout the entire genome of SARS-CoV-2. Moreover, nucleotide (nt) deletion analysis found twelve deletion sites throughout the genome other than previously reported deletions at coding sequence of the ORF8 (open reading frame), spike, and ORF7a proteins, specifically in polyprotein ORF1ab (n = 9), ORF10 (n = 1), and 3´-UTR (n = 2). Evidence from the systematic gene-level mutational and protein profile analyses revealed a large number of amino acid (aa) substitutions (n = 744), demonstrating the viral proteins heterogeneous. Notably, residues of receptor-binding domain (RBD) showing crucial interactions with angiotensin-converting enzyme 2 (ACE2) and cross-reacting neutralizing antibody were found to be conserved among the analyzed virus strains, except for replacement of lysine with arginine at 378th position of the cryptic epitope of a Shanghai isolate, hCoV-19/Shanghai/SH0007/2020 (EPI_ISL_416320). Furthermore, our results of the preliminary epidemiological data on SARS-CoV-2 infections revealed that frequency of aa mutations were relatively higher in the SARS-CoV-2 genome sequences of Europe (43.07%) followed by Asia (38.09%), and North America (29.64%) while case fatality rates remained higher in the European temperate countries, such as Italy, Spain, Netherlands, France, England and Belgium. Thus, the present method of genome annotation employed at this early pandemic stage could be a promising tool for monitoring and tracking the continuously evolving pandemic situation, the associated genetic variants, and their implications for the development of effective control and prophylaxis strategies.
In plants, fluctuation of the redox balance by altered levels of reactive oxygen species (ROS) can affect many aspects of cellular physiology. ROS homeostasis is governed by a diversified set of ...antioxidant systems. Perturbation of this homeostasis leads to transient or permanent changes in the redox status and is exploited by plants in different stress signalling mechanisms. Understanding how plants sense ROS and transduce these stimuli into downstream biological responses is still a major challenge. ROS can provoke reversible and irreversible modifications to proteins that act in diverse signalling pathways. These oxidative post-translational modifications (Ox-PTMs) lead to oxidative damage and/or trigger structural alterations in these target proteins. Characterization of the effect of individual Ox-PTMs on individual proteins is the key to a better understanding of how cells interpret the oxidative signals that arise from developmental cues and stress conditions. This review focuses on ROS-mediated Ox-PTMs on cysteine (Cys) residues. The Cys side chain, with its high nucleophilic capacity, appears to be the principle target of ROS. Ox-PTMs on Cys residues participate in various signalling cascades initiated by plant stress hormones. We review the mechanistic aspects and functional consequences of Cys Ox-PTMs on specific target proteins in view of stress signalling events.
Cysteine sulfinic acid or S-sulfinylation is an oxidative post-translational modification (OxiPTM) that is known to be involved in redox-dependent regulation of protein function but has been ...historically difficult to analyze biochemically. To facilitate the detection of S-sulfinylated proteins, we demonstrate that a clickable, electrophilic diazene probe (DiaAlk) enables capture and site-centric proteomic analysis of this OxiPTM. Using this workflow, we revealed a striking difference between sulfenic acid modification (S-sulfenylation) and the S-sulfinylation dynamic response to oxidative stress, which is indicative of different roles for these OxiPTMs in redox regulation. We also identified >55 heretofore-unknown protein substrates of the cysteine sulfinic acid reductase sulfiredoxin, extending its function well beyond those of 2-cysteine peroxiredoxins (2-Cys PRDX1-4) and offering new insights into the role of this unique oxidoreductase as a central mediator of reactive oxygen species-associated diseases, particularly cancer. DiaAlk therefore provides a novel tool to profile S-sulfinylated proteins and study their regulatory mechanisms in cells.
As an analytical matrix, saliva has superior characteristics than blood and urine. Saliva collection is, first and foremost, non-invasive, making it convenient, painless, and secure for more ...susceptible people. Second, it does not need professional training for medical personnel, resulting in cost-effectiveness and suitability for extensive collection in support of research. In this study, we developed a method and used it to quantify 13 salivary-free amino acid (SFAA) profiles to support the early clinical diagnosis of diseases using LC-MS/MS. Using an Intrada Amino Acid column (100 × 3 mm, 3 μm), chromatographic separation was accomplished with a binary gradient elution, and an electrospray ionisation source running in the positive ionisation mode was chosen for data collection using the multiple reaction monitoring (MRM) modes. Amino acids were extracted from saliva using acetonitrile. In the MRM mode, LODs and LOQs for ten amino acids were in the range of 0.06-2.50 μM and 0.19-7.58 μM, respectively, and those values were in the range of 1.00-3.00 μM and 3.00-8.50 μM, respectively, for three amino acids. Matrix-matched six-point calibration curves showed a linear correlation coefficient (
r
2
) of ≥0.998. Recovery experiments validated the method by spiking the control sample at three different concentration levels (5, 50 and 100 μM), and the accuracy level was 85-110%. Except for Thr and Ser, intra- (
n
= 3) and inter-day (
n
= 3) precision fell between 0.02 and 7.28. Salivary amino acids can serve as possible biomarkers for various malignancies, with fluctuations in body fluids being crucial for cancer diagnosis; therefore, examining amino acid patterns in saliva can assist in early cancer detection. LC-MS offers improved selectivity and sensitivity for non-derivatised amino acid analysis, surpassing conventional methods and offering proactive quality assurance, making it suitable for complicated sample matrices. These discoveries could be significant in investigating new pathways and cancer treatments and looking for possible AA biomarkers for other malignancies and diseases.
As an analytical matrix, saliva has superior characteristics than blood and urine.
The emerged novel coronavirus severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) has created a global health crisis that warrants an accurate and detailed characterization of the rapidly ...evolving viral genome for understanding its epidemiology, pathogenesis, and containment. Here, we explored 61,485 sequences of the nucleocapsid (N) protein, a potent diagnostic and prophylactic target, for identifying the mutations to review their roles in real‐time polymerase chain reaction based diagnosis and observe consequent impacts. Compared to the Wuhan reference strain, a total of 1034 unique nucleotide mutations were identified in the mutant strains (49.15%, n = 30,221) globally. Of these mutations, 367 occupy primer binding sites including the 3′‐end mismatch to the primer‐pair of 11 well‐characterized primer sets. Noteworthily, CDC (USA) recommended the N2 primer set contained a lower mismatch than the other primer sets. Moreover, 684 amino acid (aa) substitutions were located across 317 (75.66% of total aa) unique positions including 82, 21, and 83 of those in the RNA binding N‐terminal domain (NTD), SR‐rich region, and C‐terminal dimerization domain, respectively. Moreover, 11 in‐frame deletions, mostly (n = 10) within the highly flexible linker region, were revealed, and the rest was within the NTD region. Furthermore, we predicted the possible consequence of high‐frequency mutations (≥20) and deletions on the tertiary structure of the N protein. Remarkably, we observed that a high frequency (67.94% of mutated sequences) co‐occuring mutations (R203K and G204R) destabilized and decreased overall structural flexibility. The N protein of SARS‐CoV‐2 comprises an average of 1.2 mutations per strain compared to 4.4 and 0.4 in Middle East respiratory syndrome‐related coronavirus and SARS‐CoV, respectively. Despite being proposed as the alternative target to spike protein for vaccine and therapeutics, the ongoing evolution of the N protein may challenge these endeavors, thus needing further immunoinformatics analyses. Therefore, continuous monitoring is required for tracing the ongoing evolution of the SARS‐CoV‐2 N protein in prophylactic and diagnostic interventions.
Highlights
Analyzing 61,485 sequences of the nucleocapsid (N) protein, 1034 unique nucleotide mutations were identified in the mutant strains (49.15%, n=30,221) globally.
Of these mutations, 367 occupy primer binding sites including the 3'‐end mismatch to the primer‐pair of 11 well‐characterized primer sets.
In total, 684 amino acid (aa) substitutions in 317 unique positions including 82, 21, and 83 in RNA binding N‐terminal domain (NTD), SR‐rich region, and C‐terminal dimerization domain (CTD), respectively were detected.
Eleven in‐frame deletions found, mostly (n = 10) within the highly flexible linker region of the SARS‐CoV‐2 N protein.
The N protein of SARS‐CoV‐2 comprises an average of 1.2 mutations per strain compared to 4.4 and 0.4 in MERS‐CoV and SARS‐CoV, respectively.
Sulfenome mining in Arabidopsis thaliana Waszczak, Cezary; Akter, Salma; Eeckhout, Dominique ...
Proceedings of the National Academy of Sciences - PNAS,
08/2014, Letnik:
111, Številka:
31
Journal Article
Recenzirano
Odprti dostop
Reactive oxygen species (ROS) have been shown to be potent signaling molecules. Today, oxidation of cysteine residues is a well-recognized posttranslational protein modification, but the signaling ...processes steered by such oxidations are poorly understood. To gain insight into the cysteine thiol-dependent ROS signaling in Arabidopsis thaliana, we identified the hydrogen peroxide (H 2 O 2 )-dependent sulfenome: that is, proteins with at least one cysteine thiol oxidized to a sulfenic acid. By means of a genetic construct consisting of a fusion between the C-terminal domain of the yeast (Saccharomyces cerevisiae) AP-1-like (YAP1) transcription factor and a tandem affinity purification tag, we detected ∼100 sulfenylated proteins in Arabidopsis cell suspensions exposed to H 2 O 2 stress. The in vivo YAP1-based trapping of sulfenylated proteins was validated by a targeted in vitro analysis of DEHYDROASCORBATE REDUCTASE2 (DHAR2). In DHAR2, the active site nucleophilic cysteine is regulated through a sulfenic acid-dependent switch, leading to S-glutathionylation, a protein modification that protects the protein against oxidative damage.
Authenticity and adulteration detection are primary concerns of various stakeholders, such as researchers, consumers, manufacturers, traders, and regulatory agencies. Traditional approaches for ...authenticity and adulteration detection in edible oils are time-consuming, complicated, laborious, and expensive; they require technical skills when interpreting the data. Over the last several years, much effort has been spent in academia and industry on developing vibrational spectroscopic techniques for quality, authenticity, and adulteration detection in edible oils. Among them, Fourier transforms infrared (FT-IR) spectroscopy has gained enormous attention as a green analytical technique for the rapid monitoring quality of edible oils at all stages of production and for detecting and quantifying adulteration and authenticity in edible oils. The technique has several benefits such as rapid, precise, inexpensive, and multi-analytical; hence, several parameters can be predicted simultaneously from the same spectrum. Associated with chemometrics, the technique has been successfully implemented for the rapid detection of adulteration and authenticity in edible oils. After presenting the fundamentals, the latest research outcomes in the last 10 years on quality, authenticity, and adulteration detection in edible oils using FT-IR spectroscopy will be highlighted and described in this review. Additionally, opportunities, challenges, and future trends of FT-IR spectroscopy will also be discussed.
As the sustainability of the environment is a very much concerning issue for developed countries, the drive of the paper is to reveal the effects of nuclear, environment-friendly, and non-friendly ...energy, population, and GDP on CO2 emission for Italy, a developed country. Using the extended Stochastic Regression on Population, Affluence, and Technology (STIRPAT) framework, the yearly data from 1972 to 2021 are analyzed in this paper through an Autoregressive Distributed Lag (ARDL) framework. The reliability of the study is also examined by employing Fully Modified Ordinary Least Square (FMOLS), Dynamic Ordinary Least Square (DOLS), and Canonical Cointegration Regression (CCR) estimators and also the Granger causality method which is used to see the directional relationship among the indicators. The investigation confirms the findings of previous studies by showing that in the longer period, rising Italian GDP and non-green energy by 1% can lead to higher CO2 emissions by 8.08% and 1.505%, respectively, while rising alternative and nuclear energy by 1% can lead to falling in CO2 emission by 0.624%. Although population and green energy adversely influence the upsurge of CO2, they seem insignificant. Robustness tests confirm these longer-period impacts. This analysis may be helpful in planning and developing strategies for future financial funding in the energy sector in Italy, which is essential if the country is to achieve its goals of sustainable development.
The Mre11/Rad50/Nbs1 complex initiates double-strand break repair by homologous recombination (HR). Loss of Mre11 or its nuclease activity in mouse cells is known to cause genome aberrations and ...cellular senescence, although the molecular basis for this phenotype is not clear. To identify the origin of these defects, we characterized Mre11-deficient (MRE11−/−) and nuclease-deficient Mre11 (MRE11−/H129N) chicken DT40 and human lymphoblast cell lines. These cells exhibit increased spontaneous chromosomal DSBs and extreme sensitivity to topoisomerase 2 poisons. The defects in Mre11 compromise the repair of etoposide-induced Top2-DNA covalent complexes, and MRE11−/− and MRE11−/H129N cells accumulate high levels of Top2 covalent conjugates even in the absence of exogenous damage. We demonstrate that both the genome instability and mortality of MRE11−/− and MRE11−/H129N cells are significantly reversed by overexpression of Tdp2, an enzyme that eliminates covalent Top2 conjugates; thus, the essential role of Mre11 nuclease activity is likely to remove these lesions.
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•Topoisomerase 2 (Top2) frequently fails to complete catalysis•Failed catalysis causes the formation of Top2-cleavage complex (Top2cc)•Mre11 nuclease eliminates Top2cc followed by DNA double-strand break repair•Top2cc accumulation leads mitotic chromosomal breakage and apoptosis
The MRN complex is critical for genomic stability through several mechanisms. Hoa et al. find that nuclease activity of Mre11 is critical for the removal of topoisomerase 2-cleavage complexes that naturally accumulate in the genome when topoisomerase 2 fails to complete catalysis.
Sugar plays a vital role in the structural and functional characteristics of cells. Hence, the interaction of NPs with cell membranes in the presence of sugar concentrations is important for ...medicinal and pharmacological innovations. This study integrated three tools: giant unilamellar vesicles (GUVs), anionic magnetite nanoparticles (NPs), and sugar concentrations, to understand a simplified mechanism for interactions between the vesicle membranes and NPs under various sugar concentrations. We focused on changing the sugar concentration in aqueous solution; more precisely, sucrose inside the GUVs and glucose outside with equal osmolarity. 1,2-dioleoyl-sn-glycero-3-phospho-(1'-rac-glycerol) (sodium salt) (DOPG) and 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) were used to prepare the charged membranes of 40mole%DOPG/60mole%DOPC-GUVs, whereas only DOPC was used to prepare the neutral membranes. Phase contrast fluorescence microscopy shows that the adherence of 18 nm magnetite NPs with anionic charge depends on the sugar concentration. The alterations of GUVs induced by the NPs are characterized in terms of i) vesicle compactness, ii) deformation, and iii) membrane poration. The presence of sugar provides additional structural stability to the GUVs and reduces the effects of the NPs with respect to these parameters; more precisely, the higher the sugar concentration, the smaller the alteration induced by the NPs. The differences in NPs effects are explained by the change in the type of interaction between sugar molecules and lipid membranes, namely enthalpy and entropy-driven interaction, respectively. In addition, such alterations are influenced by the surface charge density of the lipid bilayer. The surface pressure of membranes due to the adsorption of NPs is responsible for inducing the poration in membranes. The differences in deformation and poration in charged and neutral GUVs under various sugar concentrations are discussed based on the structure of the head of lipid molecules.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
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