Active Site Motif Research Articles

The atypical thioredoxin 'Alr2205', a newly identified partner of the typical 2-Cys-Peroxiredoxin, safeguards the cyanobacterium Anabaena from oxidative stress.

Thioredoxins (Trxs) are ubiquitous proteins that play vital roles in several physiological processes. Alr2205, a thioredoxin-like protein from Anabaena PCC 7120, was evolutionarily closer to the Trx-domain of the NADPH-Thioredoxin Reductase C than the other thioredoxins. The Alr2205 protein showed disulphide reductase activity despite the presence a non-canonical active site motif 'CPSC'. Alr2205 not only physically interacted with, but also acted as a physiological reductant of Alr4641 (2-Cys-Peroxiredoxin), supporting its peroxidase function. Structurally, Alr2205 was a monomeric protein that formed an intramolecular disulphide bond between the two active site cysteines. However, the Alr2205C41S protein, wherein the resolving cysteine was mutated to serine, was capable of forming intermolecular disulphide bond and exist as a dimer when treated with H2O2. Overproduction of Alr2205 in E. coli protected cells from heavy metals, but not oxidative stress. To delve into its physiological role, Alr2205/Alr2205C41S was overexpressed in Anabaena, and the ability of the corresponding strains (An2205+ or An2205C41S+) to withstand environmental stresses was assessed. An2205+ showed higher resistance to H2O2 than An2205C41S+, indicating that the disulphide reductase function of this protein was critical to protect cells from this peroxide. Although, An2205+ did not show increased capability to withstand cadmium stress, An2205C41S+ was more susceptible to this heavy metal. This is the first study that provides a vital understanding into the function of atypical thioredoxins in countering the toxic effects of heavy metals/H2O2 in prokaryotes.

Relationship between Penicillin-Binding Proteins Alterations and β-Lactams Non-Susceptibility of Diseased Pig-Isolated Streptococcus suis.

Streptococcus suis is a zoonotic pathogen causing disease in both animals and humans, and the emergence of increasingly resistant bacteria to antimicrobial agents has become a significant challenge globally. The objective of this study was to investigate the genetic basis for declining susceptibility to penicillin and other β-lactams among S. suis. Antimicrobial susceptibility testing and penicillin-binding proteins (PBP1a, PBP2a, PBP2b, and PBP2x) sequence analysis were performed on 225 S. suis isolated from diseased pigs. This study found that a growing trend of isolates displayed reduced susceptibility to β-lactams including penicillin, ampicillin, amoxicillin/clavulanic acid, and cephalosporins. A total of 342 substitutions within the transpeptidase domain of four PBPs were identified, of which 18 substitutions were most statistically associated with reduced β-lactams susceptibility. Almost all the S. suis isolates which exhibited penicillin-non-susceptible phenotype (71.9%) had single nucleotide polymorphisms, leading to alterations of PBP1a (P409T) and PBP2a (T584A and H588Y). The isolates may manifest a higher level of penicillin resistance by additional mutation of M341I in the 339STMK active site motif of PBP2x. The ampicillin-non-susceptible isolates shared the mutations in PBP1a (P409T) and PBP2a (T584A and H588Y) with additional alterations of PBP2b (T625R) and PBP2x (T467S). The substitutions, including PBP1a (M587S/T), PBP2a (M433T), PBP2b (I428L), and PBP2x (Q405E/K/L), appeared to play significant roles in mediating the reduction in amoxicillin/clavulanic acid susceptibility. Among the cephalosporins, specific mutations strongly associated with the decrease in cephalosporins susceptibility were observed for ceftiofur: PBP1a (S477D/G), PBP2a (E549Q and A568S), PBP2b (T625R), and PBP2x (Q453H). It is concluded that there was genetically widespread presence of PBPs substitutions associated with reduced susceptibility to β-lactam antibiotics.

Mechanistic insight into the effect of active site motif structures on direct oxidation of methane to methanol over Cu-ZSM-5.

Direct oxidation of methane to methanol (DMTM), a highly challenging reaction in C1 chemistry, has attracted lots of attention. Herein, we investigate the continuous H2O-mediated N2O-DMTM over a series of Cu-ZSM-5-n zeolites prepared by a solid-state ion-exchange method. Excellent CH3OH productivity (194.8 μmol gcat-1 h-1) and selectivity (67.1%) can be achieved over Cu-ZSM-5-0.3%, which surpasses most recently reported zeolite catalysts. The effect of the active site motif structure on the reaction was systematically investigated by the combined experimental and theoretical studies. It has been revealed that both the monomeric [Cu]+ and binuclear [Cu]+-[Cu]+ sites function to produce CH3OH, following the radical rebound mechanism, wherein the latter one plays a dominant role due to the synergistic effect of neighboring [Cu]+ that can efficiently reduce the N2O dissociation barrier to generate active oxygen for CH4 oxidation. Microkinetic modeling results further show that the dicopper site possesses a much higher net reaction rate (1.23 × 105 s-1) than the monomeric Cu site (0.962 s-1); moreover, H2O can shift the rate determining step from the CH3OH desorption step to the N2O dissociation step over the dicopper site, thereby efficiently favoring CH3OH production and resisting carbon deposition. Generally, the study in the present work would substantially favor other highly efficient catalyst designs.

Transcriptome analysis provides novel insights into the immune mechanisms of Macrobrachium nipponense during molting

Molting is a basic physiological behavior of the Oriental river prawn (Macrobrachium nipponense), however, the gene expression patterns and immune mechanisms during the molting process of Oriental river prawn are unclear. In the current study, the gene expression levels of the hepatopancreas of the Oriental river prawn at different molting stages (pre-molting, Prm; mid-molting, Mm; and post-molting, Pom) were detected by mRNA sequencing. A total of 1721, 551, and 1054 differentially expressed genes (DEGs) were identified between the Prm hepatopancreas (PrmHe) and Mm hepatopancreas (MmHe), MmHe and Pom hepatopancreas (PomHe) and PrmHe and PomHe, respectively. The results showed that a total of 1151 DEGs were annotated into 316 signaling pathways, and the significantly enriched immune-related pathways were "Lysosome", "Hippo signaling pathway", "Apoptosis", "Autophagy-animal", and "Endocytosis". The qRT-PCR verification results of 30 randomly selected DEGs were consistent with RNA-seq. The expression patterns of eight immune related genes in different molting stages of the Oriental river prawn were analyzed by qRT-PCR. The function of Caspase-1 (CASP1) was further investigated by bioinformatics, qRT-PCR, and RNAi analysis. CASP1 has two identical conserved domains: histidine active site and pentapeptide motif, and the expression of CASP1 is the highest in ovary. The expression levels of triosephosphate isomerase (TPI), Cathepsin B (CTSB) and Hexokinase (HXK) were evaluated after knockdown of CASP1. This research provides a valuable basis to improve our understanding the immune mechanisms of Oriental river prawns at different molting stages. The identification of immune-related genes is of great significance for enhancing the immunity of the Oriental river prawn, or other crustaceans, by transgenic methods in the future.

Electrolyte Engineering for Oxygen Evolution Reaction Over Non-Noble Metal Electrodes Achieving High Current Density in the Presence of Chloride Ion.

Direct seawater electrolysis potentially simplifies the electrolysis process and leads to a decrease in the cost of green hydrogen production. However, impurities present in the seawater, especially chloride ions (Cl- ), cause corrosion of the electrode material, and its oxidation competes with the anodic oxygen evolution reaction (OER). By carefully tuning electrode substrate and electrolyte solutions, the CoFeOx Hy /Ti electrode with high double-layer capacitance actively and stably electro-catalyzed the OER in potassium borate solutions at pH 9.2 in the presence of 0.5 mol kg-1 Cl- . The electrode possesses an active site motif composed of either a Co- or Fe-domain and benefits from an enlarged surface area. Selective OER was demonstrated in Cl- -containing electrolyte solutions at an elevated reaction temperature, stably achieving 500 mA cm-2 at a mere potential of 1.67 V vs. reversible hydrogen electrode (RHE) at 353 K for multiple on-off and long-term testing processes with a faradaic efficiency of unity toward the OER.

Effect of the Monothiol Glutaredoxin GrxD on 2,4-Diacetylphloroglucinol Biosynthesis and Biocontrol Activity of Pseudomonas fluorescens 2P24

Pseudomonas fluorescens 2P24 is a plant root-associated bacterium that suppresses several soilborne plant diseases due to its production of the antibiotic 2,4-diacetylphloroglucinol (2,4-DAPG). The biosynthesis of 2,4-DAPG is controlled by many regulatory elements, including the global regulator of the Gac/Rsm regulon and the pathway-specific repressor PhlF. In this work, a novel genetic element grxD, which encodes the monothiol glutaredoxin GrxD, was identified and characterized in the production of 2,4-DAPG in P. fluorescens 2P24. Our data showed that the mutation of grxD remarkably decreased 2,4-DAPG production. GrxD lost its ability to alter the production of 2,4-DAPG when the active-site CGFS motif of GrxD was mutated by site-directed mutagenesis. Further studies showed that the RsmA and RsmE proteins were essential for the GrxD-mediated regulation of 2,4-DAPG and exoprotease production. In addition, our data revealed that the deletion of grxD increased the expression of phlF, which negatively regulated the production of 2,4-DAPG. In addition, the grxD mutant was severely impaired in the biocontrol effect against the bacterial wilt of tomato. Overall, our results indicated that the monothiol glutaredoxin GrxD is involved in the production of 2,4-DAPG of P. fluorescens by influencing the Gac/Rsm global signaling pathway and transcriptional regulator PhlF and is essential for the biocontrol properties.

Molecular cloning and characterization of a lipase from the honeybee Apis mellifera

• Am-Lipase protein preferentially degrades triglycerides with long-chain fatty acids. • Am-Lipase is highly expressed in the fat body of foragers in comparison with the nurses. • Am-Lipase plays a role in the fat body for lipid metabolism. Lipids perform essential and important functions, such as serving as an energy source for growth, development, reproduction, flight, starvation, and diapause in insects. Lipases are key enzymes involving in lipid metabolism and have been reported in several insect species. However, the molecular characterization of the pancreatic triacylglycerol lipase-like genes in honeybees has not been elucidated. Here, we describe the cDNA cloning and characterization of lipase from the honeybee Apis mellifera (Am-Lipase). Am-Lipase consists of 321 amino acids, including a Ser-Glu-His catalytic triad and a consensus active site motif GXSXG. Recombinant Am-Lipase protein degrades triglycerides, preferentially catalyzing the hydrolysis of long-chain fatty acids. Furthermore, the expression pattern of Am-Lipase seems to be a fat body-specific lipase, shows higher expression in forager bees, and is decreased under starvation conditions. Thus, our results suggest that Am-Lipase plays a role in the utilization of lipids stored in the fat body for lipid metabolism.

Nucleoredoxin Plays a Key Role in the Maintenance of Retinal Pigmented Epithelium Differentiation.

Nucleoredoxin (Nrx) belongs to the Thioredoxin protein family and functions in redox-mediated signal transduction. It contains the dithiol active site motif Cys-Pro-Pro-Cys and interacts and regulates different proteins in distinct cellular pathways. Nrx was shown to be catalytically active in the insulin assay and recent findings indicate that Nrx functions, in fact, as oxidase. Here, we have analyzed Nrx in the mammalian retina exposed to (perinatal) hypoxia-ischemia/reoxygenation, combining ex vivo and in vitro models. Our data show that Nrx regulates cell differentiation, which is important to (i) increase the number of glial cells and (ii) replenish neurons that are lost following the hypoxic insult. Nrx is essential to maintain cell morphology. These regulatory changes are related to VEGF but do not seem to be linked to the Wnt/β-catenin pathway, which is not affected by Nrx knock-down. In conclusion, our results strongly suggest that hypoxia-ischemia could lead to alterations in the organization of the retina, related to changes in RPE cell differentiation. Nrx may play an essential role in the maintenance of the RPE cell differentiation state via the regulation of VEGF release.

Screening and Understanding Lattice Silicon‐Controlled Catalytically Active Site Motifs from a Library of Transition Metal‐Silicon Intermetallics (Small 10/2022)

Active Site Engineering In article number 2107371, Xiaoxin Zou and co-workers investigate a library of transition metal-silicon (Si) intermetallic catalysts by integrating high-throughput theoretical prediction and experimental validation. The cover design emphasizes the ability of Si to modify the arrangements of surface atoms and change adsorption sites of hydrogen intermediate for controlling catalytic activity.

Divergence of active site motifs among different classes of Populus glutaredoxins results in substrate switches.

Enzymes are essential components of all biological systems. The key characteristics of proteins functioning as enzymes are their substrate specificities and catalytic efficiencies. In plants, most genes encoding enzymes are members of large gene families. Within such families, the contributions of active site motifs to the functional divergence of duplicate genes have not been well elucidated. In this study, we identified 41 glutaredoxin (GRX) genes in the Populus trichocarpa genome. GRXs are ubiquitous enzymes in plants that play important roles in developmental and stress tolerance processes. In poplar, GRX genes were divided into four classes based on clear differences in gene structure and expression pattern, subcellular localization, enzymatic activity, and substrate specificity of the encoded proteins. Using site-directed mutagenesis, this study revealed that the divergence of the active site motif among different classes of GRX proteins resulted in substrate switches and thus provided new insights into the molecular evolution of these important plant enzymes.

Base excision repair system targeting DNA adducts of trioxacarcin/LL-D49194 antibiotics for self-resistance.

Two families of DNA glycosylases (YtkR2/AlkD, AlkZ/YcaQ) have been found to remove bulky and crosslinking DNA adducts produced by bacterial natural products. Whether DNA glycosylases eliminate other types of damage formed by structurally diverse antibiotics is unknown. Here, we identify four DNA glycosylases—TxnU2, TxnU4, LldU1 and LldU5—important for biosynthesis of the aromatic polyketide antibiotics trioxacarcin A (TXNA) and LL-D49194 (LLD), and show that the enzymes provide self-resistance to the producing strains by excising the intercalated guanine adducts of TXNA and LLD. These enzymes are highly specific for TXNA/LLD-DNA lesions and have no activity toward other, less stable alkylguanines as previously described for YtkR2/AlkD and AlkZ/YcaQ. Similarly, TXNA-DNA adducts are not excised by other alkylpurine DNA glycosylases. TxnU4 and LldU1 possess unique active site motifs that provide an explanation for their tight substrate specificity. Moreover, we show that abasic (AP) sites generated from TxnU4 excision of intercalated TXNA-DNA adducts are incised by AP endonuclease less efficiently than those formed by 7mG excision. This work characterizes a distinct class of DNA glycosylase acting on intercalated DNA adducts and furthers our understanding of specific DNA repair self-resistance activities within antibiotic producers of structurally diverse, highly functionalized DNA damaging agents.

Screening and Understanding Lattice Silicon-Controlled Catalytically Active Site Motifs from a Library of Transition Metal-Silicon Intermetallics.

A joint theoretical and experimental study is reported to systematically explore over a library of transition metal-silicon intermetallics for understanding silicon-controlled active site motifs and discovering hydrogen-evolving electrocatalysts. On the one hand, every low-index surface termination of 115 transition metal (M)-silicon (Si) intermetallics is enumerated, followed by cataloging of stable adsorption sites and prediction of catalytic activities on the main exposed facets. It is theoretically found that silicon atoms in silicon-rich structures (especially MSi2 and MSi) show a strong site-isolating effect, which can eliminate M-M-M hollow and M-M bridge sites with too strong hydrogen-binding ability and thereby provide great opportunities for the exposure of novel highly active sites (e.g., M-top and Si-related sites). On the other hand, solid-state redox reactions are developed to synthesize a set of 24 silicides containing 5 MSi, 13 MSi2 , and 6 others, most of which are phase-pure samples. The experimental studies demonstrate that too rich silicon content in silicides (e.g., MSi2 ) leads to adverse effects, such as the formation of amorphous SiOx layers on the silicide surface, masking the presence of active sites during electrocatalysis. Finally, 5 MSi (M = Rh, Pd, Pt, Ru, Ir) as highly active hydrogen-evolving electrocatalysts are identified.

Tris(imidazolyl) dicopper(I) complex and its reactivity to exert the catalytic oxidation of sterically hindered phenol substrates via a [Cu2O]2+ core.

The Cu ion ligated with histidine residues is a common active site motif of various Cu-containing metalloenzymes exerting versatile catalytic oxidation reactions. Due to the scarcity of structurally characterized biomimetic binuclear Cu(I)-imidazolyl complexes, the bonding interactions between the Cu(I) center and imidazolyl donor ligands as well as their stoichiometric/catalytic oxidation reactivities remain relatively unexplored. In this study, we successfully synthesized a tris(imidazolyl) dicopper(I) complex [CuI(μ-bimeta)3CuI][PF6]2 (1) characterized by single-crystal X-ray diffraction, cyclic voltammetry, and UV-vis absorption spectroscopy. The coordination environment around each Cu(I) center of complex 1 is best described as a regular trigonal geometry and the distance between two Cu(I) centers is ∼3.0521(18) Å. From the O2-/PhIO-titration reactions of complex 1, only 0.5 equiv. of O2(g) and one equiv. of PhIO are required to produce the corresponding oxygenated product complex 1ox, respectively, exhibiting a distinct UV-vis absorption band at ∼640 nm. From the characterization of ESI mass spectrometry, IR, UV-vis spectroscopy, and O2-/PhIO-titration reactions, the molecular identity of complex 1ox is tentatively assigned as [Cu(μ-O)(μ-bimeta)3Cu]2+, which is further corroborated by the spectroscopically calibrated DFT calculations. The oxidation reactivities of complex 1ox were investigated using the well-understood sterically hindered phenol substrates DTBP and TBBP in both stoichiometric and catalytic fashions. In stoichiometric reactions, one equiv. of 1ox is capable of fully converting TBBP into TBOBF in the CH3CN solution at room temperature within 1 h. The optimized selectivity of catalytically oxidizing DTBP into TBOBF (>95% selectivity, ∼100% conversion rate) could be achieved with a 10 mol% loading of complex 1ox using air as the oxidant. From the time-course product distributions of this catalyst system, ∼40% of DTBP was converted into the corresponding TBBP product in the first 5 min. From 10 to 120 min, the oxidation of DTBP to TBBP and the oxidation of TBBP to TBOBF simultaneously proceeded, which was evidenced by the decrease of TBBP and the increase TBOBF.

Synergistic Multisites Fe2Mo6S8 Electrocatalysts for Ambient Nitrogen Conversion to Ammonia.

Electrochemical hydrogenation of N2 under ambient conditions is attractive for sustainable and distributable NH3 production but is limited by the lack of selective electrocatalysts. Herein, we describe active site motifs based on the Chevrel phase chalcogenide Fe2Mo6S8 that exhibit intrinsic activities for converting N2 to NH3 in aqueous electrolytes. Despite having a very low specific surface area of ∼2 m2/g, this catalyst exhibited a Faradaic efficiency of 12.5% and an average rate of 70 μg h-1 mgcat-1 for NH3 production at -0.20 V vs RHE. Such activities were attributed to the unique composition and structure of Fe2Mo6S8 that provide synergistic multisites for activating and associating key reaction intermediates. Specifically, Fe/Mo sites assist adsorption and activation of N2, whereas S sites stabilize hydrogen intermediate Had* for N2 hydrogenation. Fe in Fe2Mo6S8 enhances binding of S with Had* and thus inhibits the competing hydrogen evolution reaction. The spatial geometry of Fe, Mo, and S sites in Fe2Mo6S8 promotes conversion of N2-Had* association intermediates, reaching a turnover frequency of ∼0.23 s-1 for NH3 production.

Genome sequencing and molecular characterisation of XDR Acinetobacter baumannii reveal complexities in resistance: Novel combination of sulbactam-durlobactam holds promise for therapeutic intervention.

Emerging nosocomial strains of Acinetobacter baumannii are of recent concern as they are expressing extensive drug resistance (XDR). Using whole-genome sequencing and molecular characterisation analysis, the current study reveals the presence of carbapenemase genes in 92.86% of studied Indian isolates. These included blaOXA-51 , blaOXA-23 , blaOXA-58 , and blaNDM genes, with over a third expressing dual carbapenemase genes. As per the MLST scheme, IC2Oxf /CC2Pas was the predominant clone, with 57.14% isolates belonging to this lineage. The presence of these carbapenemase genes resulted in sulbactam (SUL) resistance (MIC: 16-256 µg/ml) in all of the studied isolates. The efficacy of durlobactam (DUR), a novel β-lactamase inhibitor that also inhibits PBP2 was assessed through in silico intermolecular interaction analysis. Several nonsynonymous single nucleotide polymorphisms were identified in PBP2 (G264S, I108V, S259T) and PBP3 (A515V, T526S) sequences. Minimal variations were recorded in the protein backbone dynamics in active-site motifs of wild-type and mutants, which correlated with negligible binding energy fluctuations for the PBP3-SUL (-5.85 ± 0.04 kcal/mol) and PBP2-DUR (-5.16 ± 0.66 kcal/mol) complexes. Furthermore, higher binding affinities and low inhibition constants were noted in OXA23-DUR (-7.36 kcal/mol; 4.01 µM), OXA58-DUR (-6.44 kcal/mol; 19.07 µM), and NDM-DUR (-6.82 kcal/mol; 10.01 µM) complexes when compared with the conventional drugs avibactam and aztreonam. Stable interaction profiles of DUR with carbapenemases can possibly restore SUL activity against both PBP3WT and PBP3MTs . The study establishes the efficacy of the novel SUL-DUR combination as a successful treatment strategy in combating emerging XDR strains of A. baumannii.

Broader than expected tolerance for substitutions in the WCGPCK catalytic motif of yeast thioredoxin 2

Thioredoxins constitute a key class of oxidant defense enzymes that facilitate disulfide bond reduction in oxidized substrate proteins. While thioredoxin's WCGPCK active site motif is highly conserved in traditional model organisms, predicted thioredoxins from newly sequenced genomes show variability in this motif, making ascertaining which genes encode functional thioredoxins with robust activity a challenge. To address this problem, we generated a semi-saturation mutagenesis library of approximately 70 thioredoxin variants harboring mutations adjacent to their catalytic cysteines, making substitutions in the Saccharomyces cerevisiae thioredoxin Trx2. Using this library, we determined how such substitutions impact oxidant defense in yeast along with how they influence disulfide reduction and interaction with binding partners in vivo. The majority of thioredoxin variants screened rescued the slow growth phenotype that accompanies deletion of the yeast cytosolic thioredoxins; however, the ability of these mutant proteins to protect against H2O2-mediated toxicity, facilitate disulfide reduction, and interact with redox partners varied widely, depending on the site being mutated and the substitution made. We report that thioredoxin is less tolerant of substitutions at its conserved tryptophan and proline in the active site motif, while it is more amenable to substitutions at the conserved glycine and lysine. Our work highlights a noteworthy plasticity within the active site of this critical oxidant defense enzyme.

Kinetic and Structural Characterization of the First B3 Metallo-β-Lactamase with an Active-Site Glutamic Acid

The structural diversity in metallo-β-lactamases (MBLs), especially in the vicinity of the active site, has been a major hurdle in the development of clinically effective inhibitors. Representatives from three variants of the B3 MBL subclass, containing either the canonical HHH/DHH active-site motif (present in the majority of MBLs in this subclass) or the QHH/DHH (B3-Q) or HRH/DQK (B3-RQK) variations, were reported previously. Here, we describe the structure and kinetic properties of the first example (SIE-1) of a fourth variant containing the EHH/DHH active-site motif (B3-E). SIE-1 was identified in the hexachlorocyclohexane-degrading bacterium Sphingobium indicum, and kinetic analyses demonstrate that although it is active against a wide range of antibiotics, its efficiency is lower than that of other B3 MBLs but has increased efficiency toward cephalosporins relative to other β-lactam substrates. The overall fold of SIE-1 is characteristic of the MBLs; the notable variation is observed in the Zn1 site due to the replacement of the canonical His116 by a glutamate. The unusual preference of SIE-1 for cephalosporins and its occurrence in a widespread environmental organism suggest the scope for increased MBL-mediated β-lactam resistance. Thus, it is relevant to include SIE-1 in MBL inhibitor design studies to widen the therapeutic scope of much needed antiresistance drugs.

Identification and characterization of an Apis cerana cerana nucleoside diphosphate kinase (AccNDPK) associated with oxidative stress

Nucleoside diphosphate kinases (NDPKs) are widespread nucleotide-metabolizing enzymes that are involved in a variety of biological processes, including responses to oxidative stress. Although studies have been conducted on NDPKs in mammals and some plants, there is scant research on insect NDPKs, especially in honey bees. In the present study, we isolated AccNDPK from Apis cerana cerana. Sequence analysis showed that AccNDPK has high homology with many NDPKs and contains a highly conserved NDPK active site motif. Based on phylogenetic analysis, AccNDPK has a relatively recent evolutionary relationship with NDPKs in other hymenopteran insects. AccNDPK was found to be highly expressed in newly emerged honey bees and muscle tissues, and RT-qPCR analysis and bacteriostatic assays showed that the expression level of AccNDPK is affected by abnormal temperature, UV light, H2O2, heavy metals, and various pesticides. After AccNDPK knockdown, antioxidant-related genes, including AccCAT, AccCYP4G11, AccGSTS4, AccTpx1 and AccMsrA, were upregulated, whereas AccGSTD, AccGST1, AccHSP22.6 and AccTrx1 were downregulated. Furthermore, catalase (CAT), superoxide dismutase (SOD), and peroxidase (POD) activities were significantly increased, and the tolerance of bees to oxidative stress caused by cyhalothrin was reduced by silencing of AccNDPK. Given these findings, we speculate that AccNDPK plays an important role in the oxidative stress response of A. cerana cerana.

A novel mycothiol-dependent thiol\u2013disulfide reductase in Corynebacterium glutamicum involving oxidative stress resistance

ncgl2478 gene from Corynebacterium glutamicum encodes a thiol–disulfide oxidoreductase enzyme annotated as dithiol–disulfide isomerase DsbA. It preserves a Cys–Pro–Phe–Cys active-site motif, which is presumed to be an exclusive characteristic of the novel DsbA–mycoredoxin 1 (Mrx1) cluster. However, the real mode of action, the nature of the electron donor pathway and biological functions of NCgl2478 in C. glutamicum have remained enigmatic so far. Herein, we report that NCgl2478 plays an important role in stress resistance. Deletion of the ncgl2478 gene increases the size of growth inhibition zones. The ncgl2478 expression is induced in the stress-responsive extra-cytoplasmic function-sigma (ECF-σ) factor SigH-dependent manner by stress. It receives electrons preferentially from the mycothiol (MSH)/mycothione reductase (Mtr)/NADPH pathway. Further, NCgl2478 reduces S-mycothiolated mixed disulfides and intramolecular disulfides via a monothiol–disulfide and a dithiol–disulfide exchange mechanism, respectively. NCgl2478 lacks oxidase activity; kinetic properties of its demycothiolation are different from those of Mrx1. Site-directed mutagenesis confirms Cys24 is the resolving Cys residue, while Cys21 is the nucleophilic cysteine that is oxidized to a sulfenic acid and then forms an intramolecular disulfide bond with Cys24 or a mixed disulfide with MSH under oxidative stress. In conclusion, our study presents the first evidence that NCgl2478 protects against various stresses by acting as an MSH-dependent thiol–disulfide reductase, belonging to a novel DsbA–Mrx1 cluster.

Adsorption Enthalpies for Catalysis Modeling through Machine-Learned Descriptors.

Heterogeneous catalysts are rather complex materials that come in many classes (e.g., metals, oxides, carbides) and shapes. At the same time, the interaction of the catalyst surface with even a relatively simple gas-phase environment such as syngas (CO and H2) may already produce a wide variety of reaction intermediates ranging from atoms to complex molecules. The starting point for creating predictive maps of, e.g., surface coverages or chemical activities of potential catalyst materials is the reliable prediction of adsorption enthalpies of all of these intermediates. For simple systems, direct density functional theory (DFT) calculations are currently the method of choice. However, a wider exploration of complex materials and reaction networks generally requires enthalpy predictions at lower computational cost.The use of machine learning (ML) and related techniques to make accurate and low-cost predictions of quantum-mechanical calculations has gained increasing attention lately. The employed approaches span from physically motivated models over hybrid physics-ΔML approaches to complete black-box methods such as deep neural networks. In recent works we have explored the possibilities for using a compressed sensing method (Sure Independence Screening and Sparsifying Operator, SISSO) to identify sparse (low-dimensional) descriptors for the prediction of adsorption enthalpies at various active-site motifs of metals and oxides. We start from a set of physically motivated primary features such as atomic acid/base properties, coordination numbers, or band moments and let the data and the compressed sensing method find the best algebraic combination of these features. Here we take this work as a starting point to categorize and compare recent ML-based approaches with a particular focus on model sparsity, data efficiency, and the level of physical insight that one can obtain from the model.Looking ahead, while many works to date have focused only on the mere prediction of databases of, e.g., adsorption enthalpies, there is also an emerging interest in our field to start using ML predictions to answer fundamental science questions about the functioning of heterogeneous catalysts or perhaps even to design better catalysts than we know today. This task is significantly simplified in works that make use of scaling-relation-based models (volcano curves), where the model outcome is determined by only one or two adsorption enthalpies and which consequently become the sole target for ML-based high-throughput screening or design. However, the availability of cheap ML energetics also allows going beyond scaling relations. On the basis of our own work in this direction, we will discuss the additional physical insight that can be achieved by integrating ML-based predictions with traditional catalysis modeling techniques from thermal and electrocatalysis, such as the computational hydrogen electrode and microkinetic modeling, as well as the challenges that lie ahead.