Biochemistry Biochemistry最新文献

Here, we performed biochemical andgenetic characterizationofa GppA/PPX-family phosphohydrolase from Arabidopsis thaliana (AtGPPA/PPX). Sixteen splice variants of AtGPPA/PPX are deposited in public databases and can beclassified into two types based on differences in their N-terminalsequences. Green fluorescent protein fusions with either N-terminusindicated that neither possesses a transit peptide, suggesting thatall AtGPPA/PPX splice variants localize to the cytosol. Biochemicalanalysis of the long splice variant of AtGPPA/PPX demonstrated phosphataseactivity toward guanosine 5′-triphosphate 3′-diphosphate(pppGpp) and long-chain polyphosphate in vitro, althoughits substrate affinity and catalytic efficiency were lower than thoseofEscherichia coli PPX. Heterologousexpression of AtGPPA/PPX in anEscherichia coligppA mutant reduced intracellular pppGpp levelsrelative to the mutant control, indicating that AtGPPA/PPX possessespppGpp dephosphorylation activity in vivo. Loss-of-functionmutants of AtGPPA/PPX exhibited no overt growth defects under eitherstandard or nitrogen-starvation conditions. However, chlorophyll fluorescenceimaging revealed delayed and attenuated nonphotochemical quenchingafter actinic-light illumination without changes in the PSII quantumyield, suggesting faster electron transport and reduced need for thermaldissipation. Together, these results suggest that the cytosol-localizedAtGPPA/PPX functions as a phosphatase with unknown physiological substrate(s)and plays a key role in photosynthetic acclimation to fluctuatinglight conditions.

Precise,context-sensitivecontrol of protein synthesis is criticalin eukaryotic cells, and mRNA structure has emerged as a central mechanismfor achieving this control. mRNA structures influence every stageof translation. During initiation, structures within 5′ untranslatedregions modulate ribosome association with mRNA and the balance betweentranslation of the main open reading frame and use of upstream oralternative start sites. During elongation, structures in the codingsequence govern ribosome pausing in ways that can either protect mRNAstability or trigger decay. During termination, structures downstreamof primary stop codons promote readthrough to generate protein isoformsin a tissue-specific manner. mRNA structures are remodeled by helicaseexpression, post-transcriptional modifications, and translationalprogramming to provide additional layers of regulation. We reviewrecent advances illuminating diverse mechanisms by which RNA structuremodulates translation.

Glycerol is abundantin natural environments and is utilized bymany microbes. In aerobes, it is typically converted, via glycerol-3-phosphate(G3P), to dihydroxyacetone phosphate (DHAP) by a quinone-linked dehydrogenasethereby coupling glycolysis and respiration. Under anaerobic conditions,an NAD⁺-dependent dehydrogenase has been proposed to oxidizeG3P to DHAP in several bacteria but this reaction is thermodynamicallyunfavorable. Herein, we have purified a heterotrimeric electron bifurcatingenzyme from the archaeon Pyrococcus furiosus where the simultaneous oxidation of both G3P (E_o′−190 mV) and reduced ferredoxin (E_m ∼ −450mV) enables reduction of NAD⁺(E_o′ −320mV) and production of DHAP. Surprisingly, this ferredoxin-dependent NAD⁺G3P oxidoreductase (FngABC) is unrelated evolutionarilyto the four known families of bifurcating enzyme. Analysis by UV–visiblespectroscopy and of its predicted structure suggest FngABC has a nonclassicalbifurcation mechanism. Phylogenetic and genome context analyses of4,273 P. furiosus FngA homologues revealedthey are widespread with ∼35% found mainly in Clostridia asFngABC and ∼10% found mainly in Actinomyces as FngAB, mostof which utilize polyols in addition to glycerol. The remaining ∼40%are present in Gammaproteobacteria and halophilic archaea but hereFngA is associated with homologues of E. coli GlpBC, which are unrelated to FngBC, and these enzymes typicallyonly use glycerol. It is therefore proposed that P. furiosus FngABC and the previously characterized E. coli GlpABC are disparate members of a new electronbifurcating family widespread in the microbial world that are involvedin the metabolism of a range of sugars as well as glycerol.

N-Acetylglucosamineexists in various glycoforms and linkage patternswithin organisms, playing a crucial role in numerous vital biologicalprocesses. The signal of β-1,2-N-acetylglucosamine is a keycomponent within complex biantennary N-glycans on the cell surface,leaving related research in its early exploratory stages. Currently,there is a lack of efficient tools and methods capable of directlymodifying terminal N-acetylglucosamine on living cells. In this study,we identified a novel β-N-acetylglucosaminidase from Elizabethkingia meningoseptica FMS-007, which specificallycleaves nonreducing terminal β-1,2-N-acetylglucosamine, enablingdirect removal from native glycoproteins and/or free oligosaccharides.More importantly, we demonstrate for the first time the successfulremoval of β-1,2-N-acetylglucosamine from the living cell surfaceusing this enzyme. Based on its isolation and newly characterizedcell-surface glycan-editing activity, we designated it as EmNag, alsotermed cell-surface glycan-editing N-acetylglucosaminidase (csgeNag).It showed favorable enzymatic stability between pH 5–8 andfrom 4 to 37 °C. Sequence analysis and alanine-scanning mutagenesisidentified a conserved active pocket containing the catalytic residuepair Asp317-Glu318, with Asp317 being essential for activity. In summary,our findings provide an effective and reliable method for the targetedremoval of β-1,2-N-acetylglucosamine from the living cell surface,establishing a foundation for further functional studies and practicalapplications.

Molecules that formirreversible covalent bonds with their targetsare a mainstay of drug discovery and chemical biology research. Theirability to permanently inactivate an enzyme target provides a mechanismwith significant potential to modulate disease phenotypes. This perspectivediscusses the trajectory of the field of irreversible enzyme inhibitorswith an outlook on emerging methods, warhead structures, and sentimentspresently directing practices in the discovery and design of the nextwave of covalent agents.

Long-range proteinelectron transfer (ET) often depends on tryptophanand tyrosine residues acting as radical relay sites. For example,cytochrome c peroxidase (CcP) generates a W191^•+ radical to increase ET from cytochrome c (Cc) tothe active center. W191 substitution to Tyr reduces ET rates, butintroduction of an adjacent general base (as Glu or His) at position232 (Y191:E/H232 CcP) recovers activity. E232 fluorination lowersthe pK_a of the conjugate base and confirmsthat a hydrogen bond is critical to elevate the Y191^• formal potential for effective ET. Photoinitiated ET between Zn-porphyrin(ZnP) CcP (ZnCcP) and Cc also depends on activatingY191 with a basic residue but through a different mechanism than forthe peroxide-driven system. In ZnCcP, pH dependencies and solventisotope effects indicate that proton-coupled electron transfer tothe basic residue and ZnP^•+, respectively, facilitatesY191^• formation. Replacing Cc withthe irreversible oxidant [Co(NH3)₅Cl]²⁺ isolatesdistinct protein radicals for characterization by electron paramagneticresonance (EPR) spectroscopy. Radical distributions and computationindicate that W191^•+ lies close in potential toZnP^•+ and that the two radicals exchange on a slowtime scale despite their close separation. Remarkably, Y191:E/H232ZnCcP variants propagate radicals differently to peripheral sitesdepending on the nature of the 232 residue. QM/MM calculations supportradical exchange between ZnP^•+/Trp^•+ and the importance of a hydrogen bond to Y191^• for maintaining a high potential to oxidize peripheral donors. Theseresolved reactivity patterns of CcP/ZnCcP have general relevance forengineering proton management to separate and migrate charge in proteinsand potentially other molecular systems.

Fibrillar proteinaggregates are a defining feature of neurodegenerativediseases and represent attractive biomarkers and therapeutic targets.However, the rational design of small-molecule ligands and probestargeting these aggregates is limited by a poor understanding of howligands bind to amyloid fibrils. This work outlines an experimentalapproach to determine the binding mode of ligands to amyloid fibrilsusing previously overlooked information contained within standardbinding assays. Using a mathematical framework to analyze bindingbehavior, three distinct high-affinity binding modes were identified:discrete, overlapping, and interacting binding. Reanalysis of publishedbinding data indicates that these binding modes are widespread amongcommon amyloid-binding ligand scaffolds. Two ligands were designedusingprinciples informed by these binding modes, yielding improved bindingaffinities and characteristic fluorescence responses. These findingsestablish a practical framework for determining how small moleculesbind amyloid fibrils using straightforward binding assays and forguiding the design of future fibril-binding ligands and probes.

Cnidarians possess a large number of opsins in theirgenomes fortheir various photoreceptive functions. In particular, they uniquelypossess Gs-coupled opsins that induce intracellular cAMP accumulationin a light-dependent manner. These Gs-coupled opsins, cnidopsins,are powerful optogenetic tools that manipulate cAMP-dependent cellularresponses. In this study, we characterized a cnidopsin, named AtCnidop3a,from the coral Acropora tenuis as aGs-coupled and UV-sensitive bistable pigment. This cnidopsin showeda large spectral shift upon activation from absorption maxima from395 to 560 nm, and the resting and activated states are interconvertibleby illumination with UV (or violet) and orange light. The activatedstate efficiently activates Gs proteins and elevates intracellularcAMP levels in mammalian cultured cells. To engineer an opsin mutantthat can be turned on and off upon long-wavelength light illuminationby utilizing the large spectral separation, negatively charged aminoacids were introduced near the retinal Schiff base region. Among thetested opsin mutants, the Y113^3.28E mutant is capable ofbeing activated by green light unlike the wild-type while retainingthe property of being inactivated by orange light like the wild-type,indicating successful conversion of the opsin to a visible-light-sensitivebistable pigment. The visible-light-induced cAMP regulation of theY113^3.28E mutant was enhanced by an additional L94^2.61G substitution. Our characterization and engineering ofthe cnidopsin revealed the functional diversity of cnidarian opsinsand their potential utility as optogenetic tools regulating Gs-dependentphysiological responses.

Azo dyes are widespread in the environment, and humansingest arange of these dyes present in food and drugs. The human gut microbiomesignificantly impacts the fate of ingested azo dyes primarily throughthe reduction of the azo bond (R–N = N–R′). Flavin-dependentazoreductases have been considered the key enzymatic drivers of thisprocess. To challenge this paradigm, we constructed a sequence similaritynetwork of known azoreductases and focused on AzoA of Klebsiella pneumoniae, a central representative withinthe gut microbiome cluster. Unexpectedly, K. pneumoniae AzoA displayed relatively low in vitro activityagainst a range of azo compounds. While the physiological implicationsremain unclear, these findings are consistent with the possibilitythat nonenzymatic mechanisms contribute substantially to azo compoundreduction in the gut. Furthermore, structural characterization ofAzoA, as a holoenzyme and in its ligand-bound state, revealed a previouslyunrecognized ligand-coupled mechanism involving remodeling of theactive site and oligomeric state.

Phosphorothioated (PST) oligonucleotides are extensivelyused inRNA therapeutics and biosensing applications. PST-modified linkagesremain part of 13 approved oligonucleotide drug backbones (out of23 total approved drugs). Despite the widespread utilization of PSTlinkages in oligonucleotide therapeutics, the full spectrum of theirinteractions with nontarget nucleic acids and DNA polymerases remainsinadequately characterized. In this study, we report a novel discoveryand the modalities (sequence dependence and length) of an unusual3′-mismatch bypass activity involving 3′-PST primers,circular DNA (CD) template, and strand displacement DNA polymerases.We demonstrate that this activity persists for at least 24 nt of mismatch,is sequence-independent, and occurs when processed by three majorcommercially available strand displacement DNA polymerases commonlyused in molecular diagnostics (phi29, BST large fragment (LF), BSUlarge fragment (LF)) with operational conditions spanning a largetemperature range and buffer conditions. The 3′-terminal mismatchbypass activity of these three polymerases additionally extended totherapeutically relevant modifications such as locked nucleic acid(LNA) and 2′-O-methyl (2′-OMe). Wealso found that this mismatch bypass activity could be regulated byoligonucleotides complementary to the mismatch region. The significanceof this study lies not only in the discovery and analytical investigationof the novel observation but also in its ramifications for biosensingand the nonspecific interactions of PST oligonucleotides in RNA therapeutics.