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1.
Annu Rev Biochem ; 91: 157-181, 2022 06 21.
Artículo en Inglés | MEDLINE | ID: mdl-35303790

RESUMEN

Covalent DNA-protein crosslinks (DPCs) are pervasive DNA lesions that interfere with essential chromatin processes such as transcription or replication. This review strives to provide an overview of the sources and principles of cellular DPC formation. DPCs are caused by endogenous reactive metabolites and various chemotherapeutic agents. However, in certain conditions DPCs also arise physiologically in cells. We discuss the cellular mechanisms resolving these threats to genomic integrity. Detection and repair of DPCs require not only the action of canonical DNA repair pathways but also the activity of specialized proteolytic enzymes-including proteases of the SPRTN/Wss1 family-to degrade the crosslinked protein. Loss of DPC repair capacity has dramatic consequences, ranging from genome instability in yeast and worms to cancer predisposition and premature aging in mice and humans.


Asunto(s)
Reparación del ADN , Proteínas de Saccharomyces cerevisiae , Animales , ADN/genética , ADN/metabolismo , Daño del ADN , Proteínas de Unión al ADN/genética , Proteínas de Unión al ADN/metabolismo , Inestabilidad Genómica , Ratones , Saccharomyces cerevisiae/metabolismo , Proteínas de Saccharomyces cerevisiae/metabolismo
2.
Cell ; 182(4): 933-946.e14, 2020 08 20.
Artículo en Inglés | MEDLINE | ID: mdl-32780992

RESUMEN

Methanol, being electron rich and derivable from methane or CO2, is a potentially renewable one-carbon (C1) feedstock for microorganisms. Although the ribulose monophosphate (RuMP) cycle used by methylotrophs to assimilate methanol differs from the typical sugar metabolism by only three enzymes, turning a non-methylotrophic organism to a synthetic methylotroph that grows to a high cell density has been challenging. Here we reprogrammed E. coli using metabolic robustness criteria followed by laboratory evolution to establish a strain that can efficiently utilize methanol as the sole carbon source. This synthetic methylotroph alleviated a so far uncharacterized hurdle, DNA-protein crosslinking (DPC), by insertion sequence (IS)-mediated copy number variations (CNVs) and balanced the metabolic flux by mutations. Being capable of growing at a rate comparable with natural methylotrophs in a wide range of methanol concentrations, this synthetic methylotrophic strain illustrates genome editing and evolution for microbial tropism changes and expands the scope of biological C1 conversion.


Asunto(s)
Escherichia coli/metabolismo , Ingeniería Metabólica , Metanol/metabolismo , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo , Carbono/metabolismo , Ciclo del Ácido Cítrico/genética , Variaciones en el Número de Copia de ADN , Evolución Molecular Dirigida , Escherichia coli/genética , Formaldehído/metabolismo , Glucólisis , Mutagénesis , Ribosamonofosfatos/metabolismo
3.
Cell ; 169(6): 1105-1118.e15, 2017 Jun 01.
Artículo en Inglés | MEDLINE | ID: mdl-28575672

RESUMEN

Mutations truncating a single copy of the tumor suppressor, BRCA2, cause cancer susceptibility. In cells bearing such heterozygous mutations, we find that a cellular metabolite and ubiquitous environmental toxin, formaldehyde, stalls and destabilizes DNA replication forks, engendering structural chromosomal aberrations. Formaldehyde selectively depletes BRCA2 via proteasomal degradation, a mechanism of toxicity that affects very few additional cellular proteins. Heterozygous BRCA2 truncations, by lowering pre-existing BRCA2 expression, sensitize to BRCA2 haploinsufficiency induced by transient exposure to natural concentrations of formaldehyde. Acetaldehyde, an alcohol catabolite detoxified by ALDH2, precipitates similar effects. Ribonuclease H1 ameliorates replication fork instability and chromosomal aberrations provoked by aldehyde-induced BRCA2 haploinsufficiency, suggesting that BRCA2 inactivation triggers spontaneous mutagenesis during DNA replication via aberrant RNA-DNA hybrids (R-loops). These findings suggest a model wherein carcinogenesis in BRCA2 mutation carriers can be incited by compounds found pervasively in the environment and generated endogenously in certain tissues with implications for public health.


Asunto(s)
Proteína BRCA2/genética , Aberraciones Cromosómicas/efectos de los fármacos , Formaldehído/toxicidad , Inestabilidad Genómica/efectos de los fármacos , Toxinas Biológicas/toxicidad , Daño del ADN , Replicación del ADN/efectos de los fármacos , Proteínas de Unión al ADN/metabolismo , Haploinsuficiencia , Células HeLa , Humanos , Proteína Homóloga de MRE11 , Proteoma , Ribonucleasa H/metabolismo
4.
Mol Cell ; 83(23): 4290-4303.e9, 2023 Dec 07.
Artículo en Inglés | MEDLINE | ID: mdl-37951216

RESUMEN

Reactive aldehydes are abundant endogenous metabolites that challenge homeostasis by crosslinking cellular macromolecules. Aldehyde-induced DNA damage requires repair to prevent cancer and premature aging, but it is unknown whether cells also possess mechanisms that resolve aldehyde-induced RNA lesions. Here, we establish photoactivatable ribonucleoside-enhanced crosslinking (PAR-CL) as a model system to study RNA crosslinking damage in the absence of confounding DNA damage in human cells. We find that such RNA damage causes translation stress by stalling elongating ribosomes, which leads to collisions with trailing ribosomes and activation of multiple stress response pathways. Moreover, we discovered a translation-coupled quality control mechanism that resolves covalent RNA-protein crosslinks. Collisions between translating ribosomes and crosslinked mRNA-binding proteins trigger their modification with atypical K6- and K48-linked ubiquitin chains. Ubiquitylation requires the E3 ligase RNF14 and leads to proteasomal degradation of the protein adduct. Our findings identify RNA lesion-induced translational stress as a central component of crosslinking damage.


Asunto(s)
ARN , Ubiquitina , Humanos , ARN/metabolismo , Ubiquitinación , Ubiquitina/metabolismo , Ribosomas/metabolismo , Ubiquitina-Proteína Ligasas/genética , Ubiquitina-Proteína Ligasas/metabolismo , Aldehídos , Biosíntesis de Proteínas
5.
Mol Cell ; 80(6): 996-1012.e9, 2020 12 17.
Artículo en Inglés | MEDLINE | ID: mdl-33147438

RESUMEN

Reactive aldehydes arise as by-products of metabolism and are normally cleared by multiple families of enzymes. We find that mice lacking two aldehyde detoxifying enzymes, mitochondrial ALDH2 and cytoplasmic ADH5, have greatly shortened lifespans and develop leukemia. Hematopoiesis is disrupted profoundly, with a reduction of hematopoietic stem cells and common lymphoid progenitors causing a severely depleted acquired immune system. We show that formaldehyde is a common substrate of ALDH2 and ADH5 and establish methods to quantify elevated blood formaldehyde and formaldehyde-DNA adducts in tissues. Bone-marrow-derived progenitors actively engage DNA repair but also imprint a formaldehyde-driven mutation signature similar to aging-associated human cancer mutation signatures. Furthermore, we identify analogous genetic defects in children causing a previously uncharacterized inherited bone marrow failure and pre-leukemic syndrome. Endogenous formaldehyde clearance alone is therefore critical for hematopoiesis and in limiting mutagenesis in somatic tissues.


Asunto(s)
Alcohol Deshidrogenasa/genética , Aldehído Deshidrogenasa Mitocondrial/genética , Formaldehído/sangre , Leucemia/genética , Adolescente , Aldehídos/sangre , Animales , Niño , Preescolar , Aductos de ADN/genética , Daño del ADN/efectos de los fármacos , Reparación del ADN/efectos de los fármacos , Femenino , Formaldehído/toxicidad , Hematopoyesis/genética , Células Madre Hematopoyéticas/metabolismo , Humanos , Lactante , Leucemia/sangre , Leucemia/patología , Masculino , Ratones , Mutación/genética , Especificidad por Sustrato
6.
Mol Cell ; 80(6): 1013-1024.e6, 2020 12 17.
Artículo en Inglés | MEDLINE | ID: mdl-33338401

RESUMEN

Impaired DNA crosslink repair leads to Fanconi anemia (FA), characterized by a unique manifestation of bone marrow failure and pancytopenia among diseases caused by DNA damage response defects. As a germline disorder, why the hematopoietic hierarchy is specifically affected is not fully understood. We find that reprogramming transcription during hematopoietic differentiation results in an overload of genotoxic stress, which causes aborted differentiation and depletion of FA mutant progenitor cells. DNA damage onset most likely arises from formaldehyde, an obligate by-product of oxidative protein demethylation during transcription regulation. Our results demonstrate that rapid and extensive transcription reprogramming associated with hematopoietic differentiation poses a major threat to genome stability and cell viability in the absence of the FA pathway. The connection between differentiation and DNA damage accumulation reveals a novel mechanism of genome scarring and is critical to exploring therapies to counteract the aplastic anemia for the treatment of FA patients.


Asunto(s)
Diferenciación Celular/efectos de los fármacos , Reprogramación Celular/genética , Anemia de Fanconi/genética , Formaldehído/toxicidad , Daño del ADN/efectos de los fármacos , Reparación del ADN/genética , Anemia de Fanconi/sangre , Anemia de Fanconi/patología , Formaldehído/metabolismo , Regulación del Desarrollo de la Expresión Génica/efectos de los fármacos , Regulación del Desarrollo de la Expresión Génica/genética , Inestabilidad Genómica/genética , Trasplante de Células Madre Hematopoyéticas , Células Madre Hematopoyéticas/efectos de los fármacos , Humanos , Células K562 , Transcripción Genética
7.
Mol Cell ; 80(1): 102-113.e6, 2020 10 01.
Artículo en Inglés | MEDLINE | ID: mdl-32853547

RESUMEN

Repair of covalent DNA-protein crosslinks (DPCs) by DNA-dependent proteases has emerged as an essential genome maintenance mechanism required for cellular viability and tumor suppression. However, how proteolysis is restricted to the crosslinked protein while leaving surrounding chromatin proteins unharmed has remained unknown. Using defined DPC model substrates, we show that the DPC protease SPRTN displays strict DNA structure-specific activity. Strikingly, SPRTN cleaves DPCs at or in direct proximity to disruptions within double-stranded DNA. In contrast, proteins crosslinked to intact double- or single-stranded DNA are not cleaved by SPRTN. NMR spectroscopy data suggest that specificity is not merely affinity-driven but achieved through a flexible bipartite strategy based on two DNA binding interfaces recognizing distinct structural features. This couples DNA context to activation of the enzyme, tightly confining SPRTN's action to biologically relevant scenarios.


Asunto(s)
Reactivos de Enlaces Cruzados/metabolismo , Proteínas de Unión al ADN/metabolismo , ADN/química , Línea Celular , Proteínas de Unión al ADN/química , Humanos , Espectroscopía de Resonancia Magnética , Modelos Biológicos , Dominios Proteicos , Relación Estructura-Actividad
8.
Proc Natl Acad Sci U S A ; 120(48): e2304650120, 2023 Nov 28.
Artículo en Inglés | MEDLINE | ID: mdl-37988470

RESUMEN

Atmospheric formic acid is severely underpredicted by models. A recent study proposed that this discrepancy can be resolved by abundant formic acid production from the reaction (1) between hydroxyl radical and methanediol derived from in-cloud formaldehyde processing and provided a chamber-experiment-derived rate constant, k1 = 7.5 × 10-12 cm3 s-1. High-level accuracy coupled cluster calculations in combination with E,J-resolved two-dimensional master equation analyses yield k1 = (2.4 ± 0.5) × 10-12 cm3 s-1 for relevant atmospheric conditions (T = 260-310 K and P = 0-1 atm). We attribute this significant discrepancy to HCOOH formation from other molecules in the chamber experiments. More importantly, we show that reversible aqueous processes result indirectly in the equilibration on a 10 min. time scale of the gas-phase reaction [Formula: see text] (2) with a HOCH2OH to HCHO ratio of only ca. 2%. Although HOCH2OH outgassing upon cloud evaporation typically increases this ratio by a factor of 1.5-5, as determined by numerical simulations, its in-cloud reprocessing is shown using a global model to strongly limit the gas-phase sink and the resulting production of formic acid. Based on the combined findings in this work, we derive a range of 1.2-8.5 Tg/y for the global HCOOH production from cloud-derived HOCH2OH reacting with OH. The best estimate, 3.3 Tg/y, is about 30 times less than recently reported. The theoretical equilibrium constant Keq (2) determined in this work also allows us to estimate the Henry's law constant of methanediol (8.1 × 105 M atm-1 at 280 K).

9.
Development ; 149(10)2022 05 15.
Artículo en Inglés | MEDLINE | ID: mdl-35485397

RESUMEN

Melanocyte stem cells (McSCs) in zebrafish serve as an on-demand source of melanocytes during growth and regeneration, but metabolic programs associated with their activation and regenerative processes are not well known. Here, using live imaging coupled with scRNA-sequencing, we discovered that, during regeneration, quiescent McSCs activate a dormant embryonic neural crest transcriptional program followed by an aldehyde dehydrogenase (Aldh) 2 metabolic switch to generate progeny. Unexpectedly, although ALDH2 is well known for its aldehyde-clearing mechanisms, we find that, in regenerating McSCs, Aldh2 activity is required to generate formate - the one-carbon (1C) building block for nucleotide biosynthesis - through formaldehyde metabolism. Consequently, we find that disrupting the 1C cycle with low doses of methotrexate causes melanocyte regeneration defects. In the absence of Aldh2, we find that purines are the metabolic end product sufficient for activated McSCs to generate progeny. Together, our work reveals McSCs undergo a two-step cell state transition during regeneration, and that the reaction products of Aldh2 enzymes have tissue-specific stem cell functions that meet metabolic demands in regeneration.


Asunto(s)
Melanocitos , Pez Cebra , Animales , Diferenciación Celular , Cresta Neural , Células Madre
10.
Circ Res ; 133(3): 220-236, 2023 07 21.
Artículo en Inglés | MEDLINE | ID: mdl-37377022

RESUMEN

BACKGROUND: The cardiac-protective role of GSNOR (S-nitrosoglutathione reductase) in the cytoplasm, as a denitrosylase enzyme of S-nitrosylation, has been reported in cardiac remodeling, but whether GSNOR is localized in other organelles and exerts novel effects remains unknown. We aimed to elucidate the effects of mitochondrial GSNOR, a novel subcellular localization of GSNOR, on cardiac remodeling and heart failure (HF). METHODS: GSNOR subcellular localization was observed by cellular fractionation assay, immunofluorescent staining, and colloidal gold particle staining. Overexpression of GSNOR in mitochondria was achieved by mitochondria-targeting sequence-directed adeno-associated virus 9. Cardiac-specific knockout of GSNOR mice was used to examine the role of GSNOR in HF. S-nitrosylation sites of ANT1 (adenine nucleotide translocase 1) were identified using biotin-switch and liquid chromatography-tandem mass spectrometry. RESULTS: GSNOR expression was suppressed in cardiac tissues of patients with HF. Consistently, cardiac-specific knockout mice showed aggravated pathological remodeling induced by transverse aortic constriction. We found that GSNOR is also localized in mitochondria. In the angiotensin II-induced hypertrophic cardiomyocytes, mitochondrial GSNOR levels significantly decreased along with mitochondrial functional impairment. Restoration of mitochondrial GSNOR levels in cardiac-specific knockout mice significantly improved mitochondrial function and cardiac performance in transverse aortic constriction-induced HF mice. Mechanistically, we identified ANT1 as a direct target of GSNOR. A decrease in mitochondrial GSNOR under HF leads to an elevation of S-nitrosylation ANT1 at cysteine 160 (C160). In accordance with these findings, overexpression of either mitochondrial GSNOR or ANT1 C160A, non-nitrosylated mutant, significantly improved mitochondrial function, maintained the mitochondrial membrane potential, and upregulated mitophagy. CONCLUSIONS: We identified a novel species of GSNOR localized in mitochondria and found mitochondrial GSNOR plays an essential role in maintaining mitochondrial homeostasis through ANT1 denitrosylation, which provides a potential novel therapeutic target for HF.


Asunto(s)
Insuficiencia Cardíaca , Remodelación Ventricular , Animales , Humanos , Ratones , Corazón , Insuficiencia Cardíaca/metabolismo , Ratones Noqueados , Mitocondrias/metabolismo
11.
Mol Cell ; 66(2): 258-269.e5, 2017 Apr 20.
Artículo en Inglés | MEDLINE | ID: mdl-28431232

RESUMEN

MicroRNA (miRNA) maturation is initiated by DROSHA, a double-stranded RNA (dsRNA)-specific RNase III enzyme. By cleaving primary miRNAs (pri-miRNAs) at specific positions, DROSHA serves as a main determinant of miRNA sequences and a highly selective gatekeeper for the canonical miRNA pathway. However, the sites of DROSHA-mediated processing have not been annotated, and it remains unclear to what extent DROSHA functions outside the miRNA pathway. Here, we establish a protocol termed "formaldehyde crosslinking, immunoprecipitation, and sequencing (fCLIP-seq)," which allows identification of DROSHA cleavage sites at single-nucleotide resolution. fCLIP identifies numerous processing sites, suggesting widespread end modifications during miRNA maturation. fCLIP also finds many pri-miRNAs that undergo alternative processing, yielding multiple miRNA isoforms. Moreover, we discovered dozens of DROSHA substrates on non-miRNA loci, which may serve as cis-elements for DROSHA-mediated gene regulation. We anticipate that fCLIP-seq could be a general tool for investigating interactions between dsRNA-binding proteins and structured RNAs.


Asunto(s)
Secuenciación de Nucleótidos de Alto Rendimiento , MicroARNs/metabolismo , Procesamiento Postranscripcional del ARN , Ribonucleasa III/metabolismo , Análisis de Secuencia de ARN/métodos , Secuencia de Bases , Sitios de Unión , Reactivos de Enlaces Cruzados/química , Formaldehído/química , Células HEK293 , Células HeLa , Humanos , Inmunoprecipitación , MicroARNs/química , MicroARNs/genética , Conformación de Ácido Nucleico , Unión Proteica , Interferencia de ARN , Ribonucleasa III/química , Ribonucleasa III/genética , Relación Estructura-Actividad , Especificidad por Sustrato , Transfección
12.
Proc Natl Acad Sci U S A ; 119(4)2022 01 25.
Artículo en Inglés | MEDLINE | ID: mdl-35046020

RESUMEN

Water influences critically the kinetics of the autocatalytic conversion of methanol to hydrocarbons in acid zeolites. At very low conversions but otherwise typical reaction conditions, the initiation of the reaction is delayed in presence of H2O. In absence of hydrocarbons, the main reactions are the methanol and dimethyl ether (DME) interconversion and the formation of a C1 reactive mixture-which in turn initiates the formation of first hydrocarbons in the zeolite pores. We conclude that the dominant reactions for the formation of a reactive C1 pool at this stage involve hydrogen transfer from both MeOH and DME to surface methoxy groups, leading to methane and formaldehyde in a 1:1 stoichiometry. While formaldehyde reacts further to other C1 intermediates and initiates the formation of first C-C bonds, CH4 is not reacting. The hydride transfer to methoxy groups is the rate-determining step in the initiation of the conversion of methanol and DME to hydrocarbons. Thus, CH4 formation rates at very low conversions, i.e., in the initiation stage before autocatalysis starts, are used to gauge the formation rates of first hydrocarbons. Kinetics, in good agreement with theoretical calculations, show surprisingly that hydrogen transfer from DME to methoxy species is 10 times faster than hydrogen transfer from methanol. This difference in reactivity causes the observed faster formation of hydrocarbons in dry feeds, when the concentration of methanol is lower than in presence of water. Importantly, the kinetic analysis of CH4 formation rates provides a unique quantitative parameter to characterize the activity of catalysts in the methanol-to-hydrocarbon process.

13.
Proc Natl Acad Sci U S A ; 119(6)2022 02 08.
Artículo en Inglés | MEDLINE | ID: mdl-35101978

RESUMEN

Formaldehyde (HCHO), the simplest and most abundant carbonyl in the atmosphere, contributes to particulate matter (PM) formation via two in-cloud processing pathways. First, in a catalytic pathway, HCHO reacts with hydrogen peroxide (H2O2) to form hydroxymethyl hydroperoxide (HMHP), which rapidly oxidizes dissolved sulfur dioxide (SO2,aq) to sulfate, regenerating HCHO. Second, HCHO reacts with dissolved SO2,aq to form hydroxymethanesulfonate (HMS), which upon oxidation with the hydroxyl radical (OH) forms sulfate and also reforms HCHO. Chemical transport model simulations using rate coefficients from laboratory studies of the reaction rate of HMHP with SO2,aq show that the HMHP pathways reduce the SO2 lifetime by up to a factor of 2 and contribute up to ∼18% of global sulfate. This contribution rises to >50% in isoprene-dominated regions such as the Amazon. Combined with recent results on HMS, this work demonstrates that the one-carbon molecules HMHP and HCHO contribute significantly to global PM, with HCHO playing a crucial catalytic role.

14.
J Bacteriol ; 206(4): e0008124, 2024 04 18.
Artículo en Inglés | MEDLINE | ID: mdl-38501746

RESUMEN

Paracoccus denitrificans is a facultative methylotroph that can grow on methanol and methylamine as sole sources of carbon and energy. Both are oxidized to formaldehyde and then to formate, so growth on C1 substrates induces the expression of genes encoding enzymes required for the oxidation of formaldehyde and formate. This induction involves a histidine kinase response regulator pair (FlhSR) that is likely triggered by formaldehyde. Catabolism of some complex organic substrates (e.g., choline and L-proline betaine) also generates formaldehyde. Thus, flhS and flhR mutants that fail to induce expression of the formaldehyde catabolic enzymes cannot grow on methanol, methylamine, and choline. Choline is oxidized to glycine via glycine betaine, dimethylglycine, and sarcosine. By exploring flhSR growth phenotypes and the activities of a promoter and enzyme known to be upregulated by formaldehyde, we identify the oxidative demethylations of glycine betaine, dimethylglycine, and sarcosine as sources of formaldehyde. Growth on glycine betaine, dimethylglycine, and sarcosine is accompanied by the production of up to three, two, and one equivalents of formaldehyde, respectively. Genetic evidence implicates two orthologous monooxygenases in the oxidation of glycine betaine. Interestingly, one of these appears to be a bifunctional enzyme that also oxidizes L-proline betaine (stachydrine). We present preliminary evidence to suggest that growth on L-proline betaine induces expression of a formaldehyde dehydrogenase distinct from the enzyme induced during growth on other formaldehyde-generating substrates.IMPORTANCEThe bacterial degradation of one-carbon compounds (methanol and methylamine) and some complex multi-carbon compounds (e.g., choline) generates formaldehyde. Formaldehyde is toxic and must be removed, which can be done by oxidation to formate and then to carbon dioxide. These oxidations provide a source of energy; in some species, the CO2 thus generated can be assimilated into biomass. Using the Gram-negative bacterium Paracoccus denitrificans as the experimental model, we infer that oxidation of choline to glycine generates up to three equivalents of formaldehyde, and we identify the three steps in the catabolic pathway that are responsible. Our work sheds further light on metabolic pathways that are likely important in a variety of environmental contexts.


Asunto(s)
Betaína , Paracoccus denitrificans , Betaína/metabolismo , Sarcosina/metabolismo , Paracoccus denitrificans/genética , Paracoccus denitrificans/metabolismo , Metanol , Colina/metabolismo , Glicina , Formaldehído , Formiatos , Metilaminas
15.
J Proteome Res ; 23(4): 1370-1378, 2024 04 05.
Artículo en Inglés | MEDLINE | ID: mdl-38472149

RESUMEN

Messenger ribonucleoprotein particles (mRNPs) are vital for tissue-specific gene expression via mediating posttranscriptional regulations. However, proteomic profiling of proteins in mRNPs, i.e., mRNA-associated proteins (mRAPs), has been challenging at the tissue level. Herein, we report the development of formaldehyde cross-linking-based mRNA-associated protein profiling (FAXRAP), a chemical strategy that enables the identification of mRAPs in both cultured cells and intact mouse organs. Applying FAXRAP, tissue-specific mRAPs were systematically profiled in the mouse liver, kidney, heart, and brain. Furthermore, brain mRAPs in Parkinson's disease (PD) mouse model were investigated, which revealed a global decrease of mRNP assembly in the brain of mice with PD. We envision that FAXRAP will facilitate uncovering the posttranscriptional regulation networks in various biological systems.


Asunto(s)
Proteómica , Ribonucleoproteínas , Ratones , Animales , Ribonucleoproteínas/genética , Ribonucleoproteínas/metabolismo , ARN Mensajero/genética , ARN Mensajero/metabolismo , Formaldehído
16.
J Biol Chem ; 299(5): 104648, 2023 05.
Artículo en Inglés | MEDLINE | ID: mdl-36965616

RESUMEN

IsdG-type enzymes catalyze the noncanonical degradation of heme to iron, staphylobilin (SB), and formaldehyde (HCHO), presumably by binding heme in an unusually distorted conformation. Their unique mechanism has been elucidated for MhuD from Mycobacterium tuberculosis, revealing an unusual ring opening of hydroxyheme by dioxygenation. A similar mechanism has been postulated for other IsdG enzymes; however, MhuD, which is special as an IsdG-type enzyme, retains a formyl group in the linearized tetrapyrrole. Recent reports on Staphylococcus aureus IsdG have suggested the formation of SB retaining a formyl group (formyl-SB), but its identification is preliminary. Furthermore, the reaction properties of formyl-SB and the mechanism of HCHO release remain unclear. In this study, the complex reaction of S. aureus IsdG was reexamined to elucidate its mechanism, including the identification of reaction products and their control mechanisms. Depending on the reaction conditions, IsdG produced both SB and formyl-SB as the main product, the latter of which was isolated and characterized by MS and NMR measurements. The formyl-SB product was generated upon the reaction between hydroxyheme-IsdG and O2 without reduction, indicating the dioxygenation mechanism as found for MhuD. Under reducing conditions, hydroxyheme-IsdG was converted also to SB and HCHO by activating another O2 molecule. These results provide the first overview of the complicated IsdG reaction. The heme distortion in the IsdG-type enzymes is shown to generally promote ring cleavage by dioxygenation. The presence or absence of HCHO release can be influenced by many factors, and the direct identification of S. aureus heme catabolites is of interest.


Asunto(s)
Formaldehído , Hemo Oxigenasa (Desciclizante) , Hemo , Staphylococcus aureus , Catálisis , Formaldehído/metabolismo , Hemo/metabolismo , Hemo Oxigenasa (Desciclizante)/metabolismo , Staphylococcus aureus/enzimología , Mycobacterium tuberculosis/metabolismo
17.
J Biol Chem ; 299(9): 105121, 2023 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-37536628

RESUMEN

Single-cell transcriptomics are powerful tools to define neuronal cell types based on co-expressed gene clusters. Limited RNA input in these technologies necessarily compromises transcriptome coverage and accuracy of differential expression analysis. We propose that bulk RNA-Seq of neuronal pools defined by spatial position offers an alternative strategy to overcome these technical limitations. We report a laser-capture microdissection (LCM)-Seq method which allows deep transcriptome profiling of fluorescently tagged neuron populations isolated with LCM from histological sections of transgenic mice. Mild formaldehyde fixation of ZsGreen marker protein, LCM sampling of ∼300 pooled neurons, followed by RNA isolation, library preparation and RNA-Seq with methods optimized for nanogram amounts of moderately degraded RNA enabled us to detect ∼15,000 different transcripts in fluorescently labeled cholinergic neuron populations. The LCM-Seq approach showed excellent accuracy in quantitative studies, allowing us to detect 2891 transcripts expressed differentially between the spatially defined and clinically relevant cholinergic neuron populations of the dorsal caudate-putamen and medial septum. In summary, the LCM-Seq method we report in this study is a versatile, sensitive, and accurate bulk sequencing approach to study the transcriptome profile and differential gene expression of fluorescently tagged neuronal populations isolated from transgenic mice with high spatial precision.

18.
Small ; : e2309656, 2024 Apr 30.
Artículo en Inglés | MEDLINE | ID: mdl-38686693

RESUMEN

Bi/CeO2 (BC-x) photocatalysts are successfully prepared by solvothermal loading Bi nanoparticles and Bi-doped CeO2 derived by Ce-MOF (Ce-BTC). Formaldehyde gas (HCHO) and tetracycline hydrochloride (HTC) are used to evaluate the photocatalytic activity of the synthesized Bi/CeO2. For BC-1000 photocatalyst, the degradation of HTC by 420 nm < λ < 780 nm light reaches 91.89% for 90 min, and HCHO by 350 nm < λ < 780 nm light reaches 94.66% for 120 min. The photocatalytic cycle experiments prove that BC-1000 has good cyclic stability and repeatability. The results of photoluminescence spectra, fluorescence lifetime, photocurrent response, and electrochemical impedance spectroscopy showed that the SPR (Surface Plasmon Resonance) effect of Bi nanoparticles acted as a bridge and promoted electron transfer and enhanced the response-ability of Bi/CeO2 to visible light. Bi-doping produced more oxygen vacancies to provide adsorption sites for adsorbing oxygen and generated more ·O2 - thus promoting photocatalytic reactions. The mechanism of photocatalytic degradation is analyzed in detail utilizing active free radical capture experiments and electron paramagnetic resonance (EPR) characterization. The experimental results indicate that ·O2 - and h+ active free radicals significantly promote the degradation of pollutants.

19.
Small ; 20(29): e2310465, 2024 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-38366001

RESUMEN

The modification of metal oxides with noble metals is one of the most effective means of improving gas-sensing performance of chemiresistors, but it is often accompanied by unintended side effects such as sensor resistance increases up to unmeasurable levels. Herein, a carbonization-oxidation method is demonstrated using ultrasonic spray pyrolysis technique to realize platinum (Pt) single atom (SA) substitutional doping into SnO2 (named PtSA-SnO2). The substitutional doping strategy can obviously enhance gas-sensing properties, and meanwhile decrease sensor resistance by two orders of magnitude (decreased from ≈850 to ≈2 MΩ), which are attributed to the tuning of band gap and fermi-level position, efficient single atom catalysis, and the raising of adsorption capability of formaldehyde, as validated by the state-of-the-art characterizations, such as spherical aberration-corrected scanning transmission electron microscopy (Cs-corrected STEM), in situ diffuse reflectance infrared Fourier transformed spectra (in situ DRIFT), CO temperature-programmed reduction (CO-TPR), and theoretical calculations. As a proof of concept, the developed PtSA-SnO2 sensor shows humidity-independent (30-70% relative humidity) gas-sensing performance in the selective detection of formaldehyde with high response, distinguishable selectivity (8< Sformaldehyde/Sinterferant <14), and ultra-low detection limit (10 ppb). This work presents a generalized and facile method to design high-performance metal oxides for chemical sensing of volatile organic compounds (VOCs).

20.
Small ; : e2406107, 2024 Aug 22.
Artículo en Inglés | MEDLINE | ID: mdl-39171940

RESUMEN

Water splitting for hydrogen production is limited by high cell voltage and low energy conversion efficiencies due to the slow kinetic process of the oxygen evolution reaction (OER). Here, an electrolytic system is constructed in which the cathode and anode co-release H2 at ultra-low input voltage using formaldehyde oxidation reaction (FOR) instead of OER. The prepared RuCe co-doped Cu2O nanotubes on copper foam (RuCe-Cu2O/CF) are used as electrode materials for the HER-FOR system. A current density of 0.8 A cm-2 is achieved at 0.55 V, and a stable hydrogen production process is realized at both the cathode and anode. Density functional theory (DFT) studies show that the synergistic effect of Ru and Ce drives: i) the d-band center of RuCe-Cu2O/CF away from the Fermi energy level; ii) the energy barrier for the C─H cracking of the H2C(OH)O* intermediate in FOR is lowered, which promotes the formation of H2 from H*, and iii) ΔGH* tends to 0 (-0.1 eV), optimizing the reaction kinetics of HER. This work provides a new design for an efficient catalyst for dual hydrogen production systems from water splitting.

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