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1.
Food Microbiol ; 124: 104624, 2024 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-39244375

RESUMEN

Environmental conditions significantly impact the metabolism of Saccharomyces cerevisiae, a Crabtree-positive yeast that maintains a fermentative metabolism in high-sugar environments even in the presence of oxygen. Although the introduction of oxygen has been reported to induce alterations in yeast metabolism, knowledge of the mechanisms behind these metabolic adaptations in relation to redox cofactor metabolism and their implications in the context of wine fermentation remains limited. This study aimed to compare the intracellular redox cofactor levels, the cofactor ratios, and primary metabolite production in S. cerevisiae under aerobic and anaerobic conditions in synthetic grape juice. The molecular mechanisms underlying these metabolic differences were explored using a transcriptomic approach. Aerobic conditions resulted in an enhanced fermentation rate and biomass yield. Total NADP(H) levels were threefold higher during aerobiosis, while a decline in the total levels of NAD(H) was observed. However, there were stark differences in the ratio of NAD+/NADH between the treatments. Despite few changes in the differential expression of genes involved in redox cofactor metabolism, anaerobiosis resulted in an increased expression of genes involved in lipid biosynthesis pathways, while the presence of oxygen increased the expression of genes associated with thiamine, methionine, and sulfur metabolism. The production of fermentation by-products was linked with differences in the redox metabolism in each treatment. This study provides valuable insights that may help steer the production of metabolites of industrial interest during alcoholic fermentation (including winemaking) by using oxygen as a lever of redox metabolism.


Asunto(s)
Fermentación , Oxidación-Reducción , Oxígeno , Saccharomyces cerevisiae , Vino , Saccharomyces cerevisiae/metabolismo , Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/crecimiento & desarrollo , Oxígeno/metabolismo , Vino/microbiología , Vino/análisis , Anaerobiosis , Vitis/microbiología , Vitis/metabolismo , NAD/metabolismo , Etanol/metabolismo , NADP/metabolismo , Aerobiosis , Regulación Fúngica de la Expresión Génica , Proteínas de Saccharomyces cerevisiae/metabolismo , Proteínas de Saccharomyces cerevisiae/genética , Coenzimas/metabolismo
2.
Sci Adv ; 10(38): eadr5357, 2024 Sep 20.
Artículo en Inglés | MEDLINE | ID: mdl-39292780

RESUMEN

Experiments now support theoretical suggestions that coenzymes mediated key metabolic reactions before the emergence of enzymes. Three coenzymes believed essential to the core metabolism of the last universal common ancestor to extant life (pyridoxal phosphate, adenosine diphosphate, and nicotinamide adenine dinucleotide) were recently found to be active in their corresponding metabolic reactions in the absence of enzymes. These findings suggest an earlier contribution of coenzymes to abiogenesis, ultimately yielding insights into the prebiotic origins of metabolism.


Asunto(s)
Coenzimas , Coenzimas/metabolismo , Enzimas/metabolismo , NAD/metabolismo , Origen de la Vida , Adenosina Difosfato/metabolismo , Fosfato de Piridoxal/metabolismo
3.
Life Sci Alliance ; 7(11)2024 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-39159974

RESUMEN

Regeneration of insulin-producing ß-cells is an alternative avenue to manage diabetes, and it is crucial to unravel this process in vivo during physiological responses to the lack of ß-cells. Here, we aimed to characterize how hepatocytes can contribute to ß-cell regeneration, either directly or indirectly via secreted proteins or metabolites, in a zebrafish model of ß-cell loss. Using lineage tracing, we show that hepatocytes do not directly convert into ß-cells even under extreme ß-cell ablation conditions. A transcriptomic analysis of isolated hepatocytes after ß-cell ablation displayed altered lipid- and glucose-related processes. Based on the transcriptomics, we performed a genetic screen that uncovers a potential role of the molybdenum cofactor (Moco) biosynthetic pathway in ß-cell regeneration and glucose metabolism in zebrafish. Consistently, molybdenum cofactor synthesis 2 (Mocs2) haploinsufficiency in mice indicated dysregulated glucose metabolism and liver function. Together, our study sheds light on the liver-pancreas crosstalk and suggests that the molybdenum cofactor biosynthesis pathway should be further studied in relation to glucose metabolism and diabetes.


Asunto(s)
Coenzimas , Glucosa , Hepatocitos , Células Secretoras de Insulina , Hígado , Metaloproteínas , Cofactores de Molibdeno , Pteridinas , Pez Cebra , Animales , Células Secretoras de Insulina/metabolismo , Pteridinas/metabolismo , Coenzimas/metabolismo , Ratones , Hígado/metabolismo , Hígado/citología , Metaloproteínas/metabolismo , Metaloproteínas/genética , Hepatocitos/metabolismo , Glucosa/metabolismo , Regeneración/genética , Páncreas/metabolismo , Páncreas/citología , Proteínas de Pez Cebra/genética , Proteínas de Pez Cebra/metabolismo
4.
Appl Microbiol Biotechnol ; 108(1): 446, 2024 Aug 21.
Artículo en Inglés | MEDLINE | ID: mdl-39167161

RESUMEN

Neuraminic acid synthases are an important yet underexplored group of enzymes. Thus, in this research, we performed a detailed kinetic and stability analysis and a comparison of previously known neuraminic acid synthase from Neisseria meningitidis, and a novel enzyme, PNH5, obtained from a metagenomic library. A systematic analysis revealed a high level of similarity of PNH5 to other known neuraminic acid synthases, except for its pH optimum, which was found to be at 5.5 for the novel enzyme. This is the first reported enzyme from this family that prefers an acidic pH value. The effect of different metal cofactors on enzyme activity, i.e. Co2+, Mn2+ and Mg2+, was studied systematically. The kinetics of neuraminic acid synthesis was completely elucidated, and an appropriate kinetic model was proposed. Enzyme stability study revealed that the purified enzyme exhibits changes in its structure during time as observed by differential light scattering, which cause a drop in its activity and protein concentration. The operational enzyme stability for the neuraminic acid synthase from N. meningitidis is excellent, where no activity drop was observed during the batch reactor experiments. In the case of PNH5, some activity drop was observed at higher concentration of substrates. The obtained results present a solid platform for the future application of these enzymes in the synthesis of sialic acids. KEY POINTS: • A novel neuraminic acid synthase was characterized. • The effect of cofactors on NeuS activity was elucidated. • Kinetic and stability characterization of two neuraminic acid synthases was performed.


Asunto(s)
Estabilidad de Enzimas , Neisseria meningitidis , Cinética , Concentración de Iones de Hidrógeno , Neisseria meningitidis/enzimología , Neisseria meningitidis/genética , Oxo-Ácido-Liasas/metabolismo , Oxo-Ácido-Liasas/genética , Oxo-Ácido-Liasas/química , Coenzimas/metabolismo
5.
Int J Biol Macromol ; 278(Pt 4): 135064, 2024 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-39182884

RESUMEN

Enzyme specificity towards cofactors like NAD(P)H is crucial for applications in bioremediation and eco-friendly chemical synthesis. Despite their role in converting pollutants and creating sustainable products, predicting enzyme specificity faces challenges due to sparse data and inadequate models. To bridge this gap, we developed the cutting-edge INSIGHT platform to enhance the prediction of coenzyme specificity in NAD(P)-dependent enzymes. INSIGHT integrates extensive data from principal bioinformatics resources, concentrating on both NADH and NADPH specificities, and utilizes advanced protein language models to refine the predictions. This integration not only strengthens computational predictions but also meets the practical demands of high-throughput screening and optimization. Experimental validation confirms INSIGHT's effectiveness, boosting our ability to engineer enzymes for efficient, sustainable industrial and environmental processes. This work advances the practical use of computational tools in enzyme research, addressing industrial needs and offering scalable solutions for environmental challenges.


Asunto(s)
NADP , NAD , Ingeniería de Proteínas , NADP/metabolismo , NADP/química , Especificidad por Sustrato , NAD/metabolismo , NAD/química , Ingeniería de Proteínas/métodos , Biología Computacional/métodos , Modelos Moleculares , Coenzimas/metabolismo , Coenzimas/química
6.
Int J Biol Macromol ; 276(Pt 1): 133873, 2024 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-39013505

RESUMEN

In this study, based on the self-assembly strategy, we fused CipA with carbonyl reductase LXCARS154Y derived from Leifsonia xyli by gene coding, and successfully performed the carrier-free immobilization of LXCARS154Y. The immobilized enzyme was then characterized using scanning electron microscope (SEM), dynamic light scattering (DLS) and fourier transform infrared spectroscopy (FTIR). Compared with the free enzyme, the immobilized LXCARS154Y exhibited a 2.3-fold improvement in the catalytic efficiency kcat/km for the synthesis of a chiral pharmaceutical intermediate (R)-3,5-bis(trifluoromethyl)phenyl ethanol ((R)-BTPE) by reducing 3,5-bis(trifluoromethyl)acetophenone (BTAP). Moreover, the immobilized enzyme showed the enhanced stability while maintaining over 61 % relative activity after 18 cycles of batch reaction. Further, when CipA-fused carbonyl reductase was employed for (R)-BTPE production in a continuous flow reaction, almost complete yield (97.0 %) was achieved within 7 h at 2 M (512.3 g/L) of BTAP concentration, with a space-time yield of 1717.1 g·L-1·d-1. Notably, we observed the retention of cofactor NADH by CipA-based enzyme aggregates, resulting in a higher total turnover number (TTN) of 4815 to facilitate this bioreductive process. This research developed a concise strategy for efficient preparation of chiral intermediate with cofactor self-sufficiency via continuous flow biocatalysis, and the relevant mechanism was also explored.


Asunto(s)
Oxidorreductasas de Alcohol , Enzimas Inmovilizadas , Enzimas Inmovilizadas/química , Enzimas Inmovilizadas/metabolismo , Oxidorreductasas de Alcohol/química , Oxidorreductasas de Alcohol/metabolismo , Oxidorreductasas de Alcohol/genética , Reactores Biológicos , Cinética , Alcoholes/química , Biocatálisis , Coenzimas/química , Coenzimas/metabolismo , Estereoisomerismo
7.
Appl Microbiol Biotechnol ; 108(1): 410, 2024 Jul 08.
Artículo en Inglés | MEDLINE | ID: mdl-38976076

RESUMEN

We characterise a reversible bacterial zinc-containing benzyl alcohol dehydrogenase (BaDH) accepting either NAD+ or NADP+ as a redox cofactor. Remarkably, its redox cofactor specificity is pH-dependent with the phosphorylated cofactors favored at lower and the dephospho-forms at higher pH. BaDH also shows different steady-state kinetic behavior with the two cofactor forms. From a structural model, the pH-dependent shift may affect the charge of a histidine in the 2'-phosphate-binding pocket of the redox cofactor binding site. The enzyme is phylogenetically affiliated to a new subbranch of the Zn-containing alcohol dehydrogenases, which share this conserved residue. BaDH appears to have some specificity for its substrate, but also turns over many substituted benzyl alcohol and benzaldehyde variants, as well as compounds containing a conjugated C=C double bond with the aldehyde carbonyl group. However, compounds with an sp3-hybridised C next to the alcohol/aldehyde group are not or only weakly turned over. The enzyme appears to contain a Zn in its catalytic site and a mixture of Zn and Fe in its structural metal-binding site. Moreover, we demonstrate the use of BaDH in an enzyme cascade reaction with an acid-reducing tungsten enzyme to reduce benzoate to benzyl alcohol. KEY POINTS: •Zn-containing BaDH has activity with either NAD + or NADP+ at different pH optima. •BaDH converts a broad range of substrates. •BaDH is used in a cascade reaction for the reduction of benzoate to benzyl alcohol.


Asunto(s)
Oxidorreductasas de Alcohol , Alcohol Bencilo , Coenzimas , NADP , Oxidación-Reducción , Zinc , Concentración de Iones de Hidrógeno , NADP/metabolismo , Especificidad por Sustrato , Alcohol Bencilo/metabolismo , Alcohol Bencilo/química , Cinética , Zinc/metabolismo , Coenzimas/metabolismo , Oxidorreductasas de Alcohol/metabolismo , Oxidorreductasas de Alcohol/química , Oxidorreductasas de Alcohol/genética , NAD/metabolismo , Benzaldehídos/metabolismo , Benzaldehídos/química , Dominio Catalítico , Sitios de Unión , Filogenia , Modelos Moleculares
8.
J Am Chem Soc ; 146(30): 21025-21033, 2024 Jul 31.
Artículo en Inglés | MEDLINE | ID: mdl-39025790

RESUMEN

Artificial photosynthesis represents a sustainable strategy for accessing high-value chemicals; however, the conversion efficiency is significantly limited by its difficulty in the cycle of coenzymes such as NADH. In this study, we report a series of isostructural triazine covalent organic frameworks (COFs) and explore their N-substituted microenvironment-dependent photocatalytic activity for NADH regeneration. We discovered that the rational alteration of N-heterocyclic species, which are linked to the triazine center through an imine linkage, can significantly regulate both the electron band structure and planarity of a COF layer. This results in different separation efficiencies of the photoinduced electron-hole pairs and electron transfer behavior within and between individual layers. The optimal COF catalyst herein achieves an NADH regeneration capacity of 89% within 20 min, outperforming most of the reported nanomaterial photocatalysts. Based on this, an artificial photosynthesis system is constructed for the green synthesis of a high-value compound, L-glutamate, and its conversion efficiency significantly surpasses the enzymatic approach without the NADH photocatalytic cycle. This work offers new insights into the coenzyme regeneration by means of regulating the distal heterocyclic microenvironment of a COF skeleton, holding great potential for the green photosynthesis of important chemicals.


Asunto(s)
Estructuras Metalorgánicas , Triazinas , Triazinas/química , Catálisis , Estructuras Metalorgánicas/química , NAD/química , NAD/metabolismo , Procesos Fotoquímicos , Estructura Molecular , Coenzimas/química , Coenzimas/metabolismo , Fotosíntesis
9.
Appl Microbiol Biotechnol ; 108(1): 391, 2024 Jun 24.
Artículo en Inglés | MEDLINE | ID: mdl-38910188

RESUMEN

Metal cofactors are essential for catalysis and enable countless conversions in nature. Interestingly, the metal cofactor is not always static but mobile with movements of more than 4 Å. These movements of the metal can have different functions. In the case of the xylose isomerase and medium-chain dehydrogenases, it clearly serves a catalytic purpose. The metal cofactor moves during substrate activation and even during the catalytic turnover. On the other hand, in class II aldolases, the enzymes display resting states and active states depending on the movement of the catalytic metal cofactor. This movement is caused by substrate docking, causing the metal cofactor to take the position essential for catalysis. As these metal movements are found in structurally and mechanistically unrelated enzymes, it has to be expected that this metal movement is more common than currently perceived. KEY POINTS: • Metal ions are essential cofactors that can move during catalysis. • In class II aldolases, the metal cofactors can reside in a resting state and an active state. • In MDR, the movement of the metal cofactor is essential for substrate docking.


Asunto(s)
Coenzimas , Metales , Metales/metabolismo , Coenzimas/metabolismo , Isomerasas Aldosa-Cetosa/metabolismo , Isomerasas Aldosa-Cetosa/química , Isomerasas Aldosa-Cetosa/genética , Catálisis , Oxidorreductasas/metabolismo , Oxidorreductasas/química
10.
Enzyme Microb Technol ; 179: 110469, 2024 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-38878426

RESUMEN

Esomeprazole is the most popular proton pump inhibitor for treating gastroesophageal reflux disease. Previously, a phenylacetone monooxygenase mutant LnPAMOmu15 (LM15) was obtained by protein engineering for asymmetric synthesis of esomeprazole using pyrmetazole as substrate. To scale up the whole cell asymmetric synthesis of esomeprazole and reduce the cost, in this work, an Escherichia coli whole-cell catalyst harboring LM15 and formate dehydrogenase from Burkholderia stabilis 15516 (BstFDH) were constructed through optimized gene assembly patterns. CRISPR/Cas9 mediated insertion of Ptrc promoter in genome was done to enhance the expression of key genes to increase the cellular NADP supply in the whole cell catalyst, by which the amount of externally added NADP+ for the asymmetric synthesis of esomeprazole decreased to 0.05 mM from 0.3 mM for reducing the cost. After the optimization of reaction conditions in the reactor, the scalable synthesis of esomeprazole was performed using the efficient LM15-BstFDH whole-cell as catalyst, which showed the highest reported space-time yield of 3.28 g/L/h with 50 mM of pyrmetazole loading. Isolation procedure was conducted to obtain esomeprazole sodium of 99.55 % purity and > 99.9 % ee with 90.1 % isolation yield. This work provides the basis for production of enantio-pure esomeprazole via cost-effective whole cell biocatalysis.


Asunto(s)
Biocatálisis , Burkholderia , Escherichia coli , Esomeprazol , Esomeprazol/metabolismo , Escherichia coli/genética , Escherichia coli/metabolismo , Burkholderia/genética , Burkholderia/enzimología , Burkholderia/metabolismo , Coenzimas/metabolismo , Vías Biosintéticas , Ingeniería Metabólica , Formiato Deshidrogenasas/metabolismo , Formiato Deshidrogenasas/genética , Sistemas CRISPR-Cas , Oxigenasas de Función Mixta/metabolismo , Oxigenasas de Función Mixta/genética
11.
Faraday Discuss ; 252(0): 157-173, 2024 Sep 11.
Artículo en Inglés | MEDLINE | ID: mdl-38836629

RESUMEN

A scarcity of cofactors, necessary metabolites or substrates for in vivo enzymatic reactions, is among the major barriers for product synthesis in metabolically engineered cells. This work compares our recently developed cofactor-boosting strategy, which uses xylose reductase (XR) and lactose to increase the intracellular levels of reduced or oxidized nicotinamide adenine dinucleotide (phosphate) (NAD(P)H), adenosine triphosphate (ATP) and acetyl coenzymeA (acetyl-CoA), with other previously reported methods. We demonstrated that the XR/lactose approach enhances levels of sugar alcohols and sugar phosphates, which leads to elevated levels of crucial cofactors required by specific metabolic pathways. The patterns of cofactor enhancement are not uniform and depend upon the specific pathway components that are overexpressed. We term this model the "user-pool" model. Here, we investigated metabolite alteration in the fatty-alcohol-producing system in the presence of XR/lactose within an early time frame (5 min after the bioconversion started). All metabolite data were analyzed using untargeted metabolomics. We found that the XR/lactose system could improve fatty-alcohol production as early as 5 min after the bioconversion started. The enhancement of key cofactors and intermediates, such as hexitol, NAD(P)H, ATP, 3-phosphoglycerate, acetyl-CoA, 6-phosphogluconate (6-PG) and glutathione, was consistent with those previously reported on a longer time scale (after 1 h). However, measurements performed at the early time reported here showed detectable differences in metabolite enhancement patterns, such as those of ATP, NADPH, acetyl-CoA and glutathione. These data could serve as a basis for future analysis of metabolic flux alteration by the XR/lactose system. Comparative analysis of the cofactor enhancement by XR and other methods suggests that XR/lactose can serve as a simple tool to increase levels of various cofactors for microbial cell factories.


Asunto(s)
Biocatálisis , Aldehído Reductasa/metabolismo , NADP/metabolismo , NADP/química , Lactosa/metabolismo , Lactosa/química , Coenzimas/metabolismo , Coenzimas/química , Acetilcoenzima A/metabolismo , Acetilcoenzima A/química , Adenosina Trifosfato/metabolismo , Adenosina Trifosfato/química , Ingeniería Metabólica
12.
Neurochem Int ; 178: 105791, 2024 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-38880231

RESUMEN

Long-term studies have confirmed a causal relationship between the development of neurodegenerative processes and vitamin B1 (thiamine) deficiency. However, the biochemical mechanisms underlying the high neurotropic activity of thiamine are not fully understood. At the same time, there is increasing evidence that vitamin B1, in addition to its coenzyme functions, may have non-coenzyme activities that are particularly important for neurons. To elucidate which effects of vitamin B1 in neurons are due to its coenzyme function and which are due to its non-coenzyme activity, we conducted a comparative study of the effects of thiamine and its derivative, 3-decyloxycarbonylmethyl-5-(2-hydroxyethyl)-4-methyl-1,3-thiazolium chloride (DMHT), on selected processes in synaptosomes. The ability of DMHT to effectively compete with thiamine for binding to thiamine-binding sites on the plasma membrane of synaptosomes and to participate as a substrate in the thiamine pyrophosphokinase reaction was demonstrated. In experiments with rat brain synaptosomes, unidirectional effects of DMHT and thiamine on the activity of the pyruvate dehydrogenase complex (PDC) and on the incorporation of radiolabeled [2-14C]pyruvate into acetylcholine were demonstrated. The observed effects of thiamine and DMHT on the modulation of acetylcholine synthesis can be explained by suggesting that both compounds, which interact in cells with enzymes of thiamine metabolism, are phosphorylated and exert an inhibitory/activating effect (concentration-dependent) on PDC activity by affecting the regulatory enzymes of the complex. Such effects were not observed in the presence of structural analogues of thiamine and DMHT without a 2-hydroxyethyl substituent at position 5 of the thiazolium cycle. The effect of DMHT on the plasma membrane Ca-ATPase was similar to that of thiamine. At the same time, DMHT showed high cytostatic activity against neuroblastoma cells.


Asunto(s)
Ratas Wistar , Sinaptosomas , Tiamina , Animales , Sinaptosomas/metabolismo , Sinaptosomas/efectos de los fármacos , Ratas , Tiamina/farmacología , Tiamina/metabolismo , Masculino , Acetilcolina/metabolismo , Complejo Piruvato Deshidrogenasa/metabolismo , Tiazoles/farmacología , Coenzimas/metabolismo , Encéfalo/metabolismo , Encéfalo/efectos de los fármacos , Ácido Pirúvico/metabolismo , Ácido Pirúvico/farmacología
13.
Int J Biol Macromol ; 274(Pt 2): 133268, 2024 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-38944083

RESUMEN

p-Hydroxybenzoate hydroxylase (PHBH) catalyzes the ortho-hydroxylation of 4-hydroxybenzoate (4-HB) to protocatechuate (PCA). PHBHs are commonly known as homodimers, and the prediction of pyridine nucleotide binding and specificity remains an ongoing focus in this field. Therefore, our study aimed to determine the dimerization interface in AspPHBH from Arthrobacter sp. PAMC25564 and identify the canonical pyridine nucleotide-binding residues, along with coenzyme specificity, through site-directed mutagenesis. The results confirm a functional dimeric assembly from a tetramer that appeared in the crystallographic asymmetric unit identical to that established in previous studies. Furthermore, AspPHBH exhibits coenzyme versatility, utilizing both NADH and NADPH, with a preference for NADH. Rational engineering experiments demonstrated that targeted mutations in coenzyme surrounding residues profoundly impact NADPH binding, leading to nearly abrogated enzymatic activity compared to that of NADH. R50, R273, and S166 emerged as significant residues for NAD(P)H binding, having a near-fatal impact on NADPH binding compared to NADH. Likewise, the E44 residue plays a critical role in determining coenzyme specificity. Overall, our findings contribute to the fundamental understanding of the determinants of PHBH's active dimeric conformation, coenzyme binding and specificity holding promise for biotechnological advancements.


Asunto(s)
4-Hidroxibenzoato-3-Monooxigenasa , Arthrobacter , Multimerización de Proteína , Arthrobacter/enzimología , 4-Hidroxibenzoato-3-Monooxigenasa/metabolismo , 4-Hidroxibenzoato-3-Monooxigenasa/química , NADP/metabolismo , Modelos Moleculares , Coenzimas/metabolismo , Especificidad por Sustrato , NAD/metabolismo , Conformación Proteica , Mutagénesis Sitio-Dirigida , Unión Proteica , Sitios de Unión , Proteínas Bacterianas/química , Proteínas Bacterianas/metabolismo , Proteínas Bacterianas/genética , Parabenos
14.
Sci Rep ; 14(1): 11165, 2024 05 15.
Artículo en Inglés | MEDLINE | ID: mdl-38750092

RESUMEN

Kinetic aspects of enzymatic reactions are described by equations based on the Michaelis-Menten theory for the initial stage. However, the kinetic parameters provide little information on the atomic mechanism of the reaction. In this study, we analyzed structures of glutamate dehydrogenase in the initial and steady stages of the reaction using cryoEM at near-atomic resolution. In the initial stage, four metastable conformations displayed different domain motions and cofactor/ligand association modes. The most striking finding was that the enzyme-cofactor-substrate complex, treated as a single state in the enzyme kinetic theory, comprised at least three different metastable conformations. In the steady stage, seven conformations, including derivatives from the four conformations in the initial stage, made the reaction pathway complicated. Based on the visualized conformations, we discussed stage-dependent pathways to illustrate the dynamics of the enzyme in action.


Asunto(s)
Microscopía por Crioelectrón , Glutamato Deshidrogenasa , Conformación Proteica , Glutamato Deshidrogenasa/química , Glutamato Deshidrogenasa/metabolismo , Microscopía por Crioelectrón/métodos , Ligandos , Cinética , Modelos Moleculares , Coenzimas/metabolismo , Coenzimas/química , Catálisis , Unión Proteica
15.
Appl Environ Microbiol ; 90(6): e0023324, 2024 Jun 18.
Artículo en Inglés | MEDLINE | ID: mdl-38727223

RESUMEN

Vanillin is one of the world's most important flavor and fragrance compounds used in foods and cosmetics. In plants, vanillin is reportedly biosynthesized from ferulic acid via the hydratase/lyase-type enzyme VpVAN. However, in biotechnological and biocatalytic applications, the use of VpVAN limits the production of vanillin. Although microbial enzymes are helpful as substitutes for plant enzymes, synthesizing vanillin from ferulic acid in one step using microbial enzymes remains a challenge. Here, we developed a single enzyme that catalyzes vanillin production from ferulic acid in a coenzyme-independent manner via the rational design of a microbial dioxygenase in the carotenoid cleavage oxygenase family using computational simulations. This enzyme acquired catalytic activity toward ferulic acid by introducing mutations into the active center to increase its affinity for ferulic acid. We found that the single enzyme can catalyze not only the production of vanillin from ferulic acid but also the synthesis of other aldehydes from p-coumaric acid, sinapinic acid, and coniferyl alcohol. These results indicate that the approach used in this study can greatly expand the range of substrates available for the dioxygenase family of enzymes. The engineered enzyme enables efficient production of vanillin and other value-added aldehydes from renewable lignin-derived compounds. IMPORTANCE: The final step of vanillin biosynthesis in plants is reportedly catalyzed by the enzyme VpVAN. Prior to our study, VpVAN was the only reported enzyme that directly converts ferulic acid to vanillin. However, as many characteristics of VpVAN remain unknown, this enzyme is not yet suitable for biocatalytic applications. We show that an enzyme that converts ferulic acid to vanillin in one step could be constructed by modifying a microbial dioxygenase-type enzyme. The engineered enzyme is of biotechnological importance as a tool for the production of vanillin and related compounds via biocatalytic processes and metabolic engineering. The results of this study may also provide useful insights for understanding vanillin biosynthesis in plants.


Asunto(s)
Benzaldehídos , Ácidos Cumáricos , Dioxigenasas , Benzaldehídos/metabolismo , Ácidos Cumáricos/metabolismo , Dioxigenasas/metabolismo , Dioxigenasas/genética , Ingeniería Metabólica , Coenzimas/metabolismo , Ingeniería de Proteínas , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo
16.
Biotechnol J ; 19(4): e2300557, 2024 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-38581092

RESUMEN

The halogenase-based catalysis is one of the most environmentally friendly methods for the synthesis of halogenated products, among which flavin-dependent halogenases (FDHs) have attracted great interest as one of the most promising biocatalysts due to the remarkable site-selectivity and wide substrate range. However, the complexity of constructing the NAD+-NADH-FAD-FADH2 bicoenzyme cycle system has affected the engineering applications of FDHs. In this work, a coenzyme self-sufficient tri-enzyme fusion was constructed and successfully applied to the continuous halogenation of L-tryptophan. SpFDH was firstly identified derived from Streptomyces pratensis, a highly selective halogenase capable of generating 6-chloro-tryptophan from tryptophan. Then, using gene fusion technology, SpFDH was fused with glucose dehydrogenase (GDH) and flavin reductase (FR) to form a tri-enzyme fusion, which increased the yield by 1.46-fold and making the coenzymes self-sufficient. For more efficient halogenation of L-tryptophan, a continuous halogenation bioprocess of L-tryptophan was developed by immobilizing the tri-enzyme fusion and attaching it to a continuous catalytic device, which resulted in a reaction yield of 97.6% after 12 h reaction. An FDH from S. pratensis was successfully applied in the halogenation and our study provides a concise strategy for the preparation of halogenated tryptophan mediated by multienzyme cascade catalysis.


Asunto(s)
Halogenación , Triptófano , Coenzimas , Oxidorreductasas/genética , Oxidorreductasas/metabolismo , Flavinas/metabolismo
17.
Biochim Biophys Acta Mol Cell Res ; 1871(5): 119731, 2024 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-38631442

RESUMEN

Molybdenum cofactor (Moco) biosynthesis is a complex process that involves the coordinated function of several proteins. In the recent years it has become evident that the availability of Fe-S clusters play an important role for the biosynthesis of Moco. First, the MoaA protein binds two [4Fe-4S] clusters per monomer. Second, the expression of the moaABCDE and moeAB operons is regulated by FNR, which senses the availability of oxygen via a functional [4Fe-4S] cluster. Finally, the conversion of cyclic pyranopterin monophosphate to molybdopterin requires the availability of the L-cysteine desulfurase IscS, which is an enzyme involved in the transfer of sulfur to various acceptor proteins with a main role in the assembly of Fe-S clusters. In this review, we dissect the dependence of the production of active molybdoenzymes in detail, starting from the regulation of gene expression and further explaining sulfur delivery and Fe-S cluster insertion into target enzymes. Further, Fe-S cluster assembly is also linked to iron availability. While the abundance of selected molybdoenzymes is largely decreased under iron-limiting conditions, we explain that the expression of the genes is dependent on an active FNR protein. FNR is a very important transcription factor that represents the master-switch for the expression of target genes in response to anaerobiosis. Moco biosynthesis is further directly dependent on the presence of ArcA and also on an active Fur protein.


Asunto(s)
Coenzimas , Proteínas Hierro-Azufre , Metaloproteínas , Cofactores de Molibdeno , Pteridinas , Metaloproteínas/metabolismo , Metaloproteínas/genética , Metaloproteínas/biosíntesis , Proteínas Hierro-Azufre/metabolismo , Proteínas Hierro-Azufre/genética , Coenzimas/metabolismo , Coenzimas/biosíntesis , Coenzimas/genética , Pteridinas/metabolismo , Proteínas de Escherichia coli/metabolismo , Proteínas de Escherichia coli/genética , Hierro/metabolismo , Azufre/metabolismo , Escherichia coli/genética , Escherichia coli/metabolismo , Liasas de Carbono-Azufre/metabolismo , Liasas de Carbono-Azufre/genética , Regulación Bacteriana de la Expresión Génica , Operón , Isomerasas
18.
J Inherit Metab Dis ; 47(4): 598-623, 2024 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-38627985

RESUMEN

Sulfite intoxication is the hallmark of four ultrarare disorders that are caused by impaired sulfite oxidase activity due to genetic defects in the synthesis of the molybdenum cofactor or of the apoenzyme sulfite oxidase. Delays on the diagnosis of these disorders are common and have been caused by their unspecific presentation of acute neonatal encephalopathy with high early mortality, followed by the evolution of dystonic cerebral palsy and also by the lack of easily available and reliable diagnostic tests. There is significant variation in survival and in the quality of symptomatic management of affected children. One of the four disorders, molybdenum cofactor deficiency type A (MoCD-A) has recently become amenable to causal treatment with synthetic cPMP (fosdenopterin). The evidence base for the rational use of cPMP is very limited. This prompted the formulation of these clinical guidelines to facilitate diagnosis and support the management of patients. The guidelines were developed by experts in diagnosis and treatment of sulfite intoxication disorders. It reflects expert consensus opinion and evidence from a systematic literature search.


Asunto(s)
Errores Innatos del Metabolismo de los Metales , Sulfito-Oxidasa , Humanos , Recién Nacido , Errores Innatos del Metabolismo de los Aminoácidos/diagnóstico , Errores Innatos del Metabolismo de los Aminoácidos/terapia , Errores Innatos del Metabolismo de los Aminoácidos/genética , Coenzimas/deficiencia , Consenso , Errores Innatos del Metabolismo de los Metales/diagnóstico , Errores Innatos del Metabolismo de los Metales/terapia , Metaloproteínas/deficiencia , Cofactores de Molibdeno , Pteridinas , Sulfito-Oxidasa/deficiencia , Sulfito-Oxidasa/genética
19.
Chemphyschem ; 25(14): e202400327, 2024 Jul 15.
Artículo en Inglés | MEDLINE | ID: mdl-38602444

RESUMEN

The present work is another part of our investigation on the pathway of dissimilatory sulfate reduction and covers a theoretical study on the reaction catalyzed by dissimilatory sulfite reductase (dSIR). dSIR is the terminal enzyme involved in this metabolic pathway, which uses the siroheme-[4Fe4S] cofactor for six-electron reduction of sulfite to sulfide. In this study we use a large cluster model containing siroheme-[4Fe4S] cofactor and protein residues involved in the direct interactions with the substrate, to get insight into the most feasible reaction mechanism and to understand the role of each considered active site component. In combination with earlier studies reported in the literature, our results lead to several interesting insights. One of the most important conclusions is that the reaction mechanism consists of three steps of two-electron reduction of sulfur and the probable role of the siroheme-[4Fe4S] cofactor is to ensure the delivery of packages of two electrons to the reactant.


Asunto(s)
Hemo , Proteínas Hierro-Azufre , Proteínas Hierro-Azufre/química , Proteínas Hierro-Azufre/metabolismo , Hemo/química , Hemo/metabolismo , Hemo/análogos & derivados , Biocatálisis , Hidrogenosulfito Reductasa/metabolismo , Hidrogenosulfito Reductasa/química , Dominio Catalítico , Oxidación-Reducción , Sulfitos/química , Sulfitos/metabolismo , Coenzimas/metabolismo , Coenzimas/química , Modelos Moleculares
20.
FEMS Yeast Res ; 242024 Jan 09.
Artículo en Inglés | MEDLINE | ID: mdl-38637306

RESUMEN

Anaerobic alcoholic fermentation, particularly in high-sugar environments, presents metabolic challenges for yeasts. Crabtree-positive yeasts, including Saccharomyces cerevisiae, prefer fermentation even in the presence of oxygen. These yeasts rely on internal NAD+ recycling and extracellular assimilation of its precursor, nicotinic acid (vitamin B3), rather than de novo NAD+ production. Surprisingly, nicotinic acid assimilation is poorly characterized, even in S. cerevisiae. This study elucidated the timing of nicotinic acid uptake during grape juice-like fermentation and its impact on NAD(H) levels, the NAD+/NADH ratio, and metabolites produced. Complete uptake of extracellular nicotinic acid occurred premid-exponential phase, thereafter small amounts of vitamin B3 were exported back into the medium. Suboptimal levels of nicotinic acid were correlated with slower fermentation and reduced biomass, disrupting redox balance and impeding NAD+ regeneration, thereby affecting metabolite production. Metabolic outcomes varied with nicotinic acid concentrations, linking NAD+ availability to fermentation efficiency. A model was proposed encompassing rapid nicotinic acid uptake, accumulation during cell proliferation, and recycling with limited vitamin B3 export. This research enhances the understanding of nicotinic acid uptake dynamics during grape juice-like fermentation. These insights contribute to advancing yeast metabolism research and have profound implications for the enhancement of biotechnological practices and the wine-making industry.


Asunto(s)
Fermentación , NAD , Niacina , Oxidación-Reducción , Saccharomyces cerevisiae , Saccharomyces cerevisiae/metabolismo , Niacina/metabolismo , NAD/metabolismo , Etanol/metabolismo , Coenzimas/metabolismo
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