Academic literature on the topic 'Ubiquinone biosynthesis'

ABSTRACT Enzymatic steps from two different biosynthetic pathways were combined in Escherichia coli, directing the synthesis of a new class of biomolecules—ubiquinones with prenyl side chains containing conjugated double bonds. This was achieved by the activity of a C30 carotenoid desaturase, CrtN, from Staphylococcus aureus, which exhibited an inherent flexibility in substrate recognition compared to other carotenoid desaturases. By utilizing the known plasticity of E. coli's native ubiquinone biosynthesis pathway and the unusual activity of CrtN, modified ubiquinone structures with prenyl side chains containing conjugated double bonds were generated. The side chains of the new structures were confirmed to have different degrees of desaturation by mass spectrometry and nuclear magnetic resonance analysis. In vivo 14C labeling and in vitro activity studies showed that CrtN desaturates octaprenyl diphosphates but not the ubiquinone compounds directly. Antioxidant properties of conjugated side chain ubiquinones were analyzed in an in vitro β-carotene-linoleate model system and were found to be higher than the corresponding unmodified ubiquinones. These results demonstrate that by combining pathway steps from different branches of biosynthetic networks, classes of compounds not observed in nature can be synthesized and structural motifs that are functionally important can be combined or enhanced.

When T. pyriformis is grown in the presence of 10(-2)M-mevalonic acid, the uptake exceeds the cell's requirement for this biosynthetic intermediate. The majority of the excess mevalonic acid is diverted into ubiquinone-8 biosynthesis whereas the biosynthesis of tetrahymanol, the major product of the mevalonic acid pathway, is unchanged. In the presence of excess external mevalonic acid, the biosynthesis of mevalonic acid by the cell is inhibited. It is proposed that ubiquinone biosynthesis is normally regulated by mevalonic acid availability, whereas tetrahymanol biosynthesis is regulated primarily at a later point in the pathway.

Ubiquinone, known as coenzyme Q, was shown to be the part of the metabolic pathways by Crane et al. in 1957. Its function as a component of the mitochondrial respiratory chain is well established. However, ubiquinone has recently attracted increasing attention with regard to its function, in the reduced form, as an antioxidant. In ubiquinone synthesis the para-hydroxybenzoate ring (which is the derivative of tyrosine or phenylalanine) is condensed with a hydrophobic polyisoprenoid side chain, whose length varies from 6 to 10 isoprene units depending on the organism. para-Hydroxybenzoate (PHB) polyprenyltransferase that catalyzes the condensation of PHB with polyprenyl diphosphate has a broad substrate specificity. Most of the genes encoding (all-E)-prenyltransferases which synthesize polyisoprenoid chains, have been cloned. Their structure is either homo- or heterodimeric. Genes that encode prenyltransferases catalysing the transfer of the isoprenoid chain to para-hydroxybenzoate were also cloned in bacteria and yeast. To form ubiquinone, prenylated PHB undergoes several modifications such as hydroxylations, O-methylations, methylations and decarboxylation. In eukaryotes ubiquinones were found in the inner mitochondrial membrane and in other membranes such as the endoplasmic reticulum, Golgi vesicles, lysosomes and peroxisomes. Still, the subcellular site of their biosynthesis remains unclear. Considering the diversity of functions of ubiquinones, and their multistep biosynthesis, identification of factors regulating their cellular level remains an elusive task.

ABSTRACT The naphthoquinone atovaquone is effective againstPlasmodium and Pneumocystis carinii carinii. InPlasmodium, the primary mechanism of drug action is an irreversible binding to the mitochondrial cytochromebc 1 complex as an analog of ubiquinone. Blockage of the electron transport chain ultimately inhibits de novo pyrimidine biosynthesis since dihydroorotate dehydrogenase, a key enzyme in pyrimidine biosynthesis, is unable to transfer electrons to ubiquinone. In the present study, the effect of atovaquone was examined on Pneumocystis carinii carinii coenzyme Q biosynthesis (rather than electron transport and respiration) by measuring its effect on the incorporation of radiolabeledp-hydroxybenzoate into ubiquinone in vitro. A triphasic dose-response was observed, with inhibition at 10 nM and then stimulation up to 0.2 μM, followed by inhibition at 1 μM. Since other naphthoquinone drugs may also act as analogs of ubiquinone, diospyrin and two of its derivatives were also tested for their effects on ubiquinone biosynthesis in P. carinii carinii. In contrast to atovaquone, these drugs did not inhibit the incorporation of p-hydroxybenzoate intoP. carinii carinii ubiquinone.

ABSTRACT ArcBA is a two-component regulatory system of Escherichia coli involved in sensing oxygen availability and the concomitant transcriptional regulation of oxidative and fermentative catabolism. Based on in vitro data, it has been postulated that the redox state of the ubiquinone pool is the determinant for ArcB kinase activity. Here we report on the in vivo regulation of ArcB activation, as determined using a lacZ reporter specifically responsive to phosphorylated ArcA. Our results indicate that upon deletion of a ubiquinone biosynthetic enzyme, regulation of ArcB in the anaerobic-aerobic transition is not affected. In contrast, interference with menaquinone biosynthesis leads to inactivation of ArcB during anaerobic growth; this phenotype is fully rescued by addition of a menaquinone precursor. This clearly demonstrates that the menaquinones play a major role in ArcB activation. ArcB shows a complex pattern of regulation when E. coli is titrated through the entire aerobiosis range; ArcB is activated under anaerobic and subaerobic conditions and is much less active under fully aerobic and microaerobic conditions. Furthermore, there is no correlation between ArcB activation and the redox state of the ubiquinone pool, but there is a restricted correlation between the total cellular ubiquinone content and ArcB activity due to the considerable increase in the size of the ubiquinone pool with increasing degrees of aerobiosis. These results lead to the working hypothesis that the in vivo activity of ArcB in E. coli is modulated by the redox state of the menaquinone pool and that the ubiquinone/ubiquinol ratio in vivo surely is not the only determinant of ArcB activity.

Plants have evolved the ability to derive the benzenoid moiety of the respiratory cofactor and antioxidant, ubiquinone (coenzyme Q), either from the β-oxidative metabolism of p-coumarate or from the peroxidative cleavage of kaempferol. Here, isotopic feeding assays, gene co-expression analysis and reverse genetics identified Arabidopsis 4-COUMARATE-COA LIGASE 8 (4-CL8; At5g38120) as a contributor to the β-oxidation of p-coumarate for ubiquinone biosynthesis. The enzyme is part of the same clade (V) of acyl-activating enzymes than At4g19010, a p-coumarate CoA ligase known to play a central role in the conversion of p-coumarate into 4-hydroxybenzoate. A 4-cl8 T-DNA knockout displayed a 20% decrease in ubiquinone content compared with wild-type plants, while 4-CL8 overexpression boosted ubiquinone content up to 150% of the control level. Similarly, the isotopic enrichment of ubiquinone's ring was decreased by 28% in the 4-cl8 knockout as compared with wild-type controls when Phe-[Ring-13C6] was fed to the plants. This metabolic blockage could be bypassed via the exogenous supply of 4-hydroxybenzoate, the product of p-coumarate β-oxidation. Arabidopsis 4-CL8 displays a canonical peroxisomal targeting sequence type 1, and confocal microscopy experiments using fused fluorescent reporters demonstrated that this enzyme is imported into peroxisomes. Time course feeding assays using Phe-[Ring-13C6] in a series of Arabidopsis single and double knockouts blocked in the β-oxidative metabolism of p-coumarate (4-cl8; at4g19010; at4g19010 × 4-cl8), flavonol biosynthesis (flavanone-3-hydroxylase), or both (at4g19010 × flavanone-3-hydroxylase) indicated that continuous high light treatments (500 µE m−2 s−1; 24 h) markedly stimulated the de novo biosynthesis of ubiquinone independently of kaempferol catabolism.

C. elegans worms with mutations in the gene CLK-1 develop slowly and have an extended lifespan. CLK-1 encodes a mitochondrial protein that is responsible for the hydroxylation of 5-demethoxyubiquinone (DMQ), the penultimate step of ubiquinone (Coenzyme-Q or UQ) biosynthesis. Structural homologues of CLK-1 are found in mammals, fruit flies, yeast and some types of bacteria. Interestingly, however, there is no structural homologue of CLK-1 in the Arabidopsis genome and no plant homologue can be found in other sequence databases. Yeast with the CLK-1 homologue COQ7 deleted fail to grow on non-fermentable carbon sources. To identify a plant functional homologue of COQ7/CLK-1, an Arabidopsis cDNA expression library was screened for complementation of a yeast coq7 deletion mutant. A clone was identified that rescued the coq7 respiratory deficiency. Although the sequence of the encoded protein has no structural similarity to proteins in the COQ7/CLK-1 family, it contains a monooxygenase/hydroxylase domain that has sequence similarity with the E. coli DMQ hydroxylase encoded by the UBIF gene. Like the structural homologues of COQ7/CLK-1 found in other eukaryotes, the gene (AQX for 'Alternate Quinone monooXygenase') contains a likely mitochondrial targeting presequence at its N-terminus. HPLC analysis of quinone extracts from rescued cog7 strains does not detect ubiquinone, but instead shows another peak that may be DMQ. It is likely that AQX does not hydroxylate yeast DMQ effectively enough to generate detectable levels of UQ. A unique pathway for UQ biosynthesis in plants is proposed that is defined by AQX and Arabidopsis genes identified on the basis of homology to known E. coli and yeast UQ biosynthesis genes.

Coq6 est une enzyme impliquée dans la biosynthèse du coenzyme Q (aussi nommé ubiquinone, ou Q), un lipide benzoquinone polyprenylé essentiel à la fonction de la chaîne respiratoire mitochondriale. Dans la levure Saccharomyces cerevisiae, cette monooxygénase flavine-dépendante putatif est proposé pour hydroxyler le noyau benzénique d' un précurseur du coenzyme Q à la position C5. Nous montrons ici à travers des études biochimiques que Coq6 est une flavoprotéine utilisant le FAD comme cofacteur. Des modèles d'homologie du complexe Coq6-FAD ont étés réalisés et étudiés par dynamique moléculaire et arrimage moléculaire du 3-hexaprenyl-4-hydroxyphényl (4-HP6), un substrat modèle hydrophobe et volumineux. Nous identifions un canal d'accès putatif pour Coq6 dans un modèle de la forme sauvage et proposons des mutations in silico positionnés à l'entrée capable de partiellement (les mutations simples G248R et L382E) ou complètement (une double-mutation G248R-L382E) bloquer l'accès du substrat au site actif via le canal d' accès. Des essais in vivo soutiennent les prédictions in silico, qui expliquent l'abrogation ou la diminution des enzymes mutées. Ce travail fournit la première information structurale détaillée d'une enzyme importante et hautement conservée de biosynthèse de l'ubiquinone
Coq6 is an enzyme involved in the biosynthesis of coenzyme Q, a polyisoprenylated benzoquinone lipid essential to the function of the mitochondrial respiratory chain. In the yeast Saccharomyces cerevisiae, this putative flavin-dependent monooxygenase is proposed to hydroxylate the benzene ring of coenzyme Q (ubiquinone) precursor at position C5. We show here through biochemical studies that Coq6 is a flavoprotein using FAD as a cofactor. Homology models of the Coq6-FAD complex are constructed and studied through molecular dynamics and substrate docking calculations of 3-hexaprenyl-4-hydroxyphenol (4-HP6), a bulky hydrophobic model substrate. We identify a putative access channel for Coq6 in a wild type model and propose in silico mutations positioned at its entrance capable of partially (G248R and L382E single mutations) or completely (a G248R-L382E double-mutation) blocking access of the substrate to thechannel . Further in vivo assays support the computational predictions, thus explaining the decreased activities or inactivation of the mutated enzymes. This work provides the first detailed structural information of an important and highly conserved enzyme of ubiquinone biosynthesis

Ubiquinone (Coenzyme Q, UQ or CoQ) is a small lipophilic molecule which is essential for all life forms that rely on mitochondrial respiration for energy production. It functions as an electron carrier in the respiratory chain and plays a role in many other cellular functions as well. In the past decade, an increasing number of patients have been described to have a genetic defect in UQ biosynthesis and present with severe and diverse clinical manifestations, making UQ research relevant to patient care. This thesis focuses on a particular enzyme of the UQ biosynthetic pathway in mice, which is encoded by the Mclk1/Coq7 gene and is responsible for the penultimate step of UQ biosynthesis: the hydroxylation of DMQ (demethoxy-UQ). I generated three conditional Mclk1 knockout (KO) models which are able to bypass the embryonic lethality of Mclk1 and allow us to examine the consequences of complete loss-of-function of Mclk1 in vitro and in vivo in adult animals. First, we created Mclk1 KO mouse embryonic fibroblasts (MEFs) in vitro. These cells do not synthesize UQ and accumulate DMQ. They are viable under standard (glucose) culture conditions. More interestingly, despite lacking UQ, they still have a functionally active electron transport chain. To understand this surprising phenomenon, we generated Pdss2 KO MEFs which are devoid of both DMQ and UQ. To our surprise, Pdss2 KO MEFs also are still capable of carrying out mitochondrial respiration. These observations suggest that 1) the respiratory phenotype of Mclk1 mutants can be considered essentially as a UQ-deficiency phenotype, and 2) mitochondrial respiration can occur in the absence of UQ. Mclk1 KO MEFs cannot survive in medium containing galactose instead of glucose as this forces cells to mostly rely on mitochondrial ATP production to sustain their viability. These characteristics make them a unique tool for testing the efficacy of UQ analogues in promoting electron transport in mammalian mitochondria. Next, we generated a mouse model with liver-specific loss of Mclk1. A large depletion of UQ in hepatocytes was found to cause only a mild impairment of respiratory chain function and no gross abnormalities. Therefore, liver mitochondrial function appears to have a high tolerance of severe UQ deficiency. Using this model, we also demonstrated that dietary UQ10 can functionally rescue the endogenous UQ deficiency of Mclk1 KO liver at the respiratory chain level. Furthermore, we generated an inducible Mclk1 KO model in which Mclk1 was knocked out in adult mice. These animals have a median survival time of 9 months after induction of global KO of the Mclk1 gene. We observed a very slow gradual decrement of tissue UQ contents after inducing the ablation of Mclk1, which could explain the slowly progressive phenotype in these mice. In the heart, kidneys and skeletal muscles severe deficits of UQ were found to severely impair mitochondrial respiration. Therefore, unlike the liver, the kidneys and muscle tissues need high levels of UQ to sustain sufficient respiratory function. I examined the efficacy of dietary UQ10 supplementation against the global KO model and found that dietary UQ10 cannot be taken up by other organs beside the liver, and accordingly it was almost completely ineffective in rescuing the Mclk1 KO phenotype. On the other hand, feeding the mutant animals with 2,4-dihydroxybenzoic acid, a synthetic analogue of the UQ ring precursor 4-hydroxybenzoic acid (4-HB), led to dramatic rescue of disease phenotypes in these animals, including their early lethality. 2,4-diHB structurally differs from 4-HB by having one more hydroxyl group at the position where the MCLK1 enzyme would catalyze the hydroxylation of DMQ. This finding suggests that some types of primary UQ deficiency could be relieved by treatment with the appropriate unnatural precursors, and more generally, that biosynthetic "by-pass" precursors could be a new treatment strategy for biosynthetic pathway defects.
L'ubiquinone (coenzyme Q, UQ, CoQ) est essentielle pour toutes les formes de vie qui s'appuient sur la respiration mitochondriale pour la production d'énergie. Elle fonctionne comme un transporteur d'électrons dans la chaîne respiratoire mitochondriale (ETC) et joue un rôle dans de nombreuses autres fonctions cellulaires. Au cours de la dernière décennie, un nombre croissant de patients ont été décrits comme ayant un défaut génétique produisant un problème de synthèse de l'UQ et présentant des manifestations cliniques graves et diversifiées. Ma thèse s'est concentrée sur une enzyme particulière de la synthèse de l'UQ chez la souris, codée par le gène Mclk1/Coq7 et responsable de l'hydroxylation du DMQ (demethoxy-UQ). Ici je décris 3 modèles de knockout (KO) conditionnels que j'ai créés qui permettent de contourner la létalité embryonnaire de Mclk1. Ces modèles nous permettent d'examiner les conséquences de la perte complète de la fonction de Mclk1 in vitro et in vivo chez les animaux adultes. Premièrement, j'ai créé des lignées de fibroblastes embryonnaires (MEFs) de souris KO pour Mclk1. Ces cellules ne synthétisent pas d'UQ et accumulent le DMQ. Elles sont viables dans les conditions standards de culture et en présence de glucose. De plus, malgré le manque d'UQ, elles ont encore une ETC fonctionnelle. Pour comprendre ce phénomène, j'ai généré des MEFs KO pour Pdss2 qui sont dépourvus de DMQ et d'UQ. À notre surprise, ces cellules sont également capables de respiration mitochondriale. Ces observations suggèrent que 1) le phénotype respiratoire des mutants Mclk1 peut être considéré essentiellement comme un phénotype dû à un manque d'UQ, et 2) la respiration mitochondriale peut se produire en l'absence d'UQ. Les MEFs KO pour Mclk1 ne peuvent survivre dans un milieu qui les forcerait à dépendre de la respiration mitochondriale pour la production d'ATP. Ces caractéristiques font de ces cellules un outil unique pour tester l'efficacité des analogues de l'UQ dans la ETC de mammifères. J'ai aussi créé un modèle de souris produisant une ablation hépatique de Mclk1. Il est intéressant de noter qu'une perte sévère d'UQ dans les hépatocytes ne cause qu'une diminution légère de l'activité de la ETC et que les souris ne présentent aucune anomalie flagrante. Par conséquent, la fonction mitochondriale du foie semble être capable de tolérer de graves carences en UQ. En utilisant ce modèle, nous avons aussi démontré que de l'UQ10 exogène peut être utilisé par le foie et rétablir la fonction de la ETC. J'ai aussi construit un modèle pour lequel Mclk1 est absent chez les souris adultes. Ces animaux ont une survie moyenne de 9 mois après la perte totale de Mclk1. Une très lente diminution du contenu en UQ des tissus après l'ablation de Mclk1 a été observée, ce qui pourrait expliquer la détérioration très lente de ces souris. J'ai trouvé que dans le cœur, les reins et les muscles squelettiques de profonds déficits en UQ compromettent gravement la respiration mitochondriale. Contrairement au foie il semblerait que ces tissus nécessitent de hauts niveaux d'UQ afin de maintenir une fonction respiratoire suffisante. J'ai trouvé que l'UQ10 exogène ne peut être utilisé que par le foie et que, même dans ce cas, il était presque totalement incapable d'aider les souris déficientes en Mclk1. Par contre, le traitement des animaux mutants avec l'acide 2,4 -dihydroxybenzoïque (2,4-diHB; un analogue synthétique de l'acide 4-hydroxybenzoïque (4-HB), qui est le précurseur naturel dans la biosynthèse de l'UQ) mène à une nette amélioration des symptômes de maladie des souris mutantes incluant la létalité précoce. Le 2,4 -diHB diffère structurellement du 4-HB par un groupe hydroxyle à la position où l'enzyme MCLK1 catalyse l'hydroxylation du DMQ. Ces données suggèrent que les symptômes de certaines déficiences en UQ pourraient être allégés par le traitement à l'aide de précurseurs non-naturels qui permettraient de contourner les voies de biosynthèses défectueuses.

Coq6 est une enzyme impliquée dans la biosynthèse du coenzyme Q (aussi nommé ubiquinone, ou Q), un lipide benzoquinone polyprenylé essentiel à la fonction de la chaîne respiratoire mitochondriale. Dans la levure Saccharomyces cerevisiae, cette monooxygénase flavine-dépendante putatif est proposé pour hydroxyler le noyau benzénique d' un précurseur du coenzyme Q à la position C5. Nous montrons ici à travers des études biochimiques que Coq6 est une flavoprotéine utilisant le FAD comme cofacteur. Des modèles d'homologie du complexe Coq6-FAD ont étés réalisés et étudiés par dynamique moléculaire et arrimage moléculaire du 3-hexaprenyl-4-hydroxyphényl (4-HP6), un substrat modèle hydrophobe et volumineux. Nous identifions un canal d'accès putatif pour Coq6 dans un modèle de la forme sauvage et proposons des mutations in silico positionnés à l'entrée capable de partiellement (les mutations simples G248R et L382E) ou complètement (une double-mutation G248R-L382E) bloquer l'accès du substrat au site actif via le canal d' accès. Des essais in vivo soutiennent les prédictions in silico, qui expliquent l'abrogation ou la diminution des enzymes mutées. Ce travail fournit la première information structurale détaillée d'une enzyme importante et hautement conservée de biosynthèse de l'ubiquinone
Coq6 is an enzyme involved in the biosynthesis of coenzyme Q, a polyisoprenylated benzoquinone lipid essential to the function of the mitochondrial respiratory chain. In the yeast Saccharomyces cerevisiae, this putative flavin-dependent monooxygenase is proposed to hydroxylate the benzene ring of coenzyme Q (ubiquinone) precursor at position C5. We show here through biochemical studies that Coq6 is a flavoprotein using FAD as a cofactor. Homology models of the Coq6-FAD complex are constructed and studied through molecular dynamics and substrate docking calculations of 3-hexaprenyl-4-hydroxyphenol (4-HP6), a bulky hydrophobic model substrate. We identify a putative access channel for Coq6 in a wild type model and propose in silico mutations positioned at its entrance capable of partially (G248R and L382E single mutations) or completely (a G248R-L382E double-mutation) blocking access of the substrate to thechannel . Further in vivo assays support the computational predictions, thus explaining the decreased activities or inactivation of the mutated enzymes. This work provides the first detailed structural information of an important and highly conserved enzyme of ubiquinone biosynthesis

Les interactions protéine-protéine (PPIs) et les assemblages supramoléculaires sont essentiels pour les fonctions des cellules vivantes. Ils jouent un rôle important dans un certain nombre de fonctions biologiques, comme la transduction de signaux, la communication entre cellules, la transcription, la réplication ou le transport membranaire. La détermination et la caractérisation de telles interfaces restent un défi en biologie structurale. Cependant, les progrès dans le développement de méthodes computationnelles et la puissance des ressources informatiques disponibles de nos jours ont permis une amélioration considérable de la précision des prédictions in silico des modèles tri-dimensionnels d’assemblages protéiques.Dans le cadre de cette thèse, l’objectif était de prédire la structure d’un assemblage supramoléculaire, appelé métabolon Ubi, impliqué dans la voie de biosynthèse de l’ubiquinone (UQ8) dans Escherichia coli. L’ubiquinone est un prénol possédant des propriétés oxydo-réductrices, localisé dans les membranes, et très conservé à travers l’évolution mais également dans les différentes cellules des organismes. Elle est composée de deux parties principales, un groupe aromatique aux propriétés oxydo-réductrices, appelé quinone ou tête polaire, et une queue polyisoprénoide qui est de nature hydrophobe. Dans le cadre de cette étude, ce sont les dernières étapes de la voie de biosynthèse, notamment les modifications (méthylations et hydroxylations) de la tête polaire, qui nous intéressent. Ces réactions ont lieu au sein du métabolon Ubi. Ce dernier est constitué de sept protéines différentes (UbiE, UbiG, UbiF, UbiH, UbiI, UbiJ, UbiK) catalysant six réactions enzymatiques consécutives.Dans ce travail, nous avons cherché à prédire la structure du métabolon et nous avons ainsi été capable de proposer un sous-ensemble protéique que nous avons nommé "sous-unité centrale". Cette sous-unité comprend l’ensemble des partenaires et pourrait être biologiquement fonctionnelle. En parallèle, une étude a été menée sur l’hétérotrimère UbiJ-UbiK2, une brique moléculaire essentielle du métabolon Ubi. Un modèle tri-dimensionnel de UbiJ-UbiK2 a été proposé. A l’aide d’une étude par modélisation multi-échelles, il a pu être montré qu’il pouvait être impliqué dans le relargage de l’ubiquinone au sein des membranes. Enfin, la dernière partie de ce travail a porté sur l’étude du comportement d’une famille particulière d’enzymes, les mono-oxygénases à flavine de classe A, à laquelle appartiennent UbiF, UbiH et UbiI. Une étude comparative entre une enzyme modèle de cette famille enzymatique, appelée PHBH, et UbiI a été réalisée et concluant à la nécessité d’interactions avec des partenaires, permettant de stabiliser ces protéines au sein du métabolon Ubi.L’ensemble de ces travaux, et des hypothèses proposées, permet d’apporter un regard nouveau sur l’organisation supramoléculaire du métabolon Ubi, tant au niveau structural que fonctionnel. Ainsi, nos résultats ouvrent de nouvelles perspectives pour leur étude expérimentale
Protein-protein interactions (PPIs) and supramolecular assemblies are essential for the functions of living cells. They play an important role in various biological functions, such as signal transduction, cell-cell communication, transcription, replication and membrane transport. Determining and characterizing such interfaces remains a challenge in structural biology. However, advances in the development of computational methods and the power of the computing resources available today have led to a considerable improvement in the accuracy of in silico predictions of three-dimensional models of protein assemblies.In this thesis, the aim was to predict the structure of a supramolecular assembly, called the Ubi metabolon, involved in the ubiquinone (UQ8) biosynthesis pathway in Escherichia coli. Ubiquinone is a prenol with oxido-reducing properties, localized in membranes, and highly conserved throughout evolution but also in different cells of organisms. It is composed of two main parts, an aromatic group with oxido-reducing properties, known as quinone or polar head, and a polyisoprenoid tail which is hydrophobic in nature. In this study, we are interested in the final stages of the biosynthetic pathway, in particular the modifications (methylations and hydroxylations) of the polar head. These reactions take place within the Ubi metabolon. The latter is made up of seven different proteins (UbiE, UbiG, UbiF, UbiH, UbiI, UbiJ, UbiK) catalysing six consecutive enzymatic reactions.In this work, we sought to predict the structure of the metabolon and were thus able to propose a protein subset that we called the 'core subunit'. This sub-unit includes all the partners and could be biologically functional. In parallel, a study was carried out on the UbiJ-UbiK2 heterotrimer, an essential molecular brick of the Ubi metabolon. A three-dimensional model of UbiJ-UbiK2 was proposed. Using a multi-scale modelling study, it was shown that it could be involved in the release of ubiquinone from membranes. Finally, the last part of this work focused on studying the behavior of a particular family of enzymes, the class A flavin mono-oxygenases, to which UbiF, UbiH and UbiI belong. A comparative study between a representative enzyme from this family, called PHBH, and UbiI was carried out, concluding that interactions with partners were necessary to stabilize these proteins within the Ubi metabolon.Taken together, this work and the proposed hypotheses provide a new insight into the supramolecular organization of the Ubi metabolon, both structurally and functionally. Our results open up new prospects for their experimental study

L’ubiquinone, ou coenzyme Q (CoQ ou UQ), est un lipide polyprénylé qui joue un rôle important dans le transport des électrons dans les chaînes respiratoires chez E. coli. La biosynthèse de l'UQ en aérobie chez E. coli nécessite huit réactions et implique au moins douze protéines (UbiA-UbiK et UbiX). Dans ce travail, nous démontrons que les protéines Ubi forment le complexe Ubi, un métabolon stable qui catalyse les six dernières réactions de la voie de biosynthèse. La structure tridimensionnelle du domaine SCP2 d’UbiJ forme une cavité hydrophobe étendue qui lie les intermédiaires de l’UQ à l'intérieur du complexe d’1-MDa. Le complexe Ubi est purifié à partir des extraits cytoplasmiques et la biosynthèse de l'UQ a lieu dans cette fraction, remettant en question l’hypothèse actuelle d'un processus de biosynthèse associé à la membrane. L’UQ est connue pour être synthétisée en aérobie et anaérobie. Nous caractérisons une nouvelle voie de biosynthèse de l’UQ indépendante de l'O2. Cette voie repose sur trois protéines, UbiT, UbiU et UbiV. UbiT possède un domaine de liaison aux lipides SCP2 et est probablement un facteur accessoire de la voie de biosynthèse, tandis qu’UbiU et UbiV (UbiU-UbiV) sont impliqués dans les réactions d'hydroxylation et représentent une nouvelle classe d'hydroxylases indépendantes de l’O2. Nous démontrons qu’UbiU-UbiV d’E.coli forme un hétérodimère, chaque protéine se lie à un centre [4Fe-4S] via des cystéines conservées essentielles à l'activité. De plus, nous montrons qu’UbiU purifié de P. aeruginosa est capable de lier de l’UQ, suggérant un rôle différent d’UbiU et d’UbiV. UbiU et UbiV appartiennent à la famille des peptidases U32, dont la fonction reste discutable. Nous démontrons, par des analyses bioinformatiques, que les protéines U32 sont caractérisées par quatre cystéines conservées très importantes pour leurs activités enzymatiques et par des outils biochimiques, nous confirmons que RlhA et TrhP, deux autres protéines de la famille U32, comme UbiU et UbiV, sont des protéines Fe-S
Ubiquinone (UQ) is a polyprenylated lipid that plays an important role in electron transport in the respiratory chains of E. coli. The aerobic biosynthesis of UQ in E. coli requires eight reactions and involves at least twelve proteins (UbiA-UbiK and UbiX). In this work, we demonstrate that seven Ubi proteins form the Ubi complex, a stable metabolon that catalyzes the last six reactions of the UQ biosynthetic pathway. The X-Ray structure of the SCP2 domain of UbiJ forms an extended hydrophobic cavity that could bind UQ intermediates inside the 1-MDa Ubi complex. The Ubi complex is purified from cytoplasmic extracts and UQ biosynthesis occurs in this fraction, challenging the current thinking of a membrane-associated biosynthetic process. UQ is reported to be biosynthesized under both anerobic and anaerobic conditions. We characterize a novel, O2-independent pathway for the biosynthesis of UQ. This pathway relies on three proteins, UbiT, UbiU, and UbiV. UbiT contains an SCP2 lipid-binding domain and is likely an accessory factor of the biosynthetic pathway, while UbiU and UbiV (UbiU-UbiV) are involved in hydroxylation reactions and represent a novel class of O2-independent hydroxylases. We demonstrate that UbiU-UbiV from E.coli form a heterodimer, wherein each protein binds a [4Fe-4S] cluster via conserved cysteines that are essential for activity. Moreover, we show that purified UbiU from P. aeruginosa is able to bind UQ, suggesting a different role of UbiU and UbiV. UbiU and UbiV belong to peptidase U32 family whose function remains questionable. By bioinformatic analyses, we demonstrated that U32 proteins were characterized by four conserved cysteines important for their enzymatic activities and by biochemical tools, we confirmed that RlhA and TrhP, two others U32 subfamilies, like UbiU and UbiV, are all Fe-S proteins

Le coenzyme Q est une molécule lipophile rédox rencontrée chez les eucaryotes et chez la plupart des procaryotes. La structure de Q correspond à une benzoquinone substituée par une chaîne polyisoprényle dont la longueur varie selon les organismes. Q joue le rôle de transporteur d'électrons dans les chaînes respiratoires d'où provient la plupart de l'énergie de la cellule. La biosynthèse de Q chez la bactérie Escherichia coli comporte huit étapes et implique au moins neuf protéines (UbiA-UbiH et UbiX). Trois réactions d'hydroxylation sont nécessaires pour la biosynthèse de Q8 en conditions aérobies. Alors que les protéines UbiH et UbiF présentent des homologies de séquence avec des monooxygénases à flavine connues pour catalyser des réactions d'hydroxylation, UbiB qui a été proposée comme étant la troisième hydroxylase, présente uniquement une homologie de séquence avec des kinases. Nous rapportons dans ce travail que la protéine VisC, renommée UbiI, catalyse la réaction d'hydroxylation auparavant attribuée à UbiB. Nous avons également identifié deux nouvelles protéines (YigP et YqiC, renommées respectivement UbiJ et UbiK) importantes pour le métabolisme de Q chez Escherichia coli puisque leur mutation diminue fortement le contenu en Q des souches mutantes. Ces protéines interagissent avec la plupart des protéines connues pour participer à la biosynthèse de Q ce qui implique l'existence d'un complexe de biosynthèse de Q. En utilisant des approches biochimiques et protéomiques, nous avons pu mettre en évidence un complexe impliquant plusieurs protéines Ubi et notamment UbiJ et UbiK. Ces deux protéines semblent avoir un rôle dans l'assemblage et/ou la stabilisation de ce complexe multiprotéique. Enfin, nous nous sommes intéressés à la biosynthèse de Q dans des conditions de cultures anaérobies. Nos résultats montrent l'existence « d'hydroxylases anaérobies », inconnues à ce jour, qui remplaçent les hydroxylases aérobies UbiH, UbiI et UbiF. Grâce à une approche phylogénétique, nous identifions un gène important pour la biosynthèse de Q uniquement en conditions anaérobies suggérant une réorganisation de la biosynthèse de Q entre ces deux environnements fréquemment rencontrés par E. coli. L'ensemble de nos résultats a permis d'améliorer notre connaissance de la voie de biosynthèse procaryote de Q grâce à la découverte de nouveaux gènes impliqués dans ce processus et grâce à l'identification de la fonction moléculaire de certaines protéines
Ubiquinone (Q) is a lipophilic compound that plays an important role in electron and proton transport in the respiratory chains of Escherichia coli. Besides this important role in energy production, Q also functions as a membrane soluble antioxidant. The biosynthesis of Q8 requires eight reactions and involves at least nine proteins (UbiA-UbiH and UbiX) in Escherichia coli. Three of these reactions are hydroxylations resulting in the introduction of a hydroxyl group on carbon atoms at position 1, 5 and 6 of the aromatic ring. The C1 and C6 hydroxylation are well characterized whereas the C5 hydroxylation has been proposed to involve UbiB, a protein kinase without any sequence homology with monooxygenase. In this work, by genetic and biochemical methods we provide evidence that VisC which we renamed UbiI, displays sequence homology with monooxygenases and catalyzes the C5 hydroxylation, not UbiB. We have identified two new genes, yqiC and yigP (renammed UbiJ and UbiK) which are required only for Q8 biosynthesis in aerobic conditions. The exact role of the corresponding proteins, renamed UbiJ and UbiK, remains unknown. These proteins are able to interact with other Ubi proteins to be able to produce Q supporting the protein complex hypothesis. Our progress on the characterization of an Ubi-complex regrouping several Ubi proteins suggest that UbiJ and UbiK may fulfill functions related to the Ubi-complex stability. Mutants affected in hydroxylation steps are deficient for Q8 in aerobic conditions but recover a wild type Q8 content when grown in anaerobic conditions. This intriguing observation supports the existence of an alternative hydroxylation system independent from dioxygen which has not been characterized so far. By phylogenetic studies, we have identified a new gene in which the deletion affect the biosynthesis of Q only in anaerobic conditions suggesting a reorganization of Q biosynthesis in these two conditions. Our results has improved our knowledge of the prokaryotic Q biosynthetic pathway through the discovery of new genes involved in this process and through the identification of the molecular function of some proteins

Terpenoids are a class of chemicals with over 50,000 individual compounds, highly diverse in chemical structure, founded in all kingdoms of life, and are the largest group of secondary plant metabolites. Also known as isoprenoids, their structure began to be elucidated between the 1940s and 1960s, when their basic isoprenoid building blocks were characterized. They play several basic and specialized physiological functions in plants through direct and indirect interactions. Terpenoids are essential to metabolic processes, including post-translational protein modifications, photosynthesis, and intracellular signaling. All terpenoids are built through C5 units condensed to prenyl diphosphate intermediates. The fusion of these C5 units generates short C15-C25, medium C30-C35, and long-chain C40-Cn terpenoids. Along with the extension of the chain, the introduction of functional groups, such as ketones, alcohol, esters and, ethers, forms the precursors to hormones, sterols, carotenoids, and ubiquinone synthesis. The biosynthesis of terpenoids is regulated by spatial, temporal, transcriptional, and post-transcriptional factors. This chapter gives an overview of terpenoid biosynthesis, focusing on both cytoplasmic and plastid pathways, and highlights recent advances in the regulation of its metabolic pathways.