A Soluble Metabolon Synthesizes the Isoprenoid Lipid Ubiquinone

Chehade, Mahmoud Hajj; Pélosi, Ludovic; Fyfe, Cameron David; Loiseau, Laurent; Rascalou, Bérengère; Brugière, Sabine; Kazemzadeh, Katayoun; Vo, Chau-Duy-Tam; Ciccone, Lidia; Aussel, Laurent; Couté, Yohann; Fontecave, Marc; Barras, Frédéric; Lombard, Murielle; Pierrel, Fabien

doi:10.1016/j.chembiol.2018.12.001

Cited by 49 publications

(71 citation statements)

References 68 publications

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“…S2). Recently, we reported that UbiJ binds UQ biosynthetic intermediates in its SCP2 domain and organizes a multiprotein complex composed of several Ubi enzymes (16). We propose that UbiT and its SCP2 domain fulfill similar functions in the O 2 -independent UQ pathway, as UbiJ is required exclusively for the O 2 -dependent biosynthesis of UQ (Fig.…”

Section: Resultsmentioning

confidence: 99%

“…In addition to the enzymes that catalyze the various steps, three accessory factors, UbiB, UbiJ, and UbiK, are also needed. UbiB has an ATPase activity (13), and we showed that UbiJ and UbiK (14, 15) belong to a multiprotein UQ biosynthesis complex, in which the SCP2 domain (sterol carrier protein 2) of UbiJ binds the hydrophobic UQ biosynthetic intermediates (16). This UQ biosynthetic pathway is dependent upon O 2 , since all three hydroxylases, UbiI, UbiH, and UbiF, use O 2 as a cosubstrate (Fig.…”

Section: Introductionmentioning

confidence: 99%

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Ubiquinone Biosynthesis over the Entire O ₂ Range: Characterization of a Conserved O ₂ -Independent Pathway

Pélosi

Abby

et al. 2019

mBio

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Most bacteria can generate ATP by respiratory metabolism, in which electrons are shuttled from reduced substrates to terminal electron acceptors, via quinone molecules like ubiquinone. Dioxygen (O2) is the terminal electron acceptor of aerobic respiration and serves as a co-substrate in the biosynthesis of ubiquinone. Here, we characterize a novel, O2-independent pathway for the biosynthesis of ubiquinone. This pathway relies on three proteins, UbiT (YhbT), UbiU (YhbU), and UbiV (YhbV). 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 form a heterodimer, wherein each protein binds a 4Fe-4S cluster via conserved cysteines that are essential for activity. The UbiT, -U, and -V proteins are found in alpha-, beta-, and gammaproteobacterial clades, including several human pathogens, supporting the widespread distribution of a previously unrecognized capacity to synthesize ubiquinone in the absence of O2. Together, the O2-dependent and O2-independent ubiquinone biosynthesis pathways contribute to optimizing bacterial metabolism over the entire O2 range. IMPORTANCE In order to colonize environments with large O2 gradients or fluctuating O2 levels, bacteria have developed metabolic responses that remain incompletely understood. Such adaptations have been recently linked to antibiotic resistance, virulence, and the capacity to develop in complex ecosystems like the microbiota. Here, we identify a novel pathway for the biosynthesis of ubiquinone, a molecule with a key role in cellular bioenergetics. We link three uncharacterized genes of Escherichia coli to this pathway and show that the pathway functions independently from O2. In contrast, the long-described pathway for ubiquinone biosynthesis requires O2 as a substrate. In fact, we find that many proteobacteria are equipped with the O2-dependent and O2-independent pathways, supporting that they are able to synthesize ubiquinone over the entire O2 range. Overall, we propose that the novel O2-independent pathway is part of the metabolic plasticity developed by proteobacteria to face various environmental O2 levels.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Ubiquinone Biosynthesis over the Entire O ₂ Range: Characterization of a Conserved O ₂ -Independent Pathway

Pélosi

Abby

et al. 2019

mBio

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“…We have recently demonstrated that isoprenoid quinones were able to co-elute with the Ubi-proteins such as UbiJ (11) and that UbiT exhibits a sterol carrier protein 2 (SCP2) domain (9). In this direction, we performed lipid content analysis of the UbiTPa, UbiUPa and UbiVPa fractions purified from E. coli extracts.…”

Section: Heterologously Overproduced Ubiupa and Ubitpa Co-purify Withmentioning

confidence: 99%

“…The typical UQ biosynthesis pathway requires O2 for three hydroxylation steps (10). Obviously, the flavin-dependent monooxygenases UbiI, UbiF, and UbiH, which catalyze the O2-dependent hydroxylation steps are not involved in the anaerobic pathway, nor are the accessory UbiK and UbiJ proteins implicated in the assembly and/or stability of the aerobic Ubi complex (11). The enzymes, catalyzing the prenylation, decarboxylation and methylation of the phenyl ring of the 4-hydroxybenzoate precursor, in total seven proteins (UbiA, B, C, D, E, G, X), are common to both pathways.…”

Section: Introductionmentioning

confidence: 99%

The O₂-independent pathway of ubiquinone biosynthesis is essential for denitrification inPseudomonas aeruginosa

Michaud

Elsen

et al. 2020

Preprint

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ABSTRACTMany proteobacteria, such as Escherichia coli, contain two main types of quinones, benzoquinones represented by ubiquinone (UQ) and naphthoquinones such as menaquinone (MK) and dimethyl-menaquinone (DMK). MK and DMK function predominantly in anaerobic respiratory chains, whereas UQ is the major electron carrier used for reduction of dioxygen. However, this division of labor is probably not so stric. Indeed, a pathway that produces UQ under anaerobic conditions in an UbiU-, UbiV- and UbiT-dependent manner has been recently discovered in E. coli while its physiological relevance is not yet understood because of the presence of MK and DMK in this bacterium. In the present study, we established that UQ9 is the single quinone of P. aeruginosa and that is required for growth under anaerobic respiration (denitrification). We demonstrated that ORFs PA3911, PA3912 and PA3913, which are homologues to the E. coli ubiT, ubiV and ubiU genes, respectively, were essential for UQ9 biosynthesis and thus for denitrification in P. aeruginosa. These three genes were hereafter called ubiTPa, ubiVPa and ubiUPa. We showed that UbiVPa accommodates a [4Fe-4S] cluster. Moreover, we demonstrated that UbiUPa and UbiTPa were able to bind UQ and that the isoprenoid tail of UQ was the structural determinant for the recognition by these Ubi proteins. Since the denitrification metabolism of P. aeruginosa is believed to be important for pathogenicity in cystic fibrosis patients, our results highlight the O2-independent UQ biosynthesis pathway as a new possible target to develop innovative antibiotics.

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“…Furthermore, knockdown of kdsC (56), encoding an enzyme involved in LPS biosynthesis, also led to sensitivity to LL37. Knockdown strains for rpoE, the gene encoding the envelope stress responsive sigma factor σ E (39,42,43), and the ubiquinone biosynthesis gene ubiJ (58) were sensitive to CSA13, but not to CSA131, also supporting the idea that these ceragenins have distinctive mechanisms of action. On the other hand, the knockdown strain for the fatty acid biosynthesis gene fabI (52,53) was sensitive to both CSA13 and CSA131 and not to the CAMPs, and may constitute a common molecular determinant of sensitivity to ceragenins.…”

Section: Identification Of Genetic Determinantsmentioning

confidence: 77%

Ceragenins and antimicrobial peptides kill bacteria through distinct mechanisms

Mitchell

Silvis

Talkington

et al. 2020

Preprint

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Ceragenins are a family of synthetic amphipathic molecules designed to mimic the properties of naturally-occurring cationic antimicrobial peptides (CAMPs). Although ceragenins have potent antimicrobial activity, whether their mode of action is similar to that of CAMPs has remained elusive. Here we report the results of a comparative study of the bacterial responses to two well-studied CAMPs, LL37 and colistin, and two ceragenins with related structures, CSA13 and CSA131. Using transcriptomic and proteomic analyses, we found that Escherichia coli responds similarly to both CAMPs and ceragenins by inducing a Cpx envelope stress response. However, whereas E. coli exposed to CAMPs increased expression of genes involved in colanic acid biosynthesis, bacteria exposed to ceragenins specifically modulated functions related to phosphate transport, indicating distinct mechanisms of action between these two classes of molecules. Although traditional genetic approaches failed to identify genes that confer high-level resistance to ceragenins, using a Clustered Regularly Interspaced Short Palindromic Repeats interference (CRISPRi) approach we identified E. coli essential genes that when knocked down modify sensitivity to these molecules. Comparison of the essential gene-antibiotic interactions for each of the CAMPs and ceragenins identified both overlapping and distinct dependencies for their antimicrobial activities. Overall, this study indicates that while some bacterial responses to ceragenins overlap with those induced by naturally-occurring CAMPs, these synthetic molecules target the bacterial envelope using a distinctive mode of action.

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A Soluble Metabolon Synthesizes the Isoprenoid Lipid Ubiquinone

Cited by 49 publications

References 68 publications

Ubiquinone Biosynthesis over the Entire O ₂ Range: Characterization of a Conserved O ₂ -Independent Pathway

Ubiquinone Biosynthesis over the Entire O ₂ Range: Characterization of a Conserved O ₂ -Independent Pathway

The O₂-independent pathway of ubiquinone biosynthesis is essential for denitrification inPseudomonas aeruginosa

Ceragenins and antimicrobial peptides kill bacteria through distinct mechanisms

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A Soluble Metabolon Synthesizes the Isoprenoid Lipid Ubiquinone

Cited by 49 publications

References 68 publications

Ubiquinone Biosynthesis over the Entire O 2 Range: Characterization of a Conserved O 2 -Independent Pathway

Ubiquinone Biosynthesis over the Entire O 2 Range: Characterization of a Conserved O 2 -Independent Pathway

The O2-independent pathway of ubiquinone biosynthesis is essential for denitrification inPseudomonas aeruginosa

Ceragenins and antimicrobial peptides kill bacteria through distinct mechanisms

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Ubiquinone Biosynthesis over the Entire O ₂ Range: Characterization of a Conserved O ₂ -Independent Pathway

Ubiquinone Biosynthesis over the Entire O ₂ Range: Characterization of a Conserved O ₂ -Independent Pathway

The O₂-independent pathway of ubiquinone biosynthesis is essential for denitrification inPseudomonas aeruginosa