All three quinone species play distinct roles in ensuring optimal growth under aerobic and fermentative conditions in E. coli K12

Nitzschke, Annika; Bettenbrock, Katja

doi:10.1371/journal.pone.0194699

Cited by 33 publications

(28 citation statements)

References 63 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Here, we characterized three genes, ubiTPa (PA3911), ubiUPa (PA3913) and ubiVPa (PA3912) as essential for the anaerobic UQ9 biosynthesis in P. aeruginosa and dispensable for the aerobic one. These genes are homologs to the ubiT, ubiU and UbiV previously identified in E. coli, which grows normally in anaerobic conditions in a UQindependent manner because of the presence of naphthoquinones (9) (28) (29). In contrast, we demonstrated that these three genes were essential to anaerobic denitrification metabolism of P. aeruginosa, which is in agreement with the presence of a single quinone corresponding to UQ.…”

Section: Discussionsupporting

confidence: 82%

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

Michaud

Elsen

et al. 2020

Journal of Biological Chemistry

View full text Add to dashboard Cite

Many 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 in the reduction of dioxygen. However, this division of labor is probably not very strict. Indeed, a pathway that produces UQ under anaerobic conditions in an UbiU-, UbiV-, and UbiT-dependent manner has been discovered recently in E. coli. Its physiological relevance is not yet understood, because MK and DMK are also present in E. coli. Here, we established that UQ9 is the major quinone of Pseudomonas aeruginosa and is required for growth under anaerobic respiration (i.e. denitrification). We demonstrate that the ORFs PA3911, PA3912, and PA3913, which are homologs of the E. coli ubiT, ubiV, and ubiU genes, respectively, are essential for UQ9 biosynthesis and, thus, for denitrification in P. aeruginosa. These three genes here are called ubiTPa, ubiVPa, and ubiUPa. We show that UbiVPa accommodates an iron–sulfur [4Fe-4S] cluster. Moreover, we report that UbiUPa and UbiTPa can bind UQ and that the isoprenoid tail of UQ is the structural determinant required for recognition by these two Ubi proteins. Since the denitrification metabolism of P. aeruginosa is believed to be important for the pathogenicity of this bacterium in individuals with cystic fibrosis, our results highlight that the O2-independent UQ biosynthetic pathway may represent a target for antibiotics development to manage P. aeruginosa infections.

show abstract

Section: Discussionsupporting

confidence: 82%

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

Michaud

Elsen

et al. 2020

Journal of Biological Chemistry

View full text Add to dashboard Cite

show abstract

“…Quantification of transcript levels based on qRT-PCR was performed as described previously (Nitzschke and Bettenbrock, 2018). About 1.5 × 10 9 cells from exponential growth phase were quenched in twice the volume of RNAprotect Bacterial Reagent (Qiagen, Hilden, Germany), vortexed for 5 s and incubated at room temperature for 5 min.…”

Section: Methodsmentioning

confidence: 99%

Improvement of Acetaldehyde Production in Zymomonas mobilis by Engineering of Its Aerobic Metabolism

et al. 2019

Self Cite

View full text Add to dashboard Cite

Acetaldehyde is a valuable product of microbial biosynthesis, which can be used by the chemical industry as the entry point for production of various commodity chemicals. In ethanologenic microorganisms, like yeast or the bacterium Zymomonas mobilis, this compound is the immediate metabolic precursor of ethanol. In aerobic cultures of Z. mobilis, it accumulates as a volatile, inhibitory byproduct, due to the withdrawal of reducing equivalents from the alcohol dehydrogenase reaction by respiration. The active respiratory chain of Z. mobilis with its low energy-coupling efficiency is well-suited for regeneration of NAD+ under conditions when acetaldehyde, but not ethanol, is the desired catabolic product. In the present work, we sought to improve the capacity Z. mobilis to synthesize acetaldehyde, based on predictions of a stoichiometric model of its central metabolism developed herein. According to the model analysis, the main objectives in the course of engineering acetaldehyde producer strains were determined to be: (i) reducing ethanol synthesis via reducing the activity of alcohol dehydrogenase (ADH), and (ii) enhancing the respiratory capacity, either by overexpression of the respiratory NADH dehydrogenase (NDH), or by mutation of other components of respiratory metabolism. Several mutants with elevated respiration rate, decreased alcohol dehydrogenase activity, or a combination of both, were obtained. They were extensively characterized by determining their growth rates, product yields, oxygen consumption rates, ADH, and NDH activities, transcription levels of key catabolic genes, as well as concentrations of central metabolites under aerobic culture conditions. Two mutant strains were selected, with acetaldehyde yield close to 70% of the theoretical maximum value, almost twice the previously published yield for Z. mobilis. These strains can serve as a basis for further development of industrial acetaldehyde producers.

show abstract

“…(D)MK are considered anaerobic quinones, since they function primarily in anaerobic respiration, whereas UQ is considered an aerobic quinone, because it supplies electrons mostly to the reductases that reduce O 2 (1, 8, 9). Accordingly, UQ is the main quinone of the facultative anaerobe Escherichia coli under aerobic conditions, whereas the naphtoquinones are predominant in the absence of O 2 (10, 11), with UQ nevertheless being present.…”

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

View full text Add to dashboard Cite

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.

show abstract

All three quinone species play distinct roles in ensuring optimal growth under aerobic and fermentative conditions in E. coli K12

Cited by 33 publications

References 63 publications

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

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

Improvement of Acetaldehyde Production in Zymomonas mobilis by Engineering of Its Aerobic Metabolism

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

Contact Info

Product

Resources

About

All three quinone species play distinct roles in ensuring optimal growth under aerobic and fermentative conditions in E. coli K12

Cited by 33 publications

References 63 publications

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

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

Improvement of Acetaldehyde Production in Zymomonas mobilis by Engineering of Its Aerobic Metabolism

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

Contact Info

Product

Resources

About

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