Novel enzymology in futalosine-dependent menaquinone biosynthesis

doi:10.1016/j.cbpa.2018.09.015

Current Opinion in Chemical Biology

Volume 47, December 2018, Pages 134-141

https://doi.org/10.1016/j.cbpa.2018.09.015 Get rights and content

The recently discovered futalosine-dependent menaquinone biosynthesis pathway employs radical chemistry for the naphthoquinol core assembly. Mechanistic studies on this pathway have resulted in the discovery of novel reaction motifs. MqnA is the first example of a chorismate dehydratase. MqnE is the first example of a radical SAM enzyme that catalyzes the addition of the 5′-deoxyadenosyl radical to the substrate double bond rather than hydrogen atom abstraction. Both MqnE and MqnC reaction sequences involve radical additions to a benzene ring followed by formation of an aryl radical anion intermediate. The enzymology of the tailoring reactions after dihydroxynaphthoic acid formation remains to be elucidated. Since the futalosine-dependent menaquinone biosynthesis pathway is absent in humans, mechanistic studies on this pathway may promote the development of new antibiotics.

Introduction

Menaquinone 12 is a lipid-soluble cofactor that transfers electrons between membrane-bound redox enzymes in the electron transport chain of the respiratory and photosynthetic systems in microorganisms and plants [1]. In humans and other mammals, menaquinone is an essential vitamin (vitamin K) required for the remarkable γ-carboxylation of glutamic acid residues in proteins involved in blood clotting and bone formation (Figure 1a) [2, 3, 4]. Humans do not biosynthesize vitamin K and acquire it from food (vegetables and vegetable oils) and from its biosynthesis in the gut microbiome [5]. Vitamin K deficiency in humans leads to the synthesis of abnormal forms of coagulation factors resulting in prolonged clotting time and hemorrhaging [5].

Section snippets

Biosynthesis of menaquinone

In prokaryotes, there are two different pathways for the biosynthesis of the naphthoquinol core of menaquinone. The majority of bacteria produce menaquinone by the well-studied o-succinylbenzoate (OSB) pathway (the classical pathway, Figure 1b) [6^••,7]. An alternative pathway (the futalosine pathway, Figure 1c), was recently discovered in Streptomyces coelicolor [8^••,9,10]. This pathway is distributed only in prokaryotes and no microorganism has yet been found that uses both pathways [8^••].

Chorismate dehydratase (MqnA)

MqnA catalyzes the dehydration of chorismate 3, to give 13 (Figure 2a). [24^••] While base-catalyzed non-enzymatic dehydration of chorismate has been reported [31], MqnA is the first example of an enzyme-catalyzed dehydration of chorismate making it the latest addition to the family of chorismate utilizing enzymes [32]. Since the proton and hydroxyl of chorismate involved in the elimination are syn, an E2 elimination is not possible. The reaction therefore is likely to proceed via an E1 or an

The antibiotic potential of the menaquinone biosynthesis pathways

The classical pathway to menaquinone has been validated as a target for antibiotic development and antibiotic compounds targeting the enzymes of this pathway have been reported against Gram-positive organisms such as Mycobacterium tuberculosis, Staphylococcus aureus, and Plasmodium falciparum [59, 60, 61, 62, 63, 64, 65]. Human pathogens such as H. pylori (causes gastric ulcers and cancer), Campylobacter jejuni (causes diarrhea), Chlamydia strains (causes urethritis and respiratory tract

Summary and outlook

The classical and futalosine pathway of menaquinone biosynthesis employ distinctive biochemical strategies for the assembly of the naphthoquinone head group of menaquinone. At this time, we do not understand why microorganisms utilize one pathway over the other: both pathways proceed from readily available precursors and both can proceed under aerobic and anaerobic conditions. Mechanistic studies on the futalosine pathway have resulted in the discovery of two new reaction motifs: MqnA is the

Conflict of interest statement

Nothing declared.

References and recommended reading

Papers of particular interest, published within the period of review, have been highlighted as:

• of special interest
•• of outstanding interest

Acknowledgements

This research was supported by a grant from the National Science Foundation (CHE-1507191) and by the Robert A. Welch Foundation (A0034).

References (74)

B. Nowicka et al.
Occurrence, biosynthesis and function of isoprenoid quinones
Biochim Biophys Acta (BBA) - Bioenerg
(2010)
R. Meganathan
Menaquinone/ubiquinone biosynthesis and enzymology
T. Dairi et al.
Convergent strategies in biosynthesis
Nat Prod Rep
(2011)
X.-Y. Zhi et al.
The futalosine pathway played an important role in menaquinone biosynthesis during early prokaryote evolution
Genome Biol Evol
(2014)
T.B. Thompson et al.
evolution of enzymatic activity in the enolase superfamily: structure of o-Succinylbenzoate synthase from escherichia coli in complex with Mg2+ and o-Succinylbenzoate
Biochemistry
(2000)
A.M. Goble et al.
Deamination of 6-aminodeoxyfutalosine in menaquinone biosynthesis by distantly related enzymes
Biochemistry
(2013)
R.A. Rossi et al.
Nucleophilic substitution reactions by electron transfer
Chem Rev
(2003)
C.M. Seibert et al.
Structural and catalytic diversity within the amidohydrolase superfamily
Biochemistry
(2005)
I. Barr et al.
Demonstration that the radical S-adenosylmethionine (SAM) enzyme PqqE catalyzes de novo carbon-carbon cross-linking within a peptide substrate PqqA in the presence of the peptide chaperone PqqD
J Biol Chem
(2016)
M.R. Bauerle et al.
Mechanistic diversity of radical S-adenosylmethionine (SAM)-dependent methylation
J Biol Chem
(2015)

X. Li et al.

CoA Adducts of 4-Oxo-4-phenylbut-2-enoates: inhibitors of MenB from the M. tuberculosis menaquinone biosynthesis pathway

ACS Med Chem Lett

(2011)

S.-R. Choi et al.

Discovery of bicyclic inhibitors against menaquinone biosynthesis

Future Med Chem

(2016)

X. Lu et al.

Stable analogues of OSB-AMP: potent inhibitors of MenE, the o-Succinylbenzoate-CoA synthetase from bacterial menaquinone biosynthesis

ChemBioChem

(2012)

X. Li et al.

Synthesis and SAR studies of 1,4-benzoxazine MenB inhibitors: novel antibacterial agents against Mycobacterium tuberculosis

Bioorg Med Chem Lett

(2010)

G.B. Evans et al.

Immucillins in Infectious Diseases

ACS Infect Dis

(2018)

S. Wang et al.

A picomolar transition state analogue inhibitor of MTAN as a specific antibiotic for Helicobacter pylori

Biochemistry

(2012)

E.C.M. Cranenburg et al.

Vitamin K: the coagulation vitamin that became omnipotent

Thromb Haemost

(2007)

S.M. Plaza et al.

Vitamin K2 in bone metabolism and osteoporosis

Altern Med Rev

(2005)

P. Dowd et al.

Vitamin K and energy transduction: a base strength amplification mechanism

Science

(1995)

J.W. Suttie

The importance of menaquinones in human nutrition

Annu Rev Nutr

(1995)

R. Meganathan et al.

Biosynthesis of menaquinone (vitamin K2) and ubiquinone (coenzyme Q)

EcoSal Plus

(2014)

T. Hiratsuka et al.

An alternative menaquinone biosynthetic pathway operating in microorganisms

Science

(2008)

H. Seto et al.

Studies on a new biosynthetic pathway for menaquinone

J Am Chem Soc

(2008)

T. Dairi

Menaquinone biosyntheses in microorganisms

Methods Enzymol

(2012)

T.P. Begley et al.

Cofactor biosynthesis—still yielding fascinating new biological chemistry

Curr Opin Chem Biol

(2008)

S. Kolappan et al.

Lysine 190 is the catalytic base in MenF, the menaquinone-specific isochorismate synthase from Escherichia coli: implications for an enzyme family

Biochemistry

(2007)

E.N. Jirgis et al.

Structural views along the Mycobacterium tuberculosis MenD reaction pathway illuminate key aspects of thiamin diphosphate-dependent enzyme mechanisms

Structure

(2016)

M. Jiang et al.

Catalytic mechanism of SHCHC synthase in the menaquinone biosynthesis of Escherichia coli: identification and mutational analysis of the active site residues

Biochemistry

(2009)

V. Klenchin et al.

Evolution of enzymatic activity in the enolase superfamily: structural and mutagenic studies of the mechanism of the reaction catalyzed by o-Succinylbenzoate synthase from Escherichia coli

Biochemistry

(2003)

Y. Chen et al.

Mechanistic insights from the crystal structure of Bacillus subtilis o-succinylbenzoyl-CoA synthetase complexed with the adenylate intermediate

Biochemistry

(2016)

H.-J. Li et al.

Mechanism of the intramolecular Claisen condensation reaction catalyzed by MenB, a crotonase superfamily member

Biochemistry

(2011)

J.R. Widhalm et al.

A dedicated thioesterase of the Hotdog-fold family is required for the biosynthesis of the naphthoquinone ring of vitamin K1

Proc Natl Acad Sci U S A

(2009)

R. Bentley et al.

Biosynthesis of vitamin K (menaquinone) in bacteria

Microbiol Rev

(1982)

R. Meganathan

Biosynthesis of menaquinone (vitamin K2) and ubiquinone (coenzyme Q): A perspective on enzymatic mechanisms

Vitam Horm

(2001)

N. Mahanta et al.

Menaquinone biosynthesis: formation of aminofutalosine requires a unique radical SAM enzyme

J Am Chem Soc

(2013)

C. Arakawa et al.

Diversity of the early step of the futalosine pathway

Antimicrob Agents Chemother

(2011)

L.E. Cooper et al.

In vitro reconstitution of the radical S-adenosylmethionine enzyme MqnC involved in the biosynthesis of futalosine-derived menaquinone

Biochemistry

(2013)

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Review: Bacterially produced vitamin K2 and its potential to generate health benefits in humans
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Several bacterial species associated with the human gut and with fermented foods produce menaquinones (MK-n; vitamin K2) as part of their energy metabolism. Given that MK-n offer multiple health benefits to humans, research into this topic is of increasing interest.
To outline the current understanding of bacterial MK-n production and how it relates to the gut microbiota, food fermentation, the production of dietary supplements, and health.
In bacteria, MK-n display various functions in addition to their chief role in energy production, including a role in defense mechanisms, the sensing of environmental changes, the reduction of metals, sporulation, and pathogenicity. In humans, they are relevant for health beyond the effects of phylloquinones (vitamin K1), which are primarily related to blood coagulation, as they seem to be more effective extrahepatically, impacting on cardiovascular and bone health and protecting against non-communicable diseases. While the contribution of gut microbiota to the human vitamin K budget remains unclear, more is known about fermented foods. Some fermented foods from either plant (e.g., sauerkraut and natto) or animal origin (e.g., cheese) are valuable sources of MK-n, even compared to non-fermented animal source foods, which only contain limited amounts of one specific form (MK-4). Bacillus subtilis, commonly used in the production of natto, is the most employed microorganism at industrial level for the production of dietary MK-7 supplements, a process which can be optimized by selecting the appropriate fermentation parameters.
The origins of photosynthetic systems: Clues from the phosphorus and sulphur chemical scenarios
2023, BioSystems
Photosynthesis is the predominant biochemical process of carbon dioxide assimilation in the biosphere. To reduce carbon dioxide into organic compounds, photosynthetic organisms have one or two distinct photochemical reaction centre complexes with which they capture solar energy and generate ATP and reducing power. The core polypeptides of the photosynthetic reaction centres show low homologies but share overlapping structural folds, overall architecture, similar functional properties and highly conserved positions in protein sequences suggesting a common ancestry. However, the other biochemical components of photosynthetic apparatus appear to be a mosaic resulting from different evolutionary trajectories. The current proposal focusses on the nature and biosynthetic pathways of some organic redox cofactors that participate in the photosynthetic systems: quinones, chlorophyll and heme rings and their attached isoprenoid side chains, as well as on the coupled proton motive forces and associated carbon fixation pathways. This perspective highlights clues about the involvement of the phosphorus and sulphur chemistries that would have shaped the different types of photosynthetic systems.
Biosynthesis and function of microbial methylmenaquinones
2023, Advances in Microbial Physiology
The membranous quinone/quinol pool is essential for the majority of life forms and its composition has been widely used as a biomarker in microbial taxonomy. The most abundant quinone is menaquinone (MK), which serves as an essential redox mediator in various electron transport chains of aerobic and anaerobic respiration. Several methylated derivatives of MK, designated methylmenaquinones (MMKs), have been reported to be present in members of various microbial phyla possessing either the classical MK biosynthesis pathway (Men) or the futalosine pathway (Mqn). Due to their low redox midpoint potentials, MMKs have been proposed to be specifically involved in appropriate electron transport chains of anaerobic respiration. The class C radical SAM methyltransferases MqnK, MenK and MenK2 have recently been shown to catalyse specific MK methylation reactions at position C-8 (MqnK/MenK) or C-7 (MenK2) to synthesise 8-MMK, 7-MMK and 7,8-dimethylmenaquinone (DMMK). MqnK, MenK and MenK2 from organisms such as Wolinella succinogenes, Adlercreutzia equolifaciens, Collinsella tanakaei, Ferrimonas marina and Syntrophus aciditrophicus have been functionally produced in Escherichia coli, enabling extensive quinone/quinol pool engineering of the native MK and 2-demethylmenaquinone (DMK). Cluster and phylogenetic analyses of available MK and MMK methyltransferase sequences revealed signature motifs that allowed the discrimination of MenK/MqnK/MenK2 family enzymes from other radical SAM enzymes and the identification of C-7-specific menaquinone methyltransferases of the MenK2 subfamily. It is envisaged that this knowledge will help to predict the methylation status of the menaquinone/menaquinol pool of any microbial species (or even a microbial community) from its (meta)genome.
Mechanism of chorismate dehydratase MqnA, the first enzyme of the futalosine pathway, proceeds via substrate-assisted catalysis
2022, Journal of Biological Chemistry
MqnA, the only chorismate dehydratase known so far, catalyzes the initial step in the biosynthesis of menaquinone via the futalosine pathway. Details of the MqnA reaction mechanism remain unclear. Here, we present crystal structures of Streptomyces coelicolor MqnA and its active site mutants in complex with chorismate and the product 3-enolpyruvyl-benzoate, produced during heterologous expression in Escherichia coli. Together with activity studies, our data are in line with dehydration proceeding via substrate assisted catalysis, with the enol pyruvyl group of chorismate acting as catalytic base. Surprisingly, structures of the mutant Asn17Asp with copurified ligand suggest that the enzyme converts to a hydrolase by serendipitous positioning of the carboxyl group. All complex structures presented here exhibit a closed Venus flytrap fold, with the enzyme exploiting the characteristic ligand binding properties of the fold for specific substrate binding and catalysis. The conformational rearrangements that facilitate complete burial of substrate/product, with accompanying topological changes to the enzyme surface, could foster substrate channeling within the biosynthetic pathway.
Quinones: more than electron shuttles
2022, Research in Microbiology
Citation Excerpt :
The number of isoprenoid units and modifications in the isoprenyl tail vary among species, and depending on whether the redox moiety undergoes reduction or oxidation, the molecule becomes either a quinol or quinone, respectively. The extensive degree of structural variation in bacterial isoprenoid quinones and elucidation of their complex biosynthetic pathways have been the focus of numerous studies and multiple recent reviews [2–7]. In this review, we will focus on the two main structural groups of isoprenoid quinones found in bacteria: benzoquinones and naphthoquinones.
Bacterial quinones are lipophilic redox compounds involved in important cellular roles such as electron transport in respiratory and photosynthetic chains. However, a growing body of research has now revealed that quinones have additional functions in bacterial physiology, with significant consequences for colonization and persistence in different ecological niches. The aim of this review is to provide an updated view of the functions of bacterial quinones, with particular emphasis on their importance for bacterial metabolism, gene regulation, and stress resistance. We provide evidence that quinones have also a deep impact on the composition and function of bacterial ecosystems.
Bacterial terpenome
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Terpenoids, also called isoprenoids, are the largest and most structurally diverse family of natural products. Found in all domains of life, there are over 80 000 known compounds. The majority of characterized terpenoids, which include some of the most well known, pharmaceutically relevant, and commercially valuable natural products, are produced by plants and fungi. Comparatively, terpenoids of bacterial origin are rare. This is counter-intuitive to the fact that recent microbial genomics revealed that almost all bacteria have the biosynthetic potential to create the C₅ building blocks necessary for terpenoid biosynthesis. In this review, we catalogue terpenoids produced by bacteria. We collected 1062 natural products, consisting of both primary and secondary metabolites, and classified them into two major families and 55 distinct subfamilies. To highlight the structural and chemical space of bacterial terpenoids, we discuss their structures, biosynthesis, and biological activities. Although the bacterial terpenome is relatively small, it presents a fascinating dichotomy for future research. Similarities between bacterial and non-bacterial terpenoids and their biosynthetic pathways provides alternative model systems for detailed characterization while the abundance of novel skeletons, biosynthetic pathways, and bioactivies presents new opportunities for drug discovery, genome mining, and enzymology.

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View full text

Novel enzymology in futalosine-dependent menaquinone biosynthesis

Introduction

Section snippets

Biosynthesis of menaquinone

Chorismate dehydratase (MqnA)

The antibiotic potential of the menaquinone biosynthesis pathways

Summary and outlook

Conflict of interest statement

References and recommended reading

Acknowledgements

Biochim Biophys Acta (BBA) - Bioenerg

Nat Prod Rep

Genome Biol Evol

Biochemistry

Biochemistry

Chem Rev

Biochemistry

J Biol Chem

J Biol Chem

ACS Med Chem Lett

Future Med Chem

ChemBioChem

Bioorg Med Chem Lett

ACS Infect Dis

Biochemistry

Vitamin K: the coagulation vitamin that became omnipotent

Thromb Haemost

Vitamin K2 in bone metabolism and osteoporosis

Altern Med Rev

Vitamin K and energy transduction: a base strength amplification mechanism

Science

The importance of menaquinones in human nutrition

Annu Rev Nutr

Biosynthesis of menaquinone (vitamin K2) and ubiquinone (coenzyme Q)

EcoSal Plus

An alternative menaquinone biosynthetic pathway operating in microorganisms

Science

Studies on a new biosynthetic pathway for menaquinone

J Am Chem Soc

Menaquinone biosyntheses in microorganisms

Methods Enzymol

Cofactor biosynthesis—still yielding fascinating new biological chemistry

Curr Opin Chem Biol

Lysine 190 is the catalytic base in MenF, the menaquinone-specific isochorismate synthase from Escherichia coli: implications for an enzyme family

Biochemistry

Structural views along the Mycobacterium tuberculosis MenD reaction pathway illuminate key aspects of thiamin diphosphate-dependent enzyme mechanisms

Structure

Catalytic mechanism of SHCHC synthase in the menaquinone biosynthesis of Escherichia coli: identification and mutational analysis of the active site residues

Biochemistry

Evolution of enzymatic activity in the enolase superfamily: structural and mutagenic studies of the mechanism of the reaction catalyzed by o-Succinylbenzoate synthase from Escherichia coli

Biochemistry

Mechanistic insights from the crystal structure of Bacillus subtilis o-succinylbenzoyl-CoA synthetase complexed with the adenylate intermediate

Biochemistry

Mechanism of the intramolecular Claisen condensation reaction catalyzed by MenB, a crotonase superfamily member

Biochemistry

A dedicated thioesterase of the Hotdog-fold family is required for the biosynthesis of the naphthoquinone ring of vitamin K1

Proc Natl Acad Sci U S A

Biosynthesis of vitamin K (menaquinone) in bacteria

Microbiol Rev

Biosynthesis of menaquinone (vitamin K2) and ubiquinone (coenzyme Q): A perspective on enzymatic mechanisms

Vitam Horm

Menaquinone biosynthesis: formation of aminofutalosine requires a unique radical SAM enzyme

J Am Chem Soc

Diversity of the early step of the futalosine pathway

Antimicrob Agents Chemother

In vitro reconstitution of the radical S-adenosylmethionine enzyme MqnC involved in the biosynthesis of futalosine-derived menaquinone

Biochemistry