1
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Wörner J, Panter S, Illarionov B, Bacher A, Fischer M, Weber S. Expanding Reaction Horizons: Evidence of the 5-Deazaflavin Radical Through Photochemically Induced Dynamic Nuclear Polarization. Angew Chem Int Ed Engl 2023; 62:e202309334. [PMID: 37571931 DOI: 10.1002/anie.202309334] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 08/09/2023] [Accepted: 08/10/2023] [Indexed: 08/13/2023]
Abstract
Deazaflavins are important analogues of the naturally occurring flavins: riboflavin, flavin mononucleotide (FMN), and flavin adenine dinucleotide (FAD). The use of 5-deazaflavin as a replacement coenzyme in a number of flavoproteins has proven particularly valuable in unraveling and manipulating their reaction mechanisms. It was frequently reported that one-electron-transfer reactions in flavoproteins are impeded with 5-deazaflavin as the cofactor. Based on these findings, it was concluded that the 5-deazaflavin radical is significantly less stable compared to the respective flavin semiquinone and quickly re-oxidizes or undergoes disproportionation. The long-standing paradigm of 5-deazaflavin being solely a two-electron/hydride acceptor/donor-"a nicotinamide in flavin clothing"-needs to be re-evaluated now with the indirect observation of a one-electron-reduced (paramagnetic) species using photochemically induced dynamic nuclear polarization (photo-CIDNP) 1 H nuclear magnetic resonance (NMR) under biologically relevant conditions.
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Affiliation(s)
- Jakob Wörner
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstraße 21, 79104, Freiburg, Germany
| | - Sabrina Panter
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstraße 21, 79104, Freiburg, Germany
| | - Boris Illarionov
- Institut für Lebensmittelchemie, Universität Hamburg, Grindelallee 117, 20146, Hamburg, Germany
| | - Adelbert Bacher
- TUM School of Natural Sciences, Technische Universität München, Lichtenbergstraße 4, 85747, Garching, Germany
| | - Markus Fischer
- Institut für Lebensmittelchemie, Universität Hamburg, Grindelallee 117, 20146, Hamburg, Germany
| | - Stefan Weber
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstraße 21, 79104, Freiburg, Germany
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2
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Waller NJE, Cheung CY, Cook GM, McNeil MB. The evolution of antibiotic resistance is associated with collateral drug phenotypes in Mycobacterium tuberculosis. Nat Commun 2023; 14:1517. [PMID: 36934122 PMCID: PMC10024696 DOI: 10.1038/s41467-023-37184-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 03/06/2023] [Indexed: 03/20/2023] Open
Abstract
The increasing incidence of drug resistance in Mycobacterium tuberculosis has diminished the efficacy of almost all available antibiotics, complicating efforts to combat the spread of this global health burden. Alongside the development of new drugs, optimised drug combinations are needed to improve treatment success and prevent the further spread of antibiotic resistance. Typically, antibiotic resistance leads to reduced sensitivity, yet in some cases the evolution of drug resistance can lead to enhanced sensitivity to unrelated drugs. This phenomenon of collateral sensitivity is largely unexplored in M. tuberculosis but has the potential to identify alternative therapeutic strategies to combat drug-resistant strains that are unresponsive to current treatments. Here, by using drug susceptibility profiling, genomics and evolutionary studies we provide evidence for the existence of collateral drug sensitivities in an isogenic collection M. tuberculosis drug-resistant strains. Furthermore, in proof-of-concept studies, we demonstrate how collateral drug phenotypes can be exploited to select against and prevent the emergence of drug-resistant strains. This study highlights that the evolution of drug resistance in M. tuberculosis leads to collateral drug responses that can be exploited to design improved drug regimens.
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Affiliation(s)
- Natalie J E Waller
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand
| | - Chen-Yi Cheung
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Gregory M Cook
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand
| | - Matthew B McNeil
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand.
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand.
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3
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Kang SW, Antoney J, Frkic RL, Lupton DW, Speight R, Scott C, Jackson CJ. Asymmetric Ene-Reduction of α,β-Unsaturated Compounds by F 420-Dependent Oxidoreductases A Enzymes from Mycobacterium smegmatis. Biochemistry 2023; 62:873-891. [PMID: 36637210 DOI: 10.1021/acs.biochem.2c00557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Abstract
The stereoselective reduction of alkenes conjugated to electron-withdrawing groups by ene-reductases has been extensively applied to the commercial preparation of fine chemicals. Although several different enzyme families are known to possess ene-reductase activity, the old yellow enzyme (OYE) family has been the most thoroughly investigated. Recently, it was shown that a subset of ene-reductases belonging to the flavin/deazaflavin oxidoreductase (FDOR) superfamily exhibit enantioselectivity that is generally complementary to that seen in the OYE family. These enzymes belong to one of several FDOR subgroups that use the unusual deazaflavin cofactor F420. Here, we explore several enzymes of the FDOR-A subgroup, characterizing their substrate range and enantioselectivity with 20 different compounds, identifying enzymes (MSMEG_2027 and MSMEG_2850) that could reduce a wide range of compounds stereoselectively. For example, MSMEG_2027 catalyzed the complete conversion of both isomers of citral to (R)-citronellal with 99% ee, while MSMEG_2850 catalyzed complete conversion of ketoisophorone to (S)-levodione with 99% ee. Protein crystallography combined with computational docking has allowed the observed stereoselectivity to be mechanistically rationalized for two enzymes. These findings add further support for the FDOR and OYE families of ene-reductases displaying general stereocomplementarity to each other and highlight their potential value in asymmetric ene-reduction.
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Affiliation(s)
- Suk Woo Kang
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory2601, Australia.,Natural Products Research Center, Korea Institute of Science and Technology (KIST), Gangneung25451, Republic of Korea
| | - James Antoney
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory2601, Australia.,School of Biology and Environmental Sciences, Queensland University of Technology, Brisbane, Queensland4000, Australia.,ARC Centre of Excellence in Synthetic Biology, Queensland University of Technology, Brisbane, Queensland4000, Australia
| | - Rebecca L Frkic
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory2601, Australia.,ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory2601, Australia
| | - David W Lupton
- School of Chemistry, Monash University, Melbourne, Victoria3800, Australia
| | - Robert Speight
- School of Biology and Environmental Sciences, Queensland University of Technology, Brisbane, Queensland4000, Australia.,ARC Centre of Excellence in Synthetic Biology, Queensland University of Technology, Brisbane, Queensland4000, Australia
| | - Colin Scott
- Land and Water, Commonwealth Scientific and Industrial Research Organisation, Clayton, Victoria3168, Australia.,CSIRO Synthetic Biology Future Science Platform, GPO Box 1700, Canberra, Australian Capital Territory2601, Australia
| | - Colin J Jackson
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory2601, Australia.,ARC Centre of Excellence in Synthetic Biology, Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory2601, Australia.,ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory2601, Australia
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4
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Kang SW, Antoney J, Lupton DW, Speight R, Scott C, Jackson CJ. Asymmetric Ene-Reduction by F 420 -Dependent Oxidoreductases B (FDOR-B) from Mycobacterium smegmatis. Chembiochem 2023; 24:e202200797. [PMID: 36716144 DOI: 10.1002/cbic.202200797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/29/2023] [Accepted: 01/30/2023] [Indexed: 01/31/2023]
Abstract
Asymmetric reduction by ene-reductases has received considerable attention in recent decades. While several enzyme families possess ene-reductase activity, the Old Yellow Enzyme (OYE) family has received the most scientific and industrial attention. However, there is a limited substrate range and few stereocomplementary pairs of current ene-reductases, necessitating the development of a complementary class. Flavin/deazaflavin oxidoreductases (FDORs) that use the uncommon cofactor F420 have recently gained attention as ene-reductases for use in biocatalysis due to their stereocomplementarity with OYEs. Although the enzymes of the FDOR-As sub-group have been characterized in this context and reported to catalyse ene-reductions enantioselectively, enzymes from the similarly large, but more diverse, FDOR-B sub-group have not been investigated in this context. In this study, we investigated the activity of eight FDOR-B enzymes distributed across this sub-group, evaluating their specific activity, kinetic properties, and stereoselectivity against α,β-unsaturated compounds. The stereochemical outcomes of the FDOR-Bs are compared with enzymes of the FDOR-A sub-group and OYE family. Computational modelling and induced-fit docking are used to rationalize the observed catalytic behaviour and proposed a catalytic mechanism.
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Affiliation(s)
- Suk Woo Kang
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia.,Natural Products Research Center, Korea Institute of Science and Technology (KIST), Gangneung, 25451 (Republic of, Korea
| | - James Antoney
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia.,School of Biology and Environmental Sciences, Queensland University of Technology, Brisbane, QLD 4000, Australia.,ARC Centre of Excellence in Synthetic Biology, Queensland University of Technology, Brisbane, Queensland, 4000, Australia
| | - David W Lupton
- School of Chemistry, Monash University, Melbourne, Victoria, 3800, Australia
| | - Robert Speight
- School of Biology and Environmental Sciences, Queensland University of Technology, Brisbane, QLD 4000, Australia.,ARC Centre of Excellence in Synthetic Biology, Queensland University of Technology, Brisbane, Queensland, 4000, Australia
| | - Colin Scott
- Environment, Commonwealth Scientific and Industrial Research Organization, GPO Box 1700, Canberra, ACT 2601, Australia
| | - Colin J Jackson
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia.,ARC Centre of Excellence in Synthetic Biology, Australian National University, Canberra, ACT 2601, Australia.,ARC Centre of Excellence for Innovations in Peptide and Protein Science, Australian National University, Canberra, ACT 2601, Australia
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5
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Abstract
The genus Mycobacterium contains several slow-growing human pathogens, including Mycobacterium tuberculosis, Mycobacterium leprae, and Mycobacterium avium. Mycobacterium smegmatis is a nonpathogenic and fast growing species within this genus. In 1990, a mutant of M. smegmatis, designated mc2155, that could be transformed with episomal plasmids was isolated, elevating M. smegmatis to model status as the ideal surrogate for mycobacterial research. Classical bacterial models, such as Escherichia coli, were inadequate for mycobacteria research because they have low genetic conservation, different physiology, and lack the novel envelope structure that distinguishes the Mycobacterium genus. By contrast, M. smegmatis encodes thousands of conserved mycobacterial gene orthologs and has the same cell architecture and physiology. Dissection and characterization of conserved genes, structures, and processes in genetically tractable M. smegmatis mc2155 have since provided previously unattainable insights on these same features in its slow-growing relatives. Notably, tuberculosis (TB) drugs, including the first-line drugs isoniazid and ethambutol, are active against M. smegmatis, but not against E. coli, allowing the identification of their physiological targets. Furthermore, Bedaquiline, the first new TB drug in 40 years, was discovered through an M. smegmatis screen. M. smegmatis has become a model bacterium, not only for M. tuberculosis, but for all other Mycobacterium species and related genera. With a repertoire of bioinformatic and physical resources, including the recently established Mycobacterial Systems Resource, M. smegmatis will continue to accelerate mycobacterial research and advance the field of microbiology.
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6
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Wunderer M, Markt R, Lackner N, Wagner AO. The glutamyl tail length of the cofactor F 420 in the methanogenic Archaea Methanosarcina thermophila and Methanoculleus thermophilus. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 809:151112. [PMID: 34688753 DOI: 10.1016/j.scitotenv.2021.151112] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 10/01/2021] [Accepted: 10/17/2021] [Indexed: 06/13/2023]
Abstract
The cofactor F420 is synthesized by many different organisms and as a redox cofactor, it plays a crucial role in the redox reactions of catabolic and biosynthetic metabolic pathways. It consists of a deazaflavin structure, which is linked via lactate to an oligoglutamate chain, that can vary in length. In the present study, the methanogenic Archaea Methanosarcina thermophila and Methanoculleus thermophilus were cultivated on different carbon sources and their coenzyme F420 composition has been assayed by reversed-phase ion-pair high-performance liquid chromatography with fluorometric detection regarding both, overall cofactor F420 production and distribution of F420 glutamyl tail length. In Methanosarcina thermophila cultivated on methanol, acetate, and a mixture of acetate and methanol, the most abundant cofactors were F420-5 and F420-4, whereby the last digit refers to the number of expressed glutamyl rests. By contrast, in the obligate CO2 reducing Methanoculleus thermophilus the most abundant cofactors were F420-3 and F420-4. In Methanosarcina thermophila, the relative proportions of the expressed F420 tail length changed during batch growth on all three carbon sources. Over time F420-3 and F420-4 decreased while F420-5 and F420-6 increased in their relative proportion in comparison to total F420 content. In contrast, in Methanoculleus thermophilus the relative abundance of the different F420 cofactors remained stable. It was also possible to differentiate the two methanogenic Archaea based on the glutamyl tail length of the cofactor F420. The cofactor F420-5 in concentrations >2% could only be assigned to Methanosarcina thermophila. In all four variants a trend for a positive correlation between the DNA concentration and the total concentration of the cofactor could be shown. Except for the variant Methanosarcinathermophila with acetate as sole carbon source the same could be shown between the concentration of the mcrA gene copy number and the total concentration of the cofactor.
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Affiliation(s)
- Mathias Wunderer
- Universität Innsbruck, Department of Microbiology, Technikerstraße 25d, 6020 Innsbruck, Austria.
| | - Rudolf Markt
- Universität Innsbruck, Department of Microbiology, Technikerstraße 25d, 6020 Innsbruck, Austria
| | - Nina Lackner
- Universität Innsbruck, Department of Microbiology, Technikerstraße 25d, 6020 Innsbruck, Austria
| | - Andreas O Wagner
- Universität Innsbruck, Department of Microbiology, Technikerstraße 25d, 6020 Innsbruck, Austria
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7
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Grinter R, Greening C. Cofactor F420: an expanded view of its distribution, biosynthesis and roles in bacteria and archaea. FEMS Microbiol Rev 2021; 45:fuab021. [PMID: 33851978 PMCID: PMC8498797 DOI: 10.1093/femsre/fuab021] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 04/11/2021] [Indexed: 12/11/2022] Open
Abstract
Many bacteria and archaea produce the redox cofactor F420. F420 is structurally similar to the cofactors FAD and FMN but is catalytically more similar to NAD and NADP. These properties allow F420 to catalyze challenging redox reactions, including key steps in methanogenesis, antibiotic biosynthesis and xenobiotic biodegradation. In the last 5 years, there has been much progress in understanding its distribution, biosynthesis, role and applications. Whereas F420 was previously thought to be confined to Actinobacteria and Euryarchaeota, new evidence indicates it is synthesized across the bacterial and archaeal domains, as a result of extensive horizontal and vertical biosynthetic gene transfer. F420 was thought to be synthesized through one biosynthetic pathway; however, recent advances have revealed variants of this pathway and have resolved their key biosynthetic steps. In parallel, new F420-dependent biosynthetic and metabolic processes have been discovered. These advances have enabled the heterologous production of F420 and identified enantioselective F420H2-dependent reductases for biocatalysis. New research has also helped resolve how microorganisms use F420 to influence human and environmental health, providing opportunities for tuberculosis treatment and methane mitigation. A total of 50 years since its discovery, multiple paradigms associated with F420 have shifted, and new F420-dependent organisms and processes continue to be discovered.
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Affiliation(s)
- Rhys Grinter
- Department of Microbiology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Chris Greening
- Department of Microbiology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
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8
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Zhao L, Wang XT, Chen KY, Wang ZH, Xu XJ, Zhou X, Xing DF, Ren NQ, Lee DJ, Chen C. The underlying mechanism of enhanced methane production using microbial electrolysis cell assisted anaerobic digestion (MEC-AD) of proteins. WATER RESEARCH 2021; 201:117325. [PMID: 34144484 DOI: 10.1016/j.watres.2021.117325] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 05/10/2021] [Accepted: 05/30/2021] [Indexed: 06/12/2023]
Abstract
Anaerobic digestion (AD) is a promising technology capable of converting waste matter into bio-energy. Recent studies have reported that microbial electrolysis cell assisted anaerobic digestion (MEC-AD) is an effective system for methane production from organic waste, via enhanced electron transfer. However, little is known about the effects of applied voltage on the AD of proteins. Herein, the mechanism of MEC-AD on protein digestion was investigated using varying concentrations of bovine serum albumin (BSA) as the protein substrate (500 mg/L, 4 g/L, and 20 g/L BSA). Experimental results showed that the applied voltage can not only enhance the methane production rate from 23.8% to 45.6% at low and medium organic loading (BSA concentration of 500 mg/L and 4 g/L), but also improve the methanogenesis efficiency increased by 225.4% at high BSA concentration (20 g/L) with the applied voltage of 0.6 V compared to that with open circuit. Mechanism explorations revealed that the applied voltage significantly enhanced the acidogenesis and methanogenesis processes in the AD of proteins. Microbial community characterization showed that with the applied voltage, the abundance of fermentative bacteria increased by 46.7 % at the anode, while, the abundance of Methanobacterium at the cathode increased from 10.4 to 84.3%, indicating the methanogenesis pathway transformed from acetoclastic to hydrogenotrophic. External circuit electron transfer calculations demonstrated that only 10% of the produced methane could be attributed to direct interspecies electron transfer (DIET). From a thermodynamic perspective, the applied external voltage led to a reduction in the cathodic potential to -0.9 V, which is beneficial for enhanced methane production via mediated interspecies electron transfer (MIET) by enrichment of hydrogenotrophic methanogens. The findings reported here reveal the previously unrecognized contribution of proteins to MEC-AD, while also furthering our understanding of the role of applied voltage in the MEC-AD process.
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Affiliation(s)
- Lei Zhao
- State Key Laboratory of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Xue-Ting Wang
- State Key Laboratory of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Ke-Yang Chen
- State Key Laboratory of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Zi-Han Wang
- State Key Laboratory of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Xi-Jun Xu
- State Key Laboratory of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Xu Zhou
- Engineering Laboratory of Microalgal Bioenergy, Shenzhen Graduate School, Harbin Institute of Technology, Shenzhen 518055, China
| | - De-Feng Xing
- State Key Laboratory of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Nan-Qi Ren
- State Key Laboratory of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Duu-Jong Lee
- Department of Chemical Engineering, National Taiwan University, Taipei 106, Taiwan
| | - Chuan Chen
- State Key Laboratory of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, China.
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Potency boost of a Mycobacterium tuberculosis dihydrofolate reductase inhibitor by multienzyme F 420H 2-dependent reduction. Proc Natl Acad Sci U S A 2021; 118:2025172118. [PMID: 34161270 PMCID: PMC8237569 DOI: 10.1073/pnas.2025172118] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bacterial metabolism can cause intrinsic drug resistance but can also convert inactive parent drugs into bioactive derivatives, as is the case for several antimycobacterial prodrugs. Here, we show that the intrabacterial metabolism of a Mtb dihydrofolate reductase (DHFR) inhibitor with moderate affinity for its target boosts its on-target activity by two orders of magnitude. This is a “prodrug-like” antimycobacterial that possesses baseline activity in the absence of intracellular bioactivation. By elucidating the metabolic enhancement mechanism, we have provided the basis for the rational optimization of a class of DHFR inhibitors and uncovered an antibacterial drug discovery concept. Triaza-coumarin (TA-C) is a Mycobacterium tuberculosis (Mtb) dihydrofolate reductase (DHFR) inhibitor with an IC50 (half maximal inhibitory concentration) of ∼1 µM against the enzyme. Despite this moderate target inhibition, TA-C shows exquisite antimycobacterial activity (MIC50, concentration inhibiting growth by 50% = 10 to 20 nM). Here, we investigated the mechanism underlying this potency disconnect. To confirm that TA-C targets DHFR and investigate its unusual potency pattern, we focused on resistance mechanisms. In Mtb, resistance to DHFR inhibitors is frequently associated with mutations in thymidylate synthase thyA, which sensitizes Mtb to DHFR inhibition, rather than in DHFR itself. We observed thyA mutations, consistent with TA-C interfering with the folate pathway. A second resistance mechanism involved biosynthesis of the redox coenzyme F420. Thus, we hypothesized that TA-C may be metabolized by Mtb F420–dependent oxidoreductases (FDORs). By chemically blocking the putative site of FDOR-mediated reduction in TA-C, we reproduced the F420-dependent resistance phenotype, suggesting that F420H2-dependent reduction is required for TA-C to exert its potent antibacterial activity. Indeed, chemically synthesized TA-C-Acid, the putative product of TA-C reduction, displayed a 100-fold lower IC50 against DHFR. Screening seven recombinant Mtb FDORs revealed that at least two of these enzymes reduce TA-C. This redundancy in activation explains why no mutations in the activating enzymes were identified in the resistance screen. Analysis of the reaction products confirmed that FDORs reduce TA-C at the predicted site, yielding TA-C-Acid. This work demonstrates that intrabacterial metabolism converts TA-C, a moderately active “prodrug,” into a 100-fold-more-potent DHFR inhibitor, thus explaining the disconnect between enzymatic and whole-cell activity.
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10
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Veyron-Churlet R, Saliou JM, Locht C. Interconnection of the mycobacterial heparin-binding hemagglutinin with cholesterol degradation and heme/iron pathways identified by proximity-dependent biotin identification in Mycobacterium smegmatis. Environ Microbiol 2021; 23:3212-3224. [PMID: 33913567 DOI: 10.1111/1462-2920.15547] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 04/15/2021] [Accepted: 04/26/2021] [Indexed: 11/28/2022]
Abstract
Deciphering protein-protein interactions is a critical step in the identification and the understanding of biological mechanisms deployed by pathogenic bacteria. The development of in vivo technologies to characterize these interactions is still in its infancy, especially for bacteria whose subcellular organization is particularly complex, such as mycobacteria. In this work, we used the proximity-dependent biotin identification (BioID) to define the mycobacterial heparin-binding hemagglutinin (HbhA) interactome in the saprophytic bacterium Mycobacterium smegmatis. M. smegmatis is a commonly used model to study and characterize the physiology of pathogenic mycobacteria, such as Mycobacterium tuberculosis. Here, we adapted the BioID technology to in vivo protein-protein interactions studies in M. smegmatis, which presents several advantages, such as maintaining the complex organization of the mycomembrane, offering the possibility to study membrane or cell wall-associated proteins, including HbhA, in the presence of cofactors and post-translational modifications, such as the complex methylation pattern of HbhA. Using this technology, we found that HbhA is interconnected with cholesterol degradation and heme/iron pathways. These results are in line with previous studies showing the dual localization of HbhA, associated with the cell wall and intracytoplasmic lipid inclusions, and its induction under high iron growth conditions.
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Affiliation(s)
- Romain Veyron-Churlet
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, Lille, F-59000, France
| | - Jean-Michel Saliou
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UMS 2014 - PLBS, Lille, F-59000, France
| | - Camille Locht
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, Lille, F-59000, France
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11
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Mutations in fbiD ( Rv2983) as a Novel Determinant of Resistance to Pretomanid and Delamanid in Mycobacterium tuberculosis. Antimicrob Agents Chemother 2020; 65:AAC.01948-20. [PMID: 33077652 DOI: 10.1128/aac.01948-20] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 10/07/2020] [Indexed: 11/20/2022] Open
Abstract
The nitroimidazole prodrugs delamanid and pretomanid comprise one of only two new antimicrobial classes approved to treat tuberculosis (TB) in 50 years. Prior in vitro studies suggest a relatively low barrier to nitroimidazole resistance in Mycobacterium tuberculosis, but clinical evidence is limited to date. We selected pretomanid-resistant M. tuberculosis mutants in two mouse models of TB using a range of pretomanid doses. The frequency of spontaneous resistance was approximately 10-5 CFU. Whole-genome sequencing of 161 resistant isolates from 47 mice revealed 99 unique mutations, of which 91% occurred in 1 of 5 genes previously associated with nitroimidazole activation and resistance, namely, fbiC (56%), fbiA (15%), ddn (12%), fgd (4%), and fbiB (4%). Nearly all mutations were unique to a single mouse and not previously identified. The remaining 9% of resistant mutants harbored mutations in Rv2983 (fbiD), a gene not previously associated with nitroimidazole resistance but recently shown to be a guanylyltransferase necessary for cofactor F420 synthesis. Most mutants exhibited high-level resistance to pretomanid and delamanid, although Rv2983 and fbiB mutants exhibited high-level pretomanid resistance but relatively small changes in delamanid susceptibility. Complementing an Rv2983 mutant with wild-type Rv2983 restored susceptibility to pretomanid and delamanid. By quantifying intracellular F420 and its precursor Fo in overexpressing and loss-of-function mutants, we provide further evidence that Rv2983 is necessary for F420 biosynthesis. Finally, Rv2983 mutants and other F420H2-deficient mutants displayed hypersusceptibility to some antibiotics and to concentrations of malachite green found in solid media used to isolate and propagate mycobacteria from clinical samples.
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12
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Redox Coenzyme F 420 Biosynthesis in Thermomicrobia Involves Reduction by Stand-Alone Nitroreductase Superfamily Enzymes. Appl Environ Microbiol 2020; 86:AEM.00457-20. [PMID: 32276981 DOI: 10.1128/aem.00457-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Accepted: 04/07/2020] [Indexed: 12/17/2022] Open
Abstract
Coenzyme F420 is a redox cofactor involved in hydride transfer reactions in archaea and bacteria. Since F420-dependent enzymes are attracting increasing interest as tools in biocatalysis, F420 biosynthesis is being revisited. While it was commonly accepted for a long time that the 2-phospho-l-lactate (2-PL) moiety of F420 is formed from free 2-PL, it was recently shown that phosphoenolpyruvate is incorporated in Actinobacteria and that the C-terminal domain of the FbiB protein, a member of the nitroreductase (NTR) superfamily, converts dehydro-F420 into saturated F420 Outside the Actinobacteria, however, the situation is still unclear because FbiB is missing in these organisms and enzymes of the NTR family are highly diversified. Here, we show by heterologous expression and in vitro assays that stand-alone NTR enzymes from Thermomicrobia exhibit dehydro-F420 reductase activity. Metabolome analysis and proteomics studies confirmed the proposed biosynthetic pathway in Thermomicrobium roseum These results clarify the biosynthetic route of coenzyme F420 in a class of Gram-negative bacteria, redefine functional subgroups of the NTR superfamily, and offer an alternative for large-scale production of F420 in Escherichia coli in the future.IMPORTANCE Coenzyme F420 is a redox cofactor of Archaea and Actinobacteria, as well as some Gram-negative bacteria. Its involvement in processes such as the biosynthesis of antibiotics, the degradation of xenobiotics, and asymmetric enzymatic reductions renders F420 of great relevance for biotechnology. Recently, a new biosynthetic step during the formation of F420 in Actinobacteria was discovered, involving an enzyme domain belonging to the versatile nitroreductase (NTR) superfamily, while this process remained blurred in Gram-negative bacteria. Here, we show that a similar biosynthetic route exists in Thermomicrobia, although key biosynthetic enzymes show different domain architectures and are only distantly related. Our results shed light on the biosynthesis of F420 in Gram-negative bacteria and refine the knowledge about sequence-function relationships within the NTR superfamily of enzymes. Appreciably, these results offer an alternative route to produce F420 in Gram-negative model organisms and unveil yet another biochemical facet of this pathway to be explored by synthetic microbiologists.
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Grinter R, Ney B, Brammananth R, Barlow CK, Cordero PRF, Gillett DL, Izoré T, Cryle MJ, Harold LK, Cook GM, Taiaroa G, Williamson DA, Warden AC, Oakeshott JG, Taylor MC, Crellin PK, Jackson CJ, Schittenhelm RB, Coppel RL, Greening C. Cellular and Structural Basis of Synthesis of the Unique Intermediate Dehydro-F 420-0 in Mycobacteria. mSystems 2020; 5:e00389-20. [PMID: 32430409 PMCID: PMC7253369 DOI: 10.1128/msystems.00389-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 05/04/2020] [Indexed: 11/29/2022] Open
Abstract
F420 is a low-potential redox cofactor used by diverse bacteria and archaea. In mycobacteria, this cofactor has multiple roles, including adaptation to redox stress, cell wall biosynthesis, and activation of the clinical antitubercular prodrugs pretomanid and delamanid. A recent biochemical study proposed a revised biosynthesis pathway for F420 in mycobacteria; it was suggested that phosphoenolpyruvate served as a metabolic precursor for this pathway, rather than 2-phospholactate as long proposed, but these findings were subsequently challenged. In this work, we combined metabolomic, genetic, and structural analyses to resolve these discrepancies and determine the basis of F420 biosynthesis in mycobacterial cells. We show that, in whole cells of Mycobacterium smegmatis, phosphoenolpyruvate rather than 2-phospholactate stimulates F420 biosynthesis. Analysis of F420 biosynthesis intermediates present in M. smegmatis cells harboring genetic deletions at each step of the biosynthetic pathway confirmed that phosphoenolpyruvate is then used to produce the novel precursor compound dehydro-F420-0. To determine the structural basis of dehydro-F420-0 production, we solved high-resolution crystal structures of the enzyme responsible (FbiA) in apo-, substrate-, and product-bound forms. These data show the essential role of a single divalent cation in coordinating the catalytic precomplex of this enzyme and demonstrate that dehydro-F420-0 synthesis occurs through a direct substrate transfer mechanism. Together, these findings resolve the biosynthetic pathway of F420 in mycobacteria and have significant implications for understanding the emergence of antitubercular prodrug resistance.IMPORTANCE Mycobacteria are major environmental microorganisms and cause many significant diseases, including tuberculosis. Mycobacteria make an unusual vitamin-like compound, F420, and use it to both persist during stress and resist antibiotic treatment. Understanding how mycobacteria make F420 is important, as this process can be targeted to create new drugs to combat infections like tuberculosis. In this study, we show that mycobacteria make F420 in a way that is different from other bacteria. We studied the molecular machinery that mycobacteria use to make F420, determining the chemical mechanism for this process and identifying a novel chemical intermediate. These findings also have clinical relevance, given that two new prodrugs for tuberculosis treatment are activated by F420.
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Affiliation(s)
- Rhys Grinter
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
- Department of Microbiology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Blair Ney
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
- CSIRO Land & Water, Canberra, ACT, Australia
- Research School of Chemistry, Australian National University, Canberra, ACT, Australia
| | - Rajini Brammananth
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
- Department of Microbiology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Christopher K Barlow
- Department of Biochemistry, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
- Monash Proteomics & Metabolomics Facility, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Paul R F Cordero
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
- Department of Microbiology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - David L Gillett
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
- Department of Microbiology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Thierry Izoré
- Department of Biochemistry, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Max J Cryle
- Department of Biochemistry, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Liam K Harold
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Gregory M Cook
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - George Taiaroa
- Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Deborah A Williamson
- Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | | | | | | | - Paul K Crellin
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
- Department of Microbiology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Colin J Jackson
- Research School of Chemistry, Australian National University, Canberra, ACT, Australia
| | - Ralf B Schittenhelm
- Department of Biochemistry, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
- Monash Proteomics & Metabolomics Facility, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Ross L Coppel
- Department of Microbiology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Chris Greening
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
- Department of Microbiology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
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14
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Sieniawska E, Sawicki R, Golus J, Georgiev MI. Untargetted Metabolomic Exploration of the Mycobacterium tuberculosis Stress Response to Cinnamon Essential Oil. Biomolecules 2020; 10:biom10030357. [PMID: 32111061 PMCID: PMC7175327 DOI: 10.3390/biom10030357] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 02/20/2020] [Accepted: 02/24/2020] [Indexed: 11/18/2022] Open
Abstract
The antimycobacterial activity of cinnamaldehyde has already been proven for laboratory strains and for clinical isolates. What is more, cinnamaldehyde was shown to threaten the mycobacterial plasma membrane integrity and to activate the stress response system. Following promising applications of metabolomics in drug discovery and development we aimed to explore the mycobacteria response to cinnamaldehyde within cinnamon essential oil treatment by untargeted liquid chromatography–mass spectrometry. The use of predictive metabolite pathway analysis and description of produced lipids enabled the evaluation of the stress symptoms shown by bacteria. This study suggests that bacteria exposed to cinnamaldehyde could reorganize their outer membrane as a physical barrier against stress factors. They probably lowered cell wall permeability and inner membrane fluidity, and possibly redirected carbon flow to store energy in triacylglycerols. Being a reactive compound, cinnamaldehyde may also contribute to disturbances in bacteria redox homeostasis and detoxification mechanisms.
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Affiliation(s)
- Elwira Sieniawska
- Chair and Department of Pharmacognosy, Medical University of Lublin, Chodzki 1, 20-093 Lublin, Poland
- Correspondence:
| | - Rafał Sawicki
- Chair and Department of Biochemistry and Biotechnology, Medical University of Lublin, Chodzki 1, 20-093 Lublin, Poland; (R.S.); (J.G.)
| | - Joanna Golus
- Chair and Department of Biochemistry and Biotechnology, Medical University of Lublin, Chodzki 1, 20-093 Lublin, Poland; (R.S.); (J.G.)
| | - Milen I. Georgiev
- Group of Plant Cell Biotechnology and Metabolomics, The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, 139 Ruski Blvd., 4000 Plovdiv, Bulgaria;
- Center of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria
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15
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Lee BM, Harold LK, Almeida DV, Afriat-Jurnou L, Aung HL, Forde BM, Hards K, Pidot SJ, Ahmed FH, Mohamed AE, Taylor MC, West NP, Stinear TP, Greening C, Beatson SA, Nuermberger EL, Cook GM, Jackson CJ. Predicting nitroimidazole antibiotic resistance mutations in Mycobacterium tuberculosis with protein engineering. PLoS Pathog 2020; 16:e1008287. [PMID: 32032366 PMCID: PMC7032734 DOI: 10.1371/journal.ppat.1008287] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 02/20/2020] [Accepted: 12/16/2019] [Indexed: 12/21/2022] Open
Abstract
Our inability to predict which mutations could result in antibiotic resistance has made it difficult to rapidly identify the emergence of resistance, identify pre-existing resistant populations, and manage our use of antibiotics to effectively treat patients and prevent or slow the spread of resistance. Here we investigated the potential for resistance against the new antitubercular nitroimidazole prodrugs pretomanid and delamanid to emerge in Mycobacterium tuberculosis, the causative agent of tuberculosis (TB). Deazaflavin-dependent nitroreductase (Ddn) is the only identified enzyme within M. tuberculosis that activates these prodrugs, via an F420H2-dependent reaction. We show that the native menaquinone-reductase activity of Ddn is essential for emergence from hypoxia, which suggests that for resistance to spread and pose a threat to human health, the native activity of Ddn must be at least partially retained. We tested 75 unique mutations, including all known sequence polymorphisms identified among ~15,000 sequenced M. tuberculosis genomes. Several mutations abolished pretomanid and delamanid activation in vitro, without causing complete loss of the native activity. We confirmed that a transmissible M. tuberculosis isolate from the hypervirulent Beijing family already possesses one such mutation and is resistant to pretomanid, before being exposed to the drug. Notably, delamanid was still effective against this strain, which is consistent with structural analysis that indicates delamanid and pretomanid bind to Ddn differently. We suggest that the mutations identified in this work be monitored for informed use of delamanid and pretomanid treatment and to slow the emergence of resistance.
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Affiliation(s)
- Brendon M. Lee
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Liam K. Harold
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Deepak V. Almeida
- Center for Tuberculosis Research, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Livnat Afriat-Jurnou
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory, Australia
- MIGAL, Galilee Research Institute, Kiryat Shmona, Israel
- Faculty of Sciences and Technology, Tel-Hai Academic College, Upper Galilee, Israel
| | - Htin Lin Aung
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Brian M. Forde
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Kiel Hards
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Sacha J. Pidot
- Department of Microbiology and Immunology, University of Melbourne, Melbourne, Victoria, Australia
| | - F. Hafna Ahmed
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory, Australia
| | - A. Elaaf Mohamed
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Matthew C. Taylor
- Land and Water Flagship, The Commonwealth Scientific and Industrial Organisation, Canberra, Australian Capital Territory, Australia
| | - Nicholas P. West
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Timothy P. Stinear
- Department of Microbiology and Immunology, University of Melbourne, Melbourne, Victoria, Australia
| | - Chris Greening
- Land and Water Flagship, The Commonwealth Scientific and Industrial Organisation, Canberra, Australian Capital Territory, Australia
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia
| | - Scott A. Beatson
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Eric L. Nuermberger
- Center for Tuberculosis Research, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Gregory M. Cook
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Colin J. Jackson
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory, Australia
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16
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Braga D, Last D, Hasan M, Guo H, Leichnitz D, Uzum Z, Richter I, Schalk F, Beemelmanns C, Hertweck C, Lackner G. Metabolic Pathway Rerouting in Paraburkholderia rhizoxinica Evolved Long-Overlooked Derivatives of Coenzyme F 420. ACS Chem Biol 2019; 14:2088-2094. [PMID: 31469543 DOI: 10.1021/acschembio.9b00605] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Coenzyme F420 is a specialized redox cofactor with a negative redox potential. It supports biochemical processes like methanogenesis, degradation of xenobiotics, and the biosynthesis of antibiotics. Although well-studied in methanogenic archaea and actinobacteria, not much is known about F420 in Gram-negative bacteria. Genome sequencing revealed F420 biosynthetic genes in the Gram-negative, endofungal bacterium Paraburkholderia rhizoxinica, a symbiont of phytopathogenic fungi. Fluorescence microscopy, high-resolution LC-MS, and structure elucidation by NMR demonstrated that the encoded pathway is active and yields unexpected derivatives of F420 (3PG-F420). Further analyses of a biogas-producing microbial community showed that these derivatives are more widespread in nature. Genetic and biochemical studies of their biosynthesis established that a specificity switch in the guanylyltransferase CofC reprogrammed the pathway to start from 3-phospho-d-glycerate, suggesting a rerouting event during the evolution of F420 biosynthesis. Furthermore, the cofactor activity of 3PG-F420 was validated, thus opening up perspectives for its use in biocatalysis. The 3PG-F420 biosynthetic gene cluster is fully functional in Escherichia coli, enabling convenient production of the cofactor by fermentation.
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Affiliation(s)
- Daniel Braga
- Junior Research Group Synthetic Microbiology, Leibniz Institute for Natural Product Research and Infection Biology − Hans Knöll Institute, Beutenbergstr. 11a, 07745 Jena, Germany
- Friedrich Schiller University, Jena, Germany
| | - Daniel Last
- Junior Research Group Synthetic Microbiology, Leibniz Institute for Natural Product Research and Infection Biology − Hans Knöll Institute, Beutenbergstr. 11a, 07745 Jena, Germany
| | - Mahmudul Hasan
- Junior Research Group Synthetic Microbiology, Leibniz Institute for Natural Product Research and Infection Biology − Hans Knöll Institute, Beutenbergstr. 11a, 07745 Jena, Germany
- Friedrich Schiller University, Jena, Germany
| | - Huijuan Guo
- Junior Research Group, Chemical Biology of Microbe−Host Interactions, Leibniz Institute for Natural Product Research and Infection Biology − Hans Knöll Institute, Beutenbergstr. 11a, 07745 Jena, Germany
| | - Daniel Leichnitz
- Junior Research Group, Chemical Biology of Microbe−Host Interactions, Leibniz Institute for Natural Product Research and Infection Biology − Hans Knöll Institute, Beutenbergstr. 11a, 07745 Jena, Germany
| | - Zerrin Uzum
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology − Hans Knöll Institute, Beutenbergstr. 11a, 07745 Jena, Germany
| | - Ingrid Richter
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology − Hans Knöll Institute, Beutenbergstr. 11a, 07745 Jena, Germany
| | - Felix Schalk
- Junior Research Group, Chemical Biology of Microbe−Host Interactions, Leibniz Institute for Natural Product Research and Infection Biology − Hans Knöll Institute, Beutenbergstr. 11a, 07745 Jena, Germany
| | - Christine Beemelmanns
- Junior Research Group, Chemical Biology of Microbe−Host Interactions, Leibniz Institute for Natural Product Research and Infection Biology − Hans Knöll Institute, Beutenbergstr. 11a, 07745 Jena, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology − Hans Knöll Institute, Beutenbergstr. 11a, 07745 Jena, Germany
- Friedrich Schiller University, Jena, Germany
| | - Gerald Lackner
- Junior Research Group Synthetic Microbiology, Leibniz Institute for Natural Product Research and Infection Biology − Hans Knöll Institute, Beutenbergstr. 11a, 07745 Jena, Germany
- Friedrich Schiller University, Jena, Germany
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17
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Drenth J, Trajkovic M, Fraaije MW. Chemoenzymatic Synthesis of an Unnatural Deazaflavin Cofactor That Can Fuel F420-Dependent Enzymes. ACS Catal 2019. [DOI: 10.1021/acscatal.9b01506] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Jeroen Drenth
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747AG Groningen, The Netherlands
| | - Milos Trajkovic
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747AG Groningen, The Netherlands
| | - Marco W. Fraaije
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747AG Groningen, The Netherlands
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18
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A revised biosynthetic pathway for the cofactor F 420 in prokaryotes. Nat Commun 2019; 10:1558. [PMID: 30952857 PMCID: PMC6450877 DOI: 10.1038/s41467-019-09534-x] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 03/13/2019] [Indexed: 01/19/2023] Open
Abstract
Cofactor F420 plays critical roles in primary and secondary metabolism in a range of bacteria and archaea as a low-potential hydride transfer agent. It mediates a variety of important redox transformations involved in bacterial persistence, antibiotic biosynthesis, pro-drug activation and methanogenesis. However, the biosynthetic pathway for F420 has not been fully elucidated: neither the enzyme that generates the putative intermediate 2-phospho-l-lactate, nor the function of the FMN-binding C-terminal domain of the γ-glutamyl ligase (FbiB) in bacteria are known. Here we present the structure of the guanylyltransferase FbiD and show that, along with its archaeal homolog CofC, it accepts phosphoenolpyruvate, rather than 2-phospho-l-lactate, as the substrate, leading to the formation of the previously uncharacterized intermediate dehydro-F420-0. The C-terminal domain of FbiB then utilizes FMNH2 to reduce dehydro-F420-0, which produces mature F420 species when combined with the γ-glutamyl ligase activity of the N-terminal domain. These new insights have allowed the heterologous production of F420 from a recombinant F420 biosynthetic pathway in Escherichia coli. Cofactor F420 plays crucial roles in bacterial and archaeal metabolism, but its biosynthetic pathway is not fully understood. Here, the authors present the structure of one of the enzymes and provide experimental evidence for a substantial revision of the pathway, including the identification of a new intermediate.
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19
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Reconstructing the evolutionary history of F 420-dependent dehydrogenases. Sci Rep 2018; 8:17571. [PMID: 30514849 PMCID: PMC6279831 DOI: 10.1038/s41598-018-35590-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 08/24/2018] [Indexed: 12/20/2022] Open
Abstract
During the last decade the number of characterized F420-dependent enzymes has significantly increased. Many of these deazaflavoproteins share a TIM-barrel fold and are structurally related to FMN-dependent luciferases and monooxygenases. In this work, we traced the origin and evolutionary history of the F420-dependent enzymes within the luciferase-like superfamily. By a thorough phylogenetic analysis we inferred that the F420-dependent enzymes emerged from a FMN-dependent common ancestor. Furthermore, the data show that during evolution, the family of deazaflavoproteins split into two well-defined groups of enzymes: the F420-dependent dehydrogenases and the F420-dependent reductases. By such event, the dehydrogenases specialized in generating the reduced deazaflavin cofactor, while the reductases employ the reduced F420 for catalysis. Particularly, we focused on investigating the dehydrogenase subfamily and demonstrated that this group diversified into three types of dehydrogenases: the already known F420-dependent glucose-6-phosphate dehydrogenases, the F420-dependent alcohol dehydrogenases, and the sugar-6-phosphate dehydrogenases that were identified in this study. By reconstructing and experimentally characterizing ancestral and extant representatives of F420-dependent dehydrogenases, their biochemical properties were investigated and compared. We propose an evolutionary path for the emergence and diversification of the TIM-barrel fold F420-dependent dehydrogenases subfamily.
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20
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Fujiwara M, Kawasaki M, Hariguchi N, Liu Y, Matsumoto M. Mechanisms of resistance to delamanid, a drug for Mycobacterium tuberculosis. Tuberculosis (Edinb) 2017. [PMID: 29523322 DOI: 10.1016/j.tube.2017.12.006] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Delamanid, a bicyclic nitroimidazooxazole, is effective against M. tuberculosis. Previous studies have shown that resistance to a bicyclic nitroimidazooxazine, PA-824, is caused by mutations in an F420-dependent bio-activation pathway. We investigated whether the same mechanisms are responsible for resistance to delamanid. Spontaneous resistance frequencies were determined using M. bovis BCG Tokyo (BCG) and M. tuberculosis H37Rv. F420 high-performance liquid chromatography (HPLC) elution patterns of homogenates of delamanid-resistant BCG colonies and two previously identified delamanid-resistant M. tuberculosis clinical isolates were examined, followed by sequencing of genes in the F420-dependent bio-activation pathway. Spontaneous resistance frequencies to delamanid were similar to those of isoniazid and PA-824. Four distinct F420 HPLC elution patterns were observed, corresponding to colonies with mutations on fgd1, fbiA, fbiB, and fbiC with no change in the ddn mutants from the wildtype. Complementation with the wildtype sequence of the mutated gene restored susceptibility. The two delamanid-resistant clinical isolates had ddn mutations and the wildtype F420 HPLC elution pattern. In conclusion, delamanid-resistant bacilli have mutations in one of the 5 genes in the F420-dependent bio-activation pathway with distinct F420 HPLC elution patterns. Both genetic and phenotypic changes may be considered in the development of a rapid susceptibility test for delamanid.
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Affiliation(s)
- Mamoru Fujiwara
- Department of Medical Innovations, New Drug Research Division, Otsuka Pharmaceutical Co., Ltd., Tokushima, Japan.
| | | | - Norimitsu Hariguchi
- Department of Medical Innovations, New Drug Research Division, Otsuka Pharmaceutical Co., Ltd., Tokushima, Japan.
| | - Yongge Liu
- Otsuka Pharmaceutical Development & Commercialization, Inc., Rockville, MD, USA.
| | - Makoto Matsumoto
- Pharmaceutical Business Division, Otsuka Pharmaceutical Co., Ltd., San Francisco, CA, USA.
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21
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Ney B, Carere CR, Sparling R, Jirapanjawat T, Stott MB, Jackson CJ, Oakeshott JG, Warden AC, Greening C. Cofactor Tail Length Modulates Catalysis of Bacterial F 420-Dependent Oxidoreductases. Front Microbiol 2017; 8:1902. [PMID: 29021791 PMCID: PMC5623714 DOI: 10.3389/fmicb.2017.01902] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 09/15/2017] [Indexed: 11/13/2022] Open
Abstract
F420 is a microbial cofactor that mediates a wide range of physiologically important and industrially relevant redox reactions, including in methanogenesis and tetracycline biosynthesis. This deazaflavin comprises a redox-active isoalloxazine headgroup conjugated to a lactyloligoglutamyl tail. Here we studied the catalytic significance of the oligoglutamate chain, which differs in length between bacteria and archaea. We purified short-chain F420 (two glutamates) from a methanogen isolate and long-chain F420 (five to eight glutamates) from a recombinant mycobacterium, confirming their different chain lengths by HPLC and LC/MS analysis. F420 purified from both sources was catalytically compatible with purified enzymes from the three major bacterial families of F420-dependent oxidoreductases. However, long-chain F420 bound to these enzymes with a six- to ten-fold higher affinity than short-chain F420. The cofactor side chain also significantly modulated the kinetics of the enzymes, with long-chain F420 increasing the substrate affinity (lower Km) but reducing the turnover rate (lower kcat) of the enzymes. Molecular dynamics simulations and comparative structural analysis suggest that the oligoglutamate chain of F420 makes dynamic electrostatic interactions with conserved surface residues of the oxidoreductases while the headgroup binds the catalytic site. In conjunction with the kinetic data, this suggests that electrostatic interactions made by the oligoglutamate tail result in higher-affinity, lower-turnover catalysis. Physiologically, we propose that bacteria have selected for long-chain F420 to better control cellular redox reactions despite tradeoffs in catalytic rate. Conversely, this suggests that industrial use of shorter-length F420 will greatly increase the rates of bioremediation and biocatalysis processes relying on purified F420-dependent oxidoreductases.
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Affiliation(s)
- Blair Ney
- School of Biological Sciences, Monash University, Clayton, VIC, Australia.,Land and Water Flagship, The Commonwealth Scientific and Industrial Research Organisation, Acton, ACT, Australia
| | - Carlo R Carere
- GNS Science, Wairakei Research Centre, Lower Hutt, New Zealand
| | - Richard Sparling
- GNS Science, Wairakei Research Centre, Lower Hutt, New Zealand.,Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada
| | | | - Matthew B Stott
- GNS Science, Wairakei Research Centre, Lower Hutt, New Zealand
| | - Colin J Jackson
- Research School of Chemistry, Australian National University, Acton, ACT, Australia
| | - John G Oakeshott
- Land and Water Flagship, The Commonwealth Scientific and Industrial Research Organisation, Acton, ACT, Australia
| | - Andrew C Warden
- Land and Water Flagship, The Commonwealth Scientific and Industrial Research Organisation, Acton, ACT, Australia
| | - Chris Greening
- School of Biological Sciences, Monash University, Clayton, VIC, Australia.,Land and Water Flagship, The Commonwealth Scientific and Industrial Research Organisation, Acton, ACT, Australia
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22
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Oyugi MA, Bashiri G, Baker EN, Johnson-Winters K. Mechanistic insights into F 420-dependent glucose-6-phosphate dehydrogenase using isotope effects and substrate inhibition studies. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1866:387-395. [PMID: 28807886 DOI: 10.1016/j.bbapap.2017.08.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Revised: 07/24/2017] [Accepted: 08/03/2017] [Indexed: 01/24/2023]
Abstract
F420-dependent glucose-6-phosphate dehydrogenase (FGD) is involved in the committed step of the pentose phosphate pathway within mycobacteria, where it catalyzes the reaction between glucose-6-phosphate (G6P) and the F420 cofactor to yield 6-phosphogluconolactone and the reduced cofactor, F420H2. Here, we aim to probe the FGD reaction mechanism using dead-end inhibition experiments, as well as solvent and substrate deuterium isotope effects studies. The dead-end inhibition studies performed using citrate as the inhibitor revealed competitive and uncompetitive inhibition patterns for G6P and F420 respectively, thus suggesting a mechanism of ordered addition of substrates in which the F420 cofactor must first bind to FGD before G6P binding. The solvent deuterium isotope effects studies yielded normal solvent kinetic isotope effects (SKIE) on kcat and kcat/Km for both G6P and F420. The proton inventory data yielded a fractionation factor of 0.37, suggesting that the single proton responsible for the observed SKIE is likely donated by Glu109 and protonates the cofactor at position N1. The steady state substrate deuterium isotope effects studies using G6P and G6P-d1 yielded KIE of 1.1 for both kcat and kcat/Km, while the pre-steady state KIE on kobs was 1.4. Because the hydride transferred to C5 of F420 was the one targeted for isotopic substitution, these KIE values provide further evidence to support our previous findings that hydride transfer is likely not rate-limiting in the FGD reaction.
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Affiliation(s)
- Mercy A Oyugi
- Department of Chemistry and Biochemistry, University of Texas at Arlington, TX 76019-0065, United States
| | - Ghader Bashiri
- Laboratory of Structural Biology and Maurice Wilkins Center for Molecular Biodiscovery, School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand
| | - Edward N Baker
- Laboratory of Structural Biology and Maurice Wilkins Center for Molecular Biodiscovery, School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand
| | - Kayunta Johnson-Winters
- Department of Chemistry and Biochemistry, University of Texas at Arlington, TX 76019-0065, United States.
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23
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Greening C, Jirapanjawat T, Afroze S, Ney B, Scott C, Pandey G, Lee BM, Russell RJ, Jackson CJ, Oakeshott JG, Taylor MC, Warden AC. Mycobacterial F 420H 2-Dependent Reductases Promiscuously Reduce Diverse Compounds through a Common Mechanism. Front Microbiol 2017; 8:1000. [PMID: 28620367 PMCID: PMC5449967 DOI: 10.3389/fmicb.2017.01000] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 05/18/2017] [Indexed: 01/24/2023] Open
Abstract
An unusual aspect of actinobacterial metabolism is the use of the redox cofactor F420. Studies have shown that actinobacterial F420H2-dependent reductases promiscuously hydrogenate diverse organic compounds in biodegradative and biosynthetic processes. These enzymes therefore represent promising candidates for next-generation industrial biocatalysts. In this work, we undertook the first broad survey of these enzymes as potential industrial biocatalysts by exploring the extent, as well as mechanistic and structural bases, of their substrate promiscuity. We expressed and purified 11 enzymes from seven subgroups of the flavin/deazaflavin oxidoreductase (FDOR) superfamily (A1, A2, A3, B1, B2, B3, B4) from the model soil actinobacterium Mycobacterium smegmatis. These enzymes reduced compounds from six chemical classes, including fundamental monocycles such as a cyclohexenone, a dihydropyran, and pyrones, as well as more complex quinone, coumarin, and arylmethane compounds. Substrate range and reduction rates varied between the enzymes, with the A1, A3, and B1 groups exhibiting greatest promiscuity. Molecular docking studies suggested that structurally diverse compounds are accommodated in the large substrate-binding pocket of the most promiscuous FDOR through hydrophobic interactions with conserved aromatic residues and the isoalloxazine headgroup of F420H2. Liquid chromatography-mass spectrometry (LC/MS) and gas chromatography-mass spectrometry (GC/MS) analysis of derivatized reaction products showed reduction occurred through a common mechanism involving hydride transfer from F420H- to the electron-deficient alkene groups of substrates. Reduction occurs when the hydride donor (C5 of F420H-) is proximal to the acceptor (electrophilic alkene of the substrate). These findings suggest that engineered actinobacterial F420H2-dependent reductases are promising novel biocatalysts for the facile transformation of a wide range of α,β-unsaturated compounds.
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Affiliation(s)
- Chris Greening
- Land and Water Flagship, The Commonwealth Scientific and Industrial Research Organisation, ActonACT, Australia.,School of Biological Sciences, Monash University, ClaytonVIC, Australia
| | - Thanavit Jirapanjawat
- Land and Water Flagship, The Commonwealth Scientific and Industrial Research Organisation, ActonACT, Australia.,School of Biological Sciences, Monash University, ClaytonVIC, Australia.,Research School of Chemistry, Australian National University, ActonACT, Australia
| | - Shahana Afroze
- Land and Water Flagship, The Commonwealth Scientific and Industrial Research Organisation, ActonACT, Australia.,Research School of Chemistry, Australian National University, ActonACT, Australia
| | - Blair Ney
- Land and Water Flagship, The Commonwealth Scientific and Industrial Research Organisation, ActonACT, Australia.,School of Biological Sciences, Monash University, ClaytonVIC, Australia.,Research School of Chemistry, Australian National University, ActonACT, Australia
| | - Colin Scott
- Land and Water Flagship, The Commonwealth Scientific and Industrial Research Organisation, ActonACT, Australia
| | - Gunjan Pandey
- Land and Water Flagship, The Commonwealth Scientific and Industrial Research Organisation, ActonACT, Australia
| | - Brendon M Lee
- Land and Water Flagship, The Commonwealth Scientific and Industrial Research Organisation, ActonACT, Australia.,Research School of Chemistry, Australian National University, ActonACT, Australia
| | - Robyn J Russell
- Land and Water Flagship, The Commonwealth Scientific and Industrial Research Organisation, ActonACT, Australia
| | - Colin J Jackson
- Research School of Chemistry, Australian National University, ActonACT, Australia
| | - John G Oakeshott
- Land and Water Flagship, The Commonwealth Scientific and Industrial Research Organisation, ActonACT, Australia
| | - Matthew C Taylor
- Land and Water Flagship, The Commonwealth Scientific and Industrial Research Organisation, ActonACT, Australia
| | - Andrew C Warden
- Land and Water Flagship, The Commonwealth Scientific and Industrial Research Organisation, ActonACT, Australia
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24
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Discovery and characterization of an F 420-dependent glucose-6-phosphate dehydrogenase (Rh-FGD1) from Rhodococcus jostii RHA1. Appl Microbiol Biotechnol 2016; 101:2831-2842. [PMID: 27966048 PMCID: PMC5352752 DOI: 10.1007/s00253-016-8038-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 11/22/2016] [Accepted: 11/26/2016] [Indexed: 12/16/2022]
Abstract
Cofactor F420, a 5-deazaflavin involved in obligatory hydride transfer, is widely distributed among archaeal methanogens and actinomycetes. Owing to the low redox potential of the cofactor, F420-dependent enzymes play a pivotal role in central catabolic pathways and xenobiotic degradation processes in these organisms. A physiologically essential deazaflavoenzyme is the F420-dependent glucose-6-phosphate dehydrogenase (FGD), which catalyzes the reaction F420 + glucose-6-phosphate → F420H2 + 6-phospho-gluconolactone. Thereby, FGDs generate the reduced F420 cofactor required for numerous F420H2-dependent reductases, involved e.g., in the bioreductive activation of the antitubercular prodrugs pretomanid and delamanid. We report here the identification, production, and characterization of three FGDs from Rhodococcus jostii RHA1 (Rh-FGDs), being the first experimental evidence of F420-dependent enzymes in this bacterium. The crystal structure of Rh-FGD1 has also been determined at 1.5 Å resolution, showing a high similarity with FGD from Mycobacterium tuberculosis (Mtb) (Mtb-FGD1). The cofactor-binding pocket and active-site catalytic residues are largely conserved in Rh-FGD1 compared with Mtb-FGD1, except for an extremely flexible insertion region capping the active site at the C-terminal end of the TIM-barrel, which also markedly differs from other structurally related proteins. The role of the three positively charged residues (Lys197, Lys258, and Arg282) constituting the binding site of the substrate phosphate moiety was experimentally corroborated by means of mutagenesis study. The biochemical and structural data presented here provide the first step towards tailoring Rh-FGD1 into a more economical biocatalyst, e.g., an F420-dependent glucose dehydrogenase that requires a cheaper cosubstrate and can better match the demands for the growing applications of F420H2-dependent reductases in industry and bioremediation.
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