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Dong L, Liu Y. Exploring the Substrate-Assisted Dehydration of Chorismate Catalyzed by Dehydratase MqnA from QM/MM Calculations: The Role of Pocket Residues and the Hydrolysis Mechanism of N17D Mutant. J Chem Inf Model 2023; 63:7499-7507. [PMID: 37970731 DOI: 10.1021/acs.jcim.3c01074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2023]
Abstract
MqnA is the first enzyme on the futalosine pathway to menaquinone, which catalyzes the dehydration of chorismate to yield 3-enolpyruvyl-benzoate (3-EPB). MqnA is also the only chorismate dehydratase known so far. In this work, based on the recently determined crystal structures, we constructed the enzyme-substrate complex models and conducted quantum mechanics/molecular mechanics (QM/MM) calculations to elucidate the reaction details of MqnA and the critical roles of pocket residues. The calculation results confirm that the MqnA-catalyzed dehydration of chorismate follows the substrate-assisted E1cb mechanism, in which the enol carboxylate in the side chain of the substrate is responsible for deprotonating the C3 of chorismate. This proton transfer process is much slower than C4-OH departure. Calculations on different mutants reveal that S86 and N17 are important for anchoring the enol carboxylate of the substrate in a favorable conformation to extract the C3-proton. The strong H-bonds formed between the enol carboxylate of chorismate and S86/N17 play a key role in stabilizing the reaction intermediate. Consistent with the experimental observations, our calculations demonstrate that the MqnA N17D mutant also shows hydrolase activity and the typical enzyme-catalyzed hydrolysis mechanism is elucidated. The protonated D17 is responsible for saturating the methylene group of chorismate to start the hydrolysis reaction. The orientation of the carboxyl group of D17 is key in determining MqnA to be a dehydratase or hydrolase.
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Affiliation(s)
- Lihua Dong
- School of Chemistry and Chemical Engineering, Qilu Normal University, Jinan, Shandong 250013, China
| | - Yongjun Liu
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
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2
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Liu Y, Wang J, Huang JB, Li XF, Chen Y, Liu K, Zhao M, Huang XL, Gao XL, Luo YN, Tao W, Wu J, Xue ZL. Advances in regulating vitamin K 2 production through metabolic engineering strategies. World J Microbiol Biotechnol 2023; 40:8. [PMID: 37938463 DOI: 10.1007/s11274-023-03828-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 11/02/2023] [Indexed: 11/09/2023]
Abstract
Vitamin K2 (menaquinone, VK2, MK) is an essential lipid-soluble vitamin that plays critical roles in inhibiting cell ferroptosis, improving blood clotting, and preventing osteoporosis. The increased global demand for VK2 has inspired interest in novel production strategies. In this review, various novel metabolic regulation strategies, including static and dynamic metabolic regulation, are summarized and discussed. Furthermore, the advantages and disadvantages of both strategies are analyzed in-depth to highlight the bottlenecks facing microbial VK2 production on an industrial scale. Finally, advanced metabolic engineering biotechnology for future microbial VK2 production will also be discussed. In summary, this review provides in-depth information and offers an outlook on metabolic engineering strategies for VK2 production.
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Affiliation(s)
- Yan Liu
- College of Biology and Food Engineering, Anhui Polytechnic University, 241000, Wuhu, China.
- Anhui Engineering Laboratory for Industrial Microbiology Molecular Breeding, 241000, Wuhu, China.
| | - Jian Wang
- College of Biology and Food Engineering, Anhui Polytechnic University, 241000, Wuhu, China
| | - Jun-Bao Huang
- College of Biology and Food Engineering, Anhui Polytechnic University, 241000, Wuhu, China
| | - Xiang-Fei Li
- College of Biology and Food Engineering, Anhui Polytechnic University, 241000, Wuhu, China
- Anhui Engineering Laboratory for Industrial Microbiology Molecular Breeding, 241000, Wuhu, China
| | - Yu Chen
- College of Biology and Food Engineering, Anhui Polytechnic University, 241000, Wuhu, China
- Anhui Engineering Laboratory for Industrial Microbiology Molecular Breeding, 241000, Wuhu, China
| | - Kun Liu
- College of Biology and Food Engineering, Anhui Polytechnic University, 241000, Wuhu, China
- Anhui Engineering Laboratory for Industrial Microbiology Molecular Breeding, 241000, Wuhu, China
| | - Ming Zhao
- College of Biology and Food Engineering, Anhui Polytechnic University, 241000, Wuhu, China.
- Anhui Engineering Laboratory for Industrial Microbiology Molecular Breeding, 241000, Wuhu, China.
| | - Xi-Lin Huang
- College of Biology and Food Engineering, Anhui Polytechnic University, 241000, Wuhu, China
| | - Xu-Li Gao
- College of Biology and Food Engineering, Anhui Polytechnic University, 241000, Wuhu, China
| | - Ya-Ni Luo
- College of Biology and Food Engineering, Anhui Polytechnic University, 241000, Wuhu, China
| | - Wei Tao
- College of Biology and Food Engineering, Anhui Polytechnic University, 241000, Wuhu, China
| | - Jing Wu
- College of Biology and Food Engineering, Anhui Polytechnic University, 241000, Wuhu, China
| | - Zheng-Lian Xue
- College of Biology and Food Engineering, Anhui Polytechnic University, 241000, Wuhu, China
- Anhui Engineering Laboratory for Industrial Microbiology Molecular Breeding, 241000, Wuhu, China
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3
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Kazemzadeh K, Pelosi L, Chenal C, Chobert SC, Hajj Chehade M, Jullien M, Flandrin L, Schmitt W, He Q, Bouvet E, Jarzynka M, Varoquaux N, Junier I, Pierrel F, Abby SS. Diversification of Ubiquinone Biosynthesis via Gene Duplications, Transfers, Losses, and Parallel Evolution. Mol Biol Evol 2023; 40:msad219. [PMID: 37788637 PMCID: PMC10597321 DOI: 10.1093/molbev/msad219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 09/11/2023] [Accepted: 09/26/2023] [Indexed: 10/05/2023] Open
Abstract
The availability of an ever-increasing diversity of prokaryotic genomes and metagenomes represents a major opportunity to understand and decipher the mechanisms behind the functional diversification of microbial biosynthetic pathways. However, it remains unclear to what extent a pathway producing a specific molecule from a specific precursor can diversify. In this study, we focus on the biosynthesis of ubiquinone (UQ), a crucial coenzyme that is central to the bioenergetics and to the functioning of a wide variety of enzymes in Eukarya and Pseudomonadota (a subgroup of the formerly named Proteobacteria). UQ biosynthesis involves three hydroxylation reactions on contiguous carbon atoms. We and others have previously shown that these reactions are catalyzed by different sets of UQ-hydroxylases that belong either to the iron-dependent Coq7 family or to the more widespread flavin monooxygenase (FMO) family. Here, we combine an experimental approach with comparative genomics and phylogenetics to reveal how UQ-hydroxylases evolved different selectivities within the constrained framework of the UQ pathway. It is shown that the UQ-FMOs diversified via at least three duplication events associated with two cases of neofunctionalization and one case of subfunctionalization, leading to six subfamilies with distinct hydroxylation selectivity. We also demonstrate multiple transfers of the UbiM enzyme and the convergent evolution of UQ-FMOs toward the same function, which resulted in two independent losses of the Coq7 ancestral enzyme. Diversification of this crucial biosynthetic pathway has therefore occurred via a combination of parallel evolution, gene duplications, transfers, and losses.
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Affiliation(s)
- Katayoun Kazemzadeh
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France
| | - Ludovic Pelosi
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France
| | - Clothilde Chenal
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France
| | - Sophie-Carole Chobert
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France
| | - Mahmoud Hajj Chehade
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France
| | - Margaux Jullien
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France
| | - Laura Flandrin
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France
| | - William Schmitt
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France
| | - Qiqi He
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France
| | - Emma Bouvet
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France
| | - Manon Jarzynka
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France
| | - Nelle Varoquaux
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France
| | - Ivan Junier
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France
| | - Fabien Pierrel
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France
| | - Sophie S Abby
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France
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Wilkens D, Simon J. Biosynthesis and function of microbial methylmenaquinones. Adv Microb Physiol 2023; 83:1-58. [PMID: 37507157 DOI: 10.1016/bs.ampbs.2023.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2023]
Abstract
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.
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Affiliation(s)
- Dennis Wilkens
- Microbial Energy Conversion and Biotechnology, Department of Biology, Technical University of Darmstadt, Schnittspahnstraße 10, Darmstadt, Germany
| | - Jörg Simon
- Microbial Energy Conversion and Biotechnology, Department of Biology, Technical University of Darmstadt, Schnittspahnstraße 10, Darmstadt, Germany; Centre for Synthetic Biology, Technical University of Darmstadt, Darmstadt, Germany.
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5
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Wang M, Li CJ, Zhang Z, Li PP, Yang LL, Zhi XY. The evolution of morphological development is congruent with the species phylogeny in the genus Streptomyces. Front Microbiol 2023; 14:1102250. [PMID: 37065118 PMCID: PMC10090380 DOI: 10.3389/fmicb.2023.1102250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 03/14/2023] [Indexed: 03/31/2023] Open
Abstract
As the canonical model organism to dissect bacterial morphological development, Streptomyces species has attracted much attention from the microbiological society. However, the evolution of development-related genes in Streptomyces remains elusive. Here, we evaluated the distribution of development-related genes, thus indicating that the majority of these genes were ubiquitous in Streptomyces genomes. Furthermore, the phylogenetic topologies of related strict orthologous genes were compared to the species tree of Streptomyces from both concatenation and single-gene tree analyses. Meanwhile, the reconciled gene tree and normalization based on the number of parsimony-informative sites were also employed to reduce the impact of phylogenetic conflicts, which was induced by uncertainty in single-gene tree inference based merely on the sequence and the bias in the amount of phylogenetic information caused by variable numbers of parsimony-informative sites. We found that the development-related genes had higher congruence to the species tree than other strict orthologous genes. Considering that the development-related genes could also be tracked back to the common ancestor of Streptomyces, these results suggest that morphological development follows the same pattern as species divergence.
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Affiliation(s)
- Min Wang
- Key Laboratory of Microbial Diversity in Southwest China of Ministry of Education, School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, China
- Zhaotong Health Vocational College, Zhaotong, China
| | - Cong-Jian Li
- Key Laboratory of Microbial Diversity in Southwest China of Ministry of Education, School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, China
| | - Zhen Zhang
- Key Laboratory of Microbial Diversity in Southwest China of Ministry of Education, School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, China
| | - Pan-Pan Li
- Key Laboratory of Microbial Diversity in Southwest China of Ministry of Education, School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, China
| | - Ling-Ling Yang
- Key Laboratory of Microbial Diversity in Southwest China of Ministry of Education, School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, China
| | - Xiao-Yang Zhi
- Key Laboratory of Microbial Diversity in Southwest China of Ministry of Education, School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, China
- *Correspondence: Xiao-Yang Zhi,
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6
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Freire MÁ. The origins of photosynthetic systems: Clues from the phosphorus and sulphur chemical scenarios. Biosystems 2023; 226:104873. [PMID: 36906114 DOI: 10.1016/j.biosystems.2023.104873] [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: 09/28/2022] [Revised: 02/22/2023] [Accepted: 03/06/2023] [Indexed: 03/11/2023]
Abstract
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.
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Affiliation(s)
- Miguel Ángel Freire
- Instituto Multidisciplinario de Biología Vegetal (IMBIV), CONICET, Universidad Nacional de Córdoba (UNC), Facultad de Ciencias Exactas, Físicas y Naturales. Av. Vélez Sarsfield 299, CC 495, 5000, Córdoba, Argentina.
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7
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Berg K, Hegde P, Pujari V, Brinkmann M, Wilkins DZ, Parish T, Crick DC, Aldrich CC. SAR study of piperidine derivatives as inhibitors of 1,4-dihydroxy-2-naphthoate isoprenyltransferase (MenA) from Mycobacterium tuberculosis. Eur J Med Chem 2023; 249:115125. [PMID: 36682292 PMCID: PMC9975056 DOI: 10.1016/j.ejmech.2023.115125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 01/11/2023] [Accepted: 01/14/2023] [Indexed: 01/19/2023]
Abstract
The electron transport chain (ETC) in the cell membrane consists of a series of redox complexes that transfer electrons from electron donors to acceptors and couples this electron transfer with the transfer of protons (H+) across a membrane. This process generates proton motive force which is used to produce ATP and a myriad of other functions and is essential for the long-term survival of Mycobacterium tuberculosis (Mtb), the causative organism of tuberculosis (TB), under the hypoxic conditions present within infected granulomas. Menaquinone (MK), an important carrier molecule within the mycobacterial ETC, is synthesized de novo by a cluster of enzymes known as the classic/canonical MK biosynthetic pathway. MenA (1,4-dihydroxy-2-naphthoate prenyltransferase), the antepenultimate enzyme in this pathway, is a verified target for TB therapy. In this study, we explored structure-activity relationships of a previously discovered MenA inhibitor scaffold, seeking to improve potency and drug disposition properties. Focusing our campaign upon three molecular regions, we identified two novel inhibitors with potent activity against MenA and Mtb (IC50 = 13-22 μM, GIC50 = 8-10 μM). These analogs also displayed substantially improved pharmacokinetic parameters and potent synergy with other ETC-targeting agents, achieving nearly complete sterilization of Mtb in combination therapy within two weeks in vivo. These new inhibitors of MK biosynthesis present a promising new strategy to curb the continued spread of TB.
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Affiliation(s)
- Kaja Berg
- Department of Medicinal Chemistry, University of Minnesota, 308 Harvard Street Southeast, Minneapolis, MN, 55455, USA
| | - Pooja Hegde
- Department of Medicinal Chemistry, University of Minnesota, 308 Harvard Street Southeast, Minneapolis, MN, 55455, USA
| | - Venugopal Pujari
- Mycobacteria Research Laboratories, Microbiology, Immunology, and Pathology Department, Colorado State University, Fort Collins, CO, 80523, USA
| | - Marzena Brinkmann
- Department of Medicinal Chemistry, University of Minnesota, 308 Harvard Street Southeast, Minneapolis, MN, 55455, USA
| | - David Z Wilkins
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, 98109, USA
| | - Tanya Parish
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, 98109, USA
| | - Dean C Crick
- Mycobacteria Research Laboratories, Microbiology, Immunology, and Pathology Department, Colorado State University, Fort Collins, CO, 80523, USA.
| | - Courtney C Aldrich
- Department of Medicinal Chemistry, University of Minnesota, 308 Harvard Street Southeast, Minneapolis, MN, 55455, USA.
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8
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Prasad A, Breithaupt C, Nguyen DA, Lilie H, Ziegler J, Stubbs MT. Mechanism of chorismate dehydratase MqnA, the first enzyme of the futalosine pathway, proceeds via substrate-assisted catalysis. J Biol Chem 2022; 298:102601. [PMID: 36265588 PMCID: PMC9672406 DOI: 10.1016/j.jbc.2022.102601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 10/10/2022] [Accepted: 10/12/2022] [Indexed: 11/07/2022] Open
Abstract
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.
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Affiliation(s)
- Archna Prasad
- Institut für Biochemie und Biotechnologie, Charles-Tanford-Proteinzentrum, Martin-Luther-Universität – Halle-Wittenberg, Halle/Saale, Germany
| | - Constanze Breithaupt
- Institut für Biochemie und Biotechnologie, Charles-Tanford-Proteinzentrum, Martin-Luther-Universität – Halle-Wittenberg, Halle/Saale, Germany
| | - Duc-Anh Nguyen
- Institut für Biochemie und Biotechnologie, Charles-Tanford-Proteinzentrum, Martin-Luther-Universität – Halle-Wittenberg, Halle/Saale, Germany
| | - Hauke Lilie
- Institut für Biochemie und Biotechnologie, Charles-Tanford-Proteinzentrum, Martin-Luther-Universität – Halle-Wittenberg, Halle/Saale, Germany
| | - Jörg Ziegler
- Abteilung Molekulare Signalverarbeitung, Leibniz-Institut für Pflanzenbiochemie, Halle/Saale, Germany
| | - Milton T. Stubbs
- Institut für Biochemie und Biotechnologie, Charles-Tanford-Proteinzentrum, Martin-Luther-Universität – Halle-Wittenberg, Halle/Saale, Germany,For correspondence: Milton T. Stubbs
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Abstract
Covering: up to 2022The report provides a broad approach to deciphering the evolution of coenzyme biosynthetic pathways. Here, these various pathways are analyzed with respect to the coenzymes required for this purpose. Coenzymes whose biosynthesis relies on a large number of coenzyme-mediated reactions probably appeared on the scene at a later stage of biological evolution, whereas the biosyntheses of pyridoxal phosphate (PLP) and nicotinamide (NAD+) require little additional coenzymatic support and are therefore most likely very ancient biosynthetic pathways.
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Affiliation(s)
- Andreas Kirschning
- Institute of Organic Chemistry, Leibniz University Hannover, Schneiderberg 1B, D-30167 Hannover, Germany.
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10
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Horne RG, Freedman SB, Johnson-Henry KC, Pang XL, Lee BE, Farion KJ, Gouin S, Schuh S, Poonai N, Hurley KF, Finkelstein Y, Xie J, Williamson-Urquhart S, Chui L, Rossi L, Surette MG, Sherman PM. Intestinal Microbial Composition of Children in a Randomized Controlled Trial of Probiotics to Treat Acute Gastroenteritis. Front Cell Infect Microbiol 2022; 12:883163. [PMID: 35774405 PMCID: PMC9238408 DOI: 10.3389/fcimb.2022.883163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 05/18/2022] [Indexed: 11/24/2022] Open
Abstract
Compositional analysis of the intestinal microbiome in pre-schoolers is understudied. Effects of probiotics on the gut microbiota were evaluated in children under 4-years-old presenting to an emergency department with acute gastroenteritis. Included were 70 study participants (n=32 placebo, n=38 probiotics) with stool specimens at baseline (day 0), day 5, and after a washout period (day 28). Microbiota composition and deduced functions were profiled using 16S ribosomal RNA sequencing and predictive metagenomics, respectively. Probiotics were detected at day 5 of administration but otherwise had no discernable effects, whereas detection of bacterial infection (P<0.001) and participant age (P<0.001) had the largest effects on microbiota composition, microbial diversity, and deduced bacterial functions. Participants under 1 year had lower bacterial diversity than older aged pre-schoolers; compositional changes of individual bacterial taxa were associated with maturation of the gut microbiota. Advances in age were associated with differences in gut microbiota composition and deduced microbial functions, which have the potential to impact health later in life.
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Affiliation(s)
- Rachael G. Horne
- Cell Biology Program, Research Institute, Hospital for Sick Children, Toronto, ON, Canada
| | - Stephen B. Freedman
- Sections of Pediatric Emergency Medicine and Gastroenterology, Department of Pediatrics, Alberta Children’s Hospital, Alberta Children’s Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | | | - Xiao-Li Pang
- Alberta Precision Laboratories – Public Health Laboratory (ProvLab), Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, Canada
| | - Bonita E. Lee
- Women and Children’s Research Institute, Stollery Children’s Hospital, University of Alberta, Edmonton, AB, Canada
| | - Ken J. Farion
- Children’s Hospital of Eastern Ontario, University of Ottawa, Ottawa, ON, Canada
| | - Serge Gouin
- Departments of Emergency Medicine and Pediatrics, Centre Hospitalier Universitaire (CHU) Sainte-Justine, Université de Montréal, Montréal, QC, Canada
| | - Suzanne Schuh
- Division of Emergency Medicine, Department of Paediatrics, Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Naveen Poonai
- Division of Pediatric Emergency Medicine, London Children’s Hospital Health Science Centre, Department of Pediatrics, Western University, London, ON, Canada
| | - Katrina F. Hurley
- Pediatric Emergency Medicine, Izaak Walton Killam (IWK) Children’s Hospital, Dalhousie University, Halifax, NS, Canada
| | - Yaron Finkelstein
- Division of Emergency Medicine, Department of Paediatrics, Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Jianling Xie
- Pediatric Emergency Medicine, Izaak Walton Killam (IWK) Children’s Hospital, Dalhousie University, Halifax, NS, Canada
| | - Sarah Williamson-Urquhart
- Section of Pediatric Emergency Medicine, Department of Pediatrics, Alberta Children’s Hospital, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Linda Chui
- Alberta Precision Laboratories – Public Health Laboratory (ProvLab), Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, Canada
| | - Laura Rossi
- Department of Biochemistry and Biomedical Sciences, McMaster University Medical Centre, Hamilton, ON, Canada
| | - Michael G. Surette
- Department of Biochemistry and Biomedical Sciences, McMaster University Medical Centre, Hamilton, ON, Canada
| | - Philip M. Sherman
- Cell Biology Program, Research Institute, Hospital for Sick Children, Toronto, ON, Canada
- Division of Gastroenterology, Hepatology and Nutrition, Department of Paediatrics, Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
- *Correspondence: Philip M. Sherman,
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11
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Hoke A, Chakraborty N, Gautam A, Hammamieh R, Jett M. Acute and Delayed Effects of Stress Eliciting Post-Traumatic Stress-Like Disorder Differentially Alters Fecal Microbiota Composition in a Male Mouse Model. Front Cell Infect Microbiol 2022; 12:810815. [PMID: 35300376 PMCID: PMC8921487 DOI: 10.3389/fcimb.2022.810815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Accepted: 02/04/2022] [Indexed: 11/19/2022] Open
Abstract
The association between the shift in fecal resident microbiome and social conflicts with long-term consequences on psychological plasticity, such as the development of post-traumatic stress disorder (PTSD), is yet to be comprehended. We developed an aggressor-exposed (Agg-E) social stress (SS) mouse model to mimic warzone-like conflicts, where random life-threatening interactions took place between naïve intruder mice and aggressive resident mice. Gradually these Agg-E mice developed distinct characteristics simulating PTSD-like aspects, whereas the control mice not exposed to Agg-E SS demonstrated distinct phenotypes. To further investigate the role of Agg-E SS on the resident microbiome, 16S rRNA gene sequencing was assayed using fecal samples collected at pre-, during, and post-SS time points. A time agonist shift in the fecal microbial composition of Agg-E mice in contrast to its controls suggested a persistent impact of Agg-E SS on resident microbiota. At the taxonomic level, Agg-E SS caused a significant shift in the time-resolved ratios of Firmicutes and Bacteroidetes abundance. Furthermore, Agg-E SS caused diverging shifts in the relative abundances of Verrucomicrobia and Actinobacteria. An in silico estimation of genomic potential identified a potentially perturbed cluster of bioenergetic networks, which became increasingly enriched with time since the termination of Agg-E SS. Supported by a growing number of studies, our results indicated the roles of the microbiome in a wide range of phenotypes that could mimic the comorbidities of PTSD, which would be directly influenced by energy deficiency. Together, the present work suggested the fecal microbiome as a potential tool to manage long-term effects of social conflicts, including the management of PTSD.
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Affiliation(s)
- Allison Hoke
- Oak Ridge Institute for Science and Education (ORISE), Oak Ridge, TN, United States
- Medical Readiness Systems Biology Branch, Center for Military Psychiatry and Neuroscience Research (CMPN), Walter Reed Army Institute of Research (WRAIR), Silver Spring, MD, United States
| | - Nabarun Chakraborty
- Medical Readiness Systems Biology Branch, Center for Military Psychiatry and Neuroscience Research (CMPN), Walter Reed Army Institute of Research (WRAIR), Silver Spring, MD, United States
- *Correspondence: Nabarun Chakraborty, ; Aarti Gautam,
| | - Aarti Gautam
- Medical Readiness Systems Biology Branch, Center for Military Psychiatry and Neuroscience Research (CMPN), Walter Reed Army Institute of Research (WRAIR), Silver Spring, MD, United States
- *Correspondence: Nabarun Chakraborty, ; Aarti Gautam,
| | - Rasha Hammamieh
- Medical Readiness Systems Biology Branch, Center for Military Psychiatry and Neuroscience Research (CMPN), Walter Reed Army Institute of Research (WRAIR), Silver Spring, MD, United States
| | - Marti Jett
- Medical Readiness Systems Biology Branch, Center for Military Psychiatry and Neuroscience Research (CMPN), Walter Reed Army Institute of Research (WRAIR), Silver Spring, MD, United States
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12
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Cheng J, Liu WQ, Zhu X, Zhang Q. Functional Diversity of HemN-like Proteins. ACS BIO & MED CHEM AU 2022; 2:109-119. [PMID: 37101745 PMCID: PMC10114718 DOI: 10.1021/acsbiomedchemau.1c00058] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
HemN is a radical S-adenosylmethionine (SAM) enzyme that catalyzes the anaerobic oxidative decarboxylation of coproporphyrinogen III to produce protoporphyrinogen IX, a key intermediate in heme biosynthesis. Proteins homologous to HemN (HemN-like proteins) are widespread in both prokaryotes and eukaryotes. Although these proteins are in most cases annotated as anaerobic coproporphyrinogen III oxidases (CPOs) in the public database, many of them are actually not CPOs but have diverse functions such as methyltransferases, cyclopropanases, heme chaperones, to name a few. This Perspective discusses the recent advances in the understanding of HemN-like proteins, and particular focus is placed on the diverse chemistries and functions of this growing protein family.
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Affiliation(s)
- Jinduo Cheng
- Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Wan-Qiu Liu
- Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Xiaoyu Zhu
- Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Qi Zhang
- Department of Chemistry, Fudan University, Shanghai, 200433, China
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13
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Feng M, Harijan RK, Harris LD, Tyler PC, Fröhlich RFG, Brown M, Schramm VL. Aminofutalosine Deaminase in the Menaquinone Pathway of Helicobacter pylori. Biochemistry 2021; 60:1933-1946. [PMID: 34077175 DOI: 10.1021/acs.biochem.1c00215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Helicobacter pylori is a Gram-negative bacterium that is responsible for gastric and duodenal ulcers. H. pylori uses the unusual mqn pathway with aminofutalosine (AFL) as an intermediate for menaquinone biosynthesis. Previous reports indicate that hydrolysis of AFL by 5'-methylthioadenosine nucleosidase (HpMTAN) is the direct path for producing downstream metabolites in the mqn pathway. However, genomic analysis indicates jhp0252 is a candidate for encoding AFL deaminase (AFLDA), an activity for deaminating aminofutolasine. The product, futalosine, is not a known substrate for bacterial MTANs. Recombinant jhp0252 was expressed and characterized as an AFL deaminase (HpAFLDA). Its catalytic specificity includes AFL, 5'-methylthioadenosine, 5'-deoxyadenosine, adenosine, and S-adenosylhomocysteine. The kcat/Km value for AFL is 6.8 × 104 M-1 s-1, 26-fold greater than that for adenosine. 5'-Methylthiocoformycin (MTCF) is a slow-onset inhibitor for HpAFLDA and demonstrated inhibitory effects on H. pylori growth. Supplementation with futalosine partially restored H. pylori growth under MTCF treatment, suggesting AFL deamination is significant for cell growth. The crystal structures of apo-HpAFLDA and with MTCF at the catalytic sites show a catalytic site Zn2+ or Fe2+ as the water-activating group. With bound MTCF, the metal ion is 2.0 Å from the sp3 hydroxyl group of the transition state analogue. Metabolomics analysis revealed that HpAFLDA has intracellular activity and is inhibited by MTCF. The mqn pathway in H. pylori bifurcates at aminofutalosine with HpMTAN producing adenine and depurinated futalosine and HpAFLDA producing futalosine. Inhibition of cellular HpMTAN or HpAFLDA decreased the cellular content of menaquinone-6, supporting roles for both enzymes in the pathway.
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Affiliation(s)
- Mu Feng
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Rajesh K Harijan
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Lawrence D Harris
- The Ferrier Research Institute, Victoria University of Wellington, Wellington 6140, New Zealand
| | - Peter C Tyler
- The Ferrier Research Institute, Victoria University of Wellington, Wellington 6140, New Zealand
| | - Richard F G Fröhlich
- The Ferrier Research Institute, Victoria University of Wellington, Wellington 6140, New Zealand
| | - Morais Brown
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Vern L Schramm
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
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14
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Varijakzhan D, Loh JY, Yap WS, Yusoff K, Seboussi R, Lim SHE, Lai KS, Chong CM. Bioactive Compounds from Marine Sponges: Fundamentals and Applications. Mar Drugs 2021; 19:246. [PMID: 33925365 PMCID: PMC8146879 DOI: 10.3390/md19050246] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 04/12/2021] [Accepted: 04/22/2021] [Indexed: 12/19/2022] Open
Abstract
Marine sponges are sessile invertebrates that can be found in temperate, polar and tropical regions. They are known to be major contributors of bioactive compounds, which are discovered in and extracted from the marine environment. The compounds extracted from these sponges are known to exhibit various bioactivities, such as antimicrobial, antitumor and general cytotoxicity. For example, various compounds isolated from Theonella swinhoei have showcased various bioactivities, such as those that are antibacterial, antiviral and antifungal. In this review, we discuss bioactive compounds that have been identified from marine sponges that showcase the ability to act as antibacterial, antiviral, anti-malarial and antifungal agents against human pathogens and fish pathogens in the aquaculture industry. Moreover, the application of such compounds as antimicrobial agents in other veterinary commodities, such as poultry, cattle farming and domesticated cats, is discussed, along with a brief discussion regarding the mode of action of these compounds on the targeted sites in various pathogens. The bioactivity of the compounds discussed in this review is focused mainly on compounds that have been identified between 2000 and 2020 and includes the novel compounds discovered from 2018 to 2021.
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Affiliation(s)
- Disha Varijakzhan
- Aquatic Animal Health and Therapeutics Laboratory, Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Malaysia;
| | - Jiun-Yan Loh
- Faculty of Applied Sciences, UCSI University, No. 1, Jalan Menara Gading, UCSI Heights, Cheras, Kuala Lumpur 56000, Malaysia; (J.-Y.L.); (W.-S.Y.)
| | - Wai-Sum Yap
- Faculty of Applied Sciences, UCSI University, No. 1, Jalan Menara Gading, UCSI Heights, Cheras, Kuala Lumpur 56000, Malaysia; (J.-Y.L.); (W.-S.Y.)
| | - Khatijah Yusoff
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Malaysia;
| | - Rabiha Seboussi
- Health Sciences Division, Al Ain Men’s College, Higher Colleges of Technology, Al Ain 17155, United Arab Emirates;
| | - Swee-Hua Erin Lim
- Health Sciences Division, Abu Dhabi Women’s College, Higher Colleges of Technology, Abu Dhabi 41012, United Arab Emirates;
| | - Kok-Song Lai
- Health Sciences Division, Abu Dhabi Women’s College, Higher Colleges of Technology, Abu Dhabi 41012, United Arab Emirates;
| | - Chou-Min Chong
- Aquatic Animal Health and Therapeutics Laboratory, Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Malaysia;
- Department of Aquaculture, Faculty of Agriculture, Universiti Putra Malaysia, Serdang 43400, Malaysia
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15
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Zhang Z, Liu L, Liu C, Sun Y, Zhang D. New aspects of microbial vitamin K2 production by expanding the product spectrum. Microb Cell Fact 2021; 20:84. [PMID: 33849534 PMCID: PMC8042841 DOI: 10.1186/s12934-021-01574-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 04/02/2021] [Indexed: 12/21/2022] Open
Abstract
Vitamin K2 (menaquinone, MK) is an essential lipid-soluble vitamin with critical roles in blood coagulation and bone metabolism. Chemically, the term vitamin K2 encompasses a group of small molecules that contain a common naphthoquinone head group and a polyisoprenyl side chain of variable length. Among them, menaquinone-7 (MK-7) is the most potent form. Here, the biosynthetic pathways of vitamin K2 and different types of MK produced by microorganisms are briefly introduced. Further, we provide a new aspect of MK-7 production, which shares a common naphthoquinone ring and polyisoprene biosynthesis pathway, by analyzing strategies for expanding the product spectrum. We review the findings of metabolic engineering strategies targeting the shikimate pathway, polyisoprene pathway, and menaquinone pathway, as well as membrane engineering, which provide comprehensive insights for enhancing the yield of MK-7. Finally, the current limitations and perspectives of microbial menaquinone production are also discussed. This article provides in-depth information on metabolic engineering strategies for vitamin K2 production by expanding the product spectrum.
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Affiliation(s)
- Zimeng Zhang
- School of Biological Engineering, Dalian Polytechnic University, Dalian, 116034, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Linxia Liu
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - Chuan Liu
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yumei Sun
- School of Biological Engineering, Dalian Polytechnic University, Dalian, 116034, China.
| | - Dawei Zhang
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China. .,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China. .,National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
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16
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Abby SS, Kazemzadeh K, Vragniau C, Pelosi L, Pierrel F. Advances in bacterial pathways for the biosynthesis of ubiquinone. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1861:148259. [PMID: 32663475 DOI: 10.1016/j.bbabio.2020.148259] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 05/29/2020] [Accepted: 06/04/2020] [Indexed: 12/20/2022]
Abstract
Ubiquinone is an important component of the electron transfer chains in proteobacteria and eukaryotes. The biosynthesis of ubiquinone requires multiple steps, most of which are common to bacteria and eukaryotes. Whereas the enzymes of the mitochondrial pathway that produces ubiquinone are highly similar across eukaryotes, recent results point to a rather high diversity of pathways in bacteria. This review focuses on ubiquinone in bacteria, highlighting newly discovered functions and detailing the proteins that are known to participate to its biosynthetic pathways. Novel results showing that ubiquinone can be produced by a pathway independent of dioxygen suggest that ubiquinone may participate to anaerobiosis, in addition to its well-established role for aerobiosis. We also discuss the supramolecular organization of ubiquinone biosynthesis proteins and we summarize the current understanding of the evolution of the ubiquinone pathways relative to those of other isoprenoid quinones like menaquinone and plastoquinone.
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Affiliation(s)
- Sophie Saphia Abby
- Univ. Grenoble Alpes, CNRS, CHU Grenoble Alpes, Grenoble INP, TIMC-IMAG, F-38000 Grenoble, France
| | - Katayoun Kazemzadeh
- Univ. Grenoble Alpes, CNRS, CHU Grenoble Alpes, Grenoble INP, TIMC-IMAG, F-38000 Grenoble, France
| | - Charles Vragniau
- Univ. Grenoble Alpes, CNRS, CHU Grenoble Alpes, Grenoble INP, TIMC-IMAG, F-38000 Grenoble, France
| | - Ludovic Pelosi
- Univ. Grenoble Alpes, CNRS, CHU Grenoble Alpes, Grenoble INP, TIMC-IMAG, F-38000 Grenoble, France.
| | - Fabien Pierrel
- Univ. Grenoble Alpes, CNRS, CHU Grenoble Alpes, Grenoble INP, TIMC-IMAG, F-38000 Grenoble, France.
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17
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Carl AG, Harris LD, Feng M, Nordstrøm LU, Gerfen GJ, Evans GB, Silakov A, Almo SC, Grove TL. Narrow-Spectrum Antibiotic Targeting of the Radical SAM Enzyme MqnE in Menaquinone Biosynthesis. Biochemistry 2020; 59:2562-2575. [DOI: 10.1021/acs.biochem.0c00070] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Ayala G. Carl
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Lawrence D. Harris
- The Ferrier Research Institute, Victoria University of Wellington, Wellington, New Zealand
- The Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland 5040, New Zealand
| | - Mu Feng
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Lars U. Nordstrøm
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Gary J. Gerfen
- Department of Biophysics, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Gary B. Evans
- The Ferrier Research Institute, Victoria University of Wellington, Wellington, New Zealand
- The Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland 5040, New Zealand
| | - Alexey Silakov
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Steven C. Almo
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Tyler L. Grove
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
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18
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Johnston JM, Bulloch EM. Advances in menaquinone biosynthesis: sublocalisation and allosteric regulation. Curr Opin Struct Biol 2020; 65:33-41. [PMID: 32634692 DOI: 10.1016/j.sbi.2020.05.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 05/08/2020] [Accepted: 05/11/2020] [Indexed: 12/31/2022]
Abstract
Menaquinones (vitamin K2) are a family of redox-active small molecules with critical functions across all domains of life, including energy generation in bacteria and bone health in humans. The enzymes involved in menaquinone biosynthesis also have bioengineering applications and are potential antimicrobial drug targets. New insights into the essential roles of menaquinones, and their potential to cause redox-related toxicity, have highlighted the need for this pathway to be tightly controlled. Here, we provide an overview of our current understanding of the classical menaquinone biosynthesis pathway in bacteria. We also review recent discoveries on protein-level allostery and sublocalisation of membrane-bound enzymes that have provided insight into the regulation of flux through this biosynthetic pathway.
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Affiliation(s)
- Jodie M Johnston
- School of Physical and Chemical Sciences, Biomolecular Interaction Centre, and Maurice Wilkins Centre for MolecularBiodiscovery, University of Canterbury, Christchurch 8041, New Zealand.
| | - Esther Mm Bulloch
- Laboratory of Structural Biology, School of Biological Sciences and Maurice Wilkins Centre for MolecularBiodiscovery, University of Auckland, Private Bag 92019, Auckland, New Zealand
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19
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Tan W, Liao TH, Wang J, Ye Y, Wei YC, Zhou HK, Xiao Y, Zhi XY, Shao ZH, Lyu LD, Zhao GP. A recently evolved diflavin-containing monomeric nitrate reductase is responsible for highly efficient bacterial nitrate assimilation. J Biol Chem 2020; 295:5051-5066. [PMID: 32111737 DOI: 10.1074/jbc.ra120.012859] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 02/25/2020] [Indexed: 12/11/2022] Open
Abstract
Nitrate is one of the major inorganic nitrogen sources for microbes. Many bacterial and archaeal lineages have the capacity to express assimilatory nitrate reductase (NAS), which catalyzes the rate-limiting reduction of nitrate to nitrite. Although a nitrate assimilatory pathway in mycobacteria has been proposed and validated physiologically and genetically, the putative NAS enzyme has yet to be identified. Here, we report the characterization of a novel NAS encoded by Mycolicibacterium smegmatis Msmeg_4206, designated NasN, which differs from the canonical NASs in its structure, electron transfer mechanism, enzymatic properties, and phylogenetic distribution. Using sequence analysis and biochemical characterization, we found that NasN is an NADPH-dependent, diflavin-containing monomeric enzyme composed of a canonical molybdopterin cofactor-binding catalytic domain and an FMN-FAD/NAD-binding, electron-receiving/transferring domain, making it unique among all previously reported hetero-oligomeric NASs. Genetic studies revealed that NasN is essential for aerobic M. smegmatis growth on nitrate as the sole nitrogen source and that the global transcriptional regulator GlnR regulates nasN expression. Moreover, unlike the NADH-dependent heterodimeric NAS enzyme, NasN efficiently supports bacterial growth under nitrate-limiting conditions, likely due to its significantly greater catalytic activity and oxygen tolerance. Results from a phylogenetic analysis suggested that the nasN gene is more recently evolved than those encoding other NASs and that its distribution is limited mainly to Actinobacteria and Proteobacteria. We observed that among mycobacterial species, most fast-growing environmental mycobacteria carry nasN, but that it is largely lacking in slow-growing pathogenic mycobacteria because of multiple independent genomic deletion events along their evolution.
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Affiliation(s)
- Wei Tan
- Department of Microbiology and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong 999077, China.,Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences and Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai 200032, China
| | - Tian-Hua Liao
- Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Jin Wang
- College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Yu Ye
- Department of Microbiology and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong 999077, China
| | - Yu-Chen Wei
- Department of Microbiology and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong 999077, China
| | - Hao-Kui Zhou
- Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Youli Xiao
- CAS Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Xiao-Yang Zhi
- Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming 650091, China
| | - Zhi-Hui Shao
- CAS Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Liang-Dong Lyu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences and Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai 200032, China
| | - Guo-Ping Zhao
- Department of Microbiology and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong 999077, China .,Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences and Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai 200032, China.,Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,CAS Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China.,Bio-Med Big Data Center, Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China.,Shanghai-MOST Key Laboratory for Health and Disease Genomics, Chinese National Human Genome Center, Shanghai 201203, China
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20
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Jin WB, Wu S, Xu YF, Yuan H, Tang GL. Recent advances in HemN-like radical S-adenosyl-l-methionine enzyme-catalyzed reactions. Nat Prod Rep 2020; 37:17-28. [DOI: 10.1039/c9np00032a] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
HemN-like radical S-adenosyl-l-methionine (SAM) enzymes have been recently disclosed to catalyze diverse chemically challenging reactions from primary to secondary metabolic pathways.
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Affiliation(s)
- Wen-Bing Jin
- State Key Laboratory of Bio-organic and Natural Products Chemistry
- Center for Excellence in Molecular Synthesis
- Shanghai Institute of Organic Chemistry
- University of Chinese Academy of Sciences
- Chinese Academy of Sciences
| | - Sheng Wu
- State Key Laboratory of Bio-organic and Natural Products Chemistry
- Center for Excellence in Molecular Synthesis
- Shanghai Institute of Organic Chemistry
- University of Chinese Academy of Sciences
- Chinese Academy of Sciences
| | - Yi-Fan Xu
- State Key Laboratory of Bio-organic and Natural Products Chemistry
- Center for Excellence in Molecular Synthesis
- Shanghai Institute of Organic Chemistry
- University of Chinese Academy of Sciences
- Chinese Academy of Sciences
| | - Hua Yuan
- State Key Laboratory of Bio-organic and Natural Products Chemistry
- Center for Excellence in Molecular Synthesis
- Shanghai Institute of Organic Chemistry
- University of Chinese Academy of Sciences
- Chinese Academy of Sciences
| | - Gong-Li Tang
- State Key Laboratory of Bio-organic and Natural Products Chemistry
- Center for Excellence in Molecular Synthesis
- Shanghai Institute of Organic Chemistry
- University of Chinese Academy of Sciences
- Chinese Academy of Sciences
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21
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Chen GY, Kao CY, Smith HB, Rust DP, Powers ZM, Li AY, Sauer JD. Mutation of the Transcriptional Regulator YtoI Rescues Listeria monocytogenes Mutants Deficient in the Essential Shared Metabolite 1,4-Dihydroxy-2-Naphthoate (DHNA). Infect Immun 2019; 88:e00366-19. [PMID: 31685546 PMCID: PMC6921671 DOI: 10.1128/iai.00366-19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 10/17/2019] [Indexed: 12/30/2022] Open
Abstract
Listeria monocytogenes, a Gram-positive, facultative intracellular pathogen, survives and replicates in the cytosol of host cells. Synthesis of 1,4-dihydroxy-2-naphthoate (DHNA), an intermediate of menaquinone biosynthesis, is essential for cytosolic survival of L. monocytogenes independent from its role in respiration. Here, we demonstrate that DHNA is essential for virulence in a murine model of listeriosis due to both respiration-dependent and -independent functions. In addition, DHNA can be both secreted and utilized as an extracellular shared metabolite to promote cytosolic survival inside host macrophages. To understand the role(s) of DHNA in L. monocytogenes intracellular survival and virulence, we isolated DHNA-deficient (ΔmenD strain) suppressor mutants that formed plaques in monolayers of fibroblasts. Five ΔmenD suppressor (mds) mutants additionally rescued at least 50% of the cytosolic survival defect of the parent ΔmenD mutant. Whole-genome sequencing revealed that four of the five suppressor mutants had independent missense mutations in a putative transcriptional regulator, ytoI (lmo1576). Clean deletion and complementation in trans confirmed that loss of ytoI could restore plaquing and cytosolic survival of DHNA-deficient L. monocytogenes RNA-seq transcriptome analysis revealed five genes (lmo0944, lmo1575, lmo1577, lmo2005, and lmo2006) expressed at a higher level in the ΔytoI strain than in the wild-type strain, whereas two genes (lmo1917 and lmo2103) demonstrated lower expression in the ΔytoI mutant. Intriguingly, the majority of these genes are involved in controlling pyruvate flux. Metabolic analysis confirmed that acetoin, acetate, and lactate flux were altered in a ΔytoI mutant, suggesting a critical role for regulating these metabolic programs. In conclusion, we have demonstrated that, similar to findings in select other bacteria, DHNA can act as a shared resource, and it is essential for cytosolic survival and virulence of L. monocytogenes Furthermore, we have identified a novel transcriptional regulator in L. monocytogenes and determined that its metabolic regulation is implicated in cytosolic survival of L. monocytogenes.
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Affiliation(s)
- Grischa Y Chen
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison Wisconsin, USA
| | - Cheng-Yen Kao
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison Wisconsin, USA
| | - Hans B Smith
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison Wisconsin, USA
| | - Drew P Rust
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison Wisconsin, USA
| | - Zachary M Powers
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison Wisconsin, USA
| | - Alexandria Y Li
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison Wisconsin, USA
| | - John-Demian Sauer
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison Wisconsin, USA
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22
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Verdaguer IB, Zafra CA, Crispim M, Sussmann RA, Kimura EA, Katzin AM. Prenylquinones in Human Parasitic Protozoa: Biosynthesis, Physiological Functions, and Potential as Chemotherapeutic Targets. Molecules 2019; 24:molecules24203721. [PMID: 31623105 PMCID: PMC6832408 DOI: 10.3390/molecules24203721] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 09/25/2019] [Accepted: 10/01/2019] [Indexed: 12/19/2022] Open
Abstract
Human parasitic protozoa cause a large number of diseases worldwide and, for some of these diseases, there are no effective treatments to date, and drug resistance has been observed. For these reasons, the discovery of new etiological treatments is necessary. In this sense, parasitic metabolic pathways that are absent in vertebrate hosts would be interesting research candidates for the identification of new drug targets. Most likely due to the protozoa variability, uncertain phylogenetic origin, endosymbiotic events, and evolutionary pressure for adaptation to adverse environments, a surprising variety of prenylquinones can be found within these organisms. These compounds are involved in essential metabolic reactions in organisms, for example, prevention of lipoperoxidation, participation in the mitochondrial respiratory chain or as enzymatic cofactors. This review will describe several prenylquinones that have been previously characterized in human pathogenic protozoa. Among all existing prenylquinones, this review is focused on ubiquinone, menaquinone, tocopherols, chlorobiumquinone, and thermoplasmaquinone. This review will also discuss the biosynthesis of prenylquinones, starting from the isoprenic side chains to the aromatic head group precursors. The isoprenic side chain biosynthesis maybe come from mevalonate or non-mevalonate pathways as well as leucine dependent pathways for isoprenoid biosynthesis. Finally, the isoprenic chains elongation and prenylquinone aromatic precursors origins from amino acid degradation or the shikimate pathway is reviewed. The phylogenetic distribution and what is known about the biological functions of these compounds among species will be described, as will the therapeutic strategies associated with prenylquinone metabolism in protozoan parasites.
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Affiliation(s)
- Ignasi B. Verdaguer
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508000, Brazil; (I.B.V.); (C.A.Z.); (M.C.); (E.A.K.)
| | - Camila A. Zafra
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508000, Brazil; (I.B.V.); (C.A.Z.); (M.C.); (E.A.K.)
| | - Marcell Crispim
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508000, Brazil; (I.B.V.); (C.A.Z.); (M.C.); (E.A.K.)
| | - Rodrigo A.C. Sussmann
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508000, Brazil; (I.B.V.); (C.A.Z.); (M.C.); (E.A.K.)
- Centro de Formação em Ciências Ambientais, Universidade Federal do Sul da Bahia, Porto Seguro 45810-000 Bahia, Brazil
| | - Emília A. Kimura
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508000, Brazil; (I.B.V.); (C.A.Z.); (M.C.); (E.A.K.)
| | - Alejandro M. Katzin
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508000, Brazil; (I.B.V.); (C.A.Z.); (M.C.); (E.A.K.)
- Correspondence: ; Tel.: +55-11-3091-7330; Fax: +5511-3091-7417
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23
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Sekowska A, Ashida H, Danchin A. Revisiting the methionine salvage pathway and its paralogues. Microb Biotechnol 2019; 12:77-97. [PMID: 30306718 PMCID: PMC6302742 DOI: 10.1111/1751-7915.13324] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 08/24/2018] [Accepted: 09/14/2018] [Indexed: 12/17/2022] Open
Abstract
Methionine is essential for life. Its chemistry makes it fragile in the presence of oxygen. Aerobic living organisms have selected a salvage pathway (the MSP) that uses dioxygen to regenerate methionine, associated to a ratchet-like step that prevents methionine back degradation. Here, we describe the variation on this theme, developed across the tree of life. Oxygen appeared long after life had developed on Earth. The canonical MSP evolved from ancestors that used both predecessors of ribulose bisphosphate carboxylase oxygenase (RuBisCO) and methanethiol in intermediate steps. We document how these likely promiscuous pathways were also used to metabolize the omnipresent by-products of S-adenosylmethionine radical enzymes as well as the aromatic and isoprene skeleton of quinone electron acceptors.
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Affiliation(s)
- Agnieszka Sekowska
- Institute of Cardiometabolism and NutritionHôpital de la Pitié‐SalpêtrièreParisFrance
| | - Hiroki Ashida
- Graduate School of Human Development and EnvironmentKobe UniversityKobeJapan
| | - Antoine Danchin
- Institute of Cardiometabolism and NutritionHôpital de la Pitié‐SalpêtrièreParisFrance
- Institute of Synthetic BiologyShenzhen Institutes of Advanced StudiesShenzhenChina
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24
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Taylor AJ, Kelly DJ. The function, biogenesis and regulation of the electron transport chains in Campylobacter jejuni: New insights into the bioenergetics of a major food-borne pathogen. Adv Microb Physiol 2019; 74:239-329. [PMID: 31126532 DOI: 10.1016/bs.ampbs.2019.02.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Campylobacter jejuni is a zoonotic Epsilonproteobacterium that grows in the gastrointestinal tract of birds and mammals, and is the most frequent cause of food-borne bacterial gastroenteritis worldwide. As an oxygen-sensitive microaerophile, C. jejuni has to survive high environmental oxygen tensions, adapt to oxygen limitation in the host intestine and resist host oxidative attack. Despite its small genome size, C. jejuni is a versatile and metabolically active pathogen, with a complex and highly branched set of respiratory chains allowing the use of a wide range of electron donors and alternative electron acceptors in addition to oxygen, including fumarate, nitrate, nitrite, tetrathionate and N- or S-oxides. Several novel enzymes participate in these electron transport chains, including a tungsten containing formate dehydrogenase, a Complex I that uses flavodoxin and not NADH, a periplasmic facing fumarate reductase and a cytochrome c tetrathionate reductase. This review presents an updated description of the composition and bioenergetics of these various respiratory chains as they are currently understood, including recent work that gives new insights into energy conservation during electron transport to various alternative electron acceptors. The regulation of synthesis and assembly of the electron transport chains is also discussed. A deeper appreciation of the unique features of the respiratory systems of C. jejuni may be helpful in informing strategies to control this important pathogen.
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Affiliation(s)
- Aidan J Taylor
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - David J Kelly
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Western Bank, Sheffield S10 2TN, UK
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25
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Novel enzymology in futalosine-dependent menaquinone biosynthesis. Curr Opin Chem Biol 2018; 47:134-141. [DOI: 10.1016/j.cbpa.2018.09.015] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 09/13/2018] [Accepted: 09/20/2018] [Indexed: 12/12/2022]
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26
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Degli Esposti M. A Journey across Genomes Uncovers the Origin of Ubiquinone in Cyanobacteria. Genome Biol Evol 2018; 9:3039-3053. [PMID: 29106540 PMCID: PMC5714133 DOI: 10.1093/gbe/evx225] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/31/2017] [Indexed: 12/15/2022] Open
Abstract
Ubiquinone (Q) is an isoprenoid quinone that functions as membrane electron carrier in mitochondria and bacterial organisms belonging to the alpha, beta, and gamma class of proteobacteria. The biosynthesis of Q follows various biochemical steps catalyzed by diverse proteins that are, in general, homologous in mitochondria and bacteria. Nonorthologous proteins can also contribute to some biochemical steps as originally uncovered in Escherichia coli, which is the best studied organism for Q biosynthesis in prokaryotes. However, the origin of the biosynthetic pathway of Q has remained obscure. Here, I show by genome analysis that Q biosynthesis originated in cyanobacteria and then diversified in anaerobic alpha proteobacteria which have extant relatives in members of the Rhodospirillaceae family. Two distinct biochemical pathways diverged when ambient oxygen reached current levels on earth, one leading to the well-known series of Ubi genes found in E. coli, and the other containing CoQ proteins originally found in eukaryotes. Extant alpha proteobacteria show Q biosynthesis pathways that are more similar to that present in mitochondria than to that of E. coli. Hence, this work clarifies not only the origin but also the evolution of Q biosynthesis from bacteria to mitochondria.
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Affiliation(s)
- Mauro Degli Esposti
- Italian Institute of Technology, Genoa, Italy.,Center for Genomic Sciences, Universidad National Autonoma de Mexico Campus of Cuernavaca, Cuernavaca, Morelos, Mexico
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27
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Cenci U, Qiu H, Pillonel T, Cardol P, Remacle C, Colleoni C, Kadouche D, Chabi M, Greub G, Bhattacharya D, Ball SG. Host-pathogen biotic interactions shaped vitamin K metabolism in Archaeplastida. Sci Rep 2018; 8:15243. [PMID: 30323231 PMCID: PMC6189191 DOI: 10.1038/s41598-018-33663-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 10/03/2018] [Indexed: 02/01/2023] Open
Abstract
Menaquinone (vitamin K2) shuttles electrons between membrane-bound respiratory complexes under microaerophilic conditions. In photosynthetic eukaryotes and cyanobacteria, phylloquinone (vitamin K1) participates in photosystem I function. Here we elucidate the evolutionary history of vitamin K metabolism in algae and plants. We show that Chlamydiales intracellular pathogens made major genetic contributions to the synthesis of the naphthoyl ring core and the isoprenoid side-chain of these quinones. Production of the core in extremophilic red algae is under control of a menaquinone (Men) gene cluster consisting of 7 genes that putatively originated via lateral gene transfer (LGT) from a chlamydial donor to the plastid genome. In other green and red algae, functionally related nuclear genes also originated via LGT from a non-cyanobacterial, albeit unidentified source. In addition, we show that 3-4 of the 9 required steps for synthesis of the isoprenoid side chains are under control of genes of chlamydial origin. These results are discussed in the light of the hypoxic response experienced by the cyanobacterial endosymbiont when it gained access to the eukaryotic cytosol.
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Affiliation(s)
- U Cenci
- Unité de Glycobiologie Structurale et Fonctionnelle, UMR 8576 CNRS-USTL, Université des Sciences et Technologies de Lille, Bâtiment C9, Cité Scientifique, 59655, Villeneuve d'Ascq Cedex, France
| | - H Qiu
- Department of Ecology, Evolution & Natural Resources, Rutgers University, New Brunswick, NJ, 08901, USA
| | - T Pillonel
- Center for Research on Intracellular Bacteria (CRIB), Institute of Microbiology, University Hospital Center and University of Lausanne, 1011, Lausanne, Switzerland
| | - P Cardol
- Laboratoire de Génétique et Physiologie des Microalgues, InBioS/Phytosystems, B22 Institut de Botanique, Université de Liège, 4000, Liège, Belgium
| | - C Remacle
- Laboratoire de Génétique et Physiologie des Microalgues, InBioS/Phytosystems, B22 Institut de Botanique, Université de Liège, 4000, Liège, Belgium
| | - C Colleoni
- Unité de Glycobiologie Structurale et Fonctionnelle, UMR 8576 CNRS-USTL, Université des Sciences et Technologies de Lille, Bâtiment C9, Cité Scientifique, 59655, Villeneuve d'Ascq Cedex, France
| | - D Kadouche
- Unité de Glycobiologie Structurale et Fonctionnelle, UMR 8576 CNRS-USTL, Université des Sciences et Technologies de Lille, Bâtiment C9, Cité Scientifique, 59655, Villeneuve d'Ascq Cedex, France
| | - M Chabi
- Unité de Glycobiologie Structurale et Fonctionnelle, UMR 8576 CNRS-USTL, Université des Sciences et Technologies de Lille, Bâtiment C9, Cité Scientifique, 59655, Villeneuve d'Ascq Cedex, France
| | - G Greub
- Center for Research on Intracellular Bacteria (CRIB), Institute of Microbiology, University Hospital Center and University of Lausanne, 1011, Lausanne, Switzerland
| | - D Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, 08901, USA
| | - S G Ball
- Unité de Glycobiologie Structurale et Fonctionnelle, UMR 8576 CNRS-USTL, Université des Sciences et Technologies de Lille, Bâtiment C9, Cité Scientifique, 59655, Villeneuve d'Ascq Cedex, France.
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28
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Amara A, Takano E, Breitling R. Development and validation of an updated computational model of Streptomyces coelicolor primary and secondary metabolism. BMC Genomics 2018; 19:519. [PMID: 29973148 PMCID: PMC6040156 DOI: 10.1186/s12864-018-4905-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 06/28/2018] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Streptomyces species produce a vast diversity of secondary metabolites of clinical and biotechnological importance, in particular antibiotics. Recent developments in metabolic engineering, synthetic and systems biology have opened new opportunities to exploit Streptomyces secondary metabolism, but achieving industry-level production without time-consuming optimization has remained challenging. Genome-scale metabolic modelling has been shown to be a powerful tool to guide metabolic engineering strategies for accelerated strain optimization, and several generations of models of Streptomyces metabolism have been developed for this purpose. RESULTS Here, we present the most recent update of a genome-scale stoichiometric constraint-based model of the metabolism of Streptomyces coelicolor, the major model organism for the production of antibiotics in the genus. We show that the updated model enables better metabolic flux and biomass predictions and facilitates the integrative analysis of multi-omics data such as transcriptomics, proteomics and metabolomics. CONCLUSIONS The updated model presented here provides an enhanced basis for the next generation of metabolic engineering attempts in Streptomyces.
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Affiliation(s)
- Adam Amara
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, School of Chemistry, Faculty of Science and Engineering, University of Manchester, 131 Princess Street, Manchester, M1 7DN UK
| | - Eriko Takano
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, School of Chemistry, Faculty of Science and Engineering, University of Manchester, 131 Princess Street, Manchester, M1 7DN UK
| | - Rainer Breitling
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, School of Chemistry, Faculty of Science and Engineering, University of Manchester, 131 Princess Street, Manchester, M1 7DN UK
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29
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Baek I, Kim M, Lee I, Na SI, Goodfellow M, Chun J. Phylogeny Trumps Chemotaxonomy: A Case Study Involving Turicella otitidis. Front Microbiol 2018; 9:834. [PMID: 29760685 PMCID: PMC5936774 DOI: 10.3389/fmicb.2018.00834] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 04/12/2018] [Indexed: 11/13/2022] Open
Abstract
The genus Turicella was proposed to harbor clinical strains isolated from middle-ear fluids of patients with otitis media. 16S rRNA phylogeny showed that it belonged to the mycolic acid-containing actinobacteria, currently classified in the order Corynebacteriales, and was closely related to the genus Corynebacterium. A new genus was proposed for the organisms as unlike corynebacteria they lacked mycolic acids and had different menaquinones. Here, we carried out large-scale comparative genomics on representative strains of the genera Corynebacterium and Turicella to check if this chemotaxonomic classification is justified. Three genes that are known to play an essential role in mycolic acid biosynthesis were absent in Turicella and two other mycolate-less Corynebacterium spp., explaining the lack of mycolic acids resulted from the deletion of genes and does not confer any phylogenetic context. Polyphasic phylogenetic analyses using 16S rRNA, bacterial core genes and genes responsible for synthesizing menaquinones unequivocally indicate that Turicella is a true member of the genus Corynebacterium. Here, we demonstrate that menaquinone and mycolic acid that have been used as critical taxonomic markers should be interpreted carefully, particularly when genome-based taxonomy is readily available. Based on the phylogenetic analysis, we propose to reclassify Turicella otitidis as Corynebacterium otitidis comb. nov.
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Affiliation(s)
- Inwoo Baek
- School of Biological Sciences, Seoul National University, Seoul, South Korea.,Institute of Molecular Biology and Genetics, Seoul National University, Seoul, South Korea
| | - Mincheol Kim
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon, South Korea
| | - Imchang Lee
- School of Biological Sciences, Seoul National University, Seoul, South Korea.,Institute of Molecular Biology and Genetics, Seoul National University, Seoul, South Korea
| | - Seong-In Na
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul, South Korea.,Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, South Korea
| | - Michael Goodfellow
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Jongsik Chun
- School of Biological Sciences, Seoul National University, Seoul, South Korea.,Institute of Molecular Biology and Genetics, Seoul National University, Seoul, South Korea.,Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, South Korea
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30
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Two dedicated class C radical S-adenosylmethionine methyltransferases concertedly catalyse the synthesis of 7,8-dimethylmenaquinone. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1859:300-308. [DOI: 10.1016/j.bbabio.2018.01.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 01/24/2018] [Accepted: 01/28/2018] [Indexed: 12/24/2022]
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31
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Matsui H, Takahashi T, Murayama SY, Kawaguchi M, Matsuo K, Nakamura M. Protective efficacy of a hydroxy fatty acid against gastric Helicobacter infections. Helicobacter 2017; 22. [PMID: 28834011 DOI: 10.1111/hel.12430] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
BACKGROUND We have previously revealed that omega-3 polyunsaturated fatty acids can prevent Helicobacter pylori infection by blocking the futalosine pathway, an alternative route for menaquinone (MK) biosynthesis. MATERIALS AND METHODS 1, Different H. pylori strains were grown in liquid media supplemented with linoleic acid, an omega-6 fatty acid, or its 10-hydroxy derivative, 10-hydroxy-cis-12-octadecenoic acid (HYA), in the presence or absence of MK. The bacterial numbers in the media were estimated by plating; 2, C57BL/6NCrl mice received drinking water supplemented with different fatty acids starting from 1 week before infection with H. pylori or Helicobacter suis until the end of the experiment. The gastric colonization levels of H. pylori or H. suis were determined 2 weeks after infection by plating or quantitative PCR, respectively; 3, Mice were given HYA, starting 1 week before infection with H. suis and continuing until 6 months after infection, for analysis of the gastric conditions. RESULTS 1, A low concentration (20 μmol/L) of HYA in culture broth suppressed the growth of H. pylori, and this inhibition was reduced by MK supplementation; 2, HYA treatment protected mice against H. pylori or H. suis infection; 3, HYA treatment suppressed the formation of lymphoid follicles in the gastric mucus layer after H. suis infection. CONCLUSIONS HYA prevents gastric Helicobacter infections by blocking their futalosine pathways. Daily HYA supplementation is effective for the prevention of gastric mucosa-associated lymphoid tissue lymphoma induced by persistent infection with H. suis.
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Affiliation(s)
- Hidenori Matsui
- Department of Infection Control and Immunology, Kitasato Institute for Life Sciences and Graduate School of Infection Control Sciences, Kitasato University, Minato-ku, Tokyo, Japan
| | - Tetsufumi Takahashi
- Department of Kampo Pharmacy, Yokohama University of Pharmacy, Totsuka-ku, Yokohama-shi, Kanagawa, Japan
| | - Somay Y Murayama
- Laboratory of Medical Microbiology, Graduate School of Pharmacy, Nihon University, Funabashi-shi, Chiba, Japan
| | | | - Koichi Matsuo
- Laboratory of Cell and Tissue Biology, Keio University School of Medicine, Shinjuku-ku, Tokyo, Japan
| | - Masahiko Nakamura
- Center for Clinical Pharmacy and Clinical Sciences, School of Pharmaceutical Sciences, Kitasato University, Minato-ku, Tokyo, Japan
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32
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Cotrim CA, Weidner A, Strehmel N, Bisol TB, Meyer D, Brandt W, Wessjohann LA, Stubbs MT. A Distinct Aromatic Prenyltransferase Associated with the Futalosine Pathway. ChemistrySelect 2017. [DOI: 10.1002/slct.201702151] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Camila A. Cotrim
- Institute of Biochemistry and Biotechnology; Martin Luther University Halle-Wittenberg; Kurt-Mothes-Str. 3 06120 Halle/Saale Germany
| | - Annett Weidner
- Institute of Biochemistry and Biotechnology; Martin Luther University Halle-Wittenberg; Kurt-Mothes-Str. 3 06120 Halle/Saale Germany
| | - Nadine Strehmel
- Stress and Developmental Biology; Leibniz Institute of Plant Biochemistry; Weinberg 3 06120 Halle/Saale Germany
| | - Tula B. Bisol
- Bioorganic Chemistry; Leibniz Institute of Plant Biochemistry; Weinberg 3 06120 Halle/Saale, Germany
| | - Danilo Meyer
- Bioorganic Chemistry; Leibniz Institute of Plant Biochemistry; Weinberg 3 06120 Halle/Saale, Germany
| | - Wolfgang Brandt
- Bioorganic Chemistry; Leibniz Institute of Plant Biochemistry; Weinberg 3 06120 Halle/Saale, Germany
| | - Ludger A. Wessjohann
- Bioorganic Chemistry; Leibniz Institute of Plant Biochemistry; Weinberg 3 06120 Halle/Saale, Germany
| | - Milton T. Stubbs
- Institute of Biochemistry and Biotechnology; Martin Luther University Halle-Wittenberg; Kurt-Mothes-Str. 3 06120 Halle/Saale Germany
- ZIK HALOmem; Kurt-Mothes-Str. 3 06120 Halle/Saale Germany
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33
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Aleku GA, Nowicka B, Turner NJ. Biocatalytic Potential of Enzymes Involved in the Biosynthesis of Isoprenoid Quinones. ChemCatChem 2017. [DOI: 10.1002/cctc.201700685] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Godwin A. Aleku
- School of Chemistry and Manchester Institute of Biotechnology; University of Manchester; 131 Princess Street Manchester M1 7DN UK
| | - Beatrycze Nowicka
- Department of Plant Physiology and Biochemistry; Faculty of Biochemistry, Biophysics and Biotechnology; Jagiellonian University; Gronostajowa 7 30-387 Krakow Poland
| | - Nicholas J. Turner
- School of Chemistry and Manchester Institute of Biotechnology; University of Manchester; 131 Princess Street Manchester M1 7DN UK
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34
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Loiseau L, Fyfe C, Aussel L, Hajj Chehade M, Hernández SB, Faivre B, Hamdane D, Mellot-Draznieks C, Rascalou B, Pelosi L, Velours C, Cornu D, Lombard M, Casadesús J, Pierrel F, Fontecave M, Barras F. The UbiK protein is an accessory factor necessary for bacterial ubiquinone (UQ) biosynthesis and forms a complex with the UQ biogenesis factor UbiJ. J Biol Chem 2017; 292:11937-11950. [PMID: 28559279 DOI: 10.1074/jbc.m117.789164] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 05/08/2017] [Indexed: 11/06/2022] Open
Abstract
Ubiquinone (UQ), also referred to as coenzyme Q, is a widespread lipophilic molecule in both prokaryotes and eukaryotes in which it primarily acts as an electron carrier. Eleven proteins are known to participate in UQ biosynthesis in Escherichia coli, and we recently demonstrated that UQ biosynthesis requires additional, nonenzymatic factors, some of which are still unknown. Here, we report on the identification of a bacterial gene, yqiC, which is required for efficient UQ biosynthesis, and which we have renamed ubiK Using several methods, we demonstrated that the UbiK protein forms a complex with the C-terminal part of UbiJ, another UQ biogenesis factor we previously identified. We found that both proteins are likely to contribute to global UQ biosynthesis rather than to a specific biosynthetic step, because both ubiK and ubiJ mutants accumulated octaprenylphenol, an early intermediate of the UQ biosynthetic pathway. Interestingly, we found that both proteins are dispensable for UQ biosynthesis under anaerobiosis, even though they were expressed in the absence of oxygen. We also provide evidence that the UbiK-UbiJ complex interacts with palmitoleic acid, a major lipid in E. coli Last, in Salmonella enterica, ubiK was required for proliferation in macrophages and virulence in mice. We conclude that although the role of the UbiK-UbiJ complex remains unknown, our results support the hypothesis that UbiK is an accessory factor of Ubi enzymes and facilitates UQ biosynthesis by acting as an assembly factor, a targeting factor, or both.
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Affiliation(s)
- Laurent Loiseau
- Aix Marseille Université, CNRS, Laboratoire de Chimie Bactérienne (LCB) UMR 7283, Institut de Microbiologie de la Méditerranée (IMM), 13402, Marseille, France
| | - Cameron Fyfe
- Laboratoire de Chimie des Processus Biologiques, UMR8229 CNRS, Collège de France, Université Pierre et Marie Curie, 11 place Marcelin Berthelot, 75 231 Paris Cedex 05, France
| | - Laurent Aussel
- Aix Marseille Université, CNRS, Laboratoire de Chimie Bactérienne (LCB) UMR 7283, Institut de Microbiologie de la Méditerranée (IMM), 13402, Marseille, France
| | - Mahmoud Hajj Chehade
- University Grenoble Alpes, Laboratoire Technologies de l'Ingénierie Médicale et de la Complexité-Informatique, Mathématiques et Applications, Techniques de l'Ingénierie Médicale et de la Complexité-Informatique, Mathématiques et Applications, Grenoble (TIMC-IMAG), UMR 5525, 38000 Grenoble, France; CNRS, TIMC-IMAG, 38000 Grenoble, France
| | - Sara B Hernández
- Departamento de Genética, Universidad de Sevilla, 41012 Sevilla, Spain
| | - Bruno Faivre
- Laboratoire de Chimie des Processus Biologiques, UMR8229 CNRS, Collège de France, Université Pierre et Marie Curie, 11 place Marcelin Berthelot, 75 231 Paris Cedex 05, France
| | - Djemel Hamdane
- Laboratoire de Chimie des Processus Biologiques, UMR8229 CNRS, Collège de France, Université Pierre et Marie Curie, 11 place Marcelin Berthelot, 75 231 Paris Cedex 05, France
| | - Caroline Mellot-Draznieks
- Laboratoire de Chimie des Processus Biologiques, UMR8229 CNRS, Collège de France, Université Pierre et Marie Curie, 11 place Marcelin Berthelot, 75 231 Paris Cedex 05, France
| | - Bérengère Rascalou
- University Grenoble Alpes, Laboratoire Technologies de l'Ingénierie Médicale et de la Complexité-Informatique, Mathématiques et Applications, Techniques de l'Ingénierie Médicale et de la Complexité-Informatique, Mathématiques et Applications, Grenoble (TIMC-IMAG), UMR 5525, 38000 Grenoble, France; CNRS, TIMC-IMAG, 38000 Grenoble, France
| | - Ludovic Pelosi
- University Grenoble Alpes, Laboratoire Technologies de l'Ingénierie Médicale et de la Complexité-Informatique, Mathématiques et Applications, Techniques de l'Ingénierie Médicale et de la Complexité-Informatique, Mathématiques et Applications, Grenoble (TIMC-IMAG), UMR 5525, 38000 Grenoble, France; CNRS, TIMC-IMAG, 38000 Grenoble, France
| | - Christophe Velours
- Institut de Biologie Integrative de la cellule, Plateforme Interactions des Macromolécules, I2BC, UMR 9198 CNRS, Bât 430F, 91405 Orsay Cedex, France
| | - David Cornu
- Institut de Biologie Integrative de la cellule, Plateforme SICaPS, I2BC, CNRS, Centre de Recherche de Gif, SICaPS, F-91198 Gif-sur-Yvette Cedex, France
| | - Murielle Lombard
- Laboratoire de Chimie des Processus Biologiques, UMR8229 CNRS, Collège de France, Université Pierre et Marie Curie, 11 place Marcelin Berthelot, 75 231 Paris Cedex 05, France
| | - Josep Casadesús
- Departamento de Genética, Universidad de Sevilla, 41012 Sevilla, Spain
| | - Fabien Pierrel
- University Grenoble Alpes, Laboratoire Technologies de l'Ingénierie Médicale et de la Complexité-Informatique, Mathématiques et Applications, Techniques de l'Ingénierie Médicale et de la Complexité-Informatique, Mathématiques et Applications, Grenoble (TIMC-IMAG), UMR 5525, 38000 Grenoble, France; CNRS, TIMC-IMAG, 38000 Grenoble, France.
| | - Marc Fontecave
- Laboratoire de Chimie des Processus Biologiques, UMR8229 CNRS, Collège de France, Université Pierre et Marie Curie, 11 place Marcelin Berthelot, 75 231 Paris Cedex 05, France.
| | - Frédéric Barras
- Aix Marseille Université, CNRS, Laboratoire de Chimie Bactérienne (LCB) UMR 7283, Institut de Microbiologie de la Méditerranée (IMM), 13402, Marseille, France.
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35
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Hein S, Klimmek O, Polly M, Kern M, Simon J. A class C radicalS-adenosylmethionine methyltransferase synthesizes 8-methylmenaquinone. Mol Microbiol 2017; 104:449-462. [DOI: 10.1111/mmi.13638] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Sascha Hein
- Microbial Energy Conversion and Biotechnology, Department of Biology; Technische Universität Darmstadt; Schnittspahnstraße 10 64287 Darmstadt Germany
| | - Oliver Klimmek
- Microbial Energy Conversion and Biotechnology, Department of Biology; Technische Universität Darmstadt; Schnittspahnstraße 10 64287 Darmstadt Germany
| | - Markus Polly
- Microbial Energy Conversion and Biotechnology, Department of Biology; Technische Universität Darmstadt; Schnittspahnstraße 10 64287 Darmstadt Germany
| | - Melanie Kern
- Microbial Energy Conversion and Biotechnology, Department of Biology; Technische Universität Darmstadt; Schnittspahnstraße 10 64287 Darmstadt Germany
| | - Jörg Simon
- Microbial Energy Conversion and Biotechnology, Department of Biology; Technische Universität Darmstadt; Schnittspahnstraße 10 64287 Darmstadt Germany
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36
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Sorokin DY, Messina E, Smedile F, Roman P, Damsté JSS, Ciordia S, Mena MC, Ferrer M, Golyshin PN, Kublanov IV, Samarov NI, Toshchakov SV, La Cono V, Yakimov MM. Discovery of anaerobic lithoheterotrophic haloarchaea, ubiquitous in hypersaline habitats. ISME JOURNAL 2017; 11:1245-1260. [PMID: 28106880 PMCID: PMC5437934 DOI: 10.1038/ismej.2016.203] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 11/23/2016] [Accepted: 12/05/2016] [Indexed: 12/20/2022]
Abstract
Hypersaline anoxic habitats harbour numerous novel uncultured archaea whose metabolic and ecological roles remain to be elucidated. Until recently, it was believed that energy generation via dissimilatory reduction of sulfur compounds is not functional at salt saturation conditions. Recent discovery of the strictly anaerobic acetotrophic Halanaeroarchaeum compels to change both this assumption and the traditional view on haloarchaea as aerobic heterotrophs. Here we report on isolation and characterization of a novel group of strictly anaerobic lithoheterotrophic haloarchaea, which we propose to classify as a new genus Halodesulfurarchaeum. Members of this previously unknown physiological group are capable of utilising formate or hydrogen as electron donors and elemental sulfur, thiosulfate or dimethylsulfoxide as electron acceptors. Using genome-wide proteomic analysis we have detected the full set of enzymes required for anaerobic respiration and analysed their substrate-specific expression. Such advanced metabolic plasticity and type of respiration, never seen before in haloarchaea, empower the wide distribution of Halodesulfurarchaeum in hypersaline inland lakes, solar salterns, lagoons and deep submarine anoxic brines. The discovery of this novel functional group of sulfur-respiring haloarchaea strengthens the evidence of their possible role in biogeochemical sulfur cycling linked to the terminal anaerobic carbon mineralisation in so far overlooked hypersaline anoxic habitats.
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Affiliation(s)
- Dimitry Y Sorokin
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia.,Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Enzo Messina
- Institute for Coastal Marine Environment, CNR, Messina, Italy
| | | | - Pawel Roman
- Sub-department of Environmental Technology, Wageningen University, Wageningen, The Netherlands.,Wetsus, Centre of Excellence for Sustainable Water Technology, Leeuwarden, The Netherlands
| | - Jaap S Sinninghe Damsté
- Department of Marine Organic Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Den Burg, The Netherlands
| | - Sergio Ciordia
- Proteomics Unit, National Center for Biotechnology, CSIC, Madrid, Spain
| | - Maria Carmen Mena
- Proteomics Unit, National Center for Biotechnology, CSIC, Madrid, Spain
| | | | - Peter N Golyshin
- School of Biological Sciences, Bangor University, Bangor, UK.,Immanuel Kant Baltic Federal University, Kaliningrad, Russia
| | - Ilya V Kublanov
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Nazar I Samarov
- Immanuel Kant Baltic Federal University, Kaliningrad, Russia
| | | | | | - Michail M Yakimov
- Institute for Coastal Marine Environment, CNR, Messina, Italy.,Immanuel Kant Baltic Federal University, Kaliningrad, Russia
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37
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From low- to high-potential bioenergetic chains: Thermodynamic constraints of Q-cycle function. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:1569-1579. [DOI: 10.1016/j.bbabio.2016.06.006] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 06/14/2016] [Accepted: 06/16/2016] [Indexed: 11/27/2022]
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38
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Narrow-spectrum inhibitors targeting an alternative menaquinone biosynthetic pathway of Helicobacter pylori. J Infect Chemother 2016; 22:587-92. [DOI: 10.1016/j.jiac.2016.05.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 05/13/2016] [Accepted: 05/29/2016] [Indexed: 01/14/2023]
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39
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Evolution of Ubiquinone Biosynthesis: Multiple Proteobacterial Enzymes with Various Regioselectivities To Catalyze Three Contiguous Aromatic Hydroxylation Reactions. mSystems 2016; 1:mSystems00091-16. [PMID: 27822549 PMCID: PMC5069965 DOI: 10.1128/msystems.00091-16] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 08/05/2016] [Indexed: 11/27/2022] Open
Abstract
UQ, a key molecule for cellular bioenergetics that is conserved from proteobacteria to humans, appeared in an ancestral proteobacterium more than 2 billion years ago. UQ biosynthesis has been studied only in a few model organisms, and thus, the diversity of UQ biosynthesis pathways is largely unknown. In the work reported here, we conducted a phylogenomic analysis of hydroxylases involved in UQ biosynthesis. Our results support the existence of at least two UQ hydroxylases in the proteobacterial ancestor, and yet, we show that their number varies from one to four in extant proteobacterial species. Our biochemical experiments demonstrated that bacteria containing only one or two UQ hydroxylases have developed generalist enzymes that are able to catalyze several steps of UQ biosynthesis. Our study documents a rare case where evolution favored the broadening of an enzyme’s regioselectivity, which resulted in gene loss in several proteobacterial species with small genomes. The ubiquitous ATP synthase uses an electrochemical gradient to synthesize cellular energy in the form of ATP. The production of this electrochemical gradient relies on liposoluble proton carriers like ubiquinone (UQ), which is used in the respiratory chains of eukaryotes and proteobacteria. The biosynthesis of UQ requires three hydroxylation reactions on contiguous positions of an aromatic ring. In Escherichia coli, each of three UQ flavin monooxygenases (FMOs), called UbiF, UbiH, and UbiI, modifies a single position of the aromatic ring. This pattern of three hydroxylation reactions/three proteins has been accepted as a paradigm in UQ biology. Using a phylogenetic analysis, we found that UbiF, UbiH, and UbiI are detected only in a small fraction of proteobacteria, and we identified two new types of UQ FMOs: UbiM, which is distributed in members of the alpha, beta, and gamma classes of proteobacteria, and UbiL, which is restricted to members of the alphaproteobacteria. Remarkably, the ubiL and ubiM genes were found in genomes with fewer than three UQ hydroxylase-encoding genes. We demonstrated, using biochemical approaches, that UbiL from Rhodospirillum rubrum and UbiM from Neisseria meningitidis hydroxylate, respectively, two and three positions of the aromatic ring during UQ biosynthesis. We conclude that bacteria have evolved a large repertoire of hydroxylase combinations for UQ biosynthesis, including pathways with either three specialist enzymes or pathways with one or two generalist enzymes of broader regioselectivity. The emergence of the latter is potentially related to genome reduction events. IMPORTANCE UQ, a key molecule for cellular bioenergetics that is conserved from proteobacteria to humans, appeared in an ancestral proteobacterium more than 2 billion years ago. UQ biosynthesis has been studied only in a few model organisms, and thus, the diversity of UQ biosynthesis pathways is largely unknown. In the work reported here, we conducted a phylogenomic analysis of hydroxylases involved in UQ biosynthesis. Our results support the existence of at least two UQ hydroxylases in the proteobacterial ancestor, and yet, we show that their number varies from one to four in extant proteobacterial species. Our biochemical experiments demonstrated that bacteria containing only one or two UQ hydroxylases have developed generalist enzymes that are able to catalyze several steps of UQ biosynthesis. Our study documents a rare case where evolution favored the broadening of an enzyme’s regioselectivity, which resulted in gene loss in several proteobacterial species with small genomes.
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40
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Kellermann MY, Yoshinaga MY, Valentine RC, Wörmer L, Valentine DL. Important roles for membrane lipids in haloarchaeal bioenergetics. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2940-2956. [PMID: 27565574 DOI: 10.1016/j.bbamem.2016.08.010] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2016] [Revised: 08/11/2016] [Accepted: 08/19/2016] [Indexed: 10/21/2022]
Abstract
Recent advances in lipidomic analysis in combination with various physiological experiments set the stage for deciphering the structure-function of haloarchaeal membrane lipids. Here we focused primarily on changes in lipid composition of Haloferax volcanii, but also performed a comparative analysis with four other haloarchaeal species (Halobacterium salinarum, Halorubrum lacusprofundi, Halorubrum sodomense and Haloplanus natans) all representing distinctive cell morphologies and behaviors (i.e., rod shape vs. pleomorphic behavior). Common to all five haloarchaea, our data reveal an extraordinary high level of menaquinone, reaching up to 72% of the total lipids. This ubiquity suggests that menaquinones may function beyond their ordinary role as electron and proton transporter, acting simultaneously as ion permeability barriers and as powerful shield against oxidative stress. In addition, we aimed at understanding the role of cations interacting with the characteristic negatively charged surface of haloarchaeal membranes. We propose for instance that by bridging the negative charges of adjacent anionic phospholipids, Mg2+ acts as surrogate for cardiolipin, a molecule that is known to control curvature stress of membranes. This study further provides a bioenergetic perspective as to how haloarchaea evolved following oxygenation of Earth's atmosphere. The success of the aerobic lifestyle of haloarchaea includes multiple membrane-based strategies that successfully balance the need for a robust bilayer structure with the need for high rates of electron transport - collectively representing the molecular basis to inhabit hypersaline water bodies around the planet.
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Affiliation(s)
- Matthias Y Kellermann
- Department of Earth Science and Marine Science Institute, University of California, Santa Barbara, CA 93106, USA.
| | - Marcos Y Yoshinaga
- MARUM Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, Leobener Strasse, D-28359 Bremen, Germany
| | | | - Lars Wörmer
- MARUM Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, Leobener Strasse, D-28359 Bremen, Germany
| | - David L Valentine
- Department of Earth Science and Marine Science Institute, University of California, Santa Barbara, CA 93106, USA.
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41
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Franza T, Delavenne E, Derré-Bobillot A, Juillard V, Boulay M, Demey E, Vinh J, Lamberet G, Gaudu P. A partial metabolic pathway enables group b streptococcus to overcome quinone deficiency in a host bacterial community. Mol Microbiol 2016; 102:81-91. [PMID: 27328751 DOI: 10.1111/mmi.13447] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/20/2016] [Indexed: 11/28/2022]
Abstract
Aerobic respiration metabolism in Group B Streptococcus (GBS) is activated by exogenous heme and menaquinone. This capacity enhances resistance of GBS to acid and oxidative stress and improves its survival. In this work, we discovered that GBS is able to respire in the presence of heme and 1,4-dihydroxy-2-naphthoic acid (DHNA). DHNA is a biosynthetic precursor of demethylmenaquinone (DMK) in many bacterial species. A GBS gene (gbs1789) encodes a homolog of the MenA 1,4-dihydroxy-2-naphthoate prenyltransferase enzyme, involved in the synthesis of demethylmenaquinone. In this study, we showed that gbs1789 is involved in the biosynthesis of long-chain demethylmenaquinones (DMK-10). The Δgbs1789 mutant cannot respire in the presence of heme and DHNA, indicating that endogenously synthesized DMKs are cofactors of the GBS respiratory chain. We also found that isoprenoid side chains from GBS DMKs are produced by the protein encoded by the gbs1783 gene, since this gene can complement an Escherichia coli ispB mutant defective for isoprenoids chain synthesis. In the gut or vaginal microbiote, where interspecies metabolite exchanges occur, this partial DMK biosynthetic pathway can be important for GBS respiration and survival in different niches.
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Affiliation(s)
- Thierry Franza
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, 78350, France.
| | - Emilie Delavenne
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, 78350, France
| | - Aurélie Derré-Bobillot
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, 78350, France
| | - Vincent Juillard
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, 78350, France
| | - Mylène Boulay
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, 78350, France
| | | | - Joelle Vinh
- ESPCI Paris, SMBP USR3149 CNRS, Paris, F-75005, France
| | - Gilles Lamberet
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, 78350, France
| | - Philippe Gaudu
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, 78350, France
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42
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Nowicka B, Kruk J. Powered by light: Phototrophy and photosynthesis in prokaryotes and its evolution. Microbiol Res 2016; 186-187:99-118. [PMID: 27242148 DOI: 10.1016/j.micres.2016.04.001] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 02/12/2016] [Accepted: 04/01/2016] [Indexed: 11/29/2022]
Abstract
Photosynthesis is a complex metabolic process enabling photosynthetic organisms to use solar energy for the reduction of carbon dioxide into biomass. This ancient pathway has revolutionized life on Earth. The most important event was the development of oxygenic photosynthesis. It had a tremendous impact on the Earth's geochemistry and the evolution of living beings, as the rise of atmospheric molecular oxygen enabled the development of a highly efficient aerobic metabolism, which later led to the evolution of complex multicellular organisms. The mechanism of photosynthesis has been the subject of intensive research and a great body of data has been accumulated. However, the evolution of this process is not fully understood, and the development of photosynthesis in prokaryota in particular remains an unresolved question. This review is devoted to the occurrence and main features of phototrophy and photosynthesis in prokaryotes. Hypotheses concerning the origin and spread of photosynthetic traits in bacteria are also discussed.
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Affiliation(s)
- Beatrycze Nowicka
- Department of Plant Physiology and Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland.
| | - Jerzy Kruk
- Department of Plant Physiology and Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland.
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43
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Ravcheev DA, Thiele I. Genomic Analysis of the Human Gut Microbiome Suggests Novel Enzymes Involved in Quinone Biosynthesis. Front Microbiol 2016; 7:128. [PMID: 26904004 PMCID: PMC4746308 DOI: 10.3389/fmicb.2016.00128] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 01/25/2016] [Indexed: 02/06/2023] Open
Abstract
Ubiquinone and menaquinone are membrane lipid-soluble carriers of electrons that are essential for cellular respiration. Eukaryotic cells can synthesize ubiquinone but not menaquinone, whereas prokaryotes can synthesize both quinones. So far, most of the human gut microbiome (HGM) studies have been based on metagenomic analysis. Here, we applied an analysis of individual HGM genomes to the identification of ubiquinone and menaquinone biosynthetic pathways. In our opinion, the shift from metagenomics to analysis of individual genomes is a pivotal milestone in investigation of bacterial communities, including the HGM. The key results of this study are as follows. (i) The distribution of the canonical pathways in the HGM genomes was consistent with previous reports and with the distribution of the quinone-dependent reductases for electron acceptors. (ii) The comparative genomics analysis identified four alternative forms of the previously known enzymes for quinone biosynthesis. (iii) Genes for the previously unknown part of the futalosine pathway were identified, and the corresponding biochemical reactions were proposed. We discuss the remaining gaps in the menaquinone and ubiquinone pathways in some of the microbes, which indicate the existence of further alternate genes or routes. Together, these findings provide further insight into the biosynthesis of quinones in bacteria and the physiology of the HGM.
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Affiliation(s)
- Dmitry A Ravcheev
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg Esch-sur-Alzette, Luxembourg
| | - Ines Thiele
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg Esch-sur-Alzette, Luxembourg
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44
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Elling FJ, Becker KW, Könneke M, Schröder JM, Kellermann MY, Thomm M, Hinrichs KU. Respiratory quinones in Archaea: phylogenetic distribution and application as biomarkers in the marine environment. Environ Microbiol 2015; 18:692-707. [PMID: 26472620 DOI: 10.1111/1462-2920.13086] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Revised: 07/28/2015] [Accepted: 10/10/2015] [Indexed: 11/30/2022]
Abstract
The distribution of respiratory quinone electron carriers among cultivated organisms provides clues on both the taxonomy of their producers and the redox processes these are mediating. Our study of the quinone inventories of 25 archaeal species belonging to the phyla Eury-, Cren- and Thaumarchaeota facilitates their use as chemotaxonomic markers for ecologically important archaeal clades. Saturated and monounsaturated menaquinones with six isoprenoid units forming the alkyl chain may serve as chemotaxonomic markers for Thaumarchaeota. Other diagnostic biomarkers are thiophene-bearing quinones for Sulfolobales and methanophenazines as functional quinone analogues of the Methanosarcinales. The ubiquity of saturated menaquinones in the Archaea in comparison to Bacteria suggests that these compounds may represent an ancestral and diagnostic feature of the Archaea. Overlap between quinone compositions of distinct thermophilic and halophilic archaea and bacteria may indicate lateral gene transfer. The biomarker potential of thaumarchaeal quinones was exemplarily demonstrated on a water column profile of the Black Sea. Both, thaumarchaeal quinones and membrane lipids showed similar distributions with maxima at the chemocline. Quinone distributions indicate that Thaumarchaeota dominate respiratory activity at a narrow interval in the chemocline, while they contribute only 9% to the microbial biomass at this depth, as determined by membrane lipid analysis.
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Affiliation(s)
- Felix J Elling
- Organic Geochemistry Group, MARUM - Center for Marine Environmental Sciences & Department of Geosciences, University of Bremen, 28359, Bremen, Germany
| | - Kevin W Becker
- Organic Geochemistry Group, MARUM - Center for Marine Environmental Sciences & Department of Geosciences, University of Bremen, 28359, Bremen, Germany
| | - Martin Könneke
- Organic Geochemistry Group, MARUM - Center for Marine Environmental Sciences & Department of Geosciences, University of Bremen, 28359, Bremen, Germany
| | - Jan M Schröder
- Organic Geochemistry Group, MARUM - Center for Marine Environmental Sciences & Department of Geosciences, University of Bremen, 28359, Bremen, Germany
| | - Matthias Y Kellermann
- Department of Earth Science and Marine Science Institute, University of California, Santa Barbara, CA, 93106, USA
| | - Michael Thomm
- Lehrstuhl für Mikrobiologie und Archaeenzentrum, Universität Regensburg, 93053, Regensburg, Germany
| | - Kai-Uwe Hinrichs
- Organic Geochemistry Group, MARUM - Center for Marine Environmental Sciences & Department of Geosciences, University of Bremen, 28359, Bremen, Germany
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45
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Abstract
Quinol oxidation in the catalytic quinol oxidation site (Qo site) of cytochrome (cyt) bc1 complexes is the key step of the Q cycle mechanism, which laid the ground for Mitchell’s chemiosmotic theory of energy conversion. Bifurcated electron transfer upon quinol oxidation enables proton uptake and release on opposite membrane sides, thus generating a proton gradient that fuels ATP synthesis in cellular respiration and photosynthesis. The Qo site architecture formed by cyt b and Rieske iron–sulfur protein (ISP) impedes harmful bypass reactions. Catalytic importance is assigned to four residues of cyt b formerly described as PEWY motif in the context of mitochondrial complexes, which we now denominate Qo motif as comprehensive evolutionary sequence analysis of cyt b shows substantial natural variance of the motif with phylogenetically specific patterns. In particular, the Qo motif is identified as PEWY in mitochondria, α- and ε-Proteobacteria, Aquificae, Chlorobi, Cyanobacteria, and chloroplasts. PDWY is present in Gram-positive bacteria, Deinococcus–Thermus and haloarchaea, and PVWY in β- and γ-Proteobacteria. PPWF only exists in Archaea. Distinct patterns for acidophilic organisms indicate environment-specific adaptations. Importantly, the presence of PDWY and PEWY is correlated with the redox potential of Rieske ISP and quinone species. We propose that during evolution from low to high potential electron-transfer systems in the emerging oxygenic atmosphere, cyt bc1 complexes with PEWY as Qo motif prevailed to efficiently use high potential ubiquinone as substrate, whereas cyt b with PDWY operate best with low potential Rieske ISP and menaquinone, with the latter being the likely composition of the ancestral cyt bc1 complex.
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Affiliation(s)
- Wei-Chun Kao
- Institute for Biochemistry and Molecular Biology, ZBMZ, BIOSS Centre for Biological Signalling Studies, University of Freiburg, Germany
- Faculty of Biology, University of Freiburg, Germany
| | - Carola Hunte
- Institute for Biochemistry and Molecular Biology, ZBMZ, BIOSS Centre for Biological Signalling Studies, University of Freiburg, Germany
- *Corresponding author: E-mail:
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46
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Mukherjee S, Lapidus A, Shapiro N, Cheng JF, Han J, Reddy TBK, Huntemann M, Ivanova N, Mikhailova N, Chen A, Palaniappan K, Spring S, Göker M, Markowitz V, Woyke T, Tindall BJ, Klenk HP, Kyrpides NC, Pati A. High quality draft genome sequence and analysis of Pontibacter roseus type strain SRC-1(T) (DSM 17521(T)) isolated from muddy waters of a drainage system in Chandigarh, India. Stand Genomic Sci 2015; 10:8. [PMID: 26203325 PMCID: PMC4511580 DOI: 10.1186/1944-3277-10-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 11/24/2014] [Indexed: 12/21/2022] Open
Abstract
Pontibacter roseus is a member of genus Pontibacter family Cytophagaceae, class Cytophagia. While the type species of the genus Pontibacter actiniarum was isolated in 2005 from a marine environment, subsequent species of the same genus have been found in different types of habitats ranging from seawater, sediment, desert soil, rhizosphere, contaminated sites, solar saltern and muddy water. Here we describe the features of Pontibacter roseus strain SRC-1(T) along with its complete genome sequence and annotation from a culture of DSM 17521(T). The 4,581,480 bp long draft genome consists of 12 scaffolds with 4,003 protein-coding and 50 RNA genes and is a part of Genomic Encyclopedia of Type Strains: KMG-I project.
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Affiliation(s)
| | - Alla Lapidus
- T. Dobzhansky Center for Genome Bionformatics, St. Petersburg State University, St. Petersburg, Russia
- Algorithmic Biology Lab, St. Petersburg Academic University, St. Petersburg, Russia
| | - Nicole Shapiro
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Jan-Fang Cheng
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - James Han
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - TBK Reddy
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | | | | | - Amy Chen
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Krishna Palaniappan
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Stefan Spring
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Markus Göker
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Victor Markowitz
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Brian J Tindall
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Hans-Peter Klenk
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Nikos C Kyrpides
- DOE Joint Genome Institute, Walnut Creek, California, USA
- King Abdulaziz University, Jeddah, Saudi Arabia
| | - Amrita Pati
- DOE Joint Genome Institute, Walnut Creek, California, USA
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47
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Identification of polyunsaturated fatty acid and diterpenoid biosynthesis pathways from draft genome of Aureispira sp. CCB-QB1. Mar Genomics 2014; 19:39-44. [PMID: 25468060 DOI: 10.1016/j.margen.2014.10.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 10/18/2014] [Accepted: 10/19/2014] [Indexed: 11/21/2022]
Abstract
The genus Aureispira consisting of two species, Aureispira marina and Aureispira maritima is an arachidonic acid-producing bacterium and produces secondary metabolites. In this study, we isolated a new Aureispira strain, Aureispira sp. CCB-QB1 from coastal area of Penang, Malaysia and the genome sequence of this strain was determined. The draft genome of this strain is composed of 185 contigs for 7,370,077 bases with 35.6% G+C content and contains 5911 protein-coding genes and 76 RNA genes. Linoleoyl-CoA desaturase, the key gene in arachidonic acid biosynthesis, is present in the genome. It was found that this strain uses mevalonate pathway for the synthesis of geranylgeranyl diphosphate (GGPP), which is precursor of diterpenoid, and novel pathway via futalosine for the synthesis of menaquinones. This is the first draft genome sequence of a member of the genus Aureispira.
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48
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Barta ML, Thomas K, Yuan H, Lovell S, Battaile KP, Schramm VL, Hefty PS. Structural and biochemical characterization of Chlamydia trachomatis hypothetical protein CT263 supports that menaquinone synthesis occurs through the futalosine pathway. J Biol Chem 2014; 289:32214-32229. [PMID: 25253688 DOI: 10.1074/jbc.m114.594325] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The obligate intracellular human pathogen Chlamydia trachomatis is the etiological agent of blinding trachoma and sexually transmitted disease. Genomic sequencing of Chlamydia indicated this medically important bacterium was not exclusively dependent on the host cell for energy. In order for the electron transport chain to function, electron shuttling between membrane-embedded complexes requires lipid-soluble quinones (e.g. menaquionone or ubiquinone). The sources or biosynthetic pathways required to obtain these electron carriers within C. trachomatis are poorly understood. The 1.58Å crystal structure of C. trachomatis hypothetical protein CT263 presented here supports a role in quinone biosynthesis. Although CT263 lacks sequence-based functional annotation, the crystal structure of CT263 displays striking structural similarity to 5'-methylthioadenosine nucleosidase (MTAN) enzymes. Although CT263 lacks the active site-associated dimer interface found in prototypical MTANs, co-crystal structures with product (adenine) or substrate (5'-methylthioadenosine) indicate that the canonical active site residues are conserved. Enzymatic characterization of CT263 indicates that the futalosine pathway intermediate 6-amino-6-deoxyfutalosine (kcat/Km = 1.8 × 10(3) M(-1) s(-1)), but not the prototypical MTAN substrates (e.g. S-adenosylhomocysteine and 5'-methylthioadenosine), is hydrolyzed. Bioinformatic analyses of the chlamydial proteome also support the futalosine pathway toward the synthesis of menaquinone in Chlamydiaceae. This report provides the first experimental support for quinone synthesis in Chlamydia. Menaquinone synthesis provides another target for agents to combat C. trachomatis infection.
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Affiliation(s)
- Michael L Barta
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045
| | - Keisha Thomas
- Department of Biochemistry, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York 10461
| | - Hongling Yuan
- Department of Biochemistry, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York 10461
| | - Scott Lovell
- Protein Structure Laboratory, Del Shankel Structural Biology Center, University of Kansas, Lawrence, Kansas 66047, and
| | - Kevin P Battaile
- Industrial Macromolecular Crystallography Association-Collaborative Access Team, Hauptman-Woodward Medical Research Institute, Argonne, Illinois 60439
| | - Vern L Schramm
- Department of Biochemistry, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York 10461
| | - P Scott Hefty
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045,.
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