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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Fan HH, Fang SB, Chang YC, Huang ST, Huang CH, Chang PR, Chang WC, Yang LTL, Lin PC, Cheng HY. Effects of colonization-associated gene yqiC on global transcriptome, cellular respiration, and oxidative stress in Salmonella Typhimurium. J Biomed Sci 2022; 29:102. [PMID: 36457101 PMCID: PMC9714038 DOI: 10.1186/s12929-022-00885-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 11/20/2022] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND yqiC is required for colonizing the Salmonella enterica serovar Typhimurium (S. Typhimurium) in human cells; however, how yqiC regulates nontyphoidal Salmonella (NTS) genes to influence bacteria-host interactions remains unclear. METHODS The global transcriptomes of S. Typhimurium yqiC-deleted mutant (ΔyqiC) and its wild-type strain SL1344 after 2 h of in vitro infection with Caco-2 cells were obtained through RNA sequencing to conduct comparisons and identify major yqiC-regulated genes, particularly those involved in Salmonella pathogenicity islands (SPIs), ubiquinone and menaquinone biosynthesis, electron transportation chains (ETCs), and carbohydrate/energy metabolism. A Seahorse XFp Analyzer and assays of NADH/NAD+ and H2O2 were used to compare oxygen consumption and extracellular acidification, glycolysis parameters, adenosine triphosphate (ATP) generation, NADH/NAD+ ratios, and H2O2 production between ΔyqiC and SL1344. RESULTS After S. Typhimurium interacts with Caco-2 cells, yqiC represses gene upregulation in aspartate carbamoyl transferase, type 1 fimbriae, and iron-sulfur assembly, and it is required for expressing ilvB operon, flagellin, tdcABCD, and dmsAB. Furthermore, yqiC is required for expressing mainly SPI-1 genes and specific SPI-4, SPI-5, and SPI-6 genes; however, it diversely regulates SPI-2 and SPI-3 gene expression. yqiC significantly contributes to menD expression in menaquinone biosynthesis. A Kyoto Encyclopedia of Genes and Genomes analysis revealed the extensive association of yqiC with carbohydrate and energy metabolism. yqiC contributes to ATP generation, and the analyzer results demonstrate that yqiC is required for maintaining cellular respiration and metabolic potential under energy stress and for achieving glycolysis, glycolytic capacity, and glycolytic reserve. yqiC is also required for expressing ndh, cydA, nuoE, and sdhB but suppresses cyoC upregulation in the ETC of aerobically and anaerobically grown S. Typhimurium; priming with Caco-2 cells caused a reversed regulation of yiqC toward upregulation in these ETC complex genes. Furthermore, yqiC is required for maintaining NADH/NAD+ redox status and H2O2 production. CONCLUSIONS Specific unreported genes that were considerably regulated by the colonization-associated gene yqiC in NTS were identified, and the key role and tentative mechanisms of yqiC in the extensive modulation of virulence factors, SPIs, ubiquinone and menaquinone biosynthesis, ETCs, glycolysis, and oxidative stress were discovered.
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Affiliation(s)
- Hung-Hao Fan
- grid.412955.e0000 0004 0419 7197Division of Pediatric Gastroenterology and Hepatology, Department of Pediatrics, Shuang Ho Hospital, Taipei Medical University, No. 291, Jhong Jheng Road, Jhong Ho, New Taipei City, 23561 Taiwan ,grid.412896.00000 0000 9337 0481Department of Pediatrics, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan ,grid.412955.e0000 0004 0419 7197Department of Emergency Medicine, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan
| | - Shiuh-Bin Fang
- grid.412955.e0000 0004 0419 7197Division of Pediatric Gastroenterology and Hepatology, Department of Pediatrics, Shuang Ho Hospital, Taipei Medical University, No. 291, Jhong Jheng Road, Jhong Ho, New Taipei City, 23561 Taiwan ,grid.412896.00000 0000 9337 0481Department of Pediatrics, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan ,grid.412896.00000 0000 9337 0481Master Program for Clinical Genomics and Proteomics, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Yu-Chu Chang
- grid.412896.00000 0000 9337 0481Department of Biochemistry and Molecular Cell Biology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Sheng-Tung Huang
- grid.412087.80000 0001 0001 3889Graduate Institute of Biochemical and Biomedical Engineering, National Taipei University of Technology, Taipei, Taiwan
| | - Chih-Hung Huang
- grid.412087.80000 0001 0001 3889Graduate Institute of Biochemical and Biomedical Engineering, National Taipei University of Technology, Taipei, Taiwan
| | - Pei-Ru Chang
- grid.412955.e0000 0004 0419 7197Division of Pediatric Gastroenterology and Hepatology, Department of Pediatrics, Shuang Ho Hospital, Taipei Medical University, No. 291, Jhong Jheng Road, Jhong Ho, New Taipei City, 23561 Taiwan ,grid.412896.00000 0000 9337 0481Department of Pediatrics, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Wei-Chiao Chang
- grid.412896.00000 0000 9337 0481Master Program for Clinical Genomics and Proteomics, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Lauderdale Tsai-Ling Yang
- grid.59784.370000000406229172National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Taiwan
| | - Pei-Chun Lin
- grid.412955.e0000 0004 0419 7197Division of Pediatric Gastroenterology and Hepatology, Department of Pediatrics, Shuang Ho Hospital, Taipei Medical University, No. 291, Jhong Jheng Road, Jhong Ho, New Taipei City, 23561 Taiwan
| | - Hung-Yen Cheng
- grid.412955.e0000 0004 0419 7197Division of Pediatric Gastroenterology and Hepatology, Department of Pediatrics, Shuang Ho Hospital, Taipei Medical University, No. 291, Jhong Jheng Road, Jhong Ho, New Taipei City, 23561 Taiwan
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Van Cleave C, Koehn JT, Pereira CS, Haase AA, Peters BJ, Croslow SW, McLaughlin KG, Werst KR, Goach AL, Crick DC, Arantes GM, Crans DC. Interactions of Truncated Menaquinones in Lipid Monolayers and Bilayers. Int J Mol Sci 2021; 22:9755. [PMID: 34575937 PMCID: PMC8470443 DOI: 10.3390/ijms22189755] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 09/02/2021] [Accepted: 09/05/2021] [Indexed: 11/28/2022] Open
Abstract
Menaquinones (MK) are hydrophobic molecules that consist of a naphthoquinone headgroup and a repeating isoprenyl side chain and are cofactors used in bacterial electron transport systems to generate cellular energy. We have previously demonstrated that the folded conformation of truncated MK homologues, MK-1 and MK-2, in both solution and reverse micelle microemulsions depended on environment. There is little information on how MKs associate with phospholipids in a model membrane system and how MKs affect phospholipid organization. In this manuscript, we used a combination of Langmuir monolayer studies and molecular dynamics (MD) simulations to probe these questions on truncated MK homologues, MK-1 through MK-4 within a model membrane. We observed that truncated MKs reside farther away from the interfacial water than ubiquinones are are located closer to the phospholipid tails. We also observed that phospholipid packing does not change at physiological pressure in the presence of truncated MKs, though a difference in phospholipid packing has been observed in the presence of ubiquinones. We found through MD simulations that for truncated MKs, the folded conformation varied, but MKs location and association with the bilayer remained unchanged at physiological conditions regardless of side chain length. Combined, this manuscript provides fundamental information, both experimental and computational, on the location, association, and conformation of truncated MK homologues in model membrane environments relevant to bacterial energy production.
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Affiliation(s)
- Cameron Van Cleave
- Department of Chemistry, Colorado State University, Fort Collins, CO 80523, USA; (C.V.C.); (J.T.K.); (A.A.H.); (B.J.P.); (K.R.W.)
| | - Jordan T. Koehn
- Department of Chemistry, Colorado State University, Fort Collins, CO 80523, USA; (C.V.C.); (J.T.K.); (A.A.H.); (B.J.P.); (K.R.W.)
| | - Caroline Simões Pereira
- Department of Biochemistry, Institutio de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, São Paulo 05508-900, SP, Brazil; (C.S.P.); (G.M.A.)
| | - Allison A. Haase
- Department of Chemistry, Colorado State University, Fort Collins, CO 80523, USA; (C.V.C.); (J.T.K.); (A.A.H.); (B.J.P.); (K.R.W.)
| | - Benjamin J. Peters
- Department of Chemistry, Colorado State University, Fort Collins, CO 80523, USA; (C.V.C.); (J.T.K.); (A.A.H.); (B.J.P.); (K.R.W.)
| | - Seth W. Croslow
- Department of Chemistry, Monmouth College, Monmouth, IL 61462, USA; (S.W.C.); (K.G.M.); (A.L.G.)
| | - Kyle G. McLaughlin
- Department of Chemistry, Monmouth College, Monmouth, IL 61462, USA; (S.W.C.); (K.G.M.); (A.L.G.)
| | - Katarina R. Werst
- Department of Chemistry, Colorado State University, Fort Collins, CO 80523, USA; (C.V.C.); (J.T.K.); (A.A.H.); (B.J.P.); (K.R.W.)
| | - Audra L. Goach
- Department of Chemistry, Monmouth College, Monmouth, IL 61462, USA; (S.W.C.); (K.G.M.); (A.L.G.)
| | - Dean C. Crick
- Cell and Molecular Biology Program, Colorado State University, Fort Collins, CO 80523, USA;
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA
| | - Guilherme Menegon Arantes
- Department of Biochemistry, Institutio de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, São Paulo 05508-900, SP, Brazil; (C.S.P.); (G.M.A.)
| | - Debbie C. Crans
- Department of Chemistry, Colorado State University, Fort Collins, CO 80523, USA; (C.V.C.); (J.T.K.); (A.A.H.); (B.J.P.); (K.R.W.)
- Cell and Molecular Biology Program, Colorado State University, Fort Collins, CO 80523, USA;
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Wu H, Wang H, Wang P, Zhao G, Liu H, Wang L, Sun X, Zheng Z. Gradient radiation breeding and culture domestication of menaquinone producing strains. Bioprocess Biosyst Eng 2021; 44:1373-1382. [PMID: 34008084 DOI: 10.1007/s00449-021-02508-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 01/03/2021] [Indexed: 11/27/2022]
Abstract
By comparing the survival rate and positive mutation rate of the primary mutagenic strain and progeny mutagenic strain under different radiation doses, the results showed that the tolerance of the mutagenic strain to radiation dose increased with the increase of the mutagenic generations. We adopted an improved gradient radiation breeding strategy to improve the breeding efficiency. The strains were treated with radiation in four stages. The first stage was low energy N+ ion implantation (ion energy 15 keV, dose 80 × 2.6 × 1013 cm-2). In the second stage, the energy and dose of N+ ion reached to 20 keV, 90 × 2.6 × 1013 cm-2. In the third stage, 60Co-γ radiation (dose of 1.56 kGy) was used. In the fourth stage, the radiation dose of 60Co-γ increased to 1.82 kGy. After each stage of radiation, the MK (Menaquinone) precursor 1, 4-dihydroxy-2-naphthalate (DHNA) was used as the stress factor to domesticate the mutant strains. By gradually increasing the concentration of DHNA in the culture medium, the substrate tolerance of Flavobacterium sp. was effectively improved. By measuring SOD (superoxide dismutase) activity and malondialdehyde, it showed that the cell damage caused by radiation mutagenesis to the offspring mutant was less than that of the primary mutant. Changes in membrane permeability and membrane potential of the mutant strains were reflected in changes in fluorescence intensity of luciferin diacetate and rhodamine 123, which could explain the enhanced substrate tolerance of strain F-2. After gradient radiation breeding and culture acclimation, the biomass of mutant Strain F-2 was 6.59 g/L, and the MK yield was 9.59 mg/L.
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Affiliation(s)
- Hefang Wu
- Key Laboratory of High Magnetic Field And Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Shushanhu Road No. 350, Hefei, 210031, Anhui, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Han Wang
- Key Laboratory of High Magnetic Field And Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Shushanhu Road No. 350, Hefei, 210031, Anhui, China
| | - Peng Wang
- Key Laboratory of High Magnetic Field And Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Shushanhu Road No. 350, Hefei, 210031, Anhui, China
| | - Geihai Zhao
- Key Laboratory of High Magnetic Field And Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Shushanhu Road No. 350, Hefei, 210031, Anhui, China
| | - Hui Liu
- Key Laboratory of High Magnetic Field And Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Shushanhu Road No. 350, Hefei, 210031, Anhui, China
| | - Li Wang
- Key Laboratory of High Magnetic Field And Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Shushanhu Road No. 350, Hefei, 210031, Anhui, China
| | - Xiaowen Sun
- Key Laboratory of High Magnetic Field And Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Shushanhu Road No. 350, Hefei, 210031, Anhui, China
| | - Zhiming Zheng
- Key Laboratory of High Magnetic Field And Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Shushanhu Road No. 350, Hefei, 210031, Anhui, China.
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