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Li ZM, Hu Z, Wang X, Chen S, Yu W, Liu J, Li Z. Biochemical and Structural Insights into a Thiamine Diphosphate-Dependent α-Ketoglutarate Decarboxylase from Cyanobacterium Microcystis aeruginosa NIES-843. Int J Mol Sci 2023; 24:12198. [PMID: 37569577 PMCID: PMC10418658 DOI: 10.3390/ijms241512198] [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: 06/28/2023] [Revised: 07/26/2023] [Accepted: 07/29/2023] [Indexed: 08/13/2023] Open
Abstract
α-Ketoglutarate decarboxylase is a crucial enzyme in the tricarboxylic acid cycle of cyanobacteria, catalyzing the non-oxidative decarboxylation of α-ketoglutarate to produce succinate semialdehyde and CO2. The decarboxylation process is reliant on the cofactor of thiamine diphosphate. However, this enzyme's biochemical and structural properties have not been well characterized. In this work, two α-ketoglutarate decarboxylases encoded by MAE_06010 and MiAbw_01735 genes from Microcystis aeruginosa NIES-843 (MaKGD) and NIES-4325 (MiKGD), respectively, were overexpressed and purified by using an Escherichia coli expression system. It was found that MaKGD exhibited 9.2-fold higher catalytic efficiency than MiKGD, which may be attributed to the absence of glutamate decarboxylase in Microcystis aeruginosa NIES-843. Further biochemical investigation of MaKGD demonstrated that it displayed optimum activity at pH 6.5-7.0 and was most activated by Mg2+. Additionally, MaKGD showed substrate specificity towards α-ketoglutarate. Structural modeling and autodocking results revealed that the active site of MaKGD contained a distinct binding pocket where α-ketoglutarate and thiamine diphosphate interacted with specific amino acid residues via hydrophobic interactions, hydrogen bonds and salt bridges. Furthermore, the mutagenesis study provided strong evidence supporting the importance of certain residues in the catalysis of MaKGD. These findings provide new insights into the structure-function relationships of α-ketoglutarate decarboxylases from cyanobacteria.
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Affiliation(s)
- Zhi-Min Li
- College of Chemistry and Materials, Jiangxi Agricultural University, Nanchang 330045, China;
| | - Ziwei Hu
- College of Bioscience and Bioengineering, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China
| | - Xiaoqin Wang
- College of Bioscience and Bioengineering, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China
| | - Suhang Chen
- College of Bioscience and Bioengineering, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China
| | - Weiyan Yu
- College of Bioscience and Bioengineering, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China
| | - Jianping Liu
- College of Bioscience and Bioengineering, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China
| | - Zhimin Li
- College of Bioscience and Bioengineering, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China
- Collaborative Innovation Center of Postharvest Key Technology and Quality Safety of Fruits and Vegetables in Jiangxi Province, Jiangxi Agricultural University, Nanchang 330045, China
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2
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Pujari V, Rozman K, Dhiman RK, Aldrich CC, Crick DC. Mycobacterial MenG: Partial Purification, Characterization, and Inhibition. ACS Infect Dis 2022; 8:2430-2440. [PMID: 36417754 DOI: 10.1021/acsinfecdis.2c00190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Menaquinone (MK) is an essential component of the electron transport chain (ETC) in the gram-variable Mycobacterium tuberculosis and many Gram-positive pathogens. Three genes in the M. tuberculosis genome were annotated as methyltransferases involved in lipoquinone synthesis in mycobacteria. Heterologous expression of Rv0558 complemented an ubiE (the quinone C-methyltransferase involved in ubiquinone and menaquinone synthesis) deletion in Escherichia coli, and expression in a wild-type E. coli strain increased quinone C-methyltransferase specific activity by threefold. Rv0558 encodes a canonical C-methyltransferase or, more specifically, a S-adenosylmethionine/demethylmenaquinol methyltransferase. Partially purified recombinant protein catalyzed the formation of MK from demethylmenaquinone (DMK), although the activity of the recombinant protein was low and appeared to require a cofactor or intact membrane structure for activity. Membrane preparations from irradiated M. tuberculosis also showed poor activity; however, membrane preparations from wild-type Mycobacterium smegmatis showed robust, substrate-dependent activity. The apparent Km values for demethylmenaquinone and SAM were 14 ± 5.0 and 17 ± 7.0 μM, respectively. Interestingly, addition of dithiothreitol, dithionite, NADH, or other substrates of primary dehydrogenases to reaction mixtures containing membrane preparations stimulated the activity. Thus, these observations strongly suggest that demethylmenaquinol is the actual substrate of MenG. Ro 48-8071, previously reported to inhibit mycobacterial MK synthesis and growth, inhibited Rv0558 activity with an IC50 value of 5.1 ± 0.5 μM, and DG70 (GSK1733953A), first described as a respiration inhibitor in M. tuberculosis, inhibits MenG activity with an IC50 value of 2.6 ± 0.6 μM.
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Affiliation(s)
- Venugopal Pujari
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Kaja Rozman
- Department of Medicinal Chemistry, University of Minnesota, 308 Harvard Street Southeast, Minneapolis, Minnesota 55455, United States
| | - Rakesh K Dhiman
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Courtney C Aldrich
- Department of Medicinal Chemistry, University of Minnesota, 308 Harvard Street Southeast, Minneapolis, Minnesota 55455, United States
| | - Dean C Crick
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80523, United States
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Panter F, Popoff A, Garcia R, Krug D, Müller R. Myxobacteria of the Cystobacterineae Suborder Are Producers of New Vitamin K 2 Derived Myxoquinones. Microorganisms 2022; 10:microorganisms10030534. [PMID: 35336107 PMCID: PMC8955186 DOI: 10.3390/microorganisms10030534] [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: 01/05/2022] [Revised: 02/21/2022] [Accepted: 02/25/2022] [Indexed: 02/01/2023] Open
Abstract
Vitamin K is an essential, lipid soluble vitamin that plays an important role in the human blood coagulation cascade as well as in the life cycle of bacteria and plants. In this study, we report the isolation and structure elucidation of unprecedented polyhydroxylated menaquinone variants named myxoquinones that are produced by myxobacteria and structurally belong to the Vitamin K family. We analyze the occurrence of myxoquinones across an LC-MS data collection from myxobacterial extracts and shed light on the distribution of myxoquinone-type biosynthetic gene clusters among publicly available myxobacterial genomes. Our findings indicate that myxoquinones are specifically produced by strains of the Cystobacterineae suborder within myxobacteria. Furthermore, bioinformatic analysis of the matching gene clusters allowed us to propose a biosynthetic model for myxoquinone formation. Due to their increased water-solubility, the myxoquinones could be a suitable starting point for the development of a better bioavailable treatment of vitamin K deficiency.
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Affiliation(s)
- Fabian Panter
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University, Campus E8 1, 66123 Saarbrücken, Germany; (F.P.); (A.P.); (R.G.); (D.K.)
- German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany
- Helmholtz International Lab for Anti-Infectives, Campus E8 1, 66123 Saarbrücken, Germany
| | - Alexander Popoff
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University, Campus E8 1, 66123 Saarbrücken, Germany; (F.P.); (A.P.); (R.G.); (D.K.)
- German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Ronald Garcia
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University, Campus E8 1, 66123 Saarbrücken, Germany; (F.P.); (A.P.); (R.G.); (D.K.)
- German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Daniel Krug
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University, Campus E8 1, 66123 Saarbrücken, Germany; (F.P.); (A.P.); (R.G.); (D.K.)
- German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Rolf Müller
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University, Campus E8 1, 66123 Saarbrücken, Germany; (F.P.); (A.P.); (R.G.); (D.K.)
- German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany
- Helmholtz International Lab for Anti-Infectives, Campus E8 1, 66123 Saarbrücken, Germany
- Correspondence:
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4
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Wang H, Ye YH, Wang HH, Liu J, Liu YJ, Jiang BW. HPLC-QTOF-MS/MS profiling, antioxidant, and α-glucosidase inhibitory activities of Pyracantha fortuneana fruit extracts. J Food Biochem 2019; 43:e12821. [PMID: 31353511 DOI: 10.1111/jfbc.12821] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 01/25/2019] [Accepted: 02/09/2019] [Indexed: 11/27/2022]
Abstract
This study was carried out to optimize the solvent for extracting the antioxidants and α-glucosidase inhibitors (AGIs) from Pyracantha fortuneana fruit (PFF) and the major chemical components were characterized by HPLC-QTOF-MS/MS. The results showed that 50% and 70% acetone (v/v, ml/ml) gave the best extraction efficiency on phenolics and total flavonoids, while 70% acetone and 50% methanol possess better recovery on protein and polysaccharides, respectively. In addition, the 50% and 70% acetone extracts gave the strongest radical scavenging ability and α-glucosidase inhibitory activity (p > 0.05), but the Fe3+ reducing power of the 50% acetone extract was higher than that of 70% acetone. Correlation analysis indicated that phenolic acids and flavonoids were connected to the antioxidant activity and α-glucosidase inhibitory activity closely. Moreover, 25 compounds including 7 flavonoids, 6 phenolic acids, 7 organic acids, 3 tannins, 1 terpene, and 1 alkaloid were identified or tentatively identified in the 50% acetone extract. Overall, 50% acetone can be a proper solvent for extracting antioxidants and AGIs from PFF. PRACTICAL APPLICATIONS: Imbalance between production and clearance of reactive oxygen species (ROS) in the body could induce various chronic diseases. PFF is an edible fruit beneficial to human health; it is reported to be capable of optimizing blood glucose levels and may prevent premature aging. In the present study, PFF was found to be excellent in antioxidant activities and α-glucosidase inhibitory ability; 50% acetone was found to be the best extraction solvent. In addition, the predominant phytochemical components of the 50% acetone extract were characterized. This study can promote further research of Pyracantha fortuneana in natural functional products, especially in the prevention of type II diabetes and its complication.
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Affiliation(s)
- Hao Wang
- Engineering Research Center of Freshwater Fish High-value Utilization of Jiangxi Province, National Research and Development Center of Freshwater Fish Processing, Nanchang, China
| | - Yun-Hua Ye
- Engineering Research Center of Freshwater Fish High-value Utilization of Jiangxi Province, National Research and Development Center of Freshwater Fish Processing, Nanchang, China
| | - Hong-Hong Wang
- Engineering Research Center of Freshwater Fish High-value Utilization of Jiangxi Province, National Research and Development Center of Freshwater Fish Processing, Nanchang, China
| | - Jun Liu
- Engineering Research Center of Freshwater Fish High-value Utilization of Jiangxi Province, National Research and Development Center of Freshwater Fish Processing, Nanchang, China
| | - Yan-Jiang Liu
- Engineering Research Center of Freshwater Fish High-value Utilization of Jiangxi Province, National Research and Development Center of Freshwater Fish Processing, Nanchang, China
| | - Bo-Wen Jiang
- Engineering Research Center of Freshwater Fish High-value Utilization of Jiangxi Province, National Research and Development Center of Freshwater Fish Processing, Nanchang, China
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5
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Expression and biochemical characterization of α-ketoglutarate decarboxylase from cyanobacterium Synechococcus sp. PCC7002. Int J Biol Macromol 2018; 114:188-193. [PMID: 29574001 DOI: 10.1016/j.ijbiomac.2018.03.112] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 03/19/2018] [Accepted: 03/21/2018] [Indexed: 11/22/2022]
Abstract
α-Ketoglutarate decarboxylase (α-KGD), one member of α-keto acid decarboxylases, catalyzing non-oxidative decarboxylation of α-ketoglutarate to form succinic semialdehyde, was proposed to play critical role in completing tricarboxylic acid (TCA) cycle of cyanobacteria. Although the catalytic function of α-KGD from Synechococcus sp. PCC7002 was demonstrated previously, there was no detailed biochemical characterization of α-KGD from Synechococcus sp. PCC7002 yet. In this study, the gene encoding α-KGD from Synechococcus sp. PCC7002 was amplified and soluble expression of recombinant α-KGD was achieved by coexpressing with pTf16 chaperone plasmid in E. coli BL21 (DE3). Kinetic analysis showed that the activity of α-KGD was dependent on cofactors of thiamine pyrophosphate and divalent cation. Meanwhile this α-KGD was specific for α-ketoglutarate with respect to the decarboxylation activity despite of the pretty low activity of acetolactate synthase. The catalytic efficiency of α-KGD (the values of kcat and kcat/Km for α-ketoglutarate were 1.2s-1 and 6.3×103M-1s-1, respectively) might provide evidence for its physiological role in TCA cycle of Synechococcus sp. PCC7002.
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6
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Yan A, Culp E, Perry J, Lau JT, MacNeil LT, Surette MG, Wright GD. Transformation of the Anticancer Drug Doxorubicin in the Human Gut Microbiome. ACS Infect Dis 2018; 4:68-76. [PMID: 29160065 DOI: 10.1021/acsinfecdis.7b00166] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Bacteria living in the human gut are implicated in the etiology of several diseases. Moreover, dozens of drugs are metabolized by elements of the gut microbiome, which may have further implications for human health. Here, we screened a collection of gut isolates for their ability to inactivate the widely used antineoplastic drug doxorubicin and identified a strain of Raoultella planticola as a potent inactivator under anaerobic conditions. We demonstrate that R. planticola deglycosylates doxorubicin to metabolites 7-deoxydoxorubicinol and 7-deoxydoxorubicinolone via a reductive deglycosylation mechanism. We further show that doxorubicin is degraded anaerobically by Klebsiella pneumoniae and Escherichia coli BW25113 and present evidence that this phenotype is dependent on molybdopterin-dependent enzyme(s). Deglycosylation of doxorubicin by R. planticola under anaerobic conditions is found to reduce toxicity to the model species Caenorhabditis elegans, providing a model to begin understanding the role of doxorubicin metabolism by microbes in the human gut. Understanding the in vivo metabolism of important therapeutics like doxorubicin by the gut microbiome has the potential to guide clinical dosing to maximize therapeutic benefit while limiting undesirable side effects.
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Affiliation(s)
- Austin Yan
- M. G. DeGroote Institute
for Infectious Disease Research, McMaster University, 1280 Main
Street West, Hamilton, Ontario L8S 4K1, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Elizabeth Culp
- M. G. DeGroote Institute
for Infectious Disease Research, McMaster University, 1280 Main
Street West, Hamilton, Ontario L8S 4K1, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Julie Perry
- M. G. DeGroote Institute
for Infectious Disease Research, McMaster University, 1280 Main
Street West, Hamilton, Ontario L8S 4K1, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Jennifer T. Lau
- Farncombe
Family Digestive Health Research Institute, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Lesley T. MacNeil
- M. G. DeGroote Institute
for Infectious Disease Research, McMaster University, 1280 Main
Street West, Hamilton, Ontario L8S 4K1, Canada
- Farncombe
Family Digestive Health Research Institute, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
- Department of Medicine, McMaster University, 1280 Main
Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Michael G. Surette
- M. G. DeGroote Institute
for Infectious Disease Research, McMaster University, 1280 Main
Street West, Hamilton, Ontario L8S 4K1, Canada
- Farncombe
Family Digestive Health Research Institute, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Gerard D. Wright
- M. G. DeGroote Institute
for Infectious Disease Research, McMaster University, 1280 Main
Street West, Hamilton, Ontario L8S 4K1, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
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7
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Abstract
Escherichia coli and Salmonella contain the naphthoquinones menaquinone (MK; vitamin K2) and demethylmenaquinone and the benzoquinone ubiquinone (coenzyme Q; Q). Both quinones are derived from the shikimate pathway, which has been called a "metabolic tree with many branches." There are two different pathways for the biosynthesis of the naphthoquinones. The vast majority of prokaryotes, including E. coli and Salmonella, and the plants use the o-succinylbenzoate pathway, while a minority uses the futalosine pathway. The quinone nucleus of Q is derived directly from chorismate, while that of MK is derived from chorismate via isochorismate. The prenyl side chains of both quinones are from isopentenyl diphosphate formed by the 2-C-methyl-D-erythritol 4-phosphate (non-mevalonate) pathway and the methyl groups are from S-adenosylmethionine. In addition, MK biosynthesis requires 2-ketoglutarate and cofactors ATP, coenzyme A, and thiamine pyrophosphate. Despite the fact that both quinones originate from the shikimate pathway, there are important differences in their biosyntheses. The prenyl side chain in MK biosynthesis is introduced at the penultimate step, accompanied by decarboxylation, whereas in Q biosynthesis it is introduced at the second step, with retention of the carboxyl group. In MK biosynthesis, all the reactions of the pathway up to prenylation are carried out by soluble enzymes, whereas all the enzymes involved in Q biosynthesis except the first are membrane bound. In MK biosynthesis, the last step is a C-methylation; in Q biosynthesis, the last step is an O-methylation. In Q biosynthesis a second C-methylation and O-methylation take place in the middle part of the pathway. Despite the fact that Q and MK biosyntheses diverge at chorismate, the C-methylations in both pathways are carried out by the same methyltransferase.
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Upadhyay A, Fontes F, Gonzalez-Juarrero M, McNeil MR, Crans DC, Jackson M, Crick DC. Partial Saturation of Menaquinone in Mycobacterium tuberculosis: Function and Essentiality of a Novel Reductase, MenJ. ACS CENTRAL SCIENCE 2015; 1:292-302. [PMID: 26436137 PMCID: PMC4582327 DOI: 10.1021/acscentsci.5b00212] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Indexed: 05/12/2023]
Abstract
Menaquinone (MK) with partially saturated isoprenyl moieties is found in a wide range of eubacteria and Archaea. In many Gram-positive organisms, including mycobacteria, it is the double bond found in the β-isoprene unit that is reduced. Mass spectral characterization of menaquinone from mycobacterial knockout strains and heterologous expression hosts demonstrates that Rv0561c (designated menJ) encodes an enzyme which reduces the β-isoprene unit of menaquinone in Mycobacterium tuberculosis, forming the predominant form of menaquinone found in mycobacteria. MenJ is highly conserved in mycobacteria species but is not required for growth in culture. Disruption of menJ reduces mycobacterial electron transport efficiency by 3-fold, but mycobacteria are able to maintain ATP levels by increasing the levels of the total menaquinone in the membrane; however, MenJ is required for M. tuberculosis survival in host macrophages. Thus, MK with partially hydrogenated isoprenyl moieties represents a novel virulence factor and MenJ is a contextually essential enzyme and a potential drug target in pathogenic mycobacteria and other Gram-positive pathogens.
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Affiliation(s)
- Ashutosh Upadhyay
- Department
of Microbiology, Immunology and Pathology, Department of Chemistry, and Cell and Molecular
Biology Program, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Fabio
L. Fontes
- Department
of Microbiology, Immunology and Pathology, Department of Chemistry, and Cell and Molecular
Biology Program, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Mercedes Gonzalez-Juarrero
- Department
of Microbiology, Immunology and Pathology, Department of Chemistry, and Cell and Molecular
Biology Program, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Michael R. McNeil
- Department
of Microbiology, Immunology and Pathology, Department of Chemistry, and Cell and Molecular
Biology Program, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Debbie C. Crans
- Department
of Microbiology, Immunology and Pathology, Department of Chemistry, and Cell and Molecular
Biology Program, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Mary Jackson
- Department
of Microbiology, Immunology and Pathology, Department of Chemistry, and Cell and Molecular
Biology Program, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Dean C. Crick
- Department
of Microbiology, Immunology and Pathology, Department of Chemistry, and Cell and Molecular
Biology Program, Colorado State University, Fort Collins, Colorado 80523, United States
- Mycobacteria Research Laboratories,
Department of Microbiology, Immunology and Pathology, 1682 Campus
Delivery, Fort Collins, CO 80523, USA. E-mail: . Tel: (+1) 970 491 3308. Fax: (+1) 970 491 1815
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Chen X, Xu J, Yang L, Yuan Z, Xiao S, Zhang Y, Liang C, He M, Guo Y. Production of C4 and C5 branched-chain alcohols by engineered Escherichia. coli. J Ind Microbiol Biotechnol 2015; 42:1473-9. [PMID: 26350079 DOI: 10.1007/s10295-015-1656-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 07/22/2015] [Indexed: 11/26/2022]
Abstract
Higher alcohols, longer chain alcohols, contain more than 3 carbon atoms, showed close energy advantages as gasoline, and were considered as the next generation substitution for chemical fuels. Higher alcohol biosynthesis by native microorganisms mainly needs gene expression of heterologous keto acid decarboxylase and alcohol dehydrogenases. In the present study, branched-chain α-keto acid decarboxylase gene from Lactococcus lactis subsp. lactis CICC 6246 (Kivd) and alcohol dehydrogenases gene from Zymomonas mobilis CICC 41465 (AdhB) were transformed into Escherichia coli for higher alcohol production. SDS-PAGE results showed these two proteins were expressed in the recombinant strains. The resulting strain was incubated in LB medium at 37 °C in Erlenmeyer flasks and much more 3-methyl-1-butanol (104 mg/L) than isobutanol (24 mg/L) was produced. However, in 5 g/L glucose-containing medium, the production of two alcohols was similar, 156 and 161 mg/L for C4 (isobutanol) and C5 (3-methyl-1-butanol) alcohol, respectively. Effects of fermentation factors including temperature, glucose content, and α-keto acid on alcohol production were also investigated. The increase of glucose content and the adding of α-keto acids facilitated the production of C4 and C5 alcohols. The enzyme activities of pure Kivd on α-ketoisovalerate and α-ketoisocaproate were 26.77 and 21.24 μmol min(-1) mg(-1), respectively. Due to its ability on decarboxylation of α-ketoisovalerate and α-ketoisocaproate, the recombinant E. coli strain showed potential application on isoamyl alcohol and isobutanol production.
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Affiliation(s)
- Xiaoyan Chen
- Key Laboratory of Renewable Energy and Gas Hydrate, Chinese Academy of Sciences, Guangzhou, 510640, China
| | - Jingliang Xu
- Key Laboratory of Renewable Energy and Gas Hydrate, Chinese Academy of Sciences, Guangzhou, 510640, China
| | - Liu Yang
- Key Laboratory of Renewable Energy and Gas Hydrate, Chinese Academy of Sciences, Guangzhou, 510640, China
| | - Zhenhong Yuan
- Key Laboratory of Renewable Energy and Gas Hydrate, Chinese Academy of Sciences, Guangzhou, 510640, China.
| | - Shiyuan Xiao
- Key Laboratory of Renewable Energy and Gas Hydrate, Chinese Academy of Sciences, Guangzhou, 510640, China
| | - Yu Zhang
- Key Laboratory of Renewable Energy and Gas Hydrate, Chinese Academy of Sciences, Guangzhou, 510640, China
| | - Cuiyi Liang
- Key Laboratory of Renewable Energy and Gas Hydrate, Chinese Academy of Sciences, Guangzhou, 510640, China
| | - Minchao He
- Key Laboratory of Renewable Energy and Gas Hydrate, Chinese Academy of Sciences, Guangzhou, 510640, China
| | - Ying Guo
- Key Laboratory of Renewable Energy and Gas Hydrate, Chinese Academy of Sciences, Guangzhou, 510640, China
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Meneely KM, Luo Q, Lamb AL. Redesign of MST enzymes to target lyase activity instead promotes mutase and dehydratase activities. Arch Biochem Biophys 2013; 539:70-80. [PMID: 24055536 DOI: 10.1016/j.abb.2013.09.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Revised: 09/10/2013] [Accepted: 09/11/2013] [Indexed: 11/20/2022]
Abstract
The isochorismate and salicylate synthases are members of the MST family of enzymes. The isochorismate synthases establish an equilibrium for the conversion chorismate to isochorismate and the reverse reaction. The salicylate synthases convert chorismate to salicylate with an isochorismate intermediate; therefore, the salicylate synthases perform isochorismate synthase and isochorismate-pyruvate lyase activities sequentially. While the active site residues are highly conserved, there are two sites that show trends for lyase-activity and lyase-deficiency. Using steady state kinetics and HPLC progress curves, we tested the "interchange" hypothesis that interconversion of the amino acids at these sites would promote lyase activity in the isochorismate synthases and remove lyase activity from the salicylate synthases. An alternative, "permute" hypothesis, that chorismate-utilizing enzymes are designed to permute the substrate into a variety of products and tampering with the active site may lead to identification of adventitious activities, is tested by more sensitive NMR time course experiments. The latter hypothesis held true. The variant enzymes predominantly catalyzed chorismate mutase-prephenate dehydratase activities, sequentially generating prephenate and phenylpyruvate, augmenting previously debated (mutase) or undocumented (dehydratase) adventitious activities.
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Affiliation(s)
- Kathleen M Meneely
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045, United States
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Wang M, Song F, Wu R, Allen KN, Mariano PS, Dunaway-Mariano D. Co-evolution of HAD phosphatase and hotdog-fold thioesterase domain function in the menaquinone-pathway fusion proteins BF1314 and PG1653. FEBS Lett 2013; 587:2851-9. [PMID: 23851007 DOI: 10.1016/j.febslet.2013.07.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2013] [Accepted: 07/02/2013] [Indexed: 01/25/2023]
Abstract
The function of a Bacteroidetes menaquinone biosynthetic pathway fusion protein comprised of an N-terminal haloacid dehalogenase (HAD) family domain and a C-terminal hotdog-fold family domain is described. Whereas the thioesterase domain efficiently catalyzes 1,4-dihydroxynapthoyl-CoA hydrolysis, an intermediate step in the menaquinone pathway, the HAD domain is devoid of catalytic activity. In some Bacteroidetes a homologous, catalytically active 1,4-dihydroxynapthoyl-CoA thioesterase replaces the fusion protein. Following the gene fusion event, sequence divergence resulted in a HAD domain that functions solely as the oligomerization domain of an otherwise inactive thioesterase domain.
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Affiliation(s)
- Min Wang
- Department of Chemistry & Chemical Biology, University of New Mexico, Albuquerque, NM 87131, USA
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12
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Beigi M, Waltzer S, Fries A, Eggeling L, Sprenger GA, Müller M. TCA Cycle Involved Enzymes SucA and Kgd, as well as MenD: Efficient Biocatalysts for Asymmetric C–C Bond Formation. Org Lett 2013; 15:452-5. [DOI: 10.1021/ol3031186] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Maryam Beigi
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-University of Freiburg, Albertstraße 25, 79104 Freiburg, Germany, Institute of Bio- and Geoscience, IBG-1: Biotechnology, Research Centre Jülich, 52425 Jülich, Germany, and Institute of Microbiology, Universität Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Simon Waltzer
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-University of Freiburg, Albertstraße 25, 79104 Freiburg, Germany, Institute of Bio- and Geoscience, IBG-1: Biotechnology, Research Centre Jülich, 52425 Jülich, Germany, and Institute of Microbiology, Universität Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Alexander Fries
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-University of Freiburg, Albertstraße 25, 79104 Freiburg, Germany, Institute of Bio- and Geoscience, IBG-1: Biotechnology, Research Centre Jülich, 52425 Jülich, Germany, and Institute of Microbiology, Universität Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Lothar Eggeling
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-University of Freiburg, Albertstraße 25, 79104 Freiburg, Germany, Institute of Bio- and Geoscience, IBG-1: Biotechnology, Research Centre Jülich, 52425 Jülich, Germany, and Institute of Microbiology, Universität Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Georg A. Sprenger
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-University of Freiburg, Albertstraße 25, 79104 Freiburg, Germany, Institute of Bio- and Geoscience, IBG-1: Biotechnology, Research Centre Jülich, 52425 Jülich, Germany, and Institute of Microbiology, Universität Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Michael Müller
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-University of Freiburg, Albertstraße 25, 79104 Freiburg, Germany, Institute of Bio- and Geoscience, IBG-1: Biotechnology, Research Centre Jülich, 52425 Jülich, Germany, and Institute of Microbiology, Universität Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
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13
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Fang M, Macova A, Hanson KL, Kos J, Palmer DRJ. Using substrate analogues to probe the kinetic mechanism and active site of Escherichia coli MenD. Biochemistry 2011; 50:8712-21. [PMID: 21928762 DOI: 10.1021/bi201202n] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
MenD catalyzes the thiamin diphosphate-dependent decarboxylative carboligation of α-ketoglutarate and isochorismate. The enzyme is essential for menaquinone biosynthesis in many bacteria and has been proposed to be an antibiotic target. The kinetic mechanism of this enzyme has not previously been demonstrated because of the limitations of the UV-based kinetic assay. We have reported the synthesis of an isochorismate analogue that acts as a substrate for MenD. The apparent weaker binding of this analogue is advantageous in that it allows accurate kinetic experiments at substrate concentrations near K(m). Using this substrate in concert with the dead-end inhibitor methyl succinylphosphonate, an analogue of α-ketoglutarate, we show that MenD follows a ping-pong kinetic mechanism. Using both the natural and synthetic substrates, we have measured the effects of 12 mutations of residues at the active site. The results give experimental support to previous models and hypotheses and allow observations unavailable using only the natural substrate.
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Affiliation(s)
- Maohai Fang
- Department of Chemistry, University of Saskatchewan, Saskatoon, SK S7N 5C9, Canada
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14
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Bongaerts J, Esser S, Lorbach V, Al-Momani L, Müller MA, Franke D, Grondal C, Kurutsch A, Bujnicki R, Takors R, Raeven L, Wubbolts M, Bovenberg R, Nieger M, Schürmann M, Trachtmann N, Kozak S, Sprenger GA, Müller M. Diversity-oriented production of metabolites derived from chorismate and their use in organic synthesis. Angew Chem Int Ed Engl 2011; 50:7781-6. [PMID: 21739551 DOI: 10.1002/anie.201103261] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2011] [Indexed: 11/09/2022]
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15
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Bongaerts J, Esser S, Lorbach V, Al-Momani L, Müller MA, Franke D, Grondal C, Kurutsch A, Bujnicki R, Takors R, Raeven L, Wubbolts M, Bovenberg R, Nieger M, Schürmann M, Trachtmann N, Kozak S, Sprenger GA, Müller M. Diversity-Oriented Production of Metabolites Derived from Chorismate and Their Use in Organic Synthesis. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201103261] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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16
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Dawson A, Fyfe PK, Gillet F, Hunter WN. Exploiting the high-resolution crystal structure of Staphylococcus aureus MenH to gain insight into enzyme activity. BMC STRUCTURAL BIOLOGY 2011; 11:19. [PMID: 21513522 PMCID: PMC3097144 DOI: 10.1186/1472-6807-11-19] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2011] [Accepted: 04/22/2011] [Indexed: 11/23/2022]
Abstract
Background MenH (2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase) is a key enzyme in the biosynthesis of menaquinone, catalyzing an unusual 2,5-elimination of pyruvate from 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexadiene-1-carboxylate. Results The crystal structure of Staphylococcus aureus MenH has been determined at 2 Å resolution. In the absence of a complex to inform on aspects of specificity a model of the enzyme-substrate complex has been used in conjunction with previously published kinetic analyses, site-directed mutagenesis studies and comparisons with orthologues to investigate the structure and reactivity of MenH. Conclusions The overall basic active site displays pronounced hydrophobic character on one side and these properties complement those of the substrate. A complex network of hydrogen bonds involving well-ordered water molecules serves to position key residues participating in the recognition of substrate and subsequent catalysis. We propose a proton shuttle mechanism, reliant on a catalytic triad consisting of Ser89, Asp216 and His243. The reaction is initiated by proton abstraction from the substrate by an activated Ser89. The propensity to form a conjugated system provides the driving force for pyruvate elimination. During the elimination, a methylene group is converted to a methyl and we judge it likely that His243 provides a proton, previously acquired from Ser89 for that reduction. A conformational change of the protonated His243 may be encouraged by the presence of an anionic intermediate in the active site.
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Affiliation(s)
- Alice Dawson
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
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17
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Fang M, Toogood RD, Macova A, Ho K, Franzblau SG, McNeil MR, Sanders DAR, Palmer DRJ. Succinylphosphonate Esters Are Competitive Inhibitors of MenD That Show Active-Site Discrimination between Homologous α-Ketoglutarate-Decarboxylating Enzymes. Biochemistry 2010; 49:2672-9. [DOI: 10.1021/bi901432d] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Maohai Fang
- Department of Chemistry, University of Saskatchewan, 110 Science Place, Saskatoon, SK S7N 5C9, Canada
| | - R. Daniel Toogood
- Department of Chemistry, University of Saskatchewan, 110 Science Place, Saskatoon, SK S7N 5C9, Canada
| | - Andrea Macova
- Department of Chemistry, University of Saskatchewan, 110 Science Place, Saskatoon, SK S7N 5C9, Canada
| | - Karen Ho
- Department of Chemistry, University of Saskatchewan, 110 Science Place, Saskatoon, SK S7N 5C9, Canada
| | - Scott G. Franzblau
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois, 833 South Wood Street, Chicago, Illinois 60612
| | - Michael R. McNeil
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80523
| | - David A. R. Sanders
- Department of Chemistry, University of Saskatchewan, 110 Science Place, Saskatoon, SK S7N 5C9, Canada
| | - David R. J. Palmer
- Department of Chemistry, University of Saskatchewan, 110 Science Place, Saskatoon, SK S7N 5C9, Canada
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18
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19
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Structural and functional analysis of Vitamin K2 synthesis protein MenD. Biochem Biophys Res Commun 2009; 388:748-51. [DOI: 10.1016/j.bbrc.2009.08.093] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2009] [Accepted: 08/18/2009] [Indexed: 11/23/2022]
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20
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Srinivasan N, Golbeck JH. Protein–cofactor interactions in bioenergetic complexes: The role of the A1A and A1B phylloquinones in Photosystem I. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2009; 1787:1057-88. [DOI: 10.1016/j.bbabio.2009.04.010] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2009] [Revised: 04/14/2009] [Accepted: 04/22/2009] [Indexed: 10/20/2022]
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21
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Bunik VI, Degtyarev D. Structure-function relationships in the 2-oxo acid dehydrogenase family: substrate-specific signatures and functional predictions for the 2-oxoglutarate dehydrogenase-like proteins. Proteins 2008; 71:874-90. [PMID: 18004749 DOI: 10.1002/prot.21766] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Structural relationship within the family of the thiamine diphosphate-dependent 2-oxo acid dehydrogenases was analyzed by combining different methods of sequence alignment with crystallographic and enzymological studies of the family members. For the first time, the sequence similarity of the homodimeric 2-oxoglutarate dehydrogenase to heterotetrameric 2-oxo acid dehydrogenases is established. The presented alignment of the catalytic domains of the dehydrogenases of pyruvate, branched-chain 2-oxo acids and 2-oxoglutarate unravels the sequence markers of the substrate specificity and the essential residues of the family members without the 3D structures resolved. Predicted dual substrate specificity of some of the 2-oxo acid dehydrogenases was confirmed experimentally. The results were used to decipher functions of the two hypothetical proteins of animal genomes, OGDHL and DHTKD1, similar to the 2-oxoglutarate dehydrogenase. Conservation of all the essential residues confirmed their catalytic competence. Sequence analysis indicated that OGDHL represents a previously unknown isoform of the 2-oxoglutarate dehydrogenase, whereas DHTKD1 differs from the homologs at the N-terminus and substrate binding pocket. The differences suggest changes in heterologous protein interactions and accommodation of more polar and/or bulkier structural analogs of 2-oxoglutarate, such as 2-oxoadipate, 2-oxo-4-hydroxyglutarate, or products of the carboligase reaction between a 2-oxodicarboxylate and glyoxylate or acetaldehyde. The signatures of the Ca2+-binding sites were found in the Ca2+-activated 2-oxoglutarate dehydrogenase and OGDHL, but not in DHTKD1. Mitochondrial localization was predicted for OGDHL and DHTKD1, with DHTKD1 probably localized also to nuclei. Medical implications of the obtained results are discussed in view of the possible associations of the 2-oxo acid dehydrogenases and DHTKD1 with neurodegeneration and cancer.
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Affiliation(s)
- Victoria I Bunik
- School of Bioinformatics and Bioengineering, Lomonosov Moscow State University, Moscow 119992, Russian Federation.
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22
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Oldenburg J, Marinova M, Müller-Reible C, Watzka M. The vitamin K cycle. VITAMINS AND HORMONES 2008; 78:35-62. [PMID: 18374189 DOI: 10.1016/s0083-6729(07)00003-9] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Vitamin K is a collective term for lipid-like naphthoquinone derivatives synthesized only in eubacteria and plants and functioning as electron carriers in energy transduction pathways and as free radical scavengers maintaining intracellular redox homeostasis. Paradoxically, vitamin K is a required micronutrient in animals for protein posttranslational modification of some glutamate side chains to gamma-carboxyglutamate. The majority of gamma-carboxylated proteins function in blood coagulation. Vitamin K shuttles reducing equivalents as electrons between two enzymes: VKORC1, which is itself reduced by an unknown ER lumenal reductant in order to reduce vitamin K epoxide (K>O) to the quinone form (KH2); and gamma-glutamyl carboxylase, which catalyzes posttranslational gamma-carboxylation and oxidizes KH2 to K>O. This article reviews vitamin K synthesis and the vitamin K cycle, outlines physiological roles of various vitamin K-dependent, gamma-carboxylated proteins, and summarizes the current understanding of clinical phenotypes caused by genetic mutations affecting both enzymes of the vitamin K cycle.
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Affiliation(s)
- Johannes Oldenburg
- Institute of Experimental Haematology and Transfusion Medicine, University Clinic Bonn, D-53105 Bonn, Germany
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23
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Jiang M, Chen M, Cao Y, Yang Y, Sze KH, Chen X, Guo Z. Determination of the stereochemistry of 2-succinyl-5-enolpyruvyl-6-hydroxy-3- cyclohexene-1-carboxylate, a key intermediate in menaquinone biosynthesis. Org Lett 2007; 9:4765-7. [PMID: 17956107 DOI: 10.1021/ol702126m] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The turnover product of the committed step of menaquinone biosynthesis was isolated and determined to be (1R,2S,5S,6S)-2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate. Structural determination of this key intermediate represents a critical step to complete elucidation of the biosynthetic pathway.
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Affiliation(s)
- Ming Jiang
- Department of Chemistry, Center for Cancer Research, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
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24
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Jiang M, Cao Y, Guo ZF, Chen M, Chen X, Guo Z. Menaquinone biosynthesis in Escherichia coli: identification of 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate as a novel intermediate and re-evaluation of MenD activity. Biochemistry 2007; 46:10979-89. [PMID: 17760421 DOI: 10.1021/bi700810x] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Menaquinone is an electron carrier in the respiratory chain of Escherichia coli during anaerobic growth. Its biosynthesis involves (1R,6R)-2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylic acid (SHCHC) as an intermediate, which is believed to be derived from isochorismate and 2-ketoglutarate by one of the biosynthetic enzymes-MenD. However, we found that the genuine MenD product is 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic acid (SEPHCHC), rather than SHCHC. This is supported by the following findings: (i) isochorismate consumption and SHCHC formation are not synchronized in the enzymic reaction, (ii) the rate of SHCHC formation is independent of the enzyme concentration, (iii) SHCHC is not formed in weakly acidic or neutral solutions in which the isochorismate substrate is readily consumed by MenD, and (iv) the MenD turnover product, formed under conditions disabling SHCHC formation, possesses spectroscopic characteristics consistent with the structure of SEPHCHC and spontaneously undergoes 2,5-elimination to form SHCHC and pyruvate in weakly basic solutions. Two properties of the intermediate, ultraviolet transparency and chemical instability, provide a rationale for the fact that SHCHC has been consistently mistaken as the MenD product. In accordance with these findings, MenD was rediscovered to be a highly efficient enzyme with a high second-order rate constant and should be renamed SEPHCHC synthase. Intriguingly, the enzymatic activity responsible for conversion of SEPHCHC into SHCHC appears not to associate with any of the known enzymes in menaquinone biosynthesis but is present in the crude extract of E. coli K12, suggesting that a genuine SHCHC synthase remains to be identified to fully elucidate the ubiquitous biosynthetic pathway.
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Affiliation(s)
- Ming Jiang
- Department of Chemistry, Center for Cancer Research, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
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25
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Tian J, Bryk R, Itoh M, Suematsu M, Nathan C. Variant tricarboxylic acid cycle in Mycobacterium tuberculosis: identification of alpha-ketoglutarate decarboxylase. Proc Natl Acad Sci U S A 2005; 102:10670-5. [PMID: 16027371 PMCID: PMC1180764 DOI: 10.1073/pnas.0501605102] [Citation(s) in RCA: 163] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb) has adapted its metabolism for persistence in the human macrophage. The adaptations are likely to involve Mtb's core intermediary metabolism, whose enzymes have been little studied. The tricarboxylic acid cycle is expected to yield precursors for energy, lipids, amino acids, and heme. The genome sequence of Mtb H37Rv predicts the presence of a complete tricarboxylic acid cycle, but we recently found that alpha-ketoglutarate dehydrogenase (KDH) activity is lacking in Mtb lysates. Here we showed that citrate synthase, aconitase, isocitrate dehydrogenase, fumarase, malate dehydrogenase, and succinate dehydrogenase, but not KDH, are present, raising the possibility of separate oxidative and reductive half-cycles. As a potential link between the half-cycles, we found that Rv1248c, annotated as encoding SucA, the putative E1 component of KDH, instead encodes alpha-ketoglutarate decarboxylase (Kgd) and produces succinic semialdehyde. Succinic semialdehyde dehydrogenase activity was detected in Mtb lysates and recapitulated with recombinant proteins GabD1 (encoded by Rv0234c) and GabD2 (encoded by Rv1731). Kgd and GabD1 or GabD2 form an alternative pathway from alpha-ketoglutarate to succinate. Rv1248c, which is essential or required for normal growth of Mtb [Sassetti, C., Boyd, D. H. & Rubin, E. J. (2003) Mol. Microbiol 48, 77-84] is the first gene shown to encode a Kgd. Kgd is lacking in humans and may represent a potential target for chemotherapy of tuberculosis.
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Affiliation(s)
- Jing Tian
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY 10021, USA
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26
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Smit BA, van Hylckama Vlieg JET, Engels WJM, Meijer L, Wouters JTM, Smit G. Identification, cloning, and characterization of a Lactococcus lactis branched-chain alpha-keto acid decarboxylase involved in flavor formation. Appl Environ Microbiol 2005; 71:303-11. [PMID: 15640202 PMCID: PMC544199 DOI: 10.1128/aem.71.1.303-311.2005] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The biochemical pathway for formation of branched-chain aldehydes, which are important flavor compounds derived from proteins in fermented dairy products, consists of a protease, peptidases, a transaminase, and a branched-chain alpha-keto acid decarboxylase (KdcA). The activity of the latter enzyme has been found only in a limited number of Lactococcus lactis strains. By using a random mutagenesis approach, the gene encoding KdcA in L. lactis B1157 was identified. The gene for this enzyme is highly homologous to the gene annotated ipd, which encodes a putative indole pyruvate decarboxylase, in L. lactis IL1403. Strain IL1403 does not produce KdcA, which could be explained by a 270-nucleotide deletion at the 3' terminus of the ipd gene encoding a truncated nonfunctional decarboxylase. The kdcA gene was overexpressed in L. lactis for further characterization of the decarboxylase enzyme. Of all of the potential substrates tested, the highest activity was observed with branched-chain alpha-keto acids. Moreover, the enzyme activity was hardly affected by high salinity, and optimal activity was found at pH 6.3, indicating that the enzyme might be active under cheese ripening conditions.
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Affiliation(s)
- Bart A Smit
- Department of Flavor, Nutrition and Ingredients, NIZO food research, 6710 BA Ede, The Netherlands
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27
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Shimada H, Ohno R, Shibata M, Ikegami I, Onai K, Ohto MA, Takamiya KI. Inactivation and deficiency of core proteins of photosystems I and II caused by genetical phylloquinone and plastoquinone deficiency but retained lamellar structure in a T-DNA mutant of Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2005; 41:627-37. [PMID: 15686525 DOI: 10.1111/j.1365-313x.2004.02326.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Phylloquinone, a substituted 1,4-naphthoquinone with an 18-carbon-saturated phytyl tail, functions as a bound one-electron carrier cofactor at the A1 site of photosystem I (PSI). A Feldmann tag line mutant, no. 2755 (designated as abc4 hereafter), showed pale-green young leaves and white old leaves. The mutated nuclear gene encoded 1,4-dihydroxy-2-naphtoic acid phytyltransferase, an enzyme of phylloquinone biosynthesis, and high-performance liquid chromatography analysis revealed that the abc4 mutant contained no phylloquinone, and only about 3% plastoquinone. Photooxidation of P700 of PSI in the abc4 mutant was not observed, and reduced-versus-oxidized difference spectroscopy indicated that the abc4 mutant had no P700. The maximum quantum yield of photosystem II (PSII) in the abc4 mutant was much decreased, and the electron transfer from PSII to PSI in the abc4 mutant did not occur. For the pale-green leaves of the abc4 mutant plant, the ultrastructure of the chloroplasts was almost the same as that of the wild-type plant. However, the chloroplasts in the albino leaves of the mutant were smaller and had a lot of grana thylakoids and few stroma thylakoids. The amounts of PSI and PSII core subunits in the abc4 mutant were significantly decreased compared with those in the wild type. These results suggested that a deficiency of phylloquinone in PSI caused the abolishment of PSI and a partial defect of PSII due to a significant decrease of plastoquinone, but did not influence the ultrastructure of the chloroplasts in young leaves.
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Affiliation(s)
- Hiroshi Shimada
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama, Japan.
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28
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Bhasin M, Billinsky JL, Palmer DRJ. Steady-State Kinetics and Molecular Evolution of Escherichia coli MenD [(1R,6R)-2-Succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate Synthase], an Anomalous Thiamin Diphosphate-Dependent Decarboxylase−Carboligase. Biochemistry 2003; 42:13496-504. [PMID: 14621995 DOI: 10.1021/bi035224j] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
(1R,6R)-2-Succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate (SHCHC) synthase, or MenD, catalyzes the thiamin diphosphate- (ThDP-) dependent decarboxylation of 2-oxoglutarate, the subsequent addition of the resulting succinyl-ThDP moiety to isochorismate, and the delta-elimination of pyruvate to yield SHCHC, pyruvate, and carbon dioxide. The enzyme is part of a superfamily of ThDP-dependent 2-oxo acid decarboxylases that includes pyruvate decarboxylase, benzoylformate decarboxylase, and acetohydroxy acid synthase, among others. However, this is the only enzyme known to catalyze a Stetter-like 1,4-addition of a ThDP adduct to the beta-carbon of an unsaturated carboxylate. Herein we report properties of the MenD protein from Escherichia coli, including the results of the first steady-state kinetic studies of the SHCHC synthase reaction. The protein is a dimer and shows cooperativity with respect to both substrates. The enzyme prefers divalent manganese as its metal ion cofactor and shows no dependence on FAD. MenD, required for biosynthesis of menaquinone and phylloquinone, is found in the genomes of a wide range of bacteria, as well as that of the archaeon Halobacterium sp. NRC-1 and the eukaryote Arabidopsis thaliana. Sequence alignments with other members of the superfamily are used to predict amino acid residues likely to be important in the binding and activation of ThDP. A site-directed mutant that replaces the conserved glutamic acid residue (E55), predicted to interact with N1' of the aminopyrimidine ring, with glutamine was generated, with catastrophic results for catalysis. There is no evidence for the release of succinate semialdehyde as a product; therefore, EC 4.1.1.71 should not be used for this enzyme.
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Affiliation(s)
- Milan Bhasin
- Department of Chemistry, University of Saskatchewan, 110 Science Place, Saskatoon, Saskatchewan S7N 5C9, Canada
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29
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Truglio JJ, Theis K, Feng Y, Gajda R, Machutta C, Tonge PJ, Kisker C. Crystal structure of Mycobacterium tuberculosis MenB, a key enzyme in vitamin K2 biosynthesis. J Biol Chem 2003; 278:42352-60. [PMID: 12909628 DOI: 10.1074/jbc.m307399200] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Bacterial enzymes of the menaquinone (Vitamin K2) pathway are potential drug targets because they lack human homologs. MenB, 1,4-dihydroxy-2-naphthoyl-CoA synthase, the fourth enzyme in the biosynthetic pathway leading from chorismate to menaquinone, catalyzes the conversion of O-succinylbenzoyl-CoA (OSB-CoA) to 1,4-dihydroxy-2-naphthoyl-CoA (DHNA-CoA). Based on our interest in developing novel tuberculosis chemotherapeutics, we have solved the structures of MenB from Mycobacterium tuberculosis and its complex with acetoacetyl-coenzyme A at 1.8 and 2.3 A resolution, respectively. Like other members of the crotonase superfamily, MenB folds as an (alpha3)2 hexamer, but its fold is distinct in that the C terminus crosses the trimer-trimer interface, forming a flexible part of the active site within the opposing trimer. The highly conserved active site of MenB contains a deep pocket lined by Asp-192, Tyr-287, and hydrophobic residues. Mutagenesis shows that Asp-192 and Tyr-287 are essential for enzymatic catalysis. We postulate a catalytic mechanism in which MenB enables proton transfer within the substrate to yield an oxyanion as the initial step in catalysis. Knowledge of the active site geometry and characterization of the catalytic mechanism of MenB will aid in identifying new inhibitors for this potential drug target.
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Affiliation(s)
- James J Truglio
- Department of Pharmacological Sciences, Center for Structural Biology, State University of New York at Stony Brook, NY 11794-5115, USA
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Wade Johnson T, Naithani S, Stewart C, Zybailov B, Daniel Jones A, Golbeck JH, Chitnis PR. The menD and menE homologs code for 2-succinyl-6-hydroxyl-2,4-cyclohexadiene-1-carboxylate synthase and O-succinylbenzoic acid-CoA synthase in the phylloquinone biosynthetic pathway of Synechocystis sp. PCC 6803. BIOCHIMICA ET BIOPHYSICA ACTA 2003; 1557:67-76. [PMID: 12615349 DOI: 10.1016/s0005-2728(02)00396-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The genome of the cyanobacterium Synechocystis sp. PCC 6803 contains genes identified as menD and menE, homologs of Escherichia coli genes that code for 2-succinyl-6-hydroxyl-2,4-cyclohexadiene-1-carboxylate (SHCHC) synthase and O-succinylbenzoic acid-CoA ligase in the menaquinone biosynthetic pathway. In cyanobacteria, the product of this pathway is 2-methyl-3-phytyl-1,4-naphthoquinone (phylloquinone), a molecule used exclusively as an electron transfer cofactor in Photosystem (PS) I. The menD(-) and menE(-) strains were generated, and both were found to lack phylloquinone. Hence, no alternative pathways exist in cyanobacteria to produce O-succinylbenzoyl-CoA. Q-band EPR studies of photoaccumulated quinone anion radical and optical kinetic studies of the P700(+) [F(A)/F(B)](-) backreaction indicate that in the mutant strains, plastoquinone-9 functions as the electron transfer cofactor in the A(1) site of PS I. At a light intensity of 40 microE m(-2) s(-1), the menD(-) and menE(-) mutant strains grew photoautotrophically and photoheterotrophically, but with doubling times slower than the wild type. Both of which are sensitive to high light intensities. Low-temperature fluorescence studies show that in the menD(-) and menE(-) mutants, the ratio of PS I to PS II is reduced relative to the wild type. Whole-chain electron transfer rates in the menD(-) and menE(-) mutant cells are correspondingly higher on a chlorophyll basis. The slower growth rate and high-light sensitivity of the menD(-) and menE(-) mutants are therefore attributed to a lower content of PS I per cell.
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Affiliation(s)
- T Wade Johnson
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA.
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Zheng Y, Szustakowski JD, Fortnow L, Roberts RJ, Kasif S. Computational identification of operons in microbial genomes. Genome Res 2002; 12:1221-30. [PMID: 12176930 PMCID: PMC186635 DOI: 10.1101/gr.200602] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
By applying graph representations to biochemical pathways, a new computational pipeline is proposed to find potential operons in microbial genomes. The algorithm relies on the fact that enzyme genes in operons tend to catalyze successive reactions in metabolic pathways. We applied this algorithm to 42 microbial genomes to identify putative operon structures. The predicted operons from Escherichia coli were compared with a selected metabolism-related operon dataset from the RegulonDB database, yielding a prediction sensitivity (89%) and specificity (87%) relative to this dataset. Several examples of detected operons are given and analyzed. Modular gene cluster transfer and operon fusion are observed. A further use of predicted operon data to assign function to putative genes was suggested and, as an example, a previous putative gene (MJ1604) from Methanococcus jannaschii is now annotated as a phosphofructokinase, which was regarded previously as a missing enzyme in this organism. GC content changes in the operon region and nonoperon region were examined. The results reveal a clear GC content transition at the boundaries of putative operons. We looked further into the conservation of operons across genomes. A trp operon alignment is analyzed in depth to show gene loss and rearrangement in different organisms during operon evolution.
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Affiliation(s)
- Yu Zheng
- Bioinformatics Graduate Program, Boston University, Boston, Massachusetts 02215, USA
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Meganathan R. Biosynthesis of menaquinone (vitamin K2) and ubiquinone (coenzyme Q): a perspective on enzymatic mechanisms. VITAMINS AND HORMONES 2001; 61:173-218. [PMID: 11153266 DOI: 10.1016/s0083-6729(01)61006-9] [Citation(s) in RCA: 180] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The benzoquinone ubiquinone (coenzyme Q) and the naphthoquinones menaquinone (vitamin K2) and demethylmenaquinone are derived from the shikimate pathway, which has been described as a "metabolic tree with many branches." Menaquinone (MK) is considered a vitamin, but coenzyme (Q) is not; MK is an essential nutrient (it cannot be synthesized by mammals), whereas Q is not considered an essential nutrient since it can be synthesized from the amino acid tyrosine. The quinone nucleus of Q is derived directly from chorismate, whereas that of MK is derived from chorismate via isochorismate. The prenyl side chain of both quinones is derived from prenyl diphosphate, and the methyl groups are derived from S-adenosylmethionine. MK biosynthesis requires 2-ketoglutarate and the cofactors ATP, coenzyme A (CoASH), and thiamine pyrophosphate. In spite of the fact that both quinones originate from the shikimate pathway, there are important differences in their biosynthesis. In MK biosynthesis, the prenyl side chain is introduced in the next to last step, which is accompanied by loss of the carboxyl group, whereas in Q biosynthesis, the prenyl side chain is introduced at the second step, with retention of the carboxyl group. In MK biosynthesis, all the reactions of the pathway up to the prenylation (next to last step) are carried out by soluble enzymes, whereas all the enzymes involved in Q biosynthesis except the first are membrane bound. In MK biosynthesis the last step is a C-methylation; in Q biosynthesis, the last step is an O-methylation. In Q biosynthesis a second C-methylation and O-methylation take place in the middle part of the pathway. In spite of the fact that Q and MK biosynthesis diverges at chorismate, the C-methylations involved in both pathways are carried out by the same enzyme. Finally, Q biosynthesis under aerobic conditions requires molecular oxygen; anaerobic biosynthesis of Q and MK incorporates oxygen atoms derived from water. The current status of the pathways with particular emphasis on the reaction mechanisms, is discussed in this review.
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Affiliation(s)
- R Meganathan
- Department of Biological Sciences, Northern Illinois University, DeKalb, Illinois 60115, USA
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Green LS, Li Y, Emerich DW, Bergersen FJ, Day DA. Catabolism of alpha-ketoglutarate by a sucA mutant of Bradyrhizobium japonicum: evidence for an alternative tricarboxylic acid cycle. J Bacteriol 2000; 182:2838-44. [PMID: 10781553 PMCID: PMC101993 DOI: 10.1128/jb.182.10.2838-2844.2000] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A complete tricarboxylic acid (TCA) cycle is generally considered necessary for energy production from the dicarboxylic acid substrates malate, succinate, and fumarate. However, a Bradyrhizobium japonicum sucA mutant that is missing alpha-ketoglutarate dehydrogenase is able to grow on malate as its sole source of carbon. This mutant also fixes nitrogen in symbiosis with soybean, where dicarboxylic acids are its principal carbon substrate. Using a flow chamber system to make direct measurements of oxygen consumption and ammonium excretion, we confirmed that bacteroids formed by the sucA mutant displayed wild-type rates of respiration and nitrogen fixation. Despite the absence of alpha-ketoglutarate dehydrogenase activity, whole cells of the mutant were able to decarboxylate alpha-[U-(14)C]ketoglutarate and [U-(14)C]glutamate at rates similar to those of wild-type B. japonicum, indicating that there was an alternative route for alpha-ketoglutarate catabolism. Because cell extracts from B. japonicum decarboxylated [U-(14)C]glutamate very slowly, the gamma-aminobutyrate shunt is unlikely to be the pathway responsible for alpha-ketoglutarate catabolism in the mutant. In contrast, cell extracts from both the wild type and mutant showed a coenzyme A (CoA)-independent alpha-ketoglutarate decarboxylation activity. This activity was independent of pyridine nucleotides and was stimulated by thiamine PP(i). Thin-layer chromatography showed that the product of alpha-ketoglutarate decarboxylation was succinic semialdehyde. The CoA-independent alpha-ketoglutarate decarboxylase, along with succinate semialdehyde dehydrogenase, may form an alternative pathway for alpha-ketoglutarate catabolism, and this pathway may enhance TCA cycle function during symbiotic nitrogen fixation.
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Affiliation(s)
- L S Green
- Biochemistry Department, University of Missouri, Columbia, Missouri 65211, USA.
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Johnson TW, Shen G, Zybailov B, Kolling D, Reategui R, Beauparlant S, Vassiliev IR, Bryant DA, Jones AD, Golbeck JH, Chitnis PR. Recruitment of a foreign quinone into the A(1) site of photosystem I. I. Genetic and physiological characterization of phylloquinone biosynthetic pathway mutants in Synechocystis sp. pcc 6803. J Biol Chem 2000; 275:8523-30. [PMID: 10722690 DOI: 10.1074/jbc.275.12.8523] [Citation(s) in RCA: 108] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Genes encoding enzymes of the biosynthetic pathway leading to phylloquinone, the secondary electron acceptor of photosystem (PS) I, were identified in Synechocystis sp. PCC 6803 by comparison with genes encoding enzymes of the menaquinone biosynthetic pathway in Escherichia coli. Targeted inactivation of the menA and menB genes, which code for phytyl transferase and 1,4-dihydroxy-2-naphthoate synthase, respectively, prevented the synthesis of phylloquinone, thereby confirming the participation of these two gene products in the biosynthetic pathway. The menA and menB mutants grow photoautotrophically under low light conditions (20 microE m(-2) s(-1)), with doubling times twice that of the wild type, but they are unable to grow under high light conditions (120 microE m(-2) s(-1)). The menA and menB mutants grow photoheterotrophically on media supplemented with glucose under low light conditions, with doubling times similar to that of the wild type, but they are unable to grow under high light conditions unless atrazine is present to inhibit PS II activity. The level of active PS II per cell in the menA and menB mutant strains is identical to that of the wild type, but the level of active PS I is about 50-60% that of the wild type as assayed by low temperature fluorescence, P700 photoactivity, and electron transfer rates. PS I complexes isolated from the menA and menB mutant strains contain the full complement of polypeptides, show photoreduction of F(A) and F(B) at 15 K, and support 82-84% of the wild type rate of electron transfer from cytochrome c(6) to flavodoxin. HPLC analyses show high levels of plastoquinone-9 in PS I complexes from the menA and menB mutants but not from the wild type. We propose that in the absence of phylloquinone, PS I recruits plastoquinone-9 into the A(1) site, where it functions as an efficient cofactor in electron transfer from A(0) to the iron-sulfur clusters.
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Affiliation(s)
- T W Johnson
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011, USA
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Verberne MC, Muljono RAB, Verpoorte R. Salicylic acid biosynthesis. BIOCHEMISTRY AND MOLECULAR BIOLOGY OF PLANT HORMONES 1999. [DOI: 10.1016/s0167-7306(08)60493-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Abstract
This map is an update of the edition 9 map by Berlyn et al. (M. K. B. Berlyn, K. B. Low, and K. E. Rudd, p. 1715-1902, in F. C. Neidhardt et al., ed., Escherichia coli and Salmonella: cellular and molecular biology, 2nd ed., vol. 2, 1996). It uses coordinates established by the completed sequence, expressed as 100 minutes for the entire circular map, and adds new genes discovered and established since 1996 and eliminates those shown to correspond to other known genes. The latter are included as synonyms. An alphabetical list of genes showing map location, synonyms, the protein or RNA product of the gene, phenotypes of mutants, and reference citations is provided. In addition to genes known to correspond to gene sequences, other genes, often older, that are described by phenotype and older mapping techniques and that have not been correlated with sequences are included.
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Affiliation(s)
- M K Berlyn
- Department of Biology and School of Forestry and Environmental Studies, Yale University, New Haven, Connecticut 06520-8104, USA.
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Schörken U, Sprenger GA. Thiamin-dependent enzymes as catalysts in chemoenzymatic syntheses. BIOCHIMICA ET BIOPHYSICA ACTA 1998; 1385:229-43. [PMID: 9655911 DOI: 10.1016/s0167-4838(98)00071-5] [Citation(s) in RCA: 72] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Enzymes are increasingly being used to perform regio- and enantioselective reactions in chemoenzymatic syntheses. To utilize enzymes for unphysiological reactions and to yield novel products, a broad substrate spectrum is desirable. Thiamin diphosphate (ThDP)-dependent enzymes vary in their substrate tolerance from rather strict substrate specificity (phosphoketolases, glyoxylate carboligase) to more permissive enzymes (transketolase, dihydroxyacetone synthase, pyruvate decarboxylase) and therefore differ in their potential to be used as biocatalysts. We give an overview of the known substrate spectra of ThDP-dependent enzymes and present examples of multi-enzyme or chemoenzymatic approaches which involve ThDP-dependent enzymes as biocatalysts to obtain pharmaceutical compounds as ephedrine and glycosidase inhibitors, sex pheromones as exo-brevicomin, 13C-labeled metabolites, and other intermediates as 1-deoxyxylulose 5-phosphate, a precursor of vitamins and isoprenoids.
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Affiliation(s)
- U Schörken
- Institut für Biotechnologie 1, Forschungszentrum Jülich GmbH, P.O. Box 1913, D-52425 Jülich, Germany
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38
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Suvarna K, Stevenson D, Meganathan R, Hudspeth ME. Menaquinone (vitamin K2) biosynthesis: localization and characterization of the menA gene from Escherichia coli. J Bacteriol 1998; 180:2782-7. [PMID: 9573170 PMCID: PMC107237 DOI: 10.1128/jb.180.10.2782-2787.1998] [Citation(s) in RCA: 103] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
A key reaction in the biosynthesis of menaquinone involves the conversion of the soluble bicyclic naphthalenoid compound 1, 4-dihydroxy-2-naphthoic acid (DHNA) to the membrane-bound demethylmenaquinone. The enzyme catalyzing this reaction, DHNA-octaprenyltransferase, attaches a 40-carbon side chain to DHNA. The menA gene encoding this enzyme has been cloned and localized to a 2.0-kb region of the Escherichia coli genome between cytR and glpK. DNA sequence analysis of the cloned insert revealed a 308-codon open reading frame (ORF), which by deletion analyses was shown to restore anaerobic growth of a menA mutant. Reverse-phase high-performance liquid chromatography analysis of quinones extracted from the orf-complemented cells independently confirmed the restoration of menaquinone biosynthesis, and similarly, analyses of isolated cell membranes for DHNA octaprenyltransferase activity confirmed the introduction of the menA product into the orf-complemented menA mutant. The validity of an ORF-associated putative promoter sequence was confirmed by primer extension analyses.
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Affiliation(s)
- K Suvarna
- Department of Biological Sciences, Northern Illinois University, DeKalb, Illinois 60115, USA
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Koike-Takeshita A, Koyama T, Ogura K. Identification of a novel gene cluster participating in menaquinone (vitamin K2) biosynthesis. Cloning and sequence determination of the 2-heptaprenyl-1,4-naphthoquinone methyltransferase gene of Bacillus stearothermophilus. J Biol Chem 1997; 272:12380-3. [PMID: 9139683 DOI: 10.1074/jbc.272.19.12380] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
We recently described the isolation and sequence analysis of a DNA region containing the genes of Bacillus stearothermophilus heptaprenyl diphosphate synthase, which catalyzes the synthesis of the prenyl side chain of menaquinone-7 of this bacterium. Sequence analyses revealed the presence of three open reading frames (ORFs), designated as ORF-1, ORF-2, and ORF-3, and the structural genes of the heptaprenyl diphosphate synthase were proved to consist of ORF-1 (heps-1) and ORF-3 (heps-2) (Koike-Takeshita, A., Koyama, T., Obata, S., and Ogura, K. (1995) J. Biol. Chem. 270, 18396-18400). The predicted amino acid sequence of ORF-2 (234 amino acids) contains a methyltransferase consensus sequence and shows a 22% identity with UbiG of Escherichia coli, which catalyzes S-adenosyl-L-methionine-dependent methylation of 2-octaprenyl-3-methyl-5-hydroxy-6-methoxy-1,4-benzoquinone. These pieces of information led us to identify the ORF-2 gene product. The cell-free homogenate of the transformant of E. coli with an expression vector of ORF-2 catalyzed the incorporation of S-adenosyl-L-methionine into menaquinone-8, indicating that ORF-2 encodes 2-heptaprenyl-1,4-naphthoquinone methyltransferase, which participates in the terminal step of the menaquinone biosynthesis. Thus it is concluded that the ORF-1, ORF-2, and ORF-3 genes, designated heps-1, menG, and heps-2, respectively, form another cluster involved in menaquinone biosynthesis in addition to the cluster of menB, menC, menD, and menE already identified in the Bacillus subtilis and E. coli chromosomes.
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Affiliation(s)
- A Koike-Takeshita
- Bio Research Laboratory, Toyota Motor Corporation, Toyota-cho 1, Toyota, Aichi 471-71, Japan
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41
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Daruwala R, Kwon O, Meganathan R, Hudspeth M. A new isochorismate synthase specifically involved in menaquinone (vitamin K2) biosynthesis encoded by the menF gene. FEMS Microbiol Lett 1996. [DOI: 10.1111/j.1574-6968.1996.tb08330.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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42
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Kwon O, Hudspeth ME, Meganathan R. Anaerobic biosynthesis of enterobactin Escherichia coli: regulation of entC gene expression and evidence against its involvement in menaquinone (vitamin K2) biosynthesis. J Bacteriol 1996; 178:3252-9. [PMID: 8655506 PMCID: PMC178078 DOI: 10.1128/jb.178.11.3252-3259.1996] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
In Escherichia coli, isochorismate is a common precursor for the biosynthesis of the siderophore enterobactin and menaquinone (vitamin K2). Isochorismate is formed by the shikimate pathway from chorismate by the enzyme isochorismate synthase encoded by the entC gene. Since enterobactin is involved in the aerobic assimilation of iron, and menaquinone is involved in anaerobic electron transport, we investigated the regulation of entC by iron and oxygen. An operon fusion between entC with its associated regulatory region and lacZ+ was constructed and introduced into the chromosome in a single copy. Expression of entC-lacZ was found to be regulated by the concentration of iron both aerobically and anaerobically. An established entC::kan mutant deficient in enterobactin biosynthesis was found to grow normally and synthesize wild-type levels of menaquinone under anaerobic conditions in iron-sufficient media. These results led to the demonstration of an alternate isochorismate synthase specifically involved in menaquinone synthesis encoded by the menF gene. Consistent with these findings, the entC+ strains were found to synthesize enterobactin anaerobically under iron-deficient conditions while the ent mutants failed to do so.
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Affiliation(s)
- O Kwon
- Department of Biological Sciences, Northern Illinois University, De Kalb, 60115, USA
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43
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Sharma V, Hudspeth ME, Meganathan R. Menaquinone (vitamin K2) biosynthesis: localization and characterization of the menE gene from Escherichia coli. Gene X 1996; 168:43-8. [PMID: 8626063 DOI: 10.1016/0378-1119(95)00721-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
In Escherichia coli, the biosynthesis of the electron carrier menaquinone (vitamin K2) involves at least seven identified enzymatic activities, five of which are encoded in the men cluster. One of these, the conversion of o-succinylbenzoic acid to 1,4-dihydroxy-2-naphthoic acid, requires the formation of o-succinylbenzoyl-CoA (OSB-CoA) as an intermediate. Formation of the intermediate is mediated by OSB-CoA synthetase encoded by the menE locus known to be located either 5' of menB, or 3' of menC. A DNA fragment overlapping the 3' end of menC in shown by enzymatic complementation to elevate OSB-CoA synthetase activity. Nucleotide sequence analysis of the fragment identified a 1.355-kb open reading frame (ORF) which, when deleted at either the 5' or 3' end, failed to generate increased enzymatic activity. The ORF is preceded by a consensus ribosome-binding site, but no apparent sigma-70 promoter. An oppositely transcribed unidentified gene cluster follows the menE ORF. The region 5' of menB contains an an additional ORF of unknown function (orf241) and establishes the order of genes in the men cluster as menD, orf241, menB, menC and menE. All loci are transcribed counter-clockwise.
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Affiliation(s)
- V Sharma
- Department of Biological Sciences, Northern Illinois University, DeKalb, 60115, USA
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Rowland B, Hill K, Miller P, Driscoll J, Taber H. Structural organization of a Bacillus subtilis operon encoding menaquinone biosynthetic enzymes. Gene 1995; 167:105-9. [PMID: 8566759 DOI: 10.1016/0378-1119(95)00662-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Menaquinone (MK) is a non-protein component of the Bacillus subtilis (Bs) electron transport chain synthesized from chorismate through a series of MK-specific reactions. The genes encoding biosynthesis of the naphthoquinone ring of MK are clustered at 273 degrees on the Bs chromosome. A 3.9-kb region capable of rescuing men mutants blocked in the early stages of MK biosynthesis was sequenced and found to contain three major open reading frames (ORFs). The first ORF (menF) has a predicted size of 51.8 kDa and 34% amino-acid identity with the isochorismate synthases of Escherichia coli (EntC) and Aeromonas hydrophila (AmoA), ORF2 (menD) a predicted size of 60.2 kDa and 21% identity with MenD of E. coli. ORF3 has a predicted size of 21.4 kDa and 29% identity to triacylglycerol lipase of Psychrobacter immobilis. No sequence corresponding to menC was identified. Plasmid integrational studies of the men gene cluster had suggested the presence of promoters secondary to the previously identified p1 men promoter. Sequence analysis revealed a putative promoter region upstream from ORF3.
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Affiliation(s)
- B Rowland
- Department of Microbiology, Immunology and Molecular Genetics, Albany Medical College, NY 12208, USA
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Palaniappan C, Taber H, Meganathan R. Biosynthesis of o-succinylbenzoic acid in Bacillus subtilis: identification of menD mutants and evidence against the involvement of the alpha-ketoglutarate dehydrogenase complex. J Bacteriol 1994; 176:2648-53. [PMID: 8169214 PMCID: PMC205404 DOI: 10.1128/jb.176.9.2648-2653.1994] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The biosynthesis of o-succinylbenzoic acid (OSB), the first aromatic intermediate involved in the biosynthesis of menaquinone (vitamin K2) is demonstrated for the first time in the gram-positive bacterium Bacillus subtilis. Cell extracts were found to contain isochorismate synthase, 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylic acid (SHCHC) synthase-alpha-ketoglutarate decarboxylase and o-succinylbenzoic acid synthase activities. An odhA mutant which lacks the decarboxylase component (usually termed E1, EC 1.2.4.2, oxoglutarate dehydrogenase [lipoamide]) of the alpha-ketoglutarate dehydrogenase complex was found to synthesize SHCHC and form succinic semialdehyde-thiamine pyrophosphate. Thus, the presence of an alternate alpha-ketoglutarate decarboxylase activity specifically involved in menaquinone biosynthesis is established for B. subtilis. A number of OSB-requiring mutants were also assayed for the presence of the various enzymes involved in the biosynthesis of OSB. All mutants were found to lack only the SHCHC synthase activity.
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Affiliation(s)
- C Palaniappan
- Department of Biological Sciences, Northern Illinois University, DeKalb 60115
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Abstract
A list of currently identified gene products of Escherichia coli is given, together with a bibliography that provides pointers to the literature on each gene product. A scheme to categorize cellular functions is used to classify the gene products of E. coli so far identified. A count shows that the numbers of genes concerned with small-molecule metabolism are on the same order as the numbers concerned with macromolecule biosynthesis and degradation. One large category is the category of tRNAs and their synthetases. Another is the category of transport elements. The categories of cell structure and cellular processes other than metabolism are smaller. Other subjects discussed are the occurrence in the E. coli genome of redundant pairs and groups of genes of identical or closely similar function, as well as variation in the degree of density of genetic information in different parts of the genome.
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Affiliation(s)
- M Riley
- Marine Biological Laboratory, Woods Hole, Massachusetts 02543
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Sharma V, Meganathan R, Hudspeth ME. Menaquinone (vitamin K2) biosynthesis: cloning, nucleotide sequence, and expression of the menC gene from Escherichia coli. J Bacteriol 1993; 175:4917-21. [PMID: 8335646 PMCID: PMC204947 DOI: 10.1128/jb.175.15.4917-4921.1993] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
The benzenoid aromatic compound o-succinylbenzoic acid is formed by dehydration of the prearomatic compound 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylic acid by the enzyme o-succinylbenzoate synthase, encoded by the menC gene. A 1.3-kb PstI-PvuII fragment was found to complement the menC mutation. The complete nucleotide sequence of this fragment revealed a single open reading frame of 954 bp capable of encoding a 35-kDa protein. A consensus sequence for a ribosomal binding site but no promoter consensus sequences were found. However, the first base of the initiating codon of this open reading frame overlaps the upstream menB gene termination codon, suggesting an operon-like organization for these genes. Consistent with this suggestion, the menB promoter can initiate transcription of the menC gene.
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Affiliation(s)
- V Sharma
- Department of Biological Sciences, Plant Molecular Biology Center, Northern Illinois University, DeKalb 60115
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