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Duan C, Jiang Q, Jiang X, Zeng H, Wu Q, Yu Y, Yang X. Discovery of a Novel Inhibitor Structure of Mycobacterium tuberculosis Isocitrate Lyase. Molecules 2022; 27:molecules27082447. [PMID: 35458645 PMCID: PMC9026967 DOI: 10.3390/molecules27082447] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 03/30/2022] [Accepted: 03/31/2022] [Indexed: 02/06/2023] Open
Abstract
Tuberculosis remains a global threat to public health, and dormant Mycobacterium tuberculosis leads to long-term medication that is harmful to the human body. M. tuberculosis isocitrate lyase (MtICL), which is absent in host cells, is a key rate-limiting enzyme of the glyoxylic acid cycle and is essential for the survival of dormant M. tuberculosis. The aim of this study was to evaluate natural compounds as potential MtICL inhibitors through docking and experimental verification. Screening of the TCMSP database library was done using Discovery Studio 2019 for molecular docking and interaction analysis, with the putative inhibitors of MtICL, 3-BP, and IA as reference ligands. Daphnetin (MOL005118), with a docking score of 94.8 and -CDOCKER interaction energy of 56 kcal/mol, was selected and verified on MtICL in vitro and M. smegmatis; daphnetin gave an IC50 of 4.34 μg/mL for the MtICL enzyme and an MIC value of 128 μg/mL against M. smegmatis, showing enhanced potential in comparison with 3-BP and IA. The interactions and essential amino acid residues of the protein were analyzed. In summary, natural daphnetin may be a promising new skeleton for the design of inhibitors of MtICL to combat dormant M. tuberculosis.
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Affiliation(s)
- Changyuan Duan
- Key Laboratory of Medical Laboratory Diagnostics of the Education Ministry, College of Laboratory Medicine, Chongqing Medical University, No. 1, Yixueyuan Road, Yuzhong Dist, Chongqing 400016, China; (C.D.); (X.J.); (H.Z.); (Q.W.); (Y.Y.)
| | - Qihua Jiang
- College of Pharmacy, Chongqing Medical University, Chongqing 400016, China;
| | - Xue Jiang
- Key Laboratory of Medical Laboratory Diagnostics of the Education Ministry, College of Laboratory Medicine, Chongqing Medical University, No. 1, Yixueyuan Road, Yuzhong Dist, Chongqing 400016, China; (C.D.); (X.J.); (H.Z.); (Q.W.); (Y.Y.)
| | - Hongwei Zeng
- Key Laboratory of Medical Laboratory Diagnostics of the Education Ministry, College of Laboratory Medicine, Chongqing Medical University, No. 1, Yixueyuan Road, Yuzhong Dist, Chongqing 400016, China; (C.D.); (X.J.); (H.Z.); (Q.W.); (Y.Y.)
| | - Qiaomin Wu
- Key Laboratory of Medical Laboratory Diagnostics of the Education Ministry, College of Laboratory Medicine, Chongqing Medical University, No. 1, Yixueyuan Road, Yuzhong Dist, Chongqing 400016, China; (C.D.); (X.J.); (H.Z.); (Q.W.); (Y.Y.)
| | - Yang Yu
- Key Laboratory of Medical Laboratory Diagnostics of the Education Ministry, College of Laboratory Medicine, Chongqing Medical University, No. 1, Yixueyuan Road, Yuzhong Dist, Chongqing 400016, China; (C.D.); (X.J.); (H.Z.); (Q.W.); (Y.Y.)
| | - Xiaolan Yang
- Key Laboratory of Medical Laboratory Diagnostics of the Education Ministry, College of Laboratory Medicine, Chongqing Medical University, No. 1, Yixueyuan Road, Yuzhong Dist, Chongqing 400016, China; (C.D.); (X.J.); (H.Z.); (Q.W.); (Y.Y.)
- Correspondence: ; Tel.: +86-23-6848-5240
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Mellott DM, Torres D, Krieger IV, Cameron SA, Moghadamchargari Z, Laganowsky A, Sacchettini JC, Meek TD, Harris LD. Mechanism-Based Inactivation of Mycobacterium tuberculosis Isocitrate Lyase 1 by (2 R,3 S)-2-Hydroxy-3-(nitromethyl)succinic acid. J Am Chem Soc 2021; 143:17666-17676. [PMID: 34664502 DOI: 10.1021/jacs.1c07970] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The isocitrate lyase paralogs of Mycobacterium tuberculosis (ICL1 and 2) are essential for mycobacterial persistence and constitute targets for the development of antituberculosis agents. We report that (2R,3S)-2-hydroxy-3-(nitromethyl)succinic acid (5-NIC) undergoes apparent retro-aldol cleavage as catalyzed by ICL1 to produce glyoxylate and 3-nitropropionic acid (3-NP), the latter of which is a covalent-inactivating agent of ICL1. Kinetic analysis of this reaction identified that 5-NIC serves as a robust and efficient mechanism-based inactivator of ICL1 (kinact/KI = (1.3 ± 0.1) × 103 M-1 s-1) with a partition ratio <1. Using enzyme kinetics, mass spectrometry, and X-ray crystallography, we identified that the reaction of the 5-NIC-derived 3-NP with the Cys191 thiolate of ICL1 results in formation of an ICL1-thiohydroxamate adduct as predicted. One aspect of the design of 5-NIC was to lower its overall charge compared to isocitrate to assist with cell permeability. Accordingly, the absence of the third carboxylate group will simplify the synthesis of pro-drug forms of 5-NIC for characterization in cell-infection models of M. tuberculosis.
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Affiliation(s)
- Drake M Mellott
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, United States
| | - Dan Torres
- The Ferrier Research Institute, Victoria University of Wellington, Wellington 5046, New Zealand
| | - Inna V Krieger
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, United States
| | - Scott A Cameron
- The Ferrier Research Institute, Victoria University of Wellington, Wellington 5046, New Zealand
- The Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland 1010, New Zealand
| | - Zahra Moghadamchargari
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - James C Sacchettini
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, United States
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Thomas D Meek
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, United States
| | - Lawrence D Harris
- The Ferrier Research Institute, Victoria University of Wellington, Wellington 5046, New Zealand
- The Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland 1010, New Zealand
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Hwang JY, Chung B, Kwon OS, Park SC, Cho E, Oh DC, Shin J, Oh KB. Inhibitory Effects of Epipolythiodioxopiperazine Fungal Metabolites on Isocitrate Lyase in the Glyoxylate Cycle of Candida albicans. Mar Drugs 2021; 19:md19060295. [PMID: 34067454 PMCID: PMC8224697 DOI: 10.3390/md19060295] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/20/2021] [Accepted: 05/20/2021] [Indexed: 11/16/2022] Open
Abstract
Four epipolythiodioxopiperazine fungal metabolites (1-4) isolated from the sponge-derived Aspergillus quadrilineatus FJJ093 were evaluated for their capacity to inhibit isocitrate lyase (ICL) in the glyoxylate cycle of Candida albicans. The structures of these compounds were elucidated using spectroscopic techniques and comparisons with previously reported data. We found secoemestrin C (1) (an epitetrathiodioxopiperazine derivative) to be a potent ICL inhibitor, with an inhibitory concentration of 4.77 ± 0.08 μM. Phenotypic analyses of ICL-deletion mutants via growth assays with acetate as the sole carbon source demonstrated that secoemestrin C (1) inhibited C. albicans ICL. Semi-quantitative reverse-transcription polymerase chain reaction analyses indicated that secoemestrin C (1) inhibits ICL mRNA expression in C. albicans under C2-assimilating conditions.
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Affiliation(s)
- Ji-Yeon Hwang
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Korea; (J.-Y.H.); (O.-S.K.); (S.C.P.); (D.-C.O.)
| | - Beomkoo Chung
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea; (B.C.); (E.C.)
| | - Oh-Seok Kwon
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Korea; (J.-Y.H.); (O.-S.K.); (S.C.P.); (D.-C.O.)
| | - Sung Chul Park
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Korea; (J.-Y.H.); (O.-S.K.); (S.C.P.); (D.-C.O.)
| | - Eunji Cho
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea; (B.C.); (E.C.)
| | - Dong-Chan Oh
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Korea; (J.-Y.H.); (O.-S.K.); (S.C.P.); (D.-C.O.)
| | - Jongheon Shin
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Korea; (J.-Y.H.); (O.-S.K.); (S.C.P.); (D.-C.O.)
- Correspondence: (J.S.); (K.-B.O.); Tel.: +82-2-880-2484 (J.S.); +82-2-880-4646 (K.-B.O.)
| | - Ki-Bong Oh
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea; (B.C.); (E.C.)
- Correspondence: (J.S.); (K.-B.O.); Tel.: +82-2-880-2484 (J.S.); +82-2-880-4646 (K.-B.O.)
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Pham TV, Mellott DM, Moghadamchargari Z, Chen K, Krieger I, Laganowsky A, Sacchettini JC, Meek TD. Covalent Inactivation of Mycobacterium tuberculosis Isocitrate Lyase by cis-2,3-Epoxy-Succinic Acid. ACS Chem Biol 2021; 16:463-470. [PMID: 33688722 DOI: 10.1021/acschembio.0c00740] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The isocitrate lyases (ICL1/2) are essential enzymes of Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis. At present, no ICL1/2 inhibitors have progressed to clinical evaluation, despite extensive drug discovery efforts. Herein, we surveyed succinate analogs against ICL1 and found that dicarboxylic acids constrained in their synperiplanar conformations, such as maleic acid, comprise uncompetitive inhibitors of ICL1 and inhibit more potently than their trans-isomers. From this, we identified cis-2,3 epoxysuccinic acid (cis-EpS) as a selective, irreversible covalent inactivator of Mtb ICL1 (kinact/Kinact= (5.0 ± 1.4) × 104 M-1 s-1; Kinact = 200 ± 50 nM), the most potent inactivator of ICL1 yet characterized. Crystallographic and mass spectrometric analysis demonstrated that Cys191 of ICL1 was S-malylated by cis-EpS, and a crystallographic "snapshot" of inactivation lent insight into the chemical mechanism of this inactivation. Proteomic analysis of E. coli lysates showed that cis-EpS selectively labeled plasmid-expressed Mtb ICL1. Consistently, cis-EpS, but not its trans-isomer, inhibited the growth of Mtb under conditions in which ICL function is essential. These findings encourage the development of analogs of cis-2,3-epoxysuccinate as antituberculosis agents.
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Affiliation(s)
- Truc Viet Pham
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, United States
| | - Drake M Mellott
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, United States
| | - Zahra Moghadamchargari
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Kevin Chen
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, United States
| | - Inna Krieger
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, United States
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - James C Sacchettini
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, United States
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Thomas D Meek
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, United States
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Hwang JY, Lee JH, Park SC, Lee J, Oh DC, Oh KB, Shin J. New Peptides from The Marine-Derived Fungi Aspergillus allahabadii and Aspergillus ochraceopetaliformis. Mar Drugs 2019; 17:md17090488. [PMID: 31438635 PMCID: PMC6780696 DOI: 10.3390/md17090488] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 08/19/2019] [Accepted: 08/19/2019] [Indexed: 12/29/2022] Open
Abstract
Four new peptides were isolated from the culture broths of the marine-derived fungi Aspergillus allahabadii and A. ochraceopetaliformis. Based on the results of chemical and spectroscopic analyses, two compounds (1 and 2) from A. allahabadii were determined to be cyclopentapeptides, while those from A. ochraceopetaliformis were a structurally-related cyclodepsihexapeptide (3) and its linear analog (4). In addition to the presence of a D-amino acid residue, the almost reversed sequence of peptides in 3 and 4, relative to those of the 1 and 2, is notable. These new compounds exhibited moderate inhibition against the enzyme sortase A as well as a weak inhibition against isocitrate lyase (2).
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Affiliation(s)
- Ji-Yeon Hwang
- Natural Products Research Institute, College of Pharmacy, Seoul National University, San 56-1, Sillim, Gwanak, Seoul 151-742, Korea
| | - Jung-Ho Lee
- Natural Products Research Institute, College of Pharmacy, Seoul National University, San 56-1, Sillim, Gwanak, Seoul 151-742, Korea
| | - Sung Chul Park
- Natural Products Research Institute, College of Pharmacy, Seoul National University, San 56-1, Sillim, Gwanak, Seoul 151-742, Korea
| | - Jayho Lee
- Department of Agricultural Biotechnology, College of Agriculture and Life Science, Seoul National University, San 56-1, Sillim, Gwanak, Seoul 151-921, Korea
| | - Dong-Chan Oh
- Natural Products Research Institute, College of Pharmacy, Seoul National University, San 56-1, Sillim, Gwanak, Seoul 151-742, Korea
| | - Ki-Bong Oh
- Department of Agricultural Biotechnology, College of Agriculture and Life Science, Seoul National University, San 56-1, Sillim, Gwanak, Seoul 151-921, Korea.
| | - Jongheon Shin
- Natural Products Research Institute, College of Pharmacy, Seoul National University, San 56-1, Sillim, Gwanak, Seoul 151-742, Korea.
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Kwon OS, Kim D, Kim H, Lee YJ, Lee HS, Sim CJ, Oh DC, Lee SK, Oh KB, Shin J. Bromopyrrole Alkaloids from the Sponge Agelas kosrae. Mar Drugs 2018; 16:md16120513. [PMID: 30563015 PMCID: PMC6316234 DOI: 10.3390/md16120513] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 12/12/2018] [Accepted: 12/13/2018] [Indexed: 11/23/2022] Open
Abstract
Two new sceptrin derivatives (1,2) and eight structurally-related known bromopyrrole-bearing alkaloids were isolated from the tropical sponge Agelas kosrae. By a combination of spectroscopic methods, the new compounds, designated dioxysceptrin (1) and ageleste C (2), were determined to be structural analogs of each other that differ at the imidazole moiety. Dioxysceptrin was also found to exist as a mixture of α-amido epimers. The sceptrin alkaloids exhibited weak cytotoxicity against cancer cells. Compounds 1 and 2 also moderately exhibited anti-angiogenic and isocitrate lyase-inhibitory activities, respectively.
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Affiliation(s)
- Oh-Seok Kwon
- Natural Products Research Institute, College of Pharmacy, Seoul National University, San 56-1, Sillim, Gwanak, Seoul 151-742, Korea.
| | - Donghwa Kim
- Natural Products Research Institute, College of Pharmacy, Seoul National University, San 56-1, Sillim, Gwanak, Seoul 151-742, Korea.
| | - Heegyu Kim
- Department of Agricultural Biotechnology, College of Agriculture and Life Science, Seoul National University, San 56-1, Sillim, Gwanak, Seoul 151-921, Korea.
| | - Yeon-Ju Lee
- Marine Natural Products Laboratory, Korea Institute of Ocean Science and Technology, P.O. Box 29, Seoul 425-600, Korea.
| | - Hyi-Seung Lee
- Marine Natural Products Laboratory, Korea Institute of Ocean Science and Technology, P.O. Box 29, Seoul 425-600, Korea.
| | - Chung J Sim
- Department of Biological Science, College of Life Science and Nano Technology, Hannam University, 461-6 Jeonmin, Yuseong, Daejeon 305-811, Korea.
| | - Dong-Chan Oh
- Natural Products Research Institute, College of Pharmacy, Seoul National University, San 56-1, Sillim, Gwanak, Seoul 151-742, Korea.
| | - Sang Kook Lee
- Natural Products Research Institute, College of Pharmacy, Seoul National University, San 56-1, Sillim, Gwanak, Seoul 151-742, Korea.
| | - Ki-Bong Oh
- Department of Agricultural Biotechnology, College of Agriculture and Life Science, Seoul National University, San 56-1, Sillim, Gwanak, Seoul 151-921, Korea.
| | - Jongheon Shin
- Natural Products Research Institute, College of Pharmacy, Seoul National University, San 56-1, Sillim, Gwanak, Seoul 151-742, Korea.
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Hernández-Chinea C, Maimone L, Campos Y, Mosca W, Romero PJ. Apparent isocitrate lyase activity in Leishmania amazonensis. Acta Parasitol 2017; 62:701-707. [PMID: 29035856 DOI: 10.1515/ap-2017-0084] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 06/23/2017] [Indexed: 11/15/2022]
Abstract
Early reports have demonstrated the occurrence of glyoxylate cycle enzymes in several Leishmania species. However, these results have been underestimated because genes for the two key enzymes of the cycle, isocitrate lyase (ICL) and malate synthase (MS), are not annotated in Leishmania genomes. We have re-examined this issue in promastigotes of Leishmania amazonensis. Enzyme activities were assayed spectrophotometrically in cellular extracts and characterized partially. A 40 kDa band displaying ICL activity was visualized on zymograms of the extracts. By immunoblotting with mouse antibodies against ICL from Bacillus stearothermophilus, a band of approximately 40 kDa was identified, coincident with the relative molecular mass of the activity band revealed on zymograms. Indirect immunofluorescence of intact promastigotes showed that the recognized antigen is distributed as a punctuated pattern, mainly distributed beneath the subpellicular microtubules, over a diffused cytoplasmic stain. These results clearly demonstrate the existence of an apparent ICL activity in L. amazonensis promastigotes, which is associated to a 40 kDa polypeptide and distributed both diffused and as punctuate aggregates in the cytoplasm. The relevance of this activity is discussed.
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Kamzolova SV, Allayarov RK, Lunina JN, Morgunov IG. The effect of oxalic and itaconic acids on threo-Ds-isocitric acid production from rapeseed oil by Yarrowia lipolytica. Bioresour Technol 2016; 206:128-133. [PMID: 26851896 DOI: 10.1016/j.biortech.2016.01.092] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 01/24/2016] [Accepted: 01/25/2016] [Indexed: 05/07/2023]
Abstract
The effect of oxalic and itaconic acids, the inhibitors of the isocitrate lyase, on the production of isocitric acid by the wild strain Yarrowia lipolytica VKM Y-2373 grown in the medium containing rapeseed oil was studied. In the presence of oxalic and itaconic acids, strain Y. lipolytica accumulated in the medium isocitric acid (70.0 and 82.7 g/L, respectively) and citric acid (23.0 and 18.4 g/L, respectively). In control experiment, when the inhibitors were not added to the medium, the strain accumulated isocitric and citric acids at concentrations of 62.0 and 28.0 g/L, respectively. Thus, the use of the oxalic and itaconic acids as additives to the medium is a simple and convenient method of isocitric acid production with a minimum content of citric acid.
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Affiliation(s)
- Svetlana V Kamzolova
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino 142290, Russia.
| | - Ramil K Allayarov
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino 142290, Russia
| | - Julia N Lunina
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino 142290, Russia
| | - Igor G Morgunov
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino 142290, Russia
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Kamzolova SV, Lunin YN, Allayarov RK, Puntus IF, Laptev IA, Samojlenko VA, Morgunov IG. [Biosynthesis of isocitric acid by the yeast yarrowia lipolytica and its regulation]. Prikl Biokhim Mikrobiol 2015; 51:251-257. [PMID: 26027362 DOI: 10.7868/s0555109915020075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We studied the biosynthesis of isocitric acid from rapeseed (canola) oil by the yeast Yarrowia lipolytica and its regulation. We determined a fundamental possibility for directed biosynthesis of isocitric acid by Y lipolytica yeast, with only minimal amounts of citric acid byproduct, when grown on a medium containing canola oil. Wild type strains of Y lipolytica were mutagenized by UV irradiation and treatment with N-methyl-N'-nitro-N-nitrosoguanidine (NG). Subsequent selection on media with acetate and isocitrate resulted in isolation of a UV/NG Y lipolytica UV/NG mutant that synthesized isocitrate and citrate at a ratio of 2.7:1. In the parent strain, this ratio is 1:1. Inhibition of isocitrate lyase, a key enzyme in the metabolism of isocitric acid, by the addition of itaconic acid resulted in increased synthesis of isocitrate with a ratio of isocitrate to citrate reaching 6:1. Culturing of the Y lipolytica UV/NG mutant in a pilot industrial fermenter in the presence of itaconic acid resulted in the production of 88.7 g/L of isocitric acid with a yield of 90%.
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Ko K, Lee SH, Kim SH, Kim EH, Oh KB, Shin J, Oh DC. Lajollamycins, nitro group-bearing spiro-β-lactone-γ-lactams obtained from a marine-derived Streptomyces sp. J Nat Prod 2014; 77:2099-2104. [PMID: 25211234 DOI: 10.1021/np500500t] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Lajollamycins (1-4), each of which bears a spiro-β-lactone-γ-lactam ring and a nitro-tetraene moiety, were obtained from a marine-derived Streptomyces strain isolated from the southern area of Jeju Island, Republic of Korea. The planar structures of the lajollamycins were elucidated on the basis of spectroscopic analyses by NMR, UV, IR, and MS. The absolute configuration of lajollamycin (1), the planar structure of which has been previously reported, was determined using J-based configuration analysis based on (1)H-(1)H and (1)H-(13)C coupling constants, as well as ROESY correlations, followed by the modified Mosher's method. The absolute configurations of lajollamycins B-D (2-4) were established by comparing their CD spectra with that of 1. The lajollamycins exhibited moderate inhibitory activity toward Candida albicans isocitrate lyase.
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Affiliation(s)
- Keebeom Ko
- Natural Products Research Institute, College of Pharmacy, Seoul National University , 1 Gwanak-ro, Gwanak-gu, Seoul 151-742, Republic of Korea
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do Prado RS, Alves RJ, de Oliveira CMA, Kato L, da Silva RA, Quintino GO, do Desterro Cunha S, de Almeida Soares CM, Pereira M. Inhibition of Paracoccidioides lutzii Pb01 isocitrate lyase by the natural compound argentilactone and its semi-synthetic derivatives. PLoS One 2014; 9:e94832. [PMID: 24752170 PMCID: PMC3994062 DOI: 10.1371/journal.pone.0094832] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Accepted: 03/20/2014] [Indexed: 11/08/2022] Open
Abstract
The dimorphic fungus Paracoccidioides spp. is responsible for paracoccidioidomycosis, the most prevalent systemic mycosis in Latin America, causing serious public health problems. Adequate treatment of mycotic infections is difficult, since fungi are eukaryotic organisms with a structure and metabolism similar to those of eukaryotic hosts. In this way, specific fungus targets have become important to search of new antifungal compound. The role of the glyoxylate cycle and its enzymes in microbial virulence has been reported in many fungal pathogens, including Paracoccidioides spp. Here, we show the action of argentilactone and its semi-synthetic derivative reduced argentilactone on recombinant and native isocitrate lyase from Paracoccidioides lutzii Pb01 (PbICL) in the presence of different carbon sources, acetate and glucose. Additionally, argentilactone and its semi-synthetic derivative reduced argentilactone exhibited relevant inhibitory activity against P. lutzii Pb01 yeast cells and dose-dependently influenced the transition from the mycelium to yeast phase. The other oxygenated derivatives tested, epoxy argentilactone and diol argentilactone-, did not show inhibitory action on the fungus. The results were supported by in silico experiments.
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Affiliation(s)
- Renata Silva do Prado
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | - Ricardo Justino Alves
- Laboratório de Produtos Naturais, Instituto de Química, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | | | - Lucília Kato
- Laboratório de Produtos Naturais, Instituto de Química, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | - Roosevelt Alves da Silva
- Núcleo Colaborativo de BioSistemas, Campus Jataí, Universidade Federal de Goiás, Jataí, Goiás, Brazil
| | | | - Silvio do Desterro Cunha
- Instituto de Química, Departamento de Química Orgânica, Universidade Federal da Bahia, Salvador, Bahia, Brazil
| | - Célia Maria de Almeida Soares
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | - Maristela Pereira
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
- * E-mail:
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12
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Abrahams GL, Kumar A, Savvi S, Hung AW, Wen S, Abell C, Barry CE, Sherman DR, Boshoff HIM, Mizrahi V. Pathway-selective sensitization of Mycobacterium tuberculosis for target-based whole-cell screening. ACTA ACUST UNITED AC 2014; 19:844-54. [PMID: 22840772 DOI: 10.1016/j.chembiol.2012.05.020] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Revised: 05/22/2012] [Accepted: 05/25/2012] [Indexed: 11/19/2022]
Abstract
Whole-cell screening of Mycobacterium tuberculosis (Mtb) remains a mainstay of drug discovery, but subsequent target elucidation often proves difficult. Conditional mutants that underexpress essential genes have been used to identify compounds with known mechanism of action by target-based whole-cell screening (TB-WCS). Here, the feasibility of TB-WCS in Mtb was assessed by generating mutants that conditionally express pantothenate synthetase (panC), diaminopimelate decarboxylase (lysA), and isocitrate lyase (icl1). The essentiality of panC and lysA, and conditional essentiality of icl1 for growth on fatty acids, was confirmed. Depletion of PanC and Icl1 rendered mutants hypersensitive to target-specific inhibitors. Stable reporter strains were generated for use in high-throughput screening, and their utility was demonstrated by identifying compounds that display greater potency against a PanC-depleted strain. These findings illustrate the power of TB-WCS as a tool for tuberculosis drug discovery.
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Affiliation(s)
- Garth L Abrahams
- Molecular Mycobacteriology Research Unit and DST/NRF Centre of Excellence for Biomedical TB Research, University of the Witwatersrand and the National Health Laboratory Service, Johannesburg 2000, South Africa.
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13
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Won TH, Jeon JE, Kim SH, Lee SH, Rho BJ, Oh DC, Oh KB, Shin J. Brominated aromatic furanones and related esters from the ascidian Synoicum sp. J Nat Prod 2012; 75:2055-61. [PMID: 23145909 DOI: 10.1021/np3005562] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Nine new compounds, tris-aromatic furanones (1, 2, 3a, 3b, and 4) and related bis-aromatic diesters (5a, 5b, 6a, and 6b), are described from the ascidian Synoicum sp. collected off the coast of Chuja-do, Korea. The structures of these compounds, designated as cadiolides E and G-I (1-4) and synoilides A and B (5 and 6), were determined by extensive spectroscopic analyses. The absolute configuration at the asymmetric center of cadiolide G (2) was assigned by ECD analysis. Of these new compounds, cadiolide I and the synoilides possess unprecedented carbon skeletons. Several of these compounds exhibited significant inhibition against diverse bacterial strains as well as moderate inhibition against the enzymes sortase A, isocitrate lyase, and Na(+)/K(+)-ATPase.
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Affiliation(s)
- Tae Hyung Won
- Natural Products Research Institute, College of Pharmacy, Seoul National University , San 56-1, Sillim, Gwanak, Seoul 151-742, Korea
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14
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Fahnoe KC, Flanagan ME, Gibson G, Shanmugasundaram V, Che Y, Tomaras AP. Non-traditional antibacterial screening approaches for the identification of novel inhibitors of the glyoxylate shunt in gram-negative pathogens. PLoS One 2012; 7:e51732. [PMID: 23240059 PMCID: PMC3519852 DOI: 10.1371/journal.pone.0051732] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Accepted: 11/08/2012] [Indexed: 01/06/2023] Open
Abstract
Antibacterial compounds that affect bacterial viability have traditionally been identified, confirmed, and characterized in standard laboratory media. The historical success of identifying new antibiotics via this route has justifiably established a traditional means of screening for new antimicrobials. The emergence of multi-drug-resistant (MDR) bacterial pathogens has expedited the need for new antibiotics, though many in the industry have questioned the source(s) of these new compounds. As many pharmaceutical companies' chemical libraries have been exhaustively screened via the traditional route, we have concluded that all compounds with any antibacterial potential have been identified. While new compound libraries and platforms are being pursued, it also seems prudent to screen the libraries we currently have in hand using alternative screening approaches. One strategy involves screening under conditions that better reflect the environment pathogens experience during an infection, and identifying in vivo essential targets and pathways that are dispensable for growth in standard laboratory media in vitro. Here we describe a novel screening strategy for identifying compounds that inhibit the glyoxylate shunt in Pseudomonas aeruginosa, a pathway that is required for bacterial survival in the pulmonary environment. We demonstrate that these compounds, which were not previously identified using traditional screening approaches, have broad-spectrum antibacterial activity when they are tested under in vivo-relevant conditions. We also show that these compounds have potent activity on both enzymes that comprise the glyoxylate shunt, a feature that was supported by computational homology modeling. By dual-targeting both enzymes in this pathway, we would expect to see a reduced propensity for resistance development to these compounds. Taken together, these data suggest that understanding the in vivo environment that bacterial pathogens must tolerate, and adjusting the antibacterial screening paradigm to reflect those conditions, could identify novel antibiotics for the treatment of serious MDR pathogens.
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Affiliation(s)
- Kelly C. Fahnoe
- Antibacterials Research Unit, Pfizer Worldwide Research & Development, Groton, Connecticut, United States of America
| | - Mark E. Flanagan
- Antibacterials Research Unit, Pfizer Worldwide Research & Development, Groton, Connecticut, United States of America
| | - Glenn Gibson
- Antibacterials Research Unit, Pfizer Worldwide Research & Development, Groton, Connecticut, United States of America
| | - Veerabahu Shanmugasundaram
- Antibacterials Research Unit, Pfizer Worldwide Research & Development, Groton, Connecticut, United States of America
| | - Ye Che
- Antibacterials Research Unit, Pfizer Worldwide Research & Development, Groton, Connecticut, United States of America
| | - Andrew P. Tomaras
- Antibacterials Research Unit, Pfizer Worldwide Research & Development, Groton, Connecticut, United States of America
- * E-mail:
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15
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Abstract
Eight new sesterterpenes (2, 5, and 10-15), including structurally related pentaprenyl hydroquinones (2 and 5), and seven known ones of the same structural classes were isolated from the sponge Coscinoderma sp., collected from Chuuk Island, Micronesia. On the basis of the results of combined spectroscopic analyses, the new compounds were determined to be derivatives of the halisulfates and suvanine. These compounds exhibited moderate cytotoxicity against the K562 cell line and inhibitory activities against isocitrate lyase, sortase A, and Na+/K+-ATPase; significant structure-activity relationships were evident.
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Affiliation(s)
- Jaemin Bae
- Natural Products Research Institute, College of Pharmacy, Seoul National University , San 56-1, Sillim, Gwanak, Seoul 151-742, Korea
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16
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Abstract
Five new sesterterpenes (7-11) along with six known compounds (1-6) were isolated from the sponge Hyatella sp., collected off the coast of Soheuksan-do, Korea. Spectroscopic analyses revealed these compounds as scalarane sesterterpenes with oxidized furan moieties (7-10) and a corresponding lactam (11). The compounds exhibited moderate cytotoxicity, antibacterial activity, and weak inhibitory activity against isocitrate lyase.
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Affiliation(s)
- Ju-eun Jeon
- Natural Products Research Institute, College of Pharmacy, Seoul National University, San 56-1, Sillim, Gwanak, Seoul 151-742, Korea
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17
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Abstract
Ten new sesterterpene compounds (4-13) and seven known metabolites (1-3, 14-17) were isolated from the sponge Smenospongia sp. collected from Korean coastal waters. On the basis of combined spectroscopic analyses, the new compounds exhibited diverse functionalities on a common scalarane sesterterpene structure. The presence of a 23-aldehyde on compound 6 and a 20-carboxylic acid on 11 is unprecedented among sponge-derived scalarane sesterterpenes. Several of the new compounds showed significant cytotoxicity and antimicrobial activity, as well as moderate inhibitory activity against isocitrate lyase.
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Affiliation(s)
- Jueun Song
- Natural Products Research Institute, College of Pharmacy, Seoul National University, San 56-1, Sillim, Gwanak, Seoul 151-742, Korea
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18
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Abstract
Ten new polyoxygenated diterpenes (7-16) along with six known gagunin compounds (1-6) were isolated from the sponge Phorbas sp. collected in the Korean Sea. On the basis of a combination of NMR and mass spectroscopic analyses, the molecular structures of these diterpenes, designated as gagunins H-Q, were determined to be penta- or hexa-oxygenated diterpenes of the 10,13-bis-epi-homoverrucosane class. A new diterpene acid (17) of a bisabolane-related skeletal class was also isolated and structurally defined by the spectroscopic analyses. These compounds exhibited moderate to significant cytotoxicity against the K-562 cell line as well as weak inhibitory activity against isocitrate lyase (ICL).
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Affiliation(s)
- Kyoung Hwa Jang
- Natural Products Research Institute, College of Pharmacy, Seoul National University, San 56-1, Shilim, Kwanak, Seoul 151-742, Korea
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19
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Abstract
Eleven new meroditerpenoids (7-11, 14-17, 19, 20) and nine known compounds (1-6, 12, 13, 18) were isolated from the brown alga Sargassum siliquastrum. Combined chemical and spectroscopic analyses revealed a common tetraprenyl hydroquinone structure; these compounds belonged to the nahocol, isonahocol, and sargahydroquinoic acid classes. The dihydroquinone moiety of 20 was unique and unprecedented in a brown alga. Stereochemical assignments were made for several of the known compounds based on their chemical reactivity. These compounds exhibited moderate to significant radical-scavenging activity as well as weak inhibitory activities against sortase A and isocitrate lyase.
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Affiliation(s)
- Misong Jung
- Natural Products Research Institute, College of Pharmacy, Seoul National University, San 56-1, Sillim, Gwanak, Seoul 151-742, Korea
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20
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Chang YH, Shin D, Na Z, Lee HS, Kim DD, Oh KB, Shin J. Dihydroxystyrene metabolites from an association of the sponges Poecillastra wondoensis and Jaspis sp. J Nat Prod 2008; 71:779-783. [PMID: 18407691 DOI: 10.1021/np078015z] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Five new dihydroxystyrene metabolites and six known compounds of the same structural class were isolated from an association of the sponges Poecillatra wondoensis and Jaspis sp., collected from Keomun Island, Korea. The structures of novel compounds were determined to be the sodium or N, N-dimethyl guanidinium salts of a dihydroxystyrene dimer (5) and two trimers (6, 7). Two dimers (10, 11) containing imidazole moieties were also identified on the basis of the results of combined spectroscopic analyses. Several compounds exhibited weak to moderate inhibitory effects against isocitrate lyase and sortase A enzymes derived from microorganisms.
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Affiliation(s)
- Yong Ha Chang
- College of Pharmacy, Seoul National University, Gwanak-Gu, Seoul, Korea
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21
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Abstract
Nineteen new sesterterpenoids and eight known compounds were isolated from the sponge Sarcotragus sp. collected from Soheuksan Island, Korea. The structures of these compounds were determined to be linear sesterterpenoids containing furan or related oxygenated functionalities on the basis of combined chemical and spectroscopic analyses. In addition, the configurations of several previously undetermined compounds were assigned. Several compounds exhibited moderate to major antibacterial activity (compounds 1- 3, 17, 18) and cytotoxicity ( 3, 11, 12) against the K562 cell line and inhibitory activity against isocitrate lyase ( 6, 13).
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Affiliation(s)
- Nan Wang
- Natural Products Research Institute, College of Pharmacy, Seoul National University, 599 Gwanangno, Gwanak-gu, Seoul 151-742, Korea
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22
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Yang HC, Yu J, Oh KB, Shin DS, Cho WJ, Shin J, Kim S. Synthesis and evaluation of hydroquinone derivatives as inhibitors of isocitrate lyase. Arch Pharm Res 2007; 30:955-61. [PMID: 17879748 DOI: 10.1007/bf02993963] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Isocitrate lyase (ICL) is envisaged as an attractive drug target for the development of antimicrobial agents. We have prepared a series of hydroquinone derivatives on the basis of the structure of halisulfates, a naturally occurring inhibitor of ICL. The obtained derivatives were evaluated against ICL of C. albicans. The preliminary structure-activity relationships and the minimal structural requirements for potency were established through structural modifications.
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Affiliation(s)
- Hyeong-Cheol Yang
- Department of Dental Biomaterials Science, Dental Research Institute, School of Dentistry, Seoul National University, Seoul, Korea
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23
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Lee HS, Lee TH, Lee JH, Chae CS, Chung SC, Shin DS, Shin J, Oh KB. Inhibition of the pathogenicity of Magnaporthe grisea by bromophenols, isocitrate lyase inhibitors, from the red alga Odonthalia corymbifera. J Agric Food Chem 2007; 55:6923-8. [PMID: 17655246 DOI: 10.1021/jf071125r] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Magnaporthe grisea is a fungal pathogen of rice that forms appressoria that penetrate the outer cuticle of the rice plant. Data from recent studies indicate that M. grisea isocitrate lyase (ICL), a key enzyme in the glyoxylate cycle, is highly expressed during appressorium-mediated plant infection. Bromophenols isolated from the red alga Odonthalia corymbifera exhibited potent ICL inhibitory activity and blocked appressoria formation by M. grisea in a concentration-dependent manner. In addition, these compounds protected the rice plants from infection by M. grisea. Rice plants infected with wild-type M. grisea Guy 11 exhibited significantly lower disease severity with bromophenol treatment than without, and the treatment effect was comparable to the behavior of the Deltaicl knockout mutant I-10. The protective effect of bromophenols and their strong inhibition of appressorium formation on rice plants suggest that ICL inhibitors may be promising candidates for crop protection, particularly to protect rice plants against M. grisea.
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Affiliation(s)
- Hyi-Seung Lee
- Marine Natural Products Laboratory, Korea Ocean Research and Development Institute, Ansan P.O. Box 29, Seoul 425-600, South Korea
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24
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Abstract
Halisulfate 1, a sesterterpene sulfate and an isocitrate lyase (ICL) inhibitor that is isolated from tropical sponge Hippospongia spp., reduces both appressorium formation and infection of rice plants by the fungus Magnaporthe grisea. Rice plants infected with wild-type M. grisea Guy 11 exhibited significantly lower disease severity after halisulfate 1 treatment than without, and the treatment effect was comparable to the behavior of the Delta icl knockout mutant I-10. The protection observed upon applying halisulfate 1 to rice plants suggests that the ICL inhibitor may be a promising candidate for crop protection, particularly to protect rice plants against M. grisea.
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Affiliation(s)
- Dong-Sun Shin
- Center for Agricultural Biomaterials, Seoul National University, Seoul, Korea
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25
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Lee HS, Lee TH, Yang SH, Shin HJ, Shin J, Oh KB. Sesterterpene sulfates as isocitrate lyase inhibitors from tropical sponge Hippospongia sp. Bioorg Med Chem Lett 2007; 17:2483-6. [PMID: 17317180 DOI: 10.1016/j.bmcl.2007.02.027] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2006] [Revised: 01/22/2007] [Accepted: 02/09/2007] [Indexed: 11/23/2022]
Abstract
Two sesterterpene sulfates (1-2) were isolated from tropical sponge Hippospongia sp. and their inhibitory activities against isocitrate lyase (ICL) from the rice blast fungus Mgnaporthe grisea were evaluated. Compound 3 was obtained by hydrolysis of compound 1. Compounds 1 and 3 were found to be potent ICL inhibitors, which inhibited appressorium formation and C(2) carbon utilization in M. grisea. Our results suggest that ICL plays crucial role in appressorium formation of M. grisea and is a new target for the protection of rice blast disease.
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Affiliation(s)
- Hyi-Seung Lee
- Marine Natural Products Laboratory, Korea Ocean Research and Development Institute, Ansan PO Box 29, Seoul 425-600, Republic of Korea
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26
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Ogawa T, Murakami K, Mori H, Ishii N, Tomita M, Yoshin M. Role of phosphoenolpyruvate in the NADP-isocitrate dehydrogenase and isocitrate lyase reaction in Escherichia coli. J Bacteriol 2006; 189:1176-8. [PMID: 17142397 PMCID: PMC1797289 DOI: 10.1128/jb.01628-06] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Phosphoenolpyruvate inhibited Escherichia coli NADP-isocitrate dehydrogenase allosterically (Ki of 0.31 mM) and isocitrate lyase uncompetitively (Ki' of 0.893 mM). Phosphoenolpyruvate enhances the uncompetitive inhibition of isocitrate lyase by increasing isocitrate, which protects isocitrate dehydrogenase from the inhibition, and contributes to the control through the tricarboxylic acid cycle and glyoxylate shunt.
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Affiliation(s)
- Tadashi Ogawa
- Department of Biochemistry, Aichi Medical University School of Medicine, Aichi 489-1195, Japan
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27
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Abstract
Since the determination of the Mycobacterium tuberculosis genome sequence, various groups have used the genomic information to identify and validate targets as the basis for the development of new anti-tuberculosis agents. Validation might include many components: demonstration of the biochemical activity of the enzyme, determination of its crystal structure in complex with an inhibitor or a substrate, confirmation of essentiality, and the identification of potent growth inhibitors either in vitro or in an infection model. If novel target validation and subsequent inhibition are matched by an improved understanding of disease biology, then new antibiotics could have the potential to shorten the duration of therapy, prevent resistance development and eliminate latent disease.
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Affiliation(s)
- Khisimuzi Mdluli
- Global Alliance for TB Drug Development, 80 Broad Street, 31st Floor, New York, NY 10004, USA.
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28
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Muñoz-Elías EJ, McKinney JD. Mycobacterium tuberculosis isocitrate lyases 1 and 2 are jointly required for in vivo growth and virulence. Nat Med 2005; 11:638-44. [PMID: 15895072 PMCID: PMC1464426 DOI: 10.1038/nm1252] [Citation(s) in RCA: 555] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2004] [Accepted: 04/29/2005] [Indexed: 01/01/2023]
Abstract
Genes involved in fatty acid catabolism have undergone extensive duplication in the genus Mycobacterium, which includes the etiologic agents of leprosy and tuberculosis. Here, we show that prokaryotic- and eukaryotic-like isoforms of the glyoxylate cycle enzyme isocitrate lyase (ICL) are jointly required for fatty acid catabolism and virulence in Mycobacterium tuberculosis. Although deletion of icl1 or icl2, the genes that encode ICL1 and ICL2, respectively, had little effect on bacterial growth in macrophages and mice, deletion of both genes resulted in complete impairment of intracellular replication and rapid elimination from the lungs. The feasibility of targeting ICL1 and ICL2 for chemical inhibition was shown using a dual-specific ICL inhibitor, which blocked growth of M. tuberculosis on fatty acids and in macrophages. The absence of ICL orthologs in mammals should facilitate the development of glyoxylate cycle inhibitors as new drugs for the treatment of tuberculosis.
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Affiliation(s)
| | - John D. McKinney
- Laboratory of Infection Biology, The Rockefeller University, New York, NY 10021 USA
- *Corresponding author: John D. McKinney, Ph.D. Laboratory of Infection Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10021 USA. Tel: (+1) 212-327-7081. Fax: (+1) 212-327-7083. E-mail:
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29
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López ML, Redruello B, Valdés E, Moreno F, Heinisch JJ, Rodicio R. Isocitrate lyase of the yeast Kluyveromyces lactis is subject to glucose repression but not to catabolite inactivation. Curr Genet 2003; 44:305-16. [PMID: 14569415 DOI: 10.1007/s00294-003-0453-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2003] [Revised: 09/13/2003] [Accepted: 09/19/2003] [Indexed: 10/26/2022]
Abstract
KlICL1, encoding the isocitrate lyase of Kluyveromyces lactis, was isolated by complementation of the Saccharomyces cerevisiae icl1 deletion mutant. Sequence analysis revealed an open reading frame of 1626 nucleotides encoding a protein with 542 amino acids. The deduced protein shows extensive homologies to isocitrate lyases from various organisms, with an overall identity of 69% to the enzyme from S. cerevisiae. The KlICL1 gene has two major transcription start-points, located at -113 bp and -95 bp relative to the ATG translation start codon. The gene is expressed on ethanol medium only in respiratory-competent cells. Transcription is repressed by glucose. Mutants carrying a Klcat8 deletion lack the ability to derepress KlICL1 transcription. A Klicl1 deletion mutant does not grow on ethanol medium and lacks any isocitrate lyase activity. A strain lacking the gene KlFBP1, which encodes the gluconeogenic enzyme fructose 1,6-bisphosphatase, lacks the ability to grow on non-fermentable carbon sources. This implies that K. lactis does not contain additional isoenzymes catalyzing either of the reactions. Enzyme assays revealed that neither KlIcl1p nor KlFbp1p are subject to catabolite inactivation. However, the respective enzymes from S. cerevisiae are efficiently inactivated when expressed in K. lactis. Thus, despite the extensive sequence similarities of the enzymes involved, non-fermentative carbohydrate metabolism in the two yeasts displays distinct regulatory properties.
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Affiliation(s)
- M Luz López
- Departamento de Bioquímica y Biología Molecular, Universidad de Oviedo, Edificio Santiago Gascón, 33006 Oviedo, Spain
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30
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Bi Y, Guo J, Zhang L, Wong Y. Changes in some enzymes of microbodies and plastid development in excised radish cotyledons: effect of narciclasine. J Plant Physiol 2003; 160:1041-1049. [PMID: 14593805 DOI: 10.1078/0176-1617-00911] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Narciclasine (NCS), isolated from mucilage of Narcissus bulb, showed inhibitory effects on growth and plastid development of excised radish cotyledons. NCS (0.1 mumol/L) started to show inhibitory effects on isocitrate lyase and hydroxypyruvate reductase activities after 24 h incubation in light. When NCS concentration was increased to 10 mumol/L, the activities of both enzymes are completely inhibited. From ultrastructural studies, NCS markedly prevented the degradation of protein bodies and lipid bodies, as well as chloroplast formation of excised radish cotyledons. There was only little degradation of protein and lipid bodies, and almost no chloroplast formation in the excised radish cotyledon treated with 1 mumol/L NCS. Therefore, our results provide clear evidence that NCS inhibited the transition of glyoxysomes and peroxisomes, and chloroplast development.
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Affiliation(s)
- Yurong Bi
- School of Life Sciences, State Key Laboratory of Arid Agroecology, Lanzhou 730000, Lanzhou University, P.R. China. ,
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31
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Affiliation(s)
- Mitsunori Nakata
- Discovery Laboratories, Toyama Chemical Co., Ltd. 4-1, Shimookui 2-chome, Toyama 930-8508, Japan
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32
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Rúa J, Soler J, Busto F, de Arriaga D. Specific and reversible inactivation of Phycomyces blakesleeanus isocitrate lyase by ascorbate-iron: role of two redox-active cysteines. Fungal Genet Biol 2002; 35:223-34. [PMID: 11929212 DOI: 10.1006/fgbi.2001.1324] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Phycomyces blakesleeanus isocitrate lyase (EC 4.1.3.1) is in vivo reversibly inactivated by hydrogen peroxide. The purified enzyme showed reversible inactivation by an ascorbate plus Fe(2+) system under aerobic conditions. Inactivation requires hydrogen peroxide; was prevented by catalase, EDTA, Mg(2+), isocitrate, GSH, DTT, or cysteine; and was reversed by thiols. The ascorbate served as a source of hydrogen peroxide and also reduced the Fe(3+) ions produced in a "site-specific" Fenton reaction. Two redox-active cysteine residues per enzyme subunit are targets of oxidative modification; one of them is located at the catalytic site and the other at the metal regulatory site. The oxidized enzyme showed covalent and conformational changes that led to inactivation, decreased thermal stability, and also increased inactivation by trypsin. These results represent an example of redox regulation of an enzymatic activity, which may play a role as a sensor of redox cellular status.
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Affiliation(s)
- Javier Rúa
- Departamento de Bioquímica y Biología Molecular, Universidad de León, León, 24007, Spain
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33
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Ranaldi F, Vanni P, Giachetti E. Multisite inhibition of Pinus pinea isocitrate lyase by phosphate. Plant Physiol 2000; 124:1131-8. [PMID: 11080290 PMCID: PMC59212 DOI: 10.1104/pp.124.3.1131] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2000] [Accepted: 07/12/2000] [Indexed: 05/20/2023]
Abstract
Our results show that the phosphate ion is a nonlinear competitive inhibitor of Pinus pinea isocitrate lyase. In addition, this compound induces a sigmoidal response of the enzyme, which usually exhibits standard Michaelis-Menten kinetics. This peculiar behavior of P. pinea isocitrate lyase could be explained by a dimer (two-site) model, in which phosphate binds cooperatively, but the affinity of the vacant site for substrate (the magnesium-isocitrate complex) remains the same. As a result, the interaction of phosphate with free enzyme produces an inhibitor-enzyme-inhibitor species that is of significant importance in determining reaction rate; a possible regulatory role of the glyoxylate cycle by inorganic phosphate is suggested. The mode of phosphate inhibition is consistent with both the mechanism for magnesium ion activation of P. pinea isocitrate lyase and its site heterogeneity. Our results explain the cooperative effects observed by some authors in kinetic studies of isocitrate lyase carried out in phosphate buffers and also account for the higher K(m) values determined by using such assay systems. Phosphate buffer should be avoided in performing isocitrate lyase kinetics.
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Affiliation(s)
- F Ranaldi
- Dipartimento di Scienze Biochimiche, Università di Firenze, Firenze, Italy
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34
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Abstract
The secret of the success of Mycobacterium tuberculosis, the pathogen that causes tuberculosis, is that it can linger undetected in the lungs for decades, hiding from the immune system's macrophages that aim to chew it up and spit it out. Now a team of researchers has uncovered a vulnerability in this resilient bug that suggests new ways to starve it out of its bolt-hole.
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35
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Sharma V, Sharma S, Hoener zu Bentrup K, McKinney JD, Russell DG, Jacobs WR, Sacchettini JC. Structure of isocitrate lyase, a persistence factor of Mycobacterium tuberculosis. Nat Struct Biol 2000; 7:663-8. [PMID: 10932251 DOI: 10.1038/77964] [Citation(s) in RCA: 176] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Isocitrate lyase (ICL) plays a pivotal role in the persistence of Mycobacterium tuberculosis in mice by sustaining intracellular infection in inflammatory macrophages. The enzyme allows net carbon gain by diverting acetyl-CoA from beta-oxidation of fatty acids into the glyoxylate shunt pathway. Given its potential as a drug target against persistent infections, we solved its structure without ligand and in complex with two inhibitors. Covalent modification of an active site residue, Cys 191, by the inhibitor 3-bromopyruvate traps the enzyme in a catalytic conformation with the active site completely inaccessible to solvent. The structure of a C191S mutant of the enzyme with the inhibitor 3-nitropropionate provides further insight into the reaction mechanism.
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Affiliation(s)
- V Sharma
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843-2128, USA
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36
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Amor C, Domínguez AI, De Lucas JR, Laborda F. The catabolite inactivation of Aspergillus nidulans isocitrate lyase occurs by specific autophagy of peroxisomes. Arch Microbiol 2000; 174:59-66. [PMID: 10985743 DOI: 10.1007/s002030000176] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
In Aspergillus nidulans, activity of the glyoxylate cycle enzyme isocitrate lyase is finely regulated. Isocitrate lyase is induced by growth on C2 compounds and long-chain fatty acids and repressed by glucose. In addition, activity of isocitrate lyase is subject to a second mechanism of catabolite control, glucose-induced inactivation. Here, we demonstrate that the catabolite inactivation of A. nidulans isocitrate lyase, a process that takes place during glucose adaptation of cells grown under gluconeogenic conditions, occurs by proteolysis of the enzyme. Ultrastructural analyses were carried out in order to investigate the cellular processes that govern the catabolite inactivation of this peroxisomal enzyme. Addition of glucose to oleate-induced cells triggered the specific engulfment and sequestration of peroxisomes by the vacuoles. Sequestration of various peroxisomes by a single vacuole was a frequently observed phenomenon. Results obtained by immunoelectron microscopy using antibodies against A. nidulans isocitrate lyase showed that degradation of this peroxisomal enzyme occurred inside the vacuole. In addition, ultrastructural studies demonstrated that microautophagy was the autophagic pathway involved in degradation of redundant peroxisomes during glucose adaptation of oleate-induced cells of A. nidulans.
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Affiliation(s)
- C Amor
- Departamento de Microbiología y Parasitología, Fac. Farmacia, Campus Universitario, Universidad de Alcalá, Alcalá de Henares (Madrid), Spain
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37
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Abstract
Key enzymes of the glyoxylate cycle, isocitrate lyase (ICL) and malate synthase (MS), have been detected in the liver of alloxan-treated rats. The activity of ICL in rat liver was 0.040 micromol/min/mg protein and the activity of MS was 0.022 micromol/min/mg protein. These enzymes were associated with the peroxisomal fraction. The activities of citrate synthase, malate synthase and malate dehydrogenase detected in the peroxisomal fraction were also increased by alloxan treatment. Isocitrate lyase was partially purified and displayed catalytic and regulatory properties similar to those of the enzyme isolated from the liver of starved rats (Popov, V.N. et al. (1996) FEBS Lett. 391, 87-90).
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Affiliation(s)
- V N Popov
- Department of Plant Physiology and Biochemistry, Voronezh State University, Russia.
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38
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Hämmerle M, Bauer J, Rose M, Szallies A, Thumm M, Düsterhus S, Mecke D, Entian KD, Wolf DH. Proteins of newly isolated mutants and the amino-terminal proline are essential for ubiquitin-proteasome-catalyzed catabolite degradation of fructose-1,6-bisphosphatase of Saccharomyces cerevisiae. J Biol Chem 1998; 273:25000-5. [PMID: 9737955 DOI: 10.1074/jbc.273.39.25000] [Citation(s) in RCA: 72] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Addition of glucose to cells of the yeast Saccharomyces cerevisiae growing on a non-fermentable carbon source leads to selective and rapid degradation of fructose-1,6-bisphosphatase. This so called catabolite inactivation of the enzyme is brought about by the ubiquitin-proteasome system. To identify additional components of the catabolite inactivation machinery, we isolated three mutant strains, gid1, gid2, and gid3, defective in glucose-induced degradation of fructose-1,6-bisphospha-tase. All mutant strains show in addition a defect in catabolite inactivation of three other gluconeogenic enzymes: cytosolic malate dehydrogenase, isocitrate lyase, and phosphoenolpyruvate carboxykinase. These findings indicate a common mechanism for the inactivation of all four enzymes. The mutants were also impaired in degradation of short-lived N-end rule substrates, which are degraded via the ubiquitin-proteasome system. Site-directed mutagenesis of the amino-terminal proline residue yielded fructose-1,6-bisphosphatase forms that were no longer degraded via the ubiquitin-proteasome pathway. All amino termini other than proline made fructose-1,6-bisphosphatase inaccessible to degradation. However, the exchange of the amino-terminal proline had no effect on the phosphorylation of the mutated enzyme. Our findings suggest an essential function of the amino-terminal proline residue for the degradation process of fructose-1,6-bisphosphatase. Phosphorylation of the enzyme was not necessary for degradation to occur.
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Affiliation(s)
- M Hämmerle
- Institut für Biochemie, Universität Stuttgart, Pfaffenwaldring 55, D-70569 Stuttgart, Germany
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39
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Ordiz I, Herrero P, Rodicio R, Moreno F. Glucose-induced inactivation of isocitrate lyase in Saccharomyces cerevisiae is mediated by the cAMP-dependent protein kinase catalytic subunits Tpk1 and Tpk2. FEBS Lett 1996; 385:43-6. [PMID: 8641464 DOI: 10.1016/0014-5793(96)00344-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Glucose-induced inactivation of isocitrate lyase (Icl) has been related to protein phosphorylation. Moreover, since rapid reversible inactivation preceded irreversible inactivation of the enzyme, phosphorylation was proposed as the triggering reaction that makes the enzyme accessible to the proteolytic machinery. The protein kinase involved in the process is unknown at the moment. In this work we demonstrate that Tpk1 and Tpk2, the catalytic subunits of cAMP-dependent protein kinase, are involved in the signalling of short-term and long-term inactivation processes of Icl. We also demonstrate that threonine 53 is involved in a regulatory mechanism necessary for short-term reversible inactivation of Icl, probably mediated through its phosphorylation. Other, as yet unidentified, residues are likely to be the target of distinct protein kinases mediating the irreversible long-term inactivation of Icl.
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Affiliation(s)
- I Ordiz
- Departamento de Bioquímica y Biología Molecular, Universidad de Oviedo, Spain
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40
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Rúa J, Soler J, Busto F, de Arriaga D. The pH dependence and modification by diethyl pyrocarbonate of isocitrate lyase from Phycomyces blakesleeanus. Eur J Biochem 1995; 232:381-90. [PMID: 7556185 DOI: 10.1111/j.1432-1033.1995.tb20822.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
We determined the variation with pH of the kinetic parameters for the isocitrate cleavage reaction catalyzed by Phycomyces isocitrate lyase, with the aim of elucidating the role played by ionising amino acid residues in binding and catalysis. The log VmaxpH profile shows that the enzyme possesses two ionising groups with pK values of 6.1 and 8.3. The first group is also observed in the VmaxpH/KmpH and pKmpH profiles, so this group is involved in catalysis. The last two profiles exhibit a similar pK value of 16 on the basic side, which represents the sum of the pK values for two ionising groups with pK values that differ by less than two pH units. Diethyl pyrocarbonate inactivated isocitrate lyase from Phycomyces with a second-order rate constant of 18.58 M-1 s-1 (at pH 6.0 and 20 degrees C). The difference spectra of the modified enzyme revealed an absorption maximum at 242 nm, characteristic of N-carbethoxyhistidine isocitrate lyase. No trough at around 280 nm due to O-carbethoxytyrosine is observed. Quantification of the increase in absorbance to 242 nm due to N-carbethoxyhistidine showed that ten histidine residues/active site were modified during total inactivation. However, only one of them was essential for catalysis. Treatment of the partially inactivated enzyme with hydroxylamine led to recovery of a substantial part of the original activity. The reactivity of isocitrate lyase towards diethyl pyrocarbonate declined with pH, following a titration curve for a group of pK 6.1. The presence of substrate decreased the rate of inactivation. Data-protection analyses indicate that the reactive histidine residues are within the active site of the enzyme.
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Affiliation(s)
- J Rúa
- Departamento de Bioquímica y Biología Molecular, Universidad de León, Spain
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41
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Ordiz I, Herrero P, Rodicio R, Moreno F. Glucose-induced inactivation of isocitrate lyase in Saccharomyces cerevisiae is mediated by an internal decapeptide sequence. FEBS Lett 1995; 367:219-22. [PMID: 7607310 DOI: 10.1016/0014-5793(95)00538-k] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
In this work we have investigated the role of specific peptide sequences for glucose-inactivation of the yeast isocitrate lyase. Thus, different fragments of the ICL1 coding region were fused to the lacZ gene of E. coli to provide a reporter construction. Determinations of beta-galactosidase activities indicated that the decapeptide sequence KTKRNYSARD, located between amino acid residues 37 and 46 of isocitrate lyase, is important for glucose induced proteolytic inactivation. Further experimental evidence was provided by insertion of this sequence into a glucokinase-beta-galactosidase fusion protein, which is not sensitive to glucose regulation. The decapeptide inserted conferred glucose inactivation to this construct, confirming that it is both necessary and sufficient as a signal.
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Affiliation(s)
- I Ordiz
- Departamento de Biología Functional (Bioquímica), Universidad de Oviedo, Spain
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42
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Abstract
The existence of a second mechanism of catabolite control of isocitrate lyase of Aspergillus nidulans, in addition to the carbon catabolite repression phenomenon recently reported was analysed. Isocitrate lyase was rapidly and specifically inactivated by glucose. The inactivation was irreversible at all stages in the presence of cycloheximide, showing that reactivation depends on de novo protein synthesis. In addition, analysis of glucose-induced inactivation of isocitrate lyase in a creAd-30 strain showed that the creA gene is not involved in this process.
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Affiliation(s)
- J R De Lucas
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad de Alcalá de Henares, Madrid, Spain
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43
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Minard KI, McAlister-Henn L. Glucose-induced degradation of the MDH2 isozyme of malate dehydrogenase in yeast. J Biol Chem 1992; 267:17458-64. [PMID: 1324938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
MDH2, the nonmitochondrial isozyme of malate dehydrogenase in Saccharomyces cerevisiae, was determined to be a target of glucose-induced proteolytic degradation. Shifting a yeast culture growing with acetate to medium containing glucose as a carbon source resulted in a 25-fold increase in turnover of MDH2. A truncated form of MDH2 lacking amino acid residues 1-12 was constructed by mutagenesis of the MDH2 gene and expressed in a haploid yeast strain containing a deletion disruption of the corresponding chromosomal gene. Measurements of malate dehydrogenase specific activity and determination of growth rates with diagnostic carbon sources indicated that the truncated form of MDH2 was expressed at authentic MDH2 levels and was fully active. However, the truncated enzyme proved to be less susceptible to glucose-induced proteolysis, exhibiting a 3.75-fold reduction in turnover rate following a shift to glucose medium. Rates of loss of activity for other cellular enzymes known to be subject to glucose inactivation were similarly reduced. An extended lag in attaining wild type rates of growth on glucose measured for strains expressing the truncated MDH2 enzyme represents the first evidence of a selective advantage for the phenomenon of glucose-induced proteolysis in yeast.
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Affiliation(s)
- K I Minard
- Department of Biological Chemistry, College of Medicine, University of California, Irvine 92717
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44
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Rua J, Robertson AG, Nimmo HG. Identification of the histidine residue in Escherichia coli isocitrate lyase that reacts with diethylpyrocarbonate. Biochim Biophys Acta 1992; 1122:212-8. [PMID: 1643095 DOI: 10.1016/0167-4838(92)90326-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Escherichia coli isocitrate lyase was inactivated by diethylpyrocarbonate in a pseudo-first-order process. The enzyme was completely inactivated by modification of a single histidine residue, but slower modification of further residues also occurred. The substrate, isocitrate, and products, glyoxylate and succinate, protected against inactivation by diethylpyrocarbonate but this was not simply due to binding at the active site. Treatment of the inactivated enzyme with hydroxylamine led to only partial recovery of activity. Diethylpyrocarbonate also reacted with sulphydryl groups in isocitrate lyase, as judged by titrations with Nbs2, but this reaction was not responsible for the failure of hydroxylamine to reactivate the enzyme fully. The reactivity of isocitrate lyase to diethylpyrocarbonate declined with pH, following a titration curve for a group of pKa 6.1. Isolation and sequencing of ethoxyformylated peptides showed that the major site of modification by diethylpyrocarbonate was histidine residue 306.
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Affiliation(s)
- J Rua
- Department of Biochemistry, University of Glasgow, UK
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45
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Olano J, de Arriaga D, Rúa J, Busto F, Soler J. Inactivation of Phycomyces isocitrate lyase by thiol-reactive reagents. Evidence for an essential thiol group. Biochim Biophys Acta 1992; 1119:287-95. [PMID: 1547274 DOI: 10.1016/0167-4838(92)90216-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Isocitrate lyase from the mycelium of Phycomyces blakesleeanus was inactivated with thiol-reactive reagents, 5,5'-dithiobis-(2-nitrobenzoic)acid, p-hydroxymercuribenzoic acid, N-ethylmaleimide or iodoacetate, at pH 6.8 and 25 degrees C. In all cases the inactivation is characterized by a biphasic kinetic profile. The rapid initial phase of inactivation does not increase linearly with increasing reagent concentration, but exhibits an apparent saturation effect, suggesting the formation of a reversible complex between the enzyme and the reagent prior to the inactivation step. Re-activation of the enzyme was observed under thiol excess treatment. The pH dependence of the initial phase of inactivation suggests that a group on the enzyme with pKa = 6.8 is being modified. The effect of ligands was tested on the inactivation reaction. Mg(2+)-Ds-isocitrate and Ds-isocitrate provided total protection, whereas Mg2+ ions, succinate and oxalate provided only partial protection of the enzyme against inactivation. On the basis of these results, we would suggest that the thiol-reactive reagents modify at least one thiol group crucial for the enzymatic activity and probably located in the interface between succinate and glyoxylate subsite.
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Affiliation(s)
- J Olano
- Departamento de Bioquímica y Biología Molecular, Universidad de León, Spain
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46
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Abstract
Acinetobacter calcoaceticus is capable of growing on acetate or compounds that are metabolized to acetate. During adaptation to growth on acetate, A. calcoaceticus B4 exhibits an increase in NADP(+)-isocitrate dehydrogenase and isocitrate lyase activities. In contrast, during adaptation to growth on acetate, Escherichia coli exhibits a decrease in NADP(+)-isocitrate dehydrogenase activity that is caused by reversible phosphorylation of specific serine residues on this enzyme. Also, in E. coli, isocitrate lyase is believed to be active only in the phosphorylated form. This phosphorylation of isocitrate lyase may regulate entry of isocitrate into the glyoxylate bypass. To understand the relationships between these two isocitrate-metabolizing enzymes and the metabolism of acetate in A. calcoaceticus B4 better, we have purified isocitrate lyase to homogeneity. Physical and kinetic characterization of the enzyme as well as the inhibitor specificity and divalent cation requirement have been examined.
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Affiliation(s)
- J C Hoyt
- Department of Microbiology, Arizona State University, Tempe 85287-2701
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47
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Ko YH, Vanni P, Munske GR, McFadden BA. Substrate-decreased modification by diethyl pyrocarbonate of two histidines in isocitrate lyase from Escherichia coli. Biochemistry 1991; 30:7451-6. [PMID: 1854747 DOI: 10.1021/bi00244a012] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The inactivation of tetrameric 188-kDa isocitrate lyase from Escherichia coli at pH 6.8 (37 degrees C) by diethyl pyrocarbonate, exhibiting saturation kinetics, is accompanied by modification of histidine residues 266 and 306. Substrates isocitrate, glyoxylate, or glyoxylate plus succinate protect the enzyme from inactivation, but succinate alone does not. Removal of the carbethoxy groups from inactivated enzyme by treatment with hydroxylamine restores activity of isocitrate lyase. The present results suggest that the group-specific modifying reagent diethyl pyrocarbonate may be generally useful in determining the position of active site histidine residues in enzymes.
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Affiliation(s)
- Y H Ko
- Department of Biochemistry and Biophysics, Washington State University, Pullman 99164-4660
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48
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Abstract
Mycenon (C11H5Cl3O3), a new inhibitor of isocitrate lyase (EC 4.1.3.1) was isolated from the culture broth of a basidiomycete, Mycena sp. Mycenon is a novel chlorinated benzoquinone derivative which is also active against bacteria and fungi. Malate synthase (EC 4.1.3.2) the second key enzyme of the glyoxylate cycle was not affected by mycenon. Isocitrate lyase preparations from plants, bacteria and fungi were sensitive. The following Ki-values for mycenon have been determined: Ricinus communis, 5.2 microM; Acinetobacter calcoaceticus, 11 microM; Neurospora crassa, 7.4 microM. The structure of mycenon has been determined by a single crystal X-ray analysis.
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Affiliation(s)
- R Hautzel
- University of Kaiserslautern, Department of Biotechnology, FRG
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49
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Dwivedi UN, Malhotra OP. Site-site heterogeneity in isocitrate lyase of castor seed endosperm: evidence from kinetics of inactivation by tetranitromethane. Indian J Biochem Biophys 1989; 26:386-9. [PMID: 2632362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Inactivation of isocitrate lyase (native and EDTA-dialysed) by excess tetranitromethane (TNM) exhibits, biphasic kinetics, in which half of the initial activity is lost in a fast and the remaining half in a slow phase each following the pseudo-first order kinetics. Rate constants of the two phases are proportional to the TNM concentration. High succinate concentration protects the enzyme against TNM inactivation only in the slow phase without any effect on the fast phase. With the EDTA-dialysed enzyme, no such protection (against inactivation by TNM) is observed in the presence of succinate or Mg2+ ions. Addition of both these ligands together brings about protection against the slow phase (as with the native enzyme). It has been proposed that the site-site heterogeneity of isocitrate lyase is a consequence of its quaternary structure constraints.
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50
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Polnisch E, Hofmann K. Cyclic AMP, fructose-2,6-bisphosphate and catabolite inactivation of enzymes in the hydrocarbon-assimilating yeast Candida maltosa. Arch Microbiol 1989; 152:269-72. [PMID: 2549901 DOI: 10.1007/bf00409662] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The inactivation of fructose-1,6-bisphosphatase, isocitrate lyase and cytoplasmic malate dehydrogenase in Candida maltosa was found to occur after the addition of glucose to starved cells. The concentration of cyclic AMP and fructose-2,6-bisphosphate increased drastically within 30 s when glucose was added to the intact cells of this yeast. From these results it was concluded that catabolite inactivation, with participation of cyclic AMP and fructose-2,6-bisphosphate, is an important control mechanism of the gluconeogenetic sequence in the n-alkane-assimilating yeast Candida maltosa, as described for Saccharomyces cerevisiae.
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Affiliation(s)
- E Polnisch
- Sektion Biologie, Ernst-Moritz-Arndt-Universität Greifswald, German Democratic Republic
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