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Dembech E, Malatesta M, De Rito C, Mori G, Cavazzini D, Secchi A, Morandin F, Percudani R. Identification of hidden associations among eukaryotic genes through statistical analysis of coevolutionary transitions. Proc Natl Acad Sci U S A 2023; 120:e2218329120. [PMID: 37043529 PMCID: PMC10120013 DOI: 10.1073/pnas.2218329120] [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: 10/28/2022] [Accepted: 03/10/2023] [Indexed: 04/13/2023] Open
Abstract
Coevolution at the gene level, as reflected by correlated events of gene loss or gain, can be revealed by phylogenetic profile analysis. The optimal method and metric for comparing phylogenetic profiles, especially in eukaryotic genomes, are not yet established. Here, we describe a procedure suitable for large-scale analysis, which can reveal coevolution based on the assessment of the statistical significance of correlated presence/absence transitions between gene pairs. This metric can identify coevolution in profiles with low overall similarities and is not affected by similarities lacking coevolutionary information. We applied the procedure to a large collection of 60,912 orthologous gene groups (orthogroups) in 1,264 eukaryotic genomes extracted from OrthoDB. We found significant cotransition scores for 7,825 orthogroups associated in 2,401 coevolving modules linking known and unknown genes in protein complexes and biological pathways. To demonstrate the ability of the method to predict hidden gene associations, we validated through experiments the involvement of vertebrate malate synthase-like genes in the conversion of (S)-ureidoglycolate into glyoxylate and urea, the last step of purine catabolism. This identification explains the presence of glyoxylate cycle genes in metazoa and suggests an anaplerotic role of purine degradation in early eukaryotes.
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Affiliation(s)
- Elena Dembech
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma43124, Italy
| | - Marco Malatesta
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma43124, Italy
| | - Carlo De Rito
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma43124, Italy
| | - Giulia Mori
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma43124, Italy
| | - Davide Cavazzini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma43124, Italy
| | - Andrea Secchi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma43124, Italy
| | - Francesco Morandin
- Department of Mathematical, Physical and Computer Sciences, University of Parma, Parma43124, Italy
| | - Riccardo Percudani
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma43124, Italy
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2
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Guerrero M. GG. Sporulation, Structure Assembly, and Germination in the Soil Bacterium Bacillus thuringiensis: Survival and Success in the Environment and the Insect Host. MICROBIOLOGY RESEARCH 2023. [DOI: 10.3390/microbiolres14020035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023] Open
Abstract
Bacillus thuringiensis (Bt) is a rod-shaped, Gram-positive soil bacterium that belongs to the phylum Firmicutes and the genus Bacillus. It is a spore-forming bacterium. During sporulation, it produces a wide range of crystalline proteins that are toxic to different orders of insects. Sporulation, structure assembly, and germination are essential stages in the cell cycle of B. thuringiensis. The majority of studies on these issues have focused on the model organism Bacillus subtilis, followed by Bacillus cereus and Bacillus anthracis. The machinery for sporulation and germination extrapolated to B. thuringiensis. However, in the light of recent findings concerning the role of the sporulation proteins (SPoVS), the germination receptors (Gr), and the cortical enzymes in Bt, the theory strengthened that conservation in sporulation, structure assembly, and germination programs drive the survival and success of B. thuringiensis in the environment and the insect host. In the present minireview, the latter pinpointed and reviewed.
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Affiliation(s)
- Gloria G. Guerrero M.
- Unidad Académica de Ciencias Biológicas, Laboratorio de Immunobiología, Universidad Autónoma de Zacatecas, Av. Preparatoria S/N, Col. Agronomicas, Zacatecas 98066, Mexico
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3
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Antimicrobial activity, inhibition of biofilm formation, and molecular docking study of novel Ag-NHC complexes. J Organomet Chem 2021. [DOI: 10.1016/j.jorganchem.2021.122082] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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4
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Üstün E, Şahin N, Çelik C, Tutar U, Özdemir N, Gürbüz N, Özdemir İ. Synthesis, characterization, antimicrobial and antibiofilm activity, and molecular docking analysis of NHC precursors and their Ag-NHC complexes. Dalton Trans 2021; 50:15400-15412. [PMID: 34647935 DOI: 10.1039/d1dt02003j] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Microorganisms attach to surfaces and interfaces and form biofilms which create a sheltered area for host cell response. Therefore, biofilms provide troubles in fields such as medicine, food, and pharmaceuticals. Inhibition of formation of biofilms through hindering of quorum sensing could be a method for the production of new generation antibiotics. In this study, four new benzimidazole type NHC precursors (1-allyl-3-benzyl-5,6-dimethylbenzimidazolium chloride, 1-allyl-3-(2,4,6-trimethylbenzyl)-5,6-dimethylbenzimidazolium chloride, 1-allyl-3-(2,3,5,6-tetramethylbenzyl)-5,6-dimethylbenzimidazolium chloride, and 1-allyl-3-(2,3,4,5,6-pentamethylbenzyl)-5,6-dimethylbenzimidazolium chloride and Ag-NHC complexes of these molecules were synthesized and characterized by elemental analysis, FT-IR spectroscopy, 1H, and 13C{1H} NMR spectroscopy, LC-MS, and single crystal crystallography. Antimicrobial and biofilm formation inhibition activities of the molecules were evaluated. In addition, the activities of the molecules were examined in detail by molecular docking analysis. According to the results obtained, higher activity was achieved with the complex molecules when compared with the benzimidazole derivative ligands.
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Affiliation(s)
- Elvan Üstün
- Department of Chemistry, Faculty of Art and Science, Ordu University, 52200 Ordu, Turkey
| | - Neslihan Şahin
- Department of Basic Education, Faculty of Education, Cumhuriyet University, 58040, Sivas, Turkey. .,Department of Chemistry, Faculty of Science and Art, İnönü University, 44280 Malatya, Turkey.,Catalysis Research and Application Center, İnönü University, 44280, Malatya, Turkey
| | - Cem Çelik
- Department of Medical Microbiology, Faculty of Medicine, Cumhuriyet University, Sivas, Turkey
| | - Uğur Tutar
- Department of Botanica, Faculty of Pharmacy, Sivas Cumhuriyet University, Sivas, 58140, Turkey
| | - Namık Özdemir
- Department of Mathematics and Science Education, Faculty of Education, Ondokuz Mayıs University, 55139, Samsun, Turkey
| | - Nevin Gürbüz
- Department of Chemistry, Faculty of Science and Art, İnönü University, 44280 Malatya, Turkey.,Catalysis Research and Application Center, İnönü University, 44280, Malatya, Turkey.,Drug Application and Research Center, İnönü University, 44280, Malatya, Turkey
| | - İsmail Özdemir
- Department of Chemistry, Faculty of Science and Art, İnönü University, 44280 Malatya, Turkey.,Catalysis Research and Application Center, İnönü University, 44280, Malatya, Turkey.,Drug Application and Research Center, İnönü University, 44280, Malatya, Turkey
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5
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Kim Y, Lama S, Agrawal D, Kumar V, Park S. Acetate as a potential feedstock for the production of value-added chemicals: Metabolism and applications. Biotechnol Adv 2021; 49:107736. [PMID: 33781888 DOI: 10.1016/j.biotechadv.2021.107736] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 02/22/2021] [Accepted: 03/19/2021] [Indexed: 10/21/2022]
Abstract
Acetate is regarded as a promising carbon feedstock in biological production owing to its possible derivation from C1 gases such as CO, CO2 and methane. To best use of acetate, comprehensive understanding of acetate metabolisms from genes and enzymes to pathways and regulations is needed. This review aims to provide an overview on the potential of acetate as carbon feedstock for industrial biotechnology. Biochemical, microbial and biotechnological aspects of acetate metabolism are described. Especially, the current state-of-the art in the production of value-added chemicals from acetate is summarized. Challenges and future perspectives are also provided.
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Affiliation(s)
- Yeonhee Kim
- School of Energy and Chemical Engineering, UNIST, 50, UNIST-gil, Ulsan 44919, Republic of Korea
| | - Suman Lama
- School of Energy and Chemical Engineering, UNIST, 50, UNIST-gil, Ulsan 44919, Republic of Korea
| | - Deepti Agrawal
- Biochemistry and Biotechnology Area, Material Resource Efficiency Division, CSIR- Indian Institute of Petroleum, Mohkampur, Dehradun 248005, India
| | - Vinod Kumar
- Centre for Climate and Environmental Protection, School of Water, Energy and Environment, Cranfield University, Cranfield, MK430AL, United Kingdom.
| | - Sunghoon Park
- School of Energy and Chemical Engineering, UNIST, 50, UNIST-gil, Ulsan 44919, Republic of Korea.
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6
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Durall C, Kukil K, Hawkes JA, Albergati A, Lindblad P, Lindberg P. Production of succinate by engineered strains of Synechocystis PCC 6803 overexpressing phosphoenolpyruvate carboxylase and a glyoxylate shunt. Microb Cell Fact 2021; 20:39. [PMID: 33557832 PMCID: PMC7871529 DOI: 10.1186/s12934-021-01529-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 01/25/2021] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Cyanobacteria are promising hosts for the production of various industrially important compounds such as succinate. This study focuses on introduction of the glyoxylate shunt, which is naturally present in only a few cyanobacteria, into Synechocystis PCC 6803. In order to test its impact on cell metabolism, engineered strains were evaluated for succinate accumulation under conditions of light, darkness and anoxic darkness. Each condition was complemented by treatments with 2-thenoyltrifluoroacetone, an inhibitor of succinate dehydrogenase enzyme, and acetate, both in nitrogen replete and deplete medium. RESULTS We were able to introduce genes encoding the glyoxylate shunt, aceA and aceB, encoding isocitrate lyase and malate synthase respectively, into a strain of Synechocystis PCC 6803 engineered to overexpress phosphoenolpyruvate carboxylase. Our results show that complete expression of the glyoxylate shunt results in higher extracellular succinate accumulation compared to the wild type control strain after incubation of cells in darkness and anoxic darkness in the presence of nitrate. Addition of the inhibitor 2-thenoyltrifluoroacetone increased succinate titers in all the conditions tested when nitrate was available. Addition of acetate in the presence of the inhibitor further increased the succinate accumulation, resulting in high levels when phosphoenolpyruvate carboxylase was overexpressed, compared to control strain. However, the highest succinate titer was obtained after dark incubation of an engineered strain with a partial glyoxylate shunt overexpressing isocitrate lyase in addition to phosphoenolpyruvate carboxylase, with only 2-thenoyltrifluoroacetone supplementation to the medium. CONCLUSIONS Heterologous expression of the glyoxylate shunt with its central link to the tricarboxylic acid cycle (TCA) for acetate assimilation provides insight on the coordination of the carbon metabolism in the cell. Phosphoenolpyruvate carboxylase plays an important role in directing carbon flux towards the TCA cycle.
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Affiliation(s)
- Claudia Durall
- Microbial Chemistry, Department of Chemistry-Ångström, Uppsala University, Box 523, 751 20, Uppsala, Sweden
| | - Kateryna Kukil
- Microbial Chemistry, Department of Chemistry-Ångström, Uppsala University, Box 523, 751 20, Uppsala, Sweden
| | - Jeffrey A Hawkes
- Analytical Chemistry, Department of Chemistry-BMC, Uppsala University, Box 599, 751 20, Uppsala, Sweden
| | - Alessia Albergati
- Microbial Chemistry, Department of Chemistry-Ångström, Uppsala University, Box 523, 751 20, Uppsala, Sweden
| | - Peter Lindblad
- Microbial Chemistry, Department of Chemistry-Ångström, Uppsala University, Box 523, 751 20, Uppsala, Sweden
| | - Pia Lindberg
- Microbial Chemistry, Department of Chemistry-Ångström, Uppsala University, Box 523, 751 20, Uppsala, Sweden.
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7
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Liu Z, Xie J, Deng Z, Wang M, Dang D, Luo S, Wang Y, Sun Y, Xia L, Ding X. Enhancing the insecticidal activity of new Bacillus thuringiensis X023 by copper ions. Microb Cell Fact 2020; 19:195. [PMID: 33069248 PMCID: PMC7568400 DOI: 10.1186/s12934-020-01452-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 10/09/2020] [Indexed: 11/12/2022] Open
Abstract
Background A new Bacillus thuringiensis X023 (BtX023) with high insecticidal activity was isolated in Hunan Province, China. The addition of metals (Cu, Fe, Mg and Mn) to the medium could influence the formation of spores and/or insecticidal crystal proteins (ICPs). In previous studies, Cu ions considerably increased the synthesis of ICPs by enhancing the synthesis of poly-β-hydroxy butyrate. However, the present study could provide new insights into the function of Cu ions in ICPs. Results Bioassay results showed that wild strain BtX023 exhibited high insecticidal activity against Plutella xylostella. The addition of 1 × 10−5 M Cu2+ could considerably increase the expression of cry1Ac and vip3Aa, and the insecticidal activity was enhanced. Quantitative real-time polymerase chain reaction (qRT-PCR) and proteomic analyses revealed that the upregulated proteins included amino acid synthesis, the glyoxylate pathway, oxidative phosphorylation, and poly-β-hydroxy butyrate synthesis. The Cu ions enhanced energy metabolism and primary amino acid synthesis, will providing abundant raw material accumulation for ICP synthesis. Conclusion The new strain BtX023 exerted a strong insecticidal effect on P. xylostella by producing ICPs. The addition of 1 × 10−5 M Cu2+ in the medium could considerably enhance the expression of the cry1Ac and vip3Aa genes, thereby further increasing the toxicity of BtX023 to Helicoverpa armigera and P. xylostella by enhancing energy synthesis, the glyoxylate cycle, and branched-chain amino acids synthesis, but not poly-β-hydroxy butyrate synthesis.
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Affiliation(s)
- Zhuolin Liu
- Hunan Provincial Key Laboratory of Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Junyan Xie
- Hunan Provincial Key Laboratory of Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Ziru Deng
- Hunan Provincial Key Laboratory of Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Mulan Wang
- Hunan Provincial Key Laboratory of Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Dandan Dang
- Hunan Provincial Key Laboratory of Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Sha Luo
- Hunan Provincial Key Laboratory of Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Yunfeng Wang
- Hunan Provincial Key Laboratory of Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Yunjun Sun
- Hunan Provincial Key Laboratory of Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Liqiu Xia
- Hunan Provincial Key Laboratory of Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Xuezhi Ding
- Hunan Provincial Key Laboratory of Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China.
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8
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Zhao J, Zhang H, Qin B, Nikolay R, He QY, Spahn CMT, Zhang G. Multifaceted Stoichiometry Control of Bacterial Operons Revealed by Deep Proteome Quantification. Front Genet 2019; 10:473. [PMID: 31178895 PMCID: PMC6544118 DOI: 10.3389/fgene.2019.00473] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Accepted: 05/01/2019] [Indexed: 12/03/2022] Open
Abstract
More than half of the protein-coding genes in bacteria are organized in polycistronic operons composed of two or more genes. It remains under debate whether the operon organization maintains the stoichiometric expression of the genes within an operon. In this study, we performed a label-free data-independent acquisition hyper reaction monitoring mass-spectrometry (HRM-MS) experiment to quantify the Escherichia coli proteome in exponential phase and quantified 93.6% of the cytosolic proteins, covering 67.9% and 56.0% of the translating polycistronic operons in BW25113 and MG1655 strains, respectively. We found that the translational regulation contributes largely to the proteome complexity: the shorter operons tend to be more tightly controlled for stoichiometry than longer operons; the operons which mainly code for complexes is more tightly controlled for stoichiometry than the operons which mainly code for metabolic pathways. The gene interval (distance between adjacent genes in one operon) may serve as a regulatory factor for stoichiometry. The catalytic efficiency might be a driving force for differential expression of enzymes encoded in one operon. These results illustrated the multifaceted nature of the operon regulation: the operon unified transcriptional level and gene-specific translational level. This multi-level regulation benefits the host by optimizing the efficiency of the productivity of metabolic pathways and maintenance of different types of protein complexes.
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Affiliation(s)
- Jing Zhao
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, Jinan University, Guangzhou, China
| | - Hong Zhang
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, Jinan University, Guangzhou, China
| | - Bo Qin
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Rainer Nikolay
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Qing-Yu He
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, Jinan University, Guangzhou, China
| | - Christian M T Spahn
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Gong Zhang
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, Jinan University, Guangzhou, China
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9
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Tiwari A, Kumar A, Srivastava G, Sharma A. Screening of Anti-mycobacterial Phytochemical Compounds for Potential Inhibitors against Mycobacterium Tuberculosis Isocitrate Lyase. Curr Top Med Chem 2019; 19:600-608. [PMID: 30836915 DOI: 10.2174/1568026619666190304125603] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 10/12/2018] [Accepted: 11/05/2018] [Indexed: 11/22/2022]
Abstract
Background and Introduction: Tuberculosis (TB) is a leading infectious disease caused by Mycobacterium tuberculosiswith high morbidity and mortality. Isocitrate lyase (MtbICL), a key enzyme of glyoxylate pathway has been shown to be involved in mycobacterial persistence, is attractive drug target against persistent tuberculosis. METHODS Virtual screening, molecular docking and MD simulation study has been integrated for screening of phytochemical based anti-mycobacterial compounds. Docking study of reported MtbICL inhibitors has shown an average binding affinity score -7.30 Kcal/mol. In virtual screening, compounds exhibiting lower binding energy than calculated average binding energy were selected as top hit compounds followed by calculation of drug likeness property. Relationship between experimental IC50 value and calculated binding gibbs free energy of reported inhibitors was also calculated through regression analysis to predict IC50 value of potential inhibitors. RESULTS Docking and MD simulation studies of top hit compounds have identified shinjudilactone (quassinoid), lecheronol A (pimarane) and caniojane (diterpene) as potential MtbICL inhibitors. CONCLUSION Phytochemical based anti-mycobacterial compound can further developed into effective drugs against persistence tuberculosis with lesser toxicity and side effects.
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Affiliation(s)
- Ashish Tiwari
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plant (CIMAP), Lucknow-226015, Uttar Pradesh, India
| | - Akhil Kumar
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plant (CIMAP), Lucknow-226015, Uttar Pradesh, India
| | - Gaurava Srivastava
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plant (CIMAP), Lucknow-226015, Uttar Pradesh, India
| | - Ashok Sharma
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plant (CIMAP), Lucknow-226015, Uttar Pradesh, India
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10
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Bhatnagar A, Bandyopadhyay D. Characterization of cysteine thiol modifications based on protein microenvironments and local secondary structures. Proteins 2017; 86:192-209. [DOI: 10.1002/prot.25424] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 11/09/2017] [Accepted: 11/10/2017] [Indexed: 12/20/2022]
Affiliation(s)
- Akshay Bhatnagar
- Department of Biological Sciences; Birla Institute of Technology and Science, Pilani; Hyderabad India
| | - Debashree Bandyopadhyay
- Department of Biological Sciences; Birla Institute of Technology and Science, Pilani; Hyderabad India
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11
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McVey AC, Medarametla P, Chee X, Bartlett S, Poso A, Spring DR, Rahman T, Welch M. Structural and Functional Characterization of Malate Synthase G from Opportunistic Pathogen Pseudomonas aeruginosa. Biochemistry 2017; 56:5539-5549. [PMID: 28985053 DOI: 10.1021/acs.biochem.7b00852] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Pseudomonas aeruginosa is an opportunistic human pathogen recognized as a critical threat by the World Health Organization because of the dwindling number of effective therapies available to treat infections. Over the past decade, it has become apparent that the glyoxylate shunt plays a vital role in sustaining P. aeruginosa during infection scenarios. The glyoxylate shunt comprises two enzymes: isocitrate lyase and malate synthase isoform G. Inactivation of these enzymes has been reported to abolish the ability of P. aeruginosa to establish infection in a mammalian model system, yet we still lack the structural information to support drug design efforts. In this work, we describe the first X-ray crystal structure of P. aeruginosa malate synthase G in the apo form at 1.62 Å resolution. The enzyme is a monomer composed of four domains and is highly conserved with homologues found in other clinically relevant microorganisms. It is also dependent on Mg2+ for catalysis. Metal ion binding led to a change in the intrinsic fluorescence of the protein, allowing us to quantitate its affinity for Mg2+. We also identified putative drug binding sites in malate synthase G using computational analysis and, because of the high resolution of the experimental data, were further able to characterize its hydration properties. Our data reveal two promising binding pockets in malate synthase G that may be exploited for drug design.
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Affiliation(s)
- Alyssa C McVey
- Department of Biochemistry, University of Cambridge , Cambridge CB2 1QW, U.K
| | | | - Xavier Chee
- Department of Pharmacology, University of Cambridge , Cambridge CB2 1PD, U.K
| | - Sean Bartlett
- Department of Chemistry, University of Cambridge , Cambridge CB2 1EW, U.K
| | - Antti Poso
- School of Pharmacy, University of Eastern Finland , 70211 Kuopio, Finland.,Department of Internal Medicine VIII, University Hospital Tübingen , 72076 Tübingen, Germany
| | - David R Spring
- Department of Chemistry, University of Cambridge , Cambridge CB2 1EW, U.K
| | - Taufiq Rahman
- Department of Pharmacology, University of Cambridge , Cambridge CB2 1PD, U.K
| | - Martin Welch
- Department of Biochemistry, University of Cambridge , Cambridge CB2 1QW, U.K
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12
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Huang HL, Krieger IV, Parai MK, Gawandi VB, Sacchettini JC. Mycobacterium tuberculosis Malate Synthase Structures with Fragments Reveal a Portal for Substrate/Product Exchange. J Biol Chem 2016; 291:27421-27432. [PMID: 27738104 PMCID: PMC5207166 DOI: 10.1074/jbc.m116.750877] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 09/28/2016] [Indexed: 11/06/2022] Open
Abstract
Fragment screening and high throughput screening are complementary approaches that combine with structural biology to explore the binding capabilities of an active site. We have used a fragment-based approach on malate synthase (GlcB) from Mycobacterium tuberculosis and discovered several novel binding chemotypes. In addition, the crystal structures of GlcB in complex with these fragments indicated conformational changes in the active site that represent the enzyme conformations during catalysis. Additional structures of the complex with malate and of the apo form of GlcB supported that hypothesis. Comparative analysis of GlcB structures in complex with 18 fragments allowed us to characterize the preferred chemotypes and their binding modes. The fragment structures showed a hydrogen bond to the backbone carbonyl of Met-631. We successfully incorporated an indole group from a fragment into an existing phenyl-diketo acid series. The resulting indole-containing inhibitor was 100-fold more potent than the parent phenyl-diketo acid with an IC50 value of 20 nm.
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Affiliation(s)
| | - Inna V Krieger
- Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77845
| | - Maloy K Parai
- Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77845
| | - Vijay B Gawandi
- Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77845
| | - James C Sacchettini
- From the Departments of Chemistry and .,Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77845
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13
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Strittmatter L, Li Y, Nakatsuka NJ, Calvo SE, Grabarek Z, Mootha VK. CLYBL is a polymorphic human enzyme with malate synthase and β-methylmalate synthase activity. Hum Mol Genet 2013; 23:2313-23. [PMID: 24334609 DOI: 10.1093/hmg/ddt624] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
CLYBL is a human mitochondrial enzyme of unknown function that is found in multiple eukaryotic taxa and conserved to bacteria. The protein is expressed in the mitochondria of all mammalian organs, with highest expression in brown fat and kidney. Approximately 5% of all humans harbor a premature stop polymorphism in CLYBL that has been associated with reduced levels of circulating vitamin B12. Using comparative genomics, we now show that CLYBL is strongly co-expressed with and co-evolved specifically with other components of the mitochondrial B12 pathway. We confirm that the premature stop polymorphism in CLYBL leads to a loss of protein expression. To elucidate the molecular function of CLYBL, we used comparative operon analysis, structural modeling and enzyme kinetics. We report that CLYBL encodes a malate/β-methylmalate synthase, converting glyoxylate and acetyl-CoA to malate, or glyoxylate and propionyl-CoA to β-methylmalate. Malate synthases are best known for their established role in the glyoxylate shunt of plants and lower organisms and are traditionally described as not occurring in humans. The broader role of a malate/β-methylmalate synthase in human physiology and its mechanistic link to vitamin B12 metabolism remain unknown.
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Affiliation(s)
- Laura Strittmatter
- Department of Molecular Biology, Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA
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14
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Zarzycki J, Kerfeld CA. The crystal structures of the tri-functional Chloroflexus aurantiacus and bi-functional Rhodobacter sphaeroides malyl-CoA lyases and comparison with CitE-like superfamily enzymes and malate synthases. BMC STRUCTURAL BIOLOGY 2013; 13:28. [PMID: 24206647 PMCID: PMC3832036 DOI: 10.1186/1472-6807-13-28] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Accepted: 11/04/2013] [Indexed: 11/18/2022]
Abstract
Background Malyl-CoA lyase (MCL) is a promiscuous carbon-carbon bond lyase that catalyzes the reversible cleavage of structurally related Coenzyme A (CoA) thioesters. This enzyme plays a crucial, multifunctional role in the 3-hydroxypropionate bi-cycle for autotrophic CO2 fixation in Chloroflexus aurantiacus. A second, phylogenetically distinct MCL from Rhodobacter sphaeroides is involved in the ethylmalonyl-CoA pathway for acetate assimilation. Both MCLs belong to the large superfamily of CitE-like enzymes, which includes the name-giving β-subunit of citrate lyase (CitE), malyl-CoA thioesterases and other enzymes of unknown physiological function. The CitE-like enzyme superfamily also bears sequence and structural resemblance to the malate synthases. All of these different enzymes share highly conserved catalytic residues, although they catalyze distinctly different reactions: C-C bond formation and cleavage, thioester hydrolysis, or both (the malate synthases). Results Here we report the first crystal structures of MCLs from two different phylogenetic subgroups in apo- and substrate-bound forms. Both the C. aurantiacus and the R. sphaeroides MCL contain elaborations on the canonical β8/α8 TIM barrel fold and form hexameric assemblies. Upon ligand binding, changes in the C-terminal domains of the MCLs result in closing of the active site, with the C-terminal domain of one monomer forming a lid over and contributing side chains to the active site of the adjacent monomer. The distinctive features of the two MCL subgroups were compared to known structures of other CitE-like superfamily enzymes and to malate synthases, providing insight into the structural subtleties that underlie the functional versatility of these enzymes. Conclusions Although the C. aurantiacus and the R. sphaeroides MCLs have divergent primary structures (~37% identical), their tertiary and quaternary structures are very similar. It can be assumed that the C-C bond formation catalyzed by the MCLs occurs as proposed for malate synthases. However, a comparison of the two MCL structures with known malate synthases raised the question why the MCLs are not also able to hydrolyze CoA thioester bonds. Our results suggest the previously proposed reaction mechanism for malate synthases may be incomplete or not entirely correct. Further studies involving site-directed mutagenesis based on these structures may be required to solve this puzzling question.
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Affiliation(s)
| | - Cheryl A Kerfeld
- Department of Biochemistry and Molecular Biology, Plant Research Laboratories, Michigan State University, Plant Biology Building, 612 Wilson Road, East Lansing, MI 48824, USA.
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15
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Wang J, Mei H, Zheng C, Qian H, Cui C, Fu Y, Su J, Liu Z, Yu Z, He J. The metabolic regulation of sporulation and parasporal crystal formation in Bacillus thuringiensis revealed by transcriptomics and proteomics. Mol Cell Proteomics 2013; 12:1363-76. [PMID: 23408684 DOI: 10.1074/mcp.m112.023986] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Bacillus thuringiensis is a well-known entomopathogenic bacterium used worldwide as an environmentally compatible biopesticide. During sporulation, B. thuringiensis accumulates a large number of parasporal crystals consisting of insecticidal crystal proteins (ICPs) that can account for nearly 20-30% of the cell's dry weight. However, the metabolic regulation mechanisms of ICP synthesis remain to be elucidated. In this study, the combined efforts in transcriptomics and proteomics mainly uncovered the following 6 metabolic regulation mechanisms: (1) proteases and the amino acid metabolism (particularly, the branched-chain amino acids) became more active during sporulation; (2) stored poly-β-hydroxybutyrate and acetoin, together with some low-quality substances provided considerable carbon and energy sources for sporulation and parasporal crystal formation; (3) the pentose phosphate shunt demonstrated an interesting regulation mechanism involving gluconate when CT-43 cells were grown in GYS medium; (4) the tricarboxylic acid cycle was significantly modified during sporulation; (5) an obvious increase in the quantitative levels of enzymes and cytochromes involved in energy production via the electron transport system was observed; (6) most F0F1-ATPase subunits were remarkably up-regulated during sporulation. This study, for the first time, systematically reveals the metabolic regulation mechanisms involved in the supply of amino acids, carbon substances, and energy for B. thuringiensis spore and parasporal crystal formation at both the transcriptional and translational levels.
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Affiliation(s)
- Jieping Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PRC
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16
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Kumar R, Bhakuni V. Comparative analysis of malate synthase G from Mycobacterium tuberculosis and E. coli: role of ionic interaction in modulation of structural and functional properties. Int J Biol Macromol 2011; 49:917-22. [PMID: 21864568 DOI: 10.1016/j.ijbiomac.2011.08.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2011] [Revised: 08/04/2011] [Accepted: 08/06/2011] [Indexed: 10/17/2022]
Abstract
Metabolic plasticity of Mycobacterium renders high degree of adaptive advantages in the persistence through the upregulation of glyoxylate shunt. The malate synthase (MS), an important enzyme of the shunt belongs to the G isoform and expressed predominantly as monomer. Here we did a comparative unfolding studies of two homologous MS from Mycobacterium tuberculosis (MtbMS) and Escherichia coli (ecMS) using various biophysical techniques. Despite having high sequence identities, they show different structural, stability and functional properties. The study suggests that the differences in the stability and unfolding of the two enzymes are by virtue of differential electrostatic modulation unique to their respective molecular assembly.
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Affiliation(s)
- Ranjeet Kumar
- Molecular and Structural Biology Division, Central Drug Research Institute, Lucknow 226001, India.
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17
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Bracken CD, Neighbor AM, Lamlenn KK, Thomas GC, Schubert HL, Whitby FG, Howard BR. Crystal structures of a halophilic archaeal malate synthase from Haloferax volcanii and comparisons with isoforms A and G. BMC STRUCTURAL BIOLOGY 2011; 11:23. [PMID: 21569248 PMCID: PMC3112382 DOI: 10.1186/1472-6807-11-23] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2010] [Accepted: 05/10/2011] [Indexed: 01/07/2023]
Abstract
BACKGROUND Malate synthase, one of the two enzymes unique to the glyoxylate cycle, is found in all three domains of life, and is crucial to the utilization of two-carbon compounds for net biosynthetic pathways such as gluconeogenesis. In addition to the main isoforms A and G, so named because of their differential expression in E. coli grown on either acetate or glycolate respectively, a third distinct isoform has been identified. These three isoforms differ considerably in size and sequence conservation. The A isoform (MSA) comprises ~530 residues, the G isoform (MSG) is ~730 residues, and this third isoform (MSH-halophilic) is ~430 residues in length. Both isoforms A and G have been structurally characterized in detail, but no structures have been reported for the H isoform which has been found thus far only in members of the halophilic Archaea. RESULTS We have solved the structure of a malate synthase H (MSH) isoform member from Haloferax volcanii in complex with glyoxylate at 2.51 Å resolution, and also as a ternary complex with acetyl-coenzyme A and pyruvate at 1.95 Å. Like the A and G isoforms, MSH is based on a β8/α8 (TIM) barrel. Unlike previously solved malate synthase structures which are all monomeric, this enzyme is found in the native state as a trimer/hexamer equilibrium. Compared to isoforms A and G, MSH displays deletion of an N-terminal domain and a smaller deletion at the C-terminus. The MSH active site is closely superimposable with those of MSA and MSG, with the ternary complex indicating a nucleophilic attack on pyruvate by the enolate intermediate of acetyl-coenzyme A. CONCLUSIONS The reported structures of MSH from Haloferax volcanii allow a detailed analysis and comparison with previously solved structures of isoforms A and G. These structural comparisons provide insight into evolutionary relationships among these isoforms, and also indicate that despite the size and sequence variation, and the truncated C-terminal domain of the H isoform, the catalytic mechanism is conserved. Sequence analysis in light of the structure indicates that additional members of isoform H likely exist in the databases but have been misannotated.
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Affiliation(s)
- Colten D Bracken
- Department of Physical Science, Southern Utah University, Cedar City, UT 84720-2470, USA
| | - Amber M Neighbor
- Department of Physical Science, Southern Utah University, Cedar City, UT 84720-2470, USA
| | - Kenneth K Lamlenn
- Department of Physical Science, Southern Utah University, Cedar City, UT 84720-2470, USA,Department of Pharmacology, Georgetown University Medical Center, Washington, DC. 20057-1411, USA
| | - Geoffrey C Thomas
- Department of Physical Science, Southern Utah University, Cedar City, UT 84720-2470, USA,Department of Chemistry, University of Utah, Salt Lake City, UT 84112-0850, USA
| | - Heidi L Schubert
- Department of Biochemistry, University of Utah, Salt Lake City, UT 84112-5650, USA
| | - Frank G Whitby
- Department of Biochemistry, University of Utah, Salt Lake City, UT 84112-5650, USA
| | - Bruce R Howard
- Department of Physical Science, Southern Utah University, Cedar City, UT 84720-2470, USA
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18
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Chim N, Habel JE, Johnston JM, Krieger I, Miallau L, Sankaranarayanan R, Morse RP, Bruning J, Swanson S, Kim H, Kim CY, Li H, Bulloch EM, Payne RJ, Manos-Turvey A, Hung LW, Baker EN, Lott JS, James MNG, Terwilliger TC, Eisenberg DS, Sacchettini JC, Goulding CW. The TB Structural Genomics Consortium: a decade of progress. Tuberculosis (Edinb) 2011; 91:155-72. [PMID: 21247804 DOI: 10.1016/j.tube.2010.11.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2010] [Revised: 11/19/2010] [Accepted: 11/26/2010] [Indexed: 01/03/2023]
Abstract
The TB Structural Genomics Consortium is a worldwide organization of collaborators whose mission is the comprehensive structural determination and analyses of Mycobacterium tuberculosis proteins to ultimately aid in tuberculosis diagnosis and treatment. Congruent to the overall vision, Consortium members have additionally established an integrated facilities core to streamline M. tuberculosis structural biology and developed bioinformatics resources for data mining. This review aims to share the latest Consortium developments with the TB community, including recent structures of proteins that play significant roles within M. tuberculosis. Atomic resolution details may unravel mechanistic insights and reveal unique and novel protein features, as well as important protein-protein and protein-ligand interactions, which ultimately lead to a better understanding of M. tuberculosis biology and may be exploited for rational, structure-based therapeutics design.
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Affiliation(s)
- Nicholas Chim
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA
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19
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The apparent malate synthase activity of Rhodobacter sphaeroides is due to two paralogous enzymes, (3S)-Malyl-coenzyme A (CoA)/{beta}-methylmalyl-CoA lyase and (3S)- Malyl-CoA thioesterase. J Bacteriol 2010; 192:1249-58. [PMID: 20047909 DOI: 10.1128/jb.01267-09] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Assimilation of acetyl coenzyme A (acetyl-CoA) is an essential process in many bacteria that proceeds via the glyoxylate cycle or the ethylmalonyl-CoA pathway. In both assimilation strategies, one of the final products is malate that is formed by the condensation of acetyl-CoA with glyoxylate. In the glyoxylate cycle this reaction is catalyzed by malate synthase, whereas in the ethylmalonyl-CoA pathway the reaction is separated into two proteins: malyl-CoA lyase, a well-known enzyme catalyzing the Claisen condensation of acetyl-CoA with glyoxylate and yielding malyl-CoA, and an unidentified malyl-CoA thioesterase that hydrolyzes malyl-CoA into malate and CoA. In this study the roles of Mcl1 and Mcl2, two malyl-CoA lyase homologs in Rhodobacter sphaeroides, were investigated by gene inactivation and biochemical studies. Mcl1 is a true (3S)-malyl-CoA lyase operating in the ethylmalonyl-CoA pathway. Notably, Mcl1 is a promiscuous enzyme and catalyzes not only the condensation of acetyl-CoA and glyoxylate but also the cleavage of beta-methylmalyl-CoA into glyoxylate and propionyl-CoA during acetyl-CoA assimilation. In contrast, Mcl2 was shown to be the sought (3S)-malyl-CoA thioesterase in the ethylmalonyl-CoA pathway, which specifically hydrolyzes (3S)-malyl-CoA but does not use beta-methylmalyl-CoA or catalyze a lyase or condensation reaction. The identification of Mcl2 as thioesterase extends the enzyme functions of malyl-CoA lyase homologs that have been known only as "Claisen condensation" enzymes so far. Mcl1 and Mcl2 are both related to malate synthase, an enzyme which catalyzes both a Claisen condensation and thioester hydrolysis reaction.
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20
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Dunn MF, Ramírez-Trujillo JA, Hernández-Lucas I. Major roles of isocitrate lyase and malate synthase in bacterial and fungal pathogenesis. MICROBIOLOGY-SGM 2009; 155:3166-3175. [PMID: 19684068 DOI: 10.1099/mic.0.030858-0] [Citation(s) in RCA: 198] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The glyoxylate cycle is an anaplerotic pathway of the tricarboxylic acid (TCA) cycle that allows growth on C(2) compounds by bypassing the CO(2)-generating steps of the TCA cycle. The unique enzymes of this route are isocitrate lyase (ICL) and malate synthase (MS). ICL cleaves isocitrate to glyoxylate and succinate, and MS converts glyoxylate and acetyl-CoA to malate. The end products of the bypass can be used for gluconeogenesis and other biosynthetic processes. The glyoxylate cycle occurs in Eukarya, Bacteria and Archaea. Recent studies of ICL- and MS-deficient strains as well as proteomic and transcriptional analyses show that these enzymes are often important in human, animal and plant pathogenesis. These studies have extended our understanding of the metabolic pathways essential for the survival of pathogens inside the host and provide a more complete picture of the physiology of pathogenic micro-organisms. Hopefully, the recent knowledge generated about the role of the glyoxylate cycle in virulence can be used for the development of new vaccines, or specific inhibitors to combat bacterial and fungal diseases.
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Affiliation(s)
- M F Dunn
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, Mexico
| | - J A Ramírez-Trujillo
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, Mexico
| | - I Hernández-Lucas
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, Mexico
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