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Fonseca BDR, das Neves RN, Strothmann AL, Sena-Lopes Â, da Silva CC, Birmann PT, Savegnago L, de Pereira CMP, Borsuk S. Antiparasitic activity of chalcones analogue against Trichomonas vaginalis: biochemical, molecular and in silico aspects. Exp Parasitol 2024; 265:108809. [PMID: 39094997 DOI: 10.1016/j.exppara.2024.108809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 06/27/2024] [Accepted: 07/30/2024] [Indexed: 08/04/2024]
Abstract
Trichomonas vaginalis is the etiologic agent of trichomoniasis, a worldwide distributed sexually transmitted infection (STI) that affects the genitourinary tract. Even though this disease already has a treatment in the prescription of drugs of the 5-nitroimidazole class, described low treatments adhesion, adverse side effects and cases of resistant isolates demonstrate the need for new formulations. With this in mind, chalcones emerge as a potential alternative to be tested, being compounds widely distributed in nature, easy to chemically synthesize and presenting several biological activities already reported. In this experiment, we evaluated the antiparasitic activity of 10 chalcone at a concentration of 100 μM against ATCC 30236 T. vaginalis isolates, considering negative (live trophozoites), positive (Metronidazole 100 μM) and vehicle (DMSO 0.6%) controls. Compounds 3a, 3c, 3 g and 3i showed promising results, with MICs set at 70 μM, 80 μM, 90 μM and 90 μM, respectively (p < 0,05). Cytotoxicity assays were performed on VERO and HMVII cell lines and revealed low inhibition rates at concentrations bellow 20 μM. To elucidate a possible mechanism of action for these molecules, the DPPH, ABTS and FRAP assays were performed, in which none of the four compounds presented antioxidant activity. Assays to verify ROS and lipid peroxidation in the parasite membrane were performed. None of the tested compounds identified ROS accumulation after incubation with trophozoites. 3 g molecule promoted an increase in MDA production after incubation. Results presented in this paper demonstrate the promising trichomonicidal profile, although further tests are still needed to optimize their performance and better elucidate the mechanisms of action involved.
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Affiliation(s)
- Bárbara da Rocha Fonseca
- Laboratório de Biotecnologia Infecto-parasitária, Centro de Desenvolvimento Tecnológico, Biotecnologia, UFPel, Pelotas, RS, 96010-900, Brazil.
| | - Raquel Nascimento das Neves
- Laboratório de Biotecnologia Infecto-parasitária, Centro de Desenvolvimento Tecnológico, Biotecnologia, UFPel, Pelotas, RS, 96010-900, Brazil
| | - Adriane Leites Strothmann
- Laboratório de Biotecnologia Infecto-parasitária, Centro de Desenvolvimento Tecnológico, Biotecnologia, UFPel, Pelotas, RS, 96010-900, Brazil
| | - Ângela Sena-Lopes
- Laboratório de Biotecnologia Infecto-parasitária, Centro de Desenvolvimento Tecnológico, Biotecnologia, UFPel, Pelotas, RS, 96010-900, Brazil
| | - Caroline Carapina da Silva
- Laboratório de Lipidômica e Bio-orgânica, Grupo de Ciências Químicas Farmacêuticas e de Alimentos, UFPel, Pelotas, RS, 96010-900, Brazil
| | - Paloma Taborda Birmann
- Laboratório de Neurobiotecnologia, Centro de Desenvolvimento Tecnológico, Biotecnologia, UFPel, Pelotas, RS, Brazil
| | - Lucielli Savegnago
- Laboratório de Neurobiotecnologia, Centro de Desenvolvimento Tecnológico, Biotecnologia, UFPel, Pelotas, RS, Brazil
| | - Claudio Martin Pereira de Pereira
- Laboratório de Lipidômica e Bio-orgânica, Grupo de Ciências Químicas Farmacêuticas e de Alimentos, UFPel, Pelotas, RS, 96010-900, Brazil
| | - Sibele Borsuk
- Laboratório de Biotecnologia Infecto-parasitária, Centro de Desenvolvimento Tecnológico, Biotecnologia, UFPel, Pelotas, RS, 96010-900, Brazil.
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2
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Raboni S, Faggiano S, Bettati S, Mozzarelli A. Methionine gamma lyase: Structure-activity relationships and therapeutic applications. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2024; 1872:140991. [PMID: 38147934 DOI: 10.1016/j.bbapap.2023.140991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 12/19/2023] [Accepted: 12/20/2023] [Indexed: 12/28/2023]
Abstract
Methionine gamma lyase (MGL) is a bacterial and plant enzyme that catalyzes the conversion of methionine in methanthiol, 2-oxobutanoate and ammonia. The enzyme belongs to fold type I of the pyridoxal 5'-dependent family. The catalytic mechanism and the structure of wild type MGL and variants were determined in the presence of the natural substrate as well as of many sulfur-containing derivatives. Structure-function relationship studies were pivotal for MGL exploitation in the treatment of cancer, bacterial infections, and other diseases. MGL administration to cancer cells leads to methionine starvation, thus decreasing cells viability and increasing their vulnerability towards other drugs. In antibiotic therapy, MGL acts by transforming prodrugs in powerful drugs. Numerous strategies have been pursued for the delivering of MGL in vivo to prolong its bioavailability and decrease its immunogenicity. These include conjugation with polyethylene glycol and encapsulation in synthetic or natural vesicles, eventually decorated with tumor targeting molecules, such as the natural phytoestrogens daidzein and genistein. The scientific achievements in studying MGL structure, function and perspective therapeutic applications came from the efforts of many talented scientists, among which late Tatyana Demidkina to whom we dedicate this review.
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Affiliation(s)
- Samanta Raboni
- Department of Food and Drug, University of Parma, Parma, Italy; Institute of Biophysics, National Research Council, Pisa, Italy.
| | - Serena Faggiano
- Department of Food and Drug, University of Parma, Parma, Italy; Institute of Biophysics, National Research Council, Pisa, Italy
| | - Stefano Bettati
- Institute of Biophysics, National Research Council, Pisa, Italy; National Institute of Biostructures and Biosystems (INBB), Rome, Italy; Department of Medicine, University of Parma, Parma, Italy
| | - Andrea Mozzarelli
- Department of Food and Drug, University of Parma, Parma, Italy; Institute of Biophysics, National Research Council, Pisa, Italy
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3
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Kumar V, Barwal A, Sharma N, Mir DS, Kumar P, Kumar V. Therapeutic proteins: developments, progress, challenges, and future perspectives. 3 Biotech 2024; 14:112. [PMID: 38510462 PMCID: PMC10948735 DOI: 10.1007/s13205-024-03958-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 02/13/2024] [Indexed: 03/22/2024] Open
Abstract
Proteins are considered magic molecules due to their enormous applications in the health sector. Over the past few decades, therapeutic proteins have emerged as a promising treatment option for various diseases, particularly cancer, cardiovascular disease, diabetes, and others. The formulation of protein-based therapies is a major area of research, however, a few factors still hinder the large-scale production of these therapeutic products, such as stability, heterogenicity, immunogenicity, high cost of production, etc. This review provides comprehensive information on various sources and production of therapeutic proteins. The review also summarizes the challenges currently faced by scientists while developing protein-based therapeutics, along with possible solutions. It can be concluded that these proteins can be used in combination with small molecular drugs to give synergistic benefits in the future.
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Affiliation(s)
- Vimal Kumar
- University Institute of Biotechnology, Chandigarh University, Gharuan, Mohali, Punjab 140413 India
| | - Arti Barwal
- Department of Microbial Biotechnology, Panjab University, South Campus, Sector-25, Chandigarh, 160014 India
| | - Nitin Sharma
- Department of Biotechnology, Chandigarh Group of Colleges, Mohali, Punjab 140307 India
| | - Danish Shafi Mir
- University Institute of Biotechnology, Chandigarh University, Gharuan, Mohali, Punjab 140413 India
| | - Pradeep Kumar
- Faculty of Applied Sciences and Biotechnology, Shoolini University of Biotechnology and Management Sciences, Solan, 173229 India
| | - Vikas Kumar
- University Institute of Biotechnology, Chandigarh University, Gharuan, Mohali, Punjab 140413 India
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Javia BM, Gadhvi MS, Vyas SJ, Ghelani A, Wirajana N, Dudhagara DR. A review on L-methioninase in cancer therapy: Precision targeting, advancements and diverse applications for a promising future. Int J Biol Macromol 2024; 265:130997. [PMID: 38508568 DOI: 10.1016/j.ijbiomac.2024.130997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Revised: 03/04/2024] [Accepted: 03/17/2024] [Indexed: 03/22/2024]
Abstract
Cancer remains a global health challenge, demanding novel therapeutic options due to the debilitating side effects of conventional treatments on healthy tissues. The review highlights the potential of L-methioninase, a pyridoxal-5-phosphate (PLP)-dependent enzyme, as a promising avenue in alternative cancer therapy. L-methioninase offers a unique advantage, its ability to selectively target and inhibit the growth of cancer cells without harming healthy cells. This selectivity arises because tumor cells lack an essential enzyme called methionine synthase, which healthy cells use to make the vital amino acid L-methionine. Several sources harbor L-methioninase, including bacteria, fungi, plants, and protozoa. Future research efforts can explore and exploit this diverse range of sources to improve the therapeutic potential of L-methioninase in the fight against cancer. Despite challenges, research actively explores microbial L-methioninase for its anticancer potential. This review examines the enzyme's side effects, advancements in combination therapies, recombinant technologies, polymer conjugation and novel delivery methods like nanoparticles, while highlighting the success of oral administration in preclinical trials. Beyond its promising role in cancer therapy, L-methioninase holds potential applications in food science, antioxidants, and various health concerns like diabetes, cardiovascular issues, and neurodegenerative diseases. This review provides a piece of current knowledge and future prospects of L-methioninase, exploring its diverse therapeutic potential.
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Affiliation(s)
- Bhumi M Javia
- Department of Life Sciences, Bhakta Kavi Narsinh Mehta University, Khadiya, 362263 Junagadh, Gujarat, India
| | - Megha S Gadhvi
- Department of Life Sciences, Bhakta Kavi Narsinh Mehta University, Khadiya, 362263 Junagadh, Gujarat, India
| | - Suhas J Vyas
- Department of Life Sciences, Bhakta Kavi Narsinh Mehta University, Khadiya, 362263 Junagadh, Gujarat, India
| | - Anjana Ghelani
- Shree Ramkrishna Institute of Computer Education and Applied Sciences, Surat 395 001, Gujarat, India
| | - Nengah Wirajana
- Faculty of Mathematics and Natural Sciences, Udayana University, Jimbaran Campus, Kuta-Badung, Bali, Indonesia
| | - Dushyant R Dudhagara
- Department of Life Sciences, Bhakta Kavi Narsinh Mehta University, Khadiya, 362263 Junagadh, Gujarat, India.
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Sonal, Yuan AE, Yang X, Shou W. Collective production of hydrogen sulfide gas enables budding yeast lacking MET17 to overcome their metabolic defect. PLoS Biol 2023; 21:e3002439. [PMID: 38060626 PMCID: PMC10729969 DOI: 10.1371/journal.pbio.3002439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 12/19/2023] [Accepted: 11/20/2023] [Indexed: 12/20/2023] Open
Abstract
Assimilation of sulfur is vital to all organisms. In S. cerevisiae, inorganic sulfate is first reduced to sulfide, which is then affixed to an organic carbon backbone by the Met17 enzyme. The resulting homocysteine can then be converted to all other essential organosulfurs such as methionine, cysteine, and glutathione. This pathway has been known for nearly half a century, and met17 mutants have long been classified as organosulfur auxotrophs, which are unable to grow on sulfate as their sole sulfur source. Surprisingly, we found that met17Δ could grow on sulfate, albeit only at sufficiently high cell densities. We show that the accumulation of hydrogen sulfide gas underpins this density-dependent growth of met17Δ on sulfate and that the locus YLL058W (HSU1) enables met17Δ cells to assimilate hydrogen sulfide. Hsu1 protein is induced during sulfur starvation and under exposure to high sulfide concentrations in wild-type cells, and the gene has a pleiotropic role in sulfur assimilation. In a mathematical model, the low efficiency of sulfide assimilation in met17Δ can explain the observed density-dependent growth of met17Δ on sulfate. Thus, having uncovered and explained the paradoxical growth of a commonly used "auxotroph," our findings may impact the design of future studies in yeast genetics, metabolism, and volatile-mediated microbial interactions.
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Affiliation(s)
- Sonal
- Centre for Life’s Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Alex E. Yuan
- University of Washington, Seattle, Washington, United States of America
| | - Xueqin Yang
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, China
| | - Wenying Shou
- Centre for Life’s Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
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6
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Ashkan MF, Younis SA, Elazab NT. Isolation and characterization of Trichoderma harzianum L-methioninase with promising a powerful anticancer. Saudi J Biol Sci 2023; 30:103870. [PMID: 38020221 PMCID: PMC10663931 DOI: 10.1016/j.sjbs.2023.103870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 10/24/2023] [Accepted: 11/02/2023] [Indexed: 12/01/2023] Open
Abstract
Bioactive components derived from medicinal herbs have recently acquired popularity due to their efficacy in treating various ailments, including cancer and infectious diseases. In this study, the anticancer enzyme, L-methioninase isolated from medicinal plants endophytic fungi, then evaluated its promising therapeutic agents against different types of human cancers. L methionine was purified using column chromatography with the stationary phase of Sephadex G-200 with 6.6-fold purification, which increased the specific activity of 71.3 U/mg of protein with a recovery rate of 48.2 %. On the SDS-PAGE chromatogram, the apparent molecular mass of the isolated enzyme was 48 kDa, and its highest activity was observed at pH 8 and 35 °C. The enzyme was catalytically stable within the pH range of 6.0-9.0 and below 40 °C. This study demonstrates that isolated L-methioninase is particularly efficient against tumour cell lines in vitro. The crude and purified L-methioninase inhibited 60 and 80 % of the growth of the breast cancer cell line (MCF-7), respectively, with an estimated IC50 = 12.6 μg/ml (crude) and IC50 = 5.0 μg/ml for purified L-methioninase from isolate 8 with accession no MZ675362. Because of this, pure L-methioninase has better catalytic characteristics and significant thermal stability, which could be used as a cancer-fighting substance than the enzyme purified from other sources.
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Affiliation(s)
- Mada F. Ashkan
- Biological Sciences Department, College of Science & Arts, King Abdulaziz University, Rabigh 21911, Saudi Arabia
| | - Sadia A. Younis
- Department of Botany, Molecular Microbial Lab, Faculty of Science, Mansoura University, Egypt
| | - Nahla T. Elazab
- Botany Department, Faculty of Science, Mansoura University, Mansoura 35516, Egypt
- Department of Biology, College of Science, Qassim University, Qassim, Saudi Arabia
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7
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Philipp TM, Scheller AS, Krafczyk N, Klotz LO, Steinbrenner H. Methanethiol: A Scent Mark of Dysregulated Sulfur Metabolism in Cancer. Antioxidants (Basel) 2023; 12:1780. [PMID: 37760083 PMCID: PMC10525899 DOI: 10.3390/antiox12091780] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 09/15/2023] [Accepted: 09/16/2023] [Indexed: 09/29/2023] Open
Abstract
In order to cope with increased demands for energy and metabolites as well as to enhance stress resilience, tumor cells develop various metabolic adaptations, representing a hallmark of cancer. In this regard, the dysregulation of sulfur metabolism that may result in elevated levels of volatile sulfur compounds (VSCs) in body fluids, breath, and/or excretions of cancer patients has recently gained attention. Besides hydrogen sulfide (H2S), methanethiol is the predominant cancer-associated VSC and has been proposed as a promising biomarker for non-invasive cancer diagnosis. Gut bacteria are the major exogenous source of exposure to this foul-smelling toxic gas, with methanethiol-producing strains such as Fusobacterium nucleatum highly abundant in the gut microbiome of colorectal carcinoma (CRC) patients. Physiologically, methanethiol becomes rapidly degraded through the methanethiol oxidase (MTO) activity of selenium-binding protein 1 (SELENBP1). However, SELENBP1, which is considered a tumor suppressor, is often downregulated in tumor tissues, and this has been epidemiologically linked to poor clinical outcomes. In addition to impaired removal, an increase in methanethiol levels may derive from non-enzymatic reactions, such as a Maillard reaction between glucose and methionine, two metabolites enriched in cancer cells. High methionine concentrations in cancer cells may also result in enzymatic methanethiol production in mitochondria. Moreover, enzymatic endogenous methanethiol production may occur through methyltransferase-like protein 7B (METTL7B), which is present at elevated levels in some cancers, including CRC and hepatocellular carcinoma (HCC). In conclusion, methanethiol contributes to the scent of cancer as part of the cancer-associated signature combination of volatile organic compounds (VOCs) that are increasingly being exploited for non-invasive early cancer diagnosis.
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Affiliation(s)
| | | | | | | | - Holger Steinbrenner
- Institute of Nutritional Sciences, Nutrigenomics Section, Friedrich Schiller University Jena, D-07743 Jena, Germany; (T.M.P.); (A.S.S.); (N.K.); (L.-O.K.)
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8
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Chen X, Ferchaud N, Briozzo P, Machover D, Simonson T. PLP-Dependent Enzyme Methionine γ-Lyase: Insights into the Michaelis Complex from Molecular Dynamics and Free Energy Simulations. Biochemistry 2023; 62:2791-2801. [PMID: 37668546 DOI: 10.1021/acs.biochem.3c00355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
Abstract
Methionine γ-lyase (MGL) breaks down methionine, with the help of its cofactor pyridoxal-5'-phosphate (PLP), or vitamin B6. Methionine depletion is damaging for cancer cells but not normal cells, so MGL is of interest as a therapeutic protein. To increase our understanding and help engineer improved activity, we focused on the reactive, Michaelis complex M between MGL, covalently bound PLP, and substrate Met. M is not amenable to crystallography, as it proceeds to products. Experimental activity measurements helped exclude a mechanism that would bypass M . We then used molecular dynamics and alchemical free energy simulations to elucidate its structure and dynamics. We showed that the PLP phosphate has a pKa strongly downshifted by the protein, whether Met is present or not. Met binding affects the structure surrounding the reactive atoms. With Met, the Schiff base linkage between PLP and a nearby lysine shifts from a zwitterionic, keto form to a neutral, enol form that makes it easier for Met to approach its labile, target atom. The Met ligand also stabilizes the correct orientation of the Schiff base, more strongly than in simulations without Met, and in agreement with structures in the Protein Data Bank, where the Schiff base orientation correlates with the presence or absence of a co-bound anion or substrate analogue in the active site. Overall, the Met ligand helps organize the active site for the enzyme reaction by reducing fluctuations and shifting protonation states and conformational populations.
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Affiliation(s)
- Xingyu Chen
- Laboratoire de Biologie Structurale de la Cellule (CNRS UMR7654), Ecole Polytechnique, Palaiseau 91128, France
| | - Nathan Ferchaud
- Institut Jean-Pierre Bourgin, INRAE-AgroParisTech, University Paris-Saclay, Versailles 78026, France
| | - Pierre Briozzo
- Institut Jean-Pierre Bourgin, INRAE-AgroParisTech, University Paris-Saclay, Versailles 78026, France
| | - David Machover
- INSERM U935-UA09, University Paris-Saclay, Hôpital Paul-Brousse, 12, Avenue Paul Vaillant-Couturier, 94800 Villejuif, France
| | - Thomas Simonson
- Laboratoire de Biologie Structurale de la Cellule (CNRS UMR7654), Ecole Polytechnique, Palaiseau 91128, France
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Zmich A, Perkins LJ, Bingman C, Acheson JF, Buller AR. Multiplexed Assessment of Promiscuous Non-Canonical Amino Acid Synthase Activity in a Pyridoxal Phosphate-Dependent Protein Family. ACS Catal 2023; 13:11644-11655. [PMID: 37720819 PMCID: PMC10501158 DOI: 10.1021/acscatal.3c02498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/19/2023]
Abstract
Pyridoxal phosphate (PLP)-dependent enzymes afford access to a variety of non-canonical amino acids (ncAAs), which are premier buildings blocks for the construction of complex bioactive molecules. The vinylglycine ketimine (VGK) subfamily of PLP-dependent enzymes plays a critical role in sulfur metabolism and is home to a growing set of secondary metabolic enzymes that synthesize γ-substituted ncAAs. Identification of VGK enzymes for biocatalysis faces a distinct challenge because the subfamily contains both desirable synthases as well as lyases that break down ncAAs. Some enzymes have both activities, which may contribute to pervasive mis-annotation. To navigate this complex functional landscape, we used a substrate multiplexed screening approach to rapidly measure the substrate promiscuity of 40 homologs in the VGK subfamily. We found that enzymes involved in transsulfuration are less likely to have promiscuous activities and often possess undesirable lyase activity. Enzymes from direct sulfuration and secondary metabolism generally had a high degree of substrate promiscuity. From this cohort, we identified an exemplary γ-synthase from Caldicellulosiruptor hydrothermalis (CahyGS). This enzyme is thermostable and has high expression (~400 mg protein per L culture), enabling preparative scale synthesis of thioether containing ncAAs. When assayed with l-allylglycine, CahyGS catalyzes a stereoselective γ-addition reaction to afford access to a unique set of γ-methyl branched ncAAs. We determined high-resolution crystal structures of this enzyme that define an open-close transition associated with ligand binding and set the stage for future engineering within this enzyme subfamily.
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Affiliation(s)
- Anna Zmich
- Department of Biochemistry, University of Wisconsin−Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Lydia J. Perkins
- Department of Chemistry, University of Wisconsin−Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Craig Bingman
- Department of Biochemistry, University of Wisconsin−Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Justin F Acheson
- Department of Biochemistry, University of Wisconsin−Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Andrew R. Buller
- Department of Biochemistry, University of Wisconsin−Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
- Department of Chemistry, University of Wisconsin−Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
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10
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Kavya D, Nadumane VK. Enhanced l-Methioninase production by Methylobacterium sp. JUBTK33 through RSM and its anticancer potential. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2023. [DOI: 10.1016/j.bcab.2023.102621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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11
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Singh SS, Mansuri MS, Naiyer S, Kaur D, Agrahari M, Srinivasan S, Jhingan GD, Bhattacharya A, Bhattacharya S. Multi-omics analysis to characterize molecular adaptation of Entamoeba histolytica during serum stress. Proteomics 2022; 22:e2200148. [PMID: 36066285 DOI: 10.1002/pmic.202200148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 08/07/2022] [Accepted: 08/19/2022] [Indexed: 12/29/2022]
Abstract
Entamoeba histolytica is responsible for dysentery and extraintestinal disease in humans. To establish successful infection, it must generate adaptive response against stress due to host defense mechanisms. We have developed a robust proteomics workflow by combining miniaturized sample preparation, low flow-rate chromatography, and ultra-high sensitivity mass spectrometry, achieving increased proteome coverage, and further integrated proteomics and RNA-seq data to decipher regulation at translational and transcriptional levels. Label-free quantitative proteomics led to identification of 2344 proteins, an improvement over the maximum number identified in E. histolytica proteomic studies. In serum-starved cells, 127 proteins were differentially abundant and were associated with functions including antioxidant activity, cytoskeleton, translation, catalysis, and transport. The virulence factor, Gal/GalNAc-inhibitable lectin subunits, was significantly altered. Integration of transcriptomic and proteomic data revealed that only 30% genes were coordinately regulated at both transcriptional and translational levels. Some highly expressed transcripts did not change in protein abundance. Conversely, genes with no transcriptional change showed enhanced protein abundance, indicating post-transcriptional regulation. This multi-omics approach enables more refined gene expression analysis to understand the adaptive response of E. histolytica during growth stress.
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Affiliation(s)
- Shashi Shekhar Singh
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, India.,Center for RNA Science and Therapeutics, Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Mohammad Shahid Mansuri
- Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Sarah Naiyer
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, India.,Department of Immunology and Microbiology, University of Illinois Chicago, Chicago, Illinois, USA
| | - Devinder Kaur
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, India.,Central University of Punjab, Bathinda, Punjab, India
| | - Mridula Agrahari
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, India.,Vproteomics, Valerian Chem Private Limited, New Delhi, India
| | | | | | - Alok Bhattacharya
- Ashoka University, Rajiv Gandhi Education City, Sonipat, Haryana, India
| | - Sudha Bhattacharya
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, India.,Ashoka University, Rajiv Gandhi Education City, Sonipat, Haryana, India
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12
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Chen X, Briozzo P, Machover D, Simonson T. A Computational Model for the PLP-Dependent Enzyme Methionine γ-Lyase. Front Mol Biosci 2022; 9:886358. [PMID: 35558556 PMCID: PMC9087591 DOI: 10.3389/fmolb.2022.886358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/01/2022] [Indexed: 11/13/2022] Open
Abstract
Pyridoxal-5′-phosphate (PLP) is a cofactor in the reactions of over 160 enzymes, several of which are implicated in diseases. Methionine γ-lyase (MGL) is of interest as a therapeutic protein for cancer treatment. It binds PLP covalently through a Schiff base linkage and digests methionine, whose depletion is damaging for cancer cells but not normal cells. To improve MGL activity, it is important to understand and engineer its PLP binding. We develop a simulation model for MGL, starting with force field parameters for PLP in four main states: two phosphate protonation states and two tautomeric states, keto or enol for the Schiff base moiety. We used the force field to simulate MGL complexes with each form, and showed that those with a fully-deprotonated PLP phosphate, especially keto, led to the best agreement with MGL structures in the PDB. We then confirmed this result through alchemical free energy simulations that compared the keto and enol forms, confirming a moderate keto preference, and the fully-deprotonated and singly-protonated phosphate forms. Extensive simulations were needed to adequately sample conformational space, and care was needed to extrapolate the protonation free energy to the thermodynamic limit of a macroscopic, dilute protein solution. The computed phosphate pKa was 5.7, confirming that the deprotonated, −2 form is predominant. The PLP force field and the simulation methods can be applied to all PLP enzymes and used, as here, to reveal fine details of structure and dynamics in the active site.
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Affiliation(s)
- Xingyu Chen
- Laboratoire de Biologie Structurale de la Cellule (CNRS UMR7654), Ecole Polytechnique, Palaiseau, France
| | - Pierre Briozzo
- Institut Jean-Pierre Bourgin, INRAE-AgroParisTech, University Paris-Saclay, Paris, France
| | - David Machover
- INSERM U935-UA09, University Paris-Saclay, Hôpital Paul-Brousse, Paris, France
| | - Thomas Simonson
- Laboratoire de Biologie Structurale de la Cellule (CNRS UMR7654), Ecole Polytechnique, Palaiseau, France
- *Correspondence: Thomas Simonson,
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13
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Hauth F, Buck H, Stanoppi M, Hartig JS. Canavanine utilization via homoserine and hydroxyguanidine by a PLP-dependent γ-lyase in Pseudomonadaceae and Rhizobiales. RSC Chem Biol 2022; 3:1240-1250. [PMID: 36320885 PMCID: PMC9533460 DOI: 10.1039/d2cb00128d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 08/18/2022] [Indexed: 12/02/2022] Open
Abstract
Canavanine, the δ-oxa-analogue of arginine, is produced as one of the main nitrogen storage compounds in legume seeds and has repellent properties. Its toxicity originates from incorporation into proteins as well as arginase-mediated hydrolysis to canaline that forms stable oximes with carbonyls. So far no pathway or enzyme has been identified acting specifically on canavanine. Here we report the characterization of a novel PLP-dependent enzyme, canavanine-γ-lyase, that catalyzes the elimination of hydroxyguanidine from canavanine to subsequently yield homoserine. Homoserine-dehydrogenase, aspartate–semialdehyde–dehydrogenase and ammonium–aspartate–lyase activities are also induced for facilitating canavanine utilization. We demonstrate that this novel pathway is found in certain Pseudomonas species and the Rhizobiales symbionts of legumes. The findings broaden the diverse reactions that the versatile class of PLP-dependent enzymes is able to catalyze. Since canavanine utilization is found prominently in root-associated bacteria, it could have important implications for the establishment and maintenance of the legume rhizosphere. A novel degradation pathway enables rhizosphere-associated bacteria to utilize canavanine.![]()
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Affiliation(s)
- Franziskus Hauth
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
- Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Hiltrun Buck
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Marco Stanoppi
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Jörg S. Hartig
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
- Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
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14
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Philipp TM, Will A, Richter H, Winterhalter PR, Pohnert G, Steinbrenner H, Klotz LO. A coupled enzyme assay for detection of selenium-binding protein 1 (SELENBP1) methanethiol oxidase (MTO) activity in mature enterocytes. Redox Biol 2021; 43:101972. [PMID: 33901808 PMCID: PMC8099554 DOI: 10.1016/j.redox.2021.101972] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/09/2021] [Accepted: 04/10/2021] [Indexed: 01/23/2023] Open
Abstract
Methanethiol, a gas with the characteristic smell of rotten cabbage, is a product of microbial methionine degradation. In the human body, methanethiol originates primarily from bacteria residing in the lumen of the large intestine. Selenium-binding protein 1 (SELENBP1), a marker protein of mature enterocytes, has recently been identified as a methanethiol oxidase (MTO). It catalyzes the conversion of methanethiol to hydrogen sulfide (H2S), hydrogen peroxide (H2O2) and formaldehyde. Here, human Caco-2 intestinal epithelial cells were subjected to enterocyte-like differentiation, followed by analysis of SELENBP1 levels and MTO activity. To that end, we established a novel coupled assay to assess MTO activity mimicking the proximity of microbiome and intestinal epithelial cells in vivo. The assay is based on in situ-generation of methanethiol as catalyzed by a bacterial recombinant l-methionine gamma-lyase (MGL), followed by detection of H2S and H2O2. Applying this assay, we verified the loss and impairment of MTO function in SELENBP1 variants (His329Tyr; Gly225Trp) previously identified in individuals with familial extraoral halitosis. MTO activity was strongly enhanced in Caco-2 cells upon enterocyte differentiation, in parallel with increased SELENBP1 levels. This suggests that mature enterocytes located at the tip of colonic crypts are capable of eliminating microbiome-derived methanethiol.
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Affiliation(s)
- Thilo Magnus Philipp
- Institute of Nutritional Sciences, Nutrigenomics Section, Friedrich Schiller University Jena, Jena, Germany
| | - Andreas Will
- Institute of Nutritional Sciences, Nutrigenomics Section, Friedrich Schiller University Jena, Jena, Germany
| | - Hannes Richter
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Jena, Germany
| | | | - Georg Pohnert
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Jena, Germany
| | - Holger Steinbrenner
- Institute of Nutritional Sciences, Nutrigenomics Section, Friedrich Schiller University Jena, Jena, Germany
| | - Lars-Oliver Klotz
- Institute of Nutritional Sciences, Nutrigenomics Section, Friedrich Schiller University Jena, Jena, Germany.
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15
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Foo TC, Meacham JE, Terentis AC, Venkatachalam KV. Gamma cleavage is a rate-determining step in the gamma-elimination reaction of L-methionine analogues catalyzed by methionine-gamma-lyase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2021; 1869:140652. [PMID: 33746063 DOI: 10.1016/j.bbapap.2021.140652] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 03/12/2021] [Accepted: 03/17/2021] [Indexed: 11/15/2022]
Abstract
Methionine-γ-lyase (MGL) is a pyridoxal-5'-phosphate dependent enzyme found in bacteria and protozoa that catalyzes a variety of reactions, including the γ-elimination of L-methionine (L-Met). Here we report experimental kinetic data and density functional theory (DFT) computational data for the γ-elimination reaction of L-Met and several other substrate analogues by a recombinant MGL from P. gingivalis (MGL_Pg). UV-Visible spectrophotometry experiments revealed a heavily populated species with maximum absorbance at 478 nm during steady-state catalysis of L-Met, L-ethionine, L-methionine sulfone and L-homoserine, which we assign to a late crotonate intermediate formed after the γ-cleavage step in the reaction and thus common to all substrates. A more red-shifted (498 nm) species was observed during the reaction of L-homoserine lactone, which we assign to an early quinonoid intermediate with the aid of time-dependent self-consistent field calculations. Significant differences in both binding and the rate of turnover were observed for the substrates. MGL_Pg's highest catalytic efficiency was recorded for L-vinylglycine (kcat/Km = 6455 s-1 M-1), exceeding that of L-Met (kcat/Km = 4211 s-1 M-1), while L-Met sulfone displayed the largest turnover number (kcat = 1638 min-1). A direct correlation between experimental kcat values and DFT-calculated γ-cleavage Gibbs activation energies was identified for the various substrates. In light of these data, we propose that the γ-cleavage step in the catalytic reaction pathway is rate-limiting. This conclusion has direct implications for the rational design of substrates or inhibitors aimed at regulating MGL activity.
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Affiliation(s)
- Timothy C Foo
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, FL 33431, United States
| | - Jesse E Meacham
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, FL 33431, United States
| | - Andrew C Terentis
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, FL 33431, United States.
| | - Kallidaikurichi V Venkatachalam
- Division of Biochemistry, College of Allopathic Medicine, Nova Southeastern University, Fort Lauderdale, FL 33328, United States.
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16
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Zhou S, Chen X, Ni X, Liu Y, Zhang H, Dong M, Xia H. Pyridoxal-5'-phosphate-dependent enzyme GenB3 Catalyzes C-3',4'-dideoxygenation in gentamicin biosynthesis. Microb Cell Fact 2021; 20:65. [PMID: 33750386 PMCID: PMC7941887 DOI: 10.1186/s12934-021-01558-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 03/03/2021] [Indexed: 11/20/2022] Open
Abstract
Background The C-3′,4′-dideoxygenation structure in gentamicin can prevent deactivation by aminoglycoside 3′-phosphotransferase (APH(3′)) in drug-resistant pathogens. However, the enzyme catalyzing the dideoxygenation step in the gentamicin biosynthesis pathway remains unknown. Results Here, we report that GenP catalyzes 3′ phosphorylation of the gentamicin biosynthesis intermediates JI-20A, JI-20Ba, and JI-20B. We further demonstrate that the pyridoxal-5′-phosphate (PLP)-dependent enzyme GenB3 uses these phosphorylated substrates to form 3′,4′-dideoxy-4′,5′-ene-6′-oxo products. The following C-6′-transamination and the GenB4-catalyzed reduction of 4′,5′-olefin lead to the formation of gentamicin C. To the best of our knowledge, GenB3 is the first PLP-dependent enzyme catalyzing dideoxygenation in aminoglycoside biosynthesis. Conclusions This discovery solves a long-standing puzzle in gentamicin biosynthesis and enriches our knowledge of the chemistry of PLP-dependent enzymes. Interestingly, these results demonstrate that to evade APH(3′) deactivation by pathogens, the gentamicin producers evolved a smart strategy, which utilized their own APH(3′) to activate hydroxyls as leaving groups for the 3′,4′-dideoxygenation in gentamicin biosynthesis. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01558-7.
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Affiliation(s)
- Shaotong Zhou
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Benxi, 117004, China
| | - Xiaotang Chen
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Benxi, 117004, China
| | - Xianpu Ni
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Benxi, 117004, China.
| | - Yu Liu
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Benxi, 117004, China
| | - Hui Zhang
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Benxi, 117004, China
| | - Min Dong
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
| | - Huanzhang Xia
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Benxi, 117004, China.
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17
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Irajie C, Mohkam M, Vakili B, Nezafat N. Computational Elucidation of Phylogenetic, Functional and Structural Features of Methioninase from Pseudomonas, Escherichia, Clostridium and Citrobacter Strains. Recent Pat Biotechnol 2021; 15:286-301. [PMID: 34515017 DOI: 10.2174/1872208315666210910091438] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 06/30/2021] [Accepted: 07/26/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND L-Methioninase (EC 4.4.1.11; MGL) is a pyridoxal phosphate (PLP)-dependent enzyme that is produced by a variety of bacteria, fungi, and plants. L-methioninase, especially from Pseudomonas and Citrobacter sp., is considered as the efficient therapeutic enzyme, particularly in cancers such as glioblastomas, medulloblastoma, and neuroblastoma that are more sensitive to methionine starvation. OBJECTIVE The low stability is one of the main drawbacks of the enzyme; in this regard, in the current study, different features of the enzyme, including phylogenetic, functional, and structural from Pseudomonas, Escherichia, Clostridium, and Citrobacter strains were evaluated to find the best bacterial L-Methioninase. METHODS After the initial screening of L-Methioninase sequences from the above-mentioned bacterial strains, the three-dimensional structures of enzymes from Escherichia fergusonii, Pseudomonas fluorescens, and Clostridium homopropionicum were determined through homology modeling via GalaxyTBM server and refined by GalaxyRefine server. RESULTS AND CONCLUSION Afterwards, PROCHECK, verify 3D, and ERRAT servers were used for verification of the obtained models. Moreover, antigenicity, allergenicity, and physico-chemical analysis of enzymes were also carried out. In order to get insight into the interaction of the enzyme with other proteins, the STRING server was used. The secondary structure of the enzyme is mainly composed of random coils and alpha-helices. However, these outcomes should further be validated by wet-lab investigations.
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Affiliation(s)
- Cambyz Irajie
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Milad Mohkam
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Bahareh Vakili
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Navid Nezafat
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
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18
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Phillips L, Chu L, Kolodrubetz D. Multiple enzymes can make hydrogen sulfide from cysteine in Treponema denticola. Anaerobe 2020; 64:102231. [PMID: 32603680 PMCID: PMC7484134 DOI: 10.1016/j.anaerobe.2020.102231] [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: 04/16/2020] [Revised: 06/15/2020] [Accepted: 06/17/2020] [Indexed: 10/24/2022]
Abstract
Treponema denticola is a spirochete that is involved in causing periodontal diseases. This bacterium can produce H2S from thiol compounds found in the gingival crevicular fluid. Determining how H2S is made by oral bacteria is important since this molecule is present at high levels in periodontally-diseased pockets and the biological effects of H2S can explain some of the pathologies seen in periodontitis. Thus, it is of interest to identify the enzyme, or enzymes, involved in the synthesis of H2S by T. denticola. We, and others, have previously identified and characterized a T. denticola cystalysin, called HlyA, which hydrolyzes cysteine into H2S (and pyruvate and ammonia). However, there have been no studies to show that HlyA is, or is not, the only pathway that T. denticola can use to make H2S. To address this question, allelic replacement mutagenesis was used to make a deletion mutant (ΔhlyA) in the gene encoding HlyA. The mutant produces the same amount of H2S from cysteine as do wild type spirochetes, indicating that T. denticola has at least one other enzyme that can generate H2S from cysteine. To identify candidates for this other enzyme, a BLASTp search of T. denticola strain 33520 was done. There was one gene that encoded an HlyA homolog so we named it HlyB. Recombinant His-tagged HlyB was expressed in E. coli and partially purified. This enzyme was able to make H2S from cysteine in vitro. To test the role of HlyB in vivo, an HlyB deletion mutant (ΔhlyB) was constructed in T. denticola. This mutant still made normal levels of H2S from cysteine, but a strain mutated in both hly genes (ΔhlyA ΔhlyB) synthesizes significantly less H2S from cysteine. We conclude that the HlyA and HlyB enzymes perform redundant functions in vivo and are the major contributors to H2S production in T. denticola. However, at least one other enzyme can still convert cysteine to H2S in the ΔhlyA ΔhlyB mutant. An in silico analysis that identifies candidate genes for this other enzyme is presented.
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Affiliation(s)
- Linda Phillips
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA.
| | - Lianrui Chu
- Department of Developmental Dentistry, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA.
| | - David Kolodrubetz
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA.
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19
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Saksrithai K, King AJ. Lactobacillus species in drinking water had no main effects on sulphur compounds from manure, egg quality, and selected serum parameters of second cycle hens. Br Poult Sci 2020; 61:328-335. [PMID: 31899948 DOI: 10.1080/00071668.2019.1709618] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
1. The aim of this study was to investigate the effects of a combined probiotic product (Lactobacillus paracasei, L. plantarum, and L. rhamnosus) on egg quality, sulphur compounds in manure and serum biochemistry of second cycle hens. 2. A total of 48 White Leghorn hens, at 52- to 54 weeks of age, were treated in a completely randomised design with water containing 0 or 1.8375 × 1010 cfu/l of probiotics for 8 weeks. 3. Probiotic supplementation did not affect egg quality. Albumen height and Haugh units were in general lowest in week 2 and highest in week 6. 4. For manure and serum parameters, water with or without probiotics produced statistically similar effects. An interacting trend for increasing concentrations of methyl mercaptan in manure was noted for probiotics x week, and should be further investigated. The week of supplementation significantly affected hydrogen sulphide, dimethyl sulphide, and triglycerides.
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Affiliation(s)
- K Saksrithai
- Department of Animal Science, University of California , Davis, CA, USA
| | - A J King
- Department of Animal Science, University of California , Davis, CA, USA
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20
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Cui Z, Overbay J, Wang X, Liu X, Zhang Y, Bhardwaj M, Lemke A, Wiegmann D, Niro G, Thorson JS, Ducho C, Van Lanen SG. Pyridoxal-5'-phosphate-dependent alkyl transfer in nucleoside antibiotic biosynthesis. Nat Chem Biol 2020; 16:904-911. [PMID: 32483377 PMCID: PMC7377962 DOI: 10.1038/s41589-020-0548-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 04/10/2020] [Indexed: 11/09/2022]
Abstract
Several nucleoside antibiotics are structurally characterized by a 5′′-amino-5′′-deoxyribose (ADR) appended via a glycosidic bond to a high-carbon sugar nucleoside, (5′S,6′S)-5′-C-glycyluridine (GlyU). GlyU is further modified with an N-alkylamine linker, the biosynthetic origins of which have yet to be established. By using a combination of feeding experiments with isotopically labeled precursors and characterization of recombinant proteins from multiple pathways, the biosynthetic mechanism for N-alkylamine installation for ADR-GlyU-containing nucleoside antibiotics has been uncovered. The data reveal S-adenosyl-l-methionine (AdoMet) as the direct precursor of the N-alkylamine, but unlike conventional AdoMet- or decarboxylated AdoMet-dependent alkyltransferases, the reaction is catalyzed by a pyridoxal-5′-phophosate (PLP)-dependent aminobutyryltransferase (ABTase) using a stepwise γ-replacement mechanism that couples γ-elimination of AdoMet with aza-γ-addition onto the disaccharide alkyl acceptor. In addition to utilizing a conceptually different strategy for AdoMet-dependent alkylation, the newly discovered ABTases require a phosphorylated disaccharide alkyl acceptor, revealing a cryptic intermediate in the biosynthetic pathway.
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Affiliation(s)
- Zheng Cui
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, USA
| | - Jonathan Overbay
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, USA
| | - Xiachang Wang
- Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, KY, USA.,Jiangsu Key Laboratory for Functional Substance of Chinese Medicine, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, People's Republic of China
| | - Xiaodong Liu
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, USA
| | - Yinan Zhang
- Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, KY, USA.,Jiangsu Key Laboratory for Functional Substance of Chinese Medicine, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, People's Republic of China
| | - Minakshi Bhardwaj
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, USA
| | - Anke Lemke
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Saarbrücken, Germany
| | - Daniel Wiegmann
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Saarbrücken, Germany
| | - Giuliana Niro
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Saarbrücken, Germany
| | - Jon S Thorson
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, USA.,Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, KY, USA
| | - Christian Ducho
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Saarbrücken, Germany
| | - Steven G Van Lanen
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, USA.
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21
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Adams JD, Røise JJ, Lee DS, Murthy N. The methionase chain reaction: an enzyme-based autocatalytic amplification system for the detection of thiols. Chem Commun (Camb) 2020; 56:3175-3178. [PMID: 32065188 DOI: 10.1039/c9cc09136j] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present an autocatalytic system for the detection and amplification of thiols termed the Methionase Chain Reaction (MCR). MCR is based on the reversible modification of the thiol producing enzyme Methionine Gamma-Lyase (MGL). MCR was able to amplify the concentration of thiols by a factor of 560 and was able to visually detect thiols at concentrations as low as 50 nM.
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Affiliation(s)
- Jeremy David Adams
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA 94720, USA
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22
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Alves MSD, das Neves RN, Sena-Lopes Â, Domingues M, Casaril AM, Segatto NV, Nogueira TCM, de Souza MVN, Savegnago L, Seixas FK, Collares T, Borsuk S. Antiparasitic activity of furanyl N-acylhydrazone derivatives against Trichomonas vaginalis: in vitro and in silico analyses. Parasit Vectors 2020; 13:59. [PMID: 32046788 PMCID: PMC7014680 DOI: 10.1186/s13071-020-3923-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 02/01/2020] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Trichomonas vaginalis is the causative agent of trichomoniasis, which is one of the most common sexually transmitted diseases worldwide. Trichomoniasis has a high incidence and prevalence and is associated with serious complications such as HIV transmission and acquisition, pelvic inflammatory disease and preterm birth. Although trichomoniasis is treated with oral metronidazole (MTZ), the number of strains resistant to this drug is increasing (2.5-9.6%), leading to treatment failure. Therefore, there is an urgent need to find alternative drugs to combat this disease. METHODS Herein, we report the in vitro and in silico analysis of 12 furanyl N-acylhydrazone derivatives (PFUR 4, a-k) against Trichomonas vaginalis. Trichomonas vaginalis ATCC 30236 isolate was treated with seven concentrations of these compounds to determine the minimum inhibitory concentration (MIC) and 50% inhibitory concentration (IC50). In addition, compounds that displayed anti-T. vaginalis activity were analyzed using thiobarbituric acid reactive substances (TBARS) assay and molecular docking. Cytotoxicity analysis was also performed in CHO-K1 cells. RESULTS The compounds PFUR 4a and 4b, at 6.25 µM, induced complete parasite death after 24 h of exposure with IC50 of 1.69 µM and 1.98 µM, respectively. The results showed that lipid peroxidation is not involved in parasite death. Molecular docking studies predicted strong interactions of PFUR 4a and 4b with T. vaginalis enzymes, purine nucleoside phosphorylase, and lactate dehydrogenase, while only PFUR 4b interacted in silico with thioredoxin reductase and methionine gamma-lyase. PFUR 4a and 4b led to a growth inhibition (< 20%) in CHO-K1 cells that was comparable to the drug of choice, with a promising selectivity index (> 7.4). CONCLUSIONS Our results showed that PFUR 4a and 4b are promising molecules that can be used for the development of new trichomonacidal agents for T. vaginalis.
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Affiliation(s)
- Mirna Samara Dié Alves
- Laboratório de Biotecnologia Infecto-parasitária, Centro de Desenvolvimento Tecnológico, Biotecnologia, UFPel, Pelotas, RS 96010-900 Brazil
| | - Raquel Nascimento das Neves
- Laboratório de Biotecnologia Infecto-parasitária, Centro de Desenvolvimento Tecnológico, Biotecnologia, UFPel, Pelotas, RS 96010-900 Brazil
| | - Ângela Sena-Lopes
- Laboratório de Biotecnologia Infecto-parasitária, Centro de Desenvolvimento Tecnológico, Biotecnologia, UFPel, Pelotas, RS 96010-900 Brazil
| | - Micaela Domingues
- Laboratório de Neurobiotecnologia, Centro de Desenvolvimento Tecnológico, Biotecnologia, UFPel, Pelotas, RS 96010-900 Brazil
| | - Angela Maria Casaril
- Laboratório de Neurobiotecnologia, Centro de Desenvolvimento Tecnológico, Biotecnologia, UFPel, Pelotas, RS 96010-900 Brazil
| | - Natália Vieira Segatto
- Laboratório de Biotecnologia do Câncer, Centro de Desenvolvimento Tecnológico, Biotecnologia, UFPel, Pelotas, RS 96010-900 Brazil
| | | | - Marcus Vinicius Nora de Souza
- Instituto de Tecnologia em Fármacos-Far-Manguinhos, Fiocruz-Fundação Oswaldo Cruz, Rio de Janeiro, RJ 21041-250 Brazil
- Programa de Pós-Graduação em Química, Instituto de Química, Universidade Federal do Rio de Janeiro, Cidade Universitária, Rio de Janeiro, RJ 21945-970 Brazil
| | - Lucielli Savegnago
- Laboratório de Neurobiotecnologia, Centro de Desenvolvimento Tecnológico, Biotecnologia, UFPel, Pelotas, RS 96010-900 Brazil
| | - Fabiana Kömmling Seixas
- Laboratório de Biotecnologia do Câncer, Centro de Desenvolvimento Tecnológico, Biotecnologia, UFPel, Pelotas, RS 96010-900 Brazil
| | - Tiago Collares
- Laboratório de Biotecnologia do Câncer, Centro de Desenvolvimento Tecnológico, Biotecnologia, UFPel, Pelotas, RS 96010-900 Brazil
| | - Sibele Borsuk
- Laboratório de Biotecnologia Infecto-parasitária, Centro de Desenvolvimento Tecnológico, Biotecnologia, UFPel, Pelotas, RS 96010-900 Brazil
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23
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Li Z, Zhao Y, Zhou H, Luo HB, Zhan CG. Catalytic Roles of Coenzyme Pyridoxal-5'-phosphate (PLP) in PLP-dependent Enzymes: Reaction Pathway for Methionine-γ-lyase-catalyzed L-methionine Depletion. ACS Catal 2020; 10:2198-2210. [PMID: 33344000 DOI: 10.1021/acscatal.9b03907] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Pyridoxal-5'-phosphate (PLP), the active form of vitamin B6, is an important and versatile coenzyme involved in a variety of enzymatic reactions, accounting for about 4% of all classified activities. However, the detailed catalytic reaction pathways for PLP-dependent enzymes remain to be explored. Methionine-γ-lyase (MGL), a promising alternative anti-tumor agent to conventional chemotherapies whose catalytic mechanism is highly desired for guiding further development of re-engineered enzymes, was used as a representative PLP-dependent enzyme, and the catalytic mechanism for L-Met elimination by MGL was explored at the first-principles quantum mechanical/molecular mechanical (QM/MM) level with umbrella sampling. The QM/MM calculations revealed that the enzymatic reaction pathway consists of 4 stages for a total of 19 reaction steps with five intermediates captured in available crystal structures. Furthermore, the more comprehensive role of PLP was revealed. Besides the commonly known role of "electron sink", coenzyme PLP can also assist proton transfer and temporarily store the excess proton generated in some intermediate states by using its hydroxyl group and phosphate group. Thus, PLP is participated in most of the 19 steps. This study not only provided a theoretical basis for further development and re-engineering MGL as a potential anti-tumor agent, but also revealed the comprehensive role of PLP which could be used to explore the mechanisms of other PLP-dependent enzymes.
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Affiliation(s)
- Zhe Li
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, People’s Republic of China
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536, United States
| | - Yunsong Zhao
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, People’s Republic of China
| | - Huifang Zhou
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, People’s Republic of China
| | - Hai-Bin Luo
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, People’s Republic of China
| | - Chang-Guo Zhan
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536, United States
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Calcagnile M, Tredici SM, Talà A, Alifano P. Bacterial Semiochemicals and Transkingdom Interactions with Insects and Plants. INSECTS 2019; 10:E441. [PMID: 31817999 PMCID: PMC6955855 DOI: 10.3390/insects10120441] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 12/02/2019] [Accepted: 12/05/2019] [Indexed: 01/08/2023]
Abstract
A peculiar feature of all living beings is their capability to communicate. With the discovery of the quorum sensing phenomenon in bioluminescent bacteria in the late 1960s, it became clear that intraspecies and interspecies communications and social behaviors also occur in simple microorganisms such as bacteria. However, at that time, it was difficult to imagine how such small organisms-invisible to the naked eye-could influence the behavior and wellbeing of the larger, more complex and visible organisms they colonize. Now that we know this information, the challenge is to identify the myriad of bacterial chemical signals and communication networks that regulate the life of what can be defined, in a whole, as a meta-organism. In this review, we described the transkingdom crosstalk between bacteria, insects, and plants from an ecological perspective, providing some paradigmatic examples. Second, we reviewed what is known about the genetic and biochemical bases of the bacterial chemical communication with other organisms and how explore the semiochemical potential of a bacterium can be explored. Finally, we illustrated how bacterial semiochemicals managing the transkingdom communication may be exploited from a biotechnological point of view.
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Affiliation(s)
| | | | | | - Pietro Alifano
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Via Prov.le Lecce-Monteroni, 73100 Lecce, Italy; (M.C.); (S.M.T.); (A.T.)
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25
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Machover D, Rossi L, Hamelin J, Desterke C, Goldschmidt E, Chadefaux-Vekemans B, Bonnarme P, Briozzo P, Kopečný D, Pierigè F, Magnani M, Mollicone R, Haghighi-Rad F, Gaston-Mathé Y, Dairou J, Boucheix C, Saffroy R. Effects in Cancer Cells of the Recombinant l-Methionine Gamma-Lyase fromBrevibacterium aurantiacum.Encapsulation in Human Erythrocytes for Sustained l-Methionine Elimination. J Pharmacol Exp Ther 2019; 369:489-502. [DOI: 10.1124/jpet.119.256537] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Accepted: 04/01/2019] [Indexed: 01/20/2023] Open
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Spallholz JE. Selenomethionine and Methioninase: Selenium Free Radical Anticancer Activity. Methods Mol Biol 2019; 1866:199-210. [PMID: 30725417 DOI: 10.1007/978-1-4939-8796-2_15] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Colloidal selenium, was first used to treat cancer as early as 1911 in both humans and mice. Selenium was identified as the toxic component in forage plants of sheep, cattle, and horses in the 1930s. The animal toxicity of selenium compounds was determined to be from the metabolism by animals of the elevated concentrations of Se-methylselenocysteine and selenomethionine in plants. The metabolism of both Se-methylselenocysteine and selenomethionine by animals gives rise to the metabolite, methylselenide (CH3Se-), which if in sufficient concentration oxidizes thiols and generates superoxide and other reactive oxygen species. Cancer cells that may overly express methionine gamma-lyase, or beta-lyase (methioninase), by induced viral genomic expression, are susceptible to free radical-induced apoptosis from selenomethionine or Se-methylselenocysteine supplementation.
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Affiliation(s)
- Julian E Spallholz
- Departments of Nutritional Sciences, Texas Tech University, Lubbock, TX, USA.
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27
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Maggi M, Scotti C. Enzymes in Metabolic Anticancer Therapy. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1148:173-199. [PMID: 31482500 DOI: 10.1007/978-981-13-7709-9_9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Cancer treatment has greatly improved over the last 50 years, but it remains challenging in several cases. Useful therapeutic targets are normally unique peculiarities of cancer cells that distinguish them from normal cells and that can be tackled with appropriate drugs. It is now known that cell metabolism is rewired during tumorigenesis and metastasis as a consequence of oncogene activation and oncosuppressors inactivation, leading to a new cellular homeostasis typically directed towards anabolism. Because of these modifications, cells can become strongly or absolutely dependent on specific substrates, like sugars, lipids or amino acids. Cancer addictions are a relevant target for therapy, as removal of an essential substrate can lead to their selective cell-cycle arrest or even to cell death, leaving normal cells untouched. Enzymes can act as powerful agents in this respect, as demonstrated by asparaginase, which has been included in the treatment of Acute Lymphoblastic Leukemia for half a century. In this review, a short outline of cancer addictions will be provided, focusing on the main cancer amino acid dependencies described so far. Therapeutic enzymes which have been already experimented at the clinical level will be discussed, along with novel potential candidates that we propose as new promising molecules. The intrinsic limitations of their present molecular forms, along with molecular engineering solutions to explore, will also be presented.
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Affiliation(s)
- Maristella Maggi
- Department of Molecular Medicine, Unit of Immunology and General Pathology, University of Pavia, Pavia, Italy.
| | - Claudia Scotti
- Department of Molecular Medicine, Unit of Immunology and General Pathology, University of Pavia, Pavia, Italy
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Hassabo AA, Mousa AM, Abdel-Gawad H, Selim MH, Abdelhameed RM. Immobilization ofl-methioninase on a zirconium-based metal–organic framework as an anticancer agent. J Mater Chem B 2019. [DOI: 10.1039/c9tb00198k] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A new composite (METase@UiO-66) was prepared froml-methioninase and UiO-66-(COOH), which exhibited enhanced thermostability, pH and storage lifetime compared tol-methioninase. Moreover,in vivoexperiments showed that the drug inhibited tumor growth in mice.
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Affiliation(s)
- Amany A. Hassabo
- Microbial Chemistry Department
- National Research Centre
- Cairo
- Egypt
| | - Amria M. Mousa
- Biochemistry Department
- National Research Centre
- Cairo
- Egypt
| | - Hassan Abdel-Gawad
- Applied Organic Chemistry Department
- Chemical Industries Research Division
- National Research Centre
- Dokki
- Egypt
| | - Mohsen H. Selim
- Microbial Chemistry Department
- National Research Centre
- Cairo
- Egypt
| | - Reda M. Abdelhameed
- Applied Organic Chemistry Department
- Chemical Industries Research Division
- National Research Centre
- Dokki
- Egypt
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29
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Li P, Fung YME, Yin X, Seneviratne CJ, Che CM, Jin L. Controlled cellular redox, repressive hemin utilization and adaptive stress responses are crucial to metronidazole tolerance of Porphyromonas gingivalis
persisters. J Clin Periodontol 2018; 45:1211-1221. [DOI: 10.1111/jcpe.13002] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 07/24/2018] [Accepted: 08/01/2018] [Indexed: 11/26/2022]
Affiliation(s)
- Peng Li
- Faculty of Dentistry; The University of Hong Kong; Hong Kong China
- Department of Periodontology; Peking University School and Hospital of Stomatology; Beijing China
| | - Yi-Man Eva Fung
- State Key Laboratory of Synthetic Chemistry and Chemical Biology Center; Department of Chemistry; The University of Hong Kong; Hong Kong China
| | - Xiaohui Yin
- Department of Periodontology; First Clinical Division; Peking University School and Hospital of Stomatology; Beijing China
| | | | - Chi-Ming Che
- State Key Laboratory of Synthetic Chemistry and Chemical Biology Center; Department of Chemistry; The University of Hong Kong; Hong Kong China
| | - Lijian Jin
- Faculty of Dentistry; The University of Hong Kong; Hong Kong China
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Two Distinct Aerobic Methionine Salvage Pathways Generate Volatile Methanethiol in Rhodopseudomonas palustris. mBio 2018; 9:mBio.00407-18. [PMID: 29636438 PMCID: PMC5893883 DOI: 10.1128/mbio.00407-18] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
5'-Methyl-thioadenosine (MTA) is a dead-end, sulfur-containing metabolite and cellular inhibitor that arises from S-adenosyl-l-methionine-dependent reactions. Recent studies have indicated that there are diverse bacterial methionine salvage pathways (MSPs) for MTA detoxification and sulfur salvage. Here, via a combination of gene deletions and directed metabolite detection studies, we report that under aerobic conditions the facultatively anaerobic bacterium Rhodopseudomonas palustris employs both an MTA-isoprenoid shunt identical to that previously described in Rhodospirillum rubrum and a second novel MSP, both of which generate a methanethiol intermediate. The additional R. palustris aerobic MSP, a dihydroxyacetone phosphate (DHAP)-methanethiol shunt, initially converts MTA to 2-(methylthio)ethanol and DHAP. This is identical to the initial steps of the recently reported anaerobic ethylene-forming MSP, the DHAP-ethylene shunt. The aerobic DHAP-methanethiol shunt then further metabolizes 2-(methylthio)ethanol to methanethiol, which can be directly utilized by O-acetyl-l-homoserine sulfhydrylase to regenerate methionine. This is in contrast to the anaerobic DHAP-ethylene shunt, which metabolizes 2-(methylthio)ethanol to ethylene and an unknown organo-sulfur intermediate, revealing functional diversity in MSPs utilizing a 2-(methylthio)ethanol intermediate. When MTA was fed to aerobically growing cells, the rate of volatile methanethiol release was constant irrespective of the presence of sulfate, suggesting a general housekeeping function for these MSPs up through the methanethiol production step. Methanethiol and dimethyl sulfide (DMS), two of the most important compounds of the global sulfur cycle, appear to arise not only from marine ecosystems but from terrestrial ones as well. These results reveal a possible route by which methanethiol might be biologically produced in soil and freshwater environments.IMPORTANCE Biologically available sulfur is often limiting in the environment. Therefore, many organisms have developed methionine salvage pathways (MSPs) to recycle sulfur-containing by-products back into the amino acid methionine. The metabolically versatile bacterium Rhodopseudomonas palustris is unusual in that it possesses two RuBisCOs and two RuBisCO-like proteins. While RuBisCO primarily serves as the carbon fixation enzyme of the Calvin cycle, RuBisCOs and certain RuBisCO-like proteins have also been shown to function in methionine salvage. This work establishes that only one of the R. palustris RuBisCO-like proteins functions as part of an MSP. Moreover, in the presence of oxygen, to salvage sulfur, R. palustris employs two pathways, both of which result in production of volatile methanethiol, a key compound of the global sulfur cycle. When total available sulfur was plentiful, methanethiol was readily released into the environment. However, when sulfur became limiting, methanethiol release decreased, presumably due to methanethiol utilization to regenerate needed methionine.
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Lazard M, Dauplais M, Blanquet S, Plateau P. Recent advances in the mechanism of selenoamino acids toxicity in eukaryotic cells. Biomol Concepts 2018; 8:93-104. [PMID: 28574376 DOI: 10.1515/bmc-2017-0007] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 05/03/2017] [Indexed: 12/31/2022] Open
Abstract
Selenium is an essential trace element due to its incorporation into selenoproteins with important biological functions. However, at high doses it is toxic. Selenium toxicity is generally attributed to the induction of oxidative stress. However, it has become apparent that the mode of action of seleno-compounds varies, depending on its chemical form and speciation. Recent studies in various eukaryotic systems, in particular the model organism Saccharomyces cerevisiae, provide new insights on the cytotoxic mechanisms of selenomethionine and selenocysteine. This review first summarizes current knowledge on reactive oxygen species (ROS)-induced genotoxicity of inorganic selenium species. Then, we discuss recent advances on our understanding of the molecular mechanisms of selenocysteine and selenomethionine cytotoxicity. We present evidences indicating that both oxidative stress and ROS-independent mechanisms contribute to selenoamino acids cytotoxicity. These latter mechanisms include disruption of protein homeostasis by selenocysteine misincorporation in proteins and/or reaction of selenols with protein thiols.
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32
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Westrop GD, Wang L, Blackburn GJ, Zhang T, Zheng L, Watson DG, Coombs GH. Metabolomic profiling and stable isotope labelling of Trichomonas vaginalis and Tritrichomonas foetus reveal major differences in amino acid metabolism including the production of 2-hydroxyisocaproic acid, cystathionine and S-methylcysteine. PLoS One 2017; 12:e0189072. [PMID: 29267346 PMCID: PMC5739422 DOI: 10.1371/journal.pone.0189072] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 11/17/2017] [Indexed: 11/19/2022] Open
Abstract
Trichomonas vaginalis and Tritrichomonas foetus are pathogens that parasitise, respectively, human and bovine urogenital tracts causing disease. Using LC-MS, reference metabolomic profiles were obtained for both species and stable isotope labelling with D-[U-13C6] glucose was used to analyse central carbon metabolism. This facilitated a comparison of the metabolic pathways of T. vaginalis and T. foetus, extending earlier targeted biochemical studies. 43 metabolites, whose identities were confirmed by comparison of their retention times with authentic standards, occurred at more than 3-fold difference in peak intensity between T. vaginalis and T. foetus. 18 metabolites that were removed from or released into the medium during growth also showed more than 3-fold difference between the species. Major differences were observed in cysteine and methionine metabolism in which homocysteine, produced as a bi-product of trans-methylation, is catabolised by methionine γ-lyase in T. vaginalis but converted to cystathionine in T. foetus. Both species synthesise methylthioadenosine by an unusual mechanism, but it is not used as a substrate for methionine recycling. T. vaginalis also produces and exports high levels of S-methylcysteine, whereas only negligible levels were found in T. foetus which maintains significantly higher intracellular levels of cysteine. 13C-labeling confirmed that both cysteine and S-methylcysteine are synthesised by T. vaginalis; S-methylcysteine can be generated by recombinant T. vaginalis cysteine synthase using phosphoserine and methanethiol. T. foetus contained higher levels of ornithine and citrulline than T. vaginalis and exported increased levels of putrescine, suggesting greater flux through the arginine dihydrolase pathway. T. vaginalis produced and exported hydroxy acid derivatives of certain amino acids, particularly 2-hydroxyisocaproic acid derived from leucine, whereas negligible levels of these metabolites occurred in T. foetus.
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Affiliation(s)
- Gareth D. Westrop
- Strathclyde Institute of Pharmacy and Biomedical Science, Strathclyde University, Glasgow, United Kingdom
- * E-mail:
| | - Lijie Wang
- Strathclyde Institute of Pharmacy and Biomedical Science, Strathclyde University, Glasgow, United Kingdom
| | | | - Tong Zhang
- Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Liang Zheng
- Pediatric Translational Medicine Institute, Shanghai Children’s Medical Center, Shanghai, China
| | - David G. Watson
- Strathclyde Institute of Pharmacy and Biomedical Science, Strathclyde University, Glasgow, United Kingdom
| | - Graham H. Coombs
- Strathclyde Institute of Pharmacy and Biomedical Science, Strathclyde University, Glasgow, United Kingdom
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Lin B, Tian G, Liu Y. Mechanistic insights into the γ-elimination reaction of l-methionine catalyzed by methionine γ-lyase (MGL). Theor Chem Acc 2017. [DOI: 10.1007/s00214-017-2140-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Barton LL, Ritz NL, Fauque GD, Lin HC. Sulfur Cycling and the Intestinal Microbiome. Dig Dis Sci 2017; 62:2241-2257. [PMID: 28766244 DOI: 10.1007/s10620-017-4689-5] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 07/19/2017] [Indexed: 02/08/2023]
Abstract
In this review, we focus on the activities transpiring in the anaerobic segment of the sulfur cycle occurring in the gut environment where hydrogen sulfide is produced. While sulfate-reducing bacteria are considered as the principal agents for hydrogen sulfide production, the enzymatic desulfhydration of cysteine by heterotrophic bacteria also contributes to production of hydrogen sulfide. For sulfate-reducing bacteria respiration, molecular hydrogen and lactate are suitable as electron donors while sulfate functions as the terminal electron acceptor. Dietary components provide fiber and macromolecules that are degraded by bacterial enzymes to monomers, and these are fermented by intestinal bacteria with the production to molecular hydrogen which promotes the metabolic dominance by sulfate-reducing bacteria. Sulfate is also required by the sulfate-reducing bacteria, and this can be supplied by sulfate- and sulfonate-containing compounds that are hydrolyzed by intestinal bacterial with the release of sulfate. While hydrogen sulfide in the intestinal biosystem may be beneficial to bacteria by increasing resistance to antibiotics, and protecting them from reactive oxygen species, hydrogen sulfide at elevated concentrations may become toxic to the host.
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Affiliation(s)
- Larry L Barton
- Department of Biology, MSCO3 2020, University of New Mexico, Albuquerque, NM, 87131, USA.
| | - Nathaniel L Ritz
- New Mexico VA Health Care System, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Guy D Fauque
- CNRS, IRD, Mediterranean Institute of Oceanography (MIO) UM 110, Aix-Marseille Université, Université de Toulon, Campus de Luminy, Case 901, 13288, Marseille Cedex 09, France
| | - Henry C Lin
- New Mexico VA Health Care System, University of New Mexico, Albuquerque, NM, 87131, USA
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Sato D, Shiba T, Karaki T, Yamagata W, Nozaki T, Nakazawa T, Harada S. X-Ray snapshots of a pyridoxal enzyme: a catalytic mechanism involving concerted [1,5]-hydrogen sigmatropy in methionine γ-lyase. Sci Rep 2017; 7:4874. [PMID: 28687762 PMCID: PMC5501846 DOI: 10.1038/s41598-017-05032-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 05/19/2017] [Indexed: 11/30/2022] Open
Abstract
Pyridoxal 5′-phosphate (PLP)-enzymes are essentially involved in amino acid and amine metabolism of a wide variety of organisms. Despite their extensive biochemical studies, there are little evidence and structural data to comprehensively elaborate the catalytic mechanism. We obtained X-ray snapshots of l-methionine γ-lyase from Entamoeba histolytica (EhMGL), a PLP-enzyme catalyzing the γ-elimination reaction of methionine. Here, we suggest a catalytic mechanism of EhMGL by using the X-ray snapshots covering all stages of this multistep catalysis reaction. Initial formation of a Michaelis complex is followed by the migration of double bond from the C4′=Nα–Cα moiety in an intermediate PLP-methionine imine to C4′–Nα=Cα in pyridoxamine 5′-phosphate (PMP)-α,β-dehydromethionine imine without intervention of a putative quinonoid intermediate. The enzyme can facilitate the subsequent γ-elimination of methanethiol by the possible general acid-base catalysis of Tyr108 for the E1cB mechanism, enabling to form the ene-imine C4′–Nα=Cα–Cβ=Cγ structure with the s-cis conformation, which is prerequisite for the non-enzymatic symmetry-allowed suprafacial [1,5]-hydrogen shift to complete the catalytic cycle by releasing α-ketobutyrate. The mechanism based on the X-ray snapshots is consistent with the reactivity of MGL toward methionine analogues. The generality of such a mechanism involving non-enzymatic concerted reaction in other PLP enzymes is discussed.
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Affiliation(s)
- Dan Sato
- Graduate School of Science and Technology, Department of Applied Biology, Kyoto Institute of Technology, Sakyo-ku, Kyoto, 606-8585, Japan
| | - Tomoo Shiba
- Graduate School of Science and Technology, Department of Applied Biology, Kyoto Institute of Technology, Sakyo-ku, Kyoto, 606-8585, Japan
| | - Tsuyoshi Karaki
- Graduate School of Science and Technology, Department of Applied Biology, Kyoto Institute of Technology, Sakyo-ku, Kyoto, 606-8585, Japan
| | - Wataru Yamagata
- Graduate School of Science and Technology, Department of Applied Biology, Kyoto Institute of Technology, Sakyo-ku, Kyoto, 606-8585, Japan
| | - Tomoyoshi Nozaki
- Department of Parasitology, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo, 162-8640, Japan
| | - Takashi Nakazawa
- Department of Chemistry, Nara Women's University, Nara, 630-8506, Japan
| | - Shigeharu Harada
- Graduate School of Science and Technology, Department of Applied Biology, Kyoto Institute of Technology, Sakyo-ku, Kyoto, 606-8585, Japan.
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Sato D, Shiba T, Yunoto S, Furutani K, Fukumoto M, Kudou D, Tamura T, Inagaki K, Harada S. Structural and mechanistic insights into homocysteine degradation by a mutant of methionine γ-lyase based on substrate-assisted catalysis. Protein Sci 2017; 26:1224-1230. [PMID: 28329912 DOI: 10.1002/pro.3158] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Revised: 03/14/2017] [Accepted: 03/17/2017] [Indexed: 01/26/2023]
Abstract
Methionine γ-lyse (MGL) catalyzes the α, γ-elimination of l-methionine and its derivatives as well as the α, β-elimination of l-cysteine and its derivatives to produce α-keto acids, volatile thiols, and ammonia. The reaction mechanism of MGL has been characterized by enzymological studies using several site-directed mutants. The Pseudomonas putida MGL C116H mutant showed drastically reduced degradation activity toward methionine while retaining activity toward homocysteine. To understand the underlying mechanism and to discern the subtle differences between these substrates, we analyzed the crystal structures of the reaction intermediates. The complex formed between the C116H mutant and methionine demonstrated that a loop structure (Ala51-Asn64) in the adjacent subunit of the catalytic dimer cannot approach the cofactor pyridoxal 5'-phosphate (PLP) because His116 disrupts the interaction of Asp241 with Lys240, and the liberated side chain of Lys240 causes steric hindrance with this loop. Conversely, in the complex formed between C116H mutant and homocysteine, the thiol moiety of the substrate conjugated with PLP offsets the imidazole ring of His116 via a water molecule, disrupting the interaction of His116 and Asp241 and restoring the interaction of Asp241 with Lys240. These structural data suggest that the Cys116 to His mutation renders the enzyme inactive toward the original substrate, but activity is restored when the substrate is homocysteine due to substrate-assisted catalysis.
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Affiliation(s)
- Dan Sato
- Department of Applied Biology, Graduate School of Science Technology, Kyoto Institute of Technology, Kyoto, 606-8585, Japan
| | - Tomoo Shiba
- Department of Applied Biology, Graduate School of Science Technology, Kyoto Institute of Technology, Kyoto, 606-8585, Japan
| | - Shunsuke Yunoto
- Department of Applied Biology, Graduate School of Science Technology, Kyoto Institute of Technology, Kyoto, 606-8585, Japan
| | - Kazuo Furutani
- Department of Applied Biology, Graduate School of Science Technology, Kyoto Institute of Technology, Kyoto, 606-8585, Japan
| | - Mitsuki Fukumoto
- Department of Biofunctional Chemistry, Graduate School of Environmental and Life Science, Okayama University, Okayama, 700-8530, Japan
| | - Daizou Kudou
- Department of Biofunctional Chemistry, Graduate School of Environmental and Life Science, Okayama University, Okayama, 700-8530, Japan
| | - Takashi Tamura
- Department of Biofunctional Chemistry, Graduate School of Environmental and Life Science, Okayama University, Okayama, 700-8530, Japan
| | - Kenji Inagaki
- Department of Biofunctional Chemistry, Graduate School of Environmental and Life Science, Okayama University, Okayama, 700-8530, Japan
| | - Shigeharu Harada
- Department of Applied Biology, Graduate School of Science Technology, Kyoto Institute of Technology, Kyoto, 606-8585, Japan
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Sato D, Shiba T, Mizuno S, Kawamura A, Hanada S, Yamada T, Shinozaki M, Yanagitani M, Tamura T, Inagaki K, Harada S. The hyperthermophilic cystathionine γ-synthase from the aerobic crenarchaeon Sulfolobus tokodaii: expression, purification, crystallization and structural insights. Acta Crystallogr F Struct Biol Commun 2017; 73:152-158. [PMID: 28291751 PMCID: PMC5349309 DOI: 10.1107/s2053230x17002011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Accepted: 02/07/2017] [Indexed: 11/10/2022] Open
Abstract
Cystathionine γ-synthase (CGS; EC 2.5.1.48), a pyridoxal 5'-phosphate (PLP)-dependent enzyme, catalyzes the formation of cystathionine from an L-homoserine derivative and L-cysteine in the first step of the transsulfuration pathway. Recombinant CGS from the thermoacidophilic archaeon Sulfolobus tokodaii (StCGS) was overexpressed in Escherichia coli and purified to homogeneity by heat treatment followed by hydroxyapatite and gel-filtration column chromatography. The purified enzyme shows higher enzymatic activity at 353 K under basic pH conditions compared with that at 293 K. Crystallization trials yielded three crystal forms from different temperature and pH conditions. Form I crystals (space group P21; unit-cell parameters a = 58.4, b = 149.3, c = 90.2 Å, β = 108.9°) were obtained at 293 K under acidic pH conditions using 2-methyl-2,4-pentanediol as a precipitant, whereas under basic pH conditions the enzyme crystallized in form II at 293 K (space group C2221; unit-cell parameters a = 117.7, b = 117.8, c = 251.3 Å) and in form II' at 313 K (space group C2221; unit-cell parameters a = 107.5, b = 127.7, c = 251.1 Å) using polyethylene glycol 3350 as a precipitant. X-ray diffraction data were collected to 2.2, 2.9 and 2.7 Å resolution for forms I, II and II', respectively. Structural analysis of these crystal forms shows that the orientation of the bound PLP in form II is significantly different from that in form II', suggesting that the change in orientation of PLP with temperature plays a role in the thermophilic enzymatic activity of StCGS.
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Affiliation(s)
- Dan Sato
- Department of Applied Biology, Kyoto Institute of Technology, Gosho Kaido-cho, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Tomoo Shiba
- Department of Applied Biology, Kyoto Institute of Technology, Gosho Kaido-cho, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Sae Mizuno
- Department of Applied Biology, Kyoto Institute of Technology, Gosho Kaido-cho, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Ayaka Kawamura
- Department of Applied Biology, Kyoto Institute of Technology, Gosho Kaido-cho, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Shoko Hanada
- Department of Applied Biology, Kyoto Institute of Technology, Gosho Kaido-cho, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Tetsuya Yamada
- Department of Biofunctional Chemistry, Okayama University, Tsushima-naka 1-1-1, Kita-ku, Okayama 700-8530, Japan
| | - Mai Shinozaki
- Department of Biofunctional Chemistry, Okayama University, Tsushima-naka 1-1-1, Kita-ku, Okayama 700-8530, Japan
| | - Masahiko Yanagitani
- Department of Biofunctional Chemistry, Okayama University, Tsushima-naka 1-1-1, Kita-ku, Okayama 700-8530, Japan
| | - Takashi Tamura
- Department of Biofunctional Chemistry, Okayama University, Tsushima-naka 1-1-1, Kita-ku, Okayama 700-8530, Japan
| | - Kenji Inagaki
- Department of Biofunctional Chemistry, Okayama University, Tsushima-naka 1-1-1, Kita-ku, Okayama 700-8530, Japan
| | - Shigeharu Harada
- Department of Applied Biology, Kyoto Institute of Technology, Gosho Kaido-cho, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
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Setzer MS, Byler KG, Ogungbe IV, Setzer WN. Natural Products as New Treatment Options for Trichomoniasis: A Molecular Docking Investigation. Sci Pharm 2017; 85:scipharm85010005. [PMID: 28134827 PMCID: PMC5388143 DOI: 10.3390/scipharm85010005] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 01/23/2017] [Indexed: 11/22/2022] Open
Abstract
Trichomoniasis, caused by the parasitic protozoan Trichomonas vaginalis, is the most common non-viral sexually-transmitted disease, and there can be severe complications from trichomoniasis. Antibiotic resistance in T. vaginalis is increasing, but there are currently no alternatives treatment options. There is a need to discover and develop new chemotherapeutic alternatives. Plant-derived natural products have long served as sources for new medicinal agents, as well as new leads for drug discovery and development. In this work, we have carried out an in silico screening of 952 antiprotozoal phytochemicals with specific protein drug targets of T. vaginalis. A total of 42 compounds showed remarkable docking properties to T. vaginalis methionine gamma-lyase (TvMGL) and to T. vaginalis purine nucleoside phosphorylase (TvPNP). The most promising ligands were polyphenolic compounds, and several of these showed docking properties superior to either co-crystallized ligands or synthetic enzyme inhibitors.
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Affiliation(s)
- Mary Snow Setzer
- Department of Chemistry, University of Alabama in Huntsville, Huntsville, AL 35899, USA.
| | - Kendall G Byler
- Department of Chemistry, University of Alabama in Huntsville, Huntsville, AL 35899, USA.
| | - Ifedayo Victor Ogungbe
- Department of Chemistry & Biochemistry, Jackson State University, Jackson, MS 39217, USA.
| | - William N Setzer
- Department of Chemistry, University of Alabama in Huntsville, Huntsville, AL 35899, USA.
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Stephen AS, Millhouse E, Sherry L, Aduse-Opoku J, Culshaw S, Ramage G, Bradshaw DJ, Burnett GR, Allaker RP. In Vitro Effect of Porphyromonas gingivalis Methionine Gamma Lyase on Biofilm Composition and Oral Inflammatory Response. PLoS One 2016; 11:e0169157. [PMID: 28033374 PMCID: PMC5199072 DOI: 10.1371/journal.pone.0169157] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 12/13/2016] [Indexed: 02/07/2023] Open
Abstract
Methanethiol (methyl mercaptan) is an important contributor to oral malodour and periodontal tissue destruction. Porphyromonas gingivalis, Prevotella intermedia and Fusobacterium nucleatum are key oral microbial species that produce methanethiol via methionine gamma lyase (mgl) activity. The aim of this study was to compare an mgl knockout strain of P. gingivalis with its wild type using a 10-species biofilm co-culture model with oral keratinocytes and its effect on biofilm composition and inflammatory cytokine production. A P. gingivalis mgl knockout strain was constructed using insertion mutagenesis from wild type W50 with gas chromatographic head space analysis confirming lack of methanethiol production. 10-species biofilms consisting of Streptococcus mitis, Streptococcus oralis, Streptococcus intermedius, Fusobacterium nucleatum ssp polymorphum, Fusobacterium nucleatum ssp vincentii, Veillonella dispar, Actinomyces naeslundii, Prevotella intermedia and Aggregatibacter actinomycetemcomitans with either the wild type or mutant P. gingivalis were grown on Thermanox cover slips and used to stimulate oral keratinocytes (OKF6-TERT2), under anaerobic conditions for 4 and 24 hours. Biofilms were analysed by quantitative PCR with SYBR Green for changes in microbial ecology. Keratinocyte culture supernatants were analysed using a multiplex bead immunoassay for cytokines. Significant population differences were observed between mutant and wild type biofilms; V. dispar proportions increased (p<0.001), whilst A. naeslundii (p<0.01) and Streptococcus spp. (p<0.05) decreased in mutant biofilms. Keratinocytes produced less IL-8, IL-6 and IL-1α when stimulated with the mutant biofilms compared to wild type. Lack of mgl in P. gingivalis has been shown to affect microbial ecology in vitro, giving rise to a markedly different biofilm composition, with a more pro-inflammatory cytokine response from the keratinocytes observed. A possible role for methanethiol in biofilm formation and cytokine response with subsequent effects on oral malodor and periodontitis is suggested.
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Affiliation(s)
- Abish S. Stephen
- Research Centre for Clinical & Diagnostic Oral Sciences, Blizard Institute, Queen Mary University of London, London, United Kingdom
| | - Emma Millhouse
- Infection and Immunity Research Group, Dental School, University of Glasgow, Glasgow, United Kingdom
| | - Leighann Sherry
- Infection and Immunity Research Group, Dental School, University of Glasgow, Glasgow, United Kingdom
| | - Joseph Aduse-Opoku
- Research Centre for Clinical & Diagnostic Oral Sciences, Blizard Institute, Queen Mary University of London, London, United Kingdom
| | - Shauna Culshaw
- Infection and Immunity Research Group, Dental School, University of Glasgow, Glasgow, United Kingdom
| | - Gordon Ramage
- Infection and Immunity Research Group, Dental School, University of Glasgow, Glasgow, United Kingdom
| | | | - Gary R. Burnett
- GlaxoSmithKline Consumer Healthcare, Weybridge, United Kingdom
| | - Robert P. Allaker
- Research Centre for Clinical & Diagnostic Oral Sciences, Blizard Institute, Queen Mary University of London, London, United Kingdom
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Repression of the Chromatin-Tethering Domain of Murine Leukemia Virus p12. J Virol 2016; 90:11197-11207. [PMID: 27707926 DOI: 10.1128/jvi.01084-16] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 09/28/2016] [Indexed: 12/28/2022] Open
Abstract
Murine leukemia virus (MLV) p12, encoded within Gag, binds the viral preintegration complex (PIC) to the mitotic chromatin. This acts to anchor the viral PIC in the nucleus as the nuclear envelope re-forms postmitosis. Mutations within the p12 C terminus (p12 PM13 to PM15) block early stages in viral replication. Within the p12 PM13 region (p12 60PSPMA65), our studies indicated that chromatin tethering was not detected when the wild-type (WT) p12 protein (M63) was expressed as a green fluorescent protein (GFP) fusion; however, constructs bearing p12-I63 were tethered. N-terminal truncations of the activated p12-I63-GFP indicated that tethering increased further upon deletion of p12 25DLLTEDPPPY34, which includes the late domain required for viral assembly. The p12 PM15 sequence (p12 70RREPP74) is critical for wild-type viral viability; however, virions bearing the PM15 mutation (p12 70AAAAA74) with a second M63I mutant were viable, with a titer 18-fold lower than that of the WT. The p12 M63I mutation amplified chromatin tethering and compensated for the loss of chromatin binding of p12 PM15. Rescue of the p12-M63-PM15 nonviable mutant with prototype foamy virus (PFV) and Kaposi's sarcoma herpesvirus (KSHV) tethering sequences confirmed the function of p1270-74 in chromatin binding. Minimally, full-strength tethering was seen with only p12 61SPIASRLRGRR71 fused to GFP. These results indicate that the p12 C terminus alone is sufficient for chromatin binding and that the presence of the p12 25DLLTEDPPPY34 motif in the N terminus suppresses the ability to tether. IMPORTANCE This study defines a regulatory mechanism controlling the differential roles of the MLV p12 protein in early and late replication. During viral assembly and egress, the late domain within the p12 N terminus functions to bind host vesicle release factors. During viral entry, the C terminus of p12 is required for tethering to host mitotic chromosomes. Our studies indicate that the p12 domain including the PPPY late sequence temporally represses the p12 chromatin tethering motif. Maximal p12 tethering was identified with only an 11-amino-acid minimal chromatin tethering motif encoded at p1261-71 Within this region, the p12-M63I substitution switches p12 into a tethering-competent state, partially rescuing the p12-PM15 tethering mutant. A model for how this conformational change regulates early versus late functions is presented.
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Fernandes HS, Silva Teixeira CS, Fernandes PA, Ramos MJ, Cerqueira NMFSA. Amino acid deprivation using enzymes as a targeted therapy for cancer and viral infections. Expert Opin Ther Pat 2016; 27:283-297. [DOI: 10.1080/13543776.2017.1254194] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- H. S. Fernandes
- UCIBIO-REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - C. S. Silva Teixeira
- UCIBIO-REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - P. A. Fernandes
- UCIBIO-REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - M. J. Ramos
- UCIBIO-REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - N. M. F. S. A. Cerqueira
- UCIBIO-REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
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Watson SB, Jüttner F. Malodorous volatile organic sulfur compounds: Sources, sinks and significance in inland waters. Crit Rev Microbiol 2016; 43:210-237. [DOI: 10.1080/1040841x.2016.1198306] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Susan B. Watson
- Watershed Hydrology and Ecology Research Division, Environment and Climate Change Canada, Canada Center for Inland Waters, Burlington, Ontario, Canada
| | - Friedrich Jüttner
- University of Zurich, Department of Limnology, Limnological Station, Kilchberg, Switzerland
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43
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El-Sayed AS, Hassan AE, Shindia AA, Mohamed SG, Sitohy MZ. Aspergillus flavipes methionine γ-lyase-dextran conjugates with enhanced structural, proteolytic stability and anticancer efficiency. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.molcatb.2016.11.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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44
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Foo TC, Terentis AC, Venkatachalam KV. A continuous spectrophotometric assay and nonlinear kinetic analysis of methionine γ-lyase catalysis. Anal Biochem 2016; 507:21-6. [DOI: 10.1016/j.ab.2016.05.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Revised: 04/08/2016] [Accepted: 05/13/2016] [Indexed: 10/21/2022]
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45
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Selim M, Elshikh H, El-Hadedy D, Saad M, Eliwa E, Abdelraof M. l-Methioninase from some Streptomyces isolates I: Isolation, identification of best producers and some properties of the crude enzyme produced. J Genet Eng Biotechnol 2015; 13:129-137. [PMID: 30647576 PMCID: PMC6299813 DOI: 10.1016/j.jgeb.2015.08.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Revised: 08/10/2015] [Accepted: 08/25/2015] [Indexed: 11/28/2022]
Abstract
Among 60 isolates of Streptomyces tested; only 40 isolates were capable to utilize l-methionine as the only source of nitrogen in medium. In addition, 24 of these isolates could grow in medium amended with l-methionine as a source of nitrogen and carbon. Qualitative rapid plate assay test shows the ability of 18 of these isolates to grow with a pink color surrounding their colonial growth, while 6 of these isolates could grow and utilize l-methionine without any pink color around their colonial growth. Quantitative assay test shows the rate of l-methioninase production by all isolates tested. Permeabilization treatment including chemical and physical methods proved that l-methioninase was found to be extracellularly produced. The results also indicate that l-methioninase production was not correlated with growth rate or l-methionine consumption in medium. On the other hand, quantitative assay test shows that these six isolates were l-methioninase negative and failed to produce any amount of l-methioninase. In addition, results also show that isolates No. 4 and No. 60 were the most suitable for l-methioninase production, these two isolates were characterized and identified as Streptomyces sp. DMMMH 4 and Streptomyces sp. MDMMH 60 using 16S rRNA with accession No. in gene bank. Furthermore, optimal conditions for enzyme activity produced by the two isolates were established in relation to temperature, pH, reaction time and type of buffer used and its molarities.
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Affiliation(s)
- M.H. Selim
- Microbial Chemistry Dep., National Research Center (NRC), Giza, Egypt
| | - H.H. Elshikh
- Botany and Microbiology Dep., Faculty of Science (Boys), Al-Azhar University, Cairo, Egypt
| | - D.E. El-Hadedy
- Biotechnology Division, National Center for Radiation Research and Technology (NCRRT), 3 Ahmed Elzumor St., 8th Sector, Nasr City, Cairo, Egypt
| | - M.M. Saad
- Microbial Chemistry Dep., National Research Center (NRC), Giza, Egypt
| | - E. Eliwa
- Microbial Chemistry Dep., National Research Center (NRC), Giza, Egypt
| | - M. Abdelraof
- Microbial Chemistry Dep., National Research Center (NRC), Giza, Egypt
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46
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Selim MH, Karm Eldin EZ, Saad MM, Mostafa ESE, Shetia YH, Anise AAH. Purification, Characterization of L-Methioninase from Candida tropicalis, and Its Application as an Anticancer. BIOTECHNOLOGY RESEARCH INTERNATIONAL 2015; 2015:173140. [PMID: 26691554 PMCID: PMC4672112 DOI: 10.1155/2015/173140] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 10/10/2015] [Accepted: 10/13/2015] [Indexed: 02/08/2023]
Abstract
The aim of the present study is to purify L-methioninase from Candida tropicalis 34.19-fold with 27.98% recovery after ion exchange chromatography followed by gel filtration. The purified enzyme revealed a single band on SDS-PAGE gel with a molecular weight of 46 KDa. Its optimum temperature was 45 to 55 and thermal stability was 55°C for 15 min. The enzyme had optimum pH at 6.5 and stability at a pH range of 5.5 to 7.0 for 24 hr. The maximum activity was observed with substrate concentration of 30 µM and Km was 0.5 mM. The enzyme was strongly inhibited by Cd(+2) and Cu(+2) while it was enhanced by Na(+), Ni(+2), and Mg(+2) at 10 mM while Ca(+2) had slight activation at 20 mM. In addition, the potential application of the L-methioninase as an anticancer agent against various types of tumor cell lines is discussed.
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Abstract
Carbon–sulfur biological chemistry encompasses a fascinating area of biochemistry and medicinal chemistry and includes the roles that methionine and S-adenosyl-l-methionine play in cells as well as the chemistry of intracellular thiols such as glutathione. This article, based on the 2014 Bernard Belleau Award lecture, provides an overview of some of the key investigations that were undertaken in this area from a bioorganic perspective. The research has ameliorated our fundamental knowledge of several of the enzymes utilizing these sulfur-containing molecules, has led to the development of several novel 19F biophysical probes, and has explored some of the medicinal chemistry associated with these processes.
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Affiliation(s)
- John F. Honek
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1, Canada
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1, Canada
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A Matter of Timing: Contrasting Effects of Hydrogen Sulfide on Oxidative Stress Response in Shewanella oneidensis. J Bacteriol 2015; 197:3563-72. [PMID: 26324455 DOI: 10.1128/jb.00603-15] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 08/25/2015] [Indexed: 01/29/2023] Open
Abstract
UNLABELLED Hydrogen sulfide (H2S), well known for its toxic properties, has recently become a research focus in bacteria, in part because it has been found to prevent oxidative stress caused by treatment with some antibiotics. H2S has the ability to scavenge reactive oxygen species (ROS), thus preventing oxidative stress, but it is also toxic, leading to conflicting reports of its effects in different organisms. Here, with Shewanella oneidensis as a model, we report that the effects of H2S on the response to oxidative stress are time dependent. When added simultaneously with H2O2, H2S promoted H2O2 toxicity by inactivating catalase, KatB, a heme-containing enzyme involved in H2O2 degradation. Such an inhibitory effect may apply to other heme-containing proteins, such as cytochrome cbb3 oxidase. When H2O2 was supplied 20 min or later after the addition of H2S, the oxidative-stress-responding regulator OxyR was activated, resulting in increased resistance to H2O2. The activation of OxyR was likely triggered by the influx of iron, a response to lowered intracellular iron due to the iron-sequestering property of H2S. Given that Shewanella bacteria thrive in redox-stratified environments that have abundant sulfur and iron species, our results imply that H2S is more important for bacterial survival in such environmental niches than previously believed. IMPORTANCE Previous studies have demonstrated that H2S is either detrimental or beneficial to bacterial cells. While it can act as a growth-inhibiting molecule by damaging DNA and denaturing proteins, it helps cells to combat oxidative stress. Here we report that H2S indeed has these contrasting biological functions and that its effects are time dependent. Immediately after H2S treatment, there is growth inhibition due to damage of heme-containing proteins, at least to catalase and cytochrome c oxidase. In contrast, when added a certain time later, H2S confers an enhanced ability to combat oxidative stress by activating the H2O2-responding regulator OxyR. Our data reconcile conflicting observations about the functions of H2S.
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Wu G, Li N, Mao Y, Zhou G, Gao H. Endogenous generation of hydrogen sulfide and its regulation in Shewanella oneidensis. Front Microbiol 2015; 6:374. [PMID: 25972854 PMCID: PMC4412017 DOI: 10.3389/fmicb.2015.00374] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Accepted: 04/12/2015] [Indexed: 11/21/2022] Open
Abstract
Hydrogen sulfide (H2S) has been recognized as a physiological mediator with a variety of functions across all domains of life. In this study, mechanisms of endogenous H2S generation in Shewanella oneidensis were investigated. As a research model with highly diverse anaerobic respiratory pathways, the microorganism is able to produce H2S by respiring on a variety of sulfur-containing compounds with SirACD and PsrABC enzymatic complexes, as well as through cysteine degradation with three enzymes, MdeA, SO_1095, and SseA. We showed that the SirACD and PsrABC complexes, which are predominantly, if not exclusively, responsible for H2S generation via respiration of sulfur species, do not interplay with each other. Strikingly, a screen for regulators controlling endogenous H2S generation by transposon mutagenesis identified global regulator Crp to be essential to all H2S-generating processes. In contrast, Fnr and Arc, two other global regulators that have a role in respiration, are dispensable in regulating H2S generation via respiration of sulfur species. Interestingly, Arc is involved in the H2S generation through cysteine degradation by repressing expression of the mdeA gene. We further showed that expression of the sirA and psrABC operons is subjected to direct regulation of Crp, but the mechanisms underlying the requirement of Crp for H2S generation through cysteine degradation remain elusive.
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Affiliation(s)
- Genfu Wu
- Institute of Microbiology and College of Life Sciences, Zhejiang University Hangzhou, China
| | - Ning Li
- Institute of Microbiology and College of Life Sciences, Zhejiang University Hangzhou, China
| | - Yinting Mao
- Institute of Microbiology and College of Life Sciences, Zhejiang University Hangzhou, China
| | - Guangqi Zhou
- Institute of Microbiology and College of Life Sciences, Zhejiang University Hangzhou, China
| | - Haichun Gao
- Institute of Microbiology and College of Life Sciences, Zhejiang University Hangzhou, China
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50
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Song H, Xu R, Guo Z. Identification and characterization of a methionine γ-lyase in the calicheamicin biosynthetic cluster of Micromonospora echinospora. Chembiochem 2014; 16:100-9. [PMID: 25404066 DOI: 10.1002/cbic.201402489] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2014] [Indexed: 11/07/2022]
Abstract
CalE6 is a previously uncharacterized protein involved in the biosynthesis of calicheamicins in Micromonospora echinospora. It is a pyridoxal-5'-phosphate-dependent enzyme and exhibits high sequence homology to cystathionine γ-lyases and cystathionine γ-synthases. However, it was found to be active towards methionine and to convert this amino acid into α-ketobutyrate, ammonium, and methanethiol. The crystal structure of the cofactor-bound holoenzyme was resolved at 2.0 Å; it contains two active site residues, Gly105 and Val322, specific for methionine γ-lyases. Modeling of methionine into the active site allows identification of the active site residues responsible for substrate recognition and catalysis. These findings support that CalE6 is a putative methionine γ-lyase producing methanethiol as a building block in biosynthesis of calicheamicins.
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Affiliation(s)
- Haigang Song
- Department of Chemistry and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon (Hong Kong)
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