1
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Xu JT, Yu JF, Cheng T, Feng A, Yang P, Gu J, Yu HJ, Deng JY. The T120P or M172V mutation on rv2172c confers high level para-aminosalicylic acid resistance in Mycobacterium tuberculosis. Emerg Microbes Infect 2024; 13:2374030. [PMID: 39023395 PMCID: PMC11271092 DOI: 10.1080/22221751.2024.2374030] [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: 04/10/2024] [Revised: 06/12/2024] [Accepted: 06/22/2024] [Indexed: 07/20/2024]
Abstract
Although para-aminosalicylic acid (PAS) has been used to treat tuberculosis for decades, mechanisms of resistance to this drug in Mycobacterium tuberculosis (M. tuberculosis) clinical isolates have not been thoroughly investigated. Previously, we found that decreased methylenetetrahydrofolate reductase (MTHFR) activity of Rv2172c led to increased sensitivity to antifolates in M. tuberculosis. In this study, we collected the genome-sequencing data of 173 PAS-resistant and 803 PAS-sensitive clinical isolates and analyzed rv2172c mutations in those 976 isolates. The results showed that two mutations (T120P and M172V) on rv2172c could be identified in a certain proportion (6.36%) of PAS-resistant isolates. The results of AlphaFold2 prediction indicated that the T120P or M172V mutation might affect the enzymatic activity of Rv2172c by influencing nicotinamide adenine dinucleotide (NADH) binding, and this was verified by subsequent biochemical analysis, demonstrating the role of residues Thr120 and Met172 on NADH binding and enzymatic activity of Rv2172c. In addition, the effect of rv2172c T120P or M172V mutation on methionine production and PAS resistance was determined in M. tuberculosis. The results showed that both T120P and M172V mutations caused increased intracellular methionine concentrations and high level PAS resistance. In summary, we discovered new molecular markers and also a novel mechanism of PAS resistance in M. tuberculosis clinical isolates and broadened the understanding of the NADH-dependent MTHFR catalytic mechanism of Rv2172c in M. tuberculosis, which will facilitate the molecular diagnosis of PAS resistance and also the development of new drugs targeting Rv2172c.
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Affiliation(s)
- Jin-Tian Xu
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Ji-Fang Yu
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, People's Republic of China
| | - Tao Cheng
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Ao Feng
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Ping Yang
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People’s Republic of China
| | - Jing Gu
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, People's Republic of China
| | - Hong-Jun Yu
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People’s Republic of China
| | - Jiao-Yu Deng
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, People's Republic of China
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2
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Pérez-Castaño R, Aranda J, Widner FJ, Kieninger C, Deery E, Warren MJ, Orozco M, Elías-Arnanz M, Padmanabhan S, Kräutler B. The Rhodium Analogue of Coenzyme B 12 as an Anti-Photoregulatory Ligand Inhibiting Bacterial CarH Photoreceptors. Angew Chem Int Ed Engl 2024; 63:e202401626. [PMID: 38416546 DOI: 10.1002/anie.202401626] [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: 01/23/2024] [Revised: 02/23/2024] [Accepted: 02/23/2024] [Indexed: 02/29/2024]
Abstract
Coenzyme B12 (AdoCbl; 5'-deoxy-5'-adenosylcobalamin), the quintessential biological organometallic radical catalyst, has a formerly unanticipated, yet extensive, role in photoregulation in bacteria. The light-responsive cobalt-corrin AdoCbl performs this nonenzymatic role by facilitating the assembly of CarH photoreceptors into DNA-binding tetramers in the dark, suppressing gene expression. Conversely, exposure to light triggers the decomposition of this AdoCbl-bound complex by a still elusive photochemical mechanism, activating gene expression. Here, we have examined AdoRhbl, the non-natural rhodium analogue of AdoCbl, as a photostable isostructural surrogate for AdoCbl. We show that AdoRhbl closely emulates AdoCbl in its uptake by bacterial cells and structural functionality as a regulatory ligand for CarH tetramerization, DNA binding, and repressor activity. Remarkably, we find AdoRhbl is photostable even when bound "base-off/His-on" to CarH in vitro and in vivo. Thus, AdoRhbl, an antivitamin B12, also represents an unprecedented anti-photoregulatory ligand, opening a pathway to precisely target biomimetic inhibition of AdoCbl-based photoregulation, with new possibilities for selective antibacterial applications. Computational biomolecular analysis of AdoRhbl binding to CarH yields detailed structural insights into this complex, which suggest that the adenosyl group of photoexcited AdoCbl bound to CarH may specifically undergo a concerted non-radical syn-1,2-elimination mechanism, an aspect not previously considered for this photoreceptor.
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Affiliation(s)
- Ricardo Pérez-Castaño
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, 30100, Murcia, Spain
| | - Juan Aranda
- Institute for Research in Biomedicine, IRB Barcelona), Baldiri Reixac 10-12, 08028, Barcelona, Spain
| | - Florian J Widner
- Institute of Organic Chemistry & Center for Molecular Biosciences, University of Innsbruck, Innrain 80/82, A-6020, Innsbruck, Austria
| | - Christoph Kieninger
- Institute of Organic Chemistry & Center for Molecular Biosciences, University of Innsbruck, Innrain 80/82, A-6020, Innsbruck, Austria
| | - Evelyne Deery
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK
| | - Martin J Warren
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Modesto Orozco
- Institute for Research in Biomedicine, IRB Barcelona), Baldiri Reixac 10-12, 08028, Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona (Spain); the Joint BSC-IRB Research Program in Computational Biology, and Department of Biochemistry and Biomedicine, University of Barcelona, Baldiri Reixac 10-12, 08028, Barcelona, Spain
| | - Montserrat Elías-Arnanz
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, 30100, Murcia, Spain
| | - S Padmanabhan
- Instituto de Química Física Blas Cabrera (IQF-CSIC), Consejo Superior de Investigaciones Científicas (CSIC), 119 c/Serrano, 28006, Madrid, Spain
| | - Bernhard Kräutler
- Institute of Organic Chemistry & Center for Molecular Biosciences, University of Innsbruck, Innrain 80/82, A-6020, Innsbruck, Austria
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3
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Lima SF, Pires S, Rupert A, Oguntunmibi S, Jin WB, Marderstein A, Funez-dePagnier G, Maldarelli G, Viladomiu M, Putzel G, Yang W, Tran N, Xiang G, Grier A, Guo CJ, Lukin D, Mandl LA, Scherl EJ, Longman RS. The gut microbiome regulates the clinical efficacy of sulfasalazine therapy for IBD-associated spondyloarthritis. Cell Rep Med 2024; 5:101431. [PMID: 38378002 PMCID: PMC10982976 DOI: 10.1016/j.xcrm.2024.101431] [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: 07/03/2023] [Revised: 11/28/2023] [Accepted: 01/25/2024] [Indexed: 02/22/2024]
Abstract
Sulfasalazine is a prodrug known to be effective for the treatment of inflammatory bowel disease (IBD)-associated peripheral spondyloarthritis (pSpA), but the mechanistic role for the gut microbiome in regulating its clinical efficacy is not well understood. Here, treatment of 22 IBD-pSpA subjects with sulfasalazine identifies clinical responders with a gut microbiome enriched in Faecalibacterium prausnitzii and the capacity for butyrate production. Sulfapyridine promotes butyrate production and transcription of the butyrate synthesis gene but in F. prausnitzii in vitro, which is suppressed by excess folate. Sulfasalazine therapy enhances fecal butyrate production and limits colitis in wild-type and gnotobiotic mice colonized with responder, but not non-responder, microbiomes. F. prausnitzii is sufficient to restore sulfasalazine protection from colitis in gnotobiotic mice colonized with non-responder microbiomes. These findings reveal a mechanistic link between the efficacy of sulfasalazine therapy and the gut microbiome with the potential to guide diagnostic and therapeutic approaches for IBD-pSpA.
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Affiliation(s)
- Svetlana F Lima
- Jill Roberts Institute for Research in IBD, Weill Cornell Medicine, New York, NY 10065, USA; Division of Gastroenterology and Hepatology, Department of Medicine, NewYork-Presbyterian Hospital/Weill Cornell Medical Center, New York, NY 10065, USA
| | - Silvia Pires
- Jill Roberts Institute for Research in IBD, Weill Cornell Medicine, New York, NY 10065, USA; Division of Gastroenterology and Hepatology, Department of Medicine, NewYork-Presbyterian Hospital/Weill Cornell Medical Center, New York, NY 10065, USA
| | - Amanda Rupert
- Division of Gastroenterology and Hepatology, Department of Medicine, NewYork-Presbyterian Hospital/Weill Cornell Medical Center, New York, NY 10065, USA; Jill Roberts Center for IBD, NewYork-Presbyterian Hospital/Weill Cornell Medical Center, New York, NY 10065, USA
| | - Seun Oguntunmibi
- Jill Roberts Institute for Research in IBD, Weill Cornell Medicine, New York, NY 10065, USA; Division of Gastroenterology and Hepatology, Department of Medicine, NewYork-Presbyterian Hospital/Weill Cornell Medical Center, New York, NY 10065, USA
| | - Wen-Bing Jin
- Jill Roberts Institute for Research in IBD, Weill Cornell Medicine, New York, NY 10065, USA
| | - Andrew Marderstein
- Jill Roberts Institute for Research in IBD, Weill Cornell Medicine, New York, NY 10065, USA
| | - Gabriela Funez-dePagnier
- Division of Gastroenterology and Hepatology, Department of Medicine, NewYork-Presbyterian Hospital/Weill Cornell Medical Center, New York, NY 10065, USA; Jill Roberts Center for IBD, NewYork-Presbyterian Hospital/Weill Cornell Medical Center, New York, NY 10065, USA
| | - Grace Maldarelli
- Jill Roberts Institute for Research in IBD, Weill Cornell Medicine, New York, NY 10065, USA; Division of Gastroenterology and Hepatology, Department of Medicine, NewYork-Presbyterian Hospital/Weill Cornell Medical Center, New York, NY 10065, USA
| | - Monica Viladomiu
- Jill Roberts Institute for Research in IBD, Weill Cornell Medicine, New York, NY 10065, USA; Division of Gastroenterology and Hepatology, Department of Medicine, NewYork-Presbyterian Hospital/Weill Cornell Medical Center, New York, NY 10065, USA
| | - Gregory Putzel
- Jill Roberts Institute for Research in IBD, Weill Cornell Medicine, New York, NY 10065, USA
| | - Wei Yang
- Jill Roberts Institute for Research in IBD, Weill Cornell Medicine, New York, NY 10065, USA; Division of Gastroenterology and Hepatology, Department of Medicine, NewYork-Presbyterian Hospital/Weill Cornell Medical Center, New York, NY 10065, USA
| | - Nancy Tran
- Division of Gastroenterology and Hepatology, Department of Medicine, NewYork-Presbyterian Hospital/Weill Cornell Medical Center, New York, NY 10065, USA; Jill Roberts Center for IBD, NewYork-Presbyterian Hospital/Weill Cornell Medical Center, New York, NY 10065, USA
| | - Grace Xiang
- Division of Gastroenterology and Hepatology, Department of Medicine, NewYork-Presbyterian Hospital/Weill Cornell Medical Center, New York, NY 10065, USA; Jill Roberts Center for IBD, NewYork-Presbyterian Hospital/Weill Cornell Medical Center, New York, NY 10065, USA
| | - Alex Grier
- Jill Roberts Institute for Research in IBD, Weill Cornell Medicine, New York, NY 10065, USA
| | - Chun-Jun Guo
- Jill Roberts Institute for Research in IBD, Weill Cornell Medicine, New York, NY 10065, USA
| | - Dana Lukin
- Division of Gastroenterology and Hepatology, Department of Medicine, NewYork-Presbyterian Hospital/Weill Cornell Medical Center, New York, NY 10065, USA; Jill Roberts Center for IBD, NewYork-Presbyterian Hospital/Weill Cornell Medical Center, New York, NY 10065, USA
| | - Lisa A Mandl
- Division of Rheumatology, Hospital for Special Surgery and Department of Medicine, NewYork-Presbyterian Hospital/Weill Cornell Medical Center, New York, NY 10065, USA
| | - Ellen J Scherl
- Division of Gastroenterology and Hepatology, Department of Medicine, NewYork-Presbyterian Hospital/Weill Cornell Medical Center, New York, NY 10065, USA; Jill Roberts Center for IBD, NewYork-Presbyterian Hospital/Weill Cornell Medical Center, New York, NY 10065, USA
| | - Randy S Longman
- Jill Roberts Institute for Research in IBD, Weill Cornell Medicine, New York, NY 10065, USA; Division of Gastroenterology and Hepatology, Department of Medicine, NewYork-Presbyterian Hospital/Weill Cornell Medical Center, New York, NY 10065, USA; Jill Roberts Center for IBD, NewYork-Presbyterian Hospital/Weill Cornell Medical Center, New York, NY 10065, USA.
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4
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Li J, Nian Y, Liu J, Yang M, Jin Y, Kang X, Xu H, Shang Z, Lin W. Identification of a Potential Antimycobacterial Drug Sensitizer Targeting a Flavin-Independent Methylenetetrahydrofolate Reductase. ACS OMEGA 2023; 8:38406-38417. [PMID: 37867661 PMCID: PMC10586308 DOI: 10.1021/acsomega.3c05021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 09/19/2023] [Indexed: 10/24/2023]
Abstract
The increasing antibiotic resistance of Mycobacterium tuberculosis and pathogenic nontuberculosis mycobacteria highlights the urgent need for new prevention and treatment strategies. Recently, the cocrystal structure of a Mycobacterium smegmatis flavin-independent 5,10-methylenetetrahydrofolate reductase (MsmMTHFR) that binds with a reduced nicotinamide adenine dinucleotide (NADH) has been well-determined, providing a structural basis for the screening of antimycobacterial leads targeting MsmMTHFR, a new enzyme involved in tetrahydrofolic acid (THF) biosynthesis. In this study, we identified compound AB131 as a promising candidate that fits well into the NADH binding pocket of MsmMTHFR through virtual screening. We discovered that AB131 and its derivatives (13 and 14) can sensitize the antimycobacterial activity of the antitubercular drug para-aminosalicyclic acid (PAS) by 2-5-fold against various species of mycobacteria. Although the compounds themselves do not exhibit any antimycobacterial activity, the high binding affinity of AB131 with MsmMTHFR or Rv2172c was evaluated by microscale thermophoresis analysis. Additionally, we predicted and validated the key residues (V115, V117, P118, and R163) of MsmMTHFR that are involved in the interaction with AB131 by using molecular docking and mutagenesis analysis. These findings offer a potential exploitable target for developing potent and specific antimycobacterial drug sensitizers.
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Affiliation(s)
- Jiacong Li
- Department
of Pathogen Biology, School of Medicine & Holistic Integrative
Medicine, Nanjing University of Chinese
Medicine, 210023 Nanjing, China
- School
of Pharmacy, Nanjing University of Chinese
Medicine, 210023 Nanjing, China
- State
Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 200237 Shanghai, China
| | - Yong Nian
- School
of Pharmacy, Nanjing University of Chinese
Medicine, 210023 Nanjing, China
| | - Jian Liu
- School
of Pharmacy, Nanjing University of Chinese
Medicine, 210023 Nanjing, China
| | - Mingxia Yang
- Department
of Pathogen Biology, School of Medicine & Holistic Integrative
Medicine, Nanjing University of Chinese
Medicine, 210023 Nanjing, China
- The
Center for Microbes, Development and Health, Institut Pasteur of Shanghai, Chinese Academy of Sciences, 200031 Shanghai, China
| | - Yuanling Jin
- Department
of Pathogen Biology, School of Medicine & Holistic Integrative
Medicine, Nanjing University of Chinese
Medicine, 210023 Nanjing, China
| | - Xiaoman Kang
- CAS
Key Laboratory of Synthetic Biology, Centre
of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, 200032 Shanghai, China
| | - Haodong Xu
- School
of Pharmacy, Nanjing University of Chinese
Medicine, 210023 Nanjing, China
| | - Zhuo Shang
- School of
Pharmaceutical Sciences, Shandong University, 250100 Jinan, China
| | - Wei Lin
- Department
of Pathogen Biology, School of Medicine & Holistic Integrative
Medicine, Nanjing University of Chinese
Medicine, 210023 Nanjing, China
- School
of Pharmacy, Nanjing University of Chinese
Medicine, 210023 Nanjing, China
- State
Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 200237 Shanghai, China
- Jiangsu
Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, 210023 Nanjing, China
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5
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Li J, Yang M, Li W, Lu C, Feng D, Shang Z, Wang C, Lin W. Structural and functional characterization of a mycobacterial methylenetetrahydrofolate reductase utilizing NADH as the exclusive cofactor. Biochem J 2023; 480:1129-1146. [PMID: 37435857 DOI: 10.1042/bcj20230138] [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: 04/11/2023] [Revised: 07/05/2023] [Accepted: 07/12/2023] [Indexed: 07/13/2023]
Abstract
5,10-Methylenetetraydrofolate reductase (MTHFR) is a key enzyme in folate metabolism. MSMEG_6649, a non-canonical MTHFR from Mycobacterium smegmatis, was previously reported as a monomeric protein lacking the flavin coenzyme. However, the structural basis for its unique flavin-independent catalytic mechanism remains poorly understood. Here, we determined the crystal structures of apo MTHFR MSMEG_6649 and its complex with NADH from M. smegmatis. Structural analysis revealed that the groove formed by the loops 4 and 5 of non-canonical MSMEG_6649 interacting with FAD was significantly larger than that of canonical MTHFR. Meanwhile, the NADH-binding site in MSMEG_6649 is highly similar to the FAD binding site in canonical MTHFR, suggesting that NADH plays the same role (immediate hydride donor for methylenetetraydrofolate) as FAD in the catalytic reaction. Using biochemical analysis, molecular modeling, and site-directed mutagenesis, the critical residues participating in the binding of NADH and the substrate 5,10-methylenetetrahydrofolate as well as the product 5-methyltetrahydrofolate were identified and validated. Taken together, this work not only provides a good starting point for understanding the potential catalytic mechanism for MSMEG_6649, but also identifies an exploitable target for the development of anti-mycobacterial drugs.
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Affiliation(s)
- Jiacong Li
- Department of Pathogen Biology, School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Mingxia Yang
- The Center for Microbes, Development and Health, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Weijia Li
- Department of Pathogen Biology, School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Chujie Lu
- Department of Pathogen Biology, School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Deyu Feng
- The Center for Microbes, Development and Health, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Zhuo Shang
- School of Pharmaceutical Sciences, Shandong University, Jinan, China
| | - Chengyuan Wang
- The Center for Microbes, Development and Health, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Wei Lin
- Department of Pathogen Biology, School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
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6
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Sah S, Varshney U. Methionyl-tRNA formyltransferase utilizes 10-formyldihydrofolate as an alternative substrate and impacts antifolate drug action. MICROBIOLOGY (READING, ENGLAND) 2023; 169. [PMID: 36745551 DOI: 10.1099/mic.0.001297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Methionyl-tRNA formyltransferase (Fmt)-mediated formylation of Met-tRNAfMet to fMet-tRNAfMet is crucial for efficient initiation of translation in bacteria and the eukaryotic organelles. Folate dehydrogenase-cyclohydrolase (FolD), a bifunctional enzyme, carries out conversion of 5,10-methylene tetrahydrofolate (5,10-CH2-THF) to 10-formyl-THF (10-CHO-THF), a metabolite utilized by Fmt as a formyl group donor. In this study, using in vivo and in vitro approaches, we show that 10-CHO-DHF may also be utilized by Fmt as an alternative substrate (formyl group donor) to formylate Met-tRNAfMet. Dihydrofolate (DHF) formed as a by-product in the in vitro assay was verified by LC-MS/MS analysis. FolD-deficient mutants and Fmt over-expressing strains were more sensitive to trimethoprim (TMP) than the ∆fmt strain, suggesting that the domino effect of TMP leads to inhibition of protein synthesis and strain growth. Antifolate treatment to Escherichia coli showed a decrease in the reduced folate species (THF, 5,10-CH2-THF, 5-CH3-THF, 5,10-CH+-THF and 5-CHO-THF) and increase in the oxidized folate species (folic acid and DHF). In cells, 10-CHO-DHF and 10-CHO-folic acid were enriched in the stationary phase. This suggests that 10-CHO-DHF is a bioactive metabolite in the folate pathway for generating other folate intermediates and fMet-tRNAfMet.
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Affiliation(s)
- Shivjee Sah
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India
| | - Umesh Varshney
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India
- Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, 560064, India
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7
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Khan SR, Kuzminov A. Thymine-starvation-induced chromosomal fragmentation is not required for thymineless death in Escherichia coli. Mol Microbiol 2022; 117:1138-1155. [PMID: 35324030 DOI: 10.1111/mmi.14897] [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: 11/29/2021] [Revised: 03/15/2022] [Accepted: 03/16/2022] [Indexed: 11/29/2022]
Abstract
Thymine or thymidine starvation induces robust chromosomal fragmentation in E. coli thyA deoCABD mutants, and is proposed to be the cause of thymineless death (TLD). However, fragmentation kinetics challenges the idea that fragmentation causes TLD, by peaking before the onset of TLD and disappearing by the time TLD accelerates. Quantity and kinetics of fragmentation also stays unchanged in hyper-TLD-exhibiting recBCD mutant, making its faster and deeper TLD independent of fragmentation as well. Elimination of fragmentation without affecting cellular metabolism did not abolish TLD in the thyA mutant, but reduced early TLD in the thyA recBCD mutant, suggesting replication-dependent, but undetectable by pulsed field gel, double-strand breaks contributed to TLD. Chromosomal fragmentation, but not TLD, was eliminated in both the thyA and thyA recBCD mutants harboring deoCABD operon. Expression of a single gene, deoA, encoding thymidine phosphorylase, was sufficient to abolish fragmentation, suggesting thymidine-to-thymine interconversion during T-starvation being a key factor. Overall, this study reveals that chromosomal fragmentation, a direct consequence of T-starvation, is either dispensable or redundant for the overall TLD pathology, including hyper-TLD in the recBCD mutant. Replication forks, unlike chromosomal fragmentation, may provide minor contribution to TLD, but only in the repair-deficient thyA deoCABD recBCD mutant.
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Affiliation(s)
- Sharik R Khan
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Andrei Kuzminov
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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8
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Mahwish N, Bairy LK, Srinivasamurthy S. Antivitamins: A Silver Lining in the Era of Antimicrobial Resistance. J Pharmacol Pharmacother 2022. [DOI: 10.1177/0976500x221080378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Antivitamins are compounds that negate the biological effects of vitamins. They have been successfully exploited for the development of various classes of drugs. In the early 19th century, the antifolate prontosil was developed for the treatment of puerperal fever. Since then, numerous other antifolates have been used to treat a wide range of infections. Antifolates, such as methotrexate, are potent anticancer agents and antivitamin K, such as warfarin, are used as anticoagulants. Despite several years of research, most antivitamin-based drugs are limited to vitamin K and B9, and the development of antagonists for other vitamins is still in the nascent stage. In the era of antimicrobial resistance, antivitamins can be considered as a promising alternative to develop newer antimicrobials and are worth exploring further. This review discusses key antivitamins at different stages of development which have potential utility as antibiotic drug candidates. The summary of studies of antivitamins in clinical development is also narrated.
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Affiliation(s)
- Nayesha Mahwish
- Department of Pharmacology, Ras Al Khaimah College of Medical Sciences (RAKCOMS), RAK Medical and Health Sciences University Ras Al Khaimah (RAKMHSU), Ras Al Khaimah, United Arab Emirates
| | - Laxminarayana Kurady Bairy
- Department of Pharmacology, Ras Al Khaimah College of Medical Sciences (RAKCOMS), RAK Medical and Health Sciences University Ras Al Khaimah (RAKMHSU), Ras Al Khaimah, United Arab Emirates
| | - Sureshkumar Srinivasamurthy
- Department of Pharmacology, Ras Al Khaimah College of Medical Sciences (RAKCOMS), RAK Medical and Health Sciences University Ras Al Khaimah (RAKMHSU), Ras Al Khaimah, United Arab Emirates
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9
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Affiliation(s)
- Bernhard Kräutler
- Institute of Organic Chemistry and Centre of Molecular Biosciences, University of Innsbruck, Innsbruck, Austria.
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10
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Ruetz M, Koutmos M, Kräutler B. Antivitamins B 12: Synthesis and application as inhibitory ligand of the B 12-tailoring enzyme CblC. Methods Enzymol 2022; 668:157-178. [PMID: 35589193 DOI: 10.1016/bs.mie.2021.12.016] [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] [Indexed: 10/19/2022]
Abstract
Antivitamins B12 are non-natural corrinoids that have been designed to counteract the metabolic effects of vitamin B12 and related cobalamins (Cbls) in humans and other mammals. A basic structure- and reactivity-based concept typifies antivitamins B12 as close structural mimics of vitamin B12 that are not transformed by the cellular metabolism into organometallic B12-cofactors. Antivitamins B12 have the correct structure for efficient take-up and transport via the natural mammalian pathway for cobalamin assimilation. Thus they can be delivered to every cell in the body, where they are proposed to target and inhibit the Cbl tailoring enzyme CblC. Antivitamins B12 may be specifically inert Cbls or isostructural Cbl-analogues that carry a metal centre other than a cobalt-ion. The syntheses of two antivitamins B12 are detailed here, as are biochemical and crystallographic studies that provide insights into the crucial binding interactions of Cbl-based antivitamins B12 with the human B12-tailoring enzyme CblC. This key enzyme binds genuine antivitamins B12 as inert substrate mimics and enzyme inhibitors, effectively repressing the metabolic generation of the B12-cofactors. Hence, antivitamins B12 induce the diagnostic symptoms of (functional) B12-deficiency, as observed in healthy laboratory mice.
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Affiliation(s)
- Markus Ruetz
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, United States
| | - Markos Koutmos
- Department of Chemistry, Program in Biophysics, Program in Chemical Biology, University of Michigan, Ann Arbor, MI, United States.
| | - Bernhard Kräutler
- Institute of Organic Chemistry and Center of Molecular Biosciences, University of Innsbruck, Innsbruck, Austria.
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11
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Decreased methylenetetrahydrofolate reductase activity leads to increased sensitivity to para-aminosalicylic acid in Mycobacterium tuberculosis. Antimicrob Agents Chemother 2021; 66:e0146521. [PMID: 34780266 PMCID: PMC8765232 DOI: 10.1128/aac.01465-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Tuberculosis (TB), caused by Mycobacterium tuberculosis, is one of the most fatal diseases in the world. Methylenetetrahydrofolate reductase (MTHFR) catalyzes the production of 5-methyltetrahydrofolate (5-CH3-THF), which is required for the de novo biosynthesis of methionine in bacteria. Here, we identified Rv2172c as an MTHFR in M. tuberculosis through in vitro and in vivo analyses and determined that the protein is essential for the in vitro growth of the bacterium. Subsequently, we constructed rv2172c R159N and L214A mutants in M. tuberculosis and found that these mutants were more sensitive to the antifolates para-aminosalicylic acid (PAS) and sulfamethoxazole (SMX). Combining biochemical and genetic methods, we found that rv2172c R159N or L214A mutation impaired methionine production, leading to increased susceptibility of M. tuberculosis to PAS, which was largely restored by adding exogenous methionine. Moreover, overexpression of rv2172c in M. tuberculosis could increase methionine production and lead to PAS resistance. This research is the first to identify an MTHFR in M. tuberculosis and reveals that the activity of this enzyme is associated with susceptibility to antifolates. These findings have particular value for antitubercular drug design for the treatment of drug-resistant TB.
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12
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Abstract
To resolve the growing problem of drug resistance in the treatment of bacterial and fungal pathogens, specific cellular targets and pathways can be used as targets for new antimicrobial agents. Endogenous riboflavin biosynthesis is a conserved pathway that exists in most bacteria and fungi. In this review, the roles of endogenous and exogenous riboflavin in infectious disease as well as several antibacterial agents, which act as analogues of the riboflavin biosynthesis pathway, are summarized. In addition, the effects of exogenous riboflavin on immune cells, cytokines, and heat shock proteins are described. Moreover, the immune response of endogenous riboflavin metabolites in infectious diseases, recognized by MHC-related protein-1, and then presented to mucosal associated invariant T cells, is highlighted. This information will provide a strategy to identify novel drug targets as well as highlight the possible clinical use of riboflavin.
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Affiliation(s)
- Junwen Lei
- Molecular Biotechnology Platform, Public Center of Experimental Technology, School of Basic Medical Sciences, Southwest Medical University, Luzhou People's Republic of China
| | - Caiyan Xin
- Molecular Biotechnology Platform, Public Center of Experimental Technology, School of Basic Medical Sciences, Southwest Medical University, Luzhou People's Republic of China
| | - Wei Xiao
- Molecular Biotechnology Platform, Public Center of Experimental Technology, School of Basic Medical Sciences, Southwest Medical University, Luzhou People's Republic of China
| | - Wenbi Chen
- Molecular Biotechnology Platform, Public Center of Experimental Technology, School of Basic Medical Sciences, Southwest Medical University, Luzhou People's Republic of China
| | - Zhangyong Song
- Molecular Biotechnology Platform, Public Center of Experimental Technology, School of Basic Medical Sciences, Southwest Medical University, Luzhou People's Republic of China
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13
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Shi H, Li T, Xu J, Yu J, Yang S, Zhang XE, Tao S, Gu J, Deng JY. MgrB Inactivation Confers Trimethoprim Resistance in Escherichia coli. Front Microbiol 2021; 12:682205. [PMID: 34394028 PMCID: PMC8355897 DOI: 10.3389/fmicb.2021.682205] [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: 03/18/2021] [Accepted: 06/30/2021] [Indexed: 11/22/2022] Open
Abstract
After several decades of use, trimethoprim (TMP) remains one of the key access antimicrobial drugs listed by the World Health Organization. To circumvent the problem of trimethoprim resistance worldwide, a better understanding of drug-resistance mechanisms is required. In this study, we screened the single-gene knockout library of Escherichia coli, and identified mgrB and other several genes involved in trimethoprim resistance. Subsequent comparative transcriptional analysis between ΔmgrB and the wild-type strain showed that expression levels of phoP, phoQ, and folA were significantly upregulated in ΔmgrB. Further deleting phoP or phoQ could partially restore trimethoprim sensitivity to ΔmgrB, and co-overexpression of phoP/Q caused TMP resistance, suggesting the involvement of PhoP/Q in trimethoprim resistance. Correspondingly, MgrB and PhoP were shown to be able to modulated folA expression in vivo. After that, efforts were made to test if PhoP could directly modulate the expression of folA. Though phosphorylated PhoP could bind to the promotor region of folA in vitro, the former only provided a weak protection on the latter as shown by the DNA footprinting assay. In addition, deleting the deduced PhoP box in ΔmgrB could only slightly reverse the TMP resistance phenotype, suggesting that it is less likely for PhoP to directly modulate the transcription of folA. Taken together, our data suggested that, in E. coli, MgrB affects susceptibility to trimethoprim by modulating the expression of folA with the involvement of PhoP/Q. This work broadens our understanding of the regulation of folate metabolism and the mechanisms of TMP resistance in bacteria.
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Affiliation(s)
- Hongmei Shi
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Ting Li
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jintian Xu
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jifang Yu
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Shanshan Yang
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xian-En Zhang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Shengce Tao
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
| | - Jing Gu
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Jiao-Yu Deng
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.,Guangdong Province Key Laboratory of TB Systems Biology and Translational Medicine, Foshan, China
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14
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Cobalamin is present in cells of non-tuberculous mycobacteria, but not in Mycobacterium tuberculosis. Sci Rep 2021; 11:12267. [PMID: 34112827 PMCID: PMC8192938 DOI: 10.1038/s41598-021-91430-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 05/26/2021] [Indexed: 01/22/2023] Open
Abstract
Cobalamin (vitamin B12) is a structurally complex molecule that acts as a cofactor for enzymes and regulates gene expression through so-called riboswitches. The existing literature on the vitamin B12 synthesis capacity in Mycobacterium tuberculosis is ambiguous, while in non-tuberculous mycobacteria (NTM) is rather marginal. Here we present the results of our investigation into the occurrence of vitamin B12 in mycobacteria. For detection purposes, immunoassay methods were applied to cell lysates of NTM and M. tuberculosis clinical and laboratory strains grown under different conditions. We show that whereas vitamin B12 is present in cells of various NTM species, it cannot be evidenced in strains of differently cultured M. tuberculosis, even though the genes responsible for vitamin B12 synthesis are actively expressed based on RNA-Seq data. In summary, we conclude that the production of vitamin B12 does occur in mycobacteria, with the likely exception of M. tuberculosis. Our results provide direct evidence of vitamin B12 synthesis in a clinically important group of bacteria.
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15
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Tsybizova A, Brenig C, Kieninger C, Kräutler B, Chen P. Surprising Homolytic Gas Phase Co-C Bond Dissociation Energies of Organometallic Aryl-Cobinamides Reveal Notable Non-Bonded Intramolecular Interactions. Chemistry 2021; 27:7252-7264. [PMID: 33560580 PMCID: PMC8251903 DOI: 10.1002/chem.202004589] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Indexed: 01/12/2023]
Abstract
Aryl-cobalamins are a new class of organometallic structural mimics of vitamin B12 designed as potential 'antivitamins B12 '. Here, the first cationic aryl-cobinamides are described, which were synthesized using the newly developed diaryl-iodonium method. The aryl-cobinamides were obtained as pairs of organometallic coordination isomers, the stereo-structure of which was unambiguously assigned based on homo- and heteronuclear NMR spectra. The availability of isomers with axial attachment of the aryl group, either at the 'beta' or at the 'alpha' face of the cobalt-center allowed for an unprecedented comparison of the organometallic reactivity of such pairs. The homolytic gas-phase bond dissociation energies (BDEs) of the coordination-isomeric phenyl- and 4-ethylphenyl-cobinamides were determined by ESI-MS threshold CID experiments, furnishing (Co-Csp 2 )-BDEs of 38.4 and 40.6 kcal mol-1 , respectively, for the two β-isomers, and the larger BDEs of 46.6 and 43.8 kcal mol-1 for the corresponding α-isomers. Surprisingly, the observed (Co-Csp 2 )-BDEs of the Coβ -aryl-cobinamides were smaller than the (Co-Csp 3 )-BDE of Coβ -methyl-cobinamide. DFT studies and the magnitudes of the experimental (Co-Csp 2 )-BDEs revealed relevant contributions of non-bonded interactions in aryl-cobinamides, notably steric strain between the aryl and the cobalt-corrin moieties and non-bonded interactions with and among the peripheral sidechains.
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Affiliation(s)
- Alexandra Tsybizova
- Laboratorium für Organische ChemieDepartment of Chemistry and Applied BiosciencesETH ZürichZürichSwitzerland
| | - Christopher Brenig
- Institute of Organic Chemistry & Center of Molecular BiosciencesUniversity of InnsbruckInnsbruckAustria
| | - Christoph Kieninger
- Institute of Organic Chemistry & Center of Molecular BiosciencesUniversity of InnsbruckInnsbruckAustria
| | - Bernhard Kräutler
- Institute of Organic Chemistry & Center of Molecular BiosciencesUniversity of InnsbruckInnsbruckAustria
| | - Peter Chen
- Laboratorium für Organische ChemieDepartment of Chemistry and Applied BiosciencesETH ZürichZürichSwitzerland
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16
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The Pup-Proteasome System Protects Mycobacteria from Antimicrobial Antifolates. Antimicrob Agents Chemother 2021; 65:AAC.01967-20. [PMID: 33468462 DOI: 10.1128/aac.01967-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 12/30/2020] [Indexed: 12/21/2022] Open
Abstract
Protein turnover via the Pup-proteasome system (PPS) is essential for nitric oxide resistance and virulence of Mycobacterium tuberculosis, the causative agent of tuberculosis. Our study revealed components of PPS as novel determinants of intrinsic antifolate resistance in both M. tuberculosis and nonpathogenic M. smegmatis The lack of expression of the prokaryotic ubiquitin-like protein (Pup) or the ligase, PafA, responsible for ligating Pup to its protein targets, enhanced antifolate susceptibility in M. smegmatis Cross-species expression of M. tuberculosis homologs restored wild-type resistance to M. smegmatis proteasomal mutants. Targeted deletion of prcA and prcB, encoding the structural components of the PPS proteolytic core, similarly resulted in reduced antifolate resistance. Furthermore, sulfonamides were synergistic with acidified nitrite, and the synergy against mycobacteria was enhanced in the absence of proteasomal activity. In M. tuberculosis, targeted mutagenesis followed by genetic complementation of mpa, encoding the regulatory subunit responsible for translocating pupylated proteins to the proteolytic core, demonstrated a similar function of PPS in antifolate resistance. The overexpression of dihydrofolate reductase, responsible for the reduction of dihydrofolate to tetrahydrofolate, or disruption of the Lonely Guy gene, responsible for PPS-controlled production of cytokinins, abolished PPS-mediated antifolate sensitivity. Together, our results show that PPS protects mycobacteria from antimicrobial antifolates via regulating both folate reduction and cytokinin production.
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17
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De Novo Cobalamin Biosynthesis, Transport, and Assimilation and Cobalamin-Mediated Regulation of Methionine Biosynthesis in Mycobacterium smegmatis. J Bacteriol 2021; 203:JB.00620-20. [PMID: 33468593 PMCID: PMC8088520 DOI: 10.1128/jb.00620-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Accepted: 01/08/2021] [Indexed: 02/07/2023] Open
Abstract
Alterations in cobalamin-dependent metabolism have marked the evolution of Mycobacterium tuberculosis into a human pathogen. However, the role(s) of cobalamin in mycobacterial physiology remain poorly understood. Cobalamin is an essential cofactor in all domains of life, yet its biosynthesis is restricted to some bacteria and archaea. Mycobacterium smegmatis, an environmental saprophyte frequently used as surrogate for the obligate human pathogen M. tuberculosis, carries approximately 30 genes predicted to be involved in de novo cobalamin biosynthesis. M. smegmatis also encodes multiple cobalamin-dependent enzymes, including MetH, a methionine synthase that catalyzes the final reaction in methionine biosynthesis. In addition to metH, M. smegmatis possesses a cobalamin-independent methionine synthase, metE, suggesting that enzyme use—MetH versus MetE—is regulated by cobalamin availability. Consistent with this notion, we previously described a cobalamin-sensing riboswitch controlling metE expression in M. tuberculosis. Here, we apply a targeted mass spectrometry-based approach to confirm de novo cobalamin biosynthesis in M. smegmatis during aerobic growth in vitro. We also demonstrate that M. smegmatis can transport and assimilate exogenous cyanocobalamin (CNCbl; also known as vitamin B12) and its precursor, dicyanocobinamide ([CN]2Cbi). However, the uptake of CNCbl and (CN)2Cbi in this organism is restricted and seems dependent on the conditional essentiality of the cobalamin-dependent methionine synthase. Using gene and protein expression analyses combined with single-cell growth kinetics and live-cell time-lapse microscopy, we show that transcription and translation of metE are strongly attenuated by endogenous cobalamin. These results support the inference that metH essentiality in M. smegmatis results from riboswitch-mediated repression of MetE expression. Moreover, differences observed in cobalamin-dependent metabolism between M. smegmatis and M. tuberculosis provide some insight into the selective pressures which might have shaped mycobacterial metabolism for pathogenicity. IMPORTANCE Alterations in cobalamin-dependent metabolism have marked the evolution of Mycobacterium tuberculosis into a human pathogen. However, the role(s) of cobalamin in mycobacterial physiology remains poorly understood. Using the nonpathogenic saprophyte M. smegmatis, we investigated the production of cobalamin, transport and assimilation of cobalamin precursors, and the role of cobalamin in regulating methionine biosynthesis. We confirm constitutive de novo cobalamin biosynthesis in M. smegmatis, in contrast with M. tuberculosis, which appears to lack de novo cobalamin biosynthetic capacity. We also show that uptake of cyanocobalamin (vitamin B12) and its precursors is restricted in M. smegmatis, apparently depending on the cofactor requirements of the cobalamin-dependent methionine synthase. These observations establish M. smegmatis as an informative foil to elucidate key metabolic adaptations enabling mycobacterial pathogenicity.
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18
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Abstract
The recently delineated structure- and reactivity-based concept of antivitamins B12 has begun to bear fruit by the generation, and study, of a range of such B12 -dummies, either vitamin B12 -derived, or transition metal analogues that also represent potential antivitamins B12 or specific B12 -antimetabolites. As reviewed here, this has opened up new research avenues in organometallic B12 -chemistry and bioinorganic coordination chemistry. Exploratory studies with antivitamins B12 have, furthermore, revealed some of their potential, as pharmacologically interesting compounds, for inducing B12 -deficiency in a range of organisms, from hospital resistant bacteria to laboratory mice. The derived capacity of antivitamins B12 to induce functional B12 -deficiency in mammalian cells and organs also suggest their valuable potential as growth inhibitors of cancerous human and animal cells.
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Affiliation(s)
- Bernhard Kräutler
- Institute of Organic Chemistry and Center for Molecular Biosciences (CMBI)University of Innsbruck6020InnsbruckAustria
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19
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Czubat B, Minias A, Brzostek A, Żaczek A, Struś K, Zakrzewska-Czerwińska J, Dziadek J. Functional Disassociation Between the Protein Domains of MSMEG_4305 of Mycolicibacterium smegmatis ( Mycobacterium smegmatis) in vivo. Front Microbiol 2020; 11:2008. [PMID: 32973726 PMCID: PMC7466739 DOI: 10.3389/fmicb.2020.02008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 07/29/2020] [Indexed: 12/02/2022] Open
Abstract
MSMEG_4305 is a two-domain protein of Mycolicibacterium smegmatis (Mycobacterium smegmatis) (Mycolicibacterium smegmatis). The N-terminal domain of MSMEG_4305 encodes an RNase H type I. The C-terminal domain is a presumed CobC, predicted to be involved in the aerobic synthesis of vitamin B12. Both domains reach their maximum at distinct pH, approximately 8.5 and 4.5, respectively. The presence of the CobC domain influenced RNase activity in vitro in homolog Rv2228c. Here, we analyzed the role of MSMEG_4305 in vitamin B12 synthesis and the functional association between both domains in vivo in M. smegmatis. We used knock-out mutant of M. smegmatis, deficient in MSMEG_4305. Whole-cell lysates of the mutants strain contained a lower concentration of vitamin B12, as it determined with immunoenzimatic assay. We observed growth deficits, related to vitamin B12 production, on media containing sulfamethazine and propionate. Removal of the CobC domain of MSMEG_4305 in ΔrnhA background hardly affected the growth rate of M. smegmatis in vivo. The strain carrying truncation showed no fitness deficit in the competitive assay and it did not show increased level of RNA/DNA hybrids in its genome. We show that homologs of MSMEG_4305 are present only in the Actinomycetales phylogenetic branch (according to the old classification system). The domains of MSMEG_4305 homologs accumulate mutations at a different rate, while the linker region is highly variable. We conclude that MSMEG_4305 is a multidomain protein that most probably was fixed in the phylogenetic tree of life due to genetic drift.
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Affiliation(s)
- Bożena Czubat
- Department of Experimental and Clinical Pharmacology, University of Rzeszów, Rzeszów, Poland.,Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, łLódź, Poland
| | - Alina Minias
- Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, łLódź, Poland
| | - Anna Brzostek
- Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, łLódź, Poland
| | - Anna Żaczek
- Institute of Medical Sciences, Medical College of Rzeszów University, Rzeszów, Poland
| | - Katarzyna Struś
- Department of Bioenergetics, Food Analysis and Microbiology, Institute of Food Technology and Nutrition, University of Rzeszów, Rzeszów, Poland
| | | | - Jarosław Dziadek
- Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, łLódź, Poland
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20
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Monomeric NADH-Oxidizing Methylenetetrahydrofolate Reductases from Mycobacterium smegmatis Lack Flavin Coenzyme. J Bacteriol 2020; 202:JB.00709-19. [PMID: 32253341 DOI: 10.1128/jb.00709-19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 03/27/2020] [Indexed: 01/16/2023] Open
Abstract
5,10-Methylenetetrahydrofolate reductase (MetF/MTHFR) is an essential enzyme in one-carbon metabolism for de novo biosynthesis of methionine. Our in vivo and in vitro analyses of MSMEG_6664/MSMEI_6484, annotated as putative MTHFR in Mycobacterium smegmatis, failed to reveal their function as MTHFRs. However, we identified two hypothetical proteins, MSMEG_6596 and MSMEG_6649, as noncanonical MTHFRs in the bacterium. MTHFRs are known to be oligomeric flavoproteins. Both MSMEG_6596 and MSMEG_6649 are monomeric proteins and lack flavin coenzymes. In vitro, the catalytic efficiency (k cat/Km ) of MSMEG_6596 (MTHFR1) for 5,10-CH2-THF and NADH was ∼13.5- and 15.3-fold higher than that of MSMEG_6649 (MTHFR2). Thus, MSMEG_6596 is the major MTHFR. This interpretation was further supported by better rescue of the E. coli Δmthfr strain by MTHFR1 than by MTHFR2. As identified by liquid chromatography-tandem mass spectrometry, the product of MTHFR1- or MTHFR2-catalyzed reactions was 5-CH3-THF. The M. smegmatis Δmsmeg_6596 strain was partially auxotrophic for methionine and grew only poorly without methionine or without being complemented with a functional copy of MTHFR1 or MTHFR2. Furthermore, the Δmsmeg_6596 strain was more sensitive to folate pathway inhibitors (sulfachloropyridazine, p-aminosalicylic acid, sulfamethoxazole, and trimethoprim). The studies reveal that MTHFR1 and MTHFR2 are two noncanonical MTHFR proteins that are monomeric and lack flavin coenzyme. Both MTHFR1 and MTHFR2 are involved in de novo methionine biosynthesis and required for antifolate resistance in mycobacteria.IMPORTANCE MTHFR/MetF is an essential enzyme in a one-carbon metabolic pathway for de novo biosynthesis of methionine. MTHFRs are known to be oligomeric flavoproteins. Our in vivo and in vitro analyses of Mycobacterium smegmatis MSMEG_6664/MSMEI_6484, annotated as putative MTHFR, failed to reveal their function as MTHFRs. However, we identified two of the hypothetical proteins, MSMEG_6596 and MSMEG_6649, as MTHFR1 and MTHFR2, respectively. Interestingly, both MTHFRs are monomeric and lack flavin coenzymes. M. smegmatis deleted for the major mthfr (mthfr1) was partially auxotroph for methionine and more sensitive to folate pathway inhibitors (sulfachloropyridazine, para-aminosalicylic acid, sulfamethoxazole, and trimethoprim). The studies reveal that MTHFR1 and MTHFR2 are novel MTHFRs involved in de novo methionine biosynthesis and required for antifolate resistance in mycobacteria.
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21
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Salerno EV, Miller NA, Konar A, Salchner R, Kieninger C, Wurst K, Spears KG, Kräutler B, Sension RJ. Exceptional Photochemical Stability of the Co-C Bond of Alkynyl Cobalamins, Potential Antivitamins B 12 and Core Elements of B 12-Based Biological Vectors. Inorg Chem 2020; 59:6422-6431. [PMID: 32311266 PMCID: PMC7201400 DOI: 10.1021/acs.inorgchem.0c00453] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
![]()
Alkynylcorrinoids
are a class of organometallic B12 derivatives,
recently rediscovered for use as antivitamins B12 and as
core components of B12-based biological vectors. They feature
exceptional photochemical and thermal stability of their characteristic
extra-short Co–C bond. We describe here the synthesis and structure
of 3-hydroxypropynylcobalamin (HOPryCbl) and photochemical experiments
with HOPryCbl, as well as of the related alkynylcobalamins: phenylethynylcobalamin
and difluoro-phenylethynylcobalamin. Ultrafast spectroscopic studies
of the excited state dynamics and mechanism for ground state recovery
demonstrate that the Co–C bond of alkynylcobalamins is stable,
with the Co–N bond and ring deformations mediating internal
conversion and ground state recovery within 100 ps. These studies
provide insights required for the rational design of photostable or
photolabile B12-based cellular vectors. Most alkylcobalamins are photolabile; in contrast, alkynylcobalamins
are photostable. Through time-resolved measurements, we demonstrate
for three alkynylcobalamins that the Co−C bond is stable (i.e.
“locked”), while expansion of the Co−N axial
bond (which is “unlocked”) and ring deformations mediate
internal conversion and ground state recovery within 100 ps. The barrier
for ground state recovery is independent of the R group on the alkynyl
ligand.
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Affiliation(s)
- Elvin V Salerno
- Department of Chemistry, University of Michigan, 930 N University Ave. Ann Arbor, Michigan 48109-1055, United States
| | - Nicholas A Miller
- Department of Chemistry, University of Michigan, 930 N University Ave. Ann Arbor, Michigan 48109-1055, United States
| | - Arkaprabha Konar
- Department of Physics, University of Michigan, 450 Church Street, Ann Arbor, Michigan 48109-1040, United States
| | - Robert Salchner
- Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
| | - Christoph Kieninger
- Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
| | - Klaus Wurst
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
| | - Kenneth G Spears
- Department of Chemistry, University of Michigan, 930 N University Ave. Ann Arbor, Michigan 48109-1055, United States
| | - Bernhard Kräutler
- Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
| | - Roseanne J Sension
- Department of Chemistry, University of Michigan, 930 N University Ave. Ann Arbor, Michigan 48109-1055, United States.,Department of Physics, University of Michigan, 450 Church Street, Ann Arbor, Michigan 48109-1040, United States.,Biophysics, University of Michigan, 930 N University Ave. Ann Arbor, Michigan 48109-1055, United States
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22
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Minias A, Minias P, Czubat B, Dziadek J. Purifying Selective Pressure Suggests the Functionality of a Vitamin B12 Biosynthesis Pathway in a Global Population of Mycobacterium tuberculosis. Genome Biol Evol 2019; 10:2326-2337. [PMID: 30060031 PMCID: PMC6363050 DOI: 10.1093/gbe/evy153] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/27/2018] [Indexed: 12/20/2022] Open
Abstract
Mycobacterium tuberculosis is one of the deadliest and most challenging pathogens to study in current microbiological research. One of the issues that remains to be resolved is the importance of cobalamin in the metabolism of M. tuberculosis. The functionality of a vitamin B12 biosynthesis pathway in M. tuberculosis is under dispute, and the ability of this pathogen to scavenge vitamin B12 from the host is unknown. Here, we quantified the ratios of nonsynonymous and synonymous nucleotide substitution rates (dN/dS) in the genes involved in vitamin B12 biosynthesis and transport and in genes encoding cobalamin-dependent enzymes in nearly four thousand strains of M. tuberculosis. We showed that purifying selection is the dominant force acting on cobalamin-related genes at the levels of individual codons, genes and groups of genes. We conclude that cobalamin-related genes may not be essential but are adaptive for M. tuberculosis in clinical settings. Furthermore, the cobalamin biosynthesis pathway is likely to be functional in this species.
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Affiliation(s)
- Alina Minias
- Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, Łódź, Poland
| | - Piotr Minias
- Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental Protection University of Łódź, Łódź, Poland
| | - Bożena Czubat
- Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, Łódź, Poland.,Department of Biochemistry and Cell Biology, Faculty of Biology and Agriculture, University of Rzeszów, Rzeszów, Poland
| | - Jarosław Dziadek
- Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, Łódź, Poland
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23
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Thymineless Death in Escherichia coli Is Unaffected by Chromosomal Replication Complexity. J Bacteriol 2019; 201:JB.00797-18. [PMID: 30745374 DOI: 10.1128/jb.00797-18] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 02/06/2019] [Indexed: 11/20/2022] Open
Abstract
Thymineless death (TLD) is a rapid loss of viability of unclear mechanism in cultures of thyA mutants starved for thymine/thymidine (T starvation). It is accepted that T starvation repeatedly breaks replication forks, while recombinational repair restores them, but when the resulting futile breakage-repair cycle affects the small replication bubbles at oriC, the origin is degraded, killing the cell. Indeed, cells with increased chromosomal replication complexity (CRC), expressed as an elevated origin/terminus (ori/ter) ratio, die more extensively during TLD. Here we tested this logic by elevating the CRC in Escherichia coli thyA mutants before T starvation, anticipating exaggerated TLD. Unexpectedly, TLD remained unaffected by a CRC increase to either the natural limit (ori/ter ratio, ∼6) or the functional limit (ori/ter ratio, ∼16). Moreover, when we forced the CRC over the functional limit (ori/ter ratio, ∼30), TLD lessened. Thus, prior overinitiation does not sensitize cells to TLD. In contradiction with the published results, even blocking new replication initiations by the dnaA(Ts) defect at 42°C fails to prevent TLD. Using the thyA dnaA(Ts) mutant in a new T starvation protocol that excludes new initiations, we show that at 42°C, the same degree of TLD still occurs when chromosomes are demonstrably nonreplicating. Remarkably, 80% of the chromosomal DNA in these nonreplicating T-starved cells is still lost, by an unclear mechanism.IMPORTANCE Thymineless death kills cells of any type and is used in anticancer and antimicrobial treatments. We tested the idea that the more replication forks there are in the chromosome during growth, the more extensive the resulting thymineless death. We varied the number of replication forks in the Escherichia coli chromosome, as measured by the origin-to-terminus ratio, ranging it from the normal 2 to 60, and even completely eliminated replication forks in the nonreplicating chromosomes (ori/ter ratio = 1). Unexpectedly, we found that thymineless death is unaffected by the intensity of replication or by its complete absence; we also found that even nonreplicating chromosomes still disappear during thymine starvation. We conclude that thymineless death can kill E. coli independently of chromosomal replication.
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24
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Yang SS, Hu YB, Wang XD, Gao YR, Li K, Zhang XE, Chen SY, Zhang TY, Gu J, Deng JY. Deletion of sigB Causes Increased Sensitivity to para-Aminosalicylic Acid and Sulfamethoxazole in Mycobacterium tuberculosis. Antimicrob Agents Chemother 2017; 61:e00551-17. [PMID: 28717039 PMCID: PMC5610497 DOI: 10.1128/aac.00551-17] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 07/09/2017] [Indexed: 12/18/2022] Open
Abstract
Although the de novo folate biosynthesis pathway has been well studied in bacteria, little is known about its regulation. In the present study, the sigB gene in Mycobacterium tuberculosis was deleted. Subsequent drug susceptibility tests revealed that the M. tuberculosis ΔsigB strain was more sensitive to para-aminosalicylic acid (PAS) and sulfamethoxazole. Comparative transcriptional analysis was performed, and downregulation of pabB was observed in the ΔsigB strain, which was further verified by a quantitative reverse transcription-PCR and Western blot assay. Then, the production levels of para-aminobenzoic acid (pABA) were compared between the sigB deletion mutant and wild-type strain, and the results showed that sigB deletion resulted in decreased production of pABA. In addition, SigB was able to recognize the promoter of pabB in vitro Furthermore, we found that deleting pabC also caused increased susceptibility to PAS. Taken together, our data revealed that, in M. tuberculosis, sigB affects susceptibility to antifolates through multiple ways, primarily by regulating the expression of pabB To our knowledge, this is the first report showing that SigB modulates pABA biosynthesis and thus affecting susceptibility to antifolates, which broadens our understanding of the regulation of bacterial folate metabolism and mechanisms of susceptibility to antifolates.
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Affiliation(s)
- Shan-Shan Yang
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yang-Bo Hu
- Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Xu-De Wang
- School of Stomatology and Medicine, Foshan University, Foshan, China
| | - Yun-Rong Gao
- The Joint Center of Translational Precision Medicine, Guangzhou Institute of Pediatrics, Guangzhou Women and Children Medical Center, Guangzhou, China
| | - Kun Li
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Xian-En Zhang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Shi-Yun Chen
- Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Tian-Yu Zhang
- University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Jing Gu
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Jiao-Yu Deng
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- Guangdong Province Key Laboratory of TB Systems Biology and Translational Medicine, Foshan, China
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25
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Brenig C, Ruetz M, Kieninger C, Wurst K, Kräutler B. Alpha- and Beta-Diastereoisomers of Phenylcobalamin from Cobalt-Arylation with Diphenyliodonium Chloride. Chemistry 2017; 23:9726-9731. [PMID: 28557054 DOI: 10.1002/chem.201701514] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Indexed: 11/07/2022]
Abstract
Organometallic aryl-cobalamins are B12 -derivatives featuring properties of potential 'B12 antivitamins'. Herein, we describe a new method for the preparation of aryl-cobalamins using versatile diaryliodonium salts as arylation agents. Formate or sodium borohydride reduction of aquocobalamin in presence of diphenyliodonium chloride furnished Coβ -phenyl-cobalamin PhCbl in a roughly 3:1 to 1:1 ratio with its coordination isomer αPhCbl, a first representative 'base-off' Coα -aryl-cobalamin. The new structures were secured by detailed spectroscopic analysis, supplemented by an X-ray crystal structure analysis of PhCbl. Both types of coordination isomers of the aryl-cobalamins promise to be useful molecular tools in biomedical and biological studies.
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Affiliation(s)
- Christopher Brenig
- Institute of Organic Chemistry and Centre of Molecular Biosciences, University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria
| | - Markus Ruetz
- Institute of Organic Chemistry and Centre of Molecular Biosciences, University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria
| | - Christoph Kieninger
- Institute of Organic Chemistry and Centre of Molecular Biosciences, University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria
| | - Klaus Wurst
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria
| | - Bernhard Kräutler
- Institute of Organic Chemistry and Centre of Molecular Biosciences, University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria
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26
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Ruetz M, Shanmuganathan A, Gherasim C, Karasik A, Salchner R, Kieninger C, Wurst K, Banerjee R, Koutmos M, Kräutler B. Inhibierung des humanen B12-verarbeitenden Enzyms CblC durch Antivitamine B12- Kristallstruktur des inaktiven ternären Komplexes mit dem Kosubstrat Glutathion. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201701583] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Markus Ruetz
- Institut für Organische Chemie und Zentrum für Molekulare, Biowissenschaften; Universität Innsbruck; 6020 Innsbruck Österreich
- University of Michigan Medical School; Ann Arbor MI 48109-0600 USA
| | | | - Carmen Gherasim
- University of Michigan Medical School; Ann Arbor MI 48109-0600 USA
- Department of Pathology; University of Utah School of Medicine; Salt Lake City UT USA
| | - Agnes Karasik
- Department of Biochemistry; Uniformed Services University of the Health Sciences; Bethesda MD 28104 USA
| | - Robert Salchner
- Institut für Organische Chemie und Zentrum für Molekulare, Biowissenschaften; Universität Innsbruck; 6020 Innsbruck Österreich
- Watercryst GmbH & Co; Kematen Österreich
| | - Christoph Kieninger
- Institut für Organische Chemie und Zentrum für Molekulare, Biowissenschaften; Universität Innsbruck; 6020 Innsbruck Österreich
| | - Klaus Wurst
- Institut für Allgemeine, Anorganische Chemie und Theoretische Chemie; Universität Innsbruck; Österreich
| | - Ruma Banerjee
- University of Michigan Medical School; Ann Arbor MI 48109-0600 USA
| | - Markos Koutmos
- Department of Biochemistry; Uniformed Services University of the Health Sciences; Bethesda MD 28104 USA
| | - Bernhard Kräutler
- Institut für Organische Chemie und Zentrum für Molekulare, Biowissenschaften; Universität Innsbruck; 6020 Innsbruck Österreich
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27
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Ruetz M, Shanmuganathan A, Gherasim C, Karasik A, Salchner R, Kieninger C, Wurst K, Banerjee R, Koutmos M, Kräutler B. Antivitamin B 12 Inhibition of the Human B 12 -Processing Enzyme CblC: Crystal Structure of an Inactive Ternary Complex with Glutathione as the Cosubstrate. Angew Chem Int Ed Engl 2017; 56:7387-7392. [PMID: 28544088 DOI: 10.1002/anie.201701583] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Indexed: 02/06/2023]
Abstract
B12 antivitamins are important and robust tools for investigating the biological roles of vitamin B12 . Here, the potential antivitamin B12 2,4-difluorophenylethynylcobalamin (F2PhEtyCbl) was prepared, and its 3D structure was studied in solution and in the crystal. Chemically inert F2PhEtyCbl resisted thermolysis of its Co-C bond at 100 °C, was stable in bright daylight, and also remained intact upon prolonged storage in aqueous solution at room temperature. It binds to the human B12 -processing enzyme CblC with high affinity (KD =130 nm) in the presence of the cosubstrate glutathione (GSH). F2PhEtyCbl withstood tailoring by CblC, and it also stabilized the ternary complex with GSH. The crystal structure of this inactivated assembly provides first insight into the binding interactions between an antivitamin B12 and CblC, as well as into the organization of GSH and a base-off cobalamin in the active site of this enzyme.
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Affiliation(s)
- Markus Ruetz
- Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, 6020, Innsbruck, Austria.,University of Michigan Medical School, Ann Arbor, USA
| | | | - Carmen Gherasim
- University of Michigan Medical School, Ann Arbor, USA.,Current address: Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Agnes Karasik
- Department of Biochemistry, Uniformed Services University of the Health Sciences, Bethesda, USA
| | - Robert Salchner
- Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, 6020, Innsbruck, Austria.,Current address: Watercryst GmbH & Co, Kematen, Austria
| | - Christoph Kieninger
- Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, 6020, Innsbruck, Austria
| | - Klaus Wurst
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Austria
| | - Ruma Banerjee
- University of Michigan Medical School, Ann Arbor, USA
| | - Markos Koutmos
- Department of Biochemistry, Uniformed Services University of the Health Sciences, Bethesda, USA
| | - Bernhard Kräutler
- Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, 6020, Innsbruck, Austria
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28
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Jakubowski H. Homocysteine Editing, Thioester Chemistry, Coenzyme A, and the Origin of Coded Peptide Synthesis †. Life (Basel) 2017; 7:life7010006. [PMID: 28208756 PMCID: PMC5370406 DOI: 10.3390/life7010006] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 02/03/2017] [Indexed: 12/22/2022] Open
Abstract
Aminoacyl-tRNA synthetases (AARSs) have evolved “quality control” mechanisms which prevent tRNA aminoacylation with non-protein amino acids, such as homocysteine, homoserine, and ornithine, and thus their access to the Genetic Code. Of the ten AARSs that possess editing function, five edit homocysteine: Class I MetRS, ValRS, IleRS, LeuRS, and Class II LysRS. Studies of their editing function reveal that catalytic modules of these AARSs have a thiol-binding site that confers the ability to catalyze the aminoacylation of coenzyme A, pantetheine, and other thiols. Other AARSs also catalyze aminoacyl-thioester synthesis. Amino acid selectivity of AARSs in the aminoacyl thioesters formation reaction is relaxed, characteristic of primitive amino acid activation systems that may have originated in the Thioester World. With homocysteine and cysteine as thiol substrates, AARSs support peptide bond synthesis. Evolutionary origin of these activities is revealed by genomic comparisons, which show that AARSs are structurally related to proteins involved in coenzyme A/sulfur metabolism and non-coded peptide bond synthesis. These findings suggest that the extant AARSs descended from ancestral forms that were involved in non-coded Thioester-dependent peptide synthesis, functionally similar to the present-day non-ribosomal peptide synthetases.
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Affiliation(s)
- Hieronim Jakubowski
- Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, NJ 07103, USA.
- Department of Biochemistry and Biotechnology, University of Life Sciences, Poznan 60-632, Poland.
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