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Greco GLC, Segretti N, Abad-Zapatero C, Movahedzadeh F, Hirata MH, Ferreira EI, Ferreira GM. Exploring the dark side of tertiary and quaternary structure dynamics in MtbFBPaseII. J Biomol Struct Dyn 2023:1-9. [PMID: 37837432 DOI: 10.1080/07391102.2023.2270528] [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: 06/05/2023] [Accepted: 10/08/2023] [Indexed: 10/16/2023]
Abstract
Tuberculosis (TB) is a major global cause of mortality, primarily stemming from latent tuberculosis infection (LTBI). Failure to fully treat LTBI can result in drug-resistant forms of TB. Therefore, it is essential to develop novel drugs with unique mechanisms of action to combat TB effectively. One crucial metabolic pathway in Mycobacterium tuberculosis (Mtb), which contributes to TB infection and persistence, is gluconeogenesis. Within this pathway, the enzyme fructose bisphosphatase (FBPase) plays a significant role and is considered a promising target for drug development. By targeting MtbFBPaseII, a specific class of FBPase, researchers have employed molecular dynamics simulations to identify regions capable of binding new drugs, thereby inhibiting the enzyme's activity and potentially paving the way for the development of effective treatments.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | | | - Celerino Abad-Zapatero
- Institute for Tuberculosis Research, University of Illinois at Chicago, Chicago, IL, USA
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | - Farahnaz Movahedzadeh
- Institute for Tuberculosis Research, University of Illinois at Chicago, Chicago, IL, USA
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | - Mario Hiroyuki Hirata
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, São Paulo, Brazil
| | - Elizabeth Igne Ferreira
- Department of Pharmacy, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Glaucio Monteiro Ferreira
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, São Paulo, Brazil
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Guo L, Liu M, Bi Y, Qi Q, Xian M, Zhao G. Using a synthetic machinery to improve carbon yield with acetylphosphate as the core. Nat Commun 2023; 14:5286. [PMID: 37648707 PMCID: PMC10468489 DOI: 10.1038/s41467-023-41135-7] [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: 05/15/2023] [Accepted: 08/23/2023] [Indexed: 09/01/2023] Open
Abstract
In microbial cell factory, CO2 release during acetyl-CoA production from pyruvate significantly decreases the carbon atom economy. Here, we construct and optimize a synthetic carbon conserving pathway named as Sedoheptulose-1,7-bisphosphatase Cycle with Trifunctional PhosphoKetolase (SCTPK) in Escherichia coli. This cycle relies on a generalist phosphoketolase Xfspk and converts glucose into the stoichiometric amounts of acetylphosphate (AcP). Furthermore, genetic circuits responding to AcP positively or negatively are created. Together with SCTPK, they constitute a gene-metabolic oscillator that regulates Xfspk and enzymes converting AcP into valuable chemicals in response to intracellular AcP level autonomously, allocating metabolic flux rationally and improving the carbon atom economy of bioconversion process. Using this synthetic machinery, mevalonate is produced with a yield higher than its native theoretical yield, and the highest titer and yield of 3-hydroxypropionate via malonyl-CoA pathway are achieved. This study provides a strategy for improving the carbon yield of microbial cell factories.
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Affiliation(s)
- Likun Guo
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Min Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Yujia Bi
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Qingsheng Qi
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Mo Xian
- CAS Key Lab of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
| | - Guang Zhao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China.
- CAS Key Lab of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China.
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Selezneva AI, Harding LNM, Gutka HJ, Movahedzadeh F, Abad-Zapatero C. New structures of Class II Fructose-1,6-Bisphosphatase from Francisella tularensis provide a framework for a novel catalytic mechanism for the entire class. PLoS One 2023; 18:e0274723. [PMID: 37352301 PMCID: PMC10289334 DOI: 10.1371/journal.pone.0274723] [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: 09/03/2022] [Accepted: 06/06/2023] [Indexed: 06/25/2023] Open
Abstract
Class II Fructose-1,6-bisphosphatases (FBPaseII) (EC: 3.1.3.11) are highly conserved essential enzymes in the gluconeogenic pathway of microorganisms. Previous crystallographic studies of FBPasesII provided insights into various inactivated states of the enzyme in different species. Presented here is the first crystal structure of FBPaseII in an active state, solved for the enzyme from Francisella tularensis (FtFBPaseII), containing native metal cofactor Mn2+ and complexed with catalytic product fructose-6-phosphate (F6P). Another crystal structure of the same enzyme complex is presented in the inactivated state due to the structural changes introduced by crystal packing. Analysis of the interatomic distances among the substrate, product, and divalent metal cations in the catalytic centers of the enzyme led to a revision of the catalytic mechanism suggested previously for class II FBPases. We propose that phosphate-1 is cleaved from the substrate fructose-1,6-bisphosphate (F1,6BP) by T89 in a proximal α-helix backbone (G88-T89-T90-I91-T92-S93-K94) in which the substrate transition state is stabilized by the positive dipole of the 〈-helix backbone. Once cleaved a water molecule found in the active site liberates the inorganic phosphate from T89 completing the catalytic mechanism. Additionally, a crystal structure of Mycobacterium tuberculosis FBPaseII (MtFBPaseII) containing a bound F1,6BP is presented to further support the substrate binding and novel catalytic mechanism suggested for this class of enzymes.
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Affiliation(s)
- Anna I. Selezneva
- Institute for Tuberculosis Research, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Luke N. M. Harding
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Hiten J. Gutka
- Institute for Tuberculosis Research, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Farahnaz Movahedzadeh
- Institute for Tuberculosis Research, University of Illinois at Chicago, Chicago, Illinois, United States of America
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Celerino Abad-Zapatero
- Institute for Tuberculosis Research, University of Illinois at Chicago, Chicago, Illinois, United States of America
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, Illinois, United States of America
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Abad-Zapatero C. Notes of a protein crystallographer: the advantages of combining new integrated methods of structure solution with traditional data visuals. Acta Crystallogr D Struct Biol 2022; 78:260-267. [PMID: 35102891 PMCID: PMC8805300 DOI: 10.1107/s205979832101336x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 12/16/2021] [Indexed: 11/06/2023] Open
Abstract
The suggestion is made that combining analysis using the most advanced crystallographic software with the integrated visual tools of the field will result in more knowledgeable and better trained future generations of structural biologists. The use of integrated visuals could also expedite the structure solution of some recalcitrant and complex macromolecular crystal structures that resist automatic workflows.
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Affiliation(s)
- Celerino Abad-Zapatero
- Institute of Tuberculosis Research and Center for Biomolecular Sciences, Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
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Dong W, Nie X, Zhu H, Liu Q, Shi K, You L, Zhang Y, Fan H, Yan B, Niu C, Lyu LD, Zhao GP, Yang C. Mycobacterial fatty acid catabolism is repressed by FdmR to sustain lipogenesis and virulence. Proc Natl Acad Sci U S A 2021; 118:e2019305118. [PMID: 33853942 PMCID: PMC8072231 DOI: 10.1073/pnas.2019305118] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Host-derived fatty acids are an important carbon source for pathogenic mycobacteria during infection. How mycobacterial cells regulate the catabolism of fatty acids to serve the pathogenicity, however, remains unknown. Here, we identified a TetR-family transcriptional factor, FdmR, as the key regulator of fatty acid catabolism in the pathogen Mycobacterium marinum by combining use of transcriptomics, chromatin immunoprecipitation followed by sequencing, dynamic 13C-based flux analysis, metabolomics, and lipidomics. An M. marinum mutant deficient in FdmR was severely attenuated in zebrafish larvae and adult zebrafish. The mutant showed defective growth but high substrate consumption on fatty acids. FdmR was identified as a long-chain acyl-coenzyme A (acyl-CoA)-responsive repressor of genes involved in fatty acid degradation and modification. We demonstrated that FdmR functions as a valve to direct the flux of exogenously derived fatty acids away from β-oxidation toward lipid biosynthesis, thereby avoiding the overactive catabolism and accumulation of biologically toxic intermediates. Moreover, we found that FdmR suppresses degradation of long-chain acyl-CoAs endogenously synthesized through the type I fatty acid synthase. By modulating the supply of long-chain acyl-CoAs for lipogenesis, FdmR controls the abundance and chain length of virulence-associated lipids and mycolates and plays an important role in the impermeability of the cell envelope. These results reveal that despite the fact that host-derived fatty acids are used as an important carbon source, overactive catabolism of fatty acids is detrimental to mycobacterial cell growth and pathogenicity. This study thus presents FdmR as a potentially attractive target for chemotherapy.
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Affiliation(s)
- Wenyue Dong
- CAS Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS), Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoqun Nie
- CAS Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS), Shanghai 200032, China
| | - Hong Zhu
- CAS Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS), Shanghai 200032, China
| | - Qingyun Liu
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA 02115
| | - Kunxiong Shi
- Key Laboratory of Medical Molecular Virology of the Ministry of Education/National Health Commission/Chinese Academy of Medical Sciences (MOE/NHC/CAMS), School of Basic Medical Sciences, Department of Microbiology, School of Life Sciences, Shanghai Public Health Clinical Center, Fudan University, Shanghai 200000, China
| | - Linlin You
- CAS Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS), Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yu Zhang
- CAS Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS), Shanghai 200032, China
| | - Hongyan Fan
- Key Laboratory of Medical Molecular Virology of the Ministry of Education/National Health Commission/Chinese Academy of Medical Sciences (MOE/NHC/CAMS), School of Basic Medical Sciences, Department of Microbiology, School of Life Sciences, Shanghai Public Health Clinical Center, Fudan University, Shanghai 200000, China
| | - Bo Yan
- Key Laboratory of Medical Molecular Virology of the Ministry of Education/National Health Commission/Chinese Academy of Medical Sciences (MOE/NHC/CAMS), School of Basic Medical Sciences, Department of Microbiology, School of Life Sciences, Shanghai Public Health Clinical Center, Fudan University, Shanghai 200000, China
| | - Chen Niu
- Key Laboratory of Medical Molecular Virology of the Ministry of Education/National Health Commission/Chinese Academy of Medical Sciences (MOE/NHC/CAMS), School of Basic Medical Sciences, Department of Microbiology, School of Life Sciences, Shanghai Public Health Clinical Center, Fudan University, Shanghai 200000, China;
| | - Liang-Dong Lyu
- Key Laboratory of Medical Molecular Virology of the Ministry of Education/National Health Commission/Chinese Academy of Medical Sciences (MOE/NHC/CAMS), School of Basic Medical Sciences, Department of Microbiology, School of Life Sciences, Shanghai Public Health Clinical Center, Fudan University, Shanghai 200000, China;
| | - Guo-Ping Zhao
- CAS Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS), Shanghai 200032, China
- Key Laboratory of Medical Molecular Virology of the Ministry of Education/National Health Commission/Chinese Academy of Medical Sciences (MOE/NHC/CAMS), School of Basic Medical Sciences, Department of Microbiology, School of Life Sciences, Shanghai Public Health Clinical Center, Fudan University, Shanghai 200000, China
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai 200032, China
| | - Chen Yang
- CAS Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS), Shanghai 200032, China;
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Selezneva AI, Gutka HJ, Wolf NM, Qurratulain F, Movahedzadeh F, Abad-Zapatero C. Structural and biochemical characterization of the class II fructose-1,6-bisphosphatase from Francisella tularensis. Acta Crystallogr F Struct Biol Commun 2020; 76:524-535. [PMID: 33135671 PMCID: PMC7605111 DOI: 10.1107/s2053230x20013370] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 10/05/2020] [Indexed: 11/10/2022] Open
Abstract
The crystal structure of the class II fructose-1,6-bisphosphatase (FBPaseII) from the important pathogen Francisella tularensis is presented at 2.4 Å resolution. Its structural and functional relationships to the closely related phosphatases from Mycobacterium tuberculosis (MtFBPaseII) and Escherichia coli (EcFBPaseII) and to the dual phosphatase from Synechocystis strain 6803 are discussed. FBPaseII from F. tularensis (FtFBPaseII) was crystallized in a monoclinic crystal form (space group P21, unit-cell parameters a = 76.30, b = 100.17, c = 92.02 Å, β = 90.003°) with four chains in the asymmetric unit. Chain A had two coordinated Mg2+ ions in its active center, which is distinct from previous findings, and is presumably deactivated by their presence. The structure revealed an approximate 222 (D2) symmetry homotetramer analogous to that previously described for MtFBPaseII, which is formed by a crystallographic dyad and which differs from the exact tetramer found in EcFBPaseII at a 222 symmetry site in the crystal. Instead, the approximate homotetramer is very similar to that found in the dual phosphatase from Synechocystis, even though no allosteric effector was found in FtFBPase. The amino-acid sequence and folding of the active site of FtFBPaseII result in structural characteristics that are more similar to those of the previously published EcFBPaseII than to those of MtFBPaseII. The kinetic parameters of native FtFBPaseII were found to be in agreement with published studies. Kinetic analyses of the Thr89Ser and Thr89Ala mutations in the active site of the enzyme are consistent with the previously proposed mechanism for other class II bisphosphatases. The Thr89Ala variant enzyme was inactive but the Thr89Ser variant was partially active, with an approximately fourfold lower Km and Vmax than the native enzyme. The structural and functional insights derived from the structure of FtFBPaseII will provide valuable information for the design of specific inhibitors.
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Affiliation(s)
- Anna I. Selezneva
- Institute for Tuberculosis Research, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Hiten J. Gutka
- Institute for Tuberculosis Research, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Nina M. Wolf
- Institute for Tuberculosis Research, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Fnu Qurratulain
- Institute for Tuberculosis Research, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Farahnaz Movahedzadeh
- Institute for Tuberculosis Research, University of Illinois at Chicago, Chicago, Illinois, USA
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Celerino Abad-Zapatero
- Institute for Tuberculosis Research, University of Illinois at Chicago, Chicago, Illinois, USA
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, Illinois, USA
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