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Wu T, Gómez-Coronado PA, Kubis A, Lindner SN, Marlière P, Erb TJ, Bar-Even A, He H. Engineering a synthetic energy-efficient formaldehyde assimilation cycle in Escherichia coli. Nat Commun 2023; 14:8490. [PMID: 38123535 PMCID: PMC10733421 DOI: 10.1038/s41467-023-44247-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 12/05/2023] [Indexed: 12/23/2023] Open
Abstract
One-carbon (C1) substrates, such as methanol or formate, are attractive feedstocks for circular bioeconomy. These substrates are typically converted into formaldehyde, serving as the entry point into metabolism. Here, we design an erythrulose monophosphate (EuMP) cycle for formaldehyde assimilation, leveraging a promiscuous dihydroxyacetone phosphate dependent aldolase as key enzyme. In silico modeling reveals that the cycle is highly energy-efficient, holding the potential for high bioproduct yields. Dissecting the EuMP into four modules, we use a stepwise strategy to demonstrate in vivo feasibility of the modules in E. coli sensor strains with sarcosine as formaldehyde source. From adaptive laboratory evolution for module integration, we identify key mutations enabling the accommodation of the EuMP reactions with endogenous metabolism. Overall, our study demonstrates the proof-of-concept for a highly efficient, new-to-nature formaldehyde assimilation pathway, opening a way for the development of a methylotrophic platform for a C1-fueled bioeconomy in the future.
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Affiliation(s)
- Tong Wu
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Institute of Biochemistry, Charitéplatz 1, 10117, Berlin, Germany
| | - Paul A Gómez-Coronado
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043, Marburg, Germany
| | - Armin Kubis
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Steffen N Lindner
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Institute of Biochemistry, Charitéplatz 1, 10117, Berlin, Germany
| | - Philippe Marlière
- TESSSI, The European Syndicate of Synthetic Scientists and Industrialists, 81 rue Réaumur, 75002, Paris, France
| | - Tobias J Erb
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043, Marburg, Germany
| | - Arren Bar-Even
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Hai He
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany.
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043, Marburg, Germany.
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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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3
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Deng H, Zhu J, Li L, Meng X. A multi-omics analysis strategy reveals the molecular mechanism of the inhibition of Escherichia coli O157:H7 by anthocyanins from Aronia melanocarpa and its application. Food Funct 2023; 14:8575-8585. [PMID: 37664957 DOI: 10.1039/d3fo00406f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Water pollution causes the propagation of pathogenic microorganisms, which poses a serious threat to human life. Escherichia coli O157:H7, as a representative organism that can directly exhibit molecular response to stress, was selected as the indicator bacteria for the study. Tandem mass tag (TMT) quantitative proteomics and non-targeted metabolomics were used to study the response of Escherichia coli O157:H7 to Aronia melanocarpa anthocyanin (AMA) treatment. The results showed that 628 proteins and 1338 metabolites changed significantly after treatment with AMAs. According to bioinformatics analysis, integrated proteomics and metabolomics analysis differentially expressed proteins (DEPs) and metabolites participate in pyruvate metabolism, glycolysis/gluconeogenesis, alanine, aspartate and glutamate metabolism and the pentose phosphate pathway. This study preliminarily proposed the inhibition mechanism of AMAs on Escherichia coli O157:H7 from the perspective of multi-omics, providing a theoretical basis for the application of natural preservatives in fresh cut vegetables.
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Affiliation(s)
- Haotian Deng
- College of Food Science, Shenyang Agricultural University, Shenyang, Liaoning Province, 110866, China.
| | - Jinyan Zhu
- Food Inspection Monitoring Center of Zhuanghe, Dalian, Liaoning Province, 116400, China
| | - Li Li
- College of Food Science, Shenyang Agricultural University, Shenyang, Liaoning Province, 110866, China.
| | - Xianjun Meng
- College of Food Science, Shenyang Agricultural University, Shenyang, Liaoning Province, 110866, China.
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4
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Sporre E, Karlsen J, Schriever K, Asplund-Samuelsson J, Janasch M, Strandberg L, Karlsson A, Kotol D, Zeckey L, Piazza I, Syrén PO, Edfors F, Hudson EP. Metabolite interactions in the bacterial Calvin cycle and implications for flux regulation. Commun Biol 2023; 6:947. [PMID: 37723200 PMCID: PMC10507043 DOI: 10.1038/s42003-023-05318-8] [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: 01/27/2023] [Accepted: 09/01/2023] [Indexed: 09/20/2023] Open
Abstract
Metabolite-level regulation of enzyme activity is important for microbes to cope with environmental shifts. Knowledge of such regulations can also guide strain engineering for biotechnology. Here we apply limited proteolysis-small molecule mapping (LiP-SMap) to identify and compare metabolite-protein interactions in the proteomes of two cyanobacteria and two lithoautotrophic bacteria that fix CO2 using the Calvin cycle. Clustering analysis of the hundreds of detected interactions shows that some metabolites interact in a species-specific manner. We estimate that approximately 35% of interacting metabolites affect enzyme activity in vitro, and the effect is often minor. Using LiP-SMap data as a guide, we find that the Calvin cycle intermediate glyceraldehyde-3-phosphate enhances activity of fructose-1,6/sedoheptulose-1,7-bisphosphatase (F/SBPase) from Synechocystis sp. PCC 6803 and Cupriavidus necator in reducing conditions, suggesting a convergent feed-forward activation of the cycle. In oxidizing conditions, glyceraldehyde-3-phosphate inhibits Synechocystis F/SBPase by promoting enzyme aggregation. In contrast, the glycolytic intermediate glucose-6-phosphate activates F/SBPase from Cupriavidus necator but not F/SBPase from Synechocystis. Thus, metabolite-level regulation of the Calvin cycle is more prevalent than previously appreciated.
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Affiliation(s)
- Emil Sporre
- Department of Protein Science, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Jan Karlsen
- Department of Protein Science, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Karen Schriever
- Department of Fiber and Polymer Technology, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Johannes Asplund-Samuelsson
- Department of Protein Science, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Markus Janasch
- Department of Protein Science, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
- Department of Biotechnology and Nanomedicine, SINTEF Industry, 7465, Trondheim, Norway
| | - Linnéa Strandberg
- Department of Protein Science, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Anna Karlsson
- Department of Protein Science, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - David Kotol
- Department of Protein Science, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Luise Zeckey
- Department of Protein Science, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Ilaria Piazza
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Per-Olof Syrén
- Department of Fiber and Polymer Technology, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Fredrik Edfors
- Department of Protein Science, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Elton P Hudson
- Department of Protein Science, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden.
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5
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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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6
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Feng Y, Gu D, Wang Z, Lu C, Fan J, Zhou J, Wang R, Su X. Comprehensive evaluation and analysis of the salinity stress response mechanisms based on transcriptome and metabolome of Staphylococcus aureus. Arch Microbiol 2021; 204:28. [PMID: 34921629 DOI: 10.1007/s00203-021-02624-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 10/03/2021] [Accepted: 10/07/2021] [Indexed: 10/19/2022]
Abstract
Staphylococcus aureus possesses an extraordinary ability to deal with a wide range of osmotic pressure. This study performed transcriptomic and metabolomic analyses on the potential mechanism of gradient salinity stress adaptation in S. aureus ZS01. The results revealed that CPS biosynthetic protein genes were candidate target genes for directly regulating the phenotypic changes of biofilm. Inositol phosphate metabolism was downregulated to reduce the conversion of functional molecules. The gluconeogenesis pathway and histidine synthesis were downregulated to reduce the production of endogenous glucose. The pyruvate metabolism pathway was upregulated to promote the accumulation of succinate. TCA cycle metabolism pathway was downregulated to reduce unnecessary energy loss. L-Proline was accumulated to regulate osmotic pressure. Therefore, these self-protection mechanisms can protect cells from hypertonic environments and help them focus on survival. In addition, we identified ten hub genes. The findings will aid in the prevention and treatment strategies of S. aureus infections.
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Affiliation(s)
- Ying Feng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, China.,College of Life Sciences, Tonghua Normal University, Tonghua, China.,School of Marine Sciences, Ningbo University, 169 Qixing South Road, Ningbo City, 315211, Zhejiang Province, China
| | - Dizhou Gu
- College of Life Sciences, Tonghua Normal University, Tonghua, China
| | - Ziyan Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, China.,School of Marine Sciences, Ningbo University, 169 Qixing South Road, Ningbo City, 315211, Zhejiang Province, China
| | - Chenyang Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, China.,School of Marine Sciences, Ningbo University, 169 Qixing South Road, Ningbo City, 315211, Zhejiang Province, China
| | - Jingfeng Fan
- National Marine Environmental Monitoring Center, Dalian, China
| | - Jun Zhou
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, China.,School of Marine Sciences, Ningbo University, 169 Qixing South Road, Ningbo City, 315211, Zhejiang Province, China
| | - Rixin Wang
- School of Marine Sciences, Ningbo University, 169 Qixing South Road, Ningbo City, 315211, Zhejiang Province, China.
| | - Xiurong Su
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, China. .,School of Marine Sciences, Ningbo University, 169 Qixing South Road, Ningbo City, 315211, Zhejiang Province, China.
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7
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Clomburg JM, Cintolesi A, Gonzalez R. In silico and in vivo analyses reveal key metabolic pathways enabling the fermentative utilization of glycerol in Escherichia coli. Microb Biotechnol 2021; 15:289-304. [PMID: 34699695 PMCID: PMC8719807 DOI: 10.1111/1751-7915.13938] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Accepted: 09/16/2021] [Indexed: 11/29/2022] Open
Abstract
Most microorganisms can metabolize glycerol when external electron acceptors are available (i.e. under respiratory conditions). However, few can do so under fermentative conditions owing to the unique redox constraints imposed by the high degree of reduction of glycerol. Here, we utilize in silico analysis combined with in vivo genetic and biochemical approaches to investigate the fermentative metabolism of glycerol in Escherichia coli. We found that E. coli can achieve redox balance at alkaline pH by reducing protons to H2 , complementing the previously reported role of 1,2-propanediol synthesis under acidic conditions. In this new redox balancing mode, H2 evolution is coupled to a respiratory glycerol dissimilation pathway composed of glycerol kinase (GK) and glycerol-3-phosphate (G3P) dehydrogenase (G3PDH). GK activates glycerol to G3P, which is further oxidized by G3PDH to generate reduced quinones that drive hydrogenase-dependent H2 evolution. Despite the importance of the GK-G3PDH route under alkaline conditions, we found that the NADH-generating glycerol dissimilation pathway via glycerol dehydrogenase (GldA) and phosphoenolpyruvate (PEP)-dependent dihydroxyacetone kinase (DHAK) was essential under both alkaline and acidic conditions. We assessed system-wide metabolic impacts of the constraints imposed by the PEP dependency of the GldA-DHAK route. This included the identification of enzymes and pathways that were not previously known to be involved in glycerol metabolisms such as PEP carboxykinase, PEP synthetase, multiple fructose-1,6-bisphosphatases and the fructose phosphate bypass.
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Affiliation(s)
- James M Clomburg
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA.,Department of Chemical, Biological, and Materials Engineering, University of South Florida, Tampa, FL, USA
| | - Angela Cintolesi
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA
| | - Ramon Gonzalez
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA.,Department of Chemical, Biological, and Materials Engineering, University of South Florida, Tampa, FL, USA
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9
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Chen L, Zhao X, He Y, Yang H. Cloning, purification and characterisation of cytosolic fructose-1,6-bisphosphatase from mung bean (Vigna radiata). Food Chem 2021; 347:128973. [PMID: 33444888 DOI: 10.1016/j.foodchem.2020.128973] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 11/26/2020] [Accepted: 12/28/2020] [Indexed: 10/22/2022]
Abstract
To improve the crop yield and quality, the cytosolic fructose-1,6-bisphosphatase (cFBPase) from mung bean (Vigna radiata), a rate-limiting enzyme in gluconeogenesis, was cloned, purified, and structurally characterised. To function it required Mg2+ and Mn2+ at 0.01-10 mM. The Michaelis-Menton constant and adenosine monophosphate (AMP) inhibitory constant (Ki) were 7.96 and 111.09 μM, respectively. The functional site residues of AMP binding (Arg30, Asp32, and Phe33) and the active site residues (Asn218 and Met251) were tested via site-directed mutagenesis and molecular docking. Asn218 and Met251 were replaced by Tyr and Leu, respectively. The M251L mutant showed enhanced substrate affinity and activity, resulting from decreased binding energy (-2.58 kcal·mol-1) and molecular distance (4.2 Å). AMP binding site mutations changed the enzyme activities, indicating a connection between the binding and active sites. Furthermore, Ki and docking analysis revealed that Asp32 plays a key role in maintaining the AMP binding conformation.
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Affiliation(s)
- Lin Chen
- Department of Food Science and Technology, National University of Singapore, Singapore 117542, Singapore; National University of Singapore (Suzhou) Research Institute, 377 Lin Quan Street, Suzhou Industrial Park, Suzhou, Jiangsu 215123, PR China
| | - Xue Zhao
- Department of Food Science and Technology, National University of Singapore, Singapore 117542, Singapore; National University of Singapore (Suzhou) Research Institute, 377 Lin Quan Street, Suzhou Industrial Park, Suzhou, Jiangsu 215123, PR China
| | - Yun He
- Department of Food Science and Technology, National University of Singapore, Singapore 117542, Singapore; National University of Singapore (Suzhou) Research Institute, 377 Lin Quan Street, Suzhou Industrial Park, Suzhou, Jiangsu 215123, PR China
| | - Hongshun Yang
- Department of Food Science and Technology, National University of Singapore, Singapore 117542, Singapore; National University of Singapore (Suzhou) Research Institute, 377 Lin Quan Street, Suzhou Industrial Park, Suzhou, Jiangsu 215123, PR China.
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10
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Dynamic 3D proteomes reveal protein functional alterations at high resolution in situ. Cell 2020; 184:545-559.e22. [PMID: 33357446 PMCID: PMC7836100 DOI: 10.1016/j.cell.2020.12.021] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 08/21/2020] [Accepted: 12/11/2020] [Indexed: 02/02/2023]
Abstract
Biological processes are regulated by intermolecular interactions and chemical modifications that do not affect protein levels, thus escaping detection in classical proteomic screens. We demonstrate here that a global protein structural readout based on limited proteolysis-mass spectrometry (LiP-MS) detects many such functional alterations, simultaneously and in situ, in bacteria undergoing nutrient adaptation and in yeast responding to acute stress. The structural readout, visualized as structural barcodes, captured enzyme activity changes, phosphorylation, protein aggregation, and complex formation, with the resolution of individual regulated functional sites such as binding and active sites. Comparison with prior knowledge, including other ‘omics data, showed that LiP-MS detects many known functional alterations within well-studied pathways. It suggested distinct metabolite-protein interactions and enabled identification of a fructose-1,6-bisphosphate-based regulatory mechanism of glucose uptake in E. coli. The structural readout dramatically increases classical proteomics coverage, generates mechanistic hypotheses, and paves the way for in situ structural systems biology. Dynamic structural proteomic screens detect functional changes at high resolution Detect enzyme activity, phosphorylation, and molecular interactions in situ Generate new molecular hypotheses and increase functional proteomics coverage Enabled discovery of a regulatory mechanism of glucose uptake in E. coli
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11
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Neves HI, Machado GT, Ramos TCDS, Yang HM, Yagil E, Spira B. Competition for nutritional resources masks the true frequency of bacterial mutants. BMC Biol 2020; 18:194. [PMID: 33317515 PMCID: PMC7737367 DOI: 10.1186/s12915-020-00913-1] [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: 07/22/2020] [Accepted: 11/03/2020] [Indexed: 12/02/2022] Open
Abstract
Background It is widely assumed that all mutant microorganisms present in a culture are able to grow and form colonies, provided that they express the features required for selection. Unlike wild-type Escherichia coli, PHO-constitutive mutants overexpress alkaline phosphatase and hence can hydrolyze glycerol-2-phosphate (G2P) to glycerol and form colonies on plates having G2P as the sole carbon source. These mutations mostly occur in the pst operon. However, the frequency of PHO-constitutive colonies on the G2P selective plate is exceptionally low. Results We show that the rate in which spontaneous PHO-constitutive mutations emerge is about 8.0 × 10−6/generation, a relatively high rate, but the growth of most existing mutants is inhibited by their neighboring wild-type cells. This inhibition is elicited only by non-mutant viable bacteria that can take up and metabolize glycerol formed by the mutants. Evidence indicates that the few mutants that do form colonies derive from microclusters of mutants on the selective plate. A mathematical model that describes the fate of the wild-type and mutant populations under these circumstances supports these results. Conclusion This scenario in which neither the wild-type nor the majority of the mutants are able to grow resembles an unavoidable “tragedy of the commons” case which results in the collapse of the majority of the population. Cooperation between rare adjacent mutants enables them to overcome the competition and eventually form mutant colonies. The inhibition of PHO-constitutive mutants provides an example of mutant frequency masked by orders of magnitude due to a competition between mutants and their ancestral wild-type cells. Similar “tragedy of the commons-like” cases may occur in other settings and should be taken into consideration while estimating true mutant frequencies and mutation rates. Supplementary Information The online version contains supplementary material available at (doi:10.1186/s12915-020-00913-1).
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Affiliation(s)
- Henrique Iglesias Neves
- Departamento de Microbiologia, Instituto de Ciências Biomédicas Universidade de São Paulo, São Paulo, SP, Brazil
| | - Gabriella Trombini Machado
- Departamento de Microbiologia, Instituto de Ciências Biomédicas Universidade de São Paulo, São Paulo, SP, Brazil
| | | | - Hyun Mo Yang
- Departamento de Matemática Aplicada, Instituto de Matemática, Estatística e Computação Científica, Campinas, SP, Brazil
| | - Ezra Yagil
- Departament of Biochemistry and Molecular Biology, Faculty of Life Sciences, Tel-Aviv University, Tel Aviv, Israel
| | - Beny Spira
- Departamento de Microbiologia, Instituto de Ciências Biomédicas Universidade de São Paulo, São Paulo, SP, Brazil.
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12
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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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13
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Hellgren J, Godina A, Nielsen J, Siewers V. Promiscuous phosphoketolase and metabolic rewiring enables novel non-oxidative glycolysis in yeast for high-yield production of acetyl-CoA derived products. Metab Eng 2020; 62:150-160. [DOI: 10.1016/j.ymben.2020.09.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 08/11/2020] [Accepted: 09/03/2020] [Indexed: 01/31/2023]
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14
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Li Y, Ye Q, He D, Bai H, Wen J. The ubiquity and coexistence of two FBPases in chloroplasts of photosynthetic eukaryotes and its evolutionary and functional implications. PLANT DIVERSITY 2020; 42:120-125. [PMID: 32373770 PMCID: PMC7195585 DOI: 10.1016/j.pld.2019.09.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 08/27/2019] [Accepted: 09/04/2019] [Indexed: 05/24/2023]
Abstract
In photosynthetic eukaryotes, there are two well-characterized fructose-1,6-bisphosphatases (FBPases): the redox-insensitive cytosolic FBPase (cyFBPase), which participates in gluconeogenesis, and the redox-sensitive chloroplastic FBPase (cpFBPase1), which is a critical enzyme in the Calvin cycle. Recent studies have identified a new chloroplastic FBPase, cpFBPase2; however, its phylogenetic distribution, evolutionary origin, and physiological function remain unclear. In this study, we identified and characterized these three FBPase isoforms in diverse, representative photosynthetic lineages and analyzed their phylogeny. In contrast to previous hypotheses, we found that cpFBPase2 is ubiquitous in photosynthetic eukaryotes. Additionally, all cpFBPase2s from diverse lineages form a monophyly, suggesting cpFBPase2 is not a recently evolved enzyme restricted to land plants but rather evolved early in the evolution of photosynthetic organisms, and most likely, in the common ancestor of photosynthetic eukaryotes. cyFBPase was probably first duplicated to produce cpFBPase2, and then the latter duplicated to produce cpFBPase1. The ubiquitous coexistence of these two cpFBPases in chloroplasts is most likely the consequence of adaptation to different redox conditions of photosynthesis, especially those caused by recurrent changes in light conditions.
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Affiliation(s)
- Yujin Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, 650204, China
| | - Qingqing Ye
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - De He
- College of Life Sciences, Southwest Forestry University, Kunming, Yunnan, 650224, China
| | - Huixian Bai
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Jianfan Wen
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
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15
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Huddleston JP, Raushel FM. Functional Characterization of YdjH, a Sugar Kinase of Unknown Specificity in Escherichia coli K12. Biochemistry 2019; 58:3354-3364. [PMID: 31314509 DOI: 10.1021/acs.biochem.9b00327] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The ydj gene cluster is annotated to catalyze the catabolism of an unknown carbohydrate. Previously, YdjI, a class II aldolase, was shown to catalyze the retro-aldol cleavage of l-glycero-l-galacto-octuluronate-1-phosphate into DHAP and l-arabinuronate. In this report, the functional characterization of YdjH is presented. YdjH catalyzes the phosphorylation of 2-keto-monosaccharides at the C1 hydroxyl group with a substrate profile significantly more stringent than that of YdjI. Similar to YdjI, YdjH shows a strong preference for higher-order monosaccharides (seven to nine carbons) with a carboxylate terminus. The best substrate was determined to be l-glycero-l-galacto-octuluronate, yielding l-glycero-l-galacto-octuluronate-1-phosphate with a kcat of 16 s-1 and a kcat/Km of 2.1 × 104 M-1 s-1. This is apparently the first reported example of kinase activity with eight-carbon monosaccharides. Two crystal structures of YdjH were previously determined to 2.15 and 1.8 Å resolution (Protein Data Bank entries 3H49 and 3IN1 ). We present an analysis of the active site layout and use computational docking to identify potential key residues in the binding of l-glycero-l-galacto-octuluronate.
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Affiliation(s)
- Jamison P Huddleston
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
| | - Frank M Raushel
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
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16
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An energetic reformulation of kinetic rate laws enables scalable parameter estimation for biochemical networks. J Theor Biol 2019; 461:145-156. [DOI: 10.1016/j.jtbi.2018.10.041] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 09/20/2018] [Accepted: 10/19/2018] [Indexed: 11/18/2022]
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17
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Goswami R, Bondoc JMG, Wheeler PR, Jafari A, Gonzalez T, Mehboob S, Movahedzadeh F. Inositol Monophosphatase: A Bifunctional Enzyme in Mycobacterium smegmatis. ACS OMEGA 2018; 3:13876-13881. [PMID: 30411052 PMCID: PMC6217659 DOI: 10.1021/acsomega.8b01753] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 10/01/2018] [Indexed: 06/08/2023]
Abstract
Inositol monophosphatase (IMPase) is a crucial enzyme for the biosynthesis of phosphatidylinositol, an essential component in mycobacterial cell walls. IMPase A (ImpA) from Mycobacterium smegmatis is a bifunctional enzyme that also functions as a fructose-1,6-bisphosphatase (FBPase). To better understand the bifunctional nature of this enzyme, point mutagenesis was conducted on several key residues and their enzyme activity was tested. Our results along with active site models support the fact that ImpA is a bifunctional enzyme with residues Gly94, Thr95 hypothesized to be contributing to the FBPase activity and residues Trp220, Asp221 hypothesized to be contributing to the IMPase activity. Double mutants, W220A + D221A reduced both FBPase and IMPase activity drastically while the double mutant G94A + T95A surprisingly partially restored the IMPase activity compared to the single mutants. This study establishes the foundation toward obtaining a better understanding of the bifunctional nature of this enzyme.
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Affiliation(s)
- Rajendra Goswami
- Institute
for Tuberculosis Research, College of Pharmacy, and Department of
Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S Wood Street, Chicago, Illinois 60612, United States
| | - Jasper Marc G. Bondoc
- Institute
for Tuberculosis Research, College of Pharmacy, and Department of
Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S Wood Street, Chicago, Illinois 60612, United States
| | - Paul R. Wheeler
- Tuberculosis
Research, Animal and Plant Health Agency, Addlestone, Surrey KT15 3NB, U.K.
| | - Alireza Jafari
- Institute
for Tuberculosis Research, College of Pharmacy, and Department of
Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S Wood Street, Chicago, Illinois 60612, United States
- Inflammatory
Lung Disease Research Center, Faculty of Medicine, Guilan University of Medical Sciences, Rasht, Iran
- Cellular
and Molecular Research Center, Faculty of Medicine, Guilan University of Medical Sciences, Rasht, Iran
| | - Trinidad Gonzalez
- Institute
for Tuberculosis Research, College of Pharmacy, and Department of
Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S Wood Street, Chicago, Illinois 60612, United States
| | - Shahila Mehboob
- Neugenica
LLC, 2242 W Harrison
Street, #201, Chicago, Illinois 60612, United States
| | - Farahnaz Movahedzadeh
- Institute
for Tuberculosis Research, College of Pharmacy, and Department of
Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S Wood Street, Chicago, Illinois 60612, United States
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18
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Improved production of 1-deoxynojirymicin in Escherichia coli through metabolic engineering. World J Microbiol Biotechnol 2018; 34:77. [PMID: 29796897 DOI: 10.1007/s11274-018-2462-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 05/21/2018] [Indexed: 12/11/2022]
Abstract
Azasugars, such as 1-deoxynojirymicin (1-DNJ), are associated with diverse pharmaceutical applications, such as antidiabetic, anti-obesity, anti-HIV, and antitumor properties. Different azasugars have been isolated from diverse microbial and plant sources though complicated purification steps, or generated by costly chemical synthesis processes. But the biosynthesis of such potent molecules using Escherichia coli as a heterologous host provides a broader opportunity to access these molecules, particularly by utilizing synthetic biological, metabolic engineering, and process optimization approaches. This work used an integrated approach of synthetic biology, enzyme engineering, and pathway optimization for rational metabolic engineering, leading to the improved production of 1-DNJ. The production of 1-DNJ in recombinant E. coli culture broth was confirmed by enzymatic assays and mass spectrometric analysis. Specifically, the pathway engineering for its key precursor, fructose-6-phosphate, along with optimized media condition, results in the highest production levels. When combined, 1-DNJ production was extended to ~ 273 mg/L, which is the highest titer of production of 1-DNJ reported using E. coli.
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19
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Discovery and structure-activity relationships study of thieno[2,3-b]pyridine analogues as hepatic gluconeogenesis inhibitors. Eur J Med Chem 2018; 152:307-317. [DOI: 10.1016/j.ejmech.2018.04.028] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 03/31/2018] [Accepted: 04/14/2018] [Indexed: 12/17/2022]
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20
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Wolf NM, Gutka HJ, Movahedzadeh F, Abad-Zapatero C. Structures of the Mycobacterium tuberculosis GlpX protein (class II fructose-1,6-bisphosphatase): implications for the active oligomeric state, catalytic mechanism and citrate inhibition. Acta Crystallogr D Struct Biol 2018; 74:321-331. [PMID: 29652259 PMCID: PMC5892879 DOI: 10.1107/s2059798318002838] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 02/16/2018] [Indexed: 11/19/2022] Open
Abstract
The crystal structures of native class II fructose-1,6-bisphosphatase (FBPaseII) from Mycobacterium tuberculosis at 2.6 Å resolution and two active-site protein variants are presented. The variants were complexed with the reaction product fructose 6-phosphate (F6P). The Thr84Ala mutant is inactive, while the Thr84Ser mutant has a lower catalytic activity. The structures reveal the presence of a 222 tetramer, similar to those described for fructose-1,6/sedoheptulose-1,7-bisphosphatase from Synechocystis (strain 6803) as well as the equivalent enzyme from Thermosynechococcus elongatus. This homotetramer corresponds to a homologous oligomer that is present but not described in the crystal structure of FBPaseII from Escherichia coli and is probably conserved in all FBPaseIIs. The constellation of amino-acid residues in the active site of FBPaseII from M. tuberculosis (MtFBPaseII) is conserved and is analogous to that described previously for the E. coli enzyme. Moreover, the structure of the active site of the partially active (Thr84Ser) variant and the analysis of the kinetics are consistent with the previously proposed catalytic mechanism. The presence of metabolites in the crystallization medium (for example citrate and malonate) and in the corresponding crystal structures of MtFBPaseII, combined with their observed inhibitory effect, could suggest the existence of an uncharacterized inhibition of this class of enzymes besides the allosteric inhibition by adenosine monophosphate observed for the Synechocystis enzyme. The structural and functional insights derived from the structure of MtFBPaseII will provide critical information for the design of lead inhibitors, which will be used to validate this target for future chemical intervention.
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Affiliation(s)
- Nina M. Wolf
- 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
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, Chicago, Illinois, USA
- Oncobiologics Inc., Cranbury, New Jersey, USA
| | - Farahnaz Movahedzadeh
- Institute for Tuberculosis Research, University of Illinois at Chicago, Chicago, Illinois, USA
- Department of Medicinal Chemistry and Pharmacognosy, 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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21
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Bondoc JMG, Wolf NM, Ndichuck M, Abad-Zapatero C, Movahedzadeh F. Mutagenesis of threonine to serine in the active site of Mycobacterium tuberculosis fructose-1,6-bisphosphatase (Class II) retains partial enzyme activity. ACTA ACUST UNITED AC 2017; 15:48-54. [PMID: 28702369 PMCID: PMC5485559 DOI: 10.1016/j.btre.2017.06.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 06/08/2017] [Accepted: 06/08/2017] [Indexed: 01/08/2023]
Abstract
The glpX gene encodes for the Class II fructose-1,6-bisphosphatase enzyme in Mycobacterium tuberculosis (Mt), an essential enzyme for pathogenesis. We have performed site directed mutagenesis to introduce two mutations at residue Thr84, T84A and T84S, to explore the binding affinity of the substrate and the catalytic mechanism. The T84A mutant fully abolishes enzyme activity while retaining substrate binding affinity. In contrast, the T84S mutant retains some activity having a 10 times reduction in Vmax and exhibited similar sensitivity to lithium when compared to the wildtype. Homology modeling using the Escherichia coli enzyme structure suggests that the replacement of the critical nucleophile OH- in the Thr84 residue of the wildtype of MtFBPase by Ser84 results in subtle alterations of the position and orientation that reduce the catalytic efficiency. This mutant could be used to trap reaction intermediates, through crystallographic methods, facilitating the design of potent inhibitors via structure-based drug design.
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Affiliation(s)
- Jasper Marc G Bondoc
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, United States
| | - Nina M Wolf
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, United States
| | - Michael Ndichuck
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, United States
| | - Celerino Abad-Zapatero
- Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, United States
| | - Farahnaz Movahedzadeh
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, United States.,Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, United States
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22
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Gutka HJ, Wolf NM, Bondoc JMG, Movahedzadeh F. Enzymatic Characterization of Fructose 1,6-Bisphosphatase II from Francisella tularensis, an Essential Enzyme for Pathogenesis. Appl Biochem Biotechnol 2017; 183:1439-1454. [PMID: 28547120 PMCID: PMC5698383 DOI: 10.1007/s12010-017-2512-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 05/11/2017] [Indexed: 11/27/2022]
Abstract
The glpX gene from Francisella tularensis encodes for the class II fructose 1,6-bisphosphatase (FBPaseII) enzyme. The glpX gene has been verified to be essential in F. tularensis, and the inactivation of this gene leads to impaired bacterial growth on gluconeogenic substrates. In the present work, we have complemented a ∆glpX mutant of Escherichia coli with the glpX gene of F. tularensis (FTF1631c). Our complementation work independently verifies that the glpX gene (FTF1631c) in F. tularensis is indeed an FBPase and supports the growth of the ΔglpX E. coli mutant on glycerol-containing media. We have performed heterologous expression and purification of the glpX encoded FBPaseII in F. tularensis. We have confirmed the function of glpX as an FBPase and optimized the conditions for enzymatic activity. Mn2+ was found to be an absolute requirement for activity, with no other metal substitutions rendering the enzyme active. The kinetic parameters for this enzyme were found as follows: Km 11 μM, Vmax 2.0 units/mg, kcat 1.2 s-1, kcat/Km 120 mM-1 s-1, and a specific activity of 2.0 units/mg. Size exclusion data suggested an abundance of a tetrameric species in solution. Our findings on the enzyme's properties will facilitate the initial stages of a structure-based drug design program targeting this essential gene of F. tularensis.
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Affiliation(s)
- Hiten J Gutka
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA
- Oncobiologics Inc., Cranbury, NJ, USA
| | - Nina M Wolf
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA
| | - Jasper Marc G Bondoc
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA
| | - Farahnaz Movahedzadeh
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA.
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA.
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23
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Cotton CAR, Kabasakal BV, Miah NA, Murray JW. Structure of the dual-function fructose-1,6/sedoheptulose-1,7-bisphosphatase from Thermosynechococcus elongatus bound with sedoheptulose-7-phosphate. Acta Crystallogr F Struct Biol Commun 2015; 71:1341-5. [PMID: 26457528 PMCID: PMC4601601 DOI: 10.1107/s2053230x15016829] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 09/08/2015] [Indexed: 11/11/2022] Open
Abstract
The dual-function fructose-1,6/sedoheptulose-1,7-bisphosphatase (FBP/SBPase) in cyanobacteria carries out two activities in the Calvin cycle. Structures of this enzyme from the cyanobacterium Synechocystis sp. PCC 6803 exist, but only with adenosine monophosphate (AMP) or fructose-1,6-bisphosphate and AMP bound. The mechanisms which control both selectivity between the two sugars and the structural mechanisms for redox control are still unresolved. Here, the structure of the dual-function FBP/SBPase from the thermophilic cyanobacterium Thermosynechococcus elongatus is presented with sedoheptulose-7-phosphate bound and in the absence of AMP. The structure is globally very similar to the Synechocystis sp. PCC 6803 enzyme, but highlights features of selectivity at the active site and loop ordering at the AMP-binding site. Understanding the selectivity and control of this enzyme is critical for understanding the Calvin cycle in cyanobacteria and for possible biotechnological application in plants.
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Affiliation(s)
- Charles A. R. Cotton
- Department of Life Sciences, Imperial College London, Exhibition Road, London SW7 2AZ, England
| | - Burak V. Kabasakal
- Department of Life Sciences, Imperial College London, Exhibition Road, London SW7 2AZ, England
| | - Nishat A. Miah
- Department of Life Sciences, Imperial College London, Exhibition Road, London SW7 2AZ, England
| | - James W. Murray
- Department of Life Sciences, Imperial College London, Exhibition Road, London SW7 2AZ, England
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24
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Brissac T, Ziveri J, Ramond E, Tros F, Kock S, Dupuis M, Brillet M, Barel M, Peyriga L, Cahoreau E, Charbit A. Gluconeogenesis, an essential metabolic pathway for pathogenic Francisella. Mol Microbiol 2015; 98:518-34. [PMID: 26192619 DOI: 10.1111/mmi.13139] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/16/2015] [Indexed: 01/23/2023]
Abstract
Intracellular multiplication and dissemination of the infectious bacterial pathogen Francisella tularensis implies the utilization of multiple host-derived nutrients. Here, we demonstrate that gluconeogenesis constitutes an essential metabolic pathway in Francisella pathogenesis. Indeed, inactivation of gene glpX, encoding the unique fructose 1,6-bisphosphatase of Francisella, severely impaired bacterial intracellular multiplication when cells were supplemented by gluconeogenic substrates such as glycerol or pyruvate. The ΔglpX mutant also showed a severe virulence defect in the mouse model, confirming the importance of this pathway during the in vivo life cycle of the pathogen. Isotopic profiling revealed the major role of the Embden-Meyerhof (glycolysis) pathway in glucose catabolism in Francisella and confirmed the importance of glpX in gluconeogenesis. Altogether, the data presented suggest that gluconeogenesis allows Francisella to cope with the limiting glucose availability it encounters during its infectious cycle by relying on host amino acids. Hence, targeting the gluconeogenic pathway might constitute an interesting therapeutic approach against this pathogen.
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Affiliation(s)
- Terry Brissac
- Université Paris Descartes, Sorbonne Paris Cité, Bâtiment Leriche, Paris, France.,INSERM U1151 - CNRS UMR 8253, Institut Necker-Enfants Malades, Equipe 11: Pathogénie des Infections Systémiques, Paris, France
| | - Jason Ziveri
- Université Paris Descartes, Sorbonne Paris Cité, Bâtiment Leriche, Paris, France.,INSERM U1151 - CNRS UMR 8253, Institut Necker-Enfants Malades, Equipe 11: Pathogénie des Infections Systémiques, Paris, France
| | - Elodie Ramond
- Université Paris Descartes, Sorbonne Paris Cité, Bâtiment Leriche, Paris, France.,INSERM U1151 - CNRS UMR 8253, Institut Necker-Enfants Malades, Equipe 11: Pathogénie des Infections Systémiques, Paris, France
| | - Fabiola Tros
- Université Paris Descartes, Sorbonne Paris Cité, Bâtiment Leriche, Paris, France.,INSERM U1151 - CNRS UMR 8253, Institut Necker-Enfants Malades, Equipe 11: Pathogénie des Infections Systémiques, Paris, France
| | - Stephanie Kock
- Université Paris Descartes, Sorbonne Paris Cité, Bâtiment Leriche, Paris, France.,INSERM U1151 - CNRS UMR 8253, Institut Necker-Enfants Malades, Equipe 11: Pathogénie des Infections Systémiques, Paris, France
| | - Marion Dupuis
- Université Paris Descartes, Sorbonne Paris Cité, Bâtiment Leriche, Paris, France.,INSERM U1151 - CNRS UMR 8253, Institut Necker-Enfants Malades, Equipe 11: Pathogénie des Infections Systémiques, Paris, France
| | - Magali Brillet
- Université Paris Descartes, Sorbonne Paris Cité, Bâtiment Leriche, Paris, France.,INSERM U1151 - CNRS UMR 8253, Institut Necker-Enfants Malades, Equipe 11: Pathogénie des Infections Systémiques, Paris, France
| | - Monique Barel
- Université Paris Descartes, Sorbonne Paris Cité, Bâtiment Leriche, Paris, France.,INSERM U1151 - CNRS UMR 8253, Institut Necker-Enfants Malades, Equipe 11: Pathogénie des Infections Systémiques, Paris, France
| | - Lindsay Peyriga
- Université de Toulouse, INSA, UPS, INP, LISBP, 135 Avenue de Rangueil, Toulouse, 31077, France.,INRA, UMR792, Ingénierie des Systèmes Biologiques et des Procédés, Toulouse, 31400, France.,CNRS, UMR5504, Toulouse, 31400, France
| | - Edern Cahoreau
- Université de Toulouse, INSA, UPS, INP, LISBP, 135 Avenue de Rangueil, Toulouse, 31077, France.,INRA, UMR792, Ingénierie des Systèmes Biologiques et des Procédés, Toulouse, 31400, France.,CNRS, UMR5504, Toulouse, 31400, France
| | - Alain Charbit
- Université Paris Descartes, Sorbonne Paris Cité, Bâtiment Leriche, Paris, France.,INSERM U1151 - CNRS UMR 8253, Institut Necker-Enfants Malades, Equipe 11: Pathogénie des Infections Systémiques, Paris, France
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25
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Ganapathy U, Marrero J, Calhoun S, Eoh H, de Carvalho LPS, Rhee K, Ehrt S. Two enzymes with redundant fructose bisphosphatase activity sustain gluconeogenesis and virulence in Mycobacterium tuberculosis. Nat Commun 2015; 6:7912. [PMID: 26258286 PMCID: PMC4535450 DOI: 10.1038/ncomms8912] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 06/25/2015] [Indexed: 01/23/2023] Open
Abstract
The human pathogen Mycobacterium tuberculosis (Mtb) likely utilizes host fatty acids as a carbon source during infection. Gluconeogenesis is essential for the conversion of fatty acids into biomass. A rate-limiting step in gluconeogenesis is the conversion of fructose 1,6-bisphosphate to fructose 6-phosphate by a fructose bisphosphatase (FBPase). The Mtb genome contains only one annotated FBPase gene, glpX. Here we show that, unexpectedly, an Mtb mutant lacking GLPX grows on gluconeogenic carbon sources and has detectable FBPase activity. We demonstrate that the Mtb genome encodes an alternative FBPase (GPM2, Rv3214) that can maintain gluconeogenesis in the absence of GLPX. Consequently, deletion of both GLPX and GPM2 is required for disruption of gluconeogenesis and attenuation of Mtb in a mouse model of infection. Our work affirms a role for gluconeogenesis in Mtb virulence and reveals previously unidentified metabolic redundancy at the FBPase-catalysed reaction step of the pathway. Mycobacterium tuberculosis feeds on host fatty acids during infection, a process that requires a fructose bisphosphatase (FBPase) enzyme for gluconeogenesis. Here, Ganapathy et al. show that the bacterium has two different FBPases and that this enzymatic activity is required for full virulence.
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Affiliation(s)
- Uday Ganapathy
- Department of Microbiology and Immunology, Weill Cornell Medical College, 413 East 69th Street, New York, New York 10021, USA
| | - Joeli Marrero
- Department of Microbiology and Immunology, Weill Cornell Medical College, 413 East 69th Street, New York, New York 10021, USA
| | - Susannah Calhoun
- Department of Microbiology and Immunology, Weill Cornell Medical College, 413 East 69th Street, New York, New York 10021, USA
| | - Hyungjin Eoh
- Department of Medicine, Weill Cornell Medical College, New York, New York 10021, USA
| | | | - Kyu Rhee
- Department of Medicine, Weill Cornell Medical College, New York, New York 10021, USA
| | - Sabine Ehrt
- Department of Microbiology and Immunology, Weill Cornell Medical College, 413 East 69th Street, New York, New York 10021, USA
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Balsera M, Uberegui E, Schürmann P, Buchanan BB. Evolutionary development of redox regulation in chloroplasts. Antioxid Redox Signal 2014; 21:1327-55. [PMID: 24483204 DOI: 10.1089/ars.2013.5817] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
SIGNIFICANCE The post-translational modification of thiol groups stands out as a key strategy that cells employ for metabolic regulation and adaptation to changing environmental conditions. Nowhere is this more evident than in chloroplasts-the O2-evolving photosynthetic organelles of plant cells that are fitted with multiple redox systems, including the thioredoxin (Trx) family of oxidoreductases functional in the reversible modification of regulatory thiols of proteins in all types of cells. The best understood member of this family in chloroplasts is the ferredoxin-linked thioredoxin system (FTS) by which proteins are modified via light-dependent disulfide/dithiol (S-S/2SH) transitions. RECENT ADVANCES Discovered in the reductive activation of enzymes of the Calvin-Benson cycle in illuminated chloroplast preparations, recent studies have extended the role of the FTS far beyond its original boundaries to include a spectrum of cellular processes. Together with the NADP-linked thioredoxin reductase C-type (NTRC) and glutathione/glutaredoxin systems, the FTS also plays a central role in the response of chloroplasts to different types of stress. CRITICAL ISSUES The comparisons of redox regulatory networks functional in chloroplasts of land plants with those of cyanobacteria-prokaryotes considered to be the ancestors of chloroplasts-and different types of algae summarized in this review have provided new insight into the evolutionary development of redox regulation, starting with the simplest O2-evolving organisms. FUTURE DIRECTIONS The evolutionary appearance, mode of action, and specificity of the redox regulatory systems functional in chloroplasts, as well as the types of redox modification operating under diverse environmental conditions stand out as areas for future study.
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Affiliation(s)
- Monica Balsera
- 1 Instituto de Recursos Naturales y Agrobiología de Salamanca , Consejo Superior de Investigaciones Científicas, Salamanca, Spain
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Brucella abortus depends on pyruvate phosphate dikinase and malic enzyme but not on Fbp and GlpX fructose-1,6-bisphosphatases for full virulence in laboratory models. J Bacteriol 2014; 196:3045-57. [PMID: 24936050 DOI: 10.1128/jb.01663-14] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The brucellae are the etiological agents of brucellosis, a worldwide-distributed zoonosis. These bacteria are facultative intracellular parasites and thus are able to adjust their metabolism to the extra- and intracellular environments encountered during an infectious cycle. However, this aspect of Brucella biology is imperfectly understood, and the nutrients available in the intracellular niche are unknown. Here, we investigated the central pathways of C metabolism used by Brucella abortus by deleting the putative fructose-1,6-bisphosphatase (fbp and glpX), phosphoenolpyruvate carboxykinase (pckA), pyruvate phosphate dikinase (ppdK), and malic enzyme (mae) genes. In gluconeogenic but not in rich media, growth of ΔppdK and Δmae mutants was severely impaired and growth of the double Δfbp-ΔglpX mutant was reduced. In macrophages, only the ΔppdK and Δmae mutants showed reduced multiplication, and studies with the ΔppdK mutant confirmed that it reached the replicative niche. Similarly, only the ΔppdK and Δmae mutants were attenuated in mice, the former being cleared by week 10 and the latter persisting longer than 12 weeks. We also investigated the glyoxylate cycle. Although aceA (isocitrate lyase) promoter activity was enhanced in rich medium, aceA disruption had no effect in vitro or on multiplication in macrophages or mouse spleens. The results suggest that B. abortus grows intracellularly using a limited supply of 6-C (and 5-C) sugars that is compensated by glutamate and possibly other amino acids entering the Krebs cycle without a critical role of the glyoxylate shunt.
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Feng L, Sun Y, Deng H, Li D, Wan J, Wang X, Wang W, Liao X, Ren Y, Hu X. Structural and biochemical characterization of fructose-1,6/sedoheptulose-1,7-bisphosphatase from the cyanobacterium Synechocystis strain 6803. FEBS J 2013; 281:916-26. [PMID: 24286336 DOI: 10.1111/febs.12657] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Revised: 11/22/2013] [Accepted: 11/25/2013] [Indexed: 12/01/2022]
Abstract
Cyanobacterial fructose-1,6/sedoheptulose-1,7-bisphosphatase (cy-FBP/SBPase) plays a vital role in gluconeogenesis and in the photosynthetic carbon reduction pathway, and is thus a potential enzymatic target for inhibition of harmful cyanobacterial blooms. Here, we describe the crystal structure of cy-FBP/SBPase in complex with AMP and fructose-1,6-bisphosphate (FBP). The allosteric inhibitor AMP and the substrate FBP exhibit an unusual binding mode when in complex with cy-FBP/SBPase. Binding mode analysis suggested that AMP bound to the allosteric sites near the interface across the up/down subunit pairs C1C4 and C2C3 in the center of the tetramer, while FBP binds opposite to the interface between the horizontal subunit pairs C1C2 or C3C4. We identified a series of residues important for FBP and AMP binding, and suggest formation of a disulfide linkage between Cys75 and Cys99. Further analysis indicates that cy-FBP/SBPase may be regulated through ligand binding and alteration of the structure of the enzyme complex. The interactions between ligands and cy-FBP/SBPase are different from those of ligand-bound structures of other FBPase family members, and thus provide new insight into the molecular mechanisms of structure and catalysis of cy-FBP/SBPase. Our studies provide insight into the evolution of this enzyme family, and may help in the design of inhibitors aimed at preventing toxic cyanobacterial blooms.
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Affiliation(s)
- Lingling Feng
- Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, and College of Chemistry, Central China Normal University, Wuhan, 430079, China
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Characterization of fructose 1,6-bisphosphatase and sedoheptulose 1,7-bisphosphatase from the facultative ribulose monophosphate cycle methylotroph Bacillus methanolicus. J Bacteriol 2013; 195:5112-22. [PMID: 24013630 DOI: 10.1128/jb.00672-13] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The genome of the facultative ribulose monophosphate (RuMP) cycle methylotroph Bacillus methanolicus encodes two bisphosphatases (GlpX), one on the chromosome (GlpX(C)) and one on plasmid pBM19 (GlpX(P)), which is required for methylotrophy. Both enzymes were purified from recombinant Escherichia coli and were shown to be active as fructose 1,6-bisphosphatases (FBPases). The FBPase-negative Corynebacterium glutamicum Δfbp mutant could be phenotypically complemented with glpX(C) and glpX(P) from B. methanolicus. GlpX(P) and GlpX(C) share similar functional properties, as they were found here to be active as homotetramers in vitro, activated by Mn(2+) ions and inhibited by Li(+), but differed in terms of the kinetic parameters. GlpX(C) showed a much higher catalytic efficiency and a lower Km for fructose 1,6-bisphosphate (86.3 s(-1) mM(-1) and 14 ± 0.5 μM, respectively) than GlpX(P) (8.8 s(-1) mM(-1) and 440 ± 7.6 μM, respectively), indicating that GlpX(C) is the major FBPase of B. methanolicus. Both enzymes were tested for activity as sedoheptulose 1,7-bisphosphatase (SBPase), since a SBPase variant of the ribulose monophosphate cycle has been proposed for B. methanolicus. The substrate for the SBPase reaction, sedoheptulose 1,7-bisphosphate, could be synthesized in vitro by using both fructose 1,6-bisphosphate aldolase proteins from B. methanolicus. Evidence for activity as an SBPase could be obtained for GlpX(P) but not for GlpX(C). Based on these in vitro data, GlpX(P) is a promiscuous SBPase/FBPase and might function in the RuMP cycle of B. methanolicus.
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Tu QD, Li D, Sun Y, Han XY, Yi F, Sha Y, Ren YL, Ding MW, Feng LL, Wan J. Design and syntheses of novel N'-((4-oxo-4H-chromen-3-yl)methylene)benzohydrazide as inhibitors of cyanobacterial fructose-1,6-/sedoheptulose-1,7-bisphosphatase. Bioorg Med Chem 2013; 21:2826-31. [PMID: 23623712 DOI: 10.1016/j.bmc.2013.04.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Revised: 04/04/2013] [Accepted: 04/05/2013] [Indexed: 10/27/2022]
Abstract
Cyanobacterial fructose-1,6-/sedoheptulose-1,7-bisphoshatase (Cy-FBP/SBPase) is an important target enzyme for finding inhibitors to solve harmful algal bloom (HAB). In this study, as potential inhibitors of Cy-FBP/SBPase, a series of novel chromone-connecting benzohydrazone compounds (Novel N'-((4-oxo-4H-chromen-3-yl)methylene)benzohydrazide) were designed and synthesized. Their inhibitory activities against Cy-FBP/SBPase were further examined in vitro. Some of these compounds, such as f6-f8, f11, f12 and f16, exhibit higher inhibitory activities (IC50=11.2-16.1 μM), especially, the compound f7 was identified as the most potent inhibitor with IC50 value of 11.2 μM. The probable binding-mode of compound f7 was further analyzed carefully by molecular docking methods. These results indicate that compound f7 could be used as a lead compound for further optimization and might have potential to be developed as a new algicide.
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Affiliation(s)
- Qi-Dong Tu
- Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, Wuhan 430079, China
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Jiang YH, Wang DY, Wen JF. The independent prokaryotic origins of eukaryotic fructose-1, 6-bisphosphatase and sedoheptulose-1, 7-bisphosphatase and the implications of their origins for the evolution of eukaryotic Calvin cycle. BMC Evol Biol 2012; 12:208. [PMID: 23083334 PMCID: PMC3503850 DOI: 10.1186/1471-2148-12-208] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2012] [Accepted: 10/17/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In the Calvin cycle of eubacteria, the dephosphorylations of both fructose-1, 6-bisphosphate (FBP) and sedoheptulose-1, 7-bisphosphate (SBP) are catalyzed by the same bifunctional enzyme: fructose-1, 6-bisphosphatase/sedoheptulose-1, 7-bisphosphatase (F/SBPase), while in that of eukaryotic chloroplasts by two distinct enzymes: chloroplastic fructose-1, 6-bisphosphatase (FBPase) and sedoheptulose-1, 7-bisphosphatase (SBPase), respectively. It was proposed that these two eukaryotic enzymes arose from the divergence of a common ancestral eubacterial bifunctional F/SBPase of mitochondrial origin. However, no specific affinity between SBPase and eubacterial FBPase or F/SBPase can be observed in the previous phylogenetic analyses, and it is hard to explain why SBPase and/or F/SBPase are/is absent from most extant nonphotosynthetic eukaryotes according to this scenario. RESULTS Domain analysis indicated that eubacterial F/SBPase of two different resources contain distinct domains: proteobacterial F/SBPases contain typical FBPase domain, while cyanobacterial F/SBPases possess FBPase_glpX domain. Therefore, like prokaryotic FBPase, eubacterial F/SBPase can also be divided into two evolutionarily distant classes (Class I and II). Phylogenetic analysis based on a much larger taxonomic sampling than previous work revealed that all eukaryotic SBPase cluster together and form a close sister group to the clade of epsilon-proteobacterial Class I FBPase which are gluconeogenesis-specific enzymes, while all eukaryotic chloroplast FBPase group together with eukaryotic cytosolic FBPase and form another distinct clade which then groups with the Class I FBPase of diverse eubacteria. Motif analysis of these enzymes also supports these phylogenetic correlations. CONCLUSIONS There are two evolutionarily distant classes of eubacterial bifunctional F/SBPase. Eukaryotic FBPase and SBPase do not diverge from either of them but have two independent origins: SBPase share a common ancestor with the gluconeogenesis-specific Class I FBPase of epsilon-proteobacteria (or probably originated from that of the ancestor of epsilon-proteobacteria), while FBPase arise from Class I FBPase of an unknown kind of eubacteria. During the evolution of SBPase from eubacterial Class I FBPase, the SBP-dephosphorylation activity was acquired through the transition "from specialist to generalist". The evolutionary substitution of the endosymbiotic-origin cyanobacterial bifunctional F/SBPase by the two light-regulated substrate-specific enzymes made the regulation of the Calvin cycle more delicate, which contributed to the evolution of eukaryotic photosynthesis and even the entire photosynthetic eukaryotes.
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Affiliation(s)
- Yong-Hai Jiang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunan 650223, China
- Graduate School of the Chinese Academy of Sciences, Beijing 100039, China
| | - De-Yong Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunan 650223, China
- Graduate School of the Chinese Academy of Sciences, Beijing 100039, China
| | - Jian-Fan Wen
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunan 650223, China
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Moraes TF, Reithmeier RAF. Membrane transport metabolons. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2012; 1818:2687-706. [PMID: 22705263 DOI: 10.1016/j.bbamem.2012.06.007] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2011] [Revised: 05/28/2012] [Accepted: 06/05/2012] [Indexed: 10/28/2022]
Abstract
In this review evidence from a wide variety of biological systems is presented for the genetic, functional, and likely physical association of membrane transporters and the enzymes that metabolize the transported substrates. This evidence supports the hypothesis that the dynamic association of transporters and enzymes creates functional membrane transport metabolons that channel substrates typically obtained from the extracellular compartment directly into their cellular metabolism. The immediate modification of substrates on the inner surface of the membrane prevents back-flux through facilitated transporters, increasing the efficiency of transport. In some cases products of the enzymes are themselves substrates for the transporters that efflux the products in an exchange or antiport mechanism. Regulation of the binding of enzymes to transporters and their mutual activities may play a role in modulating flux through transporters and entry of substrates into metabolic pathways. Examples showing the physical association of transporters and enzymes are provided, but available structural data is sparse. Genetic and functional linkages between membrane transporters and enzymes were revealed by an analysis of Escherichia coli operons encoding polycistronic mRNAs and provide a list of predicted interactions ripe for further structural studies. This article supports the view that membrane transport metabolons are important throughout Nature in organisms ranging from bacteria to humans.
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Affiliation(s)
- Trevor F Moraes
- Department of Biochemistry, University of Toronto, Ontario, Canada
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Xu YF, Amador-Noguez D, Reaves ML, Feng XJ, Rabinowitz JD. Ultrasensitive regulation of anapleurosis via allosteric activation of PEP carboxylase. Nat Chem Biol 2012; 8:562-8. [PMID: 22522319 PMCID: PMC3433955 DOI: 10.1038/nchembio.941] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2011] [Accepted: 02/23/2012] [Indexed: 11/09/2022]
Abstract
Anapleurosis is the filling of the tricarboxylic acid cycle with four-carbon units. The common substrate for both anapleurosis and glucose phosphorylation in bacteria is the terminal glycolytic metabolite phosphoenolpyruvate (PEP). Here we show that Escherichia coli quickly and almost completely turns off PEP consumption upon glucose removal. The resulting buildup of PEP is used to quickly import glucose if it becomes available again. The switch-like termination of anapleurosis results from depletion of fructose-1,6-bisphosphate (FBP), an ultrasensitive allosteric activator of PEP carboxylase. E. coli expressing an FBP-insensitive point mutant of PEP carboxylase grow normally when glucose is steadily available. However, they fail to build up PEP upon glucose removal, grow poorly when glucose availability oscillates and suffer from futile cycling at the PEP node on gluconeogenic substrates. Thus, bacterial central carbon metabolism is intrinsically programmed with ultrasensitive allosteric regulation to enable rapid adaptation to changing environmental conditions.
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Affiliation(s)
- Yi-Fan Xu
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, USA
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Sun Y, Liao X, Li D, Feng L, Li J, Wang X, Jin J, Yi F, Zhou L, Wan J. Study on the interaction between cyanobacteria FBP/SBPase and metal ions. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2012; 89:337-344. [PMID: 22244776 DOI: 10.1016/j.saa.2011.12.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2011] [Revised: 12/05/2011] [Accepted: 12/08/2011] [Indexed: 05/31/2023]
Abstract
Fructose-1,6-/sedoheptulose-1,7-bisphosphatase (FBP/SBPase) is a potential important target enzyme for finding inhibitors to solve harmful algal bloom. In this paper, the interactions between FBP/SBPase and metal ions were studied by enzyme activity analysis, fluorescence and molecular modeling method. The enzyme activity analysis showed that FBP/SBPase can be activated by Mg2+ or Mn2+ but cannot be activated by Ca2+ or Zn2+. Spectroscopic analysis of emission quenching showed that quenching mechanism of FBP/SBPase with Mg2+ or Mn2+ was static quenching mechanism while that of Ca2+ or Zn2+ was dynamic quenching process. Hydrogen bonds and van der Waals interaction might be the predominant intermolecular forces in stabilizing FBP/SBPase-Mg2+ while hydrophobic forces were the predominant intermolecular forces in stabilizing FBP/SBPase-Mn2+. Microenvironment and conformation of FBP/SBPase were changed in binding reaction. The effect of metal ions and important amino acid residues on FBP/SBPase-metal ion complex was also discussed by molecular modeling study.
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Affiliation(s)
- Yao Sun
- Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, PR China
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Abstract
Glucose is catabolized in yeast via two fundamental routes, glycolysis and the oxidative pentose phosphate pathway, which produces NADPH and the essential nucleotide component ribose-5-phosphate. Here, we describe riboneogenesis, a thermodynamically driven pathway that converts glycolytic intermediates into ribose-5-phosphate without production of NADPH. Riboneogenesis begins with synthesis, by the combined action of transketolase and aldolase, of the seven-carbon bisphosphorylated sugar sedoheptulose-1,7-bisphosphate. In the pathway's committed step, sedoheptulose bisphosphate is hydrolyzed to sedoheptulose-7-phosphate by the enzyme sedoheptulose-1,7-bisphosphatase (SHB17), whose activity we identified based on metabolomic analysis of the corresponding knockout strain. The crystal structure of Shb17 in complex with sedoheptulose-1,7-bisphosphate reveals that the substrate binds in the closed furan form in the active site. Sedoheptulose-7-phosphate is ultimately converted by known enzymes of the nonoxidative pentose phosphate pathway to ribose-5-phosphate. Flux through SHB17 increases when ribose demand is high relative to demand for NADPH, including during ribosome biogenesis in metabolically synchronized yeast cells.
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Shimada T, Fujita N, Yamamoto K, Ishihama A. Novel roles of cAMP receptor protein (CRP) in regulation of transport and metabolism of carbon sources. PLoS One 2011; 6:e20081. [PMID: 21673794 PMCID: PMC3105977 DOI: 10.1371/journal.pone.0020081] [Citation(s) in RCA: 188] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2011] [Accepted: 04/18/2011] [Indexed: 12/17/2022] Open
Abstract
CRP (cAMP receptor protein), the global regulator of genes for carbon source utilization in the absence of glucose, is the best-studied prokaryotic transcription factor. A total of 195 target promoters on the Escherichia coli genome have been proposed to be under the control of cAMP-bound CRP. Using the newly developed Genomic SELEX screening system of transcription factor-binding sequences, however, we have identified a total of at least 254 CRP-binding sites. Based on their location on the E. coli genome, we predict a total of at least 183 novel regulation target operons, altogether with the 195 hitherto known targets, reaching to the minimum of 378 promoters as the regulation targets of cAMP-CRP. All the promoters selected from the newly identified targets and examined by using the lacZ reporter assay were found to be under the control of CRP, indicating that the Genomic SELEX screening allowed to identify the CRP targets with high accuracy. Based on the functions of novel target genes, we conclude that CRP plays a key regulatory role in the whole processes from the selective transport of carbon sources, the glycolysis-gluconeogenesis switching to the metabolisms downstream of glycolysis, including tricarboxylic acid (TCA) cycle, pyruvate dehydrogenase (PDH) pathway and aerobic respiration. One unique regulation mode is that a single and the same CRP molecule bound within intergenic regions often regulates both of divergently transcribed operons.
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Affiliation(s)
- Tomohiro Shimada
- Department of Frontier Bioscience, Hosei University, Koganei, Tokyo, Japan
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Gutka HJ, Franzblau SG, Movahedzadeh F, Abad-Zapatero C. Crystallization and preliminary X-ray characterization of the glpX-encoded class II fructose-1,6-bisphosphatase from Mycobacterium tuberculosis. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:710-3. [PMID: 21636919 PMCID: PMC3107150 DOI: 10.1107/s1744309111014722] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2011] [Accepted: 04/19/2011] [Indexed: 11/11/2022]
Abstract
Fructose-1,6-bisphosphatase (FBPase; EC 3.1.3.11), which is a key enzyme in gluconeogenesis, catalyzes the hydrolysis of fructose 1,6-bisphosphate to form fructose 6-phosphate and orthophosphate. The present investigation reports the crystallization and preliminary crystallographic studies of the glpX-encoded class II FBPase from Mycobacterium tuberculosis H37Rv. The recombinant protein, which was cloned using an Escherichia coli expression system, was purified and crystallized using the hanging-drop vapor-diffusion method. The crystals diffracted to a resolution of 2.7 Å and belonged to the hexagonal space group P6(1)22, with unit-cell parameters a = b = 131.3, c = 143.2 Å. The structure has been solved by molecular replacement and is currently undergoing refinement.
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Affiliation(s)
- Hiten J. Gutka
- Institute for Tuberculosis Research, University of Illinois at Chicago, Chicago, IL 60607, USA
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, Chicago, IL 60607, USA
- Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Scott G. Franzblau
- Institute for Tuberculosis Research, University of Illinois at Chicago, Chicago, IL 60607, USA
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Farahnaz Movahedzadeh
- Institute for Tuberculosis Research, University of Illinois at Chicago, Chicago, IL 60607, USA
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Cele Abad-Zapatero
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, Chicago, IL 60607, USA
- Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, Chicago, IL 60607, USA
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The poor growth of Rhodospirillum rubrum mutants lacking RubisCO is due to the accumulation of ribulose-1,5-bisphosphate. J Bacteriol 2011; 193:3293-303. [PMID: 21531802 DOI: 10.1128/jb.00265-11] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) catalyzes the first step of CO(2) fixation in the Calvin-Benson-Bassham (CBB) cycle. Besides its function in fixing CO(2) to support photoautotrophic growth, the CBB cycle is also important under photoheterotrophic growth conditions in purple nonsulfur photosynthetic bacteria. It has been assumed that the poor photoheterotrophic growth of RubisCO-deficient strains was due to the accumulation of excess intracellular reductant, which implied that the CBB cycle is important for maintaining the redox balance under these conditions. However, we present analyses of cbbM mutants in Rhodospirillum rubrum that indicate that toxicity is the result of an elevated intracellular pool of ribulose-1,5-bisphosphate (RuBP). There is a redox effect on growth, but it is apparently an indirect effect on the accumulation of RuBP, perhaps by the regulation of the activities of enzymes involved in RuBP regeneration. Our studies also show that the CBB cycle is not essential for R. rubrum to grow under photoheterotrophic conditions and that its role in controlling the redox balance needs to be further elucidated. Finally, we also show that CbbR is a positive transcriptional regulator of the cbb operon (cbbEFPT) in R. rubrum, as seen with related organisms, and define the transcriptional organization of the cbb genes.
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Gutka HJ, Rukseree K, Wheeler PR, Franzblau SG, Movahedzadeh F. glpX gene of Mycobacterium tuberculosis: heterologous expression, purification, and enzymatic characterization of the encoded fructose 1,6-bisphosphatase II. Appl Biochem Biotechnol 2011; 164:1376-89. [PMID: 21451980 DOI: 10.1007/s12010-011-9219-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2010] [Accepted: 03/01/2011] [Indexed: 12/22/2022]
Abstract
The glpX gene (Rv1099c) of Mycobacterium tuberculosis (Mtb) encodes Fructose 1,6-bisphosphatase II (FBPase II; EC 3.1.3.11); a key gluconeogenic enzyme. Mtb possesses glpX homologue as the major known FBPase. This study explored the expression, purification and enzymatic characterization of functionally active FBPase II from Mtb. The glpX gene was cloned, expressed and purified using a two step purification strategy including affinity and size exclusion chromatography. The specific activity of Mtb FBPase II is 1.3 U/mg. The enzyme is oligomeric, followed Michaelis-Menten kinetics with an apparent km = 44 μM. Enzyme activity is dependent on bivalent metal ions and is inhibited by lithium and inorganic phosphate. The pH optimum and thermostability of the enzyme have been determined. The robust expression, purification and assay protocols ensure sufficient production of this protein for structural biology and screening of inhibitors against this enzyme.
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Affiliation(s)
- Hiten J Gutka
- Institute for Tuberculosis Research (M/C 964), College of Pharmacy, Room 412, University of Illinois at Chicago, 833 S. Wood St, Chicago, IL 60612-7231, USA
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Liu Z, Ma Y, Yang J, Qin H. Upregulated and Downregulated Proteins in Hepatocellular Carcinoma: A Systematic Review of Proteomic Profiling Studies. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2011; 15:61-71. [PMID: 20726783 DOI: 10.1089/omi.2010.0061] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Zhihua Liu
- Evidence-Based Medicine Group, Department of Surgery, the Sixth People's Hospital Affiliated to Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Yanlei Ma
- Evidence-Based Medicine Group, Department of Surgery, the Sixth People's Hospital Affiliated to Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Jianjun Yang
- Evidence-Based Medicine Group, Department of Surgery, the Sixth People's Hospital Affiliated to Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Huanlong Qin
- Evidence-Based Medicine Group, Department of Surgery, the Sixth People's Hospital Affiliated to Shanghai Jiao Tong University, Shanghai, People's Republic of China
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Novel members of the Cra regulon involved in carbon metabolism in Escherichia coli. J Bacteriol 2010; 193:649-59. [PMID: 21115656 DOI: 10.1128/jb.01214-10] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cra (catabolite repressor activator) is a global regulator of the genes for carbon metabolism in Escherichia coli. To gain insights into the regulatory roles of Cra, attempts were made to identify the whole set of regulation targets using an improved genomic SELEX (systematic evolution of ligands by exponential enrichment) system. Surprisingly, a total of 164 binding sites were identified for Cra, 144 (88%) of which were newly identified. The majority of known targets were included in the SELEX chip pattern. The promoters examined by the lacZ reporter assay in vivo were all regulated by Cra. These two lines of evidence indicate that a total of as many as 178 promoters are under the control of Cra. The majority of Cra targets are the genes coding for the enzymes involved in central carbon metabolism, covering all the genes for the enzymes involved in glycolysis and metabolism downstream of glycolysis, including the tricarboxylic acid (TCA) cycle and aerobic respiration. Taken together, we propose that Cra plays a key role in balancing the levels of the enzymes for carbon metabolism.
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Kuznetsova E, Xu L, Singer A, Brown G, Dong A, Flick R, Cui H, Cuff M, Joachimiak A, Savchenko A, Yakunin AF. Structure and activity of the metal-independent fructose-1,6-bisphosphatase YK23 from Saccharomyces cerevisiae. J Biol Chem 2010; 285:21049-59. [PMID: 20427268 DOI: 10.1074/jbc.m110.118315] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Fructose-1,6-bisphosphatase (FBPase), a key enzyme of gluconeogenesis and photosynthetic CO(2) fixation, catalyzes the hydrolysis of fructose 1,6-bisphosphate (FBP) to produce fructose 6-phosphate, an important precursor in various biosynthetic pathways. All known FBPases are metal-dependent enzymes, which are classified into five different classes based on their amino acid sequences. Eukaryotes are known to contain only the type-I FBPases, whereas all five types exist in various combinations in prokaryotes. Here we demonstrate that the uncharacterized protein YK23 from Saccharomyces cerevisiae efficiently hydrolyzes FBP in a metal-independent reaction. YK23 is a member of the histidine phosphatase (phosphoglyceromutase) superfamily with homologues found in all organisms. The crystal structure of the YK23 apo-form was solved at 1.75-A resolution and revealed the core domain with the alpha/beta/alpha-fold covered by two small cap domains. Two liganded structures of this protein show the presence of two phosphate molecules (an inhibitor) or FBP (a substrate) bound to the active site. FBP is bound in its linear, open conformation with the cleavable C1-phosphate positioned deep in the active site. Alanine replacement mutagenesis of YK23 identified six conserved residues absolutely required for activity and suggested that His(13) and Glu(99) are the primary catalytic residues. Thus, YK23 represents the first family of metal-independent FBPases and a second FBPase family in eukaryotes.
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Affiliation(s)
- Ekaterina Kuznetsova
- Banting and Best Department of Medical Research, Centre for Structural Proteomics in Toronto, University of Toronto, Toronto, Ontario M5G 1L6, Canada
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Joachimiak A. High-throughput crystallography for structural genomics. Curr Opin Struct Biol 2009; 19:573-84. [PMID: 19765976 DOI: 10.1016/j.sbi.2009.08.002] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2009] [Revised: 08/14/2009] [Accepted: 08/20/2009] [Indexed: 11/20/2022]
Abstract
Protein X-ray crystallography recently celebrated its 50th anniversary. The structures of myoglobin and hemoglobin determined by Kendrew and Perutz provided the first glimpses into the complex protein architecture and chemistry. Since then, the field of structural molecular biology has experienced extraordinary progress and now more than 55000 protein structures have been deposited into the Protein Data Bank. In the past decade many advances in macromolecular crystallography have been driven by world-wide structural genomics efforts. This was made possible because of third-generation synchrotron sources, structure phasing approaches using anomalous signal, and cryo-crystallography. Complementary progress in molecular biology, proteomics, hardware and software for crystallographic data collection, structure determination and refinement, computer science, databases, robotics and automation improved and accelerated many processes. These advancements provide the robust foundation for structural molecular biology and assure strong contribution to science in the future. In this report we focus mainly on reviewing structural genomics high-throughput X-ray crystallography technologies and their impact.
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Affiliation(s)
- Andrzej Joachimiak
- Midwest Center for Structural Genomics, Structural Biology Center, Biosciences Division, Argonne National Laboratory, 9700 S Class Ave., Argonne, IL 60439, USA.
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