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Yin Z, Xu H, Dickschat JS. A clickable coenzyme A derived probe for investigating phosphopantetheinyl transferase activity in natural product biosynthesis. Org Biomol Chem 2024. [PMID: 39381996 DOI: 10.1039/d4ob01485e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/10/2024]
Abstract
Phosphopantetheinyl transferases activate carrier proteins through attachment of a coenzyme A derived phosphopantetheinyl linker. This study describes a method to monitor this process through a modified HSCoA with an alkyne group, allowing for the Cu-catalysed alkyne-azide cycloaddition of a fluorescent tag. Application of the method in an enzyme screening resulted in the identification of new promiscuous PPTases.
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Affiliation(s)
- Zhiyong Yin
- Kekulé-Institute for Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany.
| | - Houchao Xu
- Kekulé-Institute for Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany.
| | - Jeroen S Dickschat
- Kekulé-Institute for Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany.
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2
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Sapkota K, Lucas JK, Faulkner JW, Lichte MF, Guo YL, Burke DH, Huang F. Post-transcriptional capping generates coenzyme A-linked RNA. RNA Biol 2024; 21:1-12. [PMID: 38032240 PMCID: PMC10761072 DOI: 10.1080/15476286.2023.2288740] [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] [Accepted: 11/21/2023] [Indexed: 12/01/2023] Open
Abstract
NAD can be inserted co-transcriptionally via non-canonical initiation to form NAD-RNA. However, that mechanism is unlikely for CoA-linked RNAs due to low intracellular concentration of the required initiator nucleotide, 3'-dephospho-CoA (dpCoA). We report here that phosphopantetheine adenylyltransferase (PPAT), an enzyme of CoA biosynthetic pathway, accepts RNA transcripts as its acceptor substrate and transfers 4'-phosphopantetheine to yield CoA-RNA post-transcriptionally. Synthetic natural (RNAI) and small artificial RNAs were used to identify the features of RNA that are needed for it to serve as PPAT substrate. RNAs with 4-10 unpaired nucleotides at the 5' terminus served as PPAT substrates, but RNAs having <4 unpaired nucleotides did not undergo capping. No capping was observed when the +1A was changed to G or when 5' triphosphate was removed by RNA pyrophosphohydrolase (RppH), suggesting the enzyme recognizes pppA-RNA as an ATP analog. PPAT binding affinities were equivalent for transcripts with +1A, +1 G, or 5'OH (+1A), indicating that productive enzymatic recognition is driven more by local positioning effects than by overall binding affinity. Capping rates were independent of the number of unpaired nucleotides in the range of 4-10 nucleotides. Capping was strongly inhibited by ATP, reducing CoA-RNA production ~70% when equimolar ATP and substrate RNA were present. Dual bacterial expression of candidate RNAs with different 5' structures followed by CoA-RNA CaptureSeq revealed 12-fold enrichment of the better PPAT substrate, consistent with in vivo CoA-capping of RNA transcripts by PPAT. These results suggest post-transcriptional RNA capping as a possible mechanism for the biogenesis of CoA-RNAs in bacteria.
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Affiliation(s)
- Krishna Sapkota
- Department of Chemistry and Biochemistry, University of Southern Mississippi, Hattiesburg, MS, USA
| | - Jordyn K. Lucas
- Department of Biochemistry, University of Missouri, Columbia, MO, USA
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Jarrett W. Faulkner
- Department of Chemistry and Biochemistry, University of Southern Mississippi, Hattiesburg, MS, USA
| | - Matt F. Lichte
- Department of Biochemistry, University of Missouri, Columbia, MO, USA
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Yan-Lin Guo
- Department of Cell and Molecular Biology, University of Southern Mississippi, Hattiesburg, MS, USA
| | - Donald H. Burke
- Department of Biochemistry, University of Missouri, Columbia, MO, USA
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
- Department of Molecular Microbiology & Immunology, University of Missouri, Columbia, MO, USA
| | - Faqing Huang
- Department of Chemistry and Biochemistry, University of Southern Mississippi, Hattiesburg, MS, USA
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3
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Marincin KA, Hwang Y, Kengmana ES, Meyers DJ, Frueh DP. NMR as a readout to monitor and restore the integrity of complex chemoenzymatic reactions. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2022; 342:107265. [PMID: 35849973 PMCID: PMC9463103 DOI: 10.1016/j.jmr.2022.107265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 06/22/2022] [Accepted: 06/28/2022] [Indexed: 06/15/2023]
Abstract
The non-invasive nature of NMR offers a means to monitor biochemical reactions in situ at the atomic level. We harness this advantage to monitor a complex chemoenzymatic reaction that sequentially modifies reagents and loads the product on a nonribosomal peptide synthetase carrier protein. We present a protocol including a pulse sequence that permits to assess both the integrity of reagents and the completion of each step in the reaction, thus alleviating otherwise time-consuming and costly approaches to debug and repeat inefficient reactions. This study highlights the importance of NMR as a tool to establish reliable and reproducible experimental conditions in biochemical studies.
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Affiliation(s)
- Kenneth A Marincin
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Yousang Hwang
- Department of Pharmacology and Molecular Sciences Synthetic Core Facility, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Everett S Kengmana
- Department of Chemical and Biomolecular Engineering, Johns Hopkins Whiting School of Engineering, Baltimore, MD 21218, USA
| | - David J Meyers
- Department of Pharmacology and Molecular Sciences Synthetic Core Facility, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Dominique P Frueh
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA.
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4
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Staphylococcus aureus Small RNAs Possess Dephospho-CoA 5′-Caps, but No CoAlation Marks. Noncoding RNA 2022; 8:ncrna8040046. [PMID: 35893229 PMCID: PMC9326634 DOI: 10.3390/ncrna8040046] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 06/23/2022] [Accepted: 06/24/2022] [Indexed: 11/16/2022] Open
Abstract
Novel features of coenzyme A (CoA) and its precursor, 3′-dephospho-CoA (dpCoA), recently became evident. dpCoA was found to attach to 5′-ends of small ribonucleic acids (dpCoA-RNAs) in two bacterial species (Escherichia coli and Streptomyces venezuelae). Furthermore, CoA serves, in addition to its well-established coenzymatic roles, as a ubiquitous posttranslational protein modification (‘CoAlation’), thought to prevent the irreversible oxidation of cysteines. Here, we first identified and quantified dpCoA-RNAs in the small RNA fraction of the human pathogen Staphylococcus aureus, using a newly developed enzymatic assay. We found that the amount of dpCoA caps was similar to that of the other two bacteria. We furthermore tested the hypothesis that, in the environment of a cell, the free thiol of the dpCoA-RNAs, as well as other sulfur-containing RNA modifications, may be oxidized by disulfide bond formation, e.g., with CoA. While we could not find evidence for such an ‘RNA CoAlation’, we observed that CoA disulfide reductase, the enzyme responsible for reducing CoA homodisulfides in S. aureus, did efficiently reduce several synthetic dpCoA-RNA disulfides to dpCoA-RNAs in vitro. This activity may imply a role in reversing RNA CoAlation.
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5
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Thomas SE, McCarthy WJ, El Bakali J, Brown KP, Kim SY, Blaszczyk M, Mendes V, Abell C, Floto RA, Coyne AG, Blundell TL. Structural Characterization of Mycobacterium abscessus Phosphopantetheine Adenylyl Transferase Ligand Interactions: Implications for Fragment-Based Drug Design. Front Mol Biosci 2022; 9:880432. [PMID: 35712348 PMCID: PMC9197168 DOI: 10.3389/fmolb.2022.880432] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 05/09/2022] [Indexed: 02/02/2023] Open
Abstract
Anti-microbial resistance is a rising global healthcare concern that needs urgent attention as growing number of infections become difficult to treat with the currently available antibiotics. This is particularly true for mycobacterial infections like tuberculosis and leprosy and those with emerging opportunistic pathogens such as Mycobacterium abscessus, where multi-drug resistance leads to increased healthcare cost and mortality. M. abscessus is a highly drug-resistant non-tuberculous mycobacterium which causes life-threatening infections in people with chronic lung conditions such as cystic fibrosis. In this study, we explore M. abscessus phosphopantetheine adenylyl transferase (PPAT), an enzyme involved in the biosynthesis of Coenzyme A, as a target for the development of new antibiotics. We provide structural insights into substrate and feedback inhibitor binding modes of M. abscessus PPAT, thereby setting the basis for further chemical exploration of the enzyme. We then utilize a multi-dimensional fragment screening approach involving biophysical and structural analysis, followed by evaluation of compounds from a previous fragment-based drug discovery campaign against M. tuberculosis PPAT ortholog. This allowed the identification of an early-stage lead molecule exhibiting low micro molar affinity against M. abscessus PPAT (Kd 3.2 ± 0.8 µM) and potential new ways to design inhibitors against this enzyme. The resulting crystal structures reveal striking conformational changes and closure of solvent channel of M. abscessus PPAT hexamer providing novel strategies of inhibition. The study thus validates the ligandability of M. abscessus PPAT as an antibiotic target and identifies crucial starting points for structure-guided drug discovery against this bacterium.
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Affiliation(s)
- Sherine E. Thomas
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - William J. McCarthy
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Jamal El Bakali
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Karen P. Brown
- MRC Laboratory of Molecular Biology, Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - So Yeon Kim
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Michal Blaszczyk
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Vítor Mendes
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
- MRC Laboratory of Molecular Biology, Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Chris Abell
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - R. Andres Floto
- MRC Laboratory of Molecular Biology, Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
- Cambridge Centre for Lung Infection, Royal Papworth Hospital, Cambridge, United Kingdom
| | - Anthony G. Coyne
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Tom L. Blundell
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
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6
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Dinoflagellate Phosphopantetheinyl Transferase (PPTase) and Thiolation Domain Interactions Characterized Using a Modified Indigoidine Synthesizing Reporter. Microorganisms 2022; 10:microorganisms10040687. [PMID: 35456738 PMCID: PMC9027781 DOI: 10.3390/microorganisms10040687] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 03/07/2022] [Accepted: 03/14/2022] [Indexed: 02/01/2023] Open
Abstract
Photosynthetic dinoflagellates synthesize many toxic but also potential therapeutic compounds therapeutics via polyketide/non-ribosomal peptide synthesis, a common means of producing natural products in bacteria and fungi. Although canonical genes are identifiable in dinoflagellate transcriptomes, the biosynthetic pathways are obfuscated by high copy numbers and fractured synteny. This study focuses on the carrier domains that scaffold natural product synthesis (thiolation domains) and the phosphopantetheinyl transferases (PPTases) that thiolate these carriers. We replaced the thiolation domain of the indigoidine producing BpsA gene from Streptomyces lavendulae with those of three multidomain dinoflagellate transcripts and coexpressed these constructs with each of three dinoflagellate PPTases looking for specific pairings that would identify distinct pathways. Surprisingly, all three PPTases were able to activate all the thiolation domains from one transcript, although with differing levels of indigoidine produced, demonstrating an unusual lack of specificity. Unfortunately, constructs with the remaining thiolation domains produced almost no indigoidine and the thiolation domain for lipid synthesis could not be expressed in E. coli. These results combined with inconsistent protein expression for different PPTase/thiolation domain pairings present technical hurdles for future work. Despite these challenges, expression of catalytically active dinoflagellate proteins in E. coli is a novel and useful tool going forward.
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Zhu R, Mathur V. Prophages Present in Acinetobacter pittii Influence Bacterial Virulence, Antibiotic Resistance, and Genomic Rearrangements. PHAGE (NEW ROCHELLE, N.Y.) 2022; 3:38-49. [PMID: 36161193 PMCID: PMC9041518 DOI: 10.1089/phage.2021.0014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Introduction: Antibiotic resistance and virulence are common among bacterial populations, posing a global clinical challenge. The bacterial species Acinetobacter pittii, an infectious agent in clinical environments, has shown increasing rates of antibiotic resistance. Viruses that integrate as prophages into A. pittii could be a potential cause of this pathogenicity, as they often contain antibiotic resistance or virulence factor gene sequences. Methods: In this study, we analyzed 25 A. pittii strains for potential prophages. Using virulence factor databases, we identified many common and virulent prophages in A. pittii. Results: The analysis also included a specific catalogue of the virulence factors and antibiotic resistance genes contributed by A. pittii prophages. Finally, our results illustrate multiple similarities between A. pittii and its bacterial relatives with regard to prophage integration sites and prevalence. Discussion: These findings provide a broader insight into prophage behavior that can be applied to future studies on similar species in the Acinetobacter calcoaceticus-baumannii complex.
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Affiliation(s)
| | - Vinayak Mathur
- Department of Science, Cabrini University, Radnor, Pennsylvania, USA.,Address correspondence to: Vinayak Mathur, PhD, Department of Science, Cabrini University, 610 King of Prussia Road, IAD 224, Radnor, PA 19087-3698, USA
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8
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Evans JC, Murugesan D, Post JM, Mendes V, Wang Z, Nahiyaan N, Lynch SL, Thompson S, Green SR, Ray PC, Hess J, Spry C, Coyne AG, Abell C, Boshoff HIM, Wyatt PG, Rhee KY, Blundell TL, Barry CE, Mizrahi V. Targeting Mycobacterium tuberculosis CoaBC through Chemical Inhibition of 4'-Phosphopantothenoyl-l-cysteine Synthetase (CoaB) Activity. ACS Infect Dis 2021; 7:1666-1679. [PMID: 33939919 PMCID: PMC8205227 DOI: 10.1021/acsinfecdis.0c00904] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Indexed: 02/02/2023]
Abstract
Coenzyme A (CoA) is a ubiquitous cofactor present in all living cells and estimated to be required for up to 9% of intracellular enzymatic reactions. Mycobacterium tuberculosis (Mtb) relies on its own ability to biosynthesize CoA to meet the needs of the myriad enzymatic reactions that depend on this cofactor for activity. As such, the pathway to CoA biosynthesis is recognized as a potential source of novel tuberculosis drug targets. In prior work, we genetically validated CoaBC as a bactericidal drug target in Mtb in vitro and in vivo. Here, we describe the identification of compound 1f, a small molecule inhibitor of the 4'-phosphopantothenoyl-l-cysteine synthetase (PPCS; CoaB) domain of the bifunctional Mtb CoaBC, and show that this compound displays on-target activity in Mtb. Compound 1f was found to inhibit CoaBC uncompetitively with respect to 4'-phosphopantothenate, the substrate for the CoaB-catalyzed reaction. Furthermore, metabolomic profiling of wild-type Mtb H37Rv following exposure to compound 1f produced a signature consistent with perturbations in pantothenate and CoA biosynthesis. As the first report of a direct small molecule inhibitor of Mtb CoaBC displaying target-selective whole-cell activity, this study confirms the druggability of CoaBC and chemically validates this target.
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Affiliation(s)
- Joanna C. Evans
- MRC/NHLS/UCT
Molecular Mycobacteriology Research Unit & DST/NRF Centre of Excellence
for Biomedical TB Research & Wellcome Centre for Infectious Diseases
Research in Africa, Institute of Infectious Disease and Molecular
Medicine and Department of Pathology, Faculty of Health Sciences, University of Cape Town, Anzio Road, Observatory 7925, South Africa
| | - Dinakaran Murugesan
- Drug
Discovery Unit, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1
5EH, Scotland, U.K.
| | - John M. Post
- Drug
Discovery Unit, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1
5EH, Scotland, U.K.
| | - Vitor Mendes
- Department
of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, U.K.
| | - Zhe Wang
- Department
of Microbiology and Immunology, Weill Cornell
Medical College, New York, New York 10065, United States
| | - Navid Nahiyaan
- Department
of Microbiology and Immunology, Weill Cornell
Medical College, New York, New York 10065, United States
| | - Sasha L. Lynch
- MRC/NHLS/UCT
Molecular Mycobacteriology Research Unit & DST/NRF Centre of Excellence
for Biomedical TB Research & Wellcome Centre for Infectious Diseases
Research in Africa, Institute of Infectious Disease and Molecular
Medicine and Department of Pathology, Faculty of Health Sciences, University of Cape Town, Anzio Road, Observatory 7925, South Africa
| | - Stephen Thompson
- Drug
Discovery Unit, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1
5EH, Scotland, U.K.
| | - Simon R. Green
- Drug
Discovery Unit, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1
5EH, Scotland, U.K.
| | - Peter C. Ray
- Drug
Discovery Unit, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1
5EH, Scotland, U.K.
| | - Jeannine Hess
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Christina Spry
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Anthony G. Coyne
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Chris Abell
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Helena I. M. Boshoff
- Tuberculosis
Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Disease,
National Institutes of Health, 9000 Rockville Pike, Bethesda, Maryland 20892, United States
| | - Paul G. Wyatt
- Drug
Discovery Unit, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1
5EH, Scotland, U.K.
| | - Kyu Y. Rhee
- Department
of Microbiology and Immunology, Weill Cornell
Medical College, New York, New York 10065, United States
| | - Tom L. Blundell
- Department
of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, U.K.
| | - Clifton E. Barry
- MRC/NHLS/UCT
Molecular Mycobacteriology Research Unit & DST/NRF Centre of Excellence
for Biomedical TB Research & Wellcome Centre for Infectious Diseases
Research in Africa, Institute of Infectious Disease and Molecular
Medicine and Department of Pathology, Faculty of Health Sciences, University of Cape Town, Anzio Road, Observatory 7925, South Africa
- Tuberculosis
Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Disease,
National Institutes of Health, 9000 Rockville Pike, Bethesda, Maryland 20892, United States
| | - Valerie Mizrahi
- MRC/NHLS/UCT
Molecular Mycobacteriology Research Unit & DST/NRF Centre of Excellence
for Biomedical TB Research & Wellcome Centre for Infectious Diseases
Research in Africa, Institute of Infectious Disease and Molecular
Medicine and Department of Pathology, Faculty of Health Sciences, University of Cape Town, Anzio Road, Observatory 7925, South Africa
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9
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Wang J, Ma W, Wang X. Insights into the structure of Escherichia coli outer membrane as the target for engineering microbial cell factories. Microb Cell Fact 2021; 20:73. [PMID: 33743682 PMCID: PMC7980664 DOI: 10.1186/s12934-021-01565-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 03/12/2021] [Indexed: 12/16/2022] Open
Abstract
Escherichia coli is generally used as model bacteria to define microbial cell factories for many products and to investigate regulation mechanisms. E. coli exhibits phospholipids, lipopolysaccharides, colanic acid, flagella and type I fimbriae on the outer membrane which is a self-protective barrier and closely related to cellular morphology, growth, phenotypes and stress adaptation. However, these outer membrane associated molecules could also lead to potential contamination and insecurity for fermentation products and consume lots of nutrients and energy sources. Therefore, understanding critical insights of these membrane associated molecules is necessary for building better microbial producers. Here the biosynthesis, function, influences, and current membrane engineering applications of these outer membrane associated molecules were reviewed from the perspective of synthetic biology, and the potential and effective engineering strategies on the outer membrane to improve fermentation features for microbial cell factories were suggested.
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Affiliation(s)
- Jianli Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China.,International Joint Laboratory On Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Wenjian Ma
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China.,Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
| | - Xiaoyuan Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China. .,Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.
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10
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Lingel A, Vulpetti A, Reinsperger T, Proudfoot A, Denay R, Frommlet A, Henry C, Hommel U, Gossert AD, Luy B, Frank AO. Comprehensive and High-Throughput Exploration of Chemical Space Using Broadband 19 F NMR-Based Screening. Angew Chem Int Ed Engl 2020; 59:14809-14817. [PMID: 32363632 DOI: 10.1002/anie.202002463] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 04/27/2020] [Indexed: 12/20/2022]
Abstract
Fragment-based lead discovery has become a fundamental approach to identify ligands that efficiently interact with disease-relevant targets. Among the numerous screening techniques, fluorine-detected NMR has gained popularity owing to its high sensitivity, robustness, and ease of use. To effectively explore chemical space, a universal NMR experiment, a rationally designed fragment library, and a sample composition optimized for a maximal number of compounds and minimal measurement time are required. Here, we introduce a comprehensive method that enabled the efficient assembly of a high-quality and diverse library containing nearly 4000 fragments and screening for target-specific binders within days. At the core of the approach is a novel broadband relaxation-edited NMR experiment that covers the entire chemical shift range of drug-like 19 F motifs in a single measurement. Our approach facilitates the identification of diverse binders and the fast ligandability assessment of new targets.
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Affiliation(s)
- Andreas Lingel
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, CA, 94608, USA.,Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Campus, 4056, Basel, Switzerland
| | - Anna Vulpetti
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Campus, 4056, Basel, Switzerland
| | - Tony Reinsperger
- Institute of Organic Chemistry and Institute for Biological Interfaces 4 - Magnetic Resonance, Karlsruhe Institute of Technology (KIT), 76131, Karlsruhe, Germany
| | - Andrew Proudfoot
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, CA, 94608, USA
| | - Regis Denay
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Campus, 4056, Basel, Switzerland
| | - Alexandra Frommlet
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, CA, 94608, USA
| | - Christelle Henry
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Novartis Campus, 4056, Basel, Switzerland
| | - Ulrich Hommel
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Novartis Campus, 4056, Basel, Switzerland
| | - Alvar D Gossert
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Novartis Campus, 4056, Basel, Switzerland
| | - Burkhard Luy
- Institute of Organic Chemistry and Institute for Biological Interfaces 4 - Magnetic Resonance, Karlsruhe Institute of Technology (KIT), 76131, Karlsruhe, Germany
| | - Andreas O Frank
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, CA, 94608, USA
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11
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Lingel A, Vulpetti A, Reinsperger T, Proudfoot A, Denay R, Frommlet A, Henry C, Hommel U, Gossert AD, Luy B, Frank AO. Comprehensive and High‐Throughput Exploration of Chemical Space Using Broadband
19
F NMR‐Based Screening. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202002463] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Andreas Lingel
- Global Discovery Chemistry Novartis Institutes for BioMedical Research 5300 Chiron Way Emeryville CA 94608 USA
- Global Discovery Chemistry Novartis Institutes for BioMedical Research Novartis Campus 4056 Basel Switzerland
| | - Anna Vulpetti
- Global Discovery Chemistry Novartis Institutes for BioMedical Research Novartis Campus 4056 Basel Switzerland
| | - Tony Reinsperger
- Institute of Organic Chemistry and Institute for Biological Interfaces 4 – Magnetic Resonance Karlsruhe Institute of Technology (KIT) 76131 Karlsruhe Germany
| | - Andrew Proudfoot
- Global Discovery Chemistry Novartis Institutes for BioMedical Research 5300 Chiron Way Emeryville CA 94608 USA
| | - Regis Denay
- Global Discovery Chemistry Novartis Institutes for BioMedical Research Novartis Campus 4056 Basel Switzerland
| | - Alexandra Frommlet
- Global Discovery Chemistry Novartis Institutes for BioMedical Research 5300 Chiron Way Emeryville CA 94608 USA
| | - Christelle Henry
- Chemical Biology and Therapeutics Novartis Institutes for BioMedical Research Novartis Campus 4056 Basel Switzerland
| | - Ulrich Hommel
- Chemical Biology and Therapeutics Novartis Institutes for BioMedical Research Novartis Campus 4056 Basel Switzerland
| | - Alvar D. Gossert
- Chemical Biology and Therapeutics Novartis Institutes for BioMedical Research Novartis Campus 4056 Basel Switzerland
| | - Burkhard Luy
- Institute of Organic Chemistry and Institute for Biological Interfaces 4 – Magnetic Resonance Karlsruhe Institute of Technology (KIT) 76131 Karlsruhe Germany
| | - Andreas O. Frank
- Global Discovery Chemistry Novartis Institutes for BioMedical Research 5300 Chiron Way Emeryville CA 94608 USA
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12
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Gupta A, Singh PK, Sharma P, Kaur P, Sharma S, Singh TP. Structural and biochemical studies of phosphopantetheine adenylyltransferase from Acinetobacter baumannii with dephospho-coenzyme A and coenzyme A. Int J Biol Macromol 2019; 142:181-190. [PMID: 31525415 DOI: 10.1016/j.ijbiomac.2019.09.090] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 09/11/2019] [Accepted: 09/11/2019] [Indexed: 11/29/2022]
Abstract
Phosphopantetheine adenylyl transferase catalyzes a rate limiting penultimate step of the multistep reaction which produces coenzyme A (CoA) as a final product. CoA is required as an essential cofactor in a number of metabolic reactions. Therefore inhibiting the function of this enzyme will lead to cell death in bacteria. Acinetobacter baumannii is multi drug resistant pathogen and causes infections in immunocompromised patients. AbPPAT has been cloned, expressed, purified and crystallized and structures of two complexes of AbPPAT with dephospho coenzyme A (dPCoA) and coenzyme A (CoA) have been determined. Both dPCoA and CoA molecules are observed in the substrate binding site of AbPPAT. A comparison with the structures of the complexes of PPAT from other species shows that the orientations of dPCoA are identical in all the structures. On the other hand, as observed from the structures of the complexes of CoA with PPAT, the orientations of CoA are found to differ considerably. This shows that the substrates occupy identical positions in the substrate binding sites of enzymes whereas the positions of inhibitors may differ. The binding studies carried out using fluorescence method and surface plasmon resonance techniques showed that binding affinity of CoA towards AbPPAT is nearly three times higher than that of dPCoA.
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Affiliation(s)
- A Gupta
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - P K Singh
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - P Sharma
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - P Kaur
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - S Sharma
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - T P Singh
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India.
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13
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Structural and binding studies of phosphopantetheine adenylyl transferase from Acinetobacter baumannii. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1867:537-547. [DOI: 10.1016/j.bbapap.2019.03.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 02/25/2019] [Accepted: 03/13/2019] [Indexed: 11/21/2022]
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14
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Mouterde LMM, Stewart JD. Isolation and Synthesis of One of the Most Central Cofactors in Metabolism: Coenzyme A. Org Process Res Dev 2018. [DOI: 10.1021/acs.oprd.8b00348] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Jon D. Stewart
- Department of Chemistry, 126 Sisler Hall, University of Florida, Gainesville, Florida 32611, United States
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15
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Skepper CK, Moreau RJ, Appleton BA, Benton BM, Drumm JE, Feng BY, Geng M, Hu C, Li C, Lingel A, Lu Y, Mamo M, Mergo W, Mostafavi M, Rath CM, Steffek M, Takeoka KT, Uehara K, Wang L, Wei JR, Xie L, Xu W, Zhang Q, de Vicente J. Discovery and Optimization of Phosphopantetheine Adenylyltransferase Inhibitors with Gram-Negative Antibacterial Activity. J Med Chem 2018; 61:3325-3349. [DOI: 10.1021/acs.jmedchem.7b01861] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Colin K. Skepper
- Novartis Institutes for Biomedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Robert J. Moreau
- Novartis Institutes for Biomedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Brent A. Appleton
- Novartis Institutes for Biomedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Bret M. Benton
- Novartis Institutes for Biomedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Joseph E. Drumm
- Novartis Institutes for Biomedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Brian Y. Feng
- Novartis Institutes for Biomedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Mei Geng
- Novartis Institutes for Biomedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Cheng Hu
- Novartis Institutes for Biomedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Cindy Li
- Novartis Institutes for Biomedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Andreas Lingel
- Novartis Institutes for Biomedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Yipin Lu
- Novartis Institutes for Biomedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Mulugeta Mamo
- Novartis Institutes for Biomedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Wosenu Mergo
- Novartis Institutes for Biomedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Mina Mostafavi
- Novartis Institutes for Biomedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Christopher M. Rath
- Novartis Institutes for Biomedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Micah Steffek
- Novartis Institutes for Biomedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Kenneth T. Takeoka
- Novartis Institutes for Biomedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Kyoko Uehara
- Novartis Institutes for Biomedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Lisha Wang
- Novartis Institutes for Biomedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Jun-Rong Wei
- Novartis Institutes for Biomedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Lili Xie
- Novartis Institutes for Biomedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Wenjian Xu
- Novartis Institutes for Biomedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Qiong Zhang
- Novartis Institutes for Biomedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Javier de Vicente
- Novartis Institutes for Biomedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
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16
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Plesa C, Sidore AM, Lubock NB, Zhang D, Kosuri S. Multiplexed gene synthesis in emulsions for exploring protein functional landscapes. Science 2018; 359:343-347. [PMID: 29301959 PMCID: PMC6261299 DOI: 10.1126/science.aao5167] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 12/18/2017] [Indexed: 12/14/2022]
Abstract
Improving our ability to construct and functionally characterize DNA sequences would broadly accelerate progress in biology. Here, we introduce DropSynth, a scalable, low-cost method to build thousands of defined gene-length constructs in a pooled (multiplexed) manner. DropSynth uses a library of barcoded beads that pull down the oligonucleotides necessary for a gene's assembly, which are then processed and assembled in water-in-oil emulsions. We used DropSynth to successfully build more than 7000 synthetic genes that encode phylogenetically diverse homologs of two essential genes in Escherichia coli We tested the ability of phosphopantetheine adenylyltransferase homologs to complement a knockout E. coli strain in multiplex, revealing core functional motifs and reasons underlying homolog incompatibility. DropSynth coupled with multiplexed functional assays allows us to rationally explore sequence-function relationships at an unprecedented scale.
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Affiliation(s)
- Calin Plesa
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California, USA
| | - Angus M. Sidore
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, California, USA
| | - Nathan B. Lubock
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California, USA
| | - Di Zhang
- Genomics and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Sriram Kosuri
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California, USA
- UCLA-DOE Institute for Genomics and Proteomics, Molecular Biology Institute, Quantitative and Computational Biology Institute, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, California, USA
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17
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Efficient one-pot enzymatic synthesis of dephospho coenzyme A. Bioorg Chem 2017; 76:23-27. [PMID: 29107839 DOI: 10.1016/j.bioorg.2017.10.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 10/06/2017] [Accepted: 10/22/2017] [Indexed: 11/23/2022]
Abstract
Dephospho coenzyme A (depCoA) is the last intermediate for CoA biosynthesis, and it can be used as a transcription initiator to prepare CoA-linked RNA by in vitro transcription. However, commercially available depCoA is expensive. We hereby describe a simple and efficient enzymatic synthesis of depCoA in a single-step from commercially available and inexpensive oxidized pantethine (Ox-Pan) and ATP. A plasmid (pCoaDAa) was constructed to co-express and co-purify two enzymes pantothenate kinase (PanK/coaA) and phosphopantetheine adenylyltransferase (PPAT/coaD). Starting from Ox-Pan and ATP, two different synthetic routes of one-pot reaction catalyzed by PanK and PPAT, followed by a simple column purification step, afforded depCoA and its oxidized dimer (Ox-depCoA) with high yields and purity. The simplicity and low cost of our method should make depCoA easily accessible to a broad scientific community, and promote research on CoA-related areas in biology and biomedicine.
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18
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Thomas SE, Mendes V, Kim SY, Malhotra S, Ochoa-Montaño B, Blaszczyk M, Blundell TL. Structural Biology and the Design of New Therapeutics: From HIV and Cancer to Mycobacterial Infections: A Paper Dedicated to John Kendrew. J Mol Biol 2017; 429:2677-2693. [PMID: 28648615 DOI: 10.1016/j.jmb.2017.06.014] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 06/19/2017] [Indexed: 10/19/2022]
Abstract
Interest in applications of protein crystallography to medicine was evident, as the first high-resolution structures emerged in the 50s and 60s. In Cambridge, Max Perutz and John Kendrew sought to understand mutations in sickle cell and other genetic diseases related to hemoglobin, while in Oxford, the group of Dorothy Hodgkin became interested in long-lasting zinc-insulin crystals for treatment of diabetes and later considered insulin redesign, as synthetic insulins became possible. The use of protein crystallography in structure-guided drug discovery emerged as enzyme structures allowed the identification of potential inhibitor-binding sites and optimization of interactions of hits using the structure of the target protein. Early examples of this approach were the use of the structure of renin to design antihypertensives and the structure of HIV protease in design of AIDS antivirals. More recently, use of structure-guided design with fragment-based drug discovery, which reduces the size of screening libraries by decreasing complexity, has improved ligand efficiency in drug design and has been used to progress three oncology drugs through clinical trials to FDA approval. We exemplify current developments in structure-guided target identification and fragment-based lead discovery with efforts to develop new antimicrobials for mycobacterial infections.
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Affiliation(s)
- Sherine E Thomas
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA UK
| | - Vitor Mendes
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA UK
| | - So Yeon Kim
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA UK
| | - Sony Malhotra
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA UK
| | - Bernardo Ochoa-Montaño
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA UK
| | - Michal Blaszczyk
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA UK
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA UK.
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19
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The Complete Structure of the Core Oligosaccharide from Edwardsiella tarda EIB 202 Lipopolysaccharide. Int J Mol Sci 2017; 18:ijms18061163. [PMID: 28561753 PMCID: PMC5485987 DOI: 10.3390/ijms18061163] [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: 02/18/2017] [Revised: 04/10/2017] [Accepted: 05/24/2017] [Indexed: 11/17/2022] Open
Abstract
The chemical structure and genomics of the lipopolysaccharide (LPS) core oligosaccharide of pathogenic Edwardsiella tarda strain EIB 202 were studied for the first time. The complete gene assignment for all LPS core biosynthesis gene functions was acquired. The complete structure of core oligosaccharide was investigated by 1H and 13C nuclear magnetic resonance (NMR) spectroscopy, electrospray ionization mass spectrometry MSn, and matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry. The following structure of the undecasaccharide was established:
The heterogeneous appearance of the core oligosaccharide structure was due to the partial lack of β-d-Galp and the replacement of α-d-GlcpNAcGly by α-d-GlcpNGly. The glycine location was identified by mass spectrometry.
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20
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Sun T, Pei G, Wang J, Chen L, Zhang W. A novel small RNA CoaR regulates coenzyme A biosynthesis and tolerance of Synechocystis sp. PCC6803 to 1-butanol possibly via promoter-directed transcriptional silencing. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:42. [PMID: 28239414 PMCID: PMC5319066 DOI: 10.1186/s13068-017-0727-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 02/09/2017] [Indexed: 05/24/2023]
Abstract
BACKGROUND Microbial small RNAs (sRNAs) have been proposed as valuable regulatory elements for optimizing cellular metabolism for industrial purposes. However, little information is currently available on functional relevance of sRNAs to biofuels tolerance in cyanobacteria. RESULTS Here, we described the identification and functional characterization of a novel 124 nt sRNA Ncl1460 involved in tolerance to biofuel 1-butanol in Synechocystis sp. PCC 6803. The expression of Ncl1460 was verified by blotting assay and its length was determined through 3' RACE. Further analysis showed that Ncl1460 was a negative regulator of slr0847 (coaD) and slr0848 operon responsible for coenzyme A (CoA) synthesis possibly via promoter-directed transcriptional silencing mechanisms which has been widely discovered in eukaryote; thus Ncl1460 was designated as CoaR (CoA Biosynthesis Regulatory sRNA). The possible interaction between CoaR and target genes was suggested by CoA quantification and green fluorescent protein assays. Finally, a quantitative proteomics analysis showed that CoaR regulated tolerance to 1-butanol possibly by down-regulating CoA biosynthesis, resulting in a decrease of fatty acid metabolism and energy metabolism. CONCLUSIONS As the first reported sRNA involved CoA synthesis and 1-butanol tolerance in cyanobacteria, this study provides not only novel insights in regulating mechanisms of essential pathways in cyanobacteria, but also valuable target for biofuels tolerance and productivity modifications.
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Affiliation(s)
- Tao Sun
- Laboratory of Synthetic Microbiology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 People’s Republic of China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072 People’s Republic of China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, 300072 People’s Republic of China
| | - Guangsheng Pei
- Laboratory of Synthetic Microbiology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 People’s Republic of China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072 People’s Republic of China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, 300072 People’s Republic of China
| | - Jiangxin Wang
- Shenzhen Engineering Lab for Marine Algal Biotechnology, College of Life Science, Shenzhen University, Shenzhen, 518060 People’s Republic of China
| | - Lei Chen
- Laboratory of Synthetic Microbiology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 People’s Republic of China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072 People’s Republic of China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, 300072 People’s Republic of China
| | - Weiwen Zhang
- Laboratory of Synthetic Microbiology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 People’s Republic of China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072 People’s Republic of China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, 300072 People’s Republic of China
- Center for Biosafety Research and Strategy, Tianjin University, Tianjin, People’s Republic of China
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21
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Shen HJ, Cheng BY, Zhang YM, Tang L, Li Z, Bu YF, Li XR, Tian GQ, Liu JZ. Dynamic control of the mevalonate pathway expression for improved zeaxanthin production in Escherichia coli and comparative proteome analysis. Metab Eng 2016; 38:180-190. [DOI: 10.1016/j.ymben.2016.07.012] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2016] [Revised: 06/07/2016] [Accepted: 07/25/2016] [Indexed: 01/13/2023]
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22
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Noah C, Brabetz W, Gronow S, Brade H. Cloning, sequencing, and functional analysis of three glycosyltransferases involved in the biosynthesis of the inner core region of Klebsiella pneumoniae lipopolysaccharide. ACTA ACUST UNITED AC 2016. [DOI: 10.1177/09680519010070010401] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The genes encoding the 3-deoxy-D- manno-oct-2-ulosonic acid (Kdo) transferase ( waaA) and heptosyltransferases I ( waaC) and II ( waaF) in Klebsiella pneumoniae were cloned from a DNA library by functional complementation of corresponding Escherichia coli and Salmonella enterica mutants. Sequence analyses revealed extensive homologies of the deduced proteins to their counterparts in other Enterobacteriaceae. However, differences were evident with regard to the chromosomal organization of the genes. To perform in vitro studies, the waaA, waaC and waaF genes were subcloned and expressed in the Gram-positive host Corynebacterium glutamicum. WaaA was characterized as a bifunctional enzyme capable of transferring two Kdo residues to a synthetic bisphosphorylated tetraacyl-lipid A precursor of E. coli (compound 406). In contrast, waaC and waaF were shown to encode specific glycosyltransferases catalyzing the consecutive transfer of two L- glycero-D- manno-heptose residues to Kdo2-406.
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Affiliation(s)
- Christian Noah
- Division of Medical and Biochemical Microbiology, Research Center Borstel, Center for Medicine and Biosciences, Borstel, Germany,
| | - Werner Brabetz
- Division of Medical and Biochemical Microbiology, Research Center Borstel, Center for Medicine and Biosciences, Borstel, Germany
| | - Sabine Gronow
- Division of Medical and Biochemical Microbiology, Research Center Borstel, Center for Medicine and Biosciences, Borstel, Germany
| | - Helmut Brade
- Division of Medical and Biochemical Microbiology, Research Center Borstel, Center for Medicine and Biosciences, Borstel, Germany
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23
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Gronow S, Brade H. Invited review: Lipopolysaccharide biosynthesis: which steps do bacteria need to survive? ACTA ACUST UNITED AC 2016. [DOI: 10.1177/09680519010070010301] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
A detailed knowledge of LPS biosynthesis is of the utmost importance in understanding the function of the outer membrane of Gram-negative bacteria. The regulation of LPS biosynthesis affects many more compartments of the bacterial cell than the outer membrane and thus contributes to the understanding of the physiology of Gram-negative bacteria in general, on the basis of which only mechanisms of virulence and antibiotic resistance can be studied to find new targets for antibacterial treatment. The study of LPS biosynthesis is also an excellent example to demonstrate the limitations of `genomics' and `proteomics', since secondary gene products can be studied only by the combined tools of molecular genetics, enzymology and analytical structural biochemistry. Thus, the door to the field of `glycomics' is opened.
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Affiliation(s)
- Sabine Gronow
- Division of Medical and Biochemical Microbiology, Research Center Borstel, Center for Medicine and Biosciences, Borstel, Germany,
| | - Helmut Brade
- Division of Medical and Biochemical Microbiology, Research Center Borstel, Center for Medicine and Biosciences, Borstel, Germany
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24
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Proudfoot A, Frank AO, Ruggiu F, Mamo M, Lingel A. Facilitating unambiguous NMR assignments and enabling higher probe density through selective labeling of all methyl containing amino acids. JOURNAL OF BIOMOLECULAR NMR 2016; 65:15-27. [PMID: 27130242 DOI: 10.1007/s10858-016-0032-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Accepted: 04/19/2016] [Indexed: 05/05/2023]
Abstract
The deuteration of proteins and selective labeling of side chain methyl groups has greatly enhanced the molecular weight range of proteins and protein complexes which can be studied using solution NMR spectroscopy. Protocols for the selective labeling of all six methyl group containing amino acids individually are available, however to date, only a maximum of five amino acids have been labeled simultaneously. Here, we describe a new methodology for the simultaneous, selective labeling of all six methyl containing amino acids using the 115 kDa homohexameric enzyme CoaD from E. coli as a model system. The utility of the labeling protocol is demonstrated by efficiently and unambiguously assigning all methyl groups in the enzymatic active site using a single 4D (13)C-resolved HMQC-NOESY-HMQC experiment, in conjunction with a crystal structure. Furthermore, the six fold labeled protein was employed to characterize the interaction between the substrate analogue (R)-pantetheine and CoaD by chemical shift perturbations, demonstrating the benefit of the increased probe density.
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Affiliation(s)
- Andrew Proudfoot
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, CA, 94608, USA
| | - Andreas O Frank
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, CA, 94608, USA
| | - Fiorella Ruggiu
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, CA, 94608, USA
| | - Mulugeta Mamo
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, CA, 94608, USA
| | - Andreas Lingel
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, CA, 94608, USA.
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25
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Mouterde LMM, Stewart JD. An Efficient Chemoenzymatic Synthesis of Coenzyme A and Its Disulfide. Org Process Res Dev 2016. [DOI: 10.1021/acs.oprd.6b00059] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Louis M. M. Mouterde
- Department
of Chemistry, University of Florida, 126 Sisler Hall, Gainesville, Florida 32611, United States
| | - Jon D. Stewart
- Department
of Chemistry, University of Florida, 126 Sisler Hall, Gainesville, Florida 32611, United States
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26
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Alanazi IO, Benabdelkamel H, Alfadda AA, AlYahya SA, Alghamdi WM, Aljohi HA, Almalik A, Masood A. Proteomic Analysis of the Protein Expression Profile in the Mature Nigella sativa (Black Seed). Appl Biochem Biotechnol 2016; 179:1184-201. [DOI: 10.1007/s12010-016-2058-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 03/16/2016] [Indexed: 12/20/2022]
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27
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Ding Y, Jones GM, Brimacombe C, Uchida K, Aizawa SI, Logan SM, Kelly JF, Jarrell KF. Identification of a gene involved in the biosynthesis pathway of the terminal sugar of the archaellin N-linked tetrasaccharide in Methanococcus maripaludis. Antonie van Leeuwenhoek 2015; 109:131-48. [PMID: 26590834 DOI: 10.1007/s10482-015-0615-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 10/28/2015] [Indexed: 10/22/2022]
Abstract
In Methanococcus maripaludis, the three archaellins which comprise the archaellum are modified at multiple sites with an N-linked tetrasaccharide with the structure of Sug-4-β-ManNAc3NAmA6Thr-4-β-GlcNAc3NAcA-3-β-GalNAc, where Sug is a unique sugar (5S)-2-acetamido-2,4-dideoxy-5-O-methyl-L-erythro-hexos-5-ulo-1,5-pyranose, so far found exclusively in this species. In this study, a six-gene cluster mmp1089-1094, neighboring one of the genomic regions already known to contain genes involved with the archaellin N-glycosylation pathway, was examined for its potential involvement in the archaellin N-glycosylation or sugar biosynthesis pathway. The co-transcription of these six genes was demonstrated by RT-PCR. Mutants carrying an in-frame deletion in mmp1090, mmp1091 or mmp1092 were successfully generated. The Δmmp1090 deletion mutant was archaellated when examined by electron microscopy and mass spectrometry analysis of purified archaella showed that the archaellins were modified with a truncated N-glycan in which the terminal sugar residue and the threonine linked to the third sugar residue were missing. Both gene annotation and bioinformatic analyses indicate that MMP1090 is a UDP-glucose 4-epimerase, suggesting that the unique terminal sugar of the archaellin N-glycan might be synthesised from UDP-glucose or UDP-N-acetylglucosamine with an essential early step in synthesis catalysed by MMP1090. In contrast, no detectable phenotype related to archaellin glycosylation was observed in mutants deleted for either mmp1091 or mmp1092 while attempts to delete mmp1089, mmp1093 and mmp1094 were unsuccessful. Based on its demonstrated involvement in the archaellin N-glycosylation pathway, we designated mmp1090 as aglW.
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Affiliation(s)
- Yan Ding
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, K7L 3N6, Canada
| | - Gareth M Jones
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, K7L 3N6, Canada
| | - Cedric Brimacombe
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, K7L 3N6, Canada
| | - Kaoru Uchida
- Department of Life Sciences, Prefectural University of Hiroshima, Shobara, Hiroshima, 727-0023, Japan
| | - Shin-Ichi Aizawa
- Department of Life Sciences, Prefectural University of Hiroshima, Shobara, Hiroshima, 727-0023, Japan
| | - Susan M Logan
- Human Health Therapeutics Portfolio, National Research Council, Ottawa, K1A 0R6, Canada
| | - John F Kelly
- Human Health Therapeutics Portfolio, National Research Council, Ottawa, K1A 0R6, Canada.
| | - Ken F Jarrell
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, K7L 3N6, Canada.
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28
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Abstract
Pantothenate is vitamin B5 and is the key precursor for the biosynthesis of coenzyme A (CoA), a universal and essential cofactor involved in a myriad of metabolic reactions, including the synthesis of phospholipids, the synthesis and degradation of fatty acids, and the operation of the tricarboxylic acid cycle. CoA is also the only source of the phosphopantetheine prosthetic group for enzymes that shuttle intermediates between the active sites of enzymes involved in fatty acid, nonribosomal peptide, and polyketide synthesis. Pantothenate can be synthesized de novo and/or transported into the cell through a pantothenatepermease. Pantothenate uptake is essential for those organisms that lack the genes to synthesize this vitamin. The intracellular levels of CoA are controlled by the balance between synthesis and degradation. In particular, CoA is assembled in five enzymatic steps, starting from the phosphorylation of pantothenate to phosphopantothenatecatalyzed by pantothenate kinase, the product of the coaA gene. In some bacteria, the production of phosphopantothenate by pantothenate kinase is the rate limiting and most regulated step in the biosynthetic pathway. CoA synthesis additionally networks with other vitamin-associated pathways, such as thiamine and folic acid.
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29
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Chen C, Cao R, Shrestha R, Ward C, Katz BB, Fischer CJ, Tomich JM, Li P. Trapping of intermediates with substrate analog HBOCoA in the polymerizations catalyzed by class III polyhydroxybutyrate (PHB) synthase from Allochromatium vinosum. ACS Chem Biol 2015; 10:1330-1339. [PMID: 25686368 DOI: 10.1021/cb5009958] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Polyhydroxybutyrate (PHB) synthases (PhaCs) catalyze the formation of biodegradable PHB polymers that are considered as an ideal alternative to petroleum-based plastics. To provide strong evidence for the preferred mechanistic model involving covalent and noncovalent intermediates, a substrate analog HBOCoA was synthesized chemoenzymatically. Substitution of sulfur in the native substrate HBCoA with an oxygen in HBOCoA enabled detection of (HB)nOCoA (n = 2-6) intermediates when the polymerization was catalyzed by wild-type (wt-)PhaECAv at 5.84 h(-1). This extremely slow rate is due to thermodynamically unfavorable steps that involve the formation of enzyme-bound PHB species (thioesters) from corresponding CoA oxoesters. Synthesized standards (HB)nOCoA (n = 2-3) were found to undergo both reacylation and hydrolysis catalyzed by the synthase. Distribution of the hydrolysis products highlights the importance of the penultimate ester group as previously suggested. Importantly, the reaction between primed synthase [(3)H]-sT-PhaECAv and HBOCoA yielded [(3)H]-sTet-O-CoA at a rate constant faster than 17.4 s(-1), which represents the first example that a substrate analog undergoes PHB chain elongation at a rate close to that of the native substrate (65.0 s(-1)). Therefore, for the first time with a wt-synthase, strong evidence was obtained to support our favored PHB chain elongation model.
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Affiliation(s)
| | | | | | - Christina Ward
- University of Saint Mary, Leavenworth, Kansas 66048, United States
| | | | - Christopher J. Fischer
- Department
of Physics and Astronomy, University of Kansas, Lawrence, Kansas 66045, United States
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30
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Zhang W, Chen C, Cao R, Maurmann L, Li P. Inhibitors of polyhydroxyalkanoate (PHA) synthases: synthesis, molecular docking, and implications. Chembiochem 2014; 16:156-166. [PMID: 25394180 DOI: 10.1002/cbic.201402380] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Indexed: 11/06/2022]
Abstract
Polyhydroxyalkanoate (PHA) synthases (PhaCs) catalyze the formation of biodegradable PHAs that are considered to be ideal alternatives to non-biodegradable synthetic plastics. However, study of PhaCs has been challenging because the rate of PHA chain elongation is much faster than that of initiation. This difficulty, along with lack of a crystal structure, has become the main hurdle to understanding and engineering PhaCs for economical PHA production. Here we report the synthesis of two carbadethia CoA analogues--sT-CH2-CoA (26 a) and sTet-CH2-CoA (26 b)--as well as sT-aldehyde (saturated trimer aldehyde, 29), as new PhaC inhibitors. Study of these analogues with PhaECAv revealed that 26 a/b and 29 are competitive and mixed inhibitors, respectively. Both the CoA moiety and extension of PHA chain will increase binding affinity; this is consistent with our docking study. Estimation of the Kic values of 26 a and 26 b predicts that a CoA analogue incorporating an octameric hydroxybutanoate (HB) chain might facilitate the formation of a kinetically well-behaved synthase.
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Affiliation(s)
- Wei Zhang
- Department of Chemistry, Kansas State Univerity, Manhattan, KS 66506 (USA)
| | - Chao Chen
- Department of Chemistry, Kansas State Univerity, Manhattan, KS 66506 (USA)
| | - Ruikai Cao
- Department of Chemistry, Kansas State Univerity, Manhattan, KS 66506 (USA)
| | - Leila Maurmann
- Department of Chemistry, Kansas State Univerity, Manhattan, KS 66506 (USA)
| | - Ping Li
- Department of Chemistry, Kansas State Univerity, Manhattan, KS 66506 (USA)
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31
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Zhang W, Shrestha R, Buckley RM, Jewell J, Bossmann SH, Stubbe J, Li P. Mechanistic insight with HBCH2CoA as a probe to polyhydroxybutyrate (PHB) synthases. ACS Chem Biol 2014; 9:1773-9. [PMID: 24896226 PMCID: PMC4136709 DOI: 10.1021/cb5002735] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
![]()
Polyhydroxybutyrate (PHB) synthases
catalyze the polymerization
of 3-(R)-hydroxybutyrate coenzyme A (HBCoA) to produce
polyoxoesters of 1–2 MDa. A substrate analogue HBCH2CoA, in which the S in HBCoA is replaced with a
CH2 group, was synthesized in 13 steps using a chemoenzymatic
approach in a 7.5% overall yield. Kinetic studies reveal it is a competitive
inhibitor of a class I and a class III PHB synthases, with Kis of 40 and 14 μM, respectively. To probe
the elongation steps of the polymerization, HBCH2CoA was
incubated with a synthase acylated with a [3H]-saturated
trimer-CoA ([3H]-sTCoA). The products of the reaction were
shown to be the methylene analogue of [3H]-sTCoA ([3H]-sT-CH2-CoA), saturated dimer-([3H]-sD-CO2H), and trimer-acid ([3H]-sT-CO2H),
distinct from the expected methylene analogue of [3H]-saturated
tetramer-CoA ([3H]-sTet-CH2-CoA). Detection
of [3H]-sT-CH2-CoA and its slow rate of formation
suggest that HBCH2CoA may be reporting on the termination
and repriming process of the synthases, rather than elongation.
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Affiliation(s)
- Wei Zhang
- Department
of Chemistry, Kansas State University, Manhattan, Kansas 66506, United States
| | - Ruben Shrestha
- Department
of Chemistry, Kansas State University, Manhattan, Kansas 66506, United States
| | | | - Jamie Jewell
- Department
of Chemistry, Ohio Dominican University, Columbus, Ohio 43219, United States
| | - Stefan H. Bossmann
- Department
of Chemistry, Kansas State University, Manhattan, Kansas 66506, United States
| | | | - Ping Li
- Department
of Chemistry, Kansas State University, Manhattan, Kansas 66506, United States
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32
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Yu D, Chen X, Xu Z, Ge H. Crystallization and preliminary X-ray characterization of the dephospho-CoA kinase from Legionella pneumophila. Acta Crystallogr F Struct Biol Commun 2014; 70:608-10. [PMID: 24817720 PMCID: PMC4014329 DOI: 10.1107/s2053230x14006542] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Accepted: 03/24/2014] [Indexed: 11/10/2022] Open
Abstract
Dephospho-CoA kinases (DPCKs) are members of the kinase family that catalyze the final step in CoA biosynthesis. Their function is phosphorylation of the 3-hydroxyl group of the ribose using ATP as a phosphate donor. Structural changes induced by ATP binding play an important role during the DPCK catalytic cycle. In this work, DPCK from Legionella pneumophila was overexpressed in Escherichia coli. The purification, crystallization and preliminary X-ray analysis of crystals of this protein are described. The protein was crystallized in space group P21212, with unit-cell parameters a = 36.29, b = 82.20, c = 81.80 Å, using the hanging-drop vapour-diffusion method. Diffraction data were collected at 100 K and the phases were determined using the molecular-replacement method.
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Affiliation(s)
- Dongmin Yu
- Institute of Health Sciences and School of Life Sciences, Anhui University, Hefei 230601, People’s Republic of China
- Department of Life Sciences, Hefei Normal University, Hefei 230601, People’s Republic of China
| | - Xiaofang Chen
- Institute of Health Sciences and School of Life Sciences, Anhui University, Hefei 230601, People’s Republic of China
| | - Zhongdong Xu
- Department of Life Sciences, Hefei Normal University, Hefei 230601, People’s Republic of China
| | - Honghua Ge
- Institute of Health Sciences and School of Life Sciences, Anhui University, Hefei 230601, People’s Republic of China
- Modern Experiment Technology Center, Anhui University, Hefei 230039, People’s Republic of China
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33
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Genomic and proteomic studies on Plesiomonas shigelloides lipopolysaccharide core biosynthesis. J Bacteriol 2013; 196:556-67. [PMID: 24244003 DOI: 10.1128/jb.01100-13] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
We report here the identification of waa clusters with the genes required for the biosynthesis of the core lipopolysaccharides (LPS) of two Plesiomonas shigelloides strains. Both P. shigelloides waa clusters shared all of the genes besides the ones flanking waaL. In both strains, all of the genes were found in the waa gene cluster, although one common core biosynthetic gene (wapG) was found in a different chromosome location outside the cluster. Since P. shigelloides and Klebsiella pneumoniae share a core LPS carbohydrate backbone extending up at least to the second outer-core residue, the functions of the common P. shigelloides genes were elucidated by genetic complementation studies using well-defined K. pneumoniae mutants. The function of strain-specific inner- or outer-core genes was identified by using as a surrogate acceptor LPS from three well-defined K. pneumoniae core LPS mutants. Using this strategy, we were able to assign a proteomic function to all of the P. shigelloides waa genes identified in the two strains encoding six new glycosyltransferases (WapA, -B, -C, -D, -F, and -G). P. shigelloides demonstrated an important variety of core LPS structures, despite being a single species of the genus, as well as high homologous recombination in housekeeping genes.
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34
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Discovery of inhibitors of 4'-phosphopantetheine adenylyltransferase (PPAT) to validate PPAT as a target for antibacterial therapy. Antimicrob Agents Chemother 2013; 57:6005-15. [PMID: 24041904 DOI: 10.1128/aac.01661-13] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Inhibitors of 4'-phosphopantetheine adenylyltransferase (PPAT) were identified through high-throughput screening of the AstraZeneca compound library. One series, cycloalkyl pyrimidines, showed inhibition of PPAT isozymes from several species, with the most potent inhibition of enzymes from Gram-positive species. Mode-of-inhibition studies with Streptococcus pneumoniae and Staphylococcus aureus PPAT demonstrated representatives of this series to be reversible inhibitors competitive with phosphopantetheine and uncompetitive with ATP, binding to the enzyme-ATP complex. The potency of this series was optimized using structure-based design, and inhibition of cell growth of Gram-positive species was achieved. Mode-of-action studies, using generation of resistant mutants with targeted sequencing as well as constructs that overexpress PPAT, demonstrated that growth suppression was due to inhibition of PPAT. An effect on bacterial burden was demonstrated in mouse lung and thigh infection models, but further optimization of dosing requirements and compound properties is needed before these compounds can be considered for progress into clinical development. These studies validated PPAT as a novel target for antibacterial therapy.
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35
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Cheng CS, Jia KF, Chen T, Chang SY, Lin MS, Yin HS. Experimentally validated novel inhibitors of Helicobacter pylori phosphopantetheine adenylyltransferase discovered by virtual high-throughput screening. PLoS One 2013; 8:e74271. [PMID: 24040220 PMCID: PMC3764209 DOI: 10.1371/journal.pone.0074271] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Accepted: 07/30/2013] [Indexed: 11/23/2022] Open
Abstract
Helicobacter pylori is a major etiologic agent associated with the development and maintenance of human gastritis. The goal of this study was to develop novel antibiotics against H. pylori, and we thus targeted H. pylori phosphopantetheine adenylyltransferase (HpPPAT). PPAT catalyzes the penultimate step in coenzyme A biosynthesis. Its inactivation effectively prevents bacterial viability, making it an attractive target for antibacterial drug discovery. We employed virtual high-throughput screening and the HpPPAT crystal structure to identify compounds in the PubChem database that might act as inhibitors of HpPPAT. d-amethopterin is a potential inhibitor for blocking HpPPAT activity and suppressing H. pylori viability. Following treatment with d-amethopterin, H. pylori exhibited morphological characteristics associated with cell death. d-amethopterin is a mixed inhibitor of HpPPAT activity; it simultaneously occupies the HpPPAT 4'-phosphopantetheine- and ATP-binding sites. Its binding affinity is in the micromolar range, implying that it is sufficiently potent to serve as a lead compound in subsequent drug development. Characterization of the d-amethopterin and HpPPAT interaction network in a docked model will allow us to initiate rational drug optimization to improve the inhibitory efficacy of d-amethopterin. We anticipate that novel, potent, and selective HpPPAT inhibitors will emerge for the treatment of H. pylori infection.
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Affiliation(s)
- Chao-Sheng Cheng
- Institute of Bioinformatics and Structural Biology and College of Life Sciences, National Tsing Hua University, Hsinchu, Taiwan
| | - Kai-Fan Jia
- Institute of Bioinformatics and Structural Biology and College of Life Sciences, National Tsing Hua University, Hsinchu, Taiwan
| | - Ting Chen
- Institute of Bioinformatics and Structural Biology and College of Life Sciences, National Tsing Hua University, Hsinchu, Taiwan
| | - Shun-Ya Chang
- Institute of Bioinformatics and Structural Biology and College of Life Sciences, National Tsing Hua University, Hsinchu, Taiwan
| | | | - Hsien-Sheng Yin
- Institute of Bioinformatics and Structural Biology and College of Life Sciences, National Tsing Hua University, Hsinchu, Taiwan
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36
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Chaudhury S, Abdulhameed MDM, Singh N, Tawa GJ, D’haeseleer PM, Zemla AT, Navid A, Zhou CE, Franklin MC, Cheung J, Rudolph MJ, Love J, Graf JF, Rozak DA, Dankmeyer JL, Amemiya K, Daefler S, Wallqvist A. Rapid countermeasure discovery against Francisella tularensis based on a metabolic network reconstruction. PLoS One 2013; 8:e63369. [PMID: 23704901 PMCID: PMC3660459 DOI: 10.1371/journal.pone.0063369] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2013] [Accepted: 03/30/2013] [Indexed: 11/29/2022] Open
Abstract
In the future, we may be faced with the need to provide treatment for an emergent biological threat against which existing vaccines and drugs have limited efficacy or availability. To prepare for this eventuality, our objective was to use a metabolic network-based approach to rapidly identify potential drug targets and prospectively screen and validate novel small-molecule antimicrobials. Our target organism was the fully virulent Francisella tularensis subspecies tularensis Schu S4 strain, a highly infectious intracellular pathogen that is the causative agent of tularemia and is classified as a category A biological agent by the Centers for Disease Control and Prevention. We proceeded with a staggered computational and experimental workflow that used a strain-specific metabolic network model, homology modeling and X-ray crystallography of protein targets, and ligand- and structure-based drug design. Selected compounds were subsequently filtered based on physiological-based pharmacokinetic modeling, and we selected a final set of 40 compounds for experimental validation of antimicrobial activity. We began screening these compounds in whole bacterial cell-based assays in biosafety level 3 facilities in the 20th week of the study and completed the screens within 12 weeks. Six compounds showed significant growth inhibition of F. tularensis, and we determined their respective minimum inhibitory concentrations and mammalian cell cytotoxicities. The most promising compound had a low molecular weight, was non-toxic, and abolished bacterial growth at 13 µM, with putative activity against pantetheine-phosphate adenylyltransferase, an enzyme involved in the biosynthesis of coenzyme A, encoded by gene coaD. The novel antimicrobial compounds identified in this study serve as starting points for lead optimization, animal testing, and drug development against tularemia. Our integrated in silico/in vitro approach had an overall 15% success rate in terms of active versus tested compounds over an elapsed time period of 32 weeks, from pathogen strain identification to selection and validation of novel antimicrobial compounds.
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Affiliation(s)
- Sidhartha Chaudhury
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Fort Detrick, Maryland, United States of America
| | - Mohamed Diwan M. Abdulhameed
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Fort Detrick, Maryland, United States of America
| | - Narender Singh
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Fort Detrick, Maryland, United States of America
| | - Gregory J. Tawa
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Fort Detrick, Maryland, United States of America
| | - Patrik M. D’haeseleer
- Pathogen Bioinformatics, Lawrence Livermore National Laboratory, Livermore, California, United States of America
| | - Adam T. Zemla
- Pathogen Bioinformatics, Lawrence Livermore National Laboratory, Livermore, California, United States of America
| | - Ali Navid
- Pathogen Bioinformatics, Lawrence Livermore National Laboratory, Livermore, California, United States of America
| | - Carol E. Zhou
- Pathogen Bioinformatics, Lawrence Livermore National Laboratory, Livermore, California, United States of America
| | - Matthew C. Franklin
- New York Structural Biology Center, New York, New York, United States of America
| | - Jonah Cheung
- New York Structural Biology Center, New York, New York, United States of America
| | - Michael J. Rudolph
- New York Structural Biology Center, New York, New York, United States of America
| | - James Love
- New York Structural Biology Center, New York, New York, United States of America
| | - John F. Graf
- Computational Biology and Biostatistics Laboratory, Diagnostics and Biomedical Technologies, GE Global Research, General Electric Company, Niskayuna, New York, United States of America
| | - David A. Rozak
- Bacteriology Division, U.S. Army Medical Research Institute for Infectious Diseases, Fort Detrick, Maryland, United States of America
| | - Jennifer L. Dankmeyer
- Bacteriology Division, U.S. Army Medical Research Institute for Infectious Diseases, Fort Detrick, Maryland, United States of America
| | - Kei Amemiya
- Bacteriology Division, U.S. Army Medical Research Institute for Infectious Diseases, Fort Detrick, Maryland, United States of America
| | - Simon Daefler
- Mount Sinai School of Medicine, New York, New York, United States of America
| | - Anders Wallqvist
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Fort Detrick, Maryland, United States of America
- * E-mail:
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37
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Timofeev V, Smirnova E, Chupova L, Esipov R, Kuranova I. X-ray study of the conformational changes in the molecule of phosphopantetheine adenylyltransferase from Mycobacterium tuberculosis during the catalyzed reaction. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:1660-70. [PMID: 23151631 DOI: 10.1107/s0907444912040206] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Accepted: 09/22/2012] [Indexed: 11/11/2022]
Abstract
Structures of recombinant phosphopantetheine adenylyltransferase (PPAT) from Mycobacterium tuberculosis (PPATMt) in the apo form and in complex with the substrate ATP were determined at 1.62 and 1.70 Å resolution, respectively, using crystals grown in microgravity by the counter-diffusion method. The ATP molecule of the PPATMt-ATP complex was located with full occupancy in the active-site cavity. Comparison of the solved structures with previously determined structures of PPATMt complexed with the reaction product dephosphocoenzyme A (dPCoA) and the feedback inhibitor coenzyme A (CoA) was performed using superposition on C(α) atoms. The peculiarities of the arrangement of the ligands in the active-site cavity of PPATMt are described. The conformational states of the PPAT molecule in the consequent steps of the catalyzed reaction in the apo enzyme and the enzyme-substrate and enzyme-product complexes are characterized. It is shown that the binding of ATP and dPCoA induces the rearrangement of a short part of the polypeptide chain restricting the active-site cavity in the subunits of the hexameric enzyme molecule. The changes in the quaternary structure caused by this rearrangement are accompanied by a variation of the size of the inner water-filled channel which crosses the PPAT molecule along the threefold axis of the hexamer. The molecular mechanism of the observed changes is described.
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Affiliation(s)
- Vladimir Timofeev
- Laboratory of X-ray Analysis Methods and Synchrotron Radiation, Shubnikov Institute of Crystallography, Russian Academy of Sciences, Leninsky Prospect 59, Moscow, Russian Federation.
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38
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Cheng CS, Chen WT, Chen YW, Chen CH, Luo YC, Lyu PC, Yin HS. Substitution of asparagine 76 by a tyrosine residue induces domain swapping in Helicobacter pylori phosphopantetheine adenylyltransferase. J Biomol Struct Dyn 2012; 30:488-502. [PMID: 22694317 DOI: 10.1080/07391102.2012.682213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Phosphopantetheine adenylyltransferase (PPAT) catalyses the penultimate step in coenzyme A biosynthesis in bacteria and is therefore a candidate target for antibacterial drug development. We randomly mutated the residues in the Helicobacter pylori PPAT sequence to identify those that govern protein folding and ligand binding, and we describe the crystal structure of one of these mutants (I4V/N76Y) that contains the mutations I4 → V and N76 → Y. Unlike other PPATs, which are homohexamers, I4V/N76Y is a domain-swapped homotetramer. The protomer structure of this mutant is an open conformation in which the 65 C-terminal residues are intertwined with those of a neighbouring protomer. Despite structural differences between wild-type PPAT and IV4/N76Y, they had similar ligand-binding properties. ATP binding to these two proteins was enthalpically driven, whereas that for Escherichia coli PPAT is entropically driven. The structural packing of the subunits may affect the thermal denaturation of wild-type PPAT and I4V/N76Y. Mutations in hinge regions often induce domain swapping, i.e. the spatial exchange of portions of adjacent protomers, but residues 4 and 76 of H. pylori PPAT are not located in or near to the hinge region. However, one or both of these residues is responsible for the large conformational change in the C-terminal region of each protomer. To identify the residue(s) responsible, we constructed the single-site mutant, N76Y, and found a large displacement of α-helix 4, which indicated that its flexibility allowed the domain swap to occur.
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Affiliation(s)
- Chao-Sheng Cheng
- Institute of Bioinformatics and Structural Biology, and College of Life Sciences, National Tsing Hua University, Hsinchu, 300, Taiwan
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39
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Vong K, Tam IS, Yan X, Auclair K. Inhibitors of aminoglycoside resistance activated in cells. ACS Chem Biol 2012; 7:470-5. [PMID: 22217014 DOI: 10.1021/cb200366u] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The most common mechanism of resistance to aminoglycoside antibiotics entails bacterial expression of drug-metabolizing enzymes, such as the clinically widespread aminoglycoside N-6'-acetyltransferase (AAC(6')). Aminoglycoside-CoA bisubstrates are highly potent AAC(6') inhibitors; however, their inability to penetrate cells precludes in vivo studies. Some truncated bisubstrates are known to cross cell membranes, yet their activities against AAC(6') are in the micromolar range at best. We report here the synthesis and biological activity of aminoglycoside-pantetheine derivatives that, although devoid of AAC(6') inhibitory activity, can potentiate the antibacterial activity of kanamycin A against an aminoglycoside-resistant strain of Enterococcus faecium. Biological studies demonstrate that these molecules are potentially extended to their corresponding full-length bisubstrates by enzymes of the coenzyme A biosynthetic pathway. This work provides a proof-of-concept for the utility of prodrug compounds activated by enzymes of the coenzyme A biosynthetic pathway, to resensitize resistant strains of bacteria to aminoglycoside antibiotics.
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Affiliation(s)
- Kenward Vong
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montréal,
Québec, Canada
H3A 2K6
| | - Ingrid S. Tam
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montréal,
Québec, Canada
H3A 2K6
| | - Xuxu Yan
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montréal,
Québec, Canada
H3A 2K6
| | - Karine Auclair
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montréal,
Québec, Canada
H3A 2K6
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40
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Yoon HJ, Kang JY, Mikami B, Lee HH, Suh SW. Crystal structure of phosphopantetheine adenylyltransferase from Enterococcus faecalis in the ligand-unbound state and in complex with ATP and pantetheine. Mol Cells 2011; 32:431-5. [PMID: 21912874 PMCID: PMC3887696 DOI: 10.1007/s10059-011-0102-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Revised: 08/21/2011] [Accepted: 08/23/2011] [Indexed: 11/29/2022] Open
Abstract
Phosphopantetheine adenylyltransferase (PPAT) catalyzes the reversible transfer of an adenylyl group from ATP to 4'-phosphopantetheine (Ppant) to form dephospho-CoA (dPCoA) and pyrophosphate in the Coenzyme A (CoA) biosynthetic pathway. Importantly, PPATs are the potential target for developing antibiotics because bacterial and mammalian PPATs share little sequence homology. Previous structural studies revealed the mechanism of the recognizing substrates and products. The binding modes of ATP, ADP, Ppant, and dPCoA are highly similar in all known structures, whereas the binding modes of CoA or 3'-phosphoadenosine 5'-phosphosulfate binding are novel. To provide further structural information on ligand binding by PPATs, the crystal structure of PPAT from Enterococcus faecalis was solved in three forms: (i) apo form, (ii) binary complex with ATP, and (iii) binary complex with pantetheine. The substrate analog, pantetheine, binds to the active site in a similar manner to Ppant. The new structural information reported in this study including pantetheine as a potent inhibitor of PPAT will supplement the existing structural data and should be useful for structure-based antibacterial discovery against PPATs.
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Affiliation(s)
- Hye-Jin Yoon
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 151-742, Korea
| | - Ji Yong Kang
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 151-742, Korea
| | - Bunzo Mikami
- Laboratory of Quality Design and Exploitation, Division of Agronomy and Horticultural Science, Graduate School of Agriculture, Kyoto University, Kyoto 611-0011, Japan
| | - Hyung Ho Lee
- Department of Bio and Nano Chemistry, Kookmin University, Seoul 136-702, Korea
- Department of Integrative Biomedical Science and Engineering, Kookmin University, Seoul 136-702, Korea
| | - Se Won Suh
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 151-742, Korea
- Department of Biophysics and Chemical Biology, College of Natural Sciences, Seoul National University, Seoul 151-742, Korea
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Walia G, Surolia A. Insights into the regulatory characteristics of the mycobacterial dephosphocoenzyme A kinase: implications for the universal CoA biosynthesis pathway. PLoS One 2011; 6:e21390. [PMID: 21731728 PMCID: PMC3123319 DOI: 10.1371/journal.pone.0021390] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2011] [Accepted: 05/26/2011] [Indexed: 11/18/2022] Open
Abstract
Being vastly different from the human counterpart, we suggest that the last enzyme of the Mycobacterium tuberculosis Coenzyme A biosynthetic pathway, dephosphocoenzyme A kinase (CoaE) could be a good anti-tubercular target. Here we describe detailed investigations into the regulatory features of the enzyme, affected via two mechanisms. Enzymatic activity is regulated by CTP which strongly binds the enzyme at a site overlapping that of the leading substrate, dephosphocoenzyme A (DCoA), thereby obscuring the binding site and limiting catalysis. The organism has evolved a second layer of regulation by employing a dynamic equilibrium between the trimeric and monomeric forms of CoaE as a means of regulating the effective concentration of active enzyme. We show that the monomer is the active form of the enzyme and the interplay between the regulator, CTP and the substrate, DCoA, affects enzymatic activity. Detailed kinetic data have been corroborated by size exclusion chromatography, dynamic light scattering, glutaraldehyde crosslinking, limited proteolysis and fluorescence investigations on the enzyme all of which corroborate the effects of the ligands on the enzyme oligomeric status and activity. Cysteine mutagenesis and the effects of reducing agents on mycobacterial CoaE oligomerization further validate that the latter is not cysteine-mediated or reduction-sensitive. These studies thus shed light on the novel regulatory features employed to regulate metabolite flow through the last step of a critical biosynthetic pathway by keeping the latter catalytically dormant till the need arises, the transition to the active form affected by a delicate crosstalk between an essential cellular metabolite (CTP) and the precursor to the pathway end-product (DCoA).
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Affiliation(s)
- Guneet Walia
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Avadhesha Surolia
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
- National Institute of Immunology, New Delhi, India
- * E-mail:
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Wubben T, Mesecar AD. Structure of Mycobacterium tuberculosis phosphopantetheine adenylyltransferase in complex with the feedback inhibitor CoA reveals only one active-site conformation. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:541-5. [PMID: 21543857 PMCID: PMC3087636 DOI: 10.1107/s1744309111010761] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2011] [Accepted: 03/23/2011] [Indexed: 11/10/2022]
Abstract
Phosphopantetheine adenylyltransferase (PPAT) catalyzes the penultimate step in the coenzyme A (CoA) biosynthetic pathway, reversibly transferring an adenylyl group from ATP to 4'-phosphopantetheine to form dephosphocoenzyme A (dPCoA). To complement recent biochemical and structural studies on Mycobacterium tuberculosis PPAT (MtPPAT) and to provide further insight into the feedback regulation of MtPPAT by CoA, the X-ray crystal structure of the MtPPAT enzyme in complex with CoA was determined to 2.11 Å resolution. Unlike previous X-ray crystal structures of PPAT-CoA complexes from other bacteria, which showed two distinct CoA conformations bound to the active site, only one conformation of CoA is observed in the MtPPAT-CoA complex.
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Affiliation(s)
- T. Wubben
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois, USA
| | - A. D. Mesecar
- Departments of Biological Sciences and Chemistry, Purdue University, West Lafayette, Indiana, USA
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43
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Cheng CS, Chen CH, Luo YC, Chen WT, Chang SY, Lyu PC, Kao MC, Yin HS. Crystal structure and biophysical characterisation of Helicobacter pylori phosphopantetheine adenylyltransferase. Biochem Biophys Res Commun 2011; 408:356-61. [PMID: 21527250 DOI: 10.1016/j.bbrc.2011.04.058] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2011] [Accepted: 04/12/2011] [Indexed: 12/11/2022]
Abstract
Helicobacter pylori is a bacterium that causes chronic active gastritis and peptic ulcers. Drugs targeting H. pylori phosphopantetheine adenylyltransferase (HpPPAT), which is involved in CoA biosynthesis, may be useful. Herein, we report the expression in Escherichia coli and purification of recombinant HpPPAT and describe a crystal structure for an HpPPAT/CoA complex. As is the case for E. coli PPAT (EcPPAT), HpPPAT is hexameric in solution and as a crystal. Each protomer has a well-packed dinucleotide-binding fold in which CoA binds. Structural characterisation demonstrated that CoA derived from the E. coli expression system bound tightly to HpPPAT, presumably to initiate feedback inhibition. However, the interactions between the active-site residues of HpPPAT and CoA are not identical to those of other PPATs. Finally, CoA binding affects HpPPAT thermal denaturation.
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Affiliation(s)
- Chao-Sheng Cheng
- Institute of Bioinformatics and Structural Biology, College of Life Sciences, National Tsing Hua University, No. 101, Section 2, Kuang-Fu Road, Hsinchu 30013, Taiwan
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Timofeev VI, Smirnova EA, Chupova LA, Esipov RS, Kuranova IP. Preparation of the Crystal Complex of Phosphopantetheine Adenylyltransferase from Mycobacterium tuberculosis with Coenzyme A and Investigation of Its Three-Dimensional Structure at 2.1-Å Resolution. CRYSTALLOGR REP+ 2010. [DOI: 10.1134/s1063774510060234] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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45
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Aquilini E, Azevedo J, Merino S, Jimenez N, Tomás JM, Regué M. Three enzymatic steps required for the galactosamine incorporation into core lipopolysaccharide. J Biol Chem 2010; 285:39739-49. [PMID: 20959463 DOI: 10.1074/jbc.m110.168385] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The core lipopolysaccharides (LPS) of Proteus mirabilis as well as those of Klebsiella pneumoniae and Serratia marcescens are characterized by the presence of a hexosamine-galacturonic acid disaccharide (αHexN-(1,4)-αGalA) attached by an α1,3 linkage to L-glycero-D-manno-heptopyranose II (L-glycero-α-D-manno-heptosepyranose II). In K. pneumoniae, S. marcescens, and some P. mirabilis strains, HexN is D-glucosamine, whereas in other P. mirabilis strains, it corresponds to D-galactosamine. Previously, we have shown that two enzymes are required for the incorporation of D-glucosamine into the core LPS of K. pneumoniae; the WabH enzyme catalyzes the incorporation of GlcNAc from UDP-GlcNAc to outer core LPS, and WabN catalyzes the deacetylation of the incorporated GlcNAc. Here we report the presence of two different HexNAc transferases depending on the nature of the HexN in P. mirabilis core LPS. In vivo and in vitro assays using LPS truncated at the level of galacturonic acid as acceptor show that these two enzymes differ in their specificity for the transfer of GlcNAc or GalNAc. By contrast, only one WabN homologue was found in the studied P. mirabilis strains. Similar assays suggest that the P. mirabilis WabN homologue is able to deacetylate both GlcNAc and GalNAc. We conclude that incorporation of d-galactosamine requires three enzymes: Gne epimerase for the generation of UDP-GalNAc from UDP-GlcNAc, N-acetylgalactosaminyltransferase (WabP), and LPS:HexNAc deacetylase.
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Affiliation(s)
- Eleonora Aquilini
- Departamento de Microbiología y Parasitología Sanitarias, Facultad de Farmacia, Universidad de Barcelona, 08028 Barcelona, Spain
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Wubben TJ, Mesecar AD. Kinetic, thermodynamic, and structural insight into the mechanism of phosphopantetheine adenylyltransferase from Mycobacterium tuberculosis. J Mol Biol 2010; 404:202-19. [PMID: 20851704 DOI: 10.1016/j.jmb.2010.09.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2010] [Revised: 08/23/2010] [Accepted: 09/01/2010] [Indexed: 11/30/2022]
Abstract
Phosphopantetheine adenylyltransferase (PPAT) catalyzes the penultimate step in the coenzyme A (CoA) biosynthetic pathway, reversibly transferring an adenylyl group from ATP to 4'-phosphopantetheine (PhP) to form dephosphocoenzyme A. This reaction sits at the branch point between the de novo pathway and the salvage pathway, and has been shown to be a rate-limiting step in the biosynthesis of CoA. Importantly, bacterial and mammalian PPATs share little sequence homology, making the enzyme a potential target for antibiotic development. A series of steady-state kinetic, product inhibition, and direct binding studies with Mycobacterium tuberculosis PPAT (MtPPAT) was conducted and suggests that the enzyme utilizes a nonrapid-equilibrium random bi-bi mechanism. The kinetic response of MtPPAT to the binding of ATP was observed to be sigmoidal under fixed PhP concentrations, but substrate inhibition was observed at high PhP concentrations under subsaturating ATP concentrations, suggesting a preferred pathway to ternary complex formation. Negative cooperativity in the kinetic response of MtPPAT to PhP binding was observed under certain conditions and confirmed thermodynamically by isothermal titration calorimetry, suggesting the formation of an asymmetric quaternary structure during sequential ligation of substrates. Asymmetry in binding was also observed in isothermal titration calorimetry experiments with dephosphocoenzyme A and CoA. X-ray structures of MtPPAT in complex with PhP and the nonhydrolyzable ATP analogue adenosine-5'-[(α,β)-methyleno]triphosphate were solved to 1.57 Å and 2.68 Å, respectively. These crystal structures reveal small conformational changes in enzyme structure upon ligand binding, which may play a role in the nonrapid-equilibrium mechanism. We suggest that the proposed kinetic mechanism and asymmetric character in MtPPAT ligand binding may provide a means of reaction and pathway regulation in addition to that of the previously determined CoA feedback.
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Affiliation(s)
- Thomas J Wubben
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL 60607, USA
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The use of biochemical and biophysical tools for triage of high-throughput screening hits - A case study with Escherichia coli phosphopantetheine adenylyltransferase. Chem Biol Drug Des 2010; 75:444-54. [PMID: 20486930 DOI: 10.1111/j.1747-0285.2010.00957.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
High-throughput screening is utilized by pharmaceutical researchers and, increasingly, academic investigators to identify agents that act upon enzymes, receptors, and cellular processes. Screening hits include molecules that specifically bind the target and a greater number of non-specific compounds. It is necessary to 'triage' these hits to identify the subset worthy of further exploration. As part of our antibacterial drug discovery effort, we applied a suite of biochemical and biophysical tools to accelerate the triage process. We describe application of these tools to a series of 9-oxo-4,9-dihydropyrazolo[5,1-b]quinazoline-2-carboxylic acids (PQ) hits from a screen of Escherichia coli phosphopantetheine adenylyltransferase (PPAT). Initial confirmation of specific binding to phosphopantetheine adenylyltransferase was obtained using biochemical and biophysical tools, including a novel orthogonal assay, isothermal titration calorimetry, and saturation transfer difference NMR. To identify the phosphopantetheine adenylyltransferase sub-site bound by these inhibitors, two techniques were utilized: steady-state enzyme kinetics and a novel (19)F NMR method in which fluorine-containing fragments that bind the ATP and/or phosphopantetheine sites serve as competitive reporter probes. These data are consistent with PQs binding the ATP sub-site. In addition to identification of a series of PPAT inhibitors, the described hit triage process is broadly applicable to other enzyme targets in which milligram quantities of purified target protein are available.
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Functional identification of the Proteus mirabilis core lipopolysaccharide biosynthesis genes. J Bacteriol 2010; 192:4413-24. [PMID: 20622068 DOI: 10.1128/jb.00494-10] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In this study, we report the identification of genes required for the biosynthesis of the core lipopolysaccharides (LPSs) of two strains of Proteus mirabilis. Since P. mirabilis and Klebsiella pneumoniae share a core LPS carbohydrate backbone extending up to the second outer-core residue, the functions of the common P. mirabilis genes was elucidated by genetic complementation studies using well-defined mutants of K. pneumoniae. The functions of strain-specific outer-core genes were identified by using as surrogate acceptors LPSs from two well-defined K. pneumoniae core LPS mutants. This approach allowed the identification of two new heptosyltransferases (WamA and WamC), a galactosyltransferase (WamB), and an N-acetylglucosaminyltransferase (WamD). In both strains, most of these genes were found in the so-called waa gene cluster, although one common core biosynthetic gene (wabO) was found outside this cluster.
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Lee HH, Yoon HJ, Kang JY, Park JH, Kim DJ, Choi KH, Lee SK, Song J, Kim HJ, Suh SW. The structure of Staphylococcus aureus phosphopantetheine adenylyltransferase in complex with 3'-phosphoadenosine 5'-phosphosulfate reveals a new ligand-binding mode. Acta Crystallogr Sect F Struct Biol Cryst Commun 2009; 65:987-91. [PMID: 19851003 DOI: 10.1107/s1744309109036616] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2009] [Accepted: 09/10/2009] [Indexed: 11/10/2022]
Abstract
Bacterial phosphopantetheine adenylyltransferase (PPAT) catalyzes the penultimate step in the coenzyme A (CoA) biosynthetic pathway. It catalyzes the reversible transfer of an adenylyl group from ATP to 4'-phosphopantetheine (Ppant) to form dephospho-CoA (dPCoA) and pyrophosphate. Previous structural studies have revealed how several ligands are recognized by bacterial PPATs. ATP, ADP, Ppant and dPCoA bind to the same binding site in a highly similar manner, while CoA binds to a partially overlapping site in a different mode. To provide further structural insights into ligand binding, the crystal structure of Staphylococcus aureus PPAT was solved in a binary complex with 3'-phosphoadenosine 5'-phosphosulfate (PAPS). This study unexpectedly revealed a new mode of ligand binding to PPAT, thus providing potentially useful information for structure-based discovery of inhibitors of bacterial PPATs.
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Affiliation(s)
- Hyung Ho Lee
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 151-742, Republic of Korea
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