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Beard DK, Subramanian S, Abendroth J, Dranow DM, Edwards TE, Myler PJ, Asojo OA. Crystal structure of betaine aldehyde dehydrogenase from Burkholderia pseudomallei. Acta Crystallogr F Struct Biol Commun 2022; 78:45-51. [PMID: 35102892 PMCID: PMC8805214 DOI: 10.1107/s2053230x21013455] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 12/19/2021] [Indexed: 11/10/2022] Open
Abstract
Burkholderia pseudomallei infection causes melioidosis, which is often fatal if untreated. There is a need to develop new and more effective treatments for melioidosis. This study reports apo and cofactor-bound crystal structures of the potential drug target betaine aldehyde dehydrogenase (BADH) from B. pseudomallei. A structural comparison identified similarities to BADH from Pseudomonas aeruginosa which is inhibited by the drug disulfiram. This preliminary analysis could facilitate drug-repurposing studies for B. pseudomallei.
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Affiliation(s)
- Dylan K Beard
- Department of Chemistry and Biochemistry, Hampton University, 100 William R. Harvey Way, Hampton, VA 23668, USA
| | - Sandhya Subramanian
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, 307 Westlake Avenue North Suite 500, Seattle, WA 98109, USA
| | - Jan Abendroth
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
| | | | - Thomas E Edwards
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
| | - Peter J Myler
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, 307 Westlake Avenue North Suite 500, Seattle, WA 98109, USA
| | - Oluwatoyin A Asojo
- Department of Chemistry and Biochemistry, Hampton University, 100 William R. Harvey Way, Hampton, VA 23668, USA
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2
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Abstract
Dissociation of a ligand isoniazid from a protein catalase was investigated using all-atom molecular dynamics (MD) simulations. Random acceleration MD (τ-RAMD) was used, in which a random artificial force applied to the ligand facilitates its dissociation. We have suggested a novel approach to extrapolate such obtained dissociation times to the zero-force limit assuming never before attempted universal exponential dependence of the bond strength on the applied force, allowing direct comparison with experimentally measured values. We have found that our calculated dissociation time was equal to 36.1 s with statistically significant values distributed in the interval of 0.2-72.0 s, which quantitatively matches the experimental value of 50 ± 8 s despite the extrapolation over 9 orders of magnitude in time.
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Affiliation(s)
- Ekaterina Maximova
- Department of Nanobiotechnology, Alferov University, Khlopina Street, 8/3 A, 194021 Saint Petersburg, Russia
- Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Helmholtzstr. 10, 01069 Dresden, Germany
| | - Eugene B Postnikov
- Department of Theoretical Physics, Kursk State University, Radishcheva Street, 33, 305000 Kursk, Russia
| | - Anastasia I Lavrova
- Saint-Petersburg State University, 7/9 Universitetskaya Emb., 199034 Saint Petersburg, Russia
- Saint-Petersburg State Research Institute of Phthisiopulmonology, 2-4 Ligovskiy Avenue, 194064 Saint-Petersburg, Russia
| | - Vladimir Farafonov
- V. N. Karazin Kharkiv National University, 4 Svobody sq., Kharkiv 61022, Ukraine
| | - Dmitry Nerukh
- Department of Mathematics, Aston University, Birmingham B4 7ET, U.K
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3
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Nebl S, Alwan WS, Williams ML, Sharma G, Taylor A, Doak BC, Wilde KL, McMahon RM, Halili MA, Martin JL, Capuano B, Fenwick RB, Mohanty B, Scanlon MJ. NMR fragment screening reveals a novel small molecule binding site near the catalytic surface of the disulfide-dithiol oxidoreductase enzyme DsbA from Burkholderia pseudomallei. J Biomol NMR 2020; 74:595-611. [PMID: 32761504 DOI: 10.1007/s10858-020-00339-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 07/21/2020] [Indexed: 06/11/2023]
Abstract
The presence of suitable cavities or pockets on protein structures is a general criterion for a therapeutic target protein to be classified as 'druggable'. Many disease-related proteins that function solely through protein-protein interactions lack such pockets, making development of inhibitors by traditional small-molecule structure-based design methods much more challenging. The 22 kDa bacterial thiol oxidoreductase enzyme, DsbA, from the gram-negative bacterium Burkholderia pseudomallei (BpsDsbA) is an example of one such target. The crystal structure of oxidized BpsDsbA lacks well-defined surface pockets. BpsDsbA is required for the correct folding of numerous virulence factors in B. pseudomallei, and genetic deletion of dsbA significantly attenuates B. pseudomallei virulence in murine infection models. Therefore, BpsDsbA is potentially an attractive drug target. Herein we report the identification of a small molecule binding site adjacent to the catalytic site of oxidized BpsDsbA. 1HN CPMG relaxation dispersion NMR measurements suggest that the binding site is formed transiently through protein dynamics. Using fragment-based screening, we identified a small molecule that binds at this site with an estimated affinity of KD ~ 500 µM. This fragment inhibits BpsDsbA enzymatic activity in vitro. The binding mode of this molecule has been characterized by NMR data-driven docking using HADDOCK. These data provide a starting point towards the design of more potent small molecule inhibitors of BpsDsbA.
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Affiliation(s)
- Stefan Nebl
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC, 3052, Australia
| | - Wesam S Alwan
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC, 3052, Australia
| | - Martin L Williams
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC, 3052, Australia
| | - Gaurav Sharma
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC, 3052, Australia
| | - Ashley Taylor
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC, 3052, Australia
| | - Bradley C Doak
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC, 3052, Australia
| | - Karyn L Wilde
- National Deuteration Facility, Australian Nuclear Science and Technology Organization (ANSTO), Locked Bag 2001, Kirrawee DC, NSW, 2232, Australia
| | - Róisín M McMahon
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, Australia
| | - Maria A Halili
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, Australia
| | - Jennifer L Martin
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, Australia
- Vice-Chancellor's Unit, University of Wollongong, Northfields Avenue, Wollongong, NSW, 2522, Australia
| | - Ben Capuano
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC, 3052, Australia
| | - R Bryn Fenwick
- Department of Integrative Structural and Computational Biology, Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Biswaranjan Mohanty
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC, 3052, Australia.
- ARC Centre for Fragment-Based Design, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC, 3052, Australia.
| | - Martin J Scanlon
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC, 3052, Australia.
- ARC Centre for Fragment-Based Design, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC, 3052, Australia.
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Pederzoli R, Tarantino D, Gourlay LJ, Chaves-Sanjuan A, Bolognesi M. Detecting the nature and solving the crystal structure of a contaminant protein from an opportunistic pathogen. Acta Crystallogr F Struct Biol Commun 2020; 76:392-397. [PMID: 32880586 PMCID: PMC7470038 DOI: 10.1107/s2053230x20010626] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Accepted: 08/02/2020] [Indexed: 03/26/2023] Open
Abstract
The unintentional crystallization of contaminant proteins in the place of target recombinant proteins is sporadically reported, despite the availability of stringent expression/purification protocols and of software for the detection of contaminants. Typically, the contaminant protein originates from the expression organism (for example Escherichia coli), but in rare circumstances contaminants from different sources have been reported. Here, a case of contamination from a Serratia bacterial strain that occurred while attempting to crystallize an unrelated protein from Burkholderia pseudomallei (overexpressed in E. coli) is presented. The contamination led to the unintended crystallization and structure analysis of a cyanase hydratase from a bacterial strain of the Serratia genus, an opportunistic enterobacterium that grows under conditions similar to those of E. coli and that is found in a variety of habitats, including the laboratory environment. In this context, the procedures that were adopted to identify the contaminant based on crystallographic data only are presented and the crystal structure of Serrata spp. cyanase hydratase is briefly discussed.
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Affiliation(s)
- Riccardo Pederzoli
- Hamburg Unit c/o DESY, European Molecular Biology Laboratory, Notkestrasse 85, 22603 Hamburg, Germany
| | - Delia Tarantino
- Department of Biosciences, University of Milano, Via Celoria 26, 20133 Milano, Italy
| | - Louise J. Gourlay
- Department of Biosciences, University of Milano, Via Celoria 26, 20133 Milano, Italy
| | - Antonio Chaves-Sanjuan
- Department of Biosciences, University of Milano, Via Celoria 26, 20133 Milano, Italy
- Invernizzi Pediatric Research Center, University of Milano, Via Celoria 26, 20133 Milano, Italy
| | - Martino Bolognesi
- Department of Biosciences, University of Milano, Via Celoria 26, 20133 Milano, Italy
- Invernizzi Pediatric Research Center, University of Milano, Via Celoria 26, 20133 Milano, Italy
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5
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Angeli A, Ferraroni M, Pinteala M, Maier SS, Simionescu BC, Carta F, Del Prete S, Capasso C, Supuran CT. Crystal Structure of a Tetrameric Type II β-Carbonic Anhydrase from the Pathogenic Bacterium Burkholderia pseudomallei. Molecules 2020; 25:molecules25102269. [PMID: 32408533 PMCID: PMC7287614 DOI: 10.3390/molecules25102269] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 04/29/2020] [Accepted: 05/08/2020] [Indexed: 01/07/2023] Open
Abstract
Carbonic anhydrase (CA) is a zinc enzyme that catalyzes the reversible conversion of carbon dioxide to bicarbonate and proton. Currently, CA inhibitors are widely used as antiglaucoma, anticancer, and anti-obesity drugs and for the treatment of neurological disorders. Recently, the potential use of CA inhibitors to fight infections caused by protozoa, fungi, and bacteria has emerged as a new research line. In this article, the X-ray crystal structure of β-CA from Burkholderia pseudomallei was reported. The X-ray crystal structure of this new enzyme was solved at 2.7 Å resolution, revealing a tetrameric type II β-CA with a “closed” active site in which the zinc is tetrahedrally coordinated to Cys46, Asp48, His102, and Cys105. B. pseudomallei is known to encode at least two CAs, a β-CA, and a γ-CA. These proteins, playing a pivotal role in its life cycle and pathogenicity, offer a novel therapeutic opportunity to obtain antibiotics with a different mechanism of action. Furthermore, the new structure can provide a clear view of the β-CA mechanism of action and the possibility to find selective inhibitors for this class of CAs.
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Affiliation(s)
- Andrea Angeli
- NEUROFARBA Department, Sezione di Scienze Farmaceutiche, Via Ugo Schiff 6, Università degli Studi di Firenze, 50019 Sesto Fiorentino (Florence), Italy; (A.A.); (F.C.)
- Centre of Advanced Research in Bionanoconjugates and Biopolymers Department, “Petru Poni” Institute of Macromolecular Chemistry, 700487 Iasi, Romania; (M.P.); (S.S.M.); (B.C.S.)
| | - Marta Ferraroni
- Department of Chemistry “Ugo Schiff”, Via della Lastruccia 13, Università degli Studi di Firenze, I-50019 Sesto Fiorentino (Florence), Italy
- Correspondence: (M.F.); (C.T.S.)
| | - Mariana Pinteala
- Centre of Advanced Research in Bionanoconjugates and Biopolymers Department, “Petru Poni” Institute of Macromolecular Chemistry, 700487 Iasi, Romania; (M.P.); (S.S.M.); (B.C.S.)
| | - Stelian S. Maier
- Centre of Advanced Research in Bionanoconjugates and Biopolymers Department, “Petru Poni” Institute of Macromolecular Chemistry, 700487 Iasi, Romania; (M.P.); (S.S.M.); (B.C.S.)
- Polymers Research Center, Polymeric Release Systems Research Group, “Gheorghe Asachi” Technical University of Iasi, 700487 Iasi, Romania
| | - Bogdan C. Simionescu
- Centre of Advanced Research in Bionanoconjugates and Biopolymers Department, “Petru Poni” Institute of Macromolecular Chemistry, 700487 Iasi, Romania; (M.P.); (S.S.M.); (B.C.S.)
| | - Fabrizio Carta
- NEUROFARBA Department, Sezione di Scienze Farmaceutiche, Via Ugo Schiff 6, Università degli Studi di Firenze, 50019 Sesto Fiorentino (Florence), Italy; (A.A.); (F.C.)
| | - Sonia Del Prete
- Istituto di Bioscienze e Biorisorse, CNR, Via Pietro Castellino 111, 80131 Napoli, Italy; (S.D.P.); (C.C.)
| | - Clemente Capasso
- Istituto di Bioscienze e Biorisorse, CNR, Via Pietro Castellino 111, 80131 Napoli, Italy; (S.D.P.); (C.C.)
| | - Claudiu T. Supuran
- NEUROFARBA Department, Sezione di Scienze Farmaceutiche, Via Ugo Schiff 6, Università degli Studi di Firenze, 50019 Sesto Fiorentino (Florence), Italy; (A.A.); (F.C.)
- Correspondence: (M.F.); (C.T.S.)
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Somprasong N, Hall CM, Webb JR, Sahl JW, Wagner DM, Keim P, Currie BJ, Schweizer HP. Burkholderia ubonensis Meropenem Resistance: Insights into Distinct Properties of Class A β-Lactamases in Burkholderia cepacia Complex and Burkholderia pseudomallei Complex Bacteria. mBio 2020; 11:e00592-20. [PMID: 32291300 PMCID: PMC7157819 DOI: 10.1128/mbio.00592-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 03/16/2020] [Indexed: 12/12/2022] Open
Abstract
Burkholderia pseudomallei, the founding member of the B. pseudomallei complex (Bpc), is a biothreat agent and causes melioidosis, a disease whose treatment mainly relies on ceftazidime and meropenem. The concern is that B. pseudomallei could enhance its drug resistance repertoire by the acquisition of DNA from resistant near-neighbor species. Burkholderia ubonensis, a member of the B. cepacia complex (Bcc), is commonly coisolated from environments where B. pseudomallei is present. Unlike B. pseudomallei, in which significant primary carbapenem resistance is rare, it is not uncommon in B. ubonensis, but the underlying mechanisms are unknown. We established that carbapenem resistance in B. ubonensis is due to an inducible class A PenB β-lactamase, as has been shown for other Bcc bacteria. Inducibility is not sufficient for high-level resistance but also requires other determinants, such as a PenB that is more robust than that present in susceptible isolates, as well as other resistance factors. Curiously and diagnostic for the two complexes, both Bpc and Bcc bacteria contain distinct annotated PenA class A β-lactamases. However, the protein from Bcc bacteria is missing its essential active-site serine and, therefore, is not a β-lactamase. Regulated expression of a transcriptional penB'-lacZ (β-galactosidase) fusion in the B. pseudomallei surrogate B. thailandensis confirms that although Bpc bacteria lack an inducible β-lactamase, they contain the components required for responding to aberrant peptidoglycan synthesis resulting from β-lactam challenge. Understanding the diversity of antimicrobial resistance in Burkholderia species is informative about how the challenges arising from potential resistance transfer between them can be met.IMPORTANCEBurkholderia pseudomallei causes melioidosis, a tropical disease that is highly fatal if not properly treated. Our data show that, in contrast to B. pseudomallei, B. ubonensis β-lactam resistance is fundamentally different because intrinsic resistance is mediated by an inducible class A β-lactamase. This includes resistance to carbapenems. Our work demonstrates that studies with near-neighbor species are informative about the diversity of antimicrobial resistance in Burkholderia and can also provide clues about the potential of resistance transfer between bacteria inhabiting the same environment. Knowledge about potential adverse challenges resulting from the horizontal transfer of resistance genes between members of the two complexes enables the design of effective countermeasures.
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Affiliation(s)
- Nawarat Somprasong
- Department of Molecular Genetics & Microbiology, College of Medicine, Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
| | - Carina M Hall
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Jessica R Webb
- Global and Tropical Heath Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Jason W Sahl
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - David M Wagner
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Paul Keim
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Bart J Currie
- Global and Tropical Heath Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
- Department of Infectious Diseases, Royal Darwin Hospital, Darwin, Northern Territory, Australia
- Northern Territory Medical Program, Royal Darwin Hospital, Darwin, Northern Territory, Australia
| | - Herbert P Schweizer
- Department of Molecular Genetics & Microbiology, College of Medicine, Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
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Angeli A, Pinteala M, Maier SS, Del Prete S, Capasso C, Simionescu BC, Supuran CT. Inhibition of bacterial α-, β- and γ-class carbonic anhydrases with selenazoles incorporating benzenesulfonamide moieties. J Enzyme Inhib Med Chem 2019; 34:244-249. [PMID: 30734601 PMCID: PMC6327980 DOI: 10.1080/14756366.2018.1547287] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 11/07/2018] [Indexed: 10/27/2022] Open
Abstract
A series of benzenesulfonamides incorporating selenazoles with diverse substitution patterns were investigated as inhibitors of six bacterial carbonic anhydrases (CAs, EC 4.2.1.1) from bacterial pathogens, such as Helicobacter pylori (hpCAα was the investigated enzyme), Vibrio cholerae (all the three CAs from this pathogen were considered, VchCAα, VchCAβ and VchCAγ) and Burkholderia pseudomallei (with its two CAs, BpsCAβ and BpsCAγ). All these sulfonamides were effective CA inhibitors, with potencies in the low micromolar or submicromolar range, making them attractive as lead compounds for designing antibacterials with a novel mechanism of action, which could counteract the extensive resistance problem observed with many clinically used antibiotics.
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Affiliation(s)
- Andrea Angeli
- Dipartimento Neurofarba, Sezione di Scienze Farmaceutiche e Nutraceutiche, Università degli Studi di Firenze, Florence, Italy
| | - Mariana Pinteala
- Centre of Advanced Research in Bionanoconjugates and Biopolymers Department, “Petru Poni” Institute of Macromolecular Chemistry, Iasi, Romania
| | - Stelian S. Maier
- Centre of Advanced Research in Bionanoconjugates and Biopolymers Department, “Petru Poni” Institute of Macromolecular Chemistry, Iasi, Romania
- Polymers Research Center, Polymeric Release Systems Research Group, “Gheorghe Asachi” Technical University of Iasi, Iasi, Romania
| | | | | | - Bogdan C. Simionescu
- Centre of Advanced Research in Bionanoconjugates and Biopolymers Department, “Petru Poni” Institute of Macromolecular Chemistry, Iasi, Romania
| | - Claudiu T. Supuran
- Dipartimento Neurofarba, Sezione di Scienze Farmaceutiche e Nutraceutiche, Università degli Studi di Firenze, Florence, Italy
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Yu Y, Williams A, Zhang X, Fu L, Xia K, Xu Y, Zhang F, Liu J, Koffas M, Linhardt RJ. Specificity and action pattern of heparanase Bp, a β-glucuronidase from Burkholderia pseudomallei. Glycobiology 2019; 29:572-581. [PMID: 31143933 PMCID: PMC6639543 DOI: 10.1093/glycob/cwz039] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 05/16/2019] [Accepted: 05/23/2019] [Indexed: 12/12/2022] Open
Abstract
The specificity and action pattern of a β-glucuronidase derived from the pathogenic bacteria Burkholderia pseudomallei and expressed in Escherichia coli as a recombinant protein has been evaluated. While this enzyme shows activity on a number of glycosaminoglycans, our study has focused on its action on heparin, heparan sulfate and their biosynthetic intermediates as well as chemoenzymatically synthesized, structurally defined heparan sulfate oligosaccharides. These heparin/heparan sulfate (HP/HS) substrates examined varied in size and structure, but all contained an uronic acid (UA) residue β-(1→4) linked to a glucosamine residue. On the substrates tested, this enzyme (heparanase Bp) acted only on a glucuronic acid residue β-(1→4) linked to an N-acetylglucosamine, N-sulfoglucosamine or N-acetyl-6-O-sulfoglucosamine residue. A substrate was required to have a length of pentasaccharide or longer and heparanase Bp acted with a random endolytic action pattern on HP/HS. The specificity and glycohydrolase mechanism of action of heparanase Bp resembles mammalian heparanase and is complementary to the bacterial heparin lyases, which act through an eliminase mechanism on a glucosamine residue (1→4) linked to a UA residue, suggesting its utility as a tool for the structural determination of HP/HS as well as representing a possible model for the medically relevant mammalian heparanase. The utility heparanase Bp was demonstrated by the oligosaccharide mapping of heparin, which afforded resistant intact highly sulfated domains ranging from tetrasaccharide to >28-mer with a molecular weight >9000.
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Affiliation(s)
- Yanlei Yu
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, USA
| | - Asher Williams
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY, USA
| | - Xing Zhang
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, USA
| | - Li Fu
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, USA
| | - Ke Xia
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, USA
| | - Yongmei Xu
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA
| | - Fuming Zhang
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY, USA
| | - Jian Liu
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA
| | - Mattheos Koffas
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY, USA
- Department of Biology, Rensselaer Polytechnic Institute, Troy, NY, USA
| | - Robert J Linhardt
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, USA
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY, USA
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY, USA
- Department of Biology, Rensselaer Polytechnic Institute, Troy, NY, USA
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9
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Vullo D, Del Prete S, Osman SM, Alasmary FAS, AlOthman Z, Donald WA, Capasso C, Supuran CT. Comparison of the amine/amino acid activation profiles of the β- and γ-carbonic anhydrases from the pathogenic bacterium Burkholderia pseudomallei. J Enzyme Inhib Med Chem 2018; 33:25-30. [PMID: 29098887 PMCID: PMC6009869 DOI: 10.1080/14756366.2017.1387544] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 09/29/2017] [Accepted: 09/29/2017] [Indexed: 01/04/2023] Open
Abstract
The β-class carbonic anhydrase (CA, EC 4.2.1.1) from the pathogenic bacterium Burkholderia pseudomallei, BpsCAβ, that is responsible for the tropical disease melioidosis was investigated for its activation with natural and non-natural amino acids and amines. Previously, the γ-CA from this bacterium has been investigated with the same library of 19 amines/amino acids, which show very potent activating effects on both enzymes. The most effective BpsCAβ activators were L- and D-DOPA, L- and D-Trp, L-Tyr, 4-amino-L-Phe, histamine, dopamine, serotonin, 2-pyridyl-methylamine, 1-(2-aminoethyl)-piperazine and L-adrenaline with KAs of 0.9-27 nM. Less effective activators were D-His, L- and D-Phe, D-Tyr, 2-(2-aminoethyl)pyridine and 4-(2-aminoethyl)-morpholine with KAs of 73 nM-3.42 µM. The activation of CAs from bacteria, such as BpsCAγ/β, has not been considered previously for possible biomedical applications. It would be of interest to perform studies in which bacteria are cultivated in the presence of CA activators, which may contribute to understanding processes connected with the virulence and colonization of the host by pathogenic bacteria.
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Affiliation(s)
- Daniela Vullo
- Dipartimento Di Chimica, Laboratorio di Chimica Bioinorganica, Polo Scientifico, Università degliStudi di Firenze, Florence, Italy
| | - Sonia Del Prete
- CNR, Istituto di Bioscienze e Biorisorse, Napoli, Italy
- Dipartimento Neurofarba, Sezione di Scienze Farmaceutiche e Nutraceutiche, Università degli Studi di Firenze, Florence, Italy
| | - Sameh M. Osman
- Department of Chemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Fatmah A. S. Alasmary
- Department of Chemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Zeid AlOthman
- Department of Chemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - William A. Donald
- School of Chemistry, University of New South Wales, Sydney, New South Wales, Australia
| | | | - Claudiu T. Supuran
- Dipartimento Neurofarba, Sezione di Scienze Farmaceutiche e Nutraceutiche, Università degli Studi di Firenze, Florence, Italy
- School of Chemistry, University of New South Wales, Sydney, New South Wales, Australia
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10
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Stefanucci A, Angeli A, Dimmito MP, Luisi G, Del Prete S, Capasso C, Donald WA, Mollica A, Supuran CT. Activation of β- and γ-carbonic anhydrases from pathogenic bacteria with tripeptides. J Enzyme Inhib Med Chem 2018; 33:945-950. [PMID: 29747543 PMCID: PMC6009936 DOI: 10.1080/14756366.2018.1468530] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Six tripeptides incorporating acidic amino acid residues were prepared for investigation as activators of β- and γ-carbonic anhydrases (CAs, EC 4.2.1.1) from the pathogenic bacteria Vibrio cholerae, Mycobacterium tuberculosis, and Burkholderia pseudomallei. The primary amino acid residues that are involved in the catalytic mechanisms of these CA classes are poorly understood, although glutamic acid residues near the active site appear to be involved. The tripeptides that contain Glu or Asp residues can effectively activate VchCAβ and VchCAγ (enzymes from V. cholerae), Rv3273 CA (mtCA3, a β-CA from M. tuberculosis) and BpsCAγ (γ-CA from B. pseudomallei) at 0.21-18.1 µM levels. The position of the acidic residues in the peptide sequences can significantly affect bioactivity. For three of the enzymes, tripeptides were identified that are more effective activators than both l-Glu and l-Asp. The tripeptides are also relatively selective because they do not activate prototypical α-CAs (human carbonic anhydrases I and II). Because the role of CA activators in the pathogenicity and life cycles of these infectious bacteria are poorly understood, this study provides new molecular probes to explore such processes.
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Affiliation(s)
- Azzurra Stefanucci
- Department of Pharmacy, “Gabriele d’Annunzio” University of Chieti-Pescara, Chieti, Italy
| | - Andrea Angeli
- Department of Neurofarba, Università degli Studi di Firenze, Sezione di Scienze Farmaceutiche e Nutraceutiche, Sesto Fiorentino, Florence, Italy
| | - Marilisa Pia Dimmito
- Department of Pharmacy, “Gabriele d’Annunzio” University of Chieti-Pescara, Chieti, Italy
| | - Grazia Luisi
- Department of Pharmacy, “Gabriele d’Annunzio” University of Chieti-Pescara, Chieti, Italy
| | - Sonia Del Prete
- Department of Neurofarba, Università degli Studi di Firenze, Sezione di Scienze Farmaceutiche e Nutraceutiche, Sesto Fiorentino, Florence, Italy
- Istituto di Bioscienze e Biorisorse, CNR, Napoli, Italy
| | | | - William A. Donald
- School of Chemistry, University of New South Wales, Sydney, New South Wales, Australia
| | - Adriano Mollica
- Department of Pharmacy, “Gabriele d’Annunzio” University of Chieti-Pescara, Chieti, Italy
| | - Claudiu T. Supuran
- Department of Neurofarba, Università degli Studi di Firenze, Sezione di Scienze Farmaceutiche e Nutraceutiche, Sesto Fiorentino, Florence, Italy
- School of Chemistry, University of New South Wales, Sydney, New South Wales, Australia
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11
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Angeli A, Abbas G, Del Prete S, Capasso C, Supuran CT. Selenides bearing benzenesulfonamide show potent inhibition activity against carbonic anhydrases from pathogenic bacteria Vibrio cholerae and Burkholderia pseudomallei. Bioorg Chem 2018; 79:319-322. [PMID: 29803078 DOI: 10.1016/j.bioorg.2018.05.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Revised: 05/15/2018] [Accepted: 05/16/2018] [Indexed: 10/16/2022]
Abstract
A series of selenides bearing benzenesulfonamide moieties was evaluated as carbonic anhydrase (CA, EC 4.2.1.1) inhibitors against the pathogenic bacteria Vibrio cholerae (VchCAα and VchCAβ) and Burkholderia pseudomallei (BpsCAβ) enzymes. The molecules represent an interesting lead for antibacterial agents with a possibly new mechanism of action showing excellent inhibitory action and selectivity for inhibiting VchCAα and BpsCAβ over the human (h) off-target isoforms hCA I and II. Identification of potent and possibly selective inhibitors of bacteria CAs over the human counterparts may lead to pharmacological tools useful for understanding the physiological role(s) of these under-investigated proteins.
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Affiliation(s)
- Andrea Angeli
- Università degli Studi di Firenze, NEUROFARBA Dept., Sezione di Scienze Farmaceutiche, Via Ugo Schiff 6, 50019 Sesto Fiorentino (Florence), Italy
| | - Ghulam Abbas
- Università degli Studi di Firenze, NEUROFARBA Dept., Sezione di Scienze Farmaceutiche, Via Ugo Schiff 6, 50019 Sesto Fiorentino (Florence), Italy; Department of Biological Sciences and Chemistry, University of Nizwa, Birkat Al-Mauz, P.O. Box 33, Nizwa 616, Oman
| | - Sonia Del Prete
- Istituto di Bioscienze e Biorisorse, CNR, Via Pietro Castellino 111, 80131 Napoli, Italy
| | - Clemente Capasso
- Istituto di Bioscienze e Biorisorse, CNR, Via Pietro Castellino 111, 80131 Napoli, Italy
| | - Claudiu T Supuran
- Università degli Studi di Firenze, NEUROFARBA Dept., Sezione di Scienze Farmaceutiche, Via Ugo Schiff 6, 50019 Sesto Fiorentino (Florence), Italy.
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12
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Bond TEH, Sorenson AE, Schaeffer PM. Functional characterisation of Burkholderia pseudomallei biotin protein ligase: A toolkit for anti-melioidosis drug development. Microbiol Res 2017; 199:40-48. [PMID: 28454708 DOI: 10.1016/j.micres.2017.03.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 03/06/2017] [Accepted: 03/15/2017] [Indexed: 01/17/2023]
Abstract
Burkholderia pseudomallei (Bp) is the causative agent of melioidosis. The bacterium is responsible for 20% of community-acquired sepsis cases and 40% of sepsis-related mortalities in northeast Thailand, and is intrinsically resistant to aminoglycosides, macrolides, rifamycins, cephalosporins, and nonureidopenicillins. There is no vaccine and its diagnosis is problematic. Biotin protein ligase (BirA) which is essential for fatty acid synthesis has been proposed as a drug target in bacteria. Very few bacterial BirA have been characterized, and a better understanding of these enzymes is necessary to further assess their value as drug targets. BirA within the Burkholderia genus have not yet been investigated. We present for the first time the cloning, expression, purification and functional characterisation of the putative Bp BirA and orthologous B. thailandensis (Bt) biotin carboxyl carrier protein (BCCP) substrate. A GFP-tagged Bp BirA was produced and applied for the development of a high-throughput (HT) assay based on our differential scanning fluorimetry of GFP-tagged proteins (DSF-GTP) principle as well as an electrophoretic mobility shift assay. Our biochemical data in combination with the new HT DSF-GTP and biotinylation activity assay could facilitate future drug screening efforts against this drug-resistant organism.
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Affiliation(s)
- Thomas E H Bond
- Comparative Genomics Centre, James Cook University, DB21, James Cook Drive, Townsville, QLD 4811, Australia
| | - Alanna E Sorenson
- Comparative Genomics Centre, James Cook University, DB21, James Cook Drive, Townsville, QLD 4811, Australia
| | - Patrick M Schaeffer
- Comparative Genomics Centre, James Cook University, DB21, James Cook Drive, Townsville, QLD 4811, Australia.
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13
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Vullo D, Del Prete S, Di Fonzo P, Carginale V, Donald WA, Supuran CT, Capasso C. Comparison of the Sulfonamide Inhibition Profiles of the β- and γ-Carbonic Anhydrases from the Pathogenic Bacterium Burkholderia pseudomallei. Molecules 2017; 22:E421. [PMID: 28272358 PMCID: PMC6155308 DOI: 10.3390/molecules22030421] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 02/16/2017] [Accepted: 03/03/2017] [Indexed: 11/25/2022] Open
Abstract
We have cloned, purified, and characterized a β-carbonic anhydrase (CA, EC 4.2.1.1), BpsCAβ, from the pathogenic bacterium Burkholderia pseudomallei, responsible for the tropical disease melioidosis. The enzyme showed high catalytic activity for the physiologic CO₂ hydration reaction to bicarbonate and protons, with the following kinetic parameters: kcat of 1.6 × 10⁵ s-1 and kcat/KM of 3.4 × 10⁷ M-1 s-1. An inhibition study with a panel of 38 sulfonamides and one sulfamate-including 15 compounds that are used clinically-revealed an interesting structure-activity relationship for the interaction of this enzyme with these inhibitors. Many simple sulfonamides and clinically used agents such as topiramate, sulpiride, celecoxib, valdecoxib, and sulthiame were ineffective BpsCAβ inhibitors (KI > 50 µM). Other drugs, such as ethoxzolamide, dorzolamide, brinzolamide, zonisamide, indisulam, and hydrochlorothiazide were moderately potent micromolar inhibitors. The best inhibition was observed with benzene-1,3-disulfonamides-benzolamide and its analogs acetazolamide and methazolamide-which showed KI in the range of 185-745 nM. The inhibition profile of BpsCAβ is very different from that of the γ-class enzyme from the same pathogen, BpsCAγ. Thus, identifying compounds that would effectively interact with both enzymes is relatively challenging. However, benzolamide was one of the best inhibitors of both of these CAs with KI of 653 and 185 nM, respectively, making it an interesting lead compound for the design of more effective agents, which may be useful tools for understanding the pathogenicity of this bacterium.
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Affiliation(s)
- Daniela Vullo
- Laboratorio di Chimica Bioinorganica, Dipartimento Di Chimica, Università degli Studi di Firenze, Polo Scientifico, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy.
| | - Sonia Del Prete
- Istituto di Bioscienze e Biorisorse, CNR, Via Pietro Castellino 111, 80131 Napoli, Italy.
- Sezione di Scienze Farmaceutiche e Nutraceutiche, Dipartimento Neurofarba, Università degli Studi di Firenze, Via U. Schiff 6, 50019 Sesto Fiorentino, Florence, Italy.
| | - Pietro Di Fonzo
- Istituto di Bioscienze e Biorisorse, CNR, Via Pietro Castellino 111, 80131 Napoli, Italy.
| | - Vincenzo Carginale
- Istituto di Bioscienze e Biorisorse, CNR, Via Pietro Castellino 111, 80131 Napoli, Italy.
| | - W Alexander Donald
- School of Chemistry, University of New South Wales, Sydney, New South Wales 2052, Australia.
| | - Claudiu T Supuran
- Sezione di Scienze Farmaceutiche e Nutraceutiche, Dipartimento Neurofarba, Università degli Studi di Firenze, Via U. Schiff 6, 50019 Sesto Fiorentino, Florence, Italy.
- School of Chemistry, University of New South Wales, Sydney, New South Wales 2052, Australia.
| | - Clemente Capasso
- Istituto di Bioscienze e Biorisorse, CNR, Via Pietro Castellino 111, 80131 Napoli, Italy.
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14
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Vanaporn M, Sarkar-Tyson M, Kovacs-Simon A, Ireland PM, Pumirat P, Korbsrisate S, Titball RW, Butt A. Trehalase plays a role in macrophage colonization and virulence of Burkholderia pseudomallei in insect and mammalian hosts. Virulence 2017; 8:30-40. [PMID: 27367830 PMCID: PMC5963195 DOI: 10.1080/21505594.2016.1199316] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 06/01/2016] [Accepted: 06/03/2016] [Indexed: 10/21/2022] Open
Abstract
Trehalose is a disaccharide formed from two glucose molecules. This sugar molecule can be isolated from a range of organisms including bacteria, fungi, plants and invertebrates. Trehalose has a variety of functions including a role as an energy storage molecule, a structural component of glycolipids and plays a role in the virulence of some microorganisms. There are many metabolic pathways that control the biosynthesis and degradation of trehalose in different organisms. The enzyme trehalase forms part of a pathway that converts trehalose into glucose. In this study we set out to investigate whether trehalase plays a role in both stress adaptation and virulence of Burkholderia pseudomallei. We show that a trehalase deletion mutant (treA) had increased tolerance to thermal stress and produced less biofilm than the wild type B. pseudomallei K96243 strain. We also show that the ΔtreA mutant has reduced ability to survive in macrophages and that it is attenuated in both Galleria mellonella (wax moth larvae) and a mouse infection model. This is the first report that trehalase is important for bacterial virulence.
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Affiliation(s)
- Muthita Vanaporn
- College of Life and Environmental Sciences, University of Exeter, Exeter, UK
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | | | - Andrea Kovacs-Simon
- College of Life and Environmental Sciences, University of Exeter, Exeter, UK
| | - Philip M. Ireland
- CBR Division, Defense Science and Technology Laboratory, Salisbury, UK
| | - Pornpan Pumirat
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Sunee Korbsrisate
- Department of Immunology, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Richard W. Titball
- College of Life and Environmental Sciences, University of Exeter, Exeter, UK
| | - Aaron Butt
- College of Life and Environmental Sciences, University of Exeter, Exeter, UK
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15
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Del Prete S, Vullo D, Di Fonzo P, Osman SM, AlOthman Z, Supuran CT, Capasso C. Anion inhibition profiles of the γ-carbonic anhydrase from the pathogenic bacterium Burkholderia pseudomallei responsible of melioidosis and highly drug resistant to common antibiotics. Bioorg Med Chem 2016; 25:575-580. [PMID: 27914949 DOI: 10.1016/j.bmc.2016.11.021] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 11/11/2016] [Accepted: 11/12/2016] [Indexed: 12/13/2022]
Abstract
Burkholderia pseudomallei is a Gram-negative saprophytic bacterium responsible of melioidosis, an endemic disease of tropical and sub-tropical regions of the world. A recombinant γ-CA (BpsγCA) identified in the genome of this bacterium was cloned and purified. Its catalytic activity and anion inhibition profiles were investigated. The enzyme was an efficient catalyst for the CO2 hydration showing a kcat of 5.3×105s-1 and kcat/Km of 2.5×107M-1×s-1. The best BpsγCA inhibitors were sulfamide, sulfamic acid, phenylboronic acid and phenylarsonic acid, which showed KI in the range of 49-83μM (these inhibitors showed millimolar inhibition constant against hCA II), followed by diethyldithiocarbamate, selenate, tellurate, perrhenate, selenocyanate, trithiocarbonate, tetraborato, pyrophosphate, stannate, carbonate, bicarbonate, azide, cyanide, thiocyanate and cyanate with KIs in the range of 0.55-9.1mM. In our laboratories, work is in progress to resolve the X-ray crystal structures of BpsγCA, which may allow the development of small molecule inhibitors with desired properties for targeting and inhibiting specifically the bacterial over the human CAs, considering the fact that B. pseudomallei is involved in a serious bacterial disease.
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Affiliation(s)
- Sonia Del Prete
- Istituto di Bioscienze e Biorisorse, CNR, Via Pietro Castellino 111, Napoli, Italy; Università degliStudi di Firenze, Dipartimento Di Chimica, Laboratorio di Chimica Bioinorganica, Polo Scientifico, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy
| | - Daniela Vullo
- Università degliStudi di Firenze, Dipartimento Di Chimica, Laboratorio di Chimica Bioinorganica, Polo Scientifico, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy
| | - Pietro Di Fonzo
- Istituto di Bioscienze e Biorisorse, CNR, Via Pietro Castellino 111, Napoli, Italy
| | - Sameh M Osman
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Zeid AlOthman
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Claudiu T Supuran
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia; Università degli Studi di Firenze, Dipartimento Neurofarba, Sezione di ScienzeFarmaceutiche e Nutraceutiche, Via U. Schiff 6, 50019 Sesto Fiorentino, Florence, Italy.
| | - Clemente Capasso
- Istituto di Bioscienze e Biorisorse, CNR, Via Pietro Castellino 111, Napoli, Italy.
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16
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Park J, Lee D, Kim MS, Kim DY, Shin DH. A preliminary X-ray study of 3-deoxy-D-manno-oct-2-ulosonic acid 8-phosphate phosphatase (YrbI) from Burkholderia pseudomallei. Acta Crystallogr F Struct Biol Commun 2015; 71:790-3. [PMID: 26057814 PMCID: PMC4461349 DOI: 10.1107/s2053230x15006135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 03/25/2015] [Indexed: 11/10/2022] Open
Abstract
3-Deoxy-D-manno-oct-2-ulosonic acid 8-phosphate phosphatase (YrbI), the third enzyme in the pathway for the biosynthesis of 3-deoxy-D-manno-oct-2-ulosonic acid (KDO), hydrolyzes KDO 8-phosphate to KDO and inorganic phosphate. YrbI belongs to the haloacid dehalogenase (HAD) superfamily, which is a large family of magnesium-dependent phosphatase/phosphotransferase enzymes. In this study, YrbI from Burkholderia pseudomallei, the causative agent of melioidosis, has been cloned, expressed, purified and crystallized. Synchrotron X-ray data were also collected to 2.25 Å resolution. The crystal belonged to the primitive orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 63.7, b = 97.5, c = 98.0 Å. A full structural determination is in progress to elucidate the structure-function relationship of this protein.
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Affiliation(s)
- Jimin Park
- Global Top 5 Research Program, College of Pharmacy, Ewha Womans University, Seoul 120-750, Republic of Korea
| | - Daeun Lee
- Global Top 5 Research Program, College of Pharmacy, Ewha Womans University, Seoul 120-750, Republic of Korea
| | - Mi-Sun Kim
- Global Top 5 Research Program, College of Pharmacy, Ewha Womans University, Seoul 120-750, Republic of Korea
| | - Dae Yong Kim
- 402-803 Technopark, 65 Pyeongchon-ro, Wonmi-gu, Bucheon-si, Gyeonggi-do 420-734, Republic of Korea
| | - Dong Hae Shin
- Global Top 5 Research Program, College of Pharmacy, Ewha Womans University, Seoul 120-750, Republic of Korea
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17
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Narasimha Rao K, Lakshminarasimhan A, Joseph S, Lekshmi SU, Lau MS, Takhi M, Sreenivas K, Nathan S, Yusof R, Abd Rahman N, Ramachandra M, Antony T, Subramanya H. AFN-1252 is a potent inhibitor of enoyl-ACP reductase from Burkholderia pseudomallei--Crystal structure, mode of action, and biological activity. Protein Sci 2015; 24:832-40. [PMID: 25644789 PMCID: PMC4420531 DOI: 10.1002/pro.2655] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Revised: 01/30/2015] [Accepted: 01/30/2015] [Indexed: 12/20/2022]
Abstract
Melioidosis is a tropical bacterial infection caused by Burkholderia pseudomallei (B. pseudomallei; Bpm), a Gram-negative bacterium. Current therapeutic options are largely limited to trimethoprim-sulfamethoxazole and β-lactam drugs, and the treatment duration is about 4 months. Moreover, resistance has been reported to these drugs. Hence, there is a pressing need to develop new antibiotics for Melioidosis. Inhibition of enoyl-ACP reducatase (FabI), a key enzyme in the fatty acid biosynthesis pathway has shown significant promise for antibacterial drug development. FabI has been identified as the major enoyl-ACP reductase present in B. pseudomallei. In this study, we evaluated AFN-1252, a Staphylococcus aureus FabI inhibitor currently in clinical development, for its potential to bind to BpmFabI enzyme and inhibit B. pseudomallei bacterial growth. AFN-1252 stabilized BpmFabI and inhibited the enzyme activity with an IC50 of 9.6 nM. It showed good antibacterial activity against B. pseudomallei R15 strain, isolated from a melioidosis patient (MIC of 2.35 mg/L). X-ray structure of BpmFabI with AFN-1252 was determined at a resolution of 2.3 Å. Complex of BpmFabI with AFN-1252 formed a symmetrical tetrameric structure with one molecule of AFN-1252 bound to each monomeric subunit. The kinetic and thermal melting studies supported the finding that AFN-1252 can bind to BpmFabI independent of cofactor. The structural and mechanistic insights from these studies might help the rational design and development of new FabI inhibitors.
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Affiliation(s)
- Krishnamurthy Narasimha Rao
- Aurigene Discovery Technologies Ltd, 39-40, KIADB Industrial area, Electronic city Phase IIHosur Road, Bangalore, 560 100, India
| | - Anirudha Lakshminarasimhan
- Aurigene Discovery Technologies Ltd, 39-40, KIADB Industrial area, Electronic city Phase IIHosur Road, Bangalore, 560 100, India
| | - Sarah Joseph
- Aurigene Discovery Technologies Ltd, 39-40, KIADB Industrial area, Electronic city Phase IIHosur Road, Bangalore, 560 100, India
| | - Swathi U Lekshmi
- Aurigene Discovery Technologies Ltd, 39-40, KIADB Industrial area, Electronic city Phase IIHosur Road, Bangalore, 560 100, India
| | - Ming-Seong Lau
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia43600, Bangi, Selangor, Malaysia
| | - Mohammed Takhi
- Aurigene Discovery Technologies LtdBollaram Road, Miyapur, Hyderabad, 500 049, India
| | - Kandepu Sreenivas
- Aurigene Discovery Technologies LtdBollaram Road, Miyapur, Hyderabad, 500 049, India
| | - Sheila Nathan
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia43600, Bangi, Selangor, Malaysia
| | - Rohana Yusof
- Department of Molecular Medicine, Faculty of Medicine, University of Malaya50603, Kuala Lumpur, Malaysia
| | - Noorsaadah Abd Rahman
- Department of Chemistry, Faculty of Science, University of Malaya50603, Kuala Lumpur, Malaysia
| | - Murali Ramachandra
- Aurigene Discovery Technologies Ltd, 39-40, KIADB Industrial area, Electronic city Phase IIHosur Road, Bangalore, 560 100, India
| | - Thomas Antony
- Aurigene Discovery Technologies Ltd, 39-40, KIADB Industrial area, Electronic city Phase IIHosur Road, Bangalore, 560 100, India
| | - Hosahalli Subramanya
- Aurigene Discovery Technologies Ltd, 39-40, KIADB Industrial area, Electronic city Phase IIHosur Road, Bangalore, 560 100, India
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18
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Gong L, Lai SC, Treerat P, Prescott M, Adler B, Boyce JD, Devenish RJ. Burkholderia pseudomallei type III secretion system cluster 3 ATPase BsaS, a chemotherapeutic target for small-molecule ATPase inhibitors. Infect Immun 2015; 83:1276-85. [PMID: 25605762 PMCID: PMC4363454 DOI: 10.1128/iai.03070-14] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 01/05/2015] [Indexed: 12/18/2022] Open
Abstract
Melioidosis is an infectious disease of high mortality for humans and other animal species; it is prevalent in tropical regions worldwide. The pathogenesis of melioidosis depends on the ability of its causative agent, the Gram-negative bacterium Burkholderia pseudomallei, to enter and survive in host cells. B. pseudomallei can escape from the phagosome into the cytosol of phagocytic cells where it replicates and acquires actin-mediated motility, avoiding killing by the autophagy-dependent process, LC3 (microtubule-associated protein light chain 3)-associated phagocytosis (LAP). The type III secretion system cluster 3 (TTSS3) facilitates bacterial escape from phagosomes, although the mechanism has not been fully elucidated. Given the recent identification of small-molecule inhibitors of the TTSS ATPase, we sought to determine the potential of the predicted TTSS3 ATPase, encoded by bsaS, as a target for chemotherapeutic treatment of infection. A B. pseudomallei bsaS deletion mutant was generated and used as a control against which to assess the effect of inhibitor treatment. Infection of RAW 264.7 cells with wild-type bacteria and subsequent treatment with the ATPase inhibitor compound 939 resulted in reduced intracellular bacterial survival, reduced escape from phagosomes, and increased colocalization with both LC3 and the lysosomal marker LAMP1 (lysosome-associated membrane protein 1). These changes were similar to those observed for infection of RAW 264.7 cells with the bsaS deletion mutant. We propose that treatment with the ATPase inhibitor compound 939 decreased intracellular bacterial survival through a reduced ability of bacteria to escape from phagosomes and increased killing via LAP. Therefore, small-molecule inhibitors of the TTSS3 ATPase have potential as therapeutic treatments against melioidosis.
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Affiliation(s)
- Lan Gong
- Department of Biochemistry and Molecular Biology, Monash University, Victoria, Clayton, Australia Australian Research Council Centre of Excellence in Structural and Functional Microbial Genomics, Monash University, Victoria, Clayton, Australia
| | - Shu-Chin Lai
- Department of Biochemistry and Molecular Biology, Monash University, Victoria, Clayton, Australia
| | - Puthayalai Treerat
- Department of Microbiology, Monash University, Victoria, Clayton, Australia Australian Research Council Centre of Excellence in Structural and Functional Microbial Genomics, Monash University, Victoria, Clayton, Australia
| | - Mark Prescott
- Department of Biochemistry and Molecular Biology, Monash University, Victoria, Clayton, Australia
| | - Ben Adler
- Department of Microbiology, Monash University, Victoria, Clayton, Australia Australian Research Council Centre of Excellence in Structural and Functional Microbial Genomics, Monash University, Victoria, Clayton, Australia
| | - John D Boyce
- Department of Microbiology, Monash University, Victoria, Clayton, Australia Australian Research Council Centre of Excellence in Structural and Functional Microbial Genomics, Monash University, Victoria, Clayton, Australia
| | - Rodney J Devenish
- Department of Biochemistry and Molecular Biology, Monash University, Victoria, Clayton, Australia Australian Research Council Centre of Excellence in Structural and Functional Microbial Genomics, Monash University, Victoria, Clayton, Australia
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19
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Abstract
The isolation of therapeutic and functional protease inhibitors in vitro via combinatorial chemistry and phage display technology has been described previously. Here we report the construction of a combinatorial mouse-human chimeric antibody fragment (Fab) antibody library targeted against the protease of the tropical pathogen, Burkholderia pseudomallei. The resulting library was biopanned against the protease, and selected clones were analyzed for their ability to function as protease inhibitors. Three families of Fabs were identified by restriction fingerprinting, all of which demonstrated high specificity towards the protease of B. pseudomallei. Purified Fabs also demonstrated the capacity to inhibit B. pseudomallei protease activity in vitro, and this inhibitory property was exclusive to the pathogenic protease. Thus these recombinant antibodies are candidates for immunotherapy and tools to aid in further elucidation of the mechanism of action of the B. pseudomallei protease.
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Affiliation(s)
- Sheila Nathan
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Selanger
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20
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Kim MS, Lim A, Yang SW, Lee D, Park J, Shin DH. A preliminary X-ray study of transketolase from Burkholderia pseudomallei. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:1554-6. [PMID: 23192046 PMCID: PMC3509987 DOI: 10.1107/s1744309112044375] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Accepted: 10/25/2012] [Indexed: 11/10/2022]
Abstract
TktA is the most critical enzyme in the nonoxidative pentose phosphate pathway. It catalyzes the conversion of xylulose 5-phosphate and ribose 5-phosphate into sedoheptulose 7-phosphate and glyceraldehyde 3-phosphate, and its products are used in the biosynthesis of acetyl-CoA, aromatic amino acids, nucleic acids and ADP-L-glycero-β-D-manno-heptose. TktA also has an unexpected role in chromosome structure that is independent of its metabolic responsibilities. Therefore, it is a new potent antibiotic target. In this study, TktA from Burkholderia pseudomallei has been cloned, expressed, purified and crystallized. Synchrotron X-ray data were also collected to 2.0 Å resolution. The crystal belonged to the monoclinic space group C2, with unit-cell parameters a=146.2, b=74.6, c=61.6 Å, β=113.0°. A full structural determination is under way in order to provide insight into the structure-function relationship of this protein.
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Affiliation(s)
- Mi-Sun Kim
- The Center for Cell Signaling and Drug Discovery Research, College of Pharmacy, Division of Life and Pharmaceutical Sciences, Ewha Womans University, Seoul 120-750, Republic of Korea
| | - Areum Lim
- The Center for Cell Signaling and Drug Discovery Research, College of Pharmacy, Division of Life and Pharmaceutical Sciences, Ewha Womans University, Seoul 120-750, Republic of Korea
| | - Seung Won Yang
- The Center for Cell Signaling and Drug Discovery Research, College of Pharmacy, Division of Life and Pharmaceutical Sciences, Ewha Womans University, Seoul 120-750, Republic of Korea
| | - Daeun Lee
- The Center for Cell Signaling and Drug Discovery Research, College of Pharmacy, Division of Life and Pharmaceutical Sciences, Ewha Womans University, Seoul 120-750, Republic of Korea
| | - Jimin Park
- The Center for Cell Signaling and Drug Discovery Research, College of Pharmacy, Division of Life and Pharmaceutical Sciences, Ewha Womans University, Seoul 120-750, Republic of Korea
| | - Dong Hae Shin
- The Center for Cell Signaling and Drug Discovery Research, College of Pharmacy, Division of Life and Pharmaceutical Sciences, Ewha Womans University, Seoul 120-750, Republic of Korea
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21
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Liew SM, Tay ST, Wongratanacheewin S, Puthucheary SD. Enzymatic profiling of clinical and environmental isolates of Burkholderia pseudomallei. Trop Biomed 2012; 29:160-168. [PMID: 22543616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Melioidosis has been recognized as an important cause of sepsis in the tropics. The disease caused by an environmental saprophyte Burkholderia pseudomallei, affects mostly adults with underlying immunocompromised conditions. In this study, the enzymatic profiles of 91 clinical and 9 environmental isolates of B. pseudomallei were evaluated using the APIZYM system, in addition to assessment of protease, phospholipase C and sialidase activities using agar plate methods and other assays. The activity of 10 enzymes - alkaline phosphatase, esterase, esterase lipase, lipase, leucine arylamidase, valine arylamidase, cystine arylamidase, acid phosphatase, naphthol-AS-BI-phosphohydrolase and N-acetyl-β-glucosaminidase were detected in >75% of the clinical isolates. The majority of B. pseudomallei isolates in this study exhibited protease and phospholipase activities. No sialidase activity was detected. Five Burkholderia thailandensis isolates had similar APIZYM profiles as B. pseudomallei clinical isolates except for the lower detection rate for N-acetyl-β-glucosaminidase. The subtle differences in the number of enzymes secreted and the levels of enzymatic activities of phenotypically identical clinical and environmental strains of B. pseudomallei give weight to the fact that the causative agent of melioidodis originates from the environment.
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Affiliation(s)
- S M Liew
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
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22
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Davies DR, Staker BL, Abendroth JA, Edwards TE, Hartley R, Leonard J, Kim H, Rychel AL, Hewitt SN, Myler PJ, Stewart LJ. An ensemble of structures of Burkholderia pseudomallei 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:1044-50. [PMID: 21904048 PMCID: PMC3169400 DOI: 10.1107/s1744309111030405] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2011] [Accepted: 07/28/2011] [Indexed: 11/29/2022]
Abstract
Burkholderia pseudomallei is a soil-dwelling bacterium endemic to Southeast Asia and Northern Australia. Burkholderia is responsible for melioidosis, a serious infection of the skin. The enzyme 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase (PGAM) catalyzes the interconversion of 3-phosphoglycerate and 2-phosphoglycerate, a key step in the glycolytic pathway. As such it is an extensively studied enzyme and X-ray crystal structures of PGAM enzymes from multiple species have been elucidated. Vanadate is a phosphate mimic that is a powerful tool for studying enzymatic mechanisms in phosphoryl-transfer enzymes such as phosphoglycerate mutase. However, to date no X-ray crystal structures of phosphoglycerate mutase have been solved with vanadate acting as a substrate mimic. Here, two vanadate complexes together with an ensemble of substrate and fragment-bound structures that provide a comprehensive picture of the function of the Burkholderia enzyme are reported.
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Affiliation(s)
- Douglas R Davies
- Seattle Structural Genomics Center for Infectious Disease (http://www.ssgcid.org), USA.
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23
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Begley DW, Davies DR, Hartley RC, Hewitt SN, Rychel AL, Myler PJ, Van Voorhis WC, Staker BL, Stewart LJ. Probing conformational states of glutaryl-CoA dehydrogenase by fragment screening. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:1060-9. [PMID: 21904051 PMCID: PMC3169403 DOI: 10.1107/s1744309111014436] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2010] [Accepted: 04/17/2011] [Indexed: 11/10/2022]
Abstract
Glutaric acidemia type 1 is an inherited metabolic disorder which can cause macrocephaly, muscular rigidity, spastic paralysis and other progressive movement disorders in humans. The defects in glutaryl-CoA dehydrogenase (GCDH) associated with this disease are thought to increase holoenzyme instability and reduce cofactor binding. Here, the first structural analysis of a GCDH enzyme in the absence of the cofactor flavin adenine dinucleotide (FAD) is reported. The apo structure of GCDH from Burkholderia pseudomallei reveals a loss of secondary structure and increased disorder in the FAD-binding pocket relative to the ternary complex of the highly homologous human GCDH. After conducting a fragment-based screen, four small molecules were identified which bind to GCDH from B. pseudomallei. Complex structures were determined for these fragments, which cause backbone and side-chain perturbations to key active-site residues. Structural insights from this investigation highlight differences from apo GCDH and the utility of small-molecular fragments as chemical probes for capturing alternative conformational states of preformed protein crystals.
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Affiliation(s)
- Darren W Begley
- Seattle Structural Genomics Center for Infectious Disease (http://www.ssgcid.org), USA.
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24
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Edwards TE, Leibly DJ, Bhandari J, Statnekov JB, Phan I, Dieterich SH, Abendroth J, Staker BL, Van Voorhis WC, Myler PJ, Stewart LJ. Structures of phosphopantetheine adenylyltransferase from Burkholderia pseudomallei. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:1032-7. [PMID: 21904046 PMCID: PMC3169398 DOI: 10.1107/s1744309111004349] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2010] [Accepted: 02/04/2011] [Indexed: 11/10/2022]
Abstract
Phosphopantetheine adenylyltransferase (PPAT) catalyzes the fourth of five steps in the coenzyme A biosynthetic pathway, reversibly transferring an adenylyl group from ATP onto 4'-phosphopantetheine to yield dephospho-coenzyme A and pyrophosphate. Burkholderia pseudomallei is a soil- and water-borne pathogenic bacterium and the etiologic agent of melioidosis, a potentially fatal systemic disease present in southeast Asia. Two crystal structures are presented of the PPAT from B. pseudomallei with the expectation that, because of the importance of the enzyme in coenzyme A biosynthesis, they will aid in the search for defenses against this pathogen. A crystal grown in ammonium sulfate yielded a 2.1 Å resolution structure that contained dephospho-coenzyme A with partial occupancy. The overall structure and ligand-binding interactions are quite similar to other bacterial PPAT crystal structures. A crystal grown at low pH in the presence of coenzyme A yielded a 1.6 Å resolution structure in the same crystal form. However, the experimental electron density was not reflective of fully ordered coenzyme A, but rather was only reflective of an ordered 4'-diphosphopantetheine moiety.
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Affiliation(s)
- Thomas E Edwards
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA.
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25
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Zajdowicz SLW, Jones-Carson J, Vazquez-Torres A, Jobling MG, Gill RE, Holmes RK. Alanine racemase mutants of Burkholderia pseudomallei and Burkholderia mallei and use of alanine racemase as a non-antibiotic-based selectable marker. PLoS One 2011; 6:e21523. [PMID: 21720554 PMCID: PMC3123353 DOI: 10.1371/journal.pone.0021523] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2011] [Accepted: 05/31/2011] [Indexed: 12/20/2022] Open
Abstract
Burkholderia pseudomallei and Burkholderia mallei are category B select agents and must be studied under BSL3 containment in the United States. They are typically resistant to multiple antibiotics, and the antibiotics used to treat B. pseudomallei or B. mallei infections may not be used as selective agents with the corresponding Burkholderia species. Here, we investigated alanine racemase deficient mutants of B. pseudomallei and B. mallei for development of non-antibiotic-based genetic selection methods and for attenuation of virulence. The genome of B. pseudomallei K96243 has two annotated alanine racemase genes (bpsl2179 and bpss0711), and B. mallei ATCC 23344 has one (bma1575). Each of these genes encodes a functional enzyme that can complement the alanine racemase deficiency of Escherichia coli strain ALA1. Herein, we show that B. pseudomallei with in-frame deletions in both bpsl2179 and bpss0711, or B. mallei with an in-frame deletion in bma1575, requires exogenous D-alanine for growth. Introduction of bpsl2179 on a multicopy plasmid into alanine racemase deficient variants of either Burkholderia species eliminated the requirement for D-alanine. During log phase growth without D-alanine, the viable counts of alanine racemase deficient mutants of B. pseudomallei and B. mallei decreased within 2 hours by about 1000-fold and 10-fold, respectively, and no viable bacteria were present at 24 hours. We constructed several genetic tools with bpsl2179 as a selectable genetic marker, and we used them without any antibiotic selection to construct an in-frame ΔflgK mutant in the alanine racemase deficient variant of B. pseudomallei K96243. In murine peritoneal macrophages, wild type B. mallei ATCC 23344 was killed much more rapidly than wild type B. pseudomallei K96243. In addition, the alanine racemase deficient mutant of B. pseudomallei K96243 exhibited attenuation versus its isogenic parental strain with respect to growth and survival in murine peritoneal macrophages.
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Affiliation(s)
- Sheryl L. W. Zajdowicz
- Department of Microbiology, University of Colorado School of Medicine, Aurora, Colorado, United States of America
- Department of Biology, Metropolitan State College of Denver, Denver, Colorado, United States of America
| | - Jessica Jones-Carson
- Department of Microbiology, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - Andres Vazquez-Torres
- Department of Microbiology, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - Michael G. Jobling
- Department of Microbiology, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - Ronald E. Gill
- Department of Microbiology, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - Randall K. Holmes
- Department of Microbiology, University of Colorado School of Medicine, Aurora, Colorado, United States of America
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26
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Vanaporn M, Wand M, Michell SL, Sarkar-Tyson M, Ireland P, Goldman S, Kewcharoenwong C, Rinchai D, Lertmemongkolchai G, Titball RW. Superoxide dismutase C is required for intracellular survival and virulence of Burkholderia pseudomallei. Microbiology (Reading) 2011; 157:2392-2400. [PMID: 21659326 DOI: 10.1099/mic.0.050823-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Burkholderia pseudomallei is an intracellular pathogen and the causative agent of melioidosis, a life-threatening disease of humans. Within host cells, superoxide is an important mediator of pathogen killing. In this study, we have identified the B. pseudomallei K96243 sodC gene, shown that it has superoxide dismutase activity, and constructed an allelic deletion mutant of this gene. Compared with the wild-type, the mutant was more sensitive to killing by extracellular superoxide, but not to superoxide generated intracellularly. The sodC mutant showed a markedly decreased survival in J774A.1 mouse macrophages, and reduced numbers of bacteria were recovered from human polymorphonuclear neutrophils (PMNs) when compared with the wild-type. The numbers of wild-type or mutant bacteria recovered from human diabetic neutrophils were significantly lower than from normal human neutrophils. The sodC mutant was attenuated in BALB/c mice. Our results indicate that SodC plays a key role in the virulence of B. pseudomallei, but that diabetics are not more susceptible to infection because of a reduced ability of PMNs to kill by superoxide.
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Affiliation(s)
- Muthita Vanaporn
- Department of Microbiology and Immunology, Mahidol University, Rajvithi Road, Bangkok 10400, Thailand
- College of Life and Environmental Sciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK
| | - Matthew Wand
- Health Protection Agency, Porton Down, Salisbury SP4 0JG, UK
| | - Stephen L Michell
- College of Life and Environmental Sciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK
| | - Mitali Sarkar-Tyson
- Department of Biomedical Sciences, Defence Science and Technology Laboratory, Porton Down, Salisbury SP4 0JQ, UK
| | - Philip Ireland
- Department of Biomedical Sciences, Defence Science and Technology Laboratory, Porton Down, Salisbury SP4 0JQ, UK
| | - Stan Goldman
- Genetic Chemistry Inc., 200 Page Mill Road, Palo Alto, CA 94306, USA
| | - Chidchamai Kewcharoenwong
- The Center for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand
| | - Darawan Rinchai
- The Center for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand
| | - Ganjana Lertmemongkolchai
- The Center for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand
| | - Richard W Titball
- College of Life and Environmental Sciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK
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27
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Begley DW, Hartley RC, Davies DR, Edwards TE, Leonard JT, Abendroth J, Burris CA, Bhandari J, Myler PJ, Staker BL, Stewart LJ. Leveraging structure determination with fragment screening for infectious disease drug targets: MECP synthase from Burkholderia pseudomallei. ACTA ACUST UNITED AC 2011; 12:63-76. [PMID: 21359640 PMCID: PMC3123455 DOI: 10.1007/s10969-011-9102-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2010] [Accepted: 02/15/2011] [Indexed: 11/25/2022]
Abstract
As part of the Seattle Structural Genomics Center for Infectious Disease, we seek to enhance structural genomics with ligand-bound structure data which can serve as a blueprint for structure-based drug design. We have adapted fragment-based screening methods to our structural genomics pipeline to generate multiple ligand-bound structures of high priority drug targets from pathogenic organisms. In this study, we report fragment screening methods and structure determination results for 2C-methyl-D-erythritol-2,4-cyclo-diphosphate (MECP) synthase from Burkholderia pseudomallei, the gram-negative bacterium which causes melioidosis. Screening by nuclear magnetic resonance spectroscopy as well as crystal soaking followed by X-ray diffraction led to the identification of several small molecules which bind this enzyme in a critical metabolic pathway. A series of complex structures obtained with screening hits reveal distinct binding pockets and a range of small molecules which form complexes with the target. Additional soaks with these compounds further demonstrate a subset of fragments to only bind the protein when present in specific combinations. This ensemble of fragment-bound complexes illuminates several characteristics of MECP synthase, including a previously unknown binding surface external to the catalytic active site. These ligand-bound structures now serve to guide medicinal chemists and structural biologists in rational design of novel inhibitors for this enzyme.
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Affiliation(s)
- Darren W Begley
- Emerald BioStructures, 7869 NE Day Road West, Bainbridge Island, WA 98110, USA.
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28
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Wiseman B, Carpena X, Feliz M, Donald LJ, Pons M, Fita I, Loewen PC. Isonicotinic acid hydrazide conversion to Isonicotinyl-NAD by catalase-peroxidases. J Biol Chem 2010; 285:26662-73. [PMID: 20554537 PMCID: PMC2924108 DOI: 10.1074/jbc.m110.139428] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2010] [Revised: 05/28/2010] [Indexed: 11/06/2022] Open
Abstract
Activation of the pro-drug isoniazid (INH) as an anti-tubercular drug in Mycobacterium tuberculosis involves its conversion to isonicotinyl-NAD, a reaction that requires the catalase-peroxidase KatG. This report shows that the reaction proceeds in the absence of KatG at a slow rate in a mixture of INH, NAD(+), Mn(2+), and O(2), and that the inclusion of KatG increases the rate by >7 times. Superoxide, generated by either Mn(2+)- or KatG-catalyzed reduction of O(2), is an essential intermediate in the reaction. Elimination of the peroxidatic process by mutation slows the rate of reaction by 60% revealing that the peroxidatic process enhances, but is not essential for isonicotinyl-NAD formation. The isonicotinyl-NAD(*+) radical is identified as a reaction intermediate, and its reduction by superoxide is proposed. Binding sites for INH and its co-substrate, NAD(+), are identified for the first time in crystal complexes of Burkholderia pseudomallei catalase-peroxidase with INH and NAD(+) grown by co-crystallization. The best defined INH binding sites were identified, one in each subunit, on the opposite side of the protein from the entrance to the heme cavity in a funnel-shaped channel. The NAD(+) binding site is approximately 20 A from the entrance to the heme cavity and involves interactions primarily with the AMP portion of the molecule in agreement with the NMR saturation transfer difference results.
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Affiliation(s)
| | - Xavi Carpena
- the Institute for Research in Biomedicine and
- Institut de Biologia Molecular, Parc Científic, Baldiri Reixac 10, 08028 Barcelona, Spain, and
| | - Miguel Feliz
- the Department of Organic Chemistry, University of Barcelona, Martí i Franquès 1-11, 08028 Barcelona, Spain
| | | | - Miquel Pons
- the Institute for Research in Biomedicine and
- the Department of Organic Chemistry, University of Barcelona, Martí i Franquès 1-11, 08028 Barcelona, Spain
| | - Ignacio Fita
- the Institute for Research in Biomedicine and
- Institut de Biologia Molecular, Parc Científic, Baldiri Reixac 10, 08028 Barcelona, Spain, and
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Abstract
This paper describes a microfluidic approach to perform multiplexed nanoliter-scale experiments by combining a sample with multiple different reagents, each at multiple mixing ratios. This approach employs a user-loaded, equipment-free SlipChip. The mixing ratios, characterized by diluting a fluorescent dye, could be controlled by the volume of each of the combined wells. The SlipChip design was validated on an approximately 12 nL scale by screening the conditions for crystallization of glutaryl-CoA dehydrogenase from Burkholderia pseudomallei against 48 different reagents; each reagent was tested at 11 different mixing ratios, for a total of 528 crystallization trials. The total consumption of the protein sample was approximately 10 microL. Conditions for crystallization were successfully identified. The crystallization experiments were successfully scaled up in well plates using the conditions identified in the SlipChip. Crystals were characterized by X-ray diffraction and provided a protein structure in a different space group and at a higher resolution than the structure obtained by conventional methods. In this work, this user-loaded SlipChip has been shown to reliably handle fluids of diverse physicochemical properties, such as viscosities and surface tensions. Quantitative measurements of fluorescent intensities and high-resolution imaging were straighforward to perform in these glass SlipChips. Surface chemistry was controlled using fluorinated lubricating fluid, analogous to the fluorinated carrier fluid used in plug-based crystallization. Thus, we expect this approach to be valuable in a number of areas beyond protein crystallization, especially those areas where droplet-based microfluidic systems have demonstrated successes, including measurements of enzyme kinetics and blood coagulation, cell-based assays, and chemical reactions.
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Affiliation(s)
- Liang Li
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, IL 60637
| | - Wenbin Du
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, IL 60637
| | - Rustem Ismagilov
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, IL 60637
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30
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Korbsrisate S, Tomaras AP, Damnin S, Ckumdee J, Srinon V, Lengwehasatit I, Vasil ML, Suparak S. Characterization of two distinct phospholipase C enzymes from Burkholderia pseudomallei. Microbiology (Reading) 2007; 153:1907-1915. [PMID: 17526847 DOI: 10.1099/mic.0.2006/003004-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Burkholderia pseudomallei is a serious bacterial pathogen that can cause a lethal infection in humans known as melioidosis. In this study two of its phospholipase C (PLC) enzymes (Plc-1 and Plc-2) were characterized. Starting with a virulent strain, two single mutants were constructed, each with one plc gene inactivated, and one double mutant with both plc genes inactivated. The single plc mutants exhibited decreased extracellular PLC activity in comparison to the wild-type strain, thereby demonstrating that the two genes encoded functional extracellular PLCs. Growth comparisons between the wild-type and PLC mutants in egg-yolk-supplemented medium indicated that both PLCs contributed to egg-yolk phospholipid utilization. Both PLCs hydrolysed phosphatidylcholine and sphingomyelin but neither was haemolytic for human erythrocytes. Experimental infections of eukaryotic cells demonstrated that Plc-1 itself had no effect on plaque-forming efficiency but it had an additive effect on increasing the efficiency of Plc-2 to form plaques. Only Plc-2 had a significant role in host cell cytotoxicity. In contrast, neither Plc-1 nor Plc-2 appeared to play any role in multinucleated giant cell (MNGC) formation or induction of apoptotic death in the cells studied. These data suggested that PLCs contribute, at least in part, to B. pseudomallei virulence and support the view that Plc-1 and Plc-2 are not redundant virulence factors.
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Affiliation(s)
- Sunee Korbsrisate
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Andrew P Tomaras
- Department of Microbiology, University of Colorado at Denver and Health Sciences Center Aurora, CO 80045, USA
| | - Suwat Damnin
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Jutturong Ckumdee
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Varintip Srinon
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | | | - Michael L Vasil
- Department of Microbiology, University of Colorado at Denver and Health Sciences Center Aurora, CO 80045, USA
| | - Supaporn Suparak
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
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31
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Jakopitsch C, Vlasits J, Wiseman B, Loewen PC, Obinger C. Redox intermediates in the catalase cycle of catalase-peroxidases from Synechocystis PCC 6803, Burkholderia pseudomallei, and Mycobacterium tuberculosis. Biochemistry 2007; 46:1183-93. [PMID: 17260948 DOI: 10.1021/bi062266+] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Monofunctional catalases (EC 1.11.1.6) and catalase-peroxidases (KatGs, EC 1.11.1.7) have neither sequence nor structural homology, but both catalyze the dismutation of hydrogen peroxide (2H2O2 --> 2H2O + O2). In monofunctional catalases, the catalatic mechanism is well-characterized with conventional compound I [oxoiron(IV) porphyrin pi-cation radical intermediate] being responsible for hydrogen peroxide oxidation. The reaction pathway in KatGs is not as clearly defined, and a comprehensive rapid kinetic and spectral analysis of the reactions of KatGs from three different sources (Synechocystis PCC 6803, Burkholderia pseudomallei, and Mycobacterium tuberculosis) with peroxoacetic acid and hydrogen peroxide has focused on the pathway. Independent of KatG, but dependent on pH, two low-spin forms dominated in the catalase cycle with absorbance maxima at 415, 545, and 580 nm at low pH and 418 and 520 nm at high pH. By contrast, oxidation of KatGs with peroxoacetic acid resulted in intermediates with different spectral features that also differed among the three KatGs. Following the rate of H2O2 degradation by stopped-flow allowed the linking of reaction intermediate species with substrate availability to confirm which species were actually present during the catalase cycle. Possible reaction intermediates involved in H2O2 dismutation by KatG are discussed.
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Affiliation(s)
- Christa Jakopitsch
- Department of Chemistry, Division of Biochemistry, BOKU-University of Natural Resources and Applied Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
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Diggle SP, Lumjiaktase P, Dipilato F, Winzer K, Kunakorn M, Barrett DA, Chhabra SR, Cámara M, Williams P. Functional genetic analysis reveals a 2-Alkyl-4-quinolone signaling system in the human pathogen Burkholderia pseudomallei and related bacteria. ACTA ACUST UNITED AC 2006; 13:701-10. [PMID: 16873018 DOI: 10.1016/j.chembiol.2006.05.006] [Citation(s) in RCA: 142] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2006] [Revised: 04/27/2006] [Accepted: 05/01/2006] [Indexed: 10/24/2022]
Abstract
Pseudomonas aeruginosa synthesizes diverse 2-alkyl-4(1H)-quinolones (AHQs), including the signaling molecule 2-heptyl-3-hydroxy-4(1H)-quinolone (PQS), via the pqsABCDE locus. By examining the genome databases, homologs of the pqs genes were identified in other bacteria. However, apart from P. aeruginosa, only Burkholderia pseudomallei and B. thailandensis contained a complete pqsA-E operon (termed hhqA-E). By introducing the B. pseudomallei hhqA and hhqE genes into P. aeruginosa pqsA and pqsE mutants, we show that they are functionally conserved and restore virulence factor and PQS production. B. pseudomallei, B. thailandensis, B. cenocepacia, and P. putida each produced 2-heptyl-4(1H)-quinolone (HHQ), but not PQS. Mutation of hhqA in B. pseudomallei resulted in the loss of AHQ production, altered colony morphology, and enhanced elastase production, which was reduced to parental levels by exogenous HHQ. These data reveal a role for AHQs in bacterial cell-to-cell communication beyond that seen in P. aeruginosa.
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Affiliation(s)
- Stephen P Diggle
- Institute of Infection, Immunity & Inflammation, Centre for Biomolecular Sciences, University Park, University of Nottingham, UK.
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Deemagarn T, Wiseman B, Carpena X, Ivancich A, Fita I, Loewen PC. Two alternative substrate paths for compound I formation and reduction in catalase-peroxidase KatG from Burkholderia pseudomallei. Proteins 2006; 66:219-28. [PMID: 17063492 DOI: 10.1002/prot.21209] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Five residues in the multifunctional catalase-peroxidase KatG of Burkholderia pesudomallei are essential for catalase, but not peroxidase, activity. Asp141 is the only one of these catalase-specific residues not related with the covalent adduct found in KatGs that when replaced with a nonacidic residue reduces catalase activity to 5% of native levels. Replacing the nearby catalytic residue Arg108 causes a reduction in catalase activity to 35% of native levels, whereas a variant with both Asp141 and Arg108 replaced exhibits near normal catalase activity (82% of native), suggesting a synergism in the roles of the two residues in support of catalase activity in the enzyme. Among the Asp141 variants, D141E is unique in retaining normal catalase activity but with modified kinetics, suggesting more favorable compound I formation and less favorable compound I reduction. The crystal structure of the D141E variant has been determined at 1.8-A resolution, revealing that the carboxylate of Glu141 is moved only slightly compared with Asp141, but retains its hydrogen bond interaction with the main chain nitrogen of Ile237. In contrast, the low temperature ferric Electron Paramagnetic Resonance spectra of the D141A, R108A, and R108A/D141A variants are consistent with modifications of the water matrix and/or the relative positioning of the distal residue side chains. Such changes explain the reduction in catalase activity in all but the double variant R108A/D141A. Two pathways of hydrogen bonded solvent lead from the entrance channel into the heme active site, one running between Asp141 and Arg108 and the second between Asp141 and the main chain atoms of residues 237-239. It is proposed that binding of substrate H(2)O(2) to Asp141 and Arg108 controls H(2)O(2) access to the heme active site, thereby modulating the catalase reaction.
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Affiliation(s)
- Taweewat Deemagarn
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
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Carpena X, Wiseman B, Deemagarn T, Herguedas B, Ivancich A, Singh R, Loewen PC, Fita I. Roles for Arg426 and Trp111 in the modulation of NADH oxidase activity of the catalase-peroxidase KatG from Burkholderia pseudomallei inferred from pH-induced structural changes. Biochemistry 2006; 45:5171-9. [PMID: 16618106 DOI: 10.1021/bi060017f] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Crystals of Burkholderia pseudomallei KatG retain their ability to diffract X-rays at high resolution after adjustment of the pH from 5.6 to 4.5, 6.5, 7.5, and 8.5, providing a unique view of the effect of pH on protein structure. One significant pH-sensitive change lies in the appearance of a perhydroxy group attached to the indole nitrogen of the active site Trp111 above pH 7, similar to a modification originally observed in the Ser324Thr variant of the enzyme at pH 5.6. The modification forms rapidly from molecular oxygen in the buffer with 100% occupancy after one minute of soaking of the crystal at room temperature and pH 8.5. The low temperature (4 K) ferric EPR spectra of the resting enzyme, being very sensitive to changes in the heme iron microenvironment, confirm the presence of the modification above pH 7 in native enzyme and variants lacking Arg426 or Met264 and its absence in variants lacking Trp111 or Tyr238. The indole-perhydroxy group is very likely the reactive intermediate of molecular oxygen in the NADH oxidase reaction, and Arg426 is required for its reduction. The second significant pH-sensitive change involves the buried side chain of Arg426 that changes from one predominant conformation at low pH to a second at high pH. The pH profiles of the peroxidase, catalase, and NADH oxidase reactions can be correlated with the distribution of Arg426 conformations. Other pH-induced structural changes include a number of surface-situated side chains, but there is only one change involving a displacement of main chain atoms triggered by the protonation of His53 in a deep pocket in the vicinity of the molecular 2-fold axis.
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Affiliation(s)
- Xavier Carpena
- Departament de Biologia Estructural (IBMB-CSIC), Parc Científic de Barcelona, Josep Samitier 1-5, 08028 Barcelona, Spain
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Carpena X, Wiseman B, Deemagarn T, Singh R, Switala J, Ivancich A, Fita I, Loewen PC. A molecular switch and electronic circuit modulate catalase activity in catalase-peroxidases. EMBO Rep 2006; 6:1156-62. [PMID: 16211084 PMCID: PMC1369206 DOI: 10.1038/sj.embor.7400550] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2005] [Revised: 07/29/2005] [Accepted: 09/09/2005] [Indexed: 11/08/2022] Open
Abstract
The catalase reaction of catalase-peroxidases involves catalase-specific features built into a peroxidase core. An arginine, 20 A from the active-site heme, acts as a molecular switch moving between two conformations, one that activates heme oxidation and one that activates oxoferryl heme reduction by H(2)O(2), facilitating the catalatic pathway in a peroxidase. The influence of the arginine is imparted to the heme through its association with or dissociation from a tyrosinate that modulates reactivity through a Met-Tyr-Trp crosslinked adduct and a pi electron interaction of the heme with the adduct Trp.
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Affiliation(s)
- Xavier Carpena
- Department of Microbiology, University of Manitoba, Winnipeg MB R3T 2N2, Canada
| | - Ben Wiseman
- Department of Microbiology, University of Manitoba, Winnipeg MB R3T 2N2, Canada
| | - Taweewat Deemagarn
- Department of Microbiology, University of Manitoba, Winnipeg MB R3T 2N2, Canada
| | - Rahul Singh
- Department of Microbiology, University of Manitoba, Winnipeg MB R3T 2N2, Canada
| | - Jacek Switala
- Department of Microbiology, University of Manitoba, Winnipeg MB R3T 2N2, Canada
| | - Anabella Ivancich
- Service de Bioénergétique, URA 2096 CNRS, Département de Biologie Joliot-Curie, CEA Saclay, 91191 Gif-sur-Yvette, France
| | - Ignacio Fita
- Departament de Biologia Estructural (IBMB-CSIC), Parc Científic de Barcelona, Josep Samitier 1-5, 08028 Barcelona, Spain
| | - Peter C Loewen
- Department of Microbiology, University of Manitoba, Winnipeg MB R3T 2N2, Canada
- Tel: +1 204 474 8334; Fax: +1 204 474 7603; E-mail:
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36
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Chan SW, Nathan S. Epitope mapping of Burkholderia pseudomallei serine metalloprotease: identification of serine protease epitope mimics. ACTA ACUST UNITED AC 2005; 43:37-44. [PMID: 15607634 DOI: 10.1016/j.femsim.2004.06.025] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2004] [Revised: 06/01/2004] [Accepted: 06/30/2004] [Indexed: 10/26/2022]
Abstract
Filamentous phage random peptide libraries were used to identify the epitopes of Burkholderia pseudomallei protease by panning against IgG polyclonal sera that exhibited protease neutralizing properties. The isolated fusion peptides presented a consensus peptide sequence, TKSMALSG, which closely resembles part of the active site sequence, 435GTSMATPHVAG445, of B. pseudomallei serine metalloprotease. By comparing the consensus sequence, TKSMALSG, with the predicted three-dimensional molecular model of B. pseudomallei serine metalloprotease, it appears that the potential antibody binding epitope was buried within the molecule. This active site was conformational whereby one continuous sub-region (SMA) was located between two discontinuous sub-regions, supplied by the flanking residues in the same polypeptide. All phages selected from the biopanning with IgG polyclonal sera showed good binding towards the polyclonal antibodies when compared to the negative control. In addition, these peptide-bearing phages showed competitive inhibition of B. pseudomallei serine metalloprotease binding to the polyclonal IgG.
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Affiliation(s)
- Shzu-Wei Chan
- Centre for Gene Analysis and Technology, School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor D.E., Malaysia
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Keith KE, Oyston PC, Crossett B, Fairweather NF, Titball RW, Walsh TR, Brown KA. Functional characterization of OXA-57, a class D beta-lactamase from Burkholderia pseudomallei. Antimicrob Agents Chemother 2005; 49:1639-41. [PMID: 15793160 PMCID: PMC1068585 DOI: 10.1128/aac.49.4.1639-1641.2005] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Class D beta-lactamase OXA-57 was identified in a range of isolates of Burkholderia pseudomallei and Burkholderia thailandensis. Comparative kinetic analyses of wild-type and mutant forms of B. pseudomallei OXA-57 are reported. Implications of these data for beta-lactam resistance and the proposed role of Ser-104 in beta-lactam hydrolysis are discussed.
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Affiliation(s)
- Karen E Keith
- Department of Biological Sciences, CMMI, Flowers Building, Imperial College London, London SW7 2AZ, United Kingdom
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38
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Narbutovich NI, Lomova LV, Ageeva NP, Kucheriaeva VT, Seimova IK. [Some properties of plasmocoagulase of the causative agents of glanders and melioidosis]. Zh Mikrobiol Epidemiol Immunobiol 2005:87-9. [PMID: 16028525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Criteria for the evaluation of the plasmocoagulase activity of natural isolates and mutant strains of the causative agents of glanders and melioidosis were worked out, which made it possible to subdivide them by this sign into pathogens with high, moderate and low activity. Plasmocoagulase produced by pathogenic Burkholderia was shown to be a thermolabile enzyme, comparatively stable with respect to the action of such chemico-biological agents as hydrogen peroxide and chloramine.
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Chan SW, Ong GI, Nathan S. Neutralizing chimeric mouse-human antibodies against Burkholderia pseudomallei protease: expression, purification and characterization. BMB Rep 2005; 37:556-64. [PMID: 15479619 DOI: 10.5483/bmbrep.2004.37.5.556] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A recombinant Fab monoclonal antibody (Fab) C37, previously obtained by phage display and biopanning of a random antibody fragment library against Burkholderia pseudomallei protease, was expressed in different strains of Escherichia coli. E. coli strain HB2151 was deemed a more suitable host for Fab expression than other E. coli strains when grown in media supplemented with 0.2 % glycerol. The expressed Fab fragment was purified by affinity chromatography on a Protein G-Sepharose column, and the specificity of the recombinant Fab C37 towards B. pseudomallei protease was proven by Western blotting, enzyme-linked immunosorbent assay (ELISA) and by proteolytic activity neutralization. In addition, polyclonal antibodies against B. pseudomallei protease were produced in rabbits immunized with the protease. These were isolated from high titer serum by affinity chromatography on recombinant-Protein A-Sepharose. Purified polyclonal antibody specificity towards B. pseudomallei protease was proven by Western blotting and ELISA.
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Affiliation(s)
- Shzu-Wei Chan
- Centre for Gene Analysis and Technology, School of BioSciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor D. E., Malaysia
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Deemagarn T, Carpena X, Singh R, Wiseman B, Fita I, Loewen PC. Structural Characterization of the Ser324Thr Variant of the Catalase-peroxidase (KatG) from Burkholderia pseudomallei. J Mol Biol 2005; 345:21-8. [PMID: 15567407 DOI: 10.1016/j.jmb.2004.10.020] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2004] [Revised: 09/27/2004] [Accepted: 10/11/2004] [Indexed: 11/18/2022]
Abstract
The Ser315Thr variant of the catalase-peroxidase KatG from Mycobacterium tuberculosis imparts resistance to the pro-drug isonicotinic acid hydrazide (isoniazid) through a failure to convert it to the active drug, isonicotinoyl-NAD. The equivalent variant in KatG from Burkholderia pseudomallei, Ser324Thr, has been constructed, revealing catalase and peroxidase activities that are similar to those of the native enzyme. The other activities of the variant protein, including the NADH oxidase, the isoniazid hydrazinolysis and isonicotinoyl-NAD synthase activities are reduced by 60-70%. The crystal structure of the variant differs from that of the native enzyme in having the methyl group of Thr324 situated in the entrance channel to the heme cavity, in a modified water matrix in the entrance channel and heme cavity, in lacking the putative perhydroxy modification on the heme, in the multiple locations of a few side-chains, and in the presence of an apparent perhydroxy modification on the indole nitrogen atom of the active-site Trp111. The position of the methyl group of Thr324 creates a constriction or narrowing of the channel leading to the heme cavity, providing an explanation for the lower reactivity towards isoniazid and the slower rate of isonicotinoyl-NAD synthesis.
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Affiliation(s)
- Taweewat Deemagarn
- Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada R3T 2N2
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41
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Rainbow L, Wilkinson MC, Sargent PJ, Hart CA, Winstanley C. Identification and Expression of a Burkholderia pseudomallei Collagenase in Escherichia coli. Curr Microbiol 2004; 48:300-4. [PMID: 15057457 DOI: 10.1007/s00284-003-4192-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Extracellular protein profiles were compared for broth-grown cultures of Burkholderia pseudomallei and its avirulent close relative Burkholderia thailandensis. A number of protein bands were present in the B. pseudomallei profile but absent or less abundant in the B. thailandensis profile. Four such prominent secreted proteins were identified by using N-terminal sequencing coupled to searches of the B. pseudomallei genome sequence database. The genes for two proteins with similarity to carbohydrate-binding proteins, and a further protein homologous to known bacterial collagenases, were present in both B. pseudomallei and B. thailandensis. The putative collagenase gene was cloned and expressed as a fusion protein in Escherichia coli. Cell lysates from Escherichia coli containing the recombinant protein exhibited detectable gelatinase and collagenase activities.
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Affiliation(s)
- Lucille Rainbow
- Department of Medical Microbiology and Genitourinary Medicine, University of Liverpool, Duncan Building, Daulby Street, Liverpool L69 3GA, United Kingdom
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42
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Prachayasittikul V, Isarankura Na Ayudhya C, Piacham T, Kiatfuengfoo R. One-step purification of chimeric green fluorescent protein providing metal-binding avidity and protease recognition sequence. Asian Pac J Allergy Immunol 2003; 21:259-67. [PMID: 15198344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Gene fusion technique was successfully applied as a potential approach to create a metal-binding site to assist one-step purification of green fluorescent protein (GFP). The chimeric GFP carrying hexapolyhistidine (H6GFPuv) was purified to homogeneous protein via the Immobilized Metal Affinity Chromatography charged with zinc ions. Removal of metal tagger could readily be performed by using enterokinase enzyme. Engineering of the hexahistidine and enterokinase cleavage sites (DDDDK) onto the chimeric protein did not significantly affect the fluorescent property and the binding avidity to Burkholderia pseudomallei protease of a chimeric protease-binding GFP (H6PBGFPuv). This concludes that engineering of repetitive histidine regions onto interested target protein along with the enterokinase cleavage sites will ease the complication of protein purification.
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Affiliation(s)
- Virapong Prachayasittikul
- Department of Clinical Microbiology, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand
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43
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Donald LJ, Krokhin OV, Duckworth HW, Wiseman B, Deemagarn T, Singh R, Switala J, Carpena X, Fita I, Loewen PC. Characterization of the catalase-peroxidase KatG from Burkholderia pseudomallei by mass spectrometry. J Biol Chem 2003; 278:35687-92. [PMID: 12832453 DOI: 10.1074/jbc.m304053200] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The electron density maps of the catalase-peroxidase from Burkholderia pseudomallei (BpKatG) presented two unusual covalent modifications. A covalent structure linked the active site Trp111 with Tyr238 and Tyr238 with Met264, and the heme was modified, likely by a perhydroxy group added to the vinyl group on ring I. Mass spectrometry analysis of tryptic digests of BpKatG revealed a cluster of ions at m/z 6585, consistent with the fusion of three peptides through Trp111, Tyr238, and Met264, and a cluster at m/z approximately 4525, consistent with the fusion of two peptides linked through Trp111 and Tyr238. MS/MS analysis of the major ions at m/z 4524 and 4540 confirmed the expected sequence and suggested that the multiple ions in the cluster were the result of multiple oxidation events and transfer of CH3-S to the tyrosine. Neither cluster of ions at m/z 4525 or 6585 was present in the spectrum of a tryptic digest of the W111F variant of BpKatG. The spectrum of the tryptic digest of native BpKatG also contained a major ion for a peptide in which Met264 had been converted to homoserine, consistent with the covalent bond between Tyr238 and Met264 being susceptible to hydrolysis, including the loss of the CH3-S from the methionine. Analysis of the tryptic digests of hydroperoxidase I (KatG) from Escherichia coli provided direct evidence for the covalent linkage between Trp105 and Tyr226 and indirect evidence for a covalent linkage between Tyr226 and Met252. Tryptic peptide analysis and N-terminal sequencing revealed that the N-terminal residue of BpKatG is Ser22.
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Affiliation(s)
- Lynda J Donald
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
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Corbett CR, Burtnick MN, Kooi C, Woods DE, Sokol PA. An extracellular zinc metalloprotease gene of Burkholderia cepacia. Microbiology (Reading) 2003; 149:2263-2271. [PMID: 12904566 DOI: 10.1099/mic.0.26243-0] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Burkholderia cepacia produces at least one extracellular zinc metalloprotease that may be involved in virulence. A B. cepacia zinc metalloprotease gene was cloned using a Burkholderia pseudomallei zinc metalloprotease gene as a probe. The predicted amino acid sequences of these B. cepacia and a B. pseudomallei extracellular zinc metalloproteases indicate that they are similar to the thermolysin-like family of metalloproteases (M4 family of metalloendopeptidases) and they are likely to be secreted via the general secretory pathway. zmpA isogenic mutants were constructed in B. cepacia genomovar III strains Pc715j and K56-2 by insertional inactivation of the zmpA genes. The zmpA mutants produced less protease than the parent strains. The B. cepacia strain K56-2 zmpA mutant was significantly less virulent than its parent strain in a chronic respiratory infection model; however, there was no difference between the virulence of B. cepacia strain Pc715j and a Pc715j zmpA mutant. The results indicate that this extracellular zinc metalloprotease may play a greater role in virulence in some strains of B. cepacia.
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Affiliation(s)
- C R Corbett
- Department of Microbiology and Infectious Diseases, University of Calgary Health Sciences Center, 3330 Hospital Dr. NW, Calgary, Alberta, Canada T2N 4N1
| | - M N Burtnick
- Department of Microbiology and Infectious Diseases, University of Calgary Health Sciences Center, 3330 Hospital Dr. NW, Calgary, Alberta, Canada T2N 4N1
| | - C Kooi
- Department of Microbiology and Infectious Diseases, University of Calgary Health Sciences Center, 3330 Hospital Dr. NW, Calgary, Alberta, Canada T2N 4N1
| | - D E Woods
- Department of Microbiology and Infectious Diseases, University of Calgary Health Sciences Center, 3330 Hospital Dr. NW, Calgary, Alberta, Canada T2N 4N1
| | - P A Sokol
- Department of Microbiology and Infectious Diseases, University of Calgary Health Sciences Center, 3330 Hospital Dr. NW, Calgary, Alberta, Canada T2N 4N1
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45
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Tribuddharat C, Moore RA, Baker P, Woods DE. Burkholderia pseudomallei class a beta-lactamase mutations that confer selective resistance against ceftazidime or clavulanic acid inhibition. Antimicrob Agents Chemother 2003; 47:2082-7. [PMID: 12821450 PMCID: PMC161859 DOI: 10.1128/aac.47.7.2082-2087.2003] [Citation(s) in RCA: 79] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Burkholderia pseudomallei, the causative agent of melioidosis, is inherently resistant to a variety of antibiotics including aminoglycosides, macrolides, polymyxins, and beta-lactam antibiotics. Despite resistance to many beta-lactams, ceftazidime and beta-lactamase inhibitor-beta-lactam combinations are commonly used for treatment of melioidosis. Here, we examine the enzyme kinetics of beta-lactamase isolated from mutants resistant to ceftazidime and clavulanic acid inhibition and describe specific mutations within conserved motifs of the beta-lactamase enzyme which account for these resistance patterns. Sequence analysis of regions flanking the B. pseudomallei penA gene revealed a putative regulator gene located downstream of penA. We have cloned and sequenced the penA gene from B. mallei and found it to be identical to penA from B. pseudomallei.
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46
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Abstract
The catalase-peroxidase encoded by katG of Burkholderia pseudomallei (BpKatG) is 65% identical with KatG of Mycobacterium tuberculosis, the enzyme responsible for the activation of isoniazid as an antibiotic. The structure of a complex of BpKatG with an unidentified ligand, has been solved and refined at 1.7A resolution using X-ray synchrotron data collected from crystals flash-cooled with liquid nitrogen. The crystallographic agreement factors R and R(free) are 15.3% and 18.6%, respectively. The crystallized enzyme is a dimer with one modified heme group and one metal ion, likely sodium, per subunit. The modification on the heme group involves the covalent addition of two or three atoms, likely a perhydroxy group, to the secondary carbon atom of the vinyl group on ring I. The added group can form hydrogen bonds with two water molecules that are also in contact with the active-site residues Trp111 and His112, suggesting that the modification may have a catalytic role. The heme modification is in close proximity to an unusual covalent adduct among the side-chains of Trp111, Tyr238 and Met264. In addition, Trp111 appears to be oxidized on C(delta1) of the indole ring. The main channel, providing access of substrate hydrogen peroxide to the heme, contains a region of unassigned electron density consistent with the binding of a pyridine nucleotide-like molecule. An interior cavity, containing the sodium ion and an additional region of unassigned density, is evident adjacent to the adduct and is accessible to the outside through a second funnel-shaped channel. A large cleft in the side of the subunit is evident and may be a potential substrate-binding site with a clear pathway for electron transfer to the active-site heme group through the adduct.
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Affiliation(s)
- Xavi Carpena
- CID-CSIC, Jordi-Girona 18-26, 08034 Barcelona, Spain
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47
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Abstract
Deoxyribonuclease IIalpha (DNase IIalpha) is an acidic endonuclease found in lysosomes and nuclei, and it is also secreted. Though its Caenorhabditis elegans homolog, NUC-1, is required for digesting DNA of apoptotic cell corpses and dietary DNA, it is not required for viability. However, DNase IIalpha is required in mice for correct development and viability, because undigested cell corpses lead to lesions throughout the body. Recently, we showed that, in contrast to previous reports, active DNase IIalpha consists of one contiguous polypeptide. To better analyze DNase II protein structure and determine residues important for activity, extensive database searches were conducted to find distantly related family members. We report 29 new partial or complete homologs from 21 species. Four homologs with differences at the purported active site histidine residue were detected in the parasitic nematodes Trichinella spiralis and Trichinella pseudospiralis. When these mutations were reconstructed in human DNase IIalpha, the expressed proteins were inactive. DNase II homologs were also identified in non-metazoan species. In particular, the slime-mold Dictyostelium, the protozoan Trichomonas vaginalis, and the bacterium Burkholderia pseudomallei all contain sequences with significant similarity and identity to previously cloned DNase II family members. We report an analysis of their sequences and implications for DNase II protein structure and evolution.
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Affiliation(s)
- Kyle S MacLea
- Department of Pharmacology and Toxicology, Dartmouth Medical School, 7650 Remsen, Hanover, NH 03755, USA
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Choeycharoen A, Vinichnaiyapark N, Vichchathorn P, Tunpiboonsak S, Tungpradabkul S. A transposase-like gene isolated from Burkholderia pseudomallei by DDRT-PCR technique. J GEN APPL MICROBIOL 2003; 49:59-61. [PMID: 12682867 DOI: 10.2323/jgam.49.59] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Amaraporn Choeycharoen
- Department of Biochemistry, Faculty of Science, Mahidol University, Rama VI Road, Bangkok 10400, Thailand
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Carpena X, Switala J, Loprasert S, Mongkolsuk S, Fita I, Loewen PC. Crystallization and preliminary X-ray analysis of the catalase-peroxidase KatG from Burkholderia pseudomallei. Acta Crystallogr D Biol Crystallogr 2002; 58:2184-6. [PMID: 12454496 DOI: 10.1107/s0907444902017869] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2002] [Accepted: 09/30/2002] [Indexed: 02/27/2023]
Abstract
The bifunctional catalase-peroxidase KatG encoded by the katG gene of Burkholderia pseudomallei has a predicted subunit size of 81.6 kDa. It shows high sequence similarity to other catalase-peroxidases of bacterial, archaebacterial and fungal origin, including 64% identity to KatG from Mycobacterium tuberculosis and lesser sequence similarity to members of the plant peroxidase family. Crystals from this protein were grown in 16-20% PEG 4000, 20% 2-methyl-2,4-pentanediol and 0.1 M sodium citrate pH 5.6 by the hanging-drop vapour-diffusion method at 293 K. These crystals diffracted beyond 1.8 A resolution and belong to space group P2(1)2(1)2(1), with unit-cell parameters a = 100.9, b = 115.6, c = 175.2 A. The data are consistent with either a monomer or a dimer in the crystal asymmetric unit.
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Affiliation(s)
- Xavier Carpena
- Institut de Biología Molecular de Barcelona CSIC, Jordi-Girona 18-26, 08034 Barcelona, Spain
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Ho PL, Cheung TKM, Yam WC, Yuen KY. Characterization of a laboratory-generated variant of BPS beta-lactamase from Burkholderia pseudomallei that hydrolyses ceftazidime. J Antimicrob Chemother 2002; 50:723-6. [PMID: 12407130 DOI: 10.1093/jac/dkf208] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Burkholderia pseudomallei produces an Ambler class A beta-lactamase, known as BPS-1. The beta-lactamase gene from a laboratory-derived, ceftazidime-resistant strain of B. pseudomallei (LH-1-2) was cloned and expressed in Escherichia coli. The beta-lactamase, named BPS-1m, had an identical isoelectric focusing point (pI 7.7) to that of BPS-1, but differed in having a stronger hydrolytic activity against ceftazidime. Susceptibility testing showed that BPS-1m when expressed in E. coli conferred resistance to ceftazidime (MIC >or= 32 mg/L). The amino acid sequence of BPS-1m differed from that of BPS-1 by a Pro-to-Ser change at position 167 in the omega loop.
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Affiliation(s)
- P L Ho
- Department of Microbiology and HKU-Pasteur Research Centre, Faculty of Medicine, The University of Hong Kong, Queen Mary Hospital, Pokfulam Road, Pokfulam, Hong Kong SAR, China.
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