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Hu ZX, Cheng C, Li YQ, Qi XH, Wang T, Liu L, Voglmeir J. Recombinant snail sialic acid aldolase is promiscuous towards aliphatic aldehydes. Chembiochem 2022; 23:e202200074. [PMID: 35543120 DOI: 10.1002/cbic.202200074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 05/10/2022] [Indexed: 11/08/2022]
Abstract
Aldolases are enzymes that reversibly catalyze the cleavage of carbon-carbon bonds. Here we describe a recombinant sialic acid aldolase originating from the freshwater snail Biomphalaria glabrata (sNPL), and compare its substrate spectrum with a sialic acid aldolase originating from chicken (chNPL). In contrast to vertebrate animals which can synthesize, degrade, and incorporate sialic acids on glycoconjugate ubiquitously, snails (as all mollusks) cannot synthesize sialic acids endogenously, and therefore the biological function and substrate scope of sNPL ought to differ significantly from vertebrate sialic aldolases such as chNPL. sNPL was active towards a series of sialic acid derivatives but was in contrast to chNPL unable to catalyze the cleavage of N-acetylneuraminic acid into N-acetylmannosamine and pyruvate. Interestingly, chNPL and sNPL showed contrasting C4 (R) / (S) diastereoselectivity towards the substrates d-mannose and d-galactose in the presence of pyruvate. In addition, sNPL was also able to synthesize a series of 4-hydroxy-2-oxoates using the corresponding aliphatic aldehyde substrates in the presence of pyruvate, which could be not achieved by chNPL.
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Affiliation(s)
- Zi-Xuan Hu
- Nanjing Agricultural University - Weigang Campus: Nanjing Agricultural University, College of Food Science and Technology, CHINA
| | - Cheng Cheng
- Nanjing Agricultural University - Weigang Campus: Nanjing Agricultural University, College of Food Science and Technology, CHINA
| | - Yu-Qian Li
- Nanjing Agricultural University - Weigang Campus: Nanjing Agricultural University, College of Food Science and Technology, CHINA
| | - Xiao-Han Qi
- Nanjing Agricultural University - Weigang Campus: Nanjing Agricultural University, College of Food Science and Technology, CHINA
| | - Ting Wang
- Nanjing Agricultural University - Weigang Campus: Nanjing Agricultural University, College of Food Science and Technology, CHINA
| | - Li Liu
- Nanjing Agricultural University - Weigang Campus: Nanjing Agricultural University, College of Food Science and Technology, CHINA
| | - Josef Voglmeir
- Nanjing Agricultural University, College of Food Science And Technology, 1 Weigang, 210095, Nanjing, CHINA
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2
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Coombes D, Davies JS, Newton-Vesty MC, Horne CR, Setty TG, Subramanian R, Moir JWB, Friemann R, Panjikar S, Griffin MDW, North RA, Dobson RCJ. The basis for non-canonical ROK family function in the N-acetylmannosamine kinase from the pathogen Staphylococcus aureus. J Biol Chem 2020; 295:3301-3315. [PMID: 31949045 DOI: 10.1074/jbc.ra119.010526] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 12/31/2019] [Indexed: 12/31/2022] Open
Abstract
In environments where glucose is limited, some pathogenic bacteria metabolize host-derived sialic acid as a nutrient source. N-Acetylmannosamine kinase (NanK) is the second enzyme of the bacterial sialic acid import and degradation pathway and adds phosphate to N-acetylmannosamine using ATP to prime the molecule for future pathway reactions. Sequence alignments reveal that Gram-positive NanK enzymes belong to the Repressor, ORF, Kinase (ROK) family, but many lack the canonical Zn-binding motif expected for this function, and the sugar-binding EXGH motif is altered to EXGY. As a result, it is unclear how they perform this important reaction. Here, we study the Staphylococcus aureus NanK (SaNanK), which is the first characterization of a Gram-positive NanK. We report the kinetic activity of SaNanK along with the ligand-free, N-acetylmannosamine-bound and substrate analog GlcNAc-bound crystal structures (2.33, 2.20, and 2.20 Å resolution, respectively). These demonstrate, in combination with small-angle X-ray scattering, that SaNanK is a dimer that adopts a closed conformation upon substrate binding. Analysis of the EXGY motif reveals that the tyrosine binds to the N-acetyl group to select for the "boat" conformation of N-acetylmannosamine. Moreover, SaNanK has a stacked arginine pair coordinated by negative residues critical for thermal stability and catalysis. These combined elements serve to constrain the active site and orient the substrate in lieu of Zn binding, representing a significant departure from canonical NanK binding. This characterization provides insight into differences in the ROK family and highlights a novel area for antimicrobial discovery to fight Gram-positive and S. aureus infections.
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Affiliation(s)
- David Coombes
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
| | - James S Davies
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
| | - Michael C Newton-Vesty
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
| | - Christopher R Horne
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
| | - Thanuja G Setty
- Institute for Stem Cell Biology and Regenerative Medicine, NCBS, GKVK Campus, Bellary Road, Bangalore, Karnataka 560 065, India; The University of Trans-Disciplinary Health Sciences and Technology (TDU), Bangalore, KA 560064, India
| | - Ramaswamy Subramanian
- Institute for Stem Cell Biology and Regenerative Medicine, NCBS, GKVK Campus, Bellary Road, Bangalore, Karnataka 560 065, India
| | - James W B Moir
- Department of Biology, University of York, Helsington, York YO10 5DD, United Kingdom
| | - Rosmarie Friemann
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Guldhedsgatan 10A, 413 46 Gothenburg, Sweden; Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, 40530 Gothenburg, Sweden
| | - Santosh Panjikar
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia; Australian Synchrotron, ANSTO, Victoria 3168, Australia
| | - Michael D W Griffin
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Rachel A North
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand.
| | - Renwick C J Dobson
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand; Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia.
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3
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Gurung MK, Altermark B, Helland R, Smalås AO, Ræder ILU. Features and structure of a cold active N-acetylneuraminate lyase. PLoS One 2019; 14:e0217713. [PMID: 31185017 PMCID: PMC6559660 DOI: 10.1371/journal.pone.0217713] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 05/16/2019] [Indexed: 11/23/2022] Open
Abstract
N-acetylneuraminate lyases (NALs) are enzymes that catalyze the reversible cleavage and synthesis of sialic acids. They are therefore commonly used for the production of these high-value sugars. This study presents the recombinant production, together with biochemical and structural data, of the NAL from the psychrophilic bacterium Aliivibrio salmonicida LFI1238 (AsNAL). Our characterization shows that AsNAL possesses high activity and stability at alkaline pH. We confirm that these properties allow for the use in a one-pot reaction at alkaline pH for the synthesis of N-acetylneuraminic acid (Neu5Ac, the most common sialic acid) from the inexpensive precursor N-acetylglucosamine. We also show that the enzyme has a cold active nature with an optimum temperature for Neu5Ac synthesis at 20°C. The equilibrium constant for the reaction was calculated at different temperatures, and the formation of Neu5Ac acid is favored at low temperatures, making the cold active enzyme a well-suited candidate for use in such exothermic reactions. The specific activity is high compared to the homologue from Escherichia coli at three tested temperatures, and the enzyme shows a higher catalytic efficiency and turnover number for cleavage at 37°C. Mutational studies reveal that amino acid residue Asn 168 is important for the high kcat. The crystal structure of AsNAL was solved to 1.65 Å resolution and reveals a compact, tetrameric protein similar to other NAL structures. The data presented provides a framework to guide further optimization of its application in sialic acid production and opens the possibility for further design of the enzyme.
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Affiliation(s)
- Man Kumari Gurung
- The Norwegian Structural Biology Center (NorStruct), Department of Chemistry, UiT- The Arctic University of Norway, Tromsø, Norway
| | - Bjørn Altermark
- The Norwegian Structural Biology Center (NorStruct), Department of Chemistry, UiT- The Arctic University of Norway, Tromsø, Norway
| | - Ronny Helland
- The Norwegian Structural Biology Center (NorStruct), Department of Chemistry, UiT- The Arctic University of Norway, Tromsø, Norway
| | - Arne O. Smalås
- The Norwegian Structural Biology Center (NorStruct), Department of Chemistry, UiT- The Arctic University of Norway, Tromsø, Norway
| | - Inger Lin U. Ræder
- The Norwegian Structural Biology Center (NorStruct), Department of Chemistry, UiT- The Arctic University of Norway, Tromsø, Norway
- * E-mail:
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4
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North RA, Wahlgren WY, Remus DM, Scalise M, Kessans SA, Dunevall E, Claesson E, Soares da Costa TP, Perugini MA, Ramaswamy S, Allison JR, Indiveri C, Friemann R, Dobson RCJ. The Sodium Sialic Acid Symporter From Staphylococcus aureus Has Altered Substrate Specificity. Front Chem 2018; 6:233. [PMID: 30023356 PMCID: PMC6039549 DOI: 10.3389/fchem.2018.00233] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 06/01/2018] [Indexed: 11/13/2022] Open
Abstract
Mammalian cell surfaces are decorated with complex glycoconjugates that terminate with negatively charged sialic acids. Commensal and pathogenic bacteria can use host-derived sialic acids for a competitive advantage, but require a functional sialic acid transporter to import the sugar into the cell. This work investigates the sodium sialic acid symporter (SiaT) from Staphylococcus aureus (SaSiaT). We demonstrate that SaSiaT rescues an Escherichia coli strain lacking its endogenous sialic acid transporter when grown on the sialic acids N-acetylneuraminic acid (Neu5Ac) or N-glycolylneuraminic acid (Neu5Gc). We then develop an expression, purification and detergent solubilization system for SaSiaT and demonstrate that the protein is largely monodisperse in solution with a stable monomeric oligomeric state. Binding studies reveal that SaSiaT has a higher affinity for Neu5Gc over Neu5Ac, which was unexpected and is not seen in another SiaT homolog. We develop a homology model and use comparative sequence analyses to identify substitutions in the substrate-binding site of SaSiaT that may explain the altered specificity. SaSiaT is shown to be electrogenic, and transport is dependent upon more than one Na+ ion for every sialic acid molecule. A functional sialic acid transporter is essential for the uptake and utilization of sialic acid in a range of pathogenic bacteria, and developing new inhibitors that target these transporters is a valid mechanism for inhibiting bacterial growth. By demonstrating a route to functional recombinant SaSiaT, and developing the in vivo and in vitro assay systems, our work underpins the design of inhibitors to this transporter.
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Affiliation(s)
- Rachel A North
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.,Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand.,Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Weixiao Y Wahlgren
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden.,Centre for Antibiotic Resistance Research, University of Gothenburg, Gothenburg, Sweden
| | - Daniela M Remus
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.,Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand
| | - Mariafrancesca Scalise
- Unit of Biochemistry and Molecular Biotechnology, Department DiBEST (Biologia, Ecologia, Scienze della Terra), University of Calabria, Arcavacata di Rende, Italy
| | - Sarah A Kessans
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.,Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand
| | - Elin Dunevall
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Elin Claesson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Tatiana P Soares da Costa
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
| | - Matthew A Perugini
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
| | - S Ramaswamy
- The Institute for Stem Cell Biology and Regenerative Medicine, Bangalore, India
| | - Jane R Allison
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand.,Centre for Theoretical Chemistry and Physics, Institute of Natural and Mathematical Sciences, Massey University, Auckland, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand
| | - Cesare Indiveri
- Unit of Biochemistry and Molecular Biotechnology, Department DiBEST (Biologia, Ecologia, Scienze della Terra), University of Calabria, Arcavacata di Rende, Italy
| | - Rosmarie Friemann
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden.,Centre for Antibiotic Resistance Research, University of Gothenburg, Gothenburg, Sweden
| | - Renwick C J Dobson
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.,Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, Australia
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5
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North RA, Horne CR, Davies JS, Remus DM, Muscroft-Taylor AC, Goyal P, Wahlgren WY, Ramaswamy S, Friemann R, Dobson RCJ. "Just a spoonful of sugar...": import of sialic acid across bacterial cell membranes. Biophys Rev 2017; 10:219-227. [PMID: 29222808 DOI: 10.1007/s12551-017-0343-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 11/13/2017] [Indexed: 12/24/2022] Open
Abstract
Eukaryotic cell surfaces are decorated with a complex array of glycoconjugates that are usually capped with sialic acids, a large family of over 50 structurally distinct nine-carbon amino sugars, the most common member of which is N-acetylneuraminic acid. Once made available through the action of neuraminidases, bacterial pathogens and commensals utilise host-derived sialic acid by degrading it for energy or repurposing the sialic acid onto their own cell surface to camouflage the bacterium from the immune system. A functional sialic acid transporter has been shown to be essential for the uptake of sialic acid in a range of human bacterial pathogens and important for host colonisation and persistence. Here, we review the state-of-play in the field with respect to the molecular mechanisms by which these bio-nanomachines transport sialic acids across bacterial cell membranes.
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Affiliation(s)
- Rachel A North
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, P.O. Box 4800, Christchurch, 8140, New Zealand
| | - Christopher R Horne
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, P.O. Box 4800, Christchurch, 8140, New Zealand
| | - James S Davies
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, P.O. Box 4800, Christchurch, 8140, New Zealand
| | - Daniela M Remus
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, P.O. Box 4800, Christchurch, 8140, New Zealand
| | - Andrew C Muscroft-Taylor
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, P.O. Box 4800, Christchurch, 8140, New Zealand
| | - Parveen Goyal
- Department of Chemistry and Molecular Biology, Biochemistry and Structural Biology, University of Gothenburg, Box 462, 40530, Gothenburg, Sweden.,Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Box 440, 40530, Gothenburg, Sweden
| | - Weixiao Yuan Wahlgren
- Department of Chemistry and Molecular Biology, Biochemistry and Structural Biology, University of Gothenburg, Box 462, 40530, Gothenburg, Sweden.,Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Box 440, 40530, Gothenburg, Sweden
| | - S Ramaswamy
- The Institute for Stem Cell Biology and Regenerative Medicine (InStem), G.K.V.K. Post Office, Bangalore, Karnataka, 560065, India
| | - Rosmarie Friemann
- Department of Chemistry and Molecular Biology, Biochemistry and Structural Biology, University of Gothenburg, Box 462, 40530, Gothenburg, Sweden. .,Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Box 440, 40530, Gothenburg, Sweden.
| | - Renwick C J Dobson
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, P.O. Box 4800, Christchurch, 8140, New Zealand. .,Bio21 Molecular Science and Biotechnology Institute, Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria, 3010, Australia.
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6
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Caing-Carlsson R, Goyal P, Sharma A, Ghosh S, Setty TG, North RA, Friemann R, Ramaswamy S. Crystal structure of N-acetylmannosamine kinase from Fusobacterium nucleatum. Acta Crystallogr F Struct Biol Commun 2017; 73:356-362. [PMID: 28580924 PMCID: PMC5458393 DOI: 10.1107/s2053230x17007439] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 05/19/2017] [Indexed: 12/15/2022] Open
Abstract
Sialic acids comprise a varied group of nine-carbon amino sugars that are widely distributed among mammals and higher metazoans. Some human commensals and bacterial pathogens can scavenge sialic acids from their environment and degrade them for use as a carbon and nitrogen source. The enzyme N-acetylmannosamine kinase (NanK; EC 2.7.1.60) belongs to the transcriptional repressors, uncharacterized open reading frames and sugar kinases (ROK) superfamily. NanK catalyzes the second step of the sialic acid catabolic pathway, transferring a phosphate group from adenosine 5'-triphosphate to the C6 position of N-acetylmannosamine to generate N-acetylmannosamine 6-phosphate. The structure of NanK from Fusobacterium nucleatum was determined to 2.23 Å resolution by X-ray crystallography. Unlike other NanK enzymes and ROK family members, F. nucleatum NanK does not have a conserved zinc-binding site. In spite of the absence of the zinc-binding site, all of the major structural features of enzymatic activity are conserved.
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Affiliation(s)
- Rhawnie Caing-Carlsson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | - Parveen Goyal
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Box 440, 40530 Gothenburg, Sweden
| | - Amit Sharma
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
- Atomic Physics, Department of Physics, Lund University, Professorsgatan 1, 22363 Lund, Sweden
| | - Swagatha Ghosh
- Institute for Stem Cell Biology and Regenerative Medicine, GKVK Post, Bangalore 560 065, India
| | - Thanuja Gangi Setty
- Institute for Stem Cell Biology and Regenerative Medicine, GKVK Post, Bangalore 560 065, India
- School of Life Sciences, TransDisciplinary University, Bangalore 560 064, India
| | - Rachel A. North
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8041, New Zealand
| | - Rosmarie Friemann
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Box 440, 40530 Gothenburg, Sweden
- Department of Structural Biology, Stanford University School of Medicine, 299 Campus Drive West, Stanford, CA 94305-5126, USA
| | - S. Ramaswamy
- Institute for Stem Cell Biology and Regenerative Medicine, GKVK Post, Bangalore 560 065, India
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7
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North RA, Watson AJA, Pearce FG, Muscroft-Taylor AC, Friemann R, Fairbanks AJ, Dobson RCJ. Structure and inhibition of N-acetylneuraminate lyase from methicillin-resistant Staphylococcus aureus. FEBS Lett 2016; 590:4414-4428. [PMID: 27943302 DOI: 10.1002/1873-3468.12462] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 10/04/2016] [Accepted: 10/09/2016] [Indexed: 01/07/2023]
Abstract
N-Acetylneuraminate lyase is the first committed enzyme in the degradation of sialic acid by bacterial pathogens. In this study, we analyzed the kinetic parameters of N-acetylneuraminate lyase from methicillin-resistant Staphylococcus aureus (MRSA). We determined that the enzyme has a relatively high KM of 3.2 mm, suggesting that flux through the catabolic pathway is likely to be controlled by this enzyme. Our data indicate that sialic acid alditol, a known inhibitor of N-acetylneuraminate lyase enzymes, is a stronger inhibitor of MRSA N-acetylneuraminate lyase than of Clostridium perfringens N-acetylneuraminate lyase. Our analysis of the crystal structure of ligand-free and 2R-sialic acid alditol-bound MRSA N-acetylneuraminate lyase suggests that subtle dynamic differences in solution and/or altered binding interactions within the active site may account for species-specific inhibition.
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Affiliation(s)
- Rachel A North
- Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Andrew J A Watson
- Department of Chemistry, University of Canterbury, Christchurch, New Zealand
| | - F Grant Pearce
- Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Andrew C Muscroft-Taylor
- Protein Science and Engineering, Callaghan Innovation, University of Canterbury, Christchurch, New Zealand
| | - Rosmarie Friemann
- Department of Chemistry and Molecular Biology, University of Gothenburg, Sweden.,Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Sweden.,Department of Structural Biology, School of Medicine, Stanford University, CA, USA
| | - Antony J Fairbanks
- Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.,Department of Chemistry, University of Canterbury, Christchurch, New Zealand
| | - Renwick C J Dobson
- Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.,Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Australia
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8
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Ji W, Sun W, Feng J, Song T, Zhang D, Ouyang P, Gu Z, Xie J. Characterization of a novel N-acetylneuraminic acid lyase favoring industrial N-acetylneuraminic acid synthesis. Sci Rep 2015; 5:9341. [PMID: 25799411 PMCID: PMC5380162 DOI: 10.1038/srep09341] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Accepted: 02/26/2015] [Indexed: 01/22/2023] Open
Abstract
N-Acetylneuraminic acid lyase (NAL, E.C. number 4.1.3.3) is a Class I aldolase that catalyzes the reversible aldol cleavage of N-acetylneuraminic acid (Neu5Ac) from pyruvate and N-acetyl-D-mannosamine (ManNAc). Due to the equilibrium favoring Neu5Ac cleavage, the enzyme catalyzes the rate-limiting step of two biocatalytic reactions producing Neu5Ac in industry. We report the biochemical characterization of a novel NAL from a “GRAS” (General recognized as safe) strain C. glutamicum ATCC 13032 (CgNal). Compared to all previously reported NALs, CgNal exhibited the lowest kcat/Km value for Neu5Ac and highest kcat/Km values for ManNAc and pyruvate, which makes CgNal favor Neu5Ac synthesis the most. The recombinant CgNal reached the highest expression level (480 mg/L culture), and the highest reported yield of Neu5Ac was achieved (194 g/L, 0.63 M). All these unique properties make CgNal a promising biocatalyst for industrial Neu5Ac biosynthesis. Additionally, although showing the best Neu5Ac synthesis activity among the NAL family, CgNal is more related to dihydrodipicolinate synthase (DHDPS) by phylogenetic analysis. The activities of CgNal towards both NAL's and DHDPS' substrates are fairly high, which indicates CgNal a bi-functional enzyme. The sequence analysis suggests that CgNal might have adopted a unique set of residues for substrates recognition.
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Affiliation(s)
- Wenyan Ji
- 1] State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing, PR China [2] College of Life Science and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, PR China [3] National Engineering Technique Research Center for Biotechnology, Nanjing, PR China
| | - Wujin Sun
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, Raleigh, United States
| | - Jinmei Feng
- Department of Pathogenic Biology, School of Medicine, Jianghan University, Wuhan, China
| | - Tianshun Song
- College of Life Science and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, PR China
| | - Dalu Zhang
- International Cooperation Division, China National Center for Biotechnology Development, Beijing, PR China
| | - Pingkai Ouyang
- 1] State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing, PR China [2] College of Life Science and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, PR China [3] National Engineering Technique Research Center for Biotechnology, Nanjing, PR China
| | - Zhen Gu
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, Raleigh, United States
| | - Jingjing Xie
- 1] State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing, PR China [2] College of Life Science and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, PR China [3] National Engineering Technique Research Center for Biotechnology, Nanjing, PR China
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9
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North RA, Seizova S, Stampfli A, Kessans SA, Suzuki H, Griffin MDW, Kvansakul M, Dobson RCJ. Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of N-acetylmannosamine kinase from methicillin-resistant Staphylococcus aureus. Acta Crystallogr F Struct Biol Commun 2014; 70:643-9. [PMID: 24817729 PMCID: PMC4014338 DOI: 10.1107/s2053230x14007250] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Accepted: 04/01/2014] [Indexed: 11/10/2022] Open
Abstract
N-Acetylmannosamine kinase (EC 2.7.1.60) is involved in the catabolism of sialic acid for many bacterial pathogens implicated in human disease such as Escherichia coli, Staphylococcus aureus, Vibrio cholerae and V. vulnificus. Interestingly, some human commensals and bacterial pathogens can scavenge sialic acids from their surrounding environment and degrade them as a source of carbon, nitrogen and energy. This process requires a cluster of genes known as the `Nan-Nag cluster', which have proven to be essential for S. aureus growth on sialic acids, suggesting that the pathway is a viable antimicrobial drug target. The enzyme N-acetylmannosamine kinase is involved in the catabolism of sialic acid, transferring a phosphate group from adenosine-5'-triphosphate to the C6 position of N-acetylmannosamine to generate N-acetylmannosamine-6-phosphate. The gene was cloned into an appropriate expression vector; recombinant protein was expressed in E. coli BL21 (DE3) cells and purified via anion-exchange chromatography, hydrophobic interaction chromatography and size-exclusion chromatography. Purified N-acetylmannosamine kinase was screened for crystallization. The best crystal diffracted to a resolution of beyond 2.6 Å in space group P2. Understanding the structural nature of this enzyme from methicillin-resistant S. aureus will provide insights necessary for the development of future antimicrobials.
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Affiliation(s)
- Rachel A. North
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8041, New Zealand
| | - Simona Seizova
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8041, New Zealand
| | - Anja Stampfli
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8041, New Zealand
| | - Sarah A. Kessans
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8041, New Zealand
| | - Hironori Suzuki
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8041, New Zealand
| | - Michael D. W. Griffin
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, 30 Flemington Road, Parkville, Victoria 3010, Australia
| | - Marc Kvansakul
- Department of Biochemistry, La Trobe University, Melbourne, Victoria, Australia
| | - Renwick C. J. Dobson
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8041, New Zealand
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, 30 Flemington Road, Parkville, Victoria 3010, Australia
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North RA, Kessans SA, Griffin MDW, Watson AJA, Fairbanks AJ, Dobson RCJ. Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of N-acetylmannosamine-6-phosphate 2-epimerase from methicillin-resistant Staphylococcus aureus. Acta Crystallogr F Struct Biol Commun 2014; 70:650-5. [PMID: 24817730 PMCID: PMC4014339 DOI: 10.1107/s2053230x14007171] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Accepted: 03/31/2014] [Indexed: 12/12/2022] Open
Abstract
Sialic acids are one of the most important carbohydrate classes in biology. Some bacterial pathogens can scavenge sialic acids from their surrounding environment and degrade them as a source of carbon, nitrogen and energy. This sequestration and subsequent catabolism of sialic acid require a cluster of genes known as the `Nan-Nag' cluster. The enzymes coded by these genes are important for pathogen colonization and persistence. Importantly, the Nan-Nag genes have proven to be essential for Staphylococcus aureus growth on sialic acids, suggesting that the pathway is a viable antibiotic drug target. The enzyme N-acetylmannosamine-6-phosphate 2-epimerase is involved in the catabolism of sialic acid; specifically, the enzyme converts N-acetylmannosamine-6-phosphate into N-acetylglucosamine-6-phosphate. The gene was cloned into an appropriate expression vector, and recombinant protein was expressed in Escherichia coli BL21 (DE3) cells and purified via a three-step procedure. Purified N-acetylmannosamine-6-phosphate 2-epimerase was screened for crystallization. The best crystal diffracted to a resolution of beyond 1.84 Å in space group P21212. Understanding the structural nature of this enzyme from methicillin-resistant S. aureus will provide us with the insights necessary for the development of future antibiotics.
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Affiliation(s)
- Rachel A. North
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8041, New Zealand
| | - Sarah A. Kessans
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8041, New Zealand
| | - Michael D. W. Griffin
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, 30 Flemington Road, Parkville, Victoria 3010, Australia
| | - Andrew J. A. Watson
- Department of Chemistry, University of Canterbury, Private Bag 4800, Christchurch 8041, New Zealand
| | - Antony J. Fairbanks
- Department of Chemistry, University of Canterbury, Private Bag 4800, Christchurch 8041, New Zealand
| | - Renwick C. J. Dobson
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8041, New Zealand
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, 30 Flemington Road, Parkville, Victoria 3010, Australia
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