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Mo Y, Li X, Li Q, Han Y, Su T, Zhao P, Qiao L, Xiang M, Li F, Guo X, Liu M, Qi Q. Rational Design of N-Acetylglucosamine-2-epimerase and N-Acetylneuraminic Lyase for Efficient N-Acetylneuraminic Acid Biosynthesis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2025; 73:5320-5327. [PMID: 39969151 DOI: 10.1021/acs.jafc.4c10307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2025]
Abstract
N-Acetylneuraminic acid (NeuAc) performs a variety of biological activities where it is used as a nutraceutical and pharmaceutical intermediate. N-Acetylglucosamine-2-epimerase (AGE) and N-acetylneuraminic lyase (NAL) are the most widely used key enzymes in the industrial production of NeuAc through whole-cell catalytic synthesis. However, both AGE and NAL catalyze reversible reactions, and the equilibrium of these two reactions lies between substrates and products, resulting in a lower conversion rate of NeuAc. In this study, affinity analysis based on the dynamic docking (ADD) strategy was used to rationally design the AGE and NAL to improve enzymes properties. The variant AGEA172S/C118A showed a 2.19-fold improvement in the catalytic rate. Then, we combinatorially expressed the variant of AGE and NAL in two plasmids for whole cell catalytic synthesis. NeuAc production was 35% higher with the combination of AGEA172S/C118A and NALF252M compared with the wild type. When substrate GlcNAc/Pyruvate was 3:8 and AGEA172S/C118A and NALF252M expressed strains were 1:0.6, the molar conversion rate was 62%. Thus, our modification of AGE and NAL, the key enzymes in producing NeuAc, gave a better AGE variant AGEA172S/C118A, which could produce 128 g/L NeuAc when using low substrate concentration (0.6 M GlcNAc).
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Affiliation(s)
- Yuxia Mo
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Xiaojiang Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Qingbin Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Yuanfei Han
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Tianyuan Su
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Peng Zhao
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao 266109, China
| | - Liping Qiao
- Bloomage Biotechnology Corporation Limited, Jinan 250101, China
| | - Maogong Xiang
- Bloomage Biotechnology Corporation Limited, Jinan 250101, China
| | - Fan Li
- Bloomage Biotechnology Corporation Limited, Jinan 250101, China
| | - Xueping Guo
- Bloomage Biotechnology Corporation Limited, Jinan 250101, China
| | - Mengmeng Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Qingsheng Qi
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
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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: 0.7] [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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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: 1.8] [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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Jiang P, Vegge A, Thymann T, Wan JMF, Sangild PT. Glucagon-Like Peptide 2 Stimulates Postresection Intestinal Adaptation in Preterm Pigs by Affecting Proteins Related to Protein, Carbohydrate, and Sulphur Metabolism. JPEN J Parenter Enteral Nutr 2016; 41:1293-1300. [DOI: 10.1177/0148607116662971] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Pingping Jiang
- Department of Veterinary Clinical and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Andreas Vegge
- Department of Veterinary Clinical and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
- Global Research, Novo Nordisk, Måløv, Denmark
| | - Thomas Thymann
- Department of Veterinary Clinical and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | | | - Per Torp Sangild
- Department of Veterinary Clinical and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
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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: 1.4] [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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North RA, Kessans SA, Atkinson SC, Suzuki H, Watson AJA, Burgess BR, Angley LM, Hudson AO, Varsani A, Griffin MDW, Fairbanks AJ, Dobson RCJ. Cloning, expression, purification, crystallization and preliminary X-ray diffraction studies of N-acetylneuraminate lyase from methicillin-resistant Staphylococcus aureus. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:306-12. [PMID: 23519810 PMCID: PMC3606580 DOI: 10.1107/s1744309113003060] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 01/30/2013] [Indexed: 01/13/2023]
Abstract
The enzyme N-acetylneuraminate lyase (EC 4.1.3.3) is involved in the metabolism of sialic acids. Specifically, the enzyme catalyzes the retro-aldol cleavage of N-acetylneuraminic acid to form N-acetyl-D-mannosamine and pyruvate. Sialic acids comprise a large family of nine-carbon amino sugars, all of which are derived from the parent compound N-acetylneuraminic acid. In recent years, N-acetylneuraminate lyase has received considerable attention from both mechanistic and structural viewpoints and has been recognized as a potential antimicrobial drug target. The N-acetylneuraminate lyase gene was cloned from methicillin-resistant Staphylococcus aureus genomic DNA, and recombinant protein was expressed and purified from Escherichia coli BL21 (DE3). The enzyme crystallized in a number of crystal forms, predominantly from PEG precipitants, with the best crystal diffracting to beyond 1.70 Å resolution in space group P2₁. Molecular replacement indicates the presence of eight monomers per asymmetric unit. Understanding the structural biology of N-acetylneuraminate lyase in pathogenic bacteria, such as methicillin-resistant S. aureus, will provide insights 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
| | - Sarah A. Kessans
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8041, New Zealand
| | - Sarah C. Atkinson
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Victoria, Australia
| | - Hironori Suzuki
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8041, New Zealand
| | - Andrew J. A. Watson
- Department of Chemistry, University of Canterbury, Christchurch 8140, New Zealand
| | - Benjamin R. Burgess
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, 30 Flemington Road, Parkville, Victoria 3010, Australia
| | - Lauren M. Angley
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, 30 Flemington Road, Parkville, Victoria 3010, Australia
| | - André O. Hudson
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY 14623, USA
| | - Arvind Varsani
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8041, New Zealand
- Electron Microscope Unit, University of Cape Town, Rondebosch, Cape Town 7701, South Africa
| | - 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
| | - Antony J. Fairbanks
- Department of Chemistry, University of Canterbury, Christchurch 8140, 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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Mechanistic model for the synthesis of N-acetylneuraminic acid using N-acetylneuraminate lyase from Escherichia coli K12. ACTA ACUST UNITED AC 2012. [DOI: 10.1016/j.molcatb.2012.05.016] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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Pearce FG, Dobson RCJ, Jameson GB, Perugini MA, Gerrard JA. Characterization of monomeric dihydrodipicolinate synthase variant reveals the importance of substrate binding in optimizing oligomerization. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2011; 1814:1900-9. [PMID: 21803176 DOI: 10.1016/j.bbapap.2011.07.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2011] [Revised: 07/14/2011] [Accepted: 07/15/2011] [Indexed: 01/15/2023]
Abstract
To gain insights into the role of quaternary structure in the TIM-barrel family of enzymes, we introduced mutations to the DHDPS enzyme of Thermotoga maritima, which we have previously shown to be a stable tetramer in solution. These mutations were aimed at reducing the number of salt bridges at one of the two tetramerization interface of the enzyme, which contains many more interactions than the well characterized equivalent interface of the mesophilic Escherichia coli DHDPS enzyme. The resulting variants had altered quaternary structure, as shown by analytical ultracentrifugation, gel filtration liquid chromatography, and small angle X-ray scattering, and X-ray crystallographic studies confirmed that one variant existed as an independent monomer, but with few changes to the secondary and tertiary structure. Reduction of higher order assembly resulted in a loss of thermal stability, as measured by a variety of methods, and impaired catalytic function. Binding of pyruvate increased the oligomeric status of the variants, with a concomitant increase in thermal stability, suggesting a role for substrate binding in optimizing stable, higher order structures. The results of this work show that the salt bridges located at the tetramerization interface of DHDPS play a significant role in maintaining higher order structures, and demonstrate the importance of quaternary structure in determining protein stability and in the optimization of enzyme catalysis.
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Affiliation(s)
- F Grant Pearce
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.
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Disruption of quaternary structure in Escherichia coli dihydrodipicolinate synthase (DHDPS) generates a functional monomer that is no longer inhibited by lysine. Arch Biochem Biophys 2010; 503:202-6. [PMID: 20709017 DOI: 10.1016/j.abb.2010.08.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2010] [Revised: 08/07/2010] [Accepted: 08/10/2010] [Indexed: 11/22/2022]
Abstract
Escherichia coli dihydrodipicolinate synthase (DHDPS, E.C. 4.2.1.52), a natively homotetrameric enzyme was converted to a monomeric species through the introduction of destabilising interactions at two different subunit interfaces allowing exploration of the roles of the quaternary structure in affecting catalytic competency. The double mutant DHDPS-L197D/Y107W displays gel filtration characteristics consistent with a single non-interacting monomeric species, which was confirmed by sedimentary velocity experiments. This monomer was shown to be catalytically active, but with reduced catalytic efficiency (k(cat)=9.8±0.5s(-1)), displaying 8% of the specific activity of the wild-type enzyme. The Michaelis constants for the substrates pyruvate and for (S)-aspartate semialdehyde increased by an order of magnitude, indicating that quaternary structure plays a significant role in substrate specificity. This monomeric species exhibited an enhanced propensity for aggregation and inactivation, indicating that whilst the oligomerization is not an intrinsic criterion for catalysis, higher oligomeric forms may benefit from both increased catalytic efficiency and diminished aggregation propensity. Furthermore, allosteric inhibition by (S)-lysine was abolished for DHDPS-L197D/Y107W, confirming the importance of the dimeric unit as the minimal functional assembly for efficient (S)-lysine binding.
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Griffin MD, Dobson RC, Gerrard JA, Perugini MA. Exploring the dihydrodipicolinate synthase tetramer: How resilient is the dimer–dimer interface? Arch Biochem Biophys 2010; 494:58-63. [DOI: 10.1016/j.abb.2009.11.014] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2009] [Revised: 11/10/2009] [Accepted: 11/10/2009] [Indexed: 11/15/2022]
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