51
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Dong J, Fernández-Fueyo E, Hollmann F, Paul CE, Pesic M, Schmidt S, Wang Y, Younes S, Zhang W. Biokatalytische Oxidationsreaktionen - aus der Sicht eines Chemikers. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201800343] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- JiaJia Dong
- Department of Biotechnology; Delft University of Technology; van der Maasweg 9 2629HZ Delft Niederlande
| | - Elena Fernández-Fueyo
- Department of Biotechnology; Delft University of Technology; van der Maasweg 9 2629HZ Delft Niederlande
| | - Frank Hollmann
- Department of Biotechnology; Delft University of Technology; van der Maasweg 9 2629HZ Delft Niederlande
| | - Caroline E. Paul
- Department of Biotechnology; Delft University of Technology; van der Maasweg 9 2629HZ Delft Niederlande
| | - Milja Pesic
- Department of Biotechnology; Delft University of Technology; van der Maasweg 9 2629HZ Delft Niederlande
| | - Sandy Schmidt
- Department of Biotechnology; Delft University of Technology; van der Maasweg 9 2629HZ Delft Niederlande
| | - Yonghua Wang
- School of Food Science and Engineering; South China University of Technology; Guangzhou 510640 P. R. China
| | - Sabry Younes
- Department of Biotechnology; Delft University of Technology; van der Maasweg 9 2629HZ Delft Niederlande
| | - Wuyuan Zhang
- Department of Biotechnology; Delft University of Technology; van der Maasweg 9 2629HZ Delft Niederlande
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52
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Subramanian K, Góra A, Spruijt R, Mitusińska K, Suarez-Diez M, Martins dos Santos V, Schaap PJ. Modulating D-amino acid oxidase (DAAO) substrate specificity through facilitated solvent access. PLoS One 2018; 13:e0198990. [PMID: 29906280 PMCID: PMC6003678 DOI: 10.1371/journal.pone.0198990] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 05/30/2018] [Indexed: 11/28/2022] Open
Abstract
D-amino acid oxidase (DAAO) degrades D-amino acids to produce α-ketoacids, hydrogen peroxide and ammonia. DAAO has often been investigated and engineered for industrial and clinical applications. We combined information from literature with a detailed analysis of the structure to engineer mammalian DAAOs. The structural analysis was complemented with molecular dynamics simulations to characterize solvent accessibility and product release mechanisms. We identified non-obvious residues located on the loops on the border between the active site and the secondary binding pocket essential for pig and human DAAO substrate specificity and activity. We engineered DAAOs by mutating such critical residues and characterised the biochemical activity of the resulting variants. The results highlight the importance of the selected residues in modulating substrate specificity, product egress and enzyme activity, suggesting further steps of DAAO re-engineering towards desired clinical and industrial applications.
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Affiliation(s)
- Kalyanasundaram Subramanian
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng WE, Wageningen, The Netherlands
| | - Artur Góra
- Tunneling Group, Biotechnology Centre, Silesian University of Technology, ul. Krzywoustego, Gliwice, Poland
| | - Ruud Spruijt
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng WE, Wageningen, The Netherlands
| | - Karolina Mitusińska
- Tunneling Group, Biotechnology Centre, Silesian University of Technology, ul. Krzywoustego, Gliwice, Poland
- Department of Chemistry, Silesian University of Technology, ks. Marcina Strzody, Gliwice, Poland
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng WE, Wageningen, The Netherlands
| | - Vitor Martins dos Santos
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng WE, Wageningen, The Netherlands
| | - Peter J. Schaap
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng WE, Wageningen, The Netherlands
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53
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Orrego AH, López-Gallego F, Espaillat A, Cava F, Guisan JM, Rocha-Martin J. One-step Synthesis of α-Keto Acids from Racemic Amino Acids by A Versatile Immobilized Multienzyme Cell-free System. ChemCatChem 2018. [DOI: 10.1002/cctc.201800359] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Alejandro H. Orrego
- Department of Biocatalysis; Institute of Catalysis and Petrochemistry (ICP) CSIC; Campus UAM. Cantoblanco. 28049 Madrid Spain
| | - Fernando López-Gallego
- Departamento de Química Orgánica; Instituto de Síntesis Química y Catálisis Homogénea (ISQCH); CSIC-Universidad de Zaragoza; 50009 Zaragoza Spain
- ARAID Foundation; Zaragoza Spain
| | - Akbar Espaillat
- Department of Molecular Biology and Laboratory for Molecular Infection Medicine Sweden; Umea Centre for Microbial Research; Umea University; Umea Sweden
| | - Felipe Cava
- Department of Molecular Biology and Laboratory for Molecular Infection Medicine Sweden; Umea Centre for Microbial Research; Umea University; Umea Sweden
| | - José M. Guisan
- Department of Biocatalysis; Institute of Catalysis and Petrochemistry (ICP) CSIC; Campus UAM. Cantoblanco. 28049 Madrid Spain
| | - Javier Rocha-Martin
- Department of Biocatalysis; Institute of Catalysis and Petrochemistry (ICP) CSIC; Campus UAM. Cantoblanco. 28049 Madrid Spain
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54
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Imine Deaminase Activity and Conformational Stability of UK114, the Mammalian Member of the Rid Protein Family Active in Amino Acid Metabolism. Int J Mol Sci 2018; 19:ijms19040945. [PMID: 29565811 PMCID: PMC5979572 DOI: 10.3390/ijms19040945] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 03/16/2018] [Accepted: 03/18/2018] [Indexed: 12/18/2022] Open
Abstract
Reactive intermediate deaminase (Rid) protein family is a recently discovered group of enzymes that is conserved in all domains of life and is proposed to play a role in the detoxification of reactive enamines/imines. UK114, the mammalian member of RidA subfamily, was identified in the early 90s as a component of perchloric acid-soluble extracts from goat liver and exhibited immunomodulatory properties. Multiple activities were attributed to this protein, but its function is still unclear. This work addressed the question of whether UK114 is a Rid enzyme. Biochemical analyses demonstrated that UK114 hydrolyzes α-imino acids generated by l- or d-amino acid oxidases with a preference for those deriving from Ala > Leu = l-Met > l-Gln, whereas it was poorly active on l-Phe and l-His. Circular Dichroism (CD) analyses of UK114 conformational stability highlighted its remarkable resistance to thermal unfolding, even at high urea concentrations. The half-life of heat inactivation at 95 °C, measured from CD and activity data, was about 3.5 h. The unusual conformational stability of UK114 could be relevant in the frame of a future evaluation of its immunogenic properties. In conclusion, mammalian UK114 proteins are RidA enzymes that may play an important role in metabolism homeostasis also in these organisms.
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55
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Andreo-Vidal A, Mamounis KJ, Sehanobish E, Avalos D, Campillo-Brocal JC, Sanchez-Amat A, Yukl ET, Davidson VL. Structure and Enzymatic Properties of an Unusual Cysteine Tryptophylquinone-Dependent Glycine Oxidase from Pseudoalteromonas luteoviolacea. Biochemistry 2018; 57:1155-1165. [PMID: 29381339 DOI: 10.1021/acs.biochem.8b00009] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Glycine oxidase from Pseudoalteromonas luteoviolacea (PlGoxA) is a cysteine tryptophylquinone (CTQ)-dependent enzyme. Sequence analysis and phylogenetic analysis place it in a newly designated subgroup (group IID) of a recently identified family of LodA-like proteins, which are predicted to possess CTQ. The crystal structure of PlGoxA reveals that it is a homotetramer. It possesses an N-terminal domain with no close structural homologues in the Protein Data Bank. The active site is quite small because of intersubunit interactions, which may account for the observed cooperativy toward glycine. Steady-state kinetic analysis yielded the following values: kcat = 6.0 ± 0.2 s-1, K0.5 = 187 ± 18 μM, and h = 1.77 ± 0.27. In contrast to other quinoprotein amine dehydrogenases and oxidases that exhibit anomalously large primary kinetic isotope effects on the rate of reduction of the quinone cofactor by the amine substrate, no significant primary kinetic isotope effect was observed for this reaction of PlGoxA. The absorbance spectrum of glycine-reduced PlGoxA exhibits features in the range of 400-650 nm that have not previously been seen in other quinoproteins. Thus, in addition to the unusual structural features of PlGoxA, the kinetic and chemical reaction mechanisms of the reductive half-reaction of PlGoxA appear to be distinct from those of other amine dehydrogenases and amine oxidases that use tryptophylquinone and tyrosylquinone cofactors.
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Affiliation(s)
- Andres Andreo-Vidal
- Department of Genetics and Microbiology, University of Murcia , Murcia 30100, Spain
| | - Kyle J Mamounis
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida , Orlando, Florida 32827, United States
| | - Esha Sehanobish
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida , Orlando, Florida 32827, United States
| | - Dante Avalos
- Department of Chemistry and Biochemistry, New Mexico State University , Las Cruces, New Mexico 88003, United States
| | | | - Antonio Sanchez-Amat
- Department of Genetics and Microbiology, University of Murcia , Murcia 30100, Spain
| | - Erik T Yukl
- Department of Chemistry and Biochemistry, New Mexico State University , Las Cruces, New Mexico 88003, United States
| | - Victor L Davidson
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida , Orlando, Florida 32827, United States
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56
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Rosini E, Caldinelli L, Piubelli L. Assays of D-Amino Acid Oxidase Activity. Front Mol Biosci 2018; 4:102. [PMID: 29404340 PMCID: PMC5785730 DOI: 10.3389/fmolb.2017.00102] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 12/28/2017] [Indexed: 11/13/2022] Open
Abstract
D-amino acid oxidase (DAAO) is a well-known flavoenzyme that catalyzes the oxidative FAD-dependent deamination of D-amino acids. As a result of the absolute stereoselectivity and broad substrate specificity, microbial DAAOs have been employed as industrial biocatalysts in the production of semi-synthetic cephalosporins and enantiomerically pure amino acids. Moreover, in mammals, DAAO is present in specific brain areas and degrades D-serine, an endogenous coagonist of the N-methyl-D-aspartate receptors (NMDARs). Dysregulation of D-serine metabolism due to an altered DAAO functionality is related to pathological NMDARs dysfunctions such as in amyotrophic lateral sclerosis and schizophrenia. In this protocol paper, we describe a variety of direct assays based on the determination of molecular oxygen consumption, reduction of alternative electron acceptors, or α-keto acid production, of coupled assays to detect the hydrogen peroxide or the ammonium production, and an indirect assay of the α-keto acid production based on a chemical derivatization. These analytical assays allow the determination of DAAO activity both on recombinant enzyme preparations, in cells, and in tissue samples.
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Affiliation(s)
- Elena Rosini
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
- The Protein Factory Research Center, Politecnico of Milan and University of Insubria, Milan, Italy
| | - Laura Caldinelli
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
- The Protein Factory Research Center, Politecnico of Milan and University of Insubria, Milan, Italy
| | - Luciano Piubelli
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
- The Protein Factory Research Center, Politecnico of Milan and University of Insubria, Milan, Italy
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57
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Melis R, Rosini E, Pirillo V, Pollegioni L, Molla G. In vitro evolution of an l-amino acid deaminase active on l-1-naphthylalanine. Catal Sci Technol 2018. [DOI: 10.1039/c8cy01380b] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
l-Amino acid deaminase from Proteus myxofaciens (PmaLAAD) is a promising biocatalyst for enantioselective biocatalysis that can be exploited to produce optically pure d-amino acids or α-keto acids.
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Affiliation(s)
- Roberta Melis
- Dipartimento di Biotecnologie e Scienze della Vita
- Università degli Studi dell'Insubria
- 21100 Varese
- Italy
| | - Elena Rosini
- Dipartimento di Biotecnologie e Scienze della Vita
- Università degli Studi dell'Insubria
- 21100 Varese
- Italy
| | - Valentina Pirillo
- Dipartimento di Biotecnologie e Scienze della Vita
- Università degli Studi dell'Insubria
- 21100 Varese
- Italy
| | - Loredano Pollegioni
- Dipartimento di Biotecnologie e Scienze della Vita
- Università degli Studi dell'Insubria
- 21100 Varese
- Italy
| | - Gianluca Molla
- Dipartimento di Biotecnologie e Scienze della Vita
- Università degli Studi dell'Insubria
- 21100 Varese
- Italy
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58
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Hahn K, Hertle Y, Bloess S, Kottke T, Hellweg T, Fischer von Mollard G. Activation of Recombinantly Expressed l-Amino Acid Oxidase from Rhizoctonia solani by Sodium Dodecyl Sulfate. Molecules 2017; 22:E2272. [PMID: 29261108 PMCID: PMC6149798 DOI: 10.3390/molecules22122272] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 12/15/2017] [Accepted: 12/18/2017] [Indexed: 11/17/2022] Open
Abstract
l-Amino acid oxidases (l-AAO) catalyze the oxidative deamination of l-amino acids to the corresponding α-keto acids. The non-covalently bound cofactor FAD is reoxidized by oxygen under formation of hydrogen peroxide. We expressed an active l-AAO from the fungus Rhizoctonia solani as a fusion protein in E. coli. Treatment with small amounts of the detergent sodium dodecyl sulfate (SDS) stimulated the activity of the enzyme strongly. Here, we investigated whether other detergents and amphiphilic molecules activate 9His-rsLAAO1. We found that 9His-rsLAAO1 was also activated by sodium tetradecyl sulfate. Other detergents and fatty acids were not effective. Moreover, effects of SDS on the oligomerization state and the protein structure were analyzed. Native and SDS-activated 9His-rsLAAO1 behaved as dimers by size-exclusion chromatography. SDS treatment induced an increase in hydrodynamic radius as observed by size-exclusion chromatography and dynamic light scattering. The activated enzyme showed accelerated thermal inactivation and an exposure of additional protease sites. Changes in tryptophan fluorescence point to a more hydrophilic environment. Moreover, FAD fluorescence increased and a lower concentration of sulfites was sufficient to form adducts with FAD. Taken together, these data point towards a more open conformation of SDS-activated l-amino acid oxidase facilitating access to the active site.
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Affiliation(s)
- Katharina Hahn
- Biochemistry III, Department of Chemistry, Universitätsstrasse 25, Bielefeld University, 33615 Bielefeld, Germany.
| | - Yvonne Hertle
- Physical and Biophysical Chemistry, Department of Chemistry, Universitätsstrasse 25, Bielefeld University, 33615 Bielefeld, Germany.
| | - Svenja Bloess
- Biochemistry III, Department of Chemistry, Universitätsstrasse 25, Bielefeld University, 33615 Bielefeld, Germany.
| | - Tilman Kottke
- Physical and Biophysical Chemistry, Department of Chemistry, Universitätsstrasse 25, Bielefeld University, 33615 Bielefeld, Germany.
| | - Thomas Hellweg
- Physical and Biophysical Chemistry, Department of Chemistry, Universitätsstrasse 25, Bielefeld University, 33615 Bielefeld, Germany.
| | - Gabriele Fischer von Mollard
- Biochemistry III, Department of Chemistry, Universitätsstrasse 25, Bielefeld University, 33615 Bielefeld, Germany.
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59
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Park YK, Nicaud JM, Ledesma-Amaro R. The Engineering Potential of Rhodosporidium toruloides as a Workhorse for Biotechnological Applications. Trends Biotechnol 2017; 36:304-317. [PMID: 29132754 DOI: 10.1016/j.tibtech.2017.10.013] [Citation(s) in RCA: 125] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 10/18/2017] [Accepted: 10/19/2017] [Indexed: 12/30/2022]
Abstract
Moving our society towards a bioeconomy requires efficient and sustainable microbial production of chemicals and fuels. Rhodotorula (Rhodosporidium) toruloides is a yeast that naturally synthesizes substantial amounts of specialty chemicals and has been recently engineered to (i) enhance its natural production of lipids and carotenoids, and (ii) produce novel industrially relevant compounds. The use of R. toruloides by companies and research groups has exponentially increased in recent years as a result of recent improvements in genetic engineering techniques and the availability of multiomics information on its genome and metabolism. This review focuses on recent engineering approaches in R. toruloides for bioproduction and explores its potential as a biotechnological chassis.
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Affiliation(s)
- Young-Kyoung Park
- Micalis Institute, Institut National de la Recherche Agronomique (INRA), AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Jean-Marc Nicaud
- Micalis Institute, Institut National de la Recherche Agronomique (INRA), AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
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60
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Rosini E, Melis R, Molla G, Tessaro D, Pollegioni L. Deracemization and Stereoinversion of α-Amino Acids byl-Amino Acid Deaminase. Adv Synth Catal 2017. [DOI: 10.1002/adsc.201700806] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Elena Rosini
- Department of Biotechnology and Life Sciences; Università degli Studi dell'Insubria; via J.H. Dunant 3 21100 Varese Italy
- The Protein Factory; Politecnico di Milano and Università degli Studi dell'Insubria; via Mancinelli 7 20131 Milano Italy
| | - Roberta Melis
- Department of Biotechnology and Life Sciences; Università degli Studi dell'Insubria; via J.H. Dunant 3 21100 Varese Italy
- The Protein Factory; Politecnico di Milano and Università degli Studi dell'Insubria; via Mancinelli 7 20131 Milano Italy
| | - Gianluca Molla
- Department of Biotechnology and Life Sciences; Università degli Studi dell'Insubria; via J.H. Dunant 3 21100 Varese Italy
- The Protein Factory; Politecnico di Milano and Università degli Studi dell'Insubria; via Mancinelli 7 20131 Milano Italy
| | - Davide Tessaro
- The Protein Factory; Politecnico di Milano and Università degli Studi dell'Insubria; via Mancinelli 7 20131 Milano Italy
- Department of Chemistry, Materials and Chemical Engineering “Giulio Natta”; Politecnico di Milano; p.zza Leonardo da Vinci 32 20133 Milano Italy
| | - Loredano Pollegioni
- Department of Biotechnology and Life Sciences; Università degli Studi dell'Insubria; via J.H. Dunant 3 21100 Varese Italy
- The Protein Factory; Politecnico di Milano and Università degli Studi dell'Insubria; via Mancinelli 7 20131 Milano Italy
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61
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Molla G, Melis R, Pollegioni L. Breaking the mirror: l-Amino acid deaminase, a novel stereoselective biocatalyst. Biotechnol Adv 2017; 35:657-668. [DOI: 10.1016/j.biotechadv.2017.07.011] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 07/04/2017] [Accepted: 07/30/2017] [Indexed: 12/27/2022]
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62
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PH-Dependent Enantioselectivity of D-amino Acid Oxidase in Aqueous Solution. Sci Rep 2017; 7:2994. [PMID: 28592826 PMCID: PMC5462808 DOI: 10.1038/s41598-017-03177-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 04/26/2017] [Indexed: 11/30/2022] Open
Abstract
D-amino acid oxidases (DAAO) are stereospecific enzymes which are generally almost inactive towards L-enantiomer in neutral solution when L-, D-amino acids are supplied as substrates. In this paper, the D-amino acid oxidase can catalytic oxidize L-amino acids by modulating pH of aqueous solution. With L-Pro as substrate, the catalytic rate (kcat) and the affinity (Km) of DAAO were 6.71 s−1 and 33 mM at pH 8.0, respectively, suggesting that optimal pH condition enhanced the activity of DAAO towards L-Pro. Similar results were obtained when L-Ala (pH 9.8), L-Arg (pH 6.5), L-Phe (pH 9.0), L-Thr (pH 9.4), and L-Val (pH 8.5) were catalyzed by DAAO at various pH values. The racemization of the L-amino acids was not found by capillary electrophoresis analysis during oxidation, and quantification analysis of L-amino acids before and after catalytic reaction was performed, which confirmed that the modulation of enantioselectivity of DAAO resulted from the oxidation of L-amino acids rather than D-amino acids by changing pH. A mechanistic model was proposed to explain enhanced activity of DAAO towards L-amino acids under optimal pH condition.
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63
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Du K, Zhao J, Sun J, Feng W. Specific Ligation of Two Multimeric Enzymes with Native Peptides and Immobilization with Controlled Molar Ratio. Bioconjug Chem 2017; 28:1166-1175. [DOI: 10.1021/acs.bioconjchem.7b00043] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Kun Du
- Department of Biochemical
Engineering, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Jinjin Zhao
- Department of Biochemical
Engineering, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Jian Sun
- Department of Biochemical
Engineering, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Wei Feng
- Department of Biochemical
Engineering, Beijing University of Chemical Technology, Beijing, 100029, China
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64
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Armenia I, Balzaretti R, Pirrone C, Allegretti C, D'Arrigo P, Valentino M, Gornati R, Bernardini G, Pollegioni L. l-aspartate oxidase magnetic nanoparticles: synthesis, characterization and l-aspartate bioconversion. RSC Adv 2017. [DOI: 10.1039/c7ra00384f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
l-aspartate oxidase (LASPO) catalyses the stereospecific oxidative deamination of l-aspartate. Here, we describe the efficient immobilization of this enzyme on Fe3O4 NPs resulting in a stable NP-LASPO dispersion with a good reusability.
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Affiliation(s)
- Ilaria Armenia
- Dipartimento di Biotecnologie e Scienze della Vita
- Università degli Studi dell'Insubria
- 21100 Varese
- Italy
| | - Riccardo Balzaretti
- Dipartimento di Biotecnologie e Scienze della Vita
- Università degli Studi dell'Insubria
- 21100 Varese
- Italy
| | - Cristina Pirrone
- Dipartimento di Biotecnologie e Scienze della Vita
- Università degli Studi dell'Insubria
- 21100 Varese
- Italy
| | - Chiara Allegretti
- Dipartimento di Chimica
- Materiali e Ingegneria Chimica “Giulio Natta”
- Politecnico di Milano
- 20133 Milano
- Italy
| | - Paola D'Arrigo
- Dipartimento di Chimica
- Materiali e Ingegneria Chimica “Giulio Natta”
- Politecnico di Milano
- 20133 Milano
- Italy
| | - Mattia Valentino
- The Protein Factory, Politecnico di Milano
- ICRM CNR Milano
- Università degli Studi dell'Insubria
- 20131 Milano
- Italy
| | - Rosalba Gornati
- Dipartimento di Biotecnologie e Scienze della Vita
- Università degli Studi dell'Insubria
- 21100 Varese
- Italy
- The Protein Factory, Politecnico di Milano
| | - Giovanni Bernardini
- Dipartimento di Biotecnologie e Scienze della Vita
- Università degli Studi dell'Insubria
- 21100 Varese
- Italy
- The Protein Factory, Politecnico di Milano
| | - Loredano Pollegioni
- Dipartimento di Biotecnologie e Scienze della Vita
- Università degli Studi dell'Insubria
- 21100 Varese
- Italy
- The Protein Factory, Politecnico di Milano
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65
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Recombinant expression and characterization of a L-amino acid oxidase from the fungus Rhizoctonia solani. Appl Microbiol Biotechnol 2016; 101:2853-2864. [PMID: 27986991 DOI: 10.1007/s00253-016-8054-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Revised: 11/30/2016] [Accepted: 12/05/2016] [Indexed: 01/29/2023]
Abstract
L-Amino acid oxidases (L-AAOs) catalyze the oxidative deamination of L-amino acids to the corresponding α-keto acids, ammonia, and hydrogen peroxide. L-AAOs are homodimeric enzymes with FAD as a non-covalently bound cofactor. They are of potential interest for biotechnological applications. However, heterologous expression has not succeeded in producing large quantities of active recombinant L-AAOs with a broad substrate spectrum so far. Here, we report the heterologous expression of an active L-AAO from the fungus Rhizoctonia solani in Escherichia coli as a fusion protein with maltose-binding protein (MBP) as a solubility tag. After purification, it was possible to remove the MBP-tag proteolytically without influencing the enzyme activity. MBP-rsLAAO1 and 9His-rsLAAO1 converted basic and large hydrophobic L-amino acids as well as methyl esters of these L-amino acids. The progress of the conversion of L-phenylalanine and L-leucine into the corresponding α-keto acids was determined by HPLC and 1H-NMR analysis of reaction mixtures, respectively. Enzymatic activity was stimulated 50-100-fold by SDS treatment. K m values ranging from 0.9-10 mM and v max values from 3 to 10 U mg-1 were determined after SDS activation of 9His-rsLAAO1 for the best substrates. The enzyme displayed a broad pH optimum between pH 7.0 and 9.5. In summary, a successful overexpression of recombinant L-AAO in E. coli was established that results in a promising enzymatic activity and a broad substrate spectrum for biotechnological application.
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66
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Nakano S, Yasukawa K, Tokiwa T, Ishikawa T, Ishitsubo E, Matsuo N, Ito S, Tokiwa H, Asano Y. Origin of Stereoselectivity and Substrate/Ligand Recognition in an FAD-Dependent R-Selective Amine Oxidase. J Phys Chem B 2016; 120:10736-10743. [DOI: 10.1021/acs.jpcb.6b09328] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shogo Nakano
- Biotechnology
Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
- School
of Food and Nutritional Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
- Asano Active Enzyme Molecule Project, ERATO, JST, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Kazuyuki Yasukawa
- Biotechnology
Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
- Asano Active Enzyme Molecule Project, ERATO, JST, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Takaki Tokiwa
- Department
of Chemistry, Graduate School of Science, Tohoku University, Aramaki,
Aoba-ku, Sendai, Miyagi 980-8578, Japan
| | - Takeshi Ishikawa
- Department
of Molecular Microbiology and Immunology, Graduate School of Biomedical
Sciences, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan
| | - Erika Ishitsubo
- Department
of Chemistry, Rikkyo University, Nishi-ikebukuro, Toshimaku, Tokyo 171-8501, Japan
| | - Naoya Matsuo
- Department
of Chemistry, Rikkyo University, Nishi-ikebukuro, Toshimaku, Tokyo 171-8501, Japan
| | - Sohei Ito
- School
of Food and Nutritional Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Hiroaki Tokiwa
- Department
of Chemistry, Rikkyo University, Nishi-ikebukuro, Toshimaku, Tokyo 171-8501, Japan
- Research
Center of Smart Molecules, Rikkyo University, Nishi-ikebukuro, Toshimaku, Tokyo 171-8501, Japan
| | - Yasuhisa Asano
- Biotechnology
Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
- Asano Active Enzyme Molecule Project, ERATO, JST, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
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67
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Asn336 is involved in the substrate affinity of glycine oxidase from Bacillus cereus. ELECTRON J BIOTECHN 2016. [DOI: 10.1016/j.ejbt.2016.02.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
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68
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Immobilization of Genetically-Modified d-Amino Acid Oxidase and Catalase on Carbon Nanotubes to Improve the Catalytic Efficiency. Catalysts 2016. [DOI: 10.3390/catal6050066] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
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69
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Motta P, Molla G, Pollegioni L, Nardini M. Structure-Function Relationships in l-Amino Acid Deaminase, a Flavoprotein Belonging to a Novel Class of Biotechnologically Relevant Enzymes. J Biol Chem 2016; 291:10457-75. [PMID: 27022028 DOI: 10.1074/jbc.m115.703819] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Indexed: 01/11/2023] Open
Abstract
l-Amino acid deaminase from Proteus myxofaciens (PmaLAAD) is a membrane flavoenzyme that catalyzes the deamination of neutral and aromatic l-amino acids into α-keto acids and ammonia. PmaLAAD does not use dioxygen to re-oxidize reduced FADH2 and thus does not produce hydrogen peroxide; instead, it uses a cytochrome b-like protein as an electron acceptor. Although the overall fold of this enzyme resembles that of known amine or amino acid oxidases, it shows the following specific structural features: an additional novel α+β subdomain placed close to the putative transmembrane α-helix and to the active-site entrance; an FAD isoalloxazine ring exposed to solvent; and a large and accessible active site suitable to bind large hydrophobic substrates. In addition, PmaLAAD requires substrate-induced conformational changes of part of the active site, particularly in Arg-316 and Phe-318, to achieve the correct geometry for catalysis. These studies are expected to pave the way for rationally improving the versatility of this flavoenzyme, which is critical for biocatalysis of enantiomerically pure amino acids.
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Affiliation(s)
- Paolo Motta
- From the Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi deII'Insubria, via J. H. Dunant 3, 21100 Varese
| | - Gianluca Molla
- From the Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi deII'Insubria, via J. H. Dunant 3, 21100 Varese, The Protein Factory, Politecnico di Milano and Università degli Studi deII'Insubria, 21100 Varese, and
| | - Loredano Pollegioni
- From the Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi deII'Insubria, via J. H. Dunant 3, 21100 Varese, The Protein Factory, Politecnico di Milano and Università degli Studi deII'Insubria, 21100 Varese, and
| | - Marco Nardini
- the Dipartimento di Bioscienze, Università degli Studi di Milano, via Celoria 26, 20133 Milano, Italy
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70
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Zhang K, Guo Y, Yao P, Lin Y, Kumar A, Liu Z, Wu G, Zhang L. Characterization and directed evolution of BliGO, a novel glycine oxidase from Bacillus licheniformis. Enzyme Microb Technol 2016; 85:12-8. [PMID: 26920475 DOI: 10.1016/j.enzmictec.2015.12.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Revised: 12/22/2015] [Accepted: 12/29/2015] [Indexed: 12/18/2022]
Abstract
Glycine oxidase (GO) has great potential for use in biosensors, industrial catalysis and agricultural biotechnology. In this study, a novel GO (BliGO) from a marine bacteria Bacillus licheniformis was cloned and characterized. BliGO showed 62% similarity to the well-studied GO from Bacillus subtilis. The optimal activity of BliGO was observed at pH 8.5 and 40°C. Interestingly, BliGO retained 60% of the maximum activity at 0°C, suggesting it is a cold-adapted enzyme. The kinetic parameters on glyphosate (Km, kcat and k(cat)/K(m)) of BliGO were 11.22 mM, 0.08 s(-1), and 0.01 mM(-1) s(-1), respectively. To improve the catalytic activity to glyphosate, the BliGO was engineered by directed evolution. With error-prone PCR and two rounds of DNA shuffling, the most evolved mutant SCF-4 was obtained from 45,000 colonies, which showed 7.1- and 8-fold increase of affinity (1.58 mM) and catalytic efficiency (0.08 mM(-1) s(-1)) to glyphosate, respectively. In contrast, its activity to glycine (the natural substrate of GO) decreased by 113-fold. Structure modeling and site-directed mutation study indicated that Ser51 in SCF-4 involved in the binding of enzyme with glyphosate and played a crucial role in the improvement of catalytic efficiency.
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Affiliation(s)
- Kai Zhang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yiming Guo
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Pei Yao
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yongjun Lin
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Ashok Kumar
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Ziduo Liu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Gaobing Wu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Lili Zhang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin of Xinjiang Production and Construction Crops, College of Life Science, Tarim University, Alar 843300, China.
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71
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Luo X, Wu J, Jing S, Yan LJ. Hyperglycemic Stress and Carbon Stress in Diabetic Glucotoxicity. Aging Dis 2016; 7:90-110. [PMID: 26816666 DOI: 10.14336/ad.2015.0702] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2015] [Accepted: 07/02/2015] [Indexed: 12/16/2022] Open
Abstract
Diabetes and its complications are caused by chronic glucotoxicity driven by persistent hyperglycemia. In this article, we review the mechanisms of diabetic glucotoxicity by focusing mainly on hyperglycemic stress and carbon stress. Mechanisms of hyperglycemic stress include reductive stress or pseudohypoxic stress caused by redox imbalance between NADH and NAD(+) driven by activation of both the polyol pathway and poly ADP ribose polymerase; the hexosamine pathway; the advanced glycation end products pathway; the protein kinase C activation pathway; and the enediol formation pathway. Mechanisms of carbon stress include excess production of acetyl-CoA that can over-acetylate a proteome and excess production of fumarate that can over-succinate a proteome; both of which can increase glucotoxicity in diabetes. For hyperglycemia stress, we also discuss the possible role of mitochondrial complex I in diabetes as this complex, in charge of NAD(+) regeneration, can make more reactive oxygen species (ROS) in the presence of excess NADH. For carbon stress, we also discuss the role of sirtuins in diabetes as they are deacetylases that can reverse protein acetylation thereby attenuating diabetic glucotoxicity and improving glucose metabolism. It is our belief that targeting some of the stress pathways discussed in this article may provide new therapeutic strategies for treatment of diabetes and its complications.
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Affiliation(s)
- Xiaoting Luo
- 1 Department of Pharmaceutical Sciences, UNT System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, TX 76107, USA; 2 Department of Biochemistry and Molecular Biology, Gannan Medical University, Ganzhou, Jiangxi province, China, 341000
| | - Jinzi Wu
- 1 Department of Pharmaceutical Sciences, UNT System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, TX 76107, USA
| | - Siqun Jing
- 1 Department of Pharmaceutical Sciences, UNT System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, TX 76107, USA; 3 College of Life Sciences and Technology, Xinjiang University, Urumqi, Xinjiang, China, 830046
| | - Liang-Jun Yan
- 1 Department of Pharmaceutical Sciences, UNT System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, TX 76107, USA
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72
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Campillo-Brocal JC, Lucas-Elío P, Sanchez-Amat A. Distribution in Different Organisms of Amino Acid Oxidases with FAD or a Quinone As Cofactor and Their Role as Antimicrobial Proteins in Marine Bacteria. Mar Drugs 2015; 13:7403-18. [PMID: 26694422 PMCID: PMC4699246 DOI: 10.3390/md13127073] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 11/27/2015] [Accepted: 12/08/2015] [Indexed: 12/27/2022] Open
Abstract
Amino acid oxidases (AAOs) catalyze the oxidative deamination of amino acids releasing ammonium and hydrogen peroxide. Several kinds of these enzymes have been reported. Depending on the amino acid isomer used as a substrate, it is possible to differentiate between l-amino acid oxidases and d-amino acid oxidases. Both use FAD as cofactor and oxidize the amino acid in the alpha position releasing the corresponding keto acid. Recently, a novel class of AAOs has been described that does not contain FAD as cofactor, but a quinone generated by post-translational modification of residues in the same protein. These proteins are named as LodA-like proteins, after the first member of this group described, LodA, a lysine epsilon oxidase synthesized by the marine bacterium Marinomonas mediterranea. In this review, a phylogenetic analysis of all the enzymes described with AAO activity has been performed. It is shown that it is possible to recognize different groups of these enzymes and those containing the quinone cofactor are clearly differentiated. In marine bacteria, particularly in the genus Pseudoalteromonas, most of the proteins described as antimicrobial because of their capacity to generate hydrogen peroxide belong to the group of LodA-like proteins.
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Affiliation(s)
- Jonatan C Campillo-Brocal
- Department of Genetics and Microbiology, Faculty of Biology, University of Murcia, Murcia 30100, Spain.
| | - Patricia Lucas-Elío
- Department of Genetics and Microbiology, Faculty of Biology, University of Murcia, Murcia 30100, Spain.
| | - Antonio Sanchez-Amat
- Department of Genetics and Microbiology, Faculty of Biology, University of Murcia, Murcia 30100, Spain.
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73
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Han H, Zhu B, Fu X, You S, Wang B, Li Z, Zhao W, Peng R, Yao Q. Overexpression of D-amino acid oxidase from Bradyrhizobium japonicum, enhances resistance to glyphosate in Arabidopsis thaliana. PLANT CELL REPORTS 2015; 34:2043-51. [PMID: 26350405 DOI: 10.1007/s00299-015-1850-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Revised: 07/21/2015] [Accepted: 07/27/2015] [Indexed: 05/17/2023]
Abstract
KEY MESSAGE The glyphosate resistance in Escherichia coli and Arabidopsis was due to D-amino acid oxidase expression. Transgenic glyphosate-resistant crops have a high percentage in the total area devoted to transgenic crops worldwide. D-amino acid oxidase (DAAO) can metabolize glyphosate by oxidative cleavage of the carbon-nitrogen bond on the carboxyl side and yield aminomethyl phosphonic acid and glyoxylate, which are less toxic to plants than glyphosate. To date, reports on the use of DAAO to enhance glyphosate resistance in plants are lacking. In this paper, we report synthesis, and codon usage optimization for plant expression, of the DAAO gene by successive polymerase chain reaction from Bradyrhizobium japonicum. To confirm the glyphosate resistance of the DAAO gene, the recombinant plasmid pYPX251 (GenBank Accession No: AY178046) harboring the wild-type DAAO gene was transformed into DH5α. The positive transformants grew well both on solid and in liquid M9 medium containing 200 mM glyphosate. The optimized DAAO gene was transformed into Arabidopsis and 9 days after application of 10 mM glyphosate, the 4-week-old wild-type plants all died; by contrast, transgenic plants could grow normally. The proline content and peroxidase activity showed that glyphosate could induce proline accumulation and produce reactive oxygen species.
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Affiliation(s)
- Hongjuan Han
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, 2901 Beidi Rd, Shanghai, 201106, People's Republic of China
| | - Bo Zhu
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, 2901 Beidi Rd, Shanghai, 201106, People's Republic of China
| | - Xiaoyan Fu
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, 2901 Beidi Rd, Shanghai, 201106, People's Republic of China
| | - Shuanghong You
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, 2901 Beidi Rd, Shanghai, 201106, People's Republic of China
- College of Horticulture Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Bo Wang
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, 2901 Beidi Rd, Shanghai, 201106, People's Republic of China
| | - Zhenjun Li
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, 2901 Beidi Rd, Shanghai, 201106, People's Republic of China
| | - Wei Zhao
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, 2901 Beidi Rd, Shanghai, 201106, People's Republic of China
| | - Rihe Peng
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, 2901 Beidi Rd, Shanghai, 201106, People's Republic of China
| | - Quanhong Yao
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, 2901 Beidi Rd, Shanghai, 201106, People's Republic of China.
- College of Horticulture Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.
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74
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Mollica L, Conti G, Pollegioni L, Cavalli A, Rosini E. Unveiling the Atomic-Level Determinants of Acylase–Ligand Complexes: An Experimental and Computational Study. J Chem Inf Model 2015; 55:2227-41. [DOI: 10.1021/acs.jcim.5b00535] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Luca Mollica
- CompuNet, Istituto Italiano di Tecnologia, via Morego 30, 16163 Genova, Italy
| | - Gianluca Conti
- Dipartimento
di Biotecnologie e Scienze della Vita, Università degli studi dell’Insubria, via J. H. Dunant 3, 21100 Varese, Italy
| | - Loredano Pollegioni
- Dipartimento
di Biotecnologie e Scienze della Vita, Università degli studi dell’Insubria, via J. H. Dunant 3, 21100 Varese, Italy
- The
Protein Factory, Centro Interuniversitario di Biotecnologie Proteiche, Politecnico di Milano and Università degli studi dell’Insubria, via Mancinelli 7, 20131 Milano, Italy
| | - Andrea Cavalli
- CompuNet, Istituto Italiano di Tecnologia, via Morego 30, 16163 Genova, Italy
- Department
of Pharmacy and Biotechnology, Alma Mater Studiorum, University of Bologna, via Belmeloro 6, 40126 Bologna, Italy
| | - Elena Rosini
- Dipartimento
di Biotecnologie e Scienze della Vita, Università degli studi dell’Insubria, via J. H. Dunant 3, 21100 Varese, Italy
- The
Protein Factory, Centro Interuniversitario di Biotecnologie Proteiche, Politecnico di Milano and Università degli studi dell’Insubria, via Mancinelli 7, 20131 Milano, Italy
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75
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New synthesis and biodistribution of the D-amino acid oxidase-magnetic nanoparticle system. Future Sci OA 2015; 1:FSO67. [PMID: 28031918 PMCID: PMC5138019 DOI: 10.4155/fso.15.67] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 07/15/2015] [Indexed: 01/04/2023] Open
Abstract
Background: Application of nanoenzymes, based on D-amino acid oxidase (DAAO) conjugated to magnetic nanoparticles (NPs), as anticancer system requires improvement of the synthesis protocol and in vivo distribution evaluation. Results: A new and more efficient synthesis via EDC-NHS produced an Fe3O4NP-APTES-DAAO system with a specific activity of 7 U/mg NPs. IR spectroscopy showed that all Fe3O4 NP sites are saturated with APTES and all available NH2 sites with DAAO. The acute cytotoxicity of the new system does not differ from that of the previous one. In vivo experiments showed that the system did not cause adverse effects, cross the brain–blood barrier and accumulate in the heart. Conclusions: Our results support the possibility to use enzymes conjugated to magnetic NPs for cancer treatment. Besides, we think that enzymes and other biological molecules efficiently conjugated to magnetic NPs might constitute a category of ‘bionanoparticles’ to be exploited, not only in medical, but also in industrial biotechnology. Lay abstract: We have linked magnetic nanoparticles to D-amino acid oxidase, an enzyme capable of producing, in the presence of its substrate, reactive oxygen species. The scope is to use the magnetic properties of the enzyme-nanoparticle system to direct it to a desired area where its cytotoxicity can be controlled by the addition of exogenous substrate. Besides the possible applications in cancer therapy, we think that enzymes and other biological molecules linked to magnetic nanoparticles might also be exploited in industrial biotechnology.
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76
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Yang F, Wang Z, Zhang X, Jiang L, Li Y, Wang L. A Green Chemoenzymatic Process for the Synthesis of Azoxybenzenes. ChemCatChem 2015. [DOI: 10.1002/cctc.201500720] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Fengjuan Yang
- Key Laboratory of Molecular Enzymology and Engineering of Ministry of Education; School of Life Sciences; Jilin University; 2699 Qianjin street Changchun P.R. China
| | - Zhi Wang
- Key Laboratory of Molecular Enzymology and Engineering of Ministry of Education; School of Life Sciences; Jilin University; 2699 Qianjin street Changchun P.R. China
| | - Xiaowen Zhang
- Key Laboratory of Molecular Enzymology and Engineering of Ministry of Education; School of Life Sciences; Jilin University; 2699 Qianjin street Changchun P.R. China
| | - Liyan Jiang
- Key Laboratory of Molecular Enzymology and Engineering of Ministry of Education; School of Life Sciences; Jilin University; 2699 Qianjin street Changchun P.R. China
| | - Yazhuo Li
- College of food science and Engineering; Jilin University; 2699 Qianjin street Changchun P.R. China
| | - Lei Wang
- Key Laboratory of Molecular Enzymology and Engineering of Ministry of Education; School of Life Sciences; Jilin University; 2699 Qianjin street Changchun P.R. China
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77
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Du K, Sun J, Song X, Song C, Feng W. Enhancement of the solubility and stability of D-amino acid oxidase by fusion to an elastin like polypeptide. J Biotechnol 2015. [PMID: 26216181 DOI: 10.1016/j.jbiotec.2015.07.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
An elastin-like polypeptide (ELP) was fused to D-amino acid oxidases (DAAO). ELP-DAAO exhibited a better solubility in aqueous solutions than DAAO, and its enzymatic activity is about 1.6 times that of DAAO. The stability of the proteins was investigated by interacting with urea at various concentrations. The circular dichroism and fluorescence spectra were measured. The results demonstrated that that ELP-DAAO exhibited a much better stability than DAAO, and ELP-DAAO has retained the α-helix content with a high percentage even at a high urea concentration. The results of this work have demonstrated that the ELP tag can be utilized to purify DAAO, in the meantime the solubility and stability of the enzyme are improved.
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Affiliation(s)
- Kun Du
- Department of Biochemical Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Jian Sun
- Department of Biochemical Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Xiaoqiang Song
- Department of Biochemical Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Cuidan Song
- Department of Biochemical Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Wei Feng
- Department of Biochemical Engineering, Beijing University of Chemical Technology, Beijing 100029, China.
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78
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Takahashi S, Abe K, Kera Y. Bacterial d-amino acid oxidases: Recent findings and future perspectives. Bioengineered 2015; 6:237-41. [PMID: 25996186 DOI: 10.1080/21655979.2015.1052917] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
D-Amino acid oxidase (DAO) is a flavin enzyme that catalyzes the oxidative deamination of d-amino acids. This enzyme has been studied extensively both biochemically and structurally as a model for the oxidase-dehydrogenase class of flavoproteins. This enzyme also has various applications, such as the determination of d-amino acids and production of building blocks for a number of pharmaceuticals. DAO has been found mainly in eukaryotic organisms and has been suggested to play a significant role in various cellular processes, one of which includes neurotransmission in the human brain. In contrast, this enzyme has not been identified in prokaryotic organisms. Some studies have recently identified and characterized DAO enzyme in some actinobacteria. In addition, a genome database search reveals a wide distribution of DAO homologous genes in this bacterial group. The bacterial DAOs characterized so far have certain distinct properties in comparison to eukaryotic DAOs. These enzymes also exhibit some important applicable properties, suggesting that bacteria could be used as a source for obtaining novel and useful DAOs. The physiological function of bacterial DAO have been proposed to include the degradation of non-canonical d-amino acids released from cell wall, but is still largely unknown and need to be studied in depth.
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Affiliation(s)
- Shouji Takahashi
- a Department of Bioengineering ; Nagaoka University of Technology ; Nagaoka , Niigata , Japan
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79
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Ou Q, Liu Y, Deng J, Chen G, Yang Y, Shen P, Wu B, Jiang C. A novel D-amino acid oxidase from a contaminated agricultural soil metagenome and its characterization. Antonie van Leeuwenhoek 2015; 107:1615-23. [PMID: 25900453 DOI: 10.1007/s10482-015-0457-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Accepted: 04/15/2015] [Indexed: 01/07/2023]
Abstract
A novel D-amino acid oxidase (DAAO) gene designated as daoE was cloned by the sequence-based screening of a plasmid metagenomic library of uncultured microorganisms from contaminated agricultural soil. The deduced amino acid sequence comparison and phylogenetic analysis indicated that daoE and other putative DAAOs are closely related. The putative DAAO gene was subcloned into a pETBlue-2 vector and overexpressed in Escherichia coli Tunner(DE3)pLacI. The recombinant protein was purified to homogeneity. The maximum activity of DaoE protein occurred at pH 8.0 and 37 °C. DaoE recombinant protein had an apparent K m of 2.96 mM, V max of 0.018 mM/min, k cat of 10.9/min, and k cat/K m of 1.16 × 10(4)/mol/min. The identification of this novel DAAO gene demonstrated the importance of metagenomic libraries in exploring new D-amino acid oxidases from environmental microorganisms to optimize their applications.
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Affiliation(s)
- Qian Ou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, The Key Laboratory of Ministry of Education for Microbial and Plant Genetic Engineering, College of Life Science and Technology, Guangxi University, 100 Daxue East Road, Nanning, 530004, Guangxi, China
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80
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Tessaro D, Pollegioni L, Piubelli L, D’Arrigo P, Servi S. Systems Biocatalysis: An Artificial Metabolism for Interconversion of Functional Groups. ACS Catal 2015. [DOI: 10.1021/cs502064s] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- D. Tessaro
- Dipartimento
di Chimica, Materiali e Ingegneria Chimica “Giulio Natta”, Politecnico di Milano, p.za L. da Vinci 32, 20133 Milano, Italy
- The
Protein Factory, Centro Interuniversitario di Biotecnologie Proteiche, Politecnico di Milano and Università degli Studi dell’Insubria, via Mancinelli 7, 20131 Milano, Italy
| | - L. Pollegioni
- Dipartimento
di Biotecnologie e Scienze della Vita, Università degli Studi dell’Insubria, via J.H. Dunant 3, 21100 Varese, Italy
- The
Protein Factory, Centro Interuniversitario di Biotecnologie Proteiche, Politecnico di Milano and Università degli Studi dell’Insubria, via Mancinelli 7, 20131 Milano, Italy
| | - L. Piubelli
- Dipartimento
di Biotecnologie e Scienze della Vita, Università degli Studi dell’Insubria, via J.H. Dunant 3, 21100 Varese, Italy
- The
Protein Factory, Centro Interuniversitario di Biotecnologie Proteiche, Politecnico di Milano and Università degli Studi dell’Insubria, via Mancinelli 7, 20131 Milano, Italy
| | - P. D’Arrigo
- Dipartimento
di Chimica, Materiali e Ingegneria Chimica “Giulio Natta”, Politecnico di Milano, p.za L. da Vinci 32, 20133 Milano, Italy
- The
Protein Factory, Centro Interuniversitario di Biotecnologie Proteiche, Politecnico di Milano and Università degli Studi dell’Insubria, via Mancinelli 7, 20131 Milano, Italy
| | - S. Servi
- The
Protein Factory, Centro Interuniversitario di Biotecnologie Proteiche, Politecnico di Milano and Università degli Studi dell’Insubria, via Mancinelli 7, 20131 Milano, Italy
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81
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Conti G, Pollegioni L, Rosini E. One-pot conversion of cephalosporin C by using an optimized two-enzyme process. Catal Sci Technol 2015. [DOI: 10.1039/c4cy01522c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Setup of a low cost one-pot enzymatic system to directly convert cephalosporin C into 7-aminocephalosporanic acid with high purity.
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Affiliation(s)
- Gianluca Conti
- Dipartimento di Biotecnologie e Scienze della Vita
- Università degli Studi dell'Insubria
- 21100 Varese
- Italy
| | - Loredano Pollegioni
- Dipartimento di Biotecnologie e Scienze della Vita
- Università degli Studi dell'Insubria
- 21100 Varese
- Italy
- The Protein Factory
| | - Elena Rosini
- Dipartimento di Biotecnologie e Scienze della Vita
- Università degli Studi dell'Insubria
- 21100 Varese
- Italy
- The Protein Factory
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82
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D'Arrigo P, Allegretti C, Fiorati A, Piubelli L, Rosini E, Tessaro D, Valentino M, Pollegioni L. Immobilization of l-aspartate oxidase from Sulfolobus tokodaii as a biocatalyst for resolution of aspartate solutions. Catal Sci Technol 2015. [DOI: 10.1039/c4cy00968a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
l-Aspartate oxidase from the thermophilic archaebacterium Sulfolobus tokodaii (StLASPO) catalyzes the stereoselective oxidative deamination of l-aspartate to yield oxaloacetate, ammonia and hydrogen peroxide.
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Affiliation(s)
- Paola D'Arrigo
- Dipartimento di Chimica
- Materiali e Ingegneria Chimica “Giulio Natta”
- Politecnico di Milano
- 20133 Milano
- Italy
| | - Chiara Allegretti
- Dipartimento di Chimica
- Materiali e Ingegneria Chimica “Giulio Natta”
- Politecnico di Milano
- 20133 Milano
- Italy
| | - Andrea Fiorati
- Dipartimento di Chimica
- Materiali e Ingegneria Chimica “Giulio Natta”
- Politecnico di Milano
- 20133 Milano
- Italy
| | - Luciano Piubelli
- The Protein Factory
- Politecnico di Milano
- ICRM CNR Milano
- and Università degli Studi dell'Insubria
- 20131 Milano
| | - Elena Rosini
- The Protein Factory
- Politecnico di Milano
- ICRM CNR Milano
- and Università degli Studi dell'Insubria
- 20131 Milano
| | - Davide Tessaro
- Dipartimento di Chimica
- Materiali e Ingegneria Chimica “Giulio Natta”
- Politecnico di Milano
- 20133 Milano
- Italy
| | - Mattia Valentino
- The Protein Factory
- Politecnico di Milano
- ICRM CNR Milano
- and Università degli Studi dell'Insubria
- 20131 Milano
| | - Loredano Pollegioni
- The Protein Factory
- Politecnico di Milano
- ICRM CNR Milano
- and Università degli Studi dell'Insubria
- 20131 Milano
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83
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Molla G, Nardini M, Motta P, D'Arrigo P, Panzeri W, Pollegioni L. Aminoacetone oxidase from Streptococcus oligofermentans belongs to a new three-domain family of bacterial flavoproteins. Biochem J 2014; 464:387-99. [PMID: 25269103 DOI: 10.1042/bj20140972] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023]
Abstract
The aaoSo gene from Streptococcus oligofermentans encodes a 43 kDa flavoprotein, aminoacetone oxidase (SoAAO), which was reported to possess a low catalytic activity against several different L-amino acids; accordingly, it was classified as an L-amino acid oxidase. Subsequently, SoAAO was demonstrated to oxidize aminoacetone (a pro-oxidant metabolite), with an activity ~25-fold higher than the activity displayed on L-lysine, thus lending support to the assumption of aminoacetone as the preferred substrate. In the present study, we have characterized the SoAAO structure-function relationship. SoAAO is an FAD-containing enzyme that does not possess the classical properties of the oxidase/dehydrogenase class of flavoproteins (i.e. no flavin semiquinone formation is observed during anaerobic photoreduction as well as no reaction with sulfite) and does not show a true L-amino acid oxidase activity. From a structural point of view, SoAAO belongs to a novel protein family composed of three domains: an α/β domain corresponding to the FAD-binding domain, a β-domain partially modulating accessibility to the coenzyme, and an additional α-domain. Analysis of the reaction products of SoAAO on aminoacetone showed 2,5-dimethylpyrazine as the main product; we propose that condensation of two aminoacetone molecules yields 3,6-dimethyl-2,5-dihydropyrazine that is subsequently oxidized to 2,5-dimethylpyrazine. The ability of SoAAO to bind two molecules of the substrate analogue O-methylglycine ligand is thought to facilitate the condensation reaction. A specialized role for SoAAO in the microbial defence mechanism related to aminoacetone catabolism through a pathway yielding dimethylpyrazine derivatives instead of methylglyoxal can be proposed.
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Affiliation(s)
- Gianluca Molla
- *Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi deII'Insubria, via J.H. Dunant 3, 21100 Varese, ltaly
| | - Marco Nardini
- ‡Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milano, Italy
| | - Paolo Motta
- *Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi deII'Insubria, via J.H. Dunant 3, 21100 Varese, ltaly
| | - Paola D'Arrigo
- †The Protein Factory, Centro Interuniversitario di Biotecnologie Proteiche, Politecnico di Milano, ICRM CNR Milano, and Università degli Studi deII'Insubria, Varese, Italy
| | - Walter Panzeri
- ║CNR-Istituto di Chimica del Riconoscimento Molecolare, Politecnico di Milano, via Mancinelli 7, 20131 Milano, Italy
| | - Loredano Pollegioni
- *Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi deII'Insubria, via J.H. Dunant 3, 21100 Varese, ltaly
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84
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Rosini E, Piubelli L, Molla G, Frattini L, Valentino M, Varriale A, D'Auria S, Pollegioni L. Novel biosensors based on optimized glycine oxidase. FEBS J 2014; 281:3460-72. [DOI: 10.1111/febs.12873] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Revised: 05/27/2014] [Accepted: 06/09/2014] [Indexed: 12/16/2022]
Affiliation(s)
- Elena Rosini
- Dipartimento di Biotecnologie e Scienze della Vita; Università degli studi dell'Insubria; Varese Italy
- The Protein Factory; Centro Interuniversitario di Biotecnologie Proteiche; Politecnico di Milano; ICRM CNR Milano; Università degli studi dell'Insubria; Milano Italy
| | - Luciano Piubelli
- Dipartimento di Biotecnologie e Scienze della Vita; Università degli studi dell'Insubria; Varese Italy
- The Protein Factory; Centro Interuniversitario di Biotecnologie Proteiche; Politecnico di Milano; ICRM CNR Milano; Università degli studi dell'Insubria; Milano Italy
| | - Gianluca Molla
- Dipartimento di Biotecnologie e Scienze della Vita; Università degli studi dell'Insubria; Varese Italy
- The Protein Factory; Centro Interuniversitario di Biotecnologie Proteiche; Politecnico di Milano; ICRM CNR Milano; Università degli studi dell'Insubria; Milano Italy
| | - Luca Frattini
- Dipartimento di Biotecnologie e Scienze della Vita; Università degli studi dell'Insubria; Varese Italy
| | - Mattia Valentino
- The Protein Factory; Centro Interuniversitario di Biotecnologie Proteiche; Politecnico di Milano; ICRM CNR Milano; Università degli studi dell'Insubria; Milano Italy
- CNR - Istituto di Chimica del Riconoscimento Molecolare; Sezione Adolfo Quilico; Milano Italy
| | | | - Sabato D'Auria
- CNR - Istituto di Biochimica delle Proteine; Napoli Italy
| | - Loredano Pollegioni
- Dipartimento di Biotecnologie e Scienze della Vita; Università degli studi dell'Insubria; Varese Italy
- The Protein Factory; Centro Interuniversitario di Biotecnologie Proteiche; Politecnico di Milano; ICRM CNR Milano; Università degli studi dell'Insubria; Milano Italy
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85
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Pollegioni L, Motta P, Molla G. L-amino acid oxidase as biocatalyst: a dream too far? Appl Microbiol Biotechnol 2014; 97:9323-41. [PMID: 24077723 DOI: 10.1007/s00253-013-5230-1] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Revised: 08/29/2013] [Accepted: 09/02/2013] [Indexed: 12/27/2022]
Abstract
L-amino acid oxidase (LAAO) is a flavoenzyme containing non-covalently bound flavin adenine dinucleotide, which catalyzes the stereospecific oxidative deamination of l-amino acids to α-keto acids and also produces ammonia and hydrogen peroxide via an imino acid intermediate. LAAOs purified from snake venoms are the best-studied members of this family of enzymes, although a number of LAAOs from bacterial and fungal sources have been also reported. From a biochemical point of view, LAAOs from different sources are distinguished by molecular mass, substrate specificity, post-translational modifications and regulation. In analogy to the well-known biotechnological applications of d-amino acid oxidase, important results are expected from the availability of suitable LAAOs; however, these expectations have not been fulfilled yet because none of the "true" LAAOs has successfully been expressed as a recombinant protein in prokaryotic hosts, such as Escherichia coli. In enzyme biotechnology, recombinant production of a protein is mandatory both for the production of large amounts of the catalyst and to improve its biochemical properties by protein engineering. As an alternative, flavoenzymes active on specific l-amino acids have been identified, e.g., l-aspartate oxidase, l-lysine oxidase, l-phenylalanine oxidase, etc. According to presently available information, amino acid oxidases with "narrow" or "strict" substrate specificity represent as good candidates to obtain an enzyme more suitable for biotechnological applications by enlarging their substrate specificity by means of protein engineering.
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86
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L-Amino acid oxidases from microbial sources: types, properties, functions, and applications. Appl Microbiol Biotechnol 2013; 98:1507-15. [PMID: 24352734 DOI: 10.1007/s00253-013-5444-2] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Revised: 11/26/2013] [Accepted: 11/27/2013] [Indexed: 10/25/2022]
Abstract
L-Amino acid oxidases (LAAOs), which catalyze the stereospecific oxidative deamination of L-amino acids to α-keto acids and ammonia, are flavin adenine dinucleotide-containing homodimeric proteins. L-Amino acid oxidases are widely distributed in diverse organisms and have a range of properties. Because expressing LAAOs as recombinant proteins in heterologous hosts is difficult, their biotechnological applications have not been thoroughly advanced. LAAOs are thought to contribute to amino acid catabolism, enhance iron acquisition, display antimicrobial activity, and catalyze keto acid production, among other roles. Here, we review the types, properties, structures, biological functions, heterologous expression, and applications of LAAOs obtained from microbial sources. We expect this review to increase interest in LAAO studies.
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87
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Mutant d-amino acid oxidase with higher catalytic efficiency toward d-amino acids with bulky side chains. Russ Chem Bull 2013. [DOI: 10.1007/s11172-012-0193-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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88
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Woodley JM. Protein engineering of enzymes for process applications. Curr Opin Chem Biol 2013; 17:310-6. [PMID: 23562542 DOI: 10.1016/j.cbpa.2013.03.017] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Revised: 03/11/2013] [Accepted: 03/12/2013] [Indexed: 12/14/2022]
Abstract
Scientific progress in the field of enzyme modification today enables the opportunity to tune a given biocatalyst for a specific industrial application. Much work has been focused on extending the substrate repertoire and altering selectivity. Nevertheless, it is clear that many new forthcoming opportunities will be targeted on modification to enable process application. This article discusses the challenges involved in enzyme modification focused on process requirements, such as the need to fulfill reaction thermodynamics, specific activity under the required conditions, kinetics at required concentrations, and stability. Finally, future research directions are discussed, including the integration of biocatalysis with neighboring chemical steps.
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Affiliation(s)
- John M Woodley
- Center for Process Engineering and Technology, Department of Chemical and Biochemical Engineering, Technical University of Denmark, DK-2800 Lyngby, Denmark.
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89
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Structure of a class III engineered cephalosporin acylase: comparisons with class I acylase and implications for differences in substrate specificity and catalytic activity. Biochem J 2013; 451:217-26. [DOI: 10.1042/bj20121715] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The crystal structure of the wild-type form of glutaryl-7-ACA (7-aminocephalosporanic acid) acylase from Pseudomonas N176 and a double mutant of the protein (H57βS/H70βS) that displays enhanced catalytic efficiency on cephalosporin C over glutaryl-7-aminocephalosporanic acid has been determined. The structures show a heterodimer made up of an α-chain (229 residues) and a β-chain (543 residues) with a deep cavity, which constitutes the active site. Comparison of the wild-type and mutant structures provides insights into the molecular reasons for the observed enhanced specificity on cephalosporin C over glutaryl-7-aminocephalosporanic acid and offers the basis to evolve a further improved enzyme variant. The nucleophilic catalytic serine residue, Ser1β, is situated at the base of the active site cavity. The electron density reveals a ligand covalently bound to the catalytic serine residue, such that a tetrahedral adduct is formed. This is proposed to mimic the transition state of the enzyme for both the maturation step and the catalysis of the substrates. A view of the transition state configuration of the enzyme provides important insights into the mechanism of substrate binding and catalysis.
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90
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Pollegioni L, Rosini E, Molla G. Cephalosporin C acylase: dream and(/or) reality. Appl Microbiol Biotechnol 2013; 97:2341-55. [PMID: 23417342 DOI: 10.1007/s00253-013-4741-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Revised: 01/24/2013] [Accepted: 01/24/2013] [Indexed: 11/30/2022]
Abstract
Cephalosporins currently constitute the most widely prescribed class of antibiotics and are used to treat diseases caused by both Gram-positive and Gram-negative bacteria. Cephalosporins contain a 7-aminocephalosporanic acid (7-ACA) nucleus which is derived from cephalosporin C (CephC). The 7-ACA nucleus is not sufficiently potent for clinical use; however, a series of highly effective antibiotic agents could be produced by modifying the side chains linked to the 7-ACA nucleus. The industrial production of higher-generation semi-synthetic cephalosporins starts from 7-ACA, which is obtained by deacylation of the naturally occurring antibiotic CephC. CephC can be converted to 7-ACA either chemically or enzymatically using D-amino acid oxidase and glutaryl-7-aminocephalosporanic acid acylase. Both these methods show limitation, including the production of toxic waste products (chemical process) and the expense (the enzymatic one). In order to circumvent these problems, attempts have been undertaken to design a single-step means of enzymatically converting CephC to 7-ACA in the course of the past 10 years. The most suitable approach is represented by engineering the activity of a known glutaryl-7-aminocephalosporanic acid acylase such that it will bind and deacylate CephC more preferentially over glutaryl-7-aminocephalosporanic acid. Here, we describe the state of the art in the production of an effective and specific CephC acylase.
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Affiliation(s)
- Loredano Pollegioni
- Dipartimento di Biotecnologie e Scienze della Vita, Università degli studi dell'Insubria, Varese, Italy.
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91
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A thermostable L-aspartate oxidase: a new tool for biotechnological applications. Appl Microbiol Biotechnol 2013; 97:7285-95. [PMID: 23371294 DOI: 10.1007/s00253-013-4688-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Revised: 12/22/2012] [Accepted: 12/27/2012] [Indexed: 11/27/2022]
Abstract
L-Amino acid oxidases (LAAOs) are homodimeric flavin adenine dinucleotide (FAD)-containing flavoproteins that catalyze the stereospecific oxidative deamination of L-amino acids to α-keto acids, ammonia, and hydrogen peroxide. Unlike the D-selective counterpart, the biotechnological application of LAAOs has not been thoroughly advanced because of the difficulties in their expression as recombinant protein in prokaryotic hosts. In this work, L-aspartate oxidase from the thermophilic archea Sulfolobus tokodaii (StLASPO, specific for L-aspartate and L-asparagine only) was efficiently produced as recombinant protein in E. coli in the active form as holoenzyme. This recombinant flavoenzyme shows the classical properties of FAD-containing oxidases. Indeed, StLASPO shows distinctive features that makes it attractive for biotechnological applications: high thermal stability (it is fully stable up to 80 °C) and high temperature optimum, stable activity in a broad range of pH (7.0-10.0), weak inhibition by the product oxaloacetate and by D-aspartate, and tight binding of the FAD cofactor. This latter property significantly distinguishes StLASPO from the E. coli counterpart. StLASPO represents an appropriate novel biocatalyst for the production of D-aspartate and a well-suited protein scaffold to evolve a LAAO activity by protein engineering.
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92
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Lata S, Batra B, Pundir C. Construction of d-amino acid biosensor based on d-amino acid oxidase immobilized onto poly (indole-5-carboxylic acid)/zinc sulfide nanoparticles hybrid film. Process Biochem 2012. [DOI: 10.1016/j.procbio.2012.07.034] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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93
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Abstract
Oligolamellar phospholipid vesicles incorporated with d-amino acid oxidase from porcine kidney (OV-DAO) were prepared by encapsulating pre-formed enzyme-bound unilamellar vesicles (UV-DAO) with bilayers of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC). The bilayer of UV-DAO was composed of POPC, 30 mol% of cholesterol and 15 mol% of 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine-N-(glutaryl) (NGPE) that was responsible for covalent linking to D-amino acid oxidase (DAO). OV-DAO and UV-DAO showed the activity to catalyze the oxidation of D-alanine as measured based on the hydrogen peroxide produced. The oligolamellar and unilamellar structure of OV-DAO and UV-DAO, respectively was elucidated based on the quenching characteristics of bilayers-incorporated fluorescent lipid 7-nitro-2,1,3-benzoxadiazol-4-yl-phosphoethanolamine (NBD-PE) and the size distribution of the vesicles measured with the dynamic light scattering method. The enzyme activity of OV-DAO and UV-DAO was significantly stabilized at 50°C compared to that of free DAO at the fixed enzyme concentration of 3.29 μg/mL. At the temperature, OV-DAO and UV-DAO showed the remaining activity of 52.7 and 29.6%, respectively at the incubation time of 20 min while free DAO was completely deactivated. Thus the dimeric form of DAO could be stabilized by its coupling to the surface of UV-DAO membrane being the inner bilayer of OV-DAO. Furthermore, the thermal denaturation of DAO and dissociation of flavin adenine dinucleotide (FAD) from the subunits of enzyme were prevented in the aqueous phase formed between the bilayers of OV-DAO.
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94
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Verma R, Schwaneberg U, Roccatano D. MAP(2.0)3D: a sequence/structure based server for protein engineering. ACS Synth Biol 2012; 1:139-50. [PMID: 23651115 DOI: 10.1021/sb200019x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The Mutagenesis Assistant Program (MAP) is a web-based tool to provide statistical analyses of the mutational biases of directed evolution experiments on amino acid substitution patterns. MAP analysis assists protein engineers in the benchmarking of random mutagenesis methods that generate single nucleotide mutations in a codon. Herein, we describe a completely renewed and improved version of the MAP server, the MAP(2.0)3D server, which correlates the generated amino acid substitution patterns to the structural information of the target protein. This correlation aids in the selection of a more suitable random mutagenesis method with specific biases on amino acid substitution patterns. In particular, the new server represents MAP indicators on secondary and tertiary structure and correlates them to specific structural components such as hydrogen bonds, hydrophobic contacts, salt bridges, solvent accessibility, and crystallographic B-factors. Three model proteins (D-amino oxidase, phytase, and N-acetylneuraminic acid aldolase) are used to illustrate the novel capability of the server. MAP(2.0)3D server is available publicly at http://map.jacobs-university.de/map3d.html.
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Affiliation(s)
- Rajni Verma
- School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, 28759 Bremen,
Germany
- Department of Biotechnology, RWTH Aachen University, Worringer Weg 1, 52074 Aachen,
Germany
| | - Ulrich Schwaneberg
- Department of Biotechnology, RWTH Aachen University, Worringer Weg 1, 52074 Aachen,
Germany
| | - Danilo Roccatano
- School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, 28759 Bremen,
Germany
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95
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Rosini E, Monelli CS, Pollegioni L, Riva S, Monti D. On the substrate preference of glutaryl acylases. ACTA ACUST UNITED AC 2012. [DOI: 10.1016/j.molcatb.2011.12.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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96
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Wang Y, Yu H, Zhang J, Luo H, Shen Z. Double knockout of β-lactamase and cephalosporin acetyl esterase genes from Escherichia coli reduces cephalosporin C decomposition. J Biosci Bioeng 2012; 113:737-41. [PMID: 22382016 DOI: 10.1016/j.jbiosc.2012.02.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2011] [Revised: 01/23/2012] [Accepted: 02/02/2012] [Indexed: 11/28/2022]
Abstract
The phenomenon of CPC decomposition occurs in Escherichia coli JM105/pMKC-sCPCacy during the one-step enzymatic conversion of cephalosporin C (CPC) into 7-aminocephalosporanic acid (7-ACA) by CPC acylase (sCPCAcy) for synthesis of cephalosporin antibiotics. E. coli JM105/pMKC-sCPCacy can constitutively produce sCPCacy as a fusion protein with maltose binding protein (MBP). Control experiments verified that the cell lysis solution from the host E. coli JM105 resulted in CPC decomposition by approximately 15%. Two miscellaneous enzymes, β-lactamase (AmpC) and cephalosporin acetyl esterase (Aes), are believed to play a major role in the degradation of CPC. Using the Red recombination system, the genes ampC, aes or both ampC and aes were knocked out from the chromosome of E. coli JM105 to generate the engineers: E. coli JM105(ΔampC), E. coli JM105(Δaes) and E. coli JM105(ΔampC, Δaes). The CPC decomposition was reduced to 12.2% in E. coli JM105(Δaes), 1.3% in E. coli JM105(ΔampC), and even undetectable in ampC-aes double knockout cells of E. coli JM105(ΔampC, Δaes). When catalyzed by crude MBP-sCPCAcy isolated from E. coli JM105(ΔampC, Δaes)/pMKC-sCPCacy (3377U·l(-1)), the CPC utilization efficiency increased to 98.4% from the original 88.7%. Similar results were obtained for the ampC-aes double knockout host derived from E. coli JM109(DE3) and the CPC utilization efficiency enhanced to 99.3% in the catalysis of crude sCPCAcy harvested from E. coli JM109(DE3, ΔampC, Δaes)/pET28-sCPCacy.
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Affiliation(s)
- Ying Wang
- Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, P R China
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97
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Bolivar JM, Nidetzky B. Oriented and selective enzyme immobilization on functionalized silica carrier using the cationic binding module Zbasic2: Design of a heterogeneous D-amino acid oxidase catalyst on porous glass. Biotechnol Bioeng 2012; 109:1490-8. [DOI: 10.1002/bit.24423] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2011] [Revised: 12/10/2011] [Accepted: 12/19/2011] [Indexed: 11/08/2022]
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98
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Wang Y, Yu H, Song W, An M, Zhang J, Luo H, Shen Z. Overexpression of synthesized cephalosporin C acylase containing mutations in the substrate transport tunnel. J Biosci Bioeng 2012; 113:36-41. [DOI: 10.1016/j.jbiosc.2011.08.027] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2011] [Revised: 08/05/2011] [Accepted: 08/30/2011] [Indexed: 10/17/2022]
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Pollegioni L, Schonbrunn E, Siehl D. Molecular basis of glyphosate resistance-different approaches through protein engineering. FEBS J 2011; 278:2753-66. [PMID: 21668647 PMCID: PMC3145815 DOI: 10.1111/j.1742-4658.2011.08214.x] [Citation(s) in RCA: 109] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Glyphosate (N-phosphonomethyl-glycine) is the most widely used herbicide in the world: glyphosate-based formulations exhibit broad-spectrum herbicidal activity with minimal human and environmental toxicity. The extraordinary success of this simple, small molecule is mainly attributable to the high specificity of glyphosate for the plant enzyme enolpyruvyl shikimate-3-phosphate synthase in the shikimate pathway, leading to the biosynthesis of aromatic amino acids. Starting in 1996, transgenic glyphosate-resistant plants were introduced, thus allowing application of the herbicide to the crop (post-emergence) to remove emerged weeds without crop damage. This review focuses on mechanisms of resistance to glyphosate as obtained through natural diversity, the gene-shuffling approach to molecular evolution, and a rational, structure-based approach to protein engineering. In addition, we offer a rationale for the means by which the modifications made have had their intended effect.
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Affiliation(s)
- Loredano Pollegioni
- Dipartimento di Biotecnologie e Scienze Molecolari, Università degli Studi dell'Insubria, Varese, Italy.
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