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Characterization of proteins from the 3N5M family reveals an operationally stable amine transaminase. Appl Microbiol Biotechnol 2022; 106:5563-5574. [PMID: 35932295 PMCID: PMC9418295 DOI: 10.1007/s00253-022-12071-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 06/22/2022] [Accepted: 07/05/2022] [Indexed: 01/24/2023]
Abstract
Abstract Amine transaminases (ATA) convert ketones into optically active amines and are used to prepare active pharmaceutical ingredients and building blocks. Novel ATA can be identified in protein databases due to the extensive knowledge of sequence-function relationships. However, predicting thermo- and operational stability from the amino acid sequence is a persisting challenge and a vital step towards identifying efficient ATA biocatalysts for industrial applications. In this study, we performed a database mining and characterized selected putative enzymes of the β-alanine:pyruvate transaminase cluster (3N5M) — a subfamily with so far only a few described members, whose tetrameric structure was suggested to positively affect operational stability. Four putative transaminases (TA-1: Bilophilia wadsworthia, TA-5: Halomonas elongata, TA-9: Burkholderia cepacia, and TA-10: Burkholderia multivorans) were obtained in a soluble form as tetramers in E. coli. During comparison of these tetrameric with known dimeric transaminases we found that indeed novel ATA with high operational stabilities can be identified in this protein subfamily, but we also found exceptions to the hypothesized correlation that a tetrameric assembly leads to increased stability. The discovered ATA from Burkholderia multivorans features a broad substrate specificity, including isopropylamine acceptance, is highly active (6 U/mg) in the conversion of 1-phenylethylamine with pyruvate and shows a thermostability of up to 70 °C under both, storage and operating conditions. In addition, 50% (v/v) of isopropanol or DMSO can be employed as co-solvents without a destabilizing effect on the enzyme during an incubation time of 16 h at 30 °C. Key points • Database mining identified a thermostable amine transaminase in the β-alanine:pyruvate transaminase subfamily. • The tetrameric transaminase tolerates 50% DMSO and isopropanol under operating conditions at 30 °C. • A tetrameric structure is not necessarily associated with a higher operational stability Graphical abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1007/s00253-022-12071-1.
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Mital S, Christie G, Dikicioglu D. Recombinant expression of insoluble enzymes in Escherichia coli: a systematic review of experimental design and its manufacturing implications. Microb Cell Fact 2021; 20:208. [PMID: 34717620 PMCID: PMC8557517 DOI: 10.1186/s12934-021-01698-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 10/22/2021] [Indexed: 02/06/2023] Open
Abstract
Recombinant enzyme expression in Escherichia coli is one of the most popular methods to produce bulk concentrations of protein product. However, this method is often limited by the inadvertent formation of inclusion bodies. Our analysis systematically reviews literature from 2010 to 2021 and details the methods and strategies researchers have utilized for expression of difficult to express (DtE), industrially relevant recombinant enzymes in E. coli expression strains. Our review identifies an absence of a coherent strategy with disparate practices being used to promote solubility. We discuss the potential to approach recombinant expression systematically, with the aid of modern bioinformatics, modelling, and ‘omics’ based systems-level analysis techniques to provide a structured, holistic approach. Our analysis also identifies potential gaps in the methods used to report metadata in publications and the impact on the reproducibility and growth of the research in this field.
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Affiliation(s)
- Suraj Mital
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, CB3 0AS, UK
| | - Graham Christie
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, CB3 0AS, UK
| | - Duygu Dikicioglu
- Department of Biochemical Engineering, University College London, London, WC1E 6BT, UK.
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Ferrandi EE, Bassanini I, Sechi B, Vanoni M, Tessaro D, Guðbergsdóttir SR, Riva S, Peng X, Monti D. Discovery and Characterization of a Novel Thermostable β-Amino Acid Transaminase from a Meiothermus Strain Isolated in an Icelandic Hot Spring. Biotechnol J 2020; 15:e2000125. [PMID: 32893504 DOI: 10.1002/biot.202000125] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 07/29/2020] [Indexed: 02/02/2023]
Abstract
A Meiothermus strain capable of using β-phenylalanine for growth is isolated by culture enrichment of samples collected in hot environments and the genome is sequenced showing the presence of 22 putative transaminase (TA) sequences. On the basis of phylogenetic and sequence analysis, a TA termed Ms-TA2 is selected for further studies. The enzyme is successfully produced in Escherichia coli Rosetta(DE3) cells, with 70 mg of pure protein obtained from 1 L culture after purification by affinity chromatography. Ms-TA2 shows high activity toward (S)-β-phenylalanine and other (S)-β-amino acids, as well as a preference for α-ketoglutarate and aromatic aldehydes as amino acceptors. Moreover, Ms-TA2 is shown to be a thermostable enzyme by maintaining about 60% of the starting activity after 3 h incubation at 50 °C and showing a melting temperature of about 73 °C. Finally, a homology-based structural model of Ms-TA2 is built and key active site interactions for substrate and cofactor binding are analyzed.
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Affiliation(s)
- Erica E Ferrandi
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta" (SCITEC), CNR, Via Mario Bianco 9, Milan, 20131, Italy.,Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen, 2200, Denmark
| | - Ivan Bassanini
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta" (SCITEC), CNR, Via Mario Bianco 9, Milan, 20131, Italy.,Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via Mangiagalli 25, Milan, 20133, Italy
| | - Barbara Sechi
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta" (SCITEC), CNR, Via Mario Bianco 9, Milan, 20131, Italy
| | - Marta Vanoni
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta" (SCITEC), CNR, Via Mario Bianco 9, Milan, 20131, Italy
| | - Davide Tessaro
- Dipartimento di Chimica, Materiali e Ingegneria Chimica, Politecnico di Milano, Via Mancinelli 7, Milan, 20131, Italy
| | | | - Sergio Riva
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta" (SCITEC), CNR, Via Mario Bianco 9, Milan, 20131, Italy
| | - Xu Peng
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen, 2200, Denmark
| | - Daniela Monti
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta" (SCITEC), CNR, Via Mario Bianco 9, Milan, 20131, Italy
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Roura Padrosa D, Alaux R, Smith P, Dreveny I, López-Gallego F, Paradisi F. Enhancing PLP-Binding Capacity of Class-III ω-Transaminase by Single Residue Substitution. Front Bioeng Biotechnol 2019; 7:282. [PMID: 31681755 PMCID: PMC6813460 DOI: 10.3389/fbioe.2019.00282] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 10/04/2019] [Indexed: 11/25/2022] Open
Abstract
Transaminases are pyridoxal-5′-phosphate (PLP) binding enzymes, broadly studied for their potential industrial application. Their affinity for PLP has been related to their performance and operational stability and while significant differences in PLP requirements have been reported, the environment of the PLP-binding pocket is highly conserved. In this study, thorough analysis of the residue interaction network of three homologous transaminases Halomonas elongata (HeTA), Chromobacterium violaceum (CvTA), and Pseudomonas fluorescens (PfTA) revealed a single residue difference in their PLP binding pocket: an asparagine at position 120 in HeTA. N120 is suitably positioned to interact with an aspartic acid known to protonate the PLP pyridinium nitrogen, while the equivalent position is occupied by a valine in the other two enzymes. Three different mutants were constructed (HeTA-N120V, CvTA-V124N, and PfTA-V129N) and functionally analyzed. Notably, in HeTA and CvTA, the asparagine variants, consistently exhibited a higher thermal stability and a significant decrease in the dissociation constant (Kd) for PLP, confirming the important role of N120 in PLP binding. Moreover, the reaction intermediate pyridoxamine-5′-phosphate (PMP) was released more slowly into the bulk, indicating that the mutation also enhances their PMP binding capacity. The crystal structure of PfTA, elucidated in this work, revealed a tetrameric arrangement with the PLP binding sites near the subunit interface. In this case, the V129N mutation had a negligible effect on PLP-binding, but it reduced its temperature stability possibly destabilizing the quaternary structure.
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Affiliation(s)
| | - Raphael Alaux
- School of Chemistry, University of Nottingham, Nottingham, United Kingdom
| | - Phillip Smith
- Centre for Biomolecular Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Ingrid Dreveny
- Centre for Biomolecular Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Fernando López-Gallego
- Instituto de Síntesis Química y Catálisis Homogénea, Zaragoza, Spain.,ARAID Foundation, Zaragoza, Spain
| | - Francesca Paradisi
- School of Chemistry, University of Nottingham, Nottingham, United Kingdom.,Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
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Mattio LM, Marengo M, Parravicini C, Eberini I, Dallavalle S, Bonomi F, Iametti S, Pinto A. Inhibition of Pancreatic α-amylase by Resveratrol Derivatives: Biological Activity and Molecular Modelling Evidence for Cooperativity between Viniferin Enantiomers. Molecules 2019; 24:E3225. [PMID: 31491840 PMCID: PMC6766848 DOI: 10.3390/molecules24183225] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 08/29/2019] [Accepted: 09/02/2019] [Indexed: 02/06/2023] Open
Abstract
To improve the current understanding of the role of stilbenoids in the management of diabetes, the inhibition of the pancreatic α-amylase by resveratrol derivatives was investigated. To approach in a systematic way, the mechanistic and structural aspects of the interaction, potential bioactive agents were prepared as single molecules, that were used for the biological evaluation of the determinants of inhibitory binding. Some dimeric stilbenoids-in particular, viniferin isomers- were found to be better than the reference drug acarbose in inhibiting the pancreatic α-amylase. Racemic mixtures of viniferins were more effective inhibitors than the respective isolated pure enantiomers at an equivalent total concentration, and displayed cooperative effects not observed with the individual enantiomers. The molecular docking analysis provided a thermodynamics-based rationale for the measured inhibitory ability and for the observed synergistic effects. Indeed, the binding of additional ligands on the surface of the alpha-amylase was found to decrease the dissociation constant of inhibitors bound to the active site of the enzyme, thus providing a mechanistic rationale for the observed inhibitory synergies.
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Affiliation(s)
- Luce M Mattio
- Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, Via Celoria 2, 20133 Milano, Italy
| | - Mauro Marengo
- Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, Via Celoria 2, 20133 Milano, Italy
| | - Chiara Parravicini
- Department of Pharmacological and Biomolecular Sciences (DiSFeB) & cDSRC, University of Milan, Via Balzaretti 9, 20133 Milano, Italy
| | - Ivano Eberini
- Department of Pharmacological and Biomolecular Sciences (DiSFeB) & cDSRC, University of Milan, Via Balzaretti 9, 20133 Milano, Italy
| | - Sabrina Dallavalle
- Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, Via Celoria 2, 20133 Milano, Italy
| | - Francesco Bonomi
- Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, Via Celoria 2, 20133 Milano, Italy
| | - Stefania Iametti
- Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, Via Celoria 2, 20133 Milano, Italy
| | - Andrea Pinto
- Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, Via Celoria 2, 20133 Milano, Italy.
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Zeaiter Z, Marasco R, Booth JM, Prosdocimi EM, Mapelli F, Callegari M, Fusi M, Michoud G, Molinari F, Daffonchio D, Borin S, Crotti E. Phenomics and Genomics Reveal Adaptation of Virgibacillus dokdonensis Strain 21D to Its Origin of Isolation, the Seawater-Brine Interface of the Mediterranean Sea Deep Hypersaline Anoxic Basin Discovery. Front Microbiol 2019; 10:1304. [PMID: 31244812 PMCID: PMC6581673 DOI: 10.3389/fmicb.2019.01304] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 05/27/2019] [Indexed: 12/03/2022] Open
Abstract
The adaptation of sporeformers to extreme environmental conditions is frequently questioned due to their capacity to produce highly resistant endospores that are considered as resting contaminants, not representing populations adapted to the system. In this work, in order to gain a better understanding of bacterial adaptation to extreme habitats, we investigated the phenotypic and genomic characteristics of the halophile Virgibacillus sp. 21D isolated from the seawater-brine interface (SBI) of the MgCl2-saturated deep hypersaline anoxic basin Discovery located in the Eastern Mediterranean Sea. Vegetative cells of strain 21D showed the ability to grow in the presence of high concentrations of MgCl2, such as 14.28% corresponding to 1.5 M. Biolog phenotype MicroArray (PM) was adopted to investigate the strain phenotype, with reference to carbon energy utilization and osmotic tolerance. The strain was able to metabolize only 8.4% of 190 carbon sources provided in the PM1 and PM2 plates, mainly carbohydrates, in accordance with the low availability of nutrients in its habitat of origin. By using in silico DNA-DNA hybridization the analysis of strain 21D genome, assembled in one circular contig, revealed that the strain belongs to the species Virgibacillus dokdonensis. The genome presented compatible solute-based osmoadaptation traits, including genes encoding for osmotically activated glycine-betaine/carnitine/choline ABC transporters, as well as ectoine synthase enzymes. Osmoadaptation of the strain was then confirmed with phenotypic assays by using the osmolyte PM9 Biolog plate and growth experiments. Furthermore, the neutral isoelectric point of the reconstructed proteome suggested that the strain osmoadaptation was mainly mediated by compatible solutes. The presence of genes involved in iron acquisition and metabolism indicated that osmoadaptation was tailored to the iron-depleted saline waters of the Discovery SBI. Overall, both phenomics and genomics highlighted the potential capability of V. dokdonensis 21D vegetative cells to adapt to the environmental conditions in Discovery SBI.
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Affiliation(s)
- Zahraa Zeaiter
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l’Ambiente (DeFENS), Università degli Studi di Milano, Milan, Italy
| | - Ramona Marasco
- Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Jenny M. Booth
- Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Erica M. Prosdocimi
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l’Ambiente (DeFENS), Università degli Studi di Milano, Milan, Italy
| | - Francesca Mapelli
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l’Ambiente (DeFENS), Università degli Studi di Milano, Milan, Italy
| | - Matteo Callegari
- Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Marco Fusi
- Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Grégoire Michoud
- Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Francesco Molinari
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l’Ambiente (DeFENS), Università degli Studi di Milano, Milan, Italy
| | - Daniele Daffonchio
- Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Sara Borin
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l’Ambiente (DeFENS), Università degli Studi di Milano, Milan, Italy
| | - Elena Crotti
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l’Ambiente (DeFENS), Università degli Studi di Milano, Milan, Italy
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Galman JL, Gahloth D, Parmeggiani F, Slabu I, Leys D, Turner NJ. Characterization of a Putrescine Transaminase From Pseudomonas putida and its Application to the Synthesis of Benzylamine Derivatives. Front Bioeng Biotechnol 2018; 6:205. [PMID: 30622946 PMCID: PMC6308316 DOI: 10.3389/fbioe.2018.00205] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 12/12/2018] [Indexed: 01/08/2023] Open
Abstract
The reductive amination of prochiral ketones using biocatalysts has been of great interest to the pharmaceutical industry in the last decade for integrating novel strategies in the production of chiral building blocks with the intent of minimizing impact on the environment. Amongst the enzymes able to catalyze the direct amination of prochiral ketones, pyridoxal 5'-phosphate (PLP) dependent ω-transaminases have shown great promise as versatile industrial biocatalysts with high selectivity, regioselectivity, and broad substrate scope. Herein the biochemical characterization of a putrescine transaminase from Pseudomonas putida (Pp-SpuC) was performed, which showed an optimum pH and temperature of 8.0 and 60°C, respectively. To gain further structural insight of this enzyme, we crystallized the protein in the apo form and determined the structure to 2.1 Å resolution which revealed a dimer that adopts a class I transaminase fold comparable to other class III transaminases. Furthermore we exploited its dual substrate recognition for biogenic diamines (i.e., cadaverine) and readily available monoamines (i.e., isopropylamine) for the synthesis of benzylamine derivatives with excellent product conversions and extremely broad substrate tolerance.
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Affiliation(s)
| | | | | | | | | | - Nicholas J. Turner
- School of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester, United Kingdom
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