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Santos H, Zeoly LA, Rodrigues MT, Fernandes FS, Gomes RC, Almeida WP, Coelho F. Recent Advances in Catalytic Systems for the Mechanistically Complex Morita–Baylis–Hillman Reaction. ACS Catal 2023. [DOI: 10.1021/acscatal.2c06420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Affiliation(s)
- Hugo Santos
- Institute of Chemistry, University of Campinas, Campinas 13083-970, São Paulo, Brazil
| | - Lucas A. Zeoly
- Institute of Chemistry, University of Campinas, Campinas 13083-970, São Paulo, Brazil
| | - Manoel T. Rodrigues
- Institute of Chemistry, University of Campinas, Campinas 13083-970, São Paulo, Brazil
| | - Fábio S. Fernandes
- Institute of Chemistry, University of Campinas, Campinas 13083-970, São Paulo, Brazil
| | - Ralph C. Gomes
- Institute of Chemistry, University of Campinas, Campinas 13083-970, São Paulo, Brazil
| | - Wanda P. Almeida
- Institute of Chemistry, University of Campinas, Campinas 13083-970, São Paulo, Brazil
| | - Fernando Coelho
- Institute of Chemistry, University of Campinas, Campinas 13083-970, São Paulo, Brazil
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2
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Assessing the genomic composition, putative ecological relevance and biotechnological potential of plasmids from sponge bacterial symbionts. Microbiol Res 2022; 265:127183. [PMID: 36108440 DOI: 10.1016/j.micres.2022.127183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 02/24/2022] [Accepted: 09/01/2022] [Indexed: 11/24/2022]
Abstract
Plasmid-mediated transfer of genes can have direct consequences in several biological processes within sponge microbial communities. However, very few studies have attempted genomic and functional characterization of plasmids from marine host-associated microbial communities in general and those of sponges in particular. In the present study, we used an endogenous plasmid isolation method to obtain plasmids from bacterial symbionts of the marine sponges Stylissa carteri and Paratetilla sp. and investigated the genomic composition, putative ecological relevance and biotechnological potential of these plasmids. In total, we isolated and characterized three complete plasmids, three plasmid prophages and one incomplete plasmid. Our results highlight the importance of plasmids to transfer relevant genetic traits putatively involved in microbial symbiont adaptation and host-microbe and microbe-microbe interactions. For example, putative genes involved in bacterial response to chemical stress, competition, metabolic versatility and mediation of bacterial colonization and pathogenicity were detected. Genes coding for enzymes and toxins of biotechnological potential were also detected. Most plasmid prophage coding sequences were, however, hypothetical proteins with unknown functions. Overall, this study highlights the ecological relevance of plasmids in the marine sponge microbiome and provides evidence that plasmids of sponge bacterial symbionts may represent an untapped resource of genes of biotechnological interest.
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3
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Unusual commonality in active site structural features of substrate promiscuous and specialist enzymes. J Struct Biol 2022; 214:107835. [DOI: 10.1016/j.jsb.2022.107835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 12/26/2021] [Accepted: 01/23/2022] [Indexed: 11/21/2022]
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5
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Abstract
Cold-active enzymes increase their catalytic efficiency at low-temperature, introducing structural flexibility at or near the active sites. Inevitably, this feat seems to be accompanied by lower thermal stability. These characteristics have made cold-active enzymes into attractive targets for the industrial applications, since they could reduce the energy cost in the reaction, attenuate side-reactions, and simply be inactivated. In addition, the increased structural flexibility could result in broad substrate specificity for various non-native substrates, which is called substrate promiscuity. In this perspective, we deal with a less addressed aspect of cold-active enzymes, substrate promiscuity, which has enormous potential for semi-synthesis or enzymatic modification of fine chemicals and drugs. Further structural and directed-evolutional studies on substrate promiscuity of cold-active enzymes will provide a new workhorse in white biotechnology.
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6
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Gupta MN, Roy I. Drugs, host proteins and viral proteins: how their promiscuities shape antiviral design. Biol Rev Camb Philos Soc 2020; 96:205-222. [PMID: 32918378 DOI: 10.1111/brv.12652] [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: 08/24/2020] [Accepted: 08/27/2020] [Indexed: 12/12/2022]
Abstract
The reciprocal nature of drug specificity and target specificity implies that the same is true for their respective promiscuities. Protein promiscuity has two broadly different types of footprint in drug design. The first is relaxed specificity of binding sites for substrates, inhibitors, effectors or cofactors. The second involves protein-protein interactions of regulatory processes such as signal transduction and transcription, and here protein intrinsic disorder plays an important role. Both viruses and host cells exploit intrinsic disorder for their survival, as do the design and discovery programs for antivirals. Drug action, strictly speaking, always relies upon promiscuous activity, with drug promiscuity enlarging its scope. Drug repurposing searches for additional promiscuity on the part of both the drug and the target in the host. Understanding the subtle nuances of these promiscuities is critical in the design of novel and more effective antivirals.
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Affiliation(s)
- Munishwar Nath Gupta
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, Hauz Khas, New Delhi, 110016, India
| | - Ipsita Roy
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research (NIPER), Sector 67, S.A.S. Nagar, Punjab, 160062, India
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7
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Gupta MN, Alam A, Hasnain SE. Protein promiscuity in drug discovery, drug-repurposing and antibiotic resistance. Biochimie 2020; 175:50-57. [PMID: 32416199 DOI: 10.1016/j.biochi.2020.05.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 04/29/2020] [Accepted: 05/04/2020] [Indexed: 12/01/2022]
Abstract
Proteins are supposed to bind to their substrates/ligands in a specific manner via their pre-formed binding sites, according to classical biochemistry. In recent years, several types of deviations from this norm have been observed and called promiscuous behavior. Enzymatic promiscuities allow several biochemical functions to be carried out by the same enzyme. The promiscuous activity can also be the origin of "new proteins" via gene duplication. In more recent years, proteins from prokaryotes, eukaryotes and viruses have been found to have intrinsic disorder and lack a preformed binding site. Intrinsic disorder is exploited in regulatory proteins such as those that are involved in transcription and signal transduction. Such proteins function by folding locally while binding to their ligands or interacting with other proteins. These phenomena have also been classified as examples of protein promiscuity and encompass diverse kinds of ligands that can bind to a protein. Given the significant extent of structural homology in many protein families, it is not surprising that ligands also have been found to display promiscuity. Promiscuous behavior of proteins offers both challenges and opportunities to the drug discovery programs such as drug repurposing. Pathogens when exposed to antibiotics exploit protein promiscuity in several ways to develop resistance to the drug. There is increasing evidence now to support that the disorder in proteins is a major tool used by pathogens for virulence and evade drug action by exploiting protein promiscuity. This review provides a holistic view of this multi-faceted phenomenon called protein promiscuity.
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Affiliation(s)
- Munishwar N Gupta
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, 110016, India
| | - Anwar Alam
- ICMR-National Institute of Pathology, Safdarjung Hospital Campus, New Delhi, 110029, India
| | - Seyed E Hasnain
- JH-Institute of Molecular Medicine, Jamia Hamdard, New Delhi, 110062, India; Dr Reddy's Institute of Life Sciences, University of Hyderabad Campus, Professor CR Rao Road, Hyderabad, 500046, India.
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8
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Affiliation(s)
- Munishwar Nath Gupta
- Former Professor, Department of Chemistry, Indian Institute of Technology, Hauz Khas, New Delhi 110016, India
| | - Ipsita Roy
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research (NIPER), Sector 67, S.A.S. Nagar, Punjab 160062, India
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9
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Biocatalysis as Useful Tool in Asymmetric Synthesis: An Assessment of Recently Granted Patents (2014–2019). Catalysts 2019. [DOI: 10.3390/catal9100802] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The broad interdisciplinary nature of biocatalysis fosters innovation, as different technical fields are interconnected and synergized. A way to depict that innovation is by conducting a survey on patent activities. This paper analyses the intellectual property activities of the last five years (2014–2019) with a specific focus on biocatalysis applied to asymmetric synthesis. Furthermore, to reflect the inventive and innovative steps, only patents that were granted during that period are considered. Patent searches using several keywords (e.g., enzyme names) have been conducted by using several patent engine servers (e.g., Espacenet, SciFinder, Google Patents), with focus on granted patents during the period 2014–2019. Around 200 granted patents have been identified, covering all enzyme types. The inventive pattern focuses on the protection of novel protein sequences, as well as on new substrates. In some other cases, combined processes, multi-step enzymatic reactions, as well as process conditions are the innovative basis. Both industries and academic groups are active in patenting. As a conclusion of this survey, we can assert that biocatalysis is increasingly recognized as a useful tool for asymmetric synthesis and being considered as an innovative option to build IP and protect synthetic routes.
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Rodrigues RC, Virgen-Ortíz JJ, dos Santos JC, Berenguer-Murcia Á, Alcantara AR, Barbosa O, Ortiz C, Fernandez-Lafuente R. Immobilization of lipases on hydrophobic supports: immobilization mechanism, advantages, problems, and solutions. Biotechnol Adv 2019; 37:746-770. [DOI: 10.1016/j.biotechadv.2019.04.003] [Citation(s) in RCA: 287] [Impact Index Per Article: 57.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 04/02/2019] [Accepted: 04/03/2019] [Indexed: 12/13/2022]
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Amin SA, Chavez E, Porokhin V, Nair NU, Hassoun S. Towards creating an extended metabolic model (EMM) for E. coli using enzyme promiscuity prediction and metabolomics data. Microb Cell Fact 2019; 18:109. [PMID: 31196115 PMCID: PMC6567437 DOI: 10.1186/s12934-019-1156-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 06/05/2019] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Metabolic models are indispensable in guiding cellular engineering and in advancing our understanding of systems biology. As not all enzymatic activities are fully known and/or annotated, metabolic models remain incomplete, resulting in suboptimal computational analysis and leading to unexpected experimental results. We posit that one major source of unaccounted metabolism is promiscuous enzymatic activity. It is now well-accepted that most, if not all, enzymes are promiscuous-i.e., they transform substrates other than their primary substrate. However, there have been no systematic analyses of genome-scale metabolic models to predict putative reactions and/or metabolites that arise from enzyme promiscuity. RESULTS Our workflow utilizes PROXIMAL-a tool that uses reactant-product transformation patterns from the KEGG database-to predict putative structural modifications due to promiscuous enzymes. Using iML1515 as a model system, we first utilized a computational workflow, referred to as Extended Metabolite Model Annotation (EMMA), to predict promiscuous reactions catalyzed, and metabolites produced, by natively encoded enzymes in Escherichia coli. We predict hundreds of new metabolites that can be used to augment iML1515. We then validated our method by comparing predicted metabolites with the Escherichia coli Metabolome Database (ECMDB). CONCLUSIONS We utilized EMMA to augment the iML1515 metabolic model to more fully reflect cellular metabolic activity. This workflow uses enzyme promiscuity as basis to predict hundreds of reactions and metabolites that may exist in E. coli but may have not been documented in iML1515 or other databases. We provide detailed analysis of 23 predicted reactions and 16 associated metabolites. Interestingly, nine of these metabolites, which are in ECMDB, have not previously been documented in any other E. coli databases. Four of the predicted reactions provide putative transformations parallel to those already in iML1515. We suggest adding predicted metabolites and reactions to iML1515 to create an extended metabolic model (EMM) for E. coli.
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Affiliation(s)
- Sara A. Amin
- Department of Computer Science, Tufts University, Medford, MA USA
| | - Elizabeth Chavez
- Department of Biology, University of North Carolina, Chapel Hill, NC USA
| | | | - Nikhil U. Nair
- Department of Chemical and Biological Engineering, Tufts University, Medford, MA USA
| | - Soha Hassoun
- Department of Computer Science, Tufts University, Medford, MA USA
- Department of Chemical and Biological Engineering, Tufts University, Medford, MA USA
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12
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Djoumbou-Feunang Y, Fiamoncini J, Gil-de-la-Fuente A, Greiner R, Manach C, Wishart DS. BioTransformer: a comprehensive computational tool for small molecule metabolism prediction and metabolite identification. J Cheminform 2019; 11:2. [PMID: 30612223 PMCID: PMC6689873 DOI: 10.1186/s13321-018-0324-5] [Citation(s) in RCA: 218] [Impact Index Per Article: 43.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 12/22/2018] [Indexed: 12/17/2022] Open
Abstract
Background A number of computational tools for metabolism prediction have been developed over the last 20 years to predict the structures of small molecules undergoing biological transformation or environmental degradation. These tools were largely developed to facilitate absorption, distribution, metabolism, excretion, and toxicity (ADMET) studies, although there is now a growing interest in using such tools to facilitate metabolomics and exposomics studies. However, their use and widespread adoption is still hampered by several factors, including their limited scope, breath of coverage, availability, and performance. Results To address these limitations, we have developed BioTransformer, a freely available software package for accurate, rapid, and comprehensive in silico metabolism prediction and compound identification. BioTransformer combines a machine learning approach with a knowledge-based approach to predict small molecule metabolism in human tissues (e.g. liver tissue), the human gut as well as the environment (soil and water microbiota), via its metabolism prediction tool. A comprehensive evaluation of BioTransformer showed that it was able to outperform two state-of-the-art commercially available tools (Meteor Nexus and ADMET Predictor), with precision and recall values up to 7 times better than those obtained for Meteor Nexus or ADMET Predictor on the same sets of pharmaceuticals, pesticides, phytochemicals or endobiotics under similar or identical constraints. Furthermore BioTransformer was able to reproduce 100% of the transformations and metabolites predicted by the EAWAG pathway prediction system. Using mass spectrometry data obtained from a rat experimental study with epicatechin supplementation, BioTransformer was also able to correctly identify 39 previously reported epicatechin metabolites via its metabolism identification tool, and suggest 28 potential metabolites, 17 of which matched nine monoisotopic masses for which no evidence of a previous report could be found. Conclusion BioTransformer can be used as an open access command-line tool, or a software library. It is freely available at https://bitbucket.org/djoumbou/biotransformerjar/. Moreover, it is also freely available as an open access RESTful application at www.biotransformer.ca, which allows users to manually or programmatically submit queries, and retrieve metabolism predictions or compound identification data. Electronic supplementary material The online version of this article (10.1186/s13321-018-0324-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Jarlei Fiamoncini
- INRA, Human Nutrition Unit, Université Clermont Auvergne, 63000, Clermont-Ferrand, France.,Department of Food and Experimental Nutrition, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | | | - Russell Greiner
- Department of Computing Science, University of Alberta, Edmonton, AB, T6G 2E8, Canada.,Alberta Machine Intelligence Institute, University of Alberta, Edmonton, AB, T6G 2E8, Canada
| | - Claudine Manach
- INRA, Human Nutrition Unit, Université Clermont Auvergne, 63000, Clermont-Ferrand, France
| | - David S Wishart
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada. .,Department of Computing Science, University of Alberta, Edmonton, AB, T6G 2E8, Canada.
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13
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Hen Egg White Lysozyme Catalyzed Efficient Synthesis of 3-Indolyl-3-hydroxy Oxindole in Aqueous Ethanol. Catal Letters 2018. [DOI: 10.1007/s10562-018-2551-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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Beer B, Pick A, Döring M, Lommes P, Sieber V. Substrate scope of a dehydrogenase from Sphingomonas species A1 and its potential application in the synthesis of rare sugars and sugar derivatives. Microb Biotechnol 2018; 11:747-758. [PMID: 29697194 PMCID: PMC6011931 DOI: 10.1111/1751-7915.13272] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 03/31/2018] [Accepted: 04/02/2018] [Indexed: 12/24/2022] Open
Abstract
Rare sugars and sugar derivatives that can be obtained from abundant sugars are of great interest to biochemical and pharmaceutical research. Here, we describe the substrate scope of a short‐chain dehydrogenase/reductase from Sphingomonas species A1 (SpsADH) in the oxidation of aldonates and polyols. The resulting products are rare uronic acids and rare sugars respectively. We provide insight into the substrate recognition of SpsADH using kinetic analyses, which show that the configuration of the hydroxyl groups adjacent to the oxidized carbon is crucial for substrate recognition. Furthermore, the specificity is demonstrated by the oxidation of d‐sorbitol leading to l‐gulose as sole product instead of a mixture of d‐glucose and l‐gulose. Finally, we applied the enzyme to the synthesis of l‐gulose from d‐sorbitol in an in vitro system using a NADH oxidase for cofactor recycling. This study shows the usefulness of exploring the substrate scope of enzymes to find new enzymatic reaction pathways from renewable resources to value‐added compounds.
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Affiliation(s)
- Barbara Beer
- Chair of Chemistry of Biogenic Resources, Technical University of Munich, Schulgasse 16, 94315, Straubing, Germany
| | - André Pick
- Chair of Chemistry of Biogenic Resources, Technical University of Munich, Schulgasse 16, 94315, Straubing, Germany
| | - Manuel Döring
- Chair of Chemistry of Biogenic Resources, Technical University of Munich, Schulgasse 16, 94315, Straubing, Germany
| | - Petra Lommes
- Chair of Chemistry of Biogenic Resources, Technical University of Munich, Schulgasse 16, 94315, Straubing, Germany
| | - Volker Sieber
- Chair of Chemistry of Biogenic Resources, Technical University of Munich, Schulgasse 16, 94315, Straubing, Germany.,Catalysis Research Center, Technical University of Munich, Ernst-Otto-Fischer-Str. 1, 85748, Garching, Germany.,Fraunhofer Institute of Interfacial Engineering and Biotechnology (IGB), Bio-, Electro- and Chemo Catalysis (BioCat) Branch, Schulgasse 11a, Straubing, 94315, Germany.,School of Chemistry and Molecular Biosciences, The University of Queensland, 68 Cooper Road, St. Lucia, 4072, Qld, Australia
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Guezane-Lakoud S, Toffano M, Aribi-Zouioueche L. Promiscuous lipase catalyzed a new P-C bond formation: Green and efficient protocol for one-pot synthesis of α-aminophosphonates. HETEROATOM CHEMISTRY 2017. [DOI: 10.1002/hc.21408] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Samia Guezane-Lakoud
- Ecocompatible Asymmetric Catalysis Laboratory (LCAE); Badji Mokhtar Annaba-University; Annaba Algeria
| | - Martial Toffano
- Equipe de Catalyse Moléculaire-ICMMO- CNRS UMR8182 Bât 420; Université Paris-Sud; Orsay France
| | - Louisa Aribi-Zouioueche
- Ecocompatible Asymmetric Catalysis Laboratory (LCAE); Badji Mokhtar Annaba-University; Annaba Algeria
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Sellés Vidal L, Kelly CL, Mordaka PM, Heap JT. Review of NAD(P)H-dependent oxidoreductases: Properties, engineering and application. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1866:327-347. [PMID: 29129662 DOI: 10.1016/j.bbapap.2017.11.005] [Citation(s) in RCA: 164] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 10/27/2017] [Accepted: 11/08/2017] [Indexed: 11/27/2022]
Abstract
NAD(P)H-dependent oxidoreductases catalyze the reduction or oxidation of a substrate coupled to the oxidation or reduction, respectively, of a nicotinamide adenine dinucleotide cofactor NAD(P)H or NAD(P)+. NAD(P)H-dependent oxidoreductases catalyze a large variety of reactions and play a pivotal role in many central metabolic pathways. Due to the high activity, regiospecificity and stereospecificity with which they catalyze redox reactions, they have been used as key components in a wide range of applications, including substrate utilization, the synthesis of chemicals, biodegradation and detoxification. There is great interest in tailoring NAD(P)H-dependent oxidoreductases to make them more suitable for particular applications. Here, we review the main properties and classes of NAD(P)H-dependent oxidoreductases, the types of reactions they catalyze, some of the main protein engineering techniques used to modify their properties and some interesting examples of their modification and application.
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Affiliation(s)
- Lara Sellés Vidal
- Centre for Synthetic Biology and Innovation, Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - Ciarán L Kelly
- Centre for Synthetic Biology and Innovation, Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - Paweł M Mordaka
- Centre for Synthetic Biology and Innovation, Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - John T Heap
- Centre for Synthetic Biology and Innovation, Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom.
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Martínez-Núñez MA, Rodríguez-Escamilla Z, Rodríguez-Vázquez K, Pérez-Rueda E. Tracing the Repertoire of Promiscuous Enzymes along the Metabolic Pathways in Archaeal Organisms. Life (Basel) 2017; 7:life7030030. [PMID: 28703743 PMCID: PMC5617955 DOI: 10.3390/life7030030] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 07/09/2017] [Accepted: 07/10/2017] [Indexed: 01/10/2023] Open
Abstract
The metabolic pathways that carry out the biochemical transformations sustaining life depend on the efficiency of their associated enzymes. In recent years, it has become clear that promiscuous enzymes have played an important role in the function and evolution of metabolism. In this work we analyze the repertoire of promiscuous enzymes in 89 non-redundant genomes of the Archaea cellular domain. Promiscuous enzymes are defined as those proteins with two or more different Enzyme Commission (E.C.) numbers, according the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. From this analysis, it was found that the fraction of promiscuous enzymes is lower in Archaea than in Bacteria. A greater diversity of superfamily domains is associated with promiscuous enzymes compared to specialized enzymes, both in Archaea and Bacteria, and there is an enrichment of substrate promiscuity rather than catalytic promiscuity in the archaeal enzymes. Finally, the presence of promiscuous enzymes in the metabolic pathways was found to be heterogeneously distributed at the domain level and in the phyla that make up the Archaea. These analyses increase our understanding of promiscuous enzymes and provide additional clues to the evolution of metabolism in Archaea.
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Affiliation(s)
- Mario Alberto Martínez-Núñez
- Laboratorio de Estudios Ecogenómicos, Facultad de Ciencias, Unidad Académica de Ciencias y Tecnología de la UNAM en Yucatán, Universidad Nacional Autónoma de México, Carretera Sierra Papacal-Chuburna Km. 5, C.P. 97302, Mérida, Yucatán, Mexico.
| | - Zuemy Rodríguez-Escamilla
- Departamento de Microbiología, Instituto de Biotecnología, Universidad Nacional, Autónoma de México, C.P. 62210, Cuernavaca, Morelos, Mexico.
| | - Katya Rodríguez-Vázquez
- Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Ciudad Universitaria, C.P. 04510, Ciudad de México, Mexico.
| | - Ernesto Pérez-Rueda
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, C.P. 62210, Cuernavaca, Morelos, Mexico.
- Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Unidad Académica Yucatán, Carretera Sierra Papacal-Chuburna Km. 5, C.P. 97302, Mérida, Yucatán, Mexico.
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Sakuta R, Takeda K, Igarashi K, Ohno H, Nakamura N. Pyrroloquinoline quinone-dependent glucose dehydrogenase anode: d-Galacturonic acid oxidation and galactaric acid production. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.molcatb.2016.11.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Pabis A, Duarte F, Kamerlin SCL. Promiscuity in the Enzymatic Catalysis of Phosphate and Sulfate Transfer. Biochemistry 2016; 55:3061-81. [PMID: 27187273 PMCID: PMC4899807 DOI: 10.1021/acs.biochem.6b00297] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
![]()
The
enzymes that facilitate phosphate and sulfate hydrolysis are
among the most proficient natural catalysts known to date. Interestingly,
a large number of these enzymes are promiscuous catalysts that exhibit
both phosphatase and sulfatase activities in the same active site
and, on top of that, have also been demonstrated to efficiently catalyze
the hydrolysis of other additional substrates with varying degrees
of efficiency. Understanding the factors that underlie such multifunctionality
is crucial both for understanding functional evolution in enzyme superfamilies
and for the development of artificial enzymes. In this Current Topic,
we have primarily focused on the structural and mechanistic basis
for catalytic promiscuity among enzymes that facilitate both phosphoryl
and sulfuryl transfer in the same active site, while comparing this
to how catalytic promiscuity manifests in other promiscuous phosphatases.
We have also drawn on the large number of experimental and computational
studies of selected model systems in the literature to explore the
different features driving the catalytic promiscuity of such enzymes.
Finally, on the basis of this comparative analysis, we probe the plausible
origins and determinants of catalytic promiscuity in enzymes that
catalyze phosphoryl and sulfuryl transfer.
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Affiliation(s)
- Anna Pabis
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University , BMC Box 596, S-751 24 Uppsala, Sweden
| | - Fernanda Duarte
- Chemistry Research Laboratory, University of Oxford , 12 Mansfield Road, Oxford OX1 3TA, U.K.,Physical and Theoretical Chemistry Laboratory, University of Oxford , South Parks Road, Oxford OX1 3QZ, U.K
| | - Shina C L Kamerlin
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University , BMC Box 596, S-751 24 Uppsala, Sweden
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Martínez-Núñez MA, Pérez-Rueda E. Do lifestyles influence the presence of promiscuous enzymes in bacteria and Archaea metabolism? ACTA ACUST UNITED AC 2016. [DOI: 10.1186/s40508-016-0047-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Kumar M, Mukherjee J, Sinha M, Kaur P, Sharma S, Gupta MN, Singh TP. Enhancement of stability of a lipase by subjecting to three phase partitioning (TPP): structures of native and TPP-treated lipase from Thermomyces lanuginosa. ACTA ACUST UNITED AC 2015. [DOI: 10.1186/s40508-015-0042-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Abstract
Enzymes require some flexibility for catalysis. Biotechnologists prefer stable enzymes but often this stabilization comes at the cost of reduced efficiency. Enzymes from thermophiles have low flexibility but poor catalytic rates. Enzymes from psychrophiles are less stable but show good catalytic rates at low temperature. In organic solvents enzymes perform poorly as the prior drying makes the enzyme molecules very rigid. Adding water or increasing reaction temperature improves flexibility and catalytic rates. In case of hydrolases, flexibility and enantioselectivity have interdependence. Understanding the complex role of protein flexibility in biocatalysis can help in designing biotechnological processes.
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Affiliation(s)
- Joyeeta Mukherjee
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Munishwar Nath Gupta
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
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Ren H, Li Q, Fang X, Yu D. Exploring substrate promiscuity of chlorophenol hydroxylase against biphenyl derivatives. RSC Adv 2015. [DOI: 10.1039/c5ra16935f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The substrate promiscuity of 2,4-dichlorophenol hydroxylase against biphenyl derivatives was explored. This enzyme may be used as a potentially useful catalyst in the bioremediation of aromatic contaminants.
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Affiliation(s)
- Hejun Ren
- Key Laboratory of Ground Water Resources and Environment of the Ministry of Education
- College of Environment and Resources
- Jilin University
- Changchun
- P. R. China
| | - Qingchao Li
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education
- College of Life Science
- Jilin University
- Changchun
- P. R. China
| | - Xuexun Fang
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education
- College of Life Science
- Jilin University
- Changchun
- P. R. China
| | - Dahai Yu
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education
- College of Life Science
- Jilin University
- Changchun
- P. R. China
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