1
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Jackson SA, Duan M, Zhang P, Ihua MW, Stengel DB, Duan D, Dobson ADW. Isolation, identification, and biochemical characterization of a novel bifunctional phosphomannomutase/phosphoglucomutase from the metagenome of the brown alga Laminaria digitata. Front Microbiol 2022; 13:1000634. [PMID: 36212884 PMCID: PMC9537760 DOI: 10.3389/fmicb.2022.1000634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 08/15/2022] [Indexed: 11/17/2022] Open
Abstract
Macroalgae host diverse epiphytic bacterial communities with potential symbiotic roles including important roles influencing morphogenesis and growth of the host, nutrient exchange, and protection of the host from pathogens. Macroalgal cell wall structures, exudates, and intra-cellular environments possess numerous complex and valuable carbohydrates such as cellulose, hemi-cellulose, mannans, alginates, fucoidans, and laminarin. Bacterial colonizers of macroalgae are important carbon cyclers, acquiring nutrition from living macroalgae and also from decaying macroalgae. Seaweed epiphytic communities are a rich source of diverse carbohydrate-active enzymes which may have useful applications in industrial bioprocessing. With this in mind, we constructed a large insert fosmid clone library from the metagenome of Laminaria digitata (Ochrophyta) in which decay was induced. Subsequent sequencing of a fosmid clone insert revealed the presence of a gene encoding a bifunctional phosphomannomutase/phosphoglucomutase (PMM/PGM) enzyme 10L6AlgC, closely related to a protein from the halophilic marine bacterium, Cobetia sp. 10L6AlgC was subsequently heterologously expressed in Escherichia coli and biochemically characterized. The enzyme was found to possess both PMM and PGM activity, which had temperature and pH optima of 45°C and 8.0, respectively; for both activities. The PMM activity had a Km of 2.229 mM and Vmax of 29.35 mM min−1 mg−1, while the PGM activity had a Km of 0.5314 mM and a Vmax of 644.7 mM min−1 mg−1. Overall characterization of the enzyme including the above parameters as well as the influence of various divalent cations on these activities revealed that 10L6AlgC has a unique biochemical profile when compared to previously characterized PMM/PGM bifunctional enzymes. Thus 10L6AlgC may find utility in enzyme-based production of biochemicals with different potential industrial applications, in which other bacterial PMM/PGMs have previously been used such as in the production of low-calorie sweeteners in the food industry.
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Affiliation(s)
- Stephen A. Jackson
- School of Microbiology, University College Cork, Cork, Ireland
- Environmental Research Institute, University College Cork, Cork, Ireland
| | - Maohang Duan
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Pengyan Zhang
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Maureen W. Ihua
- School of Microbiology, University College Cork, Cork, Ireland
| | - Dagmar B. Stengel
- Botany and Plant Science, School of Natural Sciences, Ryan Institute for Environmental, Marine and Energy Research, University of Galway, Galway, Ireland
| | - Delin Duan
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
- *Correspondence: Delin Duan,
| | - Alan D. W. Dobson
- School of Microbiology, University College Cork, Cork, Ireland
- Environmental Research Institute, University College Cork, Cork, Ireland
- Alan D. W. Dobson,
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2
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Woods DF, Kozak IM, O'Gara F. Genome analysis and phenotypic characterization of Halomonas hibernica isolated from a traditional food process with novel quorum quenching and catalase activities. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 36099016 DOI: 10.1099/mic.0.001238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Traditional food processes can utilize bacteria to promote positive organoleptic qualities and increase shelf life. Wiltshire curing has a vital bacterial component that has not been fully investigated from a microbial perspective. During the investigation of a Wiltshire brine, a culturable novel bacterium of the genus Halomonas was identified by 16S rRNA gene (MN822133) sequencing and analysis. The isolate was confirmed as representing a novel species (Halomonas hibernica B1.N12) using a housekeeping (HK) gene phylogenetic tree reconstruction with the selected genes 16S rRNA, 23S rRNA, atpA, gyrB, rpoD and secA. The genome of the new isolate was sequenced and annotated and comparative genome analysis was conducted. Functional analysis revealed that the isolate has a unique phenotypic signature including high salt tolerance, a wide temperature growth range and substrate metabolism. Phenotypic and biochemical profiling demonstrated that H. hibernica B1.N12 possesses strong catalase activity which is an important feature for an industrial food processing bacterium, as it can promote an increased product shelf life and improve organoleptic qualities. Moreover, H. hibernica exhibits biocontrol properties based on its quorum quenching capabilities. Our work on this novel isolate advances knowledge on potential mechanistic interplays operating in complex microbial communities that mediate traditional food processes.
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Affiliation(s)
- David F Woods
- BIOMERIT Research Centre, School of Microbiology, University College Cork, Cork, Ireland
| | - Iwona M Kozak
- BIOMERIT Research Centre, School of Microbiology, University College Cork, Cork, Ireland
| | - Fergal O'Gara
- BIOMERIT Research Centre, School of Microbiology, University College Cork, Cork, Ireland.,Wal-yan Respiratory Research Centre, Telethon Kids Institute, Perth, WA, Australia.,Synthesis and Solid State Pharmaceutical Centre, University College Cork, Cork, Ireland
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3
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Misra N, Rawat S, Goel NK, Shelkar SA, Kumar A, Kumar V. Radiation facilitated-immobilized lipase ( RaFIL) mini biocatalytic reactor based on epoxy decorated PP tubes: Rapid colorimetric estimation of pesticide Chlorpyrifos. JOURNAL OF MACROMOLECULAR SCIENCE PART A-PURE AND APPLIED CHEMISTRY 2022. [DOI: 10.1080/10601325.2022.2098143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Nilanjal Misra
- Radiation Technology Development Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Swarnima Rawat
- Radiation Technology Development Division, Bhabha Atomic Research Centre, Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
| | - Narender Kumar Goel
- Radiation Technology Development Division, Bhabha Atomic Research Centre, Mumbai, India
| | | | - Asheesh Kumar
- Chemistry Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Virendra Kumar
- Radiation Technology Development Division, Bhabha Atomic Research Centre, Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
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4
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Purification and Characterization of Trochus radiatus Derived Low Molecular Weight Bactericidal Polypeptide Active Against ESKAPE Pathogens. Int J Pept Res Ther 2021. [DOI: 10.1007/s10989-021-10195-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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5
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Varrella S, Barone G, Tangherlini M, Rastelli E, Dell’Anno A, Corinaldesi C. Diversity, Ecological Role and Biotechnological Potential of Antarctic Marine Fungi. J Fungi (Basel) 2021; 7:jof7050391. [PMID: 34067750 PMCID: PMC8157204 DOI: 10.3390/jof7050391] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 05/07/2021] [Accepted: 05/13/2021] [Indexed: 11/28/2022] Open
Abstract
The Antarctic Ocean is one of the most remote and inaccessible environments on our planet and hosts potentially high biodiversity, being largely unexplored and undescribed. Fungi have key functions and unique physiological and morphological adaptations even in extreme conditions, from shallow habitats to deep-sea sediments. Here, we summarized information on diversity, the ecological role, and biotechnological potential of marine fungi in the coldest biome on Earth. This review also discloses the importance of boosting research on Antarctic fungi as hidden treasures of biodiversity and bioactive molecules to better understand their role in marine ecosystem functioning and their applications in different biotechnological fields.
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Affiliation(s)
- Stefano Varrella
- Department of Materials, Environmental Sciences and Urban Planning, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
- Correspondence: (S.V.); (C.C.)
| | - Giulio Barone
- Institute for Biological Resources and Marine Biotechnologies, National Research Council (IRBIM-CNR), Largo Fiera della Pesca, 60125 Ancona, Italy;
| | - Michael Tangherlini
- Department of Research Infrastructures for Marine Biological Resources, Stazione Zoologica “Anton Dohrn”, Fano Marine Centre, Viale Adriatico 1-N, 61032 Fano, Italy;
| | - Eugenio Rastelli
- Department of Marine Biotechnology, Stazione Zoologica “Anton Dohrn”, Fano Marine Centre, Viale Adriatico 1-N, 61032 Fano, Italy;
| | - Antonio Dell’Anno
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy;
| | - Cinzia Corinaldesi
- Department of Materials, Environmental Sciences and Urban Planning, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
- Correspondence: (S.V.); (C.C.)
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6
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Barzkar N, Sohail M, Tamadoni Jahromi S, Gozari M, Poormozaffar S, Nahavandi R, Hafezieh M. Marine Bacterial Esterases: Emerging Biocatalysts for Industrial Applications. Appl Biochem Biotechnol 2021; 193:1187-1214. [PMID: 33411134 DOI: 10.1007/s12010-020-03483-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 11/30/2020] [Indexed: 12/17/2022]
Abstract
The marine ecosystem has been known to be a significant source of novel enzymes. Esterase enzymes (EC 3.1.1.1) represent a diverse group of hydrolases that catalyze the cleavage and formation of ester bonds. Although esterases are widely distributed among marine organisms, only microbial esterases are of paramount industrial importance. This article discusses the importance of marine microbial esterases, their biochemical and kinetic properties, and their stability under extreme conditions. Since culture-dependent techniques provide limited insights into microbial diversity of the marine ecosystem, therefore, genomics and metagenomics approaches have widely been adopted in search of novel esterases. Additionally, the article also explains industrial applications of marine bacterial esterases particularly for the synthesis of optically pure substances, the preparation of enantiomerically pure drugs, the degradation of human-made plastics and organophosphorus compounds, degradation of the lipophilic components of the ink, and production of short-chain flavor esters.
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Affiliation(s)
- Noora Barzkar
- Department of Marine Biology, Faculty of Marine Science and Technology, University of Hormozgan, Bandar Abbas, 7931674576, Iran.
| | - Muhammad Sohail
- Department of Microbiology, University of Karachi, Karachi, 75270, Pakistan
| | - Saeid Tamadoni Jahromi
- Persian Gulf and Oman Sea Ecological Research Center, Iranian Fisheries Science Research Institute (IFSRI), Agricultural Research Education and Extension Organization (AREEO), Bandar Abbas, Iran
| | - Mohsen Gozari
- Persian Gulf and Oman Sea Ecological Research Center, Iranian Fisheries Science Research Institute (IFSRI), Agricultural Research Education and Extension Organization (AREEO), Bandar Abbas, Iran
| | - Sajjad Poormozaffar
- Persian Gulf Mollusks Research Station, Persian Gulf and Oman Sea Ecology Research Center, Agricultural Research Education and Extension Organization (AREEO), Iranian Fisheries Sciences Research Institute, Bandar-e-Lengeh, Iran
| | - Reza Nahavandi
- Animal Science Research Institute of Iran, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Mahmoud Hafezieh
- Iranian Fisheries Science Research Institute (ASRI), Agricultural Research, Education and Extension Organization (AREEO), Tehran, Iran
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7
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Schwarz M, Murphy EJ, Foley AM, Woods DF, Castilla IA, Reen FJ, Collins SG, O'Gara F, Maguire AR. Exploring the synthetic potential of a marine transaminase including discrimination at a remote stereocentre. Org Biomol Chem 2021; 19:188-198. [PMID: 33119023 DOI: 10.1039/d0ob01848a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The marine transaminase, P-ω-TA, can be employed for the transamination from 1-aminotetralins and 1-aminoindanes with differentiation of stereochemistry at both the site of reaction and at a remote stereocentre resulting in formation of ketone products with up to 93% ee. While 4-substituents are tolerated on the tetralin core, the presence of 3- or 8-substituents is not tolerated by the transaminase. In general P-ω-TA shows capacity for remote diastereoselectivity, although both the stereoselectivity and efficiency are dependent on the specific substrate structure. Optimum efficiency and selectivity are seen with 4-haloaryl-1-aminotetralins and 3-haloaryl-1-aminoindanes, which may be associated with the marine origin of this enzyme.
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Affiliation(s)
- Maria Schwarz
- School of Chemistry, Analytical and Biological Chemistry Research Facility, University College Cork, T12 K8AF, Cork, Ireland.
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8
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Enantioselective Transesterification of Allyl Alcohols with (E)-4-Arylbut-3-en-2-ol Motif by Immobilized Lecitase™ Ultra. Catalysts 2020. [DOI: 10.3390/catal10070798] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Lecitase™ Ultra was immobilized on four different supports and tested for the first time as the biocatalyst in the kinetic resolution of racemic allyl alcohols with the (E)-4-arylbut-3-en-2-ol system in the process of transesterification. The most effective biocatalyst turned out to be the enzyme immobilized on agarose activated with cyanogen bromide (LU-CNBr). The best results (E > 200, ees and eep = 95–99%) were obtained for (E)-4-phenylbut-3-en-2-ol and its analog with a 2,5-dimethylphenyl ring whereas the lowest ee of kinetic resolution products (90%) was achieved for the substrate with a 4-methoxyphenyl substituent. For all substrates, (R)-enantiomers were esterified faster than their (S)-antipodes. The results showed that LU-CNBr is a versatile biocatalyst, showing high activity and enantioselectivity in a wide range of organic solvents in the presence of commonly used acyl donors. High operational stability of LU-CNBr allows it to be reused in three subsequent reaction cycles without negative effects on the efficiency and enantioselectivity of transesterification. This biocatalyst can become attractive to the commercial lipases in the process of the kinetic resolution of allyl alcohols.
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9
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Caparco AA, Pelletier E, Petit JL, Jouenne A, Bommarius BR, Berardinis V, Zaparucha A, Champion JA, Bommarius AS, Vergne‐Vaxelaire C. Metagenomic Mining for Amine Dehydrogenase Discovery. Adv Synth Catal 2020. [DOI: 10.1002/adsc.202000094] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Adam A. Caparco
- School of Chemical & Biomolecular EngineeringGeorgia Institute of Technology Atlanta, GA USA
| | - Eric Pelletier
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ EvryUniversité Paris-Saclay 91057 Evry France
| | - Jean Louis Petit
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ EvryUniversité Paris-Saclay 91057 Evry France
| | - Aurélie Jouenne
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ EvryUniversité Paris-Saclay 91057 Evry France
| | - Bettina R. Bommarius
- School of Chemical & Biomolecular EngineeringGeorgia Institute of Technology Atlanta, GA USA
| | - Véronique Berardinis
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ EvryUniversité Paris-Saclay 91057 Evry France
| | - Anne Zaparucha
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ EvryUniversité Paris-Saclay 91057 Evry France
| | - Julie A. Champion
- School of Chemical & Biomolecular EngineeringGeorgia Institute of Technology Atlanta, GA USA
| | - Andreas S. Bommarius
- School of Chemical & Biomolecular EngineeringGeorgia Institute of Technology Atlanta, GA USA
| | - Carine Vergne‐Vaxelaire
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ EvryUniversité Paris-Saclay 91057 Evry France
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10
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Kornecki JF, Carballares D, Tardioli PW, Rodrigues RC, Berenguer-Murcia Á, Alcántara AR, Fernandez-Lafuente R. Enzyme production ofd-gluconic acid and glucose oxidase: successful tales of cascade reactions. Catal Sci Technol 2020. [DOI: 10.1039/d0cy00819b] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
This review mainly focuses on the use of glucose oxidase in the production ofd-gluconic acid, which is a reactant of undoubtable interest in different industrial areas. As example of diverse enzymatic cascade reactions.
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Affiliation(s)
- Jakub F. Kornecki
- Departamento de Biocatálisis
- ICP-CSIC
- Campus UAM-CSIC
- 28049 Madrid
- Spain
| | - Diego Carballares
- Departamento de Biocatálisis
- ICP-CSIC
- Campus UAM-CSIC
- 28049 Madrid
- Spain
| | - Paulo W. Tardioli
- Postgraduate Program in Chemical Engineering (PPGEQ)
- Department of Chemical Engineering
- Federal University of São Carlos
- 13565-905 São Carlos
- Brazil
| | - Rafael C. Rodrigues
- Biocatalysis and Enzyme Technology Lab
- Institute of Food Science and Technology
- Federal University of Rio Grande do Sul
- Porto Alegre
- Brazil
| | - Ángel Berenguer-Murcia
- Departamento de Química Inorgánica e Instituto Universitario de Materiales
- Universidad de Alicante
- Alicante 03080
- Spain
| | - Andrés R. Alcántara
- Departamento de Química en Ciencias Farmacéuticas
- Facultad de Farmacia
- Universidad Complutense de Madrid
- 28040-Madrid
- Spain
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11
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Gavin DP, Reen FJ, Rocha-Martin J, Abreu-Castilla I, Woods DF, Foley AM, Sánchez-Murcia PA, Schwarz M, O'Neill P, Maguire AR, O'Gara F. Genome mining and characterisation of a novel transaminase with remote stereoselectivity. Sci Rep 2019; 9:20285. [PMID: 31889089 PMCID: PMC6937235 DOI: 10.1038/s41598-019-56612-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 11/20/2019] [Indexed: 01/27/2023] Open
Abstract
Microbial enzymes from pristine niches can potentially deliver disruptive opportunities in synthetic routes to Active Pharmaceutical Ingredients and intermediates in the Pharmaceutical Industry. Advances in green chemistry technologies and the importance of stereochemical control, further underscores the application of enzyme-based solutions in chemical synthesis. The rich tapestry of microbial diversity in the oceanic ecosystem encodes a capacity for novel biotransformations arising from the chemical complexity of this largely unexplored bioactive reservoir. Here we report a novel ω-transaminase discovered in a marine sponge Pseudovibrio sp. isolate. Remote stereoselection using a transaminase has been demonstrated for the first time using this novel protein. Application to the resolution of an intermediate in the synthesis of sertraline highlights the synthetic potential of this novel biocatalyst discovered through genomic mining. Integrated chemico-genomics revealed a unique substrate profile, while molecular modelling provided structural insights into this ‘first in class’ selectivity at a remote chiral centre.
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Affiliation(s)
- D P Gavin
- School of Chemistry; Analytical and Biological Chemistry Research Facility, University College Cork, Cork, Ireland.,Synthesis and Solid State Pharmaceutical Centre, University College Cork, Cork, Ireland
| | - F J Reen
- BIOMERIT Research Centre, School of Microbiology, University College Cork, Cork, Ireland.,School of Microbiology, University College Cork, T12 K8AF, Cork, Ireland
| | - J Rocha-Martin
- BIOMERIT Research Centre, School of Microbiology, University College Cork, Cork, Ireland
| | - I Abreu-Castilla
- BIOMERIT Research Centre, School of Microbiology, University College Cork, Cork, Ireland
| | - D F Woods
- BIOMERIT Research Centre, School of Microbiology, University College Cork, Cork, Ireland
| | - A M Foley
- School of Chemistry, School of Pharmacy, Analytical and Biological Chemistry Research Facility, University College Cork, Cork, Ireland
| | - P A Sánchez-Murcia
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 17, A-1090, Vienna, Austria
| | - M Schwarz
- School of Chemistry; Analytical and Biological Chemistry Research Facility, University College Cork, Cork, Ireland
| | - P O'Neill
- Pfizer Process Development Centre, Loughbeg, Cork, Ireland
| | - A R Maguire
- Synthesis and Solid State Pharmaceutical Centre, University College Cork, Cork, Ireland. .,School of Chemistry, School of Pharmacy, Analytical and Biological Chemistry Research Facility, University College Cork, Cork, Ireland.
| | - F O'Gara
- Synthesis and Solid State Pharmaceutical Centre, University College Cork, Cork, Ireland. .,BIOMERIT Research Centre, School of Microbiology, University College Cork, Cork, Ireland. .,Human Microbiome Programme, School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Institute, Curtin University, Perth, WA 6102, Australia and Telethon Kids Institute, Perth, WA, 6008, Australia.
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12
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Genipin as An Emergent Tool in the Design of Biocatalysts: Mechanism of Reaction and Applications. Catalysts 2019. [DOI: 10.3390/catal9121035] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Genipin is a reagent isolated from the Gardenia jasminoides fruit extract, and whose low toxicity and good crosslinking properties have converted it into a reactive whose popularity is increasing by the day. These properties have made it widely used in many medical applications, mainly in the production of chitosan materials (crosslinked by this reactive), biological scaffolds for tissue engineering, and nanoparticles of chitosan and nanogels of proteins for controlled drug delivery, the genipin crosslinking being a key point to strengthen the stability of these materials. This review is focused on the mechanism of reaction of this reagent and its use in the design of biocatalysts, where genipin plays a double role, as a support activating agent and as inter- or intramolecular crosslinker. Its low toxicity makes this compound an ideal alterative to glutaraldehyde in these processes. Moreover, in some cases the features of the biocatalysts prepared using genipin surpassed those of the biocatalysts prepared using other standard crosslinkers, even disregarding toxicity. In this way, genipin is a very promising reagent in the design of biocatalysts.
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13
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Bauer TL, Buchholz PCF, Pleiss J. The modular structure of α/β-hydrolases. FEBS J 2019; 287:1035-1053. [PMID: 31545554 DOI: 10.1111/febs.15071] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 08/15/2019] [Accepted: 09/19/2019] [Indexed: 12/22/2022]
Abstract
The α/β-hydrolase fold family is highly diverse in sequence, structure and biochemical function. To investigate the sequence-structure-function relationships, the Lipase Engineering Database (https://led.biocatnet.de) was updated. Overall, 280 638 protein sequences and 1557 protein structures were analysed. All α/β-hydrolases consist of the catalytically active core domain, but they might also contain additional structural modules, resulting in 12 different architectures: core domain only, additional lids at three different positions, three different caps, additional N- or C-terminal domains and combinations of N- and C-terminal domains with caps and lids respectively. In addition, the α/β-hydrolases were distinguished by their oxyanion hole signature (GX-, GGGX- and Y-types). The N-terminal domains show two different folds, the Rossmann fold or the β-propeller fold. The C-terminal domains show a β-sandwich fold. The N-terminal β-propeller domain and the C-terminal β-sandwich domain are structurally similar to carbohydrate-binding proteins such as lectins. The classification was applied to the newly discovered polyethylene terephthalate (PET)-degrading PETases and MHETases, which are core domain α/β-hydrolases of the GX- and the GGGX-type respectively. To investigate evolutionary relationships, sequence networks were analysed. The degree distribution followed a power law with a scaling exponent γ = 1.4, indicating a highly inhomogeneous network which consists of a few hubs and a large number of less connected sequences. The hub sequences have many functional neighbours and therefore are expected to be robust toward possible deleterious effects of mutations. The cluster size distribution followed a power law with an extrapolated scaling exponent τ = 2.6, which strongly supports the connectedness of the sequence space of α/β-hydrolases. DATABASE: Supporting data about domains from other proteins with structural similarity to the N- or C-terminal domains of α/β-hydrolases are available in Data Repository of the University of Stuttgart (DaRUS) under doi: https://doi.org/10.18419/darus-458.
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Affiliation(s)
- Tabea L Bauer
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Germany
| | - Patrick C F Buchholz
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Germany
| | - Jürgen Pleiss
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Germany
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14
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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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15
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16
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Andreu C, del Olmo M. Improved Biocatalytic Activity of the DebaryomycesSpecies in Seawater. ChemCatChem 2019. [DOI: 10.1002/cctc.201900558] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Cecilia Andreu
- Departament de Química OrgànicaUniversitat de València (UVEG) Vicent Andrés Estellés s.n. 46100 Burjassot, València Spain
| | - Marcel⋅lí del Olmo
- Departament de Bioquímica i Biologia MolecularUniversitat de València (UVEG) Dr. Moliner 50 46100 Burjassot, València Spain
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17
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Gavin DP, Murphy EJ, Foley AM, Castilla IA, Reen FJ, Woods DF, Collins SG, O'Gara F, Maguire AR. Identification of an Esterase Isolated Using Metagenomic Technology which Displays an Unusual Substrate Scope and its Characterisation as an Enantioselective Biocatalyst. Adv Synth Catal 2019. [DOI: 10.1002/adsc.201801691] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Declan P. Gavin
- School of Chemistry; Analytical and Biological Chemistry Research Facility; Synthesis and Solid State Pharmaceutical Centre; University College Cork; T12 K8AF Cork Ireland
| | - Edel J. Murphy
- School of Chemistry; Analytical and Biological Chemistry Research Facility; University College Cork; T12 K8AF Cork Ireland
| | - Aoife M. Foley
- School of Chemistry; Analytical and Biological Chemistry Research Facility; Synthesis and Solid State Pharmaceutical Centre; University College Cork; T12 K8AF Cork Ireland
| | - Ignacio Abreu Castilla
- BIOMERIT Research Centre; School of Microbiology; University College Cork; T12 K8AF Cork Ireland
| | - F. Jerry Reen
- School of Microbiology; University College Cork; T12 K8AF Cork Ireland
| | - David F. Woods
- BIOMERIT Research Centre; School of Microbiology; University College Cork; T12 K8AF Cork Ireland
| | - Stuart G. Collins
- School of Chemistry; Analytical and Biological Chemistry Research Facility; Synthesis and Solid State Pharmaceutical Centre; University College Cork; T12 K8AF Cork Ireland
| | - Fergal O'Gara
- BIOMERIT Research Centre; School of Microbiology; University College Cork; T12 K8AF Cork Ireland
- Human Microbiome Programme, School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Institute; Curtin University; Perth WA 6102 Australia
- Telethon Kids Institute; Perth WA 6008 Australia
| | - Anita R. Maguire
- School of Chemistry; School of Pharmacy; Analytical and Biological Chemistry Research Facility; Synthesis and Solid State Pharmaceutical Centre; University College Cork; T12 K8AF Cork Ireland
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18
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Ortiz C, Ferreira ML, Barbosa O, dos Santos JCS, Rodrigues RC, Berenguer-Murcia Á, Briand LE, Fernandez-Lafuente R. Novozym 435: the “perfect” lipase immobilized biocatalyst? Catal Sci Technol 2019. [DOI: 10.1039/c9cy00415g] [Citation(s) in RCA: 263] [Impact Index Per Article: 52.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Novozym 435 (N435) is a commercially available immobilized lipase produced by Novozymes with its advantages and drawbacks.
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Affiliation(s)
- Claudia Ortiz
- Escuela de Microbiología
- Universidad Industrial de Santander
- Bucaramanga
- Colombia
| | - María Luján Ferreira
- Planta Piloto de Ingeniería Química – PLAPIQUI
- CONICET
- Universidad Nacional del Sur
- 8000 Bahía Blanca
- Argentina
| | - Oveimar Barbosa
- Departamento de Química
- Facultad de Ciencias
- Universidad del Tolima
- Ibagué
- Colombia
| | - José C. S. dos Santos
- Instituto de Engenharias e Desenvolvimento Sustentável
- Universidade da Integração Internacional da Lusofonia Afro-Brasileira
- Redenção
- Brazil
| | - Rafael C. Rodrigues
- Biotechnology, Bioprocess, and Biocatalysis Group, Food Science and Technology Institute
- Federal University of Rio Grande do Sul
- Porto Alegre
- Brazil
| | - Ángel Berenguer-Murcia
- Instituto Universitario de Materiales
- Departamento de Química Inorgánica
- Universidad de Alicante
- Alicante
- Spain
| | - Laura E. Briand
- Centro de Investigación y Desarrollo en Ciencias Aplicadas-Dr. Jorge J. Ronco
- Universidad Nacional de La Plata
- CONICET
- Buenos Aires
- Argentina
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