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Scortica A, Capone M, Narzi D, Frezzini M, Scafati V, Giovannoni M, Angelucci F, Guidoni L, Mattei B, Benedetti M. A molecular dynamics-guided mutagenesis identifies two aspartic acid residues involved in the pH-dependent activity of OG-OXIDASE 1. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 169:171-182. [PMID: 34800821 DOI: 10.1016/j.plaphy.2021.11.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 10/19/2021] [Accepted: 11/10/2021] [Indexed: 06/13/2023]
Abstract
During the infection, plant cells secrete different OG-oxidase (OGOX) paralogs, defense flavoproteins that oxidize the oligogalacturonides (OGs), homogalacturonan fragments released from the plant cell wall that act as Damage Associated Molecular Patterns. OGOX-mediated oxidation inactivates their elicitor nature, but on the other hand makes OGs less hydrolysable by microbial endo-polygalacturonases (PGs). Among the different plant defense responses, apoplastic alkalinization can further reduce the degrading potential of PGs by boosting the oxidizing activity of OGOXs. Accordingly, the different OGOXs so far characterized showed an optimal activity at pH values greater than 8. Here, an approach of molecular dynamics (MD)-guided mutagenesis succeeded in identifying the amino acids responsible for the pH dependent activity of OGOX1 from Arabidopsis thaliana. MD simulations indicated that in alkaline conditions (pH 8.5), the residues Asp325 and Asp344 are engaged in the formation of two salt bridges with Arg327 and Lys415, respectively, at the rim of enzyme active site. According to MD analysis, the presence of such ionic bonds modulates the size and flexibility of the cavity used to accommodate the OGs, in turn affecting the activity of OGOX1. Based on functional properties of the site-directed mutants OGOX1.D325A and OGOX.D344A, we demonstrated that Asp325 and Asp344 are major determinants of the alkaline-dependent activity of OGOX1.
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Affiliation(s)
- Anna Scortica
- Dept. of Life, Health and Environmental Sciences, University of L'Aquila, 67100, L'Aquila, Italy
| | - Matteo Capone
- Dept. of Physical and Chemical Sciences, University of L'Aquila, 67100, L'Aquila, Italy
| | - Daniele Narzi
- Dept. of Physical and Chemical Sciences, University of L'Aquila, 67100, L'Aquila, Italy.
| | - Mario Frezzini
- Dept. of Information Engineering, Computer Science and Mathematics, University of L'Aquila, 67100, L'Aquila, Italy
| | - Valentina Scafati
- Dept. of Life, Health and Environmental Sciences, University of L'Aquila, 67100, L'Aquila, Italy
| | - Moira Giovannoni
- Dept. of Life, Health and Environmental Sciences, University of L'Aquila, 67100, L'Aquila, Italy
| | - Francesco Angelucci
- Dept. of Life, Health and Environmental Sciences, University of L'Aquila, 67100, L'Aquila, Italy
| | - Leonardo Guidoni
- Dept. of Physical and Chemical Sciences, University of L'Aquila, 67100, L'Aquila, Italy
| | - Benedetta Mattei
- Dept. of Life, Health and Environmental Sciences, University of L'Aquila, 67100, L'Aquila, Italy.
| | - Manuel Benedetti
- Dept. of Life, Health and Environmental Sciences, University of L'Aquila, 67100, L'Aquila, Italy
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Pontiggia D, Benedetti M, Costantini S, De Lorenzo G, Cervone F. Dampening the DAMPs: How Plants Maintain the Homeostasis of Cell Wall Molecular Patterns and Avoid Hyper-Immunity. FRONTIERS IN PLANT SCIENCE 2020; 11:613259. [PMID: 33391327 PMCID: PMC7773757 DOI: 10.3389/fpls.2020.613259] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 11/23/2020] [Indexed: 05/05/2023]
Abstract
Several oligosaccharide fragments derived from plant cell walls activate plant immunity and behave as typical damage-associated molecular patterns (DAMPs). Some of them also behave as negative regulators of growth and development, and due to their antithetic effect on immunity and growth, their concentrations, activity, time of formation, and localization is critical for the so-called "growth-defense trade-off." Moreover, like in animals, over accumulation of DAMPs in plants provokes deleterious physiological effects and may cause hyper-immunity if the cellular mechanisms controlling their homeostasis fail. Recently, a mechanism has been discovered that controls the activity of two well-known plant DAMPs, oligogalacturonides (OGs), released upon hydrolysis of homogalacturonan (HG), and cellodextrins (CDs), products of cellulose breakdown. The potential homeostatic mechanism involves specific oxidases belonging to the family of berberine bridge enzyme-like (BBE-like) proteins. Oxidation of OGs and CDs not only inactivates their DAMP activity, but also makes them a significantly less desirable food source for microbial pathogens. The evidence that oxidation and inactivation of OGs and CDs may be a general strategy of plants for controlling the homeostasis of DAMPs is discussed. The possibility exists of discovering additional oxidative and/or inactivating enzymes targeting other DAMP molecules both in the plant and in animal kingdoms.
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Affiliation(s)
- Daniela Pontiggia
- Dipartimento di Biologia e Biotecnologie “Charles Darwin,” Sapienza Università di Roma, Rome, Italy
| | - Manuel Benedetti
- Dipartimento di Medicina Clinica, Sanità Pubblica e Scienze della Vita e dell’Ambiente, Università degli Studi dell’Aquila, L’Aquila, Italy
| | - Sara Costantini
- Dipartimento di Biologia e Biotecnologie “Charles Darwin,” Sapienza Università di Roma, Rome, Italy
| | - Giulia De Lorenzo
- Dipartimento di Biologia e Biotecnologie “Charles Darwin,” Sapienza Università di Roma, Rome, Italy
| | - Felice Cervone
- Dipartimento di Biologia e Biotecnologie “Charles Darwin,” Sapienza Università di Roma, Rome, Italy
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Savino S, Fraaije MW. The vast repertoire of carbohydrate oxidases: An overview. Biotechnol Adv 2020; 51:107634. [PMID: 32961251 DOI: 10.1016/j.biotechadv.2020.107634] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 08/12/2020] [Accepted: 09/06/2020] [Indexed: 01/01/2023]
Abstract
Carbohydrates are widely abundant molecules present in a variety of forms. For their biosynthesis and modification, nature has evolved a plethora of carbohydrate-acting enzymes. Many of these enzymes are of particular interest for biotechnological applications, where they can be used as biocatalysts or biosensors. Among the enzymes catalysing conversions of carbohydrates are the carbohydrate oxidases. These oxidative enzymes belong to different structural families and use different cofactors to perform the oxidation reaction of CH-OH bonds in carbohydrates. The variety of carbohydrate oxidases available in nature reflects their specificity towards different sugars and selectivity of the oxidation site. Thanks to their properties, carbohydrate oxidases have received a lot of attention in basic and applied research, such that nowadays their role in biotechnological processes is of paramount importance. In this review we provide an overview of the available knowledge concerning the known carbohydrate oxidases. The oxidases are first classified according to their structural features. After a description on their mechanism of action, substrate acceptance and characterisation, we report on the engineering of the different carbohydrate oxidases to enhance their employment in biocatalysis and biotechnology. In the last part of the review we highlight some practical applications for which such enzymes have been exploited.
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Affiliation(s)
- Simone Savino
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747AG Groningen, the Netherlands
| | - Marco W Fraaije
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747AG Groningen, the Netherlands.
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