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Torres de Oliveira C, Alexandrino de Assis M, Lourenço Franco Cairo JP, Damasio A, Guimarães Pereira GA, Mazutti MA, de Oliveira D. Functional characterization and structural insights of three cutinases from the ascomycete Fusarium verticillioides. Protein Expr Purif 2024; 216:106415. [PMID: 38104791 DOI: 10.1016/j.pep.2023.106415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 12/05/2023] [Accepted: 12/06/2023] [Indexed: 12/19/2023]
Abstract
Cutinases are serine esterases that belong to the α/β hydrolases superfamily. The natural substrates for these enzymes are cutin and suberin, components of the plant cuticle, the first barrier in the defense system against pathogen invasion. It is well-reported that plant pathogens produce cutinases to facilitate infection. Fusarium verticillioides, one important corn pathogens, is an ascomycete upon which its cutinases are poorly explored. Consequently, the objective of this study was to perform the biochemical characterization of three precursor cutinases (FvCut1, FvCut2, and FvCut3) from F. verticillioides and to obtain structural insights about them. The cutinases were produced in Escherichia coli and purified. FvCut1, FvCut2, and FvCut3 presented optimal temperatures of 20, 40, and 35 °C, and optimal pH of 9, 7, and 8, respectively. Some chemicals stimulated the enzymatic activity. The kinetic parameters revealed that FvCut1 has higher catalytic efficiency (Kcat/Km) in the p-nitrophenyl-butyrate (p-NPB) substrate. Nevertheless, the enzymes were not able to hydrolyze polyethylene terephthalate (PET). Furthermore, the three-dimensional models of these enzymes showed structural differences among them, mainly FvCut1, which presented a narrower opening cleft to access the catalytic site. Therefore, our study contributes to exploring the diversity of fungal cutinases and their potential biotechnological applications.
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Affiliation(s)
- Caroline Torres de Oliveira
- Department of Chemical and Food Engineering, Technology Center, Federal University of Santa Catarina, UFSC, Florianópolis, Brazil
| | - Michelle Alexandrino de Assis
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, UNICAMP, Campinas, Brazil
| | | | - André Damasio
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, UNICAMP, Campinas, Brazil
| | | | - Marcio Antonio Mazutti
- Department of Chemical Engineering, Technology Center, Federal University of Santa Maria, UFSM, Santa Maria, Brazil
| | - Débora de Oliveira
- Department of Chemical and Food Engineering, Technology Center, Federal University of Santa Catarina, UFSC, Florianópolis, Brazil.
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2
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Haernvall K, Fladischer P, Schoeffmann H, Zitzenbacher S, Pavkov-Keller T, Gruber K, Schick M, Yamamoto M, Kuenkel A, Ribitsch D, Guebitz GM, Wiltschi B. Residue-Specific Incorporation of the Non-Canonical Amino Acid Norleucine Improves Lipase Activity on Synthetic Polyesters. Front Bioeng Biotechnol 2022; 10:769830. [PMID: 35155387 PMCID: PMC8826565 DOI: 10.3389/fbioe.2022.769830] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 01/07/2022] [Indexed: 11/19/2022] Open
Abstract
Environmentally friendly functionalization and recycling processes for synthetic polymers have recently gained momentum, and enzymes play a central role in these procedures. However, natural enzymes must be engineered to accept synthetic polymers as substrates. To enhance the activity on synthetic polyesters, the canonical amino acid methionine in Thermoanaerobacter thermohydrosulfuricus lipase (TTL) was exchanged by the residue-specific incorporation method for the more hydrophobic non-canonical norleucine (Nle). Strutural modelling of TTL revealed that residues Met-114 and Met-142 are in close vicinity of the active site and their replacement by the norleucine could modulate the catalytic activity of the enzyme. Indeed, hydrolysis of the polyethylene terephthalate model substrate by the Nle variant resulted in significantly higher amounts of release products than the Met variant. A similar trend was observed for an ionic phthalic polyester containing a short alkyl diol (C5). Interestingly, a 50% increased activity was found for TTL [Nle] towards ionic phthalic polyesters containing different ether diols compared to the parent enzyme TTL [Met]. These findings clearly demonstrate the high potential of non-canonical amino acids for enzyme engineering.
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Affiliation(s)
| | - Patrik Fladischer
- Acib–Austrian Centre of Industrial Biotechnology, Graz, Austria
- Institute of Molecular Biotechnology, Graz University of Technology, Graz, Austria
| | | | | | - Tea Pavkov-Keller
- Acib–Austrian Centre of Industrial Biotechnology, Graz, Austria
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
- Field of Excellence BioHealth—University of Graz, Graz, Austria
| | - Karl Gruber
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
- Field of Excellence BioHealth—University of Graz, Graz, Austria
| | | | | | | | - Doris Ribitsch
- Acib–Austrian Centre of Industrial Biotechnology, Graz, Austria
- Institute for Environmental Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
- *Correspondence: Doris Ribitsch,
| | - Georg M. Guebitz
- Acib–Austrian Centre of Industrial Biotechnology, Graz, Austria
- Institute for Environmental Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Birgit Wiltschi
- Acib–Austrian Centre of Industrial Biotechnology, Graz, Austria
- Institute of Molecular Biotechnology, Graz University of Technology, Graz, Austria
- BioTechMed-Graz, Graz, Austria
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3
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Johnson AN, Barlow DE, Kelly AL, Varaljay VA, Crookes‐Goodson WJ, Biffinger JC. Current progress towards understanding the biodegradation of synthetic condensation polymers with active hydrolases. POLYM INT 2020. [DOI: 10.1002/pi.6131] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
| | - Daniel E Barlow
- Chemistry Division Naval Research Laboratory Washington, DC USA
| | | | - Vanessa A Varaljay
- Soft Matter Materials Branch, Materials and Manufacturing Directorate Air Force Research Laboratory Wright‐Patterson Air Force Base OH USA
| | - Wendy J Crookes‐Goodson
- Soft Matter Materials Branch, Materials and Manufacturing Directorate Air Force Research Laboratory Wright‐Patterson Air Force Base OH USA
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Plastic Pollution in Soils: Governance Approaches to Foster Soil Health and Closed Nutrient Cycles. ENVIRONMENTS 2020. [DOI: 10.3390/environments7050038] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Plastic pollution in soils pose a major threat to soil health and soil fertility that are directly linked to food security and human health. In contrast to marine plastic pollution, this ubiquitous problem is thus far scientifically poorly understood and policy approaches that tackle plastic pollution in soils comprehensively do not exist. In this article, we apply a qualitative governance analysis to assess the effectiveness of existing policy instruments to avoid harmful plastic pollution in (agricultural) soils against the background of international environmental agreements. In particular, environmental and fertiliser legislation relevant to soil protection in the European Union and in Germany are assessed. Regulatory weaknesses and gaps of the respective legislation are identified, and proposals for enhanced command-and-control provisions developed. However, the legal analysis furthermore shows that plastic pollution ecologically is also a problem of quantity, which is difficult to solve exclusively through command-and-control legislation. Instead, comprehensive quantity-control instruments to phase out fossil fuels (worldwide and in all sectors) as required by climate protection law can be effective approaches to tackle plastic pollution in environmental media like agricultural soils as well.
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Bollinger A, Thies S, Knieps-Grünhagen E, Gertzen C, Kobus S, Höppner A, Ferrer M, Gohlke H, Smits SHJ, Jaeger KE. A Novel Polyester Hydrolase From the Marine Bacterium Pseudomonas aestusnigri - Structural and Functional Insights. Front Microbiol 2020; 11:114. [PMID: 32117139 PMCID: PMC7031157 DOI: 10.3389/fmicb.2020.00114] [Citation(s) in RCA: 114] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 01/17/2020] [Indexed: 11/17/2022] Open
Abstract
Biodegradation of synthetic polymers, in particular polyethylene terephthalate (PET), is of great importance, since environmental pollution with PET and other plastics has become a severe global problem. Here, we report on the polyester degrading ability of a novel carboxylic ester hydrolase identified in the genome of the marine hydrocarbonoclastic bacterium Pseudomonas aestusnigri VGXO14T. The enzyme, designated PE-H, belongs to the type IIa family of PET hydrolytic enzymes as indicated by amino acid sequence homology. It was produced in Escherichia coli, purified and its crystal structure was solved at 1.09 Å resolution representing the first structure of a type IIa PET hydrolytic enzyme. The structure shows a typical α/β-hydrolase fold and high structural homology to known polyester hydrolases. PET hydrolysis was detected at 30°C with amorphous PET film (PETa), but not with PET film from a commercial PET bottle (PETb). A rational mutagenesis study to improve the PET degrading potential of PE-H yielded variant PE-H (Y250S) which showed improved activity, ultimately also allowing the hydrolysis of PETb. The crystal structure of this variant solved at 1.35 Å resolution allowed to rationalize the improvement of enzymatic activity. A PET oligomer binding model was proposed by molecular docking computations. Our results indicate a significant potential of the marine bacterium P. aestusnigri for PET degradation.
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Affiliation(s)
- Alexander Bollinger
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Jülich, Germany
| | - Stephan Thies
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Jülich, Germany
| | - Esther Knieps-Grünhagen
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Jülich, Germany
| | - Christoph Gertzen
- Center for Structural Studies, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.,Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Stefanie Kobus
- Center for Structural Studies, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Astrid Höppner
- Center for Structural Studies, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Manuel Ferrer
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.,Institute of Biological Information Processing (IBI-7: Structural Biochemistry), John von Neumann Institute for Computing and Jülich Supercomputing Centre, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Sander H J Smits
- Center for Structural Studies, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.,Institute of Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Jülich, Germany.,Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
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Molitor R, Bollinger A, Kubicki S, Loeschcke A, Jaeger K, Thies S. Agar plate-based screening methods for the identification of polyester hydrolysis by Pseudomonas species. Microb Biotechnol 2020; 13:274-284. [PMID: 31016871 PMCID: PMC6922526 DOI: 10.1111/1751-7915.13418] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 04/05/2019] [Accepted: 04/08/2019] [Indexed: 12/24/2022] Open
Abstract
Hydrolases acting on polyesters like cutin, polycaprolactone or polyethylene terephthalate (PET) are of interest for several biotechnological applications like waste treatment, biocatalysis and sustainable polymer modifications. Recent studies suggest that a large variety of such enzymes are still to be identified and explored in a variety of microorganisms, including bacteria of the genus Pseudomonas. For activity-based screening, methods have been established using agar plates which contain nanoparticles of polycaprolactone or PET prepared by solvent precipitation and evaporation. In this protocol article, we describe a straightforward agar plate-based method using emulsifiable artificial polyesters as substrates, namely Impranil® DLN and liquid polycaprolactone diol (PLD). Thereby, the currently quite narrow set of screening substrates is expanded. We also suggest optional pre-screening with short-chain and middle-chain-length triglycerides as substrates to identify enzymes with lipolytic activity to be further tested for polyesterase activity. We applied these assays to experimentally demonstrate polyesterase activity in bacteria from the P. pertucinogena lineage originating from contaminated soils and diverse marine habitats.
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Affiliation(s)
- Rebecka Molitor
- Institute of Molecular Enzyme TechnologyHeinrich‐Heine‐University DüsseldorfForschungszentrum JülichD‐52425JülichGermany
| | - Alexander Bollinger
- Institute of Molecular Enzyme TechnologyHeinrich‐Heine‐University DüsseldorfForschungszentrum JülichD‐52425JülichGermany
| | - Sonja Kubicki
- Institute of Molecular Enzyme TechnologyHeinrich‐Heine‐University DüsseldorfForschungszentrum JülichD‐52425JülichGermany
| | - Anita Loeschcke
- Institute of Molecular Enzyme TechnologyHeinrich‐Heine‐University DüsseldorfForschungszentrum JülichD‐52425JülichGermany
| | - Karl‐Erich Jaeger
- Institute of Molecular Enzyme TechnologyHeinrich‐Heine‐University DüsseldorfForschungszentrum JülichD‐52425JülichGermany
- Institute of Bio‐ and Geosciences IBG‐1: BiotechnologyForschungszentrum Jülich GmbHD‐52425JülichGermany
| | - Stephan Thies
- Institute of Molecular Enzyme TechnologyHeinrich‐Heine‐University DüsseldorfForschungszentrum JülichD‐52425JülichGermany
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Bollinger A, Thies S, Katzke N, Jaeger K. The biotechnological potential of marine bacteria in the novel lineage of Pseudomonas pertucinogena. Microb Biotechnol 2020; 13:19-31. [PMID: 29943398 PMCID: PMC6922532 DOI: 10.1111/1751-7915.13288] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 05/24/2018] [Accepted: 05/25/2018] [Indexed: 01/20/2023] Open
Abstract
Marine habitats represent a prolific source for molecules of biotechnological interest. In particular, marine bacteria have attracted attention and were successfully exploited for industrial applications. Recently, a group of Pseudomonas species isolated from extreme habitats or living in association with algae or sponges were clustered in the newly established Pseudomonas pertucinogena lineage. Remarkably for the predominantly terrestrial genus Pseudomonas, more than half (9) of currently 16 species within this lineage were isolated from marine or saline habitats. Unlike other Pseudomonas species, they seem to have in common a highly specialized metabolism. Furthermore, the marine members apparently possess the capacity to produce biomolecules of biotechnological interest (e.g. dehalogenases, polyester hydrolases, transaminases). Here, we summarize the knowledge regarding the enzymatic endowment of the marine Pseudomonas pertucinogena bacteria and report on a genomic analysis focusing on the presence of genes encoding esterases, dehalogenases, transaminases and secondary metabolites including carbon storage compounds.
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Affiliation(s)
- Alexander Bollinger
- Institute of Molecular Enzyme TechnologyHeinrich‐Heine‐University DüsseldorfForschungszentrum JülichD‐52425JülichGermany
| | - Stephan Thies
- Institute of Molecular Enzyme TechnologyHeinrich‐Heine‐University DüsseldorfForschungszentrum JülichD‐52425JülichGermany
| | - Nadine Katzke
- Institute of Molecular Enzyme TechnologyHeinrich‐Heine‐University DüsseldorfForschungszentrum JülichD‐52425JülichGermany
| | - Karl‐Erich Jaeger
- Institute of Molecular Enzyme TechnologyHeinrich‐Heine‐University DüsseldorfForschungszentrum JülichD‐52425JülichGermany
- Institute of Bio‐ and Geosciences IBG‐1: BiotechnologyForschungszentrum Jülich GmbHD‐52425JülichGermany
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8
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Current knowledge on enzymatic PET degradation and its possible application to waste stream management and other fields. Appl Microbiol Biotechnol 2019; 103:4253-4268. [PMID: 30957199 PMCID: PMC6505623 DOI: 10.1007/s00253-019-09717-y] [Citation(s) in RCA: 232] [Impact Index Per Article: 46.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 02/20/2019] [Accepted: 02/22/2019] [Indexed: 11/21/2022]
Abstract
Enzymatic hydrolysis of polyethylene terephthalate (PET) has been the subject of extensive previous research that can be grouped into two categories, viz. enzymatic surface modification of polyester fibers and management of PET waste by enzymatic hydrolysis. Different enzymes with rather specific properties are required for these two processes. Enzymatic surface modification is possible with several hydrolases, such as lipases, carboxylesterases, cutinases, and proteases. These enzymes should be designated as PET surface–modifying enzymes and should not degrade the building blocks of PET but should hydrolyze the surface polymer chain so that the intensity of PET is not weakened. Conversely, management of PET waste requires substantial degradation of the building blocks of PET; therefore, only a limited number of cutinases have been recognized as PET hydrolases since the first PET hydrolase was discovered by Müller et al. (Macromol Rapid Commun 26:1400–1405, 2005). Here, we introduce current knowledge on enzymatic degradation of PET with a focus on the key class of enzymes, PET hydrolases, pertaining to the definition of enzymatic requirements for PET hydrolysis, structural analyses of PET hydrolases, and the reaction mechanisms. This review gives a deep insight into the structural basis and dynamics of PET hydrolases based on the recent progress in X-ray crystallography. Based on the knowledge accumulated to date, we discuss the potential for PET hydrolysis applications, such as in designing waste stream management.
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Abstract
Cutinases are α/β hydrolases, and their role in nature is the degradation of cutin. Such enzymes are usually produced by phytopathogenic microorganisms in order to penetrate their hosts. The first focused studies on cutinases started around 50 years ago. Since then, numerous cutinases have been isolated and characterized, aiming at the elucidation of their structure–function relations. Our deeper understanding of cutinases determines the applications by which they could be utilized; from food processing and detergents, to ester synthesis and polymerizations. However, cutinases are mainly efficient in the degradation of polyesters, a natural function. Therefore, these enzymes have been successfully applied for the biodegradation of plastics, as well as for the delicate superficial hydrolysis of polymeric materials prior to their functionalization. Even though research on this family of enzymes essentially began five decades ago, they are still involved in many reports; novel enzymes are being discovered, and new fields of applications arise, leading to numerous related publications per year. Perhaps the future of cutinases lies in their evolved descendants, such as polyesterases, and particularly PETases. The present article reviews the biochemical and structural characteristics of cutinases and cutinase-like hydrolases, and their applications in the field of bioremediation and biocatalysis.
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