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Jiménez JD, Godoy MS, Del Cerro C, Prieto MA. Hints from nature for a PHA circular economy: Carbon synthesis and sharing by Pseudomonas solani GK13. N Biotechnol 2024; 84:9-23. [PMID: 39245322 DOI: 10.1016/j.nbt.2024.09.002] [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: 06/19/2024] [Revised: 09/05/2024] [Accepted: 09/05/2024] [Indexed: 09/10/2024]
Abstract
Polyhydroxyalkanoates (PHAs) are a well-known group of biodegradable and biocompatible bioplastics that are synthesised and stored by microorganisms as carbon and energy reservoirs. Extracellular PHA depolymerases (ePhaZs), secreted by a limited range of microorganisms, are the main hydrolytic enzymes responsible for their environmental degradation. Pseudomonas sp. GK13, initially identified as P. fluorescens GK13, produces PHA and a prototypic ePhaZ that specifically degrades mcl-PHA. In this study, a comprehensive characterization of strain GK13 was performed. The whole genomic sequence of GK13 was consolidated into one complete chromosome, leading to its reclassification as P. solani GK13. We conducted a detailed in silico examination of the bacteria genomic sequence, specifically targeting PHA metabolic functions. From the different growth conditions explored, PHA accumulation occurred only under carbon/nitrogen (C/N) imbalance, whereas ePhaZ production was induced even at balanced C/N ratios in mineral media. We extend our study to other bacteria belonging to the Pseudomonas genus revealing that the ePhaZ production capacity is closely associated with mcl-PHA synthesis capacity, as also suggested by metagenomic samples. This finding suggests that these types of microorganisms could contribute to the carbon economy of the microbial community, by storing PHA in carbon-rich times, and sharing it with the rest of the population during times of carbon scarcity through PHA hydrolysis. The conclusion pointed that carbon cycle metabolism performed by P. solani GK13 may contribute to the environmental circular economy at a microscopic scale.
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Affiliation(s)
- José D Jiménez
- Polymer Biotechnology Lab, Biological Research Center Margarita Salas, Spanish National Research Council (CIB-CSIC), Madrid, Spain; Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy-CSIC (SusPlast-CSIC), Madrid, Spain
| | - Manuel S Godoy
- Polymer Biotechnology Lab, Biological Research Center Margarita Salas, Spanish National Research Council (CIB-CSIC), Madrid, Spain; Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy-CSIC (SusPlast-CSIC), Madrid, Spain.
| | - Carlos Del Cerro
- Environmental Microbiology Lab, Biological Research Center Margarita Salas, Spanish National Research Council (CIB-CSIC), Madrid, Spain
| | - M Auxiliadora Prieto
- Polymer Biotechnology Lab, Biological Research Center Margarita Salas, Spanish National Research Council (CIB-CSIC), Madrid, Spain; Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy-CSIC (SusPlast-CSIC), Madrid, Spain.
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2
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Mohanan N, Wong MCH, Budisa N, Levin DB. Polymer-Degrading Enzymes of Pseudomonas chloroaphis PA23 Display Broad Substrate Preferences. Int J Mol Sci 2023; 24:ijms24054501. [PMID: 36901931 PMCID: PMC10003648 DOI: 10.3390/ijms24054501] [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: 01/02/2023] [Revised: 01/27/2023] [Accepted: 02/14/2023] [Indexed: 03/02/2023] Open
Abstract
Although many bacterial lipases and PHA depolymerases have been identified, cloned, and characterized, there is very little information on the potential application of lipases and PHA depolymerases, especially intracellular enzymes, for the degradation of polyester polymers/plastics. We identified genes encoding an intracellular lipase (LIP3), an extracellular lipase (LIP4), and an intracellular PHA depolymerase (PhaZ) in the genome of the bacterium Pseudomonas chlororaphis PA23. We cloned these genes into Escherichia coli and then expressed, purified, and characterized the biochemistry and substrate preferences of the enzymes they encode. Our data suggest that the LIP3, LIP4, and PhaZ enzymes differ significantly in their biochemical and biophysical properties, structural-folding characteristics, and the absence or presence of a lid domain. Despite their different properties, the enzymes exhibited broad substrate specificity and were able to hydrolyze both short- and medium-chain length polyhydroxyalkanoates (PHAs), para-nitrophenyl (pNP) alkanoates, and polylactic acid (PLA). Gel Permeation Chromatography (GPC) analyses of the polymers treated with LIP3, LIP4, and PhaZ revealed significant degradation of both the biodegradable as well as the synthetic polymers poly(ε-caprolactone) (PCL) and polyethylene succinate (PES).
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Affiliation(s)
- Nisha Mohanan
- Department of Biosystems Engineering, University of Manitoba, Winnipeg, MB R3T 5V6, Canada
| | - Michael C.-H. Wong
- Department of Chemistry, University of Manitoba, 144 Dysart Rd., Winnipeg, MB R3T 2N2, Canada
| | - Nediljko Budisa
- Department of Chemistry, University of Manitoba, 144 Dysart Rd., Winnipeg, MB R3T 2N2, Canada
- Biocatalysis Group, Technical University of Berlin, Müller-Breslau-Str. 10, D-10623 Berlin, Germany
- Correspondence: or (N.B.); (D.B.L.); Tel.: +1-204-474-7429
| | - David B. Levin
- Department of Biosystems Engineering, University of Manitoba, Winnipeg, MB R3T 5V6, Canada
- Correspondence: or (N.B.); (D.B.L.); Tel.: +1-204-474-7429
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3
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El-Malek FA, Steinbüchel A. Post-Synthetic Enzymatic and Chemical Modifications for Novel Sustainable Polyesters. Front Bioeng Biotechnol 2022; 9:817023. [PMID: 35071219 PMCID: PMC8766639 DOI: 10.3389/fbioe.2021.817023] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 12/20/2021] [Indexed: 11/13/2022] Open
Abstract
Because of their biodegradability, compostability, compatibility and flexible structures, biodegradable polymers such as polyhydroxyalkanoates (PHA) are an important class of biopolymers with various industrial and biological uses. PHAs are thermoplastic polyesters with a limited processability due to their low heat resistance. Furthermore, due to their high crystallinity, some PHAs are stiff and brittle. These features result sometimes in very poor mechanical characteristics with low extension at break values which limit the application range of some natural PHAs. Several in vivo approaches for PHA copolymer modifications range from polymer production to enhance PHA-based material performance after synthesis. The methods for enzymatic and chemical polymer modifications are aiming at modifying the structures of the polyesters and thereby their characteristics while retaining the biodegradability. This survey illustrates the efficient use of enzymes and chemicals in post-synthetic PHA modifications, offering insights on these green techniques for modifying and improving polymer performance. Important studies in this sector will be reviewed, as well as chances and obstacles for their stability and hyper-production.
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Affiliation(s)
- Fady Abd El-Malek
- International Center for Research on Innovative Biobased Materials (ICRI-BioM)-International Research Agenda, Lodz University of Technology, Lodz, Poland
| | - Alexander Steinbüchel
- International Center for Research on Innovative Biobased Materials (ICRI-BioM)-International Research Agenda, Lodz University of Technology, Lodz, Poland
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Nikolaivits E, Pantelic B, Azeem M, Taxeidis G, Babu R, Topakas E, Brennan Fournet M, Nikodinovic-Runic J. Progressing Plastics Circularity: A Review of Mechano-Biocatalytic Approaches for Waste Plastic (Re)valorization. Front Bioeng Biotechnol 2021; 9:696040. [PMID: 34239864 PMCID: PMC8260098 DOI: 10.3389/fbioe.2021.696040] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 05/28/2021] [Indexed: 01/10/2023] Open
Abstract
Inspirational concepts, and the transfer of analogs from natural biology to science and engineering, has produced many excellent technologies to date, spanning vaccines to modern architectural feats. This review highlights that answers to the pressing global petroleum-based plastic waste challenges, can be found within the mechanics and mechanisms natural ecosystems. Here, a suite of technological and engineering approaches, which can be implemented to operate in tandem with nature's prescription for regenerative material circularity, is presented as a route to plastics sustainability. A number of mechanical/green chemical (pre)treatment methodologies, which simulate natural weathering and arthropodal dismantling activities are reviewed, including: mechanical milling, reactive extrusion, ultrasonic-, UV- and degradation using supercritical CO2. Akin to natural mechanical degradation, the purpose of the pretreatments is to render the plastic materials more amenable to microbial and biocatalytic activities, to yield effective depolymerization and (re)valorization. While biotechnological based degradation and depolymerization of both recalcitrant and bioplastics are at a relatively early stage of development, the potential for acceleration and expedition of valuable output monomers and oligomers yields is considerable. To date a limited number of independent mechano-green chemical approaches and a considerable and growing number of standalone enzymatic and microbial degradation studies have been reported. A convergent strategy, one which forges mechano-green chemical treatments together with the enzymatic and microbial actions, is largely lacking at this time. An overview of the reported microbial and enzymatic degradations of petroleum-based synthetic polymer plastics, specifically: low-density polyethylene (LDPE), high-density polyethylene (HDPE), polystyrene (PS), polyethylene terephthalate (PET), polyurethanes (PU) and polycaprolactone (PCL) and selected prevalent bio-based or bio-polymers [polylactic acid (PLA), polyhydroxyalkanoates (PHAs) and polybutylene succinate (PBS)], is detailed. The harvesting of depolymerization products to produce new materials and higher-value products is also a key endeavor in effectively completing the circle for plastics. Our challenge is now to effectively combine and conjugate the requisite cross disciplinary approaches and progress the essential science and engineering technologies to categorically complete the life-cycle for plastics.
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Affiliation(s)
- Efstratios Nikolaivits
- Industrial Biotechnology & Biocatalysis Group, Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Brana Pantelic
- Eco-Biotechnology & Drug Development Group, Laboratory for Microbial Molecular Genetics and Ecology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | | | - George Taxeidis
- Industrial Biotechnology & Biocatalysis Group, Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Ramesh Babu
- AMBER Centre, CRANN Institute, School of Chemistry, Trinity College Dublin, Dublin, Ireland
| | - Evangelos Topakas
- Industrial Biotechnology & Biocatalysis Group, Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | | | - Jasmina Nikodinovic-Runic
- Eco-Biotechnology & Drug Development Group, Laboratory for Microbial Molecular Genetics and Ecology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
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Characterization of an intracellular poly(3-hydroxyalkanoate) depolymerase from the soil bacterium, Pseudomonas putida LS46. Polym Degrad Stab 2020. [DOI: 10.1016/j.polymdegradstab.2020.109127] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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6
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Sharma PK, Mohanan N, Sidhu R, Levin DB. Colonization and degradation of polyhydroxyalkanoates by lipase-producing bacteria. Can J Microbiol 2019; 65:461-475. [PMID: 30897336 DOI: 10.1139/cjm-2019-0042] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Biodegradation of short-chain-length polyhydroxyalkanoates (scl-PHAs) and medium-chain-length polyhydroxyalkanoates (mcl-PHAs) was studied using 2 bacteria, Pseudomonas chlororaphis and Acinetobacter lwoffii, which secrete an enzyme, or enzymes, with lipase activity. These bacteria produced clear zones of depolymerization on Petri plates containing colloidal solutions of PHA polymers with different monomer compositions. Lipase activity in these bacteria was measured using p-nitrophenyl octanoate as a substrate. In liquid medium, scl-PHA (e.g., PHBV) and mcl-PHA (e.g., PHO) films were used as the sole carbon source for growth, and after 7 days, 5%-18% loss in mass of PHA films was observed. Scanning electron microscopy of these films revealed bacterial colonization of the polymers, with cracks and pitting in the film surfaces. Degradation of polymers released 3-hydroxyhexanoate, 3-hydroxyoctanoate, and 3-hydroxydecanoate monomers into the liquid medium, depending on the starting polymer. Genes encoding secretory lipases, with amino acid consensus sequences for lipase boxes and oxyanion holes, were identified in the genomes of P. chlororaphis and A. lwoffii. Although amino acid consensus sequences for lipase boxes and oxyanion holes are also present in PHA depolymerases identified in the genomes of other PHA-degrading bacteria, the P. chlororaphis and A. lwoffii lipases had low homology with these depolymerases.
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Affiliation(s)
- Parveen K Sharma
- a Department of Biosystems Engineering, University of Manitoba, Winnipeg, MB R3T 5V6, Canada
| | - Nisha Mohanan
- a Department of Biosystems Engineering, University of Manitoba, Winnipeg, MB R3T 5V6, Canada
| | - Ravinder Sidhu
- b Manitoba Institute for Materials & Faculty of Science, University of Manitoba, Winnipeg, MB R3T 5V6, Canada
| | - David B Levin
- a Department of Biosystems Engineering, University of Manitoba, Winnipeg, MB R3T 5V6, Canada
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Infanzón B, Cesarini S, Martínez J, Pastor FIJ, Diaz P. Alternative Oils Tested as Feedstocks for Enzymatic FAMEs Synthesis: Toward a More Sustainable Process. Biotechnol Prog 2017; 33:1209-1217. [DOI: 10.1002/btpr.2558] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 07/20/2017] [Indexed: 11/11/2022]
Affiliation(s)
- Belén Infanzón
- Department of Genetics, Microbiology and Statistics; University of Barcelona; Barcelona 08028 Spain
| | - Silvia Cesarini
- Department of Genetics, Microbiology and Statistics; University of Barcelona; Barcelona 08028 Spain
| | - Josefina Martínez
- Department of Genetics, Microbiology and Statistics; University of Barcelona; Barcelona 08028 Spain
- Institute of Nanoscience and Nanotechnology (IN2UB), University of Barcelona; Spain
| | - F. I. Javier Pastor
- Department of Genetics, Microbiology and Statistics; University of Barcelona; Barcelona 08028 Spain
- Institute of Nanoscience and Nanotechnology (IN2UB), University of Barcelona; Spain
| | - Pilar Diaz
- Department of Genetics, Microbiology and Statistics, Faculty of Biology; University of Barcelona, Barcelona, Av. Diagonal 643, 08028; Barcelona Spain
- Institute of Nanoscience and Nanotechnology (IN2UB), University of Barcelona; Spain
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8
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Ensari Y, Dhoke GV, Davari MD, Bocola M, Ruff AJ, Schwaneberg U. Inversion of cpADH5 Enantiopreference and Altered Chain Length Specificity for Methyl 3-Hydroxyalkanoates. Chemistry 2017; 23:12636-12645. [DOI: 10.1002/chem.201702581] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Indexed: 11/12/2022]
Affiliation(s)
- Yunus Ensari
- Lehrstuhl für Biotechnologie; RWTH Aachen University; Worringerweg 3 52074 Aachen Germany
- Faculty of Engineering and Architecture; Department of Bioengineering; Kafkas University; Kars Turkey
| | - Gaurao V. Dhoke
- Lehrstuhl für Biotechnologie; RWTH Aachen University; Worringerweg 3 52074 Aachen Germany
| | - Mehdi D. Davari
- Lehrstuhl für Biotechnologie; RWTH Aachen University; Worringerweg 3 52074 Aachen Germany
| | - Marco Bocola
- Lehrstuhl für Biotechnologie; RWTH Aachen University; Worringerweg 3 52074 Aachen Germany
| | - Anna Joëlle Ruff
- Lehrstuhl für Biotechnologie; RWTH Aachen University; Worringerweg 3 52074 Aachen Germany
| | - Ulrich Schwaneberg
- Lehrstuhl für Biotechnologie; RWTH Aachen University; Worringerweg 3 52074 Aachen Germany
- DWI-Leibniz Institut für Interaktive Materialien; Forckenbeckstraße 50 52056 Aachen Germany
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9
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Martínez V, de Santos PG, García-Hidalgo J, Hormigo D, Prieto MA, Arroyo M, de la Mata I. Novel extracellular medium-chain-length polyhydroxyalkanoate depolymerase from Streptomyces exfoliatus K10 DSMZ 41693: a promising biocatalyst for the efficient degradation of natural and functionalized mcl-PHAs. Appl Microbiol Biotechnol 2015; 99:9605-15. [PMID: 26156240 DOI: 10.1007/s00253-015-6780-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Revised: 06/15/2015] [Accepted: 06/17/2015] [Indexed: 11/30/2022]
Abstract
Cloning and biochemical characterization of a novel extracellular medium-chain-length polyhydroxyalkanoate (mcl-PHA) depolymerase from Streptomyces exfoliatus K10 DSMZ 41693 are described. The primary structure of the depolymerase (PhaZSex2) includes the lipase consensus sequence (serine-histidine-aspartic acid) which is known for serine hydrolases. Secondary structure analysis shows 7.9 % α-helix, 43.9 % β-sheet, 19.4 % β-turns, and 31.2 % random coil, suggesting that this enzyme belongs to the α/β hydrolase fold family, in agreement with other PHA depolymerases and lipases. The enzyme was efficiently produced as an extracellular active form in Rhodococcus and purified by two consecutive hydrophobic chromatographic steps. Matrix-assisted laser desorption-time-of-flight (MALDI-TOF) analysis of the purified enzyme revealed a monomer of 27.6 kDa with a midpoint transition temperature of 44.2 °C. Remarkably, the activity is significantly enhanced by low concentrations of nonionic and anionic detergents and thermal stability is improved by the presence of 10 % glycerol. PhaZSex2 is an endo-exohydrolase that cleaves both large and small PHA molecules, producing (R)-3-hydroxyoctanoic acid monomers as the main reaction product. Markedly, PhaZSex2 is able to degrade functionalized polymers containing thioester groups in the side chain (PHACOS), releasing functional thioester-based monomers and oligomers demonstrating the potentiality of this novel biocatalyst for the industrial production of enantiopure (R)-3-hydroxyalkanoic acids.
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Affiliation(s)
- Virginia Martínez
- Department of Biochemistry and Molecular Biology, Facultad de Biología, Universidad Complutense de Madrid, Madrid, Spain.,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
| | - Patricia Gómez de Santos
- Department of Biochemistry and Molecular Biology, Facultad de Biología, Universidad Complutense de Madrid, Madrid, Spain.,Department of Biocatalysis, Institute of Catalysis, CSIC, Madrid, Spain
| | - Javier García-Hidalgo
- Department of Biochemistry and Molecular Biology, Facultad de Biología, Universidad Complutense de Madrid, Madrid, Spain
| | - Daniel Hormigo
- Department of Biochemistry and Molecular Biology, Facultad de Biología, Universidad Complutense de Madrid, Madrid, Spain.,Department of Pharmacy and Biotechnology, Biomedical Sciences Faculty, European University of Madrid, Madrid, Spain
| | - M Auxiliadora Prieto
- Department of Environmental Biology, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Miguel Arroyo
- Department of Biochemistry and Molecular Biology, Facultad de Biología, Universidad Complutense de Madrid, Madrid, Spain
| | - Isabel de la Mata
- Department of Biochemistry and Molecular Biology, Facultad de Biología, Universidad Complutense de Madrid, Madrid, Spain.
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Prieto A, Escapa IF, Martínez V, Dinjaski N, Herencias C, de la Peña F, Tarazona N, Revelles O. A holistic view of polyhydroxyalkanoate metabolism inPseudomonas putida. Environ Microbiol 2015; 18:341-57. [DOI: 10.1111/1462-2920.12760] [Citation(s) in RCA: 129] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 12/12/2014] [Accepted: 12/20/2014] [Indexed: 11/29/2022]
Affiliation(s)
- Auxiliadora Prieto
- Department of Environmental Biology; Centro de Investigaciones Biológicas; CSIC; Madrid 28040 Spain
| | - Isabel F. Escapa
- Department of Environmental Biology; Centro de Investigaciones Biológicas; CSIC; Madrid 28040 Spain
| | - Virginia Martínez
- Department of Environmental Biology; Centro de Investigaciones Biológicas; CSIC; Madrid 28040 Spain
| | - Nina Dinjaski
- Department of Environmental Biology; Centro de Investigaciones Biológicas; CSIC; Madrid 28040 Spain
| | - Cristina Herencias
- Department of Environmental Biology; Centro de Investigaciones Biológicas; CSIC; Madrid 28040 Spain
| | - Fernando de la Peña
- Department of Environmental Biology; Centro de Investigaciones Biológicas; CSIC; Madrid 28040 Spain
| | - Natalia Tarazona
- Department of Environmental Biology; Centro de Investigaciones Biológicas; CSIC; Madrid 28040 Spain
| | - Olga Revelles
- Department of Environmental Biology; Centro de Investigaciones Biológicas; CSIC; Madrid 28040 Spain
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12
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Lignin valorization through integrated biological funneling and chemical catalysis. Proc Natl Acad Sci U S A 2014; 111:12013-8. [PMID: 25092344 DOI: 10.1073/pnas.1410657111] [Citation(s) in RCA: 429] [Impact Index Per Article: 42.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Lignin is an energy-dense, heterogeneous polymer comprised of phenylpropanoid monomers used by plants for structure, water transport, and defense, and it is the second most abundant biopolymer on Earth after cellulose. In production of fuels and chemicals from biomass, lignin is typically underused as a feedstock and burned for process heat because its inherent heterogeneity and recalcitrance make it difficult to selectively valorize. In nature, however, some organisms have evolved metabolic pathways that enable the utilization of lignin-derived aromatic molecules as carbon sources. Aromatic catabolism typically occurs via upper pathways that act as a "biological funnel" to convert heterogeneous substrates to central intermediates, such as protocatechuate or catechol. These intermediates undergo ring cleavage and are further converted via the β-ketoadipate pathway to central carbon metabolism. Here, we use a natural aromatic-catabolizing organism, Pseudomonas putida KT2440, to demonstrate that these aromatic metabolic pathways can be used to convert both aromatic model compounds and heterogeneous, lignin-enriched streams derived from pilot-scale biomass pretreatment into medium chain-length polyhydroxyalkanoates (mcl-PHAs). mcl-PHAs were then isolated from the cells and demonstrated to be similar in physicochemical properties to conventional carbohydrate-derived mcl-PHAs, which have applications as bioplastics. In a further demonstration of their utility, mcl-PHAs were catalytically converted to both chemical precursors and fuel-range hydrocarbons. Overall, this work demonstrates that the use of aromatic catabolic pathways enables an approach to valorize lignin by overcoming its inherent heterogeneity to produce fuels, chemicals, and materials.
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Cesarini S, Infanzón B, Pastor FIJ, Diaz P. Fast and economic immobilization methods described for non-commercial Pseudomonas lipases. BMC Biotechnol 2014; 14:27. [PMID: 24755191 PMCID: PMC4003287 DOI: 10.1186/1472-6750-14-27] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Accepted: 04/09/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND There is an increasing interest to seek new enzyme preparations for the development of new products derived from bioprocesses to obtain alternative bio-based materials. In this context, four non-commercial lipases from Pseudomonas species were prepared, immobilized on different low-cost supports, and examined for potential biotechnological applications. RESULTS To reduce costs of eventual scaling-up, the new lipases were obtained directly from crude cell extracts or from growth culture supernatants, and immobilized by simple adsorption on Accurel EP100, Accurel MP1000 and Celite®545. The enzymes evaluated were LipA and LipC from Pseudomonas sp. 42A2, a thermostable mutant of LipC, and LipI.3 from Pseudomonas CR611, which were produced in either homologous or heterologous hosts. Best immobilization results were obtained on Accurel EP100 for LipA and on Accurel MP1000 for LipC and its thermostable variant. Lip I.3, requiring a refolding step, was poorly immobilized on all supports tested (best results for Accurel MP1000). To test the behavior of immobilized lipases, they were assayed in triolein transesterification, where the best results were observed for lipases immobilized on Accurel MP1000. CONCLUSIONS The suggested protocol does not require protein purification and uses crude enzymes immobilized by a fast adsorption technique on low-cost supports, which makes the method suitable for an eventual scaling up aimed at biotechnological applications. Therefore, a fast, simple and economic method for lipase preparation and immobilization has been set up. The low price of the supports tested and the simplicity of the procedure, skipping the tedious and expensive purification steps, will contribute to cost reduction in biotechnological lipase-catalyzed processes.
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Affiliation(s)
- Silvia Cesarini
- Department of Microbiology, University of Barcelona, Av. Diagonal 643, 08028 Barcelona, Spain
| | - Belén Infanzón
- Department of Microbiology, University of Barcelona, Av. Diagonal 643, 08028 Barcelona, Spain
| | - F I Javier Pastor
- Department of Microbiology, University of Barcelona, Av. Diagonal 643, 08028 Barcelona, Spain
| | - Pilar Diaz
- Department of Microbiology, University of Barcelona, Av. Diagonal 643, 08028 Barcelona, Spain
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Martínez V, Dinjaski N, de Eugenio LI, de la Peña F, Prieto MA. Cell system engineering to produce extracellular polyhydroxyalkanoate depolymerase with targeted applications. Int J Biol Macromol 2014; 71:28-33. [PMID: 24751505 DOI: 10.1016/j.ijbiomac.2014.04.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Revised: 03/19/2014] [Accepted: 04/05/2014] [Indexed: 11/19/2022]
Abstract
Novel platforms based on the application of bacterial cell systems as factories for production of new bioproducts open avenues and dramatically expand the catalogue of existing biomaterials. Herein, we designed the strategy based on in vivo production of extracellular Pseudomonas fluorescens GK13 (PhaZGK13) depolymerase to degrade previously biosynthesized polyhydroxyalkanotes (PHAs) or to obtain 3-hydroxyalkanoic acids (HAs). With this aim, extracellular PhaZGK13 was produced in recombinant strains and the optimal conditions for controlled release of HAs and oligomers by growing cells were set up with a particle suspension of (14)C-labelled PHA, being maximal after 24h of incubation. Genetic modification of key factors involved in fatty acids metabolism revealed the influence of an active β-oxidation pathway on the extracellular degradation of PHA and subsequent HAs isolation. The highest HAs production was obtained using Pseudomonas putida KT2442 fadB mutant (0.27mg/mL) due to the reduced ability of this strain to metabolize the degradation products. The system was applied to produce new added value HAs harboring thioester groups in the side chain from the functionalized mcl-PHA, PHACOS. Remarkably, hydrolyzed PHACOS showed greater potential to inhibit Staphylococcus aureus(T) growth when compared to that of degradation products of non functionalized polyhydroxyoctanoate-co-hexanoate P(HO-co-HH).
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Affiliation(s)
- Virginia Martínez
- Environmental Biology Department, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Nina Dinjaski
- Environmental Biology Department, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Laura I de Eugenio
- Environmental Biology Department, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Fernando de la Peña
- Environmental Biology Department, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - María Auxiliadora Prieto
- Environmental Biology Department, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain.
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Wang Y, Liu S. Production of (R)-3-hydroxybutyric acid by Burkholderia cepacia from wood extract hydrolysates. AMB Express 2014; 4:28. [PMID: 24949263 PMCID: PMC4052727 DOI: 10.1186/s13568-014-0028-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2014] [Accepted: 01/06/2014] [Indexed: 11/10/2022] Open
Abstract
(R)-hydroxyalkanoic acids (R-HAs) are valuable building blocks for the synthesis of fine chemicals and biopolymers because of the chiral center and the two active functional groups. Hydroxyalkanoic acids fermentation can revolutionize the polyhydroxyalkanoic acids (PHA) production by increasing efficiency and enhancing product utility. Modifying the fermentation conditions that promotes the in vivo depolymerization and secretion to fermentation broth in wild type bacteria is a novel and promising approach to produce R-HAs. Wood extract hydrolysate (WEH) was found to be a suitable substrate for R-3-hydroxybutyric acid (R-3-HB) production by Burkholderia cepacia. Using Paulownia elongate WEH as a feedstock, the R-3-HB concentration in fermentation broth reached as high as 14.2 g/L after 3 days of batch fermentation and the highest concentration of 16.8 g/L was obtained at day 9. Further investigation indicated that the composition of culture medium contributed to the enhanced R-3-HB production.
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Chung AL, Zeng GD, Jin HL, Wu Q, Chen JC, Chen GQ. Production of medium-chain-length 3-hydroxyalkanoic acids by β-oxidation and phaC operon deleted Pseudomonas entomophila harboring thioesterase gene. Metab Eng 2013; 17:23-9. [DOI: 10.1016/j.ymben.2013.02.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2012] [Revised: 02/13/2013] [Accepted: 02/25/2013] [Indexed: 10/27/2022]
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Production of long-chain hydroxy fatty acids by microbial conversion. Appl Microbiol Biotechnol 2013; 97:3323-31. [PMID: 23494626 DOI: 10.1007/s00253-013-4815-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2012] [Revised: 02/24/2013] [Accepted: 02/26/2013] [Indexed: 10/27/2022]
Abstract
Hydroxy fatty acids (HFAs) are very important chemicals for versatile applications in biodegradable polymer materials and cosmetic and pharmaceutical industries. They are difficult to be synthesized via chemical routes due to the inertness of the fatty acyl chain. In contrast, these fatty acids make up a major class of natural products widespread among bacteria, yeasts, and fungi. A number of microorganisms capable of producing HFAs from fatty acids or vegetable oils have been reported. Therefore, HFAs could be produced by biotechnological strategies, especially by microbial conversion processes. Microorganisms could oxidize fatty acids either at the terminal carbon or inside the acyl chain to produce various HFAs, including α-HFAs, β-HFAs, mid-position HFAs, ω-HFAs, di-HFAs, and tri-HFAs. The enzymes and their encoded genes responsible for the hydroxylation of the carbon chain have been identified and characterized during the past few years. The involved microbes and catalytic mechanisms for the production of different types of HFAs are systematically demonstrated in this review. It provides a better view of HFA biosynthesis and lays the foundation for further industrial production.
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Seo BS, Kim DY, Ni YY, Son KH, Park HY, Rhee YH. Non-ionic polysorbate surfactants: alternative inducers of medium-chain-length poly(3-hydroxyalkanoates) (MCL-PHAs) for production of extracellular MCL-PHA depolymerases. BIORESOURCE TECHNOLOGY 2012; 121:47-53. [PMID: 22858467 DOI: 10.1016/j.biortech.2012.06.118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2012] [Revised: 06/19/2012] [Accepted: 06/20/2012] [Indexed: 06/01/2023]
Abstract
The potential of non-ionic polysorbate surfactants as alternative inducers of medium-chain-length poly(3-hydroxyalkanoates) (MCL-PHAs) for the production of diverse bacterial MCL-PHA depolymerases was evaluated. When grown with corn oil as the sole carbon substrate, Pseudomonas alcaligenes LB19 preferentially produced lipolytic enzymes, but its MCL-PHA depolymerase was not induced by the substrate. However, the results of activity staining and sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis clearly revealed that Tween 20 induced simultaneous production of lipolytic enzymes and the MCL-PHA depolymerase with the molecular mass (26.5 kDa) of P. alcaligenes LB19, which has been previously identified. Moreover, the co-production of two functionally distinct hydrolytic enzymes induced by Tween 20 was commonly observed in various Gram-positive and Gram-negative bacteria that were fed the substrate. Thus, it is expected that non-ionic polysorbate surfactants including Tween 20 can be widely exploited as promising universal substrates for the facile and efficient production of diverse MCL-PHA depolymerases.
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Affiliation(s)
- Bong Su Seo
- Department of Microbiology and Molecular Biology, Chungnam National University, Daejeon 305-764, Republic of Korea
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Characterization of a novel subgroup of extracellular medium-chain-length polyhydroxyalkanoate depolymerases from actinobacteria. Appl Environ Microbiol 2012; 78:7229-37. [PMID: 22865072 DOI: 10.1128/aem.01707-12] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nineteen medium-chain-length (mcl) poly(3-hydroxyalkanoate) (PHA)-degrading microorganisms were isolated from natural sources. From them, seven Gram-positive and three Gram-negative bacteria were identified. The ability of these microorganisms to hydrolyze other biodegradable plastics, such as short-chain-length (scl) PHA, poly(ε-caprolactone) (PCL), poly(ethylene succinate) (PES), and poly(l-lactide) (PLA), has been studied. On the basis of the great ability to degrade different polyesters, Streptomyces roseolus SL3 was selected, and its extracellular depolymerase was biochemically characterized. The enzyme consisted of one polypeptide chain of 28 kDa with a pI value of 5.2. Its maximum activity was observed at pH 9.5 with chromogenic substrates. The purified enzyme hydrolyzed mcl PHA and PCL but not scl PHA, PES, and PLA. Moreover, the mcl PHA depolymerase can hydrolyze various substrates for esterases, such as tributyrin and p-nitrophenyl (pNP)-alkanoates, with its maximum activity being measured with pNP-octanoate. Interestingly, when poly(3-hydroxyoctanoate-co-3-hydroxyhexanoate [11%]) was used as the substrate, the main hydrolysis product was the monomer (R)-3-hydroxyoctanoate. In addition, the genes of several Actinobacteria strains, including S. roseolus SL3, were identified on the basis of the peptide de novo sequencing of the Streptomyces venezuelae SO1 mcl PHA depolymerase by tandem mass spectrometry. These enzymes did not show significant similarity to mcl PHA depolymerases characterized previously. Our results suggest that these distinct enzymes might represent a new subgroup of mcl PHA depolymerases.
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Identification and biochemical evidence of a medium-chain-length polyhydroxyalkanoate depolymerase in the Bdellovibrio bacteriovorus predatory hydrolytic arsenal. Appl Environ Microbiol 2012; 78:6017-26. [PMID: 22706067 DOI: 10.1128/aem.01099-12] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The obligate predator Bdellovibrio bacteriovorus HD100 shows a large set of proteases and other hydrolases as part of its hydrolytic arsenal needed for its predatory life cycle. We present genetic and biochemical evidence that open reading frame (ORF) Bd3709 of B. bacteriovorus HD100 encodes a novel medium-chain-length polyhydroxyalkanoate (mcl-PHA) depolymerase (PhaZ(Bd)). The primary structure of PhaZ(Bd) suggests that this enzyme belongs to the α/β-hydrolase fold family and has a typical serine hydrolase catalytic triad (serine-histidine-aspartic acid) in agreement with other PHA depolymerases and lipases. PhaZ(Bd) has been extracellularly produced using different hypersecretor Tol-pal mutants of Escherichia coli and Pseudomonas putida as recombinant hosts. The recombinant PhaZ(Bd) has been characterized, and its biochemical properties have been compared to those of other PHA depolymerases. The enzyme behaves as a serine hydrolase that is inhibited by phenylmethylsulfonyl fluoride. It is also affected by the reducing agent dithiothreitol and nonionic detergents like Tween 80. PhaZ(Bd) is an endoexohydrolase that cleaves both large and small PHA molecules, producing mainly dimers but also monomers and trimers. The enzyme specifically degrades mcl-PHA and is inactive toward short-chain-length polyhydroxyalkanoates (scl-PHA) like polyhydroxybutyrate (PHB). These studies shed light on the potentiality of these predators as sources of new biocatalysts, such as an mcl-PHA depolymerase, for the production of enantiopure hydroxyalkanoic acids and oligomers as building blocks for the synthesis of biobased polymers.
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Santos M, Gangoiti J, Keul H, Möller M, Serra JL, Llama MJ. Polyester hydrolytic and synthetic activity catalyzed by the medium-chain-length poly(3-hydroxyalkanoate) depolymerase from Streptomyces venezuelae SO1. Appl Microbiol Biotechnol 2012; 97:211-22. [PMID: 22695803 DOI: 10.1007/s00253-012-4210-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2012] [Revised: 05/23/2012] [Accepted: 05/24/2012] [Indexed: 11/25/2022]
Abstract
The extracellular medium-chain-length polyhydroxyalkanote (MCL-PHA) depolymerase from an isolate identified as Streptomyces venezuelae SO1 was purified to electrophoretic homogeneity and characterized. The molecular mass and pI of the purified enzyme were approximately 27 kDa and 5.9, respectively. The depolymerase showed its maximum activity in the alkaline pH range and 50 °C and retained more than 70 % of its initial activity after 8 h at 40 °C. The MCL-PHA depolymerase hydrolyzes various p-nitrophenyl-alkanoates and polycaprolactone but not polylactide, poly-3-hydroxybutyrate, and polyethylene succinate. The enzymatic activity was markedly enhanced by the presence of low concentrations of detergents and organic solvents, being inhibited by dithiothreitol and EDTA. The potential of using the enzyme to produce (R)-3-hydroxyoctanoate in aqueous media or to catalyze ester-forming reactions in anhydrous media was investigated. In this sense, the MCL-PHA depolymerase catalyzes the hydrolysis of poly-3-hydroxyoctanoate to monomeric units and the ring-opening polymerization of β-butyrolactone and lactides, while ε-caprolactone and pentadecalactone were hardly polymerized.
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Affiliation(s)
- Marta Santos
- Enzyme and Cell Technology Group, Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), P.O. Box 644, 48080, Bilbao, Spain
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Santos M, Gangoiti J, Llama MJ, Serra JL, Keul H, Möller M. Poly(3-hydroxyoctanoate) depolymerase from Pseudomonas fluorescens GK13: Catalysis of ester-forming reactions in non-aqueous media. ACTA ACUST UNITED AC 2012. [DOI: 10.1016/j.molcatb.2012.01.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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Revellame ED, Hernandez R, French W, Holmes WE, Benson TJ, Pham PJ, Forks A, Callahan II R. Lipid storage compounds in raw activated sludge microorganisms for biofuels and oleochemicals production. RSC Adv 2012. [DOI: 10.1039/c2ra01078j] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
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Arroyo M, García-Hidalgo J, Villalón M, de Eugenio L, Hormigo D, Acebal C, García JL, Prieto MA, de la Mata I. Characterization of a novel immobilized biocatalyst obtained by matrix-assisted refolding of recombinant polyhydroxyoctanoate depolymerase from Pseudomonas putida KT2442 isolated from inclusion bodies. J Ind Microbiol Biotechnol 2010; 38:1203-9. [DOI: 10.1007/s10295-010-0898-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2010] [Accepted: 10/30/2010] [Indexed: 10/18/2022]
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