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Gasse C, Srivastava P, Schepers G, Jose J, Hollenstein M, Marlière P, Herdewijn P. Controlled E. coli Aggregation Mediated by DNA and XNA Hybridization. Chembiochem 2023; 24:e202300191. [PMID: 37119472 DOI: 10.1002/cbic.202300191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 04/26/2023] [Accepted: 04/27/2023] [Indexed: 05/01/2023]
Abstract
Chemical cell surface modification is a fast-growing field of research, due to its enormous potential in tissue engineering, cell-based immunotherapy, and regenerative medicine. However, engineering of bacterial tissues by chemical cell surface modification has been vastly underexplored and the identification of suitable molecular handles is in dire need. We present here, an orthogonal nucleic acid-protein conjugation strategy to promote artificial bacterial aggregation. This system gathers the high selectivity and stability of linkage to a protein Tag expressed at the cell surface and the modularity and reversibility of aggregation due to oligonucleotide hybridization. For the first time, XNA (xeno nucleic acids in the form of 1,5-anhydrohexitol nucleic acids) were immobilized via covalent, SNAP-tag-mediated interactions on cell surfaces to induce bacterial aggregation.
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Affiliation(s)
- Cécile Gasse
- Génomique Métabolique, Genoscope Institut François Jacob, CEA, CNRS Univ Evry, Université Paris-Saclay, 2 Rue Gaston Crémieux, 91057, Evry, France
| | - Puneet Srivastava
- Laboratory of Medicinal Chemistry, Rega Institute for Biomedical Research, KU Leuven, Herestraat 49, Box 1041, 3000, Leuven, Belgium
| | - Guy Schepers
- Laboratory of Medicinal Chemistry, Rega Institute for Biomedical Research, KU Leuven, Herestraat 49, Box 1041, 3000, Leuven, Belgium
| | - Joachim Jose
- Institute of Pharmaceutical and Medicinal Chemistry, University of Münster, Corrensstr. 48, D-48149, Münster, Germany
| | - Marcel Hollenstein
- Institut Pasteur, Université Paris Cité, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724, Paris Cedex 15, France
| | - Philippe Marlière
- The European Syndicate of Synthetic Scientists and Industrialists (TESSSI), 81 rue Réaumur, 75002, Paris, France
| | - Piet Herdewijn
- Laboratory of Medicinal Chemistry, Rega Institute for Biomedical Research, KU Leuven, Herestraat 49, Box 1041, 3000, Leuven, Belgium
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2
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Fraile S, Briones M, Revenga-Parra M, de Lorenzo V, Lorenzo E, Martínez-García E. Engineering Tropism of Pseudomonas putida toward Target Surfaces through Ectopic Display of Recombinant Nanobodies. ACS Synth Biol 2021; 10:2049-2059. [PMID: 34337948 PMCID: PMC8397431 DOI: 10.1021/acssynbio.1c00227] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Indexed: 12/15/2022]
Abstract
Gram-negative bacteria are endowed with complex outer membrane (OM) structures that allow them to both interact with other organisms and attach to different physical structures. However, the design of reliable bacterial coatings of solid surfaces is still a considerable challenge. In this work, we report that ectopic expression of a fibrinogen-specific nanobody on the envelope of Pseudomonas putida cells enables controllable formation of a bacterial monolayer strongly bound to an antigen-coated support. To this end, either the wild type or a surface-naked derivative of P. putida was engineered to express a hybrid between the β-barrel of an intimin-type autotransporter inserted in the outer membrane and a nanobody (VHH) moiety that targets fibrinogen as its cognate interaction partner. The functionality of the thereby presented VHH and the strength of the resulting cell attachment to a solid surface covered with the cognate antigen were tested and parametrized with Quartz Crystal Microbalance technology. The results not only demonstrated the value of using bacteria with reduced OM complexity for efficient display of artificial adhesins, but also the potential of this approach to engineer specific bacterial coverings of predetermined target surfaces.
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Affiliation(s)
- Sofía Fraile
- Systems Biology Department, Centro Nacional
de Biotecnología (CNB-CSIC), Campus de Cantoblanco, 28049 Madrid, Spain
| | - María Briones
- Departamento de Química Analítica y Análisis
Instrumental, Universidad Autónoma
de Madrid, Campus de Cantoblanco, 28049 Madrid, Spain
| | - Mónica Revenga-Parra
- Departamento de Química Analítica y Análisis
Instrumental, Universidad Autónoma
de Madrid, Campus de Cantoblanco, 28049 Madrid, Spain
| | - Víctor de Lorenzo
- Systems Biology Department, Centro Nacional
de Biotecnología (CNB-CSIC), Campus de Cantoblanco, 28049 Madrid, Spain
| | - Encarnación Lorenzo
- Departamento de Química Analítica y Análisis
Instrumental, Universidad Autónoma
de Madrid, Campus de Cantoblanco, 28049 Madrid, Spain
| | - Esteban Martínez-García
- Systems Biology Department, Centro Nacional
de Biotecnología (CNB-CSIC), Campus de Cantoblanco, 28049 Madrid, Spain
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Gercke D, Furtmann C, Tozakidis IEP, Jose J. Highly Crystalline Post‐Consumer PET Waste Hydrolysis by Surface Displayed PETase Using a Bacterial Whole‐Cell Biocatalyst. ChemCatChem 2021. [DOI: 10.1002/cctc.202100443] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- David Gercke
- Institut für Pharmazeutische und Medizinische Chemie PharmaCampus Westfälische Wilhelms-Universität Münster Corrensstrasse 48 48149 Münster Germany
| | - Christoph Furtmann
- Institut für Pharmazeutische und Medizinische Chemie PharmaCampus Westfälische Wilhelms-Universität Münster Corrensstrasse 48 48149 Münster Germany
| | - Iasson E. P. Tozakidis
- Institut für Pharmazeutische und Medizinische Chemie PharmaCampus Westfälische Wilhelms-Universität Münster Corrensstrasse 48 48149 Münster Germany
| | - Joachim Jose
- Institut für Pharmazeutische und Medizinische Chemie PharmaCampus Westfälische Wilhelms-Universität Münster Corrensstrasse 48 48149 Münster Germany
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Dvořák P, Bayer EA, de Lorenzo V. Surface Display of Designer Protein Scaffolds on Genome-Reduced Strains of Pseudomonas putida. ACS Synth Biol 2020; 9:2749-2764. [PMID: 32877604 DOI: 10.1021/acssynbio.0c00276] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The bacterium Pseudomonas putida KT2440 is gaining considerable interest as a microbial platform for biotechnological valorization of polymeric organic materials, such as lignocellulosic residues or plastics. However, P. putida on its own cannot make much use of such complex substrates, mainly because it lacks an efficient extracellular depolymerizing apparatus. We seek to address this limitation by adopting a recombinant cellulosome strategy for this host. In this work, we report an essential step in this endeavor-a display of designer enzyme-anchoring protein "scaffoldins", encompassing cohesin binding domains from divergent cellulolytic bacterial species on the P. putida surface. Two P. putida chassis strains, EM42 and EM371, with streamlined genomes and differences in the composition of the outer membrane were employed in this study. Scaffoldin variants were optimally delivered to their surface with one of four tested autotransporter systems (Ag43 from Escherichia coli), and the efficient display was confirmed by extracellular attachment of chimeric β-glucosidase and fluorescent proteins. Our results not only highlight the value of cell surface engineering for presentation of recombinant proteins on the envelope of Gram-negative bacteria but also pave the way toward designer cellulosome strategies tailored for P. putida.
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Affiliation(s)
- Pavel Dvořák
- Department of Experimental Biology (Section of Microbiology), Faculty of Science, Masaryk University, Kamenice 753/5, 62500 Brno, Czech Republic
| | - Edward A Bayer
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Víctor de Lorenzo
- Systems and Synthetic Biology Program, Centro Nacional de Biotecnología CNB-CSIC, Cantoblanco, Darwin 3, 28049 Madrid, Spain
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Meyers A, Furtmann C, Gesing K, Tozakidis IEP, Jose J. Cell density-dependent auto-inducible promoters for expression of recombinant proteins in Pseudomonas putida. Microb Biotechnol 2019; 12:1003-1013. [PMID: 31237428 PMCID: PMC6680623 DOI: 10.1111/1751-7915.13455] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 06/05/2019] [Accepted: 06/05/2019] [Indexed: 02/06/2023] Open
Abstract
Inducible promoters such as Plac are of limited usability for industrial protein production with Pseudomonas putida. We therefore utilized cell density-dependent auto-inducible promoters for recombinant gene expression in P. putida KT2440 based on the RoxS/RoxR Quorum Sensing (QS) system of the bacterium. To this end, genetic regions upstream of the RoxS/RoxR-regulated genes ddcA (PR ox132 ) and PP_3332 (PR ox306 ) were inserted into plasmids that mediated the expression of superfolder green fluorescent protein (sfGFP) and surface displayed mCherry, confirming their promoter functionalities. Mutation of the Pribnow box of PR ox306 to the σ70 consensus sequence (PR ox3061 ) resulted in a more than threefold increase of sfGFP production. All three promoters caused cell density-dependent expression, starting transcription at optical densities (OD578 ) of approximately 1.0 (PR ox132 , PR ox306 ) or 0.7 (PR ox3061 ) as determined by RT-qPCR. The QS dependency of PR ox306 was further shown by cultivating P. putida in media that had already been used for cultivation and thus contained bacterial signal molecules. The longer P. putida had grown in these media before, the earlier protein expression in freshly inoculated P. putida appeared with PR ox306 . This confirmed previous findings that a bacterial compound accumulates within the culture and induces protein expression.
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Affiliation(s)
- Annika Meyers
- Institut für Pharmazeutische und Medizinische ChemieWestfälische Wilhelms‐Universität MünsterPharmaCampus, Corrensstr. 4848149MünsterGermany
| | - Christoph Furtmann
- Institut für Pharmazeutische und Medizinische ChemieWestfälische Wilhelms‐Universität MünsterPharmaCampus, Corrensstr. 4848149MünsterGermany
| | - Katrin Gesing
- Institut für Pharmazeutische und Medizinische ChemieWestfälische Wilhelms‐Universität MünsterPharmaCampus, Corrensstr. 4848149MünsterGermany
| | - Iasson E. P. Tozakidis
- Institut für Pharmazeutische und Medizinische ChemieWestfälische Wilhelms‐Universität MünsterPharmaCampus, Corrensstr. 4848149MünsterGermany
| | - Joachim Jose
- Institut für Pharmazeutische und Medizinische ChemieWestfälische Wilhelms‐Universität MünsterPharmaCampus, Corrensstr. 4848149MünsterGermany
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Wang X, Feng X, Lv B, Zhou A, Hou Y, Li C. Enhanced yeast surface display of β‐glucuronidase using dual anchor motifs for high‐temperature glycyrrhizin hydrolysis. AIChE J 2019. [DOI: 10.1002/aic.16629] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Xudong Wang
- Institute for Synthetic Biosystem/Department of Biochemical Engineering, School of Chemistry and Chemical EngineeringBeijing Institute of Technology Beijing China
| | - Xudong Feng
- Institute for Synthetic Biosystem/Department of Biochemical Engineering, School of Chemistry and Chemical EngineeringBeijing Institute of Technology Beijing China
| | - Bo Lv
- Institute for Synthetic Biosystem/Department of Biochemical Engineering, School of Chemistry and Chemical EngineeringBeijing Institute of Technology Beijing China
| | - Anqi Zhou
- Institute for Synthetic Biosystem/Department of Biochemical Engineering, School of Chemistry and Chemical EngineeringBeijing Institute of Technology Beijing China
| | - Yuhui Hou
- Institute for Synthetic Biosystem/Department of Biochemical Engineering, School of Chemistry and Chemical EngineeringBeijing Institute of Technology Beijing China
| | - Chun Li
- Institute for Synthetic Biosystem/Department of Biochemical Engineering, School of Chemistry and Chemical EngineeringBeijing Institute of Technology Beijing China
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Tozakidis IEP, Lüken LM, Üffing A, Meyers A, Jose J. Improving the autotransporter-based surface display of enzymes in Pseudomonas putida KT2440. Microb Biotechnol 2019; 13:176-184. [PMID: 31044490 PMCID: PMC6922575 DOI: 10.1111/1751-7915.13419] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 04/15/2019] [Accepted: 04/16/2019] [Indexed: 12/14/2022] Open
Abstract
Pseudomonas putida can be used as a host for the autotransporter‐mediated surface display of enzymes (autodisplay), resulting in whole‐cell biocatalysts with recombinant functionalities on their cell envelope. The efficiency of autotransporter‐mediated secretion depends on the N‐terminal signal peptide as well as on the C‐terminal translocator domain of autotransporter fusion proteins. We set out to optimize autodisplay for P. putida as the host bacterium by comparing different signal peptides and translocator domains for the surface display of an esterase. The translocator domain did not have a considerable effect on the activity of the whole‐cell catalysts. In contrast, by using the signal peptide of the P. putida outer membrane protein OprF, the activity was more than 12‐fold enhanced to 638 mU ml−1 OD−1 compared with the signal peptide of V. cholerae CtxB (52 mU ml−1 OD−1). This positive effect was confirmed with a β‐glucosidase as a second example enzyme. Here, cells expressing the protein with N‐terminal OprF signal peptide showed more than fourfold higher β‐glucosidase activity (181 mU ml−1 OD−1) than with the CtxB signal peptide (42 mU ml−1 OD−1). SDS‐PAGE and flow cytometry analyses indicated that the increased activities correlated with an increased amount of recombinant protein in the outer membrane and a higher number of enzymes detectable on the cell surface.
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Affiliation(s)
- Iasson E P Tozakidis
- Institut für Pharmazeutische und Medizinische Chemie, PharmaCampus, Westfälische Wilhelms-Universität Münster, Corrensstr. 48, 48149, Münster, Germany
| | - Lena M Lüken
- Institut für Pharmazeutische und Medizinische Chemie, PharmaCampus, Westfälische Wilhelms-Universität Münster, Corrensstr. 48, 48149, Münster, Germany
| | - Alina Üffing
- Institut für Pharmazeutische und Medizinische Chemie, PharmaCampus, Westfälische Wilhelms-Universität Münster, Corrensstr. 48, 48149, Münster, Germany
| | - Annika Meyers
- Institut für Pharmazeutische und Medizinische Chemie, PharmaCampus, Westfälische Wilhelms-Universität Münster, Corrensstr. 48, 48149, Münster, Germany
| | - Joachim Jose
- Institut für Pharmazeutische und Medizinische Chemie, PharmaCampus, Westfälische Wilhelms-Universität Münster, Corrensstr. 48, 48149, Münster, Germany
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Diversity and Biotechnological Potential of Xylan-Degrading Microorganisms from Orange Juice Processing Waste. WATER 2019. [DOI: 10.3390/w11020274] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The orange juice processing sector produces worldwide massive amounts of waste, which is characterized by high lignin, cellulose and hemicellulose content, and which exceeds 40% of the fruit’s dry weight (d.w.). In this work, the diversity and the biotechnological potential of xylan-degrading microbiota in orange juice processing waste were investigated through the implementation of an enrichment isolation strategy followed by enzyme assays for the determination of xylanolytic activities, and via next generation sequencing for microbial diversity identification. Intracellular rather than extracellular endo-1,4-β-xylanase activities were detected, indicating that peripheral cell-bound (surface) xylanases are involved in xylan hydrolysis by the examined microbial strains. Among the isolated microbial strains, bacterial isolates belonging to Pseudomonas psychrotolerans/P. oryzihabitans spectrum (99.9%/99.8% similarity, respectively) exhibited activities of 280 U/mg protein. In contrast, almost all microbial strains isolated exerted low extracellular 1,4-β-xylosidase activities (<5 U/mg protein), whereas no intracellular 1,4-β-xylosidase activities were detected for any of them. Illumina data showed the dominance of lactic and acetic acid bacteria and of the yeasts Hanseniaspora and Zygosaccharomyces. This is the first report on indigenous xylanolytic microbiota isolated from orange juice processing waste, possessing the biotechnological potential to serve as biocatalysts for citrus biomass valorization through the production of high-added value products and energy recovery.
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The workability of Escherichia coli BL21 (DE3) and Pseudomonas putida KT2440 expression platforms with autodisplayed cellulases: a comparison. Appl Microbiol Biotechnol 2018; 102:4829-4841. [DOI: 10.1007/s00253-018-8987-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 04/02/2018] [Accepted: 04/05/2018] [Indexed: 02/07/2023]
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