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Varadarajan AR, Allan RN, Valentin JDP, Castañeda Ocampo OE, Somerville V, Pietsch F, Buhmann MT, West J, Skipp PJ, van der Mei HC, Ren Q, Schreiber F, Webb JS, Ahrens CH. An integrated model system to gain mechanistic insights into biofilm-associated antimicrobial resistance in Pseudomonas aeruginosa MPAO1. NPJ Biofilms Microbiomes 2020; 6:46. [PMID: 33127897 PMCID: PMC7603352 DOI: 10.1038/s41522-020-00154-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 10/07/2020] [Indexed: 12/11/2022] Open
Abstract
Pseudomonas aeruginosa MPAO1 is the parental strain of the widely utilized transposon mutant collection for this important clinical pathogen. Here, we validate a model system to identify genes involved in biofilm growth and biofilm-associated antibiotic resistance. Our model employs a genomics-driven workflow to assemble the complete MPAO1 genome, identify unique and conserved genes by comparative genomics with the PAO1 reference strain and genes missed within existing assemblies by proteogenomics. Among over 200 unique MPAO1 genes, we identified six general essential genes that were overlooked when mapping public Tn-seq data sets against PAO1, including an antitoxin. Genomic data were integrated with phenotypic data from an experimental workflow using a user-friendly, soft lithography-based microfluidic flow chamber for biofilm growth and a screen with the Tn-mutant library in microtiter plates. The screen identified hitherto unknown genes involved in biofilm growth and antibiotic resistance. Experiments conducted with the flow chamber across three laboratories delivered reproducible data on P. aeruginosa biofilms and validated the function of both known genes and genes identified in the Tn-mutant screens. Differential protein abundance data from planktonic cells versus biofilm confirmed the upregulation of candidates known to affect biofilm formation, of structural and secreted proteins of type VI secretion systems, and provided proteogenomic evidence for some missed MPAO1 genes. This integrated, broadly applicable model promises to improve the mechanistic understanding of biofilm formation, antimicrobial tolerance, and resistance evolution in biofilms.
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Affiliation(s)
- Adithi R Varadarajan
- Research Group Molecular Diagnostics Genomics & Bioinformatics, Agroscope and SIB Swiss Institute of Bioinformatics, Wädenswil, Switzerland.
| | - Raymond N Allan
- School of Biological Sciences and Institute for Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK
- National Biofilms Innovation Centre, University of Southampton, Southampton, SO17 1BJ, UK
- School of Pharmacy, Faculty of Health and Life Sciences, De Montfort University, Leicester, LE1 9BH, UK
| | - Jules D P Valentin
- Laboratory for Biointerfaces, Empa, Swiss Federal Laboratories for Materials Science and Technology, St. Gallen, Switzerland
- Department of BioMedical Engineering, University of Groningen and University Medical Center Groningen, Groningen, Netherlands
| | - Olga E Castañeda Ocampo
- Department of BioMedical Engineering, University of Groningen and University Medical Center Groningen, Groningen, Netherlands
| | - Vincent Somerville
- Research Group Molecular Diagnostics Genomics & Bioinformatics, Agroscope and SIB Swiss Institute of Bioinformatics, Wädenswil, Switzerland
| | - Franziska Pietsch
- Division of Biodeterioration and Reference Organisms, Federal Institute for Materials Research and Testing (BAM), Berlin, Germany
| | - Matthias T Buhmann
- Laboratory for Biointerfaces, Empa, Swiss Federal Laboratories for Materials Science and Technology, St. Gallen, Switzerland
| | - Jonathan West
- Faculty of Medicine, University of Southampton, Southampton, SO17 1BJ, UK
- Centre for Hybrid Biodevices, University of Southampton, Southampton, SO17 1BJ, UK
| | - Paul J Skipp
- Centre for Proteomics Research, University of Southampton, Southampton, SO17 1BJ, UK
| | - Henny C van der Mei
- Department of BioMedical Engineering, University of Groningen and University Medical Center Groningen, Groningen, Netherlands
| | - Qun Ren
- Laboratory for Biointerfaces, Empa, Swiss Federal Laboratories for Materials Science and Technology, St. Gallen, Switzerland
| | - Frank Schreiber
- Division of Biodeterioration and Reference Organisms, Federal Institute for Materials Research and Testing (BAM), Berlin, Germany
| | - Jeremy S Webb
- School of Biological Sciences and Institute for Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK
- National Biofilms Innovation Centre, University of Southampton, Southampton, SO17 1BJ, UK
| | - Christian H Ahrens
- Research Group Molecular Diagnostics Genomics & Bioinformatics, Agroscope and SIB Swiss Institute of Bioinformatics, Wädenswil, Switzerland.
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Mukhopadhyay S, Karuppannan SK, Guo C, Fereiro JA, Bergren A, Mukundan V, Qiu X, Castañeda Ocampo OE, Chen X, Chiechi RC, McCreery R, Pecht I, Sheves M, Pasula RR, Lim S, Nijhuis CA, Vilan A, Cahen D. Solid-State Protein Junctions: Cross- Laboratory Study Shows Preservation of Mechanism at Varying Electronic Coupling. iScience 2020; 23:101099. [PMID: 32438319 PMCID: PMC7235645 DOI: 10.1016/j.isci.2020.101099] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 03/01/2020] [Accepted: 04/20/2020] [Indexed: 12/14/2022] Open
Abstract
Successful integration of proteins in solid-state electronics requires contacting them in a non-invasive fashion, with a solid conducting surface for immobilization as one such contact. The contacts can affect and even dominate the measured electronic transport. Often substrates, substrate treatments, protein immobilization, and device geometries differ between laboratories. Thus the question arises how far results from different laboratories and platforms are comparable and how to distinguish genuine protein electronic transport properties from platform-induced ones. We report a systematic comparison of electronic transport measurements between different laboratories, using all commonly used large-area schemes to contact a set of three proteins of largely different types. Altogether we study eight different combinations of molecular junction configurations, designed so that Ageoof junctions varies from 105 to 10-3 μm2. Although for the same protein, measured with similar device geometry, results compare reasonably well, there are significant differences in current densities (an intensive variable) between different device geometries. Likely, these originate in the critical contact-protein coupling (∼contact resistance), in addition to the actual number of proteins involved, because the effective junction contact area depends on the nanometric roughness of the electrodes and at times, even the proteins may increase this roughness. On the positive side, our results show that understanding what controls the coupling can make the coupling a design knob. In terms of extensive variables, such as temperature, our comparison unanimously shows the transport to be independent of temperature for all studied configurations and proteins. Our study places coupling and lack of temperature activation as key aspects to be considered in both modeling and practice of protein electronic transport experiments.
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Affiliation(s)
- Sabyasachi Mukhopadhyay
- Weizmann Institute of Science, Rehovot 76100, Israel
- Department of Physics, SRM University – AP, Amaravati, Andhra Pradesh 522502, India
| | - Senthil Kumar Karuppannan
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore
| | - Cunlan Guo
- Weizmann Institute of Science, Rehovot 76100, Israel
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | | | - Adam Bergren
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Dr., Edmonton AB T6G 2G2, Canada
| | - Vineetha Mukundan
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Dr., Edmonton AB T6G 2G2, Canada
| | - Xinkai Qiu
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, the Netherlands
| | - Olga E. Castañeda Ocampo
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, the Netherlands
| | - Xiaoping Chen
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore
| | - Ryan C. Chiechi
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, the Netherlands
| | - Richard McCreery
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Dr., Edmonton AB T6G 2G2, Canada
| | - Israel Pecht
- Weizmann Institute of Science, Rehovot 76100, Israel
| | | | - Rupali Reddy Pasula
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 70 Nanyang Drive, Singapore 637457, Singapore
| | - Sierin Lim
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 70 Nanyang Drive, Singapore 637457, Singapore
| | - Christian A. Nijhuis
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore
- Centre for Advanced 2D Materials, National University of Singapore, 6 Science Drive 2, Singapore 117546, Singapore
| | - Ayelet Vilan
- Weizmann Institute of Science, Rehovot 76100, Israel
| | - David Cahen
- Weizmann Institute of Science, Rehovot 76100, Israel
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Gordiichuk P, Pesce D, Ocampo OEC, Marcozzi A, Wetzelaer GAH, Paul A, Loznik M, Gloukhikh E, Richter S, Chiechi RC, Herrmann A. Orientation and Incorporation of Photosystem I in Bioelectronics Devices Enabled by Phage Display. Adv Sci (Weinh) 2017; 4:1600393. [PMID: 28546908 PMCID: PMC5441502 DOI: 10.1002/advs.201600393] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 12/04/2016] [Indexed: 05/23/2023]
Abstract
Interfacing proteins with electrode surfaces is important for the field of bioelectronics. Here, a general concept based on phage display is presented to evolve small peptide binders for immobilizing and orienting large protein complexes on semiconducting substrates. Employing this method, photosystem I is incorporated into solid-state biophotovoltaic cells.
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Affiliation(s)
- Pavlo Gordiichuk
- Department of Polymer Chemistry and BioengineeringZernike Institute for Advanced MaterialsUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
| | - Diego Pesce
- Department of Polymer Chemistry and BioengineeringZernike Institute for Advanced MaterialsUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
| | - Olga E. Castañeda Ocampo
- Stratingh Institute for Chemistry and Zernike Institute for Advanced MaterialsUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
| | - Alessio Marcozzi
- Department of Polymer Chemistry and BioengineeringZernike Institute for Advanced MaterialsUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
| | - Gert‐Jan A. H. Wetzelaer
- Department of Polymer Chemistry and BioengineeringZernike Institute for Advanced MaterialsUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
| | - Avishek Paul
- Department of Polymer Chemistry and BioengineeringZernike Institute for Advanced MaterialsUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
| | - Mark Loznik
- Department of Polymer Chemistry and BioengineeringZernike Institute for Advanced MaterialsUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
| | - Ekaterina Gloukhikh
- The Bio and Molecular Electronics GroupDepartment of Materials Science and EngineeringFaculty of Engineering and University Center for Nano Science and NanotechnologyTel Aviv UniversityTel‐Aviv69978Israel
| | - Shachar Richter
- The Bio and Molecular Electronics GroupDepartment of Materials Science and EngineeringFaculty of Engineering and University Center for Nano Science and NanotechnologyTel Aviv UniversityTel‐Aviv69978Israel
| | - Ryan C. Chiechi
- Stratingh Institute for Chemistry and Zernike Institute for Advanced MaterialsUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
| | - Andreas Herrmann
- Department of Polymer Chemistry and BioengineeringZernike Institute for Advanced MaterialsUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
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Castañeda Ocampo OE, Gordiichuk P, Catarci S, Gautier DA, Herrmann A, Chiechi RC. Mechanism of Orientation-Dependent Asymmetric Charge Transport in Tunneling Junctions Comprising Photosystem I. J Am Chem Soc 2015; 137:8419-27. [PMID: 26057523 PMCID: PMC4558993 DOI: 10.1021/jacs.5b01241] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Recently, photoactive proteins have gained a lot of attention due to their incorporation into bioinspired (photo)electrochemical and solar cells. This paper describes the measurement of the asymmetry of current transport of self-assembled monolayers (SAMs) of the entire photosystem I (PSI) protein complex (not the isolated reaction center, RCI), on two different "director SAMs" supported by ultraflat Au substrates. The director SAMs induce the preferential orientation of PSI, which manifest as asymmetry in tunneling charge-transport. We measured the oriented SAMs of PSI using eutectic Ga-In (EGaIn), a large-area technique, and conducting probe atomic force microscopy (CP-AFM), a single-complex technique, and determined that the transport properties are comparable. By varying the temperatures at which the measurements were performed, we found that there is no measurable dependence of the current on temperature from ±0.1 to ±1.0 V bias, and thus, we suggest tunneling as the mechanism for transport; there are no thermally activated (e.g., hopping) processes. Therefore, it is likely that relaxation in the electron transport chain is not responsible for the asymmetry in the conductance of SAMs of PSI complexes in these junctions, which we ascribe instead to the presence of a large, net dipole moment present in PSI.
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Affiliation(s)
- Olga E Castañeda Ocampo
- †Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.,‡Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Pavlo Gordiichuk
- ‡Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Stefano Catarci
- ‡Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Daniel A Gautier
- ‡Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Andreas Herrmann
- ‡Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Ryan C Chiechi
- †Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.,‡Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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