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Jonkergouw C, Savola P, Osmekhina E, van Strien J, Batys P, Linder MB. Exploration of Chemical Diversity in Intercellular Quorum Sensing Signalling Systems in Prokaryotes. Angew Chem Int Ed Engl 2024; 63:e202314469. [PMID: 37877232 DOI: 10.1002/anie.202314469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 10/24/2023] [Accepted: 10/24/2023] [Indexed: 10/26/2023]
Abstract
Quorum sensing (QS) serves as a vital means of intercellular signalling in a variety of prokaryotes, which enables single cells to act in multicellular configurations. The potential to control community-wide responses has also sparked numerous recent biotechnological innovations. However, our capacity to utilize intercellular communication is hindered due to a scarcity of complementary signalling systems and a restricted comprehension of interconnections between these systems caused by variations in their dynamic range. In this study, we utilize uniform manifold approximation and projection and extended-connectivity fingerprints to explore the available chemical space of QS signalling molecules. We investigate and experimentally characterize a set of closely related QS signalling ligands, consisting of N-acyl homoserine lactones and the aryl homoserine lactone p-coumaroyl, as well as a set of more widely diverging QS ligands, consisting of photopyrones, dialkylresorcinols, 3,5-dimethylpyrazin-2-ol and autoinducer-2, and define their performance. We report on a set of six signal- and promoter-orthogonal intercellular QS signalling systems, significantly expanding the toolkit for engineering community-wide behaviour. Furthermore, we demonstrate that ligand diversity can serve as a statistically significant tool to predict much more complicated ligand-receptor interactions. This approach highlights the potential of dimensionality reduction to explore chemical diversity in microbial dynamics.
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Affiliation(s)
- Christopher Jonkergouw
- Aalto University, School of Chemical Engineering, Department of Bioproducts and Biosystems, Kemistintie 1, 02150, Espoo, Finland
| | - Pihla Savola
- Aalto University, School of Chemical Engineering, Department of Bioproducts and Biosystems, Kemistintie 1, 02150, Espoo, Finland
| | - Ekaterina Osmekhina
- Aalto University, School of Chemical Engineering, Department of Bioproducts and Biosystems, Kemistintie 1, 02150, Espoo, Finland
| | - Joeri van Strien
- Medical BioSciences Department, Radboud University Medical Center, Geert Grooteplein 28, 6525 GA, Nijmegen, The Netherlands
| | - Piotr Batys
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30239, Krakow, Poland
| | - Markus B Linder
- Aalto University, School of Chemical Engineering, Department of Bioproducts and Biosystems, Kemistintie 1, 02150, Espoo, Finland
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Feng J, Gabryelczyk B, Tunn I, Osmekhina E, Linder MB. A Minispidroin Guides the Molecular Design for Cellular Condensation Mechanisms in S. cerevisiae. ACS Synth Biol 2023; 12:3050-3063. [PMID: 37688556 PMCID: PMC10594646 DOI: 10.1021/acssynbio.3c00374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Indexed: 09/11/2023]
Abstract
Structural engineering of molecules for condensation is an emerging technique within synthetic biology. Liquid-liquid phase separation of biomolecules leading to condensation is a central step in the assembly of biological materials into their functional forms. Intracellular condensates can also function within cells in a regulatory manner to facilitate reaction pathways and to compartmentalize interactions. We need to develop a strong understanding of how to design molecules for condensates and how their in vivo-in vitro properties are related. The spider silk protein NT2RepCT undergoes condensation during its fiber-forming process. Using parallel in vivo and in vitro characterization, in this study, we mapped the effects of intracellular conditions for NT2RepCT and its several structural variants. We found that intracellular conditions may suppress to some extent condensation whereas molecular crowding affects both condensate properties and their formation. Intracellular characterization of protein condensation allowed experiments on pH effects and solubilization to be performed within yeast cells. The growth of intracellular NT2RepCT condensates was restricted, and Ostwald ripening was not observed in yeast cells, in contrast to earlier observations in E. coli. Our results lead the way to using intracellular condensation to screen for properties of molecular assembly. For characterizing different structural variants, intracellular functional characterization can eliminate the need for time-consuming batch purification and in vitro condensation. Therefore, we suggest that the in vivo-in vitro understanding will become useful in, e.g., high-throughput screening for molecular functions and in strategies for designing tunable intracellular condensates.
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Affiliation(s)
- Jianhui Feng
- Department of Bioproducts
and Biosystems, School of Chemical Engineering and Academy of Finland
Center of Excellence in Life-Inspired Hybrid Materials (LIBER), Aalto University, Espoo 02150, Finland
| | - Bartosz Gabryelczyk
- Department of Bioproducts
and Biosystems, School of Chemical Engineering and Academy of Finland
Center of Excellence in Life-Inspired Hybrid Materials (LIBER), Aalto University, Espoo 02150, Finland
| | - Isabell Tunn
- Department of Bioproducts
and Biosystems, School of Chemical Engineering and Academy of Finland
Center of Excellence in Life-Inspired Hybrid Materials (LIBER), Aalto University, Espoo 02150, Finland
| | - Ekaterina Osmekhina
- Department of Bioproducts
and Biosystems, School of Chemical Engineering and Academy of Finland
Center of Excellence in Life-Inspired Hybrid Materials (LIBER), Aalto University, Espoo 02150, Finland
| | - Markus B. Linder
- Department of Bioproducts
and Biosystems, School of Chemical Engineering and Academy of Finland
Center of Excellence in Life-Inspired Hybrid Materials (LIBER), Aalto University, Espoo 02150, Finland
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Jonkergouw C, Beyeh NK, Osmekhina E, Leskinen K, Taimoory SM, Fedorov D, Anaya-Plaza E, Kostiainen MA, Trant JF, Ras RHA, Saavalainen P, Linder MB. Repurposing host-guest chemistry to sequester virulence and eradicate biofilms in multidrug resistant Pseudomonas aeruginosa and Acinetobacter baumannii. Nat Commun 2023; 14:2141. [PMID: 37059703 PMCID: PMC10104825 DOI: 10.1038/s41467-023-37749-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 03/29/2023] [Indexed: 04/16/2023] Open
Abstract
The limited diversity in targets of available antibiotic therapies has put tremendous pressure on the treatment of bacterial pathogens, where numerous resistance mechanisms that counteract their function are becoming increasingly prevalent. Here, we utilize an unconventional anti-virulence screen of host-guest interacting macrocycles, and identify a water-soluble synthetic macrocycle, Pillar[5]arene, that is non-bactericidal/bacteriostatic and has a mechanism of action that involves binding to both homoserine lactones and lipopolysaccharides, key virulence factors in Gram-negative pathogens. Pillar[5]arene is active against Top Priority carbapenem- and third/fourth-generation cephalosporin-resistant Pseudomonas aeruginosa and Acinetobacter baumannii, suppressing toxins and biofilms and increasing the penetration and efficacy of standard-of-care antibiotics in combined administrations. The binding of homoserine lactones and lipopolysaccharides also sequesters their direct effects as toxins on eukaryotic membranes, neutralizing key tools that promote bacterial colonization and impede immune defenses, both in vitro and in vivo. Pillar[5]arene evades both existing antibiotic resistance mechanisms, as well as the build-up of rapid tolerance/resistance. The versatility of macrocyclic host-guest chemistry provides ample strategies for tailored targeting of virulence in a wide range of Gram-negative infectious diseases.
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Affiliation(s)
- Christopher Jonkergouw
- Aalto University, School of Chemical Engineering, Department of Bioproducts and Biosystems, Kemistintie 1, 02150, Espoo, Finland.
| | - Ngong Kodiah Beyeh
- Oakland University, Department of Chemistry, 146 Library Drive, Rochester, MI, 48309-4479, USA
- Aalto University, School of Science, Department of Applied Physics, Puumiehenkuja 2, Espoo, Finland
| | - Ekaterina Osmekhina
- Aalto University, School of Chemical Engineering, Department of Bioproducts and Biosystems, Kemistintie 1, 02150, Espoo, Finland
| | - Katarzyna Leskinen
- University of Helsinki, Translational Immunology Research Program, Haartmaninkatu 8, 0014, Helsinki, Finland
| | - S Maryamdokht Taimoory
- University of Windsor, Department of Chemistry and Biochemistry, Windsor, ON, N9B 3P4, Canada
- University of Michigan, Department of Chemistry, Ann Arbor, MI, USA
| | - Dmitrii Fedorov
- Aalto University, School of Chemical Engineering, Department of Bioproducts and Biosystems, Kemistintie 1, 02150, Espoo, Finland
| | - Eduardo Anaya-Plaza
- Aalto University, School of Chemical Engineering, Department of Bioproducts and Biosystems, Kemistintie 1, 02150, Espoo, Finland
| | - Mauri A Kostiainen
- Aalto University, School of Chemical Engineering, Department of Bioproducts and Biosystems, Kemistintie 1, 02150, Espoo, Finland
| | - John F Trant
- University of Windsor, Department of Chemistry and Biochemistry, Windsor, ON, N9B 3P4, Canada
| | - Robin H A Ras
- Aalto University, School of Chemical Engineering, Department of Bioproducts and Biosystems, Kemistintie 1, 02150, Espoo, Finland
- Aalto University, School of Science, Department of Applied Physics, Puumiehenkuja 2, Espoo, Finland
| | - Päivi Saavalainen
- University of Helsinki, Translational Immunology Research Program, Haartmaninkatu 8, 0014, Helsinki, Finland.
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland.
| | - Markus B Linder
- Aalto University, School of Chemical Engineering, Department of Bioproducts and Biosystems, Kemistintie 1, 02150, Espoo, Finland.
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Osmekhina E, Jonkergouw C, Schmidt G, Jahangiri F, Jokinen V, Franssila S, Linder MB. Controlled communication between physically separated bacterial populations in a microfluidic device. Commun Biol 2018; 1:97. [PMID: 30271977 PMCID: PMC6123784 DOI: 10.1038/s42003-018-0102-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 06/28/2018] [Indexed: 12/29/2022] Open
Abstract
The engineering of microbial systems increasingly strives to achieve a co-existence and co-functioning of different populations. By creating interactions, one can utilize combinations of cells where each population has a specialized function, such as regulation or sharing of metabolic burden. Here we describe a microfluidic system that enables long-term and independent growth of fixed and distinctly separate microbial populations, while allowing communication through a thin nano-cellulose filter. Using quorum-sensing signaling, we can couple the populations and show that this leads to a rapid and stable connection over long periods of time. We continue to show that this control over communication can be utilized to drive nonlinear responses. The coupling of separate populations, standardized interaction, and context-independent function lay the foundation for the construction of increasingly complex community-wide dynamic genetic regulatory mechanisms.
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Affiliation(s)
- Ekaterina Osmekhina
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, 02150, Espoo, Finland
| | - Christopher Jonkergouw
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, 02150, Espoo, Finland
| | - Georg Schmidt
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, 02150, Espoo, Finland
| | - Farzin Jahangiri
- Department of Chemistry and Materials Science, School of Chemical Engineering, 02150, Espoo, Finland
| | - Ville Jokinen
- Department of Chemistry and Materials Science, School of Chemical Engineering, 02150, Espoo, Finland
| | - Sami Franssila
- Department of Chemistry and Materials Science, School of Chemical Engineering, 02150, Espoo, Finland
| | - Markus B Linder
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, 02150, Espoo, Finland.
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Osmekhina E, Shvetsova A, Ruottinen M, Neubauer P. Quantitative and sensitive RNA based detection of Bacillus spores. Front Microbiol 2014; 5:92. [PMID: 24653718 PMCID: PMC3949131 DOI: 10.3389/fmicb.2014.00092] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [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: 01/21/2014] [Accepted: 02/19/2014] [Indexed: 11/13/2022] Open
Abstract
The fast and reliable detection of bacterial spores is of great importance and still remains a challenge. Here we describe a direct RNA-based diagnostic method for the specific detection of viable bacterial spores which does not depends on an enzymatic amplification step and therefore is directly appropriate for quantification. The procedure includes the following steps: (i) heat activation of spores, (ii) germination and enrichment cultivation, (iii) cell lysis, and (iv) analysis of 16S rRNA in crude cell lysates using a sandwich hybridization assay. The sensitivity of the method is dependent on the cultivation time and the detection limit; it is possible to detect 10 spores per ml when the RNA analysis is performed after 6 h of enrichment cultivation. At spore concentrations above 10(6) spores per ml the cultivation time can be shortened to 30 min. Total analysis times are in the range of 2-8 h depending on the spore concentration in samples. The developed procedure is optimized at the example of Bacillus subtilis spores but should be applicable to other organisms. The new method can easily be modified for other target RNAs and is suitable for specific detection of spores from known groups of organisms.
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Affiliation(s)
- Ekaterina Osmekhina
- Department of Process and Environmental Engineering and Biocenter Oulu, University of Oulu Oulu, Finland
| | - Antonina Shvetsova
- Department of Biochemistry and Biocenter Oulu, University of Oulu Oulu, Finland
| | - Maria Ruottinen
- Department of Process and Environmental Engineering and Biocenter Oulu, University of Oulu Oulu, Finland
| | - Peter Neubauer
- Department of Process and Environmental Engineering and Biocenter Oulu, University of Oulu Oulu, Finland ; Laboratory of Bioprocess Engineering, Department of Biotechnology, Technische Universität Berlin Berlin, Germany
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Taskila S, Osmekhina E, Tuomola M, Ruuska J, Neubauer P. Modification of Buffered Peptone Water for Improved Recovery of Heat-Injured Salmonella Typhimurium. J Food Sci 2011; 76:M157-62. [DOI: 10.1111/j.1750-3841.2010.02050.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Osmekhina E, Neubauer A, Klinzing K, Myllyharju J, Neubauer P. Sandwich ELISA for quantitative detection of human collagen prolyl 4-hydroxylase. Microb Cell Fact 2010; 9:48. [PMID: 20565744 PMCID: PMC2895579 DOI: 10.1186/1475-2859-9-48] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [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] [Received: 03/31/2010] [Accepted: 06/17/2010] [Indexed: 11/28/2022] Open
Abstract
Background We describe a method for specific, quantitative and quick detection of human collagen prolyl 4-hydroxylase (C-P4H), the key enzyme for collagen prolyl-4 hydroxylation, in crude samples based on a sandwich ELISA principle. The method is relevant to active C-P4H level monitoring during recombinant C-P4H and collagen production in different expression systems. The assay proves to be specific for the active C-P4H α2β2 tetramer due to the use of antibodies against its both subunits. Thus in keeping with the method C-P4H is captured by coupled to an anti-α subunit antibody magnetic beads and an anti-β subunit antibody binds to the PDI/β subunit of the protein. Then the following holoenzyme detection is accomplished by a goat anti-rabbit IgG labeled with alkaline phosphatase which AP catalyzes the reaction of a substrate transformation with fluorescent signal generation. Results We applied an experimental design approach for the optimization of the antibody concentrations used in the sandwich ELISA. The assay sensitivity was 0.1 ng of C-P4H. The method was utilized for the analysis of C-P4H accumulation in crude cell extracts of E. coli overexpressing C-P4H. The sandwich ELISA signals obtained demonstrated a very good correlation with the detected protein activity levels measured with the standard radioactive assay. The developed assay was applied to optimize C-P4H production in E. coli Origami in a system where the C-P4H subunits expression acted under control by different promoters. The experiments performed in a shake flask fed-batch system (EnBase®) verified earlier observations that cell density and oxygen supply are critical factors for the use of the inducer anhydrotetracycline and thus for the soluble C-P4H yield. Conclusions Here we show an example of sandwich ELISA usage for quantifying multimeric proteins. The method was developed for monitoring the amount of recombinant C-P4H tetramer in crude E. coli extracts. Due to the specificity of the antibodies used in the assay against the different C-P4H subunits, the method detects the entire holoenzyme, and the signal is not disturbed by background expression of the separate subunits.
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Affiliation(s)
- Ekaterina Osmekhina
- Bioprocess Engineering Laboratory, Department of Process and Environmental Engineering, P.O. Box 4300, FIN-90014 University of Oulu, Finland.
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