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La Corte SG, Stevens CA, Cárcamo-Oyarce G, Ribbeck K, Wingreen NS, Datta SS. Morphogenesis of bacterial colonies in polymeric environments. bioRxiv 2024:2024.04.18.590088. [PMID: 38712130 PMCID: PMC11071276 DOI: 10.1101/2024.04.18.590088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Many bacteria live in polymeric fluids, such as mucus, environmental polysaccharides, and extracellular polymers in biofilms. However, lab studies typically focus on cells in polymer-free fluids. Here, we show that interactions with polymers shape a fundamental feature of bacterial life-how they proliferate in space in multicellular colonies. Using experiments, we find that when polymer is sufficiently concentrated, cells generically and reversibly form large serpentine "cables" as they proliferate. By combining experiments with biophysical theory and simulations, we demonstrate that this distinctive form of colony morphogenesis arises from an interplay between polymer-induced entropic attraction between neighboring cells and their hindered ability to diffusely separate from each other in a viscous polymer solution. Our work thus reveals a pivotal role of polymers in sculpting proliferating bacterial colonies, with implications for how they interact with hosts and with the natural environment, and uncovers quantitative principles governing colony morphogenesis in such complex environments.
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Deiss-Yehiely E, Cárcamo-Oyarce G, Berger AG, Ribbeck K, Hammond PT. pH-Responsive, Charge-Reversing Layer-by-Layer Nanoparticle Surfaces Enhance Biofilm Penetration and Eradication. ACS Biomater Sci Eng 2023; 9:4794-4804. [PMID: 37390118 DOI: 10.1021/acsbiomaterials.3c00481] [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] [Indexed: 07/02/2023]
Abstract
Microbes entrenched within biofilms can withstand 1000-fold higher concentrations of antibiotics, in part due to the viscous extracellular matrix that sequesters and attenuates antimicrobial activity. Nanoparticle (NP)-based therapeutics can aid in delivering higher local concentrations throughout biofilms as compared to free drugs alone, thereby enhancing the efficacy. Canonical design criteria dictate that positively charged nanoparticles can multivalently bind to anionic biofilm components and increase biofilm penetration. However, cationic particles are toxic and are rapidly cleared from circulation in vivo, limiting their use. Therefore, we sought to design pH-responsive NPs that change their surface charge from negative to positive in response to the reduced biofilm pH microenvironment. We synthesized a family of pH-dependent, hydrolyzable polymers and employed the layer-by-layer (LbL) electrostatic assembly method to fabricate biocompatible NPs with these polymers as the outermost surface. The NP charge conversion rate, dictated by polymer hydrophilicity and the side-chain structure, ranged from hours to undetectable within the experimental timeframe. LbL NPs with an increasingly fast charge conversion rate more effectively penetrated through, and accumulated throughout, wildtype (PAO1) and mutant overexpressing biomass (ΔwspF) Pseudomonas aeruginosa biofilms. Finally, tobramycin, an antibiotic known to be trapped by anionic biofilm components, was loaded into the final layer of the LbL NP. There was a 3.2-fold reduction in ΔwspF colony forming units for the fastest charge-converting NP as compared to both the slowest charge converter and free tobramycin. These studies provide a framework for the design of biofilm-penetrating NPs that respond to matrix interactions, ultimately increasing the efficacious delivery of antimicrobials.
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Affiliation(s)
- Elad Deiss-Yehiely
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, 182 Memorial Drive, Cambridge, Massachusetts 02142, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street Bld. 76, Cambridge, Massachusetts 02139, United States
| | - Gerardo Cárcamo-Oyarce
- Department of Biological Engineering, Massachusetts Institute of Technology, 21 Ames St. #56-651, Cambridge, Massachusetts 02139, United States
| | - Adam G Berger
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street Bld. 76, Cambridge, Massachusetts 02139, United States
- Institute for Soldier Nanotechnologies, Massachusetts Institute of Technology, 500 Technology Square, NE47-4F, Cambridge, Massachusetts 02139, United States
- Harvard-MIT Health Sciences and Technology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Katharina Ribbeck
- Department of Biological Engineering, Massachusetts Institute of Technology, 21 Ames St. #56-651, Cambridge, Massachusetts 02139, United States
| | - Paula T Hammond
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street Bld. 76, Cambridge, Massachusetts 02139, United States
- Institute for Soldier Nanotechnologies, Massachusetts Institute of Technology, 500 Technology Square, NE47-4F, Cambridge, Massachusetts 02139, United States
- Department of Chemical Engineering, Massachusetts Institute of Technology, 25 Ames Street, Cambridge, Massachusetts 02139, United States
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Wu CM, Wheeler KM, Cárcamo-Oyarce G, Aoki K, McShane A, Datta SS, Mark Welch JL, Tiemeyer M, Griffen AL, Ribbeck K. Mucin glycans drive oral microbial community composition and function. NPJ Biofilms Microbiomes 2023; 9:11. [PMID: 36959210 PMCID: PMC10036478 DOI: 10.1038/s41522-023-00378-4] [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: 10/03/2022] [Accepted: 02/20/2023] [Indexed: 03/25/2023] Open
Abstract
Human microbiome composition is closely tied to health, but how the host manages its microbial inhabitants remains unclear. One important, but understudied, factor is the natural host environment: mucus, which contains gel-forming glycoproteins (mucins) that display hundreds of glycan structures with potential regulatory function. Leveraging a tractable culture-based system to study how mucins influence oral microbial communities, we found that mucin glycans enable the coexistence of diverse microbes, while resisting disease-associated compositional shifts. Mucins from tissues with unique glycosylation differentially tuned microbial composition, as did isolated mucin glycan libraries, uncovering the importance of specific glycan patterns in microbiome modulation. We found that mucins shape microbial communities in several ways: serving as nutrients to support metabolic diversity, organizing spatial structure through reduced aggregation, and possibly limiting antagonism between competing taxa. Overall, this work identifies mucin glycans as a natural host mechanism and potential therapeutic intervention to maintain healthy microbial communities.
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Affiliation(s)
- Chloe M Wu
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kelsey M Wheeler
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Microbiology Graduate Program, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Gerardo Cárcamo-Oyarce
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kazuhiro Aoki
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Abigail McShane
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sujit S Datta
- Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
| | | | - Michael Tiemeyer
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Ann L Griffen
- Department of Dentistry, Nationwide Children's Hospital, Columbus, OH, USA
- Divisions of Biosciences and Pediatric Dentistry, College of Dentistry, The Ohio State University, Columbus, OH, USA
| | - Katharina Ribbeck
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
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Mawla GD, Hall BM, Cárcamo-Oyarce G, Grant RA, Zhang JJ, Kardon JR, Ribbeck K, Sauer RT, Baker TA. ClpP1P2 peptidase activity promotes biofilm formation in Pseudomonas aeruginosa. Mol Microbiol 2021; 115:1094-1109. [PMID: 33231899 PMCID: PMC8141546 DOI: 10.1111/mmi.14649] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [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: 07/06/2020] [Revised: 11/15/2020] [Accepted: 11/16/2020] [Indexed: 01/07/2023]
Abstract
Caseinolytic proteases (Clp) are central to bacterial proteolysis and control cellular physiology and stress responses. They are composed of a double-ring compartmentalized peptidase (ClpP) and a AAA+ unfoldase (ClpX or ClpA/ClpC). Unlike many bacteria, the opportunistic pathogen Pseudomonas aeruginosa contains two ClpP homologs: ClpP1 and ClpP2. The specific functions of these homologs, however, are largely elusive. Here, we report that the active form of PaClpP2 is a part of a heteromeric PaClpP17 P27 tetradecamer that is required for proper biofilm development. PaClpP114 and PaClpP17 P27 complexes exhibit distinct peptide cleavage specificities and interact differentially with P. aeruginosa ClpX and ClpA. Crystal structures reveal that PaClpP2 has non-canonical features in its N- and C-terminal regions that explain its poor interaction with unfoldases. However, experiments in vivo indicate that the PaClpP2 peptidase active site uniquely contributes to biofilm development. These data strongly suggest that the specificity of different classes of ClpP peptidase subunits contributes to the biological outcome of proteolysis. This specialized role of PaClpP2 highlights it as an attractive target for developing antimicrobial agents that interfere specifically with late-stage P. aeruginosa development.
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Affiliation(s)
- Gina D. Mawla
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Branwen M. Hall
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Gerardo Cárcamo-Oyarce
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Robert A. Grant
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Jia Jia Zhang
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Julia R. Kardon
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Katharina Ribbeck
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Robert T. Sauer
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Tania A. Baker
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
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Calderón CE, Tienda S, Heredia-Ponce Z, Arrebola E, Cárcamo-Oyarce G, Eberl L, Cazorla FM. The Compound 2-Hexyl, 5-Propyl Resorcinol Has a Key Role in Biofilm Formation by the Biocontrol Rhizobacterium Pseudomonas chlororaphis PCL1606. Front Microbiol 2019; 10:396. [PMID: 30873149 PMCID: PMC6403133 DOI: 10.3389/fmicb.2019.00396] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [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: 10/30/2018] [Accepted: 02/14/2019] [Indexed: 11/13/2022] Open
Abstract
The production of the compound 2-hexyl-5-propyl resorcinol (HPR) by the biocontrol rhizobacterium Pseudomonas chlororaphis PCL1606 (PcPCL1606) is crucial for fungal antagonism and biocontrol activity that protects plants against the phytopathogenic fungus Rosellinia necatrix. The production of HPR is also involved in avocado root colonization during the biocontrol process. This pleiotrophic response prompted us to study the potential role of HPR production in biofilm formation. The swimming motility of PcPLL1606 is enhanced by the disruption of HPR production. Mutants impaired in HPR production, revealed that adhesion, colony morphology, and typical air–liquid interphase pellicles were all dependent on HPR production. The role of HPR production in biofilm architecture was also analyzed in flow chamber experiments. These experiments revealed that the HPR mutant cells had less tight unions than those producing HPR, suggesting an involvement of HPR in the production of the biofilm matrix.
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Affiliation(s)
- Claudia E Calderón
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain.,Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora," Consejo Superior de Investigaciones Científicas, Universidad de Málaga, IHSM-UMA-CSIC, Málaga, Spain
| | - Sandra Tienda
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain.,Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora," Consejo Superior de Investigaciones Científicas, Universidad de Málaga, IHSM-UMA-CSIC, Málaga, Spain
| | - Zaira Heredia-Ponce
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain.,Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora," Consejo Superior de Investigaciones Científicas, Universidad de Málaga, IHSM-UMA-CSIC, Málaga, Spain
| | - Eva Arrebola
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain.,Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora," Consejo Superior de Investigaciones Científicas, Universidad de Málaga, IHSM-UMA-CSIC, Málaga, Spain
| | | | - Leo Eberl
- Department of Plant and Microbial Biology, University of Zürich, Zurich, Switzerland
| | - Francisco M Cazorla
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain.,Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora," Consejo Superior de Investigaciones Científicas, Universidad de Málaga, IHSM-UMA-CSIC, Málaga, Spain
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Turnbull L, Toyofuku M, Hynen AL, Kurosawa M, Pessi G, Petty NK, Osvath SR, Cárcamo-Oyarce G, Gloag ES, Shimoni R, Omasits U, Ito S, Yap X, Monahan LG, Cavaliere R, Ahrens CH, Charles IG, Nomura N, Eberl L, Whitchurch CB. Explosive cell lysis as a mechanism for the biogenesis of bacterial membrane vesicles and biofilms. Nat Commun 2016; 7:11220. [PMID: 27075392 PMCID: PMC4834629 DOI: 10.1038/ncomms11220] [Citation(s) in RCA: 372] [Impact Index Per Article: 46.5] [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: 09/06/2015] [Accepted: 03/02/2016] [Indexed: 02/07/2023] Open
Abstract
Many bacteria produce extracellular and surface-associated components such as membrane vesicles (MVs), extracellular DNA and moonlighting cytosolic proteins for which the biogenesis and export pathways are not fully understood. Here we show that the explosive cell lysis of a sub-population of cells accounts for the liberation of cytosolic content in Pseudomonas aeruginosa biofilms. Super-resolution microscopy reveals that explosive cell lysis also produces shattered membrane fragments that rapidly form MVs. A prophage endolysin encoded within the R- and F-pyocin gene cluster is essential for explosive cell lysis. Endolysin-deficient mutants are defective in MV production and biofilm development, consistent with a crucial role in the biogenesis of MVs and liberation of extracellular DNA and other biofilm matrix components. Our findings reveal that explosive cell lysis, mediated through the activity of a cryptic prophage endolysin, acts as a mechanism for the production of bacterial MVs.
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Affiliation(s)
- Lynne Turnbull
- The ithree institute, University of Technology Sydney, Ultimo, New South Wales 2007, Australia
| | - Masanori Toyofuku
- Department of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan.,Department of Plant and Microbial Biology, University of Zurich, Zürich 8008, Switzerland
| | - Amelia L Hynen
- The ithree institute, University of Technology Sydney, Ultimo, New South Wales 2007, Australia
| | - Masaharu Kurosawa
- Department of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - Gabriella Pessi
- Department of Plant and Microbial Biology, University of Zurich, Zürich 8008, Switzerland
| | - Nicola K Petty
- The ithree institute, University of Technology Sydney, Ultimo, New South Wales 2007, Australia
| | - Sarah R Osvath
- The ithree institute, University of Technology Sydney, Ultimo, New South Wales 2007, Australia
| | - Gerardo Cárcamo-Oyarce
- Department of Plant and Microbial Biology, University of Zurich, Zürich 8008, Switzerland
| | - Erin S Gloag
- The ithree institute, University of Technology Sydney, Ultimo, New South Wales 2007, Australia
| | - Raz Shimoni
- The ithree institute, University of Technology Sydney, Ultimo, New South Wales 2007, Australia
| | - Ulrich Omasits
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zürich 8093, Switzerland
| | - Satoshi Ito
- Department of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - Xinhui Yap
- The ithree institute, University of Technology Sydney, Ultimo, New South Wales 2007, Australia
| | - Leigh G Monahan
- The ithree institute, University of Technology Sydney, Ultimo, New South Wales 2007, Australia
| | - Rosalia Cavaliere
- The ithree institute, University of Technology Sydney, Ultimo, New South Wales 2007, Australia
| | - Christian H Ahrens
- Agroscope, Institute for Plant Production Sciences, Research Group Molecular Diagnostics, Genomics and Bioinformatics, &Swiss Institute of Bioinformatics (SIB), Wädenswil 8820, Switzerland
| | - Ian G Charles
- The ithree institute, University of Technology Sydney, Ultimo, New South Wales 2007, Australia
| | - Nobuhiko Nomura
- Department of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - Leo Eberl
- Department of Plant and Microbial Biology, University of Zurich, Zürich 8008, Switzerland
| | - Cynthia B Whitchurch
- The ithree institute, University of Technology Sydney, Ultimo, New South Wales 2007, Australia
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Cárcamo-Oyarce G, Lumjiaktase P, Kümmerli R, Eberl L. Quorum sensing triggers the stochastic escape of individual cells from Pseudomonas putida biofilms. Nat Commun 2015; 6:5945. [PMID: 25592773 PMCID: PMC4309448 DOI: 10.1038/ncomms6945] [Citation(s) in RCA: 133] [Impact Index Per Article: 14.8] [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: 05/26/2014] [Accepted: 11/24/2014] [Indexed: 12/18/2022] Open
Abstract
The term ‘quorum sensing’ (QS) is generally used to describe the phenomenon that bacteria release and perceive signal molecules to coordinate cooperative behaviour in response to their population size. QS-based communication has therefore been considered a social trait. Here we show that QS signals (N-acyl-homoserine lactones, AHLs) are stochastically produced in young biofilms of Pseudomonas putida and act mainly as self-regulatory signals rather than inducing neighbouring cells. We demonstrate that QS induces the expression of putisolvin biosurfactants that are not public goods, thereby triggering asocial motility of induced cells out of microcolonies. Phenotypic heterogeneity is most prominent in the early stages of biofilm development, whereas at later stages behaviour patterns across cells become more synchronized. Our findings broaden our perspective on QS by showing that AHLs can control the expression of asocial (self-directed) traits, and that heterogeneity in QS can serve as a mechanism to drive phenotypic heterogeneity in self-directed behaviour. Bacteria secrete signalling molecules (AHLs) to coordinate actions such as biofilm formation and the release of public goods, in a process called quorum sensing. Here, the authors show that AHLs are stochastically produced and control asocial (self-directed) traits in young biofilms of P. putida.
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Affiliation(s)
- Gerardo Cárcamo-Oyarce
- Department of Microbiology, Institute of Plant Biology, University of Zürich, Zollikerstrasse 107, Zürich CH-8008, Switzerland
| | - Putthapoom Lumjiaktase
- Department of Microbiology, Institute of Plant Biology, University of Zürich, Zollikerstrasse 107, Zürich CH-8008, Switzerland
| | - Rolf Kümmerli
- Department of Microbial Evolutionary Ecology, Institute of Plant Biology, University of Zürich, Winterthurerstrasse 190, Zürich CH-8057, Switzerland
| | - Leo Eberl
- Department of Microbiology, Institute of Plant Biology, University of Zürich, Zollikerstrasse 107, Zürich CH-8008, Switzerland
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