1
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McCaughey C, Trebino MA, McAtamney A, Isenberg RY, Mandel MJ, Yildiz FH, Sanchez LM. A Label-Free Approach for Relative Spatial Quantitation of c-di-GMP in Microbial Biofilms. Anal Chem 2024; 96:8308-8316. [PMID: 38752543 PMCID: PMC11140670 DOI: 10.1021/acs.analchem.3c04687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 04/27/2024] [Accepted: 05/07/2024] [Indexed: 05/19/2024]
Abstract
Microbial biofilms represent an important lifestyle for bacteria and are dynamic three-dimensional structures. Cyclic dimeric guanosine monophosphate (c-di-GMP) is a ubiquitous signaling molecule that is known to be tightly regulated with biofilm processes. While measurements of global levels of c-di-GMP have proven valuable toward understanding the genetic control of c-di-GMP production, there is a need for tools to observe the local changes of c-di-GMP production in biofilm processes. We have developed a label-free method for the direct detection of c-di-GMP in microbial colony biofilms using matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI). We applied this method to the enteric pathogen Vibrio cholerae, the marine symbiont V. fischeri, and the opportunistic pathogen Pseudomonas aeruginosa PA14 and detected spatial and temporal changes in c-di-GMP signal that accompanied genetic alterations in factors that synthesize and degrade the compound. We further demonstrated how this method can be simultaneously applied to detect additional metabolites of interest from a single sample.
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Affiliation(s)
- Catherine
S. McCaughey
- Department
of Chemistry and Biochemistry, University
of California, Santa Cruz, Santa Cruz, California 95064, United States
| | - Michael A. Trebino
- Department
of Microbiology and Environmental Toxicology, University of California, Santa Cruz, Santa Cruz, California 95064, United States
| | - Allyson McAtamney
- Department
of Chemistry and Biochemistry, University
of California, Santa Cruz, Santa Cruz, California 95064, United States
| | - Ruth Y. Isenberg
- Department
of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Microbiology
Doctoral Training Program, University of
Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Mark J. Mandel
- Department
of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Microbiology
Doctoral Training Program, University of
Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Fitnat H. Yildiz
- Department
of Microbiology and Environmental Toxicology, University of California, Santa Cruz, Santa Cruz, California 95064, United States
| | - Laura M. Sanchez
- Department
of Chemistry and Biochemistry, University
of California, Santa Cruz, Santa Cruz, California 95064, United States
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2
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Weaver AA, Jia J, Cutri AR, Madukoma CS, Vaerewyck CM, Bohn PW, Shrout JD. Alkyl quinolones mediate heterogeneous colony biofilm architecture that improves community-level survival. J Bacteriol 2024; 206:e0009524. [PMID: 38564677 PMCID: PMC11025328 DOI: 10.1128/jb.00095-24] [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: 03/05/2024] [Accepted: 03/11/2024] [Indexed: 04/04/2024] Open
Abstract
Bacterial communities exhibit complex self-organization that contributes to their survival. To better understand the molecules that contribute to transforming a small number of cells into a heterogeneous surface biofilm community, we studied acellular aggregates, structures seen by light microscopy in Pseudomonas aeruginosa colony biofilms using light microscopy and chemical imaging. These structures differ from cellular aggregates, cohesive clusters of cells important for biofilm formation, in that they are visually distinct from cells using light microscopy and are reliant on metabolites for assembly. To investigate how these structures benefit a biofilm community we characterized three recurrent types of acellular aggregates with distinct geometries that were each abundant in specific areas of these biofilms. Alkyl quinolones (AQs) were essential for the formation of all aggregate types with AQ signatures outside the aggregates below the limit of detection. These acellular aggregates spatially sequester AQs and differentiate the biofilm space. However, the three types of aggregates showed differing properties in their size, associated cell death, and lipid content. The largest aggregate type co-localized with spatially confined cell death that was not mediated by Pf4 bacteriophage. Biofilms lacking AQs were absent of localized cell death but exhibited increased, homogeneously distributed cell death. Thus, these AQ-rich aggregates regulate metabolite accessibility, differentiate regions of the biofilm, and promote survival in biofilms.IMPORTANCEPseudomonas aeruginosa is an opportunistic pathogen with the ability to cause infection in the immune-compromised. It is well established that P. aeruginosa biofilms exhibit resilience that includes decreased susceptibility to antimicrobial treatment. This work examines the self-assembled heterogeneity in biofilm communities studying acellular aggregates, regions of condensed matter requiring alkyl quinolones (AQs). AQs are important to both virulence and biofilm formation. Aggregate structures described here spatially regulate the accessibility of these AQs, differentiate regions of the biofilm community, and despite their association with autolysis, correlate with improved P. aeruginosa colony biofilm survival.
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Affiliation(s)
- Abigail A. Weaver
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, Indiana, USA
| | - Jin Jia
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Allison R. Cutri
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Chinedu S. Madukoma
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, Indiana, USA
| | - Catherine M. Vaerewyck
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, Indiana, USA
| | - Paul W. Bohn
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana, USA
| | - Joshua D. Shrout
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, Indiana, USA
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA
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3
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Chung HH, Huang P, Chen CL, Lee C, Hsu CC. Next-generation pathology practices with mass spectrometry imaging. MASS SPECTROMETRY REVIEWS 2023; 42:2446-2465. [PMID: 35815718 DOI: 10.1002/mas.21795] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 04/13/2022] [Accepted: 04/22/2022] [Indexed: 06/15/2023]
Abstract
Mass spectrometry imaging (MSI) is a powerful technique that reveals the spatial distribution of various molecules in biological samples, and it is widely used in pathology-related research. In this review, we summarize common MSI techniques, including matrix-assisted laser desorption/ionization and desorption electrospray ionization MSI, and their applications in pathological research, including disease diagnosis, microbiology, and drug discovery. We also describe the improvements of MSI, focusing on the accumulation of imaging data sets, expansion of chemical coverage, and identification of biological significant molecules, that have prompted the evolution of MSI to meet the requirements of pathology practices. Overall, this review details the applications and improvements of MSI techniques, demonstrating the potential of integrating MSI techniques into next-generation pathology practices.
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Affiliation(s)
- Hsin-Hsiang Chung
- Department of Chemistry, National Taiwan University, Taipei City, Taiwan
| | - Penghsuan Huang
- Department of Chemistry, National Taiwan University, Taipei City, Taiwan
| | - Chih-Lin Chen
- Department of Chemistry, National Taiwan University, Taipei City, Taiwan
| | - Chuping Lee
- Department of Chemistry, Fu Jen Catholic University, New Taipei City, Taiwan
| | - Cheng-Chih Hsu
- Department of Chemistry, National Taiwan University, Taipei City, Taiwan
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4
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McCaughey CS, Trebino MA, McAtamney A, Isenberg R, Mandel MJ, Yildiz FH, Sanchez LM. A label-free approach for relative spatial quantitation of c-di-GMP in microbial biofilms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.10.561783. [PMID: 37873360 PMCID: PMC10592747 DOI: 10.1101/2023.10.10.561783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Microbial biofilms represent an important lifestyle for bacteria and are dynamic three dimensional structures. Cyclic dimeric guanosine monophosphate (c-di-GMP) is a ubiquitous signaling molecule that is known to be tightly regulated with biofilm processes. While measurements of global levels of c-di-GMP have proven valuable towards understanding the genetic control of c-di-GMP production, there is a need for tools to observe the local changes of c-di-GMP production in biofilm processes. We have developed a label-free method for the direct detection of c-di-GMP in microbial colony biofilms using matrix-assisted laser desorption ionization mass spectrometry imaging (MALDI-MSI). We applied this method to the enteric pathogen Vibrio cholerae, the marine symbiont V. fischeri, and the opportunistic pathogen Pseudomonas aeruginosa PA14 and detected spatial and temporal changes in c-di-GMP signal that accompanied genetic alterations in factors that synthesize and degrade the compound. We further demonstrated how this method can be simultaneously applied to detect additional metabolites of interest in a single experiment.
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Affiliation(s)
- Catherine S McCaughey
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA 95064
| | - Michael A Trebino
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, Santa Cruz, CA 95064
| | - Allyson McAtamney
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA 95064
| | - Ruth Isenberg
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI 53706
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI 53706
- Current Address: Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, MN 55455
| | - Mark J Mandel
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI 53706
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI 53706
| | - Fitnat H Yildiz
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, Santa Cruz, CA 95064
| | - Laura M Sanchez
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA 95064
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5
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Bru JL, Kasallis SJ, Chang R, Zhuo Q, Nguyen J, Pham P, Warren E, Whiteson K, Høyland-Kroghsbo NM, Limoli DH, Siryaporn A. The great divide: rhamnolipids mediate separation between P. aeruginosa and S. aureus. Front Cell Infect Microbiol 2023; 13:1245874. [PMID: 37780859 PMCID: PMC10540625 DOI: 10.3389/fcimb.2023.1245874] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 08/23/2023] [Indexed: 10/03/2023] Open
Abstract
The interactions between bacterial species during infection can have significant impacts on pathogenesis. Pseudomonas aeruginosa and Staphylococcus aureus are opportunistic bacterial pathogens that can co-infect hosts and cause serious illness. The factors that dictate whether one species outcompetes the other or whether the two species coexist are not fully understood. We investigated the role of surfactants in the interactions between these two species on a surface that enables P. aeruginosa to swarm. We found that P. aeruginosa swarms are repelled by colonies of clinical S. aureus isolates, creating physical separation between the two strains. This effect was abolished in mutants of S. aureus that were defective in the production of phenol-soluble modulins (PSMs), which form amyloid fibrils around wild-type S. aureus colonies. We investigated the mechanism that establishes physical separation between the two species using Imaging of Reflected Illuminated Structures (IRIS), which is a non-invasive imaging method that tracks the flow of surfactants produced by P. aeruginosa. We found that PSMs produced by S. aureus deflected the surfactant flow, which in turn, altered the direction of P. aeruginosa swarms. These findings show that rhamnolipids mediate physical separation between P. aeruginosa and S. aureus, which could facilitate coexistence between these species. Additionally, we found that a number of molecules repelled P. aeruginosa swarms, consistent with a surfactant deflection mechanism. These include Bacillus subtilis surfactant, the fatty acids oleic acid and linoleic acid, and the synthetic lubricant polydimethylsiloxane. Lung surfactant repelled P. aeruginosa swarms and inhibited swarm expansion altogether at higher concentration. Our results suggest that surfactant interactions could have major impacts on bacteria-bacteria and bacteria-host relationships. In addition, our findings uncover a mechanism responsible for P. aeruginosa swarm development that does not rely solely on sensing but instead is based on the flow of surfactant.
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Affiliation(s)
- Jean-Louis Bru
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, United States
| | - Summer J. Kasallis
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, United States
- Department of Physics & Astronomy, University of California, Irvine, Irvine, CA, United States
| | - Rendell Chang
- School of Biological Sciences, University of California, Irvine, Irvine, CA, United States
| | - Quantum Zhuo
- Department of Physics & Astronomy, University of California, Irvine, Irvine, CA, United States
| | - Jacqueline Nguyen
- School of Biological Sciences, University of California, Irvine, Irvine, CA, United States
| | - Phillip Pham
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, United States
| | - Elizabeth Warren
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA, United States
| | - Katrine Whiteson
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, United States
| | | | - Dominique H. Limoli
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA, United States
| | - Albert Siryaporn
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, United States
- Department of Physics & Astronomy, University of California, Irvine, Irvine, CA, United States
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6
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Bru JL, Kasallis SJ, Zhuo Q, Høyland-Kroghsbo NM, Siryaporn A. Swarming of P. aeruginosa: Through the lens of biophysics. BIOPHYSICS REVIEWS 2023; 4:031305. [PMID: 37781002 PMCID: PMC10540860 DOI: 10.1063/5.0128140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 08/29/2023] [Indexed: 10/03/2023]
Abstract
Swarming is a collective flagella-dependent movement of bacteria across a surface that is observed across many species of bacteria. Due to the prevalence and diversity of this motility modality, multiple models of swarming have been proposed, but a consensus on a general mechanism for swarming is still lacking. Here, we focus on swarming by Pseudomonas aeruginosa due to the abundance of experimental data and multiple models for this species, including interpretations that are rooted in biology and biophysics. In this review, we address three outstanding questions about P. aeruginosa swarming: what drives the outward expansion of a swarm, what causes the formation of dendritic patterns (tendrils), and what are the roles of flagella? We review models that propose biologically active mechanisms including surfactant sensing as well as fluid mechanics-based models that consider swarms as thin liquid films. Finally, we reconcile recent observations of P. aeruginosa swarms with early definitions of swarming. This analysis suggests that mechanisms associated with sliding motility have a critical role in P. aeruginosa swarm formation.
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Affiliation(s)
- Jean-Louis Bru
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, California 92697, USA
| | - Summer J. Kasallis
- Department of Physics and Astronomy, University of California Irvine, Irvine, California 92697, USA
| | - Quantum Zhuo
- Department of Physics and Astronomy, University of California Irvine, Irvine, California 92697, USA
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7
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Jia J, Parmar D, Ellis JF, Cao T, Cutri AR, Shrout JD, Sweedler JV, Bohn PW. Effect of Micro-Patterned Mucin on Quinolone and Rhamnolipid Profiles of Mucoid Pseudomonas aeruginosa under Antibiotic Stress. ACS Infect Dis 2023; 9:150-161. [PMID: 36538577 PMCID: PMC10116410 DOI: 10.1021/acsinfecdis.2c00519] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Pseudomonas aeruginosa (P. aeruginosa) is commonly implicated in hospital-acquired infections where its capacity to form biofilms on a variety of surfaces and the resulting enhanced antibiotic resistance seriously limit treatment choices. Because surface attachment sensitizes P. aeruginosa to quorum sensing (QS) and induces virulence through both chemical and mechanical cues, we investigate the effect of surface properties through spatially patterned mucin, combined with sub-inhibitory concentrations of tobramycin on QS and virulence factors in both mucoid and non-mucoid P. aeruginosa strains using multi-modal chemical imaging combining confocal Raman microscopy and matrix-assisted laser desorption/ionization-mass spectrometry. Samples comprise surface-adherent static biofilms at a solid-water interface, supernatant liquid, and pellicle biofilms at an air-water interface at various time points. Although the presence of a sub-inhibitory concentration of tobramycin in the supernatant retards growth and development of static biofilms independent of strain and surface mucin patterning, we observe clear differences in the behavior of mucoid and non-mucoid strains. Quinolone signals in a non-mucoid strain are induced earlier and are influenced by mucin surface patterning to a degree not exhibited in the mucoid strain. Additionally, phenazine virulence factors, such as pyocyanin, are observed in the pellicle biofilms of both mucoid and non-mucoid strains but are not detected in the static biofilms from either strain, highlighting the differences in stress response between pellicle and static biofilms. Differences between mucoid and non-mucoid strains are consistent with their strain-specific phenology, in which the mucoid strain develops highly protected biofilms.
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Affiliation(s)
- Jin Jia
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Dharmeshkumar Parmar
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Joanna F Ellis
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Tianyuan Cao
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Allison R Cutri
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Joshua D Shrout
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, Indiana 46556, United States.,Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Jonathan V Sweedler
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Paul W Bohn
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States.,Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, United States
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8
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Ogbechi J, Huang YS, Clanchy FIL, Pantazi E, Topping LM, Darlington LG, Williams RO, Stone TW. Modulation of immune cell function, IDO expression and kynurenine production by the quorum sensor 2-heptyl-3-hydroxy-4-quinolone (PQS). Front Immunol 2022; 13:1001956. [PMID: 36389710 PMCID: PMC9650388 DOI: 10.3389/fimmu.2022.1001956] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 10/05/2022] [Indexed: 12/29/2023] Open
Abstract
Many invasive micro-organisms produce 'quorum sensor' molecules which regulate colony expansion and may modulate host immune responses. We have examined the ability of Pseudomonas Quorum Sensor (PQS) to influence cytokine expression under conditions of inflammatory stress. The administration of PQS in vivo to mice with collagen-induced arthritis (CIA) increased the severity of disease. Blood and inflamed paws from treated mice had fewer regulatory T cells (Tregs) but normal numbers of Th17 cells. However, PQS (1μM) treatment of antigen-stimulated lymph node cells from collagen-immunised mice in vitro inhibited the differentiation of CD4+IFNγ+ cells, with less effect on CD4+IL-17+ cells and no change in CD4+FoxP3+Tregs. PQS also inhibited T cell activation by anti-CD3/anti-CD28 antibodies. PQS reduced murine macrophage polarisation and inhibited expression of IL1B and IL6 genes in murine macrophages and human THP-1 cells. In human monocyte-derived macrophages, IDO1 gene, protein and enzyme activity were all inhibited by exposure to PQS. TNF gene expression was inhibited in THP-1 cells but not murine macrophages, while LPS-induced TNF protein release was increased by high PQS concentrations. PQS is known to have iron scavenging activity and its suppression of cytokine release was abrogated by iron supplementation. Unexpectedly, PQS decreased the expression of indoleamine-2, 3-dioxygenase genes (IDO1 and IDO2), IDO1 protein expression and enzyme activity in mouse and human macrophages. This is consistent with evidence that IDO1 inhibition or deletion exacerbates arthritis, while kynurenine reduces its severity. It is suggested that the inhibition of IDO1 and cytokine expression may contribute to the quorum sensor and invasive actions of PQS.
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Affiliation(s)
- Joy Ogbechi
- The Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculo-skeletal Sciences (NDORMS), University of Oxford, Oxford, United Kingdom
| | - Yi-Shu Huang
- The Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculo-skeletal Sciences (NDORMS), University of Oxford, Oxford, United Kingdom
| | - Felix I. L. Clanchy
- The Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculo-skeletal Sciences (NDORMS), University of Oxford, Oxford, United Kingdom
| | - Eirini Pantazi
- The Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculo-skeletal Sciences (NDORMS), University of Oxford, Oxford, United Kingdom
| | - Louise M. Topping
- The Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculo-skeletal Sciences (NDORMS), University of Oxford, Oxford, United Kingdom
| | | | - Richard O. Williams
- The Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculo-skeletal Sciences (NDORMS), University of Oxford, Oxford, United Kingdom
| | - Trevor W. Stone
- The Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculo-skeletal Sciences (NDORMS), University of Oxford, Oxford, United Kingdom
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9
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Hills OJ, Yong CW, Scott AJ, Devine DA, Smith J, Chappell HF. Atomic-scale interactions between quorum sensing autoinducer molecules and the mucoid P. aeruginosa exopolysaccharide matrix. Sci Rep 2022; 12:7724. [PMID: 35545629 PMCID: PMC9095684 DOI: 10.1038/s41598-022-11499-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 04/18/2022] [Indexed: 12/22/2022] Open
Abstract
Mucoid Pseudomonas aeruginosa is a prevalent cystic fibrosis (CF) lung coloniser whose chronicity is associated with the formation of cation cross-linked exopolysaccharide (EPS) matrices, which form a biofilm that acts as a diffusion barrier, sequestering cationic and neutral antimicrobials, and making it extremely resistant to pharmacological challenge. Biofilm chronicity and virulence of the colony is regulated by quorum sensing autoinducers (QSAIs), small signalling metabolites that pass between bacteria, through the biofilm matrix, regulating genetic responses on a population-wide scale. The nature of how these molecules interact with the EPS is poorly understood, despite the fact that they must pass through EPS matrix to reach neighbouring bacteria. Interactions at the atomic-scale between two QSAI molecules, C4-HSL and PQS—both utilised by mucoid P. aeruginosa in the CF lung—and the EPS, have been studied for the first time using a combined molecular dynamics (MD) and density functional theory (DFT) approach. A large-scale, calcium cross-linked, multi-chain EPS molecular model was developed and MD used to sample modes of interaction between QSAI molecules and the EPS that occur at physiological equilibrium. The thermodynamic stability of the QSAI-EPS adducts were calculated using DFT. These simulations provide a thermodynamic rationale for the apparent free movement of C4-HSL, highlight key molecular functionality responsible for EPS binding and, based on its significantly reduced mobility, suggest PQS as a viable target for quorum quenching.
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Affiliation(s)
- Oliver J Hills
- School of Food Science & Nutrition, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK.
| | - Chin W Yong
- Daresbury Laboratory, Scientific Computing Department, Science and Technology Facilities Council, Keckwick Lane, Daresbury, Warrington, WA4 4AD, UK.,Division of Pharmacy and Optometry, School of Health Sciences, University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Andrew J Scott
- School of Chemical & Process Engineering, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | - Deirdre A Devine
- School of Dentistry, University of Leeds, Clarendon Way, Leeds, LS2 9LU, UK
| | - James Smith
- School of Food Science & Nutrition, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | - Helen F Chappell
- School of Food Science & Nutrition, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK.
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10
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Mass spectrometry imaging and its potential in food microbiology. Int J Food Microbiol 2022; 371:109675. [DOI: 10.1016/j.ijfoodmicro.2022.109675] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 03/23/2022] [Accepted: 04/04/2022] [Indexed: 11/20/2022]
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11
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Junkins EN, McWhirter JB, McCall LI, Stevenson BS. Environmental structure impacts microbial composition and secondary metabolism. ISME COMMUNICATIONS 2022; 2:15. [PMID: 37938679 PMCID: PMC9723690 DOI: 10.1038/s43705-022-00097-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 01/03/2022] [Accepted: 01/18/2022] [Indexed: 05/11/2023]
Abstract
Determining the drivers of microbial community assembly is a central theme of microbial ecology, and chemical ecologists seek to characterize how secondary metabolites mediate these assembly patterns. Environmental structure affects how communities assemble and what metabolic pathways aid in that assembly. Here, we bridged these two perspectives by addressing the chemical drivers of community assembly within a spatially structured landscape with varying oxygen availability. We hypothesized that structured environments would favor higher microbial diversity and metabolite diversity. We anticipated that the production of a compound would be more advantageous in a structured environment (less mixing) compared to an unstructured environment (more mixing), where the molecule would have a diminished local effect. We observed this to be partially true in our experiments: structured environments had similar microbial diversity compared to unstructured environments but differed significantly in the metabolites produced. We also found that structured environments selected for communities with higher evenness, rather than communities with higher richness. This supports the idea that when characterizing the drivers of community assembly, it matters less about who is there and more about what they are doing. Overall, these data contribute to a growing effort to approach microbial community assembly with interdisciplinary tools and perspectives.
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Affiliation(s)
- Emily N Junkins
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA.
| | - Joseph B McWhirter
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Laura-Isobel McCall
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, USA
| | - Bradley S Stevenson
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
- Department of Earth and Planetary Science, Northwestern University, Chicago, IL, USA
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12
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Cao T, Weaver AA, Baek S, Jia J, Shrout JD, Bohn PW. Depth distributions of signaling molecules in Pseudomonas aeruginosa biofilms mapped by confocal Raman microscopy. J Chem Phys 2021; 154:204201. [PMID: 34241187 DOI: 10.1063/5.0052785] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Pseudomonas aeruginosa is an opportunistic human pathogen implicated in both acute and chronic diseases, which resists antibiotic treatment, in part by forming physical and chemical barriers such as biofilms. Here, we explore the use of confocal Raman imaging to characterize the three-dimensional (3D) spatial distribution of alkyl quinolones (AQs) in P. aeruginosa biofilms by reconstructing depth profiles from hyperspectral Raman data. AQs are important to quorum sensing (QS), virulence, and other actions of P. aeruginosa. Three-dimensional distributions of three different AQs (PQS, HQNO, and HHQ) were observed to have a significant depth, suggesting 3D anisotropic shapes-sheet-like rectangular solids for HQNO and extended cylinders for PQS. Similar to observations from 2D imaging studies, spectral features characteristic of AQs (HQNO or PQS) and the amide I vibration from peptide-containing species were found to correlate with the PQS cylinders typically located at the tips of the HQNO rectangular solids. In the QS-deficient mutant lasIrhlI, a small globular component was observed, whose highly localized nature and similarity in size to a P. aeruginosa cell suggest that the feature arises from HHQ localized in the vicinity of the cell from which it was secreted. The difference in the shapes and sizes of the aggregates of the three AQs in wild-type and mutant P. aeruginosa is likely related to the difference in the cellular response to growth conditions, environmental stress, metabolic levels, or other structural and biochemical variations inside biofilms. This study provides a new route to characterizing the 3D structure of biofilms and shows the potential of confocal Raman imaging to elucidate the nature of heterogeneous biofilms in all three spatial dimensions. These capabilities should be applicable as a tool in studies of infectious diseases.
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Affiliation(s)
- Tianyuan Cao
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Abigail A Weaver
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Seol Baek
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Jin Jia
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Joshua D Shrout
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Paul W Bohn
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
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13
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Biological and clinical significance of quorum sensing alkylquinolones: current analytical and bioanalytical methods for their quantification. Anal Bioanal Chem 2021; 413:4599-4618. [PMID: 33959788 DOI: 10.1007/s00216-021-03356-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 03/21/2021] [Accepted: 04/16/2021] [Indexed: 12/27/2022]
Abstract
Quorum sensing (QS) is a sophisticated bacterial communication system which plays a key role in the virulence and biofilm formation of many pathogens. The Pseudomonas aeruginosa QS network consists of four sets of connected systems (las, rlh, pqs and iqs) hierarchically organized. The pqs system involves characteristic autoinducers (AI), most of them sharing an alkylquinolone (AQ) structure, and is able to carry out several relevant biological functions besides its main signalling activity. Their role in bacterial physiology and pathogenicity has been widely studied. Indeed, the presence of these metabolites in several body fluids and infected tissues has pointed to their potential value as biomarkers of infection. In this review, we summarize the most recent findings about the biological implications and the clinical significance of the main P. aeruginosa AQs. These findings have encouraged the development of analytical and bioanalytical techniques addressed to assess the role of these metabolites in bacterial growth and survival, during pathogenesis or as biomarkers of infections. The availability of highly sensitive reliable analytical methods suitable for clinical analysis would allow getting knowledge about pathogenesis and disease prognosis or progression, supporting clinicians on the decision-making process for the management of these infections and guiding them on the application of more effective and appropriate treatments. The benefits from the implementation of the point-of-care (PoC)-type testing in infectious disease diagnostics, which are seen to improve patient outcomes by promoting earlier therapeutic interventions, are also discussed.
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14
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Iakab SA, Ràfols P, Correig-Blanchar X, García-Altares M. Perspective on Multimodal Imaging Techniques Coupling Mass Spectrometry and Vibrational Spectroscopy: Picturing the Best of Both Worlds. Anal Chem 2021; 93:6301-6310. [PMID: 33856207 PMCID: PMC8491157 DOI: 10.1021/acs.analchem.0c04986] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
![]()
Studies
on complex biological phenomena often combine two or more
imaging techniques to collect high-quality comprehensive data directly in situ, preserving the biological context. Mass spectrometry
imaging (MSI) and vibrational spectroscopy imaging (VSI) complement
each other in terms of spatial resolution and molecular information.
In the past decade, several combinations of such multimodal strategies
arose in research fields as diverse as microbiology, cancer, and forensics,
overcoming many challenges toward the unification of these techniques.
Here we focus on presenting the advantages and challenges of multimodal
imaging from the point of view of studying biological samples as well
as giving a perspective on the upcoming trends regarding this topic.
The latest efforts in the field are discussed, highlighting the purpose
of the technique for clinical applications.
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Affiliation(s)
- Stefania Alexandra Iakab
- Rovira i Virgili University, Department of Electronic Engineering, IISPV, 43007 Tarragona, Spain.,Spanish Biomedical Research Centre in Diabetes and Associated Metabolic Disorders (CIBERDEM), 28029 Madrid, Spain
| | - Pere Ràfols
- Rovira i Virgili University, Department of Electronic Engineering, IISPV, 43007 Tarragona, Spain.,Spanish Biomedical Research Centre in Diabetes and Associated Metabolic Disorders (CIBERDEM), 28029 Madrid, Spain
| | - Xavier Correig-Blanchar
- Rovira i Virgili University, Department of Electronic Engineering, IISPV, 43007 Tarragona, Spain.,Spanish Biomedical Research Centre in Diabetes and Associated Metabolic Disorders (CIBERDEM), 28029 Madrid, Spain
| | - María García-Altares
- Rovira i Virgili University, Department of Electronic Engineering, IISPV, 43007 Tarragona, Spain.,Spanish Biomedical Research Centre in Diabetes and Associated Metabolic Disorders (CIBERDEM), 28029 Madrid, Spain
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15
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Jia J, Ellis JF, Cao T, Fu K, Morales-Soto N, Shrout JD, Sweedler JV, Bohn PW. Biopolymer Patterning-Directed Secretion in Mucoid and Nonmucoid Strains of Pseudomonas aeruginosa Revealed by Multimodal Chemical Imaging. ACS Infect Dis 2021; 7:598-607. [PMID: 33620198 DOI: 10.1021/acsinfecdis.0c00765] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Quinolone, pyocyanin, and rhamnolipid production were studied in Pseudomonas aeruginosa by spatially patterning mucin, a glycoprotein important to infection of lung epithelia. Mass spectrometric imaging and confocal Raman microscopy are combined to probe P. aeruginosa biofilms from mucoid and nonmucoid strains grown on lithographically defined patterns. Quinolone signatures from biofilms on patterned vs unpatterned and mucin vs mercaptoundecanoic acid (MUA) surfaces were compared. Microbial attachment is accompanied by secretion of 2-alkyl-4-quinolones as well as rhamnolipids from the mucoid and nonmucoid strains. Pyocyanin was also detected both in the biofilm and in the supernatant in the mucoid strain only. Significant differences in the spatiotemporal distributions of secreted factors are observed between strains and among different surface patterning conditions. The mucoid strain is sensitive to composition and patterning while the nonmucoid strain is not, and in promoting community development in the mucoid strain, nonpatterned surfaces are better than patterned, and mucin is better than MUA. Also, the mucoid strain secretes the virulence factor pyocyanin in a way that correlates with distress. A change in the relative abundance for two rhamnolipids is observed in the mucoid strain during exposure to mucin, whereas minimal variation is observed in the nonmucoid strain. Differences between mucoid and nonmucoid strains are consistent with their strain-specific phenology, in which the mucoid strain develops highly protected and withdrawn biofilms that achieve Pseudomonas quinolone signal production under limited conditions.
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Affiliation(s)
- Jin Jia
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Joanna F. Ellis
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801,United States
| | - Tianyuan Cao
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Kaiyu Fu
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Nydia Morales-Soto
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, Indiana 46556,United States
| | - Joshua D. Shrout
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, Indiana 46556,United States
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Jonathan V. Sweedler
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801,United States
| | - Paul W. Bohn
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, United States
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16
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Neumann EK, Djambazova KV, Caprioli RM, Spraggins JM. Multimodal Imaging Mass Spectrometry: Next Generation Molecular Mapping in Biology and Medicine. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:2401-2415. [PMID: 32886506 PMCID: PMC9278956 DOI: 10.1021/jasms.0c00232] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Imaging mass spectrometry has become a mature molecular mapping technology that is used for molecular discovery in many medical and biological systems. While powerful by itself, imaging mass spectrometry can be complemented by the addition of other orthogonal, chemically informative imaging technologies to maximize the information gained from a single experiment and enable deeper understanding of biological processes. Within this review, we describe MALDI, SIMS, and DESI imaging mass spectrometric technologies and how these have been integrated with other analytical modalities such as microscopy, transcriptomics, spectroscopy, and electrochemistry in a field termed multimodal imaging. We explore the future of this field and discuss forthcoming developments that will bring new insights to help unravel the molecular complexities of biological systems, from single cells to functional tissue structures and organs.
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Affiliation(s)
- Elizabeth K Neumann
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States
| | - Katerina V Djambazova
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, Tennessee 37235, United States
| | - Richard M Caprioli
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, Tennessee 37235, United States
- Department of Pharmacology, Vanderbilt University, 2220 Pierce Avenue, Nashville, Tennessee 37232, United States
- Department of Medicine, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States
| | - Jeffrey M Spraggins
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, Tennessee 37235, United States
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17
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Interrogation of chemical changes on, and through, the bacterial envelope of
Escherichia coli
FabF mutant using time‐of‐flight secondary ion mass spectrometry. SURF INTERFACE ANAL 2020. [DOI: 10.1002/sia.6905] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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18
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Spatiotemporal Distribution of Pseudomonas aeruginosa Alkyl Quinolones under Metabolic and Competitive Stress. mSphere 2020; 5:5/4/e00426-20. [PMID: 32699119 PMCID: PMC7376503 DOI: 10.1128/msphere.00426-20] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Alkyl quinolones (AQs), including Pseudomonas quinolone signal (PQS), made by the opportunistic pathogen Pseudomonas aeruginosa have been associated with both population density and stress. The regulation of AQ production is known to be complex, and the stimuli that modulate AQ responses are not fully clear. Here, we have used hyperspectral Raman chemical imaging to examine the temporal and spatial profiles of AQs exhibited by P. aeruginosa under several potentially stressful conditions. We found that metabolic stress, effected by carbon limitation, or competition stress, effected by proximity to other species, resulted in accelerated PQS production. This competition effect did not require cell-to-cell interaction, as evidenced by the fact that the addition of supernatants from either Escherichia coli or Staphylococcus aureus led to early appearance of PQS. Lastly, the fact that these modulations were observed for PQS but not for all AQs suggests a high level of complexity in AQ regulation that remains to be discerned. Pseudomonas aeruginosa is an opportunistic human pathogen important to diseases such as cystic fibrosis. P. aeruginosa has multiple quorum-sensing (QS) systems, one of which utilizes the signaling molecule 2-heptyl-3-hydroxy-4-quinolone (Pseudomonas quinolone signal [PQS]). Here, we use hyperspectral Raman imaging to elucidate the spatiotemporal PQS distributions that determine how P. aeruginosa regulates surface colonization and its response to both metabolic stress and competition from other bacterial strains. These chemical imaging experiments illustrate the strong link between environmental challenges, such as metabolic stress caused by nutritional limitations or the presence of another bacterial species, and PQS signaling. Metabolic stress elicits a complex response in which limited nutrients induce the bacteria to produce PQS earlier, but the bacteria may also pause PQS production entirely if the nutrient concentration is too low. Separately, coculturing P. aeruginosa in the proximity of another bacterial species, or its culture supernatant, results in earlier production of PQS. However, these differences in PQS appearance are not observed for all alkyl quinolones (AQs) measured; the spatiotemporal response of 2-heptyl-4-hydroxyquinoline N-oxide (HQNO) is highly uniform for most conditions. These insights on the spatiotemporal distributions of quinolones provide additional perspective on the behavior of P. aeruginosa in response to different environmental cues. IMPORTANCE Alkyl quinolones (AQs), including Pseudomonas quinolone signal (PQS), made by the opportunistic pathogen Pseudomonas aeruginosa have been associated with both population density and stress. The regulation of AQ production is known to be complex, and the stimuli that modulate AQ responses are not fully clear. Here, we have used hyperspectral Raman chemical imaging to examine the temporal and spatial profiles of AQs exhibited by P. aeruginosa under several potentially stressful conditions. We found that metabolic stress, effected by carbon limitation, or competition stress, effected by proximity to other species, resulted in accelerated PQS production. This competition effect did not require cell-to-cell interaction, as evidenced by the fact that the addition of supernatants from either Escherichia coli or Staphylococcus aureus led to early appearance of PQS. Lastly, the fact that these modulations were observed for PQS but not for all AQs suggests a high level of complexity in AQ regulation that remains to be discerned.
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19
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Sämfors S, Fletcher JS. Lipid Diversity in Cells and Tissue Using Imaging SIMS. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2020; 13:249-271. [PMID: 32212820 DOI: 10.1146/annurev-anchem-091619-103512] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Lipids are an important class of biomolecules with many roles within cells and tissue. As targets for study, they present several challenges. They are difficult to label, as many labels lack the specificity to the many different lipid species or the labels maybe larger than the lipids themselves, thus severely perturbing the natural chemical environment. Mass spectrometry provides exceptional specificity and is often used to examine lipid extracts from different samples. However, spatial information is lost during extraction. Of the different imaging mass spectrometry methods available, secondary ion mass spectrometry (SIMS) is unique in its ability to analyze very small features, with probe sizes <50 nm available. It also offers high surface sensitivity and 3D imaging capability on a subcellular scale. This article reviews the current capabilities and some remaining challenges associated with imaging the diverse lipids present in cell and tissue samples. We show how the technique has moved beyond show-and-tell, proof-of-principle analysis and is now being used to address real biological challenges. These include imaging the microenvironment of cancer tumors, probing the pathophysiology of traumatic brain injury, or tracking the lipid composition through bacterial membranes.
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Affiliation(s)
- Sanna Sämfors
- Department of Chemistry and Molecular Biology, University of Gothenburg, 41296 Gothenburg, Sweden;
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - John S Fletcher
- Department of Chemistry and Molecular Biology, University of Gothenburg, 41296 Gothenburg, Sweden;
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20
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Bloxham CJ, Foster SR, Thomas WG. A Bitter Taste in Your Heart. Front Physiol 2020; 11:431. [PMID: 32457649 PMCID: PMC7225360 DOI: 10.3389/fphys.2020.00431] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 04/08/2020] [Indexed: 12/11/2022] Open
Abstract
The human genome contains ∼29 bitter taste receptors (T2Rs), which are responsible for detecting thousands of bitter ligands, including toxic and aversive compounds. This sentinel function varies between individuals and is underpinned by naturally occurring T2R polymorphisms, which have also been associated with disease. Recent studies have reported the expression of T2Rs and their downstream signaling components within non-gustatory tissues, including the heart. Though the precise role of T2Rs in the heart remains unclear, evidence points toward a role in cardiac contractility and overall vascular tone. In this review, we summarize the extra-oral expression of T2Rs, focusing on evidence for expression in heart; we speculate on the range of potential ligands that may activate them; we define the possible signaling pathways they activate; and we argue that their discovery in heart predicts an, as yet, unappreciated cardiac physiology.
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Affiliation(s)
- Conor J Bloxham
- School of Biomedical Sciences, Faculty of Medicine, The University of Queensland, St Lucia, QLD, Australia
| | - Simon R Foster
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Walter G Thomas
- School of Biomedical Sciences, Faculty of Medicine, The University of Queensland, St Lucia, QLD, Australia
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21
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PQS Produced by the Pseudomonas aeruginosa Stress Response Repels Swarms Away from Bacteriophage and Antibiotics. J Bacteriol 2019; 201:JB.00383-19. [PMID: 31451543 DOI: 10.1128/jb.00383-19] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 08/21/2019] [Indexed: 11/20/2022] Open
Abstract
We investigate the effect of bacteriophage infection and antibiotic treatment on the coordination of swarming, a collective form of flagellum- and pilus-mediated motility in bacteria. We show that phage infection of the opportunistic bacterial pathogen Pseudomonas aeruginosa abolishes swarming motility in the infected subpopulation and induces the release of the Pseudomonas quinolone signaling molecule PQS, which repulses uninfected subpopulations from approaching the infected area. These mechanisms have the overall effect of limiting the infection to a subpopulation, which promotes the survival of the overall population. Antibiotic treatment of P. aeruginosa elicits the same response, abolishing swarming motility and repulsing approaching swarms away from the antibiotic-treated area through a PQS-dependent mechanism. Swarms are entirely repelled from the zone of antibiotic-treated P. aeruginosa, consistent with a form of antibiotic evasion, and are not repelled by antibiotics alone. PQS has multiple functions, including serving as a quorum-sensing molecule, activating an oxidative stress response, and regulating the release of virulence and host-modifying factors. We show that PQS serves additionally as a stress warning signal that causes the greater population to physically avoid cell stress. The stress response at the collective level observed here in P. aeruginosa is consistent with a mechanism that promotes the survival of bacterial populations.IMPORTANCE We uncover a phage- and antibiotic-induced stress response in the clinically important opportunistic pathogen Pseudomonas aeruginosa Phage-infected P. aeruginosa subpopulations are isolated from uninfected subpopulations by the production of a stress-induced signal. Activation of the stress response by antibiotics causes P. aeruginosa to physically be repelled from the area containing antibiotics altogether, consistent with a mechanism of antibiotic evasion. The stress response observed here could increase P. aeruginosa resilience against antibiotic treatment and phage therapy in health care settings, as well as provide a simple evolutionary strategy to avoid areas containing stress.
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22
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PQS Signaling for More than a Quorum: the Collective Stress Response Protects Healthy Pseudomonas aeruginosa Populations. J Bacteriol 2019; 201:JB.00568-19. [PMID: 31527112 DOI: 10.1128/jb.00568-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
In this issue, Bru et al. connect Pseudomonas aeruginosa PQS signaling secretion during stress response to swarming behavior (J.-L. Bru, B. Rawson, C. Trinh, K. Whiteson, et al., J Bacteriol 201:e00383-19, 2019, https://doi.org/10.1128/JB.00383-19). Phage-infected or antibiotic-treated bacterial cells secrete PQS to repel healthy, unexposed cells away from the source of the stress. Thus, the collective stress response mechanism driven by PQS signaling influences spatial organization and population dynamics in P. aeruginosa that may provide competitive advantages in certain niches.
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23
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Brockmann EU, Steil D, Bauwens A, Soltwisch J, Dreisewerd K. Advanced Methods for MALDI-MS Imaging of the Chemical Communication in Microbial Communities. Anal Chem 2019; 91:15081-15089. [DOI: 10.1021/acs.analchem.9b03772] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Eike Ulrich Brockmann
- Institute of Hygiene, University of Münster, Münster 48149, Germany
- Interdisciplinary Center for Clinical Research (IZKF), University of Münster, Münster 48149, Germany
| | - Daniel Steil
- Institute of Hygiene, University of Münster, Münster 48149, Germany
- Interdisciplinary Center for Clinical Research (IZKF), University of Münster, Münster 48149, Germany
| | - Andreas Bauwens
- Institute of Hygiene, University of Münster, Münster 48149, Germany
| | - Jens Soltwisch
- Institute of Hygiene, University of Münster, Münster 48149, Germany
- Interdisciplinary Center for Clinical Research (IZKF), University of Münster, Münster 48149, Germany
| | - Klaus Dreisewerd
- Institute of Hygiene, University of Münster, Münster 48149, Germany
- Interdisciplinary Center for Clinical Research (IZKF), University of Münster, Münster 48149, Germany
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24
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Dimovska Nilsson K, Palm M, Hood J, Sheriff J, Farewell A, Fletcher JS. Chemical Changes On, and Through, The Bacterial Envelope in Escherichia coli Mutants Exhibiting Impaired Plasmid Transfer Identified Using Time-of-Flight Secondary Ion Mass Spectrometry. Anal Chem 2019; 91:11355-11361. [PMID: 31359753 DOI: 10.1021/acs.analchem.9b02533] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Time-of-flight secondary ion mass spectrometry (ToF-SIMS) using a (CO2)6k+ gas cluster ion beam (GCIB) was used to analyze Escherichia coli mutants previously identified as having impaired plasmid transfer capability related to the spread of antibiotic resistance. The subset of mutants selected were expected to result in changes in the bacterial envelope composition through the deletion of genes encoding for FabF, DapF, and Lpp, where the surface sensitivity of ToF-SIMS can be most useful. Analysis of arrays of spotted bacteria allowed changes in the lipid composition of the bacteria to be elucidated using multivariate analysis and confirmed through imaging of individual ion signals. Significant changes in chemical composition were observed, including a surprising loss of cyclopropanated fatty acids in the fabF mutant where FabF is associated with the elongation of FA(16:1) to FA(18:1) and not cyclopropane formation. The ability of the GCIB to generate increased higher mass signals from biological samples allowed intact lipid A (m/z 1796) to be detected on the bacteria and, despite a 40 keV impact energy, depth profiled through the bacterial envelope along with other high mass ions including species at m/z 1820 and 2428, attributed to ECACYC, that were only observed below the surface of the bacteria and were notably absent in the depth profile of the lpp mutant. The analysis provides new insights into the action of the specific pathways targeted in this study and paves the way for whole new avenues for the characterization of intact molecules within the bacterial envelope.
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Affiliation(s)
- Kelly Dimovska Nilsson
- Department of Chemistry and Molecular Biology , University of Gothenburg , Gothenburg 405 30 , Sweden
| | - Martin Palm
- Department of Chemistry and Molecular Biology , University of Gothenburg , Gothenburg 405 30 , Sweden.,Centre for Antibiotic Resistance Research , University of Gothenburg , Gothenburg 405 30 , Sweden
| | - James Hood
- School of Engineering , Newcastle University , Newcastle upon Tyne NE1 7RU , United Kingdom
| | - Jake Sheriff
- School of Engineering , Newcastle University , Newcastle upon Tyne NE1 7RU , United Kingdom
| | - Anne Farewell
- Department of Chemistry and Molecular Biology , University of Gothenburg , Gothenburg 405 30 , Sweden.,Centre for Antibiotic Resistance Research , University of Gothenburg , Gothenburg 405 30 , Sweden
| | - John S Fletcher
- Department of Chemistry and Molecular Biology , University of Gothenburg , Gothenburg 405 30 , Sweden
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25
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Do H, Kwon SR, Fu K, Morales-Soto N, Shrout JD, Bohn PW. Electrochemical Surface-Enhanced Raman Spectroscopy of Pyocyanin Secreted by Pseudomonas aeruginosa Communities. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:7043-7049. [PMID: 31042392 PMCID: PMC8006532 DOI: 10.1021/acs.langmuir.9b00184] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Pyocyanin (PYO) is one of many toxins secreted by the opportunistic human pathogenic bacterium Pseudomonas aeruginosa. Direct detection of PYO in biofilms is crucial because PYO can provide important information about infection-related virulence mechanisms in P. aeruginosa. Because PYO is both redox-active and Raman-active, we seek to simultaneously acquire both spectroscopic and redox state information about PYO. The combination of surface-enhanced Raman spectroscopy (SERS) and voltammetry is used here to provide insights into the molecular redox behavior of PYO while controlling the SERS and electrochemical (EC) response of PYO with external stimuli, such as pH and applied potential. Furthermore, PYO secretion from biofilms of different P. aeruginosa strains is compared. Both SERS spectra and EC behavior are observed to change with pH, and several pH-dependent bands are identified in the SERS spectra, which can potentially be used to probe the local environment. Comparison of the voltammetric behavior of wild-type and a PYO-deficient mutant unequivocally identifies PYO as a major component of the secretome. Spectroelectrochemical studies of the PYO standard reveal decreasing SERS intensities of PYO bands under reducing conditions. Extending these experiments to pellicle biofilms shows similar behavior with applied potential, and SERS imaging indicates that secreted PYO is localized in regions approximately the size of P. aeruginosa cells. The in situ spectroelectrochemical biofilm characterization approach developed here suggests that EC-SERS monitoring of secreted molecules can be used diagnostically and correlated with the progress of infection.
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Affiliation(s)
- Hyein Do
- Department of Chemistry and Biochemistry,
University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Seung-Ryong Kwon
- Department of Chemical and Biomolecular
Engineering, University of Notre Dame, Notre Dame, Indiana 46556, United
States
| | - Kaiyu Fu
- Department of Chemistry and Biochemistry,
University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Nydia Morales-Soto
- Department of Civil and Environmental
Engineering and Earth Sciences, University of Notre Dame, Notre Dame, Indiana
46556, United States
| | - Joshua D. Shrout
- Department of Civil and Environmental
Engineering and Earth Sciences, University of Notre Dame, Notre Dame, Indiana
46556, United States
- Department of Biological Sciences, University of
Notre Dame, Notre Dame, Indiana 46556, United States
| | - Paul W. Bohn
- Department of Chemistry and Biochemistry,
University of Notre Dame, Notre Dame, Indiana 46556, United States
- Department of Chemical and Biomolecular
Engineering, University of Notre Dame, Notre Dame, Indiana 46556, United
States
- Corresponding Author
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26
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Cao T, Morales-Soto N, Jia J, Baig NF, Dunham SJB, Ellis J, Sweedler JV, Shrout JD, Bohn PW. Spatiotemporal Dynamics of Molecular Messaging in Bacterial Co-Cultures Studied by Multimodal Chemical Imaging. PROCEEDINGS OF SPIE--THE INTERNATIONAL SOCIETY FOR OPTICAL ENGINEERING 2019; 10863:108630A. [PMID: 33790492 PMCID: PMC8009051 DOI: 10.1117/12.2501349] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Microbial community behavior is coupled to a set of genetically-regulated chemical signals that correlate with cell density - the quorum sensing (QS) system - and there is growing appreciation that the QS-regulated behavior of bacteria is chemically, spatially, and temporally complex. In addition, while it has been known for some time that different species use different QS networks, we are beginning to appreciate that different strains of the same bacterial species also differ in their QS networks. Here we combine mass spectrometric imaging (MSI) and confocal Raman microscopy (CRM) approaches to investigate co-cultures involving different strains (FRD1 and PAO1C) of the same species (Pseudomonas aeruginosa) as well as those involving different species (P. aeruginosa and E. coli). Combining MSI and CRM makes it possible to supersede the limits imposed by individual imaging approaches and enables the spatial mapping of individual bacterial species and their microbial products within a mixed bacterial community growing in situ on surfaces. MSI is used to delineate the secretion of a specific rhamnolipid surfactant as well as alkyl quinolone (AQ) messengers between FRD1 and PAO1C strains of P. aeruginosa, showing that the spatial distribution and production rate of AQ messengers in PAO1C far outstrips that of FRD1. In the case of multiple species, CRM is used to show that the prolific secretion of AQs by the PAO1C strain of P. aeruginosa is used to mediate its interaction with co-cultured E. coli.
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Affiliation(s)
- Tianyuan Cao
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA
| | - Nydia Morales-Soto
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Jin Jia
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA
| | - Nameera F Baig
- Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720
| | - Sage J B Dunham
- Entech Instruments, 2207 Agate Court, Simi Valley, CA 93065
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL 61801
| | - Joseph Ellis
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL 61801
| | - Jonathan V Sweedler
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL 61801
| | - Joshua D Shrout
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, IN, USA
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Paul W Bohn
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN, USA
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27
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Morales-Soto N, Cao T, Baig NF, Kramer KM, Bohn PW, Shrout JD. Surface-Growing Communities of Pseudomonas aeruginosa Exhibit Distinct Alkyl Quinolone Signatures. Microbiol Insights 2018; 11:1178636118817738. [PMID: 30573968 PMCID: PMC6295745 DOI: 10.1177/1178636118817738] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 11/06/2018] [Indexed: 12/24/2022] Open
Abstract
A cascade of events leads to the development of microbial biofilm communities that are thought to be responsible for over 80% of infections in humans. However, not all surface-growing bacteria reside in a stationary biofilm state. Here, we have employed confocal Raman microscopy to analyze and compare variations in the alkyl quinolone (AQ) family of molecules during the transition between surface-attached motile-swarming and stationary biofilm communities. The AQs have been established previously as important to Pseudomonas aeruginosa biofilms, interspecies competition, and virulence. The AQ Pseudomonas quinolone signal (PQS) is also a known quorum-sensing signal. We detail spatial identification of AQ, PQS, and 2-alkyl-4-hydroxyquinoline N-oxide (AQNO) metabolites in both swarm and biofilm communities. We find that AQNO metabolites are abundant signatures in active swarming communities.
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Affiliation(s)
- Nydia Morales-Soto
- Department of Civil & Environmental Engineering & Earth Sciences, University of Notre Dame, Notre Dame, IN, USA.,Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, USA
| | - Tianyuan Cao
- Department of Chemistry & Biochemistry, University of Notre Dame, Notre Dame, IN, USA
| | - Nameera F Baig
- Department of Chemistry & Biochemistry, University of Notre Dame, Notre Dame, IN, USA
| | - Kristen M Kramer
- Department of Civil & Environmental Engineering & Earth Sciences, University of Notre Dame, Notre Dame, IN, USA.,Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Paul W Bohn
- Department of Chemistry & Biochemistry, University of Notre Dame, Notre Dame, IN, USA.,Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN, USA.,Advanced Diagnostics & Therapeutics, University of Notre Dame, Notre Dame, IN, USA
| | - Joshua D Shrout
- Department of Civil & Environmental Engineering & Earth Sciences, University of Notre Dame, Notre Dame, IN, USA.,Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, USA.,Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA.,Advanced Diagnostics & Therapeutics, University of Notre Dame, Notre Dame, IN, USA
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28
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Garg N, Whiteley M. The chemical topology of a bacterial swarm. J Biol Chem 2018; 293:9553-9554. [PMID: 29907734 DOI: 10.1074/jbc.h118.003178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Microbes respond to antibiotics by initiating a suite of defense mechanisms, including the production of small-molecule effectors. However, it is not well-known how these defenses vary according to the particular effector or antibiotic and bacterial state, due in part to the challenges of monitoring small molecules in complex environments. A new study uses state-of-the-art imaging techniques to track the location of secreted small molecules produced by a bacterial swarm in response to different antibiotics, providing unexpected insights into the spatial heterogeneity of bacterial stress responses.
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Affiliation(s)
- Neha Garg
- From the School of Chemistry and Biochemistry and .,Emory-Children's Cystic Fibrosis Center, Atlanta, Georgia 30322
| | - Marvin Whiteley
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332 and.,Emory-Children's Cystic Fibrosis Center, Atlanta, Georgia 30322
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29
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Freund JR, Mansfield CJ, Doghramji LJ, Adappa ND, Palmer JN, Kennedy DW, Reed DR, Jiang P, Lee RJ. Activation of airway epithelial bitter taste receptors by Pseudomonas aeruginosa quinolones modulates calcium, cyclic-AMP, and nitric oxide signaling. J Biol Chem 2018; 293:9824-9840. [PMID: 29748385 DOI: 10.1074/jbc.ra117.001005] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2017] [Revised: 04/17/2018] [Indexed: 12/12/2022] Open
Abstract
Bitter taste receptors (taste family 2 bitter receptor proteins; T2Rs), discovered in many tissues outside the tongue, have recently become potential therapeutic targets. We have shown previously that airway epithelial cells express several T2Rs that activate innate immune responses that may be important for treatment of airway diseases such as chronic rhinosinusitis. It is imperative to more clearly understand what compounds activate airway T2Rs as well as their full range of functions. T2R isoforms in airway motile cilia (T2R4, -14, -16, and -38) produce bactericidal levels of nitric oxide (NO) that also increase ciliary beating, promoting clearance of mucus and trapped pathogens. Bacterial quorum-sensing acyl-homoserine lactones activate T2Rs and stimulate these responses in primary airway cells. Quinolones are another type of quorum-sensing molecule used by Pseudomonas aeruginosa To elucidate whether bacterial quinolones activate airway T2Rs, we analyzed calcium, cAMP, and NO dynamics using a combination of fluorescent indicator dyes and FRET-based protein biosensors. T2R-transfected HEK293T cells, several lung epithelial cell lines, and primary sinonasal cells grown and differentiated at the air-liquid interface were tested with 2-heptyl-3-hydroxy-4-quinolone (known as Pseudomonas quinolone signal; PQS), 2,4-dihydroxyquinolone, and 4-hydroxy-2-heptylquinolone (HHQ). In HEK293T cells, PQS activated T2R4, -16, and -38, whereas HHQ activated T2R14. 2,4-Dihydroxyquinolone had no effect. PQS and HHQ increased calcium and decreased both baseline and stimulated cAMP levels in cultured and primary airway cells. In primary cells, PQS and HHQ activated levels of NO synthesis previously shown to be bactericidal. This study suggests that airway T2R-mediated immune responses are activated by bacterial quinolones as well as acyl-homoserine lactones.
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Affiliation(s)
- Jenna R Freund
- From the Departments of Otorhinolaryngology-Head and Neck Surgery and
| | | | | | - Nithin D Adappa
- From the Departments of Otorhinolaryngology-Head and Neck Surgery and
| | - James N Palmer
- From the Departments of Otorhinolaryngology-Head and Neck Surgery and
| | - David W Kennedy
- From the Departments of Otorhinolaryngology-Head and Neck Surgery and
| | - Danielle R Reed
- the Monell Chemical Senses Center, Philadelphia, Pennsylvania 19104
| | - Peihua Jiang
- the Monell Chemical Senses Center, Philadelphia, Pennsylvania 19104
| | - Robert J Lee
- From the Departments of Otorhinolaryngology-Head and Neck Surgery and .,Physiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104 and
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30
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Dunham SJB, Ellis JF, Baig NF, Morales-Soto N, Cao T, Shrout JD, Bohn PW, Sweedler JV. Quantitative SIMS Imaging of Agar-Based Microbial Communities. Anal Chem 2018; 90:5654-5663. [PMID: 29623707 PMCID: PMC5930052 DOI: 10.1021/acs.analchem.7b05180] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
After several decades of widespread use for mapping elemental ions and small molecular fragments in surface science, secondary ion mass spectrometry (SIMS) has emerged as a powerful analytical tool for molecular imaging in biology. Biomolecular SIMS imaging has primarily been used as a qualitative technique; although the distribution of a single analyte can be accurately determined, it is difficult to map the absolute quantity of a compound or even to compare the relative abundance of one molecular species to that of another. We describe a method for quantitative SIMS imaging of small molecules in agar-based microbial communities. The microbes are cultivated on a thin film of agar, dried under nitrogen, and imaged directly with SIMS. By use of optical microscopy, we show that the area of the agar is reduced by 26 ± 2% (standard deviation) during dehydration, but the overall biofilm morphology and analyte distribution are largely retained. We detail a quantitative imaging methodology, in which the ion intensity of each analyte is (1) normalized to an external quadratic regression curve, (2) corrected for isomeric interference, and (3) filtered for sample-specific noise and lower and upper limits of quantitation. The end result is a two-dimensional surface density image for each analyte. The sample preparation and quantitation methods are validated by quantitatively imaging four alkyl-quinolone and alkyl-quinoline N-oxide signaling molecules (including Pseudomonas quinolone signal) in Pseudomonas aeruginosa colony biofilms. We show that the relative surface densities of the target biomolecules are substantially different from values inferred through direct intensity comparison and that the developed methodologies can be used to quantitatively compare as many ions as there are available standards.
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Affiliation(s)
- Sage J. B. Dunham
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana- Champaign, Urbana, IL 61801
| | - Joseph F. Ellis
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana- Champaign, Urbana, IL 61801
| | - Nameera F. Baig
- Department of Chemistry and Biochemistry, and Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556
| | - Nydia Morales-Soto
- Department of Civil and Environmental Engineering and Earth Sciences, and Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556
| | - Tianyuan Cao
- Department of Chemistry and Biochemistry, and Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556
| | - Joshua D. Shrout
- Department of Civil and Environmental Engineering and Earth Sciences, and Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556
| | - Paul W. Bohn
- Department of Chemistry and Biochemistry, and Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556
| | - Jonathan V. Sweedler
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana- Champaign, Urbana, IL 61801
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