1
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Zheng X, Gomez-Rivas EJ, Lamont SI, Daneshjoo K, Shieh A, Wozniak DJ, Parsek MR. The surface interface and swimming motility influence surface-sensing responses in Pseudomonas aeruginosa. Proc Natl Acad Sci U S A 2024; 121:e2411981121. [PMID: 39284057 PMCID: PMC11441478 DOI: 10.1073/pnas.2411981121] [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: 06/14/2024] [Accepted: 08/01/2024] [Indexed: 10/02/2024] Open
Abstract
Bacterial biofilms have been implicated in several chronic infections. After initial attachment, a critical first step in biofilm formation is a cell inducing a surface-sensing response. In the Gram-negative opportunistic pathogen Pseudomonas aeruginosa, two second messengers, cyclic diguanylate monophosphate (c-di-GMP) and cyclic adenosine monophosphate (cAMP), are produced by different surface-sensing mechanisms. However, given the disparate cellular behaviors regulated by these second messengers, how newly attached cells coordinate these pathways remains unclear. Some of the uncertainty relates to studies using different strains, experimental systems, and usually focusing on a single second messenger. In this study, we developed a tricolor reporter system to simultaneously gauge c-di-GMP and cAMP levels in single cells. Using PAO1, we show that c-di-GMP and cAMP are selectively activated in two commonly used experimental systems to study surface sensing. By further examining the conditions that differentiate a c-di-GMP or cAMP response, we demonstrate that an agarose-air interface activates cAMP signaling through type IV pili and the Pil-Chp system. However, a liquid-agarose interface favors the activation of c-di-GMP signaling. This response is dependent on flagellar motility and correlated with higher swimming speed. Collectively, this work indicates that c-di-GMP and cAMP signaling responses are dependent on the surface context.
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Affiliation(s)
- Xuhui Zheng
- Department of Microbiology, University of Washington, Seattle, WA
| | | | - Sabrina I. Lamont
- Departments of Microbial Infection and Immunity, Microbiology, The Ohio State University, Columbus, OH
| | | | - Angeli Shieh
- Department of Microbiology, University of Washington, Seattle, WA
| | - Daniel J. Wozniak
- Departments of Microbial Infection and Immunity, Microbiology, The Ohio State University, Columbus, OH
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2
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Warrell DL, Zarrella TM, Machalek C, Khare A. Interspecies surfactants serve as public goods enabling surface motility in Pseudomonas aeruginosa. J Bacteriol 2024:e0028124. [PMID: 39235232 DOI: 10.1128/jb.00281-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2024] [Accepted: 08/02/2024] [Indexed: 09/06/2024] Open
Abstract
In most natural environments, bacteria live in polymicrobial communities where secreted molecules from neighboring species alter bacterial behaviors, including motility, but such interactions are understudied. Pseudomonas aeruginosa is a motile opportunistic pathogen that exists in diverse multispecies environments, such as the soil, and is frequently found in human wound and respiratory tract co-infections with other bacteria, including Staphylococcus aureus. Here, we show that P. aeruginosa can co-opt secreted surfactants from other species for flagellar-based surface motility. We found that exogenous surfactants from S. aureus, other bacteria, and interkingdom species enabled P. aeruginosa to switch from swarming to an alternative surface spreading motility on semi-solid surfaces and allowed for the emergence of surface motility on hard agar where P. aeruginosa was otherwise unable to move. Although active flagellar function was required for surface spreading, known motility regulators were not essential, indicating that surface spreading may be regulated by an as yet unknown mechanism. This motility was distinct from the response of most other motile bacterial species in the presence of exogenous surfactants. Mutant analysis indicated that this P. aeruginosa motility was similar to a previously described mucin-based motility, "surfing," albeit with divergent regulation. Thus, our study demonstrates that secreted surfactants from the host as well as neighboring bacterial and interkingdom species act as public goods facilitating P. aeruginosa flagella-mediated surfing-like surface motility, thereby allowing it to access different environmental niches. IMPORTANCE Bacterial motility is an important determinant of bacterial fitness and pathogenesis, allowing expansion and invasion to access nutrients and adapt to new environments. Here, we demonstrate that secreted surfactants from a variety of foreign species, including other bacterial species, infection hosts, fungi, and plants, facilitate surface spreading motility in the opportunistic pathogen Pseudomonas aeruginosa that is distinct from established motility phenotypes. This response to foreign surfactants also occurs in Pseudomonas putida, but not in more distantly related bacterial species. Our systematic characterization of surfactant-based surface spreading shows that these interspecies surfactants serve as public goods to enable P. aeruginosa to move and explore environmental conditions when it would be otherwise immotile.
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Affiliation(s)
- Delayna L Warrell
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Tiffany M Zarrella
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
- Postdoctoral Research Associate Training Program, National Institute of General Medical Sciences, National Institutes of Health, Bethesda, Maryland, USA
- Department of Biology, Georgetown University, Washington, DC, USA
| | - Christopher Machalek
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Anupama Khare
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
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3
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Yin J, Li J, Xie H, Wang Y, Zhao J, Wang L, Wu L. Unveiling cold Code: Acinetobacter calcoaceticus TY1's adaptation strategies and applications in nitrogen treatment. BIORESOURCE TECHNOLOGY 2024; 413:131449. [PMID: 39244103 DOI: 10.1016/j.biortech.2024.131449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2024] [Revised: 09/01/2024] [Accepted: 09/04/2024] [Indexed: 09/09/2024]
Abstract
Overcoming low nitrogen removal efficiency at low temperatures is a challenge in biological treatment. This study investigated the cold-tolerant heterotrophic nitrification-aerobic denitrification by Acinetobacter calcoaceticus TY1. Transcriptomic and biochemical analyses indicated that strain TY1 upregulated genes for energy production, assimilation, cell motility, and antioxidant enzyme production under cold stress, maintaining functions such as energy supply, nitrogen utilization, and oxidative defense. Increasing the synthesis of extracellular polysaccharides, unsaturated fatty acids, and medium-chain fatty acids and secreting large amounts of antioxidant enzymes ensured cell membrane flexibility while enhancing the antioxidant system. Immobilization experiments showed that biofilms accelerated the removal of nitrogen pollutants and demonstrated good stability, with carriers being reusable to five times, maintaining high ammonia nitrogen (63.90 %) and total nitrogen (50.66 %) removal rates. These findings reveal the cold tolerance mechanisms of strain TY1 and its excellent practical potential as a candidate for wastewater treatment in cold regions.
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Affiliation(s)
- Jiahui Yin
- School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, PR China
| | - Junyi Li
- School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, PR China
| | - Hongliang Xie
- School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, PR China
| | - Yongman Wang
- School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, PR China
| | - Jialin Zhao
- School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, PR China
| | - Lixin Wang
- School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, PR China
| | - Linhui Wu
- School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, PR China; Inner Mongolia Key Laboratory of Environmental Pollution Prevention and Waste Resource Recycle, Hohhot 010021, PR China.
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4
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Wheeler JHR, Foster KR, Durham WM. Individual bacterial cells can use spatial sensing of chemical gradients to direct chemotaxis on surfaces. Nat Microbiol 2024; 9:2308-2322. [PMID: 39227714 PMCID: PMC11371657 DOI: 10.1038/s41564-024-01729-3] [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: 08/02/2023] [Accepted: 05/10/2024] [Indexed: 09/05/2024]
Abstract
Swimming bacteria navigate chemical gradients using temporal sensing to detect changes in concentration over time. Here we show that surface-attached bacteria use a fundamentally different mode of sensing during chemotaxis. We combined microfluidic experiments, massively parallel cell tracking and fluorescent reporters to study how Pseudomonas aeruginosa senses chemical gradients during pili-based 'twitching' chemotaxis on surfaces. Unlike swimming cells, we found that temporal changes in concentration did not induce motility changes in twitching cells. We then quantified the chemotactic behaviour of stationary cells by following changes in the sub-cellular localization of fluorescent proteins as cells are exposed to a gradient that alternates direction. These experiments revealed that P. aeruginosa cells can directly sense differences in concentration across the lengths of their bodies, even in the presence of strong temporal fluctuations. Our work thus overturns the widely held notion that bacterial cells are too small to directly sense chemical gradients in space.
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Affiliation(s)
- James H R Wheeler
- Department of Physics and Astronomy, University of Sheffield, Sheffield, UK
- Department of Biology, University of Oxford, Oxford, UK
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Kevin R Foster
- Department of Biology, University of Oxford, Oxford, UK.
- Department of Biochemistry, University of Oxford, Oxford, UK.
| | - William M Durham
- Department of Physics and Astronomy, University of Sheffield, Sheffield, UK.
- Department of Biology, University of Oxford, Oxford, UK.
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5
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Geiger CJ, Wong GCL, O'Toole GA. A bacterial sense of touch: T4P retraction motor as a means of surface sensing by Pseudomonas aeruginosa PA14. J Bacteriol 2024; 206:e0044223. [PMID: 38832786 PMCID: PMC11270903 DOI: 10.1128/jb.00442-23] [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] [Indexed: 06/05/2024] Open
Abstract
Most microbial cells found in nature exist in matrix-covered, surface-attached communities known as biofilms. This mode of growth is initiated by the ability of the microbe to sense a surface on which to grow. The opportunistic pathogen Pseudomonas aeruginosa (Pa) PA14 utilizes a single polar flagellum and type 4 pili (T4P) to sense surfaces. For Pa, T4P-dependent "twitching" motility is characterized by effectively pulling the cell across a surface through a complex process of cooperative binding, pulling, and unbinding. T4P retraction is powered by hexameric ATPases. Pa cells that have engaged a surface increase production of the second messenger cyclic AMP (cAMP) over multiple generations via the Pil-Chp system. This rise in cAMP allows cells and their progeny to become better adapted for surface attachment and activates virulence pathways through the cAMP-binding transcription factor Vfr. While many studies have focused on mechanisms of T4P twitching and regulation of T4P production and function by the Pil-Chp system, the mechanism by which Pa senses and relays a surface-engagement signal to the cell is still an open question. Here we review the current state of the surface sensing literature for Pa, with a focus on T4P, and propose an integrated model of surface sensing whereby the retraction motor PilT senses and relays the signal to the Pil-Chp system via PilJ to drive cAMP production and adaptation to a surface lifestyle.
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Affiliation(s)
- C. J. Geiger
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - G. C. L. Wong
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, California, USA
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California, USA
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California, USA
| | - G. A. O'Toole
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
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6
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David A, Tahrioui A, Tareau AS, Forge A, Gonzalez M, Bouffartigues E, Lesouhaitier O, Chevalier S. Pseudomonas aeruginosa Biofilm Lifecycle: Involvement of Mechanical Constraints and Timeline of Matrix Production. Antibiotics (Basel) 2024; 13:688. [PMID: 39199987 PMCID: PMC11350761 DOI: 10.3390/antibiotics13080688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2024] [Revised: 07/22/2024] [Accepted: 07/23/2024] [Indexed: 09/01/2024] Open
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen causing acute and chronic infections, especially in immunocompromised patients. Its remarkable adaptability and resistance to various antimicrobial treatments make it difficult to eradicate. Its persistence is enabled by its ability to form a biofilm. Biofilm is a community of sessile micro-organisms in a self-produced extracellular matrix, which forms a scaffold facilitating cohesion, cell attachment, and micro- and macro-colony formation. This lifestyle provides protection against environmental stresses, the immune system, and antimicrobial treatments, and confers the capacity for colonization and long-term persistence, often characterizing chronic infections. In this review, we retrace the events of the life cycle of P. aeruginosa biofilm, from surface perception/contact to cell spreading. We focus on the importance of extracellular appendages, mechanical constraints, and the kinetics of matrix component production in each step of the biofilm life cycle.
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Affiliation(s)
| | | | | | | | | | | | | | - Sylvie Chevalier
- Univ Rouen Normandie, Univ Caen Normandie, Normandie Univ, CBSA UR 4312, F-76000 Rouen, France
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7
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Warrell DL, Zarrella TM, Machalek C, Khare A. Interspecies surfactants serve as public goods enabling surface motility in Pseudomonas aeruginosa. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.03.573969. [PMID: 38260674 PMCID: PMC10802355 DOI: 10.1101/2024.01.03.573969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
In most natural environments, bacteria live in polymicrobial communities where secreted molecules from neighboring species alter bacterial behaviors including motility, but such interactions are understudied. Pseudomonas aeruginosa is a motile opportunistic pathogen that exists in diverse multispecies environments such as the soil and is frequently found in human wound and respiratory tract co-infections with other bacteria including Staphylococcus aureus. Here we show that P. aeruginosa can co-opt secreted surfactants from other species for flagellar-based surface motility. We found that exogenous surfactants from S. aureus, other bacteria, and interkingdom species enabled P. aeruginosa to switch from swarming to an alternative surface spreading motility on semi-solid surfaces and allowed for the emergence of surface motility on hard agar where P. aeruginosa was otherwise unable to move. This motility was distinct from the response of other motile bacteria in the presence of exogenous surfactants. Mutant analysis indicated that this P. aeruginosa motility was similar to a previously described mucin-based motility, 'surfing', albeit with divergent regulation. Thus, our study demonstrates that secreted surfactants from the host as well as neighboring bacterial and interkingdom species act as public goods facilitating P. aeruginosa flagella-mediated surfing-like surface motility, thereby allowing it to access different environmental niches.
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Affiliation(s)
- Delayna L. Warrell
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Tiffany M. Zarrella
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Postdoctoral Research Associate Training Program, National Institute of General Medical Sciences, National Institutes of Health, Bethesda, MD, USA
- Current address: Department of Biology, Georgetown University, Washington, DC, USA
| | - Christopher Machalek
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Anupama Khare
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
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8
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Patino R, Kühn MJ, Macmillan H, Inclan YF, Chavez I, Von Dollen J, Johnson JR, Swaney DL, Krogan NJ, Persat A, Engel JN. Spatial control of sensory adaptation modulates mechanosensing in Pseudomonas aeruginosa. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.27.582188. [PMID: 38464290 PMCID: PMC10925122 DOI: 10.1101/2024.02.27.582188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Sensory signaling pathways use adaptation to dynamically respond to changes in their environment. Here, we report the mechanism of sensory adaptation in the Pil-Chp mechanosensory system, which the important human pathogen Pseudomonas aeruginosa uses to sense mechanical stimuli during surface exploration. Using biochemistry, genetics, and cell biology, we discovered that the enzymes responsible for adaptation, a methyltransferase and a methylesterase, are segregated to opposing cell poles as P. aeruginosa explore surfaces. By coordinating the localization of both enzymes, we found that the Pil-Chp response regulators influence local receptor methylation, the molecular basis of bacterial sensory adaptation. We propose a model in which adaptation during mechanosensing spatially resets local receptor methylation, and thus Pil-Chp signaling, to modulate the pathway outputs, which are involved in P. aeruginosa virulence. Despite decades of bacterial sensory adaptation studies, our work has uncovered an unrecognized mechanism that bacteria use to achieve adaptation to sensory stimuli.
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9
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Schroven K, Putzeys L, Kerremans A, Ceyssens PJ, Vallino M, Paeshuyse J, Haque F, Yusuf A, Koch MD, Lavigne R. The phage-encoded PIT4 protein affects multiple two-component systems of Pseudomonas aeruginosa. Microbiol Spectr 2023; 11:e0237223. [PMID: 37962408 PMCID: PMC10714779 DOI: 10.1128/spectrum.02372-23] [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: 06/08/2023] [Accepted: 10/04/2023] [Indexed: 11/15/2023] Open
Abstract
IMPORTANCE More and more Pseudomonas aeruginosa isolates have become resistant to antibiotics like carbapenem. As a consequence, P. aeruginosa ranks in the top three of pathogens for which the development of novel antibiotics is the most crucial. The pathogen causes both acute and chronic infections, especially in patients who are the most vulnerable. Therefore, efforts are urgently needed to develop alternative therapies. One path explored in this article is the use of bacteriophages and, more specifically, phage-derived proteins. In this study, a phage-derived protein was studied that impacts key virulence factors of the pathogen via interaction with multiple histidine kinases of TCSs. The fundamental insights gained for this protein can therefore serve as inspiration for the development of an anti-virulence compound that targets the bacterial TCS.
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Affiliation(s)
- Kaat Schroven
- Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
| | - Leena Putzeys
- Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
| | | | | | - Marta Vallino
- Institute of Sustainable Plant Protection, National Research Council of Italy, Turin, Italy
| | - Jan Paeshuyse
- Host and Pathogen Interactions, KU Leuven, Leuven, Belgium
| | - Farhana Haque
- Department of Biology, Texas A&M University, College Station, Texas, USA
| | - Ahmed Yusuf
- Department of Biology, Texas A&M University, College Station, Texas, USA
| | - Matthias D. Koch
- Department of Biology, Texas A&M University, College Station, Texas, USA
| | - Rob Lavigne
- Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
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10
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Singh A, Schnürer A, Dolfing J, Westerholm M. Syntrophic entanglements for propionate and acetate oxidation under thermophilic and high-ammonia conditions. THE ISME JOURNAL 2023; 17:1966-1978. [PMID: 37679429 PMCID: PMC10579422 DOI: 10.1038/s41396-023-01504-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 08/22/2023] [Accepted: 08/25/2023] [Indexed: 09/09/2023]
Abstract
Propionate is a key intermediate in anaerobic digestion processes and often accumulates in association with perturbations, such as elevated levels of ammonia. Under such conditions, syntrophic ammonia-tolerant microorganisms play a key role in propionate degradation. Despite their importance, little is known about these syntrophic microorganisms and their cross-species interactions. Here, we present metagenomes and metatranscriptomic data for novel thermophilic and ammonia-tolerant syntrophic bacteria and the partner methanogens enriched in propionate-fed reactors. A metagenome for a novel bacterium for which we propose the provisional name 'Candidatus Thermosyntrophopropionicum ammoniitolerans' was recovered, together with mapping of its highly expressed methylmalonyl-CoA pathway for syntrophic propionate degradation. Acetate was degraded by a novel thermophilic syntrophic acetate-oxidising candidate bacterium. Electron removal associated with syntrophic propionate and acetate oxidation was mediated by the hydrogen/formate-utilising methanogens Methanoculleus sp. and Methanothermobacter sp., with the latter observed to be critical for efficient propionate degradation. Similar dependence on Methanothermobacter was not seen for acetate degradation. Expression-based analyses indicated use of both H2 and formate for electron transfer, including cross-species reciprocation with sulphuric compounds and microbial nanotube-mediated interspecies interactions. Batch cultivation demonstrated degradation rates of up to 0.16 g propionate L-1 day-1 at hydrogen partial pressure 4-30 Pa and available energy was around -20 mol-1 propionate. These observations outline the multiple syntrophic interactions required for propionate oxidation and represent a first step in increasing knowledge of acid accumulation in high-ammonia biogas production systems.
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Affiliation(s)
- Abhijeet Singh
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, SE-750 07, Uppsala, Sweden
| | - Anna Schnürer
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, SE-750 07, Uppsala, Sweden
| | - Jan Dolfing
- Faculty of Energy and Environment, Northumbria University, Newcastle-upon-Tyne, NE18QH, UK
| | - Maria Westerholm
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, SE-750 07, Uppsala, Sweden.
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11
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McDaniel MS, Sumpter NA, Lindgren NR, Billiot CE, Swords WE. Comparative genomics of clinical Stenotrophomonas maltophilia isolates reveals genetic diversity which correlates with colonization and persistence in vivo. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001408. [PMID: 37942787 PMCID: PMC10710838 DOI: 10.1099/mic.0.001408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 10/18/2023] [Indexed: 11/10/2023]
Abstract
Stenotrophomonas maltophilia is a Gram-negative emerging opportunistic pathogen often present in people with respiratory diseases such as cystic fibrosis (CF). People with CF (pwCF) experience lifelong polymicrobial infections of the respiratory mucosa. Our prior work showed that Pseudomonas aeruginosa promotes persistence of S. maltophilia in mouse respiratory infections. As is typical for environmental opportunistic pathogens, S. maltophilia has a large genome and a high degree of genetic diversity. In this study, we evaluated the genomic content of S. maltophilia, combining short and long read sequencing to construct nearly complete genomes of 10 clinical isolates. The genomes of these isolates were then compared with all publicly available S. maltophilia genome assemblies, and each isolate was then evaluated for colonization/persistence in vivo, both alone and in coinfection with P. aeruginosa. We found that while the overall genome size and GC content were fairly consistent between strains, there was considerable variability in both genome structure and gene content. Similarly, there was significant variability in S. maltophilia colonization and persistence in experimental mouse respiratory infections in the presence or absence of P. aeruginosa. Ultimately, this study gives us a greater understanding of the genomic diversity of clinical S. maltophilia isolates, and how this genomic diversity relates to both interactions with other pulmonary pathogens and to host disease progression. Identifying the molecular determinants of infection with S. maltophilia can facilitate development of novel antimicrobial strategies for a highly drug-resistant pathogen.
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Affiliation(s)
- Melissa S. McDaniel
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Birmingham, AL, US
- Gregory Fleming James Center for Cystic Fibrosis Research, Birmingham, AL, US
| | - Nicholas A. Sumpter
- Department of Medicine, Division of Clinical Immunology and Rheumatology, Birmingham, AL, US
| | - Natalie R. Lindgren
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Birmingham, AL, US
- Gregory Fleming James Center for Cystic Fibrosis Research, Birmingham, AL, US
| | - Caitlin E. Billiot
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Birmingham, AL, US
- Gregory Fleming James Center for Cystic Fibrosis Research, Birmingham, AL, US
| | - W. Edward Swords
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Birmingham, AL, US
- Gregory Fleming James Center for Cystic Fibrosis Research, Birmingham, AL, US
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12
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Meacock OJ, Durham WM. Tracking bacteria at high density with FAST, the Feature-Assisted Segmenter/Tracker. PLoS Comput Biol 2023; 19:e1011524. [PMID: 37812642 PMCID: PMC10586697 DOI: 10.1371/journal.pcbi.1011524] [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: 03/10/2023] [Revised: 10/19/2023] [Accepted: 09/17/2023] [Indexed: 10/11/2023] Open
Abstract
Most bacteria live attached to surfaces in densely-packed communities. While new experimental and imaging techniques are beginning to provide a window on the complex processes that play out in these communities, resolving the behaviour of individual cells through time and space remains a major challenge. Although a number of different software solutions have been developed to track microorganisms, these typically require users either to tune a large number of parameters or to groundtruth a large volume of imaging data to train a deep learning model-both manual processes which can be very time consuming for novel experiments. To overcome these limitations, we have developed FAST, the Feature-Assisted Segmenter/Tracker, which uses unsupervised machine learning to optimise tracking while maintaining ease of use. Our approach, rooted in information theory, largely eliminates the need for users to iteratively adjust parameters manually and make qualitative assessments of the resulting cell trajectories. Instead, FAST measures multiple distinguishing 'features' for each cell and then autonomously quantifies the amount of unique information each feature provides. We then use these measurements to determine how data from different features should be combined to minimize tracking errors. Comparing our algorithm with a naïve approach that uses cell position alone revealed that FAST produced 4 to 10 fold fewer tracking errors. The modular design of FAST combines our novel tracking method with tools for segmentation, extensive data visualisation, lineage assignment, and manual track correction. It is also highly extensible, allowing users to extract custom information from images and seamlessly integrate it into downstream analyses. FAST therefore enables high-throughput, data-rich analyses with minimal user input. It has been released for use either in Matlab or as a compiled stand-alone application, and is available at https://bit.ly/3vovDHn, along with extensive tutorials and detailed documentation.
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Affiliation(s)
- Oliver J. Meacock
- Department of Biology, University of Oxford, Oxford, United Kingdom
- Department of Physics and Astronomy, University of Sheffield, Sheffield, United Kingdom
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - William M. Durham
- Department of Biology, University of Oxford, Oxford, United Kingdom
- Department of Physics and Astronomy, University of Sheffield, Sheffield, United Kingdom
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13
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Geiger CJ, O’Toole GA. Evidence for the Type IV Pilus Retraction Motor PilT as a Component of the Surface Sensing System in Pseudomonas aeruginosa. J Bacteriol 2023; 205:e0017923. [PMID: 37382531 PMCID: PMC10367593 DOI: 10.1128/jb.00179-23] [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: 06/05/2023] [Accepted: 06/07/2023] [Indexed: 06/30/2023] Open
Abstract
Biofilm formation begins when bacteria contacting a surface induce cellular changes to become better adapted for surface growth. One of the first changes to occur for Pseudomonas aeruginosa after surface contact is an increase in the nucleotide second messenger 3',5'-cyclic AMP (cAMP). It has been demonstrated that this increase in intracellular cAMP is dependent on functional type IV pili (T4P) relaying a signal to the Pil-Chp system, but the mechanism by which this signal is transduced remains poorly understood. Here, we investigate the role of the type IV pilus retraction motor PilT in sensing a surface and relaying that signal to cAMP production. We show that mutations in PilT, and in particular those impacting the ATPase activity of this motor protein, reduce surface-dependent cAMP production. We identify a novel interaction between PilT and PilJ, a member of the Pil-Chp system, and propose a new model whereby P. aeruginosa uses its PilT retraction motor to sense a surface and to relay that signal via PilJ to increased production of cAMP. We discuss these findings in light of current T4P-dependent surface sensing models for P. aeruginosa. IMPORTANCE T4P are cellular appendages that allow P. aeruginosa to sense a surface, leading to the production of cAMP. This second messenger not only activates virulence pathways but leads to further surface adaptation and irreversible attachment of cells. Here, we demonstrate the importance of the retraction motor PilT in surface sensing. We also present a new surface sensing model in P. aeruginosa whereby the T4P retraction motor PilT senses and transmits the surface signal, likely via its ATPase domain and interaction with PilJ, to mediate production of the second messenger cAMP.
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Affiliation(s)
- C. J. Geiger
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - G. A. O’Toole
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
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14
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McDaniel MS, Sumpter NA, Lindgren NR, Billiot CE, Swords WE. Comparative genomics of clinical Stenotrophomonas maltophilia isolates reveals regions of diversity which correlate with colonization and persistence in vivo. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.14.549068. [PMID: 37503051 PMCID: PMC10369963 DOI: 10.1101/2023.07.14.549068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Stenotrophomonas maltophilia is a Gram-negative emerging opportunistic pathogen often found in respiratory diseases such as cystic fibrosis (CF). Patients with CF experience lifelong polymicrobial infections of the respiratory mucosa. Our prior work showed that P. aeruginosa promotes persistence of S. maltophilia mouse respiratory infections. As is typical for environmental opportunistic pathogens, S. maltophilia has a large genome and a high degree of genetic diversity. In this study, we evaluated the genomic content of S. maltophilia, combining short and long read sequencing to construct complete genomes of 10 clinical isolates which were then compared with the larger phylogeny of S. maltophilia genomic sequence data, and compared colonization/persistence in vivo, alone and in coinfection with P. aeruginosa. We found that while the overall genome size and GC content were fairly consistent, there was considerable variability in arrangement and gene content. Similarly, there was significant variability in S. maltophilia colonization and persistence in vivo in experimental mouse respiratory infection. Ultimately, this study gives us a greater understanding of the genomic diversity of S. maltophilia isolated from patients, and how this genomic diversity relates to interactions with other pulmonary pathogens, and to host disease progression. Identifying the molecular determinants of infection with S. maltophilia can facilitate development of novel antimicrobial strategies for a highly drug-resistant pathogen.
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Affiliation(s)
- Melissa S. McDaniel
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Alabama at Birmingham
- Gregory Fleming James Center for Cystic Fibrosis Research, University of Alabama at Birmingham
| | - Nicholas A. Sumpter
- Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham
| | - Natalie R. Lindgren
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Alabama at Birmingham
- Gregory Fleming James Center for Cystic Fibrosis Research, University of Alabama at Birmingham
| | - Caitlin E. Billiot
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Alabama at Birmingham
- Gregory Fleming James Center for Cystic Fibrosis Research, University of Alabama at Birmingham
| | - W. Edward Swords
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Alabama at Birmingham
- Gregory Fleming James Center for Cystic Fibrosis Research, University of Alabama at Birmingham
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15
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Bhattacharyya A, Mavrodi O, Bhowmik N, Weller D, Thomashow L, Mavrodi D. Bacterial biofilms as an essential component of rhizosphere plant-microbe interactions. METHODS IN MICROBIOLOGY 2023; 53:3-48. [PMID: 38415193 PMCID: PMC10898258 DOI: 10.1016/bs.mim.2023.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/29/2024]
Affiliation(s)
- Ankita Bhattacharyya
- School of Biological, Environmental and Earth Sciences, The University of Southern Mississippi, Hattiesburg, MS, United States
| | - Olga Mavrodi
- School of Biological, Environmental and Earth Sciences, The University of Southern Mississippi, Hattiesburg, MS, United States
| | - Niladri Bhowmik
- School of Biological, Environmental and Earth Sciences, The University of Southern Mississippi, Hattiesburg, MS, United States
| | - David Weller
- USDA-ARS Wheat Health, Genetics and Quality Research Unit, Pullman, WA, United States
| | - Linda Thomashow
- USDA-ARS Wheat Health, Genetics and Quality Research Unit, Pullman, WA, United States
| | - Dmitri Mavrodi
- School of Biological, Environmental and Earth Sciences, The University of Southern Mississippi, Hattiesburg, MS, United States
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16
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Simsek AN, Koch MD, Sanfilippo JE, Gitai Z, Gompper G, Sabass B. Type-IV pili tune an adhesion-migration trade-off during surface colonization of Pseudomonas aeruginosa. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.09.538458. [PMID: 37215001 PMCID: PMC10197611 DOI: 10.1101/2023.05.09.538458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Bacterial pathogenicity relies on both firm surface adhesion and cell dissemination. How twitching bacteria resolve the fundamental contradiction between adhesion and migration is unknown. To address this question, we employ live-cell imaging of type-IV pili (T4P) and therewith construct a comprehensive mathematical model of Pseudomonas aeruginosa migration. The data show that only 10% to 50% of T4P bind to substrates and contribute to migration through random extension and retraction. Individual T4P do not display a measurable sensory response to surfaces, but their number increases on cellular surface contact. Attachment to surfaces is mediated, besides T4P, by passive adhesive forces acting on the cell body. Passive adhesions slow down cell migration and result in local random motion on short time scales, which is followed by directionally persistent, superdiffusive motion on longer time scales. Moreover, passive adhesions strongly enhance surface attachment under shear flow. Δ pilA mutants, which produce no T4P, robustly stick to surfaces under shear flow. In contrast, rapidly migrating Δ pilH cells, which produce an excessive number of T4P, are easily detached by shear. Wild-type cells sacrifice migration speed for robust surface attachment by maintaining a low number of active pili. The different cell strains pertain to disjunct regimes in a generic adhesion-migration trait space. Depending on the nature of the adhesion structures, adhesion and migration are either compatible or a trade-off is required for efficient bacterial surface colonization under different conditions.
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17
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Geiger CJ, O'Toole GA. Evidence for the Type IV Pili Retraction Motor PilT as a Component of the Surface Sensing System in Pseudomonas aeruginosa. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.02.539127. [PMID: 37205505 PMCID: PMC10187167 DOI: 10.1101/2023.05.02.539127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Biofilm formation begins when bacteria contacting a surface induce cellular changes to become better adapted for surface growth. One of the first changes to occur for Pseudomonas aeruginosa after surface contact is an increase in the nucleotide second messenger 3',5'-cyclic adenosine monophosphate (cAMP). It has been demonstrated that this increase in intracellular cAMP is dependent on functional Type IV pili (T4P) relaying a signal to the Pil-Chp system, but the mechanism by which this signal is transduced remains poorly understood. Here, we investigate the role of the Type IV pili retraction motor PilT in sensing a surface and relaying that signal to cAMP production. We show that mutations affecting the structure of PilT and in particular ATPase activity of this motor protein, reduce surface-dependent cAMP production. We identify a novel interaction between PilT and PilJ, a member of the Pil-Chp system, and propose a new model whereby P. aeruginosa uses its retraction motor to sense a surface and to relay that signal via PilJ to increased production of cAMP. We discuss these findings in light of current TFP-dependent surface sensing models for P. aeruginosa . Importance T4P are cellular appendages that allow P. aeruginosa to sense a surface leading to the production of cAMP. This second messenger not only activates virulence pathways but leads to further surface adaptation and irreversible attachment of cells. Here, we demonstrate the importance of the retraction motor PilT in surface sensing. We also present a new surface sensing model in P. aeruginosa whereby the T4P retraction motor PilT senses and transmits the surface signal, likely via its ATPase domain and interaction with PilJ, to mediate production of the second messenger cAMP.
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Affiliation(s)
- C J Geiger
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth
| | - G A O'Toole
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth
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Kühn MJ, Macmillan H, Talà L, Inclan Y, Patino R, Pierrat X, Al‐Mayyah Z, Engel JN, Persat A. Two antagonistic response regulators control Pseudomonas aeruginosa polarization during mechanotaxis. EMBO J 2023; 42:e112165. [PMID: 36795017 PMCID: PMC10519157 DOI: 10.15252/embj.2022112165] [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: 07/20/2022] [Revised: 01/24/2023] [Accepted: 01/30/2023] [Indexed: 02/17/2023] Open
Abstract
The opportunistic pathogen Pseudomonas aeruginosa adapts to solid surfaces to enhance virulence and infect its host. Type IV pili (T4P), long and thin filaments that power surface-specific twitching motility, allow single cells to sense surfaces and control their direction of movement. T4P distribution is polarized to the sensing pole by the chemotaxis-like Chp system via a local positive feedback loop. However, how the initial spatially resolved mechanical signal is translated into T4P polarity is incompletely understood. Here, we demonstrate that the two Chp response regulators PilG and PilH enable dynamic cell polarization by antagonistically regulating T4P extension. By precisely quantifying the localization of fluorescent protein fusions, we show that phosphorylation of PilG by the histidine kinase ChpA controls PilG polarization. Although PilH is not strictly required for twitching reversals, it becomes activated upon phosphorylation and breaks the local positive feedback mechanism established by PilG, allowing forward-twitching cells to reverse. Chp thus uses a main output response regulator, PilG, to resolve mechanical signals in space and employs a second regulator, PilH, to break and respond when the signal changes. By identifying the molecular functions of two response regulators that dynamically control cell polarization, our work provides a rationale for the diversity of architectures often found in non-canonical chemotaxis systems.
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Affiliation(s)
- Marco J Kühn
- Institute of Bioengineering and Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de LausanneLausanneSwitzerland
| | | | - Lorenzo Talà
- Institute of Bioengineering and Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de LausanneLausanneSwitzerland
| | - Yuki Inclan
- Department of MedicineUniversity of CaliforniaSan FranciscoCAUSA
| | - Ramiro Patino
- Department of MedicineUniversity of CaliforniaSan FranciscoCAUSA
| | - Xavier Pierrat
- Institute of Bioengineering and Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de LausanneLausanneSwitzerland
| | - Zainebe Al‐Mayyah
- Institute of Bioengineering and Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de LausanneLausanneSwitzerland
| | - Joanne N Engel
- Department of MedicineUniversity of CaliforniaSan FranciscoCAUSA
- Department of Microbiology and ImmunologyUniversity of CaliforniaSan FranciscoCAUSA
| | - Alexandre Persat
- Institute of Bioengineering and Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de LausanneLausanneSwitzerland
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Kavela S, Vyas P, CP J, Kushwaha SK, Majumdar SS, Faisal SM. Use of an Integrated Multi-Omics Approach To Identify Molecular Mechanisms and Critical Factors Involved in the Pathogenesis of Leptospira. Microbiol Spectr 2023; 11:e0313522. [PMID: 36853003 PMCID: PMC10100824 DOI: 10.1128/spectrum.03135-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 02/06/2023] [Indexed: 03/01/2023] Open
Abstract
Leptospirosis, a bacterial zoonosis caused by pathogenic Leptospira spp., is prevalent worldwide and has become a serious threat in recent years. Limited understanding of Leptospira pathogenesis and host response has hampered the development of effective vaccine and diagnostics. Although Leptospira is phagocytosed by innate immune cells, it resists its destruction, and the evading mechanism involved is unclear. In the present study, we used an integrative multi-omics approach to identify the critical molecular factors of Leptospira involved in pathogenesis during interaction with human macrophages. Transcriptomic and proteomic analyses were performed at 24 h postinfection of human macrophages (phorbol-12-myristate-13-acetate differentiated THP-1 cells) with the pathogenic Leptospira interrogans serovar Icterohaemorrhagiae strain RGA (LEPIRGA). Our results identified a total of 1,528 transcripts and 871 proteins that were significantly expressed with an adjusted P value of <0.05. The correlations between the transcriptomic and proteomic data were above average (r = 0.844), suggesting the role of the posttranscriptional processes during host interaction. The conjoint analysis revealed the expression of several virulence-associated proteins such as adhesins, invasins, and secretory and chemotaxis proteins that might be involved in various processes of attachment and invasion and as effectors during pathogenesis in the host. Further, the interaction of bacteria with the host cell (macrophages) was a major factor in the differential expression of these proteins. Finally, eight common differentially expressed RNA-protein pairs, predicted as virulent, outer membrane/extracellular proteins were validated by quantitative PCR. This is the first report using integrated multi-omics approach to identify critical factors involved in Leptospira pathogenesis. Validation of these critical factors may lead to the identification of target antigens for the development of improved diagnostics and vaccines against leptospirosis. IMPORTANCE Leptospirosis is a zoonotic disease of global importance. It is caused by a Gram-negative bacterial spirochete of the genus Leptospira. The current challenge is to detect the infection at early stage for treatment or to develop potent vaccines that can induce cross-protection against various pathogenic serovars. Understanding host-pathogen interactions is important to identify the critical factors involved in pathogenesis and host defense for developing improved vaccines and diagnostics. Utilizing an integrated multi-omics approach, our study provides important insight into the interaction of Leptospira with human macrophages and identifies a few critical factors (such as virulence-associated proteins) involved in pathogenesis. These factors can be exploited for the development of novel tools for the detection, treatment, or prevention of leptospirosis.
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Affiliation(s)
- Sridhar Kavela
- Laboratory of Vaccine Immunology, National Institute of Animal Biotechnology, Hyderabad, India
| | - Pallavi Vyas
- Laboratory of Vaccine Immunology, National Institute of Animal Biotechnology, Hyderabad, India
- Regional Centre for Biotechnology, Faridabad, India
| | - Jusail CP
- Laboratory of Vaccine Immunology, National Institute of Animal Biotechnology, Hyderabad, India
- Regional Centre for Biotechnology, Faridabad, India
| | - Sandeep K. Kushwaha
- Bioinformatics Lab, National Institute of Animal Biotechnology, Hyderabad, India
| | - Subeer S. Majumdar
- Gene and Protein Engineering Lab, National Institute of Animal Biotechnology, Hyderabad, India
| | - Syed M. Faisal
- Laboratory of Vaccine Immunology, National Institute of Animal Biotechnology, Hyderabad, India
- Regional Centre for Biotechnology, Faridabad, India
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20
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Pseudomonas aeruginosa Promotes Persistence of Stenotrophomonas maltophilia via Increased Adherence to Depolarized Respiratory Epithelium. Microbiol Spectr 2023; 11:e0384622. [PMID: 36472421 PMCID: PMC9927254 DOI: 10.1128/spectrum.03846-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Stenotrophomonas maltophilia is an emerging opportunistic respiratory pathogen in people with cystic fibrosis (CF). S. maltophilia is frequently observed in polymicrobial infections, and we have previously shown that Pseudomonas aeruginosa promotes colonization and persistence of S. maltophilia in mouse respiratory infections. In this study, we used host and bacterial RNA sequencing to further understand the molecular underpinnings of this interaction. To evaluate S. maltophilia transcript profiles, we used a recently described method for selective capture of bacterial mRNA transcripts with strain-specific RNA probes. We found that factors associated with the type IV pilus, including the histidine kinase subunit of a chemotactic two-component signaling system (chpA), had increased transcript levels during dual-species infection. Using immortalized CF respiratory epithelial cells, we found that infection with P. aeruginosa increases adherence of S. maltophilia, at least in part due to disruption of epithelial tight junctions. In contrast, an isogenic S. maltophilia chpA mutant strain lacked cooperative adherence to CF epithelia and decreased bacterial burden in vivo in dual-species infections with P. aeruginosa. Similarly, P. aeruginosa lacking elastase (lasB) failed to promote S. maltophilia adherence or bacterial colonization and persistence in vivo. Based on these results, we propose that disruption of lung tissue integrity by P. aeruginosa facilitates adherence of S. maltophilia to the lung epithelia, likely in a type IV pilus-dependent manner. These data lend insight into S. maltophilia colonization and persistence in people in later stages of CF disease and may have implications for interactions with other bacterial opportunists. IMPORTANCE Despite advances in treatment options for people with CF, complications of bacterial infections remain the greatest driver of morbidity and mortality in this patient population. These infections often involve more than one bacterial pathogen, and our understanding of how interspecies interactions impact disease progression is lacking. Previous work in our lab found that two CF pathogens, Stenotrophomonas maltophilia and Pseudomonas aeruginosa, can work together in the lung to cause more severe infection. In the present study, we found that infection with P. aeruginosa promotes persistence of S. maltophilia by interfering with epithelial barrier integrity. Depolarization of the epithelial cell layer by P. aeruginosa-secreted elastase increased S. maltophilia adherence, likely in a type IV pilus-dependent manner. Ultimately, this work sheds light on the molecular mechanisms governing an important multispecies interaction seen in pulmonary diseases such as CF.
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21
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In Vivo Role of Two-Component Regulatory Systems in Models of Urinary Tract Infections. Pathogens 2023; 12:pathogens12010119. [PMID: 36678467 PMCID: PMC9861413 DOI: 10.3390/pathogens12010119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 12/23/2022] [Accepted: 01/08/2023] [Indexed: 01/12/2023] Open
Abstract
Two-component signaling systems (TCSs) are finely regulated mechanisms by which bacteria adapt to environmental conditions by modifying the expression of target genes. In bacterial pathogenesis, TCSs play important roles in modulating adhesion to mucosal surfaces, resistance to antibiotics, and metabolic adaptation. In the context of urinary tract infections (UTI), one of the most common types infections causing significant health problems worldwide, uropathogens use TCSs for adaptation, survival, and establishment of pathogenicity. For example, uropathogens can exploit TCSs to survive inside bladder epithelial cells, sense osmolar variations in urine, promote their ascension along the urinary tract or even produce lytic enzymes resulting in exfoliation of the urothelium. Despite the usefulness of studying the function of TCSs in in vitro experimental models, it is of primary necessity to study bacterial gene regulation also in the context of host niches, each displaying its own biological, chemical, and physical features. In light of this, the aim of this review is to provide a concise description of several bacterial TCSs, whose activity has been described in mouse models of UTI.
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Abstract
Bacteria commonly live in surface-associated communities where steep gradients of antibiotics and other chemical compounds can occur. While many bacterial species move on surfaces, we know surprisingly little about how such antibiotic gradients affect cell motility. Here, we study the behaviour of the opportunistic pathogen Pseudomonas aeruginosa in stable spatial gradients of several antibiotics by tracking thousands of cells in microfluidic devices as they form biofilms. Unexpectedly, these experiments reveal that bacteria use pili-based ('twitching') motility to navigate towards antibiotics. Our analyses suggest that this behaviour is driven by a general response to the effects of antibiotics on cells. Migrating bacteria reach antibiotic concentrations hundreds of times higher than their minimum inhibitory concentration within hours and remain highly motile. However, isolating cells - using fluid-walled microfluidic devices - reveals that these bacteria are terminal and unable to reproduce. Despite moving towards their death, migrating cells are capable of entering a suicidal program to release bacteriocins that kill other bacteria. This behaviour suggests that the cells are responding to antibiotics as if they come from a competing colony growing nearby, inducing them to invade and attack. As a result, clinical antibiotics have the potential to lure bacteria to their death.
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23
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Ellison CK, Fei C, Dalia TN, Wingreen NS, Dalia AB, Shaevitz JW, Gitai Z. Subcellular localization of type IV pili regulates bacterial multicellular development. Nat Commun 2022; 13:6334. [PMID: 36284096 PMCID: PMC9596432 DOI: 10.1038/s41467-022-33564-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 09/22/2022] [Indexed: 12/25/2022] Open
Abstract
In mammals, subcellular protein localization of factors like planar cell polarity proteins is a key driver of the multicellular organization of tissues. Bacteria also form organized multicellular communities, but these patterns are largely thought to emerge from regulation of whole-cell processes like growth, motility, cell shape, and differentiation. Here we show that a unique intracellular patterning of appendages known as type IV pili (T4P) can drive multicellular development of complex bacterial communities. Specifically, dynamic T4P appendages localize in a line along the long axis of the cell in the bacterium Acinetobacter baylyi. This long-axis localization is regulated by a functionally divergent chemosensory Pil-Chp system, and an atypical T4P protein homologue (FimV) bridges Pil-Chp signaling and T4P positioning. We further demonstrate through modeling and empirical approaches that subcellular T4P localization controls how individual cells interact with one another, independently of T4P dynamics, with different patterns of localization giving rise to distinct multicellular architectures. Our results reveal how subcellular patterning of single cells regulates the development of multicellular bacterial communities.
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Affiliation(s)
- Courtney K Ellison
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
- Department of Microbiology, University of Georgia, Athens, GA, USA.
| | - Chenyi Fei
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Triana N Dalia
- Department of Biology, Indiana University, Bloomington, IN, USA
| | - Ned S Wingreen
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Ankur B Dalia
- Department of Biology, Indiana University, Bloomington, IN, USA.
| | - Joshua W Shaevitz
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.
| | - Zemer Gitai
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
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24
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Surface-Induced cAMP Signaling Requires Multiple Features of the Pseudomonas aeruginosa Type IV Pili. J Bacteriol 2022; 204:e0018622. [PMID: 36073942 PMCID: PMC9578403 DOI: 10.1128/jb.00186-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Pseudomonas aeruginosa type IV pili (TFP) are important for twitching motility and biofilm formation. TFP have been implicated in surface sensing, a process whereby surface-engaged cells upregulate the synthesis of the second messenger cAMP to propagate a signaling cascade leading to biofilm initiation and repression of motility. Here, we showed that mutations in PilA impairing proteolytic processing of the prepilin into mature pilin as well as the disruption of essential TFP components, including the PilC platform protein and PilB assembly motor protein, fail to induce surface-dependent cAMP signaling. We showed that TFP retraction by surface-engaged cells was required to induce signaling and that the retractile motor PilT was both necessary and sufficient to power surface-specific induction of cAMP. Furthermore, full TFP function required to support twitching motility is not required for robust cAMP signalling. The PilU retraction motor, in contrast, was unable to support full signaling in the absence of PilT. Finally, while we confirmed that PilA and PilJ interacted by bacterial two-hybrid analysis, our data do not support the current model that PilJ-PilA interaction drives cAMP signaling. IMPORTANCE Surface sensing by P. aeruginosa requires TFP. TFP plays a critical role in the induction of the second messenger cAMP upon surface contact; this second messenger is part of a larger cascade involved in the transition from a planktonic to a biofilm lifestyle. Here, we showed that TFP must be deployed and actively retracted by the PilT motor for the full induction of cAMP signaling. Furthermore, the mechanism whereby TFP retraction triggers cAMP induction is not well understood, and our data argue against one of the current models in the field proposed to address this knowledge gap.
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Luo J, Cheng X, Su Y, Zhang L, Du W, Bao X, Huang W, Feng Q, Cao J, Wu Y. Metagenomic assembly deciphered the type-dependent effects of surfactants on the fates of antibiotics resistance genes during sludge fermentation and the underlying mechanisms. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 807:150822. [PMID: 34627892 DOI: 10.1016/j.scitotenv.2021.150822] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 09/29/2021] [Accepted: 10/01/2021] [Indexed: 06/13/2023]
Abstract
Waste activated sludge (WAS) is an important reservoir of antibiotic resistance genes (ARGs). However, the interactive effects of co-existed substances in WAS on ARGs fates have yet to be disclosed. This study demonstrated the type-dependent effects of surfactants (potentially effective chemicals for WAS disposal) on the reduction of ARGs during WAS fermentation, which followed the order of linear alkylbenzene sulphonates (LAS) > alkyl polyglucoside (APG) > hexadecyl trimethyl ammonium bromide (HTAB). Interestingly, the ratio of ARGs affiliated to efflux pump showed an upward trend in the surfactant-treated reactor. Mechanistic investigations revealed that the extracellular polymeric substances (EPS) destruction induced by surfactants increased the permeability of bacterial cells and caused the ARGs being released and susceptible for subsequent elimination. Besides, the surfactants significantly altered the microbial community, resulting in the ARGs reduction via changing the potential hosts. Also, the metabolic pathways participated in the dissemination of ARGs were remarkably down-regulated, thereby resulting in the reduction of ARGs abundances. This work broadened the understanding of ARGs fates during WAS fermentation and provided insights on the interactive functions of exogenous chemicals in multiple matrics.
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Affiliation(s)
- Jingyang Luo
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, 1 Xikang Road, Nanjing 210098, PR China; College of Environment, Hohai University, 1 Xikang Road, Nanjing 210098, PR China
| | - Xiaoshi Cheng
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, 1 Xikang Road, Nanjing 210098, PR China; College of Environment, Hohai University, 1 Xikang Road, Nanjing 210098, PR China
| | - Yinglong Su
- Shanghai Engineering Research Center of Biotransformation on Organic Solid Waste, School of Ecological and Environmental Sciences, East China University, Shanghai 200241, China
| | - Le Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, 1 Xikang Road, Nanjing 210098, PR China; College of Environment, Hohai University, 1 Xikang Road, Nanjing 210098, PR China
| | - Wei Du
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, 1 Xikang Road, Nanjing 210098, PR China; College of Environment, Hohai University, 1 Xikang Road, Nanjing 210098, PR China
| | - Xingchen Bao
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, 1 Xikang Road, Nanjing 210098, PR China; College of Environment, Hohai University, 1 Xikang Road, Nanjing 210098, PR China
| | - Wenxuan Huang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, 1 Xikang Road, Nanjing 210098, PR China; College of Environment, Hohai University, 1 Xikang Road, Nanjing 210098, PR China
| | - Qian Feng
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, 1 Xikang Road, Nanjing 210098, PR China; College of Environment, Hohai University, 1 Xikang Road, Nanjing 210098, PR China
| | - Jiashun Cao
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, 1 Xikang Road, Nanjing 210098, PR China; College of Environment, Hohai University, 1 Xikang Road, Nanjing 210098, PR China
| | - Yang Wu
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China.
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26
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Ducret V, Perron K, Valentini M. Role of Two-Component System Networks in Pseudomonas aeruginosa Pathogenesis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1386:371-395. [PMID: 36258080 DOI: 10.1007/978-3-031-08491-1_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Two-component systems (TCS) are the largest family of signaling systems in the bacterial kingdom. They enable bacteria to cope with a wide range of environmental conditions via the sensing of stimuli and the transduction of the signal into an appropriate cellular adaptation response. Pseudomonas aeruginosa possesses one of the richest arrays of TCSs in bacteria and they have been the subject of intense investigation for more than 20 years. Most of the P. aeruginosa TCSs characterized to date affect its pathogenesis, via the regulation of virulence factors expression, modulation of the synthesis of antibiotic/antimicrobial resistance mechanisms, and/or via linking virulence to energy metabolism. Here, we give an overview of the current knowledge on P. aeruginosa TCSs, citing key examples for each of the above-mentioned regulatory actions. We then conclude by mentioning few small molecule inhibitors of P. aeruginosa TCSs that have shown an antimicrobial action in vitro.
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Affiliation(s)
- Verena Ducret
- Microbiology Unit, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland
| | - Karl Perron
- Microbiology Unit, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland
| | - Martina Valentini
- Department of Microbiology and Molecular Medicine, CMU, Faculty of Medicine, University of Geneva, Geneva, Switzerland.
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Han Y, Jakob A, Engel S, Wilde A, Nils S. PATAN-domain regulators interact with the Type IV pilus motor to control phototactic orientation in the cyanobacterium Synechocystis. Mol Microbiol 2021; 117:790-801. [PMID: 34936151 DOI: 10.1111/mmi.14872] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 12/19/2021] [Accepted: 12/20/2021] [Indexed: 11/28/2022]
Abstract
Many prokaryotes show complex behaviors that require the intricate spatial and temporal organization of cellular protein machineries, leading to asymmetrical protein distribution and cell polarity. One such behavior is cyanobacterial phototaxis which relies on the dynamic localization of the Type IV pilus motor proteins in response to light. In the cyanobacterium Synechocystis, various signaling systems encompassing chemotaxis-related CheY- and PatA-like response regulators are critical players in switching between positive and negative phototaxis depending on the light intensity and wavelength. In this study, we show that PatA-type regulators evolved from chemosensory systems. Using fluorescence microscopy and yeast-two-hybrid analysis, we demonstrate that they localize to the inner membrane, where they interact with the N-terminal cytoplasmic domain of PilC and the pilus assembly ATPase PilB1. By separately expressing the subdomains of the response regulator PixE, we confirm that only the N-terminal PATAN domain interacts with PilB1, localizes to the membrane, and is sufficient to reverse phototactic orientation. These experiments established that the PATAN domain is the principal output domain of PatA-type regulators which we presume to modulate pilus extension by binding to the pilus motor components.
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Affiliation(s)
- Yu Han
- Molecular Genetics, Institute of Biology III, University of Freiburg, 79104, Freiburg, Germany
| | - Annik Jakob
- Molecular Genetics, Institute of Biology III, University of Freiburg, 79104, Freiburg, Germany
| | - Sophia Engel
- Molecular Genetics, Institute of Biology III, University of Freiburg, 79104, Freiburg, Germany
| | - Annegret Wilde
- Molecular Genetics, Institute of Biology III, University of Freiburg, 79104, Freiburg, Germany
| | - Schuergers Nils
- Molecular Genetics, Institute of Biology III, University of Freiburg, 79104, Freiburg, Germany
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Ellison CK, Whitfield GB, Brun YV. Type IV Pili: Dynamic Bacterial Nanomachines. FEMS Microbiol Rev 2021; 46:6425739. [PMID: 34788436 DOI: 10.1093/femsre/fuab053] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 11/08/2021] [Indexed: 01/19/2023] Open
Abstract
Bacteria and archaea rely on appendages called type IV pili (T4P) to participate in diverse behaviors including surface sensing, biofilm formation, virulence, protein secretion, and motility across surfaces. T4P are broadly distributed fibers that dynamically extend and retract, and this dynamic activity is essential for their function in broad processes. Despite the essentiality of dynamics in T4P function, little is known about the role of these dynamics and molecular mechanisms controlling them. Recent advances in microscopy have yielded insight into the role of T4P dynamics in their diverse functions and recent structural work has expanded what is known about the inner workings of the T4P motor. This review discusses recent progress in understanding the function, regulation, and mechanisms of T4P dynamics.
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Affiliation(s)
- Courtney K Ellison
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.,Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Gregory B Whitfield
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, Québec, Canada
| | - Yves V Brun
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, Québec, Canada
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Sultan M, Arya R, Kim KK. Roles of Two-Component Systems in Pseudomonas aeruginosa Virulence. Int J Mol Sci 2021; 22:12152. [PMID: 34830033 PMCID: PMC8623646 DOI: 10.3390/ijms222212152] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 11/01/2021] [Accepted: 11/02/2021] [Indexed: 12/28/2022] Open
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen that synthesizes and secretes a wide range of virulence factors. P. aeruginosa poses a potential threat to human health worldwide due to its omnipresent nature, robust host accumulation, high virulence, and significant resistance to multiple antibiotics. The pathogenicity of P. aeruginosa, which is associated with acute and chronic infections, is linked with multiple virulence factors and associated secretion systems, such as the ability to form and utilize a biofilm, pili, flagella, alginate, pyocyanin, proteases, and toxins. Two-component systems (TCSs) of P. aeruginosa perform an essential role in controlling virulence factors in response to internal and external stimuli. Therefore, understanding the mechanism of TCSs to perceive and respond to signals from the environment and control the production of virulence factors during infection is essential to understanding the diseases caused by P. aeruginosa infection and further develop new antibiotics to treat this pathogen. This review discusses the important virulence factors of P. aeruginosa and the understanding of their regulation through TCSs by focusing on biofilm, motility, pyocyanin, and cytotoxins.
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Affiliation(s)
| | - Rekha Arya
- Department of Precision Medicine, Graduate School of Basic Medical Science (GSBMS), Institute for Antimicrobial Resistance Research and Therapeutics, Sungkyunkwan University School of Medicine, Suwon 16419, Korea;
| | - Kyeong Kyu Kim
- Department of Precision Medicine, Graduate School of Basic Medical Science (GSBMS), Institute for Antimicrobial Resistance Research and Therapeutics, Sungkyunkwan University School of Medicine, Suwon 16419, Korea;
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Abstract
Single cells across kingdoms of life explore, prey, escape, or congregate using surface-specific motility. Motile eukaryotic cells use chemotaxis to direct migration on surfaces. However, how bacteria control surface motility remains underexplored. Pseudomonas aeruginosa twitches on surfaces by successive extension and retraction of extracellular filaments called type IV pili. Here, we show that P. aeruginosa directs twitching by sensing mechanical input generated by type IV pili. The Chp sensory system performs spatially resolved mechanosensing by harnessing two response regulators with antagonistic functions. Our results demonstrate that sensory systems, whose input often remains elusive, can sense mechanical signals to actively steer motility. Furthermore, Chp establishes a signaling principle shared with higher-order organisms, identifying a conserved strategy to transduce spatially resolved signals. The opportunistic pathogen Pseudomonas aeruginosa explores surfaces using twitching motility powered by retractile extracellular filaments called type IV pili (T4P). Single cells twitch by sequential T4P extension, attachment, and retraction. How single cells coordinate T4P to efficiently navigate surfaces remains unclear. We demonstrate that P. aeruginosa actively directs twitching in the direction of mechanical input from T4P in a process called mechanotaxis. The Chp chemotaxis-like system controls the balance of forward and reverse twitching migration of single cells in response to the mechanical signal. Collisions between twitching cells stimulate reversals, but Chp mutants either always or never reverse. As a result, while wild-type cells colonize surfaces uniformly, collision-blind Chp mutants jam, demonstrating a function for mechanosensing in regulating group behavior. On surfaces, Chp senses T4P attachment at one pole, thereby sensing a spatially resolved signal. As a result, the Chp response regulators PilG and PilH control the polarization of the extension motor PilB. PilG stimulates polarization favoring forward migration, while PilH inhibits polarization, inducing reversal. Subcellular segregation of PilG and PilH efficiently orchestrates their antagonistic functions, ultimately enabling rapid reversals upon perturbations. The distinct localization of response regulators establishes a signaling landscape known as local excitation–global inhibition in higher-order organisms, identifying a conserved strategy to transduce spatially resolved signals.
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Abstract
Bacteria thrive both in liquids and attached to surfaces. The concentration of bacteria on surfaces is generally much higher than in the surrounding environment, offering bacteria ample opportunity for mutualistic, symbiotic, and pathogenic interactions. To efficiently populate surfaces, they have evolved mechanisms to sense mechanical or chemical cues upon contact with solid substrata. This is of particular importance for pathogens that interact with host tissue surfaces. In this review we discuss how bacteria are able to sense surfaces and how they use this information to adapt their physiology and behavior to this new environment. We first survey mechanosensing and chemosensing mechanisms and outline how specific macromolecular structures can inform bacteria about surfaces. We then discuss how mechanical cues are converted to biochemical signals to activate specific cellular processes in a defined chronological order and describe the role of two key second messengers, c-di-GMP and cAMP, in this process.
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Affiliation(s)
| | - Urs Jenal
- Biozentrum, University of Basel, CH-4056 Basel, Switzerland; ,
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Two-Component Signaling Systems Regulate Diverse Virulence-Associated Traits in Pseudomonas aeruginosa. Appl Environ Microbiol 2021; 87:AEM.03089-20. [PMID: 33771779 DOI: 10.1128/aem.03089-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 03/18/2021] [Indexed: 12/30/2022] Open
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen that can cause problematic infections at different sites throughout the human body. P. aeruginosa encodes a large suite of over 60 two-component signaling systems that enable cells to rapidly sense and respond to external signals. Previous work has shown that some of these sensory systems contribute to P. aeruginosa pathogenesis, but the virulence-associated processes and phenotypic traits that each of these systems controls are still largely unclear. To aid investigations of these sensory systems, we have generated deletion strains for each of 64 genes encoding histidine kinases and one histidine phosphotransferase in P. aeruginosa PA14. We carried out initial phenotypic characterizations of this collection by assaying these mutants for over a dozen virulence-associated traits, and we found that each of these phenotypes is regulated by multiple sensory systems. Our work highlights the usefulness of this collection for further studies of P. aeruginosa two-component signaling systems and provides insight into how these systems may contribute to P. aeruginosa infection.IMPORTANCE Pseudomonas aeruginosa can grow and survive under a wide range of conditions, including as a human pathogen. As such, P. aeruginosa must be able to sense and respond to diverse signals and cues in its environment. This sensory capability is endowed in part by the hundreds of two-component signaling proteins encoded in the P. aeruginosa genome, but the precise roles of each remain poorly defined. To facilitate systematic study of the signaling repertoire of P. aeruginosa PA14, we generated a library of deletion strains, each lacking one of the 64 histidine kinases. By subjecting these strains to a battery of phenotypic assays, we confirmed the functions of many and unveiled roles for dozens of previously uncharacterized histidine kinases in controlling various traits, many of which are associated with P. aeruginosa virulence. Thus, this work provides new insight into the functions of two-component signaling proteins and provides a resource for future investigations.
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Grier JT, Arivett BA, Ramírez MS, Chosed RJ, Bigner JA, Ohneck EJ, Metz ML, Wood CR, Arce S, Tartaro A, Relich RF, Actis LA, Fiester SE. Two Acinetobacter baumannii Isolates Obtained From a Fatal Necrotizing Fasciitis Infection Display Distinct Genomic and Phenotypic Characteristics in Comparison to Type Strains. Front Cell Infect Microbiol 2021; 11:635673. [PMID: 33912474 PMCID: PMC8072282 DOI: 10.3389/fcimb.2021.635673] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 03/11/2021] [Indexed: 11/23/2022] Open
Abstract
Acinetobacter baumannii has been recognized as a critical pathogen that causes severe infections worldwide not only because of the emergence of extensively drug-resistant (XDR) derivatives, but also because of its ability to persist in medical environments and colonize compromised patients. While there are numerous reports describing the mechanisms by which this pathogen acquires resistance genes, little is known regarding A. baumannii’s virulence functions associated with rare manifestations of infection such as necrotizing fasciitis, making the determination and implementation of alternative therapeutic targets problematic. To address this knowledge gap, this report describes the analysis of the NFAb-1 and NFAb-2 XDR isolates, which were obtained at two time points during a fatal case of necrotizing fasciitis, at the genomic and functional levels. The comparative genomic analysis of these isolates with the ATCC 19606T and ATCC 17978 strains showed that the NFAb-1 and NFAb-2 isolates are genetically different from each other as well as different from the ATCC 19606T and ATCC 17978 clinical isolates. These genomic differences could be reflected in phenotypic differences observed in these NFAb isolates. Biofilm, cell viability and flow cytometry assays indicate that all tested strains caused significant decreases in A549 human alveolar epithelial cell viability with ATCC 17978, NFAb-1 and NFAb-2 producing significantly less biofilm and significantly more hemolysis and capacity for intracellular invasion than ATCC 19606T. NFAb-1 and NFAb-2 also demonstrated negligible surface motility but significant twitching motility compared to ATCC 19606T and ATCC 17978, likely due to the presence of pili exceeding 2 µm in length, which are significantly longer and different from those previously described in the ATCC 19606T and ATCC 17978 strains. Interestingly, infection with cells of the NFAb-1 isolate, which were obtained from a premortem blood sample, lead to significantly higher mortality rates than NFAb-2 bacteria, which were obtained from postmortem tissue samples, when tested using the Galleria mellonella in vivo infection model. These observations suggest potential changes in the virulence phenotype of the A. baumannii necrotizing fasciitis isolates over the course of infection by mechanisms and cell processes that remain to be identified.
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Affiliation(s)
- Jennifer T Grier
- Department of Biomedical Sciences, University of South Carolina School of Medicine Greenville, Greenville, SC, United States
| | - Brock A Arivett
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN, United States
| | - Maria S Ramírez
- Department of Biological Science, California State University Fullerton, Fullerton, CA, United States
| | - Renee J Chosed
- Department of Biomedical Sciences, University of South Carolina School of Medicine Greenville, Greenville, SC, United States
| | - Jessica A Bigner
- Department of Biomedical Sciences, University of South Carolina School of Medicine Greenville, Greenville, SC, United States
| | - Emily J Ohneck
- Department of Microbiology, Miami University, Oxford, OH, United States
| | - Maeva L Metz
- Department of Microbiology, Miami University, Oxford, OH, United States
| | - Cecily R Wood
- Department of Microbiology, Miami University, Oxford, OH, United States
| | - Sergio Arce
- Department of Biomedical Sciences, University of South Carolina School of Medicine Greenville, Greenville, SC, United States.,Cancer Institute, Prisma Health, Greenville, SC, United States
| | - Andrea Tartaro
- Computer Science Department, Furman University, Greenville, SC, United States
| | - Ryan F Relich
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Luis A Actis
- Department of Microbiology, Miami University, Oxford, OH, United States
| | - Steven E Fiester
- Department of Biomedical Sciences, University of South Carolina School of Medicine Greenville, Greenville, SC, United States.,Department of Pathology, Prisma Health, Greenville, SC, United States
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Pilus Production in Acinetobacter baumannii Is Growth Phase Dependent and Essential for Natural Transformation. J Bacteriol 2021; 203:JB.00034-21. [PMID: 33495250 PMCID: PMC8088505 DOI: 10.1128/jb.00034-21] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 01/19/2021] [Indexed: 12/17/2022] Open
Abstract
Rapid bacterial evolution has alarming negative impacts on animal and human health which can occur when pathogens acquire antimicrobial resistance traits. As a major cause of antibiotic-resistant opportunistic infections, A. baumannii is a high-priority health threat which has motivated renewed interest in studying how this pathogen acquires new, dangerous traits. Acinetobacter baumannii is a severe threat to human health as a frequently multidrug-resistant hospital-acquired pathogen. Part of the danger from this bacterium comes from its genome plasticity and ability to evolve quickly by taking up and recombining external DNA into its own genome in a process called natural competence for transformation. This mode of horizontal gene transfer is one of the major ways that bacteria can acquire new antimicrobial resistances and toxic traits. Because these processes in A. baumannii are not well studied, we herein characterized new aspects of natural transformability in this species that include the species’ competence window. We uncovered a strong correlation with a growth phase-dependent synthesis of a type IV pilus (TFP), which constitutes the central part of competence-induced DNA uptake machinery. We used bacterial genetics and microscopy to demonstrate that the TFP is essential for the natural transformability and surface motility of A. baumannii, whereas pilus-unrelated proteins of the DNA uptake complex do not affect the motility phenotype. Furthermore, TFP biogenesis and assembly is subject to input from two regulatory systems that are homologous to Pseudomonas aeruginosa, namely, the PilSR two-component system and the Pil-Chp chemosensory system. We demonstrated that these systems affect not only the piliation status of cells but also their ability to take up DNA for transformation. Importantly, we report on discrepancies between TFP biogenesis and natural transformability within the same genus by comparing data for our work on A. baumannii to data reported for Acinetobacter baylyi, the latter of which served for decades as a model for natural competence. IMPORTANCE Rapid bacterial evolution has alarming negative impacts on animal and human health which can occur when pathogens acquire antimicrobial resistance traits. As a major cause of antibiotic-resistant opportunistic infections, A. baumannii is a high-priority health threat which has motivated renewed interest in studying how this pathogen acquires new, dangerous traits. In this study, we deciphered a specific time window in which these bacteria can acquire new DNA and correlated that with its ability to produce the external appendages that contribute to the DNA acquisition process. These cell appendages function doubly for motility on surfaces and for DNA uptake. Collectively, we showed that A. baumannii is similar in its TFP production to Pseudomonas aeruginosa, though it differs from the well-studied species A. baylyi.
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Transcriptional Responses of Pseudomonas aeruginosa to Inhibition of Lipoprotein Transport by a Small Molecule Inhibitor. J Bacteriol 2020; 202:JB.00452-20. [PMID: 32989085 PMCID: PMC7685553 DOI: 10.1128/jb.00452-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 09/21/2020] [Indexed: 12/16/2022] Open
Abstract
A key set of lipoprotein transport components, LolCDE, were inhibited by both a small molecule as well as genetic downregulation of their expression. The data show a unique signature in the Pseudomonas aeruginosa transcriptome in response to perturbation of outer membrane biogenesis. In addition, we demonstrate a transcriptional response in key genes with marked specificity compared to several antibiotic classes with different mechanisms of action. As a result of this work, we identified genes that could be of potential use as biomarkers in a cell-based screen for novel antibiotic inhibitors of lipoprotein transport in P. aeruginosa. Lipoprotein transport from the inner to the outer membrane, carried out by the Lol machinery, is essential for the biogenesis of the Gram-negative cell envelope and, consequently, for bacterial viability. Recently, small molecule inhibitors of the Lol system in Escherichia coli have been identified and shown to inhibit the growth of this organism by interfering with the function of the LolCDE complex. Analysis of the transcriptome of E. coli treated with one such molecule (compound 2) revealed that a number of envelope stress response pathways were induced in response to LolCDE inhibition. However, Pseudomonas aeruginosa is refractory to inhibition by the same small molecule, but we could demonstrate that E. colilolCDE could be substituted for the P. aeruginosa orthologues, where it functions in the correct transport of Pseudomonas lipoproteins, and the cells are inhibited by the more potent compound 2A. In the present study, we took advantage of the functionality of E. coli LolCDE in P. aeruginosa and determined the P. aeruginosa transcriptional response to LolCDE inhibition by compound 2A. We identified key genes that responded to LolCDE inhibition and also demonstrated that the same genes appeared to be affected by genetic depletion of the native P. aeruginosa LolCDE proteins. Several of the major changes were in an upregulated cluster of genes that encode determinants of alginate biosynthesis and transport, and the levels of alginate were found to be increased either by treatment with the small molecule inhibitor or upon depletion of native LolCDE. Finally, we tested several antibiotics with differing mechanisms of action to identify potential specific reporter genes for the further development of compounds that would inhibit the native P. aeruginosa Lol system. IMPORTANCE A key set of lipoprotein transport components, LolCDE, were inhibited by both a small molecule as well as genetic downregulation of their expression. The data show a unique signature in the Pseudomonas aeruginosa transcriptome in response to perturbation of outer membrane biogenesis. In addition, we demonstrate a transcriptional response in key genes with marked specificity compared to several antibiotic classes with different mechanisms of action. As a result of this work, we identified genes that could be of potential use as biomarkers in a cell-based screen for novel antibiotic inhibitors of lipoprotein transport in P. aeruginosa.
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36
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Zboralski A, Filion M. Genetic factors involved in rhizosphere colonization by phytobeneficial Pseudomonas spp. Comput Struct Biotechnol J 2020; 18:3539-3554. [PMID: 33304453 PMCID: PMC7711191 DOI: 10.1016/j.csbj.2020.11.025] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 11/10/2020] [Accepted: 11/12/2020] [Indexed: 12/13/2022] Open
Abstract
Plant growth-promoting rhizobacteria (PGPR) actively colonize the soil portion under the influence of plant roots, called the rhizosphere. Many plant-beneficial Pseudomonas spp. have been characterized as PGPR. They are ubiquitous rod-shaped motile Gram-negative bacteria displaying a high metabolic versatility. Their capacity to protect plants from pathogens and improve plant growth closely depends on their rhizosphere colonization abilities. Various molecular and cellular mechanisms are involved in this complex process, such as chemotaxis, biofilm formation, secondary metabolites biosynthesis, metabolic versatility, and evasion of plant immunity. The burst in Pseudomonas spp. genome sequencing in recent years has been crucial to better understand how they colonize the rhizosphere. In this review, we discuss the recent advances regarding these mechanisms and the underlying bacterial genetic factors required for successful rhizosphere colonization.
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Affiliation(s)
- Antoine Zboralski
- Department of Biology, Université de Moncton, Moncton, NB E1A 3E9, Canada
| | - Martin Filion
- Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, QC J3B 3E6, Canada
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Antar A, Lee MA, Yoo Y, Cho MH, Lee SW. PXO_RS20535, Encoding a Novel Response Regulator, Is Required for Chemotactic Motility, Biofilm Formation, and Tolerance to Oxidative Stress in Xanthomonas oryzae pv. oryzae. Pathogens 2020; 9:pathogens9110956. [PMID: 33212951 PMCID: PMC7698356 DOI: 10.3390/pathogens9110956] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 11/13/2020] [Accepted: 11/13/2020] [Indexed: 11/16/2022] Open
Abstract
Xanthomonas oryzae pv. oryzae (Xoo), a causal agent of bacterial leaf blight of rice, possesses two-component regulatory systems (TCSs) as an intracellular signaling pathway. In this study, we observed changes in virulence, biofilm formation, motility, chemotaxis, and tolerance against oxidative stress of a knockout mutant strain for the PXO_RS20535 gene, encoding an orphan response regulator (RR). The mutant strain lost virulence, produced significantly less biofilm, and showed remarkably reduced motility in swimming, swarming, and twitching. Furthermore, the mutant strain lost glucose-guided movement and showed clear diminution of growth and survival in the presence of H2O2. These results indicate that the RR protein encoded in the PXO_RS20535 gene (or a TCS mediated by the protein) is closely involved in regulation of biofilm formation, all types of motility, chemotaxis, and tolerance against reactive oxygen species (ROS) in Xoo. Moreover we found that the expression of most genes required for a type six secretion system (T6SS) was decreased in the mutant, suggesting that lack of the RR gene most likely leads to defect of T6SS in Xoo.
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Affiliation(s)
- Abdulwahab Antar
- Department of Genetic Engineering and Graduate School of Biotechnology, Kyung Hee University, Yongin 17104, Korea; (A.A.); (M.-A.L.); (Y.Y.); (M.-H.C.)
- Crop Biotech Institute, Kyung Hee University, Yongin 17104, Korea
| | - Mi-Ae Lee
- Department of Genetic Engineering and Graduate School of Biotechnology, Kyung Hee University, Yongin 17104, Korea; (A.A.); (M.-A.L.); (Y.Y.); (M.-H.C.)
- Crop Biotech Institute, Kyung Hee University, Yongin 17104, Korea
| | - Youngchul Yoo
- Department of Genetic Engineering and Graduate School of Biotechnology, Kyung Hee University, Yongin 17104, Korea; (A.A.); (M.-A.L.); (Y.Y.); (M.-H.C.)
- Crop Biotech Institute, Kyung Hee University, Yongin 17104, Korea
| | - Man-Ho Cho
- Department of Genetic Engineering and Graduate School of Biotechnology, Kyung Hee University, Yongin 17104, Korea; (A.A.); (M.-A.L.); (Y.Y.); (M.-H.C.)
| | - Sang-Won Lee
- Department of Genetic Engineering and Graduate School of Biotechnology, Kyung Hee University, Yongin 17104, Korea; (A.A.); (M.-A.L.); (Y.Y.); (M.-H.C.)
- Crop Biotech Institute, Kyung Hee University, Yongin 17104, Korea
- Correspondence:
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Hik36-Hik43 and Rre6 act as a two-component regulatory system to control cell aggregation in Synechocystis sp. PCC6803. Sci Rep 2020; 10:19405. [PMID: 33173131 PMCID: PMC7656254 DOI: 10.1038/s41598-020-76264-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 10/12/2020] [Indexed: 11/08/2022] Open
Abstract
In response to environmental stress the model cyanobacterium, Synechocystis sp. PCC6803 can switch from a planktonic state to autoaggregation and biofilm formation. The precise mechanism of this transition remains unknown. Here we investigated the role of a candidate two-component regulatory system (TCS) in controlling morphological changes, as a way to understand the intermediate molecular steps that are part of the signaling pathway. A bacterial two-hybrid assay showed that the response regulator Rre6 formed a TCS together with a split histidine kinase consisting of Hik36 and Hik43. Individual disruption mutants displayed autoaggregation in a static culture. In contrast, unlike in the wild type, high salinity did not induce biofilm formation in Δhik36, Δhik43 and Δrre6. The expression levels of exopolysaccharide (EPS) production genes were higher in Δhik36 and Δhik43, compared with the wild type, but lower in Δrre6, suggesting that the TCS regulated EPS production in Synechocystis. Rre6 interacted physically with the motor protein PilT2, that is a component of the type IV pilus system. This interaction was enhanced in a phosphomimic version of Rre6. Taken together, Hik36-Hik43-Rre6 function as an upstream component of the pili-related signal transduction cascade and control the prevention of cell adhesion and biofilm formation.
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Graham KJ, Burrows LL. More than a feeling: microscopy approaches to understanding surface-sensing mechanisms. J Bacteriol 2020; 203:JB.00492-20. [PMID: 33077631 PMCID: PMC8095462 DOI: 10.1128/jb.00492-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The mechanisms by which bacteria sense and respond to surface attachment have long been a mystery. Our understanding of the structure and dynamics of bacterial appendages, notably type IV pili (T4P), provided new insights into the potential ways that bacteria sense surfaces. T4P are ubiquitous, retractable hair-like adhesins that until recently were difficult to image in the absence of fixation due to their nanoscale size. This review focuses on recent microscopy innovations used to visualize T4P in live cells to reveal the dynamics of their retraction and extension. We discuss recently proposed mechanisms by which T4P facilitate bacterial surface sensing, including the role of surface-exposed PilY1, two-component signal transduction pathways, force-induced structural modifications of the major pilin, and altered dynamics of the T4P motor complex.
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Affiliation(s)
- Katherine J Graham
- Department of Biochemistry and Biomedical Sciences, and the Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton ON Canada L8S4K1
| | - Lori L Burrows
- Department of Biochemistry and Biomedical Sciences, and the Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton ON Canada L8S4K1
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Overexpression of the Small RNA PA0805.1 in Pseudomonas aeruginosa Modulates the Expression of a Large Set of Genes and Proteins, Resulting in Altered Motility, Cytotoxicity, and Tobramycin Resistance. mSystems 2020; 5:5/3/e00204-20. [PMID: 32430407 PMCID: PMC7253367 DOI: 10.1128/msystems.00204-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
P. aeruginosa is an opportunistic pathogen of humans. With roughly 10% of its genes encoding transcriptional regulators, and hundreds of small noncoding RNAs (sRNAs) interspersed throughout the genome, P. aeruginosa is able to fine-tune its response to adapt and survive in the host and resist antimicrobial agents. Understanding mechanisms of genetic regulation is therefore crucial to combat pathogenesis. The previously uncharacterized sRNA PA0805.1 was overexpressed in P. aeruginosa strain PAO1, resulting in decreased motility, increased adherence, cytotoxicity, and tobramycin resistance. In contrast, a ΔPA0805.1 deletion mutant had increased susceptibility to tobramycin under swarming conditions. Omic approaches uncovered 1,121 transcriptomic and 258 proteomic changes in the overexpression strain compared with the empty-vector strain, which included 106 regulatory factors. Downstream of these regulators were upregulated adherence factors, multidrug efflux systems, and virulence factors in both transcriptomics and proteomics. This study provides insights into the role of the sRNA PA0805.1 in modulating bacterial adaptations. Pseudomonas aeruginosa is a motile species that initiates swarming motility in response to specific environmental cues, i.e., a semisolid surface with amino acids as a nitrogen source (relevant to the human lung). Swarming is an intricately regulated process, but to date posttranscriptional regulation has not been extensively investigated. Small noncoding RNAs (sRNAs) are hypothesized to play posttranscriptional regulatory roles, largely through suppression of translation, and we previously demonstrated 20 sRNA species that were dysregulated under swarming conditions. One of these, sRNA PA0805.1 (which was 5-fold upregulated under swarming conditions), when cloned, transformed into wild-type (WT) PAO1, and overexpressed, led to broad phenotypic changes, including reduced swarming, swimming, and twitching motilities, as well as increased adherence, cytotoxicity, and tobramycin resistance. A ΔPA0805.1 deletion mutant was more susceptible to tobramycin than the WT under swarming conditions. The strain overexpressing PA0805.1 was compared to the empty-vector strain by transcriptome sequencing (RNA-Seq) and proteomics under swarming conditions to determine sRNA targets. Broad transcriptional and proteomic profiles showed 1,121 differentially expressed genes and 258 proteins with significantly different abundance. Importantly, these included 106 transcriptional regulators, two-component regulatory systems, and sigma and anti-sigma factors. Downstream of these regulators were found downregulated type IV pilus genes, many upregulated adherence and virulence factors, and two multidrug efflux systems, mexXY and mexGHI-opmD. Therefore, the sRNA PA0805.1 appears to be a global regulator that influences diverse bacterial lifestyles, most likely through a regulatory cascade. IMPORTANCEP. aeruginosa is an opportunistic pathogen of humans. With roughly 10% of its genes encoding transcriptional regulators, and hundreds of small noncoding RNAs (sRNAs) interspersed throughout the genome, P. aeruginosa is able to fine-tune its response to adapt and survive in the host and resist antimicrobial agents. Understanding mechanisms of genetic regulation is therefore crucial to combat pathogenesis. The previously uncharacterized sRNA PA0805.1 was overexpressed in P. aeruginosa strain PAO1, resulting in decreased motility, increased adherence, cytotoxicity, and tobramycin resistance. In contrast, a ΔPA0805.1 deletion mutant had increased susceptibility to tobramycin under swarming conditions. Omic approaches uncovered 1,121 transcriptomic and 258 proteomic changes in the overexpression strain compared with the empty-vector strain, which included 106 regulatory factors. Downstream of these regulators were upregulated adherence factors, multidrug efflux systems, and virulence factors in both transcriptomics and proteomics. This study provides insights into the role of the sRNA PA0805.1 in modulating bacterial adaptations.
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Beeby M, Ferreira JL, Tripp P, Albers SV, Mitchell DR. Propulsive nanomachines: the convergent evolution of archaella, flagella and cilia. FEMS Microbiol Rev 2020; 44:253-304. [DOI: 10.1093/femsre/fuaa006] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 03/06/2020] [Indexed: 02/06/2023] Open
Abstract
ABSTRACT
Echoing the repeated convergent evolution of flight and vision in large eukaryotes, propulsive swimming motility has evolved independently in microbes in each of the three domains of life. Filamentous appendages – archaella in Archaea, flagella in Bacteria and cilia in Eukaryotes – wave, whip or rotate to propel microbes, overcoming diffusion and enabling colonization of new environments. The implementations of the three propulsive nanomachines are distinct, however: archaella and flagella rotate, while cilia beat or wave; flagella and cilia assemble at their tips, while archaella assemble at their base; archaella and cilia use ATP for motility, while flagella use ion-motive force. These underlying differences reflect the tinkering required to evolve a molecular machine, in which pre-existing machines in the appropriate contexts were iteratively co-opted for new functions and whose origins are reflected in their resultant mechanisms. Contemporary homologies suggest that archaella evolved from a non-rotary pilus, flagella from a non-rotary appendage or secretion system, and cilia from a passive sensory structure. Here, we review the structure, assembly, mechanism and homologies of the three distinct solutions as a foundation to better understand how propulsive nanomachines evolved three times independently and to highlight principles of molecular evolution.
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Affiliation(s)
- Morgan Beeby
- Department of Life Sciences, Frankland Road, Imperial College of London, London, SW7 2AZ, UK
| | - Josie L Ferreira
- Department of Life Sciences, Frankland Road, Imperial College of London, London, SW7 2AZ, UK
| | - Patrick Tripp
- Molecular Biology of Archaea, Institute of Biology, University of Freiburg, Schaenzlestrasse 1, 79211 Freiburg, Germany
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Institute of Biology, University of Freiburg, Schaenzlestrasse 1, 79211 Freiburg, Germany
| | - David R Mitchell
- Department of Cell and Developmental Biology, SUNY Upstate Medical University, 750 E. Adams St., Syracuse, NY 13210, USA
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Abstract
Twitching and swimming are two bacterial movements governed by pili and flagella. The present work identifies for the first time in the Gram-negative plant pathogen Ralstonia solanacearum a pilus-mediated chemotaxis pathway analogous to that governing flagellum-mediated chemotaxis. We show that regulatory genes in this pathway control all of the phenotypes related to pili, including twitching motility, natural transformation, and biofilm formation, and are also directly implicated in virulence, mainly during the first steps of the plant infection. Our results show that pili have a higher impact than flagella on the interaction of R. solanacearum with tomato plants and reveal new types of cross-talk between the swimming and twitching motility phenotypes: enhanced swimming in bacteria lacking pili and a role for the flagellum in root attachment. Ralstonia solanacearum is a bacterial plant pathogen causing important economic losses worldwide. In addition to the polar flagella responsible for swimming motility, this pathogen produces type IV pili (TFP) that govern twitching motility, a flagellum-independent movement on solid surfaces. The implication of chemotaxis in plant colonization, through the control flagellar rotation by the proteins CheW and CheA, has been previously reported in R. solanacearum. In this work, we have identified in this bacterium homologues of the Pseudomonas aeruginosapilI and chpA genes, suggested to play roles in TFP-associated motility analogous to those played by the cheW and cheA genes, respectively. We demonstrate that R. solanacearum strains with a deletion of the pilI or the chpA coding region show normal swimming and chemotaxis but altered biofilm formation and reduced twitching motility, transformation efficiency, and root attachment. Furthermore, these mutants displayed wild-type growth in planta and impaired virulence on tomato plants after soil-drench inoculations but not when directly applied to the xylem. Comparison with deletion mutants for pilA and fliC—encoding the major pilin and flagellin subunits, respectively—showed that both twitching and swimming are required for plant colonization and full virulence. This work proves for the first time the functionality of a pilus-mediated pathway encoded by pil-chp genes in R. solanacearum, demonstrating that pilI and chpA genes are bona fide motility regulators controlling twitching motility and its three related phenotypes: virulence, natural transformation, and biofilm formation. IMPORTANCE Twitching and swimming are two bacterial movements governed by pili and flagella. The present work identifies for the first time in the Gram-negative plant pathogen Ralstonia solanacearum a pilus-mediated chemotaxis pathway analogous to that governing flagellum-mediated chemotaxis. We show that regulatory genes in this pathway control all of the phenotypes related to pili, including twitching motility, natural transformation, and biofilm formation, and are also directly implicated in virulence, mainly during the first steps of the plant infection. Our results show that pili have a higher impact than flagella on the interaction of R. solanacearum with tomato plants and reveal new types of cross-talk between the swimming and twitching motility phenotypes: enhanced swimming in bacteria lacking pili and a role for the flagellum in root attachment.
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Mechanomicrobiology: how bacteria sense and respond to forces. Nat Rev Microbiol 2020; 18:227-240. [DOI: 10.1038/s41579-019-0314-2] [Citation(s) in RCA: 99] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/06/2019] [Indexed: 12/26/2022]
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Chen H, De La Fuente L. Calcium transcriptionally regulates movement, recombination and other functions of Xylella fastidiosa under constant flow inside microfluidic chambers. Microb Biotechnol 2019; 13:548-561. [PMID: 31729188 PMCID: PMC7017821 DOI: 10.1111/1751-7915.13512] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 10/25/2019] [Accepted: 10/28/2019] [Indexed: 01/08/2023] Open
Abstract
Xylella fastidiosa is a xylem‐limited bacterial pathogen causing devastating diseases in many economically important crops. Calcium (Ca) is a major inorganic nutrient in xylem sap that influences virulence‐related traits of this pathogen, including biofilm formation and twitching motility. This study aimed to adapt a microfluidic system, which mimics the natural habitat of X. fastidiosa, for whole transcriptome analysis under flow conditions. A microfluidic chamber with two parallel channels was used, and RNA isolated from cells grown inside the system was analysed by RNA‐Seq. Ca transcriptionally regulated the machinery of type IV pili and other genes related to pathogenicity and host adaptation. Results were compared to our previous RNA‐Seq study in biofilm cells in batch cultures (Parker et al., 2016, Environ Microbiol 18, 1620). Ca‐regulated genes in both studies belonged to similar functional categories, but the number and tendencies (up‐/downregulation) of regulated genes were different. Recombination‐related genes were upregulated by Ca, and we proved experimentally that 2 mM Ca enhances natural transformation frequency. Taken together, our results suggest that the regulatory role of Ca in X. fastidiosa acts differently during growth in flow or batch conditions, and this can correlate to the different phases of growth (planktonic and biofilm) during the infection process.
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Affiliation(s)
- Hongyu Chen
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, 36849, USA
| | - Leonardo De La Fuente
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, 36849, USA
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Limoli DH, Warren EA, Yarrington KD, Donegan NP, Cheung AL, O'Toole GA. Interspecies interactions induce exploratory motility in Pseudomonas aeruginosa. eLife 2019; 8:47365. [PMID: 31713513 PMCID: PMC6910820 DOI: 10.7554/elife.47365] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 10/30/2019] [Indexed: 11/13/2022] Open
Abstract
Microbes often live in multispecies communities where interactions among community members impact both the individual constituents and the surrounding environment. Here, we developed a system to visualize interspecies behaviors at initial encounters. By imaging two prevalent pathogens known to be coisolated from chronic illnesses, Pseudomonas aeruginosa and Staphylococcus aureus, we observed P. aeruginosa can modify surface motility in response to secreted factors from S. aureus. Upon sensing S. aureus, P. aeruginosa transitioned from collective to single-cell motility with an associated increase in speed and directedness – a behavior we refer to as ‘exploratory motility’. Explorer cells moved preferentially towards S. aureus and invaded S. aureus colonies through the action of the type IV pili. These studies reveal previously undescribed motility behaviors and lend insight into how P. aeruginosa senses and responds to other species. Identifying strategies to harness these interactions may open avenues for new antimicrobial strategies.
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Affiliation(s)
- Dominique H Limoli
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, United States.,Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, United States
| | - Elizabeth A Warren
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, United States
| | - Kaitlin D Yarrington
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, United States
| | - Niles P Donegan
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, United States
| | - Ambrose L Cheung
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, United States
| | - George A O'Toole
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, United States
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DMBT1 inhibition of Pseudomonas aeruginosa twitching motility involves its N-glycosylation and cannot be conferred by the Scavenger Receptor Cysteine-Rich bacteria-binding peptide domain. Sci Rep 2019; 9:13146. [PMID: 31511582 PMCID: PMC6739395 DOI: 10.1038/s41598-019-49543-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 08/22/2019] [Indexed: 01/18/2023] Open
Abstract
The scavenging capacity of glycoprotein DMBT1 helps defend mucosal epithelia against microbes. DMBT1 binding to multiple bacterial species involves its conserved Scavenger Receptor Cysteine-Rich (SRCR) domains, localized to a 16-mer consensus sequence peptide, SRCRP2. Previously, we showed that DMBT1 bound Pseudomonas aeruginosa pili, and inhibited twitching motility, a pilus-mediated movement important for virulence. Here, we determined molecular characteristics required for twitching motility inhibition. Heat-denatured DMBT1 lost capacity to inhibit twitching motility and showed reduced pili binding (~40%). Size-exclusion chromatography of Lys-C-digested native DMBT1 showed that only high-Mw fractions retained activity, suggesting involvement of the N-terminal containing repeated SRCR domains with glycosylated SRCR-Interspersed Domains (SIDs). However, individual or pooled consensus sequence peptides (SRCRPs 1 to 7) showed no activity and did not bind P. aeruginosa pili; nor did recombinant DMBT1 (aa 1–220) or another SRCR-rich glycoprotein, CD163. Enzymatic de-N-glycosylation of DMBT1, but not de-O-glycosylation, reduced its capacity to inhibit twitching motility (~57%), without reducing pili binding. Therefore, DMBT1 inhibition of P. aeruginosa twitching motility involves its N-glycosylation, its pili-binding capacity is insufficient, and it cannot be conferred by the SRCR bacteria-binding peptide domain, either alone or mixed with other unlinked SRCRPs, suggesting an additional mechanism for DMBT1-mediated mucosal defense.
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Adams DW, Pereira JM, Stoudmann C, Stutzmann S, Blokesch M. The type IV pilus protein PilU functions as a PilT-dependent retraction ATPase. PLoS Genet 2019; 15:e1008393. [PMID: 31525185 PMCID: PMC6762196 DOI: 10.1371/journal.pgen.1008393] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 09/26/2019] [Accepted: 08/29/2019] [Indexed: 11/18/2022] Open
Abstract
Type IV pili are dynamic cell surface appendages found throughout the bacteria. The ability of these structures to undergo repetitive cycles of extension and retraction underpins their crucial roles in adhesion, motility and natural competence for transformation. In the best-studied systems a dedicated retraction ATPase PilT powers pilus retraction. Curiously, a second presumed retraction ATPase PilU is often encoded immediately downstream of pilT. However, despite the presence of two potential retraction ATPases, pilT deletions lead to a total loss of pilus function, raising the question of why PilU fails to take over. Here, using the DNA-uptake pilus and mannose-sensitive haemagglutinin (MSHA) pilus of Vibrio cholerae as model systems, we show that inactivated PilT variants, defective for either ATP-binding or hydrolysis, have unexpected intermediate phenotypes that are PilU-dependent. In addition to demonstrating that PilU can function as a bona fide retraction ATPase, we go on to make the surprising discovery that PilU functions exclusively in a PilT-dependent manner and identify a naturally occurring pandemic V. cholerae PilT variant that renders PilU essential for pilus function. Finally, we show that Pseudomonas aeruginosa PilU also functions as a PilT-dependent retraction ATPase, providing evidence that the functional coupling between PilT and PilU could be a widespread mechanism for optimal pilus retraction.
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Affiliation(s)
- David W. Adams
- Laboratory of Molecular Microbiology, Global Health Institute, School of Life Sciences, EPFL-SV-UPBLO, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH, Lausanne, Switzerland
| | - Jorge M. Pereira
- Laboratory of Molecular Microbiology, Global Health Institute, School of Life Sciences, EPFL-SV-UPBLO, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH, Lausanne, Switzerland
| | - Candice Stoudmann
- Laboratory of Molecular Microbiology, Global Health Institute, School of Life Sciences, EPFL-SV-UPBLO, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH, Lausanne, Switzerland
| | - Sandrine Stutzmann
- Laboratory of Molecular Microbiology, Global Health Institute, School of Life Sciences, EPFL-SV-UPBLO, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH, Lausanne, Switzerland
| | - Melanie Blokesch
- Laboratory of Molecular Microbiology, Global Health Institute, School of Life Sciences, EPFL-SV-UPBLO, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH, Lausanne, Switzerland
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Lee YS, Park W. Enhanced calcium carbonate-biofilm complex formation by alkali-generating Lysinibacillus boronitolerans YS11 and alkaliphilic Bacillus sp. AK13. AMB Express 2019; 9:49. [PMID: 30976947 PMCID: PMC6459448 DOI: 10.1186/s13568-019-0773-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 04/02/2019] [Indexed: 12/11/2022] Open
Abstract
Microbially induced calcium carbonate (CaCO3) precipitation (MICP) is a process where microbes induce condition favorable for CaCO3 formation through metabolic activities by increasing the pH or carbonate ions when calcium is near. The molecular and ecological basis of CaCO3 precipitating (CCP) bacteria has been poorly illuminated. Here, we showed that increased pH levels by deamination of amino acids is a driving force toward MICP using alkalitolerant Lysinibacillus boronitolerans YS11 as a model species of non-ureolytic CCP bacteria. This alkaline generation also facilitates the growth of neighboring alkaliphilic Bacillus sp. AK13, which could alter characteristics of MICP by changing the size and shape of CaCO3 minerals. Furthermore, we showed CaCO3 that precipitates earlier in an experiment modifies membrane rigidity of YS11 strain via upregulation of branched chain fatty acid synthesis. This work closely examines MICP conditions by deamination and the effect of MICP on cell membrane rigidity and crystal formation for the first time.
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Rosenzweig R, Perinbam K, Ly VK, Ahrar S, Siryaporn A, Yee AF. Nanopillared Surfaces Disrupt Pseudomonas aeruginosa Mechanoresponsive Upstream Motility. ACS APPLIED MATERIALS & INTERFACES 2019; 11:10532-10539. [PMID: 30789254 DOI: 10.1021/acsami.8b22262] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Pseudomonas aeruginosa is an opportunistic, multidrug-resistant, human pathogen that forms biofilms in environments with fluid flow, such as the lungs of cystic fibrosis patients, industrial pipelines, and medical devices. P. aeruginosa twitches upstream on surfaces by the cyclic extension and retraction of its mechanoresponsive type IV pili motility appendages. The prevention of upstream motility, host invasion, and infectious biofilm formation in fluid flow systems remains an unmet challenge. Here, we describe the design and application of scalable nanopillared surface structures fabricated using nanoimprint lithography that reduce upstream motility and colonization by P. aeruginosa. We used flow channels to induce shear stress typically found in catheter tubes and microscopy analysis to investigate the impact of nanopillared surfaces with different packing fractions on upstream motility trajectory, displacement, velocity, and surface attachment. We found that densely packed, subcellular nanopillared surfaces, with pillar periodicities ranging from 200 to 600 nm and widths ranging from 70 to 215 nm, inhibit the mechanoresponsive upstream motility and surface attachment. This bacteria-nanostructured surface interface effect allows us to tailor surfaces with specific nanopillared geometries for disrupting cell motility and attachment in fluid flow systems.
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Abstract
Complex chemosensory systems control multiple biological functions in bacteria, such as chemotaxis, gene regulation, and cell cycle progression. Many species contain more than one chemosensory system per genome, but little is known about their potential interplay. In this study, we reveal cross talk between two chemosensory pathways that modulate chemotaxis and biofilm formation in Comamonas testosteroni We demonstrate that some chemoreceptors that govern chemotaxis also contribute to biofilm formation and these chemoreceptors can physically interact with components of both pathways. Finally, we show that the chemotaxis histidine kinase CheA can phosphorylate not only its cognate response regulator CheY2 but also one of the response regulators from the pathway mediating biofilm formation, FlmD. The phosphoryl group transfer from CheA to CheY2 is much faster than that from CheA to FlmD, which is consistent with chemotaxis being a fast response and biofilm formation being a much slower developmental process. We propose that cross talk between chemosensory pathways may play a role in coordination of complex behaviors in bacteria.IMPORTANCE In many bacteria, two or more homologous chemosensory pathways control several cellular functions, such as motility and gene regulation, in response to changes in the cell's microenvironment. Cross talk between signal transduction systems is poorly understood; while generally it is considered to be undesired, in some instances it might be beneficial for coregulation of complex behaviors. We demonstrate that several receptors from the pathway controlling motility can physically interact with downstream components of the pathway controlling biofilm formation. We further show that a kinase from the pathway controlling motility can also phosphorylate a response regulator from the pathway controlling biofilm formation. We propose that cross talk between two chemosensory pathways might be involved in coordination of two types of cell behavior-chemotaxis and biofilm formation.
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