1
|
Chen G, Fanouraki G, Anandhi Rangarajan A, Winkelman BT, Winkelman JT, Waters CM, Mukherjee S. Combinatorial control of Pseudomonas aeruginosa biofilm development by quorum-sensing and nutrient-sensing regulators. mSystems 2024; 9:e0037224. [PMID: 39140783 PMCID: PMC11406991 DOI: 10.1128/msystems.00372-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 06/23/2024] [Indexed: 08/15/2024] Open
Abstract
The human pathogen Pseudomonas aeruginosa, a leading cause of hospital-acquired infections, inhabits and forms sessile antibiotic-resistant communities called biofilms in a wide range of biotic and abiotic environments. In this study, we examined how two global sensory signaling pathways-the RhlR quorum-sensing system and the CbrA/CbrB nutritional adaptation system-intersect to control biofilm development. Previous work has shown that individually these two systems repress biofilm formation. Here, we used biofilm analyses, RNA-seq, and reporter assays to explore the combined effect of information flow through RhlR and CbrA on biofilm development. We find that the ΔrhlRΔcbrA double mutant exhibits a biofilm morphology and an associated transcriptional response distinct from wildtype and the parent ΔrhlR and ΔcbrA mutants indicating codominance of each signaling pathway. The ΔrhlRΔcbrA mutant gains suppressor mutations that allow biofilm expansion; these mutations map to the crc gene resulting in loss of function of the carbon catabolite repression protein Crc. Furthermore, the combined absence of RhlR and CbrA leads to a drastic reduction in the abundance of the Crc antagonist small RNA CrcZ. Thus, CrcZ acts as the molecular convergence point for quorum- and nutrient-sensing cues. We find that in the absence of antagonism by CrcZ, Crc promotes the expression of biofilm matrix components-Pel exopolysaccharide, and CupB and CupC fimbriae. Therefore, this study uncovers a regulatory link between nutritional adaption and quorum sensing with potential implications for anti-biofilm targeting strategies.IMPORTANCEBacteria often form multicellular communities encased in an extracytoplasmic matrix called biofilms. Biofilm development is controlled by various environmental stimuli that are decoded and converted into appropriate cellular responses. To understand how information from two distinct stimuli is integrated, we used biofilm formation in the human pathogen Pseudomonas aeruginosa as a model and studied the intersection of two global sensory signaling pathways-quorum sensing and nutritional adaptation. Global transcriptomics on biofilm cells and reporter assays suggest parallel regulation of biofilms by each pathway that converges on the abundance of a small RNA antagonist of the carbon catabolite repression protein, Crc. We find a new role of Crc as it modulates the expression of biofilm matrix components in response to the environment. These results expand our understanding of the genetic regulatory strategies that allow P. aeruginosa to successfully develop biofilm communities.
Collapse
Affiliation(s)
- Gong Chen
- Department of Molecular Genetics & Cell Biology, The University of Chicago, Chicago, Illinois, USA
| | - Georgia Fanouraki
- Department of Molecular Genetics & Cell Biology, The University of Chicago, Chicago, Illinois, USA
| | | | | | - Jared T Winkelman
- Department of Molecular Genetics & Cell Biology, The University of Chicago, Chicago, Illinois, USA
| | - Christopher M Waters
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Sampriti Mukherjee
- Department of Molecular Genetics & Cell Biology, The University of Chicago, Chicago, Illinois, USA
| |
Collapse
|
2
|
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.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Sylvie Chevalier
- Univ Rouen Normandie, Univ Caen Normandie, Normandie Univ, CBSA UR 4312, F-76000 Rouen, France
| |
Collapse
|
3
|
Zyla DS, Wiegand T, Bachmann P, Zdanowicz R, Giese C, Meier BH, Waksman G, Hospenthal MK, Glockshuber R. The assembly platform FimD is required to obtain the most stable quaternary structure of type 1 pili. Nat Commun 2024; 15:3032. [PMID: 38589417 PMCID: PMC11001860 DOI: 10.1038/s41467-024-47212-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 03/22/2024] [Indexed: 04/10/2024] Open
Abstract
Type 1 pili are important virulence factors of uropathogenic Escherichia coli that mediate bacterial attachment to epithelial cells in the urinary tract. The pilus rod is comprised of thousands of copies of the main structural subunit FimA and is assembled in vivo by the assembly platform FimD. Although type 1 pilus rods can self-assemble from FimA in vitro, this reaction is slower and produces structures with lower kinetic stability against denaturants compared to in vivo-assembled rods. Our study reveals that FimD-catalysed in vitro-assembled type 1 pilus rods attain a similar stability as pilus rods assembled in vivo. Employing structural, biophysical and biochemical analyses, we show that in vitro assembly reactions lacking FimD produce pilus rods with structural defects, reducing their stability against dissociation. Overall, our results indicate that FimD is not only required for the catalysis of pilus assembly, but also to control the assembly of the most stable quaternary structure.
Collapse
Affiliation(s)
- Dawid S Zyla
- Institute of Molecular Biology and Biophysics, ETH Zürich, Otto-Stern-Weg 5, 8093, Zürich, Switzerland
- La Jolla Institute for Immunology, 9420 Athena Cir, La Jolla, CA, 92037, USA
| | - Thomas Wiegand
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093, Zürich, Switzerland
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 2, 52074, Aachen, Germany
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470, Mülheim/Ruhr, Germany
| | - Paul Bachmann
- Institute of Molecular Biology and Biophysics, ETH Zürich, Otto-Stern-Weg 5, 8093, Zürich, Switzerland
| | - Rafal Zdanowicz
- Institute of Molecular Biology and Biophysics, ETH Zürich, Otto-Stern-Weg 5, 8093, Zürich, Switzerland
| | - Christoph Giese
- Institute of Molecular Biology and Biophysics, ETH Zürich, Otto-Stern-Weg 5, 8093, Zürich, Switzerland
| | - Beat H Meier
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093, Zürich, Switzerland
| | - Gabriel Waksman
- Institute of Structural and Molecular Biology, University College London and Birkbeck, London, WC1E 7HX, UK
| | - Manuela K Hospenthal
- Institute of Molecular Biology and Biophysics, ETH Zürich, Otto-Stern-Weg 5, 8093, Zürich, Switzerland.
- Institute of Structural and Molecular Biology, University College London and Birkbeck, London, WC1E 7HX, UK.
| | - Rudi Glockshuber
- Institute of Molecular Biology and Biophysics, ETH Zürich, Otto-Stern-Weg 5, 8093, Zürich, Switzerland
| |
Collapse
|
4
|
Böhning J, Tarafder AK, Bharat TA. The role of filamentous matrix molecules in shaping the architecture and emergent properties of bacterial biofilms. Biochem J 2024; 481:245-263. [PMID: 38358118 PMCID: PMC10903470 DOI: 10.1042/bcj20210301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 01/29/2024] [Accepted: 01/31/2024] [Indexed: 02/16/2024]
Abstract
Numerous bacteria naturally occur within spatially organised, multicellular communities called biofilms. Moreover, most bacterial infections proceed with biofilm formation, posing major challenges to human health. Within biofilms, bacterial cells are embedded in a primarily self-produced extracellular matrix, which is a defining feature of all biofilms. The biofilm matrix is a complex, viscous mixture primarily composed of polymeric substances such as polysaccharides, filamentous protein fibres, and extracellular DNA. The structured arrangement of the matrix bestows bacteria with beneficial emergent properties that are not displayed by planktonic cells, conferring protection against physical and chemical stresses, including antibiotic treatment. However, a lack of multi-scale information at the molecular level has prevented a better understanding of this matrix and its properties. Here, we review recent progress on the molecular characterisation of filamentous biofilm matrix components and their three-dimensional spatial organisation within biofilms.
Collapse
Affiliation(s)
- Jan Böhning
- Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, U.K
| | - Abul K. Tarafder
- Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, U.K
| | - Tanmay A.M. Bharat
- Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, U.K
| |
Collapse
|
5
|
Ahmad I, Nadeem A, Mushtaq F, Zlatkov N, Shahzad M, Zavialov AV, Wai SN, Uhlin BE. Csu pili dependent biofilm formation and virulence of Acinetobacter baumannii. NPJ Biofilms Microbiomes 2023; 9:101. [PMID: 38097635 PMCID: PMC10721868 DOI: 10.1038/s41522-023-00465-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 11/23/2023] [Indexed: 12/17/2023] Open
Abstract
Acinetobacter baumannii has emerged as one of the most common extensive drug-resistant nosocomial bacterial pathogens. Not only can the bacteria survive in hospital settings for long periods, but they are also able to resist adverse conditions. However, underlying regulatory mechanisms that allow A. baumannii to cope with these conditions and mediate its virulence are poorly understood. Here, we show that bi-stable expression of the Csu pili, along with the production of poly-N-acetyl glucosamine, regulates the formation of Mountain-like biofilm-patches on glass surfaces to protect bacteria from the bactericidal effect of colistin. Csu pilus assembly is found to be an essential component of mature biofilms formed on glass surfaces and of pellicles. By using several microscopic techniques, we show that clinical isolates of A. baumannii carrying abundant Csu pili mediate adherence to epithelial cells. In addition, Csu pili suppressed surface-associated motility but enhanced colonization of bacteria into the lungs, spleen, and liver in a mouse model of systemic infection. The screening of c-di-GMP metabolizing protein mutants of A. baumannii 17978 for the capability to adhere to epithelial cells led us to identify GGDEF/EAL protein AIS_2337, here denoted PdeB, as a major regulator of Csu pili-mediated virulence and biofilm formation. Moreover, PdeB was found to be involved in the type IV pili-regulated robustness of surface-associated motility. Our findings suggest that the Csu pilus is not only a functional component of mature A. baumannii biofilms but also a major virulence factor promoting the initiation of disease progression by mediating bacterial adherence to epithelial cells.
Collapse
Affiliation(s)
- Irfan Ahmad
- Department of Molecular Biology and Umeå Centre for Microbial Research (UCMR), Umeå University, SE-90187, Umeå, Sweden.
- Institute of Biomedical and Allied Health Sciences, University of Health Sciences, Lahore, Pakistan.
| | - Aftab Nadeem
- Department of Molecular Biology and Umeå Centre for Microbial Research (UCMR), Umeå University, SE-90187, Umeå, Sweden
| | - Fizza Mushtaq
- Department of Molecular Biology and Umeå Centre for Microbial Research (UCMR), Umeå University, SE-90187, Umeå, Sweden
- Institute of Biomedical and Allied Health Sciences, University of Health Sciences, Lahore, Pakistan
| | - Nikola Zlatkov
- Department of Molecular Biology and Umeå Centre for Microbial Research (UCMR), Umeå University, SE-90187, Umeå, Sweden
| | - Muhammad Shahzad
- Department of Pharmacology, University of Health Sciences, Lahore, Pakistan
| | - Anton V Zavialov
- Department of Biochemistry, University of Turku, Tykistökatu 6A, 20520, Turku, Finland
| | - Sun Nyunt Wai
- Department of Molecular Biology and Umeå Centre for Microbial Research (UCMR), Umeå University, SE-90187, Umeå, Sweden
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, SE-90187, Umeå, Sweden
| | - Bernt Eric Uhlin
- Department of Molecular Biology and Umeå Centre for Microbial Research (UCMR), Umeå University, SE-90187, Umeå, Sweden
| |
Collapse
|
6
|
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.
Collapse
|
7
|
Caldwell M, Hughes M, Wei F, Ngo C, Pascua R, Pugazhendhi AS, Coathup MJ. Promising applications of D-amino acids in periprosthetic joint infection. Bone Res 2023; 11:14. [PMID: 36894568 PMCID: PMC9998894 DOI: 10.1038/s41413-023-00254-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 02/02/2023] [Accepted: 02/10/2023] [Indexed: 03/11/2023] Open
Abstract
Due to the rise in our aging population, a disproportionate demand for total joint arthroplasty (TJA) in the elderly is forecast. Periprosthetic joint infection (PJI) represents one of the most challenging complications that can occur following TJA, and as the number of primary and revision TJAs continues to rise, an increasing PJI burden is projected. Despite advances in operating room sterility, antiseptic protocols, and surgical techniques, approaches to prevent and treat PJI remain difficult, primarily due to the formation of microbial biofilms. This difficulty motivates researchers to continue searching for an effective antimicrobial strategy. The dextrorotatory-isoforms of amino acids (D-AAs) are essential components of peptidoglycan within the bacterial cell wall, providing strength and structural integrity in a diverse range of species. Among many tasks, D-AAs regulate cell morphology, spore germination, and bacterial survival, evasion, subversion, and adhesion in the host immune system. When administered exogenously, accumulating data have demonstrated that D-AAs play a pivotal role against bacterial adhesion to abiotic surfaces and subsequent biofilm formation; furthermore, D-AAs have substantial efficacy in promoting biofilm disassembly. This presents D-AAs as promising and novel targets for future therapeutic approaches. Despite their emerging antibacterial efficacy, their role in disrupting PJI biofilm formation, the disassembly of established TJA biofilm, and the host bone tissue response remains largely unexplored. This review aims to examine the role of D-AAs in the context of TJAs. Data to date suggest that D-AA bioengineering may serve as a promising future strategy in the prevention and treatment of PJI.
Collapse
Affiliation(s)
- Matthew Caldwell
- Biionix Cluster & College of Medicine, University of Central Florida, 6900 Lake Nona Blvd, Orlando, FL, 32827, USA
| | - Megan Hughes
- School of Biosciences, Cardiff University, CF10 3AT, Wales, UK
| | - Fei Wei
- Biionix Cluster & College of Medicine, University of Central Florida, 6900 Lake Nona Blvd, Orlando, FL, 32827, USA
| | - Christopher Ngo
- Biionix Cluster & College of Medicine, University of Central Florida, 6900 Lake Nona Blvd, Orlando, FL, 32827, USA
| | - Raven Pascua
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, 6900 Lake Nona Blvd, Orlando, FL, 32827, USA
| | - Abinaya Sindu Pugazhendhi
- Biionix Cluster & College of Medicine, University of Central Florida, 6900 Lake Nona Blvd, Orlando, FL, 32827, USA
| | - Melanie J Coathup
- Biionix Cluster & College of Medicine, University of Central Florida, 6900 Lake Nona Blvd, Orlando, FL, 32827, USA.
| |
Collapse
|
8
|
Adamer MF, Brüningk SC, Tejada-Arranz A, Estermann F, Basler M, Borgwardt K. reComBat: batch-effect removal in large-scale multi-source gene-expression data integration. BIOINFORMATICS ADVANCES 2022; 2:vbac071. [PMID: 36699372 PMCID: PMC9710604 DOI: 10.1093/bioadv/vbac071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/01/2022] [Accepted: 09/26/2022] [Indexed: 01/28/2023]
Abstract
Motivation With the steadily increasing abundance of omics data produced all over the world under vastly different experimental conditions residing in public databases, a crucial step in many data-driven bioinformatics applications is that of data integration. The challenge of batch-effect removal for entire databases lies in the large number of batches and biological variation, which can result in design matrix singularity. This problem can currently not be solved satisfactorily by any common batch-correction algorithm. Results We present reComBat, a regularized version of the empirical Bayes method to overcome this limitation and benchmark it against popular approaches for the harmonization of public gene-expression data (both microarray and bulkRNAsq) of the human opportunistic pathogen Pseudomonas aeruginosa. Batch-effects are successfully mitigated while biologically meaningful gene-expression variation is retained. reComBat fills the gap in batch-correction approaches applicable to large-scale, public omics databases and opens up new avenues for data-driven analysis of complex biological processes beyond the scope of a single study. Availability and implementation The code is available at https://github.com/BorgwardtLab/reComBat, all data and evaluation code can be found at https://github.com/BorgwardtLab/batchCorrectionPublicData. Supplementary information Supplementary data are available at Bioinformatics Advances online.
Collapse
Affiliation(s)
| | | | | | | | - Marek Basler
- Biozentrum, University of Basel, Basel 4056, Switzerland
| | - Karsten Borgwardt
- Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland,Swiss Institute for Bioinformatics (SIB), Lausanne 1015, Switzerland
| |
Collapse
|
9
|
Romero M, Mayer C, Heeb S, Wattanavaekin K, Cámara M, Otero A, Williams P. Mushroom-shaped structures formed in Acinetobacter baumannii biofilms grown in a roller bioreactor are associated with quorum sensing-dependent Csu-pilus assembly. Environ Microbiol 2022; 24:4329-4339. [PMID: 35352448 PMCID: PMC9790458 DOI: 10.1111/1462-2920.15985] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 02/11/2022] [Accepted: 03/21/2022] [Indexed: 12/31/2022]
Abstract
There is currently a need to develop simple biofilm models that facilitate investigation of the architecture/biology of mature bacterial biofilms in a consistent/standardized manner given their environmental and clinical importance and the need for new anti-biofilm interventions. This study introduces a novel biofilm culture system termed the rolling biofilm bioreactor (RBB). This easily operated system allows adherent microbial cells to be repeatedly exposed to air/solid/liquid interfaces optimizing biofilm growth. The RBB was exploited to investigate biofilm formation in Acinetobacter baumannii. High levels of A. baumannii biofilm biomass reproducibly accumulate in the RBB and, importantly, undergo a maturation step to form large mushroom-shaped structures that had not been observed in other models. Based on image analysis of biofilm development and genetic manipulation, we show how N-acylhomoserine lactone-dependent quorum sensing (QS) impacts on biofilm differentiation, composition and antibiotic tolerance. Our results indicate that extracellular DNA (eDNA) is a key matrix component in mature Acinetobacter biofilms as the mushroom-like structures consist of dense cellular masses encased in an eDNA mesh. Moreover, this study reveals the contribution of QS to A. baumannii biofilm differentiation through Csu pilus assembly regulation. Understanding the mechanisms of structural development of mature biofilms helps to identify new biofilm eradication and removal strategies.
Collapse
Affiliation(s)
- Manuel Romero
- National Biofilms Innovation Centre, Biodiscovery Institute and School of Life SciencesUniversity of NottinghamNottinghamUK
| | - Celia Mayer
- National Biofilms Innovation Centre, Biodiscovery Institute and School of Life SciencesUniversity of NottinghamNottinghamUK,Instituto de Investigacion Sanitaria de Santiago de Compostela (IDIS)Santiago de CompostelaSpain
| | - Stephan Heeb
- National Biofilms Innovation Centre, Biodiscovery Institute and School of Life SciencesUniversity of NottinghamNottinghamUK
| | | | - Miguel Cámara
- National Biofilms Innovation Centre, Biodiscovery Institute and School of Life SciencesUniversity of NottinghamNottinghamUK
| | - Ana Otero
- Departamento de Microbioloxía e Parasitoloxía, Facultade de Bioloxía, Edificio CIBUSUniversidade de Santiago de CompostelaSantiago de CompostelaSpain
| | - Paul Williams
- National Biofilms Innovation Centre, Biodiscovery Institute and School of Life SciencesUniversity of NottinghamNottinghamUK
| |
Collapse
|
10
|
Sivakumar R, Gunasekaran P, Rajendhran J. Extracytoplasmic sigma factor AlgU contributes to fitness of Pseudomonas aeruginosa PGPR2 during corn root colonization. Mol Genet Genomics 2022; 297:1537-1552. [PMID: 35980488 DOI: 10.1007/s00438-022-01938-7] [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: 08/25/2020] [Accepted: 07/29/2022] [Indexed: 11/28/2022]
Abstract
In bacteria, sigma factors are crucial in determining the plasticity of core RNA polymerase (RNAP) while promoter recognition during transcription initiation. This process is modulated through an intricate regulatory network in response to environmental cues. Previously, an extracytoplasmic function (ECF) sigma factor, AlgU, was identified to positively influence the fitness of Pseudomonas aeruginosa PGPR2 during corn root colonization. In this study, we report that the inactivation of the algU gene encoded by PGPR2_23995 hampers the root colonization ability of PGPR2. An insertion mutant in the algU gene was constructed by allele exchange mutagenesis. The mutant strains displayed threefold decreased root colonization efficiency compared with the wild-type strain when inoculated individually and in the competition assay. The mutant strain was more sensitive to osmotic and antibiotic stresses and showed higher resistance to oxidative stress. On the other hand, the mutant strain showed increased biofilm formation on the abiotic surface, and the expression of the pelB and pslA genes involved in the biofilm matrix formation were up-regulated. In contrast, the expression of algD, responsible for alginate production, was significantly down-regulated in the mutant strain, which is directly regulated by the AlgU sigma factor. The mutant strain also displayed altered motility. The expression of RNA binding protein RsmA was also impeded in the mutant strain. Further, the transcript levels of genes associated with the type III secretion system (T3SS) were analyzed, which revealed a significant down-regulation in the mutant strain. These results collectively provide evidence for the regulatory role of the AlgU sigma factor in modulating gene expression during root colonization.
Collapse
Affiliation(s)
- Ramamoorthy Sivakumar
- Department of Genetics, School of Biological Sciences, Madurai Kamaraj University, Madurai, 625 021, India
| | | | - Jeyaprakash Rajendhran
- Department of Genetics, School of Biological Sciences, Madurai Kamaraj University, Madurai, 625 021, India.
| |
Collapse
|
11
|
Eilers K, Kuok Hoong Yam J, Morton R, Mei Hui Yong A, Brizuela J, Hadjicharalambous C, Liu X, Givskov M, Rice SA, Filloux A. Phenotypic and integrated analysis of a comprehensive Pseudomonas aeruginosa PAO1 library of mutants lacking cyclic-di-GMP-related genes. Front Microbiol 2022; 13:949597. [PMID: 35935233 PMCID: PMC9355167 DOI: 10.3389/fmicb.2022.949597] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Accepted: 06/27/2022] [Indexed: 11/13/2022] Open
Abstract
Pseudomonas aeruginosa is a Gram-negative bacterium that is able to survive and adapt in a multitude of niches as well as thrive within many different hosts. This versatility lies within its large genome of ca. 6 Mbp and a tight control in the expression of thousands of genes. Among the regulatory mechanisms widespread in bacteria, cyclic-di-GMP signaling is one which influences all levels of control. c-di-GMP is made by diguanylate cyclases and degraded by phosphodiesterases, while the intracellular level of this molecule drives phenotypic responses. Signaling involves the modification of enzymes' or proteins' function upon c-di-GMP binding, including modifying the activity of regulators which in turn will impact the transcriptome. In P. aeruginosa, there are ca. 40 genes encoding putative DGCs or PDEs. The combined activity of those enzymes should reflect the overall c-di-GMP concentration, while specific phenotypic outputs could be correlated to a given set of dgc/pde. This notion of specificity has been addressed in several studies and different strains of P. aeruginosa. Here, we engineered a mutant library for the 41 individual dgc/pde genes in P. aeruginosa PAO1. In most cases, we observed a significant to slight variation in the global c-di-GMP pool of cells grown planktonically, while several mutants display a phenotypic impact on biofilm including initial attachment and maturation. If this observation of minor changes in c-di-GMP level correlating with significant phenotypic impact appears to be true, it further supports the idea of a local vs global c-di-GMP pool. In contrast, there was little to no effect on motility, which differs from previous studies. Our RNA-seq analysis indicated that all PAO1 dgc/pde genes were expressed in both planktonic and biofilm growth conditions and our work suggests that c-di-GMP networks need to be reconstructed for each strain separately and cannot be extrapolated from one to another.
Collapse
Affiliation(s)
- Kira Eilers
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Joey Kuok Hoong Yam
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Richard Morton
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Adeline Mei Hui Yong
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Jaime Brizuela
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, United Kingdom
- Department of Medical Microbiology, Amsterdam UMC, Universitair Medische Centra, University of Amsterdam, Amsterdam, Netherlands
| | - Corina Hadjicharalambous
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, United Kingdom
- Department of Biology, Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule Zürich, Zurich, Switzerland
| | - Xianghui Liu
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Michael Givskov
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, Costerton Biofilm Center, University of Copenhagen, Copenhagen, Denmark
| | - Scott A. Rice
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Westmead and Microbiomes for One Systems Health, Melbourne, VIC, Australia
| | - Alain Filloux
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, United Kingdom
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| |
Collapse
|
12
|
The c-di-GMP Phosphodiesterase PipA (PA0285) Regulates Autoaggregation and Pf4 Bacteriophage Production in Pseudomonas aeruginosa PAO1. Appl Environ Microbiol 2022; 88:e0003922. [PMID: 35638845 DOI: 10.1128/aem.00039-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
In Pseudomonas aeruginosa PAO1, 41 genes encode proteins predicted to be involved in the production or degradation of c-di-GMP, a ubiquitous secondary messenger that regulates a variety of physiological behaviors closely related to biofilm and aggregate formation. Despite extensive effort, the entire picture of this important signaling network is still unclear, with one-third of these proteins remaining uncharacterized. Here, we show that the deletion of pipA, which produces a protein containing two PAS domains upstream of a GGDEF-EAL tandem, significantly increased the intracellular c-di-GMP level and promoted the formation of aggregates both on surfaces and in planktonic cultures. However, this regulatory effect was not contributed by either of the two classic pathways modulating biofilm formation, exopolysaccharide (EPS) overproduction or motility inhibition. Transcriptome sequencing (RNA-Seq) data revealed that the expression levels of 361 genes were significantly altered in a ΔpipA mutant strain compared to the wild type (WT), indicating the critical role of PipA in PAO1. The most remarkably downregulated genes were located on the Pf4 bacteriophage gene cluster, which corresponded to a 2-log reduction in the Pf4 phage production in the ΔpipA mutant. The sizes of aggregates in ΔpipA cultures were affected by exogenously added Pf4 phage in a concentration-dependent manner, suggesting the quantity of phage plays a part in regulating the formation of aggregates. Further analysis demonstrated that PipA is highly conserved across 83 P. aeruginosa strains. Our work therefore for the first time showed that a c-di-GMP phosphodiesterase can regulate bacteriophage production and provided new insights into the relationship between bacteriophage and bacterial aggregation. IMPORTANCE The c-di-GMP signaling pathways in P. aeruginosa are highly organized and well coordinated, with different diguanylate cyclases and phosphodiesterases playing distinct roles in a complex network. Understanding the function of each enzyme and the underlying regulatory mechanisms not only is crucial for revealing how bacteria decide the transition between motile and sessile lifestyles, but also greatly facilitates the development of new antibiofilm strategies. This work identified bacteriophage production as a novel phenotypic output controlled transcriptionally by a phosphodiesterase, PipA. Further analysis suggested that the quantity of phage may be important in regulating autoaggregation, as either a lack of phage or overproduction was associated with higher levels of aggregation. Our study therefore extended the scope of c-di-GMP-controlled phenotypes and discovered a potential signaling circuit that can be target for biofilm treatment.
Collapse
|
13
|
Filloux A. Bacterial protein secretion systems: Game of types. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35536734 DOI: 10.1099/mic.0.001193] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Protein trafficking across the bacterial envelope is a process that contributes to the organisation and integrity of the cell. It is the foundation for establishing contact and exchange between the environment and the cytosol. It helps cells to communicate with one another, whether they establish symbiotic or competitive behaviours. It is instrumental for pathogenesis and for bacteria to subvert the host immune response. Understanding the formation of envelope conduits and the manifold strategies employed for moving macromolecules across these channels is a fascinating playground. The diversity of the nanomachines involved in this process logically resulted in an attempt to classify them, which is where the protein secretion system types emerged. As our knowledge grew, so did the number of types, and their rightful nomenclature started to be questioned. While this may seem a semantic or philosophical issue, it also reflects scientific rigour when it comes to assimilating findings into textbooks and science history. Here I give an overview on bacterial protein secretion systems, their history, their nomenclature and why it can be misleading for newcomers in the field. Note that I do not try to suggest a new nomenclature. Instead, I explore the reasons why naming could have escaped our control and I try to reiterate basic concepts that underlie protein trafficking cross membranes.
Collapse
Affiliation(s)
- Alain Filloux
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| |
Collapse
|
14
|
Wang X, Zhang X, Lu BH, Gao J. The periplasmic chaperone protein Psg_2795 contributes to the virulence of Pseudomonas savastanoi pv. glycinea: the causal agent of bacterial blight of soybean. J Microbiol 2022; 60:478-487. [PMID: 35246805 DOI: 10.1007/s12275-022-1469-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 01/10/2022] [Accepted: 01/12/2022] [Indexed: 11/29/2022]
Abstract
Pseudomonas savastanoi pv. glycinea (Psg also named P. syringae pv. glycinea and P. amygdali pv. glycinea) is the causative agent of bacterial blight in soybean. The identification of virulence factors is essential for understanding the pathogenesis of Psg. In this study, a mini-Tn5 transposon mutant library of Psg strain PsgNC12 was screened on soybean, and one low-virulent mini-Tn5 mutant, designated as 4573, was identified. Sequence analysis of the 4573-mutant revealed that the mini-Tn5 transposon was inserted in the Psg_2795 gene. Psg_2795 encodes a FimC-domain protein that is highly conserved in Pseudomonas. Further analysis revealed that the mutation and knockout of Psg_2795 results in a reduced virulence phenotype on soybean, decreased motility, weakened bacterial attachment to a glass surface and delayed the population growth within soybean leaves. The phenotype of the 4573-mutant could be complemented nearly to wild-type levels using an intact Psg_2795 gene. Collectively, our results demonstrate that Psg_2795 plays an important role in the virulence, motility, attachment and the population growth of PsgNC12 in soybean. This finding provides a new insight into the function of periplasmic chaperone proteins in a type I pilus and provides reference information for identifying Psg_2795 homologues in P. savastanoi and other bacteria.
Collapse
Affiliation(s)
- Xiuhua Wang
- College of Plant Protection, Jilin Agricultural University, Changchun, 130118, P. R. China
| | - Xiaoyan Zhang
- College of Plant Protection, Jilin Agricultural University, Changchun, 130118, P. R. China
| | - Bao-Hui Lu
- College of Plant Protection, Jilin Agricultural University, Changchun, 130118, P. R. China.
| | - Jie Gao
- College of Plant Protection, Jilin Agricultural University, Changchun, 130118, P. R. China.
| |
Collapse
|
15
|
Deshamukhya C, Saikia R, Das BJ, Paul D, (Chanda) DD, Bhattacharjee A. Expression of cupA gene cluster responsible for biofilm formation in Pseudomonas aeruginosa is enhanced against subinhibitory concentration of carbapenems. GENE REPORTS 2022. [DOI: 10.1016/j.genrep.2021.101427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
|
16
|
Jeske A, Arce-Rodriguez A, Thöming JG, Tomasch J, Häussler S. Evolution of biofilm-adapted gene expression profiles in lasR-deficient clinical Pseudomonas aeruginosa isolates. NPJ Biofilms Microbiomes 2022; 8:6. [PMID: 35165270 PMCID: PMC8844440 DOI: 10.1038/s41522-022-00268-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 01/05/2022] [Indexed: 12/13/2022] Open
Abstract
The overall success of a pathogenic microbe depends on its ability to efficiently adapt to challenging conditions in the human host. Long-term evolution experiments track and predict adaptive trajectories and have contributed significantly to our understanding of the driving forces of bacterial adaptation. In this study, we conducted a cross-sectional study instead of long-term longitudinal evolution experiments. We analyzed the transcriptional profiles as well as genomic sequence variations of a large number of clinical Pseudomonas aeruginosa isolates that have been recovered from different infected human sites. Convergent changes in gene expression patterns were found in different groups of clinical isolates. The majority of repeatedly observed expression patterns could be attributed to a defective lasR gene, which encodes the major quorum-sensing regulator LasR. Strikingly, the gene expression pattern of the lasR-defective strains appeared to reflect a transcriptional response that evolves in a direction consistent with growth within a biofilm. In a process of genetic assimilation, lasR-deficient P. aeruginosa isolates appear to constitutively express a biofilm-adapted transcriptional profile and no longer require a respective environmental trigger. Our results demonstrate that profiling the functional consequences of pathoadaptive mutations in clinical isolates reveals long-term evolutionary pathways and may explain the success of lasR mutants in the opportunistic pathogen P. aeruginosa in a clinical context.
Collapse
Affiliation(s)
- Alexander Jeske
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, 38124, Braunschweig, Germany
- Institute for Molecular Bacteriology, TWINCORE, Centre for Experimental and Clinical Infection Research, 30265, Hannover, Germany
| | - Alejandro Arce-Rodriguez
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, 38124, Braunschweig, Germany
- Institute for Molecular Bacteriology, TWINCORE, Centre for Experimental and Clinical Infection Research, 30265, Hannover, Germany
| | - Janne G Thöming
- Institute for Molecular Bacteriology, TWINCORE, Centre for Experimental and Clinical Infection Research, 30265, Hannover, Germany
- Department of Clinical Microbiology, Copenhagen University Hospital-Rigshospitalet, 2100, Copenhagen, Denmark
| | - Jürgen Tomasch
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, 38124, Braunschweig, Germany
| | - Susanne Häussler
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, 38124, Braunschweig, Germany.
- Institute for Molecular Bacteriology, TWINCORE, Centre for Experimental and Clinical Infection Research, 30265, Hannover, Germany.
- Department of Clinical Microbiology, Copenhagen University Hospital-Rigshospitalet, 2100, Copenhagen, Denmark.
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, 30265, Hannover, Germany.
| |
Collapse
|
17
|
Bacteria.guru: Comparative Transcriptomics and Co-Expression Database for Bacterial Pathogens. J Mol Biol 2021; 434:167380. [PMID: 34838806 DOI: 10.1016/j.jmb.2021.167380] [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: 09/21/2021] [Revised: 11/11/2021] [Accepted: 11/21/2021] [Indexed: 12/12/2022]
Abstract
While bacteria can be beneficial to our health, their deadly pathogenic potential has been an ever-present concern exacerbated by the emergence of drug-resistant strains. As such, there is a pressing urgency for an enhanced understanding of their gene function and regulation, which could mediate the development of novel antimicrobials. Transcriptomic analyses have been established as insightful and indispensable to the functional characterization of genes and identification of new biological pathways, but in the context of bacterial studies, they remain limited to species-specific datasets. To address this, we integrated the genomic and transcriptomic data of the 17 most notorious and researched bacterial pathogens, creating bacteria.guru, an interactive database that can identify, visualize, and compare gene expression profiles, coexpression networks, functionally enriched clusters, and gene families across species. Through illustrating antibiotic resistance mechanisms in P. aeruginosa, we demonstrate that bacteria.guru could potentially aid in discovering multi-faceted antibiotic targets and, overall, facilitate future bacterial research. AVAILABILITY: The database and coexpression networks are freely available from https://bacteria.guru/. Sample annotations can be found in the supplemental data.
Collapse
|
18
|
Hagras SAA, Hosny AEDMS, Helmy OM, Salem-Bekhit MM, Shakeel F, Farrag HA. Effect of sub-inhibitory concentrations of cefepime on biofilm formation by Pseudomonas aeruginosa. Can J Microbiol 2021; 67:894-901. [PMID: 34731576 DOI: 10.1139/cjm-2021-0229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
This study investigated the effect of cefepime at sub-minimum inhibitory concentrations (sub-MICs) on in vitro biofilm formation (BF) by clinical isolates of Pseudomonas aeruginosa. The effect of cefepime at sub-MIC levels (½-1/256 MIC) on in vitro BF by six clinical isolates of P. aeruginosa was phenotypically assessed following 24 and 48 h of challenge using the tissue culture plate (TCP) assay. Quantitative real-time polymerase chain reaction (qRT-PCR) was employed to observe the change in expression of three biofilm-related genes, namely, a protease-encoding gene (lasA), fimbrial protein-encoding gene (cupA1), and alginate-encoding gene (algC), in a weak biofilm-producing strain of P. aeruginosa following 24 and 48 h of challenge with sub-MICs of cefepime. The BF morphology in response to cefepime was imaged using scanning electron microscopy (SEM). The TCP assay showed strain-, time-, and concentration-dependent changes in in vitro BF in P. aeruginosa following challenge with sub-MICs of cefepime, with a profound increase in strains with inherently no or weak biofilm-producing ability. RT-PCR revealed time-dependent upregulation in the expression of the investigated genes following challenge with ½ and ¼ MIC levels, as confirmed by SEM. Cefepime at sub-MICs could upregulate the expression of BF-related genes and enhance BF by P. aeruginosa clinical isolates.
Collapse
Affiliation(s)
- Soheir A A Hagras
- Department of Drug Radiation Research, National Center for Radiation Research and Technology (NCRRT), Egyptian Atomic Energy Authority, Cairo, Egypt.,Inaya Medical Colleges, Riyadh, Saudi Arabia
| | - Alaa El-Dien M S Hosny
- Department of Microbiology & Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Omneya M Helmy
- Department of Microbiology & Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Mounir M Salem-Bekhit
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia.,Department of Microbiology & Immunology, Faculty of Pharmacy, Al-Azhar University, Cairo, Egypt
| | - Faiyaz Shakeel
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Hala A Farrag
- Department of Drug Radiation Research, National Center for Radiation Research and Technology (NCRRT), Egyptian Atomic Energy Authority, Cairo, Egypt
| |
Collapse
|
19
|
Bäumler W, Eckl D, Holzmann T, Schneider-Brachert W. Antimicrobial coatings for environmental surfaces in hospitals: a potential new pillar for prevention strategies in hygiene. Crit Rev Microbiol 2021; 48:531-564. [PMID: 34699296 DOI: 10.1080/1040841x.2021.1991271] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Recent reports provide evidence that contaminated healthcare environments represent major sources for the acquisition and transmission of pathogens. Antimicrobial coatings (AMC) may permanently and autonomously reduce the contamination of such environmental surfaces complementing standard hygiene procedures. This review provides an overview of the current status of AMC and the demands to enable a rational application of AMC in health care settings. Firstly, a suitable laboratory test norm is required that adequately quantifies the efficacy of AMC. In particular, the frequently used wet testing (e.g. ISO 22196) must be replaced by testing under realistic, dry surface conditions. Secondly, field studies should be mandatory to provide evidence for antimicrobial efficacy under real-life conditions. The antimicrobial efficacy should be correlated to the rate of nosocomial transmission at least. Thirdly, the respective AMC technology should not add additional bacterial resistance development induced by the biocidal agents and co- or cross-resistance with antibiotic substances. Lastly, the biocidal substances used in AMC should be safe for humans and the environment. These measures should help to achieve a broader acceptance for AMC in healthcare settings and beyond. Technologies like the photodynamic approach already fulfil most of these AMC requirements.
Collapse
Affiliation(s)
- Wolfgang Bäumler
- Department of Dermatology, University Hospital, Regensburg, Germany
| | - Daniel Eckl
- Department of Microbiology, University of Regensburg, Regensburg, Germany
| | - Thomas Holzmann
- Department of Infection Control and Infectious Diseases, University Hospital, Regensburg, Germany
| | - Wulf Schneider-Brachert
- Department of Infection Control and Infectious Diseases, University Hospital, Regensburg, Germany
| |
Collapse
|
20
|
Tabassum R, Abbas G, Azam SS. Immunoinformatics based designing and simulation of multi-epitope vaccine against multi-drug resistant Stenotrophomonas maltophilia. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116899] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
|
21
|
Redfern J, Wallace J, van Belkum A, Jaillard M, Whittard E, Ragupathy R, Verran J, Kelly P, Enright MC. Biofilm associated genotypes of multiple antibiotic resistant Pseudomonas aeruginosa. BMC Genomics 2021; 22:572. [PMID: 34311706 PMCID: PMC8314537 DOI: 10.1186/s12864-021-07818-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 06/14/2021] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Pseudomonas aeruginosa is a ubiquitous environmental microorganism and also a common cause of infection. Its ability to survive in many different environments and persistently colonize humans is linked to its presence in biofilms formed on indwelling device surfaces. Biofilm promotes adhesion to, and survival on surfaces, protects from desiccation and the actions of antibiotics and disinfectants. RESULTS We examined the genetic basis for biofilm production on polystyrene at room (22 °C) and body temperature (37 °C) within 280 P. aeruginosa. 193 isolates (69 %) produced more biofilm at 22 °C than at 37 °C. Using GWAS and pan-GWAS, we found a number of accessory genes significantly associated with greater biofilm production at 22 °C. Many of these are present on a 165 kb region containing genes for heavy metal resistance (arsenic, copper, mercury and cadmium), transcriptional regulators and methytransferases. We also discovered multiple core genome SNPs in the A-type flagellin gene and Type II secretion system gene xpsD. Analysis of biofilm production of isolates of the MDR ST111 and ST235 lineages on stainless-steel revealed several accessory genes associated with enhanced biofilm production. These include a putative translocase with homology to a Helicobacter pylori type IV secretion system protein, a TA system II toxin gene and the alginate biosynthesis gene algA, several transcriptional regulators and methytransferases as well as core SNPs in genes involved in quorum sensing and protein translocation. CONCLUSIONS Using genetic association approaches we discovered a number of accessory genes and core-genome SNPs that were associated with enhanced early biofilm formation at 22 °C compared to 37 °C. These included a 165 kb genomic island containing multiple heavy metal resistance genes, transcriptional regulators and methyltransferases. We hypothesize that this genomic island may be associated with overall genotypes that are environmentally adapted to survive at lower temperatures. Further work to examine their importance in, for example gene-knockout studies, are required to confirm their relevance. GWAS and pan-GWAS approaches have great potential as a first step in examining the genetic basis of novel bacterial phenotypes.
Collapse
Affiliation(s)
- James Redfern
- Faculty of Science and Engineering, Manchester Metropolitan University, Chester Street, Manchester, United Kingdom
| | - Janine Wallace
- Faculty of Science and Engineering, Manchester Metropolitan University, Chester Street, Manchester, United Kingdom
| | | | | | - Elliot Whittard
- Faculty of Science and Engineering, Manchester Metropolitan University, Chester Street, Manchester, United Kingdom
| | - Roobinidevi Ragupathy
- Faculty of Science and Engineering, Manchester Metropolitan University, Chester Street, Manchester, United Kingdom
| | - Joanna Verran
- Faculty of Science and Engineering, Manchester Metropolitan University, Chester Street, Manchester, United Kingdom
| | - Peter Kelly
- Faculty of Science and Engineering, Manchester Metropolitan University, Chester Street, Manchester, United Kingdom
| | - Mark Charles Enright
- Faculty of Science and Engineering, Manchester Metropolitan University, Chester Street, Manchester, United Kingdom.
| |
Collapse
|
22
|
González-Montalvo MA, Tavares-Carreón F, González GM, Villanueva-Lozano H, García-Romero I, Zomosa-Signoret VC, Valvano MA, Andrade A. Defining chaperone-usher fimbriae repertoire in Serratia marcescens. Microb Pathog 2021; 154:104857. [PMID: 33762200 DOI: 10.1016/j.micpath.2021.104857] [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: 01/06/2021] [Accepted: 03/12/2021] [Indexed: 11/28/2022]
Abstract
Chaperone-usher (CU) fimbriae are surface organelles particularly prevalent among the Enterobacteriaceae. Mainly associated to their adhesive properties, CU fimbriae play key roles in biofilm formation and host cell interactions. Little is known about the fimbriome composition of the opportunistic human pathogen Serratia marcescens. Here, by using a search based on consensus fimbrial usher protein (FUP) sequences, we identified 421 FUPs across 39 S. marcescens genomes. Further analysis of the FUP-containing loci allowed us to classify them into 20 conserved CU operons, 6 of which form the S. marcescens core CU fimbriome. A new systematic nomenclature is proposed according to FUP sequence phylogeny. We also established an in vivo transcriptional assay comparing CU promoter expression between an environmental and a clinical isolate of S. marcescens, which revealed that promoters from 3 core CU operons (referred as fgov, fpo, and fps) are predominantly expressed in the two strains and might represent key core adhesion appendages contributing to S. marcescens pathogenesis.
Collapse
Affiliation(s)
- Martín A González-Montalvo
- Universidad Autónoma de Nuevo León, Facultad de Medicina, Departamento de Microbiología, Monterrey, Nuevo León, 64460, Mexico
| | - Faviola Tavares-Carreón
- Universidad Autónoma de Nuevo León, Facultad de Ciencias Biológicas, San Nicolás de los Garza, Nuevo León, 66455, Mexico
| | - Gloria M González
- Universidad Autónoma de Nuevo León, Facultad de Medicina, Departamento de Microbiología, Monterrey, Nuevo León, 64460, Mexico
| | - Hiram Villanueva-Lozano
- Universidad Autónoma de Nuevo León, Facultad de Medicina, Departamento de Microbiología, Monterrey, Nuevo León, 64460, Mexico
| | - Inmaculada García-Romero
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, BT9 7BL, United Kingdom
| | - Viviana C Zomosa-Signoret
- Universidad Autónoma de Nuevo León, Facultad de Medicina, Departamento de Bioquímica y Medicina Molecular, Monterrey, Nuevo León, 64460, Mexico
| | - Miguel A Valvano
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, BT9 7BL, United Kingdom
| | - Angel Andrade
- Universidad Autónoma de Nuevo León, Facultad de Medicina, Departamento de Microbiología, Monterrey, Nuevo León, 64460, Mexico.
| |
Collapse
|
23
|
Martínez-García E, Fraile S, Rodríguez Espeso D, Vecchietti D, Bertoni G, de Lorenzo V. Naked Bacterium: Emerging Properties of a Surfome-Streamlined Pseudomonas putida Strain. ACS Synth Biol 2020; 9:2477-2492. [PMID: 32786355 DOI: 10.1021/acssynbio.0c00272] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Environmental bacteria are most often endowed with native surface-attachment programs that frequently conflict with efforts to engineer biofilms and synthetic communities with given tridimensional architectures. In this work, we report the editing of the genome of Pseudomonas putida KT2440 for stripping the cells of most outer-facing structures of the bacterial envelope that mediate motion, binding to surfaces, and biofilm formation. To this end, 23 segments of the P. putida chromosome encoding a suite of such functions were deleted, resulting in the surface-naked strain EM371, the physical properties of which changed dramatically in respect to the wild type counterpart. As a consequence, surface-edited P. putida cells were unable to form biofilms on solid supports and, because of the swimming deficiency and other alterations, showed a much faster sedimentation in liquid media. Surface-naked bacteria were then used as carriers of interacting partners (e.g., Jun-Fos domains) ectopically expressed by means of an autotransporter display system on the now easily accessible cell envelope. Abstraction of individual bacteria as adhesin-coated spherocylinders enabled rigorous quantitative description of the multicell interplay brought about by thereby engineered physical interactions. The model was then applied to parametrize the data extracted from automated analysis of confocal microscopy images of the experimentally assembled bacterial flocks for analyzing their structure and distribution. The resulting data not only corroborated the value of P. putida EM371 over the parental strain as a platform for display artificial adhesins but also provided a strategy for rational engineering of catalytic communities.
Collapse
Affiliation(s)
- Esteban Martínez-García
- Systems Biology Program, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, 28049 Madrid, Spain
| | - Sofía Fraile
- Systems Biology Program, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, 28049 Madrid, Spain
| | - David Rodríguez Espeso
- Systems Biology Program, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, 28049 Madrid, Spain
| | - Davide Vecchietti
- Department of Biosciences, Università degli Studi di Milano, 20133 Milan, Italy
| | - Giovanni Bertoni
- Department of Biosciences, Università degli Studi di Milano, 20133 Milan, Italy
| | - Víctor de Lorenzo
- Systems Biology Program, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, 28049 Madrid, Spain
| |
Collapse
|
24
|
Kimkes TEP, Heinemann M. How bacteria recognise and respond to surface contact. FEMS Microbiol Rev 2020; 44:106-122. [PMID: 31769807 PMCID: PMC7053574 DOI: 10.1093/femsre/fuz029] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 11/23/2019] [Indexed: 12/27/2022] Open
Abstract
Bacterial biofilms can cause medical problems and issues in technical systems. While a large body of knowledge exists on the phenotypes of planktonic and of sessile cells in mature biofilms, our understanding of what happens when bacteria change from the planktonic to the sessile state is still very incomplete. Fundamental questions are unanswered: for instance, how do bacteria sense that they are in contact with a surface, and what are the very initial cellular responses to surface contact. Here, we review the current knowledge on the signals that bacteria could perceive once they attach to a surface, the signal transduction systems that could be involved in sensing the surface contact and the cellular responses that are triggered as a consequence to surface contact ultimately leading to biofilm formation. Finally, as the main obstacle in investigating the initial responses to surface contact has been the difficulty to experimentally study the dynamic response of single cells upon surface attachment, we also review recent experimental approaches that could be employed to study bacterial surface sensing, which ultimately could lead to an improved understanding of how biofilm formation could be prevented.
Collapse
Affiliation(s)
- Tom E P Kimkes
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, the Netherlands
| | - Matthias Heinemann
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, the Netherlands
| |
Collapse
|
25
|
Romero M, Silistre H, Lovelock L, Wright VJ, Chan KG, Hong KW, Williams P, Cámara M, Heeb S. Genome-wide mapping of the RNA targets of the Pseudomonas aeruginosa riboregulatory protein RsmN. Nucleic Acids Res 2018; 46:6823-6840. [PMID: 29718466 PMCID: PMC6061880 DOI: 10.1093/nar/gky324] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 04/10/2018] [Accepted: 04/17/2018] [Indexed: 01/01/2023] Open
Abstract
Pseudomonads typically carry multiple non-identical alleles of the post-transcriptional regulator rsmA. In Pseudomonas aeruginosa, RsmN is notable in that its structural rearrangement confers distinct and overlapping functions with RsmA. However, little is known about the specificities of RsmN for its target RNAs and overall impact on the biology of this pathogen. We purified and mapped 503 transcripts directly bound by RsmN in P. aeruginosa. About 200 of the mRNAs identified encode proteins of demonstrated function including some determining acute and chronic virulence traits. For example, RsmN reduces biofilm development both directly and indirectly via multiple pathways, involving control of Pel exopolysaccharide biosynthesis and c-di-GMP levels. The RsmN targets identified are also shared with RsmA, although deletion of rsmN generally results in less pronounced phenotypes than those observed for ΔrsmA or ΔrsmArsmNind mutants, probably as a consequence of different binding affinities. Targets newly identified for the Rsm system include the small non-coding RNA CrcZ involved in carbon catabolite repression, for which differential binding of RsmN and RsmA to specific CrcZ regions is demonstrated. The results presented here provide new insights into the intricacy of riboregulatory networks involving multiple but distinct RsmA homologues.
Collapse
Affiliation(s)
- Manuel Romero
- School of Life Sciences, Centre for Biomolecular Sciences, University Park, University of Nottingham, Nottingham NG7 2RD, UK
| | - Hazel Silistre
- School of Life Sciences, Centre for Biomolecular Sciences, University Park, University of Nottingham, Nottingham NG7 2RD, UK
| | - Laura Lovelock
- School of Life Sciences, Centre for Biomolecular Sciences, University Park, University of Nottingham, Nottingham NG7 2RD, UK
| | - Victoria J Wright
- School of Life Sciences, Centre for Biomolecular Sciences, University Park, University of Nottingham, Nottingham NG7 2RD, UK
| | - Kok-Gan Chan
- International Genome Centre, Jiangsu University,Zhenjiang, China
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Kar-Wai Hong
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Paul Williams
- School of Life Sciences, Centre for Biomolecular Sciences, University Park, University of Nottingham, Nottingham NG7 2RD, UK
| | - Miguel Cámara
- School of Life Sciences, Centre for Biomolecular Sciences, University Park, University of Nottingham, Nottingham NG7 2RD, UK
| | - Stephan Heeb
- School of Life Sciences, Centre for Biomolecular Sciences, University Park, University of Nottingham, Nottingham NG7 2RD, UK
| |
Collapse
|
26
|
Anti-biofilm effects of anthranilate on a broad range of bacteria. Sci Rep 2017; 7:8604. [PMID: 28819217 PMCID: PMC5561115 DOI: 10.1038/s41598-017-06540-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 06/14/2017] [Indexed: 01/16/2023] Open
Abstract
Anthranilate, one of tryptophan degradation products has been reported to interfere with biofilm formation by Pseudomonas aeruginosa. Here, we investigated the effects of anthranilate on biofilm formation by various bacteria and the mechanisms responsible. Anthranilate commonly inhibited biofilm formation by P. aeruginosa, Vibrio vulnificus, Bacillus subtilis, Salmonella enterica serovar Typhimurium, and Staphylococcus aureus, and disrupted biofilms preformed by these bacteria. Because anthranilate reduced intracellular c-di-GMP and enhanced swimming and swarming motilities in P. aeruginosa, V. vulnificus, B. subtilis, and S. enterica, it is likely that anthranilate disrupts biofilms by inducing the dispersion of these bacteria. On the other hand, in S. aureus, a non-flagellate bacterium that has no c-di-GMP signaling, anthranilate probably inhibits biofilm formation by reducing slime production. These results suggest that anthranilate has multiple ways for biofilm inhibition. Furthermore, because of its good biofilm inhibitory effects and lack of cytotoxicity to human cells even at high concentration, anthranilate appears to be a promising agent for inhibiting biofilm formation by a broad range of bacteria.
Collapse
|
27
|
Rashid MI, Naz A, Ali A, Andleeb S. Prediction of vaccine candidates against Pseudomonas aeruginosa: An integrated genomics and proteomics approach. Genomics 2017; 109:274-283. [PMID: 28487172 DOI: 10.1016/j.ygeno.2017.05.001] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Revised: 04/10/2017] [Accepted: 05/05/2017] [Indexed: 11/27/2022]
Abstract
Pseudomonas aeruginosa is among top critical nosocomial infectious agents due to its persistent infections and tendency for acquiring drug resistance mechanisms. To date, there is no vaccine available for this pathogen. We attempted to exploit the genomic and proteomic information of P. aeruginosa though reverse-vaccinology approaches to unveil the prospective vaccine candidates. P. aeruginosa strain PAO1 genome was subjected to sequential prioritization approach following genomic, proteomics and structural analyses. Among, the predicted vaccine candidates: surface components of antibiotic efflux pumps (Q9HY88, PA2837), chaperone-usher pathway components (CupC2, CupB3), penicillin binding protein of bacterial cell wall (PBP1a/mrcA), extracellular component of Type 3 secretory system (PscC) and three uncharacterized secretory proteins (PA0629, PA2822, PA0978) were identified as potential candidates qualifying all the set criteria. These proteins were then analyzed for potential immunogenic surface exposed epitopes. These predicted epitopes may provide a basis for development of a reliable subunit vaccine against P. aeruginosa.
Collapse
Affiliation(s)
- Muhammad Ibrahim Rashid
- Department of Industrial Biotechnology, Atta ur Rahman School of Applied Biosciences (ASAB), National University of Sciences & Technology (NUST), Islamabad, Pakistan
| | - Anam Naz
- Department of Industrial Biotechnology, Atta ur Rahman School of Applied Biosciences (ASAB), National University of Sciences & Technology (NUST), Islamabad, Pakistan
| | - Amjad Ali
- Department of Industrial Biotechnology, Atta ur Rahman School of Applied Biosciences (ASAB), National University of Sciences & Technology (NUST), Islamabad, Pakistan.
| | - Saadia Andleeb
- Department of Industrial Biotechnology, Atta ur Rahman School of Applied Biosciences (ASAB), National University of Sciences & Technology (NUST), Islamabad, Pakistan.
| |
Collapse
|
28
|
Rasheed M, Garnett J, Pérez-Dorado I, Muhl D, Filloux A, Matthews S. Crystal structure of the CupB6 adhesive tip from the chaperone-usher family of pili from Pseudomonas aeruginosa. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:1500-5. [PMID: 27481165 PMCID: PMC5022761 DOI: 10.1016/j.bbapap.2016.07.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Revised: 07/14/2016] [Accepted: 07/28/2016] [Indexed: 11/26/2022]
Abstract
Pseudomonas aeruginosa is a Gram-negative opportunistic bacterial pathogen that can cause chronic infection of the lungs of cystic fibrosis patients. Chaperone-usher systems in P. aeruginosa are known to translocate and assemble adhesive pili on the bacterial surface and contribute to biofilm formation within the host. Here, we report the crystal structure of the tip adhesion subunit CupB6 from the cupB1–6 gene cluster. The tip domain is connected to the pilus via the N-terminal donor strand from the main pilus subunit CupB1. Although the CupB6 adhesion domain bears structural features similar to other CU adhesins it displays an unusual polyproline helix adjacent to a prominent surface pocket, which are likely the site for receptor recognition. Crystal structure of the tip adhesion subunit CupB6 from the cupB1-6 gene cluster of Pseudomonas aeruginosa CupB6 possesses an atypical adhesion domain connected to a canonical chaperone-usher pilus subunit CupB6 caps the pilus shaft via donor strand complementation with the N-terminus of CupB1 CupB6 possesses unusual polyproline helices adjacent to a prominent surface pocket
Collapse
Affiliation(s)
- Masooma Rasheed
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - James Garnett
- Queen Mary University of London, Department of Chemistry and Biochemistry, School of Biological and Chemical Sciences, Joseph Priestley Building, Mile End Road, London E1 4NS, United Kingdom
| | | | - Daniela Muhl
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Alain Filloux
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Steve Matthews
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom.
| |
Collapse
|
29
|
Jani M, Mathee K, Azad RK. Identification of Novel Genomic Islands in Liverpool Epidemic Strain of Pseudomonas aeruginosa Using Segmentation and Clustering. Front Microbiol 2016; 7:1210. [PMID: 27536294 PMCID: PMC4971588 DOI: 10.3389/fmicb.2016.01210] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 07/20/2016] [Indexed: 02/03/2023] Open
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen implicated in a myriad of infections and a leading pathogen responsible for mortality in patients with cystic fibrosis (CF). Horizontal transfers of genes among the microorganisms living within CF patients have led to highly virulent and multi-drug resistant strains such as the Liverpool epidemic strain of P. aeruginosa, namely the LESB58 strain that has the propensity to acquire virulence and antibiotic resistance genes. Often these genes are acquired in large clusters, referred to as "genomic islands (GIs)." To decipher GIs and understand their contributions to the evolution of virulence and antibiotic resistance in P. aeruginosa LESB58, we utilized a recursive segmentation and clustering procedure, presented here as a genome-mining tool, "GEMINI." GEMINI was validated on experimentally verified islands in the LESB58 strain before examining its potential to decipher novel islands. Of the 6062 genes in P. aeruginosa LESB58, 596 genes were identified to be resident on 20 GIs of which 12 have not been previously reported. Comparative genomics provided evidence in support of our novel predictions. Furthermore, GEMINI unraveled the mosaic structure of islands that are composed of segments of likely different evolutionary origins, and demonstrated its ability to identify potential strain biomarkers. These newly found islands likely have contributed to the hyper-virulence and multidrug resistance of the Liverpool epidemic strain of P. aeruginosa.
Collapse
Affiliation(s)
- Mehul Jani
- Department of Biological Sciences, University of North Texas Denton, TX, USA
| | - Kalai Mathee
- Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine Global Health Consortium, and Biomolecular Sciences Institute, Florida International University Miami, FL, USA
| | - Rajeev K Azad
- Department of Biological Sciences, University of North TexasDenton, TX, USA; Department of Mathematics, University of North TexasDenton, TX, USA
| |
Collapse
|
30
|
Gill SK, Hui K, Farne H, Garnett JP, Baines DL, Moore LS, Holmes AH, Filloux A, Tregoning JS. Increased airway glucose increases airway bacterial load in hyperglycaemia. Sci Rep 2016; 6:27636. [PMID: 27273266 PMCID: PMC4897689 DOI: 10.1038/srep27636] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 05/19/2016] [Indexed: 01/15/2023] Open
Abstract
Diabetes is associated with increased frequency of hospitalization due to bacterial lung infection. We hypothesize that increased airway glucose caused by hyperglycaemia leads to increased bacterial loads. In critical care patients, we observed that respiratory tract bacterial colonisation is significantly more likely when blood glucose is high. We engineered mutants in genes affecting glucose uptake and metabolism (oprB, gltK, gtrS and glk) in Pseudomonas aeruginosa, strain PAO1. These mutants displayed attenuated growth in minimal medium supplemented with glucose as the sole carbon source. The effect of glucose on growth in vivo was tested using streptozocin-induced, hyperglycaemic mice, which have significantly greater airway glucose. Bacterial burden in hyperglycaemic animals was greater than control animals when infected with wild type but not mutant PAO1. Metformin pre-treatment of hyperglycaemic animals reduced both airway glucose and bacterial load. These data support airway glucose as a critical determinant of increased bacterial load during diabetes.
Collapse
Affiliation(s)
- Simren K. Gill
- Mucosal Infection & Immunity Group, Section of Virology, Imperial College London, St Mary’s Campus, London, W2 1PG, UK
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Kailyn Hui
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Hugo Farne
- Airway Disease Infection Section, National Heart & Lung Institute, Imperial College London, London, W2 1PG, UK
| | - James P. Garnett
- Institute for Infection and Immunity, St George’s, University of London, London SW17 0RE, UK
| | - Deborah L. Baines
- Institute for Infection and Immunity, St George’s, University of London, London SW17 0RE, UK
| | - Luke S.P. Moore
- Health Protection Research Unit in Healthcare Associated Infection and Antimicrobial Resistance, Imperial College London, Hammersmith Campus, London W12 0HS, UK
| | - Alison H. Holmes
- Health Protection Research Unit in Healthcare Associated Infection and Antimicrobial Resistance, Imperial College London, Hammersmith Campus, London W12 0HS, UK
| | - Alain Filloux
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - John S. Tregoning
- Mucosal Infection & Immunity Group, Section of Virology, Imperial College London, St Mary’s Campus, London, W2 1PG, UK
| |
Collapse
|
31
|
Abstract
During the first step of biofilm formation, initial attachment is dictated by physicochemical and electrostatic interactions between the surface and the bacterial envelope. Depending on the nature of these interactions, attachment can be transient or permanent. To achieve irreversible attachment, bacterial cells have developed a series of surface adhesins promoting specific or nonspecific adhesion under various environmental conditions. This article reviews the recent advances in our understanding of the secretion, assembly, and regulation of the bacterial adhesins during biofilm formation, with a particular emphasis on the fimbrial, nonfimbrial, and discrete polysaccharide adhesins in Gram-negative bacteria.
Collapse
|
32
|
Gnanadhas DP, Elango M, Datey A, Chakravortty D. Chronic lung infection by Pseudomonas aeruginosa biofilm is cured by L-Methionine in combination with antibiotic therapy. Sci Rep 2015; 5:16043. [PMID: 26521707 PMCID: PMC4629202 DOI: 10.1038/srep16043] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 10/07/2015] [Indexed: 01/29/2023] Open
Abstract
Bacterial biofilms are associated with 80-90% of infections. Within the biofilm, bacteria are refractile to antibiotics, requiring concentrations >1,000 times the minimum inhibitory concentration. Proteins, carbohydrates and DNA are the major components of biofilm matrix. Pseudomonas aeruginosa (PA) biofilms, which are majorly associated with chronic lung infection, contain extracellular DNA (eDNA) as a major component. Herein, we report for the first time that L-Methionine (L-Met) at 0.5 μM inhibits Pseudomonas aeruginosa (PA) biofilm formation and disassembles established PA biofilm by inducing DNase expression. Four DNase genes (sbcB, endA, eddB and recJ) were highly up-regulated upon L-Met treatment along with increased DNase activity in the culture supernatant. Since eDNA plays a major role in establishing and maintaining the PA biofilm, DNase activity is effective in disrupting the biofilm. Upon treatment with L-Met, the otherwise recalcitrant PA biofilm now shows susceptibility to ciprofloxacin. This was reflected in vivo, in the murine chronic PA lung infection model. Mice treated with L-Met responded better to antibiotic treatment, leading to enhanced survival as compared to mice treated with ciprofloxacin alone. These results clearly demonstrate that L-Met can be used along with antibiotic as an effective therapeutic against chronic PA biofilm infection.
Collapse
Affiliation(s)
- Divya Prakash Gnanadhas
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
- Department of Aerospace Engineering, Indian Institute of Science, Bangalore, India
| | - Monalisha Elango
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Akshay Datey
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
- Department of Aerospace Engineering, Indian Institute of Science, Bangalore, India
- The Bioengineering Program, Indian Institute of Science, Bangalore, India
| | - Dipshikha Chakravortty
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| |
Collapse
|
33
|
Varga JJ, Barbier M, Mulet X, Bielecki P, Bartell JA, Owings JP, Martinez-Ramos I, Hittle LE, Davis MR, Damron FH, Liechti GW, Puchałka J, dos Santos VAPM, Ernst RK, Papin JA, Albertí S, Oliver A, Goldberg JB. Genotypic and phenotypic analyses of a Pseudomonas aeruginosa chronic bronchiectasis isolate reveal differences from cystic fibrosis and laboratory strains. BMC Genomics 2015; 16:883. [PMID: 26519161 PMCID: PMC4628258 DOI: 10.1186/s12864-015-2069-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 10/03/2015] [Indexed: 01/24/2023] Open
Abstract
Background Pseudomonas aeruginosa is an environmentally ubiquitous Gram-negative bacterium and important opportunistic human pathogen, causing severe chronic respiratory infections in patients with underlying conditions such as cystic fibrosis (CF) or bronchiectasis. In order to identify mechanisms responsible for adaptation during bronchiectasis infections, a bronchiectasis isolate, PAHM4, was phenotypically and genotypically characterized. Results This strain displays phenotypes that have been associated with chronic respiratory infections in CF including alginate over-production, rough lipopolysaccharide, quorum-sensing deficiency, loss of motility, decreased protease secretion, and hypermutation. Hypermutation is a key adaptation of this bacterium during the course of chronic respiratory infections and analysis indicates that PAHM4 encodes a mutated mutS gene responsible for a ~1,000-fold increase in mutation rate compared to wild-type laboratory strain P. aeruginosa PAO1. Antibiotic resistance profiles and sequence data indicate that this strain acquired numerous mutations associated with increased resistance levels to β-lactams, aminoglycosides, and fluoroquinolones when compared to PAO1. Sequencing of PAHM4 revealed a 6.38 Mbp genome, 5.9 % of which were unrecognized in previously reported P. aeruginosa genome sequences. Transcriptome analysis suggests a general down-regulation of virulence factors, while metabolism of amino acids and lipids is up-regulated when compared to PAO1 and metabolic modeling identified further potential differences between PAO1 and PAHM4. Conclusions This work provides insights into the potential differential adaptation of this bacterium to the lung of patients with bronchiectasis compared to other clinical settings such as cystic fibrosis, findings that should aid the development of disease-appropriate treatment strategies for P. aeruginosa infections. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2069-0) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- John J Varga
- Department of Pediatrics, Division of Pulmonology, Allergy/Immunology, Cystic Fibrosis and Sleep, Children's Healthcare of Atlanta, Atlanta, GA, USA. .,Emory + Children's Center for Cystic Fibrosis Research, Emory University and Children's Healthcare of Atlanta, Atlanta, GA, USA. .,Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA, USA.
| | - Mariette Barbier
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA, USA. .,Department of Microbiology, Immunology and Cell Biology, West Virginia University School of Medicine, Morgantown, WV, USA.
| | - Xavier Mulet
- Servicio de Microbiología and Unidad de Investigación, Hospital Son Espases, Instituto de Investigación Sanitaria de Palma (IdISPa), Palma, de Mallorca, Spain.
| | - Piotr Bielecki
- Synthetic and Systems Biology Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany. .,Present address: Immunobiology Department, Yale University, School of Medicine, New Haven, CT, 06511, USA.
| | - Jennifer A Bartell
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA.
| | - Joshua P Owings
- Department of Pediatrics, Division of Pulmonology, Allergy/Immunology, Cystic Fibrosis and Sleep, Children's Healthcare of Atlanta, Atlanta, GA, USA. .,Emory + Children's Center for Cystic Fibrosis Research, Emory University and Children's Healthcare of Atlanta, Atlanta, GA, USA. .,Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA, USA.
| | | | - Lauren E Hittle
- Department of Microbial Pathogenesis, University of Maryland School of Dentistry, University of Maryland, Baltimore, MD, USA.
| | - Michael R Davis
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA, USA.
| | - F Heath Damron
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA, USA. .,Department of Microbiology, Immunology and Cell Biology, West Virginia University School of Medicine, Morgantown, WV, USA.
| | - George W Liechti
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA, USA.
| | - Jacek Puchałka
- Servicio de Microbiología and Unidad de Investigación, Hospital Son Espases, Instituto de Investigación Sanitaria de Palma (IdISPa), Palma, de Mallorca, Spain. .,Present address: Dr. von Hauner Children's Hospital, Ludwig Maximilians University, Munich, Germany.
| | - Vitor A P Martins dos Santos
- Systems and Synthetic Biology, Wageningen University, Wageningen, Netherlands. .,Present address: Chair of Systems and Synthetic Biology, Wageningen University, Wageningen, The Netherlands. .,Present address: LifeGlimmer GmbH, Berlin, Germany.
| | - Robert K Ernst
- Department of Microbial Pathogenesis, University of Maryland School of Dentistry, University of Maryland, Baltimore, MD, USA.
| | - Jason A Papin
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA.
| | - Sebastian Albertí
- IUNICS, University of the Balearic Islands, Palma, de Mallorca, Spain.
| | - Antonio Oliver
- Servicio de Microbiología and Unidad de Investigación, Hospital Son Espases, Instituto de Investigación Sanitaria de Palma (IdISPa), Palma, de Mallorca, Spain.
| | - Joanna B Goldberg
- Department of Pediatrics, Division of Pulmonology, Allergy/Immunology, Cystic Fibrosis and Sleep, Children's Healthcare of Atlanta, Atlanta, GA, USA. .,Emory + Children's Center for Cystic Fibrosis Research, Emory University and Children's Healthcare of Atlanta, Atlanta, GA, USA. .,Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA, USA.
| |
Collapse
|
34
|
The formation of biofilms by Pseudomonas aeruginosa: a review of the natural and synthetic compounds interfering with control mechanisms. BIOMED RESEARCH INTERNATIONAL 2015; 2015:759348. [PMID: 25866808 PMCID: PMC4383298 DOI: 10.1155/2015/759348] [Citation(s) in RCA: 311] [Impact Index Per Article: 34.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2014] [Revised: 09/03/2014] [Accepted: 09/07/2014] [Indexed: 12/16/2022]
Abstract
P. aeruginosa is an opportunistic pathogenic bacterium responsible for both acute and chronic infections. Beyond its natural resistance to many drugs, its ability to form biofilm, a complex biological system, renders ineffective the clearance by immune defense systems and antibiotherapy. The objective of this report is to provide an overview (i) on P. aeruginosa biofilm lifestyle cycle, (ii) on the main key actors relevant in the regulation of biofilm formation by P. aeruginosa including QS systems, GacS/GacA and RetS/LadS two-component systems and C-di-GMP-dependent polysaccharides biosynthesis, and (iii) finally on reported natural and synthetic products that interfere with control mechanisms of biofilm formation by P. aeruginosa without affecting directly bacterial viability. Concluding remarks focus on perspectives to consider biofilm lifestyle as a target for eradication of resistant infections caused by P. aeruginosa.
Collapse
|
35
|
Garnett JA, Muhl D, Douse CH, Hui K, Busch A, Omisore A, Yang Y, Simpson P, Marchant J, Waksman G, Matthews S, Filloux A. Structure-function analysis reveals that the Pseudomonas aeruginosa Tps4 two-partner secretion system is involved in CupB5 translocation. Protein Sci 2015; 24:670-87. [PMID: 25641651 PMCID: PMC4420518 DOI: 10.1002/pro.2640] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Accepted: 01/07/2015] [Indexed: 01/11/2023]
Abstract
Pseudomonas aeruginosa is a Gram-negative opportunistic bacterium, synonymous with cystic fibrosis patients, which can cause chronic infection of the lungs. This pathogen is a model organism to study biofilms: a bacterial population embedded in an extracellular matrix that provide protection from environmental pressures and lead to persistence. A number of Chaperone-Usher Pathways, namely CupA-CupE, play key roles in these processes by assembling adhesive pili on the bacterial surface. One of these, encoded by the cupB operon, is unique as it contains a nonchaperone-usher gene product, CupB5. Two-partner secretion (TPS) systems are comprised of a C-terminal integral membrane β-barrel pore with tandem N-terminal POTRA (POlypeptide TRansport Associated) domains located in the periplasm (TpsB) and a secreted substrate (TpsA). Using NMR we show that TpsB4 (LepB) interacts with CupB5 and its predicted cognate partner TpsA4 (LepA), an extracellular protease. Moreover, using cellular studies we confirm that TpsB4 can translocate CupB5 across the P. aeruginosa outer membrane, which contrasts a previous observation that suggested the CupB3 P-usher secretes CupB5. In support of our findings we also demonstrate that tps4/cupB operons are coregulated by the RocS1 sensor suggesting P. aeruginosa has developed synergy between these systems. Furthermore, we have determined the solution-structure of the TpsB4-POTRA1 domain and together with restraints from NMR chemical shift mapping and in vivo mutational analysis we have calculated models for the entire TpsB4 periplasmic region in complex with both TpsA4 and CupB5 secretion motifs. The data highlight specific residues for TpsA4/CupB5 recognition by TpsB4 in the periplasm and suggest distinct roles for each POTRA domain.
Collapse
Affiliation(s)
- James A Garnett
- Department of Life Sciences, Centre for Structural Biology, Imperial College London, South Kensington Campus, London, SW7 2AZ, United Kingdom; Department of Life Sciences, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, South Kensington Campus, London, SW7 2AZ, United Kingdom
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
36
|
de Regt AK, Yin Y, Withers TR, Wang X, Baker TA, Sauer RT, Yu HD. Overexpression of CupB5 activates alginate overproduction in Pseudomonas aeruginosa by a novel AlgW-dependent mechanism. Mol Microbiol 2014; 93:415-25. [PMID: 24913916 DOI: 10.1111/mmi.12665] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/08/2014] [Indexed: 11/29/2022]
Abstract
In Pseudomonas aeruginosa, alginate overproduction, also known as mucoidy, is negatively regulated by the transmembrane protein MucA, which sequesters the alternative sigma factor AlgU. MucA is degraded via a proteolysis pathway that frees AlgU from sequestration, activating alginate biosynthesis. Initiation of this pathway normally requires two signals: peptide sequences in unassembled outer-membrane proteins (OMPs) activate the AlgW protease, and unassembled lipopolysaccharides bind periplasmic MucB, releasing MucA and facilitating its proteolysis by activated AlgW. To search for novel alginate regulators, we screened a transposon library in the non-mucoid reference strain PAO1, and identified a mutant that confers mucoidy through overexpression of a protein encoded by the chaperone-usher pathway gene cupB5. CupB5-dependent mucoidy occurs through the AlgU pathway and can be reversed by overexpression of MucA or MucB. In the presence of activating OMP peptides, peptides corresponding to a region of CupB5 needed for mucoidy further stimulated AlgW cleavage of MucA in vitro. Moreover, the CupB5 peptide allowed OMP-activated AlgW cleavage of MucA in the presence of the MucB inhibitor. These results support a novel mechanism for conversion to mucoidy in which the proteolytic activity of AlgW and its ability to compete with MucB for MucA is mediated by independent peptide signals.
Collapse
Affiliation(s)
- Anna K de Regt
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | | | | | | | | | | | | |
Collapse
|
37
|
Neznansky A, Opatowsky Y. Expression, purification and crystallization of the phosphate-binding PstS protein from Pseudomonas aeruginosa. Acta Crystallogr F Struct Biol Commun 2014; 70:906-10. [PMID: 25005086 PMCID: PMC4089529 DOI: 10.1107/s2053230x14010279] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2014] [Accepted: 05/06/2014] [Indexed: 11/10/2022] Open
Abstract
Pseudomonas aeruginosa (PA) infections pose a serious threat to human health. PA is a leading cause of fatal lung infections in cystic fibrosis and immune-suppressed patients, of sepsis in burn victims and of nosocomial infections. An important element in PA virulence is its ability to establish biofilms that evade suppression by the host's immune system and antibiotics. PstS, a periplasmic subunit of the Pst phosphate-transport system of PA, plays a critical role in the establishment of biofilms. In some drug-resistant PA strains, PstS is secreted in large quantities from the bacteria, where it participates in the assembly of adhesion fibres that enhance bacterial virulence. In order to understand the dual function of PstS in biofilm formation and phosphate transport, the crystal structure of PA PstS was determined. Here, the overexpression in Escherichia coli and purification of PA PstS in the presence of phosphate are described. Two crystal forms were obtained using the vapour-diffusion method at 20°C and X-ray diffraction data were collected. The first crystal form belonged to the centred orthorhombic space group C222₁, with unit-cell parameters a=67.5, b=151.3, c=108.9 Å. Assuming the presence of a dimer in the asymmetric unit gives a crystal volume per protein weight (VM) of 2.09 Å3 Da(-1) and a solvent content of 41%. The second crystal form belonged to the primitive orthorhombic space group P2₁2₁2₁, with unit-cell parameters a=35.4, b=148.3, c=216.7 Å. Assuming the presence of a tetramer in the asymmetric unit gives a crystal volume per protein weight (VM) of 2.14 Å3 Da(-1) and a solvent content of 42.65%. A pseudo-translational symmetry is present in the P212121 crystal form which is consistent with a filamentous arrangement of PstS in the crystal lattice.
Collapse
Affiliation(s)
- Avi Neznansky
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Yarden Opatowsky
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
| |
Collapse
|
38
|
Latino L, Essoh C, Blouin Y, Vu Thien H, Pourcel C. A novel Pseudomonas aeruginosa bacteriophage, Ab31, a chimera formed from temperate phage PAJU2 and P. putida lytic phage AF: characteristics and mechanism of bacterial resistance. PLoS One 2014; 9:e93777. [PMID: 24699529 PMCID: PMC3974807 DOI: 10.1371/journal.pone.0093777] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 03/07/2014] [Indexed: 01/21/2023] Open
Abstract
A novel temperate bacteriophage of Pseudomonas aeruginosa, phage vB_PaeP_Tr60_Ab31 (alias Ab31) is described. Its genome is composed of structural genes related to those of lytic P. putida phage AF, and regulatory genes similar to those of temperate phage PAJU2. The virion structure resembles that of phage AF and other lytic Podoviridae (S. enterica Epsilon 15 and E. coli phiv10) with similar tail spikes. Ab31 was able to infect P. aeruginosa strain PA14 and two genetically related strains called Tr60 and Tr162, out of 35 diverse strains from cystic fibrosis patients. Analysis of resistant host variants revealed different phenotypes, including induction of pigment and alginate overproduction. Whole genome sequencing of resistant variants highlighted the existence of a large deletion of 234 kbp in two strains, encompassing a cluster of genes required for the production of CupA fimbriae. Stable lysogens formed by Ab31 in strain Tr60, permitted the identification of the insertion site. During colonization of the lung in cystic fibrosis patients, P. aeruginosa adapts by modifying its genome. We suggest that bacteriophages such as Ab31 may play an important role in this adaptation by selecting for bacterial characteristics that favor persistence of bacteria in the lung.
Collapse
Affiliation(s)
- Libera Latino
- Univ Paris-Sud, Institut de Génétique et Microbiologie, UMR 8621, Orsay, France
- CNRS, Orsay, France
| | - Christiane Essoh
- Univ Paris-Sud, Institut de Génétique et Microbiologie, UMR 8621, Orsay, France
- CNRS, Orsay, France
| | - Yann Blouin
- Univ Paris-Sud, Institut de Génétique et Microbiologie, UMR 8621, Orsay, France
- CNRS, Orsay, France
| | - Hoang Vu Thien
- Hôpital Armand Trousseau, Assistance Publique-Hôpitaux de Paris (APHP), Bactériologie, Paris, France
| | - Christine Pourcel
- Univ Paris-Sud, Institut de Génétique et Microbiologie, UMR 8621, Orsay, France
- CNRS, Orsay, France
- * E-mail:
| |
Collapse
|
39
|
Fazli M, Almblad H, Rybtke ML, Givskov M, Eberl L, Tolker-Nielsen T. Regulation of biofilm formation in Pseudomonas and Burkholderia species. Environ Microbiol 2014; 16:1961-81. [PMID: 24592823 DOI: 10.1111/1462-2920.12448] [Citation(s) in RCA: 190] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Revised: 02/12/2014] [Accepted: 02/28/2014] [Indexed: 01/28/2023]
Abstract
In the present review, we describe and compare the molecular mechanisms that are involved in the regulation of biofilm formation by Pseudomonas putida, Pseudomonas fluorescens, Pseudomonas aeruginosa and Burkholderia cenocepacia. Our current knowledge suggests that biofilm formation is regulated by cyclic diguanosine-5'-monophosphate (c-di-GMP), small RNAs (sRNA) and quorum sensing (QS) in all these bacterial species. The systems that employ c-di-GMP as a second messenger regulate the production of exopolysaccharides and surface proteins which function as extracellular matrix components in the biofilms formed by the bacteria. The systems that make use of sRNAs appear to regulate the production of exopolysaccharide biofilm matrix material in all these species. In the pseudomonads, QS regulates the production of extracellular DNA, lectins and biosurfactants which all play a role in biofilm formation. In B.cenocepacia QS regulates the expression of a large surface protein, lectins and extracellular DNA that all function as biofilm matrix components. Although the three regulatory systems all regulate the production of factors used for biofilm formation, the molecular mechanisms involved in transducing the signals into expression of the biofilm matrix components differ between the species. Under the conditions tested, exopolysaccharides appears to be the most important biofilm matrix components for P.aeruginosa, whereas large surface proteins appear to be the most important biofilm matrix components for P.putida, P.fluorescens, and B.cenocepacia.
Collapse
Affiliation(s)
- Mustafa Fazli
- Department of International Health, Immunology, and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark; Department of Genetics and Bioengineering, Faculty of Engineering and Architecture, Yeditepe University, Istanbul, Turkey
| | | | | | | | | | | |
Collapse
|
40
|
Wei Q, Ma LZ. Biofilm matrix and its regulation in Pseudomonas aeruginosa. Int J Mol Sci 2013; 14:20983-1005. [PMID: 24145749 PMCID: PMC3821654 DOI: 10.3390/ijms141020983] [Citation(s) in RCA: 193] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Revised: 09/29/2013] [Accepted: 10/09/2013] [Indexed: 01/25/2023] Open
Abstract
Biofilms are communities of microorganisms embedded in extracellular polymeric substances (EPS) matrix. Bacteria in biofilms demonstrate distinct features from their free-living planktonic counterparts, such as different physiology and high resistance to immune system and antibiotics that render biofilm a source of chronic and persistent infections. A deeper understanding of biofilms will ultimately provide insights into the development of alternative treatment for biofilm infections. The opportunistic pathogen Pseudomonas aeruginosa, a model bacterium for biofilm research, is notorious for its ability to cause chronic infections by its high level of drug resistance involving the formation of biofilms. In this review, we summarize recent advances in biofilm formation, focusing on the biofilm matrix and its regulation in P. aeruginosa, aiming to provide resources for the understanding and control of bacterial biofilms.
Collapse
Affiliation(s)
- Qing Wei
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.3, 1st Beichen West Road, Chaoyang District, Beijing 100101, China.
| | | |
Collapse
|
41
|
Mikkelsen H, Hui K, Barraud N, Filloux A. The pathogenicity island encoded PvrSR/RcsCB regulatory network controls biofilm formation and dispersal in Pseudomonas aeruginosa PA14. Mol Microbiol 2013; 89:450-63. [PMID: 23750818 PMCID: PMC3842833 DOI: 10.1111/mmi.12287] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/03/2013] [Indexed: 01/14/2023]
Abstract
Pseudomonas aeruginosa biofilm formation is linked to persistent infections in humans. Biofilm formation is facilitated by extracellular appendages, some of which are assembled by the Chaperone Usher Pathway (Cup). The cupD gene cluster is located on the PAPI-1 pathogenicity island of strain PA14 and has probably been acquired together with four genes encoding two-component signal transduction proteins. We have previously showed that the RcsB response regulator activates expression of the cupD genes, which leads to the production of CupD fimbriae and increased attachment. Here we show that RcsB activity is tightly modulated by two sensors, RcsC and PvrS. While PvrS acts as a kinase that enhances RcsB activity, RcsC has a dual function, first as a phosphorelay, and second as a phosphatase. We found that, under certain growth conditions, overexpression of RcsB readily induces biofilm dispersal. Microarray analysis shows that RcsB positively controls expression of pvrR that encodes the phosphodiesterase required for this dispersal process. Finally, in addition to the PAPI-1 encoded cupD genes, RcsB controls several genes on the core genome, some of which encode orphan response regulators. We thus discovered that RcsB is central to a large regulatory network that fine-tunes the switch between biofilm formation and dispersal.
Collapse
Affiliation(s)
- Helga Mikkelsen
- Imperial College London, Department of Life Sciences, MRC Centre for Molecular Bacteriology and Infection, South Kensington Campus, Flowers Building, SW7 2AZ, London, UK
| | | | | | | |
Collapse
|
42
|
Bezuidt OK, Klockgether J, Elsen S, Attree I, Davenport CF, Tümmler B. Intraclonal genome diversity of Pseudomonas aeruginosa clones CHA and TB. BMC Genomics 2013; 14:416. [PMID: 23799896 PMCID: PMC3697988 DOI: 10.1186/1471-2164-14-416] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Accepted: 06/19/2013] [Indexed: 01/01/2023] Open
Abstract
Background Adaptation of Pseudomonas aeruginosa to different living conditions is accompanied by microevolution resulting in genomic diversity between strains of the same clonal lineage. In order to detect the impact of colonized habitats on P. aeruginosa microevolution we determined the genomic diversity between the highly virulent cystic fibrosis (CF) isolate CHA and two temporally and geographically unrelated clonal variants. The outcome was compared with the intraclonal genome diversity between three more closely related isolates of another clonal complex. Results The three clone CHA isolates differed in their core genome in several dozen strain specific nucleotide exchanges and small deletions from each other. Loss of function mutations and non-conservative amino acid replacements affected several habitat- and lifestyle-associated traits, for example, the key regulator GacS of the switch between acute and chronic disease phenotypes was disrupted in strain CHA. Intraclonal genome diversity manifested in an individual composition of the respective accessory genome whereby the highest number of accessory DNA elements was observed for isolate PT22 from a polluted aquatic habitat. Little intraclonal diversity was observed between three spatiotemporally related outbreak isolates of clone TB. Although phenotypically different, only a few individual SNPs and deletions were detected in the clone TB isolates. Their accessory genome mainly differed in prophage-like DNA elements taken up by one of the strains. Conclusions The higher geographical and temporal distance of the clone CHA isolates was associated with an increased intraclonal genome diversity compared to the more closely related clone TB isolates derived from a common source demonstrating the impact of habitat adaptation on the microevolution of P. aeruginosa. However, even short-term habitat differentiation can cause major phenotypic diversification driven by single genomic variation events and uptake of phage DNA.
Collapse
Affiliation(s)
- Oliver Ki Bezuidt
- Klinische Forschergruppe, Klinik für Pädiatrische Pneumologie, Allergologie und Neonatologie, Medizinische Hochschule Hannover, Hannover D-30625, Germany
| | | | | | | | | | | |
Collapse
|
43
|
Qaisar U, Luo L, Haley CL, Brady SF, Carty NL, Colmer-Hamood JA, Hamood AN. The pvc operon regulates the expression of the Pseudomonas aeruginosa fimbrial chaperone/usher pathway (cup) genes. PLoS One 2013; 8:e62735. [PMID: 23646138 PMCID: PMC3639982 DOI: 10.1371/journal.pone.0062735] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Accepted: 03/25/2013] [Indexed: 02/03/2023] Open
Abstract
The Pseudomonas aeruginosa fimbrial structures encoded by the cup gene clusters (cupB and cupC) contribute to its attachment to abiotic surfaces and biofilm formation. The P. aeruginosa pvcABCD gene cluster encodes enzymes that synthesize a novel isonitrile functionalized cumarin, paerucumarin. Paerucumarin has already been characterized chemically, but this is the first report elucidating its role in bacterial biology. We examined the relationship between the pvc operon and the cup gene clusters in the P. aeruginosa strain MPAO1. Mutations within the pvc genes compromised biofilm development and significantly reduced the expression of cupB1-6 and cupC1-3, as well as different genes of the cupB/cupC two-component regulatory systems, roc1/roc2. Adjacent to pvc is the transcriptional regulator ptxR. A ptxR mutation in MPAO1 significantly reduced the expression of the pvc genes, the cupB/cupC genes, and the roc1/roc2 genes. Overexpression of the intact chromosomally-encoded pvc operon by a ptxR plasmid significantly enhanced cupB2, cupC2, rocS1, and rocS2 expression and biofilm development. Exogenously added paerucumarin significantly increased the expression of cupB2, cupC2, rocS1 and rocS2 in the pvcA mutant. Our results suggest that pvc influences P. aeruginosa biofilm development through the cup gene clusters in a pathway that involves paerucumarin, PtxR, and different cup regulators.
Collapse
Affiliation(s)
- Uzma Qaisar
- Department of Immunology and Molecular Microbiology, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
| | - Liming Luo
- Department of Immunology and Molecular Microbiology, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
| | - Cecily L. Haley
- Department of Immunology and Molecular Microbiology, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
| | - Sean F. Brady
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University and Howard Hughes Medical Institute, New York, New York, United States of America
| | - Nancy L. Carty
- Department of Immunology and Molecular Microbiology, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
| | - Jane A. Colmer-Hamood
- Department of Immunology and Molecular Microbiology, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
| | - Abdul N. Hamood
- Department of Immunology and Molecular Microbiology, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
- * E-mail:
| |
Collapse
|
44
|
Thakur PB, Vaughn-Diaz VL, Greenwald JW, Gross DC. Characterization of five ECF sigma factors in the genome of Pseudomonas syringae pv. syringae B728a. PLoS One 2013; 8:e58846. [PMID: 23516563 PMCID: PMC3597554 DOI: 10.1371/journal.pone.0058846] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Accepted: 02/07/2013] [Indexed: 11/18/2022] Open
Abstract
Pseudomonas syringae pv. syringae B728a, a bacterial pathogen of bean, utilizes large surface populations and extracellular signaling to initiate a fundamental change from an epiphytic to a pathogenic lifestyle. Extracytoplasmic function (ECF) sigma (σ) factors serve as important regulatory factors in responding to various environmental signals. Bioinformatic analysis of the B728a genome revealed 10 ECF sigma factors. This study analyzed deletion mutants of five previously uncharacterized ECF sigma factor genes in B728a, including three FecI-type ECF sigma factors (ECF5, ECF6, and ECF7) and two ECF sigma factors placed in groups ECF11 and ECF18. Transcriptional profiling by qRT-PCR analysis of ECF sigma factor mutants was used to measure expression of their associated anti-sigma and outer membrane receptor proteins, and expression of genes associated with production of extracellular polysaccharides, fimbriae, glycine betaine and syringomycin. Notably, the B728aΔecf7 mutant displayed reduced swarming and had decreased expression of CupC fimbrial genes. Growth and pathogenicity assays, using a susceptible bean host, revealed that none of the tested sigma factor genes are required for in planta growth and lesion formation.
Collapse
Affiliation(s)
- Poulami Basu Thakur
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas, United States of America
| | - Vanessa L. Vaughn-Diaz
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas, United States of America
| | - Jessica W. Greenwald
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas, United States of America
| | - Dennis C. Gross
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas, United States of America
- * E-mail: .
| |
Collapse
|
45
|
Tryptophan inhibits biofilm formation by Pseudomonas aeruginosa. Antimicrob Agents Chemother 2013; 57:1921-5. [PMID: 23318791 DOI: 10.1128/aac.00007-13] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Biofilm formation by Pseudomonas aeruginosa has been implicated in the pathology of chronic wounds. Both the d and l isoforms of tryptophan inhibited P. aeruginosa biofilm formation on tissue culture plates, with an equimolar ratio of d and l isoforms producing the greatest inhibitory effect. Addition of d-/l-tryptophan to existing biofilms inhibited further biofilm growth and caused partial biofilm disassembly. Tryptophan significantly increased swimming motility, which may be responsible in part for diminished biofilm formation by P. aeruginosa.
Collapse
|
46
|
Loper JE, Hassan KA, Mavrodi DV, Davis EW, Lim CK, Shaffer BT, Elbourne LDH, Stockwell VO, Hartney SL, Breakwell K, Henkels MD, Tetu SG, Rangel LI, Kidarsa TA, Wilson NL, van de Mortel JE, Song C, Blumhagen R, Radune D, Hostetler JB, Brinkac LM, Durkin AS, Kluepfel DA, Wechter WP, Anderson AJ, Kim YC, Pierson LS, Pierson EA, Lindow SE, Kobayashi DY, Raaijmakers JM, Weller DM, Thomashow LS, Allen AE, Paulsen IT. Comparative genomics of plant-associated Pseudomonas spp.: insights into diversity and inheritance of traits involved in multitrophic interactions. PLoS Genet 2012; 8:e1002784. [PMID: 22792073 PMCID: PMC3390384 DOI: 10.1371/journal.pgen.1002784] [Citation(s) in RCA: 398] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Accepted: 05/10/2012] [Indexed: 12/11/2022] Open
Abstract
We provide here a comparative genome analysis of ten strains within the Pseudomonas fluorescens group including seven new genomic sequences. These strains exhibit a diverse spectrum of traits involved in biological control and other multitrophic interactions with plants, microbes, and insects. Multilocus sequence analysis placed the strains in three sub-clades, which was reinforced by high levels of synteny, size of core genomes, and relatedness of orthologous genes between strains within a sub-clade. The heterogeneity of the P. fluorescens group was reflected in the large size of its pan-genome, which makes up approximately 54% of the pan-genome of the genus as a whole, and a core genome representing only 45–52% of the genome of any individual strain. We discovered genes for traits that were not known previously in the strains, including genes for the biosynthesis of the siderophores achromobactin and pseudomonine and the antibiotic 2-hexyl-5-propyl-alkylresorcinol; novel bacteriocins; type II, III, and VI secretion systems; and insect toxins. Certain gene clusters, such as those for two type III secretion systems, are present only in specific sub-clades, suggesting vertical inheritance. Almost all of the genes associated with multitrophic interactions map to genomic regions present in only a subset of the strains or unique to a specific strain. To explore the evolutionary origin of these genes, we mapped their distributions relative to the locations of mobile genetic elements and repetitive extragenic palindromic (REP) elements in each genome. The mobile genetic elements and many strain-specific genes fall into regions devoid of REP elements (i.e., REP deserts) and regions displaying atypical tri-nucleotide composition, possibly indicating relatively recent acquisition of these loci. Collectively, the results of this study highlight the enormous heterogeneity of the P. fluorescens group and the importance of the variable genome in tailoring individual strains to their specific lifestyles and functional repertoire. We sequenced the genomes of seven strains of the Pseudomonas fluorescens group that colonize plant surfaces and function as biological control agents, protecting plants from disease. In this study, we demonstrated the genomic diversity of the group by comparing these strains to each other and to three other strains that were sequenced previously. Only about half of the genes in each strain are present in all of the other strains, and each strain has hundreds of unique genes that are not present in the other genomes. We mapped the genes that contribute to biological control in each genome and found that most of the biological control genes are in the variable regions of the genome, which are not shared by all of the other strains. This finding is consistent with our knowledge of the distinctive biology of each strain. Finally, we looked for new genes that are likely to confer antimicrobial traits needed to suppress plant pathogens, but have not been identified previously. In each genome, we discovered many of these new genes, which provide avenues for future discovery of new traits with the potential to manage plant diseases in agriculture or natural ecosystems.
Collapse
Affiliation(s)
- Joyce E Loper
- Agricultural Research Service, US Department of Agriculture, Corvallis, Oregon, United States of America.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
47
|
Busch A, Waksman G. Chaperone-usher pathways: diversity and pilus assembly mechanism. Philos Trans R Soc Lond B Biol Sci 2012; 367:1112-22. [PMID: 22411982 DOI: 10.1098/rstb.2011.0206] [Citation(s) in RCA: 100] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Up to eight different types of secretion systems, and several more subtypes, have been described in Gram-negative bacteria. Here, we focus on the diversity and assembly mechanism of one of the best-studied secretion systems, the widespread chaperone-usher pathway known to assemble and secrete adhesive surface structures, called pili or fimbriae, which play essential roles in targeting bacterial pathogens to the host.
Collapse
Affiliation(s)
- Andreas Busch
- Institute of Structural and Molecular Biology, University College London, Malet Street, WC1E 7HX London, UK
| | | |
Collapse
|
48
|
Mann EE, Wozniak DJ. Pseudomonas biofilm matrix composition and niche biology. FEMS Microbiol Rev 2012; 36:893-916. [PMID: 22212072 DOI: 10.1111/j.1574-6976.2011.00322.x] [Citation(s) in RCA: 378] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2011] [Revised: 12/18/2011] [Accepted: 12/19/2011] [Indexed: 11/27/2022] Open
Abstract
Biofilms are a predominant form of growth for bacteria in the environment and in the clinic. Critical for biofilm development are adherence, proliferation, and dispersion phases. Each of these stages includes reinforcement by, or modulation of, the extracellular matrix. Pseudomonas aeruginosa has been a model organism for the study of biofilm formation. Additionally, other Pseudomonas species utilize biofilm formation during plant colonization and environmental persistence. Pseudomonads produce several biofilm matrix molecules, including polysaccharides, nucleic acids, and proteins. Accessory matrix components shown to aid biofilm formation and adaptability under varying conditions are also produced by pseudomonads. Adaptation facilitated by biofilm formation allows for selection of genetic variants with unique and distinguishable colony morphology. Examples include rugose small-colony variants and wrinkly spreaders (WS), which over produce Psl/Pel or cellulose, respectively, and mucoid bacteria that over produce alginate. The well-documented emergence of these variants suggests that pseudomonads take advantage of matrix-building subpopulations conferring specific benefits for the entire population. This review will focus on various polysaccharides as well as additional Pseudomonas biofilm matrix components. Discussions will center on structure-function relationships, regulation, and the role of individual matrix molecules in niche biology.
Collapse
Affiliation(s)
- Ethan E Mann
- Department of Microbial Infection and Immunity, Department of Microbiology, Center for Microbial Interface Biology, The Ohio State University Medical Center, Columbus, OH 43210, USA
| | | |
Collapse
|
49
|
Giraud C, de Bentzmann S. Inside the complex regulation of Pseudomonas aeruginosa chaperone usher systems. Environ Microbiol 2011; 14:1805-16. [PMID: 22187957 DOI: 10.1111/j.1462-2920.2011.02673.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Pseudomonas aeruginosa assembles several cell surface-associated organelles, including those of the chaperone usher (CU) pathway. Five different CU loci have been identified and characterized in various strains of P.aeruginosa. However, their potential functional redundancy, particularly in biofilm formation, is supported by the control of their expression by a complex and specific regulatory network. Here, we review recent findings relating to this network. The control exerted by this network involves transcriptional repressors and activators, a phase-variable mechanism, a second intracellular messenger (c-di-GMP) and chemosensory and two-component systems.
Collapse
Affiliation(s)
- Caroline Giraud
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires, CNRS - Aix Marseille Université, 31 Chemin Joseph Aiguier, 13402 Marseille, France
| | | |
Collapse
|
50
|
Yang L, Rau MH, Yang L, Høiby N, Molin S, Jelsbak L. Bacterial adaptation during chronic infection revealed by independent component analysis of transcriptomic data. BMC Microbiol 2011; 11:184. [PMID: 21851621 PMCID: PMC3224102 DOI: 10.1186/1471-2180-11-184] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2011] [Accepted: 08/18/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Bacteria employ a variety of adaptation strategies during the course of chronic infections. Understanding bacterial adaptation can facilitate the identification of novel drug targets for better treatment of infectious diseases. Transcriptome profiling is a comprehensive and high-throughput approach for characterization of bacterial clinical isolates from infections. However, exploitation of the complex, noisy and high-dimensional transcriptomic dataset is difficult and often hindered by low statistical power. RESULTS In this study, we have applied two kinds of unsupervised analysis methods, principle component analysis (PCA) and independent component analysis (ICA), to extract and characterize the most informative features from transcriptomic dataset generated from cystic fibrosis (CF) Pseudomonas aeruginosa isolates. ICA was shown to be able to efficiently extract biological meaningful features from the transcriptomic dataset and improve clustering patterns of CF isolates. Decomposition of the transcriptomic dataset by ICA also facilitates gene identification and gene ontology enrichment. CONCLUSIONS Our results show that P. aeruginosa employs multiple patient-specific adaption strategies during the early stage infections while certain essential adaptations are evolved in parallel during the chronic infections.
Collapse
Affiliation(s)
- Lei Yang
- Department of Systems Biology, Technical University of Denmark, DK-2800, Lyngby, Denmark.
| | | | | | | | | | | |
Collapse
|