151
|
Tourkya B, Boubellouta T, Dufour E, Leriche F. Fluorescence spectroscopy as a promising tool for a polyphasic approach to pseudomonad taxonomy. Curr Microbiol 2008; 58:39-46. [PMID: 18815829 DOI: 10.1007/s00284-008-9263-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2008] [Revised: 08/11/2008] [Accepted: 08/25/2008] [Indexed: 10/21/2022]
Abstract
Fluorescence spectroscopy is an emerging tool for the analysis of biomolecules from complex matrices. We explored the potentialities of the method for the pseudomonad taxonomic purpose at the genus and species level. Emission spectra of three intrinsic fluorophores (namely, NADH, tryptophan, and the complex of aromatic amino acids and nucleic acid) were collected from whole bacterial cells. Their comparisons were performed through principal component analysis and factorial discriminant analysis. Reference strains from the Xanthomonas, Stenotrophomonas, Burkholderia, and Pseudomonas genera were well separated, with sensitivity and selectivity higher than 90%. At the species level, P. lundensis, P. taetrolens, P. fragi, P. chlororaphis, and P. stutzeri were also well separated, in a distant group, from P. putida, P. pseudoalcaligenes, and P. fluorescens. These results are in agreement with the generally admitted rRNA and DNA bacterial homology grouping but they also provide additional information about strain relatedness. In the case of environmental isolates, the method allows good discrimination, even for strains for which ambiguity still remained after PCR and API 20NE identification. Rapid, easy to perform, and low cost, fluorescence spectroscopy provides substantial information on cell components. Statistical analysis of collected data allows in-depth comparison of strains. Our results strongly support the view that fluorescence spectroscopy fingerprinting can be used as a powerful tool in a polyphasic approach to pseudomonad taxonomy.
Collapse
Affiliation(s)
- Belal Tourkya
- UPRES Typicité des Produits alimentaires, ENITA Clermont-Ferrand, Site de Marmilhat, BP 35, 63370, Lempdes, France
| | | | | | | |
Collapse
|
152
|
Abstract
We studied the importance of selection and constraint in determining the limits of adaptive radiation and the consequences of adaptive radiation in an experimental system. We propagated four replicate lines of the bacterium Pseudomonas fluorescens derived from a single ancestral clone in 95 environments, where growth was limited by the availability of a single carbon source for 1,000 generations. We then assayed the growth of the ancestral clone and the evolved lines in all 95 environments. Evolved lines increased their performance in almost every selection environment and invaded 70% of the novel environments as a direct response to selection. Direct responses tended to be larger in environments where growth was initially poor. Although evolved lines lost the ability to grow on about three substrates that their ancestor could readily grow on, the correlated response to selection was, on average, positive. The correlated response allowed all of our evolved populations to expand their niches and to occupy collectively the remaining novel habitats. This is inconsistent with classical theories of niche evolution. In the most extreme cases, adaptation occurred through "roundabout selection": lineages became adapted to an environment through selection in another environment but not through selection in the environment itself. Our results indicate that mutation accumulation by neutral drift was responsible for generating the majority of costs of adaptation.
Collapse
Affiliation(s)
- R Craig MacLean
- Department of Biology, McGill University, 1205 Avenue Doctor Penfield, Montreal, Quebec H3A 1B1, Canada
| | | |
Collapse
|
153
|
Souza V, Eguiarte LE, Siefert J, Elser JJ. Microbial endemism: does phosphorus limitation enhance speciation? Nat Rev Microbiol 2008; 6:559-64. [PMID: 18521074 DOI: 10.1038/nrmicro1917] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
There is increasing evidence for the existence of unique ecosystems that are dominated by locally adapted microbiota which harbour distinct lineages and biological capabilities, much like the macrobiota of Darwin's Galapagos Islands. As a primary example of such a system, we highlight key discoveries from the Cuatro Ciénegas basin in Mexico. We argue that high microbial endemism requires a combination of geographical isolation, long-term continuity and mechanisms for reducing the intensity of horizontal gene transfer (HGT). We also propose that strong phosphorus limitation has an important role in microbial diversification by reducing the intensity of HGT.
Collapse
Affiliation(s)
- Valeria Souza
- Valeria Souza and Luis E. Eguiarte are at the Department of Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, CU, AP 70-275, Coyoacán, 04510 México DF, Mexico.
| | | | | | | |
Collapse
|
154
|
Marco D. Metagenomics and the niche concept. Theory Biosci 2008; 127:241-7. [PMID: 18421492 DOI: 10.1007/s12064-008-0028-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2007] [Accepted: 03/20/2008] [Indexed: 10/22/2022]
Abstract
The metagenomics approach has revolutionised the fields of bacterial diversity, ecology and evolution, as well as derived applications like bioremediation and obtaining bioproducts. A further associated conceptual change has also occurred since in the metagenomics methodology the species is no longer the unit of study, but rather partial genome arrangements or even isolated genes. In spite of this, concepts coming from ecological and evolutionary fields traditionally centred on the species, like the concept of niche, are still being applied without further revision. A reformulation of the niche concept is necessary to deal with the new operative and epistemological challenges posed by the metagenomics approach. To contribute to this end, I review past and present uses of the niche concept in ecology and in microbiological studies, showing that a new, updated definition need to be used in the context of the metagenomics. Finally, I give some insights into a more adequate conceptual background for the utilisation of the niche concept in metagenomic studies. In particular, I raise the necessity of including the microbial genetic background as another variable into the niche space.
Collapse
Affiliation(s)
- Diana Marco
- Laboratorio de Ecología, Area de Producción Orgánica, Facultad de Ciencias Agropecuarias, Universidad Nacional de Córdoba, Ciudad Universitaria, Av. Valparaiso s/n, Córdoba, CP 5000, CC 508, Argentina.
| |
Collapse
|
155
|
Biodegradability, antimicrobial activity and properties of PVA/PVP hydrogels prepared by γ-irradiation. JOURNAL OF POLYMER RESEARCH 2008. [DOI: 10.1007/s10965-008-9196-0] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
156
|
Application and evaluation of double digest selective label (DDSL) typing technique for Pseudomonas aeruginosa hospital isolates. J Microbiol Methods 2008; 72:283-7. [DOI: 10.1016/j.mimet.2007.12.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2007] [Revised: 12/05/2007] [Accepted: 12/18/2007] [Indexed: 11/18/2022]
|
157
|
Fajardo A, Martínez-Martín N, Mercadillo M, Galán JC, Ghysels B, Matthijs S, Cornelis P, Wiehlmann L, Tümmler B, Baquero F, Martínez JL. The neglected intrinsic resistome of bacterial pathogens. PLoS One 2008; 3:e1619. [PMID: 18286176 PMCID: PMC2238818 DOI: 10.1371/journal.pone.0001619] [Citation(s) in RCA: 207] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2007] [Accepted: 01/17/2008] [Indexed: 11/18/2022] Open
Abstract
Bacteria with intrinsic resistance to antibiotics are a worrisome health problem. It is widely believed that intrinsic antibiotic resistance of bacterial pathogens is mainly the consequence of cellular impermeability and activity of efflux pumps. However, the analysis of transposon-tagged Pseudomonas aeruginosa mutants presented in this article shows that this phenotype emerges from the action of numerous proteins from all functional categories. Mutations in some genes make P. aeruginosa more susceptible to antibiotics and thereby represent new targets. Mutations in other genes make P. aeruginosa more resistant and therefore define novel mechanisms for mutation-driven acquisition of antibiotic resistance, opening a new research field based in the prediction of resistance before it emerges in clinical environments. Antibiotics are not just weapons against bacterial competitors, but also natural signalling molecules. Our results demonstrate that antibiotic resistance genes are not merely protective shields and offer a more comprehensive view of the role of antibiotic resistance genes in the clinic and in nature.
Collapse
Affiliation(s)
- Alicia Fajardo
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Cantoblanco, Madrid, Spain
| | - Nadia Martínez-Martín
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Cantoblanco, Madrid, Spain
| | - María Mercadillo
- Unidad Asociada al Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC) “Resistencia a los antibióticos y virulencia bacteriana”, Hospital Ramón y Cajal, Madrid, Spain
| | - Juan C. Galán
- Unidad Asociada al Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC) “Resistencia a los antibióticos y virulencia bacteriana”, Hospital Ramón y Cajal, Madrid, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Hospital Ramón y Cajal, Madrid, Spain
- Departamento de Microbiología, Hospital Ramón y Cajal, Madrid, Spain
| | - Bart Ghysels
- Laboratory of Microbial Interactions, Department of Molecular and Cellular Interactions, Flanders Interuniversity Institute for Biotechnology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Sandra Matthijs
- Laboratory of Microbial Interactions, Department of Molecular and Cellular Interactions, Flanders Interuniversity Institute for Biotechnology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Pierre Cornelis
- Laboratory of Microbial Interactions, Department of Molecular and Cellular Interactions, Flanders Interuniversity Institute for Biotechnology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Lutz Wiehlmann
- Klinische Forschergruppe, Medizinische Hochschule Hannover, Hannover, Germany
| | - Burkhard Tümmler
- Klinische Forschergruppe, Medizinische Hochschule Hannover, Hannover, Germany
| | - Fernando Baquero
- Unidad Asociada al Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC) “Resistencia a los antibióticos y virulencia bacteriana”, Hospital Ramón y Cajal, Madrid, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Hospital Ramón y Cajal, Madrid, Spain
- Departamento de Microbiología, Hospital Ramón y Cajal, Madrid, Spain
| | - José L. Martínez
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Cantoblanco, Madrid, Spain
- Unidad Asociada al Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC) “Resistencia a los antibióticos y virulencia bacteriana”, Hospital Ramón y Cajal, Madrid, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Hospital Ramón y Cajal, Madrid, Spain
- * To whom correspondence should be addressed. E-mail:
| |
Collapse
|
158
|
Frey B, Pesaro M, Rüdt A, Widmer F. Resilience of the rhizosphere Pseudomonas and ammonia-oxidizing bacterial populations during phytoextraction of heavy metal polluted soil with poplar. Environ Microbiol 2008; 10:1433-49. [DOI: 10.1111/j.1462-2920.2007.01556.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
159
|
Guyard-Nicodème M, Bazire A, Hémery G, Meylheuc T, Mollé D, Orange N, Fito-Boncompte L, Feuilloley M, Haras D, Dufour A, Chevalier S. Outer membrane Modifications of Pseudomonas fluorescens MF37 in Response to Hyperosmolarity. J Proteome Res 2008; 7:1218-25. [DOI: 10.1021/pr070539x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Muriel Guyard-Nicodème
- Laboratoire de Microbiologie du Froid, UPRES EA 2123,
Université de Rouen, Evreux, France, Laboratoire de Biotechnologie
et Chimie Marines, EA 3884, Université de Bretagne-Sud. Lorient,
France, Laboratoire Bioadhésion et Hygiène des Matériaux,
UMR/INRA-ENSIA, Massy, France, and INRA-Agrocampus, UMR 1253, Science
et Technologie du Lait et de l’Oeuf, Rennes, France
| | - Alexis Bazire
- Laboratoire de Microbiologie du Froid, UPRES EA 2123,
Université de Rouen, Evreux, France, Laboratoire de Biotechnologie
et Chimie Marines, EA 3884, Université de Bretagne-Sud. Lorient,
France, Laboratoire Bioadhésion et Hygiène des Matériaux,
UMR/INRA-ENSIA, Massy, France, and INRA-Agrocampus, UMR 1253, Science
et Technologie du Lait et de l’Oeuf, Rennes, France
| | - Gaëlle Hémery
- Laboratoire de Microbiologie du Froid, UPRES EA 2123,
Université de Rouen, Evreux, France, Laboratoire de Biotechnologie
et Chimie Marines, EA 3884, Université de Bretagne-Sud. Lorient,
France, Laboratoire Bioadhésion et Hygiène des Matériaux,
UMR/INRA-ENSIA, Massy, France, and INRA-Agrocampus, UMR 1253, Science
et Technologie du Lait et de l’Oeuf, Rennes, France
| | - Thierry Meylheuc
- Laboratoire de Microbiologie du Froid, UPRES EA 2123,
Université de Rouen, Evreux, France, Laboratoire de Biotechnologie
et Chimie Marines, EA 3884, Université de Bretagne-Sud. Lorient,
France, Laboratoire Bioadhésion et Hygiène des Matériaux,
UMR/INRA-ENSIA, Massy, France, and INRA-Agrocampus, UMR 1253, Science
et Technologie du Lait et de l’Oeuf, Rennes, France
| | - Daniel Mollé
- Laboratoire de Microbiologie du Froid, UPRES EA 2123,
Université de Rouen, Evreux, France, Laboratoire de Biotechnologie
et Chimie Marines, EA 3884, Université de Bretagne-Sud. Lorient,
France, Laboratoire Bioadhésion et Hygiène des Matériaux,
UMR/INRA-ENSIA, Massy, France, and INRA-Agrocampus, UMR 1253, Science
et Technologie du Lait et de l’Oeuf, Rennes, France
| | - Nicole Orange
- Laboratoire de Microbiologie du Froid, UPRES EA 2123,
Université de Rouen, Evreux, France, Laboratoire de Biotechnologie
et Chimie Marines, EA 3884, Université de Bretagne-Sud. Lorient,
France, Laboratoire Bioadhésion et Hygiène des Matériaux,
UMR/INRA-ENSIA, Massy, France, and INRA-Agrocampus, UMR 1253, Science
et Technologie du Lait et de l’Oeuf, Rennes, France
| | - Laurène Fito-Boncompte
- Laboratoire de Microbiologie du Froid, UPRES EA 2123,
Université de Rouen, Evreux, France, Laboratoire de Biotechnologie
et Chimie Marines, EA 3884, Université de Bretagne-Sud. Lorient,
France, Laboratoire Bioadhésion et Hygiène des Matériaux,
UMR/INRA-ENSIA, Massy, France, and INRA-Agrocampus, UMR 1253, Science
et Technologie du Lait et de l’Oeuf, Rennes, France
| | - Marc Feuilloley
- Laboratoire de Microbiologie du Froid, UPRES EA 2123,
Université de Rouen, Evreux, France, Laboratoire de Biotechnologie
et Chimie Marines, EA 3884, Université de Bretagne-Sud. Lorient,
France, Laboratoire Bioadhésion et Hygiène des Matériaux,
UMR/INRA-ENSIA, Massy, France, and INRA-Agrocampus, UMR 1253, Science
et Technologie du Lait et de l’Oeuf, Rennes, France
| | - Dominique Haras
- Laboratoire de Microbiologie du Froid, UPRES EA 2123,
Université de Rouen, Evreux, France, Laboratoire de Biotechnologie
et Chimie Marines, EA 3884, Université de Bretagne-Sud. Lorient,
France, Laboratoire Bioadhésion et Hygiène des Matériaux,
UMR/INRA-ENSIA, Massy, France, and INRA-Agrocampus, UMR 1253, Science
et Technologie du Lait et de l’Oeuf, Rennes, France
| | - Alain Dufour
- Laboratoire de Microbiologie du Froid, UPRES EA 2123,
Université de Rouen, Evreux, France, Laboratoire de Biotechnologie
et Chimie Marines, EA 3884, Université de Bretagne-Sud. Lorient,
France, Laboratoire Bioadhésion et Hygiène des Matériaux,
UMR/INRA-ENSIA, Massy, France, and INRA-Agrocampus, UMR 1253, Science
et Technologie du Lait et de l’Oeuf, Rennes, France
| | - Sylvie Chevalier
- Laboratoire de Microbiologie du Froid, UPRES EA 2123,
Université de Rouen, Evreux, France, Laboratoire de Biotechnologie
et Chimie Marines, EA 3884, Université de Bretagne-Sud. Lorient,
France, Laboratoire Bioadhésion et Hygiène des Matériaux,
UMR/INRA-ENSIA, Massy, France, and INRA-Agrocampus, UMR 1253, Science
et Technologie du Lait et de l’Oeuf, Rennes, France
| |
Collapse
|
160
|
Wickert E, Machado MA, Lemos EGM. Evaluation of the Genetic Diversity of Xylella fastidiosa Strains from Citrus and Coffee Hosts by Single-Nucleotide Polymorphism Markers. PHYTOPATHOLOGY 2007; 97:1543-9. [PMID: 18943714 DOI: 10.1094/phyto-97-12-1543] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
ABSTRACT The aim of this study was to obtain information about genetic diversity and make some inferences about the relationship of 27 strains of Xylella fastidiosa from different hosts and distinct geographical areas. Single-nucleotide polymorphism (SNP) molecular markers were identified in DNA sequences from 16 distinct regions of the genome of 24 strains of X. fastidiosa from coffee and citrus plants. Among the Brazilian strains, coffee-dependent strains have a greater number of SNPs (10 to 24 SNPs) than the citrus-based strains (2 to 12 SNPs); all the strains were compared with the sequenced strain 9a5c. The identified SNP markers were able to distinguish, for the first time, strains from citrus plants and coffee and showed that strains from coffee present higher genetic diversity than the others. These markers also have proven to be efficient for discriminating strains from the same host obtained from different geographic regions. X. fastidiosa, the causal agent of citrus variegated chlorosis, possesses genetic diversity, and the SNP markers were highly efficient for discriminating genetically close organisms.
Collapse
|
161
|
Carnazza S, Foti C, Gioffrè G, Felici F, Guglielmino S. Specific and selective probes for Pseudomonas aeruginosa from phage-displayed random peptide libraries. Biosens Bioelectron 2007; 23:1137-44. [PMID: 18068970 DOI: 10.1016/j.bios.2007.11.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2007] [Revised: 11/01/2007] [Accepted: 11/02/2007] [Indexed: 11/16/2022]
Abstract
The design of novel biosensors for the detection of biological threats, such as Pseudomonas aeruginosa, requires probes that specifically bind biological agents and insure their immediate and efficient recognition. Advanced bio-selective sensors may meet the requests for isolation, concentration of the agents and their real-time detection. There is a need for robust and inexpensive affinity probes alternative to antibodies. These probes may be recruited from random peptide libraries displayed on filamentous phage. In this study, we identified from two phage-displayed random peptide libraries phage clones displaying peptides capable of specific and strong binding to P. aeruginosa cell surface. The ability of the phage clones to interact specifically with P. aeruginosa was demonstrated by using enzyme-linked immunosorbent assay (ELISA). We assessed selectivity of phage-bacteria-binding by comparing the binding ability of the selected clones to the selector bacterium and a panel of other bacterial species; we also demonstrated by dot spot and immunoblotting that the most reactive and selective phage peptide bound with high avidity the bacterial cell surface. In addition, as proof-of-concept, we tested the possibility to immobilize the affinity-selected phage to a putative biosensor surface. The quality of phage deposition was monitored by ELISA, and phage-bacterial-binding was confirmed by high-power optical phase contrast microscopy. Overall, the results of this work validate the concept of affinity-selected recombinant filamentous phages as probes for detecting and monitoring bacterial agents under any conditions that warrant their recognition, including clinical-based diagnostics and possibly biological warfare applications.
Collapse
Affiliation(s)
- Santina Carnazza
- Department of Microbiological, Genetic and Molecular Sciences, University of Messina, Sal Sperone 31, Vill S Agata, Messina, Italy.
| | | | | | | | | |
Collapse
|
162
|
Lequette Y, Rollet E, Delangle A, Greenberg EP, Bohin JP. Linear osmoregulated periplasmic glucans are encoded by the opgGH locus of Pseudomonas aeruginosa. Microbiology (Reading) 2007; 153:3255-3263. [PMID: 17906125 DOI: 10.1099/mic.0.2007/008953-0] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Osmoregulated periplasmic glucans (OPGs) are produced by many proteobacteria and are important for bacterial-host interactions. The opgG and opgH genes involved in the synthesis of OPGs are the most widely distributed genes in proteobacterial genomes. Two other non-homologous genes, both named ndvB, are also involved in OPG biosynthesis in several species. The Pseudomonas aeruginosa genome possesses two ORFs, PA5077 and PA5078, that show similarity to opgH and opgG of Pseudomonas syringae, respectively, and one ORF, PA1163, similar to ndvB of Sinorhizobium meliloti. Here, we report that the opgGH locus of P. aeruginosa PA14 is involved in the synthesis of linear polymers with beta-1,2-linked glucosyl residues branched with a few beta-1,6 glucosyl residues. Succinyl residues also substitute this glucose backbone. Transcription of opgGH is repressed by high osmolarity. Low osmolarity promotes the formation of highly structured biofilms, but biofilm development is slower and the area of biomass is reduced under high osmolarity. Biofilm development of an opgGH mutant grown under low osmolarity presents a similar phenotype to the wild-type biofilm grown under high osmolarity. These results suggest that OPGs are important for biofilm formation under conditions of low osmolarity. A previous study suggested that the P. aeruginosa ndvB gene is involved in the resistance of biofilms to antibiotics. We have shown that ndvB is not involved in the biosynthesis of the OPG described here, and opgGH do not appear to be involved in the resistance of P. aeruginosa PA14 biofilms to antibiotics.
Collapse
Affiliation(s)
- Yannick Lequette
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA
| | - Eglantine Rollet
- Unité de Glycobiologie Structurale et Fonctionnelle CNRS UMR 8576, Université des Sciences et Technologies de Lille, 59655 Villeneuve d'Ascq Cedex, France
| | - Aurélie Delangle
- Unité de Glycobiologie Structurale et Fonctionnelle CNRS UMR 8576, Université des Sciences et Technologies de Lille, 59655 Villeneuve d'Ascq Cedex, France
| | - E Peter Greenberg
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA
| | - Jean-Pierre Bohin
- Unité de Glycobiologie Structurale et Fonctionnelle CNRS UMR 8576, Université des Sciences et Technologies de Lille, 59655 Villeneuve d'Ascq Cedex, France
| |
Collapse
|
163
|
Affiliation(s)
- Rowan D. H. Barrett
- Department of Biology, McGill University, 1205 Avenue Doctor Penfield, Montreal, Quebec H3H 1B1, Canada
| | - Graham Bell
- Department of Biology, McGill University, 1205 Avenue Doctor Penfield, Montreal, Quebec H3H 1B1, Canada
| |
Collapse
|
164
|
Chevalier S, Bodilis J, Jaouen T, Barray S, Feuilloley MGJ, Orange N. Sequence diversity of the OprD protein of environmental Pseudomonas strains. Environ Microbiol 2007; 9:824-35. [PMID: 17298381 DOI: 10.1111/j.1462-2920.2006.01191.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
OprD has been widely described for Pseudomonas aeruginosa at both structural and functional levels. Here, we describe the sequence diversity of the OprD proteins from other fluorescent Pseudomonads. We analysed the sequence of the oprD gene in each of the 49 Pseudomonas isolates, mostly putida and fluorescens species, obtained from various environmental sources, including soil, rhizosphere and hospitals. Phylogeny based on OprD sequences distinguished three well-separated clusters in the P. fluorescens species whereas P. putida isolates formed only one cluster. The OprD sequences were generally well conserved within each cluster whereas on the opposite, they were highly variable from one cluster to another and particularly with regards to the cluster of P. aeruginosa. Predicted secondary structures, based on the topological model elaborated for P. aeruginosa, suggest signatures in the large extracellular loops of OprD, which are linked to the OprD-based clusters. Correlations between these OprD-based clusters and ecological niches, growth on various carbon sources and antibiotic sensitivity were investigated.
Collapse
Affiliation(s)
- Sylvie Chevalier
- LMDF (Laboratoire de Microbiologie du Froid), UPRES 2123, Université de Rouen, 55, rue St Germain 27000 Evreux, France.
| | | | | | | | | | | |
Collapse
|
165
|
Roy U, Nair D. Biodiversity of organotin resistant Pseudomonas from west coast of India. ECOTOXICOLOGY (LONDON, ENGLAND) 2007; 16:253-61. [PMID: 17131180 DOI: 10.1007/s10646-006-0125-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2006] [Accepted: 10/11/2006] [Indexed: 05/12/2023]
Abstract
Five bacterial isolates were screened for resistance to organotin compound, i.e. tributyltin chloride (TBTC) up to 2 mM. The optimum pH, temperature and salinity for the growth of the isolates were found to be 7, 28 degrees C and 2.5%, respectively. The isolates were tested for survival tolerance to heavy metals (mercury, cadmium and zinc) and co-resistance to antibiotics viz. ampicillin, kanamycin, rifampicin, streptomycin, penicillin, chloramphenicol, tetracycline, nalidixic acid and neomycin. Although our earlier study reported that these five bacterial strains are of different species of Pseudomonas, our present 16S rRNA gene sequence analysis revealed that all the strains are Pseudomonas aeruginosa. One of five isolates P. aeruginosa strain 25W could grow in mineral salt medium with 2 mM of TBTC as a sole source of carbon and survive up to 5 mM of TBTC. In presence of 2 mM of TBTC there was comparable up-regulation of 45 kDa protein in the cell extract of the 25W isolate was found indicating involvement of certain enzymes in TBTC resistance.
Collapse
Affiliation(s)
- Upal Roy
- Department of Microbiology, Goa University, Taleigaon Plateau, Goa, India.
| | | |
Collapse
|
166
|
El-Arnaouty MB, Abdel Ghaffar AM, El Shafey HM. Radiation-induced graft copolymerization of acrylic acid/acrylonitrile onto LDPE and PET films and its biodegradability. J Appl Polym Sci 2007. [DOI: 10.1002/app.27099] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
167
|
Moore FP, Barac T, Borremans B, Oeyen L, Vangronsveld J, van der Lelie D, Campbell CD, Moore ERB. Endophytic bacterial diversity in poplar trees growing on a BTEX-contaminated site: The characterisation of isolates with potential to enhance phytoremediation. Syst Appl Microbiol 2006; 29:539-56. [PMID: 16919907 DOI: 10.1016/j.syapm.2005.11.012] [Citation(s) in RCA: 120] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/15/2005] [Indexed: 10/24/2022]
Abstract
The diversity of endophytic bacteria found in association with poplar was investigated as part of a larger study to assess the possibility and practicality of using endophytic bacteria to enhance in situ phytoremediation. Endophytic bacteria were isolated from the root, stem and leaf of two cultivars of poplar tree growing on a site contaminated with BTEX compounds. They were further characterised genotypically by comparative sequence analysis of partial 16S rRNA genes and BOX-PCR genomic DNA fingerprinting, and phenotypically by their tolerance to a range of target pollutants, heavy metals and antibiotics. One hundred and 21 stable, morphologically distinct isolates were obtained, belonging to 21 genera, although six isolates could not be identified with confidence to a genus. The endophytic bacteria exhibited marked spatial compartmentalisation within the plant, suggesting there are likely to be species-specific and non-specific associations between bacteria and plants. A number of isolates demonstrated the ability to degrade BTEX compounds or to grow in the presence of TCE. This study demonstrates that within the diverse bacterial communities found in poplar several endophytic strains are present that have the potential to enhance phytoremediation strategies.
Collapse
|
168
|
Hemery G, Chevalier S, Bellon-Fontaine MN, Haras D, Orange N. Growth temperature and OprF porin affect cell surface physicochemical properties and adhesive capacities of Pseudomonas fluorescens MF37. J Ind Microbiol Biotechnol 2006; 34:49-54. [PMID: 16932888 DOI: 10.1007/s10295-006-0160-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2006] [Accepted: 07/05/2006] [Indexed: 10/24/2022]
Abstract
Pseudomonads adapt to various ecological niches by forming biofilms, which first requires bacterial adhesion on surfaces. We studied the influence of growth temperature on surface physicochemical properties of Pseudomonas fluorescens MF37 and on its adhesive capacities onto inert surfaces. It presented a global hydrophilic character, measured by microbial adhesion to solvent (MATS), and showed a cell surface more hydrophilic at 8 and 28 degrees C than at 17 degrees C. Moreover, P. fluorescens MF37 was more adhesive at 17 degrees C. This critical temperature thus should be carefully taken into account in food safety. Adhesion onto inert surfaces is thus influenced by the growth temperature, which modifies the bacteria cell wall properties through changes in the outer membrane components. Therefore, we studied the effect of the loss of OprF, the major outer membrane protein, known to act as an adhesin (root, and endothelial cells). The OprF-deficient mutant was able to adhere to surfaces, but showed the same physicochemical and adhesion properties on abiotic surfaces whatever the growth temperature. OprF is thus not essential in this adhesion process. However, we suggest that OprF is involved in the bacterial environmental temperature sensing by P. fluorescens.
Collapse
Affiliation(s)
- Gaëlle Hemery
- Laboratoire de Microbiologie Du Froid, EA 2123, Université de Rouen, 55 rue St Germain, 27000, Evreux, France
| | | | | | | | | |
Collapse
|
169
|
Abstract
It has often been argued that evolutionary diversification is the result of divergent natural selection for specialization on alternative resources. I provide a comprehensive review of experiments that examine the ecology and genetics of resource specialization and adaptive radiation in microbial microcosms. In these experiments, resource heterogeneity generates divergent selection for specialization on alternative resources. At a molecular level, the evolution of specialization is generally attributable to mutations that de-regulate the expression of existing biosynthetic and catabolic pathways. Trade-offs are associated with the evolution of resource specialization, but these trade-offs are often not the result of antagonistic pleiotropy. Replicate adaptive radiations result in the evolution of a similar assemblage of specialists, but the genetic basis of specialization differs in replicate radiations. The implications of microbial selection experiments for evolutionary theory are discussed and future directions of research are proposed.
Collapse
Affiliation(s)
- R Craig MacLean
- Department of Biology, McGill University, Montreal QC, Canada.
| |
Collapse
|
170
|
Jaouen T, Coquet L, Marvin-Guy L, Orange N, Chevalier S, Dé E. Functional characterization of Pseudomonas fluorescens OprE and OprQ membrane proteins. Biochem Biophys Res Commun 2006; 346:1048-52. [PMID: 16777062 DOI: 10.1016/j.bbrc.2006.06.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2006] [Accepted: 06/02/2006] [Indexed: 10/24/2022]
Abstract
Outer membrane (OM) proteins of the OprD family may enable bacteria of the genus Pseudomonas to adapt to various environments by modulating OM permeability. The OprE and OprQ porins from P. fluorescens strain MF0 were purified and identified by MALDI-TOF mass spectrometry and N-terminal and internal microsequencing. These proteins, when reconstituted in an artificial planar lipid bilayer, induced similar ion channels with low single-conductance values. Secondary structure prediction of both proteins showed similar folding patterns into a 16 transmembrane beta-strands barrel but a highly variable amino-acid composition and length for their putative external loops implicated in porin function. Both proteins were overexpressed under poor oxygenation conditions, but not by using several amino acids as sole carbon source, indicating a different specificity for these proteins compared to the paradigm of this protein family, OprD.
Collapse
Affiliation(s)
- Thomas Jaouen
- Laboratoire de Microbiologie du Froid, UPRES 2123, Université de Rouen, 55 rue Saint Germain, 27000 Evreux, France
| | | | | | | | | | | |
Collapse
|
171
|
Lalucat J, Bennasar A, Bosch R, García-Valdés E, Palleroni NJ. Biology of Pseudomonas stutzeri. Microbiol Mol Biol Rev 2006; 70:510-47. [PMID: 16760312 PMCID: PMC1489536 DOI: 10.1128/mmbr.00047-05] [Citation(s) in RCA: 325] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Pseudomonas stutzeri is a nonfluorescent denitrifying bacterium widely distributed in the environment, and it has also been isolated as an opportunistic pathogen from humans. Over the past 15 years, much progress has been made in elucidating the taxonomy of this diverse taxonomical group, demonstrating the clonality of its populations. The species has received much attention because of its particular metabolic properties: it has been proposed as a model organism for denitrification studies; many strains have natural transformation properties, making it relevant for study of the transfer of genes in the environment; several strains are able to fix dinitrogen; and others participate in the degradation of pollutants or interact with toxic metals. This review considers the history of the discovery, nomenclatural changes, and early studies, together with the relevant biological and ecological properties, of P. stutzeri.
Collapse
Affiliation(s)
- Jorge Lalucat
- Department de Biologia, Microbiologia, Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain.
| | | | | | | | | |
Collapse
|
172
|
Monds RD, Newell PD, Schwartzman JA, O'Toole GA. Conservation of the Pho regulon in Pseudomonas fluorescens Pf0-1. Appl Environ Microbiol 2006; 72:1910-24. [PMID: 16517638 PMCID: PMC1393216 DOI: 10.1128/aem.72.3.1910-1924.2006] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Pho regulon integrates the sensing of environmental inorganic phosphate (Pi) availability with coregulation of gene expression, mediating an adaptive response to Pi limitation. Many aspects of the Pho regulon have been addressed in studies of Escherichia coli; however, it is unclear how transferable this knowledge is to other bacterial systems. Here, we report work to discern the conservation of the Pho regulon in Pseudomonas fluorescens Pf0-1. We demonstrate by mutational studies that PhoB/PhoR and the Pst system have conserved functions in the regulation of Pi-induced phosphatase activities, as well as expression of other Pi-regulated genes. A genetic screen was carried out to isolate factors that affect Pho-regulated phosphatase activity. We identified the Pho-regulated phosphatases PhoX and PhoD and present evidence that these enzymes are exported via the Tat system. The phoX and phoD genes were shown to be members of the Pho regulon by reverse transcription-PCR, as well as by functional assessment of putative PhoB binding sites (Pho boxes). Our data also suggested that at least one other non-Tat-secreted Pho-regulated phosphatase exists. From the genetic screen, numerous siderophore mutants that displayed severe defects in Pho-activated phosphatase activity were isolated. Subsequently, iron was shown to be important for modulating the activity of Pho-regulated phosphatases, but it does not regulate this activity at the level of transcription. We also identify and demonstrate a novel role in siderophore production and Pho-regulated phosphatase activity for ApaH, the hydrolase for the nucleotide-signaling molecule AppppA. Finally, numerous mutations in multiple cellular pathways were recovered that may be required for maximal induction of the Pho regulon under Pi-limiting conditions.
Collapse
Affiliation(s)
- Russell D Monds
- Dartmouth Medical School, Department of Microbiology and Immunology, Hanover, NH 03755, USA
| | | | | | | |
Collapse
|
173
|
Barrett RDH, Bell G. THE DYNAMICS OF DIVERSIFICATION IN EVOLVING PSEUDOMONAS POPULATIONS. Evolution 2006. [DOI: 10.1554/05-673.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
174
|
Jorquera M, Yamaguchi N, Tani K, Nasu M. A Combination of Direct Viable Counting, Fluorescence in situ Hybridization, and Green Fluorescent Protein Gene Expression for Estimating Plasmid Transfer at the Single Cell Level. Microbes Environ 2006. [DOI: 10.1264/jsme2.21.101] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Milko Jorquera
- Graduate School of Pharmaceutical Sciences, Osaka University
| | | | - Katsuji Tani
- Graduate School of Pharmaceutical Sciences, Osaka University
| | - Masao Nasu
- Graduate School of Pharmaceutical Sciences, Osaka University
| |
Collapse
|
175
|
Sedlak-Weinstein E, Cripps AW, Kyd JM, Foxwell AR. Pseudomonas aeruginosa: the potential to immunise against infection. Expert Opin Biol Ther 2005; 5:967-82. [PMID: 16018741 DOI: 10.1517/14712598.5.7.967] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Pseudomonas aeruginosa remains a serious pathogen for specific cohorts of patients where chronic infection is a poor prognostic indicator, such as those with cystic fibrosis, burn wounds or those who are immunocompromised. Significant disease burden is associated with a diverse spectrum of both nosocomial and community-acquired infections. To date, vaccines against P. aeruginosa have shown limited and often conflicting efficacy data, especially against heterologous strains, which are increasingly identified as co-colonisers of biofilms. While few studies have gone beyond Phase II clinical trials, a particular concern is the ability of P. aeruginosa to evade the immune system while provoking an immune response that contributes to the destructive nature of infection. Therefore, vaccine development needs to focus on preventing attachment and colonisation, as well as preventing conversion to a mucoid phenotype that is characteristic of the chronic condition that promotes pathology.
Collapse
Affiliation(s)
- E Sedlak-Weinstein
- Griffith University Gold Coast Campus, School of Medicine, PMB 50, Gold Coast Mail Centre, Queensland 9726, Australia
| | | | | | | |
Collapse
|
176
|
Sanchez L, Weidmann S, Arnould C, Bernard AR, Gianinazzi S, Gianinazzi-Pearson V. Pseudomonas fluorescens and Glomus mosseae trigger DMI3-dependent activation of genes related to a signal transduction pathway in roots of Medicago truncatula. PLANT PHYSIOLOGY 2005; 139:1065-77. [PMID: 16183836 PMCID: PMC1256018 DOI: 10.1104/pp.105.067603] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2005] [Revised: 06/23/2005] [Accepted: 07/13/2005] [Indexed: 05/04/2023]
Abstract
Plant genes induced during early root colonization of Medicago truncatula Gaertn. J5 by a growth-promoting strain of Pseudomonas fluorescens (C7R12) have been identified by suppressive subtractive hybridization. Ten M. truncatula genes, coding proteins associated with a putative signal transduction pathway, showed an early and transient activation during initial interactions between M. truncatula and P. fluorescens, up to 8 d after root inoculation. Gene expression was not significantly enhanced, except for one gene, in P. fluorescens-inoculated roots of a Myc(-)Nod(-) genotype (TRV25) of M. truncatula mutated for the DMI3 (syn. MtSYM13) gene. This gene codes a Ca(2+) and calmodulin-dependent protein kinase, indicating a possible role of calcium in the cellular interactions between M. truncatula and P. fluorescens. When expression of the 10 plant genes was compared in early stages of root colonization by mycorrhizal and rhizobial microsymbionts, Glomus mosseae activated all 10 genes, whereas Sinorhizobium meliloti only activated one and inhibited four others. None of the genes responded to inoculation by either microsymbiont in roots of the TRV25 mutant. The similar response of the M. truncatula genes to P. fluorescens and G. mosseae points to common molecular pathways in the perception of the microbial signals by plant roots.
Collapse
Affiliation(s)
- Lisa Sanchez
- Unité Mixte de Recherche, Institut National de la Recherche Agronomique 1088/Centre National de la Recherche Scientifique 5184/Université de Bourgogne Plante-Microbe-Environnement, Dijon, France
| | | | | | | | | | | |
Collapse
|
177
|
Hõrak R, Ilves H, Pruunsild P, Kuljus M, Kivisaar M. The ColR-ColS two-component signal transduction system is involved in regulation of Tn4652 transposition in Pseudomonas putida under starvation conditions. Mol Microbiol 2005; 54:795-807. [PMID: 15491368 DOI: 10.1111/j.1365-2958.2004.04311.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bacteria use two-component signal transduction pathways to sense both extracellular and intracellular environment and to coordinate cellular events according to changing conditions. Adaptation can be either physiological or genetical. Here, we present evidence that a genome reorganization process such as transposition can be controlled by certain environmental cues sensed by a two-component signal transduction system. We demonstrate that transposition-dependent accumulation of phenol-utilizing mutants is severely decreased in Pseudomonas putida defective in a two-component system colRS. Translocation of Tn4652 is decreased both in colR- and colS-defective strains, indicating that signal transduction from a histidine kinase ColS to a response regulator ColR is necessary for the activation of Tn4652 in bacteria starving on phenol. However, overexpression of ColR in a colS-defective strain restores Tn4652 transposition, suggesting that absence of the signal from ColS can be compensated by an elevated amount of ColR. In vitro analysis of purified ColR and ColS proteins evidenced that they constitute a functional phosphorelay. Site-directed mutagenesis revealed that a conserved H221 can be the phosphoryl-accepting residue in ColS and that aspartate residues D8 and D51 of ColR are necessary for the phosphotransfer from ColS to ColR. To our knowledge, Tn4652 is the first bacterial transposon regulated by a two-component system. This finding indicates that transpositional activity can respond to signals sensed and processed by the host.
Collapse
Affiliation(s)
- Rita Hõrak
- Estonian Biocentre and Institute of Molecular and Cell Biology, Tartu University, 51010 Tartu, Estonia.
| | | | | | | | | |
Collapse
|
178
|
Zamudio-Rivera LS, George-Tellez R, López-Mendoza G, Morales-Pacheco A, Flores E, Höpfl H, Barba V, Fernández FJ, Cabirol N, Beltrán HI. Synthesis, Characterization, Biocide and Toxicological Activities of Di-n-butyl- and Diphenyl-tinIV-Salicyliden-β-Amino Alcohol Derivatives. Inorg Chem 2005; 44:5370-8. [PMID: 16022535 DOI: 10.1021/ic048628o] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The one pot reaction of salicylaldehyde 1, beta-amino alcohols 2a-2c, and di-n-butyltin(IV) oxide 3a or diphenyltin(IV) oxide 3b produced five diorganotin(IV) compounds, 4a-4c, 5a, and 5c, in good yields. All compounds were characterized by IR, (1)H, (13)C, and (119)Sn NMR spectroscopy, and elemental analysis; furthermore, compounds 4b, 4c, 5a, and 5c were characterized by X-ray diffraction analysis. After the structural characterization, all of the compounds were tested in vitro against Bacillus subtilis (Gram-positive, strain ATCC 6633), Escherichia coli (Gram-negative, strain DH5alpha), Pseudomonas aeruginosa (Gram-negative, strain BH3), Desulfovibrio longus (strain DSM 6739), and Desulfomicrobium aspheronum (strain DSM 5918) to assess their antimicrobial activity. Compounds 4 and 5 demonstrated a wide range of bactericidal activities against the tested aerobic (one Gram-positive and two Gram-negative subtypes) and anaerobic bacteria (two sulfate-reducing bacteria, SRB). Compound 5 had better bactericidal performances than compound 4. For all of the compounds, the acute toxicity was measured using luminescent bacteria toxicity (LBT-Microtox) tests to track their further environmental impact. According to these results and in order to fulfill environmental regulations, the toxicity of the compounds studied herein can be modulated through the proper selection of the disubstituted tin(IV) moiety.
Collapse
Affiliation(s)
- Luis S Zamudio-Rivera
- Programa de Ingeniería Molecular, Instituto Mexicano del Petróleo, Eje Central Lázaro Cárdenas No.152, Apartado Postal 14-805, 07730 México, D.F
| | | | | | | | | | | | | | | | | | | |
Collapse
|
179
|
Hoffmann N, Rasmussen TB, Jensen PØ, Stub C, Hentzer M, Molin S, Ciofu O, Givskov M, Johansen HK, Høiby N. Novel mouse model of chronic Pseudomonas aeruginosa lung infection mimicking cystic fibrosis. Infect Immun 2005; 73:2504-14. [PMID: 15784597 PMCID: PMC1087399 DOI: 10.1128/iai.73.4.2504-2514.2005] [Citation(s) in RCA: 138] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Pseudomonas aeruginosa causes a chronic infection in the lungs of cystic fibrosis (CF) patients by establishing an alginate-containing biofilm. The infection has been studied in several animal models; however, most of the models required artificial embedding of the bacteria. We present here a new pulmonary mouse model without artificial embedding. The model is based on a stable mucoid CF sputum isolate (NH57388A) with hyperproduction of alginate due to a deletion in mucA and functional N-acylhomoserine lactone (AHL)-based quorum-sensing systems. Chronic lung infection could be established in both CF mice (Cftr(tmlUnc-/-)) and BALB/c mice, as reflected by the detection of a high number of P. aeruginosa organisms in the lung homogenates at 7 days postinfection and alginate biofilms, surrounded by polymorphonuclear leukocytes in the alveoli. In comparison, both an AHL-producing nonmucoid revertant (NH57388C) from the mucoid isolate (NH57388A) and a nonmucoid isolate (NH57388B) deficient in AHL were almost cleared from the lungs of the mice. This model, in which P. aeruginosa is protected against the defense system of the lung by alginate, is similar to the clinical situation. Therefore, the mouse model provides an improved method for evaluating the interaction between mucoid P. aeruginosa, the host, and antibacterial therapy.
Collapse
Affiliation(s)
- Nadine Hoffmann
- Department of Bacteriology, Institute for Medical Microbiology and Immunology, Panum Institute, University of Copenhagen, Copenhagen DK-2200, Denmark.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
180
|
Jaouen T, Dé E, Chevalier S, Orange N. Pore size dependence on growth temperature is a common characteristic of the major outer membrane protein OprF in psychrotrophic and mesophilic Pseudomonas species. Appl Environ Microbiol 2005; 70:6665-9. [PMID: 15528532 PMCID: PMC525151 DOI: 10.1128/aem.70.11.6665-6669.2004] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pseudomonas species adapt well to hostile environments, which are often subjected to rapid variations. In these bacteria, the outer membrane plays an important role in the sensing of environmental conditions such as temperature. In previous studies, it has been shown that in the psychrotrophic strain P. fluorescens MF0, the major porin OprF changes its channel size according to the growth conditions and could affect outer membrane permeability. Studies of the channel-forming properties of OprFs from P. putida 01G3 and P. aeruginosa PAO1 in planar lipid bilayers generated similar results. The presence of a cysteine- or proline-rich cluster in the central linker region is not essential for channel size modulations. These findings suggest that OprF could adopt two alternative conformations in the outer membrane and that folding is thermoregulated. In contrast, no difference according to growth temperature was observed for structurally different outer membrane proteins, such as OprE3 from the Pseudomonas OprD family of specific porins. Our results are consistent with the fact that the decrease in channel size observed at low growth temperature is a particular feature of the OprF porin in various psychrotrophic and mesophilic Pseudomonas species isolated from diverse ecological niches. The ability to reduce outer membrane permeability at low growth temperature could provide these bacteria with adaptive advantages.
Collapse
Affiliation(s)
- Thomas Jaouen
- Laboratoire de Microbiologie du Froid, UPRES 2123, Université de Rouen, Evreux, France
| | | | | | | |
Collapse
|
181
|
Lloyd-Jones G, Laurie AD, Tizzard AC. Quantification of the Pseudomonas population in New Zealand soils by fluorogenic PCR assay and culturing techniques. J Microbiol Methods 2005; 60:217-24. [PMID: 15590096 DOI: 10.1016/j.mimet.2004.09.011] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2004] [Revised: 09/24/2004] [Accepted: 09/24/2004] [Indexed: 11/29/2022]
Abstract
The genus Pseudomonas contains fast-growing nutritionally versatile bacteria that are able to utilize a wide variety of carbon sources. The ubiquity of the genus has been highlighted by conventional microbiology and the genus is well represented in collections of cultured bacteria. Here we evaluate the Pseudomonas population in New Zealand soils by comparing a culture-independent (real-time PCR combined with fluorescent TaqMan technology) with a culture-dependent (Gould's S1) population estimate. We show that cultivated fluorescent pseudomonads are not numerically dominant and represent a small proportion of <1% of the total Pseudomonas population, and that the total Pseudomonas population itself represents only a small proportion of <1% of the total bacterial population.
Collapse
|
182
|
Davelos AL, Xiao K, Samac DA, Martin AP, Kinkel LL. Spatial variation in Streptomyces genetic composition and diversity in a prairie soil. MICROBIAL ECOLOGY 2004; 48:601-612. [PMID: 15696393 DOI: 10.1007/s00248-004-0031-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2004] [Accepted: 05/28/2004] [Indexed: 05/24/2023]
Abstract
Understanding how microbial genotypes are arrayed in space is crucial for identifying local factors that may influence the spatial distribution of genetic diversity. In this study we investigated variation in 16S rDNA sequences and rep-PCR fingerprints of Streptomyces stains isolated from prairie soil among three locations and four soil depths. Substantial variation in Streptomyces OTU (operational taxonomic unit) and BOX-PCR fingerprint diversity was found among locations within a limited spatial area (1 m2). Further, phylogenetic lineages at each location were distinct. However, there was little variation in genetic diversity among isolates from different soil depths and similar phylogenetic lineages were found at each depth. Some clones were found at a localized scale while other clones had a relatively widespread distribution. There was poor correspondence between 16S rDNA groupings and rep-PCR fingerprint groupings. The finding of distinct phylogenetic lineages and the variation in spatial distribution of clones suggests that selection pressures may vary over the soil landscape.
Collapse
Affiliation(s)
- A L Davelos
- Department of Plant Pathology, University of Minnesota, 495 Borlaug Hall, 1991 Upper Buford Circle, St. Paul, MN 55108, USA.
| | | | | | | | | |
Collapse
|
183
|
Jones A. The molecular cell biology of head and neck cancer with clinical applications. Section 1: Fundamental biology and the basis of cancer. ACTA ACUST UNITED AC 2004; 29:475-91. [PMID: 15373861 DOI: 10.1111/j.1365-2273.2004.00834.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
This article addresses the subject of the fundamental workings of the cell. The essential mechanisms that underlie life are discussed and explained as succinctly as intelligibility will allow and the basic principles of molecular and cell biology detailed. In preparing this article I have made reference not only to standard works but also to the most recent research. In the article I attempt to provide both the surgical and medical head and neck oncologist with the basic insights into fundamental oncology necessary to understand and treat the clinical conditions that are head and neck cancer. In addition I hope it will facilitate the understanding of the various evolving novel treatment strategies.
Collapse
Affiliation(s)
- A Jones
- Faculty of Medicine, The University of Liverpool, Clincal Sciences Centre, University Hospital Aintree, Longmoor Lane, Liverpool L9 7AL, UK.
| |
Collapse
|
184
|
Leriche F, Bordessoules A, Fayolle K, Karoui R, Laval K, Leblanc L, Dufour E. Alteration of raw-milk cheese by Pseudomonas spp.: monitoring the sources of contamination using fluorescence spectroscopy and metabolic profiling. J Microbiol Methods 2004; 59:33-41. [PMID: 15325751 DOI: 10.1016/j.mimet.2004.05.009] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2004] [Revised: 05/25/2004] [Accepted: 05/25/2004] [Indexed: 11/23/2022]
Abstract
Thirty Pseudomonas spp. strains isolated from milk, water, cheese centre and cheese surface in two traditional workshops manufacturing raw milk St. Nectaire cheese were characterised by fluorescence spectroscopy and Biolog metabolic profiling. Factorial discriminant analysis (FDA) of the two data sets revealed clear linkages between groups of isolates. In the first workshop, milk could be incriminated as the sole source of cheese contamination. In the second one, milk and cheese centre isolates were found similar but surface cheese contaminants could be linked to a secondary contamination originating from water. Thus, it is possible to characterise, differentiate and trace Pseudomonas spp. strains using the fluorescence and metabolic profiling techniques. In addition, the two data sets were found highly correlated by canonical correlation analysis (CCA). Fluorescence spectroscopy however showed several advantages because of its low cost and processing speed.
Collapse
Affiliation(s)
- Françoise Leriche
- UPRES Typicité des Produits Alimentaires, ENITA Clermont-Ferrand, Site de Marmilhat, 63370 Lempdes, France.
| | | | | | | | | | | | | |
Collapse
|
185
|
Cladera AM, Bennasar A, Barceló M, Lalucat J, García-Valdés E. Comparative genetic diversity of Pseudomonas stutzeri genomovars, clonal structure, and phylogeny of the species. J Bacteriol 2004; 186:5239-48. [PMID: 15292125 PMCID: PMC490930 DOI: 10.1128/jb.186.16.5239-5248.2004] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A combined phylogenetic and multilocus DNA sequence analysis of 26 Pseudomonas stutzeri strains distributed within the 9 genomovars of the species has been performed. Type strains of the two most closely related species (P. balearica, former genomovar 6, and P. mendocina), together with P. aeruginosa, as the type species of the genus, have been included in the study. The extremely high genetic diversity and the clonal structure of the species were confirmed by the sequence analysis. Clustering of strains in the consensus phylogeny inferred from the analysis of seven nucleotide sequences (16S ribosomal DNA, internally transcribed spacer region 1, gyrB, rpoD, nosZ, catA, and nahH) confirmed the monophyletic origin of the genomovars within the Pseudomonas branch and is in good agreement with earlier DNA-DNA similarity analysis, indicating that the selected genes are representative of the whole genome in members of the species.
Collapse
Affiliation(s)
- Aina Maria Cladera
- Departament de Biologia, Microbiologia, Universitat de les Illes Balears, and Institut Mediterrani d'Estudis Avançats (CSIC-UIB), Palma de Mallorca, Spain
| | | | | | | | | |
Collapse
|
186
|
Cerdà-Cuéllar M, Kint DP, Muñoz-Guerra S, Soledad Marqués-Calvo M. Biodegradability of aromatic building blocks for poly(ethylene terephthalate) copolyesters. Polym Degrad Stab 2004. [DOI: 10.1016/j.polymdegradstab.2004.04.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
187
|
Morales G, Wiehlmann L, Gudowius P, van Delden C, Tümmler B, Martínez JL, Rojo F. Structure of Pseudomonas aeruginosa populations analyzed by single nucleotide polymorphism and pulsed-field gel electrophoresis genotyping. J Bacteriol 2004; 186:4228-37. [PMID: 15205425 PMCID: PMC421620 DOI: 10.1128/jb.186.13.4228-4237.2004] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pseudomonas aeruginosa has a wide ecological distribution that includes natural habitats and clinical settings. To analyze the population structure and distribution of P. aeruginosa, a collection of 111 isolates of diverse habitats and geographical origin, most of which contained a genome with a different SpeI macrorestriction profile, was typed by restriction fragment length polymorphism based on 14 single nucleotide polymorphisms (SNPs) located at seven conserved loci of the core genome (oriC, oprL, fliC, alkB2, citS, oprI, and ampC). The combination of these SNPs plus the type of fliC present (a or b) allowed the assignment of a genetic fingerprint to each strain, thus providing a simple tool for the discrimination of P. aeruginosa strains. Thirteen of the 91 identified SNP genotypes were found in two or more strains. In several cases, strains sharing their SNP genotype had different SpeI macrorestriction profiles. The highly virulent CHA strain shared its SNP genotype with other strains that had different SpeI genotypes and which had been isolated from nonclinical habitats. The reference strain PAO1 also shared its SNP genotype with other strains that had different SpeI genotypes. The P. aeruginosa chromosome contains a conserved core genome and variable amounts of accessory DNA segments (genomic islands and islets) that can be horizontally transferred among strains. The fact that some SNP genotypes were overrepresented in the P. aeruginosa population studied and that several strains sharing an SNP genotype had different SpeI macrorestriction profiles supports the idea that changes occur at a higher rate in the accessory DNA segments than in the conserved core genome.
Collapse
Affiliation(s)
- Gracia Morales
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Campus de la UAM, Cantoblanco, 28049 Madrid, Spain
| | | | | | | | | | | | | |
Collapse
|
188
|
Rainey PB, Cooper TF. Evolution of bacterial diversity and the origins of modularity. Res Microbiol 2004; 155:370-5. [PMID: 15207869 DOI: 10.1016/j.resmic.2004.01.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2003] [Accepted: 01/23/2004] [Indexed: 10/26/2022]
Abstract
A characteristic feature of all organisms is modular organisation: the tendency for groups of genes to interact in such a way as to limit the extent of pleiotropic effects among characters belonging to different functional complexes. While the implications of modularity for the evolution of variability have been much discussed the evolutionary origins remain obscure. Here we develop a model, with special reference to signal transduction cascades of bacteria, which predicts that in the face of ecological opportunity and lateral gene transfer, selection will favour modular genome architectures because such architectures minimise the pleiotropic effects associated with accommodation of potentially beneficial foreign DNA.
Collapse
Affiliation(s)
- Paul B Rainey
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand.
| | | |
Collapse
|
189
|
Sarma PM, Bhattacharya D, Krishnan S, Lal B. Assessment of intra-species diversity among strains ofAcinetobacterbaumanniiisolated from sites contaminated with petroleum hydrocarbons. Can J Microbiol 2004; 50:405-14. [PMID: 15284886 DOI: 10.1139/w04-018] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A total of 96 crude oil - degrading bacterial strains were isolated from 5 geographically diverse sites in India that were contaminated with different types of petroleum hydrocarbons. The strains were identified by sequencing the genes that encode for 16S rRNA. Out of the 96 isolates, 25 strains were identified as Acinetobacter baumannii and selected for the study. All of the selected strains could degrade the total petroleum hydrocarbon fractions of crude oil. These 25 strains were biochemically profiled and grouped into 8 phenovars on the basis of multivariate analysis of their substrate utilization profiles. PCR-based DNA fingerprinting was performed using intergenic repetitive DNA sequences, which divided the selected 25 strains into 7 specific genomic clusters. tRNA intergenic spacer length polymorphism was performed to determine the intra-species relatedness among these 25 strains. It delineated the strains into 8 genomic groups. The present study detected specific variants among the A. baumannii strains with differential degradation capacities for different fractions of crude oil. This could play a significant role in in situ bioremediation. The study also revealed the impact of environmental factors that cause intra-species diversity within the selected strains of A. baumannii.Key words: genotypic diversity, phenotypic diversity, crude oil, Acinetobacter baumannii.
Collapse
Affiliation(s)
- Priyangshu Manab Sarma
- Center of Bioresources and Biotechnology, TERI School of Advanced Studies, New Delhi, India
| | | | | | | |
Collapse
|
190
|
Budzikiewicz H. Siderophores of the Pseudomonadaceae sensu stricto (fluorescent and non-fluorescent Pseudomonas spp.). FORTSCHRITTE DER CHEMIE ORGANISCHER NATURSTOFFE = PROGRESS IN THE CHEMISTRY OF ORGANIC NATURAL PRODUCTS. PROGRES DANS LA CHIMIE DES SUBSTANCES ORGANIQUES NATURELLES 2004; 87:81-237. [PMID: 15079896 DOI: 10.1007/978-3-7091-0581-8_2] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Affiliation(s)
- H Budzikiewicz
- Institut für Organische Chemie, Universität zu Köln, Germany
| |
Collapse
|
191
|
Tegova R, Tover A, Tarassova K, Tark M, Kivisaar M. Involvement of error-prone DNA polymerase IV in stationary-phase mutagenesis in Pseudomonas putida. J Bacteriol 2004; 186:2735-44. [PMID: 15090515 PMCID: PMC387815 DOI: 10.1128/jb.186.9.2735-2744.2004] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2003] [Accepted: 01/23/2004] [Indexed: 11/20/2022] Open
Abstract
In this work we studied involvement of DNA polymerase IV (Pol IV) (encoded by the dinB gene) in stationary-phase mutagenesis in Pseudomonas putida. For this purpose we constructed a novel set of assay systems that allowed detection of different types of mutations (e.g., 1-bp deletions and different base substitutions) separately. A significant effect of Pol IV became apparent when the frequency of accumulation of 1-bp deletion mutations was compared in the P. putida wild-type strain and its Pol IV-defective dinB knockout derivative. Pol IV-dependent mutagenesis caused a remarkable increase (approximately 10-fold) in the frequency of accumulation of 1-bp deletion mutations on selective plates in wild-type P. putida populations starved for more than 1 week. No effect of Pol IV on the frequency of accumulation of base substitution mutations in starving P. putida cells was observed. The occurrence of 1-bp deletions in P. putida cells did not require a functional RecA protein. RecA independence of Pol IV-associated mutagenesis was also supported by data showing that transcription from the promoter of the P. putida dinB gene was not significantly influenced by the DNA damage-inducing agent mitomycin C. Therefore, we hypothesize that mechanisms different from the classical RecA-dependent SOS response could elevate Pol IV-dependent mutagenesis in starving P. putida cells.
Collapse
Affiliation(s)
- Radi Tegova
- Department of Genetics, Institute of Molecular and Cell Biology, Tartu University and Estonian Biocentre, 23 Riia Street, 51010 Tartu, Estonia
| | | | | | | | | |
Collapse
|
192
|
Matz C, Bergfeld T, Rice SA, Kjelleberg S. Microcolonies, quorum sensing and cytotoxicity determine the survival of Pseudomonas aeruginosa biofilms exposed to protozoan grazing. Environ Microbiol 2004; 6:218-26. [PMID: 14871206 DOI: 10.1111/j.1462-2920.2004.00556.x] [Citation(s) in RCA: 152] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This study was based on the hypothesis that biofilms of the opportunistic pathogen Pseudomonas aeruginosa are successfully adapted to situations of protozoan grazing. We tested P. aeruginosa wild type and strains that were genetically altered, in structural and regulatory features of biofilm development, in response to the common surface-feeding flagellate Rhynchomonas nasuta. Early biofilms of the wild type showed the formation of grazing resistant microcolonies in the presence of the flagellate, whereas biofilms without the predator were undifferentiated. Grazing on biofilms of quorum sensing mutants (lasR and rhlR/lasR) also resulted in the formation of microcolonies, however, in lower numbers and size compared to the wild type. Considerably fewer microcolonies than the wild type were formed by mutant cells lacking type IV pili, whereas no microcolonies were formed by flagella-deficient cells. The alginate-overproducing strain PDO300 developed larger microcolonies in response to grazing. These observations suggest a role of quorum sensing in early biofilms and involvement of flagella, type IV pili, and alginate in microcolony formation in the presence of grazing. More mature biofilms of the wild type exhibited acute toxicity to the flagellate R. nasuta. Rapid growth of the flagellate on rhlR/lasR mutant biofilms indicated a key role of quorum sensing in the upregulation of lethal factors and in grazing protection of late biofilms. Both the formation of microcolonies and the production of toxins are effective mechanisms that may allow P. aeruginosa biofilms to resist protozoan grazing and to persist in the environment.
Collapse
Affiliation(s)
- Carsten Matz
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney 2052, Australia
| | | | | | | |
Collapse
|
193
|
Wehmhöner D, Häussler S, Tümmler B, Jänsch L, Bredenbruch F, Wehland J, Steinmetz I. Inter- and intraclonal diversity of the Pseudomonas aeruginosa proteome manifests within the secretome. J Bacteriol 2003; 185:5807-14. [PMID: 13129952 PMCID: PMC193958 DOI: 10.1128/jb.185.19.5807-5814.2003] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The proteomes of cultured Pseudomonas aeruginosa isolates from chronically infected cystic fibrosis (CF) lungs were compared by using genetically divergent clones and isogenic morphotypes of one strain. Cellular extracts gave very similar protein patterns in two-dimensional gels, suggesting that the conserved species-specific core genome encodes proteins that are expressed under standard culture conditions in vitro. In contrast, the protein profiles of extracts of culture supernatants were dependent on the growth phase, and there were significant differences between clones. The profiles also varied within clonally related morphotypes from one CF patient, including a hyperpiliated small-colony variant. Mass spectrometry revealed that this variant overexpressed proteins secreted by the type I secretion system (including proteins involved in iron acquisition) and by the type III secretion system. Furthermore, the proteins in the supernatant extracts from the small-colony variant which were recognized by sera from different CF patients varied greatly. We concluded that the secretome expression is a sensitive measure of P. aeruginosa strain variation.
Collapse
Affiliation(s)
- Dirk Wehmhöner
- Institute of Medical Microbiology, Hannover Medical School, 30265 Hannover, Germany
| | | | | | | | | | | | | |
Collapse
|
194
|
Nouwens AS, Walsh BJ, Cordwell SJ. Application of proteomics to Pseudomonas aeruginosa. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2003; 83:117-40. [PMID: 12934928 DOI: 10.1007/3-540-36459-5_5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
The recent completion of the Pseudomonas Genome Project, in conjunction with the Pseudomonas Community Annotation Project (PseudoCAP) has fast-tracked our ability to apply the tools encompassed under the term 'proteomics' to this pathogen. Such global approaches will allow the research community to answer long-standing questions regarding the ability of Pseudomonas aeruginosa to survive diverse habitats, its high intrinsic resistance to antibiotics and its pathogenic nature towards humans. Proteomics provides an array of tools capable of confirming the expression of Open Reading Frames (ORF), the relative levels of their expression, the environmental conditions required for this expression and the sub-cellular location of the encoded gene-products. Since proteins are important cellular effectors, the biological questions we pose can be defined in terms of changes in protein expression detectable by separation to purity using two-dimensional gel electrophoresis (2-DGE) and relation to gene sequences via mass spectrometry. As such, we can compare strains with well-characterized phenotypic differences, growth under a variety of stresses, protein interactions and complexes and aid in defining proteins of unknown function. While the complete genome has only recently been finished, a number of studies have already utilized this information and examined various protein gene-products using proteomics. This review summarizes the application of proteomics to P. aeruginosa and highlights potential areas of future research, including overcoming the traditional technical limitations associated with 2-DGE. More focused approaches that target sub-cellular fractions ('sub-proteomes') prior to 2-DGE can provide further functional information. A review of current and previous proteomic projects on P. aeruginosa is presented, as well as theoretical considerations of the importance of sub-proteomic approaches to enhance these investigations.
Collapse
|
195
|
Oda Y, Star B, Huisman LA, Gottschal JC, Forney LJ. Biogeography of the purple nonsulfur bacterium Rhodopseudomonas palustris. Appl Environ Microbiol 2003; 69:5186-91. [PMID: 12957900 PMCID: PMC194913 DOI: 10.1128/aem.69.9.5186-5191.2003] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The biogeography of the purple nonsulfur bacterium Rhodopseudomonas palustris on a local scale was investigated. Thirty clones of phototrophic bacteria were isolated from each of five unevenly spaced sampling locations in freshwater marsh sediments along a linear 10-m transect, and a total of 150 clones were characterized by BOX-PCR genomic DNA fingerprinting. Cluster analysis of 150 genomic fingerprints yielded 26 distinct genotypes, and 106 clones constituted four major genotypes that were repeatedly isolated. Representatives of these four major genotypes were tentatively identified as R. palustris based on phylogentic analyses of 16S rRNA gene sequences. The differences in the genomic fingerprint patterns among the four major genotypes were accompanied by differences in phenotypic characteristics. These phenotypic differences included differences in the kinetics of carbon source use, suggesting that there may be functional differences with possible ecological significance among these clonal linages. Morisita-Horn similarity coefficients (C(MH)), which were used to compare the numbers of common genotypes found at pairs of sampling locations, showed that there was substantial similarity between locations that were 1 cm apart (C(MH), >/=0.95) but there was almost no similarity between locations that were >/=9 m apart (C(MH), </=0.25). These calculations showed there was a gradual decrease in similarity among the five locations as a function of distance and that clones of R. palustris were lognormally distributed along the linear 10-m transect. These data indicate that natural populations of R. palustris are assemblages of genetically distinct ecotypes and that the distribution of each ecotype is patchy.
Collapse
Affiliation(s)
- Yasuhiro Oda
- Laboratory of Microbial Ecology, Center for Ecological and Evolutionary Studies, University of Groningen, 9751 NN Haren, The Netherlands
| | | | | | | | | |
Collapse
|
196
|
Marín MM, Yuste L, Rojo F. Differential expression of the components of the two alkane hydroxylases from Pseudomonas aeruginosa. J Bacteriol 2003; 185:3232-7. [PMID: 12730186 PMCID: PMC154056 DOI: 10.1128/jb.185.10.3232-3237.2003] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Oxidation of n-alkanes in bacteria is normally initiated by an enzyme system formed by a membrane-bound alkane hydroxylase and two soluble proteins, rubredoxin and rubredoxin reductase. Pseudomonas aeruginosa strains PAO1 and RR1 contain genes encoding two alkane hydroxylases (alkB1 and alkB2), two rubredoxins (alkG1 and alkG2), and a rubredoxin reductase (alkT). We have localized the promoters for these genes and analyzed their expression under different conditions. The alkB1 and alkB2 genes were preferentially expressed at different moments of the growth phase; expression of alkB2 was highest during the early exponential phase, while alkB1 was induced at the late exponential phase, when the growth rate decreased. Both genes were induced by C(10) to C(22)/C(24) alkanes but not by their oxidation derivatives. However, the alkG1, alkG2, and alkT genes were expressed at constant levels in both the absence and presence of alkanes.
Collapse
Affiliation(s)
- Mercedes M Marín
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Campus de la Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| | | | | |
Collapse
|
197
|
Coletta-Filho HD, Machado MA. Geographical Genetic Structure of Xylella fastidiosa from Citrus in São Paulo State, Brazil. PHYTOPATHOLOGY 2003; 93:28-34. [PMID: 18944153 DOI: 10.1094/phyto.2003.93.1.28] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
ABSTRACT A total of 360 Xylella fastidiosa strains were isolated from sweet orange (Citrus sinensis) cv. Pera plants growing in five geographic regions in the Brazilian state of São Paulo. The genetic variation of these strains was determined by 15 variable number tandem repeat (VNTR) and 58 random amplified polymorphic DNA (RAPD) markers. The mean values of genetic diversity (H) of X. fastidiosa strains within each geographic region determined by RAPD (H(RAPD)) were substantially lower than H(VNTR) values. H(RAPD) values ranged from 0.00 to 0.095, whereas the H(VNTR) values ranged from 0.024 to 0.285. A highly significant value of Nei's coefficient of gene differentiation (G(ST) = 0.355; P = 0.000) was detected among all five populations. Analysis of the molecular variance (AMOVA) also revealed significant genetic differentiation among regions or populations ( phi(STAT) = 0.810; P< 0.001). In addition, genetic differentiation among subpopulations (plants) within the regions (phi(STAT) = 0.699; P < 0.001) and within each plant (phi(STAT) = 368; P < 0.001) were statistically significant. These high values of genetic differentiation among X. fastidiosa strains from different regions suggest a genetic structure according to region of host origin. However, no apparent correlation between genetic distance and region of origin of populations were supported statistically by Mantel analysis (r = 0.27; P = 0.22).
Collapse
|
198
|
Saumaa S, Tover A, Kasak L, Kivisaar M. Different spectra of stationary-phase mutations in early-arising versus late-arising mutants of Pseudomonas putida: involvement of the DNA repair enzyme MutY and the stationary-phase sigma factor RpoS. J Bacteriol 2002; 184:6957-65. [PMID: 12446646 PMCID: PMC135458 DOI: 10.1128/jb.184.24.6957-6965.2002] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2002] [Accepted: 09/17/2002] [Indexed: 11/20/2022] Open
Abstract
Stationary-phase mutations occur in populations of stressed, nongrowing, and slowly growing cells and allow mutant bacteria to overcome growth barriers. Mutational processes in starving cells are different from those occurring in growing bacteria. Here, we present evidence that changes in mutational processes also take place during starvation of bacteria. Our test system for selection of mutants based on creation of functional promoters for the transcriptional activation of the phenol degradation genes pheBA in starving Pseudomonas putida enables us to study base substitutions (C-to-A or G-to-T transversions), deletions, and insertions. We observed changes in the spectrum of promoter-creating mutations during prolonged starvation of Pseudomonas putida on phenol minimal plates. One particular C-to-A transversion was the prevailing mutation in starving cells. However, with increasing time of starvation, the importance of this mutation decreased but the percentage of other types of mutations, such as 2- to 3-bp deletions, increased. The rate of transversions was markedly elevated in the P. putida MutY-defective strain. The occurrence of 2- to 3-bp deletions required the stationary-phase sigma factor RpoS, which indicates that some mutagenic pathway is positively controlled by RpoS in P. putida.
Collapse
Affiliation(s)
- Signe Saumaa
- Department of Genetics, Institute of Molecular and Cell Biology, Tartu University and Estonian Biocentre, Estonia
| | | | | | | |
Collapse
|
199
|
Pirnay JP, De Vos D, Mossialos D, Vanderkelen A, Cornelis P, Zizi M. Analysis of the Pseudomonas aeruginosa oprD gene from clinical and environmental isolates. Environ Microbiol 2002; 4:872-82. [PMID: 12534469 DOI: 10.1046/j.1462-2920.2002.00281.x] [Citation(s) in RCA: 96] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Genomes are constantly evolving. Our report highlights the wide mutational diversity of clinical as well as environmental isolates, compared with the laboratory strain(s), through the systematic genetic analysis of a chromosomal porin gene (oprD) in relation to a specific antibiotic resistance. Mutational inactivation of the oprD gene is associated with carbapenem resistance in Pseudomonas aeruginosa. The sequence of the oprD gene of 55 Pseudomonas aeruginosa natural isolates obtained from across the world--from sources as diverse as patients and rhizospheres--was analysed. A microscale mosaic structure for this gene--resulting from multiple intra- and possibly interspecies recombinational events--is reported. An array of independent and seemingly fast-occurring defective oprD mutations were found, none of which had been described before. A burn wound isolate demonstrated unusually high overall sequence variability typical of mutator strains. We also present evidence for the existence of OprD homologues in other fluorescent pseudomonads.
Collapse
Affiliation(s)
- Jean-Paul Pirnay
- Laboratory of Microbial Interactions, Department of Immunology, Parasitology, and Ultrastructure, Flanders Interuniversity Institute of Biotechnology, Brussels Free University, B-1640 Sint-Genesius-Rode, Brussels, Belgium
| | | | | | | | | | | |
Collapse
|
200
|
D'Argenio DA, Calfee MW, Rainey PB, Pesci EC. Autolysis and autoaggregation in Pseudomonas aeruginosa colony morphology mutants. J Bacteriol 2002; 184:6481-9. [PMID: 12426335 PMCID: PMC135425 DOI: 10.1128/jb.184.23.6481-6489.2002] [Citation(s) in RCA: 319] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Two distinctive colony morphologies were noted in a collection of Pseudomonas aeruginosa transposon insertion mutants. One set of mutants formed wrinkled colonies of autoaggregating cells. Suppressor analysis of a subset of these mutants showed that this was due to the action of the regulator WspR and linked this regulator (and the chemosensory pathway to which it belongs) to genes that encode a putative fimbrial adhesin required for biofilm formation. WspR homologs, related in part by a shared GGDEF domain, regulate cell surface factors, including aggregative fimbriae and exopolysaccharides, in diverse bacteria. The second set of distinctive insertion mutants formed colonies that lysed at their center. Strains with the most pronounced lysis overproduced the Pseudomonas quinolone signal (PQS), an extracellular signal that interacts with quorum sensing. Autolysis was suppressed by mutation of genes required for PQS biosynthesis, and in one suppressed mutant, autolysis was restored by addition of synthetic PQS. The mechanism of autolysis may involve activation of the endogenous prophage and phage-related pyocins in the genome of strain PAO1. The fact that PQS levels correlated with autolysis suggests a fine balance in natural populations of P. aeruginosa between survival of the many and persistence of the few.
Collapse
Affiliation(s)
- David A D'Argenio
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195-7730, USA.
| | | | | | | |
Collapse
|