Comparative genomics and functional analysis of niche-specific adaptation inPseudomonas putida
Open Access
- 1 March 2011
- journal article
- research article
- Published by Oxford University Press (OUP) in FEMS Microbiology Reviews
- Vol. 35 (2), 299-323
- https://doi.org/10.1111/j.1574-6976.2010.00249.x
Abstract
Pseudomonas putida is a gram-negative rod-shaped gammaproteobacterium that is found throughout various environments. Members of the species P. putida show a diverse spectrum of metabolic activities, which is indicative of their adaptation to various niches, which includes the ability to live in soils and sediments contaminated with high concentrations of heavy metals and organic contaminants. Pseudomonas putida strains are also found as plant growth-promoting rhizospheric and endophytic bacteria. The genome sequences of several P. putida species have become available and provide a unique tool to study the specific niche adaptation of the various P. putida strains. In this review, we compare the genomes of four P. putida strains: the rhizospheric strain KT2440, the endophytic strain W619, the aromatic hydrocarbon-degrading strain F1 and the manganese-oxidizing strain GB-1. Comparative genomics provided a powerful tool to gain new insights into the adaptation of P. putida to specific lifestyles and environmental niches, and clearly demonstrated that horizontal gene transfer played a key role in this adaptation process, as many of the niche-specific functions were found to be encoded on clearly defined genomic islands.Keywords
This publication has 150 references indexed in Scilit:
- Identification of a Two-Component Regulatory Pathway Essential for Mn(II) Oxidation in Pseudomonas putida GB-1Applied and Environmental Microbiology, 2010
- MrdH, a Novel Metal Resistance Determinant of Pseudomonas putida KT2440, Is Flanked by Metal-Inducible Mobile Genetic ElementsJournal of Bacteriology, 2009
- Genome Survey and Characterization of Endophytic Bacteria Exhibiting a Beneficial Effect on Growth and Development of Poplar TreesApplied and Environmental Microbiology, 2009
- A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: i JN746 as a cell factoryBMC Systems Biology, 2008
- Prophinder: a computational tool for prophage prediction in prokaryotic genomesBioinformatics, 2008
- Genomic, genetic and structural analysis of pyoverdine-mediated iron acquisition in the plant growth-promoting bacterium Pseudomonas fluorescens SBW25BMC Microbiology, 2008
- Plasmids pMOL28 and pMOL30 of Cupriavidus metallidurans Are Specialized in the Maximal Viable Response to Heavy MetalsJournal of Bacteriology, 2007
- The Copper-Inducible cin Operon Encodes an Unusual Methionine-Rich Azurin-Like Protein and a Pre-Q 0 Reductase in Pseudomonas putida KT2440Journal of Bacteriology, 2007
- MEGAN analysis of metagenomic dataGenome Research, 2007
- Curli Biogenesis and FunctionAnnual Review of Microbiology, 2006