Comparative genomics and functional analysis of niche-specific adaptation in Pseudomonas putida

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.

Fig. 1

Phylogenetic relationship between members of the genus Pseudomonas. 16S rRNA gene comparison was used to build the phylogenetic tree for those members of the genus Pseudomonas with publicly available genome sequences. The numbers at nodes represent the bootstrap values (1000 replicates), and the numbers in bold correspond to the number of coding sequences (CDS) preferentially shared by W619 and the corresponding organisms (with E value of 10⁻⁵). The numbers of CDS equally found in two or more organisms are indicated for this subset of organisms (boxed with dotted lines) that correspond to a group of taxa/phylum according to the NCBI taxonomy. Whole-genome comparison for shared CDS was based on megan (Huson et al., 2007).

Fig. 2

Genome atlas for the chromosome of Pseudomonas putida W619. The numbers outside the atlas indicate the locations of the predicted genomic islands on the W619 chromosome. Details of these genomic islands are provided in Table S1. From the outside to the inside the circles represent the three blast atlases for chromosome comparisons with P. putida strains F1 (a), KT2440 (b) and GB-1 (c), respectively, followed by an overview of specific W619 chromosome properties: (d) annotations for coding sequences on the +and – strand, rRNA and tRNA genes; (e) intrinsic curvature; (f) stacking energy; (g) position preference; (h) GC skew; and (i) percent AT. The explanation of the color codes is presented in the figure legend. The atlas was generated using the GeneWiz browser 0.91 (http://www.cbs.dtu.dk/services/gwBrowser/).

Fig. 3

Comparative syntheny line plots showing the orthologous relations among Pseudomonas putida W619, F1, GB-1 and KT2440. The synteny regions are displayed with strand conservation (in purple) and stand inversion (in blue). The pink bars represent the positions of transposable elements. The ‘Conserved Synteny LinePlot’ tool in MaGe was used to generate this figure (Vallenet et al., 2006). The corresponding RefSeq synteny statistics are provided in Table S2.

Fig. 4

Genetic organization of heavy metal resistance determinants located on the chromosomes of Pseudomonas putida W619, KT2440, F1 and GB-1. (a) Genetic organization of heavy metal resistance determinants on the putative genomic island region 1 of P. putida W619, and its comparison with the corresponding regions located on the chromosomes of P. putida KT2440, F1 and GB-1. PP5394, located on the P. putida KT2440 chromosomes, encodes a P-type ATPase (Ag/Cu efflux), which was reported to have a frameshift mutation (http://www.tigr.org). Identities are provided as percentages between two copies of homologous genes. ^* The position of a frame shift mutation in comparison with the full-length ORF. (b) Genetic organization of heavy metal resistance determinants on putative genomic island region 31 of P. putida W619, and its comparison with the corresponding regions located on the chromosomes of P. putida KT2440, F1 and GB-1. The arsB gene in P. putida W619 and the arsB^* genes in P. putida KT2440, F1 and GB-1 are from different sources. (c) The mercury resistance region and its flanking mobile genetic elements on the chromosome of the P. putida W619 genome. This region is absent in P. putida KT2440, F1 and GB-1.

Fig. 4

Genetic organization of heavy metal resistance determinants located on the chromosomes of Pseudomonas putida W619, KT2440, F1 and GB-1. (a) Genetic organization of heavy metal resistance determinants on the putative genomic island region 1 of P. putida W619, and its comparison with the corresponding regions located on the chromosomes of P. putida KT2440, F1 and GB-1. PP5394, located on the P. putida KT2440 chromosomes, encodes a P-type ATPase (Ag/Cu efflux), which was reported to have a frameshift mutation (http://www.tigr.org). Identities are provided as percentages between two copies of homologous genes. ^* The position of a frame shift mutation in comparison with the full-length ORF. (b) Genetic organization of heavy metal resistance determinants on putative genomic island region 31 of P. putida W619, and its comparison with the corresponding regions located on the chromosomes of P. putida KT2440, F1 and GB-1. The arsB gene in P. putida W619 and the arsB^* genes in P. putida KT2440, F1 and GB-1 are from different sources. (c) The mercury resistance region and its flanking mobile genetic elements on the chromosome of the P. putida W619 genome. This region is absent in P. putida KT2440, F1 and GB-1.