Genomotyping of Pseudomonas putida strains using P. putida KT2440-based high-density DNA microarrays: implications for transcriptomics studies

Abstract

Pseudomonas putida KT2440 is the only fully sequenced P. putida strain. Thus, for transcriptomics and proteomics studies with other P. putida strains, the P. putida KT2440 genomic database serves as standard reference. The utility of KT2440 whole-genome, high-density oligonucleotide microarrays for transcriptomics studies of other Pseudomonas strains was investigated. To this end, microarray hybridizations were performed with genomic DNAs of subcultures of P. putida KT2440 (DSM6125), the type strain (DSM291(T)), plasmid pWW0-containing KT2440-derivative strain mt-2 (DSM3931), the solvent-tolerant P. putida S12, and several other Pseudomonas strains. Depending on the strain tested, 22 to 99% of all genetic elements were identified in the genomic DNAs. The efficacy of these microarrays to study cellular function was determined for all strains included in the study. The vast majority of DSM6125 genes encoding proteins of primary metabolism and genes involved in the catabolism of aromatic compounds were identified in the genomic DNA of strain S12: a prerequisite for reliable transcriptomics analyses. The genomotypic comparisons between Pseudomonas strains were used to construct highly discriminative phylogenetic relationships. DSM6125 and DSM3931 were indistinguishable and clustered together with strain S12 in a separate group, distinct from DSM291(T). Pseudomonas monteilii (DSM14164) clustered well with P. putida strains.

Fig. 1

Genome similarity between different Pseudomonas strains. a High-density microarray genotyping tree based on absent/present designations generated by Affymetrix MAS 5.0 algorithm (Table 2) using simple matching similarity coefficient, UPGMA, and agglomerative hierarchical clustering. b AFLP-genotyping. Tree is based on the score of 757 AFLP markers using the simple matching similarity coefficient and Sahn cluster analysis

Fig. 2

Distribution of genes encoding COG proteins over different functional categories as identified in Pseudomonas strains. Functional categories were adopted from the COG database for P. putida KT2440 (http://www.ncbi.nlm.nih.gov/sutils/coxik.cgi?gi=266 ). The categories of biological function corresponding to COG codes are given in Table 3.