title: 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.
authors: TNO Quality of Life, Business Unit Food and Biotechnology Innovations, Julianalaan 67, 2628 BC, Delft, The Netherlands. hendrik.ballerstedt@tno.nl
authors: Hendrik
authors: H
authors: Ballerstedt
authors: Rita J M
authors: RJ
authors: Volkers
authors: Astrid E
authors: AE
authors: Mars
authors: John E
authors: JE
authors: Hallsworth
authors: Vitor A Martins
authors: VA
authors: dos Santos
authors: Jaçek
authors: J
authors: Puchalka
authors: Joost
authors: J
authors: van Duuren
authors: Gerrit
authors: G
authors: Eggink
authors: Ken N
authors: KN
authors: Timmis
authors: Jan A M
authors: JA
authors: de Bont
authors: Jan
authors: J
authors: Wery
mesh_terms: D016680:Genome, Bacterial; D023281:Genomics; D020411:Oligonucleotide Array Sequence Analysis; D010802:Phylogeny; D016958:Pseudomonas putida / Q000235:genetics*; D012313:RNA / Q000235:genetics*
chemical_list: D012313:RNA