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

Area of Science:

• Microbiology
• Genomics
• Systems Biology

Background:

• Pseudomonas putida KT2440 is the sole fully sequenced strain, making its genome the standard reference for other P. putida strains.
• Transcriptomics and proteomics studies require reliable genomic databases for accurate analysis.
• The utility of P. putida KT2440-based microarrays for other Pseudomonas strains is not fully established.

Purpose of the Study:

• To investigate the applicability of P. putida KT2440 whole-genome microarrays for transcriptomics studies in other Pseudomonas species.
• To assess the accuracy of these microarrays in identifying genetic elements across different strains.
• To evaluate the potential for constructing phylogenetic relationships using microarray data.

Main Methods:

• Whole-genome, high-density oligonucleotide microarrays based on P. putida KT2440 were hybridized with genomic DNAs from various P. putida strains and other Pseudomonas species.
• The percentage of identified genetic elements was quantified for each strain.
• Genotypic comparisons were performed to construct phylogenetic trees.

Main Results:

• Microarray hybridization identified between 22% and 99% of genetic elements, depending on the strain.
• Genes involved in primary metabolism and aromatic compound catabolism in P. putida KT2440 were largely identified in the genome of the solvent-tolerant P. putida S12.
• Phylogenetic analysis revealed that P. putida KT2440, a derivative strain, and strain S12 clustered together, distinct from the type strain, while Pseudomonas monteilii grouped with P. putida.

Conclusions:

• P. putida KT2440 microarrays are effective tools for transcriptomics studies in related Pseudomonas strains, enabling identification of key metabolic genes.
• The microarrays facilitate accurate genomotyping and the construction of robust phylogenetic relationships among Pseudomonas species.
• These findings support the use of KT2440-based microarrays for comparative genomics and functional studies within the Pseudomonas genus.