Title
Genomotyping of Pseudomonas putida strains using P. putida KT2440-based high-density DNA microarrays: Implications for transcriptomics studies
Author
Ballerstedt, H.
Volkers, R.J.M.
Mars, A.E.
Hallsworth, J.E.
Santos, V.A.M.D.
Puchalka, J.
van Duuren, J.
Eggink, G.
Timmis, K.N.
de Bont, J.A.M.
Wery, J.
TNO Kwaliteit van Leven
Publication year
2007
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 (DSM291T), 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 DSM291T. Pseudomonas monteilii (DSM14164) clustered well with P. putida strains. © 2007 Springer-Verlag.
Subject
Biology
Biotechnology
Genomotyping
Pseudomonas putida
Solvent-tolerant bacteria
Transcriptomics
Bacteria
Genes
Microarrays
Oligonucleotides
Proteins
Solvents
Genomotyping
Microarray hybridizations
Pseudomonas putida
Solvent tolerant bacteria
Transcriptomics
DNA
bacterial DNA
bacterial protein
genomic DNA
array
bacterium
catabolism
DNA fingerprinting
gene
hybridization
metabolism
phylogeny
protein
article
bacterial genome
bacterial strain
bacterium culture
cell function
comparative study
controlled study
DNA hybridization
DNA microarray
genetic strain
genome analysis
genotype
microarray analysis
molecular phylogeny
nonhuman
protein degradation
protein metabolism
proteomics
Pseudomonas
pseudomonas monteilii
Pseudomonas putida
reliability
transcriptomics
Genome, Bacterial
Genomics
Oligonucleotide Array Sequence Analysis
Phylogeny
Pseudomonas putida
RNA
Pseudomonas
Pseudomonas monteilii
Pseudomonas putida
To reference this document use:
http://resolver.tudelft.nl/uuid:73e7662f-531c-43b4-a9ac-be0a22f227fa
DOI
https://doi.org/10.1007/s00253-007-0914-z
TNO identifier
240047
ISSN
0175-7598
Source
Applied Microbiology and Biotechnology, 75 (5), 1133-1142
Document type
article