1). Of the most abundant mRNA species, the P. putida cell reduced its pool for transcripts that are translated into chaperonins, elongation factors EF-Tu

and EF-Ts, ATP synthase and enzymes of the core metabolism. The cells shut down the transcription of operons that encode the biosynthesis of purines, pyrimidines, coenzymes and branched amino acids and those that encode transporters for amino acids, siderophores, polyamines and sulfur compounds. The most strongly downregulated genes encode heat shock proteins and enzymes of the citric acid cycle and of the pathway for the synthesis of valine and leucine. In summary, the cells constrained its mRNA repertoire for biosynthesis, nutrient uptake, core and energy metabolism. Of the top 100 downregulated genes, the encoded function has been experimentally demonstrated for 83 genes in P. putida or in another FK866 purchase Dabrafenib cell line proteobacterium (Hoshino & Kose, 1990a, b; Auerbach et al., 1993; Best & Knauf, 1993; Holtmann et al., 2004; Carruthers & Minion, 2009; Kazakov et al., 2009; Molina-Henares

et al., 2010). In contrast, 67 of the >10-fold upregulated 169 genes at 10 °C were found to be conserved hypotheticals. Other over-represented categories were genes encoding transporters (20), transcriptional regulators (15) or phage proteins, integrases and transposons (11). During cold adaptation, P. putida activated a transcriptional program whose most key players have not been characterized so far in any organism. The most striking upregulation was seen for the two hypotheticals PP1690 and PP1691 that were expressed at a low level at 30 °C, but belonged to the 10 most abundant transcripts at 10 °C. Among the strongly upregulated genes of known encoded function, the majority of genes are orthologs of the alginate biosynthesis regulon in Pseudomonas aeruginosa and the affiliated catabolism of glycerol and glucose through the Entner–Douderoff pathway. Furthermore, the PhoPQ two-component system TCL and the multienzyme complex for the degradation of valine, leucine and isoleucine

were activated. Another interpretable key feature of the cold adaptation was the strong upregulation of the rbfA–nusA–infB operon. The orthologs in E. coli coordinate transcription and translation during cold stress (Bae et al., 2000; Bylund et al., 2001): the cold shock protein RbfA converts nonadapted translationally inactive into cold-adapted translationally competent ribosomes. InfB is necessary for efficient and accurate de novo initiation and re-initiation of translation. NusA is an essential, multidomain protein that functions in both termination and antitermination of transcription. The rbfA–infB–nusA operon is highly conserved, and hence, we assume that its upregulation fulfills similar roles during cold stress for E. coli and P. putida cells.