Upon cold shock Escherichia coli transiently stops growing and adapts to the new temperature (acclimatization phase). The major physiological effects of cold temperature are a decrease in membrane fluidity and the stabilization of secondary structures of RNA and DNA, which may affect the efficiencies of translation, transcription, and replication. Specific proteins are transiently induced in the acclimatization phase. mRNA stabilization and increased translatability play a major role in this phenomenon. Polynucleotide phosphorylase (PNPase) is one of the cold-induced proteins and is essential for E. coli growth at low temperatures. We investigated the global changes in mRNA abundance during cold adaptation both in wild type E. coli MG1655 and in a PNPase-deficient mutant. We observed a twofold or greater variation in the relative mRNA abundance of 20 genes upon cold shock, notably the cold-inducible subset of csp genes and genes not previously associated with cold shock response, among these, the extracytoplasmic stress response regulators rpoE and rseA, and eight genes with unknown function. Interestingly, we found that PNPase both negatively and positively modulated the transcript abundance of some of these genes, thus suggesting a complex role of PNPase in controlling cold adaptation.