A DNA microarray-based global transcript profiling of Escherichia coli in response to cold shock showed that in addition to the known cold shock-inducible genes, new genes such as the flagellar operon, those encoding proteins involved in sugar transport and metabolism, and remarkably, genes encoding certain heat shock proteins are induced by cold shock. In the light of strong reduction in metabolic activity of the cell after temperature downshift, the induction of sugar metabolism machinery is unexpected. The deletion of four csps (cspA, cspB, cspG, and cspE) affected cold shock induction of mostly those genes that are transiently induced in the acclimation phase, emphasizing that CspA homologues are essential in the acclimation phase. Relevance of these findings with respect to the known RNA chaperone function of CspA homologues is discussed.The cold shock response is a physiological response of living cells to temperature downshift (12) and has been studied in detail using Escherichia coli and Bacillus subtilis as model systems (for a review, see references 5, 21, 26, and 32). When an exponentially growing culture of E. coli is shifted from 37 to 15°C, an acclimation phase (lag period of cell growth) characterized by transient dramatic induction of cold shock proteins against a severe inhibition of general protein synthesis precedes the resumption of growth. Out of the nine CspA homologues of E. coli, only CspA, CspB, CspG, and CspI are cold shock inducible (6,17,20,31). Interestingly, double or triple deletions of genes encoding cold shock-inducible CspA homologues do not result in cold sensitivity. In a triple-deletion strain, the ⌬cspA ⌬cspB ⌬cspG strain, CspE that is normally produced at 37°C is overproduced at low temperatures (33). This observation suggests that the functions of the CspA family members may overlap and they are able to substitute for each other during cold acclimation. Indeed a quadruple-deletion strain (the ⌬cspA ⌬cspB ⌬cspG ⌬cspE strain) of E. coli exhibits cold sensitivity at 15°C, which can be complemented by overproduction of any one of the CspA homologues except CspD (33).In spite of a wealth of knowledge accumulated in recent years, the cold shock response is not fully elucidated. The proteomic approaches that so far have been extremely useful in identification of many cold shock-induced proteins do have certain limitations: (i) not all the proteins can be resolved well on two-dimensional gel electrophoresis, and (ii) identification of proteins from the gel may sometimes be cumbersome. To overcome these shortcomings, in the present study, we carried out analysis of global cold shock gene expression profiles of an E. coli wild-type and cold-sensitive quadruple-deletion strain. Our main objectives were (i) to identify the E. coli open reading frames that exhibit significant increase or decrease in mRNA abundance caused by the temperature downshift and (ii) to explore the effect of deletion of four csp genes that leads to cold sensitivity. In brief, the E. coli JM83 strain [F Ϫ ara⌬(l...