Escherichia Coli Cold Shock Gene Profiles in Response to Overexpression or Deletion of CsdA, RNase R, and PNPase and Relevance to low-temperature RNA Metabolism

Cold shock proteins are important for survival and continued growth of the cells at low temperature. One of the detrimental effects of cold shock is stabilization of the secondary structures in nucleic acids. This interferes with the degradation of RNAs at low temperature. The low-temperature RNA metabolism is supposedly facilitated by cold shock proteins such as RNA helicase CsdA, and exoribonucleases such as PNPase and RNase R. Interestingly, RNase R can compensate for the cold shock function of CsdA, albeit weakly, but not that of PNPase. PNPase, on the other hand, cannot compensate the cold shock function of CsdA and vice versa. This suggests that CsdA and PNPase may have distinct target genes at low temperature. A DNA microarray analysis of the global transcript profiles of cells lacking or overproducing CsdA, RNase R, or PNPase was carried out to elucidate their cellular targets at low temperature. The analysis revealed that indeed there are distinct sets of genes, which respond to changes in the cellular levels of CsdA and PNPase. This analysis is the first step to elucidate low-temperature RNA metabolism.