Systematic molecular analyses reveal extremely long and complex 5'UTR of a major cold shock protein CsdA in Escherichia coli

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Cold-shock DEAD-box protein A (CsdA) is a DEAD-box RNA helicase in E. coli. The deaD gene encodes this CsdA protein in E. coli. It is a major cold shock protein and it plays essential roles during cold shock adaption in E. coli. CsdA homolog of E. coli is present in bacteria, archaea and eukaryotes. This major cold-shock protein has been studied at the protein level, but its mechanism of gene regulation needs further study. In this regard, we have constructed a promoter-less plasmid vector with the ORF of a GFP reporter and performed incremental zone-wise DNA scanning from the immediate upstream region of the deaD gene coding region. Interestingly, we found the promoter region about 800 nucleotides upstream of its coding region. Furthermore, the drastic decrease in CsdA protein level due to the in vivo deletion of this promoter region from the E. coli chromosome has confirmed this promoter’s existence. Interestingly, we have found this promoter region i.e., -10 region and -35 region is conserved in numbers of gammaproteobacteria. In conclusion, our study established deaD gene contains an unusually long 5'UTR of about 800 nucleotides in E. coli which is exceptional in bacteria.