Transcriptomics data on E. coli lacking queuosine tRNA modification (tgt deficient strain) exposed or not to nickel stress.

Purpose: to observe differences in E. coli transcripts levels due to the absence of the tRNA modification queuosine and due to exposure to excess nickel. Methods: RNAseq was performed using the total RNA isolated from E. coli MG1655 WT and ?tgt strains grown in LB medium only or in LB added by 2 mM NiCl2. Results: in nickel-treated WT compared to untreated WT (WT_Ni/WT_LB) 734 genes were found up-regulated and 1,642 genes down-regulated in the treated cells; in the tgt mutant compared to the WT strain (tgt_LB/WT_LB), 417 genes were found up regulated and 1,053 genes down regulated in the tgt mutant. Conclusions: the gene expression pattern of the tgt deficient cell in LB medium resembles the one of the WT strain exposed to nickel, showing repression of iron-import genes and genes associated to anaerobic metabolism; increased resistance to nickel stress observed in the tgt mutant is explained by the repression of the nickel import system nikABCCDE. Overall design: mRNA profiles of E. coli K-12 MG1655 wild type (WT) and tgt mutant, in LB medium and LB supplemented with 2 mM nickel (Ni), in triplicate, were generated by deep sequencing, using HiSeq 2500 System (Illumina).