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