Tiling array study of MNNG treated Escherichia coli reveals a widespread transcriptional response

James A Booth,Alexander D Rowe,Jessica M Lindvall,Karin Lagesen,Magnar Bjørås,Torbjørn Rognes,Gard O S Thomassen,Ragnhild Weel-Sneve,Knut I Kristiansen

doi:10.1038/srep03053

Abstract

The alkylating agent N-methyl-N'-nitro-N-nitrosoguanidine (MNNG) is known to trigger the adaptive response by inducing the ada-regulon – consisting of three DNA repair enzymes Ada, AlkB, AlkA and the enigmatic AidB. We have applied custom designed tiling arrays to study transcriptional changes in Escherichia coli following a MNNG challenge. Along with the expected upregulation of the adaptive response genes (ada, alkA and alkB), we identified a number of differentially expressed transcripts, both novel and annotated. This indicates a wider regulatory response than previously documented. There were 250 differentially-expressed and 2275 similarly-expressed unannotated transcripts. We found novel upregulation of several stress-induced transcripts, including the SOS inducible genes recN and tisAB, indicating a novel role for these genes in alkylation repair. Furthermore, the ada-regulon A and B boxes were found to be insufficient to explain the regulation of the adaptive response genes after MNNG exposure, suggesting that additional regulatory elements must be involved.

Highlights

The alkylating agent N-methyl-N’-nitro-N-nitrosoguanidine (MNNG) is known to trigger the adaptive response by inducing the ada-regulon – consisting of three DNA repair enzymes Ada, AlkB, AlkA and the enigmatic AidB
After exposure of Escherichia coli (E. coli) to non-lethal doses of MNNG, transcription of the ada, alkB, alkA and aidB genes are induced under control of the ada-regulon
Through the experimental identification of expressed or suppressed transcripts due to MNNG treatment, this study provide the basis for focused studies to subsequently uncover the functions and relevance of transcripts induced by methylation, e.g. recN, tisAB, hmp, iraP and gcvT

Summary

Introduction

The alkylating agent N-methyl-N’-nitro-N-nitrosoguanidine (MNNG) is known to trigger the adaptive response by inducing the ada-regulon – consisting of three DNA repair enzymes Ada, AlkB, AlkA and the enigmatic AidB. After exposure of Escherichia coli (E. coli) to non-lethal doses of MNNG, transcription of the ada, alkB, alkA and aidB genes are induced under control of the ada-regulon. This stress response to alkylating agents is termed the adaptive response[2,4]. Investigations employing unbiased tiling of human chromosomes 21 and 22 have elegantly shown that large portions of the human genome are transcribed[19] and are not, as previously thought, ‘‘junk’’ areas Whether these transcripts represent novel mRNAs or non-coding RNAs (ncRNAs)[20] remains largely unclear. Several RNA-Seq experiments have been performed on E. coli[27,28,29,30], but to our knowledge no such experiments subjecting E. coli to MNNG have been published

Methods

Results

Conclusion