Transcription of an antisense RNA of a gadE mRNA is regulated by GadE, the central activator of the acid resistance system in Escherichia coli

Abstract

6H57, a 69-nucleotide-long small RNA, was isolated in shotgun cloning using an RNA sample derived from early stationary-phase cells. The 6H57 gene is located in a 798-bp intergenic region between two acid resistance-related genes, hdeD and gadE, and is encoded on the strand opposite these flanking genes. In this study, we carried out stringent Northern blotting to determine target mRNAs of 6H57. A band approximately 1300 nucleotides in length was detected using a probe containing a partial sequence of 6H57 and was confirmed to be the gadE mRNA T3, which has a 566-nucleotide-long 5¢ untranslated region. These results show that 6H57 is an antisense RNA of gadE mRNA T3 and can base pair with a )380 to )312 region of the translation initiation site of gadE. We analyzed the transcription of 6H57 and showed that 6H57 transcription is dependent on GadE in the early stationary phase. Furthermore, 6H57 is induced in the exponential growth phase by an acid stimulus of pH 5.5. A 189-bp DNA fragment containing the upstream region of the 6H57 gene showed clear promoter activities in these culture conditions. These results suggest that 6H57 plays several roles in acid resistance, and we renamed it acid resistance-related small RNA.

Glutamate decarboxylase‐dependent acid resistance in orally acquired bacteria: function, distribution and biomedical implications of the gadBC operon

“…B, the gadA gene is at the 3′ end of a 14 kb genome region, named acid fitness island (AFI), comprising 13 additional genes which contribute at various levels to AR. The genes gadE , gadX , gadW , yhiF ( dctR ), arrS and gadY code for four specific transcriptional regulators and two small RNAs respectively (Tramonti et al ., ; ; ; Ma et al ., ; Tucker et al ., ; Opdyke et al ., ; Aiso et al ., ); hdeA and hdeB code for pH‐regulated acid stress periplasmic chaperones, which facilitate the refolding of acid‐denatured proteins in this cellular compartment (Hong et al ., ; Kern et al ., ); slp , yhiD and hdeD code for membrane proteins required for protection from acidic metabolites (lactate, succinate and formate) and for AR at high cell densities (Mates et al ., ); the mdtE and mdtF genes code for multidrug exporters which are unique amongst the 20 known drug exporters in that their expression is induced in stationary phase and is GadX‐dependent (Kobayashi et al ., ; Nishino et al ., ). The gadA gene is either independently transcribed or transcribed with gadX (Fig.…”

“…1B, the gadA gene is at the 3′ end of a 14 kb genome region, named acid fitness island (AFI), comprising 13 additional genes which contribute at various levels to AR. The genes gadE, gadX, gadW, yhiF (dctR), arrS and gadY code for four specific transcriptional regulators and two small RNAs respectively (Tramonti et al, 2002a;Ma et al, 2003;Tucker et al, 2003;Opdyke et al, 2004;Aiso et al, 2011); hdeA and hdeB code for pH-regulated acid stress periplasmic A. Schematic representation of the role played by the major structural components of the system. Glutamate (net charge 0) is taken up by the electrogenic L-glutamate/GABA antiporter GadC, an inner membrane protein.…”

Bacterial cyclopropane fatty acid synthase mRNA is targeted by activating and repressing small RNAs

“…6B, 7), indicating that ArrS may not play a role in acid stress under the conditions tested. ArrS has been characterized as an activator of the transcriptional activator GadE and ectopic expression of ArrS increases acid resistance though its activation of gadE but a deletion phenotype has not been reported (Aiso et al, 2014, Aiso et al, 2011). ArrS may activate cfa under another condition where CFAs in the membrane contribute to stress resistance (Fig.…”

“…Together with Hfq, CpxQ represses translation of multiple targets many of which encode inner membrane proteins (Chao & Vogel, 2016, Grabowicz, Koren et al, 2016). ArrS is an antisense sRNA that is encoded upstream of gadE (encoding the major acid resistance transcription factor) and is complementary to the 5’ UTR of the longest of three gadE transcripts (Aiso, Murata et al, 2011). ArrS expression is induced by low pH through σ s and GadE, and overexpression of ArrS increases survival of cells exposed to acidic pH (Aiso, Kamiya et al, 2014).…”

Identification and Characterization of a Cis-Encoded Antisense RNA Associated with the Replication Process of Salmonella enterica Serovar Typhi

“…The known regulatory mechanisms employed by cis -encoded asRNAs include transcription attenuation, translation inhibition, inhibition of primer maturation, promotion or inhibition of mRNA degradation and prevention of RNA pseudoknot formation [4], [5]. AsRNAs are involved in a number of cellular processes in bacteria, including acid resistance [6], iron homeostasis [7], quorum sensing [8], Mg +2 /Ca +2 transport and virulence [9]–[11], ABC transport systems [12], global repression of OMP synthesis [13], [14] and control of expression of global transcription factors [15], [16].…”