# Involvement of _E. coli_ 6S RNA in Oxidative Stress Response
## 1 Introduction  
Regulation of transcription is a central mechanism in prokaryotes for adjusting gene expression to changes, in particular, under unfavorable environmental conditions [1; 2; 3]. In natural habitats, bacteria strive for survival under nutrient starvation, need to adapt quickly to, e.g., fluctuations in temperature, pressure, humidity, pH and osmotic strength, adjust their metabolism according to the density of the population, or differentiate into subpopulations for the sake of species survival [4; 5; 6]. Fast switching to an expression of stress response proteins is widely achieved by activating the transcription of specific sets of mRNAs, processes that are not only regulated by proteinogenic transcription factors [7] but also by small non-coding RNAs (ncRNAs) [8; 9; 10]. Small ncRNAs have lengths \(\leq 200\) nt and usually do not participate in translation. To date, just a few examples of bifunctional RNAs are known in bacteria that act both as riboregulator and mRNA, such as RNAIII and Psm-mee RNA from _Staphylococcus aureus_, Sgr5 RNA from _Escherichia coli_ and SR1 RNA from _Bacillus subtilis_[11]. To date, dozens of ncRNAs are known to play various regulatory roles in bacteria via binding to complementary mRNAs or by direct interaction with proteins [12; 13]. The high impact of some ncRNAs on the regulation of gene expression and successful bacterial growth also makes them prospective targets for industrial applications [14]. 6S RNA is an abundant bacterial ncRNA that directly binds to RNA polymerase (RNAP) holoenzymes, particularly in the stationary phase of cell growth [15; 16]. The resulting inhibition of transcription entails global changes in the bacterial transcriptome [17; 18] and proteome [19]. Although 6S RNA genes are found in the majority of bacterial species [20], detailed functional studies have focused mainly on 6S RNAs from _E. coli_ and _B. subtilis_. Historically, the first documented phenotype of an _E. coli_ 6S RNA knockout (\(\Delta ssr\)S) strain was reduced survival compared to the parental strain under conditions of extended cultivation (20 days) and in competitive cultivation experiments [21]. _E. coli_ 6S RNA was shown to regulate the expression of various transcription and translation factors, transporters and enzymes involved in the metabolism of purines and degradation of amino acids. Notably, a number of stress-related genes were also shown to be dysregulated in \(\Delta ssr\)S cells, especially in the stationary phase, in particular, _asr_ (acid shock protein), _dps_ (DNA protection protein), _cspA_ and _yfiA_ (cold shock proteins), _sra_ and _smpB_ (ribosome stabilizing proteins), as well as _uspG_ and _uspF_ (general stress proteins) [17]. The _E. coli_ 6S RNA knockout also caused derepression of the _relA_ gene encoding ppGpp synthase I in the early stationary phase, resulting in decreased rRNA expression and enhanced expression of genes involved in amino acid biosynthesis [22]. A pronounced effect of 6S RNA depletion was observed in the stationary phase under stringent alkaline conditions (pH 9.3). The presence of 6S RNA normally ensures controlled expression of the transcription factor PspF that is required for expression of the _pspABCDE_ and _pspG_ operons involved in alkaline stress response. Upon 6S RNA knockout, these proteins are overexpressed and improve stationary cell survival under high pH conditions [23]. Similar and overlapping phenotypes were observed for the Gram-positive _B. subtilis_, although this bacterium is quite different in terms of natural habitats, physiology and metabolism. _B. subtilis_ and other Firmicutes express two different 6S RNAs (6S-1 and 6S-2) [24]. Deletion of both 6S RNAs in the laboratory strain PY79 also caused a decrease of _B. subtilis_ culture density in the late stationary phase (24 h cultivation) and was advantageous under extremely alkaline conditions (pH 9.8) [19]. Additionally, the lack of _B. subtilis_ 6S-1 RNA (the assumed functional homolog of _E.