6S RNA: recent answers – future questions

Abstract

Summary6S RNA is a non-coding RNA, found in almost all phylogenetic branches of bacteria. Through its conserved secondary structure, resembling open DNA promoters, it binds to RNA polymerase and interferes with transcription at many promoters. That way, it functions as transcriptional regulator facilitating adaptation to stationary phase conditions. Strikingly, 6S RNA acts as template for the synthesis of small RNAs (pRNA), which trigger the disintegration of the inhibitory RNA polymerase-6S RNA complex releasing 6S RNA-dependent repression. The regulatory implications of 6S RNAs vary among different bacterial species depending on the lifestyle and specific growth conditions that they have to face. The influence of 6S RNA can be seen on many different processes including stationary growth, sporulation, light adaptation or intracellular growth of pathogenic bacteria. Recent structural and functional studies have yielded details of the interaction between E. coli 6S RNA and RNA polymerase. Genome-wide transcriptome analyses provided insight into the functional diversity of 6S RNAs. Moreover, the mechanism and physiological consequences of pRNA synthesis have been explored in several systems. A major function of 6S RNA as a guardian regulating the economic use of cellular resources under limiting conditions and stress emerges as a common perception from numerous recent studies.

Transcriptome-Wide Identification of Hfq-Associated RNAs in Brucella suis by Deep Sequencing

“…These transcripts include transfer-messenger RNA (tmRNA), 4.5S RNA, and 6S RNA. 6S RNA acts as a transcriptional regulator controlling adaptation to stationaryphase and stress conditions and was recently implicated in Legionella virulence (58,59). It is able to bind to RNA polymerase by structurally mimicking a DNA template with an open promoter; analysis of the B. suis 6S RNA sequence indeed revealed a doublestranded RNA structure with open bulges in the center (Fig.…”

Small RNAs in Bacteria and Archaea

“…A double mutant is more affected than a single mutant in outgrowth from alkaline stress conditions (Hoch et al, 2015). Differential proteomics suggests roles for 6S-2 in metabolism, an observation probably also applying to other bacterial species (Hoch et al, 2015;Steuten et al, 2014). A related case may be Ms1, a mycobacterial sRNA that interacts with core RNApol (Hnilicova et al, 2015).…”

“…The ubiquitous and abundant 6S RNA had been known for over 40 years (Steuten et al, 2014;Wassarman, 2007) but remained recalcitrant to functional analysis; deletion or overexpression gave no phenotypes. In 2000, 6S RNA was shown to form a stable complex with the s 70 -containing housekeeping form of the RNA polymerase holoenzyme (s 70 -RNApol) (Wassarman & Storz, 2000).…”

“…They are represented by the CsrB/RsmZ family (Romeo, Vakulskas, & Babitzke, 2013) and by 6S RNA (Steuten, Schneider, & Wagner, 2014;Wassarman, 2007) (Figure 3). CsrB (or any other family member) uses short sequence motifs to bind multiple copies of CsrA (carbon storage regulator), a protein that translationally represses many mRNAs (Figure 3(B)).…”

Characterization of 6S RNA in the Lyme disease spirochete

“…Accumulation of 6S RNA in stationary phase is a hallmark of adaptation in E. coli (Cavanagh & Wassarman, ; Steuten et al, ; Wassarman & Storz, ). To examine if B. burgdorferi follows suit, Bb6S RNA levels were assayed during growth from early log phase through late stationary phase by Northern blot analyses and qRT‐PCR.…”