Regulation of transcription by 6S RNAs: insights from the Escherichia coli and Bacillus subtilis model systems.
Whereas, the majority of bacterial non-coding RNAs and functional RNA elements regulate post-transcriptional processes, either by interacting with other RNAs via base-pairing or through binding of small ligands (riboswitches), 6S RNAs affect transcription itself by binding to the housekeeping holoenzyme of RNA polymerase (RNAP). Remarkably, 6S RNAs serve as RNA templates for bacterial RNAP, giving rise to the de novo synthesis of short transcripts, termed pRNAs (product RNAs). Hence, 6S RNAs prompt the enzyme to act as an RNA-dependent RNA polymerase (RdRP). Synthesis of pRNAs exceeding a certain length limit (~13 nt) persistently rearrange the 6S RNA structure, which in turn, disrupts the 6S RNA:RNAP complex. This pRNA synthesis-mediated "reanimation" of sequestered RNAP molecules represents the conceivably fastest mechanism for resuming transcription in cells that enter a new exponential growth phase. The many different 6S RNAs found in a wide variety of bacteria do not share strong sequence homology but have in common a conserved rod-shaped structure with a large internal loop, termed the central bulge; this architecture mediates specific binding to the active site of RNAP. In this article, we summarize the overall state of knowledge as well as very recent findings on the structure, function, and physiological effects of 6S RNA examples from the two model organisms, Escherichia coli and Bacillus subtilis. Comparison of the presently known properties of 6S RNAs in the two organisms highlights common principles as well as diverse features.
Heinrich-Heine-Universität Düsseldorf; Institut für Physikalische Biologie Universitätsstr; Düsseldorf, Germany.
Benedikt
B
Steuten
Philipps-Universität Marburg; Marburg, Germany.
Philipp G
PG
Hoch
Philipps-Universität Marburg; Marburg, Germany.
Katrin
K
Damm
Heinrich-Heine-Universität Düsseldorf; Institut für Physikalische Biologie Universitätsstr; Düsseldorf, Germany.
Sabine
S
Schneider
Philipps-Universität Marburg; Marburg, Germany.
Karen
K
Köhler
Heinrich-Heine-Universität Düsseldorf; Institut für Physikalische Biologie Universitätsstr; Düsseldorf, Germany.
Rolf
R
Wagner
Philipps-Universität Marburg; Marburg, Germany.
Roland K
RK
Hartmann
D001412:Bacillus subtilis / Q000235:genetics* / Q000378:metabolism; D012321:DNA-Directed RNA Polymerases / Q000737:chemistry / Q000378:metabolism; D004926:Escherichia coli / Q000235:genetics* / Q000378:metabolism; D015964:Gene Expression Regulation, Bacterial; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D012329:RNA, Bacterial / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D022661:RNA, Untranslated / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D013698:Templates, Genetic; D014158:Transcription, Genetic
C411065:6S RNA; D012329:RNA, Bacterial; D022661:RNA, Untranslated; D012321:DNA-Directed RNA Polymerases
6S RNAs; function; mechanism; physiological role; structure; transcriptional regulation