Note to users. If you're seeing this message, it means that your browser cannot find this page's style/presentation instructions -- or possibly that you are using a browser that does not support current Web standards. Find out more about why this message is appearing, and what you can do to make your experience of our site the best it can be.


Logo for

Science 314 (5805): 1601-1603

Copyright © 2006 by the American Association for the Advancement of Science

Synthesis-Mediated Release of a Small RNA Inhibitor of RNA Polymerase

Karen M. Wassarman1*, and Ruth M. Saecker2

Abstract: Noncoding small RNAs regulate gene expression in all organisms, in some cases through direct association with RNA polymerase (RNAP). Here we report that the mechanism of 6S RNA inhibition of transcription is through specific, stable interactions with the active site of Escherichia coli RNAP that exclude promoter DNA binding. In fact, the DNA-dependent RNAP uses bound 6S RNA as a template for RNA synthesis, producing 14-to 20-nucleotide RNA products (pRNA). These results demonstrate that 6S RNA is functionally engaged in the active site of RNAP. Synthesis of pRNA destabilizes 6S RNA–RNAP complexes leading to release of the pRNA-6S RNA hybrid. In vivo, 6S RNA–directed RNA synthesis occurs during outgrowth from the stationary phase and likely is responsible for liberating RNAP from 6S RNA in response to nutrient availability.

1 Department of Bacteriology, University of Wisconsin–Madison, Madison, WI 53706, USA.
2 Department of Chemistry, University of Wisconsin–Madison, Madison, WI 53706, USA.

* To whom correspondence should be addressed. E-mail: wassarman{at}

In vitro characterization of 6S RNA release-defective mutants uncovers features of pRNA-dependent release from RNA polymerase in E. coli.
M. Oviedo Ovando, L. Shephard, and P. J. Unrau (2014)
RNA 20, 670-680
   Abstract »    Full Text »    PDF »
RNAs nonspecifically inhibit RNA polymerase II by preventing binding to the DNA template.
D. A. Pai, C. D. Kaplan, H. K. Kweon, K. Murakami, P. C. Andrews, and D. R. Engelke (2014)
RNA 20, 644-655
   Abstract »    Full Text »    PDF »
Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli.
D. McCloskey, B. O. Palsson, and A. M. Feist (2014)
Mol Syst Biol 9, 661
   Abstract »    Full Text »    PDF »
Mechanistic comparison of Bacillus subtilis 6S-1 and 6S-2 RNAs--commonalities and differences.
O. Y. Burenina, P. G. Hoch, K. Damm, M. Salas, T. S. Zatsepin, M. Lechner, T. S. Oretskaya, E. A. Kubareva, and R. K. Hartmann (2014)
RNA 20, 348-359
   Abstract »    Full Text »    PDF »
Initiating nucleotide identity determines efficiency of RNA synthesis from 6S RNA templates in Bacillus subtilis but not Escherichia coli.
I. J. Cabrera-Ostertag, A. T. Cavanagh, and K. M. Wassarman (2013)
Nucleic Acids Res. 41, 7501-7511
   Abstract »    Full Text »    PDF »
6S-1 RNA Function Leads to a Delay in Sporulation in Bacillus subtilis.
A. T. Cavanagh and K. M. Wassarman (2013)
J. Bacteriol. 195, 2079-2086
   Abstract »    Full Text »    PDF »
Struggling to let go: a non-coding RNA directs its own extension and destruction.
C. Bernecky and P. Cramer (2013)
EMBO J. 32, 771-772
   Full Text »    PDF »
RNA polymerase II acts as an RNA-dependent RNA polymerase to extend and destabilize a non-coding RNA.
S. D. Wagner, P. Yakovchuk, B. Gilman, S. L. Ponicsan, L. F. Drullinger, J. F. Kugel, and J. A. Goodrich (2013)
EMBO J. 32, 781-790
   Abstract »    Full Text »    PDF »
Identification of small RNAs in Mycobacterium smegmatis using heterologous Hfq.
S.-K. Li, P. K.-S. Ng, H. Qin, J. K.-Y. Lau, J. P.-Y. Lau, S. K.-W. Tsui, T.-F. Chan, and T. C.-K. Lau (2013)
RNA 19, 74-84
   Abstract »    Full Text »    PDF »
E. coli 6S RNA release from RNA polymerase requires {sigma}70 ejection by scrunching and is orchestrated by a conserved RNA hairpin.
S. S. S. Panchapakesan and P. J. Unrau (2012)
RNA 18, 2251-2259
   Abstract »    Full Text »    PDF »
Functional Characterization of the RNA Chaperone Hfq in the Opportunistic Human Pathogen Stenotrophomonas maltophilia.
E. Roscetto, T. Angrisano, V. Costa, M. Casalino, K. U. Forstner, C. M. Sharma, P. P. Di Nocera, and E. De Gregorio (2012)
J. Bacteriol. 194, 5864-5874
   Abstract »    Full Text »    PDF »
6S RNA - an old issue became blue-green.
A. Rediger, R. Geissen, B. Steuten, B. Heilmann, R. Wagner, and I. M. Axmann (2012)
Microbiology 158, 2480-2491
   Abstract »    Full Text »    PDF »
A pRNA-induced structural rearrangement triggers 6S-1 RNA release from RNA polymerase in Bacillus subtilis.
B. M. Beckmann, P. G. Hoch, M. Marz, D. K. Willkomm, M. Salas, and R. K. Hartmann (2012)
EMBO J. 31, 1727-1738
   Abstract »    Full Text »    PDF »
Regulation of 6S RNA by pRNA synthesis is required for efficient recovery from stationary phase in E. coli and B. subtilis.
A. T. Cavanagh, J. M. Sperger, and K. M. Wassarman (2012)
Nucleic Acids Res. 40, 2234-2246
   Abstract »    Full Text »    PDF »
Lag Phase Is a Distinct Growth Phase That Prepares Bacteria for Exponential Growth and Involves Transient Metal Accumulation.
M. D. Rolfe, C. J. Rice, S. Lucchini, C. Pin, A. Thompson, A. D. S. Cameron, M. Alston, M. F. Stringer, R. P. Betts, J. Baranyi, et al. (2012)
J. Bacteriol. 194, 686-701
   Abstract »    Full Text »    PDF »
Bacterial Small RNA Regulators: Versatile Roles and Rapidly Evolving Variations.
S. Gottesman and G. Storz (2011)
Cold Spring Harb Perspect Biol 3, a003798
   Abstract »    Full Text »    PDF »
An experimentally anchored map of transcriptional start sites in the model cyanobacterium Synechocystis sp. PCC6803.
J. Mitschke, J. Georg, I. Scholz, C. M. Sharma, D. Dienst, J. Bantscheff, B. Voss, C. Steglich, A. Wilde, J. Vogel, et al. (2011)
PNAS 108, 2124-2129
   Abstract »    Full Text »    PDF »
H. Chae, K. Han, K.-s. Kim, H. Park, J. Lee, and Y. Lee (2011)
J. Biol. Chem. 286, 114-122
   Abstract »    Full Text »    PDF »
6S RNA regulation of relA alters ppGpp levels in early stationary phase.
A. T. Cavanagh, P. Chandrangsu, and K. M. Wassarman (2010)
Microbiology 156, 3791-3800
   Abstract »    Full Text »    PDF »
Northern blot detection of endogenous small RNAs (~14 nt) in bacterial total RNA extracts.
B. M. Beckmann, A. Grunweller, M. H. W. Weber, and R. K. Hartmann (2010)
Nucleic Acids Res. 38, e147
   Abstract »    Full Text »    PDF »
Binding and release of the 6S transcriptional control RNA.
L. Shephard, N. Dobson, and P. J. Unrau (2010)
RNA 16, 885-892
   Abstract »    Full Text »    PDF »
Ecological Genomics of Marine Picocyanobacteria.
D. J. Scanlan, M. Ostrowski, S. Mazard, A. Dufresne, L. Garczarek, W. R. Hess, A. F. Post, M. Hagemann, I. Paulsen, and F. Partensky (2009)
Microbiol. Mol. Biol. Rev. 73, 249-299
   Abstract »    Full Text »    PDF »
B2 RNA and Alu RNA repress transcription by disrupting contacts between RNA polymerase II and promoter DNA within assembled complexes.
P. Yakovchuk, J. A. Goodrich, and J. F. Kugel (2009)
PNAS 106, 5569-5574
   Abstract »    Full Text »    PDF »
Formation of an RNA polymerase II preinitiation complex on an RNA promoter derived from the hepatitis delta virus RNA genome.
A. Abrahem and M. Pelchat (2008)
Nucleic Acids Res. 36, 5201-5211
   Abstract »    Full Text »    PDF »
Characterization of the structure, function, and mechanism of B2 RNA, an ncRNA repressor of RNA polymerase II transcription.
C. A. Espinoza, J. A. Goodrich, and J. F. Kugel (2007)
RNA 13, 583-596
   Abstract »    Full Text »    PDF »

To Advertise     Find Products

Science Signaling. ISSN 1937-9145 (online), 1945-0877 (print). Pre-2008: Science's STKE. ISSN 1525-8882