Jump to ContentJump to Main Navigation
Show Summary Details
More options …

Biological Chemistry

Editor-in-Chief: Brüne, Bernhard

Editorial Board Member: Buchner, Johannes / Lei, Ming / Ludwig, Stephan / Sies, Helmut / Thomas, Douglas D. / Turk, Boris / Wittinghofer, Alfred

12 Issues per year

IMPACT FACTOR 2016: 3.273

CiteScore 2016: 3.01

SCImago Journal Rank (SJR) 2016: 1.679
Source Normalized Impact per Paper (SNIP) 2016: 0.800

See all formats and pricing
More options …
Volume 386, Issue 12 (Dec 2005)


How to find small non-coding RNAs in bacteria

Jörg Vogel
  • Max Planck Institute for Infection Biology, RNA Biology, Schumannstr. 21/22, D-10117 Berlin, Germany
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Cynthia Mira Sharma
  • Max Planck Institute for Infection Biology, RNA Biology, Schumannstr. 21/22, D-10117 Berlin, Germany
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
Published Online: 2005-12-09 | DOI: https://doi.org/10.1515/BC.2005.140


Small non-coding RNAs (sRNAs) have attracted considerable attention as an emerging class of gene expression regulators. In bacteria, a few regulatory RNA molecules have long been known, but the extent of their role in the cell was not fully appreciated until the recent discovery of hundreds of potential sRNA genes in the bacterium Escherichia coli. Orthologs of these E. coli sRNA genes, as well as unrelated sRNAs, were also found in other bacteria. Here we review the disparate experimental approaches used over the years to identify sRNA molecules and their genes in prokaryotes. These include genome-wide searches based on the biocomputational prediction of non-coding RNA genes, global detection of non-coding transcripts using microarrays, and shotgun cloning of small RNAs (RNomics). Other sRNAs were found by either co-purification with RNA-binding proteins, such as Hfq or CsrA/RsmA, or classical cloning of abundant small RNAs after size fractionation in polyacrylamide gels. In addition, bacterial genetics offers powerful tools that aid in the search for sRNAs that may play a critical role in the regulatory circuit of interest, for example, the response to stress or the adaptation to a change in nutrient availability. Many of the techniques discussed here have also been successfully applied to the discovery of eukaryotic and archaeal sRNAs.

Keywords: bacteria; gene expression regulation; Hfq; non-coding RNA; post-transcriptional regulation; riboregulation; RNA processing; RNomics; small RNA


About the article

Corresponding author

Published Online: 2005-12-09

Published in Print: 2005-12-01

Citation Information: Biological Chemistry, ISSN (Online) 1437-4315, ISSN (Print) 1431-6730, DOI: https://doi.org/10.1515/BC.2005.140.

Export Citation

Citing Articles

Here you can find all Crossref-listed publications in which this article is cited. If you would like to receive automatic email messages as soon as this article is cited in other publications, simply activate the “Citation Alert” on the top of this page.

Laura Álvarez-Fraga, Soraya Rumbo-Feal, Astrid Pérez, Manuel J. Gómez, Carmen Gayoso, Juan A. Vallejo, Emily J. Ohneck, Jaione Valle, Luis A. Actis, Alejandro Beceiro, Germán Bou, Margarita Poza, and Indranil Biswas
PLOS ONE, 2017, Volume 12, Number 8, Page e0182084
Muhammad Z. Nawaz, Huahua Jian, Ying He, Lei Xiong, Xiang Xiao, and Fengping Wang
Frontiers in Microbiology, 2017, Volume 8
Pierre Mandin, Francis Repoila, Massimo Vergassola, Thomas Geissmann, and Pascale Cossart
Nucleic Acids Research, 2007, Volume 35, Number 3, Page 962
Johannes H. Urban and Jörg Vogel
Nucleic Acids Research, 2007, Volume 35, Number 3, Page 1018
Branislav Večerek, Lukas Rajkowitsch, Elisabeth Sonnleitner, Renée Schroeder, and Udo Bläsi
Nucleic Acids Research, 2008, Volume 36, Number 1, Page 133
Sandra C. Viegas, Verena Pfeiffer, Alexandra Sittka, Inês J. Silva, Jörg Vogel, and Cecília M. Arraiano
Nucleic Acids Research, 2007, Volume 35, Number 22, Page 7651
Wei-Bing Liu, Yang Shi, Li-Li Yao, Ying Zhou, Bang-Ce Ye, and Marie-Joelle Virolle
PLoS ONE, 2013, Volume 8, Number 11, Page e80676
Mariam Brenneis, Jörg Soppa, and Grzegorz Kudla
PLoS ONE, 2009, Volume 4, Number 2, Page e4484
Xiaomin Ying, Yuan Cao, Jiayao Wu, Qian Liu, Lei Cha, Wuju Li, and Jonathan H. Badger
PLoS ONE, 2011, Volume 6, Number 7, Page e22705
Carsten Marr, Fabian J. Theis, Larry S. Liebovitch, Marc-Thorsten Hütt, and M. Madan Babu
PLoS Computational Biology, 2010, Volume 6, Number 7, Page e1000836
Nataly Perez, Jeanette Treviño, Zhuyun Liu, Siu Chun Michael Ho, Paul Babitzke, Paul Sumby, and Ramy K. Aziz
PLoS ONE, 2009, Volume 4, Number 11, Page e7668
Trina M. Norden-Krichmar, Andrew E. Allen, Terry Gaasterland, Mark Hildebrand, and Iddo Friedberg
PLoS ONE, 2011, Volume 6, Number 8, Page e22870
Azeem Siddique, Nicolas Buisine, Ronald Chalmers, and Josep Casadesús
PLoS Genetics, 2011, Volume 7, Number 1, Page e1001277
Gabriele Nübel, Frieda A. Sorgenfrei, and Andres Jäschke
Methods, 2017, Volume 117, Page 14
Zhouwei Chen, Lufeng Li, Zhan Shan, Hannian Huang, Huan Chen, Xianfeng Ding, Jiangfeng Guo, and Lili Liu
Microbiological Research, 2016, Volume 192, Page 122
Michael J. Ellis and David B. Haniford
Wiley Interdisciplinary Reviews: RNA, 2016, Volume 7, Number 3, Page 382
Sandra Van Puyvelde, Jozef Vanderleyden, and Sigrid C. J. De Keersmaecker
MicrobiologyOpen, 2015, Volume 4, Number 5, Page 699
María Gómez-Lozano, Rasmus L. Marvig, Carlos Molina-Santiago, Paula M. Tribelli, Juan-Luis Ramos, and Søren Molin
Environmental Microbiology Reports, 2015, Volume 7, Number 2, Page 227
C. W. Remmele, Y. Xian, M. Albrecht, M. Faulstich, M. Fraunholz, E. Heinrichs, M. T. Dittrich, T. Muller, R. Reinhardt, and T. Rudel
Nucleic Acids Research, 2014, Volume 42, Number 16, Page 10579
C. Michaux, N. Verneuil, A. Hartke, and J.-C. Giard
Microbiology, 2014, Volume 160, Number Pt_6, Page 1007
Wendy Mok and Yingfu Li
Sensors, 2008, Volume 8, Number 11, Page 7050
Nona Heueis, Michael-Paul Vockenhuber, and Beatrix Suess
RNA Biology, 2014, Volume 11, Number 5, Page 464
E. Puerta-Fernandez, J. E. Barrick, A. Roth, and R. R. Breaker
Proceedings of the National Academy of Sciences, 2006, Volume 103, Number 51, Page 19490
Álvaro D. Ortega, Jesús Gonzalo-Asensio, and Francisco García-del Portillo
RNA Biology, 2012, Volume 9, Number 4, Page 469
Eric P. Nawrocki and Sean R. Eddy
RNA Biology, 2013, Volume 10, Number 7, Page 1170
Y. H. Lee, S. Kim, J. D. Helmann, B.-H. Kim, and Y. K. Park
Microbiology, 2013, Volume 159, Number Pt_7, Page 1366
Wuju Li, Xiaomin Ying, Qixuan Lu, and Linxi Chen
Genomics, Proteomics & Bioinformatics, 2012, Volume 10, Number 5, Page 276
Yanjie Chao, Kai Papenfort, Richard Reinhardt, Cynthia M Sharma, and Jörg Vogel
The EMBO Journal, 2012, Volume 31, Number 20, Page 4005
Shaaretha Pelly, William R. Bishai, and Gyanu Lamichhane
Gene, 2012, Volume 500, Number 1, Page 85
Tingting Zhao, Ren Zhang, and Mingbo Wang
Journal of Biomedical Research, 2010, Volume 24, Number 1, Page 33
Masayuki Murata, Rashed Noor, Hiroshi Nagamitsu, Shuhei Tanaka, and Mamoru Yamada
Genes to Cells, 2012, Volume 17, Number 3, Page 234
Francis Repoila and Fabien Darfeuille
Biology of the Cell, 2009, Volume 101, Number 2, Page 117
Karen K. Carter, James J. Valdes, and William E. Bentley
Metabolic Engineering, 2012, Volume 14, Number 3, Page 281
Kai Papenfort and Jörg Vogel
Research in Microbiology, 2009, Volume 160, Number 4, Page 278
Christopher A Brosnan and Olivier Voinnet
Current Opinion in Cell Biology, 2009, Volume 21, Number 3, Page 416
Poul Valentin-Hansen, Jesper Johansen, and Anders A Rasmussen
Current Opinion in Microbiology, 2007, Volume 10, Number 2, Page 152
Jonathan Livny and Matthew K Waldor
Current Opinion in Microbiology, 2007, Volume 10, Number 2, Page 96
Alejandro Toledo-Arana, Francis Repoila, and Pascale Cossart
Current Opinion in Microbiology, 2007, Volume 10, Number 2, Page 182
Marie Beaume, David Hernandez, Patrice Francois, and Jacques Schrenzel
International Journal of Medical Microbiology, 2010, Volume 300, Number 2-3, Page 88
Johannes H. Urban, Kai Papenfort, Jens Thomsen, Ruth A. Schmitz, and Jörg Vogel
Journal of Molecular Biology, 2007, Volume 373, Number 3, Page 521
Yalin Zhao, Hua Li, Yanyan Hou, Lei Cha, Yuan Cao, Ligui Wang, Xiaomin Ying, and Wuju Li
Biochemical and Biophysical Research Communications, 2008, Volume 372, Number 2, Page 346
Agata Fratczak, Ryszard Kierzek, and Elzbieta Kierzek
Biochemistry, 2011, Volume 50, Number 35, Page 7647
Florian Eggenhofer, Hakim Tafer, Peter F. Stadler, and Ivo L. Hofacker
Nucleic Acids Research, 2011, Volume 39, Number suppl_2, Page W149
Masayuki MURATA and Mamoru YAMADA
KAGAKU TO SEIBUTSU, 2008, Volume 46, Number 8, Page 550
Jörg Vogel and E Gerhart H Wagner
Current Opinion in Microbiology, 2007, Volume 10, Number 3, Page 262
Shoshy Altuvia
Current Opinion in Microbiology, 2007, Volume 10, Number 3, Page 257
Sophie Abby and Vincent Daubin
Trends in Microbiology, 2007, Volume 15, Number 3, Page 135
Rahul V. Kulkarni and Prajna R. Kulkarni
Methods, 2007, Volume 43, Number 2, Page 131
Cynthia Mira Sharma and Jörg Vogel
Current Opinion in Microbiology, 2009, Volume 12, Number 5, Page 536
Mobarak A. Mraheil, André Billion, Walid Mohamed, Krishnendu Mukherjee, Carsten Kuenne, Jordan Pischimarov, Christian Krawitz, Julia Retey, Thomas Hartsch, Trinad Chakraborty, and Torsten Hain
Nucleic Acids Research, 2011, Volume 39, Number 10, Page 4235
C. Pichon and B. Felden
Bioinformatics, 2008, Volume 24, Number 24, Page 2807
J. Reeder, J. Reeder, and R. Giegerich
Bioinformatics, 2007, Volume 23, Number 13, Page i392
J. Panek, L. Krasny, J. Bobek, E. Jezkova, J. Korelusova, and J. Vohradsky
Nucleic Acids Research, 2011, Volume 39, Number 8, Page 3418
Jörg Vogel and Kai Papenfort
Current Opinion in Microbiology, 2006, Volume 9, Number 6, Page 605
Yexin Zhou and Jianping Xie
Journal of Cellular Physiology, 2011, Volume 226, Number 4, Page 968
Tianyan Song, Franziska Mika, Barbro Lindmark, Zhi Liu, Stefan Schild, Anne Bishop, Jun Zhu, Andrew Camilli, Jörgen Johansson, Jörg Vogel, and Sun Nyunt Wai
Molecular Microbiology, 2008, Volume 70, Number 1, Page 100
Barbara O. Gvakharia, Brian Tjaden, Neeraja Vajrala, Luis A. Sayavedra-Soto, and Daniel J. Arp
FEMS Microbiology Letters, 2010, Volume 312, Number 1, Page 46
A. C. G. Silveira, K. L. Robertson, B. Lin, Z. Wang, G. J. Vora, A. T. R. Vasconcelos, and F. L. Thompson
Microbiology, 2010, Volume 156, Number 8, Page 2452
Luay F. Abu-Qatouseh, Suresh V. Chinni, Jochen Seggewiß, Richard A. Proctor, Jürgen Brosius, Timofey S. Rozhdestvensky, Georg Peters, Christof von Eiff, and Karsten Becker
Journal of Molecular Medicine, 2010, Volume 88, Number 6, Page 565
Eun-Jin Lee and Eduardo A. Groisman
Molecular Microbiology, 2010, Volume 76, Number 4, Page 1020
Marco Albrecht, Cynthia M. Sharma, Richard Reinhardt, Jörg Vogel, and Thomas Rudel
Nucleic Acids Research, 2010, Volume 38, Number 3, Page 868
Kyung Moon and Susan Gottesman
Molecular Microbiology, 2009, Volume 74, Number 6, Page 1314
Franz Narberhaus and Jörg Vogel
Molecular Microbiology, 2009, Volume 74, Number 2, Page 261
J. M. Peters, R. A. Mooney, P. F. Kuan, J. L. Rowland, S. Keles, and R. Landick
Proceedings of the National Academy of Sciences, 2009, Volume 106, Number 36, Page 15406
Kristine B. Arnvig and Douglas B. Young
Molecular Microbiology, 2009, Volume 73, Number 3, Page 397
Jörg Vogel
Molecular Microbiology, 2009, Volume 71, Number 1, Page 1
Maude Guillier and Susan Gottesman
Nucleic Acids Research, 2008, Volume 36, Number 21, Page 6781
Katrin Weidenbach, Claudia Ehlers, Jutta Kock, Armin Ehrenreich, and Ruth A. Schmitz
Archives of Microbiology, 2008, Volume 190, Number 3, Page 319
Kai Papenfort, Verena Pfeiffer, Sacha Lucchini, Avinash Sonawane, Jay C. D. Hinton, and Jörg Vogel
Molecular Microbiology, 2008, Volume 68, Number 4, Page 890
Verena Pfeiffer, Alexandra Sittka, Raju Tomer, Karsten Tedin, Volker Brinkmann, and Jörg Vogel
Molecular Microbiology, 2007, Volume 66, Number 5, Page 1174
Cold Spring Harbor Symposia on Quantitative Biology, 2006, Volume 71, Number 0, Page 135
Kai Papenfort, Verena Pfeiffer, Franziska Mika, Sacha Lucchini, Jay C. D. Hinton, and Jörg Vogel
Molecular Microbiology, 2006, Volume 62, Number 6, Page 1674

Comments (0)

Please log in or register to comment.
Log in