Post-transcriptional regulation is an important layer of gene expression control in both pro- and eukaryotes. Besides regulatory RNAs, such as the eukaryotic microRNAs and prokaryotic small regulatory RNAs (sRNAs), RNA-binding proteins proteins have been described as key players in this regulatory process. In many bacteria, the Sm-like protein Hfq is the most important RNA chaperone and is required for diverse cellular processes and virulence of many bacterial pathogens. However, about 50% of all bacteria lack Hfq, although sRNAs had been identified in their genomes, indicating that there might be other proteins involved in riboregulation.

In this project, we will establish Campylobacter jejuni, the most common cause of bacterial gastroenteritis in humans, as a new model organism for riboregulation in bacteria without Hfq. Its small genome carries only a few transcriptional regulators and almost nothing is known about post-transcriptional regulation in this emerging pathogen. We aim at the identification and functional characterization of protein factors involved in riboregulation in Campylobacter. This will include a combination of genetic screens and isolation of RNP-complexes, followed by proteomics and RNA-seq analyses and biochemical and structural analysis. Overall, research in Campylobacter will increase our understanding of post-transcriptional regulation in a wider range of pathogens.

Gaurav Dugar

Förstner KU, Vogel J, Sharma CM (2014). READemption - A tool for the computational analysis of deep-sequencing-based transcriptome data. Bioinformatics. [Epub ahead of print]

Sharma, CM, Vogel J (2014). Differential RNA-seq: the approach behind and the biological insight gained. Curr Opin Microbiol 19:97–105.

Voigt K, Sharma CM, Mitschke J, Joke Lambrecht S, Voß B, Hess WR, Steglich C (2014). Comparative transcriptomics of two environmentally relevant cyanobacteria reveals unexpected transcriptome diversity. ISME J 8(10):2056-68.

Dugar G, Herbig A, Förstner KU, Heidrich N, Reinhardt R, Nieselt K, Sharma CM (2013). High-resolution transcriptome maps reveal strain-specific regulatory features of multiple Campylobacter jejuni isolates. PLoS Genet 9(5):e1003495. 

1. Renate Rieder, Richard Reinhardt, Cynthia M. Sharma*& Jörg Vogel* (2012) Experimental tools to identify RNA-protein interactions in Helicobacter pylori.

RNA Biology, 9(4), in press.

*Corresponding authors.

2. Pernitzsch SR & Sharma, CM (2012) Transcriptome complexity and riboregulation in the human pathogen Helicobacter pylori.

Frontiers in Cellular and Infection Microbiology, in press.

3. Zhelyazkova P, Sharma CM, Förstner KU, Liere K, Vogel J, Börner T (2012) The primary transcriptome of barley chloroplasts: numerous non-coding RNAs and the dominating role of the plastid-encoded RNA polymerase

Plant Cell, 24(1):123-36.

4. Wilms I, Overlöper A, Nowrousian M, Sharma CM, Narberhaus F (2012)

SF RNA Virulence: Deep sequencing uncovers numerous small RNAs on all four replicons of the plant pathogen Agrobacterium tumefaciens.

RNA Biology, 9(4).

5. Ramachandran VK, Shearer N, Jacob JJ, Sharma CM, Thompson A. (2012) The architecture and ppGpp-dependent expression of the primary transcriptome of Salmonella Typhimurium during invasion gene expression. BMC Genomics. 13(1):25.

6. Madhugiri R, Pessi G, Voss B, Hahn J, Sharma CM, Reinhardt R, Vogel J, Hess WR, Fischer HM, Evguenieva-Hackenberg E (2012)

Small RNAs of the Bradyrhizobium/Rhodopseudomonas lineage and their analysis.

RNA Biology, 9(1).

7. Schmidtke C, Findeiß S, Sharma CM, Kuhfuß J, Hoffmann S, Vogel J, Stadler PF, Bonas U (2011)

Genome-wide transcriptome analysis of the plant pathogen Xanthomonas identifies sRNAs with putative virulence functions.

NAR, 40(5):2020-2031.

8. Albrecht M, Sharma CM, Dittrich MT, Müller T, Reinhardt R, Vogel J, Rudel T (2011) The Transcriptional Landscape of Chlamydia pneumoniae.

Genome Biology, 12(10):R98.

9. Belair C, Baud J, Chabas S, Sharma CM, Vogel J, Staedel C, Darfeuille F (2011)

Helicobacter pylori interferes with an embryonic stem cell miRNA cluster to block cell cycle progression.

Silence, 2(1):7.

10. Deltcheva E, Chylinski K*, Sharma CM*, Gonzales K, Chao Y, Pirzada ZA, Eckert MR, Vogel J, Charpentier E (2011)

CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III.

Nature 471(7340):602-7. *Equally contributing authors.

11. Sharma CM, Papenfort K, Pernitzsch SR, Mollenkopf HJ, Hinton JC, Vogel J. (2011)

Pervasive post-transcriptional control of genes involved in amino acid metabolism by the Hfq-dependent GcvB small RNA.

Molecular Microbiology, 81(5): 1144-1165.

12. Beckmann BM, Burenina OY, Hoch PG, Kubareva EA, Sharma CM, Hartmann RK1 (2011)

In vivo and in vitro analysis of 6S RNA-templated short transcripts in Bacillus subtilis.

RNA Biology, 8(5).

13. Sharma CM, Storz G (2011)

Interesting twists on small RNA themes in Pseudomonas aeruginosa.

Molecular Microbiology 80(4):855-9.

14. Berghoff BA, Glaeser J, Sharma CM, Zobawa M, Lottspeich F, Vogel J, Klug G (2011)

Contribution of Hfq to photooxidative stress resistance and global regulation in Rhodobacter sphaeroides.

Molecular Microbiology 80(6):1479-1495.

15. Mitschke J, Georg J, Scholz I, Sharma CM, Dienst D, Bantscheff J, Voß B, Steglich C, Wilde A, Vogel J, Hess WR (2011)

An experimentally anchored map of transcriptional start sites in the model cyanobacterium Synechocystis sp. PCC6803.

PNAS 108(5):2124-9.

16. Vockenhuber MP, Sharma CM, Statt MG, Schmidt D, Xu Z, Dietrich S, Liesegang H, Mathews DH, Suess B (2011)

Deep sequencing-based identification of small non-coding RNAs in S. coelicolor.

RNA Biology 8(3).

17. Sharma CM, Hoffmann S, Darfeuille F, Reignier J, Findeiß S, Sittka A, Chabas S, Reiche K, Hackermüller J, Reinhardt R, Stadler PF, Vogel J (2010)

The primary transcriptome of the major human pathogen Helicobacter pylori.

Nature 464(7286):250-5.

18. Papenfort K, Bouvier M, Mika F, Sharma CM, Vogel J (2010)

Evidence for an autonomous 5' target recognition domain in an Hfq-associated small RNA.

PNAS 107(47):20435-40.

19. Jäger D*, Sharma CM*, Thomsen J, Ehlers C, Vogel J, Schmitz RA (2009)

Deep sequencing analysis of the Methanosarcina mazei Gö1 transcriptome in response to nitrogen availability.

PNAS 106(51):21878-82. *Equally contributing authors.

20. Irnov I, Sharma CM, Vogel J, Winkler W (2010)

Identification of regulatory RNAs in Bacillus subtilis.

Nucleic Acids Research 38(19):6637-51.

21. Bohn C, Rigoulay C, Chabelskaya S, Sharma CM, Marchais A, Skorski P, Borezee-Durant B, Barbet R, Jacquet E, Jacq A, Gautheret D, Felden B, Vogel J, Bouloc P (2010)

Experimental discovery of small RNAs in Staphylococcus aureus reveals a riboregulator of central metabolism.

Nucleic Acids Research 38(19):6620-36.

22. Albrecht M, Sharma CM, Reinhardt R, Vogel J, Rudel T (2010)

Deep sequencing-based discovery of the Chlamydia trachomatis transcriptome.

Nucleic Acids Research 38(3):868-77.

23. Berghoff BA, Glaeser J, Sharma CM, Vogel J, Klug G (2009)

Photooxidative stress induced and abundant small RNAs in Rhodobacter sphaeroides.

Molecular Microbiology 74(6), 1497-1512.

24. Sharma CM, Vogel J (2009)

Experimental approaches for the discovery and characterization of regulatory small RNA.

Current Opinion in Microbiology 12(5):536-46

25. Hoffmann S, Otto C, Kurtz S, Sharma CM, Khaitovich P, Vogel J, Stadler PF, Hackermüller J (2009) Fast mapping of short sequences with mismatches, insertions and deletions using index structures.

PLoS Computational Biology 5(9):e1000502

26. Sittka A, Sharma CM, Rolle K, Vogel J (2009)

Deep sequencing of Salmonella RNA associated with heterologous Hfq proteins in vivo reveals small RNAs as a major target class and identifies RNA processing phenotypes.

RNA Biology 6(3):266-275

27. Bouvier M, Sharma CM, Mika F, Nierhaus KH, Vogel J (2008)

Small RNA binding to 5’ mRNA coding region inhibits translational initiation.

Molecular Cell 32(6):827-37

28. Sittka A, Lucchini S, Papenfort K, Sharma CM, Rolle K, Binnewies TT, Hinton JC, Vogel J (2008) Deep sequencing analysis of small noncoding RNA and mRNA targets of the global post-transcriptional regulator, Hfq.

PLoS Genetics 4(8):e1000163

29. Sharma CM, Darfeuille F, Plantinga T, Vogel J (2007)

A small RNA regulates multiple ABC transporter mRNAs by targeting C/A-rich elements inside and upstream of ribosome binding sites. Genes & Development 21(21):2804-2817.

30. Vogel J & Sharma CM (2005)

How to find small noncoding RNAs in bacteria.

Biological Chemistry 386(11):1219-38.

BOOK CHAPTERS

Borries A, Vogel J, Sharma CM (2012) Differential RNA Sequencing (dRNA-Seq): Deep-Sequencing-Based Analysis of Primary Transcriptomes. In: Tag-based Approaches for Next-Generation Sequencing, Eds. M. Harbers, G. Kahl, Wiley-Blackwell-VCH (978-3-527-32819-2)

Dr. Cynthia Sharma has received the 2013 annual award for young scientists of the German Society for Hygiene and Microbiology. It includes a prize money of 2500 euro. Dr. Sharma received this award for her outstanding work on riboregulation in pathogenic bacteria. We would like to congratulate Dr. Sharma and her team on this great success! More information can be found here.