Selected Publications
- GEISSMANN T, CHEVALIER C, CROS MJ, BOISSET S, FECHTER P, NOIROT C, SCHRENZEL J, FRANÇOIS P, VANDENESCH F, GASPIN C, ROMBY P. A search for small noncoding RNAs in Staphylococcus aureus reveals a conserved sequence motif for regulation. Nucleic Acids Res. 2009 Nov;37(21):7239-57.
- LIOLIOU E, SHARMA CM, CALDELARI I, HELFER AC, FECHTER P, VANDENESCH F, VOGEL J, ROMBYP. (2012) Global regulatory functions of the Staphylococcus aureus endoribonuclease III in gene expression. PLoS Genet. 8(6):e1002782.
- DUVAL M, KOREPANOV A, FUCHSBAUER O, FECHTER P, HALLER A, FABBRETTI A, CHOULIER L, MICURA R, KLAHOLZ BP, ROMBY P*, SPRINGER M, MARZI S*. (2013) Escherichia coli ribosomal protein S1 unfolds structured mRNAs onto the ribosome for active translation initiation. PLoS Biol. 11(12):e1001731. *co-corresponding author
- ROMILLY C, LAYS C, TOMASINI A, CALDELARI I, BENITO Y, HAMMANN P, GEISSMANN T, BOISSET S, ROMBY P*, VANDENESCH F*. (2014) A non-coding RNA promotes bacterial persistence and decreases virulence by regulating a regulator in Staphylococcus aureus. PLoS Pathog. 10(3):e1003979. *co-corresponding authors
- TOMASINI A, MOREAU K, CHICHER J, GEISSMANN T, VANDENESCH F, ROMBY P*, MARZI S, CALDELARI I* (2017) The RNA targetome of Staphylococcus aureus non coding RNA RsaA: impact on cell surface properties and defense mechanisms. Nucleic Acid Res. Apr 3. doi: 10.1093/nar/gkx219. *co-corresponding authors
FRIAS Project
MapRNA: Mapping RNA-RNA pairings in vivo in bacteria and their importance in fast acclimation processes (stress responses, virulence)
Small non-coding RNAs (sRNAs) are a very heterogeneous class of regulatory factors in bacteria. Extensive analysis revealed that many sRNAs in Enterobacteriaceae regulate gene expression at the post-transcriptional level. These sRNAs were the missing links in the networks that are required for fast growth adaptation, and which interconnect key cellular pathways. However, the insight into the functions and mechanism of sRNA’s action in other phyla such as the Firmicutes or Cyanobacteria is still lagging behind, because these bacteria face other regulatory challenges and hence have evolved different machineries to regulate gene expression. Here, we will combine the complementary expertise of the two teams to decipher the rules that dictate the sRNA-mediated regulation in two non-enterobacterial model bacteria. These are Staphylococcus aureus, a human pathogen and Synechocystis 6803, which is targeted for developing biotechnology in photosynthetic bacteria. Because most sRNAs act through basepairing interactions, we will apply novel strategies to map pairwise sRNA-RNA interactions genome-wide in vivo with high specificity. The results will be further exploited to improve algorithms to predict RNA interactions, and to identify hubs in the regulatory networks. This project will contribute to better understand the physiology of the two targeted organisms, to find novel targets for anti-microbial drug design and to strategies to enhance the yield from photobiotechnology.