DS0401 -

Integrative Biology of mRNA degradation – IB-mRND

Submission summary

mRNA turnover is an essential process, fundamental to the control of gene expression in all organisms. In bacteria, mRNA turnover is controlled most efficiently at the initiating step of the degradation process. Studies of Escherichia coli and Bacillus subtilis, prototypical Gram negative and Gram positive bacteria separated by 3 billion years of evolution, have revealed the principal and very disparate enzymes involved in the initiation of mRNA degradation. In E. coli, the endoribonuclease RNase E has a global role and initiates the degradation of many mRNAs. In B. subtilis, the totally unrelated RNase Y has a similar function indicating that mRNA degradation might be more similar between Gram positive and Gram negative organisms than previously thought. This led to a new view that can be summarized as “different enzymes – similar strategies”. Recent work has shown that these disparate and conserved proteins have remarkably similar properties: comparable RNA substrate specificity including a preference for 5’ monophosphorylated substrates, a propensity to form multienzyme complexes (degradosomes) and localization to the inner cytoplasmic membrane. This impressive case of convergent evolution highlights that the characteristics of these enzymes are key for initiating bacterial mRNA decay. However, many aspects of their function remain elusive, notably the role of potential regulatory interactions with associated proteins and the impact of membrane localization of these ribonucleases on the mRNA degradation process.
In a collaborative and integrative project, we will study RNase Y and RNase E by a multi-scale approach that includes genome-wide analysis of substrate specificity by RNAseq, enzymology of cleavage of model RNA substrates using purified systems, substrate recognition and degradation in vivo using super-resolution fluorescence microscopy, and analysis of ribonuclease-chromatin interactions by ChIPseq. Due to the small size of bacteria, it is still technically challenging to track single molecules like RNA. However, recent progress in fluorescence microscopy technics (PALM/STORM and single molecule Fluorescence In Situ Hybridization, smFISH) has opened up new possibilities. Expected results include a comparative analysis of RNase Y and RNase E substrate specificity and elucidation of how these membrane-associated ribonucleases interact with RNA substrate in live cells. Research with these model organisms is of fundamental importance for our understanding of processes conserved in species throughout the bacterial kingdom and as such has significant impact on agricultural, industrial and biomedical research.

Project coordination

Harald Putzer (Expression Génétique Microbienne)

The author of this summary is the project coordinator, who is responsible for the content of this summary. The ANR declines any responsibility as for its contents.

Partner

CNRS UMR 8261 Expression Génétique Microbienne
CNRS / LMGM Centre Nationale de la Recherche Scientifique / Laboratoire de Microbiologie et Génétique Moléculaires

Help of the ANR 461,565 euros
Beginning and duration of the scientific project: October 2016 - 48 Months

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