Talks by Jonathan JAGODNIK and Hervé VAUCHERET

Jonathan JAGODNIK
Institut de Biologie Physico-Chimique, Paris, CNRS UMR8261 : Expression Génétique Microbienne.

Title:
30S-RiboSeq redefines the bacterial ribosome binding site

Abstract:
Translation initiation is a key step of gene expression in all living organisms. As the limiting step of translation, it is also subjected to many regulatory events. In bacteria, it typically involves the binding of the 30S subunit of the ribosome to the mRNA, through recognition of the mRNA Shine-Dalgarno (SD) and AUG start codon. However, the process through which 30S finds translation initiation regions, for instance with very degenerated SD sequences or within long mRNA 5’UTRs remains elusive. To investigate this, we developed the 30S-RiboSeq method, inspired by the translation complex profiling (TCPseq) originally developed in eukarya. 30S-RiboSeq provided the first map of 30S-covered mRNA regions in E. coli and in bateria. We found >400 non-canonical 30S binding sites, as well as many unexpected 30S binding patterns, sometimes over 100 nucleotides upstream of the start codon. We validated several of these newly identified binding sites by in vitro toeprinting assays, and further demonstrate their strong impact on gene expression. Hence, even in bacteria, ribosomes commonly bind mRNAs outside the start region to initiate translation, thereby challenging the classic ribosome binding site model.

Hervé VAUCHERET
Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin for Plant Sciences (IJPB), 78000, Versailles, France.

Title: How do plants select RNAs to eliminate?

Abstract:
In plants, 24-nt siRNAs guide transcriptional gene silencing (TGS) of transposable elements, while 21/22nt siRNAs guide post-transcriptional gene silencing (PTGS), mostly to counteract infection by pathogens. Transgenes generally have structures resembling that of endogenous genes, and thus should be expressed, but integrate in the genome like transposable elements, and thus could be potentially silenced by TGS. However, transgenes often undergo PTGS. During this seminar, I will present recent advances in our understanding of what makes certain transgene loci prone to undergo PTGS, emphasizing the role of RNA levels and its implication on the evolution of endogenous genes.