Research Themes

Task 1: Post-transcriptional gene expression from bacteria to organelles

(PARTNERS 1, 2, 3, 4, 6)

Modern chloroplasts (cp) and mitochondria (mt) have tiny genomes that only code for a fraction of the factors required for their own gene expression and function. Nevertheless, the organellar machineries for transcription, translation, and mRNA decay have a pronounced prokaryotic nature, because most of the factors involved are the products of ancestral bacterial genes that have been transferred to the nucleus. The nucleus in turn tightly controls the expression of organellar genes by encoding gene-specific factors that bind organellar mRNAs and govern their maturation/stability and translation. In Chlamydomonas reinhardtii, these factors are referred to as M- and T-factors, respectively. In contrast, the Shine-Dalgarno (SD) sequence, which is critical for translation initiation in bacteria, has been lost in most, but not all cp genes.

The principal goal of Task 1 is the comparison of post-transcriptional regulation of gene expression in bacteria (principally Escherichia coli and Bacillus subtilis) and organelles (principally cp in C. reinhardtii) with four main work-packages (WP): A comparison of the mechanisms and regulation of mRNA decay (WP1) and translation (WP2) in cp and bacteria; an investigation of the potential role of small regulatory RNAs in controlling cp gene expression (WP3); a comparison of global networks controlling gene expression at the post-transcriptional level in bacteria and cp (WP4). In addition to these direct comparisons, we made several interesting new discoveries on the post-transcriptional control of gene expression in both bacteria and cp individually. DYNAMO was highly successful in terms of our overall accomplishments for Task 1, with 103 publications in total so far (80 since 2015) and the establishment of new collaborations between the partners that can be directly credited to the project. 

Details of our studies can be found here

Task 2: Membrane biogenesis and dynamics from bacteria to organelles

(PARTNERS 2, 4, 5, 7)

The main objective of Task 2 is to compare the dynamics and biogenesis of membrane systems across evolution in three biological models: E. coli, C. reinhardtii cp, and Saccharomyces cerevisiae mt. For this study, we used integrative approaches combining genetics and physiological analyses, together with innovative tools in chemistry and biophysics. Following the recommendation of the 2015 mid-term review, we extended our focus on structure-function studies of membrane proteins (MPs). Since 2015, we have published 42 new articles (68 publications in total so far).

Details of our studies can be found here

Task 3: Supramolecular organisation of membranes and membrane proteins

(PARTNERS 1, 2, 4, 5, 6, 7)

Life crucially depends on energy harvesting. Most organisms use a unique mechanism that relies on optimised electron flow to drive photosynthesis or respiration. The main aim of DYNAMO Task 3 is to provide an integrated view of the electron transfer chain (ETC) by coupling structural and functional studies going from the electron to the supramolecular organisation of complexes. The genetic control of the expression of these complexes has been presented in Task 1 and organellar level organisation in Task 2 (above). Our studies related to Task 3 has so far yielded 73 papers in total, 55 since 2015.

The key features of the respiratory and photosynthetic ETCs were described decades ago, but the mechanisms and control of each step remain elusive. Moreover, although linear electron transfer is more or less amenable to classical approaches, networked and cyclic electron flows upset our understanding of bioenergetics. Cyclic flows may occur locally at the level of a protein complex, at the level of one ETC or at a higher level. We made breakthroughs at each of these three levels and plan to intensify this line of research, whose understanding is rooted in coupling functional and structural studies. Our goal was to better understand the individual players in electron transfer, to decipher the interactions between the different partners and ultimately to extend our comprehension to an integrated ETC in a living cell.

Details of our studies can be found here