Seminars – From bacterial gene expression decomposition to Synthetic Biology

EVENT : C3BI Seminars

From bacterial gene expression decomposition to Synthetic Biology

Main speaker : Matthieu Jules, from Head of Bacterial Molecular Systems – Institut Micalis Date : 23/02/2017 at 02:00 pm Location : Retrovirus room – LWOFF (22) ,Institut Pasteur, Paris

Synthetic biology (SB) aims at the rational engineering of novel biological functions and systems. Libraries of well-characterized components regulating gene expression were therefore essential to many SB applications [1]. The current challenge in the field is now to rationally design genetic elements that will be assembled to finely control gene expression across growth conditions. To address this challenge, we revisited the contribution of replication, transcription and translation to global mechanisms allowing bacteria to modulate abundance of single proteins with respect to the growth rate. Growth rate has long been regarded as a global variable modulating macromolecular cellular contents. Recently however, the growth-rate-dependent variation of the transcription machinery abundance was shown to clearly influence gene expression [2]. In balanced growth, bacterial protein abundances depend on the dilution rate, transcript abundances and transcript-specific translation efficiencies. By integrating genome-wide transcriptome datasets and datasets from a library of synthetic gfp-reporter fusions, we demonstrated that translation efficiencies in Bacillus subtilis decreased up to fourfold from slow to fast growth. The translation initiation regions elicited a growth rate-dependent, differential production of proteins without regulators, hence revealing a unique, hard-coded, growth rate-dependent mode of regulation. We combined model-based data analyses of transcript and protein abundances genome-wide and revealed that this global regulation is extensively used in B. subtilis. We eventually developed a knowledge-based, three-step translation initiation model, experimentally challenged the model predictions and proposed that a growth rate-dependent drop in free ribosome abundance accounted for the differential protein production [3]. Similar modi operandi were adopted to characterize the replication and transcription processes. The intrinsic properties of these hard-wired regulatory layers of gene expression open novel avenues for synthetic biology, particularly in the potential it offers to bypass the need for multiple specific regulators to modulate complex synthetic circuits. [1] Guiziou S, Sauveplane V, Chang HJ, Clerté C, Declerck N, Jules M, Bonnet J. 2016. A part toolbox to tune genetic expression in Bacillus subtilis. Nucleic Acids Res. 44:7495-508 [2] Gerosa L, Kochanowski K, Heinemann M, Sauer U. 2013. Dissecting specific and global transcriptional regulation of bacterial gene expression. Mol Syst Biol. 9:658. [3] Borkowski O, Goelzer A, Schaffer M, Calabre M, Mäder U, Aymerich S, Jules M*, Fromion V*. 2016. Translation elicits a growth rate-dependent, genome-wide, differential protein production in Bacillus subtilis. Mol Syst Biol. 12:870.

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