Biology subjects

Lalanne, J.-B.

Publications and source records attributed to Lalanne, J.-B..

22 records · Page 2Linked to original sources

bioRxiv2021

First-principles model of optimal translation factors stoichiometry

Enzymatic pathways have evolved uniquely preferred protein expression stoichiometry in living cells, but our ability to predict the optimal abundances from basic properties remains underdeveloped. Here we report a biophysical, first-principles model of growth optimization for core mRNA translation, a multi-enzyme system that involves proteins with a broadly conserved stoichiometry spanning two orders of magnitude. We show that a parsimonious flux model constrained by proteome allocation is sufficient to predict the conserved ratios of translation factors through maximization of ribosome usage The analytical solutions, without free parameters, provide an interpretable framework for the observed hierarchy of expression levels based on simple biophysical properties, such as diffusion constants and protein sizes. Our results provide an intuitive and quantitative understanding for the construction of a central process of life, as well as a path toward rational design of pathway-specific enzyme expression stoichiometry.

biophysics↗

bioRxiv2021

Translational activation by an alternative sigma factor in Bacillus subtilis

Sigma factors are an important class of bacterial transcription factors that lend specificity to RNA polymerases by binding to distinct promoter elements for genes in their regulons. Here we show that activation of the general stress sigma factor, {sigma}B, in Bacillus subtilis paradoxically leads to dramatic induction of translation for a subset of its regulon genes. These genes are translationally repressed when transcribed by the housekeeping sigma factor, {sigma}A, owing to extended RNA secondary structures as determined in vivo using DMS-MaPseq. Transcription from {sigma}B-dependent promoters liberates the secondary structures and activates translation, leading to dual induction. Translation efficiencies between {sigma}B- and {sigma}A-dependent RNA isoforms can vary by up to 100-fold, which in multiple cases exceeds the magnitude of transcriptional induction. These results highlight the role of long-range RNA folding in modulating translation and demonstrate that a transcription factor can regulate protein synthesis beyond its effects on transcript levels.

microbiology↗

bioRxiv2020

Spurious regulatory connections dictate the expression-fitness landscape of translation termination factors

During steady-state cell growth, individual enzymatic fluxes can be directly inferred from growth rate by mass conservation, but the inverse problem remains unsolved. Perturbing the flux and expression of a single enzyme could have pleiotropic effects that may or may not dominate the impact on cell fitness. Here we quantitatively dissect the molecular and global responses to varied expression of translation termination factors (peptide release factors, RFs) in bacterium Bacillus subtilis. While endogenous RF expression maximizes proliferation, deviations in expression lead to unexpected distal regulatory responses that dictate fitness reduction. Molecularly, RF depletion causes expression imbalance at specific operons, which activates master regulators and detrimentally overrides the transcriptome. Through these spurious connections, RF abundances are thus entrenched by focal points within the regulatory network, in one case located at a single stop codon. Such regulatory entrenchment suggests that predictive bottom-up models of expression-fitness landscapes will require near-exhaustive characterization of parts. HighlightsO_LIPrecision measurements enable multiscale expression-to-fitness mapping. C_LIO_LIRF depletion leads to imbalanced translation for co-transcribed gene pairs. C_LIO_LIImbalanced translation induces unintended regulons to the detriment of cell fitness. C_LIO_LISwapping a single stop codon rewires global susceptibility to RF perturbation. C_LI

biophysics↗

bioRxiv2019

Alternative transcription cycle for bacterial RNA polymerase

RNA polymerases (RNAPs) transcribe genes through a cycle of recruitment to promoter DNA, initiation, elongation, and termination. After termination, RNAP is thought to initiate the next round of transcription by detaching from DNA and rebinding a new promoter. We used single-molecule fluorescence microscopy to observe individual RNAP molecules after transcript release at a terminator. Following termination, RNAP almost always remained bound to DNA and sometimes exhibited one-dimensional sliding over thousands of basepairs. Unexpectedly, the DNA-bound RNAP often restarted transcription, usually in reverse direction, thus producing an antisense transcript. Furthermore, we report evidence of this \"secondary initiation\" in live cells, using genome-wide RNA sequencing. These findings reveal an alternative transcription cycle that allows RNAP to reinitiate without dissociating from DNA, which is likely to have important implications for gene regulation.

biophysics↗