Datasets

Title	Evolutionary Convergence of Pathway-specific Enzyme Expression Stoichiometry
Organism
Number of Samples	5
Release Date	2017/02/22 00:00
Sequencing Types
Protocol Details

Title
Authors	Lalanne JB, Taggart JC, Guo MS, Herzel L, Schieler A, Li GW
Journal	Cell
Publication Date	2018 Apr 19
Abstract	Coexpression of proteins in response to pathway-inducing signals is the founding paradigm of gene regulation. However, it remains unexplored whether the relative abundance of co-regulated proteins requires precise tuning. Here, we present large-scale analyses of protein stoichiometry and corresponding regulatory strategies for 21 pathways and 67-224 operons in divergent bacteria separated by 0.6-2 billion years. Using end-enriched RNA-sequencing (Rend-seq) with single-nucleotide resolution, we found that many bacterial gene clusters encoding conserved pathways have undergone massive divergence in transcript abundance and architectures via remodeling of internal promoters and terminators. Remarkably, these evolutionary changes are compensated post-transcriptionally to maintain preferred stoichiometry of protein synthesis rates. Even more strikingly, in eukaryotic budding yeast, functionally analogous proteins that arose independently from bacterial counterparts also evolved to convergent in-pathway expression. The broad requirement for exact protein stoichiometries despite regulatory divergence provides an unexpected principle for building biological pathways both in nature and for synthetic activities. Copyright © 2018 Elsevier Inc. All rights reserved.
PMC	PMC5978003
PMID	29606352
DOI

Run Accession	Study Accession	Scientific Name	Cell Line	Library Type	Treatment	GWIPS-viz	Trips-Viz	Reads	BAM	BigWig (F)	BigWig (R)
SRR5278491	PRJNA376419	Bacillus subtilis	0.0	Ribo-Seq	0.0
SRR5278492	PRJNA376419	Bacillus subtilis	0.0	Ribo-Seq	0.0
SRR5278493	PRJNA376419	Bacillus subtilis	0.0	Ribo-Seq	0.0
SRR5278494	PRJNA376419	Vibrio natriegens	0.0	Ribo-Seq	0.0
SRR6652803	PRJNA376419	Bacillus subtilis	0.0	Ribo-Seq	0.0
Run Accession	Study Accession	Scientific Name	Cell Line	Library Type	Treatment	GWIPS-viz	Trips-Viz	Reads	BAM	BigWig (F)	BigWig (R)

Lalanne et al. 2018 (PRJNA376419)