Favate et al. 2021 (PRJNA689830)

General Details

Title	Landscape of transcriptional and translational changes over 22 years of bacterial adaptation
Organism
Number of Samples	4
Release Date	2021/01/05 00:00
Sequencing Types
Protocol Details

Study Links

GWIPS-viz	Trips-Viz

Repository Details

SRA	SRP300526
ENA	SRP300526
GEO	GSE164308
BioProject	PRJNA689830

Publication

Title
Authors	Favate JS, Liang S, Cope AL, Yadavalli SS, Shah P
Journal	eLife
Publication Date	2022 Oct 10
Abstract	Organisms can adapt to an environment by taking multiple mutational paths. This redundancy at the genetic level, where many mutations have similar phenotypic and fitness effects, can make untangling the molecular mechanisms of complex adaptations difficult. Here, we use the Escherichia coli long-term evolution experiment (LTEE) as a model to address this challenge. To understand how different genomic changes could lead to parallel fitness gains, we characterize the landscape of transcriptional and translational changes across 12 replicate populations evolving in parallel for 50,000 generations. By quantifying absolute changes in mRNA abundances, we show that not only do all evolved lines have more mRNAs but that this increase in mRNA abundance scales with cell size. We also find that despite few shared mutations at the genetic level, clones from replicate populations in the LTEE are remarkably similar in their gene expression patterns at both the transcriptional and translational levels. Furthermore, we show that the majority of the expression changes are due to changes at the transcriptional level with very few translational changes. Finally, we show how mutations in transcriptional regulators lead to consistent and parallel changes in the expression levels of downstream genes. These results deepen our understanding of the molecular mechanisms underlying complex adaptations and provide insights into the repeatability of evolution. © 2022, Favate et al.
PMC	PMC9645810
PMID	36214449
DOI

	Run Accession	Study Accession	Scientific Name	Cell Line	Library Type	Treatment	GWIPS-viz	Trips-Viz	Reads	BAM	BigWig (F)	BigWig (R)
	SRR13362462	PRJNA689830	Escherichia coli	0.0	Ribo-Seq	0.0
	SRR13362463	PRJNA689830	Escherichia coli	0.0	Ribo-Seq	0.0
	SRR13362466	PRJNA689830	Escherichia coli	0.0	Ribo-Seq	0.0
	SRR13362467	PRJNA689830	Escherichia coli	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)

ⓘ For more Information on the columns shown here see: About