E-GEOD-53767 - Absolute quantification of protein production reveals principles underlying protein synthesis rates

Status
Released on 24 April 2014, last updated on 31 May 2014
Organism
Escherichia coli
Samples (4)
Protocols (3)
Description
A quantitative view of cellular functions requires precise measures of the rates of biomolecule production, especially proteins-the direct effectors of biological processes. Here we present a genome-wide approach, based on ribosome profiling, for measuring absolute protein synthesis rates. The resultant E. coli dataset transforms our understanding of the extent to which protein synthesis is precisely controlled to optimize function and efficiency. For example, members of multi-protein complexes are made in precise proportion to their stoichiometry, whereas components of functional modules are produced differentially according to their hierarchical role. Estimates of absolute protein abundance also reveal principles used to optimize design. These include how the level of different types of transcription factors is optimized for rapid response, and how a metabolic pathway (methionine biosynthesis) balances production cost with activity requirements. More broadly, our studies reveal how general principles, important both for understanding natural systems and for synthesizing new ones, emerge from global quantitative analyses of protein synthesis. 4 samples of E. coli ribosome profiling and mRNA-seq, including biological replicates
Experiment type
RNA-seq of coding RNA 
Contacts
Gene-Wei Li <gene-wei.li@ucsf.edu>, Carol A Gross, David Burkhardt, Jonathan S Weissman
Citation
MINSEQE
Exp. designProtocolsFactorsProcessedSeq. reads
Files
Investigation descriptionE-GEOD-53767.idf.txt
Sample and data relationshipE-GEOD-53767.sdrf.txt
Links