Journal Article

Large-scale analysis of post-translational modifications in E. coli under glucose-limiting conditions

Boutz, Daniel R., Wilke, Claus O., Barrick, Jeffrey E., Marcotte, Edward M., Sridhara, Viswanadham, Brown, Colin W., Person, Maria D.

2017

Overview

Background Post-translational modification (PTM) of proteins is central to many cellular processes across all domains of life, but despite decades of study and a wealth of genomic and proteomic data the biological function of many PTMs remains unknown. This is especially true for prokaryotic PTM systems, many of which have only recently been recognized and studied in depth. It is increasingly apparent that a deep sampling of abundance across a wide range of environmental stresses, growth conditions, and PTM types, rather than simply cataloging targets for a handful of modifications, is critical to understanding the complex pathways that govern PTM deposition and downstream effects. Results We utilized a deeply-sampled dataset of MS/MS proteomic analysis covering 9 timepoints spanning the Escherichia coli growth cycle and an unbiased PTM search strategy to construct a temporal map of abundance for all PTMs within a 400 Da window of mass shifts. Using this map, we are able to identify novel targets and temporal patterns for N-terminal N α acetylation, C-terminal glutamylation, and asparagine deamidation. Furthermore, we identify a possible relationship between N-terminal N α acetylation and regulation of protein degradation in stationary phase, pointing to a previously unrecognized biological function for this poorly-understood PTM. Conclusions Unbiased detection of PTM in MS/MS proteomics data facilitates the discovery of novel modification types and previously unobserved dynamic changes in modification across growth timepoints.

• Publisher: BioMed Central,Springer Nature B.V,BMC
• Subject: Acetylation / Amino acids / Animal Genetics and Genomics / Asparagine / Biodegradation / Biomedical and Life Sciences / Cell division / Chromatography, High Pressure Liquid / Datasets / E coli / Environmental stress / Escherichia coli - genetics / Escherichia coli - growth & development / Escherichia coli - metabolism / Escherichia coli Proteins - chemistry / Escherichia coli Proteins - genetics / Escherichia coli Proteins - metabolism / Experiments / Genomics / Glucose - metabolism / Growth conditions / Kinases / Life Sciences / Microarrays / Microbial Genetics and Genomics / Mutation / Peptides / Peptides - analysis / Peptides - chemistry / Phosphorylation / Plant Genetics and Genomics / Post-translation / Post-translational modification / Prokaryote / Protein Processing, Post-Translational / Protein synthesis / Proteins / Proteomics / Research Article / Signal transduction / Software / Stationary phase / Tandem Mass Spectrometry / Target recognition / Translation