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

Abstract：

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.

journal_name

BMC Genomics

journal_title

BMC genomics

authors

Brown CW,Sridhara V,Boutz DR,Person MD,Marcotte EM,Barrick JE,Wilke CO

doi

10.1186/s12864-017-3676-8

subject

Has Abstract

pub_date

2017-04-17 00:00:00

pages

301

issue

1

issn

1471-2164

pii

10.1186/s12864-017-3676-8

journal_volume

18

pub_type

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