The Imperial War, Personalities and Issue

Claus Wilke (448003)

Colin Brown (832030)

Daniel Boutz (3928280)

Edward Marcotte (3928283)

Jeffrey Barrick (76402)

Maria Person (3928286)

Viswanadham Sridhara (673863)

BMC Genomics

Modified and unmodified PSM counts for each AA position with a significantly stationary-phase biased +1 Da modification to asparagine. The plots show unmodified (green) and +1 Da modified (brown) PSM counts across all nine timepoints (x-axis) for the 10 asparagine residues with the most significant p-values across all three biological replicates. Counts represent the average of the three biologcial replicates. Plots are ordered by the mean p value of the Fisherâs exact test for preferential modification from left-to-right within each row, and from top-to-bottom across rows, with the most significant position at the top left. (PDF 20 kb

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Additional file 8 of 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

Colin W. Brown

Viswanadham Sridhara

Daniel R. Boutz

Maria D. Person

Edward M. Marcotte

Jeffrey E. Barrick

Claus O. Wilke

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

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