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 prokaryoti...
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| Format: | Article |
| Language: | English |
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BMC
2017-04-01
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| Series: | BMC Genomics |
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| Online Access: | http://link.springer.com/article/10.1186/s12864-017-3676-8 |
| _version_ | 1818242210674507776 |
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| author | Colin W. Brown Viswanadham Sridhara Daniel R. Boutz Maria D. Person Edward M. Marcotte Jeffrey E. Barrick Claus O. Wilke |
| author_facet | Colin W. Brown Viswanadham Sridhara Daniel R. Boutz Maria D. Person Edward M. Marcotte Jeffrey E. Barrick Claus O. Wilke |
| author_sort | Colin W. Brown |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-12T13:41:37Z |
| format | Article |
| id | doaj.art-a47212c442df447d875b7d47b760d0a7 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-12T13:41:37Z |
| publishDate | 2017-04-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-a47212c442df447d875b7d47b760d0a72022-12-22T00:22:47ZengBMCBMC Genomics1471-21642017-04-0118112110.1186/s12864-017-3676-8Large-scale analysis of post-translational modifications in E. coli under glucose-limiting conditionsColin W. Brown0Viswanadham Sridhara1Daniel R. Boutz2Maria D. Person3Edward M. Marcotte4Jeffrey E. Barrick5Claus O. Wilke6Institute for Cellular and Molecular Biology, The University of Texas at AustinCenter for Computational Biology and Bioinformatics, The University of Texas at AustinInstitute for Cellular and Molecular Biology, The University of Texas at AustinInstitute for Cellular and Molecular Biology, The University of Texas at AustinInstitute for Cellular and Molecular Biology, The University of Texas at AustinInstitute for Cellular and Molecular Biology, The University of Texas at AustinInstitute for Cellular and Molecular Biology, The University of Texas at AustinAbstract 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.http://link.springer.com/article/10.1186/s12864-017-3676-8Post-translational modificationProteomicsProkaryote |
| spellingShingle | Colin W. Brown Viswanadham Sridhara Daniel R. Boutz Maria D. Person Edward M. Marcotte Jeffrey E. Barrick Claus O. Wilke Large-scale analysis of post-translational modifications in E. coli under glucose-limiting conditions BMC Genomics Post-translational modification Proteomics Prokaryote |
| title | Large-scale analysis of post-translational modifications in E. coli under glucose-limiting conditions |
| title_full | Large-scale analysis of post-translational modifications in E. coli under glucose-limiting conditions |
| title_fullStr | Large-scale analysis of post-translational modifications in E. coli under glucose-limiting conditions |
| title_full_unstemmed | Large-scale analysis of post-translational modifications in E. coli under glucose-limiting conditions |
| title_short | Large-scale analysis of post-translational modifications in E. coli under glucose-limiting conditions |
| title_sort | large scale analysis of post translational modifications in e coli under glucose limiting conditions |
| topic | Post-translational modification Proteomics Prokaryote |
| url | http://link.springer.com/article/10.1186/s12864-017-3676-8 |
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