Characterizing posttranslational modifications in prokaryotic metabolism using a multiscale workflow

Elizabeth Brunk, Roger L. Chang, Jing Xia, Hooman Hefzi, James T. Yurkovich, Donghyuk Kim, Evan Buckmiller, Harris H. Wang, Byung-Kwan Cho, Chen Yang, Bernhard O. Palsson, George M. Church, Nathan E. Lewis*

*Corresponding author for this work

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Abstract

Understanding the complex interactions of protein posttranslational modifications (PTMs) represents a major challenge in metabolic engineering, synthetic biology, and the biomedical sciences. Here, we present a workflow that integrates multiplex automated genome editing (MAGE), genome-scale metabolic modeling, and atomistic molecular dynamics to study the effects of PTMs on metabolic enzymes and microbial fitness. This workflow incorporates complementary approaches across scientific disciplines; provides molecular insight into how PTMs influence cellular fitness during nutrient shifts; and demonstrates how mechanistic details of PTMs can be explored at different biological scales. As a proof of concept, we present a global analysis of PTMs on enzymes in the metabolic network of Escherichia coli. Based on our workflow results, we conduct a more detailed, mechanistic analysis of the PTMs in three proteins: enolase, serine hydroxymethyltransferase, and transaldolase. Application of this workflow identified the roles of specific PTMs in observed experimental phenomena and demonstrated how individual PTMs regulate enzymes, pathways, and, ultimately, cell phenotypes.
Original languageEnglish
JournalProceedings of the National Academy of Sciences of the United States of America
Volume115
Issue number43
Pages (from-to)11096-11101
ISSN0027-8424
DOIs
Publication statusPublished - 2018

Keywords

  • Systems biology
  • Posttranslational modifications
  • Metabolism
  • Protein chemistry
  • Omics data

Cite this

Brunk, E., Chang, R. L., Xia, J., Hefzi, H., Yurkovich, J. T., Kim, D., Buckmiller, E., Wang, H. H., Cho, B-K., Yang, C., Palsson, B. O., Church, G. M., & Lewis, N. E. (2018). Characterizing posttranslational modifications in prokaryotic metabolism using a multiscale workflow. Proceedings of the National Academy of Sciences of the United States of America, 115(43), 11096-11101. https://doi.org/10.1073/pnas.1811971115