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Title: Cellular responses to reactive oxygen species are predicted from molecular mechanisms

Abstract

Catalysis using iron–sulfur clusters and transition metals can be traced back to the last universal common ancestor. The damage to metalloproteins caused by reactive oxygen species (ROS) can prevent cell growth and survival when unmanaged, thus eliciting an essential stress response that is universal and fundamental in biology. Here we develop a computable multiscale description of the ROS stress response inEscherichia coli, called OxidizeME. We use OxidizeME to explain four key responses to oxidative stress: 1) ROS-induced auxotrophy for branched-chain, aromatic, and sulfurous amino acids; 2) nutrient-dependent sensitivity of growth rate to ROS; 3) ROS-specific differential gene expression separate from global growth-associated differential expression; and 4) coordinated expression of iron–sulfur cluster (ISC) and sulfur assimilation (SUF) systems for iron–sulfur cluster biosynthesis. These results show that we can now develop fundamental and quantitative genotype–phenotype relationships for stress responses on a genome-wide basis.

Authors:
 [1]; ORCiD logo [1]; ORCiD logo [1];  [1];  [1]; ORCiD logo [1];  [1];  [1]; ORCiD logo [1];  [1];  [1];  [1];  [1];  [1];  [1];  [1];  [1];  [1];  [1];  [2] more »;  [2] « less
+ Show Author Affiliations
  1. Univ. of California San Diego, La Jolla, CA (United States)
  2. Univ. of California San Diego, La Jolla, CA (United States); Technical Univ. of Denmark, Lyngby (Denmark)
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC); Univ. of California, Oakland, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1577615
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
Proceedings of the National Academy of Sciences of the United States of America
Additional Journal Information:
Journal Volume: 116; Journal Issue: 28; Journal ID: ISSN 0027-8424
Publisher:
National Academy of Sciences
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; science & technology; reactive oxygen species; oxidative stress; metabolism; protein expression; genome-scale model

Citation Formats

Yang, Laurence, Mih, Nathan, Anand, Amitesh, Park, Joon Ho, Tan, Justin, Yurkovich, James T., Monk, Jonathan M., Lloyd, Colton J., Sandberg, Troy E., Seo, Sang Woo, Kim, Donghyuk, Sastry, Anand V., Phaneuf, Patrick, Gao, Ye, Broddrick, Jared T., Chen, Ke, Heckmann, David, Szubin, Richard, Hefner, Ying, Feist, Adam M., and Palsson, Bernhard O. Cellular responses to reactive oxygen species are predicted from molecular mechanisms. United States: N. p., 2019. Web. doi:10.1073/pnas.1905039116.
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Yang, Laurence, Mih, Nathan, Anand, Amitesh, Park, Joon Ho, Tan, Justin, Yurkovich, James T., Monk, Jonathan M., Lloyd, Colton J., Sandberg, Troy E., Seo, Sang Woo, Kim, Donghyuk, Sastry, Anand V., Phaneuf, Patrick, Gao, Ye, Broddrick, Jared T., Chen, Ke, Heckmann, David, Szubin, Richard, Hefner, Ying, Feist, Adam M., & Palsson, Bernhard O. Cellular responses to reactive oxygen species are predicted from molecular mechanisms. United States. https://doi.org/10.1073/pnas.1905039116
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Yang, Laurence, Mih, Nathan, Anand, Amitesh, Park, Joon Ho, Tan, Justin, Yurkovich, James T., Monk, Jonathan M., Lloyd, Colton J., Sandberg, Troy E., Seo, Sang Woo, Kim, Donghyuk, Sastry, Anand V., Phaneuf, Patrick, Gao, Ye, Broddrick, Jared T., Chen, Ke, Heckmann, David, Szubin, Richard, Hefner, Ying, Feist, Adam M., and Palsson, Bernhard O. Wed . "Cellular responses to reactive oxygen species are predicted from molecular mechanisms". United States. https://doi.org/10.1073/pnas.1905039116. https://www.osti.gov/servlets/purl/1577615.
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@article{osti_1577615,
title = {Cellular responses to reactive oxygen species are predicted from molecular mechanisms},
author = {Yang, Laurence and Mih, Nathan and Anand, Amitesh and Park, Joon Ho and Tan, Justin and Yurkovich, James T. and Monk, Jonathan M. and Lloyd, Colton J. and Sandberg, Troy E. and Seo, Sang Woo and Kim, Donghyuk and Sastry, Anand V. and Phaneuf, Patrick and Gao, Ye and Broddrick, Jared T. and Chen, Ke and Heckmann, David and Szubin, Richard and Hefner, Ying and Feist, Adam M. and Palsson, Bernhard O.},
abstractNote = {Catalysis using iron–sulfur clusters and transition metals can be traced back to the last universal common ancestor. The damage to metalloproteins caused by reactive oxygen species (ROS) can prevent cell growth and survival when unmanaged, thus eliciting an essential stress response that is universal and fundamental in biology. Here we develop a computable multiscale description of the ROS stress response inEscherichia coli, called OxidizeME. We use OxidizeME to explain four key responses to oxidative stress: 1) ROS-induced auxotrophy for branched-chain, aromatic, and sulfurous amino acids; 2) nutrient-dependent sensitivity of growth rate to ROS; 3) ROS-specific differential gene expression separate from global growth-associated differential expression; and 4) coordinated expression of iron–sulfur cluster (ISC) and sulfur assimilation (SUF) systems for iron–sulfur cluster biosynthesis. These results show that we can now develop fundamental and quantitative genotype–phenotype relationships for stress responses on a genome-wide basis.},
doi = {10.1073/pnas.1905039116},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
number = 28,
volume = 116,
place = {United States},
year = {2019},
month = {7}
}
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Journal Article:
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https://doi.org/10.1073/pnas.1905039116
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Figures / Tables:

Fig. 1 Fig. 1: OxidizeME: a multiscale description of metabolism and macromolecular expression that accounts for damage by ROS to macromolecules. (A) Mononuclear Fe(II) proteins are demetallated by ROS and mismetallated with alternative divalent metal ions. (B) Iron–sulfur clusters are oxidized and repaired. (C) Unincorporated Fe(II) spontaneously reacts with H2O2 via Fentonmore » chemistry, generating hydroxyl radicals that damage DNA, while the Dps protein stores unincorporated iron and protects DNA from damage. (D) Protein structural properties are computed to estimate the probability of metal cofactor damage by ROS (RSA: relative solvent accessibility). (E) Processes in A–D are integrated into a multiscale oxidative model, named OxidizeME. OxidizeME is used to compute the scope of macromolecular damage and the cellular response for varying intracellular concentrations of superoxide, hydrogen peroxide, and divalent metal ions (Fe(II), Mn(II), Co(II), Zn(II)); see SI Appendix for details.« less
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    Adaptive evolution reveals a tradeoff between growth rate and oxidative stress during naphthoquinone-based aerobic respiration
    journal, November 2019

    • Anand, Amitesh; Chen, Ke; Yang, Laurence
    • Proceedings of the National Academy of Sciences, Vol. 116, Issue 50
    • DOI: 10.1073/pnas.1909987116
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