Characterizing posttranslational modifications in prokaryotic metabolism using a multiscale workflow

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

doi:10.1073/pnas.1811971115

Title: Characterizing posttranslational modifications in prokaryotic metabolism using a multiscale workflow

Journal Article · 08 October 2018 · Proceedings of the National Academy of Sciences of the United States of America

DOI: https://doi.org/10.1073/pnas.1811971115 · OSTI ID:1528919

^[1]; Chang, Roger L. ^[2]; Xia, Jing ^[3]; Hefzi, Hooman ^[4];

^[4]; Kim, Donghyuk ^[5]; Buckmiller, Evan ^[6];

^[7]; Cho, Byung-Kwan ^[8]; Yang, Chen ^[3]; Palsson, Bernhard O. ^[9]; Church, George M. ^[10]; Lewis, Nathan E. ^[4]

University of California, San Diego, La Jolla, CA (United States); Harvard Medical School
Harvard Medical School, Boston, MA (United States); University of California, San Diego, La Jolla, CA (United States)
Chinese Academy of Sciences, Shanghai (China)
University of California, San Diego, La Jolla, CA (United States)
University of California, San Diego, La Jolla, CA (United States); Kyung Hee Univ., Yongin (Korea)
Brigham Young Univ., Provo, UT (United States)
Columbia University Medical Center, New York, NY (United States); Harvard Medical School, Boston, MA (United States)
Korea Advanced Institute of Science and Technology, Daejeon (Korea)
University of California, San Diego, La Jolla, CA (United States); Technical Univ. of Denmark, Lyngby (Denmark)
Harvard Medical School, Boston, MA (United States)

Understanding the complex interactions of protein posttranslational modifications (PTMs) represents a major challenge in metabolic engineering, synthetic biology, and the biomedical sciences. In this work, 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. Finally, 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.

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Research Organization:: Harvard Medical School, Boston, MA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23). Biological Systems Science Division

Contributing Organization:: National Energy Research Scientific Computing Center and XSEDE computer facilities (MCB140152)

Grant/Contract Number:: FG02-02ER63445

OSTI ID:: 1528919

Journal Information:: Proceedings of the National Academy of Sciences of the United States of America, Journal Name: Proceedings of the National Academy of Sciences of the United States of America Journal Issue: 43 Vol. 115; ISSN 0027-8424

Publisher:: National Academy of Sciences, Washington, DC (United States)Copyright Statement

Country of Publication:: United States

Language:: English

References (40)

How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? Wang, Junmei; Cieplak, Piotr; Kollman, Peter A. Journal of Computational Chemistry, Vol. 21, Issue 12 https://doi.org/10.1002/1096-987X(200009)21:12<1049::AID-JCC3>3.0.CO;2-F	journal	January 2000
Comparison of multiple Amber force fields and development of improved protein backbone parameters Hornak, Viktor; Abel, Robert; Okur, Asim Proteins: Structure, Function, and Bioinformatics, Vol. 65, Issue 3 https://doi.org/10.1002/prot.21123	journal	November 2006
The crystal structure and identification of NQM1/YGR043C, a transaldolase from Saccharomyces cerevisiae Huang, Hua; Rong, Hui; Li, Xu Proteins: Structure, Function, and Bioinformatics, Vol. 73, Issue 4 https://doi.org/10.1002/prot.22237	journal	September 2008
AMBER force-field parameters for phosphorylated amino acids in different protonation states: phosphoserine, phosphothreonine, phosphotyrosine, and phosphohistidine Homeyer, Nadine; Horn, Anselm H. C.; Lanig, Harald Journal of Molecular Modeling, Vol. 12, Issue 3 https://doi.org/10.1007/s00894-005-0028-4	journal	October 2005
RNA Structural Determinants of Optimal Codons Revealed by MAGE-Seq Kelsic, Eric D.; Chung, Hattie; Cohen, Niv Cell Systems, Vol. 3, Issue 6 https://doi.org/10.1016/j.cels.2016.11.004	journal	December 2016
High-throughput discovery metabolomics Fuhrer, Tobias; Zamboni, Nicola Current Opinion in Biotechnology, Vol. 31 https://doi.org/10.1016/j.copbio.2014.08.006	journal	February 2015
Riding the wave of biological data Gross, Michael Current Biology, Vol. 21, Issue 6 https://doi.org/10.1016/j.cub.2011.03.009	journal	March 2011
Beyond gene expression: The impact of protein post-translational modifications in bacteria Cain, Joel A.; Solis, Nestor; Cordwell, Stuart J. Journal of Proteomics, Vol. 97 https://doi.org/10.1016/j.jprot.2013.08.012	journal	January 2014
Global dynamics of Escherichia coli phosphoproteome in central carbon metabolism under changing culture conditions Lim, SooA; Marcellin, Esteban; Jacob, Shana Journal of Proteomics, Vol. 126 https://doi.org/10.1016/j.jprot.2015.05.021	journal	August 2015
Post-translational modifications as key regulators of bacterial metabolic fluxes Pisithkul, Tippapha; Patel, Nishaben M.; Amador-Noguez, Daniel Current Opinion in Microbiology, Vol. 24 https://doi.org/10.1016/j.mib.2014.12.006	journal	April 2015
Posttranslational regulation of microbial metabolism Kochanowski, Karl; Sauer, Uwe; Noor, Elad Current Opinion in Microbiology, Vol. 27 https://doi.org/10.1016/j.mib.2015.05.007	journal	October 2015
Steinernema glaseri surface enolase: Molecular cloning, biological characterization, and role in host immune suppression Liu, Hua; Zeng, Hongmei; Yao, Qing Molecular and Biochemical Parasitology, Vol. 185, Issue 2 https://doi.org/10.1016/j.molbiopara.2012.06.006	journal	October 2012
Acetyl-Phosphate Is a Critical Determinant of Lysine Acetylation in E. coli Weinert, Brian T.; Iesmantavicius, Vytautas; Wagner, Sebastian A. Molecular Cell, Vol. 51, Issue 2 https://doi.org/10.1016/j.molcel.2013.06.003	journal	July 2013
Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald Salomon-Ferrer, Romelia; Götz, Andreas W.; Poole, Duncan Journal of Chemical Theory and Computation, Vol. 9, Issue 9 https://doi.org/10.1021/ct400314y	journal	August 2013
Programming cells by multiplex genome engineering and accelerated evolution Wang, Harris H.; Isaacs, Farren J.; Carr, Peter A. Nature, Vol. 460, Issue 7257, p. 894-898 https://doi.org/10.1038/nature08187	journal	July 2009
What is flux balance analysis? Orth, Jeffrey D.; Thiele, Ines; Palsson, Bernhard Ø Nature Biotechnology, Vol. 28, Issue 3 https://doi.org/10.1038/nbt.1614	journal	March 2010
Encoding human serine phosphopeptides in bacteria for proteome-wide identification of phosphorylation-dependent interactions Barber, Karl W.; Muir, Paul; Szeligowski, Richard V. Nature Biotechnology, Vol. 36, Issue 7 https://doi.org/10.1038/nbt.4150	journal	June 2018
Identification of lysine succinylation as a new post-translational modification Zhang, Zhihong; Tan, Minjia; Xie, Zhongyu Nature Chemical Biology, Vol. 7, Issue 1 https://doi.org/10.1038/nchembio.495	journal	December 2010
Twisted Schiff base intermediates and substrate locale revise transaldolase mechanism Lehwess-Litzmann, Anja; Neumann, Piotr; Parthier, Christoph Nature Chemical Biology, Vol. 7, Issue 10 https://doi.org/10.1038/nchembio.633	journal	August 2011
Genome-scale promoter engineering by coselection MAGE Wang, Harris H.; Kim, Hwangbeom; Cong, Le Nature Methods, Vol. 9, Issue 6, p. 591-593 https://doi.org/10.1038/nmeth.1971	journal	April 2012
Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0 Schellenberger, Jan; Que, Richard; Fleming, Ronan M. T. Nature Protocols, Vol. 6, Issue 9 https://doi.org/10.1038/nprot.2011.308	journal	August 2011
Tuning gene expression to changing environments: from rapid responses to evolutionary adaptation López-Maury, Luis; Marguerat, Samuel; Bähler, Jürg Nature Reviews Genetics, Vol. 9, Issue 8 https://doi.org/10.1038/nrg2398	journal	August 2008
Sequencing technologies — the next generation Metzker, Michael L. Nature Reviews Genetics, Vol. 11, Issue 1 https://doi.org/10.1038/nrg2626	journal	December 2009
Computational solutions for omics data Berger, Bonnie; Peng, Jian; Singh, Mona Nature Reviews Genetics, Vol. 14, Issue 5 https://doi.org/10.1038/nrg3433	journal	April 2013
Constraint-based models predict metabolic and associated cellular functions Bordbar, Aarash; Monk, Jonathan M.; King, Zachary A. Nature Reviews Genetics, Vol. 15, Issue 2 https://doi.org/10.1038/nrg3643	journal	January 2014
Genomes by design Haimovich, Adrian D.; Muir, Paul; Isaacs, Farren J. Nature Reviews Genetics, Vol. 16, Issue 9 https://doi.org/10.1038/nrg3956	journal	August 2015
Constraining the metabolic genotype–phenotype relationship using a phylogeny of in silico methods Lewis, Nathan E.; Nagarajan, Harish; Palsson, Bernhard O. Nature Reviews Microbiology, Vol. 10, Issue 4 https://doi.org/10.1038/nrmicro2737	journal	February 2012
Coordination of microbial metabolism Chubukov, Victor; Gerosa, Luca; Kochanowski, Karl Nature Reviews Microbiology, Vol. 12, Issue 5 https://doi.org/10.1038/nrmicro3238	journal	March 2014
Stoichiometry of Site-specific Lysine Acetylation in an Entire Proteome Baeza, Josue; Dowell, James A.; Smallegan, Michael J. Journal of Biological Chemistry, Vol. 289, Issue 31 https://doi.org/10.1074/jbc.M114.581843	journal	June 2014
Use of Randomized Sampling for Analysis of Metabolic Networks Schellenberger, Jan; Palsson, Bernhard Ø. Journal of Biological Chemistry, Vol. 284, Issue 9 https://doi.org/10.1074/jbc.R800048200	journal	October 2008
Phosphoproteome Analysis of E. coli Reveals Evolutionary Conservation of Bacterial Ser/Thr/Tyr Phosphorylation Macek, Boris; Gnad, Florian; Soufi, Boumediene Molecular & Cellular Proteomics, Vol. 7, Issue 2 https://doi.org/10.1074/mcp.M700311-MCP200	journal	October 2007
Lysine Acetylation Is a Highly Abundant and Evolutionarily Conserved Modification in Escherichia Coli Zhang, Junmei; Sprung, Robert; Pei, Jimin Molecular & Cellular Proteomics, Vol. 8, Issue 2 https://doi.org/10.1074/mcp.M800187-MCP200	journal	August 2008
EcoCyc: a comprehensive database resource for Escherichia coli Keseler, Ingrid M.; Collado-Vides, Julio; Gama-Castro, Socorro Nucleic Acids Research, Vol. 33, Issue suppl_1, p. D334-D337 https://doi.org/10.1093/nar/gki108	journal	December 2004
Regulation of Isocitrate Dehydrogenase Activity in Escherichia coli on Adaptation to Acetate Holms, W. H.; Bennett, P. M. Journal of General Microbiology, Vol. 65, Issue 1 https://doi.org/10.1099/00221287-65-1-57	journal	January 1971
On the Future of Genomic Data Kahn, S. D. Science, Vol. 331, Issue 6018 https://doi.org/10.1126/science.1197891	journal	February 2011
Ancient Regulatory Role of Lysine Acetylation in Central Metabolism Nakayasu, Ernesto S.; Burnet, Meagan C.; Walukiewicz, Hanna E. mBio, Vol. 8, Issue 6 https://doi.org/10.1128/mBio.01894-17	journal	November 2017
High-Throughput Proteomics Zhang, Zhaorui; Wu, Si; Stenoien, David L. Annual Review of Analytical Chemistry, Vol. 7, Issue 1 https://doi.org/10.1146/annurev-anchem-071213-020216	journal	June 2014
Robustness in Glyoxylate Bypass Regulation Shinar, Guy; Rabinowitz, Joshua D.; Alon, Uri PLoS Computational Biology, Vol. 5, Issue 3 https://doi.org/10.1371/journal.pcbi.1000297	journal	March 2009
The Escherichia coli Phosphotyrosine Proteome Relates to Core Pathways and Virulence Hansen, Anne-Marie; Chaerkady, Raghothama; Sharma, Jyoti PLoS Pathogens, Vol. 9, Issue 6 https://doi.org/10.1371/journal.ppat.1003403	journal	June 2013
GEEQBOX : A MATLAB Toolbox for Generalized Estimating Equations and Quasi-Least Squares Ratcliffe, Sarah J.; Shults, Justine Journal of Statistical Software, Vol. 25, Issue 14 https://doi.org/10.18637/jss.v025.i14	journal	January 2008

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The Impact of ackA, pta, and ackA-pta Mutations on Growth, Gene Expression and Protein Acetylation in Escherichia coli K-12 Schütze, Andrea; Benndorf, Dirk; Püttker, Sebastian Frontiers in Microbiology, Vol. 11 https://doi.org/10.3389/fmicb.2020.00233	journal	February 2020
CRAF Methylation by PRMT6 Regulates Aerobic Glycolysis–Driven Hepatocarcinogenesis via ERK‐Dependent PKM2 Nuclear Relocalization and Activation Wong, Tin‐Lok; Ng, Kai‐Yu; Tan, Kel Vin Hepatology, Vol. 71, Issue 4 https://doi.org/10.1002/hep.30923	journal	January 2020
Protein post-translational modifications in bacteria Macek, Boris; Forchhammer, Karl; Hardouin, Julie Nature Reviews Microbiology, Vol. 17, Issue 11 https://doi.org/10.1038/s41579-019-0243-0	journal	September 2019
Global Lysine Acetylation in Escherichia coli Results from Growth Conditions That Favor Acetate Fermentation Schilling, Birgit; Basisty, Nathan; Christensen, David G. Journal of Bacteriology, Vol. 201, Issue 9 https://doi.org/10.1128/jb.00768-18	journal	February 2019

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