Conservation of metabolic regulation by phosphorylation and non-covalent small-molecule interactions

Alam, 2017, The self-inhibitory nature of metabolic networks and its alleviation through compartmentalization, Nat. Commun., 8, 16018, 10.1038/ncomms16018 Brunk, 2018, Recon3D enables a three-dimensional view of gene variation in human metabolism, Nat. Biotechnol., 36, 272, 10.1038/nbt.4072 Cappelletti, 2021, Dynamic 3D proteomes reveal protein functional alterations at high resolution in situ, Cell, 184, 545, 10.1016/j.cell.2020.12.021 Chang, 2021, BRENDA, the ELIXIR core data resource in 2021: new developments and updates, Nucleic Acids Res, 49, D498, 10.1093/nar/gkaa1025 Christodoulou, 2019, Reserve flux capacity in the pentose phosphate pathway by NADPH binding is conserved across kingdoms, iScience, 19, 1133, 10.1016/j.isci.2019.08.047 Christodoulou, 2018, Reserve flux capacity in the pentose phosphate pathway enables Escherichia coli's rapid response to oxidative stress, Cell Syst, 6, 569, 10.1016/j.cels.2018.04.009 Chubukov, 2014, Coordination of microbial metabolism, Nat. Rev. Microbiol., 12, 327, 10.1038/nrmicro3238 Chubukov, 2013, Transcriptional regulation is insufficient to explain substrate-induced flux changes in Bacillus subtilis, Mol. Syst. Biol., 9, 709, 10.1038/msb.2013.66 2020, UniProt: the universal protein KnowledgeBase in 2021, Nucleic Acids Res Diether, 2019, Systematic mapping of protein-metabolite interactions in central metabolism of Escherichia coli, Mol. Syst. Biol., 15, e9008, 10.15252/msb.20199008 Diether, 2017, Towards detecting regulatory protein-metabolite interactions, Curr. Opin. Microbiol., 39, 16, 10.1016/j.mib.2017.07.006 Gerosa, 2015, Pseudo-transition analysis identifies the key regulators of dynamic metabolic adaptations from steady-state data, Cell Syst, 1, 270, 10.1016/j.cels.2015.09.008 Han, 2016, Regulation of glucose metabolism from a liver-centric perspective, Exp. Mol. Med., 48, e218, 10.1038/emm.2015.122 Hauryliuk, 2015, Recent functional insights into the role of (p)ppGpp in bacterial physiology, Nat. Rev. Microbiol., 13, 298, 10.1038/nrmicro3448 Huang, 2019, dbPTM in 2019: exploring disease association and cross-talk of post-translational modifications, Nucleic Acids Res, 47, D298, 10.1093/nar/gky1074 Huber, 2015, Proteome-wide drug and metabolite interaction mapping by thermal-stability profiling, Nat. Methods, 12, 1055, 10.1038/nmeth.3590 Irving, 2021, The stringent response and physiological roles of (pp)pGpp in bacteria, Nat. Rev. Microbiol., 19, 256, 10.1038/s41579-020-00470-y Ito, 2020, ppGpp functions as an alarmone in metazoa, Commun. Biol., 3, 671, 10.1038/s42003-020-01368-4 Jeckelmann, 2019, Carbohydrate transport by group translocation: the bacterial phosphoenolpyruvate: sugar phosphotransferase system, Subcell. Biochem., 92, 223, 10.1007/978-3-030-18768-2_8 Jensen, 2008, Nucleotides, nucleosides, and nucleobases, EcoSal Plus, 3, 1, 10.1128/ecosalplus.3.6.2 Jünger, 2014, Mass spectrometry-driven phosphoproteomics: patterning the systems biology mosaic, Wiley Interdiscip. Rev. Dev. Biol., 3, 83, 10.1002/wdev.121 Kanehisa, 2000, KEGG: kyoto encyclopedia of genes and genomes, Nucleic Acids Res, 28, 27, 10.1093/nar/28.1.27 Knorr, 2018, Widespread bacterial lysine degradation proceeding via glutarate and L-2-hydroxyglutarate, Nat. Commun., 9, 5071, 10.1038/s41467-018-07563-6 Kochanowski, 2015, Posttranslational regulation of microbial metabolism, Curr. Opin. Microbiol., 27, 10, 10.1016/j.mib.2015.05.007 Leandro, 2020, The lysine degradation pathway: subcellular compartmentalization and enzyme deficiencies, Mol. Genet. Metab., 131, 14, 10.1016/j.ymgme.2020.07.010 Li, 2010, Extensive in vivo metabolite-protein interactions revealed by large-scale systematic analyses, Cell, 143, 639, 10.1016/j.cell.2010.09.048 Lim, 2015, Global dynamics of Escherichia coli phosphoproteome in central carbon metabolism under changing culture conditions, J. Proteomics, 126, 24, 10.1016/j.jprot.2015.05.021 Link, 2013, Systematic identification of allosteric protein-metabolite interactions that control enzyme activity in vivo, Nat. Biotechnol., 31, 357, 10.1038/nbt.2489 Liu, 2019, Mapping post-translational modifications of de novo purine biosynthetic enzymes: implications for pathway regulation, J. Proteome Res., 18, 2078, 10.1021/acs.jproteome.8b00969 Manning, 2002, Evolution of protein kinase signaling from yeast to man, Trends Biochem. Sci., 27, 514, 10.1016/S0968-0004(02)02179-5 Monk, 2017, iML1515, a KnowledgeBase that computes Escherichia coli traits, Nat. Biotechnol., 35, 904, 10.1038/nbt.3956 Mor, 2011, Control of glycolysis through regulation of PFK1: old friends and recent additions, Cold Spring Harb. Symp. Quant. Biol., 76, 211, 10.1101/sqb.2011.76.010868 Narita, 2019, Functions and mechanisms of non-histone protein acetylation, Nat. Rev. Mol. Cell Biol., 20, 156, 10.1038/s41580-018-0081-3 Nyhan, 2014, Nucleotide synthesis via salvage pathway, eLS, 10.1002/9780470015902.a0001399.pub3 Ochoa, 2020, The functional landscape of the human phosphoproteome, Nat. Biotechnol., 38, 365, 10.1038/s41587-019-0344-3 Pareek, 2021, Human de novo purine biosynthesis, Crit. Rev. Biochem. Mol. Biol., 56, 1, 10.1080/10409238.2020.1832438 Piazza, 2018, A map of protein-metabolite interactions reveals principles of chemical communication, Cell, 172, 358, 10.1016/j.cell.2017.12.006 Pisithkul, 2015, Post-translational modifications as key regulators of bacterial metabolic fluxes, Curr. Opin. Microbiol., 24, 29, 10.1016/j.mib.2014.12.006 Potel, 2018, Widespread bacterial protein histidine phosphorylation revealed by mass spectrometry-based proteomics, Nat. Methods, 15, 187, 10.1038/nmeth.4580 Reznik, 2017, Genome-scale architecture of small molecule regulatory networks and the fundamental trade-off between regulation and enzymatic activity, Cell Rep, 20, 2666, 10.1016/j.celrep.2017.08.066 Rinschen, 2019, Identification of bioactive metabolites using activity metabolomics, Nat. Rev. Mol. Cell Biol., 20, 353, 10.1038/s41580-019-0108-4 Rolfes, 2006, Regulation of purine nucleotide biosynthesis: in yeast and beyond, Biochem. Soc. Trans., 34, 786, 10.1042/BST0340786 Ryan, 2019, Coupling Krebs cycle metabolites to signalling in immunity and cancer, Nat. Metab., 1, 16, 10.1038/s42255-018-0014-7 Savitski, 2014, Tracking cancer drugs in living cells by thermal profiling of the proteome, Science, 346, 1255784, 10.1126/science.1255784 Schormann, 2019, An overview of structure, function, and regulation of pyruvate kinases, Protein Sci, 28, 1771, 10.1002/pro.3691 Semanjski, 2018, The kinases HipA and HipA7 phosphorylate different substrate pools in Escherichia coli to promote multidrug tolerance, Sci. Signal., 11, eaat5750, 10.1126/scisignal.aat5750 Sridharan, 2019, Proteome-wide solubility and thermal stability profiling reveals distinct regulatory roles for ATP, Nat. Commun., 10, 1155, 10.1038/s41467-019-09107-y Studer, 2016, Evolution of protein phosphorylation across 18 fungal species, Science, 354, 229, 10.1126/science.aaf2144 Sun, 2010, A metazoan ortholog of SpoT hydrolyzes ppGpp and functions in starvation responses, Nat. Struct. Mol. Biol., 17, 1188, 10.1038/nsmb.1906 Takahashi-Íñiguez, 2016, Function, kinetic properties, crystallization, and regulation of microbial malate dehydrogenase, J. Zhejiang Univ. Sci. B, 17, 247, 10.1631/jzus.B1500219 Thorsness, 1987, Inactivation of isocitrate dehydrogenase by phosphorylation is mediated by the negative charge of the phosphate, J. Biol. Chem., 262, 10422, 10.1016/S0021-9258(18)60975-5 Tran, 2014, StableIsotope Labeling with Amino Acids in Cell Culture (SILAC)-based strategy for proteome-wide thermodynamic analysis of protein-ligand binding interactions, Mol. Cell. Proteomics, 13, 1800, 10.1074/mcp.M113.034702 Veyel, 2018, PROMIS, global analysis of PROtein-metabolite interactions using size separation in Arabidopsis thaliana, J. Biol. Chem., 293, 12440, 10.1074/jbc.RA118.003351 Virág, 2020, Current trends in the analysis of post-translational modifications, Chromatographia, 83, 1, 10.1007/s10337-019-03796-9 Wang, 2019, Affinity-based capture and identification of protein effectors of the growth regulator ppGpp, Nat. Chem. Biol., 15, 141, 10.1038/s41589-018-0183-4 Wang, 2017, O-GlcNAcylation of fumarase maintains tumour growth under glucose deficiency, Nat. Cell Biol., 19, 833, 10.1038/ncb3562 Wegner, 2015, How metabolites modulate metabolic flux, Curr. Opin. Biotechnol., 34, 16, 10.1016/j.copbio.2014.11.008 Zomorrodi, 2010, Improving the iMM904 S. cerevisiae metabolic model using essentiality and synthetic lethality data, BMC Syst. Biol., 4, 178, 10.1186/1752-0509-4-178