Approaches for completing metabolic networks through metabolite damage and repair discovery

Nam, 2012, Network context and selection in the evolution to enzyme specificity, Science, 337, 1101, 10.1126/science.1216861 Gil, 2015, Stability of energy metabolites-An often overlooked issue in metabolomics studies: a review, Electrophoresis, 36, 2156, 10.1002/elps.201500031 Keller, 2015, The widespread role of non-enzymatic reactions in cellular metabolism, Curr Opin Biotechnol, 34, 153, 10.1016/j.copbio.2014.12.020 Lerma-Ortiz, 2016, Nothing of chemistry disappears in biology: the top 30 damage-prone endogenous metabolites, Biochem Soc Trans, 44, 961, 10.1042/BST20160073 D'Ari, 1998, Underground metabolism, Bioessays, 20, 181, 10.1002/(SICI)1521-1878(199802)20:2<181::AID-BIES10>3.0.CO;2-0 Notebaart, 2014, Network-level architecture and the evolutionary potential of underground metabolism, Proc Natl Acad Sci U S A, 111, 11762, 10.1073/pnas.1406102111 Guzmán, 2019, Enzyme promiscuity shapes adaptation to novel growth substrates, Mol Syst Biol, 15, 10.15252/msb.20188462 Cotton, 2020, Underground isoleucine biosynthesis pathways in E. coli, Elife, 9, 10.7554/eLife.54207 Linster, 2013, Metabolite damage and its repair or pre-emption, Nat Chem Biol, 9, 72, 10.1038/nchembio.1141 Hanson, 2016, Metabolite damage and metabolite damage control in plants, Annu Rev Plant Biol, 67, 131, 10.1146/annurev-arplant-043015-111648 de Crécy-Lagard, 2018, Newly-discovered enzymes that function in metabolite damage-control, Curr Opin Chem Biol, 47, 101, 10.1016/j.cbpa.2018.09.014 Bommer, 2020, Metabolite repair enzymes control metabolic damage in glycolysis, Trends Biochem Sci, 45, 228, 10.1016/j.tibs.2019.07.004 Niehaus, 2020, Enzyme promiscuity, metabolite damage, and metabolite damage control systems of the tricarboxylic acid cycle, FEBS J, 287, 1343, 10.1111/febs.15284 Jeanguenin, 2010, Moonlighting glutamate formiminotransferases can functionally replace 5-formyltetrahydrofolate cycloligase, J Biol Chem, 285, 41557, 10.1074/jbc.M110.190504 Marbaix, 2019, Pyridoxamine-phosphate oxidases and pyridoxamine-phosphate oxidase-related proteins catalyze the oxidation of 6-NAD(P)H to NAD(P)+, Biochem J, 476, 3030, 10.1042/BCJ20190602 Van Schaftingen, 2013, Metabolite proofreading, a neglected aspect of intermediary metabolism, J Inherit Metab Dis, 36, 427, 10.1007/s10545-012-9571-1 Veiga-da-Cunha, 2020, Inborn errors of metabolite repair, J Inherit Metab Dis, 43, 14, 10.1002/jimd.12187 Sun, 2017, Metabolite damage and repair in metabolic engineering design, Metab Eng, 44, 150, 10.1016/j.ymben.2017.10.006 Oberhardt, 2016, Systems-wide prediction of enzyme promiscuity reveals a new underground alternative route for pyridoxal 5’-phosphate production in E. coli, PLoS Comput Biol, 12, 10.1371/journal.pcbi.1004705 Porokhin, 2021, Analysis of metabolic network disruption in engineered microbial hosts due to enzyme promiscuity, Metab Eng Commun, 12, 10.1016/j.mec.2021.e00170 Cam, 2016, Engineering of a synthetic metabolic pathway for the assimilation of (D)-xylose into value-added chemicals, ACS Synth Biol, 5, 607, 10.1021/acssynbio.5b00103 Ellens, 2017, Confronting the catalytic dark matter encoded by sequenced genomes, Nucleic Acids Res, 45, 11495, 10.1093/nar/gkx937 Fiehn, 2011, Extending biochemical databases by metabolomic surveys, J Biol Chem, 286, 23637, 10.1074/jbc.R110.173617 Showalter, 2017, Epimetabolites: discovering metabolism beyond building and burning, Curr Opin Chem Biol, 36, 70, 10.1016/j.cbpa.2017.01.012 Dumont, 2019, The metabolite repair enzyme phosphoglycolate phosphatase regulates central carbon metabolism and fosmidomycin sensitivity in Plasmodium falciparum, mBio, 10, 10.1128/mBio.02060-19 Chamchoy, 2020, Functional analysis of BPSS2242 reveals its detoxification role in Burkholderia pseudomallei under salt stress, Sci Rep, 10, 10453, 10.1038/s41598-020-67382-y Mahieu, 2014, Credentialing features: a platform to benchmark and optimize untargeted metabolomic methods, Anal Chem, 86, 9583, 10.1021/ac503092d Mahieu, 2017, Systems-level annotation of a metabolomics data set reduces 25 000 features to fewer than 1000 unique metabolites, Anal Chem, 89, 10397, 10.1021/acs.analchem.7b02380 Chokkathukalam, 2013, MzMatch-ISO: an R tool for the annotation and relative quantification of isotope-labelled mass spectrometry data, Bioinformatics, 29, 281, 10.1093/bioinformatics/bts674 Bueschl, 2014, A novel stable isotope labelling assisted workflow for improved untargeted LC-HRMS based metabolomics research, Metabolomics, 10, 754, 10.1007/s11306-013-0611-0 Huang, 2014, X13CMS: Global tracking of isotopic labels in untargeted metabolomics, Anal Chem, 86, 1632, 10.1021/ac403384n Capellades, 2016, geoRge: A computational tool to detect the presence of stable isotope labeling in LC/MS-based untargeted metabolomics, Anal Chem, 88, 621, 10.1021/acs.analchem.5b03628 Bueschl, 2017, MetExtract II: a software suite for stable isotope-assisted untargeted metabolomics, Anal Chem, 89, 9518, 10.1021/acs.analchem.7b02518 Wang, 2019, Peak annotation and verification engine for untargeted LC-MS metabolomics, Anal Chem, 91, 1838, 10.1021/acs.analchem.8b03132 Tsugawa, 2019, A cheminformatics approach to characterize metabolomes in stable-isotope-labeled organisms, Nat Methods, 16, 295, 10.1038/s41592-019-0358-2 Cobbold, 2021, Non-canonical metabolic pathways in the malaria parasite detected by isotope-tracing metabolomics, Mol Syst Biol, 17, 10.15252/msb.202010023 Lu, 2020, Improved annotation of untargeted metabolomics data through buffer modifications that shift adduct mass and intensity, Anal Chem, 92, 11573, 10.1021/acs.analchem.0c00985 Higashi, 2020, Derivatization-based sample-multiplexing for enhancing throughput in liquid chromatography/tandem mass spectrometry quantification of metabolites: an overview, J Chromatogr A, 1634, 461679, 10.1016/j.chroma.2020.461679 Zhao, 2020, Chemical derivatization in LC-MS-based metabolomics study, TrAC Trends Anal Chem (Reference Ed), 131, 115988, 10.1016/j.trac.2020.115988 Gu, 2019, Current status and applications of genome-scale metabolic models, Genome Biol, 20, 1, 10.1186/s13059-019-1730-3 Bernstein, 2021, Addressing uncertainty in genome-scale metabolic model reconstruction and analysis, Genome Biol, 22, 1, 10.1186/s13059-021-02289-z Jeffryes, 2015, MINEs: Open access databases of computationally predicted enzyme promiscuity products for untargeted metabolomics, J Cheminf, 7, 1 Djoumbou-Feunang, 2019, BioTransformer: A comprehensive computational tool for small molecule metabolism prediction and metabolite identification, J Cheminf, 11, 2 Amin, 2019, Towards creating an extended metabolic model (EMM) for E. coli using enzyme promiscuity prediction and metabolomics data, Microb Cell Factories, 18, 109, 10.1186/s12934-019-1156-3 Lai, 2017, Using accurate mass gas chromatography–mass spectrometry with the MINE database for epimetabolite annotation, Anal Chem, 89, 10171, 10.1021/acs.analchem.7b01134 Hassanpour, 2020, Biological filtering and substrate promiscuity prediction for annotating untargeted metabolomics, Metabolites, 10, 10.3390/metabo10040160 Becker-Kettern, 2018, NAD(P)HX repair deficiency causes central metabolic perturbations in yeast and human cells, FEBS J, 285, 3376, 10.1111/febs.14631 Gladyshev, 2012, On the cause of aging and control of lifespan: heterogeneity leads to inevitable damage accumulation, causing aging; control of damage composition and rate of accumulation define lifespan, Bioessays, 34, 925, 10.1002/bies.201200092 Van Schaftingen, 2009, L-2-Hydroxyglutaric aciduria, a disorder of metabolite repair, J Inherit Metab Dis, 32, 135, 10.1007/s10545-008-1042-3 Kremer, 2016, NAXE mutations disrupt the cellular NAD(P)HX repair system and cause a lethal neurometabolic disorder of early childhood, Am J Hum Genet, 99, 894, 10.1016/j.ajhg.2016.07.018 Van Bergen, 2019, NAD(P)HX dehydratase (NAXD) deficiency: a novel neurodegenerative disorder exacerbated by febrile illnesses, Brain, 142, 50, 10.1093/brain/awy310 Veiga-da-Cunha, 2019, Failure to eliminate a phosphorylated glucose analog leads to neutropenia in patients with G6PT and G6PC3 deficiency, Proc Natl Acad Sci U S A, 116, 1241, 10.1073/pnas.1816143116 Fogh, 2021, Variants in the ethylmalonyl-CoA decarboxylase (ECHDC1) gene: a novel player in ethylmalonic aciduria?, J Inherit Metab Dis, 10.1002/jimd.12394 Rzem, 2004, A gene encoding a putative FAD-dependent L-2-hydroxyglutarate dehydrogenase is mutated in L-2-hydroxyglutaric aciduria, Proc Natl Acad Sci U S A, 101, 16849, 10.1073/pnas.0404840101 Linster, 2011, Ethylmalonyl-CoA decarboxylase, a new enzyme involved in metabolite proofreading, J Biol Chem, 286, 42992, 10.1074/jbc.M111.281527 Marbaix, 2011, Extremely conserved ATP- or ADP-dependent enzymatic system for nicotinamide nucleotide, J Biol Chem, 286, 41246, 10.1074/jbc.C111.310847 Wortmann, 2020, Treating neutropenia and neutrophil dysfunction in glycogen storage disease type Ib with an SGLT2 inhibitor, Blood, 136, 1033, 10.1182/blood.2019004465 Rafter, 1954, The action of glyceraldehyde-3-phosphate dehydrogenase on reduced diphosphopyridine nucleotide, J Biol Chem, 208, 799, 10.1016/S0021-9258(18)65605-4 Huang, 2016, A family of metal-dependent phosphatases implicated in metabolite damage-control, Nat Chem Biol, 12, 621, 10.1038/nchembio.2108 Dennis, 2020, Human ARMT1 structure and substrate specificity indicates that it is a DUF89 family damage-control phosphatase, J Struct Biol, 212, 107576, 10.1016/j.jsb.2020.107576 Sun, 2019, A novel mutation of PANK4 causes autosomal dominant congenital posterior cataract, Hum Mutat, 40, 380, 10.1002/humu.23696 Collard, 2016, A conserved phosphatase destroys toxic glycolytic side products in mammals and yeast, Nat Chem Biol, 12, 601, 10.1038/nchembio.2104 Digiovanni, 2020, Two novel fish paralogs provide insights into the Rid family of imine deaminases active in pre-empting enamine/imine metabolic damage, Sci Rep, 10, 10135, 10.1038/s41598-020-66663-w Overbeek, 2005, The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes, Nucleic Acids Res, 33, 5691, 10.1093/nar/gki866 Niehaus, 2017, Discovery of a widespread prokaryotic 5-oxoprolinase that was hiding in plain sight, J Biol Chem, 292, 16360, 10.1074/jbc.M117.805028 Sachla, 2019, A bacterial checkpoint protein for ribosome assembly moonlights as an essential metabolite-proofreading enzyme, Nat Commun, 10, 1, 10.1038/s41467-019-09508-z Schuster, 2019, RNAi/CRISPR screens: from a pool to a valid hit, Trends Biotechnol, 37, 38, 10.1016/j.tibtech.2018.08.002 Wang, 2018, Genome-wide screening identifies promiscuous phosphatases impairing terpenoid biosynthesis in Escherichia coli, Appl Microbiol Biotechnol, 102, 9771, 10.1007/s00253-018-9330-9 Wehrs, 2020, Investigation of Bar-seq as a method to study population dynamics of Saccharomyces cerevisiae deletion library during bioreactor cultivation, Microb Cell Factories, 19, 1, 10.1186/s12934-020-01423-z McGlincy, 2021, A genome-scale CRISPR interference guide library enables comprehensive phenotypic profiling in yeast, BMC Genom, 22, 1, 10.1186/s12864-021-07518-0 Kampmann, 2020, CRISPR-based functional genomics for neurological disease, Nat Rev Neurol, 16, 465, 10.1038/s41582-020-0373-z Borchert, 2019, Integrated metabolomics and transcriptomics suggest the global metabolic response to 2-aminoacrylate stress in Salmonella enterica, Metabolites, 10, 12, 10.3390/metabo10010012 Niehaus, 2018, Evidence that the metabolite repair enzyme NAD(P)HX epimerase has a moonlighting function, Biosci Rep, 38, 10.1042/BSR20180223 Petrovova, 2014, NAD(P)H-hydrate dehydratase- A metabolic repair enzyme and its role in Bacillus subtilis stress adaptation, PloS One, 9, 10.1371/journal.pone.0112590 Dewulf, 2019, The synthesis of branched-chain fatty acids is limited by enzymatic decarboxylation of ethyl- and methylmalonyl-CoA, Biochem J, 476, 2427, 10.1042/BCJ20190500