Synthetic metabolism approaches: A valuable resource for systems biology

Voigt, 2020, Synthetic biology 2020–2030: six commercially-available products that are changing our world, Nat Commun, 11, 10, 10.1038/s41467-020-20122-2 Anderson, 2018, Synthetic biology strategies for improving microbial synthesis of “green” biopolymers, J Biol Chem, 293, 5053, 10.1074/jbc.TM117.000368 Dvořák, 2017, Bioremediation 3.0: engineering pollutant-removing bacteria in the times of systemic biology, Biotechnol Adv, 35, 845, 10.1016/j.biotechadv.2017.08.001 Rylott, 2020, How synthetic biology can help bioremediation, Curr Opin Chem Biol, 58, 86, 10.1016/j.cbpa.2020.07.004 Bar-Even, 2010, Design and analysis of synthetic carbon fixation pathways, Proc Natl Acad Sci Unit States Am, 107, 8889, 10.1073/pnas.0907176107 Satanowski, 2020, A one-carbon path for fixing CO2, EMBO Rep, 21, 1 Erb, 2017, Synthetic metabolism: metabolic engineering meets enzyme design, Curr Opin Chem Biol, 37, 56, 10.1016/j.cbpa.2016.12.023 Gleizer, 2019, Conversion of Escherichia coli to generate all biomass carbon from CO2, Cell, 179, 1255, 10.1016/j.cell.2019.11.009 Kim, 2020, Growth of E. coli on formate and methanol via the reductive glycine pathway, Nat Chem Biol, 10.1038/s41589-020-0473-5 Cotton, 2020, Renewable methanol and formate as microbial feedstocks, Curr Opin Biotechnol, 62, 168, 10.1016/j.copbio.2019.10.002 Yishai, 2016, The formate bio-economy, Curr Opin Chem Biol, 35, 1, 10.1016/j.cbpa.2016.07.005 Meng, 2020, The second decade of synthetic biology: 2010–2020, Nat Commun, 11, 1, 10.1038/s41467-020-19092-2 Qi, 2013, Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression, Cell, 152, 1173, 10.1016/j.cell.2013.02.022 Orsi, 2021, Growth-coupled selection of synthetic modules to accelerate cell factory development, Nat Commun, 12, 1, 10.1038/s41467-021-25665-6 Wenk, 2018 Yishai, 2018, In vivo assimilation of one-carbon via a synthetic reductive glycine pathway in Escherichia coli, ACS Synth Biol, 7, 2023, 10.1021/acssynbio.8b00131 Wang, 2019, Developing a pyruvate-driven metabolic scenario for growth-coupled microbial production, Metab Eng, 55, 191, 10.1016/j.ymben.2019.07.011 Mehrer, 2019, Growth-coupled bioconversion of levulinic acid to butanone, Metab Eng, 55, 92, 10.1016/j.ymben.2019.06.003 Portnoy, 2011, Adaptive laboratory evolution-harnessing the power of biology for metabolic engineering, Curr Opin Biotechnol, 22, 590, 10.1016/j.copbio.2011.03.007 Slatko, 2018, Overview of next-generation sequencing technologies, Curr Protoc Mol Biol, 122, 1, 10.1002/cpmb.59 Bustin, 2000, Absolute quantification of mRNA using real-time reverse transcription polymerase chain reaction assays, J Mol Endocrinol, 25, 169, 10.1677/jme.0.0250169 Claassens, 2020, Replacing the Calvin cycle with the reductive glycine pathway in Cupriavidus necator, Metab Eng, 62, 30, 10.1016/j.ymben.2020.08.004 Kim, 2018, Exploiting transcriptomic data for metabolic engineering: toward a systematic strain design, Curr Opin Biotechnol, 54, 26, 10.1016/j.copbio.2018.01.020 Lowe, 2017, Transcriptomics technologies, PLoS Comput Biol, 13, 1, 10.1371/journal.pcbi.1005457 Baidoo, 2019, Microbial metabolomics methods and protocols, 10.1007/978-1-4939-8757-3 Vavricka, 2020, Dynamic metabolomics for engineering biology: accelerating learning cycles for bioproduction, Trends Biotechnol, 38, 68, 10.1016/j.tibtech.2019.07.009 Chae, 2017, Recent advances in systems metabolic engineering tools and strategies, Curr Opin Biotechnol, 47, 67, 10.1016/j.copbio.2017.06.007 Heux, 2017, Recent advances in high-throughput 13C-fluxomics, Curr Opin Biotechnol, 43, 104, 10.1016/j.copbio.2016.10.010 Zelcbuch, 2016, Pyruvate formate-lyase enables efficient growth of Escherichia coli on acetate and formate, Biochemistry, 55, 2423, 10.1021/acs.biochem.6b00184 Satanowski, 2020, Awakening a latent carbon fixation cycle in Escherichia coli, Nat Commun, 10.1038/s41467-020-19564-5 He, 2020, An optimized methanol assimilation pathway relying on promiscuous formaldehyde-condensing aldolases in E. coli, Metab Eng, 60, 1, 10.1016/j.ymben.2020.03.002 Hernandez, 2017, Combining aldolases and transaminases for the synthesis of 2-Amino-4-hydroxybutanoic acid, ACS Catal, 7, 1707, 10.1021/acscatal.6b03181 D'Ari, 1998, Underground metabolism, Bioessays, 20, 181, 10.1002/(SICI)1521-1878(199802)20:2<181::AID-BIES10>3.0.CO;2-0 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 Michael, 2017, Evolution of biosynthetic diversity, Biochem J, 474, 2277, 10.1042/BCJ20160823 Nam, 2012, Network context and selection in the evolution to enzyme specificity, Science, 337, 1101, 10.1126/science.1216861 Rosenberg, 2019, Harnessing underground metabolism for pathway development, Trends Biotechnol, 37, 29, 10.1016/j.tibtech.2018.08.001 Cotton, 2020, Underground isoleucine biosynthesis pathways in E. coli, Elife, 9, 1, 10.7554/eLife.54207 Pontrelli, 2018, Metabolic repair through emergence of new pathways in Escherichia coli, Nat Chem Biol, 14, 1005, 10.1038/s41589-018-0149-6 Kim, 2010, Three serendipitous pathways in E. coli can bypass a block in pyridoxal-5-phosphate synthesis, Mol Syst Biol, 6, 1, 10.1038/msb.2010.88 Eisenhut, 2008, The photorespiratory glycolate metabolism is essential for cyanobacteria and might have been conveyed endosymbiontically to plants, Proc Natl Acad Sci U S A, 105, 17199, 10.1073/pnas.0807043105 Claassens, 2020, Phosphoglycolate salvage in a chemolithoautotroph using the Calvin cycle, Proc Natl Acad Sci U S A, 117, 22452, 10.1073/pnas.2012288117 Lee, 2019, Functional genomics of the rapidly replicating bacterium Vibrio natriegens by CRISPRi, Nat Microbiol, 4, 1105, 10.1038/s41564-019-0423-8 Donati, 2021, Multi-omics analysis of CRISPRi-knockdowns identifies mechanisms that buffer decreases of enzymes in E. coli metabolism, Cell Syst, 12, 56, 10.1016/j.cels.2020.10.011 Sauer, 2001, Evolutionary engineering of industrially important microbial phenotypes, Adv Biochem Eng Biotechnol, 73, 129 Antonovsky, 2016, Sugar synthesis from CO2 in Escherichia coli, Cell, 166, 115, 10.1016/j.cell.2016.05.064 Herz, 2017, The genetic basis for the adaptation of E. coli to sugar synthesis from CO2, Nat Commun, 8, 10.1038/s41467-017-01835-3 Barenholz, 2017, Design principles of autocatalytic cycles constrain enzyme kinetics and force low substrate saturation at flux branch points, Elife, 6, 1, 10.7554/eLife.20667 Chen, 2020, Converting Escherichia coli to a synthetic methylotroph growing solely on methanol, Cell, 182, 933, 10.1016/j.cell.2020.07.010 Gassler, 2020, The industrial yeast Pichia pastoris is converted from a heterotroph into an autotroph capable of growth on CO2, Nat Biotechnol, 38, 210, 10.1038/s41587-019-0363-0 Bogorad, 2013, Synthetic non-oxidative glycolysis enables complete carbon conservation, Nature, 502, 693, 10.1038/nature12575 Lin, 2018, Construction and evolution of an Escherichia coli strain relying on nonoxidative glycolysis for sugar catabolism, Proc Natl Acad Sci U S A, 115, 3538, 10.1073/pnas.1802191115 Hindré, 2012, New insights into bacterial adaptation through in vivo and in silico experimental evolution, Nat Rev Microbiol, 10, 352, 10.1038/nrmicro2750 McCloskey, 2018, Evolution of gene knockout strains of E. coli reveal regulatory architectures governed by metabolism, Nat Commun, 9, 10.1038/s41467-018-06219-9 Sandberg, 2019, The emergence of adaptive laboratory evolution as an efficient tool for biological discovery and industrial biotechnology, Metab Eng, 56, 1, 10.1016/j.ymben.2019.08.004