Metabolic engineering for sustainability and health

• Jang W.D.
• et al.

An interactive metabolic map of bio-based chemicals.

Trends Biotechnol. 2022; 41: 10-14

• Kacser H.
• Burns J.A.

The control of flux.

Symp. Soc. Exp. Biol. 1973; 27: 65-104

• Seressiotis A.
• Bailey J.E.

MPS: an algorithm and data base for metabolic pathway synthesis.

Biotechnol. Lett. 1986; 8: 837-842

• Rogers P.
• et al.

Ethanol production by Zymomonas mobilis.

in: Microbial Reactions. Springer, 1982: 37-84

• Jones D.T.
• Woods D.R.

Acetone-butanol fermentation revisited.

Microbiol. Rev. 1986; 50: 484-524

Polymer synthesis by microorganisms: technology and economics.

Trends Biotechnol. 1987; 5: 246-250

Ingram, L.O. et al. Ethanol production by Escherichia coli strains co-expressing Zymomonas PDC and ADH genes, US5000000A, University of Florida Research Foundation Inc

• Schubert P.
• et al.

Cloning of the Alcaligenes eutrophus genes for synthesis of poly-beta-hydroxybutyric acid (PHB) and synthesis of PHB in Escherichia coli.

J. Bacteriol. 1988; 170: 5837-5847

• Tong I.T.
• et al.

1,3-Propanediol production by Escherichia coli expressing genes from the Klebsiella pneumoniae dha regulon.

Appl. Environ. Microbiol. 1991; 57: 3541-3546

• Anderson S.
• et al.

Production of 2-keto-L-gulonate, an intermediate in L-ascorbate synthesis, by a genetically modified Erwinia herbicola.

Science. 1985; 230: 144-149

• Wendisch V.F.

Metabolic engineering advances and prospects for amino acid production.

Metab. Eng. 2020; 58: 17-34

• Wolf S.
• et al.

Advances in metabolic engineering of Corynebacterium glutamicum to produce high-value active ingredients for food, feed, human health, and well-being.

Essays Biochem. 2021; 65: 197-212

• Stephanopoulos G.
• et al.

Metabolic Engineering: Principles and Methodologies.

Academic Press, 1998

• Lee S.Y.
• et al.

Construction of plasmids, estimation of plasmid stability, and use of stable plasmids for the production of poly(3-hydroxybutyric acid) by recombinant Escherichia coli.

J. Biotechnol. 1994; 32: 203-211

• Wang F.
• Lee S.Y.

Production of poly(3-hydroxybutyrate) by fed-batch culture of filamentation-suppressed recombinant Escherichia coli.

Appl. Environ. Microbiol. 1997; 63: 4765-4769

• Koch A.K.
• et al.

Genetic construction of lactose-utilizing strains of Pseudomonas aeruginosa and their application in biosurfactant production.

Nat. Biotechnol. 1988; 6: 1335-1339

• Winter R.B.
• et al.

Efficient degradation of trichloroethylene by a recombinant Escherichia coli.

Nat. Biotechnol. 1989; 7: 282-285

• Bailey J.E.

Toward a science of metabolic engineering.

Science. 1991; 252: 1668-1675

• Fleischmann R.D.
• et al.

Whole-genome random sequencing and assembly of Haemophilus influenzae Rd.

Science. 1995; 269: 496-512

• Goffeau A.
• et al.

Life with 6000 genes.

Science. 1996; 274: 546-567

• Blattner F.R.
• et al.

The complete genome sequence of Escherichia coli K-12.

Science. 1997; 277: 1453-1462

• Edwards J.S.
• Palsson B.O.

Systems properties of the Haemophilus influenzae Rd metabolic genotype.

J. Biol. Chem. 1999; 274: 17410-17416

• Edwards J.S.
• Palsson B.O.

The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilities.

Proc. Natl. Acad. Sci. U. S. A. 2000; 97: 5528-5533

• Han M.J.
• Lee S.Y.

Proteome profiling and its use in metabolic and cellular engineering.

Proteomics. 2003; 3: 2317-2324

• Bro C.
• Nielsen J.

Impact of ‘ome’ analyses on inverse metabolic engineering.

Metab. Eng. 2004; 6: 204-211

• Park S.J.
• et al.

Global physiological understanding and metabolic engineering of microorganisms based on omics studies.

Appl. Microbiol. Biotechnol. 2005; 68: 567-579

• Xia X.X.
• et al.

Native-sized recombinant spider silk protein produced in metabolically engineered Escherichia coli results in a strong fiber.

Proc. Natl. Acad. Sci. U. S. A. 2010; 107: 14059-14063

• Lee S.J.
• et al.

Metabolic engineering of Escherichia coli for enhanced production of succinic acid, based on genome comparison and in silico gene knockout simulation.

Appl. Environ. Microbiol. 2005; 71: 7880-7887

• Fong S.S.
• et al.

In silico design and adaptive evolution of Escherichia coli for production of lactic acid.

Biotechnol. Bioeng. 2005; 91: 643-648

• Alper H.
• et al.

Identifying gene targets for the metabolic engineering of lycopene biosynthesis in Escherichia coli.

Metab. Eng. 2005; 7: 155-164

• Choi H.S.
• et al.

In silico identification of gene amplification targets for improvement of lycopene production.

Appl. Environ. Microbiol. 2010; 76: 3097-3105

• Park J.H.
• et al.

Metabolic engineering of Escherichia coli for the production of L-valine based on transcriptome analysis and in silico gene knockout simulation.

Proc. Natl. Acad. Sci. U. S. A. 2007; 104: 7797-7802

• Becker J.
• et al.

From zero to hero – design-based systems metabolic engineering of Corynebacterium glutamicum for L-lysine production.

Metab. Eng. 2011; 13: 159-168

• Sanchez B.J.
• et al.

Improving the phenotype predictions of a yeast genome-scale metabolic model by incorporating enzymatic constraints.

Mol. Syst. Biol. 2017; 13: 935

• O’Brien E.J.
• et al.

Genome-scale models of metabolism and gene expression extend and refine growth phenotype prediction.

Mol. Syst. Biol. 2013; 9: 693

• Gu C.
• et al.

Current status and applications of genome-scale metabolic models.

Genome Biol. 2019; 20: 121

• Fang X.
• et al.

Reconstructing organisms in silico: genome-scale models and their emerging applications.

Nat. Rev. Microbiol. 2020; 18: 731-743

• Miller J.C.
• et al.

A TALE nuclease architecture for efficient genome editing.

Nat. Biotechnol. 2011; 29: 143-148

• Carroll D.

Genome engineering with zinc-finger nucleases.

Genetics. 2011; 188: 773-782

• Wang H.H.
• et al.

Programming cells by multiplex genome engineering and accelerated evolution.

Nature. 2009; 460: 894-898

• Jiang W.
• et al.

RNA-guided editing of bacterial genomes using CRISPR-Cas systems.

Nat. Biotechnol. 2013; 31: 233-239

• Na D.
• et al.

Metabolic engineering of Escherichia coli using synthetic small regulatory RNAs.

Nat. Biotechnol. 2013; 31: 170-174

• Noh M.
• et al.

Gene expression knockdown by modulating synthetic small RNA expression in Escherichia coli.

Cell Syst. 2017; 5: 418-426

• Dong C.
• et al.

Synthetic CRISPR-Cas gene activators for transcriptional reprogramming in bacteria.

Nat. Commun. 2018; 9: 2489

• Qi L.S.
• et al.

Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression.

Cell. 2021; 184: 844

• Blazeck J.
• Alper H.S.

Promoter engineering: recent advances in controlling transcription at the most fundamental level.

Biotechnol. J. 2013; 8: 46-58

• Mutalik V.K.
• et al.

Precise and reliable gene expression via standard transcription and translation initiation elements.

Nat. Methods. 2013; 10: 354-360

• Salis H.M.
• et al.

Automated design of synthetic ribosome binding sites to control protein expression.

Nat. Biotechnol. 2009; 27: 946-950

• Ajikumar P.K.
• et al.

Isoprenoid pathway optimization for Taxol precursor overproduction in Escherichia coli.

Science. 2010; 330: 70-74

• Dueber J.E.
• et al.

Synthetic protein scaffolds provide modular control over metabolic flux.

Nat. Biotechnol. 2009; 27: 753-759

• Avalos J.L.
• et al.

Compartmentalization of metabolic pathways in yeast mitochondria improves the production of branched-chain alcohols.

Nat. Biotechnol. 2013; 31: 335-341

• Lawrence A.D.
• et al.

Solution structure of a bacterial microcompartment targeting peptide and its application in the construction of an ethanol bioreactor.

ACS Synth. Biol. 2014; 3: 454-465

• Lee J.W.
• et al.

Systems metabolic engineering of microorganisms for natural and non-natural chemicals.

Nat. Chem. Biol. 2012; 8: 536-546

• Lee S.Y.
• Kim H.U.

Systems strategies for developing industrial microbial strains.

Nat. Biotechnol. 2015; 33: 1061-1072

• Lee S.Y.
• et al.

A comprehensive metabolic map for production of bio-based chemicals.

Nat. Catal. 2019; 2: 18-33

• Lin G.-M.
• et al.

Retrosynthetic design of metabolic pathways to chemicals not found in nature.

Curr. Opin. Syst. Biol. 2019; 14: 82-107

• Yim H.
• et al.

Metabolic engineering of Escherichia coli for direct production of 1,4-butanediol.

Nat. Chem. Biol. 2011; 7: 445-452

• Rodriguez G.M.
• et al.

Expanding ester biosynthesis in Escherichia coli.

Nat. Chem. Biol. 2014; 10: 259-265

• Chae T.U.
• et al.

Metabolic engineering of Escherichia coli for the production of four-, five- and six-carbon lactams.

Metab. Eng. 2017; 41: 82-91

• Yang J.E.
• et al.

One-step fermentative production of aromatic polyesters from glucose by metabolically engineered Escherichia coli strains.

Nat. Commun. 2018; 9: 79

• Arnold F.H.

Combinatorial and computational challenges for biocatalyst design.

Nature. 2001; 409: 253-257

• Atsumi S.
• et al.

Non-fermentative pathways for synthesis of branched-chain higher alcohols as biofuels.

Nature. 2008; 451: 86-89

• Jung Y.K.
• et al.

Metabolic engineering of Escherichia coli for the production of polylactic acid and its copolymers.

Biotechnol. Bioeng. 2010; 105: 161-171

• Biz A.
• et al.

Systems biology based metabolic engineering for non-natural chemicals.

Biotechnol. Adv. 2019; 37107379

• Cho J.S.
• et al.

Designing microbial cell factories for the production of chemicals.

JACS Au. 2022; 2: 1781-1799

• Ro D.K.
• et al.

Production of the antimalarial drug precursor artemisinic acid in engineered yeast.

Nature. 2006; 440: 940-943

• Nakagawa A.
• et al.

A bacterial platform for fermentative production of plant alkaloids.

Nat. Commun. 2011; 2: 326

• Yang D.
• et al.

Metabolic engineering of Escherichia coli for natural product biosynthesis.

Trends Biotechnol. 2020; 38: 745-765

• Kim G.B.
• et al.

Machine learning applications in systems metabolic engineering.

Curr. Opin. Biotechnol. 2020; 64: 1-9

• Ahn J.H.
• et al.

Enhanced succinic acid production by Mannheimia employing optimal malate dehydrogenase.

Nat. Commun. 2020; 11: 1970

• Han T.
• et al.

Glutaric acid production by systems metabolic engineering of an L-lysine-overproducing Corynebacterium glutamicum.

Proc. Natl. Acad. Sci. U. S. A. 2020; 117: 30328-30334

• Zhao M.
• et al.

Metabolic engineering of Escherichia coli for producing adipic acid through the reverse adipate-degradation pathway.

Metab. Eng. 2018; 47: 254-262

• Raynaud C.
• et al.

Molecular characterization of the 1,3-propanediol (1,3-PD) operon of Clostridium butyricum.

Proc. Natl. Acad. Sci. U. S. A. 2003; 100: 5010-5015

• Yun J.
• et al.

Co-fermentation of glycerol and glucose by a co-culture system of engineered Escherichia coli strains for 1,3-propanediol production without vitamin B₁₂ supplementation.

Bioresour. Technol. 2021; 319124218

• Frazao C.J.R.
• et al.

Construction of a synthetic pathway for the production of 1,3-propanediol from glucose.

Sci. Rep. 2019; 9: 11576

• Zhong W.
• et al.

Metabolic engineering of a homoserine-derived non-natural pathway for the de novo production of 1,3-propanediol from glucose.

ACS Synth. Biol. 2019; 8: 587-595

• Li Z.
• et al.

Efficient production of 1,3-propanediol from diverse carbohydrates via a non-natural pathway using 3-hydroxypropionic acid as an intermediate.

ACS Synth. Biol. 2021; 10: 478-486

• Li Z.
• et al.

Systems metabolic engineering of Corynebacterium glutamicum for high-level production of 1,3-propanediol from glucose and xylose.

Metab. Eng. 2022; 70: 79-88

• Ma H.
• et al.

Rational flux-tuning of Halomonas bluephagenesis for co-production of bioplastic PHB and ectoine.

Nat. Commun. 2020; 11: 3313

• Ye J.W.
• Chen G.Q.

Halomonas as a chassis.

Essays Biochem. 2021; 65: 393-403

• Mizuno S.
• et al.

Biosynthesis of polyhydroxyalkanoates containing 2-hydroxy-4-methylvalerate and 2-hydroxy-3-phenylpropionate units from a related or unrelated carbon source.

J. Biosci. Bioeng. 2018; 125: 295-300

• Yang J.E.
• et al.

Biosynthesis of poly(2-hydroxyisovalerate-co-lactate) by metabolically engineered Escherichia coli.

Biotechnol. J. 2016; 11: 1572-1585

• Choi S.Y.
• et al.

One-step fermentative production of poly(lactate-co-glycolate) from carbohydrates in Escherichia coli.

Nat. Biotechnol. 2016; 34: 435-440

• Choi S.Y.
• et al.

Metabolic engineering for the synthesis of polyesters: a 100-year journey from polyhydroxyalkanoates to non-natural microbial polyesters.

Metab. Eng. 2020; 58: 47-81

• Liu Y.
• et al.

Biosynthesizing structurally diverse diols via a general route combining oxidative and reductive formations of OH-groups.

Nat. Commun. 2022; 13: 1595

• Kim D.I.
• et al.

Microbial production of multiple short-chain primary amines via retrobiosynthesis.

Nat. Commun. 2021; 12: 173

• Basak A.K.
• et al.

The role of microbes in biofuel production.

in: Kumar N. Biofuel from Microbes and Plants: Green Energy Alternative. 1st edn. CRC Press, 2021: 63

• Ramamurthy P.C.
• et al.

Microbial biotechnological approaches: renewable bioprocessing for the future energy systems.

Microb. Cell Factories. 2021; 20: 55

• Liu Y.
• et al.

Biofuels for a sustainable future.

Cell. 2021; 184: 1636-1647

• Keasling J.
• et al.

Microbial production of advanced biofuels.

Nat. Rev. Microbiol. 2021; 19: 701-715

• Gray K.A.
• et al.

Bioethanol.

Curr. Opin. Chem. Biol. 2006; 10: 141-146

• Moon H.G.
• et al.

One hundred years of clostridial butanol fermentation.

FEMS Microbiol. Lett. 2016; 363e02683–18

• Zabed H.
• et al.

Bioethanol production from renewable sources: current perspectives and technological progress.

Renew. Sustain. Energy Rev. 2017; 71: 475-501

• Xue C.
• et al.

Recent advances and state-of-the-art strategies in strain and process engineering for biobutanol production by Clostridium acetobutylicum.

Biotechnol. Adv. 2017; 35: 310-322

• Jang Y.S.
• et al.

Enhanced butanol production obtained by reinforcing the direct butanol-forming route in Clostridium acetobutylicum.

mBio. 2012; 3e00314–12

• Ingram L.O.
• et al.

Genetic engineering of ethanol production in Escherichia coli.

Appl. Environ. Microbiol. 1987; 53: 2420-2425

• Ohta K.
• et al.

Genetic improvement of Escherichia coli for ethanol production: chromosomal integration of Zymomonas mobilis genes encoding pyruvate decarboxylase and alcohol dehydrogenase II.

Appl. Environ. Microbiol. 1991; 57: 893-900

• Walfridsson M.
• et al.

Expression of different levels of enzymes from the Pichia stipitis XYL1 and XYL2 genes in Saccharomyces cerevisiae and its effects on product formation during xylose utilisation.

Appl. Microbiol. Biotechnol. 1997; 48: 218-224

• Bro C.
• et al.

In silico aided metabolic engineering of Saccharomyces cerevisiae for improved bioethanol production.

Metab. Eng. 2006; 8: 102-111

• Zhou H.
• et al.

Xylose isomerase overexpression along with engineering of the pentose phosphate pathway and evolutionary engineering enable rapid xylose utilization and ethanol production by Saccharomyces cerevisiae.

Metab. Eng. 2012; 14: 611-622

• Guadalupe Medina V.
• et al.

Elimination of glycerol production in anaerobic cultures of a Saccharomyces cerevisiae strain engineered to use acetic acid as an electron acceptor.

Appl. Environ. Microbiol. 2010; 76: 190-195

• Alper H.
• et al.

Engineering yeast transcription machinery for improved ethanol tolerance and production.

Science. 2006; 314: 1565-1568

• Wei N.
• et al.

Enhanced biofuel production through coupled acetic acid and xylose consumption by engineered yeast.

Nat. Commun. 2013; 4: 2580

• Choi Y.J.
• Lee S.Y.

Microbial production of short-chain alkanes.

Nature. 2013; 502: 571-574

• Sheppard M.J.
• et al.

Modular and selective biosynthesis of gasoline-range alkanes.

Metab. Eng. 2016; 33: 28-40

• Dellomonaco C.
• et al.

Engineered reversal of the beta-oxidation cycle for the synthesis of fuels and chemicals.

Nature. 2011; 476: 355-359

• Xu P.
• et al.

Modular optimization of multi-gene pathways for fatty acids production in E. coli.

Nat. Commun. 2013; 4: 1409

• Zhou Y.J.
• et al.

Production of fatty acid-derived oleochemicals and biofuels by synthetic yeast cell factories.

Nat. Commun. 2016; 7: 11709

• Yu T.
• et al.

Reprogramming yeast metabolism from alcoholic fermentation to lipogenesis.

Cell. 2018; 174: 1549-1558

• Yu T.
• et al.

Metabolic reconfiguration enables synthetic reductive metabolism in yeast.

Nat. Metab. 2022; 4: 1551-1559

• Kim H.M.
• et al.

Engineering of an oleaginous bacterium for the production of fatty acids and fuels.

Nat. Chem. Biol. 2019; 15: 721-729

• Zhang F.
• et al.

Design of a dynamic sensor-regulator system for production of chemicals and fuels derived from fatty acids.

Nat. Biotechnol. 2012; 30: 354-359

• Steen E.J.
• et al.

Microbial production of fatty-acid-derived fuels and chemicals from plant biomass.

Nature. 2010; 463: 559-562

• Xu P.
• et al.

Engineering Yarrowia lipolytica as a platform for synthesis of drop-in transportation fuels and oleochemicals.

Proc. Natl. Acad. Sci. U. S. A. 2016; 113: 10848-10853

• Yu K.O.
• et al.

Synthesis of FAEEs from glycerol in engineered Saccharomyces cerevisiae using endogenously produced ethanol by heterologous expression of an unspecific bacterial acyltransferase.

Biotechnol. Bioeng. 2012; 109: 110-115

• Ozaydin B.
• et al.

Carotenoid-based phenotypic screen of the yeast deletion collection reveals new genes with roles in isoprenoid production.

Metab. Eng. 2013; 15: 174-183

• Meadows A.L.
• et al.

Rewriting yeast central carbon metabolism for industrial isoprenoid production.

Nature. 2016; 537: 694-697

• Dusseaux S.
• et al.

Transforming yeast peroxisomes into microfactories for the efficient production of high-value isoprenoids.

Proc. Natl. Acad. Sci. U. S. A. 2020; 117: 31789-31799

• Grewal P.S.
• et al.

Peroxisome compartmentalization of a toxic enzyme improves alkaloid production.

Nat. Chem. Biol. 2021; 17: 96-103

• Liu Q.
• et al.

Engineering an iterative polyketide pathway in Escherichia coli results in single-form alkene and alkane overproduction.

Metab. Eng. 2015; 28: 82-90

• Cruz-Morales P.
• et al.

Biosynthesis of polycyclopropanated high energy biofuels.

Joule. 2022; 6: 1590-1605

• Bruder S.
• et al.

Drop-in biofuel production using fatty acid photodecarboxylase from Chlorella variabilis in the oleaginous yeast Yarrowia lipolytica.

Biotechnol. Biofuels. 2019; 12: 202

• Sorigue D.
• et al.

An algal photoenzyme converts fatty acids to hydrocarbons.

Science. 2017; 357: 903-907

• Li J.
• et al.

Synthesis of high-titer alka(e)nes in Yarrowia lipolytica is enabled by a discovered mechanism.

Nat. Commun. 2020; 11: 6198

• Qiao K.
• et al.

Lipid production in Yarrowia lipolytica is maximized by engineering cytosolic redox metabolism.

Nat. Biotechnol. 2017; 35: 173-177

• Love C.R.
• et al.

Microbial production and consumption of hydrocarbons in the global ocean.

Nat. Microbiol. 2021; 6: 489-498

• Shi S.
• et al.

Synthetic biology: a new frontier in food production.

Trends Biotechnol. 2022; 40: 781-803

• Luo Z.W.
• et al.

Microbial production of methyl anthranilate, a grape flavor compound.

Proc. Natl. Acad. Sci. U. S. A. 2019; 116: 10749-10756

• Denby C.M.
• et al.

Industrial brewing yeast engineered for the production of primary flavor determinants in hopped beer.

Nat. Commun. 2018; 9: 965

• Yang D.
• et al.

Production of rainbow colorants by metabolically engineered Escherichia coli.

Adv. Sci. 2021; 8e2100743

• Prabowo C.P.S.
• et al.

Production of natural colorants by metabolically engineered microorganisms.

Trends Chem. 2022; 4: 608-626

• Yang D.
• et al.

Production of carminic acid by metabolically engineered Escherichia coli.

J. Am. Chem. Soc. 2021; 143: 5364-5377

• Zhao X.R.
• et al.

Metabolic engineering of Escherichia coli for secretory production of free haem.

Nat. Catal. 2018; 1: 720-728

• Ishchuk O.P.
• et al.

Genome-scale modeling drives 70-fold improvement of intracellular heme production in Saccharomyces cerevisiae.

Proc. Natl. Acad. Sci. U. S. A. 2022; 119e2108245119

• Choi K.R.
• et al.

Improved production of heme using metabolically engineered Escherichia coli.

Biotechnol. Bioeng. 2022; 119: 3178-3193

• Blin K.
• et al.

antiSMASH 6.0: improving cluster detection and comparison capabilities.

Nucleic Acids Res. 2021; 49: W29-W35

• Skinnider M.A.
• et al.

Comprehensive prediction of secondary metabolite structure and biological activity from microbial genome sequences.

Nat. Commun. 2020; 11: 6058

• Zheng S.
• et al.

Deep learning driven biosynthetic pathways navigation for natural products with BioNavi-NP.

Nat. Commun. 2022; 13: 3342

• Hafner J.
• et al.

A computational workflow for the expansion of heterologous biosynthetic pathways to natural product derivatives.

Nat. Commun. 2021; 12: 1760

• Park S.Y.
• et al.

Metabolic engineering of Escherichia coli with electron channelling for the production of natural products.

Nat. Catal. 2022; : 1-12

• Galanie S.
• et al.

Complete biosynthesis of opioids in yeast.

Science. 2015; 349: 1095-1100

• Luo X.
• et al.

Complete biosynthesis of cannabinoids and their unnatural analogues in yeast.

Nature. 2019; 567: 123-126

• Srinivasan P.
• Smolke C.D.

Biosynthesis of medicinal tropane alkaloids in yeast.

Nature. 2020; 585: 614-619

• Ma Y.
• et al.

Targeting pathway expression to subcellular organelles improves astaxanthin synthesis in Yarrowia lipolytica.

Metab. Eng. 2021; 68: 152-161

• Ma Y.
• et al.

Removal of lycopene substrate inhibition enables high carotenoid productivity in Yarrowia lipolytica.

Nat. Commun. 2022; 13: 572

• Zhang J.
• et al.

A microbial supply chain for production of the anti-cancer drug vinblastine.

Nature. 2022; 609: 341-347

• Jain M.
• et al.

Current perspective of innovative strategies for bioremediation of organic pollutants from wastewater.

Bioresour. Technol. 2022; 344126305

• Singh A.
• et al.

Techno-economic, life-cycle, and socioeconomic impact analysis of enzymatic recycling of poly(ethylene terephthalate).

Joule. 2021; 5: 2479-2503

• Yoshida S.
• et al.

A bacterium that degrades and assimilates poly(ethylene terephthalate).

Science. 2016; 351: 1196-1199

• Austin H.P.
• et al.

Characterization and engineering of a plastic-degrading aromatic polyesterase.

Proc. Natl. Acad. Sci. U. S. A. 2018; 115: E4350-E4357

• Joo S.
• et al.

Structural insight into molecular mechanism of poly(ethylene terephthalate) degradation.

Nat. Commun. 2018; 9: 382

• Son H.F.
• et al.

Rational protein engineering of thermo-stable PETase from Ideonella sakaiensis for highly efficient PET degradation.

ACS Catal. 2019; 9: 3519-3526

• Son H.F.
• et al.

Structural bioinformatics-based protein engineering of thermo-stable PETase from Ideonella sakaiensis.

Enzym. Microb. Technol. 2020; 141109656

• Cui Y.
• et al.

Computational redesign of a PETase for plastic biodegradation under ambient condition by the GRAPE strategy.

ACS Catal. 2021; 11: 1340-1350

• Palm G.J.
• et al.

Structure of the plastic-degrading Ideonella sakaiensis MHETase bound to a substrate.

Nat. Commun. 2019; 10: 1717

• Sagong H.-Y.
• et al.

Decomposition of the PET film by MHETase using Exo-PETase function.

ACS Catal. 2020; 10: 4805-4812

• Knott B.C.
• et al.

Characterization and engineering of a two-enzyme system for plastics depolymerization.

Proc. Natl. Acad. Sci. U. S. A. 2020; 117: 25476-25485

• Bell E.L.
• et al.

Directed evolution of an efficient and thermostable PET depolymerase.

Nat. Catal. 2022; 5: 673-681

• Lu H.
• et al.

Machine learning-aided engineering of hydrolases for PET depolymerization.

Nature. 2022; 604: 662-667

• Tournier V.
• et al.

An engineered PET depolymerase to break down and recycle plastic bottles.

Nature. 2020; 580: 216-219

• Zhu B.
• et al.

Enzyme discovery and engineering for sustainable plastic recycling.

Trends Biotechnol. 2022; 40: 22-37

• Zhang Z.
• et al.

Polyvinyl chloride degradation by a bacterium isolated from the gut of insect larvae.

Nat. Commun. 2022; 13: 5360

• Sanluis-Verdes A.
• et al.

Wax worm saliva and the enzymes therein are the key to polyethylene degradation by Galleria mellonella.

Nat. Commun. 2022; 13: 5568

• Tiso T.
• et al.

Towards bio-upcycling of polyethylene terephthalate.

Metab. Eng. 2021; 66: 167-178

• Sullivan K.P.
• et al.

Mixed plastics waste valorization through tandem chemical oxidation and biological funneling.

Science. 2022; 378: 207-211

• Santos-Merino M.
• et al.

New applications of synthetic biology tools for cyanobacterial metabolic engineering.

Front. Bioeng. Biotechnol. 2019; 7: 33

• Pavan M.
• et al.

Advances in systems metabolic engineering of autotrophic carbon oxide-fixing biocatalysts towards a circular economy.

Metab. Eng. 2022; 71: 117-141

• Atsumi S.
• et al.

Direct photosynthetic recycling of carbon dioxide to isobutyraldehyde.

Nat. Biotechnol. 2009; 27: 1177-1180

• Liew F.E.
• et al.

Carbon-negative production of acetone and isopropanol by gas fermentation at industrial pilot scale.

Nat. Biotechnol. 2022; 40: 335-344

• Liu Z.
• et al.

Third-generation biorefineries as the means to produce fuels and chemicals from CO₂.

Nat. Catal. 2020; 3: 274-288

• Gleizer S.
• et al.

Conversion of Escherichia coli to generate all biomass carbon from CO₂.

Cell. 2019; 179: 1255-1263 e12

• Bang J.
• et al.

Escherichia coli is engineered to grow on CO₂ and formic acid.

Nat. Microbiol. 2020; 5: 1459-1463

• Chen F.Y.
• et al.

Converting Escherichia coli to a synthetic methylotroph growing solely on methanol.

Cell. 2020; 182: 933-946

• Li H.
• et al.

Integrated electromicrobial conversion of CO₂ to higher alcohols.

Science. 2012; 335: 1596

• Stockl M.
• et al.

From CO₂ to bioplastic – coupling the electrochemical CO₂ reduction with a microbial product generation by drop-in electrolysis.

ChemSusChem. 2020; 13: 4086-4093

• Cohen S.N.
• et al.

Nonchromosomal antibiotic resistance in bacteria: genetic transformation of Escherichia coli by R-factor DNA.

Proc. Natl. Acad. Sci. U. S. A. 1972; 69: 2110-2114

• Cohen S.N.
• et al.

Construction of biologically functional bacterial plasmids in vitro.

Proc. Natl. Acad. Sci. U. S. A. 1973; 70: 3240-3244

• Sanger F.
• et al.

DNA sequencing with chain-terminating inhibitors.

Proc. Natl. Acad. Sci. U. S. A. 1977; 74: 5463-5467

• Itakura K.
• et al.

Expression in Escherichia coli of a chemically synthesized gene for the hormone somatostatin.

Science. 1977; 198: 1056-1063

• Goeddel D.V.
• et al.

Expression in Escherichia coli of chemically synthesized genes for human insulin.

Proc. Natl. Acad. Sci. U. S. A. 1979; 76: 106-110

PCR: thirty-five years and counting.

Science. 2018; 360: 670-672

• Altschul S.F.
• et al.

Basic local alignment search tool.

J. Mol. Biol. 1990; 215: 403-410

• Savinell J.M.
• Palsson B.O.

Network analysis of intermediary metabolism using linear optimization. I. Development of mathematical formalism.

J. Theor. Biol. 1992; 154: 421-454

• Baudin A.
• et al.

A simple and efficient method for direct gene deletion in Saccharomyces cerevisiae.

Nucleic Acids Res. 1993; 21: 3329-3330

• Schuster S.
• Hilgetag C.

On elementary flux modes in biochemical reaction systems at steady state.

J. Biol. Syst. 2011; 02: 165-182

• Zupke C.
• Stephanopoulos G.

Intracellular flux analysis in hybridomas using mass balances and in vitro ¹³C NMR.

Biotechnol. Bioeng. 1995; 45: 292-303

• Zhang Y.
• et al.

A new logic for DNA engineering using recombination in Escherichia coli.

Nat. Genet. 1998; 20: 123-128

• Datsenko K.A.
• Wanner B.L.

One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products.

Proc. Natl. Acad. Sci. U. S. A. 2000; 97: 6640-6645

• Zhang Y.X.
• et al.

Genome shuffling leads to rapid phenotypic improvement in bacteria.

Nature. 2002; 415: 644-646

• Patnaik R.
• et al.

Genome shuffling of Lactobacillus for improved acid tolerance.

Nat. Biotechnol. 2002; 20: 707-712

• Segre D.
• et al.

Analysis of optimality in natural and perturbed metabolic networks.

Proc. Natl. Acad. Sci. U. S. A. 2002; 99: 15112-15117

• Mahadevan R.
• Schilling C.H.

The effects of alternate optimal solutions in constraint-based genome-scale metabolic models.

Metab. Eng. 2003; 5: 264-276

• Burgard A.P.
• et al.

OptKnock: a bilevel programming framework for identifying gene knockout strategies for microbial strain optimization.

Biotechnol. Bioeng. 2003; 84: 647-657

• Szczebara F.M.
• et al.

Total biosynthesis of hydrocortisone from a simple carbon source in yeast.

Nat. Biotechnol. 2003; 21: 143-149

• Margulies M.
• et al.

Genome sequencing in microfabricated high-density picolitre reactors.

Nature. 2005; 437: 376-380

• Gibson D.G.
• et al.

Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome.

Science. 2008; 319: 1215-1220

• Gibson D.G.
• et al.

Enzymatic assembly of DNA molecules up to several hundred kilobases.

Nat. Methods. 2009; 6: 343-345

• Zhang Y.
• et al.

Three-dimensional structural view of the central metabolic network of Thermotoga maritima.

Science. 2009; 325: 1544-1549

• Gibson D.G.
• et al.

Creation of a bacterial cell controlled by a chemically synthesized genome.

Science. 2010; 329: 52-56

• Medema M.H.
• et al.

antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences.

Nucleic Acids Res. 2011; 39: W339-W346

• Karr J.R.
• et al.

A whole-cell computational model predicts phenotype from genotype.

Cell. 2012; 150: 389-401

• Bogorad I.W.
• et al.

Synthetic non-oxidative glycolysis enables complete carbon conservation.

Nature. 2013; 502: 693-697

• Siegel J.B.
• et al.

Computational protein design enables a novel one-carbon assimilation pathway.

Proc. Natl. Acad. Sci. U. S. A. 2015; 112: 3704-3709

• Skinnider M.A.
• et al.

Genomes to natural products PRediction Informatics for Secondary Metabolomes (PRISM).

Nucleic Acids Res. 2015; 43: 9645-9662

• Khodayari A.
• Maranas C.D.

A genome-scale Escherichia coli kinetic metabolic model k-ecoli457 satisfying flux data for multiple mutant strains.

Nat. Commun. 2016; 7: 13806

• Nielsen A.A.
• et al.

Genetic circuit design automation.

Science. 2016; 352aac7341

• Bang J.
• Lee S.Y.

Assimilation of formic acid and CO₂ by engineered Escherichia coli equipped with reconstructed one-carbon assimilation pathways.

Proc. Natl. Acad. Sci. U. S. A. 2018; 115: E9271-E9279

• Senior A.W.
• et al.

Improved protein structure prediction using potentials from deep learning.

Nature. 2020; 577: 706-710

• Ryu J.Y.
• et al.

Deep learning enables high-quality and high-throughput prediction of enzyme commission numbers.

Proc. Natl. Acad. Sci. U. S. A. 2019; 116: 13996-14001

• Macklin D.N.
• et al.

Simultaneous cross-evaluation of heterogeneous E. coli datasets via mechanistic simulation.

Science. 2020; 369eaav3751

• Jumper J.
• et al.

Highly accurate protein structure prediction with AlphaFold.

Nature. 2021; 596: 583-589

• Baek M.
• et al.

Accurate prediction of protein structures and interactions using a three-track neural network.

Science. 2021; 373: 871-876