Metabolic engineering of Escherichia coli W3110 strain by incorporating genome-level modifications and synthetic plasmid modules to enhance L-Dopa production from glycerol

References

• Simuni, T.; Hurtig, H. Levodopa: A Pharmacologic Miracle Four Decades Later. In Parkinson’s Disease-Diagnosis and Clinical Management. Factor S., Weiner W., Eds; Demos: New York, 2008; pp. 471–490.
   Google Scholar
• Min, K.; Park, K.; Park, D.-H.; Yoo, Y.J. Overview on the Biotechnological Production of L-DOPA. Appl. Microbiol. Biotechnol. 2015, 99, 575–584.
   PubMed Web of Science ®Google Scholar
• Knowles, W.S. Asymmetric Hydrogenation. Acc. Chem. Res. 1983, 16, 106–112.
   Web of Science ®Google Scholar
• Koyanagi, T.; Katayama, T.; Suzuki, H.; Nakazawa, H.; Yokozeki, K.; Kumagai, H. Effective Production of 3,4-dihydroxyphenyl-L-alanine (L-DOPA) with Erwinia herbicola cells carrying a mutant transcriptional regulator TyrR. J. Biotechnol. 2005, 115, 303–306.
   PubMed Web of Science ®Google Scholar
• Akashi, H.; Gojobori, T. Metabolic Efficiency and Amino Acid Composition in the Proteomes of Escherichia coli and Bacillus subtilis. PNAS. 2002, 99, 3695–3700.
   PubMed Web of Science ®Google Scholar
• Bongaerts, J.; Kramer, M.; Muller, U.; Raeven, L.; Wubbolts, M. Metabolic Engineering for Microbial Production of Aromatic Amino Acids and Derived Compounds. Metab. Eng. 2001, 3, 289–300.
   PubMed Web of Science ®Google Scholar
• Yang, T.; Rao, Z.; Zhang, X.; Xu, M.; Xu, Z.; Yang, S. T. Metabolic Engineering Strategies for Acetoin and 2, 3-Butanediol Production: Advances and Prospects. Crit. Rev. Biotechnol. 2017, 37, 990–1005.
   PubMed Web of Science ®Google Scholar
• Ma, Q.; Zhang, Q.; Xu, Q.; Zhang, C.; Li, Y.; Fan, X.; Xie X.; Chen, N. Systems Metabolic Engineering Strategies for the Production of Amino Acids. Synth. Syst. Biotechnol. 2017, 2, 87–96.
   PubMed Web of Science ®Google Scholar
• Reznik, E.; Mehta, P.; Segrè, D. Flux Imbalance Analysis and the Sensitivity of Cellular Growth to Changes in Metabolite Pools. PLoS Comput. Biol. 2013, 9, e1003195.
   PubMed Web of Science ®Google Scholar
• Phillips, R.; Kondev, J.; Theriot, J.; Garcia, H. Physical Biology of the Cell. Garland Science: Abingdon, 2012.
   Google Scholar
• Alon, U. An Introduction to Systems Biology: design Principles of Biological Circuits. Chapman and Hall/CRC Press: Boca Raton, 2006.
   Google Scholar
• Tepper, N.; Noor, E.; Amador-Noguez, D.; Haraldsdóttir, H. S.; Milo, R.; Rabinowitz, J.; Liebermeister, W.; Shlomi, T. Steady-State Metabolite Concentrations Reflect a Balance between Maximizing Enzyme Efficiency and Minimizing Total Metabolite Load. PloS One 2013, 8, e75370.
   PubMed Web of Science ®Google Scholar
• Muñoz, A.J.; Hernández-Chávez, G.; de Anda, R.; Martínez, A.; Bolívar, F.; Gosset, G. Metabolic Engineering of Escherichia coli for Improving L-3, 4-Dihydroxyphenylalanine (L-DOPA) Synthesis from Glucose. J. Ind. Microbiol. Biotechnol. 2011, 38, 1845.
   PubMed Web of Science ®Google Scholar
• Wei, T.; Cheng, B.Y.; Liu, J.Z. Genome Engineering Escherichia coli for L-DOPA Overproduction from Glucose. Sci. Rep. 2016, 6, 30080.
   PubMed Web of Science ®Google Scholar
• Gosset, G. Production of Aromatic Compounds in Bacteria. Curr. Opin. Biotechnol. 2009, 20, 651–658.
   PubMed Web of Science ®Google Scholar
• Fernandez-de-Cossio-Diaz, J.; Leon, K.; Mulet, R. Characterizing Steady States of Genome-Scale Metabolic Networks in Continuous Cell Cultures. PLoS Comput. Biol. 2017, 13, e1005835.
   PubMed Web of Science ®Google Scholar
• Juminaga, D.; Baidoo, E.E.K.; Redding-Johanson, A.M.; Batth, T.S.; Burd, H.; Mukhopadhyay, A.; Petzold, C.J.; Keasling, J.D. Modular Engineering of L-Tyrosine Production in Escherichia coli. Appl. Environ. Microbiol. 2012, 78, 89–98.
   PubMed Web of Science ®Google Scholar
• Lutke-Eversloh, T.; Stephanopoulos, G. L-Tyrosine Production by Deregulated Strains of Escherichia coli. Appl. Microbiol. Biotechnol. 2007, 75, 103–110.
   PubMed Web of Science ®Google Scholar
• Olson, M.M.; Templeton, L.J.; Suh, W.; Youderian, P.; Sariaslani, F.S.; Gatenby, A.A.; Van Dyk, T.K. Production of Tyrosine from Sucrose or Glucose Achieved by Rapid Genetic Changes to Phenylalanine-Producing Escherichia coli Strains. Appl. Microbiol. Biotechnol. 2007, 74, 1031–1040.
   PubMed Web of Science ®Google Scholar
• Jensen, E.B.; Carlsen, S. Production of Recombinant Human Growth Hormone in Escherichia coli: expression of Different Precursors and Physiological Effects of Glucose, Acetate, and Salts. Biotechnol. Bioeng. 1990, 36, 1–11.
   PubMed Web of Science ®Google Scholar
• Cabiscol, E.; Tamarit, J.; Ros Salvador, J. Oxidative Stress in Bacteria and Protein Damage by Reactive Oxygen Species. Int. Microbiol. 2000, 3, 3–8.
   PubMedGoogle Scholar
• Shine, J.; Dalgarno, L. The 3′-Terminal Sequence of Escherichia coli 16S Ribosomal RNA: complementarity to Nonsense Triplets and Ribosome Binding Sites. Proc. Natl. Acad. Sci. U.S.A. 1974, 71, 1342–1346.
   PubMedGoogle Scholar
• Thomason, L.C.; Costantino, N.; Court, D.L. E. coli Genome Manipulation by P1 Transduction. Curr. Protoc. Mol. Biol. 2007, 79, 1–17.
   Google Scholar
• Cherepanov, P.P.; Wackernagel, W. Gene Disruption in Escherichia coli: Tc R and Km R Cassettes with the Option of Flp-Catalyzed Excision of the Antibiotic-Resistance Determinant. Gene 1995, 158, 9–14.
   PubMed Web of Science ®Google Scholar
• Tyagi, N.; Saini, D.; Guleria, R.; Mukherjee, K.J. Designing an Escherichia coli Strain for Phenylalanine Overproduction by Metabolic Engineering. Mol. Biotechnol. 2017, 59, 168–178.
   PubMed Web of Science ®Google Scholar
• Siddhuraju, P.; Becker, K. Rapid Reversed-Phase High Performance Liquid Chromatographic Method for the Quantification of L-Dopa (L-3, 4-Dihydroxyphenylalanine), Non-Methylated and Methylated Tetrahydroisoquinoline Compounds from Mucuna Beans. Food Chem. 2001, 72, 389–394.
   Web of Science ®Google Scholar
• Bajad, S.U.; Lu, W.; Kimball, E.H.; Yuan, J.; Peterson, C.; Rabinowitz, J.D. Separation and Quantitation of Water Soluble Cellular Metabolites by Hydrophilic Interaction Chromatography-Tandem Mass Spectrometry. J. Chromatogr. A 2006, 1125, 76–88.
   PubMed Web of Science ®Google Scholar
• Das, A.; Verma, A.; Mukherjee, K.J. Synthesis of Dopamine in E. coli Using Plasmid-Based Expression System and Its Marked Effect on Host Growth Profiles. Prep. Biochem. Biotechnol. 2017, 47, 754–760.
   PubMed Web of Science ®Google Scholar
• Owolabi, J.B.; Rosen, B.P. Differential mRNA Stability Controls Relative Gene Expression within the Plasmid-Encoded Arsenical Resistance Operon. J. Bacteriol. 1990, 172, 2367–2371.
   PubMed Web of Science ®Google Scholar
• Newbury, S.F.; Smith, N.H.; Higgins, C.F. Differential mRNA Stability Controls Relative Gene Expression within a Polycistronic Operon. Cell 1987, 51, 1131–1143.
   PubMed Web of Science ®Google Scholar
• Coulombel, L.; Nolan, L.C.; Nikodinovic, J.; Doyle, E.M.; O’Connor, K.E. Biotransformation of 4-Halophenols to 4-Halocatechols Using Escherichia coli Expressing 4-Hydroxyphenylacetate 3-Hydroxylase. Appl. Microbiol. Biotechnol. 2011, 89, 1867–1875.
   PubMed Web of Science ®Google Scholar
• Ballou, D.P.; Entsch, B.; Cole, L.J. Dynamics Involved in Catalysis by Single-Component and Two-Component Flavin-Dependent Aromatic Hydroxylases. Biochem. Biophys. Res. Commun. 2005, 338, 590–598.
   PubMed Web of Science ®Google Scholar
• Bren, A.; Park, J.O.; Towbin, B.D.; Dekel, E.; Rabinowitz, J.D.; Alon, U. Glucose Becomes One of the Worst Carbon Sources for E.coli on poor nitrogen sources due to suboptimal levels of cAMP. Sci. Rep. 2016, 6, 24834
   PubMed Web of Science ®Google Scholar
• Ginésy, M.; Rusanova-Naydenova, D.; Rova, U. Tuning of the Carbon-to-Nitrogen Ratio for the Production of L-Arginine by Escherichia coli. Fermentation 2017, 3, 60.
   Google Scholar
• El-Mansi, E.M.T.; Bryce, C.F.; Allman, A.R.; Demain, A.L. Fermentation Microbiology and Biotechnology. CRC Press: Boca Raton, 2011.
   Google Scholar
• Bennett, B.D.; Kimball, E.H.; Gao, M.; Osterhout, R.; Van Dien, S.J.; Rabinowitz, J.D. Absolute Metabolite Concentrations and Implied Enzyme Active Site Occupancy in Escherichia coli. Nat. Chem. Biol. 2009, 5, 593.
   PubMed Web of Science ®Google Scholar
• List of important data bases used 1. Brenda: https://www.brenda-enzymes.org/ For enzyme-related quarries. 2. KEGG: http://www.genome.jp/kegg/pathway.html For sequence-related quarries. 3. EcoCyc: https://ecocyc.org/ For pathway-related quarries. 4. NCBI: https://www.ncbi.nlm.nih.gov/ For BLAST algorithm tools. 5. NEB Cutter: http://nc2.neb.com/NEBcutter2/ For restriction digestion-related queries.
   Google Scholar
• List of resource repositories used 1. ADDGENE: https://www.addgene.org/ Ordering plasmid constructs. 2. CGSC: http://cgsc2.biology.yale.edu/ Ordering mutants for transferring deletions. 3. ATCC: https://www.atcc.org/Products/All/25404.aspx Ordering K-12 wild type, nonlysogenic P1 phage for transducing Escherichia coli K12.
   Google Scholar
• Mass spectra library consulted: https://chemdata.nist.gov/For compound identification from mass-spec peaks.
   Google Scholar