A comparative study of metabolic engineering anti-metabolite tolerance in Escherichia coli

Metabolic Engineering

Volumn 8, Issue 3, 2006, Pages 227-239

  Bonomo, Jeanne ^a   Warnecke, Tanya ^a   Hume, Patrick ^a   Marizcurrena, Alex ^a   Gill, Ryan T ^a  

^a UCB 450   (United States)

Author keywords

Amino acid analog; Chemical mutagenesis; Escherichia coli; Gene overexpression; Insertional mutagenesis; Metabolic engineering

Indexed keywords

AMINO ACIDS; BIOSYNTHESIS; METABOLITES; MUTAGENESIS;

AMINO ACID ANALOG; CHEMICAL MUTAGENESIS; GENE OVEREXPRESSION; INSERTIONAL MUTAGENESIS; METABOLIC ENGINEERING;

ESCHERICHIA COLI;

AMINO ACID DERIVATIVE; ASPARTIC ACID; ASPARTIC ACID BETA HYDROXAMIC ACID; GLUTAMIC ACID; GLUTAMIC ACID GAMMA HYDROXAMIC ACID; GLYCINE; HYDROXAMIC ACID DERIVATIVE; SERINE; TRYPTOPHAN;

ARTICLE; BIOSYNTHESIS; CHEMICAL MUTAGENESIS; ESCHERICHIA COLI; METABOLIC ENGINEERING; METABOLISM; MUTAGENESIS; MUTANT; NONHUMAN; PLASMID; PRIORITY JOURNAL;

DRUG TOLERANCE; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; GENETIC ENHANCEMENT; MUTAGENESIS, SITE-DIRECTED; MUTATION; PROTEIN ENGINEERING; RECOMBINANT PROTEINS;

ESCHERICHIA COLI;

EID: 33646087687     PISSN: 10967176     EISSN: 10967184     Source Type: Journal    
DOI: 10.1016/j.ymben.2005.12.005     Document Type: Article

References (44)

1. Akashi H., and Gojobori T. Metabolic efficiency and amino acid composition in the proteomes of E. coli and Bacillus subtilis. Proc. Natl. Acad. Sci. USA 99 6 (2002) 3695-3700
2. Albert R., Jeong H., and Barabasi A.L. Error and attack tolerance of complex networks. Nature 406 6794 (2000) 378-382
3. Arita M. The metabolic world of E. coli is not small. Proc. Natl. Acad. Sci. USA 101 6 (2004) 1543-1547
4. Arnold F.H., and Moore J.C. Optimizing industrial enzymes by directed evolution. Adv. Biochem. Eng. Biotechnol. 58 (1997) 1-14
5. Bailey J.E. Toward a science of metabolic engineering. Science 252 5013 (1991) 1668-1675
6. Bailey J.E. Lessons from metabolic engineering for functional genomics and drug discovery. Nat. Biotechnol. 17 7 (1999) 616-618
7. Bailey J., and Ollis D. Biochemical Engineering Fundamentals (1986), McGraw-Hill, USA
8. Balows A., and Hausler W.J. Manual of Clinical Microbiology (1991), Asm Press, Washington DC
9. Bentley W., Mirjalili N., Andersen D., Davis R., and Kompala D. Plasmid-encoded protein- The principal factor in the metabolic burden associated with recombinant bacteria. Biotechnol. Bioeng. 35 (1990) 668-681
10. Bjorkman J., Hughes D., and Andersson D.I. Virulence of antibiotic-resistant Salmonella typhimurium. Proc. Natl. Acad. Sci. USA 95 7 (1998) 3949-3953
11. Bonomo J., and Gill R.T. Antibiotic resistance as a model for strain engineering. Comput. Chem. Eng. 29 3 (2005) 509-517
12. Botstein D., and Jones E.W. Nonrandom mutagenesis of the E. coli genome by nitrosoguanidine. J. Bacteriol. 98 2 (1969) 847-848
13. Brenner S.E., Hubbard T., Murzin a., and Chothia C. Gene Duplications in Haemophilus-Influenzae. Nature 378 6553 (1995) 140
14. Cameron D.C., and Tong I.T. Cellular and metabolic engineering. An overview. Appl. Biochem. Biotechnol. 38 1-2 (1993) 105-140
15. Cerda-Olmedo E., Hanawalt P.C., and Guerola N. Mutagenesis of the replication point by nitrosoguanidine: map and pattern of replication of the E. coli chromosome. J. Mol. Biol. 33 3 (1968) 705-719
16. Demain A. Overproduction of microbial metabolites and enzymes due to alteration of regulation. Adv. Biochem. Eng. 1 (1971) 113
17. Drainas C., Kinghorn J.R., and Pateman J.a. Aspartic Hydroxamate Resistance and Asparaginase Regulation in Fungus Aspergillus-Nidulans. J. Gen. Microbiol. 98 FEB (1977) 493-501
18. Gao W.W., Jakubowski H., and Goldman E. Evidence That Uncharged Transfer-Rna Can Inhibit a Programmed Translational Frameshift in Escherichia-Coli. J. Mol. Biol. 251 2 (1995) 210-216
19. Godiska R., Patterson M., Schoenfeld T., and Mead D. Beyond pUC: Vectors for Cloning Unstable DNA. DNA Sequencing: Optimizing the Process and Analysis (2005), Jones and Bartlett Publishers, J. Kieleczawa. Subdury, MA
20. Goryshin I.Y., and Reznikoff W.S. Tn5 in vitro transposition. J. Biol. Chem. 273 13 (1998) 7367-7374
21. Jacobs M.A., Alwood A., Thaipisuttikul I., Spencer D., Haugen E., Ernst S., Will O., Kaul R., Raymond C., Levy R., Chun-Rong L., Guenthner D., Bovee D., Olson M.V., and Manoil C. Comprehensive transposon mutant library of Pseudomonas aeruginosa. Proc. Natl. Acad. Sci. USA 100 24 (2003) 14339-14344
22. Jeong H., Tombor B., Albert R., Oltvai Z.N., and Barabasi A.L. The large-scale organization of metabolic networks. Nature 407 6804 (2000) 651-654
23. Jeong H., Mason S.P., Barabasi A.L., and Oltvai Z.N. Lethality and centrality in protein networks. Nature 411 6833 (2001) 41-42
24. Kang Y., Durfee T., Glasner J.D., Qiu Y., Frisch D., Winterberg K.M., and Blattner F.R. Systematic mutagenesis of the E. coli genome. J. Bacteriol. 186 15 (2004) 4921-4930
25. Katoh M., Hiratake J., and Oda J. ATP-dependent inactivation of E. coli gamma-glutamylcysteine synthetase by l-glutamic acid gamma-monohydroxamate. Bioscience Biotechnology and Biochemistry 62 7 (1998) 1455-1457
26. Koffas M.A.G., Jung G.Y., and Stephanopoulos G. Engineering metabolism and product formation in Corynebacterium glutamicum by coordinated gene overexpression. Metabolic Engineering 5 1 (2003) 32-41
27. Lynch M., and Conery J.S. The evolutionary fate and consequences of duplicate genes. Science 290 5494 (2000) 1151-1155
28. Ma H.W., and Zeng A.P. The connectivity structure, giant strong component and centrality of metabolic networks. Bioinformatics 19 11 (2003) 1423-1430
29. Miller J. Experiments in Molecular Genetics (1972), Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
30. Moore G.L., Maranas C.D., Lutz S., and Benkovic S.J. Predicting crossover generation in DNA shuffling. Proc. Natl. Acad. Sci. USA 98 6 (2001) 3226-3231
31. Ohnishi J., Mitsuhashi S., Hayashi M., Ando S., Yokoi H., Ochiai K., and Ikeda M. A novel methodology employing Corynebacterium glutamicum genome information to generate a new l-lysine-producing mutant. Appl. Microbiol. Biotechnol. 58 2 (2002) 217-223
32. Sambrook J., Fritsch E., and Maniatis T. Molecular Cloning: A Laboratory Manual (1989), Cold Spring Harbor Laboratory Press, Plainview, New York
33. Sander P., Springer B., Prammananan T., Sturmfels A., Kappler M., Pletschette M., and Bottger E.C. Fitness cost of chromosomal drug resistance-conferring mutations. Antimicrob. Agents Chemother. 46 5 (2002) 1204-1211
34. Sauer U. Evolutionary Engineering of Industrially Important Microbial Phenotypes. Advances in Biochemical Engineering Biotechnology 73 (2001) 129-169
35. Schrag S.J., Perrot V., and Levin B.R. Adaptation to the fitness costs of antibiotic resistance in E. coli. Proc. Roy. Soc. London Ser. B-Biol. Sci. 264 1386 (1997) 1287-1291
36. Shive W., and Skinner C. Amino acid analogs in metabolic inhibitors. In: Hochaster R., and Quastel J. (Eds). Metabolic inhibitors: a comprehensive treatise vol. 1 (1963), Academic Press Inc, New York p. 2
37. Stemmer W.P. DNA shuffling by random fragmentation and reassembly: in vitro recombination for molecular evolution. Proc. Natl. Acad. Sci. USA 91 22 (1994) 10747-10751
38. Stephanopoulos G., and Vallino J.J. Network rigidity and metabolic engineering in metabolite overproduction. Science 252 5013 (1991) 1675-1681
39. Teichmann S.A., Park J., and Chothia C. Structural assignments to the Mycoplasma genitalium proteins show extensive gene duplications and domain rearrangements. Proc. Natl. Acad. Sci. USA 95 25 (1998) 14658-14663
40. Tosa T., and Pizer L.I. Biochemical basis for antimetabolite action of l- serine hydroxamate. J. Bacteriol. 106 (1971) 972-982
41. Wagner A., and Fell D.A. The small world inside large metabolic networks. Proc. Roy. Soc. London Ser. B-Biol. Sci. 268 1478 (2001) 1803-1810
42. Watts D.J., and Strogatz S.H. Collective dynamics of 'small-world' networks. Nature 393 6684 (1998) 440-442
43. Winterberg K.M., Luecke J., Bruegl A.S., and Reznikoff W.S. Phenotypic screening of E. coli K-12 Tn5 insertion libraries, using whole-genome oligonucleotide microarrays. Appl. Environ. Microbiol. 71 1 (2005) 451-459
44. Yanofsky C., and Crawford I.P. The tryptophan operon. In: Neidhardt F., Ingraham J., Magasanik B., et al. (Eds). Escherichia coli and Salmonella typhimurium: cellular and molecular biology Vol. 2 (1987), American Society for Microbiology, Washington, DC 1453-1472