Dealing with complexity: Evolutionary engineering and genome shuffling

Current Opinion in Biotechnology

Volumn 15, Issue 4, 2004, Pages 298-304

  Petri, Ralf ^a   Schmidt Dannert, Claudia ^a  

^a UNIVERSITY OF MINNESOTA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOENGINEERING; EVOLUTIONARY HOMOLOGY; GENE SEQUENCE; GENOME; MICROBIAL GENETICS; MICROORGANISM; NONHUMAN; PHENOTYPE; PLASTICITY; PRIORITY JOURNAL; PROTOPLAST; REVIEW;

BACTERIAL PROTEINS; DIRECTED MOLECULAR EVOLUTION; DNA SHUFFLING; GENETIC ENHANCEMENT; GENOME, BACTERIAL; INDUSTRIAL MICROBIOLOGY; PROTEIN ENGINEERING; RECOMBINANT PROTEINS;

EID: 3543082676     PISSN: 09581669     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.copbio.2004.05.005     Document Type: Review

References (62)

1. Szczebara F.M., Chandelier C., Villeret C., Masurel A., Bourot S., Duport C., Blanchard S., Groisillier A., Testet E., Costaglioli P., et al. Total biosynthesis of hydrocortisone from a simple carbon source in yeast. Nat Biotechnol. 21:2003;143-149 This paper represents probably the most comprehensive metabolic engineering approach described in the literature. The authors rationally re-routed the complex ergosterol biosynthetic pathway in S. cerevisiae using the metabolic engineering cycle of synthesis, analysis and design, and overproduced hydrocortisone in quantities of up to 70% of the total steroid production from a simple carbon source.
2. Koffas M.A., Jung G., Stephanopoulos G. Engineering metabolism and product formation in Corynebacterium glutamicum by coordinated gene overexpression. Metab Eng. 5:2003;32-41
3. Kwon S.J., de Boer A., Petri R., Schmidt-Dannert C. High-level production of porphyrins in metabolically engineered Escherichia coli: systematic extension of a pathway assembled from overexpressed genes involved in heme biosynthesis. Appl Environ Microbiol. 69:2003;4875-4883
4. Aldor I.S., Keasling J.D. Process design for microbial plastic factories: metabolic engineering of polyhydroxyalkanoates. Curr Opin Biotechnol. 14:2003;475-483
5. Mijts B.N., Schmidt-Dannert C. Engineering of secondary metabolite pathways. Curr Opin Biotechnol. 14:2003;597-602
6. Lutke-Eversloh T., Fischer A., Remminghorst U., Kawada J., Marchessault R.H., Bogershausen A., Kalwei M., Eckert H., Reichelt R., Liu S.J., Steinbüchel A. Biosynthesis of novel thermoplastic polythioesters by engineered Escherichia coli. Nat Mater. 1:2002;236-240
7. Steinbüchel A. Production of rubber-like polymers by microorganisms. Curr Opin Microbiol. 6:2003;261-270
8. Nielsen J. Metabolic engineering. Appl Microbiol Biotechnol. 55:2001;263-283 The author gives an exhausting overview over the field of metabolic engineering with a precise categorization of the major aims. The concept of the metabolic engineering cycle is introduced.
9. Bulter T., Bernstein J., Liao J.C. A perspective of metabolic engineering strategies: moving up the systems hierarchy. Biotechnol Bioeng. 84:2003;815-821
10. Sauer U. Evolutionary engineering of industrially important microbial phenotypes. Adv Biochem Eng Biotechnol. 73:2001;129-169
11. Butler P.R., Brown M., Oliver S.G. Improvement of antibiotic titers from Streptomyces bacteria by interactive continuous selection. Biotechnol Bioeng. 49:1996;185-196
12. ••], these articles give the first descriptions of genome shuffling as a novel approach to metabolic engineering and the proof-of-concept. In both cases substantial strain improvements have been accomplished within remarkably short time scales.
13. ••].
14. Bailey J. Toward a science of metabolic engineering. Science. 252:1991;1668-1677
15. Bailey J.E., Sburlati A., Hatzimanikatis V., Lee K., Renner W.A., Tsai P.S. Inverse metabolic engineering: a strategy for directed genetic engineering of useful phenotypes. Biotechnol Bioeng. 79:2002;568-579
16. Thykaer J., Nielsen J. Metabolic engineering of β-lactam production. Metab Eng. 5:2003;56-69
17. Kuyper M., Winkler A.A., van Dijken J.P., Pronk J.T. Minimal metabolic engineering of Saccharomyces cerevisiae for efficient anaerobic xylose fermentation: a proof of principle. FEMS Yeast Res. 4:2004;655-664
18. Campo N., Daveran-Mingot M.L., Ritzenthaler P., Le Bourgeois P. Genome plasticity in Lactococcus lactis. Antonie Van Leeuwenhoek. 82:2002;123-132
19. Omelchenko M.V., Makarova K.S., Wolf Y.I., Rogozin I.B., Koonin E.V. Evolution of mosaic operons by horizontal gene transfer and gene displacement in situ. Genome Biol. 4:2003;R55
20. Le Bourgeois P., Daveran-Mingot M-L., Ritzenthaler P. Genome plasticity among related Lactococcus strains: identification of genetic events associated with macrorestriction polymorphisms. J Bacteriol. 182:2000;2481-2491
21. Radnedge L., Agron P.G., Worsham P.L., Andersen G.L. Genome plasticity in Yersinia pestis. Microbiology. 148:2002;1687-1698
22. Weaver D., Karoonuthaisiri N., Tsai H.H., Huang C.H., Ho M.L., Gai S., Patel K.G., Huang J., Cohen S.N., Hopwood D.A., et al. Genome plasticity in Streptomyces: identification of 1 Mb TIRs in the S. coelicolor A3(2) chromosome. Mol Microbiol. 51:2004;1535-1550
23. Jain R., Rivera M.C., Lake J.A. Horizontal gene transfer among genomes: the complexity hypothesis. Proc Natl Acad Sci USA. 96:1999;3801-3806
24. Rivera M.C., Jain R., Moore J.E., Lake J.A. Genomic evidence for two functionally distinct gene classes. Proc Natl Acad Sci USA. 95:1998;6239-6244
25. Nakamura Y., Nishio Y., Ikeo K., Gojobori T. The genome stability in Corynebacterium species due to lack of the recombinational repair system. Gene. 317:2003;149-155
26. Aras R.A., Kang J., Tschumi A.I., Harasaki Y., Blaser M.J. Extensive repetitive DNA facilitates prokaryotic genome plasticity. Proc Natl Acad Sci USA. 100:2003;13579-13584 The authors unravel an interesting case of adaptation to environmental changes in prokaryotes. They demonstrate how bacteria that colonize niches without access to the gene pool of other species for intergenic gene transfer diversify through recombination between identical repeats and rearrangement of the genome.
27. Rocha E.P., Blanchard A. Genomic repeats, genome plasticity and the dynamics of Mycoplasma evolution. Nucleic Acids Res. 30:2002;2031-2042
28. McAdams H.H., Srinivasan B., Arkin A.P. The evolution of genetic regulatory systems in bacteria. Nat Rev Genet. 5:2004;169-178 The authors give an excellent overview over the evolution of regulatory circuits in bacteria. They emphasize the modularity of the circuits and the plasticity of genomes as major factors for the design of genetic circuits and conclude that the starting point for the design of a regulatory system is considerably less important than the applied methods and, especially, a consequent selective screening.
29. Makalowski W. Genomic scrap yard: how genomes utilize all that junk. Gene. 259:2000;61-67
30. Kolkman J.A., Stemmer W.P.C. Directed evolution of proteins by exon shuffling. Nat Biotechnol. 19:2001;423-428
31. Stephanopoulos G., Vallino J. Network rigidity and metabolic engineering in metabolite overproduction. Science. 252:1991;1675-1681
32. Almaas E., Kovacs B., Vicsek T., Oltvai Z.N., Barabasi A.L. Global organization of metabolic fluxes in the bacterium Escherichia coli. Nature. 427:2004;839-843 The authors used flux balance analysis and demonstrated that the intracellular fluxes vary over a range of several orders of magnitude under the same conditions. They propose that the observed flux distribution is a generic feature of flux conservation on a scale-free network with only slight changes in the flux exponent. Based on an algorithm for local flux inhomogeneities, the authors introduced the concept of a 'high-flux backbone' for the metabolism.
33. Ozbudak E.M., Thattai M., Lim H.N., Shraiman B.I., Van Oudenaarden A. Multistability in the lactose utilization network of Escherichia coli. Nature. 427:2004;737-740 The authors modulated a lactose-utilizing network response to external signals from a hysteretic to a graded response. The experiments were performed using an elegant genetic detection system that works on a single-cell basis and allows a precise evaluation of metabolic changes. The authors interpret their data as a shift between different parts of the unified phase diagram.
34. Watts K.T., Lee P.C., Schmidt-Dannert C. Exploring recombinant flavonoid biosynthesis in metabolically engineered Escherichia coli. ChemBioChem. 5:2004;1-9
35. Farmer W.R., Liao J.C. Precursor balancing for metabolic engineering of lycopene production in Escherichia coli. Biotechnol Prog. 17:2001;57-61
36. +-dependent formate dehydrogenase. Metab Eng. 4:2002;217-229 This is the first systematic report addressing the metabolic effects of increased cofactor levels achieved through overexpression of a formate dehydrogenase from Candida biodinii. The doubling of the intracellular NADH level as a principal metabolic node promoted significant network changes under anaerobic and aerobic conditions.
37. Underwood S.A., Zhou S., Causey T.B., Yomano L.P., Shanmugam K.T., Ingram L.O. Genetic changes to optimize carbon partitioning between ethanol and biosynthesis in ethanologenic Escherichia coli. Appl Environ Microbiol. 68:2002;6263-6272
38. Schmidt-Dannert C., Umeno D., Arnold F.H. Molecular breeding of carotenoid biosynthetic pathways. Nat Biotechnol. 18:2000;750-753
39. Umeno D., Arnold F. Evolution of a pathway to novel long-chain carotenoids. J Bacteriol. 186:2004;1531-1536
40. Kim S.W., Keasling J.D. Metabolic engineering of the nonmevalonate isopentenyl diphosphate synthesis pathway in Escherichia coli enhances lycopene production. Biotechnol Bioeng. 72:2001;408-415
41. Ness J.E., Welch M., Giver L., Bueno M., Cherry J.R., Borchert T.V., Stemmer W.P.C., Minshull J. DNA shuffling of subgenomic sequences of subtilisin. Nat Biotechnol. 17:1999;893-896
42. Scheinbach S. Protoplast fusion as a means of producing new industrial yeast strains. Biotechnol Adv. 1:1983;289-300
43. Hopwood D.A., Wright H.M., Bibb M.J., Cohen S.N. Genetic recombination through protoplast fusion in Streptomyces. Nature. 268:1977;171-174
44. Iwata M., Mada M., Ishiwa H. Protoplast fusion of Lactobacillus fermentum. Appl Environ Microbiol. 52:1986;392-393
45. Verma V., Qazi G.N., Parshad R. Intergeneric protoplast fusion between Gluconobacter oxydans and Corynebacterium species. J Biotechnol. 26:1992;327-330
46. Rassoulzadegan M., Binetruy B., Cuzin F. High frequency of gene transfer after fusion between bacteria and eukaryotic cells. Nature. 295:1982;257-259
47. Stephanopoulos G. Metabolic engineering by genome shuffling. Nat Biotechnol. 20:2002;666-668 This author summarizes the two publications on genome shuffling and carefully analyzes the perspectives for this approach for industrial strain improvement.
48. de Vos W.M., Hugenholtz J. Engineering metabolic highways in Lactococci and other lactic acid bacteria. Trends Biotechnol. 22:2004;72-79
49. Kleerebezem M., Hugenholtz J. Metabolic pathway engineering in lactic acid bacteria. Curr Opin Biotechnol. 14:2003;232-237
50. Hugenholtz J., Sybesma W., Groot M.N., Wisselink W., Ladero V., Burgess K., van Sinderen D., Piard J.C., Eggink G., Smid E.J., et al. Metabolic engineering of lactic acid bacteria for the production of nutraceuticals. Antonie Van Leeuwenhoek. 82:2002;217-235
51. Agbessi S., Beauséjour J., Dery C., Beaulieu C. Antagonistic properties of two recombinant strains of Streptomyces melanosporofaciens obtained by intraspecific protoplast fusion. Appl Microbiol Biotechnol. 62:2003;233-238
52. Hopwood D.A., Wright H.M., Bibb M.J., Cohen S.N. Genetic recombination through protoplast fusion in Streptomyces. Nature. 268:1977;171-174
53. Ahmed F.E. Genetically modified probiotics in foods. Trends Biotechnol. 21:2003;491-497
54. Hwang D., Schmitt W.A., Stephanopoulos G., Stephanopoulos G. Determination of minimum sample size and discriminatory expression patterns in microarray data. Bioinformatics. 18:2002;1184-1193
55. Gill R.T., Wildt W., Yang Y.T., Ziesman S., Stephanopoulos G. Genome-wide screening for trait conferring genes using DNA microarrays. Proc Natl Acad Sci USA. 99:2002;7033-7038
56. Hwang D., Stephanopoulos G., Chan C. Inverse modeling using multi-block PLS to determine the environmental conditions that provide optimal cellular function. Bioinformatics. 20:2004;487-499
57. Romero P.R., Karp P. Using functional and organizational information to improve genome-wide computational prediction of transcription units on pathway-genome databases. Bioinformatics. 20:2004;709-717
58. Bellgard M.I., Itoh T., Watanabe H., Imanishi T., Gojobori T. Dynamic evolution of genomes and the concept of genome space. Ann N Y Acad Sci. 870:1999;293-300
59. Weinbauer M.G., Rassoulzadegan F. Are viruses driving microbial diversification and diversity? Environ Microbiol. 6:2004;1-11
60. Grohmann E., Muth G., Espinosa M. Conjugative plasmid transfer in Gram-positive bacteria. Microbiol Mol Biol Rev. 67:2003;277-301
61. Gratia J.P., Thiry M. Spontaneous zygogenesis in Escherichia coli, a form of true sexuality in prokaryotes. Microbiology. 149:2003;2571-2584
62. Dai M-H., Copley S.D. Genome shuffling improves degradation of the anthropogenic pesticide pentachlorophenol by Sphingobium chlorophenolicum ATCC 39723. Appl Env Microbiol. 70:2004;2391-2397