Synthetic Evolution of Metabolic Productivity Using Biosensors

Trends in Biotechnology

Volumn 34, Issue 5, 2016, Pages 371-381

  Williams, Thomas C ^a   Pretorius, Isak S ^a   Paulsen, Ian T ^a  

^a MACQUARIE UNIVERSITY   (Australia)

Author keywords

Adaptive laboratory evolution; Biosensing; Genome engineering; Metabolic engineering; Saccharomyces cerevisiae; Synthetic biology; Yeast

Indexed keywords

BIOLOGICAL SYSTEMS; BIOSENSORS; DNA SEQUENCES; GENES; METABOLIC ENGINEERING; METABOLISM; MOLECULES; RATIONAL FUNCTIONS; YEAST;

ADAPTIVE LABORATORY EVOLUTION; BIOSENSING; GENOME ENGINEERING; GENOMIC ARCHITECTURE; INTRACELLULAR CONCENTRATION; PREDICTIVE ENGINEERING; PROCESS OF EVOLUTION; SYNTHETIC BIOLOGY;

BIOLOGY;

RNA;

BIOSENSOR; EVOLUTION; FLUORESCENCE ACTIVATED CELL SORTING; GENETIC PROCEDURES; HIGH THROUGHPUT SCREENING; HUMAN; LABORATORY; METABOLIC ENGINEERING; METABOLISM; NONHUMAN; PRIORITY JOURNAL; REVIEW; RIBOSOME; RIBOSWITCH; SINGLE NUCLEOTIDE POLYMORPHISM; SYNTHETIC BIOLOGY; TRANSCRIPTION REGULATION; ESCHERICHIA COLI; GENETICS; PROCEDURES; SACCHAROMYCES CEREVISIAE; SYSTEMS BIOLOGY;

BIOSENSING TECHNIQUES; ESCHERICHIA COLI; METABOLIC ENGINEERING; METABOLIC NETWORKS AND PATHWAYS; SACCHAROMYCES CEREVISIAE; SYNTHETIC BIOLOGY; SYSTEMS BIOLOGY;

EID: 84959504252     PISSN: 01677799     EISSN: 18793096     Source Type: Journal    
DOI: 10.1016/j.tibtech.2016.02.002     Document Type: Review

References (72)

1. Annaluru N., et al. Total synthesis of a functional designer eukaryotic chromosome. Science 2014, 344:55-58.
2. Lartigue C., et al. Genome transplantation in bacteria: changing one species to another. Science 2007, 317:632-638.
3. Woolston B.M., et al. Metabolic engineering: past and future. Annu. Rev. Chem. Biomol. Eng. 2013, 4:259-288.
4. Ro D-K., et al. Production of the antimalarial drug precursor artemisinic acid in engineered yeast. Nature 2006, 440:940-943.
5. Diaz-Torres, M. et al. Genencor International Inc. Method for the recombinant production of 1,3-propanediol, US 6136576 A.
6. Emptage, M. et al. E.I. Du Pont De Nemours and Company, Genencor International, Inc. Process for the biological production of 1,3-propanediol with high titer, CA2380616 C.
7. Laffend, L.A. et al. Du Pont, Genencor Int. Bioconversion of a fermentable carbon source to 1,3-propanediol by a single microorganism, WO1996035796 A1.
8. Yim H., et al. Metabolic engineering of Escherichia coli for direct production of 1,4-butanediol. Nat. Chem. Biol. 2011, 7:445-452.
9. Dawkins R. The Selfish Gene 2006, Oxford University Press.
10. Andrianantoandro E., et al. Synthetic biology: new engineering rules for an emerging discipline. Mol. Syst. Biol. 2006, 2:20060028.
11. Khalil A.S., Collins J.J. Synthetic biology: applications come of age. Nat. Rev. Genet. 2010, 11:367-379.
12. Purnick P.E.M., Weiss R. The second wave of synthetic biology: from modules to systems. Nat. Rev. Mol. Cell Biol. 2009, 10:410-422.
13. Zhang F., Keasling J. Biosensors and their applications in microbial metabolic engineering. Trends Microbiol. 2011, 19:323-329.
14. Gallegos M.T., et al. Arac/XylS family of transcriptional regulators. Microbiol. Mol. Biol. Rev. 1997, 61:393-410.
15. Ramos J.L., et al. The TetR family of transcriptional repressors. Microbiol. Mol. Biol. Rev. 2005, 69:326-356.
16. Tropel D., van der Meer J.R. Bacterial transcriptional regulators for degradation pathways of aromatic compounds. Microbiol. Mol. Biol. Rev. 2004, 68:474-500.
17. Müller-Hill B. The Lac Operon: A Short History of a Genetic Paradigm 1996, Walter de Gruyter.
18. Link K.H., Breaker R.R. Engineering ligand-responsive gene-control elements: lessons learned from natural riboswitches. Gene Ther. 2009, 16:1189-1201.
19. Sudarsan N., et al. An mRNA structure in bacteria that controls gene expression by binding lysine. Genes Dev. 2003, 17:2688-2697.
20. Ellington A.D., Szostak J.W. In vitro selection of RNA molecules that bind specific ligands. Nature 1990, 346:818-822.
21. Carothers J.M., et al. Selecting RNA aptamers for synthetic biology: investigating magnesium dependence and predicting binding affinity. Nucleic Acids Res. 2010, 38:2736-2747.
22. Dietrich J.A., et al. Transcription factor-based screens and synthetic selections for microbial small-molecule biosynthesis. ACS Synth. Biol. 2012, 2:47-58.
23. Tang S-Y., et al. Screening for enhanced triacetic acid lactone production by recombinant Escherichia coli expressing a designed triacetic acid lactone reporter. J. Am. Chem. Soc. 2013, 135:10099-10103.
24. DeLoache W.C., et al. An enzyme-coupled biosensor enables (S)-reticuline production in yeast from glucose. Nat. Chem. Biol. 2015, 11:465-471.
25. Lee S-W., Oh M-K. A synthetic suicide riboswitch for the high-throughput screening of metabolite production in Saccharomyces cerevisiae. Metab. Eng. 2015, 28:143-150.
26. Cheng F., et al. A competitive flow cytometry screening system for directed evolution of therapeutic enzyme. ACS Synth. Biol. 2015, 4:768-775.
27. Siedler S., et al. SoxR as a single-cell biosensor for NADPH-consuming enzymes in Escherichia coli. ACS Synth. Biol. 2014, 3:41-47.
28. Schallmey M., et al. Looking for the pick of the bunch: high-throughput screening of producing microorganisms with biosensors. Curr. Opin. Biotechnol. 2014, 26:148-154.
29. Binder S., et al. A high-throughput approach to identify genomic variants of bacterial metabolite producers at the single-cell level. Genome Biol. 2012, 13:R40.
30. Mahr R., et al. Biosensor-driven adaptive laboratory evolution of L-valine production in Corynebacterium glutamicum. Metab. Eng. 2015, 32:184-194.
31. Chou H.H., Keasling J.D. Programming adaptive control to evolve increased metabolite production. Nat. Commun. 2013, 4:2595.
32. Raman S., et al. Evolution-guided optimization of biosynthetic pathways. Proc. Natl. Acad. Sci. U.S.A. 2014, 111:17803-17808.
33. Wang H.H., et al. Programming cells by multiplex genome engineering and accelerated evolution. Nature 2009, 460:894-898.
34. Stein V., Alexandrov K. Protease-based synthetic sensing and signal amplification. Proc. Natl. Acad. Sci. U.S.A. 2014, 111:15934-15939.
35. Stein V., Alexandrov K. Synthetic protein switches: design principles and applications. Trends Biotechnol. 2015, 33:101-110.
36. Caspeta L., et al. Altered sterol composition renders yeast thermotolerant. Science 2014, 346:75-78.
37. Garcia Sanchez R., et al. Improved xylose and arabinose utilization by an industrial recombinant Saccharomyces cerevisiae strain using evolutionary engineering. Biotechnol. Biofuels 2010, 3:13.
38. Quan S., et al. Adaptive evolution of the lactose utilization network in experimentally evolved populations of Escherichia coli. PLoS Genet. 2012, 8:e1002444.
39. Wisselink H.W., et al. Novel evolutionary engineering approach for accelerated utilization of glucose, xylose, and arabinose mixtures by engineered Saccharomyces cerevisiae strains. Appl. Environ. Microbiol. 2009, 75:907-914.
40. Almario M.P., et al. Evolutionary engineering of Saccharomyces cerevisiae for enhanced tolerance to hydrolysates of lignocellulosic biomass. Biotechnol. Bioeng. 2013, 110:2616-2623.
41. Brennan T.C., et al. Evolutionary engineering improves tolerance for replacement jet fuels in Saccharomyces cerevisiae. Appl. Environ. Microbiol. 2015, 81:3316-3325.
42. Kildegaard K.R., et al. Evolution reveals a glutathione-dependent mechanism of 3-hydroxypropionic acid tolerance. Metab. Eng. 2014, 26:57-66.
43. Reyes L.H., et al. Visualizing evolution in real time to determine the molecular mechanisms of n-butanol tolerance in Escherichia coli. Metab. Eng. 2012, 14:579-590.
44. Dragosits M., Mattanovich D. Adaptive laboratory evolution - principles and applications for biotechnology. Microb. Cell. Fact. 2013, 12:64.
45. Eggeling L., et al. Novel screening methods-biosensors. Curr. Opin. Biotechnol. 2015, 35:30-36.
46. Winston F. EMS and UV mutagenesis in yeast. Curr Protoc Mol Biol 2001, John Wiley & Sons, Inc.
47. Guo Z., Houghton J.E. PcaR-mediated activation and repression of pca genes from Pseudomonas putida are propagated by its binding to both the -35 and the -10 promoter elements. Mol. Microbiol. 1999, 32:253-263.
48. Zientz E., et al. Fumarate regulation of gene expression in Escherichia coli by the DcuSR (dcuSR Genes) two-component regulatory system. J. Bacteriol. 1998, 180:5421-5425.
49. Siedler S., et al. Novel biosensors based on flavonoid-responsive transcriptional regulators introduced into Escherichia coli. Metab. Eng. 2014, 21:2-8.
50. Marin A.M., et al. Naringenin degradation by the endophytic diazotroph Herbaspirillum seropedicae SmR1. Microbiology 2013, 159:167-175.
51. Mukherjee K., et al. GPCR-based chemical biosensors for medium-chain fatty acids. ACS Synth. Biol. 2015, 4:1261-1269.
52. Hirooka K., Fujita Y. Identification of aromatic residues critical to the DNA binding and ligand response of the Bacillus subtilis QdoR (YxaF) repressor antagonized by flavonoids. Biosci. Biotechnol. Biochem. 2011, 75:1325-1334.
53. Michener J.K., Smolke C.D. High-throughput enzyme evolution in Saccharomyces cerevisiae using a synthetic RNA switch. Metab. Eng. 2012, 14:306-316.
54. Win M.N., Smolke C.D. A modular and extensible RNA-based gene-regulatory platform for engineering cellular function. Proc. Natl. Acad. Sci. U.S.A. 2007, 104:14283-14288.
55. Winkler W.C., et al. Control of gene expression by a natural metabolite-responsive ribozyme. Nature 2004, 428:281-286.
56. Kurth E.G., et al. Involvement of BmoR and BmoG in n-alkane metabolism in 'Pseudomonas butanovora'. Microbiology 2008, 154:139-147.
57. Vrljic M., et al. A new type of transporter with a new type of cellular function: L-lysine export from Corynebacterium glutamicum. Mol. Microbiol. 1996, 22:815-826.
58. Yang J., et al. Synthetic RNA devices to expedite the evolution of metabolite-producing microbes. Nat. Commun. 2013, 4:1413.
59. Patte J.C., et al. The leader sequence of the Escherichia coli lysC gene is involved in the regulation of LysC synthesis. FEMS Microbiol. Lett. 1998, 169:165-170.
60. Majerfeld I., Yarus M. A diminutive and specific RNA binding site for L-tryptophan. Nucleic Acids Res. 2005, 33:5482-5493.
61. Eckdahl T.T., et al. Programmed evolution for optimization of orthogonal metabolic output in bacteria. PLoS ONE 2015, 10:e0118322.
62. Li S., et al. Development of a synthetic malonyl-CoA sensor in Saccharomyces cerevisiae for intracellular metabolite monitoring and genetic screening. ACS Synth. Biol. 2015, 4:1308-1315.
63. Rogers J.K., et al. Synthetic biosensors for precise gene control and real-time monitoring of metabolites. Nucleic Acids Res. 2015, 43:7648-7660.
64. Pfleger B.F., et al. Microbial sensors for small molecules: development of a mevalonate biosensor. Metab. Eng. 2007, 9:30-38.
65. Newman K.L., et al. Use of a green fluorescent strain for analysis of Xylella fastidiosa colonization of Vitis vinifera. Appl. Environ. Microbiol. 2003, 69:7319-7327.
66. Pittard J., et al. The TyrR regulon. Mol. Microbiol. 2005, 55:16-26.
67. Monterrubio R., et al. A common regulator for the operons encoding the enzymes involved in D-Galactarate, D-Glucarate, and D-Glycerate utilization in Escherichia coli. J. Bacteriol. 2000, 182:2672-2674.
68. Teran W., et al. Antibiotic-dependent induction of Pseudomonas putida DOT-T1E TtgABC efflux pump is mediated by the drug binding repressor TtgR. Antimicrob. Agents Chemother. 2003, 47:3067-3072.
69. Lange C., et al. Lrp of Corynebacterium glutamicum controls expression of the brnFE operon encoding the export system for L-methionine and branched-chain amino acids. J. Biotechnol. 2012, 158:231-241.
70. Baret J-C., et al. Fluorescence-activated droplet sorting (FADS): efficient microfluidic cell sorting based on enzymatic activity. Lab Chip 2009, 9:1850-1858.
71. Sjostrom S.L., et al. High-throughput screening for industrial enzyme production hosts by droplet microfluidics. Lab Chip 2014, 14:806-813.
72. Wang B.L., et al. Microfluidic high-throughput culturing of single cells for selection based on extracellular metabolite production or consumption. Nat. Biotech. 2014, 32:473-478.