A 'bioproduction breadboard': Programming, assembling, and actuating cellular networks

Current Opinion in Biotechnology

Volumn 36, Issue , 2015, Pages 154-160

  Zargar, Amin ^a,b   Payne, Gregory F ^a,b   Bentley, William E ^a,b  

^a UNIVERSITY OF MARYLAND   (United States)

^b UNIVERSITY OF MARYLAND   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CELL CULTURE; CELL PROLIFERATION; CELLS; MOBILE TELECOMMUNICATION SYSTEMS; ORTHOGONAL FUNCTIONS; WIRELESS NETWORKS;

BIO-PRODUCTION; BIOFABRICATION; CELL POPULATIONS; CELLULAR NETWORK; DIVISION OF LABOR; FUNCTIONALIZED; PRODUCT SYNTHESIS; SYNTHETIC BIOLOGY;

CYTOLOGY;

ACETYL PHOSPHATE; FARNESYL DIPHOSPHATE; LIGNOCELLULOSE; LYCOPENE; PHOSPHATE; UNCLASSIFIED DRUG;

ACTUATING CELLULAR NETWORK; AUTONOMOUS DYNAMIC GENE EXPRESSION; BIOPRODUCTION BREADBOARD; BIOSYNTHESIS; BIOSYNTHETIC FLUX; CELL ENGINEERING; CELL POPULATION; CELL SWITCHING; CELLULAR, SUBCELLULAR AND MOLECULAR BIOLOGICAL PHENOMENA AND FUNCTIONS; EQUIPMENT DESIGN; ESCHERICHIA COLI; GENE EXPRESSION; GENERAL DEVICE; GENETIC REGULATION; GENETIC SWITCHES; HOST PATHOGEN INTERACTION; HYPOCREA JECORINA; INTRACELLULAR SIGNALING; METABOLIC REGULATION; MICROBIAL CONSORTIUM; NUCLEAR REPROGRAMMING; PATHWAY BALANCING; PATHWAY REDIRECTION; PRIORITY JOURNAL; PROCESS OPTIMIZATION; PROMOTER REGION; QUORUM SENSING; REVIEW; RNA SEQUENCE; SACCHAROMYCES CEREVISIAE; STIMULUS RESPONSE; SYNTHETIC BIOLOGY; GENE EXPRESSION REGULATION; HUMAN; SIGNAL TRANSDUCTION;

GENE EXPRESSION REGULATION; HUMANS; SIGNAL TRANSDUCTION; SYNTHETIC BIOLOGY;

EID: 84940781154     PISSN: 09581669     EISSN: 18790429     Source Type: Journal    
DOI: 10.1016/j.copbio.2015.08.017     Document Type: Review

References (63)

1. Hernandez R. Modular Manufacturing Platforms for Biologics. 2015 April 30 2015, Available from: http://www.biopharminternational.com/modular-manufacturing-platforms-biologics.
2. Vallejos J.R., et al. Dissolved oxygen and pH profile evolution after cryovial thaw and repeated cell passaging in a T-75 flask. Biotechnol Bioeng 2010, 105:1040-1047.
3. Bentley W.E., Zargar A., Payne G.F. Plug and Play? Interconnected multifunctional chips for enhancing efficiency of biopharmaceutical R&D. Pharmaceutical Bioprocessing 2013, 1:225-228.
4. Kim E., et al. Chitosan to connect biology to electronics: Fabricating the bio-device interface and communicating across this interface. Polymers 2014, 7:1-46.
5. Liu Y., et al. Biofabrication to build the biology-device interface. Biofabrication 2010, 2:022002.
6. Sackmann E.K., Fulton A.L., Beebe D.J. The present and future role of microfluidics in biomedical research. Nature 2014, 507:181-189.
7. Way J.C., et al. Integrating biological redesign: where synthetic biology came from and where it needs to go. Cell 2014, 157:151-161.
8. Toettcher J.E., et al. The promise of optogenetics in cell biology: interrogating molecular circuits in space and time. Nat Meth 2011, 8:35-38.
9. Levskaya A., et al. Synthetic biology: engineering Escherichia coli to see light. Nature 2005, 438:441-442.
10. Tabor J.J., et al. A synthetic genetic edge detection program. Cell 2009, 137:1272-1281.
11. Olson E.J., et al. Characterizing bacterial gene circuit dynamics with optically programmed gene expression signals. Nat Meth 2014, 11:449-455.
12. Schmidl S.R., et al. Refactoring and optimization of light-switchable Escherichia coli two-component systems. ACS Synth Biol 2014, 3:820-831.
13. Barakat M., Ortet P., Whitworth D.E. P2CS: a database of prokaryotic two-component systems. Nucl Acids Res 2011, 39(Suppl 1):D771-D776.
14. Betz J.F., et al. Optically clear alginate hydrogels for spatially controlled cell entrapment and culture at microfluidic electrode surfaces. Lab Chip 2013, 13:1854-1858.
15. Marchand N., Collins C.H. Peptide-based communication system enables Escherichia coli to Bacillus megaterium interspecies signaling. Biotechnol Bioeng 2013, 110:3003-3012.
16. Pereira C.S., Thompson J.A., Xavier K.B. AI-2-mediated signalling in bacteria. FEMS Microbiol Rev 2013, 37:156-181.
17. Quan D.N., Bentley W.E. Gene network homology in prokaryotes using a similarity search approach: queries of quorum sensing signal transduction. PLoS Comput Biol 2012, 8:pe1002637.
18. Fernandes R., et al. Engineered biological nanofactories trigger quorum sensing response in targeted bacteria. Nat Nanotechnol 2010, 5:213-217.
19. Fernandes R., et al. Biological nanofactories facilitate spatially selective capture and manipulation of quorum sensing bacteria in a bioMEMS device. Lab Chip 2010, 10:1128-1134.
20. Zargar A., et al. Rational design of 'controller cells' to manipulate protein and phenotype expression. Metabolic engineering 2015, 30:61-68.
21. Gordonov T., et al. Electronic modulation of biochemical signal generation. Nat Nano 2014, 9.
22. Servinsky M.D., et al. Directed assembly of a bacterial quorum. ISME J 2015.
23. Carter K.K., Valdes J.J., Bentley W.E. Pathway engineering via quorum sensing and sRNA riboregulators-interconnected networks and controllers. Metab Eng 2012, 14:281-288.
24. Callura J.M., et al. Tracking, tuning, and terminating microbial physiology using synthetic riboregulators. Proc Natl Acad Sci 2010, 107:15898-15903.
25. Callura J.M., Cantor C.R., Collins J.J. Genetic switchboard for synthetic biology applications. Proc Natl Acad Sci 2012, 109:5850-5855.
26. Green A.A., et al. Toehold switches: de-novo-designed regulators of gene expression. Cell 2014, 159:925-939.
27. Chappell J., Takahashi M.K., Lucks J.B. Creating small transcription activating RNAs. Nat Chem Biol 2015, 11:214-220.
28. Meyer S., et al. Improving fold activation of small transcription activating RNAs (STARs) with rational RNA engineering strategies. Biotechnol Bioeng 2015.
29. Brockman I.M., Prather K.L. Dynamic metabolic engineering: new strategies for developing responsive cell factories. Biotechnol J 2015.
30. Jones J.A., Toparlak Ö.D., Koffas M.A. Metabolic pathway balancing and its role in the production of biofuels and chemicals. Curr Opin Biotechnol 2015, 33:52-59.
31. Venayak N., et al. Engineering metabolism through dynamic control. Curr Opin Biotechnol 2015, 34:142-152.
32. Farmer W.R., Liao J.C. Improving lycopene production in Escherichia coli by engineering metabolic control. Nat Biotechnol 2000, 18:533-537.
33. Soma Y., et al. Metabolic flux redirection from a central metabolic pathway toward a synthetic pathway using a metabolic toggle switch. Metabolic Eng 2014, 23:175-184.
34. Solomon K.V., Sanders T.M., Prather K.L. A dynamic metabolite valve for the control of central carbon metabolism. Metabolic Eng 2012, 14:661-671.
35. Tsao C.-Y., et al. Autonomous induction of recombinant proteins by minimally rewiring native quorum sensing regulon of E. coli. Metabolic Eng 2010, 12:291-297.
36. DeLisa M.P., Valdes J.J., Bentley W.E. Quorum signaling via AI-2 communicates the 'metabolic burden' associated with heterologous protein production. Biotechnol Bioeng 2001, 75.
37. Liu H., Lu T. Autonomous production of 1,4-butanediol via a de novo biosynthesis pathway in engineered Escherichia coli. Metabolic Eng 2015, 29:135-141.
38. Soma Y., Hanai T. Self-induced metabolic state switching by a tunable cell density sensor for microbial isopropanol production. Metabolic Eng 2015, 30:7-15.
39. Dunlop M., Keasling J., Mukhopadhyay A. A model for improving microbial biofuel production using a synthetic feedback loop. Syst Synth Biol 2010, 4:95-104.
40. Dahl R.H., et al. Engineering dynamic pathway regulation using stress-response promoters. Nat Biotechnol 2013, 31:1039-1046.
41. Xu P., et al. Improving fatty acids production by engineering dynamic pathway regulation and metabolic control. Proc Natl Acad Sci 2014, 111:11299-11304.
42. Cameron D.E., Collins J.J. Tunable protein degradation in bacteria. Nat Biotech 2014, 32:1276-1281.
43. Guntas G., et al. Directed evolution of protein switches and their application to the creation of ligand-binding proteins. Proc Natl Acad Sci U S A 2005, 102:11224-11229.
44. Stein V., Alexandrov K. Synthetic protein switches: design principles and applications. Trends Biotechnol 2015, 33:101-110.
45. Sharma S.S., Blattner F.R., Harcum S.W. Recombinant protein production in an Escherichia coli reduced genome strain. Metab Eng 2007, 9:133-141.
46. Posfai G., et al. Emergent properties of reduced-genome Escherichia coli. Science 2006, 312:1044-1046.
47. Bacchus W., Fussenegger M. Engineering of synthetic intercellular communication systems. Metabolic Eng 2013, 16:33-41.
48. Koseska A., et al. Timing cellular decision making under noise via cell-cell communication. PLoS One 2009, 4:pe4872.
49. Minty J.J., et al. Design and characterization of synthetic fungal-bacterial consortia for direct production of isobutanol from cellulosic biomass. Proc Natl Acad Sci 2013, 110:14592-14597.
50. Shong J., Jimenez Diaz M.R., Collins C.H. Towards synthetic microbial consortia for bioprocessing. Curr Opin Biotechnol 2012, 23:798-802.
51. Balagaddé F.K., et al. Long-term monitoring of bacteria undergoing programmed population control in a microchemostat. Science 2005, 309:137-140.
52. Basu S., et al. A synthetic multicellular system for programmed pattern formation. Nature 2005, 434:1130-1134.
53. Luo X., et al. Biofabrication of stratified biofilm mimics for observation and control of bacterial signaling. Biomaterials 2012, 33:5136-5143.
54. You L., et al. Programmed population control by cell-cell communication and regulated killing. Nature 2004, 428:868-871.
55. Markx G.H., Andrews J.S., Mason V.P. Towards microbial tissue engineering?. Trends Biotechnol 2004, 22:417-422.
56. Song H., et al. Synthetic microbial consortia: from systematic analysis to construction and applications. Chem Soc Rev 2014, 43:6954-6981.
57. Shin H.-D., et al. Escherichia coli binary culture engineered for direct fermentation of hemicellulose to a biofuel. Appl Environ Microbiol 2010, 76:8150-8159.
58. Hong S.H., et al. Synthetic quorum-sensing circuit to control consortial biofilm formation and dispersal in a microfluidic device. Nat Commun 2012, 3:613.
59. Betz J.F., et al. Optically clear alginate hydrogels for spatially controlled cell entrapment and culture at microfluidic electrode surfaces. Lab Chip 2013, 13:1854-1858.
60. Cheng Y., et al. Biocompatible multi-address 3D cell assembly in microfluidic devices using spatially programmable gel formation. Lab Chip 2011, 11:2316-2318.
61. Terrell J.L., et al. Integrated biofabrication for electro-addressed in-film bioprocessing. Biotechnol J 2012, 7:428-439.
62. Gray K.M., et al. Electrodeposition of a biopolymeric hydrogel: potential for one-step protein electroaddressing. Biomacromolecules 2012, 13:1181-1189.
63. Lentini R., et al. Integrating artificial with natural cells to translate chemical messages that direct E. coli behaviour. Nat Commun 2014, 5.