Synthetic biology expands chemical control of microorganisms

Current Opinion in Chemical Biology

Volumn 28, Issue , 2015, Pages 20-28

  Ford, Tyler J ^a   Silver, Pamela A ^a  

^a HARVARD MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EFFECTOR CELL; METABOLISM; MICROORGANISM; NONHUMAN; PROPHYLAXIS; PSEUDOMONAS AERUGINOSA; QUORUM SENSING; REVIEW; SENSOR; SYNTHETIC BIOLOGY; WHOLE CELL; ANIMAL; BACTERIAL INFECTIONS; BACTERIUM; BIOTECHNOLOGY; GENETIC ENGINEERING; GENETIC PROCEDURES; GENETICS; HUMAN; PROCEDURES;

ANIMALS; BACTERIA; BACTERIAL INFECTIONS; BIOSENSING TECHNIQUES; BIOTECHNOLOGY; GENETIC ENGINEERING; HUMANS; METABOLIC NETWORKS AND PATHWAYS; QUORUM SENSING; SYNTHETIC BIOLOGY;

EID: 84930673058     PISSN: 13675931     EISSN: 18790402     Source Type: Journal    
DOI: 10.1016/j.cbpa.2015.05.012     Document Type: Review

References (75)

1. Callura J.M., Cantor C.R., Collins J.J. Genetic switchboard for synthetic biology applications. Proc Natl Acad Sci U S A 2012, 109:5850-5855.
2. Daniel R., Rubens J.R., Sarpeshkar R., Lu T.K. Synthetic analog computation in living cells. Nature 2013, 497:619.
3. Stanton B.C., Nielsen A.A.K., Tamsir A., Clancy K., Peterson T., Voigt C.A. Genomic mining of prokaryotic repressors for orthogonal logic gates. Nat Chem Biol 2014, 10:99-105.
4. Wang B.J., Barahona M., Buck M. A modular cell-based biosensor using engineered genetic logic circuits to detect and integrate multiple environmental signals. Biosensors Bioelectron 2013, 40:368-376.
5. Hwang I.Y., Tan M.H., Koh E., Ho C.L., Poh C.L., Chang M.W. Reprogramming microbes to be pathogen-seeking killers. ACS Synth Biol 2014, 3:228-237.
6. Saeidi N., Wong C.K., Lo T.M., Nguyen H.X., Ling H., Leong S.S.J., Poh C.L., Chang M.W. Engineering microbes to sense and eradicate Pseudomonas aeruginosa, a human pathogen. Mol Syst Biol 2011, 7.
7. Dunstan S.J., Simmons C.P., Strugnell R.A. Use of in vivo-regulated promoters to deliver antigens from attenuated Salmonella enterica var. typhimurium. Infection Immun 1999, 67:5133-5141.
8. Ganai S., Arenas R.B., Forbes N.S. Tumour-targeted delivery of TRAIL using Salmonella typhimurium enhances breast cancer survival in mice. Br J Cancer 2009, 101:1683-1691.
9. Ryan R.M., Green J., Williams P.J., Tazzyman S., Hunt S., Harmey J.H., Kehoe S.C., Lewis C.E. Bacterial delivery of a novel cytolysin to hypoxic areas of solid tumors. Gene Therapy 2009, 16:329-339.
10. Zhang L., Gao L.F., Zhao L.J., Guo B.F., Ji K., Tian Y., Wang J.G., Yu H., Hu J.D., Kalvakolanu D.V., et al. Intratumoral delivery and suppression of prostate tumor growth by attenuated Salmonella enterica serovar typhimurium carrying plasmid-based small interfering RNAs. Cancer Res 2007, 67:5859-5864.
11. Gupta S., Bram E.E., Weiss R. Genetically programmable pathogen sense and destroy. ACS Synth Biol 2013, 2:715-723.
12. Zhang F.Z., Carothers J.M., Keasling J.D. Design of a dynamic sensor-regulator system for production of chemicals and fuels derived from fatty acids. Nat Biotechnol 2012, 30:354-U166.
13. Scalcinati G., Knuf C., Partow S., Chen Y., Maury J., Schalk M., Daviet L., Nielsen J., Siewers V. Dynamic control of gene expression in Saccharomyces cerevisiae engineered for the production of plant sesquitepene alpha-santalene in a fed-batch mode. Metab Eng 2012, 14:91-103.
14. Farmer W.R., Liao J.C. Improving lycopene production in Escherichia coli by engineering metabolic control. Nat Biotechnol 2000, 18:533-537.
15. Xu P., Li L.Y., Zhang F.M., Stephanopoulos G., Koffas M. Improving fatty acids production by engineering dynamic pathway regulation and metabolic control. Proc Natl Acad Sci U S A 2014, 111:11299-11304.
16. Dahl R.H., Zhang F., Alonso-Gutierrez J., Baidoo E., Batth T.S., Redding-Johanson A.M., Petzold C.J., Mukhopadhyay A., Lee T.S., Adams P.D., et al. Engineering dynamic pathway regulation using stress-response promoters. Nat Biotechnol 2013, 31. 1039-+.
17. Liu D., Xiao Y., Evans B.S., Zhang F. Negative feedback regulation of fatty acid production based on a malonyl-CoA sensor-actuator. ACS Synth Biol 2015, 4:132-140.
18. Anderson J.C., Clarke E.J., Arkin A.P., Voigt C.A. Environmentally controlled invasion of cancer cells by engineered bacteria. J Mol Biol 2006, 355:619-627.
19. Bacchus W., Fussenegger M. Engineering of synthetic intercellular communication systems. Metab Eng 2013, 16:33-41.
20. Chen A.Y., Deng Z.T., Billings A.N., Seker U.O.S., Lu M.Y., Citorik R.J., Zakeri B., Lu T.K. Synthesis and patterning of tunable multiscale materials with engineered cells. Nat Mater 2014, 13:515-523.
21. Hong S.H., Hegde M., Kim J., Wang X.X., Jayaraman A., Wood T.K. Synthetic quorum-sensing circuit to control consortial biofilm formation and dispersal in a microfluidic device. Nat Commun 2012, 3.
22. Nocadello S., Swennen E.F. The new pLAI (lux regulon based auto-inducible) expression system for recombinant protein production in Escherichia coli. Microb Cell Factories 2012, 11.
23. Tsao C.Y., Hooshangi S., Wu H.C., Valdes J.J., Bentley W.E. Autonomous induction of recombinant proteins by minimally rewiring native quorum sensing regulon of E. coli. Metab Eng 2010, 12:291-297.
24. You L.C., Cox R.S., Weiss R., Arnold F.H. Programmed population control by cell-cell communication and regulated killing. Nature 2004, 428:868-871.
25. Zhou K., Qiao K., Edgar S., Stephanopoulos G. Distributing a metabolic pathway among a microbial consortium enhances production of natural products. Nat Biotechnol 2015, 33:377-383.
26. Bayer T.S., Widmaier D.M., Temme K., Mirsky E.A., Santi D.V., Voigt C.A. Synthesis of methyl halides from biomass using engineered microbes. J Am Chem Soc 2009, 131:6508-6515.
27. Weber W., Baba M., Fussenegger M. Synthetic ecosystems based on airborne inter- and intrakingdom communication. Proc Natl Acad Sci U S A 2007, 104:10435-10440.
28. Yang J., Seo S.W., Jang S., Shin S.I., Lim C.H., Roh T.Y., Jung G.Y. Synthetic RNA devices to expedite the evolution of metabolite-producing microbes. Nat Commun 2013, 4.
29. Buskirk A.R., Landrigan A., Liu D.R. Engineering a ligand-dependent RNA transcriptional activator. Chem Biol 2004, 11:1157-1163.
30. Jagmann N., Philipp B. Reprint of design of synthetic microbial communities for biotechnological production processes. J Biotechnol 2014, 192:293-301.
31. Ceres P., Trausch J.J., Batey R.T. Engineering modular 'ON' RNA switches using biological components. Nucleic Acids Res 2013, 41:10449-10461.
32. Muranaka N., Sharma V., Nomura Y., Yokobayashi Y. An efficient platform for genetic selection and screening of gene switches in Escherichia coli. Nucleic Acids Res 2009, 37:e39.
33. Desai S.K., Gallivan J.P. Genetic screens and selections for small molecules based on a synthetic riboswitch that activates protein translation. J Am Chem Soc 2004, 126:13247-13254.
34. Green A.A., Silver P.A., Collins J.J., Yin P. Toehold switches: de-novo-designed regulators of gene expression. Cell 2014, 159:925-939.
35. Trang P.T., Berg M., Viet P.H., Van Mui N., Van Der Meer J.R. Bacterial bioassay for rapid and accurate analysis of arsenic in highly variable groundwater samples. Environ Sc Technol 2005, 39:7625-7630.
36. Tang S.Y., Cirino P.C. Design and application of a mevalonate-responsive regulatory protein. Angew Chem 2011, 50:1084-1086.
37. Moser F., Horwitz A., Chen J., Lim W., Voigt C.A. Genetic sensor for strong methylating compounds. ACS Synth Biol 2013, 2:614-624.
38. Bereza-Malcom L.T., Mann G., Franks A.E. Environmental sensing of heavy metals through whole cell microbial biosensors: a synthetic biology approach. ACS Synth Biol 2014.
39. Gu M.B., Mitchell R.J., Kim B.C. Whole-cell-based biosensors for environmental biomonitoring and application. Advan Biochem Eng/Biotechnol 2004, 87:269-305.
40. Duan F., March J.C. Engineered bacterial communication prevents Vibrio cholerae virulence in an infant mouse model. Proc Natl Acad Sci U S A 2010, 107:11260-11264.
41. Binder S., Schendzielorz G., Stabler N., Krumbach K., Hoffmann K., Bott M., Eggeling L. A high-throughput approach to identify genomic variants of bacterial metabolite producers at the single-cell level. Genome Biol 2012, 13.
42. Behzadian F., Barjeste H., Hosseinkhani S., Zarei A.R. Construction and characterization of Escherichia coli whole-cell biosensors for toluene and related compounds. Curr Microbiol 2011, 62:690-696.
43. Flentie K., Kocher B., Gammon S.T., Novack D.V., McKinney J.S., Piwnica-Worms D. A bioluminescent transposon reporter-trap identifies tumor-specific microenvironment-induced promoters in Salmonella for conditional bacterial-based tumor therapy. Cancer Discov 2012, 2:624-637.
44. Looger L.L., Dwyer M.A., Smith J.J., Hellinga H.W. Computational design of receptor and sensor proteins with novel functions. Nature 2003, 423:185-190.
45. Tinberg C.E., Khare S.D., Dou J.Y., Doyle L., Nelson J.W., Schena A., Jankowski W., Kalodimos C.G., Johnsson K., Stoddard B.L., et al. Computational design of ligand-binding proteins with high affinity and selectivity. Nature 2013, 501:212.
46. Wittmann A., Suess B. Engineered riboswitches: expanding researchers' toolbox with synthetic RNA regulators. FEBS Lett 2012, 586:2076-2083.
47. Michener J.K., Thodey K., Liang J.C., Smolke C.D. Applications of genetically-encoded biosensors for the construction and control of biosynthetic pathways. Metab Eng 2012, 14:212-222.
48. Ellington A.D., Szostak J.W. In vitro selection of RNA molecules that bind specific ligands. Nature 1990, 818-822.
49. Tuerk C., Gold L. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 1990, 249:505-510.
50. Dietrich J.A., Shis D.L., Alikhani A., Keasling J.D. Transcription factor-based screens and synthetic selections for microbial small-molecule biosynthesis. ACS Synth Biol 2013, 2:47-58.
51. Tang S.Y., Qian S., Akinterinwa O., Frei C.S., Gredell J.A., Cirino P.C. 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.
52. Raman S., Rogers J.K., Taylor N.D., Church G.M. Evolution-guided optimization of biosynthetic pathways. Proc Natl Acad Sci U S A 2014, 111:17803-17808.
53. Wang H.H., Isaacs F.J., Carr P.A., Sun Z.Z., Xu G., Forest C.R., Church G.M. Programming cells by multiplex genome engineering and accelerated evolution. Nature 2009, 460:894-898.
54. Kotula J.W., Kerns S.J., Shaket L.A., Siraj L., Collins J.J., Way J.C., Silver P.A. Programmable bacteria detect and record an environmental signal in the mammalian gut. Proc Natl Acad Sci U S A 2014, 111:4838-4843.
55. Forbes N.S. Engineering the perfect (bacterial) cancer therapy. Nat Rev Cancer 2010, 10:785-794.
56. Thamm D.H., Kurzman I.D., King I., Li Z., Sznol M., Dubielzig R.R., Vail D.M., MacEwen E.G. Systemic administration of an attenuated, tumor-targeting Salmonella typhimurium to dogs with spontaneous neoplasia: phase I evaluation. Clin Cancer Res 2005, 11:4827-4834.
57. Toso J.F., Gill V.J., Hwu P., Marincola F.M., Restifo N.P., Schwartzentruber D.J., Sherry R.M., Topalian S.L., Yang J.C., Stock F. Phase I study of the intravenous administration of attenuated Salmonella typhimurium to patients with metastatic melanoma. J Clin Oncol 2002, 20:142-152.
58. Nemunaitis J., Cunningham C., Senzer N., Kuhn J., Cramm J., Litz C., Cavagnolo R., Cahill A., Clairmont C., Sznol M. Pilot trial of genetically modified, attenuated Salmonella expressing the E. coli cytosine deaminase gene in refractory cancer patients. Cancer Gene Therapy 2003, 10:737-744.
59. Roberts N.J., Zhang L., Janku F., Collins A., Bai R.Y., Staedtke V., Rusk A.W., Tung D., Miller M., Roix J., et al. Intratumoral injection of Clostridium novyi-NT spores induces antitumor responses. Sci Transl Med 2014, 6:249ra111.
60. Massa P.E., Paniccia A., Monegal A., de Marco A., Rescigno M. Salmonella engineered to express CD20-targeting antibodies and a drug-converting enzyme can eradicate human lymphomas. Blood 2013, 122:705-714.
61. Xiang S., Fruehauf J., Li C.J. Short hairpin RNA-expressing bacteria elicit RNA interference in mammals. Nat Biotechnol 2006, 24:697-702.
62. Li Z., Yin P.H., Yang S.S., Li Q.Y., Chang T., Fang L., Shi L.X., Fang G.E. Recombinant attenuated Salmonella typhimurium carrying a plasmid co-expressing ENDO-VEGI151 and survivin siRNA inhibits the growth of breast cancer in vivo. Mol Med Rep 2013, 7:1215-1222.
63. Torella J.P., Ford T.J., Kim S.N., Chen A.M., Way J.C., Silver P.A. Tailored fatty acid synthesis via dynamic control of fatty acid elongation. Proc Natl Acad Sci U S A 2013, 110:11290-11295.
64. Waters C.M., Bassler B.L. Quorum sensing: cell-to-cell communication in bacteria. Annu Rev Cell Dev Biol 2005, 21:319-346.
65. Kobayashi H., Kaern M., Araki M., Chung K., Gardner T.S., Cantor C.R., Collins J.J. Programmable cells: interfacing natural and engineered gene networks. Proc Natl Acad Sci U S A 2004, 101:8414-8419.
66. Adams B.L., Carter K.K., Guo M., Wu H.C., Tsao C.Y., Sintim H.O., Valdes J.J., Bentley W.E. Evolved Quorum sensing regulator, LsrR, for altered switching functions. ACS Synth Biol 2014, 3:210-219.
67. Balagadde F.K., Song H., Ozaki J., Collins C.H., Barnet M., Arnold F.H., Quake S.R., You L.C. A synthetic Escherichia coli predator-prey ecosystem. Mol Syst Biol 2008, 4.
68. Shong J., Collins C.H. Quorum sensing-modulated AND-gate promoters control gene expression in response to a combination of endogenous and exogenous signals. ACS Synth Biol 2014, 3:238-246.
69. Wu H.C., Tsao C.Y., Quan D.N., Cheng Y., Servinsky M.D., Carter K.K., Jee K.J., Terrell J.L., Zargar A., Rubloff G.W., et al. Autonomous bacterial localization and gene expression based on nearby cell receptor density. Mol Syst Biol 2013, 9:636.
70. Minty J.J., Singer M.E., Scholz S.A., Bae C.H., Ahn J.H., Foster C.E., Liao J.C., Lin X.N. Design and characterization of synthetic fungal-bacterial consortia for direct production of isobutanol from cellulosic biomass. Proc Natl Acad Sci U S A 2013, 110:14592-14597.
71. Ajikumar P.K., Xiao W.H., Tyo K.E., Wang Y., Simeon F., Leonard E., Mucha O., Phon T.H., Pfeifer B., Stephanopoulos G. Isoprenoid pathway optimization for Taxol precursor overproduction in Escherichia coli. Science 2010, 330:70-74.
72. Wintermute E.H., Silver P.A. Emergent cooperation in microbial metabolism. Mol Syst Biol 2010, 6.
73. Mee M.T., Collins J.J., Church G.M., Wang H.H. Syntrophic exchange in synthetic microbial communities. Proc Natl Acad Sci U S A 2014, 111:E2149-E2156.
74. Silva-Rocha R., de Lorenzo V. Engineering multicellular logic in bacteria with metabolic wires. ACS Synth Biol 2014, 3:204-209.
75. Harcombe W. Novel cooperation experimentally evolved between species. Evolution 2010, 64:2166-2172.