Design and implementation of a biomolecular concentration tracker

ACS Synthetic Biology

Volumn 4, Issue 2, 2015, Pages 150-161

  Hsiao, Victoria ^a   De Los Santos, Emmanuel L C ^a   Whitaker, Weston R ^b   Dueber, John E ^c   Murray, Richard M ^a,d  

^a California Institute of Technology   (United States)

^b STANFORD UNIVERSITY   (United States)

^c University of California at Berkeley   (United States)

^d CALIFORNIA INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

feedback circuits; live cell tracking; negative feedback; synthetic protein scaffolds; two component systems

Indexed keywords

SCAFFOLD PROTEIN; ESCHERICHIA COLI PROTEIN; LEUCINE ZIPPER PROTEIN; PHOSPHATASE; PROTEIN KINASE; PROTEIN-HISTIDINE KINASE;

ARTICLE; CELL CYCLE; CELL TRACKING; ESCHERICHIA COLI; MOLECULAR DYNAMICS; NEGATIVE FEEDBACK; NONHUMAN; PRIORITY JOURNAL; STEADY STATE; SYNTHETIC BIOLOGY; CHEMICAL STRUCTURE; CHEMISTRY; FEEDBACK SYSTEM; KINETICS; METABOLISM;

ESCHERICHIA COLI;

ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; FEEDBACK, PHYSIOLOGICAL; KINETICS; LEUCINE ZIPPERS; MODELS, MOLECULAR; PHOSPHORIC MONOESTER HYDROLASES; PROTEIN KINASES;

EID: 84924253478     PISSN: None     EISSN: 21615063     Source Type: Journal    
DOI: 10.1021/sb500024b     Document Type: Article

References (35)

1. Klumpp, S., Zhang, Z., and Hwa, T. (2009) Growth Rate-Dependent Global Effects on Gene Expression in Bacteria Cell 139, 1366-1375
2. Cardinale, S., Joachimiak, M. P., and Arkin, A. P. (2013) Effects of Genetic Variation on the E. coli Host-Circuit Interface Cell Rep. 4, 231-237
3. Rosenfeld, N., Elowitz, M. B., and Alon, U. (2002) Negative Autoregulation Speeds the Response Times of Transcription Networks J. Mol. Biol. 323, 785-793
4. Becskei, A. and Serrano, L. (2000) Engineering stability in gene networks by autoregulation Nature 405, 590-593
5. Ferrell, J. E., Jr. (2013) Feedback loops and reciprocal regulation: recurring motifs in the systems biology of the cell cycle Curr. Opin. Cell Biol. 1-11
6. Franco, E., Forsberg, P.-O., and Murray, R. M. (2008) Design, modeling and synthesis of an in vitro transcription rate regulatory circuit Proc. Am. Control Conf. 2786-2791
7. Stapleton, J. A., Endo, K., Fujita, Y., Hayashi, K., Takinoue, M., Saito, H., and Inoue, T. (2012) Feedback Control of Protein Expression in Mammalian Cells by Tunable Synthetic Translational Inhibition ACS Synth. Biol. 1, 83-88
8. Dublanche, Y., Michalodimitrakis, K., Kümmerer, N., Foglierini, M., and Serrano, L. (2006) Noise in transcription negative feedback loops: simulation and experimental analysis Mol. Syst. Biol. 2 41
9. Milias-Argeitis, A., Summers, S., Stewart-Ornstein, J., Zuleta, I., Pincus, D., Lygeros, J., El Samad, H., and Khammash, M. (2011) In silico feedback for in vivo regulation of a gene expression circuit Nat. Biotechnol. 29, 1114-1116
10. Whitaker, W. R., Davis, S. A., Arkin, A. P., and Dueber, J. E. (2012) Engineering robust control of two-component system phosphotransfer using modular scaffolds Proc. Natl. Acad. Sci. U.S.A. 18090-18095
11. Skerker, J. M., Prasol, M. S., Perchuk, B. S., Biondi, E. G., and Laub, M. T. (2005) Two-Component Signal Transduction Pathways Regulating Growth and Cell Cycle Progression in a Bacterium: A System-Level Analysis PLoS Biol. 3 e334
12. Acharya, A., Ruvinov, S. B., Gal, J., Moll, J. R., and Vinson, C. (2002) A Heterodimerizing Leucine Zipper Coiled Coil System for Examining the Specificity of aPosition Interactions: Amino Acids I, V, L, N, A, and K Biochemistry 41, 14122-14131
13. Whitaker, W. R. and Dueber, J. E. (2011) in Synthetic Biology, Part A (Voigt, C., Ed.), Vol. 497, pp 447-468, Methods in Enzymology; Academic Press, San Diego, CA.
14. Whitaker, W. R. (2012) Engineering Modular Post-Translational Control Strategies in Prokaryotes. PhD Thesis, UC Berkeley, USA, 1-151.
15. Zhu, Y. and Inouye, M. (2002) The role of the G2 box, a conserved motif in the histidine kinase superfamily, in modulating the function of EnvZ Mol. Microbiol. 45, 653-663
16. Andersen, J. B. and Molin, S. (1998) New Unstable Variants of Green Fluorescent Protein for Studies of Transient Gene Expression in Bacteria Appl. Environ. Microbiol. 64, 2240-2246
17. Nagai, T., Ibata, K., Park, E. S., Kubota, M., Mikoshiba, K., and Miyawaki, A. (2002) A variant of yellow fluorescent protein with fast and efficient maturation for cell-biological applications Nat. Biotechnol. 20, 87-90
18. Shaner, N. C., Campbell, R. E., Steinbach, P. A., Giepmans, B. N. G., Palmer, A. E., and Tsien, R. Y. (2004) Improved monomeric red, orange and yellow fluorescent proteins derived from Discosoma sp. red fluorescent protein Nat. Biotechnol. 22, 1567-1572
19. de los Santos, E. L., Hsiao, V., and Murray, R. M. (2013) Design and implementation of a biomolecular circuit for tracking protein concentration Proc. Am. Control Conf. 1-5
20. Pazy, Y., Wollish, A. C., Thomas, S. A., Miller, P. J., Collins, E. J., Bourret, R. B., and Silversmith, R. E. (2009) Matching Biochemical Reaction Kinetics to the Timescales of Life: Structural Determinants That Influence the Autodephosphorylation Rate of Response Regulator Proteins J. Mol. Biol. 392, 1205-1220
21. Groban, E. S., Clarke, E. J., Salis, H. M., Miller, S. M., and Voigt, C. A. (2009) Kinetic Buffering of Cross Talk between Bacterial Two-Component Sensors J. Mol. Biol. 390, 380-393
22. Solomaha, E., Szeto, F. L., Yousef, M. A., and Palfrey, H. C. (2005) Kinetics of Src homology 3 domain association with the proline-rich domain of dynamins: specificity, occlusion, and the effects of phosphorylation J. Biol. Chem. 280, 23147-23156
23. Huang, C.-Y. F. and Ferrell, J. E., Jr. (1996) Ultrasensitivity in the mitogen-activated protein kinase cascade Proc. Natl. Acad. Sci. U. S. A. 93, 10078-10083
24. Posern, G., Zheng, J., Knudsen, B. S., Kardinal, C., Muller, K. B., Hanafusa, H., and Feller, S. M. (1998) Development of highly selective SH3 binding peptides for Crk and CRKL which disrupt Crk-complexes with DOCK180, SoS and C3G Oncogene 16, 1903-1912
25. Grunberg, R., Ferrar, T. S., van der Sloot, A. M., Constante, M., and Serrano, L. (2010) Building blocks for protein interaction devices Nucleic Acids Res. 38, 2645-2662
26. Good, M. C., Zalatan, J. G., and Lim, W. A. (2011) Scaffold Proteins: Hubs for Controlling the Flow of Cellular Information Science 332, 680-686
27. Munsky, B., Trinh, B., and Khammash, M. (2009) Listening to the noise: Random fluctuations reveal gene network parameters Mol. Syst. Biol. 5 318
28. Farrell, C. M., Grossman, A. D., and Sauer, R. T. (2005) Cytoplasmic degradation of ssrA-tagged proteins Mol. Microbiol. 57, 1750-1761
29. Park, S.-H., Zarrinpar, A., and Lim, W. A. (2003) Rewiring MAP Kinase Pathways Using Alternative Scaffold Assembly Mechanisms Science 299, 1061-1064
30. Bashor, C. J., Helman, N. C., Yan, S., and Lim, W. A. (2008) Using Engineered Scaffold Interactions to Reshape MAP Kinase Pathway Signaling Dynamics Science 319, 1539-1543
31. Dueber, J. E., Wu, G. C., Malmirchegini, G. R., Moon, T. S., Petzold, C. J., Ullal, A. V., Prather, K. L. J., and Keasling, J. D. (2009) Synthetic protein scaffolds provide modular control over metabolic flux Nat. Biotechnol. 27, 753-759
32. Moon, T. S., Dueber, J. E., Shiue, E., and Prather, K. L. J. (2010) Use of modular, synthetic scaffolds for improved production of glucaric acid in engineered E. coli Metab Eng. 12, 298-305
33. Bessho, Y. (2003) Oscillations, clocks and segmentation Curr. Opin. Genet. Dev. 13, 379-384
34. Imayoshi, I., Isomura, A., Harima, Y., Kawaguchi, K., Kori, H., Miyachi, H., Fujiwara, T., Ishidate, F., and Kageyama, R. (2013) Oscillatory control of factors determining multipotency and fate in mouse neural progenitors Science 342, 1203-1208
35. Cai, L., Dalal, C. K., and Elowitz, M. B. (2008) Frequency-modulated nuclear localization bursts coordinate gene regulation Nature 455, 485-490