A synthetic three-color scaffold for monitoring genetic regulation and noise

被引：54

作者：

Cox III R.S. ^{[1
,2
,3
]}

Dunlop M.J. ^{[2
,4
]}

Elowitz M.B. ^{[1
,2
,5
]}

机构：

[1] Division of Biology, California Institute of Technology, Pasadena, CA

[2] Department of Engineering and Applied Science, California Institute of Technology, Pasadena, CA

[3] RIKEN Systems and Structural Biology Center, Yokohama

[4] Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA

[5] Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125, 1200 E. California Blvd.

来源：

Journal of Biological Engineering | / 4卷 / 1期

基金：

美国国家科学基金会; 美国国家卫生研究院;

关键词：

Cross Correlation Function; Fluorescent Reporter; Synthetic Network; Regulatory Connection; Unique Restriction Site;

D O I：

10.1186/1754-1611-4-10

中图分类号：

学科分类号：

摘要：

Background: Current methods for analyzing the dynamics of natural regulatory networks, and quantifying synthetic circuit function, are limited by the lack of well-characterized genetic measurement tools. Fluorescent reporters have been used to measure dynamic gene expression, but recent attempts to monitor multiple genes simultaneously in single cells have not focused on independent, isolated measurements. Multiple reporters can be used to observe interactions between natural genes, or to facilitate the 'debugging' of biologically engineered genetic networks. Using three distinguishable reporter genes in a single cell can reveal information not obtainable from only one or two reporters. One application of multiple reporters is the use of genetic noise to reveal regulatory connections between genes. Experiments in both natural and synthetic systems would benefit from a well-characterized platform for expressing multiple reporter genes and synthetic network components.Results: We describe such a plasmid-based platform for the design and optimization of synthetic gene networks, and for analysis of endogenous gene networks. This network scaffold consists of three distinguishable fluorescent reporter genes controlled by inducible promoters, with conveniently placed restriction sites to make modifications straightforward. We quantitatively characterize the scaffold in Escherichia coli with single-cell fluorescence imaging and time-lapse microscopy. The three spectrally distinct reporters allow independent monitoring of genetic regulation and analysis of genetic noise. As a novel application of this tool we show that the presence of genetic noise can reveal transcriptional co-regulation due to a hidden factor, and can distinguish constitutive from regulated gene expression.Conclusion: We have constructed a general chassis where three promoters from natural genes or components of synthetic networks can be easily inserted and independently monitored on a single construct using optimized fluorescent protein reporters. We have quantitatively characterized the baseline behavior of the chassis so that it can be used to measure dynamic gene regulation and noise. Overall, the system will be useful both for analyzing natural genetic networks and assembling synthetic ones. © 2010 Cox et al; licensee BioMed Central Ltd.

引用

共 56 条

[1]

Endy D., Foundations for engineering biology, Nature, 438, 7067, pp. 449-453, (2005)

[2]

Shetty R.P., Endy D., Knight T.F., Engineering BioBrick vectors from BioBrick parts, J Biol Eng, 2, (2008)

[3]

Sprinzak D., Elowitz M.B., Reconstruction of genetic circuits, Nature, 438, 7067, pp. 443-448, (2005)

[4]

Mukherji S., van Oudenaarden A., Synthetic biology: understanding biological design from synthetic circuits, Nat Rev Genet, 10, 12, pp. 859-871, (2009)

[5]

Basu S., Gerchman Y., Collins C.H., Arnold F.H., Weiss R., A synthetic multicellular system for programmed pattern formation, Nature, 434, 7037, pp. 1130-1134, (2005)

[6]

Becskei A., Serrano L., Engineering stability in gene networks by autoregulation, Nature, 405, 6786, pp. 590-593, (2000)

[7]

Ellis T., Wang X., Collins J., Diversity-based, model-guided construction of synthetic gene networks with predicted functions, Nature biotechnology, 27, 5, pp. 465-471, (2009)

[8]

Elowitz M.B., Leibler S., A synthetic oscillatory network of transcriptional regulators, Nature, 403, 6767, pp. 335-338, (2000)

[9]

Gardner T.S., Cantor C.R., Collins J.J., Construction of a genetic toggle switch in Escherichia coli, Nature, 403, 6767, pp. 339-342, (2000)

[10]

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, Proceedings of the National Academy of Sciences of the United States of America, 101, 22, pp. 8414-8419, (2004)

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