Tunable Promoters in Synthetic and Systems Biology
Synthetic and systems biologists need standardized, modular and orthogonal tools yielding predictable functions in vivo. In systems biology such tools are needed to quantitatively analyze the behavior of biological systems while the efficient engineering
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Tunable Promoters in Synthetic and Systems Biology Tore Dehli, Christian Solem, and Peter Ruhdal Jensen
Abstract Synthetic and systems biologists need standardized, modular and orthogonal tools yielding predictable functions in vivo. In systems biology such tools are needed to quantitatively analyze the behavior of biological systems while the efficient engineering of artificial gene networks is central in synthetic biology. A number of tools exist to manipulate the steps in between gene sequence and functional protein in living cells, but out of these the most straight-forward approach is to alter the gene expression level by manipulating the promoter sequence. Some of the promoter tuning tools available for accomplishing such altered gene expression levels are discussed here along with examples of their use, and ideas for new tools are described. The road ahead looks very promising for synthetic and systems biologists as tools to achieve just about anything in terms of tuning and timing multiple gene expression levels using libraries of synthetic promoters now exist. Keywords Metabolic engineering • Standardization, orthogonality and modularity • Synthetic and systems biology • Synthetic gene networks • Synthetic promoter libraries
Abbreviations ATc DXP EGFP
anhydrotetracycline 1-deoxy-D-xylulose-5-phosphate enhanced green fluorescent protein
T. Dehli • C. Solem • P.R. Jensen (*) Center for Systems Microbiology, Department of Systems Biology, Technical University of Denmark, Matematiktorvet 301/242, 2800 Lyngby, Denmark e-mail: [email protected]; [email protected]; [email protected] X. Wang et al. (eds.), Reprogramming Microbial Metabolic Pathways, Subcellular Biochemistry 64, DOI 10.1007/978-94-007-5055-5_9, © Springer Science+Business Media Dordrecht 2012
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GFP GOI gTME GusA KO MAGE MCA ORF Pfk PLS-R PSP RBS SOE PCR SPL TAL TALOR yEGFP
9.1
green fluorescent protein gene of interest global transcription machinery engineering β-glucuronidase knock-out multiplex automated genome engineering metabolic control analysis open reading frame phosphofructokinase partial least squares regression promoter strength predictive ribosome binding site splicing by overlap extension PCR synthetic promoter library transcription activator-like transcription activator-like orthogonal repressor yeast enhanced green fluorescent protein
Introduction
Synthetic biology and systems biology are related but distinct disciplines. While both use modeling and simulation as core tools, synthetic biology focuses on the rational engineering of biological systems to display functions that do not exist in nature whereas systems biology aims to quantitatively understand the behavior of biological systems. Tools to modulate gene expression are central in both disciplines, a fact that has been and is still overlooked in many studies. Changing gene expression in small steps is essential for metabolic control analysis (MCA) in systems biology (Jensen and Hammer 1998a; Koebmann et al. 2005; Solem and Jensen 2002) and in syntheti
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