U.S. Department of Energy Office of Biological and Environmental Research

BER Research Highlights

Novel Bioengineering Technique for Genome-Scale Tuning of Gene Expression
Published: August 07, 2013
Posted: September 12, 2013

Introduction of new genes encoding desired functional attributes has long been a central tool for metabolic engineering and synthetic biodesign of microorganisms. However, difficulties in accurately predicting the expression levels of these genes in their new hosts significantly slow the design cycle and hinder progress. This is particularly problematic in synthetic biology, where large genetic constructs containing multiple genes are often introduced. Now researchers present a novel technique to more accurately predict gene expression levels in engineered biosystems by combining recent advances in DNA synthesis with novel, multiplexed methods for measuring DNA, RNA, and protein levels simultaneously using next-generation sequencing. This new technique allowed the team to simultaneously measure transcription and translation rates of thousands of synthetic regulatory elements introduced into the model microbe Escherichia coli . The resulting dataset was then used to model gene and protein expression levels under various sets of regulatory elements and “compose” a designed regulatory strategy that enables accurate prediction of expression levels of introduced genetic elements. This new technique has the potential to allow much more sophisticated forward design of genetic engineering strategies to improve production of biofuels and other bioproducts.

Reference: Kosuri, S. D. B. Goodman, G. Cambray, V. K. Mutalik, Y. Gao, A. P. Arkin, D. Endy, and G. M. Church. 2013. “Composability of Regulatory Sequences Controlling Transcription and Translation in Escherichia coli ,” Proceedings of the National Academy of Sciences USA 110 , 14024–29. DOI: 10.1073/pnas.1301301110. (Reference link)

Contact: Joseph Graber, SC-23.2, (301) 903-1239
Topic Areas:

  • Research Area: Genomic Analysis and Systems Biology
  • Research Area: Microbes and Communities
  • Research Area: Sustainable Biofuels and Bioproducts
  • Research Area: Biosystems Design

Division: SC-23.2 Biological Systems Science Division, BER


BER supports basic research and scientific user facilities to advance DOE missions in energy and environment. More about BER

Recent Highlights

May 10, 2019
Quantifying Decision Uncertainty in Water Management via a Coupled Agent-Based Model
Considering risk perception can improve the representation of human decision-making processes in age [more...]

May 09, 2019
Projecting Global Urban Area Growth Through 2100 Based on Historical Time Series Data and Future Scenarios
Study provides country-specific urban area growth models and the first dataset on country-level urba [more...]

May 05, 2019
Calibrating Building Energy Demand Models to Refine Long-Term Energy Planning
A new, flexible calibration approach improved model accuracy in capturing year-to-year changes in bu [more...]

May 03, 2019
Calibration and Uncertainty Analysis of Demeter for Better Downscaling of Global Land Use and Land Cover Projections
Researchers improved the Demeter model’s performance by calibrating key parameters and establi [more...]

Apr 22, 2019
Representation of U.S. Warm Temperature Extremes in Global Climate Model Ensembles
Representation of warm temperature events varies considerably among global climate models, which has [more...]

List all highlights (possible long download time)