Composability of regulatory sequences controlling transcription and translation in Escherichia coli

Sriram Kosuri (1) , Daniel B. Goodman (1) , Guillaume Cambray (2, 3, 4) , Vivek K. Mutalik (1) , Yuan Gao (1) , Adam P. Arkin (1) , Drew Endy (1) , George M. Church (1)

1 Chercheur indépendant
2 BIOFAD - International Open Facility Advancing Biotechnology
3 Physical Biosciences Division [LBNL Berkeley]
4 Department of Bioengineering [Berkeley]

The inability to predict heterologous gene expression levels precisely hinders our ability to engineer biological systems. Using well-characterized regulatory elements offers a potential solution only if such elements behave predictably when combined. We synthesized 12,563 combinations of common promoters and ribosome binding sites and simultaneously measured DNA, RNA, and protein levels from the entire library. Using a simple model, we found that RNA and protein expression were within twofold of expected levels 80% and 64% of the time, respectively. The large dataset allowed quantitation of global effects, such as translation rate on mRNA stability and mRNA secondary structure on translation rate. However, the worst 5% of constructs deviated from prediction by 13-fold on average, which could hinder large-scale genetic engineering projects. The ease and scale this of approach indicates that rather than relying on prediction or standardization, we can screen synthetic libraries for desired behavior.

Mots clés: next-generation sequencing; synthetic biology; systems biology

Mots clés: genetique des populations; diversité des populations

Domaines: Biodiversité et Ecologie

Sriram Kosuri, Daniel B. Goodman, Guillaume Cambray, Vivek K. Mutalik, Yuan Gao, et al.. Composability of regulatory sequences controlling transcription and translation in Escherichia coli. Proceedings of the National Academy of Sciences of the United States of America, 2013, 110 (34), pp.14024-14029. ⟨10.1073/pnas.1301301110⟩. ⟨hal-01422313⟩