Multifactorial determinants of protein expression in prokaryotic open reading frames.
Journal Article (Journal Article)
A quantitative description of the relationship between protein expression levels and open reading frame (ORF) nucleotide sequences is important for understanding natural systems, designing synthetic systems, and optimizing heterologous expression. Codon identity, mRNA secondary structure, and nucleotide composition within ORFs markedly influence expression levels. Bioinformatic analysis of ORF sequences in 816 bacterial genomes revealed that these features show distinct regional trends. To investigate their effects on protein expression, we designed 285 synthetic genes and determined corresponding expression levels in vitro using Escherichia coli extracts. We developed a mathematical function, parameterized using this synthetic gene data set, which enables computation of protein expression levels from ORF nucleotide sequences. In addition to its practical application in the design of heterologous expression systems, this equation provides mechanistic insight into the factors that control translation efficiency. We found that expression is strongly dependent on the presence of high AU content and low secondary structure in the ORF 5' region. Choice of high-frequency codons contributes to a lesser extent. The 3' terminal AU content makes modest, but detectable contributions. We present a model for the effect of these factors on the three phases of ribosomal function: initiation, elongation, and termination.
Full Text
Duke Authors
Cited Authors
- Allert, M; Cox, JC; Hellinga, HW
Published Date
- October 8, 2010
Published In
Volume / Issue
- 402 / 5
Start / End Page
- 905 - 918
PubMed ID
- 20727358
Pubmed Central ID
- PMC2963087
Electronic International Standard Serial Number (EISSN)
- 1089-8638
Digital Object Identifier (DOI)
- 10.1016/j.jmb.2010.08.010
Language
- eng
Conference Location
- Netherlands