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Determination of the Optimal Chromosomal Location(s) for a DNA Element in Escherichia coli Using a Novel Transposon-mediated Approach
Published on: September 11, 2017
Translation initiation region sequence preferences in Escherichia coli
Vladimir Vimberg1, Age Tats, Maido Remm
1Institute of Technology, University of Tartu, Nooruse 1, Tartu 50411, Estonia. riboloom@hot.ee
BMC Molecular Biology
|November 2, 2007
Summary
The optimal Shine-Dalgarno (SD) sequence length for bacterial translation initiation is six nucleotides. AU-rich enhancers significantly boost translation efficiency, especially when combined with strong SD sequences.
Area of Science:
- Bacterial molecular biology
- Gene expression regulation
Background:
- The mRNA translation initiation region (TIR) includes the initiator codon, Shine-Dalgarno (SD) sequence, and translational enhancers.
- A/U-rich sequences are a common class of translational enhancers.
Purpose of the Study:
- To investigate the impact of SD sequence length and enhancer presence on translation initiation efficiency.
- To understand the interplay between SD sequences, enhancers, and bacterial growth conditions.
Main Methods:
- Experimental testing of varying SD sequence lengths and enhancer presence.
- In silico analysis of TIRs in E. coli mRNAs.
Main Results:
- A six-nucleotide SD sequence (AGGAGG) is most efficient at 37°C.
- A/U-rich enhancers significantly stimulate translation, particularly during the bacterial exponential growth phase.
- SD sequences and enhancers exhibit cooperative effects, with strong SDs showing greater enhancement.
- Bacterial growth temperature influences TIR selection, favoring shorter SD sequences at lower temperatures.
- No significant correlation was found between SD sequence base-pairing potential and codon adaptation index in E. coli.
Conclusions:
- In E. coli, Shine-Dalgarno sequence selection is primarily influenced by growth temperature, not growth rate.
- A/U-rich enhancers substantially enhance translation by acting cooperatively with SD sequences.
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