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Depletion of Shine-Dalgarno Sequences Within Bacterial Coding Regions Is Expression Dependent
Chuyue Yang1, Adam J Hockenberry1,2, Michael C Jewett3,2,4,5
1Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208.
G3 (Bethesda, Md.)
|September 9, 2016
Summary
The Shine-Dalgarno (SD) sequence, typically regulating translation initiation, appears to slow down protein synthesis when found within bacterial coding sequences. Highly expressed genes and faster growth rates correlate with fewer SD sequences in coding regions.
Area of Science:
- Molecular Biology
- Genomics
- Bacterial Physiology
Background:
- Protein synthesis efficiency is vital for bacterial survival and competitiveness.
- Translation efficiency depends on initiation, elongation, and termination rates.
- Shine-Dalgarno (SD) sequences traditionally regulate initiation, but their role in elongation is debated.
Purpose of the Study:
- To develop a metric for quantifying Shine-Dalgarno (SD) sequences within bacterial coding regions.
- To investigate the correlation between SD sequence prevalence in coding regions and gene expression levels.
- To explore the relationship between SD sequence occurrence, ribosomal protein genes, and organismal growth rates.
Main Methods:
- Analysis of hundreds of bacterial genomes to quantify SD sequence occurrence in coding DNA sequences (CDS).
- Correlation analysis between normalized SD site occurrence and measured protein abundances.
- Examination of SD sequence depletion in ribosomal protein genes in relation to bacterial growth rates.
Main Results:
- Highly expressed genes exhibit significantly fewer SD sequences in their coding regions than expected by chance.
- A robust correlation exists between the reduced occurrence of SD sites in CDS and higher protein abundance across diverse bacteria.
- Depletion of SD sequences in ribosomal protein genes is strongly correlated with faster organismal growth rates.
Conclusions:
- The presence of Shine-Dalgarno (SD) sequences within coding regions negatively impacts translation efficiency.
- Bacteria actively select against SD sequences in coding regions, particularly in highly expressed and essential genes like ribosomal proteins.
- SD sequence occurrence within coding regions is a significant factor influencing bacterial translation efficiency and growth rates.
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