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Predicting Shine-Dalgarno sequence locations exposes genome annotation errors.

J Starmer¹, A Stomp, M Vouk

¹Bioinformatics Program, North Carolina State University, Raleigh, North Carolina, USA. jdstarme@ncsu.edu

Plos Computational Biology

|May 20, 2006

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Researchers developed a new metric, relative spacing (RS), to analyze Shine-Dalgarno sequences in prokaryotes. This method helps identify translation initiation sites and improves gene annotation by revealing unusual start codon usage and SD sequence locations.

Area of Science:

Molecular Biology
Genomics
Bioinformatics

Background:

Shine-Dalgarno (SD) sequences are crucial for initiating protein synthesis in prokaryotes.
The precise location and binding stability of SD sequences influence translation rates.
Understanding SD sequence characteristics is key to linking an organism's transcriptome to its proteome.

Purpose of the Study:

To develop a novel metric for identifying Shine-Dalgarno (SD) sequences and their hybridization potential.
To investigate the location of SD sequences relative to start codons in prokaryotic genomes.
To enhance gene sequence annotation and explore rRNA-mRNA hybridization in translation initiation.

Main Methods:

Implemented the Individual Nearest Neighbor Hydrogen Bond model for oligo-oligo hybridization.

Related Experiment Videos

Developed a new metric, relative spacing (RS), to simulate mRNA-16S rRNA binding.

Analyzed 18 prokaryotic genomes, examining translation initiation regions and start codon usage.

Main Results:

Identified 2,420 genes (RS+1 genes) with the strongest mRNA-rRNA binding including the start codon, deviating from the typical SD sequence location.
Observed a bias towards GUG as the start codon in RS+1 genes, rather than the common AUG.
Found that 384 strong RS+1 genes had SD sequences near in-frame initiation codons, suggesting potential start codon mis-annotation.

Conclusions:

The relative spacing (RS) metric offers an improved approach for gene sequence annotation.
The study reveals unexpected Shine-Dalgarno sequence locations and start codon usage in prokaryotes.
The RS metric provides a new tool for studying the role of rRNA-mRNA hybridization in translation initiation.