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Journal of Bacteriology, October 2002, p. 5733-5745, Vol. 184, No. 20
0021-9193/02/$04.00+0     DOI: 10.1128/JB.184.20.5733-5745.2002
Copyright © 2002, American Society for Microbiology. All Rights Reserved.

Correlations between Shine-Dalgarno Sequences and Gene Features Such as Predicted Expression Levels and Operon Structures

Jiong Ma,1 Allan Campbell,1 and Samuel Karlin2*

Department of Biological Sciences,1 Department of Mathematics, Stanford University, Stanford, California 943052

Received 29 April 2002/ Accepted 22 July 2002

This work assesses relationships for 30 complete prokaryotic genomes between the presence of the Shine-Dalgarno (SD) sequence and other gene features, including expression levels, type of start codon, and distance between successive genes. A significant positive correlation of the presence of an SD sequence and the predicted expression level of a gene based on codon usage biases was ascertained, such that predicted highly expressed genes are more likely to possess a strong SD sequence than average genes. Genes with AUG start codons are more likely than genes with other start codons, GUG or UUG, to possess an SD sequence. Genes in close proximity to upstream genes on the same coding strand in most genomes are significantly higher in SD presence. In light of these results, we discuss the role of the SD sequence in translation initiation and its relationship with predicted gene expression levels and with operon structure in both bacterial and archaeal genomes.

* Corresponding author. Mailing address: Department of Mathematics, Stanford University, Stanford, CA 94305-2125. Phone: (650) 723-2204. Fax: (650) 725-2040. E-mail: karlin{at}math.stanford.edu.

Journal of Bacteriology, October 2002, p. 5733-5745, Vol. 184, No. 20
0021-9193/02/$04.00+0     DOI: 10.1128/JB.184.20.5733-5745.2002
Copyright © 2002, American Society for Microbiology. All Rights Reserved.



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