title: Correlations between Shine-Dalgarno sequences and gene features such as predicted expression levels and operon structures.
abstract: 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.
authors.affiliation: Department of Biological Sciences, Stanford University, Stanford, California 94305-2125, USA.
authors.forename: Jiong
authors.initials: J
authors.lastname: Ma
authors.forename: Allan
authors.initials: A
authors.lastname: Campbell
authors.forename: Samuel
authors.initials: S
authors.lastname: Karlin
mesh_terms: D019843:Archaeal Proteins / Q000235:genetics / Q000378:metabolism*; D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism*; D001483:Base Sequence; D018387:Codon, Initiator / Q000737:chemistry* / Q000235:genetics; D019848:Gene Expression Regulation, Archaeal; D015964:Gene Expression Regulation, Bacterial; D020745:Genome, Archaeal; D016680:Genome, Bacterial; D008954:Models, Biological; D008969:Molecular Sequence Data; D009876:Operon / Q000235:genetics*; D014176:Protein Biosynthesis; D012333:RNA, Messenger / Q000737:chemistry* / Q000235:genetics; D012335:RNA, Ribosomal / Q000235:genetics / Q000378:metabolism; D017422:Sequence Analysis, DNA
chemical_list: D019843:Archaeal Proteins; D001426:Bacterial Proteins; D018387:Codon, Initiator; D012333:RNA, Messenger; D012335:RNA, Ribosomal