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PMID: 12270832 Published · ppublish English Comparative Study Journal Article Research Support, U.S. Gov't, P.H.S.

Correlations between Shine-Dalgarno sequences and gene features such as predicted expression levels and operon structures.

Journal of bacteriology ·Vol. 184 ·No. 20 ·2002-10-00 ·Pages 5733-45

Ma J, Campbell A, Karlin S

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.

MeSH Terms
Archaeal Proteins/genetics,metabolism Bacterial Proteins/genetics,metabolism Base Sequence Codon, Initiator/chemistry,genetics Gene Expression Regulation, Archaeal Gene Expression Regulation, Bacterial Genome, Archaeal Genome, Bacterial Models, Biological Molecular Sequence Data Operon/genetics Protein Biosynthesis RNA, Messenger/chemistry,genetics RNA, Ribosomal/genetics,metabolism Sequence Analysis, DNA
Chemicals
Archaeal Proteins Bacterial Proteins Codon, Initiator RNA, Messenger RNA, Ribosomal
Authors & Affiliations
3 authors, click to expand affiliations / ORCID
Ma Jiong
Department of Biological Sciences, Stanford University, Stanford, California 94305-2125, USA.
Campbell Allan
Karlin Samuel
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Article Info
Journal
Journal of bacteriology
Abbr.
J Bacteriol
ISSN
0021-9193
DOI
10.1128/JB.184.20.5733-5745.2002
Published
2002-10-00
Pages
5733-45
Language
English
Region
United States
NLM ID
2985120R
PMCID
PMC139613
Subset
IM
Grants
NIGMS NIH HHS · R01 GM010452 · United States
NIGMS NIH HHS · 5R01GM10452-38 · United States
NHGRI NIH HHS · 5R01HG00335-13 · United States
Databases
RefSeq
NC_000117, NC_000853, NC_000868, NC_000907, NC_000908, NC_000909, NC_000911, NC_000912, NC_000913, NC_000915, NC_000916, NC_000917, NC_000918, NC_000919, NC_000922, NC_000961, NC_000962, NC_000963, NC_000964, NC_001263, NC_001318, NC_002162, NC_002163, NC_002183, NC_002505, NC_002506, NC_002516, NC_002578, NC_002607, NC_002754, NC_003364
External Links
PubMed source DOI: 10.1128/JB.184.20.5733-5745.2002 PMC Full Text View journal details
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