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Influences on gene expression in vivo by a Shine-Dalgarno sequence

Jin, Haining ; Zhao, Qing ; Gonzalez de Valdivia, Ernesto I LU ; Ardell, David H ; Stenström, Magnus and Isaksson, Leif A (2006) In Molecular Microbiology 60(2). p.92-480
Abstract

The Shine-Dalgarno (SD+: 5'-AAGGAGG-3') sequence anchors the mRNA by base pairing to the 16S rRNA in the small ribosomal subunit during translation initiation. We have here compared how an SD+ sequence influences gene expression, if located upstream or downstream of an initiation codon. The positive effect of an upstream SD+ is confirmed. A downstream SD+ gives decreased gene expression. This effect is also valid for appropriately modified natural Escherichia coli genes. If an SD+ is placed between two potential initiation codons, initiation takes place predominantly at the second start site. The first start site is activated if the distance between this site and the downstream SD+ is enlarged and/or if the second start site is... (More)

The Shine-Dalgarno (SD+: 5'-AAGGAGG-3') sequence anchors the mRNA by base pairing to the 16S rRNA in the small ribosomal subunit during translation initiation. We have here compared how an SD+ sequence influences gene expression, if located upstream or downstream of an initiation codon. The positive effect of an upstream SD+ is confirmed. A downstream SD+ gives decreased gene expression. This effect is also valid for appropriately modified natural Escherichia coli genes. If an SD+ is placed between two potential initiation codons, initiation takes place predominantly at the second start site. The first start site is activated if the distance between this site and the downstream SD+ is enlarged and/or if the second start site is weakened. Upstream initiation is eliminated if a stable stem-loop structure is placed between this SD+ and the upstream start site. The results suggest that the two start sites compete for ribosomes that bind to an SD+ located between them. A minor positive contribution to upstream initiation resulting from 3' to 5' ribosomal diffusion along the mRNA is suggested. Analysis of the E. coli K12 genome suggests that the SD+ or SD-like sequences are systematically avoided in the early coding region suggesting an evolutionary significance.

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author
publishing date
type
Contribution to journal
publication status
published
keywords
Base Sequence, Binding Sites, Codon, Initiator, Escherichia coli, Gene Expression Regulation, Bacterial, Genes, Bacterial, Genes, Reporter, Molecular Sequence Data, Nucleic Acid Conformation, Protein Biosynthesis, RNA, Bacterial, RNA, Messenger, RNA, Ribosomal, 16S, RNA, Transfer, Amino Acyl, Ribosomes, Journal Article, Research Support, Non-U.S. Gov't
in
Molecular Microbiology
volume
60
issue
2
pages
13 pages
publisher
Wiley-Blackwell
external identifiers
  • pmid:16573696
  • scopus:33645296046
ISSN
0950-382X
DOI
10.1111/j.1365-2958.2006.05110.x
language
English
LU publication?
no
id
383e60cc-6bee-407f-b232-021261c263d8
date added to LUP
2018-01-13 11:55:03
date last changed
2020-01-13 00:23:43
@article{383e60cc-6bee-407f-b232-021261c263d8,
  abstract     = {<p>The Shine-Dalgarno (SD+: 5'-AAGGAGG-3') sequence anchors the mRNA by base pairing to the 16S rRNA in the small ribosomal subunit during translation initiation. We have here compared how an SD+ sequence influences gene expression, if located upstream or downstream of an initiation codon. The positive effect of an upstream SD+ is confirmed. A downstream SD+ gives decreased gene expression. This effect is also valid for appropriately modified natural Escherichia coli genes. If an SD+ is placed between two potential initiation codons, initiation takes place predominantly at the second start site. The first start site is activated if the distance between this site and the downstream SD+ is enlarged and/or if the second start site is weakened. Upstream initiation is eliminated if a stable stem-loop structure is placed between this SD+ and the upstream start site. The results suggest that the two start sites compete for ribosomes that bind to an SD+ located between them. A minor positive contribution to upstream initiation resulting from 3' to 5' ribosomal diffusion along the mRNA is suggested. Analysis of the E. coli K12 genome suggests that the SD+ or SD-like sequences are systematically avoided in the early coding region suggesting an evolutionary significance.</p>},
  author       = {Jin, Haining and Zhao, Qing and Gonzalez de Valdivia, Ernesto I and Ardell, David H and Stenström, Magnus and Isaksson, Leif A},
  issn         = {0950-382X},
  language     = {eng},
  number       = {2},
  pages        = {92--480},
  publisher    = {Wiley-Blackwell},
  series       = {Molecular Microbiology},
  title        = {Influences on gene expression in vivo by a Shine-Dalgarno sequence},
  url          = {http://dx.doi.org/10.1111/j.1365-2958.2006.05110.x},
  doi          = {10.1111/j.1365-2958.2006.05110.x},
  volume       = {60},
  year         = {2006},
}