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Nucleic Acids Research 2004 32(17):5198-5205; doi:10.1093/nar/gkh857
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Published online 30 September 2004

Nucleic Acids Research, Vol. 32 No. 17 © Oxford University Press 2004; all rights reserved

A codon window in mRNA downstream of the initiation codon where NGG codons give strongly reduced gene expression in Escherichia coli

Ernesto I. Gonzalez de Valdivia and Leif A. Isaksson*

Department of Microbiology, Stockholm University, S-106 91 Stockholm, Sweden

* To whom correspondence should be addressed. Tel: +46 8 164197; Fax: +46 8 6129552; Email: leif.isaksson{at}gmt.su.se

Received July 2, 2004; Revised and Accepted September 10, 2004

The influences on gene expression by codons at positions +2, +3, +5 and +7 downstream of the initiation codon have been compared. Most of the +2 codons that are known to give low gene expression are associated with a higher expression if placed at the later positions. The NGG codons AGG, CGG, UGG and GGG, but not GGN or GNG (where N is non-G), are unique since they are associated with a very low gene expression also if located at positions +2, +3 and +5. All codons, including NGG, give a normal gene expression if placed at positions +7. The negative effect by the NGG codons is true for both the lacZ and 3A' model genes. The low expression is suggested to originate at the translational level, although it is not the result of mRNA secondary structure or a lowered intracellular mRNA pool.


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