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Journal of Bacteriology, April 1999, p. 2084-2093, Vol. 181, No. 7
0021-9193/99/$04.00+0
Copyright © 1999, American Society for Microbiology. All rights reserved.

The Acid-Inducible asr Gene in Escherichia coli: Transcriptional Control by the phoBR Operondagger

Edita Suziedeliene,1,2,* Kestutis Suziedelis,1,2 Vaida Garbenciute,2 and Staffan Normark1,Dagger

Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri 63110,1 and Department of Biochemistry and Biophysics, Vilnius University, Vilnius LT-2009, Lithuania2

Received 24 August 1998/Accepted 28 January 1999

Escherichia coli responds to external acidification (pH 4.0 to 5.0) by synthesizing a newly identified, ~450-nucleotide RNA component. At maximal levels of induction it is one of the most abundant small RNAs in the cell and is relatively stable bacterial RNA. The acid-inducible RNA was purified, and the gene encoding it, designated asr (for acid shock RNA), mapped at 35.98 min on the E. coli chromosome. Analysis of the asr DNA sequence revealed an open reading frame coding for a 111-amino-acid polypeptide with a deduced molecular mass of approximately 11.6 kDa. According to computer-assisted analysis, the predicted polypeptide contains a typical signal sequence of 30 amino acids and might represent either a periplasmic or an outer membrane protein. The asr gene cloned downstream from a T7 promoter was translated in vivo after transcription using a T7 RNA polymerase transcription system. Expression of a plasmid-encoded asr::lacZ fusion under a native asr promoter was reduced ~15-fold in a complex medium, such as Luria-Bertani medium, versus the minimal medium. Transcription of the chromosomal asr was abolished in the presence of a phoB-phoR (a two-component regulatory system, controlling the pho regulon inducible by phosphate starvation) deletion mutant. Acid-mediated induction of the asr gene in the Delta (phoB-phoR) mutant strain was restored by introduction of the plasmid with cloned phoB-phoR genes. Primer extension analysis of the asr transcript revealed a region similar to the Pho box (the consensus sequence found in promoters transcriptionally activated by the PhoB protein) upstream from the determined transcription start. The asr promoter DNA region was demonstrated to bind PhoB protein in vitro. We discuss our results in terms of how bacteria might employ the phoB-phoR regulatory system to sense an external acidity and regulate transcription of the asr gene.

* Corresponding author. Mailing address: Department of Biochemistry and Biophysics, Faculty of Natural Sciences, Vilnius University, Ciurlionio 21, Vilnius LT-2009, Lithuania. Phone: (370 2) 650381. Fax: (370 2) 235049. E-mail: kestutis.suziedelis{at}gf.vu.lt.

dagger Dedicated to David Apirion, whose death in 1992 was the loss of a devoted scientist.

Dagger Present address: Karolinska Institute, Microbiology and Tumorbiology Center, S-10401 Stockholm, Sweden.

Journal of Bacteriology, April 1999, p. 2084-2093, Vol. 181, No. 7
0021-9193/99/$04.00+0
Copyright © 1999, American Society for Microbiology. All rights reserved.


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