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Journal of Bacteriology, October 2004, p. 6714-6720, Vol. 186, No. 20
0021-9193/04/$08.00+0     DOI: 10.1128/JB.186.20.6714-6720.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.

Global Transcriptional Effects of a Suppressor tRNA and the Inactivation of the Regulator frmR

Christopher D. Herring and Frederick R. Blattner*

Laboratory of Genetics, University of Wisconsin—Madison, Madison, Wisconsin

Received 12 April 2004/ Accepted 16 July 2004

Expression of an amber suppressor tRNA should result in read-through of the 326 open reading frames (ORFs) that terminate with amber stop codons in the Escherichia coli genome, including six pseudogenes. Abnormal extension of an ORF might alter the activities of the protein and have effects on cellular physiology, while suppression of a pseudogene could lead to a gain of function. We used oligonucleotide microarrays to determine if any effects were apparent at the level of transcription in glucose minimal medium. Surprisingly, only eight genes had significantly different expression in the presence of the suppressor. Among these were the genes yaiN, adhC, and yaiM, forming a single putative operon whose likely function is the degradation of formaldehyde. Expression of wild-type yaiN was shown to result in repression of the operon, while a suppression-mimicking allele lacking the amber stop codon and extended 7 amino acids did not. The operon was shown to be induced by formaldehyde, and the genes have been renamed frmR, frmA, and frmB, respectively.

* Corresponding author. Mailing address: Laboratory of Genetics, University of Wisconsin—Madison, 445 Henry Mall, Madison, WI 53706. Phone: (608) 262-2534. Fax: (608) 263-7459. E-mail: fred{at}genome.wisc.edu.

Journal of Bacteriology, October 2004, p. 6714-6720, Vol. 186, No. 20
0021-9193/04/$08.00+0     DOI: 10.1128/JB.186.20.6714-6720.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.



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