The TetR Family of Transcriptional Repressors

Juan Ramos

Manuel Martínez-Bueno

Antonio Molina-Henares

Wilson Terán

Department of Plant Biochemistry and Molecular and Cellular Biology, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, E-18008 Granada, Spain,^{Laboratory of Applied Microbiology, Marine Biotechnology Institute 3-75-1 Heita, Kamaishi, Iwate 026-0001, Japan,}^{Department of Biological Sciences, Imperial College London, Flowers Building, Armstrong Road, South Kensington, London, SW7 2AZ, United Kingdom,}^{Department of Biochemistry & Molecular Biology, Oregon Health Sciences University, 3181 SW Sam Jackson Park Road, Portland, Oregon 97239-3098}⁴

^{Corresponding author. Mailing address: Estación Experimental del Zaidín, CSIC, Apdo. Correos 419, E-18008 Granada, Spain. Phone: 34 958 181608. Fax: 34 958 135740. E-mail:}se.cisc.zee@somarlj.

^{Present address: Esa7, Information Technologies, Las Gabias, E-18110 Granada, Spain.}

Abstract

We have developed a general profile for the proteins of the TetR family of repressors. The stretch that best defines the profile of this family is made up of 47 amino acid residues that correspond to the helix-turn-helix DNA binding motif and adjacent regions in the three-dimensional structures of TetR, QacR, CprB, and EthR, four family members for which the function and three-dimensional structure are known. We have detected a set of 2,353 nonredundant proteins belonging to this family by screening genome and protein databases with the TetR profile. Proteins of the TetR family have been found in 115 genera of gram-positive, α-, β-, and γ-proteobacteria, cyanobacteria, and archaea. The set of genes they regulate is known for 85 out of the 2,353 members of the family. These proteins are involved in the transcriptional control of multidrug efflux pumps, pathways for the biosynthesis of antibiotics, response to osmotic stress and toxic chemicals, control of catabolic pathways, differentiation processes, and pathogenicity. The regulatory network in which the family member is involved can be simple, as in TetR (i.e., TetR bound to the target operator represses tetA transcription and is released in the presence of tetracycline), or more complex, involving a series of regulatory cascades in which either the expression of the TetR family member is modulated by another regulator or the TetR family member triggers a cell response to react to environmental insults. Based on what has been learned from the cocrystals of TetR and QacR with their target operators and from their three-dimensional structures in the absence and in the presence of ligands, and based on multialignment analyses of the conserved stretch of 47 amino acids in the 2,353 TetR family members, two groups of residues have been identified. One group includes highly conserved positions involved in the proper orientation of the helix-turn-helix motif and hence seems to play a structural role. The other set of less conserved residues are involved in establishing contacts with the phosphate backbone and target bases in the operator. Information related to the TetR family of regulators has been updated in a database that can be accessed at www.bactregulators.org.

Abstract

Acknowledgments

Work in our laboratories was supported by EC grants MIFRIEND QLK3-CT 2000-017 and BIOCARTE QLRT-2001-01923 and projects CICYT-2003 (BIO2003-00515) and Petri-NBT (PTR1995-0653 PO) to J.L.R. and grant 0021/2002 from the Human Frontier Science Program to M.T.G., K.W., and X.Z.

We thank W. Hindrich and S. Horinouchi for comments on the article. We thank Inés Abril and Carmen Lorente for secretarial assistance and Karen Shashok for checking the use of English in the manuscript. R. Tobes acknowledges support from Eduardo Pareja.

Acknowledgments

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