The Bacterial Iron Sensor IdeR Recognizes Its DNA Targets by Indirect Readout

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2021 Aug 21

PMID 34417623

Citations 4

Authors

Francisco Javier Marcos-Torres

Dirk Maurer

Linda Juniar

Julia J Griese

Affiliations

Soon will be listed here.

Abstract

The iron-dependent regulator IdeR is the main transcriptional regulator controlling iron homeostasis genes in Actinobacteria, including species from the Corynebacterium, Mycobacterium and Streptomyces genera, as well as the erythromycin-producing bacterium Saccharopolyspora erythraea. Despite being a well-studied transcription factor since the identification of the Diphtheria toxin repressor DtxR three decades ago, the details of how IdeR proteins recognize their highly conserved 19-bp DNA target remain to be elucidated. IdeR makes few direct contacts with DNA bases in its target sequence, and we show here that these contacts are not required for target recognition. The results of our structural and mutational studies support a model wherein IdeR mainly uses an indirect readout mechanism, identifying its targets via the sequence-dependent DNA backbone structure rather than through specific contacts with the DNA bases. Furthermore, we show that IdeR efficiently recognizes a shorter palindromic sequence corresponding to a half binding site as compared to the full 19-bp target previously reported, expanding the number of potential target genes controlled by IdeR proteins.

Citing Articles

Structural basis for transcription activation through cooperative recruitment of MntR.

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The molecular mechanisms of the bacterial iron sensor IdeR.

Marcos-Torres F, Juniar L, Griese J Biochem Soc Trans. 2023; 51(3):1319-1329.

PMID: 37140254 PMC: 10317159. DOI: 10.1042/BST20221539.

Structural Dynamics of the MntR Transcription Factor Is Locked by Mn Binding.

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