Specificity of DNA-binding by the FAX-1 and NHR-67 nuclear receptors of Caenorhabditis elegans is partially mediated via a subclass-specific P-box residue

BMC Molecular Biology
Stephen D DeMeoBruce Wightman

Abstract

The nuclear receptors of the NR2E class play important roles in pattern formation and nervous system development. Based on a phylogenetic analysis of DNA-binding domains, we define two conserved groups of orthologous NR2E genes: the NR2E1 subclass, which includes C. elegans nhr-67, Drosophila tailless and dissatisfaction, and vertebrate Tlx (NR2E2, NR2E4, NR2E1), and the NR2E3 subclass, which includes C. elegans fax-1 and vertebrate PNR (NR2E5, NR2E3). PNR and Tll nuclear receptors have been shown to bind the hexamer half-site AAGTCA, instead of the hexamer AGGTCA recognized by most other nuclear receptors, suggesting unique DNA-binding properties for NR2E class members. We show that NR2E3 subclass member FAX-1, unlike NHR-67 and other NR2E1 subclass members, binds to hexamer half-sites with relaxed specificity: it will bind hexamers with the sequence ANGTCA, although it prefers a purine to a pyrimidine at the second position. We use site-directed mutagenesis to demonstrate that the difference between FAX-1 and NHR-67 binding preference is partially mediated by a conserved subclass-specific asparagine or aspartate residue at position 19 of the DNA-binding domain. This amino acid position is part of the "P box" that plays a crit...Continue Reading

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Citations

Jun 27, 2013·WormBook : the Online Review of C. Elegans Biology·Valerie ReinkePeter Okkema
Oct 3, 2009·The FEBS Journal·Yoshiaki Nakagawa, Vincent C Henrich
Dec 20, 2008·Developmental Dynamics : an Official Publication of the American Association of Anatomists·Carl SungSteven Robinow
Jul 2, 2014·Biochimica Et Biophysica Acta·Marta Kostrouchova, Zdenek Kostrouch
Jun 24, 2014·Biochimica Et Biophysica Acta·Karen E BatesSteven Robinow
Jul 2, 2011·Developmental Biology·Eliana VergheseBruce Wightman

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Methods Mentioned

BETA
electrophoretic mobility shift assay
one-hybrid

Software Mentioned

Lasergene Megalign
PROF
NNPREDICT
BLASTP
DNAStar
BLASTN
CLUSTAL V

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