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DNA recognition by Arabidopsis transcription factors ABI 3 and NGA 1
Author(s) -
Sasnauskas Giedrius,
Manakova Elena,
Lapėnas Kęstutis,
Kauneckaitė Kotryna,
Siksnys Virginijus
Publication year - 2018
Publication title -
the febs journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.981
H-Index - 204
eISSN - 1742-4658
pISSN - 1742-464X
DOI - 10.1111/febs.14649
Subject(s) - arabidopsis , dna , transcription factor , repressor , transcription (linguistics) , genetics , dna binding site , protein–dna interaction , base pair , binding site , dna binding protein , dna binding domain , biology , computational biology , chemistry , promoter , gene , gene expression , mutant , linguistics , philosophy
B3 transcription factors constitute a large plant‐specific protein superfamily, which plays a central role in plant life. Family members are characterized by the presence of B3 DNA ‐binding domains ( DBD s). To date, only a few B3 DBD s were structurally characterized; therefore, the DNA recognition mechanism of other family members remains to be elucidated. Here, we analyze DNA recognition mechanism of two structurally uncharacterized B3 transcription factors, ABI 3 and NGA 1. Guided by the structure of the DNA ‐bound B3 domain of Arabidopsis transcriptional repressor VAL 1, we have performed mutational analysis of the ABI 3 B3 domain. We demonstrate that both VAL 1‐B3 and ABI 3‐B3 recognize the Sph/ RY DNA sequence 5′‐ TGCATG ‐3′ via a conserved set of base‐specific contacts. We have also solved a 1.8 Å apo‐structure of NGA 1‐B3, DBD of Arabidopsis transcription factor NGA 1. We show that NGA 1‐B3, like the structurally related RAV 1‐B3 domain, is specific for the 5′‐ CACCTG ‐3′ DNA sequence, albeit tolerates single base pair substitutions at the 5′‐terminal half of the recognition site. Employing distance‐dependent fluorophore quenching, we show that NGA 1‐B3 binds the asymmetric recognition site in a defined orientation, with the ‘N‐arm’ and ‘C‐arm’ structural elements interacting with the 5′‐ and 3′‐terminal nucleotides of the 5′‐ CACCTG ‐3′ sequence, respectively. Mutational analysis guided by the model of DNA ‐bound NGA 1‐B3 helped us identify NGA 1‐B3 residues involved in base‐specific and DNA backbone contacts, providing new insights into the mechanism of DNA recognition by plant B3 domains of RAV and REM families. Databases RCSB Protein Data Bank, accession number 5OS9 .