title: DNA binding specificity of ATAF2, a NAC domain transcription factor targeted for degradation by Tobacco mosaic virus.
abstract: BACKGROUND
  Control of the host transcriptome represents a key battleground in the interaction of plants and pathogens. Specifically, plants have evolved complex defense systems that induce profound transcriptional changes in response to pathogen attack while pathogens have evolved mechanisms to subvert or disable these defenses. Several NAC transcription factors such as ATAF2 have been linked to plant defense responses, including those targeting viruses. The replication protein of Tobacco mosaic virus (TMV) has been shown to interact with and target the degradation of ATAF2. These findings suggest that the transcriptional targets of ATAF2 are involved in defense against TMV.
  
  
  RESULTS
  To detect potential ATAF2 transcriptional targets, a genomic pull-down assay was utilized to identify ATAF2 promoter binding sequences. Subsequent mobility shift and DNA footprinting assays identified a 30-bp ATAF2 binding sequence. An in vivo GUS reporter system confirmed the function of the identified 30-bp binding sequence as an ATAF2 specific transcriptional activator in planta. Gel filtration studies of purified ATAF2 protein and mutagenesis studies of the 30-bp binding sequence indicate ATAF2 functions as a dimer. Computational analysis of interacting promoter sequences identified a corresponding 25-bp A/T-rich consensus sequence with repeating [GC]AAA motifs. Upon ATAF2 induction real-time qRT-PCR studies confirmed the accumulation of select gene transcripts whose promoters contain this consensus sequence.
  
  
  CONCLUSIONS
  We report the identification of a cis-regulatory binding sequence for ATAF2. Different from other known NAC protein binding sequences, the A/T-rich ATAF2 binding motif represents a novel binding sequence for NAC family proteins. Combined this information represents a unique tool for the identification of ATAF2 target genes.
authors.affiliation: Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, MD 20742, USA.
authors.forename: Xiao
authors.initials: X
authors.lastname: Wang
authors.forename: James N
authors.initials: JN
authors.lastname: Culver
mesh_terms: D017360:Arabidopsis / Q000235:genetics / Q000378:metabolism* / Q000821:virology*; D029681:Arabidopsis Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D020029:Base Pairing / Q000235:genetics; D001483:Base Sequence; D016384:Consensus Sequence / Q000235:genetics; D018983:DNA Footprinting; D004252:DNA Mutational Analysis; D018744:DNA, Plant / Q000378:metabolism*; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant / Q000235:genetics; D005966:Glucuronidase / Q000378:metabolism; D008969:Molecular Sequence Data; D016296:Mutagenesis; D011401:Promoter Regions, Genetic / Q000235:genetics; D011485:Protein Binding; D055503:Protein Multimerization; D017434:Protein Structure, Tertiary; D059748:Proteolysis; D012097:Repressor Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D014027:Tobacco Mosaic Virus / Q000378:metabolism*; D014158:Transcription, Genetic; D015533:Transcriptional Activation / Q000235:genetics
chemical_list: C505769:ATAF2 protein, Arabidopsis; D029681:Arabidopsis Proteins; D018744:DNA, Plant; D012097:Repressor Proteins; D005966:Glucuronidase