Abstract
The family of DNA binding with one finger (DOF) transcription factors is plant specific, and these proteins contain a highly conserved domain (DOF domain) of 50-52 amino acids that includes a C2C2-type zinc finger motif at the N-terminus that is known to function in a number of plant processes. Here, we characterized 20 DOF genes in the important ornamental species chrysanthemum (Chrysanthemum morifolium) based on transcriptomic sequences. Phylogenetic analysis identified one pair of putative orthologous proteins in Arabidopsis and chrysanthemum and six pairs of paralogous proteins in chrysanthemum. Conserved motifs in the DOF proteins shared by Arabidopsis and chrysanthemum were analyzed using MEME. Bioinformatics analysis revealed that 13 CmDOFs could be targeted by 16 miRNA families. Moreover, we used 5' RLM-RACE to map the cleavage sites in CmDOF3, 15, and 21. The expression of these 20 genes in response to phytohormone treatments and abiotic stresses was characterized, and the expression patterns of six pairs of paralogous CmDOF genes were found to completely differ from one another, except for CmDOF6 and CmDOF7. This work will promote our research of the various functions of DOF gene family members in plant hormone and stress responses.
Highlights
Transcription factors (TFs) that determine gene transcription rates can be bound to cis-regulatory elements of promoters
The 20 isolated DNA binding with one finger (DOF) sequences were designated as CmDOF1 through CmDOF21, except CmDOF17, whose DOF domain is lost
To evaluate the evolutionary relationship between Arabidopsis and chrysanthemum DOF proteins, the deduced amino acid sequences of the DOF genes identified in Arabidopsis and chrysanthemum were completely aligned
Summary
Transcription factors (TFs) that determine gene transcription rates can be bound to cis-regulatory elements of promoters. Many TFs can be divided into different gene families according to their conserved domains. The DNA binding with one finger (DOF) TF family is plant specific and contains a conserved DOF domain (Yanagisawa, 2002). The DOF domain structure includes a C2C2 zinc finger that contains 50-52 amino acid residues; this zinc finger binds to an element with the sequence 5′-AAAG-3′ (Yanagisawa, 2004). In addition to the DNA-binding domain, DOF TF proteins contain a bipartite nuclear localization signal (NLS) that partly overlaps with the conserved DOF DNA-binding domain (Krebs et al, 2010) and a C-terminal transcriptional activation domain (Yanagisawa, 2001). In addition to the DNA-binding domain, DOF TF proteins contain a bipartite nuclear localization signal (NLS) that partly overlaps with the conserved DOF DNA-binding domain (Krebs et al, 2010) and a C-terminal transcriptional activation domain (Yanagisawa, 2001). Moreno-Risueno et al (2007) grouped the DOF family into seven subfamilies based on tree topology and corresponding phylogenetic relationships that probably originated from gene duplication events from a paraphyletic basal grade
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