Template-based structure prediction and classification of transcription factors in Arabidopsis thaliana

Tao Lu, Yuedong Yang, Bo Yao, Song Liu, Yaoqi Zhou, Chi Zhang

Research output: Contribution to journalArticle

2 Citations (Scopus)

Abstract

Transcription factors (TFs) play important roles in plants. However, there is no systematic study of their structures and functions of most TFs in plants. Here, we performed template-based structure prediction for all TFs in Arabidopsis thaliana, with their full-length sequences as well as C-terminal and N-terminal regions. A total of 2918 model structures were obtained with a high confidence score. We find that TF families employ only a smaller number of templates for DNA-binding domains (DBD) but a diverse number of templates for transcription regulatory domains (TRD). Although TF families are classified according to DBD, their sizes have a significant correlation with the number of unique non-DNA-binding templates employed in the family (Pearson correlation coefficient of 0.74). That is, the size of TF family is related to its functional diversity. Network analysis reveals new connections between TF families based on shared TRD or DBD templates; 81% TF families share DBD and 67% share TRD templates. Two large fully connected family clusters in this network are observed along with 69 island families. In addition, 25 genes with unknown functions are found to be DNA-binding and/or TF factors according to predicted structures. This work provides a global view of the classification of TFs based on their DBD or TRD templates, and hence, a deeper understanding of DNA-binding and regulatory functions from structural perspective. All structural models of TFs are deposited in the online database for public usage at http://sysbio.unl.edu/AthTF.

Original languageEnglish (US)
Pages (from-to)828-838
Number of pages11
JournalProtein Science
Volume21
Issue number6
DOIs
StatePublished - Jun 1 2012

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Arabidopsis
Transcription Factors
Transcription
DNA
Structural Models
Electric network analysis
Model structures
Islands
Genes
Databases

Keywords

  • Plants
  • Structure classification
  • Structure prediction
  • Transcription factors

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology

Cite this

Template-based structure prediction and classification of transcription factors in Arabidopsis thaliana. / Lu, Tao; Yang, Yuedong; Yao, Bo; Liu, Song; Zhou, Yaoqi; Zhang, Chi.

In: Protein Science, Vol. 21, No. 6, 01.06.2012, p. 828-838.

Research output: Contribution to journalArticle

Lu, Tao ; Yang, Yuedong ; Yao, Bo ; Liu, Song ; Zhou, Yaoqi ; Zhang, Chi. / Template-based structure prediction and classification of transcription factors in Arabidopsis thaliana. In: Protein Science. 2012 ; Vol. 21, No. 6. pp. 828-838.
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