Origin and evolutionary analysis of the plant-specific TIFY transcription factor family

A substantial number of transcription factor families have been investigated from all kingdoms of life, but a particular class of plant-specific TIFY transcription factors, characterized by a highly conserved TIFY domain, lacks a systemic analysis of its origin and evolutionary relationships among d...

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Bibliographic Details
Published in:Genomics (San Diego, Calif.) Calif.), 2011-08, Vol.98 (2), p.128-136
Main Authors: Bai, Youhuang, Meng, Yijun, Huang, Donglin, Qi, Yanhua, Chen, Ming
Format: Article
Language:English
Subjects:
Amino Acid Motifs
Amino Acid Sequence
Arabidopsis Proteins - genetics
Biological and medical sciences
Comparative genomic analysis
Conserved sequence
DNA-Binding Proteins - genetics
Evolution, Molecular
Exons
Fundamental and applied biological sciences. Psychology
Genes, Duplicate
Genes. Genome
Genetics of eukaryotes. Biological and molecular evolution
genome
Genome, Plant
Introns
JAZ
Molecular and cellular biology
Molecular genetics
Molecular Sequence Data
Multigene Family - genetics
Phylogeny
Plant Proteins - classification
Plant Proteins - genetics
PPD
Protein Structure, Tertiary
Repressor Proteins - genetics
Sequence Alignment
surveys
Synteny - genetics
TIFY domain
transcription (genetics)
transcription factors
Transcription Factors - classification
Transcription Factors - genetics
ZML
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Summary:A substantial number of transcription factor families have been investigated from all kingdoms of life, but a particular class of plant-specific TIFY transcription factors, characterized by a highly conserved TIFY domain, lacks a systemic analysis of its origin and evolutionary relationships among different plant species. After exhaustive genome-wide searches against 14 genomes, TIFY transcription factors were identified and classified into four subfamilies TIFY, PPD, JAZ and ZML according to their different domain architectures. Results show that the TIFY domain of the ZML subfamily possesses a core “TLS[F/Y]XG” motif rather than the “TIFYXG” motif that is dominant in the other three subfamilies. A comprehensive survey of the TIFY family allowed us to discover a new group within the JAZ subfamily and to identify several novel conserved motifs via phylogenetic analysis. Evolutional analysis indicates that whole genome duplication and tandem duplication contributed to the expansion of the TIFY family in plants.
ISSN:0888-7543
1089-8646
DOI:10.1016/j.ygeno.2011.05.002