Genome-wide study of C2H2 zinc finger gene family in Medicago truncatula
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RESEARCH ARTICLE
Open Access
Genome-wide study of C2H2 zinc finger gene family in Medicago truncatula Zhicheng Jiao1,2,3, Liping Wang4,5, Huan Du1,2,3, Ying Wang1,2,3, Weixu Wang1,2, Junjie Liu1,2, Jinhang Huang1,2, Wei Huang4,5 and Liangfa Ge1,2,3*
Abstract Background: C2H2 zinc finger proteins (C2H2 ZFPs) play vital roles in shaping many aspects of plant growth and adaptation to the environment. Plant genomes harbor hundreds of C2H2 ZFPs, which compose one of the most important and largest transcription factor families in higher plants. Although the C2H2 ZFP gene family has been reported in several plant species, it has not been described in the model leguminous species Medicago truncatula. Results: In this study, we identified 218 C2H2 type ZFPs with 337 individual C2H2 motifs in M. truncatula. We showed that the high rate of local gene duplication has significantly contributed to the expansion of the C2H2 gene family in M. truncatula. The identified ZFPs exhibit high variation in motif arrangement and expression pattern, suggesting that the short C2H2 zinc finger motif has been adopted as a scaffold by numerous transcription factors with different functions to recognize cis-elements. By analyzing the public expression datasets and quantitative RTPCR (qRT-PCR), we identified several C2H2 ZFPs that are specifically expressed in certain tissues, such as the nodule, seed, and flower. Conclusion: Our genome-wide work revealed an expanded C2H2 ZFP gene family in an important legume M. truncatula, and provides new insights into the diversification and expansion of C2H2 ZFPs in higher plants. Keywords: C2H2, Zinc finger, Local gene duplication, Gene family, EAR motif, Expression
Background Zinc finger proteins (ZFPs) have evolved and diversified into a massive transcription factor family in the plant kingdom [1, 2]. ZFPs contain one to a few zinc fingers, which are approximately 23 to 30 amino acids in length and have several cysteine and histidine residues. The cysteine and histidine residues in the motif coordinately bind one or more zinc ions through hydrogen bonds, forming a stabilized finger-like structure that can interact with nucleic acid sequences to regulate target gene * Correspondence: [email protected] 1 Department of Grassland Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, Guangdong, China 2 Guangdong Engineering Research Center for Grassland Science, Tianhe, 483 Wushan Road, Guangzhou 510642, Guangdong, China Full list of author information is available at the end of the article
expression. Based on the combination of cysteine and histidine residues, ZFPs can be classified into different types, such as C2H2, C2C2, C2HC, and C3H [3–6]. The C2H2 type zinc finger is one of the most common motifs in ZFPs, and it can be represented by the sequence X2-Cys-X2,4-Cys-X12-His-X3,4,5-His (X indicates any amino acid residue and numbers represent residue quantity) [7, 8]. This approximately 23–30amino-acid-motif contains two β-sheet strands and one α
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