Abstract
BackgroundC2H2 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.ResultsIn 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 RT-PCR (qRT-PCR), we identified several C2H2 ZFPs that are specifically expressed in certain tissues, such as the nodule, seed, and flower.ConclusionOur 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.
Highlights
C2H2 zinc finger proteins (C2H2 Zinc finger proteins (ZFPs)) play vital roles in shaping many aspects of plant growth and adaptation to the environment
Given the large number of C2H2 ZFPs reported in other species [15, 16, 27], for instance, 176 and 321 C2H2 ZFPs in the Arabidopsis and soybean genome, respectively [16, 27], we thought that there should be more C2H2 ZFPs in the M. truncatula genome
Based on the quantity and arrangement of C2H2 motifs and element binding factor-associated amphiphilic repression motif (EAR) motifs, we classified these ZFPs into different groups
Summary
C2H2 zinc finger proteins (C2H2 ZFPs) play vital roles in shaping many aspects of plant growth and adaptation to the environment. 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-helix in the N-terminus and C-terminus, respectively, which fold around the center zinc ion to establish a stabilized simple structure that binds to the major groove of the target DNA sequence [8]. With the ability to interact with the DNA segment, C2H2 ZFPs mainly play a role in
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