CCCH-Type Zinc Finger Family in Maize: Genome-Wide Identification, Classification and Expression Profiling under Abscisic Acid and Drought Treatments

Université Paris-Diderot, France
PLoS ONE (Impact Factor: 3.53). 07/2012; 7(7):e40120. DOI: 10.1371/journal.pone.0040120
Source: PubMed

ABSTRACT CCCH-type zinc finger proteins comprise a large protein family. Increasing evidence suggests that members of this family are RNA-binding proteins with regulatory functions in mRNA processing. Compared with those in animals, functions of CCCH-type zinc finger proteins involved in plant growth and development are poorly understood.
Here, we performed a genome-wide survey of CCCH-type zinc finger genes in maize (Zea mays L.) by describing the gene structure, phylogenetic relationships and chromosomal location of each family member. Promoter sequences and expression profiles of putative stress-responsive members were also investigated. A total of 68 CCCH genes (ZmC3H1-68) were identified in maize and divided into seven groups by phylogenetic analysis. These 68 genes were found to be unevenly distributed on 10 chromosomes with 15 segmental duplication events, suggesting that segmental duplication played a major role in expansion of the maize CCCH family. The Ka/Ks ratios suggested that the duplicated genes of the CCCH family mainly experienced purifying selection with limited functional divergence after duplication events. Twelve maize CCCH genes grouped with other known stress-responsive genes from Arabidopsis were found to contain putative stress-responsive cis-elements in their promoter regions. Seven of these genes chosen for further quantitative real-time PCR analysis showed differential expression patterns among five representative maize tissues and over time in response to abscisic acid and drought treatments.
The results presented in this study provide basic information on maize CCCH proteins and form the foundation for future functional studies of these proteins, especially for those members of which may play important roles in response to abiotic stresses.

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    • "CCCH domain-containing proteins have been implicated in multiple biological processes such as plant growth, development, and environmental responses. Previous studies have investigated and analyzed the features and functions of CCCH genes in plants such as Arabidopsis, rice, maize, Populus, and Medicago truncatula (Wang et al. 2008a; Chai et al. 2012; Peng et al. 2012; Zhang et al. 2013). In this study, we identified 62 non-redundant citrus CCCH genes by genome-wide analysis. "
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    ABSTRACT: The CCCH-type zinc finger proteins comprise a large gene family of regulatory proteins and are widely distributed in eukaryotic organisms. The CCCH proteins have been implicated in multiple biological processes and environmental responses in plants. Little information is available, however, about CCCH genes in plants, especially in woody plants such as citrus. The release of the whole-genome sequence of citrus allowed us to perform a genome-wide analysis of CCCH genes and to compare the identified proteins with their orthologs in model plants. In this study, 62 CCCH genes and a total of 132 CCCH motifs were identified, and a comprehensive analysis including the chromosomal locations, phylogenetic relationships, functional annotations, gene structures and conserved motifs was performed. Distribution mapping revealed that 54 of the 62 CCCH genes are unevenly dispersed on the nine citrus chromosomes. Based on phylogenetic analysis and gene structural features, we constructed 5 subfamilies of 62 CCCH members and integrative subfamilies from citrus, Arabidopsis, and rice, respectively. Importantly, large numbers of SNPs and InDels in 26 CCCH genes were identified from Poncirus trifoliata and Fortunella japonica using whole-genome deep re-sequencing. Furthermore, citrus CCCH genes showed distinct temporal and spatial expression patterns in different developmental processes and in response to various stress conditions. Our comprehensive analysis of CleC3Hs is a valuable resource that further elucidates the roles of CCCH family members in plant growth and development. In addition, variants and comparative genomics analyses deepen our understanding of the evolution of the CCCH gene family and will contribute to further genetics and genomics studies of citrus and other plant species.
    MGG Molecular & General Genetics 05/2014; 289(5). DOI:10.1007/s00438-014-0858-9 · 2.83 Impact Factor
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    • "apparently encodes a CCCH zinc finger protein, which contain 1-6 copies of the CCCH motif (Wang et al. 2008; Peng et al. 2012). CCCH zinc finger proteins are involved in regulation of gene expression at the transcriptional and post-transcriptional levels (Pomeranz et al. 2011). "
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    ABSTRACT: We isolated differentially expressed and dark-responsive genes during flower development and opening in petals of morning glory. Flower opening usually depends on petal expansion and is regulated by both genetic and environmental factors. Flower opening in morning glory (Ipomoea nil) is controlled by the dark/light regime just prior to opening. Opening was normal after 8- or 12-h dark periods but progressed very slowly after a 4-h dark period or in continuous light. Four genes (InXTH1-InXTH4) encoding xyloglucan endotransglucosylase/hydrolases (XTHs) and three genes (InEXPA1-InEXPA3) encoding alpha-expansins (EXPAs) were isolated. The expression patterns of InXTH2, InXTH3, and InXTH4 in petals were closely correlated with the rate of flower opening controlled by the length of the dark period prior to opening, but those of the EXPA genes were not. The expression pattern of InXTH1 gene was closely correlated with petal elongation. Suppression subtractive hybridization was used to isolate dark-responsive genes accompanying flower opening. The expressions of ten isolated genes were associated with the length of the dark period prior to flower opening. One gene was highly homologous to Arabidopsis PSEUDO-RESPONSE REGULATOR7, which is associated with the circadian clock and phytochrome signaling; another to Arabidopsis REVEILLE1, which affects the output of the circadian clock. Other genes were related to light responses, plant hormone effects and signal transduction. The possible roles of these genes in regulation of flower opening are discussed.
    Plant Cell Reports 03/2014; DOI:10.1007/s00299-014-1601-z · 2.94 Impact Factor
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    • "CCCH-type zinc finger proteins play important roles in many aspects of plant growth and development (Wang et al. 2008; Lee et al. 2012; Chai et al. 2012). Compared to animals, few CCCH proteins have been studied functionally in plants (Peng et al. 2012). In this study, we characterized a wheat gene, TaZnFP, encoding a plantspecific transcription factor with two CCCH-type zinc finger motifs (Fig. 1). "
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    ABSTRACT: Zinc finger protein is one of the proteins with finger-like domains. CCCH-type zinc finger proteins involved in plant stress tolerance are poorly understood. In this paper, a novel CCCH-type zinc finger protein gene TaZnFP was isolated during analysis of an abiotic stress suppression subtractive hybridization expression library from wheat (Triticum aestivum L.). The TaZnFP gene contains a 1,533 bp open reading frame with no intron and encodes a 55.2 kDa protein with 510 amino acids. Its isoelectric point (pI) is 8.94. The TaZnFP protein contains two typical CCCH-type zinc finger domains (CX9CX5CX3H and CX5CX4CX3H). Transient expression of a 35S::TaZnFP-GFP fusion protein in Arabidopsis mesophyll protoplasts showed that TaZnFP was localized in the cytoplasm. Q-RT-PCR results showed that the TaZnFP transcript was induced by cold, salt (NaCl), drought, and ABA. Overexpression of TaZnFP enhanced drought and salt stress tolerance in transgenic Arabidopsis compared to the control. TaZnFP might be an important regulator responsive to abiotic stresses in plants.
    Acta Physiologiae Plantarum 05/2013; 35(5). DOI:10.1007/s11738-012-1202-9 · 1.52 Impact Factor
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