Research Article: Genome-wide analysis of the CCCH zinc finger family identifies tissue specific and stress responsive candidates in chickpea (Cicer arietinum L.)

Date Published: July 12, 2017

Publisher: Public Library of Science

Author(s): Seema Pradhan, Chandra Kant, Subodh Verma, Sabhyata Bhatia, Lam-Son Phan Tran.

http://doi.org/10.1371/journal.pone.0180469

Abstract

The CCCH zinc finger is a group of proteins characterised by a typical motif consisting of three cysteine residues and one histidine residue. These proteins have been reported to play important roles in regulation of plant growth, developmental processes and environmental responses. In the present study, genome wide analysis of the CCCH zinc finger gene family was carried out in the available chickpea genome. Various bioinformatics tools were employed to predict 58 CCCH zinc finger genes in chickpea (designated CarC3H1-58), which were analysed for their physio-chemical properties. Phylogenetic analysis classified the proteins into 12 groups in which members of a particular group had similar structural organization. Further, the numbers as well as the types of CCCH motifs present in the CarC3H proteins were compared with those from Arabidopsis and Medicago truncatula. Synteny analysis revealed valuable information regarding the evolution of this gene family. Tandem and segmental duplication events were identified and their Ka/Ks values revealed that the CarC3H gene family in chickpea had undergone purifying selection. Digital, as well as real time qRT-PCR expression analysis was performed which helped in identification of several CarC3H members that expressed preferentially in specific chickpea tissues as well as during abiotic stresses (desiccation, cold, salinity). Moreover, molecular characterization of an important member CarC3H45 was carried out. This study provides comprehensive genomic information about the important CCCH zinc finger gene family in chickpea. The identified tissue specific and abiotic stress specific CCCH genes could be potential candidates for further characterization to delineate their functional roles in development and stress.

Partial Text

The Zinc finger (Znf) family is one of the largest transcription factor families in eukaryotes [1–4] and is known to regulate genes at the transcriptional or posttranscriptional level [1, 5]. Their binding properties depend on the presence of Zinc finger motifs which are characterised by the presence of cysteines and/or histidines which coordinate a zinc ion to form local peptide structures that facilitate specific biological functions [6]. This superfamily has been divided into nine classes depending upon the number as well as the spacing between the conserved Cys and His residues [7, 8] These classes include C2H2, C8, C6, C3HC4, C2HC, C2HC5, C4, C4HC3, and CCCH. A typical CCCH-type zinc finger protein usually contains one or more zinc finger motifs characterised by three Cys (C) residues followed by one His (H) residue. Based on the different numbers of amino acids present between cysteines and histidines in the CCCH motif, a consensus sequence for these motifs was defined as C-X4–15-C-X4–6-C-X3-4-H (X represents any amino acid) [9]. Most transcription factors regulate gene expression through their DNA or protein binding activity [10]. But most CCCH Znf proteins display RNA binding activity [11–13].

Genome wide analysis of gene families provides valuable insights into regulation of biological processes in plants and also serves as a foundation for identifying candidates for further characterisation of important genes. The in silico methods available today have made it possible to predict gene families on a genome wide level. Using these tools genome wide analysis of the CCCH Znf family in chickpea led to the prediction of 58 CCCH Zinc finger genes. Our observations revealed that the genome size does not determine the number of CCCH TFs reported for a species. The number of CCCH TFs identified in chickpea was higher than those predicted in M. truncatula [19] but lower than those reported in Arabidopsis [9], both of which have genome sizes smaller than chickpea. The number of CCCH motifs in each CarC3H gene was seen to range from one to six and even in other plants, as many as six CCCH motifs have been reported to be present in a single CCCH TF [9, 18, 19, 20]. The 58 CarC3H proteins were also seen to exhibit a wide range of isoelectric points (pI). The isoelectric point and charge of a protein are known to be important for its solubility, subcellular localization as well as interaction. There is a correlation between subcellular location and protein pI. For example, proteins in the cytoplasm possess an acidic pI (< 7.4), while those in the nucleus have a more neutral pI (7.4 http://doi.org/10.1371/journal.pone.0180469

 

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