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Comprehensive analysis of CCCH zinc-finger-type transcription factors in the Brassica rapa genome

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  • Genetics and Breeding
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Abstract

The CCCH-type zinc finger proteins are characterized by their signature motif of three cysteine and one histidine residues. These proteins are RNA binding proteins that function in plant growth, developmental processes, and responses to various environmental stress conditions. In this study, a comprehensive analysis using computational methods allowed the identification of 63 functionally important CCCH genes in the Brassica rapa genome. Several analyses were carried out on the identified genes to understand their roles in this plant. Comparative phylogenetic analysis classified CCCH genes into six clusters, while motif and structural analyses revealed four unique CCCH motifs including different functional motifs and intron/exon variations unique to plants compared to those in other species. Real-time qRT-PCR analysis of 10 randomly selected genes indicated they function at the early stages rather than the later stages of cold and salt stress. This study provides a basic understanding of potential candidate CCCH genes in B. rapa, their structural variation, expression patterns, and their roles under different stress conditions.

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Acknowledgements

This work was supported by Korea Institute of Planning and Evaluation for Technology in Food, Agriculture, and Forestry (IPET) through Golden Seed Project, funded by Ministry of Agriculture, Food and Rural Affairs (MAFRA) (No. 213006-05-2-SB110). This work was also supported by a Grant from the Korea Institute of Planning and Evaluation for Technology in Food, Agriculture and Forestry (IPET) through Agriculture, Food and Rural Affairs Research Center Support Program (Vegetable Breeding Research Center, 710011-03-1-HD340), funded by Ministry of Agriculture, Food and Rural Affairs (MAFRA).

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  1. Jana Jeevan Rameneni and Vignesh Dhandapani have contributed equally to this work.

Authors and Affiliations

  1. Molecular Genetics and Genomics Laboratory, Department of Horticulture, College of Agriculture and Life Science, Chungnam National University, Daejeon, 34134, South Korea

    Jana Jeevan Rameneni, Vignesh Dhandapani, Parameswari Paul, Sangeeth Prasath Devaraj, Su Ryun Choi, So Young Yi, Man-Sun Kim, Seongmin Hong, Sang Heon Oh & Yong Pyo Lim

  2. Department of Biological Sciences, College of Biological Sciences and Biotechnology, Chungnam National University, Daejeon, 34134, South Korea

    Man-Ho Oh

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  1. Jana Jeevan Rameneni
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Fig. S1

Multiple alignment of C3H protein sequences from B. rapa, A. thaliana, O. sativa, and P. trichocarpa plant species. We used this analysis to construct the phylogenetic tree. (PDF) (PDF 3541 kb)

Fig. S2

Phylogenetic tree of 63 C3H genes in B. rapa. The tree was constructed using a neighbor-joining method with 1000 iterations in the MEGA 6 software. The genes were grouped into six clusters and further sub-grouped into 1-27 categories based on motif conservation. (PDF) (PDF 71 kb)

Fig. S3

Intron/exon structures of 63 BrC3H genes were constructed using GSDS software and divided into 27 sub-groups (1–27). The scale at the bottom of each group indicates the gene length, while the legend defines the intron and exon shapes, intron phases, and untranslated regions (purple). (PDF) (PDF 510 kb)

Fig. S4

The amino acid conservation of C3H motifs that were identified in representative BrC3H genes. Representative proteins for each motif were randomly selected from the multiple protein alignment and show C3H motif conservation, which is highlighted in green rectangular boxes. (TIFF) (TIFF 6746 kb)

Fig. S5

The 25 motifs identified in 63 proteins were divided into 27 sub-groups based on their motif pattern (1–27). The proteins that had unique motif patterns in the respective group were not considered under any sub-group. The scale indicates protein length, while the 25 motifs are indicated by different colored boxes. (PDF) (PDF 246 kb)

Table S1

BrC3H gene-specific primers used for qRT-PCR analysis (DOCX 13 kb)

Table S2

Paralogs and tandem duplicate copies identified among the C3H genes in Brassica rapa (XLSX 15 kb)

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Rameneni, J.J., Dhandapani, V., Paul, P. et al. Comprehensive analysis of CCCH zinc-finger-type transcription factors in the Brassica rapa genome. Hortic. Environ. Biotechnol. 59, 729–747 (2018). https://doi.org/10.1007/s13580-018-0077-0

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