Abstract
BackgroundUbiquitous CCCH nucleic acid-binding motif is found in a wide-variety of organisms. CCCH genes are involved in plant developmental processes and biotic and abiotic stress responses. Brassica rapa is a vital economic crop and classical model plant of polyploidy evolution, but the functions of CCCH genes in B. rapa are unclear.ResultsIn this study, 103 CCCH genes in B. rapa were identified. A comparative analysis of the chromosomal position, gene structure, domain organization and duplication event between B. rapa and Arabidopsis thaliana were performed. Results showed that CCCH genes could be divided into 18 subfamilies, and segmental duplication might mainly contribute to this family expansion. C-X7/8-C-X5-C3-H was the most commonly found motif, but some novel CCCH motifs were also found, along with some loses of typical CCCH motifs widespread in other plant species. The multifarious gene structures and domain organizations implicated functional diversity of CCCH genes in B. rapa. Evidence also suggested functional redundancy in at least one subfamily due to high conservation between members. Finally, the expression profiles of subfamily-IX genes indicated that they are likely involved in various stress responses.ConclusionThis study provides the first genome-wide characterization of the CCCH genes in B. rapa. The results suggest that B. rapa CCCH genes are likely functionally divergent, but mostly involved in plant development and stress response. These results are expected to facilitate future functional characterization of this potential RNA-binding protein family in Brassica crops.
Highlights
IntroductionCCCH genes are involved in plant developmental processes and biotic and abiotic stress responses
Ubiquitous CCCH nucleic acid-binding motif is found in a wide-variety of organisms
We identified and reaffirmed 103 CCCH zinc finger proteins by SMART and NCBI in B. rapa (Additional file 1). 102 of the 103 corresponding CCCH genes were mapped to chromosome A01-A10 (Fig. 1)
Summary
CCCH genes are involved in plant developmental processes and biotic and abiotic stress responses. Brassica rapa is a vital economic crop and classical model plant of polyploidy evolution, but the functions of CCCH genes in B. rapa are unclear. TFs play vital roles in response to biotic stresses, such as bacterial, fungal, and viral attacks [11], as well as. Zinc finger motif is a small, functional, independently folded domain [16,17,18]. Zinc finger proteins play a multi-faceted role in numerous biological processes, including DNA recognition, RNA packaging, transcriptional activation or repression, regulation of apoptosis, protein folding and assembly, and lipid binding [18, 19]. Fourteen zinc finger families have been found in plants, in which DNA or protein binding proteins are over-represented [20]
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