Genome-wide analysis and identification of stress-responsive genes of the CCCH zinc finger family in Solanum lycopersicum

Zinc finger genes comprise a large and diverse gene family. Based on their individual finger structures and spacing, zinc finger proteins are further divided into different families according to their specific molecular functions. Genes in the CCCH family encode zinc finger proteins containing a motif with three cysteines and one histidine. They play important roles in plant growth and development, and in response to biotic and abiotic stresses. However, the limited analysis of the genome sequence has meant that there is no detailed information concerning the CCCH zinc finger family in tomato (Solanum lycopersicum). Here, we identified 80 CCCH zinc finger protein genes in the tomato genome. A complete overview of this gene family in tomato was presented, including the chromosome locations, gene duplications, phylogeny, gene structures and protein motifs. Promoter sequences and expression profiles of putative stress-responsive members were also investigated. These results revealed that, with the exception of four genes, the 80 CCCH genes are distributed over all 12 chromosomes with different densities, and include six segmental duplication events. The CCCH family in tomato could be divided into 12 groups based on their different CCCH motifs and into eight subfamilies by phylogenetic analysis. Analysis showed that almost all CCCH genes contain putative stress-responsive cis-elements in their promoter regions. Nine CCCH genes chosen for further quantitative real-time PCR analysis showed differential expression patterns in three representative tomato tissues. In addition, their expression levels indicated that these genes are mostly involved in the response to mannitol, heat, salicylic acid, ethylene or methyl jasmonate treatments. To the best of our knowledge, this is the first report of a genome-wide analysis of the tomato CCCH zinc finger family. Our data provided valuable information on tomato CCCH proteins and form a foundation for future studies of these proteins, especially for those members that may play important roles in stress responses.