A genome-wide analysis of the RNA helicase gene family in Solanum lycopersicum

Helicases belong to a class of molecular motor proteins that are found in yeast, animals, and plants. The helicase family is divided into three subfamilies, including the DEAD-box, DEAH-box and DExD/H-box helicases, which are classified based on variations within a common motif, known as motif II. The RNA helicases are involved in every step of RNA metabolism, including nuclear transcription, pre-mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay, and organellar gene expression. The RNA helicase protein family plays a crucial role in plant growth and development as well as in response to biotic and abiotic stresses. However, unlike Arabidopsis, no detailed information regarding the RNA helicase family is currently available for tomato (Solanum lycopersicum) due to a limited number of whole-genome sequences. In this study, we identified a total of 157 RNA helicase genes in the tomato genome. According to the structural features of the motif II region, we classified the tomato RNA helicase genes into DEAD-box, DEAH-box and DExD/H-box helicase genes. But there are 27 RNA helicases not belonging to this three subfamilies, we called that "other helicase". We mapped the 157 RNA helicase genes onto the tomato chromosomes, which range from chr01 to chr12. Microarray and expressed sequence tag data showed that many of these RNA helicase proteins may be involved in diverse biological processes and responses to various stresses. To our knowledge, this is the first report of a genome-wide analysis of the tomato RNA helicase gene family. This study provides valuable information for understanding the classification and putative functions of the RNA helicase gene family in Solanaceae. (c) 2012 Elsevier B.V. All rights reserved.