Genome-wide identification and characterization of cucumber bHLH family genes and the functional characterization of CsbHLH041 in NaCl and ABA tolerance in Arabidopsis and cucumber

Abstract

Background: The basic/helix-loop-helix (bHLH) transcription factor family exists in all three eukaryotic kingdoms as important participants in biological growth and development. To date, the comprehensive genomic and functional analyses of bHLH genes has not been reported in cucumber (Cucumis sativus L.). Results: Here, a total of 142 bHLH genes were identified and classified into 32 subfamilies according to the conserved motifs, phylogenetic analysis and gene structures in cucumber. The sequences of CsbHLH proteins were highly conserved based on the results of multiple sequence alignment analyses. The chromosomal distribution, synteny analysis, and gene duplications of these 142 CsbHLHs were further analysed. Many elements related to stress responsiveness and plant hormones were present in the promoter regions of CsbHLH genes based on a ciselement analysis. By comparing the phylogeny of cucumber and Arabidopsis bHLH proteins, we found that cucumber bHLH proteins were clustered into different functional clades of Arabidopsis bHLH proteins. The expression analysis of selected CsbHLHs under abiotic stresses (NaCl, ABA and low-temperature treatments) identified five CsbHLH genes that could simultaneously respond to the three abiotic stresses. Tissue-specific expression profiles of these five genes were also analysed. In addition, 35S:CsbHLH041 enhanced the tolerance to salt and ABA in transgenic Arabidopsis and in cucumber seedlings, suggesting CsbHLH041 is an important regulator in response to abiotic stresses. Lastly, the functional interoperability network among the CsbHLH proteins was analysed. Conclusion: This study provided a good foundation for further research into the functions and regulatory mechanisms of CsbHLH proteins and identified candidate genes for stress resistance in cucumber.

Current Understanding of bHLH Transcription Factors in Plant Abiotic Stress Tolerance

“…), as well as the increase of their osmotic regulatory ability and oxidative stress tolerance, which is associated with the elevated ABA content and ABA response [ 45 ]. A similar result was obtained for the CsbHLH041 gene from cucumber, which enhances the drought tolerance of Arabidopsis and cucumber seedlings [ 11 ]. These results indicate that bHLH genes play important roles in plant drought tolerance that associate with phytohormone ABA or JA and ROS scavenging, which highlight new areas of interest for research into crop drought tolerance.…”

“…In rice ( Oryza sativa L.), 167 bHLH family members were identified and classified into 22 subfamilies [ 9 ]. In potato ( Solanum tuberosum L.), 124 bHLH genes were identified during a whole-genome analysis [ 10 ], while in cucumber ( Cucumis sativus L.), 142 bHLH genes were identified and classified into 32 subfamilies [ 11 ]. In the common bean ( Phaseolus vulgaris L.), 155 bHLH genes were identified and classified into 21 subfamilies [ 12 ].…”

“…The salt tolerance of Arabidopsis plants was enhanced with the expression of AtMYC2 gene, which is activated by a mitogen-activated protein kinase (MAPK), and is associated with increasing the levels of proline [ 53 ]. The functions of bHLH genes have also been explored in non-model plants; for example, CsbHLH041 from cucumber confers ABA-induced salt tolerance in Arabidopsis and cucumber seedlings [ 11 ]. The transgenic expression of VvbHLH1 from grape ( Vitis vinifera L.) significantly increases flavonoid accumulation and enhances drought tolerance in Arabidopsis [ 54 ], while the overexpression of SlbHLH22 in tomato ( Solanum lycopersicum L.) seedlings improves salt tolerance, enhances ROS scavenging and increases the osmotic adjustment potential [ 55 ].…”

Genome-wide Analysis of Basic Helix-Loop-Helix Family Genes and Expression Analysis in Response to Drought and Salt Stresses in Hibiscus hamabo Sieb. et Zucc

“…The bHLH gene family has been identified in several organisms so far, and has been separated into 15-26 classes in plants based on sequence similarity [13]. In Arabidopsis thaliana, for example, 162 bHLH genes were discovered and divided into 21 subfamilies [14]; 115 bHLH genes, divided into 21 subfamilies, were identified in spine grapes [15]. In red walnut, 102 bHLH genes were discovered, which were split into 15 subfamilies [16].…”

Genome-wide identification and characterization of barley bHLH transcription factors and their expression in response to low nitrogen stress

“…At least 162 and 167 bHLHs have been identi ed in model plants Arabidopsis and rice, respectively [5][6][7]. Recently, 225, 208, 155, 152, 124 and 142 bHLHs were identi ed in wheat, maize, bean, tomato, potato, and cucumber, respectively [4,[8][9][10][11][12]. However, the similar research has been little done in barley, although barley is an important crop worldwide.…”