Characterization and Tissue-specific Expression of bHLH Genes in Dimocarpus longan
In plants, the basic helix-loop-helix (bHLH) transcription factors (TFs) play pivotal roles in many biological processes including growth, stress response, and secondary metabolite synthesis. To date, many bHLH genes have been identified and characterized in diverse plant species. However, little is known regarding the bHLH genes in Dimocarpus longan Lour. (D. longan). Based on RNA-seq data, we identified 42 putative bHLH genes from D. longan and determined their putative functions using the NCBI Conserved Domain Search Tool and Pfam databases. The physicochemical properties, phylogenetic relationships, conserved motifs, gene ontology (GO) annotations, protein-protein interactions, and tissue-specific expression patterns of these bHLH genes were systematically explored. In total, ten motifs were found in DlbHLH proteins using MEME, among which two were highly conserved. Phylogenetic tree analysis found that DlbHLH proteins can be divided into nine groups, with group 2 being the largest. GO annotation results showed that the DlHLH genes were involved in various molecular functions. RNA-seq and qRT-PCR results revealed important differences in the expression patterns of 17 of the DlbHLH genes. In particular, DlbHLH-9, DlbHLH-19, DlbHLH-25, DlbHLH-26, and DlbHLH-35 were found to show significantly different expression patterns in root and leaf tissues. The results of this study will further enrich our knowledge regarding bHLH transcription factor genes and lay a foundation for enhancing the production of active secondary metabolites by genetic engineering in D. longan.
Chao G, Sun J, Wang C, Dong Y, Xiao S, Wang X, Jiao Z (2017). Genome-wide analysis of basic/helix-loop-helix gene family in peanut and assessment of its roles in pod development. PLoS One 12(7):e0181843.
Chu Y, Xiao SM, Su H, Liao BS, Zhang JJ, Xu J, Chen SL (2018). Genome-wide characterization and analysis of bHLH transcription factors in Panax ginseng. Acta Pharmaceutica Sinica B 8(4):666-677.
Conesa A, Gotz S (2008). Blast2GO: A comprehensive suite for functional analysis in plant genomics. International Journal of Plant Genomics 2008:1-12.
Gantet P, Memelink J (2002). Transcription factors: tools to engineer the production of pharmacologically active plant metabolites. Trends in Pharmacological Sciences 23(12):563-569.
Goodrich J, Carpenter R, Coen ES (1992). A common gene regulates pigmentation pattern in diverse plant species. Cell 68(5):955-964.
Guo XJ, Wang JR (2017). Global identification, structural analysis and expression characterization of bHLH transcription factors in wheat. BMC Plant Biology 17(1):90.
Guruprasad K, Reddy BVB, Pandit MW (1990). Correlation between stability of a protein and its dipeptide composition: a novel approach for predicting in vivo stability of a protein from its primary sequence. Protein Engineering, Design and Selection 4(2):155-161.
Heim MA, Jakoby M, Werber M, Martin C, Weisshaar B, Bailey PC (2003). The basic helix-loop-helix transcription factor family in plants: a genome-wide study of protein structure and functional diversity. Molecular Biology and Evolution 20(5):735-747.
Hong GJ, Xue XY, Mao YB, Wang LJ, Chen XY (2012). Arabidopsis MYC2 interacts with DELLA proteins in regulating sesquiterpene synthase gene expression. Plant Cell 24(6):2635-2648.
Jaakola L, Pirttila AM, Halonen M, Hohtola A (2001). Isolation of high quality RNA from bilberry (Vaccinium myrtillus L.) fruit. Molecular Biotechnology 19(2):201-203.
Jue DW, Sang XL, Liu LQ, Shu B, Wang YC, Liu CM, ... Shi SY (2018). Identification of WRKY gene family from Dimocarpus longan and its expression analysis during flower induction and abiotic stress responses. International Journal of Molecular Sciences 19(8):2169.
Kyte J, Doolittle RF (1982). A simple method for displaying the hydropathic character of a protein. Journal of Molecular Biology 157(1):105-132.
Li X, Duan X, Jiang H, Sun Y, Tang Y, Yuan Z, ... Yin J (2006). Genome-wide analysis of basic/helix-loop-helix transcription factor family in rice and Arabidopsis. Plant Physiology 141(4):1167-1184.
Lin YL, Min JM, Lai RL, Wu ZY, Chen YK, Yu LL, ... Lai ZX (2017). Genome-wide sequencing of longan (Dimocarpus longan Lour.) provides insights into molecular basis of its polyphenol-rich characteristics. Gigascience 6(5):1-14.
Ludwig SR, Habera LF, Dellaporta SL, Wessler SR (1989). Lc, a member of the maize R gene family responsible for tissue-specific anthocyanin production, encodes a protein similar to transcriptional activators and contains the myc-homology region. Proceedings of the National Academy of Sciences 86(18):7092-7096.
Massari ME, Murre C (2000). Helix-loop-helix proteins: regulators of transcription in eucaryotic organisms. Molecular and Cellular Biology 20(2):429-440.
Niu X, Guan Y, Chen S, Li H (2017). Genome-wide analysis of basic helix-loop-helix (bHLH) transcription factors in Brachypodium distachyon. BMC Genomics 18(1):619.
Pires N, Dolan L (2010). Origin and diversification of basic-helix-loop-helix proteins in plants. Molecular Biology and Evolution 27(4):862-874.
Schmittgen TD, Livak KJ (2008). Analyzing real-time PCR data by the comparative CT method. Nature Protocols 3(6):1101-1108.
Sun X, Wang Y, Sui N (2018). Transcriptional regulation of bHLH during plant response to stress. Biochemical and Biophysical Research Communications 503(2):397-401.
Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011). MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution 28(10):2731-2739.
Toledo-Ortiz G, Huq E, Quail PH (2003). The Arabidopsis Basic/Helix-Loop-Helix transcription factor family. The Plant Cell 15(8):1749-1770.
Wang J, Hu Z, Zhao T, Yang Y, Chen T, Yang M, ... Zhang B (2015a). Genome-wide analysis of bHLH transcription factor and involvement in the infection by yellow leaf curl virus in tomato (Solanum lycopersicum). BMC Genomics 16(1):39.
Wu P, Song XM, Wang Z, Duan WK, Hu R, Wang WL, ... Hou XL (2016b). Genome-wide analysis of the BES1 transcription factor family in Chinese cabbage (Brassica rapa ssp. pekinensis ). Plant Growth Regulation 80(3):291-301.
Xing BC, Yang DF, Yu HZ, Zhang BX, Yan KJ, Zhang XM, ... Liang ZS (2018a). Overexpression of SmbHLH10 enhances tanshinones biosynthesis in Salvia miltiorrhiza hairy roots. Plant Science 276:229-238.
Xing BC, Liang LJ, Liu L, Hou ZN, Yang DF, Yan KJ, ... Liang ZS (2018b). Overexpression of SmbHLH148 induced biosynthesis of tanshinones as well as phenolic acids in Salvia miltiorrhiza hairy roots. Plant Cell Reports 37(12):1681-1692.
Xue Y, Wang W, Liu Y (2015). Two new flavonol glycosides from Dimocarpus longan leaves. Natural Product Research 29(2):163-168.
Yamamura C, Mizutani E, Okada K, Nakagawa H, Fukushima S, Tanaka A, ... Mori M (2015). Diterpenoid phytoalexin factor, a bHLH transcription factor, plays a central role in the biosynthesis of diterpenoid phytoalexins in rice. Plant Journal 84(6):1100-1113.
Yamasaki K, Kigawa T, Seki M, Shinozaki K, Yokoyama S (2013). DNA-binding domains of plant-specific transcription factors: structure, function, and evolution. Trends in Plant Science 18(5):267-276.
Yang CQ, Fang X, Wu XM, Mao YB, Wang LJ, Chen XY (2012). Transcriptional regulation of plant secondary metabolism. Journal of Integrative Plant Biology 54(10):703-712.
Yu J, Ai G, Shen DY, Chai CY, Jia YL, Liu WJ, ... Dou DL (2019). Bioinformatical analysis and prediction of Nicotiana benthamiana bHLH transcription factors in Phytophthora parasitica resistance. Genomics 111(3):473-482.
Zhang TT, Lv W, Zhang HS, Ma L, Li PH, Ge L, Li G (2018). Genome-wide analysis of the basic Helix-Loop-Helix (bHLH) transcription factor family in maize. BMC Plant Biology 18(1):235.
Zhang X, Luo H, Xu Z, Zhu Y, Ji A, Song J, Chen S (2015). Genome-wide characterization and analysis of bHLH transcription factors related to tanshinone biosynthesis in Salvia miltiorrhiza. Scientific Reports 5:11244.
Copyright (c) 2019 Notulae Botanicae Horti Agrobotanici Cluj-Napoca
This work is licensed under a Creative Commons Attribution 4.0 International License.
Open Access Journal:
The journal allows the author(s) to retain publishing rights without restriction. Users are allowed to read, download, copy, distribute, print, search, or link to the full texts of the articles, or use them for any other lawful purpose, without asking prior permission from the publisher or the author.