title: Transcriptome-wide analysis of basic helix-loop-helix transcription factors in Isatis indigotica and their methyl jasmonate responsive expression profiling.
abstract: Jasmonates (JAs) act as conserved elicitors of plant secondary metabolism. JAs perception triggers extensive transcriptional reprogramming leading to activation of the entire metabolic pathways. The family of basic helix-loop-helix (bHLH) transcription factors (TFs) has essential roles in JA signaling; however, little is known about their roles in regulation of secondary metabolites in Isatis indigotica. In this study, we identified 78 putative IibHLH sequences using the annotation of I. indigotica transcriptome. The identified proteins were characterized based on phylogenetic and conserved motif analyses. Using RNA sequencing, 16 IibHLHs showed significant positive response to MeJA (methyl jasmonate) at 1h, indicating their roles as early signaling events of JA-mediated transcriptional reprogramming. Ten IibHLHs presented co-expression pattern with biosynthetic pathway genes, suggesting their regulating role in secondary metabolite synthesis. These gene expression profiling data indicate that bHLHs can be used as candidate genes in molecular breeding programs to improve metabolite production in I. indigotica.
authors.affiliation: Department of Pharmacy, Changzheng Hospital, Second Military Medical University, Shanghai 200003, China; Department of Pharmaceutical Botany, School of Pharmacy, Second Military Medical University, Shanghai 200433, China. Electronic address: zhanglei@smmu.edu.cn.
authors.forename: Lei
authors.initials: L
authors.lastname: Zhang
authors.affiliation: Department of Pharmacy, Changzheng Hospital, Second Military Medical University, Shanghai 200003, China. Electronic address: chenjf@smmu.edu.cn.
authors.forename: Junfeng
authors.initials: J
authors.lastname: Chen
authors.affiliation: Department of Pharmacy, Changzheng Hospital, Second Military Medical University, Shanghai 200003, China. Electronic address: qli@smmu.edu.cn.
authors.forename: Qing
authors.initials: Q
authors.lastname: Li
authors.affiliation: Department of Pharmacy, Changzheng Hospital, Second Military Medical University, Shanghai 200003, China. Electronic address: chenwanshengs@smmu.edu.cn.
authors.forename: Wansheng
authors.initials: W
authors.lastname: Chen
mesh_terms: D000085:Acetates / Q000378:metabolism*; D051778:Basic Helix-Loop-Helix Leucine Zipper Transcription Factors / Q000235:genetics / Q000378:metabolism; D003517:Cyclopentanes / Q000378:metabolism*; D020869:Gene Expression Profiling / Q000379:methods; D031219:Isatis / Q000235:genetics / Q000378:metabolism; D054883:Oxylipins / Q000378:metabolism*; D015398:Signal Transduction / Q000502:physiology*; D059467:Transcriptome / Q000502:physiology*
chemical_list: D000085:Acetates; D051778:Basic Helix-Loop-Helix Leucine Zipper Transcription Factors; D003517:Cyclopentanes; D054883:Oxylipins; C072239:methyl jasmonate
keywords: Basic helix-loop-helix transcription factors; Isatis indigotica; Lignan; Methyl jasmonate; Radix isatidis; Transcriptome profiling