Genome-Wide Characterization of bHLH Genes in Grape and Analysis of their Potential Relevance to Abiotic Stress Tolerance and Secondary Metabolite Biosynthesis

Abstract

Basic helix-loop-helix (bHLH) transcription factors are involved in many abiotic stress responses as well as flavonol and anthocyanin biosynthesis. In grapes (Vitis vinifera L.), flavonols including anthocyanins and condensed tannins are most abundant in the skins of the berries. Flavonols are important phytochemicals for viticulture and enology, but grape bHLH genes have rarely been examined. We identified 94 grape bHLH genes in a genome-wide analysis and performed Nr and GO function analyses for these genes. Phylogenetic analyses placed the genes into 15 clades, with some remaining orphans. 41 duplicate gene pairs were found in the grape bHLH gene family, and all of these duplicate gene pairs underwent purifying selection. Nine triplicate gene groups were found in the grape bHLH gene family and all of these triplicate gene groups underwent purifying selection. Twenty-two grape bHLH genes could be induced by PEG treatment and 17 grape bHLH genes could be induced by cold stress treatment including a homologous form of MYC2, VvbHLH007. Based on the GO or Nr function annotations, we found three other genes that are potentially related to anthocyanin or flavonol biosynthesis: VvbHLH003, VvbHLH007, and VvbHLH010. We also performed a cis-acting regulatory element analysis on some genes involved in flavonoid or anthocyanin biosynthesis and our results showed that most of these gene promoters contained G-box or E-box elements that could be recognized by bHLH family members.

Timing and Order of the Molecular Events Marking the Onset of Berry Ripening in Grapevine

“…We performed functional analyses of two transcription factor genes selected among the positive biomarkers of transition 1: BASIC HELIX-LOOP-HELIX75 (VvibHLH075), the most relevant transcription factor gene as determined by correlation analysis, and WRKY19 (VviWRKY19), a biomarker of both transitions (Supplemental Data Set S5). Both genes belong to recently described grapevine gene families (Wang et al, 2014(Wang et al, , 2018 and were identified as switch genes of the vegetative-to-mature transition in berry (Palumbo et al, 2014). The expression profiles of both genes highlighted a similar up-regulation before the onset of ripening, but WRKY19 did not decline as much as bHLH075 post veraison ( Fig.…”

Genome-wide analysis of basic helix-loop-helix (bHLH) transcription factors in papaya (Carica papaya L.)

“…Transcription factors (TFs) play key roles in the stress regulation network and signal pathways in plants. Basic/helix-loop-helix (bHLH) TFs are the second largest TFs family in plants and have been identified in many species [6,[18][19][20][21][22][23][24][25]. However, the bHLH TF family has not previously been reported in papaya (Carica papaya L.).…”

“…The detailed information on these CpbHLHs, including protein ID, locus ID, opening reading frame (ORF) lengths, amino acid sequences/lengths, molecular weight, isoelectric point and exon/intron numbers, are listed in Additional file 1. In previous studies, 129/132, 188, 159, 147, 124, 95, 94 and 56 bHLH genes were identified in peanut [18], apple [19], tomato [20], Arabidopsis [6], potato [21], peach [22], grapes [23] and sweet orange [24], respectively. Compared with the above dicotyledonous plants, the density of bHLHs superfamily genes in papaya genome was approximately 0.26%, which is lower than the density of peanut [18], apple [19], tomato [20], arabidopsis [6], potato [21] and sweet orange [24], and similar to peach [22] and wine grapes [23] (Table 1).…”

“…Phylogenetic analyses of some atypical bHLH proteins have even extended that number to 32 [5]. With the availability of genome sequence data and the rapid development of molecular biology, increasing numbers of bHLH subfamily genes have been identified and characterized in a wide range of plant species, including Arabidopsis [6], peanut [18], apple [19], tomato [20], potato [21], peach [22], grapes [23], sweet orange [24], and bamboo [25]. The results from these studies have shown that bHLH TFs have versatile biological functions, such as regulating light morphogenesis [26,27], hormone signals [28,29], the developmental of root [30] and anther [31], regulating epidermal cell fate determination [32], participating in various biotic and abiotic stress responses [21,33,34], etc.…”

The Dominant and Poorly Penetrant Phenotypes of Maize Unstable factor for orange1 Are Caused by DNA Methylation Changes at a Linked Transposon

“…The broader GO category of response-to-stress (GO:0006950) includes many genes encoding transcription factors, such as MYB, basic helix-loop-helix (bHLH), ethylene response factors, basic leucine zipper domain, WRKY, and NAC (NAM, ATAF1,2 and CUC2) transcription factors, as well as heat shock proteins, peroxidases, Ser/Thr protein kinases, NB-ARC (Nucleotide binding-Apaf1, R proteins, Ced-4) disease resistance proteins, and several genes involved in carbohydrate/sugar metabolism, among others (Figure 8). Among the transcription factors, the bHLH family is large and has diverse functions, including abiotic stress tolerance, anthocyanin biosynthesis, phytochrome signaling, and globulin expression (Wang et al, 2018). Likewise, MYBs are a large and diverse family with members involved in secondary metabolism, cell morphogenesis, the cell cycle, defense, and stress responses (Dubos et al, 2010).…”