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.
Highlights
The Basic helix-loop-helix (bHLH) protein is a kind of transcription factor, and it has DNA binding and dimerization capabilities as bHLH domain existed. bHLH domain contains approximately 60 amino acids with two functionally distinct regions of the HLH region and the basic region (Murre et al, 1989; Ledent and Vervoort, 2001)
Our Nrannotation showed that the grape bHLH family contained some homologous bHLH genes that had been previously reported in Arabidopsis (Feller et al, 2011)
Our results indicated that many grape bHLHs may be involved in the regulation of transcription, as well as many biological processes such as abiotic stress tolerance (Abe et al, 2003; Lee et al, 2005), organ development (Feller et al, 2011), anthocyanin biosynthesis (Mol et al, 1998; Nesi et al, 2000; Winkel-Shirley, 2001), and flavonol biosynthesis (Walker et al, 1999; Nesi et al, 2000; Baudry et al, 2004)
Summary
The bHLH protein is a kind of transcription factor, and it has DNA binding and dimerization capabilities as bHLH domain existed. bHLH domain contains approximately 60 amino acids with two functionally distinct regions of the HLH region and the basic region (Murre et al, 1989; Ledent and Vervoort, 2001). BHLH domain contains approximately 60 amino acids with two functionally distinct regions of the HLH region and the basic region (Murre et al, 1989; Ledent and Vervoort, 2001). The basic region bHLH Genes from Grape contains approximately 17 amino acids, and it is located at the Nterminus of the bHLH domain which allows bHLH transcription factors to bind to a consensus E-box (5′-CANNTG-3′) or Gbox (5′-CACGTG-3′) cis elements to regulate gene expression (Atchley et al, 1999; Massari and Murre, 2000; Toledo-Ortiz et al, 2003; Li et al, 2006). PRE1, PRE2, PRE3, PRE4, and PRE5 are involved in gibberellin signaling transduction in plants (Feller et al, 2011)
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