Genome-wide analysis of bHLH transcription factor and involvement in the infection by yellow leaf curl virus in tomato (Solanum lycopersicum)

Abstract

BackgroundThe basic helix-loop-helix (bHLH) proteins are a superfamily of transcription factors that can bind to specific DNA target sites. They have been well characterized in model plants such as Arabidopsis and rice and have been shown to be important regulatory components in many different biological processes. However, no systemic analysis of the bHLH transcription factor family has yet been reported in tomatoes. Tomato yellow leaf curl virus (TYLCV) threatens tomato production worldwide by causing leaf yellowing, leaf curling, plant stunting and flower abscission.ResultsA total of 152 bHLH transcription factors were identified from the entire tomato genome. Phylogenetic analysis of bHLH domain sequences from Arabidopsis and tomato facilitated classification of these genes into 26 subfamilies. The evolutionary and possible functional relationships revealed during this analysis are supported by other criteria, including the chromosomal distribution of these genes, the conservation of motifs and exon/intron structural patterns, and the predicted DNA binding activities within subfamilies. Distribution mapping results showed bHLH genes were localized on the 12 tomato chromosomes. Among the 152 bHLH genes from the tomato genome, 96 bHLH genes were detected in the TYLCV-susceptible and resistant tomato breeding line before (0 dpi) and after TYLCV (357 dpi) infection. As anticipated, gene ontology (GO) analysis indicated that most bHLH genes are related to the regulation of macromolecule metabolic processes and gene expression. Only four bHLH genes were differentially expressed between 0 and 357 dpi. Virus-induced gene silencing (VIGS) of one bHLH genes SlybHLH131 in resistant lines can lead to the cell death.ConclusionIn the present study, 152 bHLH transcription factor genes were identified. One of which bHLH genes, SlybHLH131, was found to be involved in the TYLCV infection through qRT-PCR expression analysis and VIGS validation. The isolation and identification of these bHLH transcription factors facilitated clarification of the molecular genetic basis for the genetic improvement of tomatoes and the development of functional gene resources for transgenic research. In addition, these findings may aid in uncovering an unexplored mechanism during the TYLCV infection in tomatoes.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1249-2) contains supplementary material, which is available to authorized users.

Genome-wide analysis of basic/helix-loop-helix gene family in peanut and assessment of its roles in pod development

“…Generally, transcriptional regulators within the same clade may exhibit recent common evolutionary origins and conserved molecular functions [ 12 ]. Notably, seven peanut bHLH proteins including Aradu.5CX4U, Araip.P4GTD, Aradu.Y3AAH, Araip.UVF95, Aradu.GH2K1, Araip.RX20Z and Aradu.0K58L were highly orthologous to SlybHLH131, which has been proved to be involved in resisting to yellow leaf curl virus infection in tomato [ 13 ]. Furthermore, Aradu.QW16A, Araip.X1DZZ, Aradu.LS2KI and Araip.37BUF were orthologous to OsbHLH13 and OsbHLH16 that are involved in anthocyanin biosynthesis [ 36 ].…”

“…For example, Li detected several genes that respond to iron-deficiency and confirmed that two bHLH transcription factors in Arabidopsis , bHLH34 and bHLH104, play major roles in regulating iron homeostasis by activating the transcription of bHLH38/39/100/101 in iron deficient conditions [ 17 ]. In addition, a tomato bHLH gene, SlybHLH131 , was found to be involved in resistance to yellow leaf curl virus infection through virus-induced gene silencing [ 13 ].…”

Genome-Wide Characterization and Analysis of bHLH Transcription Factors Related to Crocin Biosynthesis in Gardenia jasminoides Ellis (Rubiaceae)

“…The subfamily 25 had the largest number of members (11 GjbHLHs), and subfamilies 5, 9, 11, 12, 16, 30, and 32 had one GjbHLH gene each. Subfamilies 17,18,19,20,21,22, and 28 commonly exist in A. thaliana, but no GjbHLH genes were found in these subfamilies. The new subfamilies 32 and 33 were speciesspecific in G. jasminoides.…”

“…The bHLH superfamily, one of the largest TF families in plants, has been indicated to be related to plant development and stress response. The genome-wide identification and analysis of bHLH TFs have been reported in many plants, such as Arabidopsis thaliana [15], Oryza sativa [16], Solanum lycopersicum [17], Brassica rapa [18], Salvia miltiorrhiza [19], Panax ginseng [20], Vitis vinifera [21], Malus domestica [22], and Arachis hypogaea [23]. bHLH TFs can bind to E-box (5 ′ -CANNTG-3 ′ ), MYCATRD22 (5′-CACATG-3′), T/G-box (5′-AACGTG-3′), or G-box (5′-CACGTG-3′) elements to regulate gene expression [24][25][26].…”

“…Thence, the bHLH genes in these species showed significant expansion, compared with V. vinifera and G. jasminoides. In addition, compared with the bHLH family of Arabidopsis, the members of subfamilies 17,18,19,20,21,22, and 28 of bHLH TFs are lost in the G. jasminoides genome, and two new subfamilies 32 and 33 were identified in G. jasminoides. Gene families in plants might primarily evolve through tandem duplication [45].…”