Systematic analysis of the basic/helix-loop-helix (bHLH) transcription factor family in pummelo (Citrus grandis) and identification of the key members involved in the response to iron deficiency

Abstract

Background: Iron (Fe) deficiency is a common problem in citrus production. As the second largest superfamily of transcription factors (TFs), the basic/helix-loop-helix (bHLH) proteins have been shown to participate in the regulation of Fe homeostasis and a series of other biological and developmental processes in plants. However, this family of members in citrus and their functions in citrus Fe deficiency are still largely unknown. Results: In this study, we identified a total of 128 CgbHLHs from pummelo (Citrus grandis) genome that were classified into 18 subfamilies by phylogenetic comparison with Arabidopsis thaliana bHLH proteins. All of these CgbHLHs were randomly distributed on nine known (125 genes) and one unknown (3 genes) chromosomes, and 12 and 47 of them were identified to be tandem and segmental duplicated genes, respectively. Sequence analysis showed detailed characteristics of their intron-exon structures, bHLH domain and conserved motifs. Gene ontology (GO) analysis suggested that most of CgbHLHs were annotated to the nucleus, DNA-binding transcription factor activity, response to abiotic stimulus, reproduction, post-embryonic development, flower development and photosynthesis. In addition, 27 CgbHLH proteins were predicted to have direct or indirect protein-protein interactions. Based on GO annotation, RNA sequencing data in public database and qRT-PCR results, several of CgbHLHs were identified as the key candidates that respond to iron deficiency. Conclusions: In total, 128 CgbHLH proteins were identified from pummelo, and their detailed sequence and structure characteristics and putative functions were analyzed. This study provides comprehensive information for further functional elucidation of CgbHLH genes in citrus.

Current Understanding of bHLH Transcription Factors in Plant Abiotic Stress Tolerance

“…In iron-restricted environments, the expression of bHLH genes, such as AtbHLH29 , is essential for plants to absorb more iron [ 85 ]. bHLH genes also play vital roles in responding to iron-deficient conditions and regulating iron uptake and balance in fruit trees, such as pummelo ( Citrus grandis L.) [ 86 ]. These results provide insights that could enable the improvement of iron absorption and utilization in environments with low iron levels ( Figure 4 ).…”

Transcriptome Analysis of Korla Fragrant Pear Reveals a Comprehensive Signaling Network in Response to Alternaria alternata Infection

“…MYB family genes are mainly involved in various functions such as anthocyanin biosynthesis, morphogenesis and abiotic stress responses, among others (Wang et al 2004). Zhang et al (2020) found that MYB family genes in wheat can mediate host resistance to the fungal pathogen Bipolaris sorokiniana by regulating the SA signaling pathway and defense-related genes. Zhu et al (2017) reported that MYB family genes might play a regulatory role in the responses of the "Starking Delicious" pear cultivar to A. alternata attack.…”

“…7). However, various studies have shown that bHLH and ARF TFs play key roles in plant growth, development and stress tolerance, but are not stronly correlated with disease resistance (Zhang et al 2020). Therefore, we will not give more details on these TF families here.…”

Automatic identification of players in the flavonoid biosynthesis with application on the biomedicinal plantCroton tiglium

“…MYB sequences of A. thaliana [64], Vitis vinifera [121], Beta vulgaris [122], and Musa acuminata [123] were subject to KIPEs as baits. bHLH bait sequences were collected from A. thaliana [124], V. vinifera [125], Nelumbo nucifera [126], Citrus grandis [127], M. acuminata [128], and Solanum melongena [129]. WD40 sequences of A. thaliana [130], Triticum aestivum [131], and Setaria italica [132] were collected as bait sequences for the identification of the WD40 protein TTG1.…”