Genome-Wide Identification and Characterization of Melon bHLH Transcription Factors in Regulation of Fruit Development

Genome-wide characterization of the bHLH gene family in Gynostemma pentaphyllum reveals its potential role in the regulation of gypenoside biosynthesis

BACKGROUND

Gynostemma pentaphyllum, an ancient Chinese herbal medicine, serves as a natural source of gypenosides with significant medicinal properties. Basic helix-loop-helix (bHLH) transcription factors play pivotal roles in numerous biological processes, especially in the regulation of secondary metabolism in plants. However, the characteristics and functions of the bHLH genes in G. pentaphyllum remain unexplored, and their regulatory role in gypenoside biosynthesis remains poorly elucidated.

RESULTS

This study identified a total of 111 bHLH members in G. pentaphyllum (GpbHLHs), categorizing them into 26 subgroups based on shared conserved motif compositions and gene structures. Collinearity analysis illustrated that segmental duplications predominately lead to the evolution of GpbHLHs, with most duplicated GpbHLH gene pairs undergoing purifying selection. Among the nine gypenoside-related GpbHLH genes, two GpbHLHs (GpbHLH15 and GpbHLH58) were selected for further investigation based on co-expression analysis and functional prediction. The expression of these two selected GpbHLHs was dramatically induced by methyl jasmonate, and their nuclear localization was confirmed. Furthermore, yeast one-hybrid and dual-luciferase assays demonstrated that GpbHLH15 and GpbHLH58 could bind to the promoters of the gypenoside biosynthesis pathway genes, such as GpFPS1, GpSS1, and GpOSC1, and activate their promoter activity to varying degrees.

CONCLUSIONS

In conclusion, our findings provide a detailed analysis of the bHLH family and valuable insights into the potential use of GpbHLHs to enhance the accumulation of gypenosides in G. pentaphyllum.

Transcriptional and Post-Translational Regulation of Plant bHLH Transcription Factors during the Response to Environmental Stresses

Over the past decades, extensive research has been conducted to identify and characterize various plant transcription factors involved in abiotic stress responses. Therefore, numerous efforts have been made to improve plant stress tolerance by engineering these transcription factor genes. The plant basic Helix-Loop-Helix (bHLH) transcription factor family represents one of the most prominent gene families and contains a bHLH motif that is highly conserved in eukaryotic organisms. By binding to specific positions in promoters, they activate or repress the transcription of specific response genes and thus affect multiple variables in plant physiology such as the response to abiotic stresses, which include drought, climatic variations, mineral deficiencies, excessive salinity, and water stress. The regulation of bHLH transcription factors is crucial to better control their activity. On the one hand, they are regulated at the transcriptional level by other upstream components; on the other hand, they undergo various modifications such as ubiquitination, phosphorylation, and glycosylation at the post-translational level. Modified bHLH transcription factors can form a complex regulatory network to regulate the expression of stress response genes and thus determine the activation of physiological and metabolic reactions. This review article focuses on the structural characteristics, classification, function, and regulatory mechanism of bHLH transcription factor expression at the transcriptional and post-translational levels during their responses to various abiotic stress conditions.

The Key Metabolic Network and Genes Regulating the Fresh Fruit Texture of Jujube (Ziziphus jujuba Mill.) Revealed via Metabolomic and Transcriptomic Analysis

The texture of fresh jujube fruit is related to its popularity and commercial value. The metabolic networks and essential genes that regulate the texture of jujube (Ziziphus jujuba) fruit are still unknown. In this study, two jujube cultivars with significantly different textures were selected by a texture analyzer. The four developmental stages of the exocarp and mesocarp of jujube fruit were studied separately using metabolomic and transcriptomic analyses. Differentially accumulated metabolites were enriched in several critical pathways related to cell wall substance synthesis and metabolism. Transcriptome analysis confirmed this by finding enriched differential expression genes in these pathways. Combined analysis showed that 'Galactose metabolism' was the most overlapping pathway in two omics. Genes such as β-Gal, MYB and DOF may affect fruit texture by regulating cell wall substances. Overall, this study provides an essential reference for the establishment of texture-related metabolic and gene networks of jujube fruit.

Drought stress tolerance mechanisms and their potential common indicators to salinity, insights from the wild watermelon (Citrullus lanatus): A review

Climate change has escalated the effect of drought on crop production as it has negatively altered the environmental condition. Wild watermelon grows abundantly in the Kgalagadi desert even though the environment is characterized by minimal rainfall, high temperatures and intense sunshine during growing season. This area is also characterized by sandy soils with low water holding capacity, thus bringing about drought stress. Drought stress affects crop productivity through its effects on development and physiological functions as dictated by molecular responses. Not only one or two physiological process or genes are responsible for drought tolerance, but a combination of various factors do work together to aid crop tolerance mechanism. Various studies have shown that wild watermelon possess superior qualities that aid its survival in unfavorable conditions. These mechanisms include resilient root growth, timely stomatal closure, chlorophyll fluorescence quenching under water deficit as key physiological responses. At biochemical and molecular level, the crop responds through citrulline accumulation and expression of genes associated with drought tolerance in this species and other plants. Previous salinity stress studies involving other plants have identified citrulline accumulation and expression of some of these genes (chloroplast APX, Type-2 metallothionein), to be associated with tolerance. Emerging evidence indicates that the upstream of functional genes are the transcription factor that regulates drought and salinity stress responses as well as adaptation. In this review we discuss the drought tolerance mechanisms in watermelons and some of its common indicators to salinity at physiological, biochemical and molecular level.

Genome-Wide Identification of bHLH Transcription Factor Family in Malus sieversii and Functional Exploration of MsbHLH155.1 Gene under Valsa Canker Infection

Xinjiang wild apple (Malus sieversii) is an ancient relic; a plant with abundant genetic diversity and disease resistance. Several transcription factors were studied in response to different biotic and abiotic stresses on the wild apple. Basic/helix-loop-helix (bHLH) is a large plant transcription factor family that plays important roles in plant responses to various biotic and abiotic stresses and has been extensively studied in several plants. However, no study has yet been conducted on the bHLH gene in M. sieversii. Based on the genome of M. sieversii, 184 putative MsbHLH genes were identified, and their physicochemical properties were studied. MsbHLH covered 23 subfamilies and lacked two subfamily genes of Arabidopsis thaliana based on the widely used classification method. Moreover, MsbHLH exon-intron structures matched subfamily classification, as evidenced by the analysis of their protein motifs. The analysis of cis-acting elements revealed that many MsbHLH genes share stress- and hormone-related cis-regulatory elements. These MsbHLH transcription factors were found to be involved in plant defense responses based on the protein-protein interactions among the differentially expressed MsbHLHs. Furthermore, 94 MsbHLH genes were differentially expressed in response to pathogenic bacteria. The qRT-PCR results also showed differential expression of MsbHLH genes. To further verify the gene function of bHLH, our study used the transient transformation method to obtain the overexpressed MsbHLH155.1 transgenic plants and inoculated them. Under Valsa canker infection, the lesion phenotype and physiological and biochemical indexes indicated that the antioxidant capacity of plants could increase and reduce the damage caused by membrane peroxidation. This study provides detailed insights into the classification, gene structure, motifs, chromosome distribution, and gene expression of bHLH genes in M. sieversii and lays a foundation for a better understanding disease resistance in plants, as well as providing candidate genes for the development of M. sieversii resistance breeding.

Genome-Wide Identification and Expression Analysis of the bHLH Transcription Factor Family and Its Response to Abiotic Stress in Mongolian Oak (Quercus mongolica)

The basic helix-loop-helix (bHLH) family, one of the largest families of transcription factors in plants, is extensively involved in the growth, development, and stress response of several woody plants. However, no systematic analysis of the bHLH gene family in Quercus mongolica has been reported. We characterize QmbHLH genes and identify the functions of QmbHLH proteins in Q. mongolica. We used bioinformatics approaches, qRT-PCR analysis, and RNA sequencing data to examine chromosomal distributions, gene structures, and conserved patterns, and identified 89 QmbHLH genes, which were divided into 21 subgroups based on the phylogenetic analysis of bHLH genes in Arabidopsis thaliana. Segmental replication played a more prominent role than tandem duplication in the expansion of the QmbHLH gene family. Based on patterns of tissue-specific expression, protein interactions, and cis-element analysis, QmbHLH genes may be extensively involved in the growth and development of Q. mongolica. In leaves, stems, and roots, 12 selected QmbHLH genes exhibited responsiveness to abiotic stresses (salt, cold, weak light, and drought). Our study facilitates follow-up functional investigations of the bHLH gene family in Q. mongolica and provides novel insights into bHLH superfamilies in woody plants.