Search Results (177)

Rice (Oryza sativa), a crucial global staple, grapples with environmental stress and resource constraints, necessitating sustainable farming. This review explores the transformative role of transcription factors (TFs) in revolutionizing rice agriculture and their potential impact on global food security. It underscores TFs’ pivotal role in gene expression, particularly in responding to environmental stimuli, presenting a promising avenue for enhancing rice resilience. Delving into key TF families in rice, it highlights their multifaceted roles in abiotic stress responses, defense mechanisms, yield improvement, nutrient uptake, seed development, photosynthesis, and flowering regulation. Specific TFs, including DREB (Dehydration-Responsive Element-Binding), WRKY, NAC, MYB (Myeloblastosis), AP2/ERF (APETALA2/Ethylene Responsive Factor), and bHLH (basic Helix–Loop–Helix), are examined for their contributions to stress resilience, defense mechanisms, and yield enhancement. Concrete examples from cutting-edge research illustrate the tangible benefits of harnessing these molecular regulators. However, manipulating TFs presents challenges, necessitating innovative approaches such as predictive models, collaborative field testing, and transparent communication to navigate intricate regulatory networks and regulatory hurdles. Ultimately, a promising future emerges where manipulating rice TFs leads to the development of resilient, high-yielding, and nutritious varieties. Embracing research advancements and addressing existing challenges is imperative to unlock the full potential of these concealed regulators, ensuring sustainable food security for a growing global population. Full article

Seed germination is a critical phase in the plant lifecycle of Camellia oleifera (oil tea), directly influencing seedling establishment and crop reproduction. In this study, we examined transcriptomic and physiological changes across five defined germination stages (G0–G4), from radicle dormancy to cotyledon emergence. Using RNA sequencing (RNA-seq), we assembled 169,652 unigenes and identified differentially expressed genes (DEGs) at each stage compared to G0, increasing from 1708 in G1 to 10,250 in G4. Functional enrichment analysis revealed upregulation of genes associated with cell wall organization, glucan metabolism, and Photosystem II assembly. Key genes involved in cell wall remodeling, including cellulose synthase (CESA), phenylalanine ammonia-lyase (PAL), 4-coumarate-CoA ligase (4CL), caffeoyl-CoA O-methyltransferase (COMT), and peroxidase (POD) showed progressive activation during germination. A Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed dynamic regulation of phenylpropanoid and flavonoid biosynthesis, photosynthesis, carbohydrate metabolism, and hormone signaling pathways. Transcription factors such as indole-3-acetic acid (IAA), ABA-responsive element binding factor (ABF), and basic helix–loop–helix (bHLH) were upregulated, suggesting hormone-mediated regulation of dormancy release and seedling development. Physiologically, cytokinin (CTK) and IAA levels peaked in G4, antioxidant enzyme activities were highest in G2, and starch content increased toward later stages. These findings provide new insights into the molecular mechanisms underlying seed germination in C. oleifera and identify candidate genes relevant to rootstock breeding and nursery propagation. Full article

Brain muscle ARNT-like1 (Bmal1) is a transcriptional factor, consisting of basic helix–loop–helix (bHLH) and PER-ARNT-SIM (PAS) domains, that plays a central role in circadian clock activity. However, the precise roles of the BMAL1-PAS domain, a circadian rhythm-regulating structure, remain unexplored in monocytes. Here, we highlight the BMAL1-PAS domain as a key structure in monocyte pleiotropic functions by using human monocytic cell line THP-1. THP-1 cells lacking the BMAL1-PAS-B domain (THP-1#207) abrogated the circadian expression of core clock genes. THP-1#207 cells exhibited less proliferation, glycolysis and oxidative phosphorylation activity, and LPS-induced IL-1β production, but exhibited more production of LPS-induced IL-10 than THP-1 cells. A quantitative proteomics analysis revealed significant expression changes in ~10% metabolic enzymes in THP-1#207 cells compared to THP-1 cells, including reduction in a rate-limiting enzyme hexokinase2 (HK2) in the glycolytic pathway. Importantly, treatment of THP-1 with 2-deoxy-D-glucose (2-DG), an HK2 inhibitor, largely recapitulated the phenotypes of THP-1#207 cells. These findings suggest that the BMAL1-PAS-B domain is an important structure for the regulation of proliferation, cellular energetics, and inflammatory response in THP-1 cells, at least in part, via the control of glycolytic activity. Thus, the BMAL1-PAS-B domain may become a promising pharmacological target to control inflammation. Full article

Background: Pinus massoniana is a significant lipid-producing tree species in China and a susceptible host for both the pine wood nematode and its insect vector, Monochamus alternatus. The basic helix–loop–helix (bHLH) family of transcription factors play a crucial role in responding to both biotic and abiotic stresses. However, the role of bHLH in terpene-induced defense in P. massoniana remains poorly studied. Results: Transcriptome sequencing using DNA Nanoball Sequencing (DNBSEQ) and PacBio Sequel platforms was performed, revealing differences in gene expression in P. massoniana branch under the simulated feeding treatment of methyl jasmonate (MeJA) spraying. Fifteen bHLH genes were cloned and analyzed, among which eight highly upregulated PmbHLH genes showed similar temporal expression after MeJA treatment and M. alternatus adult feeding. Five highly upregulated bHLH genes with nuclear localization were highly expressed in P. massoniana after M. alternatus feeding and interacted with the promoter of the terpene synthase gene Pm TPS (−)-α-pinene, confirming their involvement in the defense response of P. massoniana against the M. alternatus adult feeding. Conclusions: Our results unveil the temporal changes and the regulation of the induced defense system in P. massoniana mediated by both MeJA signaling and M. alternatus feeding treatment. The potential application for transgenic experiments and the breeding of resistant species in the future were discussed. Full article

Drought stress is one of the primary environmental factors affecting plant survival rates and productivity, and it is a key bottleneck restricting the development of the world kiwifruit industry. Therefore, studying the drought resistance-related genes and drought resistance mechanisms of kiwifruit is essential. The bHLH (basic helix-loop-helix) TF family plays a crucial role in the resistance of kiwifruit to abiotic stresses such as drought stress. In this study, we analyzed the response of the AcbHLH gene in kiwifruit under drought stress based on the kiwifruit genome database, transcriptome data, and metabolome data. One hundred eighty-seven AcbHLH genes were identified via bioinformatics and divided into eighteen subfamilies via phylogenetic analysis. The cis-acting elements of the AcbHLH gene are mainly hormone-related cis-acting elements. Under drought stress, 64 AcbHLH genes were significantly different, 5 AcbHLH genes whose expression significantly differed were randomly selected for qRT-PCR verification, and the correlation between the qRT-PCR results and the transcriptome data was high. The determination of plant hormone contents revealed that the contents of plant hormones, such as JA, changed markedly before and after drought stress. Through the combined analysis of transcriptome and metabolome data, it was speculated that AcbHLH84 and AcbHLH97 have functions similar to those of the MYC2 transcription factor and are the main downstream effectors in the JA signaling pathway; these functions could be activated and participate in the JA signaling pathway and that the activation of the JA signaling pathway would inhibit the production of reactive oxygen species. In turn, the drought resistance of kiwifruit is improved. The AcbHLH84 and AcbHLH97 genes could be candidate genes for breeding new transgenic drought-resistant kiwifruit varieties. Full article

The occurrence of anthocyanins in rice (Oryza sativa) and barley (Hordeum vulgare) varies among cultivars, with pigmented varieties (e.g., black rice and purple barley) accumulating higher concentrations due to genetic and environmental factors. The biosynthesis of anthocyanins is regulated by a complex network of structural and regulatory genes. Key enzymes in the pathway include chalcone synthase (CHS), chalcone isomerase (CHI), flavanone 3-hydroxylase (F3H), dihydroflavonol 4-reductase (DFR), anthocyanidin synthase (ANS), and UDP-glucose flavonoid 3-O-glucosyltransferase (UFGT). These genes are tightly controlled by transcription factors (TFs) from the MYB, bHLH (basic helix–loop–helix), and WD40 repeat families, which form the MBW (MYB-bHLH-WD40) regulatory complex. In rice, OsMYB transcription factors such as OsMYB3, OsC1, and OsPL (Purple Leaf) interact with OsbHLH partners (e.g., OsB1, OsB2) to activate anthocyanin biosynthesis. Similarly, in barley, HvMYB genes (e.g., HvMYB10) coordinate with HvbHLH TFs to regulate pigment accumulation. Environmental cues, such as light, temperature, and nutrient availability, further modulate these TFs, influencing the production of anthocyanin. Understanding the genetic and molecular mechanisms behind the biosynthesis of anthocyanins in rice and barley provides opportunities for the development of biofortification strategies that enhance their nutritional value. Full article

Apple (Malus domestica Borkh.) is an economically important fruit. The use of nitrate by plants plays a crucial role in their growth and development, and its absorption and dispersal are controlled by nitrate transport proteins (NRTs). In this study, we investigated the potential function of MdNRT2.4 under low-nitrogen (N) stress by overexpressing it in tobacco. Compared with plants treated with a normal nitrogen level (5 mM), the MdNRT2.4 overexpression lines under low-N stress (0.25 mM) exhibited significantly greater plant height and width, as well as larger leaves and a higher leaf density, than wild-type plants, suggesting that the overexpression of MdNRT2.4 enhances the low-N tolerance of tobacco. Enhanced antioxidant enzyme activities in the MdNRT2.4 overexpression plant lines promoted the scavenging of reactive oxygen species, which reduced damage to their cell membranes. GUS staining of pMdNRT2.4::GUS-transformed Arabidopsis thaliana lines showed that MdNRT2.4 was expressed in the roots, vascular bundles, seeds in fruit pods, and young anther sites, suggesting that MdNRT2.4 mediates the transport of nitrate to these tissues, indicating that MdNRT2.4 might promote nitrate utilization in apple and improve its tolerance to low-N stress. Experiments using yeast one-hybrid and dual-luciferase assays revealed that MdbHLH3 binds to the MdNRT2.4 promoter and activates its expression. MdbHLH3 belongs to the basic helix–loop–helix (bHLH) transcription factor (TF). It is speculated that MdbHLH3 may interact with the promoter of MdNRT2.4 to regulate N metabolism in plants and enhance their low-N tolerance. This study establishes a theoretical framework for investigating the regulatory mechanisms of low-N responsive molecules in apple, while simultaneously providing valuable genetic resources for molecular breeding programs targeting low-N tolerance. Full article

Basic helix–loop–helix (bHLH) transcription factors, such as those in the atonal family, are important in cellular fate determination. The expression of the sponge ortholog of the atonal bHLH gene family, AmqbHLH1, in Xenopus laevis previously resulted in the formation of ectodermal ectopic neurons. However, the extent to which these neurons persist through development and the effects on the inner ear and lateral line, which require a critical level and timing of bHLH genes, remains unexplored. To test these long-term effects, we injected various concentrations of AmqbHLH1 mRNA into X. laevis embryos and assessed neurosensory development at developmental stages coinciding with fully developed neurosensory structures. The expression of AmqbHLH1 mRNA in X. laevis resulted in a dose-dependent reduction in or loss of ears and the lateral line system without eliminating ectopic neurons. At the lowest concentrations examined, we found that inner ear neurosensory development consisted sometimes of only a few scattered hair cells in a single-layer epithelium. Furthermore, low concentrations of AmqbHLH1 mRNA affected inner ear afferent guidance. Our data suggest that the AmqbHLH1 gene has some anti-neurosensory abilities in frogs and that the overexpression of a single gene may not be sufficient for stable long-term transdifferentiation in cells. Full article

Basic helix–loop–helix (bHLH) transcription factors play significant roles in plant growth and organ development and diverse biochemical processes. However, the function of bHLH transcription factors in woody plants is not fully understood. In this study, the bHLH gene family in Rhododendron × pulchrum Sweet was identified and characterized using whole-genome data. A total of 109 bHLH family genes (RpbHLHs) were identified in R. pulchrum, and their expression levels were analyzed in flowers of different colors and developmental stages. The results showed that the RpbHLH family is divided into 24 subfamilies. Chromosomal localization and collinearity analyses revealed numerous duplication events during evolution, which is one of the main reasons for the diversification of gene functions. The bHLH domains showed relative conservation of RpbHLH proteins. In the promoter regions of the RpbHLHs, various cis-regulatory elements involved in light response, gibberellic acid (GA) response, and abscisic acid (ABA) response were identified. These elements may regulate flower development and pigment synthesis. A Kyoto Encyclopedia of Genes and Genomes (KEGG) functional enrichment analysis of the target RpbHLHs revealed that 25 genes are enriched in the flavonoid biosynthetic pathway. Potential RpbHLHs related to flower development and pigment synthesis were identified through a transcriptome analysis and validated through quantitative reverse transcription PCR (qRT-PCR). This study will enhance our understanding of RpbHLH functions and provide a reference for the study of flower development and coloration in R. pulchrum. Full article

The basic helix-loop-helix (bHLH) gene family has been identified in many species. However, the characteristics and functions in the Magnolia sieboldii K. Koch (M. sieboldii), which is located in one of the original groups of angiosperms, are still unclear. Here, a total of 142 MsbHLH members were identified and divided into 27 subfamilies. MsbHLH proteins are relatively conserved during evolution. Collinearity analysis illustrated that the expansion of the MsbHLH gene family primarily occurred through segmental duplication. All members contain light-responsive elements in their promoters. Different light quality treatments were carried out to simulate the light environment in the forest after seed abscission. It was found that the expression levels of MsPIF1, MsPIF3b, MsPIF4, and MsPIF7 gradually increased under far-red light and inhibited seed germination. Overall, this study lays the foundation for further exploration of the response mechanism of MsPIFs to seed germination under different light qualities. It will provide a reference for the germination of morphophysiological dormant seeds like those of M. sieboldii under light conditions. Full article

The diversity in anthocyanin flower pigmentation is vital in the ornamental plant market. To understand the regulation of the corona filament pigmentation of the Passiflora flower, we investigated the anthocyanin profiles of five distinct species (P. violacea, P. caerulea, P. edulis, P. incarnata, and P. coccinea) using HPLC-MS. A total of 14 anthocyanins, differentially distributed in the analyzed species, were identified as responsible for the differences in corona color, which can be attributed to different ratios of pelargonidin, cyanidin, and delphinidin. Additionally, we evaluated the expression of some biosynthetic genes, including dehydroflavonol reductase (DFR), flavonoid 3′-hydroxylase (F3′H), and flavonoid 3′,5′-hydroxylase (F3′5′H). F3′H seems to regulate the accumulation of cyanidins, F3′5′H determines blue pigmentation, and DFR enhances the biosynthesis of pelargonidins. Furthermore, three genes coding for key transcription factors, Myeloblastosis (MYB), basic helix-loop-helix (bHLH), and WD repeat protein (WD40), were examined using qPCR. The results confirm that such genes regulate anthocyanin biosynthesis and provide insight into the molecular mechanisms that underlie pigment biosynthesis for application in biotechnologies. Full article

As the second largest family of transcription factors (TFs) in plants, basic helix–loop–helices (bHLHs) play key roles in regulating plant growth and development and responding to environmental stress. As the fastest growing Citrus variety in China in recent years, Orah mandarin has vital economic and nutritional value. Although a comprehensive genome-wide analysis of the bHLH TF family has been performed in many plants, a systematic study of the genes of this family has not been carried out in Orah mandarin. In this study, 114 bHLH TFs were identified in Orah mandarin via genome-wide analysis and were classified into 27 subfamilies according to the evolutionary tree. The gene expression profile revealed that five genes were significantly upregulated at 12 h and 24 h after low-temperature stress treatment. In addition, soluble sugars, soluble proteins, and proline contents increased with increasing low-temperature stress, which promoted the expression of the CrbHLH46 gene, thus mediating the interconversion pathway of pentose and glucose to improve the cold tolerance of Orah mandarin. The results help explore the characteristics and functions of CrbHLH genes and provide a basis for further research on the Orah mandarin resistance to low-temperature stress. Full article

Grape (Vitis vinifera) is a popular fruit with a rich color, favorable taste, and high nutritional quality. The formation of the color of its berries is primarily determined by anthocyanin composition and concentration. Basic helix–loop–helix proteins (bHLHs) serve as critical modulators of anthocyanin synthesis, yet many bHLHs in grape have not been systematically studied and remain uncharacterized. In this study, we tracked and detected berry components in ‘Moldova’ grapes during three developmental stages using UPLC-MS/MS and identified malvidin derivatives as the primary main anthocyanins. Our transcriptome sequencing analysis revealed 40 genes and several transcription factors (TFs) involved in anthocyanin pathways and berry coloration, with VvCHS2 (Vitvi05g01044) showing the highest expression. Among TFs, six bHLH candidates were identified, and VvbHLH137 was determined to positively regulate anthocyanin synthesis. The over-expression of VvbHLH137 in Arabidopsis thaliana significantly augmented the anthocyanin content. In addition, VvbHLH137 was found to form interactions with VvMYB15, VvMYB44, and VvMYB306 to impact anthocyanin accumulation. It also directedly stimulates VvDFR and VvF3H transcription via binding to their promoters. These findings provide insights into anthocyanin synthesis in grapes and support molecular breeding efforts for grape cultivars with enhanced coloration. Full article

Background: Basic helix–loop–helix (bHLH) transcription factors (TFs) widely exist in eukaryotic organisms and play a key role in plant growth and development in response to environmental stresses. Sanghuangporus baumii, an important medicinal mushroom known for its anticancer properties, has limited research on the bHLH gene family. Methods: This research utilized the genomic data from S. baumii to identify bHLH family members, and their gene structure, conserved motifs, and phylogenetic relationship were characterized. Additionally, we conducted an analysis of promoter cis-elements and predicted protein interaction networks. We also examined the expression profiles of bHLH genes during different developmental stages and in response to four abiotic stresses: heat, cold, oxidative stress, and heavy metal exposure. Finally, we overexpressed the candidate gene SbbHLH3 in yeast to assess its tolerance to these different stress conditions. Results: A total of 12 SbbHLH genes were identified in S. baumii, and the members of the bHLH gene family displayed a variety of physicochemical characteristics, reflecting their diverse array of functions. Based on homology, the SbbHLH proteins are more closely related to those found in Lentinula edodes and Pleurotus ostreatus. The analysis of promoter cis-elements showed that SbbHLHs contain several elements associated with abiotic stress response, and a network prediction identified 28 bHLH-interacting proteins. Expression pattern analysis revealed that most SbbHLH genes exhibited a positive response to different developmental stages and abiotic stresses. Notably, the overexpression of SbbHLH3 significantly enhanced stress tolerance in yeast. Conclusions: This study provides a comprehensive assessment of the bHLH family in S. baumii, delivering new genetic resources for breeding resistant varieties. Full article

The trichomes of mustard leaves have significance due to their ability to combat unfavorable external conditions and enhance disease resistance. It was demonstrated that the MYB-bHLH-WD40 (MBW) ternary complex consists of MYB, basic Helix-Loop-Helix (bHLH), and WD40-repeat (WD40) family proteins and plays a key role in regulating trichome formation and density. The bHLH gene family, particularly the Myelocytomatosis (MYC) proteins that possess the structural bHLH domain (termed bHLH-MYC), are crucial to the formation and development of leaf trichomes in plants. bHLH constitutes one of the largest families of transcription factors in eukaryotes, of which MYC is a subfamily member. However, studies on bHLH-MYC transcription factors in mustard have yet to be reported. In this study, a total of 45 bHLH-MYC transcription factors were identified within the Brassica juncea genome, and a comprehensive series of bioinformatic analyses were conducted on their structures and properties: an examination of protein physicochemical properties, an exploration of conserved structural domains, an assessment of chromosomal positional distributions, an analysis of the conserved motifs, an evaluation of the gene structures, microsynteny analyses, three-dimensional structure prediction, and an analysis of sequence signatures. Finally, transcriptome analyses and a subcellular localization examination were performed. The results revealed that these transcription factors were unevenly distributed across 18 chromosomes, showing relatively consistent conserved motifs and gene structures and high homology. The final results of the transcriptome analysis and gene annotation showed a high degree of variability in the expression of bHLH-MYC transcription factors. Five genes that may be associated with trichome development (BjuVA09G22490, BjuVA09G13750, BjuVB04G14560, BjuVA05G24810, and BjuVA06G44820) were identified. The subcellular localization results indicated that the transcription and translation products of these five genes were expressed in the same organelle: the nucleus. This finding provides a basis for elucidating the roles of bHLH-MYC family members in plant growth and development, and the molecular mechanisms underlying trichome development in mustard leaves. Full article