Identification and function analysis of bHLH genes in response to cold stress in sweetpotato

Functions of Basic Helix-Loop-Helix (bHLH) Proteins in the Regulation of Plant Responses to Cold, Drought, Salt, and Iron Deficiency: A Comprehensive Review

Abiotic stresses including cold, drought, salt, and iron deficiency severely impair plant development, crop productivity, and geographic distribution. Several bodies of research have shed light on the pleiotropic functions of BASIC HELIX-LOOP-HELIX (bHLH) proteins in plant responses to these abiotic stresses. In this review, we mention the regulatory roles of bHLH TFs in response to stresses such as cold, drought, salt resistance, and iron deficiency, as well as in enhancing grain yield in plants, especially crops. The bHLH proteins bind to E/G-box motifs in the target promoter and interact with various other factors to form a complex regulatory network. Through this network, they cooperatively activate or repress the transcription of downstream genes, thereby regulating various stress responses. Finally, we present some perspectives for future research focusing on the molecular mechanisms that integrate and coordinate these abiotic stresses. Understanding these molecular mechanisms is crucial for the development of stress-tolerant crops.

ApCPS2 contributes to medicinal diterpenoid biosynthesis and defense against insect herbivore in Andrographis paniculata

Kalmegh (Andrographis paniculata) spatiotemporally produces medicinally-important ent-labdane-related diterpenoids (ent-LRDs); andrographolide (AD), 14-deoxy-11,12-didehydroandrographolide (DDAD), neoandrographolide (NAD). ApCPS1 and ApCPS2, the ent-copalyl pyrophosphate (ent-CPP)-producing class II diterpene synthases (diTPSs) were identified, but their contributions to ent-CPP precursor supply for ent-LRD biosynthesis were not well understood. Here, we characterized ApCPS4, an additional ent-CPP-forming diTPS. Further, we elucidated in planta function of the ent-CPP-producing diTPSs (ApCPS1,2,4) by integrating transcript-metabolite co-profiles, biochemical analysis and gene functional characterization. ApCPS1,2,4 localized to the plastids, where diterpenoid biosynthesis occurs in plants, but ApCPS1,2,4 transcript expression patterns and ent-LRD contents revealed a strong correlation of ApCPS2 expression and ent-LRD accumulation in kalmegh. ApCPS1,2,4 upstream sequences differentially activated β-glucuronidase (GUS) in Arabidopsis and transiently-transformed kalmegh. Similar to higher expression of ApCPS1 in kalmegh stem, ApCPS1 upstream sequence activated GUS in stem/hypocotyl of Arabidopsis and kalmegh. However, ApCPS2,4 upstream sequences weakly activated GUS expression in Arabidopsis, which was not well correlated with ApCPS2,4 transcript expression in kalmegh tissues. Whereas, ApCPS2,4 upstream sequences could activate GUS expression at a considerable level in kalmegh leaf and roots/calyx, respectively, suggesting the involvement of transcriptional regulator(s) of ApCPS2,4 that might participate in kalmegh-specific diterpenoid pathway. Interestingly, ApCPS2-silenced kalmegh showed a drastic reduction in AD, DDAD and NAD contents and compromised defense against insect herbivore Spodoptera litura. However, ent-LRD contents and herbivore defense in ApCPS1 or ApCPS4-silenced plants remained largely unaltered. Overall, these results suggested an important role of ApCPS2 in producing ent-CPP for medicinal ent-LRD biosynthesis and defense against insect herbivore.

Systematic identification and expression analysis of bHLH gene family reveal their relevance to abiotic stress response and anthocyanin biosynthesis in sweetpotato

BACKGROUND

bHLH transcription factors play significant roles in regulating plant growth and development, stress response, and anthocyanin biosynthesis. Sweetpotato is a pivotal food and industry crop, but little information is available on sweetpotato bHLH genes.

RESULTS

Herein, 227 putative IbbHLH genes were defined on sweetpotato chromosomes, and fragment duplications were identified as the dominant driving force for IbbHLH expansion. These IbbHLHs were divided into 26 subfamilies through phylogenetic analysis, as supported by further analysis of exon-intron structure and conserved motif composition. The syntenic analysis between IbbHLHs and their orthologs from other plants depicted evolutionary relationships of IbbHLHs. Based on the transcriptome data under salt stress, the expression of 12 IbbHLHs was screened for validation by qRT-PCR, and differential and significant transcriptions under abiotic stress were detected. Moreover, IbbHLH123 and IbbHLH215, which were remarkably upregulated by stress treatments, had obvious transactivation activity in yeasts. Protein interaction detections and yeast two-hybrid assays suggested an intricate interaction correlation between IbbHLHs. Besides, transcriptome screening revealed that multiple IbbHLHs may be closely related to anthocyanin biosynthesis based on the phenotype (purple vs. white tissues), which was confirmed by subsequent qRT-PCR analysis.

CONCLUSIONS

These results shed light on the promising functions of sweetpotato IbbHLHs in abiotic stress response and anthocyanin biosynthesis.

A comprehensive overview of omics-based approaches to enhance biotic and abiotic stress tolerance in sweet potato

Biotic and abiotic stresses negatively affect the yield and overall plant developmental process, thus causing substantial losses in global sweet potato production. To cope with stresses, sweet potato has evolved numerous strategies to tackle ever-changing surroundings and biological and environmental conditions. The invention of modern sequencing technology and the latest data processing and analysis instruments has paved the way to integrate biological information from different approaches and helps to understand plant system biology more precisely. The advancement in omics technologies has accumulated and provided a great source of information at all levels (genome, transcript, protein, and metabolite) under stressful conditions. These latest molecular tools facilitate us to understand better the plant's responses to stress signaling and help to process/integrate the biological information encoded within the biological system of plants. This review briefly addresses utilizing the latest omics strategies for deciphering the adaptive mechanisms for sweet potatoes' biotic and abiotic stress tolerance via functional genomics, transcriptomics, proteomics, and metabolomics. This information also provides a powerful reference to understand the complex, well-coordinated stress signaling genetic regulatory networks and better comprehend the plant phenotypic responses at the cellular/molecular level under various environmental stimuli, thus accelerating the design of stress-resilient sweet potato via the latest genetic engineering approaches.

Functional analysis of sweet cherry PavbHLH106 in the regulation of cold stress

KEY MESSAGE

Sweet cherry PavbHLH106 was up-regulated under cold induction and overexpressed to enhance the cold resistance in tobacco by mediating the scavenging of ROS through increasing of antioxidant enzyme activity. Sweet cherry (Prunus avium L.) is an economically important fruit. Chilling requirements are critical during dormancy, but abnormally low temperatures unfavorably affect fruit growth and development. Differences were found in the transcript level of PavbHLH106 under salt, dehydration, and low-temperature treatments, especially in response to cold stress, suggesting that this gene is involved in the regulation of different abiotic stresses. PavbHLH106 is homologous to Arabidopsis thaliana AtbHLH106 with a conserved bHLH domain, and transient expression in tobacco suggests that the protein is localized in the nucleus and has transcriptional activity in yeast. The PavbHLH106 overexpression in tobacco resulted in weaker electrolyte leakages, lower malondialdehyde, and higher proline content than the wild type at low-temperature treatment. Reactive oxygen species accumulation was significantly reduced in the overexpressed lines, negatively correlated with the antioxidant enzyme activity. In addition, overexpression of PavbHLH106 delayed the germination of tobacco seeds and promoted plant growth. Resistance-related genes were expressed more in the overexpressed plants compared to the wild type. PavbHLH106 bound to the PavACO promoter in yeast and potentially interacted with a bHLH162-like transcription factor. These results indicate that PavbHLH106 has various functions and is particularly active in controlling low-temperature stress.

Overexpression of PavbHLH28 from Prunus avium enhances tolerance to cold stress in transgenic Arabidopsis

BACKGROUND

The basic helix-loop-helix (bHLH) gene family is one of plants' largest transcription factor families. It plays an important role in regulating plant growth and abiotic stress response.

RESULTS

In this study, we determined that the PavbHLH28 gene participated in cold resistance. The PavbHLH28 gene was located in the nucleus and could be induced by low temperature. Under the treatment of ABA, PEG, and GA3, the transcript level of PavbHLH28 was affected. At low temperature, overexpression of the PavbHLH28 gene enhanced the cold resistance of plants with higher proline content, lower electrolyte leakage (EL) and malondialdehyde (MDA) content. Compared with the WT plants, the transgenic plants accumulated fewer reactive oxygen species (ROS), and the activity and expression levels of antioxidant enzymes were significantly increased. The expression of proline synthesis enzyme genes was up-regulated, and the transcripts levels of degradation genes were significantly down-regulated. The transcripts abundance of the cold stressed-related genes in the C-repeat binding factor (CBF) pathway was not significantly different between WT plants and transgenic plants after cold stress. Moreover, the PavbHLH28 could directly bind to the POD2 gene promoter and promote its gene expression.

CONCLUSIONS

Overall, PavbHLH28 enhanced the cold resistance of transgenic plants through a CBF-independent pathway, which may be partly related to ROS scavenging.

Comparative Transcriptome Analysis Reveals the Underlying Response Mechanism to Salt Stress in Maize Seedling Roots

Crop growth and development can be impeded by salt stress, leading to a significant decline in crop yield and quality. This investigation performed a comparative analysis of the physiological responses of two maize inbred lines, namely L318 (CML115) and L323 (GEMS58), under salt-stress conditions. The results elucidated that CML115 exhibited higher salt tolerance compared with GEMS58. Transcriptome analysis of the root system revealed that DEGs shared by the two inbred lines were significantly enriched in the MAPK signaling pathway-plant and plant hormone signal transduction, which wield an instrumental role in orchestrating the maize response to salt-induced stress. Furthermore, the DEGs' exclusivity to salt-tolerant genotypes was associated with sugar metabolism pathways, and these unique DEGs may account for the disparities in salt tolerance between the two genotypes. Meanwhile, we investigated the dynamic global transcriptome in the root systems of seedlings at five time points after salt treatment and compared transcriptome data from different genotypes to examine the similarities and differences in salt tolerance mechanisms of different germplasms.

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.

Transcriptome Characterization and Gene Changes Induced by Fusarium solani in Sweetpotato Roots

Sweetpotato (Ipomoea batatas) is an important root crop that is infected by Fusarium solani in both seedling and root stages, causing irregular black or brown disease spots and root rot and canker. This study aims to use RNA sequencing technology to investigate the dynamic changes in root transcriptome profiles between control check and roots at 6 h, 24 h, 3 days, and 5 days post-inoculation (hpi/dpi) with F. solani. The results showed that the defense reaction of sweetpotato could be divided into an early step (6 and 24 hpi) without symptoms and a late step to respond to F. solani infection (3 and 5 dpi). The differentially expressed genes (DEGs) in response to F. solani infection were enriched in the cellular component, biological process, and molecular function, with more DEGs in the biological process and molecular function than in the cellular component. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that the main pathways were metabolic pathways, the biosynthesis of secondary metabolites, and carbon metabolism. More downregulated genes were identified than upregulated genes in the plant-pathogen interaction and transcription factors, which might be related to the degree of host resistance to F. solani. The findings of this study provide an important basis to further characterize the complex mechanisms of sweetpotato resistance against biotic stress and identify new candidate genes for increasing the resistance of sweetpotato.

Genome-Wide Characterization and Expression Analysis of Transcription Factor Families in Desert Moss Syntrichia caninervis under Abiotic Stresses

Transcription factor (TF) families play important roles in plant stress responses. S. caninervis is a new model moss for plant desiccation tolerance studies. Here, we report a high-confidence identification and characterization of 591 TFs representing 52 families that covered all chromosomes in S. caninervis. GO term and KEGG pathway analysis showed that TFs were involved in the regulation of transcription, DNA-templated, gene expression, binding activities, plant hormone signal transduction, and circadian rhythm. A number of TF promoter regions have a mixture of various hormones-related cis-regulatory elements. AP2/ERF, bHLH, MYB, and C2H2-zinc finger TFs were the overrepresented TF families in S. caninervis, and the detailed classification of each family is performed based on structural features. Transcriptome analysis revealed the transcript abundances of some ScAP2/ERF, bHLH, MYB, and C2H2 genes were accumulated in the treated S. caninervis under cold, dehydration, and rehydration stresses. The RT-qPCR results strongly agreed with RNA-seq analysis, indicating these TFs might play a key role in S. caninervis response to abiotic stress. Our comparative TF characterization and classification provide the foundations for functional investigations of the dominant TF genes involved in S. caninervis stress response, as well as excellent stress tolerance gene resources for plant stress resistance breeding.

NAC domain transcription factor gene GhNAC3 confers drought tolerance in plants

Abiotic stress seriously affects the growth, yield, and fiber quality of cotton. It is of great importance to cultivate drought-resistant and salt-tolerant cotton. NAC (NAM, ATAF1/2, and CUC2) is a plant-specific transcription factor, which is widely involved in the response to abiotic stress. Here, we discovered the GhNAC3 gene isolated from the expression profile of drought stress in cotton and verified its functions in cotton. First, GhNAC3 was strongly induced expression by drought and salt stresses. Gene structure analysis revealed that GhNAC3 had a conserved NAC domain and was homologous to several stress-related NAC transcription factors gene of Arabidopsis. Subcellular localization and transcriptional activation assays revealed that GhNAC3 was a nuclear protein with a C-terminal transcriptional activation domain. Overexpression of GhNAC3 enhanced Arabidopsis tolerance to drought stress with reduced sensitivity to ABA, characterized by increased germination and cotyledon rates under drought stress, and promoted root elongation. VIGS silencing of GhNAC3 reduced cotton tolerance to drought stress as indicated by the low water content of the leaves under drought treatment, significantly faster water loss and lower ABA content in detached leaves, along with the accumulation of more hydrogen peroxide (H₂O₂) and malondialdehyde (MDA). In conclusion, GhNAC3 plays an important role in the abiotic stress of cotton, which might have great application potential in molecular breeding of cotton varieties with drought resistance.

Identification of bHLH family genes in Agaricus bisporus and transcriptional regulation of arginine catabolism-related genes by AbbHLH1 after harvest

Basic helix-loop-helix (bHLH) transcription factors (TFs) are widely distributed in eukaryotes and play an important role in biological growth and development. The identification and functional analyses of bHLH genes/proteins in edible mushrooms (Agaricus bisporus) have yet to be reported. In the present study, we identified 10 putative bHLH members carrying the conserved bHLH domains. Phylogenetic analyses revealed that the 10 AbbHLHs were the closest to sequences of species belonging to 7 different fungal subgroups, which was supported by loop length, intron patterns, and key amino acid residues. The substantial increase after harvest and continuously elevated expression of AbbHLH1 during the development until the disruption of mushroom velum, and the preferential expression in cap and gill tissues suggest the important function of AbbHLH1 in postharvest development of A. bisporus. The relationship of arginine catabolism-related genes with the early stage of postharvest continuing development also was revealed by expression determination. Subcellular localization showed that AbbHLH1 could be localized in nucleus. Importantly, the electrophoretic mobility shift and dual-luciferase reporter assays showed that AbbHLH1 activated the promoters of AbOAT, AbSPDS, and AbSAMDC and suppressed the expression of AbARG, AbUREA, and AbODC, probably for the modulation of arginine catabolism and thus control of postharvest mushroom development. Taken together, the available data provide valuable functional insight into the role of AbbHLH proteins in postharvest mushrooms.

Overexpression of MxbHLH18 Increased Iron and High Salinity Stress Tolerance in Arabidopsis thaliana

In the life cycle of apple, it will suffer a variety of abiotic stresses, such as iron stress and salt stress. bHLH transcription factors (TFs) play an indispensable role in the response of plants to stress. In this study, a new bHLH gene named MxbHLH18 was separated from Malus xiaojinensis. According to the results of subcellular localization, MxbHLH18 was localized in the nucleus. Salt stress and iron stress affected the expression of MxbHLH18 in Malus xiaojinensis seedlings to a large extent. Due to the introduction of MxbHLH18, the resistance of Arabidopsis thaliana to salt, high iron and low iron was significantly enhanced. Under the environmental conditions of high iron and low iron, the overexpression of MxbHLH18 increased many physiological indexes of transgenic Arabidopsis compared to wild type (WT), such as root length, fresh weight and iron content. The high level expression of MxbHLH18 in transformed Arabidopsis thaliana can not only increased the content of chlorophyll and proline, as well as increasing the activities of superoxide dismutase (SOD), peroxidase (POD) and catalase (CAT); it also reduced the content of malondialdehyde (MDA), which was more obvious under high salt conditions. In addition, the relative conductivity, H₂O₂ content and O²⁻ content in transgenic Arabidopsis decreased under salt stress. Meanwhile, MxbHLH18 can also regulate the expression of downstream genes associated with salt stress (AtCBF1/2/3, AtKIN1 and AtCOR15a/b) and iron stress (AtIRT1, AtFRO2, AtNAS2, ATACT2, AtZIF1 and AtOPT3). Therefore, MxbHLH18 can actively promote the adaptability of plants to the growth environment of salt and low and/or iron.

Comparative Transcriptome and Interaction Protein Analysis Reveals the Mechanism of IbMPK3-Overexpressing Transgenic Sweet Potato Response to Low-Temperature Stress

The sweet potato is very sensitive to low temperature. Our previous study revealed that IbMPK3-overexpressing transgenic sweet potato (M3) plants showed stronger low-temperature stress tolerance than wild-type plants (WT). However, the mechanism of M3 plants in response to low-temperature stress is unclear. To further analyze how IbMPK3 mediates low-temperature stress in sweet potato, WT and M3 plants were exposed to low-temperature stress for 2 h and 12 h for RNA-seq analysis, whereas normal conditions were used as a control (CK). In total, 3436 and 8718 differentially expressed genes (DEGs) were identified in WT at 2 h (vs. CK) and 12 h (vs. CK) under low-temperature stress, respectively, whereas 1450 and 9291 DEGs were detected in M3 plants, respectively. Many common and unique DEGs were analyzed in WT and M3 plants. DEGs related to low temperature were involved in Ca²⁺ signaling, MAPK cascades, the reactive oxygen species (ROS) signaling pathway, hormone transduction pathway, encoding transcription factor families (bHLH, NAC, and WRKY), and downstream stress-related genes. Additionally, more upregulated genes were associated with the MAPK pathway in M3 plants during short-term low-temperature stress (CK vs. 2 h), and more upregulated genes were involved in secondary metabolic synthesis in M3 plants than in the WT during the long-time low-temperature stress treatment (CK vs. 12 h), such as fatty acid biosynthesis and elongation, glutathione metabolism, flavonoid biosynthesis, carotenoid biosynthesis, and zeatin biosynthesis. Moreover, the interaction proteins of IbMPK3 related to photosynthesis, or encoding CaM, NAC, and ribosomal proteins, were identified using yeast two-hybrid (Y2H). This study may provide a valuable resource for elucidating the sweet potato low-temperature stress resistance mechanism, as well as data to support molecular-assisted breeding with the IbMPK3 gene.

Genome-wide identification of cold-tolerance genes and functional analysis of IbbHLH116 gene in sweet potato

Sweet potato (Ipomoea batatas L.) originated from South America; therefore, it is vulnerable to low temperature. Here, the evolutionary analysis of 22 cold-responsive genes in 35 plant species revealed that the identified MYC-type basic helix-loop-helix (bHLH) transcription factors exhibit diverse structures. We found that the number of bHLH gene family members was significantly lower than that of cold-tolerant species. We further systematically evaluated the gene structure, promoter analysis, synteny analysis, and expression pattern of 28 bHLH gene family members in sweet potato. The basic helix-loop-helix protein 116 (IbbHLH116) has the closest phylogeny to the AtICE1 protein of A. thaliana. However, the IbbHLH116 protein from cold-tolerant variety FS18 showed a 37.90% of sequence homology with AtICE1 protein. Subcellular localization analysis showed that IbbHLH116 is localized in the nucleus. The transcripts of IbbHLH116 were highly accumulated in cold-tolerant genotype FS18, particularly in new leaves and stems, compared to the cold-sensitive genotype NC1 under cold stress. Overexpression of IbbHLH116 in the wild type (Col-0) A. thaliana significantly enhanced cold tolerance in transgenic plants by regulating activities of oxidative protective enzymes, such as peroxidase (POD), superoxide dismutase (SOD), and the contents of malondialdehyde (MDA), proline and soluble proteins. Moreover, overexpression of IbbHLH116 in ice1 mutant A. thaliana fully rescued the cold-sensitive phenotype by promoting the expression of C-repeat binding factors 3 (CBF3). Overexpression of IbbHLH116 in the sweet potato callus also induced the expression of CBF3 under low temperature. These results imply that IbbHLH116 can perform the function of the ICE1 gene in conferring cold tolerance in sweet potato.

Fine-Tuning Cold Stress Response Through Regulated Cellular Abundance and Mechanistic Actions of Transcription Factors

Inflictions caused by cold stress can result in disastrous effects on the productivity and survival of plants. Cold stress response in plants requires crosstalk between multiple signaling pathways including cold, heat, and reactive oxygen species (ROS) signaling networks. CBF, MYB, bHLH, and WRKY families are among the TFs that function as key players in the regulation of cold stress response at the molecular level. This review discusses some of the latest understanding on the regulation of expression and the mechanistic actions of plant TFs to address cold stress response. It was shown that the plant response consists of early and late responses as well as memory reprogramming for long-term protection against cold stress. The regulatory network can be differentiated into CBF-dependent and independent pathways involving different sets of TFs. Post-transcriptional regulation by miRNAs, control during ribosomal translation process, and post-translational regulation involving 26S proteosomic degradation are processes that affect the cellular abundance of key regulatory TFs, which is an important aspect of the regulation for cold acclimation. Therefore, fine-tuning of the regulation by TFs for adjusting to the cold stress condition involving the dynamic action of protein kinases, membrane ion channels, adapters, and modifiers is emphasized in this review.