Basic leucine zipper (bZIP) transcription factor genes and their responses to drought stress in ginseng, Panax ginseng C.A. Meyer

Genome-wide identification, expression analysis, and stress response analysis of the RdbZIP gene family in Rhododendron delavayi

BACKGROUND

Basic leucine zipper (bZIP) gene family members represent one of the most diverse and largest groups of transcription factors in eukaryotes. Research has demonstrated that bZIP transcription factors play crucial roles not only in plant growth and development but also in response to various abiotic stresses. However, studies focusing on bZIP factors in Rhododendron delavayi (RdbZIPs) remain limited.

RESULT

In this study, a total of 59 RdbZIPs were identified using bioinformatics approaches, and these could be classified into 13 subfamilies based on the genomic data of R. delavayi. Members of the same RdbZIP subfamily exhibited similar gene structures and conserved motifs, and were unevenly distributed across the 13 chromosomes of R. delavayi. Collinearity analysis revealed a total of 20 duplication events, comprising 3 pairs of tandem duplications and 17 pairs of segmental duplications. Additionally, cis-acting element analysis indicated that RdbZIP family members may be involved in various biological processes, including transcription, development, hormone regulation, and responses to biotic and abiotic stresses. Transcriptomic analysis revealed that RdbZIP family genes were highly expressed in reproductive tissues. RT-qPCR expression analysis revealed that many selected RdbZIP genes were significantly upregulated under high salinity and drought conditions, suggesting their potential involvement in stress-responsive regulatory networks.

CONCLUSION

This study provides the first comprehensive characterization of the bZIP transcription factor family in Rhododendron delavayi, laying a foundational framework for functional studies of individual RdbZIP genes. The results highlight the pivotal role of RdbZIP genes in abiotic stress tolerance, which is crucial for understanding the adaptive mechanisms of R. delavayi. Future research should focus on the functional validation of key RdbZIP genes and elucidation of their regulatory pathways, which may contribute to the genetic improvement of Rhododendron species under adverse environmental conditions.

CLINICAL TRIAL

Not applicable.

Overexpression of the Transcription Factor GmbZIP60 Increases Salt and Drought Tolerance in Soybean (Glycine max)

The regulation of downstream responsive genes by transcription factors (TFs) is a critical step in the stress response system of plants. While bZIP transcription factors are known to play important roles in stress reactions, their functional characterization in soybeans remains limited. Here, we identified a soybean bZIP gene, GmbZIP60, which encodes a protein containing a typical bZIP domain with a basic region and a leucine zipper region. Subcellular localization studies confirmed that GmbZIP60 is localized in the nucleus. Expression analysis demonstrated that GmbZIP60 is induced by salt stress, drought stress, and various plant hormone treatments, including abscisic acid (ABA), ethylene (ETH), and methyl jasmonate acid (MeJA). Overexpressing GmbZIP60 (OE-GmbZIP60) in transgenic soybean and rice enhanced tolerance to both salt and drought stresses. Quantitative real-time polymerase chain reaction (qRT-PCR) analysis indicated that the expression levels of abiotic stress-responsive genes were significantly higher in transgenic plants than in wild-type (WT) plants under stress conditions. Chromatin immunoprecipitation-qPCR (ChIP-qPCR) analysis further confirmed that GmbZIP60 directly binds to the promoters of abiotic stress-related genes induced by ABA, ETH, JA, and salicylic acid (SA). Overall, these findings revealed GmbZIP60 as a positive regulator of salt and drought stress tolerance.

Regulatory networks of bZIPs in drought, salt and cold stress response and signaling

Abiotic stresses adversely impact plants survival and growth, which in turn affect plants especially crop yields worldwide. To cope with these stresses, plant responses depend on the activation of molecular networks cascades, including stress perception, signal transduction, and the expression of specific stress-related genes. Plant bZIP (basic leucine zipper) transcription factors are important regulators that respond to diverse abiotic stresses.By binding to specific cis-elements, bZIPs can control the transcription of target genes, giving plants stress resistance. This review describes the structural characteristics of bZIPs and summarizes recent progress in analyzing the molecular mechanisms regulating plant responses to salinity, drought, and cold in different plant species. The main goal is to deepen the understanding of bZIPs and explore their value in genetic improvement of plants.

Whole Genome Identification and Integrated Analysis of Long Non-Coding RNAs Responding ABA-Mediated Drought Stress in Panax ginseng C.A. Meyer

Panax ginseng C.A. Meyer is a perennial herb that is used worldwide for a number of medical purposes. Long non-coding RNAs (lncRNAs) play a crucial role in diverse biological processes but still remain poorly understood in ginseng, which has limited the application of molecular breeding in this plant. In this study, we identified 17,478 lncRNAs and 3106 novel mRNAs from ginseng by high-throughput illumine sequencing. 50 and 257 differentially expressed genes (DEGs) and DE lncRNAs (DELs) were detected under drought + ABA vs. drought conditions, respectively. The DEGs and DELs target genes main enrichment is focused on the "biosynthesis of secondary metabolites", "starch and sucrose metabolism", and "carbon metabolism" pathways under drought + ABA vs. drought conditions according to KEGG pathway enrichment analysis, suggesting that these secondary metabolites biosynthesis pathways might be crucial for ABA-mediated drought stress response in ginseng. Together, we identified drought stress response lncRNAs in ginseng for the first time and found that the target genes of these lncRNAs mainly regulate the biosynthesis of secondary metabolites pathway to response to drought stress. These findings also open up a new visual for molecular breeding in ginseng.

Transcription factor PgNAC72 activates DAMMARENEDIOL SYNTHASE expression to promote ginseng saponin biosynthesis

Ginsenosides, the primary bioactive constituents in ginseng (Panax ginseng), possess substantial pharmacological potential and are in high demand in the market. The plant hormone methyl jasmonate (MeJA) effectively elicits ginsenoside biosynthesis in P. ginseng, though the regulatory mechanism remains largely unexplored. NAC transcription factors are critical in intricate plant regulatory networks and participate in numerous plant physiological activities. In this study, we identified a MeJA-responsive NAC transcription factor gene, PgNAC72, from a transcriptome library produced from MeJA-treated P. ginseng callus. Predominantly expressed in P. ginseng flowers, PgNAC72 localizes to the nucleus. Overexpressing PgNAC72 (OE-PgNAC72) in P. ginseng callus notably elevated total saponin levels, particularly dammarane-type ginsenosides, by upregulating dammarenediol synthase (PgDDS), encoding a key enzyme in the ginsenoside biosynthesis pathway. Electrophoretic mobility shift assays and dual-luciferase assays confirmed that PgNAC72 binds to the NAC-binding elements in the PgDDS promoter, thereby activating its transcription. Further RNA-seq and terpenoid metabolomic data in the OE-PgNAC72 line confirmed that PgNAC72 enhances ginsenoside biosynthesis. These findings uncover a regulatory role of PgNAC72 in MeJA-mediated ginsenoside biosynthesis, providing insights into the ginsenoside regulatory network and presenting a valuable target gene for metabolic engineering.

Recent trends in ginseng research

Ginseng, the dried root of Panax ginseng, contains ginsenosides and has long been used in Korea, China, and Japan to treat various symptoms. Many studies on the utility of ginseng have been conducted and in this paper we investigate recent trends in ginseng research. P. ginseng studies were collected from scientific databases (PubMed, Web of Science, and SciFindern) using the keywords "Panax ginseng C.A. Meyer", "ginsenosides", "genetic diversity", "biosynthesis", "cultivation", and "pharmacology". We identified 1208 studies up to and including September 2023: 549 studies on pharmacology, 262 studies on chemical components, 131 studies on molecular biology, 58 studies on cultivation, 71 studies on tissue culture, 28 studies on clinical trials, 123 reviews, and 49 studies in other fields. Many researchers focused on the characteristic ginseng component ginsenoside to elucidate the mechanism of ginseng's pharmacological action, the relationship between component patterns and cultivation areas and conditions, and gene expression.

Genome-wide analysis of bZIP transcription factors and their expression patterns in response to methyl jasmonate and low-temperature stresses in Platycodon grandiflorus

Background

Platycodon grandiflorus belongs to the genus Platycodon and has many pharmacological effects, such as expectorant, antitussive, and anti-tumor properties. Among transcription factor families peculiar to eukaryotes, the basic leucine zipper (bZIP) family is one of the most important, which exists widely in plants and participates in many biological processes, such as plant growth, development, and stress responses. However, genomic analysis of the bZIP gene family and related stress response genes has not yet been reported in P. grandiflorus.

Methods

P. grandiflorus bZIP (PgbZIP) genes were first identified here, and the phylogenetic relationships and conserved motifs in the PgbZIPs were also performed. Meanwhile, gene structures, conserved domains, and the possible protein subcellular localizations of these PgbZIPs were characterized. Most importantly, the cis-regulatory elements and expression patterns of selected genes exposed to two different stresses were analyzed to provide further information on PgbZIPs potential biological roles in P. grandiflorus upon exposure to environmental stresses.

Conclusions

Forty-six PgbZIPs were identified in P. grandiflorus and divided into nine groups, as displayed in the phylogenetic tree. The results of the chromosomal location and the collinearity analysis showed that forty-six PgbZIP genes were distributed on eight chromosomes, with one tandem duplication event and eleven segmental duplication events identified. Most PgbZIPs in the same phylogenetic group have similar conserved motifs, domains, and gene structures. There are cis-regulatory elements related to the methyl jasmonate (MeJA) response, low-temperature response, abscisic acid response, auxin response, and gibberellin response. Ten PgbZIP genes were selected to study their expression patterns upon exposure to low-temperature and MeJA treatments, and all ten genes responded to these stresses. The real-time quantitative polymerase chain reaction (RT-qPCR) results suggest that the expression levels of most PgbZIPs decreased significantly within 6 h and then gradually increased to normal or above normal levels over the 90 h following MeJA treatment. The expression levels of all PgbZIPs were significantly reduced after 3 h of the low-temperature treatment. These results reveal the characteristics of the PgbZIP family genes and provide valuable information for improving P. grandiflorus's ability to cope with environmental stresses during growth and development.

Transcriptome-Wide Identification and Integrated Analysis of a UGT Gene Involved in Ginsenoside Ro Biosynthesis in Panax ginseng

Panax ginseng as a traditional medicinal plant with a long history of medicinal use. Ginsenoside Ro is the only oleanane-type ginsenoside in ginseng, and has various pharmacological activities, including anti-inflammatory, detoxification, and antithrombotic activities. UDP-dependent glycosyltransferase (UGT) plays a key role in the synthesis of ginsenoside, and the excavation of UGT genes involved in the biosynthesis of ginsenoside Ro has great significance in enriching ginsenoside genetic resources and further revealing the synthesis mechanism of ginsenoside. In this work, ginsenoside-Ro-synthesis-related genes were mined using the P. ginseng reference-free transcriptome database. Fourteen hub transcripts were identified by differential expression analysis and weighted gene co-expression network analysis. Phylogenetic and synteny block analyses of PgUGAT252645, a UGT transcript among the hub transcripts, showed that PgUGAT252645 belonged to the UGT73 subfamily and was relatively conserved in ginseng plants. Functional analysis showed that PgUGAT252645 encodes a glucuronosyltransferase that catalyzes the glucuronide modification of the C3 position of oleanolic acid using uridine diphosphate glucuronide as the substrate. Furthermore, the mutation at 622 bp of its open reading frame resulted in amino acid substitutions that may significantly affect the catalytic activity of the enzyme, and, as a consequence, affect the biosynthesis of ginsenoside Ro. Results of the in vitro enzyme activity assay of the heterologous expression product in E. coli of PgUGAT252645 verified the above analyses. The function of PgUGAT252645 was further verified by the result that its overexpression in ginseng adventitious roots significantly increased the content of ginsenoside Ro. The present work identified a new UGT gene involved in the biosynthesis of ginsenoside Ro, which not only enriches the functional genes in the ginsenoside synthesis pathway, but also provides the technical basis and theoretical basis for the in-depth excavation of ginsenoside-synthesis-related genes.

Functional Analysis of PbbZIP11 Transcription Factor in Response to Cold Stress in Arabidopsis and Pear

Cold stress is a prominent abiotic factor that adversely affects the growth and yield of pears, consequently restricting the cultivation range and resulting in substantial economic losses for the pear industry. Basic region-leucine zipper (bZIP) transcription factors are widely involved in multiple physiological and biochemical activities of plants, particularly in response to cold stress. In this study, the responsiveness of PbbZIP11 in pear to cold stress was investigated, and its role was explored by using pear callus and Arabidopsis thaliana. The findings revealed that overexpression of PbbZIP11 enhanced the tolerance of pear callus and Arabidopsis thaliana to cold stress. The antioxidant enzyme activities of transgenic plants were enhanced and the expression of C-repeat binding transcription factor (CBF) genes was increased as compared to wild-type plants. To better understand the biological function of PbbZIP11, mRNAs were isolated from overexpressed and wild-type Arabidopsis thaliana after cold stress for whole-genome sequencing. The results showed that the expression of some CBF downstream target genes changed after exposure to cold stress. The results suggested that the PbbZIP11 gene could participate in cold-stress signaling through the CBF-dependent pathway, which provides a theoretical basis for the PbbZIP11-mediated response to cold stress and for the genetic breeding of pear varieties with low-temperature tolerance.

Diversification of plant SUPPRESSOR OF MAX2 1 (SMAX1)-like genes and genome-wide identification and characterization of cotton SMXL gene family

BACKGROUND

Strigolactones (SLs) are a recently discovered class of plant hormones. SUPPRESSOR OF MAX2 1 (SMAX1)-like proteins, key component of the SL signaling pathway, have been studied extensively for their roles in regulating plant growth and development, such as plant branching. However, systematic identification and functional characterization of SMXL genes in cotton (Gossypium sp.), an important fiber and oil crop, has rarely been conducted.

RESULTS

We identified 210 SMXL genes from 21 plant genomes and examined their evolutionary relationships. The structural characteristics of the SMXL genes and their encoded proteins exhibited both consistency and diversity. All plant SMXL proteins possess a conserved Clp-N domain, P-loop NTPase, and EAR motif. We identified 63 SMXL genes in cotton and classified these into four evolutionary branches. Gene expression analysis revealed tissue-specific expression patterns of GhSMXL genes, with some upregulated in response to GR24 treatment. Protein co-expression network analysis showed that GhSMXL6, GhSMXL7-1, and GhSMXL7-2 mainly interact with proteins functioning in growth and development, while virus-induced gene silencing revealed that GhSMAX1-1 and GhSMAX1-2 suppress the growth and development of axillary buds.

CONCLUSIONS

SMXL gene family members show evolutionary diversification through the green plant lineage. GhSMXL6/7-1/7-2 genes play critical roles in the SL signaling pathway, while GhSMXL1-1 and GhSMXL1-2 function redundantly in growth of axillary buds. Characterization of the cotton SMXL gene family provides new insights into their roles in responding to SL signals and in plant growth and development. Genes identified in this study could be used as the candidate genes for improvement of plant architecture and crop yield.

Genome-wide analysis of the C2H2 zinc finger protein gene family and its response to salt stress in ginseng, Panax ginseng Meyer

The C2H2 zinc finger protein (C2H2-ZFP) gene family plays important roles in response to environmental stresses and several other biological processes in plants. Ginseng is a precious medicinal herb cultivated in Asia and North America. However, little is known about the C2H2-ZFP gene family and its functions in ginseng. Here, we identified 115 C2H2-ZFP genes from ginseng, defined as the PgZFP gene family. It was clustered into five groups and featured with eight conserved motifs, with each gene containing one to six of them. The family genes are categorized into 17 gene ontology subcategories and have numerous regulatory elements responsive to a variety of biological process, suggesting their functional differentiation. The 115 PgZFP genes were spliced into 228 transcripts at seed setting stage and varied dramatically in expression across tissues, developmental stages, and genotypes, but they form a co-expression network, suggesting their functional correlation. Furthermore, four genes, PgZFP31, PgZFP78-01, PgZFP38, and PgZFP39-01, were identified from the gene family that were actively involved in plant response to salt stress. These results provide new knowledge on origin, differentiation, evolution, and function of the PgZFP gene family and new gene resources for C2H2-ZFP gene research and application in ginseng and other plant species.

Genome-Wide Identification and Analysis of bZIP Gene Family and Resistance of TaABI5 (TabZIP96) under Freezing Stress in Wheat (Triticum aestivum)

The basic leucine zipper (bZIP) regulates plant growth and responds to stress as a key transcription factor of the Abscisic acid (ABA) signaling pathway. In this study, TabZIP genes were identified in wheat and the gene structure, physicochemical properties, cis-acting elements, and gene collinearity were analyzed. RNA-Seq and qRT-PCR analysis showed that ABA and abiotic stress induced most TabZIP genes expression. The ectopic expression of TaABI5 up-regulated the expression of several cold-responsive genes in Arabidopsis. Physiological indexes of seedlings of different lines under freezing stress showed that TaABI5 enhanced the freezing tolerance of plants. Subcellular localization showed that TaABI5 is localized in the nucleus. Furthermore, TaABI5 physically interacted with cold-resistant transcription factor TaICE1 in yeast two-hybrid system. In conclusion, this study identified and analyzed members of the TabZIP gene family in wheat. It proved for the first time that the gene TaABI5 affected the cold tolerance of transgenic plants and was convenient for us to understand the cold resistance molecular mechanism of TaABI5. These results will provide a new inspiration for further study on improving plant abiotic stress resistance.