Gene Family Research Articles

Genome-wide identification of SWEET gene family and the sugar transport function of three candidate genes during female flower bud induction stage of Juglans sigillata Dode

Sugar Will Eventually be Exported Transporter (SWEET) transports sugar to sink organs and regulates intercellular sugar transport to provide energy for plant growth and development. In this study, twenty-two SWEET genes were identified and distributed on eleven chromosomes. Phylogenetic tree analysis showed that these genes could be divided into four subfamilies. Metabolism and transcriptome analysis showed that sucrose and fructose were accumulated in female flower buds at physiological differentiation stage (PDS). The third branch of JsSWEET1 and the fourth branch of JsSWEET9 and JsSWEET17 were highly expressed in female flower buds at undifferentiated stage (UDS) and PDS, which promoted sugar accumulation in female flower bud differentiation, so these three candidate SWEET genes were considered to be involved in the accumulation of sugar in the flower bud differentiation of Juglans sigillata. The subcellular localization showed that all three candidate genes were located on the cell membrane, and JsSWEET17 was also expressed and functioned in the vacuolar membrane. Through overexpression in callus and silencing in female flower buds at UDS and PDS, it was found that JsSWEET1 positively regulated the accumulation of sucrose in female flower buds, and JsSWEET9 and JsSWEET17 are involved in the transport and accumulation of fructose during flower bud differentiation. These results could provide a comprehensive understanding of the JsSWEETs gene family and provide theoretical guidance for further study of the function of SWEET-induced sugar accumulation in plant flower development.

Genome-wide identification and expression analysis of genes encoding late embryogenesis proteins in Cicer arietinum

Late embryogenesis abundant (LEA) proteins play defensive roles during seed maturation and seed germination processes. However, there is no such investigation was carried out in chickpea. In present study, genome wide identification and characterization of LEA encoding genes has been investigated, and identified 65 and 74 LEA encoding genes in desi and kabuli cultivar of chickpea, respectively. All these genes have been classified into eight subfamilies on the bases of their phylogenetic analysis and conserved domain. Maximum members of LEA encoding genes were found to be a part of the LEA_2 gene family. The analysis of physicochemical properties of LEAs was also conducted. LEA encoding genes have been found to be located in all chromosomes (8 chr) of chickpea and identified as involved in response to stimulus, biological processes, molecular functions and cellular components based upon gene ontology analysis. Gene expression analysis of randomly selected 8 LEA encoding genes has been carried out during different seed developmental stages which revealed the higher expression of LEA encoding genes during later stage of seed development in chickpea and proved their potential role in desiccation process during seed maturation. During seed germination, expression analysis of LEA encoding genes was found to be higher during the initial stages of seed germination. In conclusion, this work highlights the genome wide identification and characterization of LEA encoding genes in chickpea and proposed potential roles during seed developmental processes. This information could also be useful as a reference investigation for molecular breeding of chickpea for recalcitrant behaviour of seed.

Genome-wide survey of chlorophyllase (CLH) gene family in seven Rosaceae and functional characterization of MdCLH1 in apple (Malus domestica) leaf photosynthesis

Genome-wide survey of chlorophyllase (CLH) gene family in seven Rosaceae and functional characterization of MdCLH1 in apple (Malus domestica) leaf photosynthesis

Integrated Analysis of Polymerase Family Gene Mutations in Acute Myeloid Leukemia: Clinical Features, Prognosis, and Bioinformatics Insights

Background and Objectives: The long-term prognosis of acute myeloid leukemia (AML) is challenging due to limited understanding of the molecular markers involved in its development. This study investigates the role of DNA polymerases in AML to offer new insights for diagnosis and treatment. Materials and Methods: A retrospective study on pediatric AML patients with POL gene family mutations from 2021 to 2024 was conducted. Patients were categorized based on risk stratification criteria, and the DAH regimen was used for induction chemotherapy. Bioinformatics analysis integrated data from various databases to identify key genes and develop survival analysis plots and AUC curves. Results: The study included 59 pediatric AML patients, revealing no significant differences in demographic or clinical characteristics between those with and without POL family gene mutations. However, patients with POL gene mutations showed higher complete remission rates after initial DAH chemotherapy (91.67% vs. 59.57%, p = 0.03607), indicating a potential treatment benefit. High expression of four POL genes (POLD1, POLE, POLG, and POLQ) in bone marrow and immune cells suggests their crucial role in hematopoiesis and immune response. Survival analysis across different datasets indicated that AML patients with overexpressed POL family genes had significantly worse outcomes, proposing these genes as potential prognostic biomarkers for AML. Conclusions: This study on pediatric AML demonstrates that POL gene family mutations are associated with higher remission rates post-chemotherapy, indicating their potential as prognostic markers. Bioinformatics analysis emphasizes the significance of these mutations in AML, highlighting their impact on disease prognosis.

GmSTOP1-3 regulates flavonoid synthesis to reduce ROS accumulation and enhance aluminum tolerance in soybean

Aluminum (Al) toxicity is a significant limiting factor for crop production in acid soils. The functions and regulatory mechanisms of transcription factor STOP1 (Sensitive to Proton Rhizotoxicity 1) family genes in Al-tolerance have been widely studied in many plant species, except for soybean. Here, expression of GmSTOP1-3 was significantly enhanced by Al stress in soybean roots. Overexpression of GmSTOP1-3 resulted in enhanced root elongation and decreased Al content, which was accompanied by increased antioxidant capacity under Al treatment. Furthermore, RNA-seq identified 498 downstream genes of GmSTOP1-3, including genes involved in flavonoid biosynthesis. Among them, the expression of chalcone synthase (GmCHS) and isoflavone synthase (GmIFS) were highly enhanced by GmSTOP1-3 overexpression. Further quantitative flavonoid metabolome analysis showed that overexpression of GmSTOP1-3 significantly increased the content of naringenin chalcone, naringenin, and genistein in soybean roots under Al treatment, which positively correlated with the expression level of the genes relative to flavonoid biosynthesis. Notably, genistein had a significant positive correlation with the expression levels of GmIFS. Combination of Dual Luciferase Complementation (LUC) and Electrophoretic Mobility Shift Assays (EMSA) revealed that GmSTOP1-3 directly bound to the promoters of GmCHS/GmIFS and activated both genes’ transcription. Taken together, these results suggest that GmSTOP1-3 enhances soybean Al tolerance partially through regulating the flavonoid synthesis.

Genome-wide analysis of the R2R3-MYB gene family and identification of candidate genes that regulate isoflavone biosynthesis in red clover (Trifolium pratense)

Red clover (Trifolium pratense) is a perennial legume with high feeding and medicinal value attributed to its abundant isoflavone content. Previous studies reported that R2R3-MYB transcription factors are involved in the biosynthesis of isoflavones; however, their specific role in red clover remains poorly understood. Through comprehensive genome-wide and transcriptome analyses, a total of 138 TpR2R3-MYB genes were identified and classified into 30 distinct subgroups within a phylogenetic tree. Importantly, six of these subgroups showed associations with isoflavone biosynthesis in red clover. The majority of segmental duplication events (Ka/Ks < 1) indicated that the TpR2R3-MYB gene underwent strong purifying selection during evolution. The qRT-PCR analysis demonstrated high expression levels of TpMYB79 and TpMYB53 in Minshan red clover at full flowering stage, consistent with the trend for isoflavone content determination, suggesting that TpMYB79 and TpMYB53 might be important regulators of isoflavone biosynthesis in red clover. Additionally, we observed nucleus and vacuole membrane localization of TpMYB53 and TpMYB79, with TpMYB53 primarily exerting transcriptional activation through its C-terminal activation motifs while TpMYB79 exhibited no transcriptional activity. These findings provided a foundation for the study of the biological function of R2R3-MYB transcription factors in red clover.

GhLCYε-3 characterized as a lycopene cyclase gene responding to drought stress in cotton

Drought stress significantly affects crop productivity. Carotenoids are essential photosynthetic pigment for plants, bacteria, and algae, with signaling and antioxidant functions. Lutein is a crucial branch product in the carotenoid synthesis pathway, which effectively improves the stress tolerance of higher plants. lycopene cyclase, a central enzyme for lutein synthesis, holds great significance in regulating lutein production. This research establishes a correlation between lutein content and stress resistance by measuring the drought resistance and lutein content of various cotton materials. To identify which crucial genes are associated with lutein, the lycopene cyclase family (LCYs) was analyzed. The research found that LCYs form a highly conserved family divided into two subfamilies, LCY-ε (lycopene ε-cyclase) and LCY-β (lycopene β-cyclase). Most members of the LCY family contain photoresponsive elements and abscisic acid elements. qRT-PCR demonstrates showed that most genes responded positively to drought stress, and GhLCYε-3 was expressed significantly differently under drought stress. Virus-induced gene silencing (VIGS) assay showed that the content of GhLCYε-3 was significantly increased with MDA and PRO, and the contents of chlorophyll and lutein were significantly decreased in pYL156 plants. The decrease in GhLCYε-3 expression is speculated to lead to reduced lutein content in vivo, resulting in the accumulation of reactive oxygen species (ROS) and decreased drought tolerance. This research enriched the understanding of LCY gene family and lutein function, and provided a new reference for cotton planting in arid areas. SynopsisLycopene cyclase plays an important role in enhancing the ability of scavenging ROS and drought resistance of plants.

Genome-wide identification of HIPP and mechanism of SlHIPP4/7/9/21/26/32 mediated phytohormones response to Cd, osmotic, and salt stresses in tomato

Heavy-metal-associated isoprenylated plant proteins (HIPPs) contributed to abiotic tolerance in vascular plants. Up to now, the HIPP gene family of tomato (Solanum lycopersicum L.) had not been thoroughly understood. In the present study, 34 SlHIPP genes were identified from the tomato genome using the Hidden Markov Model (HMM). The phylogenetic analysis revealed that the evolution of SlHIPPs was highly conserved. The cis-acting element analysis indicated that SlHIPP genes might be involved in phytohormones and abiotic stresses. We constructed venn diagram with 17 genes containing stress-related motifs as well as 15 genes and 19 genes expressing in leaves and roots in RNA-seq data, suggesting that SlHIPP4/7/9/21/26/32 were selected as candidate genes for study. The quantitative real-time PCR (qRT-PCR) analysis showed that 6 candidate genes were indicated to be involved in osmotic and salt stress tolerance and SlHIPP7/21/26/32 responded to cadmium (Cd) tolerance. The virus-induced silencing of 6 candidate genes caused growth inhibition in stress conditions, further illustrating that 6 candidate genes played a positive role in abiotic conditions. Importantly, the phytohormone analysis implied that 6 candidate genes mediated abscisic acid (ABA), salicylic acid (SA), gibberellin (GA3), auxin (IAA), or methyl jasmonate (MeJA) responses to Cd, osmotic, or salt stress tolerance. These findings indicated that SlHIPP4/7/9/21/26/32 were key regulators of abiotic stress responses in tomato seedlings, functioning through multiple phytohormone pathways.

Comprehensive analysis of Capsicum annuum CaLhcs uncovered the roles of CaLhca5.1 and CaLhcb1.7 in photosynthesis and stress tolerance

The light-harvesting chlorophyll a/b-binding proteins (Lhcs) are integral to plants' capture and transfer of light energy during photosynthesis. However, the Lhc gene family remains unexplored in pepper. In this study, 37 CaLhcs (Capsicum annuum Lhc) were identified from the reference genome and classified into five subfamilies (Lhca, Lhcb, CP24, CP26, and CP29) based on phylogenetic relationships and conserved domains, with members of each subfamily displaying similar conserved motifs and gene structures. cis-element analysis revealed an enrichment of light-responsive elements within CaLhcs (46.1 %). Transcriptome analysis showed that most CaLhcs are specifically expressed in leaves, flowers, and pericarp and are responsive to stressors, including NaCl, cold, heat, H2O2, and d-mannitol. Post-transcriptional regulation analysis identified 11 miRNAs that target nine CaLhcs through cleavage. RT-qPCR analysis validated the involvement of CaLhcs in response to NaCl stress. Localization studies confirmed that CaLhca4.1, CaLhcb1.1, CaLhca1.7, CaLhcb1.11, and CaLhcb6.1 are chloroplast-localized, whereas CaLhca5.1 localizes in the nucleus. Overexpression of CaLhcb1.7 and CaLhca5.1 increased chlorophyll content and net photosynthetic rate, enhancing photosynthesis. Additionally, CaLhcb1.7 and CaLhca5.1 reduced ROS accumulation, bolstering the plant's resistance to pathogens and salt stress. These findings provide a foundation for further exploration of CaLhcs in photosynthesis and stress tolerance mechanisms.

Identification of the FBN gene family in tomato and functional analysis of SlFBN11 in the electron transport under low night temperature

FBNs are lipid-associated proteins that play a critical role in plant growth and stress response. However, the mechanisms of how FBNs proteins participate in the low night temperature response in tomato still unclear. Here we conducted a comprehensive genome-wide analysis of the FBN gene family in Solanum lycopersicum. In total, 14 SlFBN genes were identified, and information on their gene structures, protein motifs, phylogenetic relationships, and stress-related cis-regulatory elements (CREs) was provided. Among these, SlFBN11 was selected as a promising candidate for further functional characterization. The silencing of SlFBN11 destroys the redox balance of the PSI reaction center under low night temperature (LNT) stress, which led to increased ROS accumulation. Surprisingly, we found that the silencing of SlFNR2 also displayed an imbalance in electron transport of the PSI under LNT stress. Further experiments showed SlFBN11 can interact with SlFNR2 to positively response electron transport low night temperature. Collectively, the study provides a comprehensive analysis of the FBN genes family in Solanum lycopersicum and provides a theoretical basis for our understanding of the function of FBN genes in adaptation to LNT stresses.

Analyses of the bHLH gene family in Populus trichocarpa reveal roles of four PtbHLHs in regulating the drought stress response

As one of the largest families of transcription factors in plants, the basic helix-loop-helix (bHLH) transcription factor family regulates a wide range of functions in plants. However, little is known about the functions of bHLH family members in Populus trichocarpa during plant growth and in the response to drought stress. In our study, 190 PtbHLH genes were identified in the P. trichocarpa genome and classified into 21 groups. Analyses of microarray datasets showed that most PtbHLH members not only have multiple functions in poplar growth, but also respond rapidly to drought stress in the leaves or roots. We selected four genes, PtbHLH35, PtbHLH121, PtbHLH137, and PtbHLH152, which were highly expressed in leaves or roots under drought stress, for functional validation analyses. These genes encoded nucleus-localized bHLH transcription factors. Transient expression of PtbHLH35, PtbHLH121, and PtbHLH152 in P. trichocarpa improved drought tolerance by activating the antioxidant system to eliminate reactive oxygen species and reduce the degree of cell damage in the leaves under drought stress. Overexpression of PtbHLH137 improved drought tolerance by activating antioxidant enzymes in the roots to eliminate reactive oxygen species, and by increasing the abscisic acid content in the roots in response to drought stress. Together, our findings provide insights into the functions of PtbHLH family members in growth and in the response to drought.

GhBZR15 improved the tolerance of cotton to cold and salt stress revealed by genome-wide characterization of BZR genes family

Brassinazole resistant (BZR) transcription factors play important roles in brassinosteroids (BRs) signaling pathway of plants, which are involved in many developmental processes and the responses to abiotic stress by regulating the expression of related genes. In order to explore the molecular mechanism of BZR transcription factors in cotton in response to abiotic stress, the BZR transcription factors in four cotton genomes were identified and analyzed. A total of 67 BZR transcription factors were identified and divided into three subfamilies according to their genetic relationship. The expression levels of BZR under cold, heat, salt, and drought treatments were analyzed to predict their function under abiotic stress. Promoter analysis of BZR proteins showed that light signaling can enhance the BZR transcriptional activity. The subcellular localization experiment showed that GhBZR15 protein was mainly distributed in the nucleus. Arabidopsis thaliana L. overexpressing GhBZR15 gene showed stronger cold tolerance and salt tolerance than wild type. These results, combined with the GhBZR protein-interaction network, suggest that the interaction of GhBZR with phytochrome interacting factors (PIF4) plays an important role in abiotic stress responses. These findings provide a basis for further understanding the function of BZR in cotton.

Genome-wide identification of gap junction gene family and their expression profiles under low temperature stress in noble scallop Chlamys nobilis

Gap junctions, formed by gap junction proteins (GJ), play crucial roles in cell signaling and immune responses. The structure and function of the GJ from vertebrates (called connexins) have been extensively studied. However, little is known about the proteins forming gap junctions in invertebrates (called innexins). In this study, 14 GJ genes of Chlamys nobilis were identified. GJ proteins are mainly distributed on the plasma membrane, and all proteins are hydrophilic Phylogenetic tree analysis showed that the GJ proteins in C. nobilis were distantly related to those in vertebrates but closely related to those in invertebrates. Conserved motifs analysis of these GJ proteins in C. nobilis identified to have 10 conserved motifs, similar to gap junction proteins in other bivalves. Moreover, expression profiles of CnGJ genes under chronic and acute low temperature stress were also investigated. Results showed that chronic low temperature stress had a significant effect on the expression levels of CnGJ genes, and the expression profiles of CnGJ genes showed significantly variation under acute low temperature stress. All these results indicated that CnGJ genes play important roles in environmental adaptation in scallops. The present study initially elucidated the function of gap junction genes in noble scallop C. nobilis, which provides new insights into the GJ genes in mollusks and will help us better understand their roles in environmental stress in scallops.

Aggregation-Prone Antimicrobial Peptides Target Gram-negative Bacterial Nucleic Acids and Protein Synthesis

Aggregation of antimicrobial peptides (AMPs) enhances their efficacy by destabilising the bacterial cell wall, membrane, and cytosolic proteins. Developing aggregation-prone AMPs offers a promising strategy to combat antibiotic resistance, though predicting such AMPs and understanding bacterial responses remain challenging. Octopus bimaculoides, a cephalopod species, lacks known AMP gene families, yet its protein fragments were used to predict AMPs via artificial intelligence tools. Four peptides (Oct-P1, Oct-P2, Oct-P3, and Oct-P4) were identified based on their aggregation propensity. Among them, Oct-P2 reduced the viability of Escherichia coli and Staphylococcus aureus by up to 90%, confirmed by confocal laser scanning microscopy and scanning electron microscopy. It further aggregated plasmid DNA in vitro, and the presence of extracellular DNA reduced their antibacterial activity. With knockout mutants, it revealed that Oct-P2 was internalised into bacterial cells, possibly through membrane transport proteins, enhancing its antibacterial effect. Aggregation-induced emission assays and molecular dynamics simulations revealed that Oct-P2 aggregates with transcription promoter DNA, inhibiting transcription and translation in vitro. This dual-target mechanism not only highlights the potential of Oct-P2 as a lead template for new antimicrobial drug development, but also opens a new window for discovering AMPs from protein fragments against the upcoming challenge of bacterial infections. Statement of significanceA popular strategy for identifying antimicrobial peptides (AMPs) in specific genomes uses the conserved regions of AMP families, but this strategy has limitations in organisms lacking classical AMP gene families, such as Octopus. Fragments from non-antimicrobial proteins serve as a rich source for the identification of new AMPs. In this study, we used artificial intelligence tools to search for potential candidate AMP sequences from non-antimicrobial proteins in Octopus bimaculoides. The successful identification of aggregation-prone AMPs was shown to decrease bacterial viability, increase permeability, and reduce biomass. One candidate, Oct-P2, kills the gram-negative bacteria E. coli by aggregating with DNA and inhibiting transcription and translation, suggesting a new intracellular mechanism of AMP activity.

Genome‑wide identifcation and expression analysis of growth-regulating factors under drought in Brassica juncea

Growth-regulating factors (GRFs) are plant-specific transcription factors involved in the regulation of plant growth, development, and abiotic stress processes. However, the function of Brassica juncea (L.) Czern & Coss GRFs remain largely unknown. In this study, 34 BjGRF genes were identified in B. juncea. BjGRF members of the same subfamily were found to share a similar motif composition and gene structure. In total, 663 cis-acting elements were found in the promoter regions of BjGRF genes, which were related to light response, hormone response, environmental stresses, and plant growth/development. Additionally, 48 pairs of segmental duplication genes were identified during gene duplication events, and no tandemly duplicated genes were identified. qRT-PCR analysis showed that the 34 BjGRF genes were primarily expressed in the roots, followed by the leaves. Furthermore, the 10 BjGRF genes were screened in response to drought stress, and the expression patterns of the genes were relatively consistent, with a maximum expression level at 3 or 24 h, and the selected BjGRF03 and BjGRF32 might be involved in drought stress. This preliminary study clarifies the response of the BjGRF gene family to drought stress and provides ideas for further analyses of the biological functions of BjGRF genes.

Genome-wide identification and expression analysis of the GT8 gene family in tomato(Solanum lycopersicum) and the functional of SlGolS1 under cold stress

Glycosyltransferases (GTs) are a diverse superfamily of enzymes involved in glycosylation reactions, with the GT8 (glycosyltransferase 8) playing a crucial role in plant growth, development, and abiotic stress responses. Tomato, widely cultivated and is a thermophilic plant. So it is significant to study how GT8 regulates cold resistance in tomato for plant growth. In this study, we screened the whole genome of tomato by using bioinformatics methods and identified 40 members of the GT8 gene family. Analysis of cold stress transcriptome data and qRT-PCR experiments revealed the potential significance of SlGolS1 in responding to cold stress. SlGolS1 was highly expressed in the stems and flowers of tomato, with its mature protein localized in the chloroplast. Used the VIGS method to transiently silence the SlGolS1 gene, the SlGolS1-silenced plants (pTRV2-SlGolS1) rendered tomato more sensitive to cold stress compared with the control (pTRV2) tomato plant phenotype after cold treatment; enzyme activity assays showed that oxidative damage was more severe in the pTRV2-SlGolS1. In summary, SlGolS1 positively regulates cold resistance in tomato.

Comprehensive analysis of the oligopeptide transporter gene family in maize: Genome-wide identification, structural characterization, and stress-responsive expression

Oligopeptide transporter (OPT) proteins are integral proteins in cell membranes that perform a crucial role in cellular metal homeostasis, mineral uptake, transport of small peptides and abiotic stress tolerance. Hence, in-depth evolutionary, structural, molecular and expression analysis could guide in exploring the mechanism of how these transporters contribute to nutrient balance and abiotic stress tolerance in maize. Following a series of bioinformatic analyses, eight OPTs in maize were identified. These transporters showed significant variations in molecular weight, and have one to five introns, 11 to 15 motifs, 11 to 18 transmembrane domains, multiple beta-strands, multiple alpha and transmembrane helices. ZmOPT1, 5, and 6 are plasma membranes and the rest are endoplasmic reticulum localized. All ZmOPTs are distributed in six different chromosomes having significant phytohormone-responsive cis-elements might be due to their great roles in hormonal regulation in maize. The significant transport activity of these transporters plays a great role in biological processes, cellular components and molecular functions in maize during gene ontology analysis. Co-expression of five genes among eight OPTs with 56 genes might be due to their great role in regulating other genes in multiple signaling pathways or vice-versa. Significant tissue-specific and drought, salinity, nitrogen starvation, and heat stress induced in silico expression following real time PCR validation of ZmOPT1, 7, and 8 genes might guide to elucidate the potential roles of these transporters in specific tissues and abiotic stress tolerance. Hence, the findings of the research might guide plant biologists to develop new varieties of maize having higher efficiency of peptide and metal ion transport, balance, and abiotic stress tolerance. Findings of these structural and expression analyzes might guide the plant biologist for single transgenesis, or developing and transforming programming-based synthetic genetic circuits in maize for advancing research in peptide transport, metal hemostasis, and increasing abiotic stress tolerance in maize.

Metabolomic and transcriptomic analysis of Panax Notoginseng root: Mechanistic insights into the effects of flower bud removal on yield and phytochemical composition

The roots of Panax notoginseng (Burk.) F. H. Chen are used to treat organ damage and cardiovascular diseases in several East Asian countries. The removal of floral buds before inflorescence formation is widely employed to increase rhizome yield in the cultivation of Panax notoginseng. However, the molecular mechanisms regulating the growth and the accumulation of secondary metabolites remain unclear. We find that after the removal of flower buds, the root biomass accumulated in three-year-old Panax notoginseng after growing for four months increased by 27 %. Comparative transcriptomic and metabolomic analyses revealed that disbudding promoted the conversion of small molecule sugars to polysaccharides by regulating the expression of genes in the glycogen metabolism (GLG) family. It facilitated the accumulation of metabolites in the 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway by upregulating the expression of isoprenoid synthase (ISP) family genes and inhibited the conversion from the tricarboxylic acid (TCA) cycle to the mevalonate (MVA) pathway by downregulating the expression of acetyl-CoA acetyltransferase (ACAT) family genes. At the same time, the total content of triterpene saponins, main active ingredients, basically remained unchanged. However, the content of intermediate saponins increased after the upregulation of cytochrome P450 monooxygenase (CYP) transcripts, while that of downstream saponins decreased after the downregulation of UDP-glucuronosyltransferase (UGT) transcripts. Additionally, scanning electron microscopy (SEM) observations of root cross-sections indicated that the disbudding potentially promoted the development of the primary root cortex and epidermis by regulating auxin-cytokinin (AUX-CTK) signaling, thus alleviating xylem cavitation. This study confirms the removal of flower buds as an effective way to enhance yield of Panax notoginseng, offering new insights into the basic mechanisms of growth regulation during plant reproductive development and providing valuable reference for studying metabolite accumulation patterns in Panax notoginseng and other medicinal plants in the Panax genus.

HOXA11-As Promotes Lymph Node Metastasis Through Regulation of IFNL and HMGB Family Genes in Pancreatic Cancer

Recent studies have shown that long noncoding RNAs (lncRNAs) play pivotal roles in the development and progression of cancer. In the present study, we aimed to identify lncRNAs associated with lymph node metastasis in pancreatic ductal adenocarcinoma (PDAC). We analyzed data from The Cancer Genome Atlas (TCGA) database to screen for genes overexpressed in primary PDAC tumors with lymph node metastasis. Our screen revealed 740 genes potentially associated with lymph node metastasis, among which were multiple lncRNA genes located in the HOXA locus, including HOXA11-AS. Elevated expression of HOXA11-AS was associated with more advanced tumor stages and shorter overall survival in PDAC patients. HOXA11-AS knockdown suppressed proliferation and migration of PDAC cells. RNA-sequencing analysis revealed that HOXA11-AS knockdown upregulated interferon lambda (IFNL) family genes and downregulated high-mobility group box (HMGB) family genes in PDAC cells. Moreover, HMGB3 knockdown suppressed proliferation and migration by PDAC cells. These results suggest that HOXA11-AS contributes to PDAC progression, at least in part, through regulation of IFNL and HMGB family genes and that HOXA11 AS is a potential therapeutic target in PDAC.

Genome-Wide Identification of FCS-Like Zinc Finger (FLZ) Family Genes in Three Brassica Plant Species and Functional Characterization of BolFLZs in Chinese Kale Under Abiotic Stresses

FCS-like zinc finger (FLZ) proteins are plant-specific regulatory proteins, which contain a highly conserved FLZ domain, and they play critical roles in plant growth and stress responses. Although the FLZ family has been systematically characterized in certain plants, it remains underexplored in Brassica species, which are vital sources of vegetables, edible oils, and condiments for human consumption and are highly sensitive to various abiotic stresses. Following the whole-genome triplication events (WGT) in Brassica, elucidating how the FLZ genes have expanded, differentiated, and responded to abiotic stresses is valuable for uncovering the genetic basis and functionality of these genes. In this study, we identified a total of 113 FLZ genes from three diploid Brassica species and classified them into four groups on the basis of their amino acid sequences. Additionally, we identified 109 collinear gene pairs across these Brassica species, which are dispersed among different chromosomes, suggesting that whole-genome duplication (WGD) has significantly contributed to the expansion of the FLZ family. Subcellular localization revealed that six representative BolFLZ proteins are located in the nucleus and cytoplasm. Yeast two-hybrid assays revealed that 13 selected BolFLZs interact with BolSnRK1α1 and BolSnRK1α2, confirming the conservation of the SnRK1α-FLZ module in Brassica species. Expression profile analysis revealed differential expression patterns of BolFLZ across various tissues. Notably, the expression levels of seven BolFLZ genes out of the fifteen genes analyzed changed significantly following treatment with various abiotic stressors, indicating that the BolFLZ genes play distinct physiological roles and respond uniquely to abiotic stresses in Brassica species. Together, our results provide a comprehensive overview of the FLZ gene family in Brassica species and insights into their potential applications for enhancing stress tolerance and growth in Chinese kale.