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27 pages, 5167 KiB  
Article
Development of Glycyrrhizic Acid Nanoparticles for Modulating Gastric Ulcer Healing: A Comparative In Vivo Study Targeting Oxidative Stress and Inflammatory Pathways
by Mody Albalawi and Sahar Khateeb
Antioxidants 2025, 14(8), 990; https://doi.org/10.3390/antiox14080990 - 12 Aug 2025
Viewed by 323
Abstract
Gastric ulcer (GU) is a common gastrointestinal disorder that impacts quality of life. Currently, several drugs are available for GU treatment, including proton pump inhibitors like omeprazole (OMP); however, their use is limited by numerous potential adverse effects. Glycyrrhizic acid (GLY), a natural [...] Read more.
Gastric ulcer (GU) is a common gastrointestinal disorder that impacts quality of life. Currently, several drugs are available for GU treatment, including proton pump inhibitors like omeprazole (OMP); however, their use is limited by numerous potential adverse effects. Glycyrrhizic acid (GLY), a natural anti-inflammatory agent, exhibits promising gastroprotective properties; however, its use is likewise limited by numerous potential adverse effects. This study aimed to synthesize GLY nanoparticles (GLY-NPs) to enhance their therapeutic potential and to comparatively evaluate their efficacy against OMP in an ethanol-induced GU in male Wistar rats. GLY-NPs were synthesized via a hydrothermal method and characterized using TEM, XRD, FTIR, and zeta potential analyses. In vivo, GLY-NPs significantly attenuated gastric mucosal damage compared to OMP, as evidenced by macroscopic and histopathological analyses. Biochemical assays revealed that GLY-NPs markedly improved antioxidant defenses by elevating SOD, catalase, and glutathione peroxidase activities while reducing MDA levels, surpassing the effects of OMP. Furthermore, GLY-NPs modulated inflammatory responses by downregulating p38 MAPK, NF-κB, and TNF-α expression, concomitant with upregulation of the anti-inflammatory cytokine IL-10. Mechanistic insights indicated that GLY-NPs favorably regulated key signaling pathways implicated in gastric mucosal protection, including suppression of the JAK2/STAT3 and TGF-β1/Smad3 pathways, alongside activation of the SIRT1/FOXO1/PGC-1α axis. In conclusion, these findings indicate that GLY-NPs offer higher gastroprotective effects relative to traditional OMP therapy through comprehensive modulation of oxidative stress, inflammation, and molecular signaling pathways. This study highlights GLY-NPs as a potent nanotherapeutic candidate for the effective management of GU. Full article
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15 pages, 2307 KiB  
Article
Two B-Box Proteins, GhBBX21 and GhBBX24, Antagonistically Modulate Anthocyanin Biosynthesis in R1 Cotton
by Shuyan Li, Kunpeng Zhang, Chenxi Fu, Chaofeng Wu, Dongyun Zuo, Hailiang Cheng, Limin Lv, Haiyan Zhao, Jianshe Wang, Cuicui Wu, Xiaoyu Guo and Guoli Song
Plants 2025, 14(15), 2367; https://doi.org/10.3390/plants14152367 - 1 Aug 2025
Viewed by 240
Abstract
The red plant phenotype of R1 cotton is a genetic marker produced by light-induced anthocyanin accumulation. GhPAP1D controls this trait. There are two 228 bp tandem repeats upstream of GhPAP1D in R1 cotton. In this study, GUS staining assays in transgenic Arabidopsis thaliana [...] Read more.
The red plant phenotype of R1 cotton is a genetic marker produced by light-induced anthocyanin accumulation. GhPAP1D controls this trait. There are two 228 bp tandem repeats upstream of GhPAP1D in R1 cotton. In this study, GUS staining assays in transgenic Arabidopsis thaliana (L.) Heynh. demonstrated that tandem repeats in the GhPAP1D promoter-enhanced transcriptional activity. GhPAP1D is a homolog of A. thaliana AtPAP1. AtPAP1’s expression is regulated by photomorphogenesis-related transcription factors such as AtHY5 and AtBBXs. We identified the homologs of A. thaliana AtHY5, AtBBX21, and AtBBX24 in R1 cotton, designated as GhHY5, GhBBX21, and GhBBX24, respectively. Y1H assays confirmed that GhHY5, GhBBX21, and GhBBX24 each bound to the GhPAP1D promoter. Dual-luciferase reporter assays revealed that GhHY5 weakly activated the promoter activity of GhPAP1D. Heterologous expression assays in A. thaliana indicated that GhBBX21 promoted anthocyanin accumulation, whereas GhBBX24 had the opposite effect. Dual-luciferase assays showed GhBBX21 activated GhPAP1D transcription, while GhBBX24 repressed it. Further study indicated that GhHY5 did not enhance GhBBX21-mediated transcriptional activation of GhPAP1D but alleviates GhBBX24-induced repression. Together, our results demonstrate that GhBBX21 and GhBBX24 antagonistically regulate anthocyanin accumulation in R1 cotton under GhHY5 mediation, providing insights into light-responsive anthocyanin biosynthesis in cotton. Full article
(This article belongs to the Section Plant Molecular Biology)
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12 pages, 1644 KiB  
Brief Report
RNA-Seq Identification of Peanut Callus-Specific Promoters and Evaluation of Base-Editing Efficiency
by Lulu Xue, Han Liu, Huanhuan Zhao, Pengyu Qu, Xiaona Li, Xiaobo Wang, Bingyan Huang, Ziqi Sun, Suoyi Han, Xiaodong Dai, Wenzhao Dong, Lei Shi and Xinyou Zhang
Plants 2025, 14(15), 2290; https://doi.org/10.3390/plants14152290 - 25 Jul 2025
Viewed by 334
Abstract
Prolonged expression of gene-editing components in CRISPR-modified plants can interfere with phenotypic analysis of target traits, increase the risk of off-target mutations, and lead to unnecessary metabolic burden. To mitigate these issues in peanut (Arachis hypogaea L.), callus-specific promoters were screened to [...] Read more.
Prolonged expression of gene-editing components in CRISPR-modified plants can interfere with phenotypic analysis of target traits, increase the risk of off-target mutations, and lead to unnecessary metabolic burden. To mitigate these issues in peanut (Arachis hypogaea L.), callus-specific promoters were screened to restrict Cas9 expression to the callus stage, minimizing its activity in regenerated plants. In this study, six callus-specific genes in peanut were identified by mining RNA sequencing datasets and validating their expression profiles using quantitative reverse transcriptase PCR. The promoters of Arahy.H0FE8D, Arahy.WT3AEF, Arahy.I20Q6X, Arahy.ELJ55T, and Arahy.N9CMH4 were cloned and assessed for their expression activity. Beta-glucuronidase (GUS) histochemical staining confirmed that all five promoters were functional in peanut callus. Further investigation revealed their ability to drive cytosine base editing via a deaminase-nCas9 fusion protein, with all promoters successfully inducing precise base substitutions in peanut. Notably, PAh-H0FE8D, PAh-WT3AEF, PAh-ELJ55T, and PAh-N9CMH4 exhibited comparable or higher editing efficiencies than the commonly used cauliflower mosaic virus 35S promoter. These findings provide valuable tools for improving the biosafety of CRISPR-based genome editing in peanut breeding programs. Full article
(This article belongs to the Special Issue Advances in Oil Regulation in Seeds and Vegetative Tissues)
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17 pages, 3134 KiB  
Article
Validation of Fiber-Dominant Expressing Gene Promoters in Populus trichocarpa
by Mengjie Guo, Ruxia Wang, Bo Wang, Wenjing Xu, Hui Hou, Hao Cheng, Yun Zhang, Chong Wang and Yuxiang Cheng
Plants 2025, 14(13), 1948; https://doi.org/10.3390/plants14131948 - 25 Jun 2025
Viewed by 591
Abstract
Wood is an important raw material for industrial applications. Its fiber-specific genetic modification provides an effective strategy to alter wood characteristics in tree breeding. Here, we performed a cross-analysis of previously reported single-cell RNA sequencing and the AspWood database during wood formation to [...] Read more.
Wood is an important raw material for industrial applications. Its fiber-specific genetic modification provides an effective strategy to alter wood characteristics in tree breeding. Here, we performed a cross-analysis of previously reported single-cell RNA sequencing and the AspWood database during wood formation to identify potential xylem fiber-dominant expressing genes in poplar. As a result, 32 candidate genes were obtained, and subsequently, we further examined the expression of these genes in fibers and/or vessels of stem secondary xylem using the laser capture microdissection technique and RT-qPCR. Analysis identified nine candidate genes, including PtrFLA12-2, PtrIRX12, PtrFLA12-6, PtrMYB52, PtrMYB103, PtrMAP70, PtrLRR-1, PtrKIFC2-3, and PtrNAC12. Next, we cloned the promoter regions of the nine candidate genes and created promoter::GUS transgenic poplars. Histochemical GUS staining was used to investigate the tissue expression activities of these gene promoters in transgenic poplars. In one month, transgenic plantlets grown in medium showed intensive GUS staining signals that were visible in the leaves and apical buds, suggesting substantial expression activities of these gene promoters in plantlets predominantly undergoing primary growth. In contrast, for three-month-old transgenic poplars in the greenhouse with predominantly developed secondary stem tissues, the promoters of seven of nine candidate genes, including PtrMYB103, PtrIRX12, and PtrMAP70, showed secondary xylem fiber-dominant GUS signals with considerable spatial specificity. Overall, this study presents xylem fiber-dominant promoters that are well-suited for specifically expressing genes of interest in wood fibers for forest tree breeding. Full article
(This article belongs to the Section Plant Physiology and Metabolism)
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14 pages, 5685 KiB  
Article
Construction of an Overexpression Library for Chinese Cabbage Orphan Genes in Arabidopsis and Functional Analysis of BOLTING RESISTANCE 4-Mediated Flowering Delay
by Ruiqi Liao, Ruiqi Zhang, Xiaonan Li and Mingliang Jiang
Plants 2025, 14(13), 1947; https://doi.org/10.3390/plants14131947 - 25 Jun 2025
Cited by 1 | Viewed by 448
Abstract
Orphan genes (OGs), which are unique to a specific taxon and have no detectable sequence homology to any known genes across other species, play a pivotal role in governing species-specific phenotypic traits and adaptive evolution. In this study, 20 OGs of [...] Read more.
Orphan genes (OGs), which are unique to a specific taxon and have no detectable sequence homology to any known genes across other species, play a pivotal role in governing species-specific phenotypic traits and adaptive evolution. In this study, 20 OGs of Chinese cabbage (Brassica rapa OGs, BrOGs) were transferred into Arabidopsis thaliana by genetic transformation to construct an overexpression library in which 50% of the transgenic lines had a delayed flowering phenotype, 15% had an early flowering phenotype, and 35% showed no difference in flowering time compared to control plants. There were many other phenotypes attached to these transgenic lines, such as leaf color, number of rosette leaves, and silique length. To understand the impact of BrOGs on delayed flowering, BrOG142OE, which showed the most significantly delayed flowering phenotype, was chosen for further analysis, and BrOG142 was renamed BOLTING RESISTANCE 4 (BR4). In BR4OE, the expression of key flowering genes, including AtFT and AtSOC1, significantly decreased, and AtFLC and AtFRI expression increased. GUS staining revealed BR4 promoter activity mainly in the roots, flower buds and leaves. qRT-PCR showed that BR4 primarily functions in the flowers, flower buds, and leaves of Chinese cabbage. BR4 is a protein localized in the nucleus, cytoplasm, and cell membrane. The accelerated flowering time phenotype of BR4OE was observed under gibberellin and vernalization treatments, indicating that BR4 regulates flowering time in response to these treatments. These results provide a foundation for elucidating the mechanism by which OGs regulate delayed flowering and have significance for the further screening of bolting-resistant Chinese cabbage varieties. Full article
(This article belongs to the Section Plant Development and Morphogenesis)
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24 pages, 5468 KiB  
Article
Pretreatment with Citrus reticulata ‘Chachi’ Polysaccharide Alleviates Alcohol-Induced Gastric Ulcer by Inhibiting NLRP3/ASC/Caspase-1 and Nrf2/HO-1 Signaling Pathways
by Huosheng Liang, Yiyao Liang, Lipeng Wu, Long Lin, Yunan Yao, Jinji Deng, Jiepei Xu, Huajian Li, Fangfang Gao, Wenlong Xing, Meng Yu, Xuejing Jia, Minyan Wei, Chuwen Li and Guodong Zheng
Nutrients 2025, 17(13), 2062; https://doi.org/10.3390/nu17132062 - 20 Jun 2025
Viewed by 676
Abstract
Objectives: This study was designed to investigate the gastroprotective effects of Citrus reticulata ‘Chachi’ polysaccharide (CRP) against alcohol-induced gastric ulcers (GUs) and to elucidate its underlying mechanisms. Methods: CRP was extracted, purified, and structurally characterized. BALB/c mice (50/250 mg/kg CRP) and GES-1 cells [...] Read more.
Objectives: This study was designed to investigate the gastroprotective effects of Citrus reticulata ‘Chachi’ polysaccharide (CRP) against alcohol-induced gastric ulcers (GUs) and to elucidate its underlying mechanisms. Methods: CRP was extracted, purified, and structurally characterized. BALB/c mice (50/250 mg/kg CRP) and GES-1 cells (1 mg/mL CRP) were subjected to alcohol-induced injury. Oxidative stress (SOD, MDA, ROS), inflammation (TNF-α, IL-1β, NLRP3 inflammasome), mucosal barrier proteins (ZO-1, occludin, Claudin-5), and Nrf2/HO-1 signaling were analyzed via histopathology, Western blot, flow cytometry, and immunohistochemistry. Results: CRP pretreatment significantly alleviated gastric lesions, decreased oxidative stress, and suppressed inflammatory responses in alcohol-induced mice. Mechanistically, CRP induced the Nrf2/HO-1 antioxidant pathway while inhibiting the activation of the NLRP3 inflammasome. CRP also restored tight junction protein expression, enhanced mucosal repair, and reduced epithelial apoptosis. In vitro, CRP promoted cell proliferation, migration, and survival of GES-1 cells under alcohol stress. Conclusions: CRP mitigated alcohol-induced GU via dual antioxidant, anti-inflammatory, and barrier-protective mechanisms, positioning it as a considerable agent for GU. Full article
(This article belongs to the Section Phytochemicals and Human Health)
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17 pages, 7981 KiB  
Article
Genome-Wide Identification and Pollen-Specific Promoter Analysis of the DIR Gene Family in Rosa chinensis
by Qijing Dong, Qian Yang, Zitong Wang, Yuan Zhao, Sixu Guo, Yifang Peng, Qi Li and Yu Han
Horticulturae 2025, 11(7), 717; https://doi.org/10.3390/horticulturae11070717 - 20 Jun 2025
Viewed by 401
Abstract
Dirigent proteins (DIRs) are pivotal regulators of lignin/lignan biosynthesis and play multifaceted roles in plant development and stress adaptation. Despite their functional significance, DIR genes remain unexplored in Rosa chinensis, a globally important woody ornamental species. This study identified 33 RcDIRs through [...] Read more.
Dirigent proteins (DIRs) are pivotal regulators of lignin/lignan biosynthesis and play multifaceted roles in plant development and stress adaptation. Despite their functional significance, DIR genes remain unexplored in Rosa chinensis, a globally important woody ornamental species. This study identified 33 RcDIRs through whole-genome analysis, including their chromosomal distribution, phylogenetic relationships, collinearity, protein and gene structure, conserved motifs, and cis-acting element distribution, and classified them into three phylogenetically independent subgroups (DIR-a, DIR-b/d, and DIR-e). Notably, the DIR-e subgroup includes an exclusive tandem cluster comprising RcDIR7-RcDIR12, representing the largest lineage-specific RcDIR expansion in R. chinensis. Structural characterization revealed that most RcDIRs exhibit a conserved single-exon architecture. Promoter cis-element analysis uncovered abundant stress-/hormone-responsive elements and three pollen-specific motifs (AAATGA, POLLEN1LELAT52, GTGANTG10), with RcDIR12 from the DIR-e cluster showing high pollen-specific regulatory potential. Experimental validation included cloning the RcDIR12 promoter from R. chinensis ‘Old Blush’, constructing proRcDIR12::GUS vectors, and conducting histochemical GUS assays with pollen viability/DAPI staining in transgenic Arabidopsis. Histochemical assays demonstrated GUS activity localization in mature trinucleate pollen grains, marking the first experimental evidence of pollen-specific DIRs in rose. Our findings not only elucidate the DIR family’s genomic organization and evolutionary innovations in R. chinensis but also establish proRcDIR12 as a molecular tool for manipulating pollen development in plants. Full article
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19 pages, 7673 KiB  
Article
Overexpression of MdNRT2.4 Improved Low-Nitrogen Tolerance in Transgenic Tobacco Lines
by Junrong Li, Ke Liu, Chunqiong Shang, Qiandong Hou, Xiangmei Nie, Qinglong Dong, Dong Huang and Qian Wang
Horticulturae 2025, 11(6), 662; https://doi.org/10.3390/horticulturae11060662 - 10 Jun 2025
Viewed by 510
Abstract
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 [...] Read more.
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
(This article belongs to the Section Biotic and Abiotic Stress)
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15 pages, 617 KiB  
Article
Italian Multicenter Real-World Study on the Twelve-Month Effectiveness, Safety, and Retention Rate of Guselkumab in Psoriatic Arthritis Patients
by Fabiola Atzeni, Cinzia Rotondo, Cesare Siragusano, Addolorata Corrado, Alberto Cauli, Roberto Caporali, Maria Sole Chimenti, Fabrizio Conti, Valentina Picerno, Elisa Gremese, Federica Camarda, Serena Guiducci, Roberta Ramonda, Luca Idolazzi, Angelo Semeraro, Marco Sebastiani, Giovanni Lapadula, Gianfranco Ferraccioli and Florenzo Iannone
J. Clin. Med. 2025, 14(12), 4111; https://doi.org/10.3390/jcm14124111 - 10 Jun 2025
Viewed by 790
Abstract
Background/Objectives: Psoriatic arthritis (PsA) is a chronic inflammatory condition that primarily affects the musculoskeletal system and skin. While biologic and targeted synthetic DMARDs have improved treatment, many patients still fail to achieve remission. Combining conventional synthetic disease modifying anti-rheumatic drugs (csDMARDs) with [...] Read more.
Background/Objectives: Psoriatic arthritis (PsA) is a chronic inflammatory condition that primarily affects the musculoskeletal system and skin. While biologic and targeted synthetic DMARDs have improved treatment, many patients still fail to achieve remission. Combining conventional synthetic disease modifying anti-rheumatic drugs (csDMARDs) with biologic (b) DMARDs or targeted synthetic (ts) DMARDs shows no added benefit over monotherapy with IL-17, IL-23 inhibitors, or JAK inhibitors, unlike TNFi, which benefit from csDMARD co-administration. Guselkumab (GUS) and risankizumab (RKZ) target IL-23 with high specificity. RCTs (DISCOVER 1 and 2, COSMOS) have confirmed GUS efficacy regardless of methotrexate (MTX) use, though liver toxicity was higher with MTX. Real-world data on GUS remain limited, with gaps in understanding its long-term effectiveness and drug survival. The aim of this study is to assess the following three points within a multicenter Italian real-life cohort of PsA patients treated with guselkumab (GUS) and followed for 12 months: (1) effectiveness and safety of GUS; (2) drug retention rate (DRR) and reasons for discontinuation; (3) impact of comorbidities on achieving minimal disease activity (MDA). Methods: This study utilized data from the GISEA registry, which includes centers in different parts of Italy (north, center, south, and islands), and included patients aged 18 and older diagnosed with PsA according to the CASPAR criteria. Results: Data on 170 PsA patients treated with GUS were collected. In the first 6 months, a prompt mean percentage improvement in all clinimetric indexes was observed compared to the baseline. At 6-month follow-up, ACR 20 was reached by 60% of patients, ACR 50 by 30%, ACR 70 by 15%, MDA by 28%, and DAPSA < 14 by 50% of patients in the overall group. Significant differences were found in the rate of ACR 50 in the bDMARD-naive group (50%) compared to one bDMARDs non-responder (NR) (8%) (p = 0.021). At 12-month follow-up, a notable gap was observed in the rate of patients reaching MDA between bDMARD-naive (60%) and one bDMARDs NR (22%) (p = 0.035) and between bDMARD-naive (60%) and ≥2 bDMARDs NRs (22%) (p = 0.024). By using multivariate binary logistic analysis, the predictors of reaching MDA at 12-month follow-up were naive bDMARDs (OR: 7.9, 95% CI: 1.3–44.8, p = 0.019) and a higher value of pGA at baseline (OR: 1.1, 95% CI: 1–1.5; p = 0.046). The presence of comorbidities, including fibromyalgia and obesity, did not seem to affect the reaching of MDA. At 12-month follow-up, the GUS retention rate was 76%, with a mean survival time of 10.5 months ± 0.2 (95% CI: 10–10.9). No significant differences in GUS survival time were found among bDMARD-naive, one bDMARDs NR, and ≥2 bDMARDs NR patients (in the latter, regardless of the previous mechanism of action: TNFi or other mechanism), as well as between patients treated with GUS in monotherapy and those treated in combination with csDMARDs. A low rate (17%) of discontinuation was found due to both primary NR and secondary NR. The high safety of GUS was recorded. In fact, discontinuation due to adverse events (all definable as minor) was observed in just 4% of patients. By using COX regression multivariate analysis, the factors associated with higher GUS discontinuation risk were a more severe baseline PASI (HR: 1.05, 95% CI: 1–1.1, p = 0.038) and higher baseline ESR (HR:1.06, 95% CI: 1–1.03, p = 0.05). Conclusions: Good performance of GUS was observed in both biologic-naive patients and those with failure of previous bDMARDs (regardless of the mechanism of action of the previous drug: TNFi or non-TNFi), presenting good persistence in therapy even when used as a third mechanism of action. Its high safety profile allows the use of GUS even in particularly complex patients. Full article
(This article belongs to the Special Issue Targeted Treatment in Chronic Inflammatory Arthritis)
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18 pages, 14476 KiB  
Article
Functional Characterization of CpPIP1;1 and Genome-Wide Analysis of PIPs in Wintersweet (Chimonanthus praecox (L.) Link)
by Fei Ren, Zhu Feng, Guo Wei, Yimeng Lv, Jia Zhao, Yeyuan Deng, Shunzhao Sui and Jing Ma
Horticulturae 2025, 11(6), 581; https://doi.org/10.3390/horticulturae11060581 - 24 May 2025
Viewed by 472
Abstract
Plant aquaporin proteins (AQPs) are categorized into seven distinct families, among which, plasma membrane intrinsic proteins (PIPs) play pivotal roles in plant growth and physiological processes. In this study, we identified 11 CpPIP genes in wintersweet (Chimonanthus praecox (L.) Link) based on [...] Read more.
Plant aquaporin proteins (AQPs) are categorized into seven distinct families, among which, plasma membrane intrinsic proteins (PIPs) play pivotal roles in plant growth and physiological processes. In this study, we identified 11 CpPIP genes in wintersweet (Chimonanthus praecox (L.) Link) based on bioinformatic characterization of gene structural organization, chromosomal localization, and phylogenetic relationships. Subsequent phylogenetic reconstruction resolved two evolutionarily distinct CpPIP subclasses. We focused on the isolation and characterization of CpPIP1;1, which showed the highest expression in floral organs. During flowering, a significant increase was observed in the expression of the CpPIP1;1 gene in response to a gradual reduction in environmental temperature. Moreover, the overexpression of CpPIP1;1 in Arabidopsis thaliana resulted in early flowering and an enhanced tolerance to salt, drought, and cold stress. We subsequently transcriptionally fused the CpPIP1;1 promoter containing MYC and MYB low-temperature response elements to the β-glucuronidase (GUS) reporter gene and introduced this construct into Nicotiana tabacum. GUS activity assays of the transgenic plants revealed that the CpPIP1;1 promoter was effectively expressed in flowers. Furthermore, the promoter transcriptional activity was enhanced in response to salt, drought, cold, gibberellic acid, and methyl jasmonate treatments. Collectively, our findings in this study revealed that CpPIP1;1 plays a key role in the regulation of flowering and stress tolerance in wintersweet plants. Full article
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16 pages, 5161 KiB  
Article
Isolation and Activity Evaluation of Callus-Specific Promoters in Rice (Oryza sativa L.)
by Xiaojiao Ma and Chuanyin Wu
Genes 2025, 16(5), 610; https://doi.org/10.3390/genes16050610 - 21 May 2025
Viewed by 632
Abstract
Background/Objectives: In crop genetic engineering, morphogenic genes have attracted increasing attention, given their ability to facilitate the transformation of a broad range of otherwise nontransformable cultivars. However, few callus-specific promoters have been identified to date that can be employed to avoid the adverse [...] Read more.
Background/Objectives: In crop genetic engineering, morphogenic genes have attracted increasing attention, given their ability to facilitate the transformation of a broad range of otherwise nontransformable cultivars. However, few callus-specific promoters have been identified to date that can be employed to avoid the adverse effects resulting from the ectopic expression of morphogenic genes on shoot regeneration and growth. Methods: A set of potential callus-specific genes were initially selected based on publicly available data. These genes were then screened using quantitative real-time polymerase chain reaction (qPCR), followed by promoter activity evaluation using a transgenic approach with the GUS gene serving as a reporter. Results: Of the 24 evaluated promoters, 12 were verified as being callus-specific using qPCR. Five genes (Os11g0295900, Os10g0207500, Os01g0300000, Os02g0252200, and Os04g0488100) were chosen, and their promoters were cloned. Based on GUS staining, the pOsTDL1B (Os10g0207500) promoter showed strong callus-specific expression, pOsEDC (Os01g0300000) was a medium-level callus-specific promoter, and pOsDLN53 (Os02g0252200) was strictly callus-specific, although its activity was low. Quantification of GUS activity indicated that all three pOsTDL1B:GUS transgenic lines exhibited strong callus specificity relative to the various tissues tested. Conclusions: A callus-specific promoter was identified that can be used to drive the expression of morphogenic genes in crop transformation. Full article
(This article belongs to the Topic Genetic Engineering in Agriculture)
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18 pages, 3632 KiB  
Article
Isolation and Functional Analysis of the DhMYB2 and DhbHLH1 Promoters from Phalaenopsis-Type Dendrobium Involved in Stress Responses and Tissue-Specific Expression
by Yachen Wang, Chonghui Li, Wenjuan Zhu, Yamei Li, Xiqiang Song and Junmei Yin
Horticulturae 2025, 11(5), 550; https://doi.org/10.3390/horticulturae11050550 - 19 May 2025
Viewed by 539
Abstract
Phalaenopsis-type Dendrobium (Den-Phals) is a commercially valuable orchid, with floral color being key to its market appeal. Despite the significance of anthocyanin biosynthesis in color development, its transcriptional regulation in Den-Phals remains unclear. This study functionally characterized the promoters of DhMYB2 and [...] Read more.
Phalaenopsis-type Dendrobium (Den-Phals) is a commercially valuable orchid, with floral color being key to its market appeal. Despite the significance of anthocyanin biosynthesis in color development, its transcriptional regulation in Den-Phals remains unclear. This study functionally characterized the promoters of DhMYB2 and DhbHLH1, two key transcription factors involved in anthocyanin biosynthesis. A 1864 bp DhMYB2 promoter and a 1995 bp DhbHLH1 promoter were isolated using genome walking. Bioinformatics analysis identified cis-acting elements associated with abiotic stress responses, phytohormone signaling, and floral-specific regulation. 5′-Deletion analysis in tobacco leaves identified core regulatory regions for the DhMYB2 promoter (−1864 to −937 bp) and DhbHLH1 promoter (−1995 to −924 bp). GUS staining and activity assays demonstrated that the activities of the DhMYB2 and DhbHLH1 promoters were significantly increased under treatments of long light, low temperature, drought, salicylic acid (SA), and abscisic acid (ABA), while the DhbHLH1 promoter was also induced by methyl jasmonate (MeJA) and indole-3-acetic acid (IAA). Furthermore, promoter activity of DhMYB2 and DhbHLH1 was detected only in transgenic Arabidopsis flowers, suggesting that these promoters exhibit floral-specific activity. This study provides the first functional analysis of Den-Phals anthocyanin promoters, revealing their stress-responsive nature and floral specificity, which will facilitate molecular breeding of novel orchid cultivars. Full article
(This article belongs to the Special Issue Color Formation and Regulation in Horticultural Plants)
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21 pages, 5820 KiB  
Article
Heterologous Expression and Enzymatic Properties of β-Glucuronidase from Clostridium perfringens and Its Application in Bilirubin Transformation
by Qianlin Wu, Qing Guo, Fo Yang, Mengru Li, Yumeng Zhu, Binpeng Xu, Lu Zhao, Shanshan Zhang, Youyu Xie, Feng Li, Xiaomin Wu and Dayong Xu
Microorganisms 2025, 13(5), 1043; https://doi.org/10.3390/microorganisms13051043 - 30 Apr 2025
Viewed by 603
Abstract
β-glucuronidase is an important hydrolase, which plays an important role in drug metabolism, clinical diagnostics, and biotransformation. This study focuses on the heterologous expression, isolation, purification, and its enzymatic properties of β-glucuronidase CpGUS from Clostridium perfringens, as well as its application in [...] Read more.
β-glucuronidase is an important hydrolase, which plays an important role in drug metabolism, clinical diagnostics, and biotransformation. This study focuses on the heterologous expression, isolation, purification, and its enzymatic properties of β-glucuronidase CpGUS from Clostridium perfringens, as well as its application in the whole-cell transformation of unconjugated bilirubin from pig bile. A recombinant E. coli BL21(DE3)/pET-28a-CpGUS was constructed for the heterologous expression of CpGUS, with the majority of the expressed enzyme being soluble. Enzymatic analysis showed that CpGUS displayed optimal activity at pH 5.0 and 45 °C, and it rapidly lost activity at pH < 4.5. Metal ions, such as Mg2+ and Fe2+, enhanced CpGUS catalysis, while Zn2+, K+, Fe3+, Mn2+, Cu2+, and Na+ inhibited it. Notably, Cu2+ and Fe3+ can significantly inhibit β-glucuronidase, resulting in the complete loss of its activity. The results of the whole-cell transformation experiment show that when E.coli BL21(DE3)/ pET-28a-CpGUS at an OD600 of 10 was incubated at pH 5.0, a temperature of 45 °C, and a rotation speed of 200 rpm for 12 h, the hydrolysis rate of the conjugated bilirubin in pig bile reached 81.1%, the yield of unconjugated bilirubin was 76.8%, and the purity of unconjugated bilirubin was 98.2%. The three-dimensional structure of CpGUS was predicted using AlphaFold2 (AlphaFold v2.0, DeepMind Technologise Limited, London, UK), and p-Nitrophenyl-β-D-Glucuronide (pNPG) and conjugated bilirubin were then docked to the CpGUS protein model using SWISSDOCK. The best docked conformations of the CpGUS–pNPG and CpGUS–conjugated bilirubin complex systems were simulated by independent 500 ns molecular dynamics (MD) runs with the RSFF2C force field, and the binding dynamic and catalytic mechanism of each system were obtained. The results indicated that π-π stacking, hydrogen bonding, and hydrophobic interactions between the key residue Tyr472 and the benzene ring of pNPG molecules are crucial for its catalytic process. Similarly, for the binding and catalysis of conjugated bilirubin by CpGUS, the π-π stacking and hydrogen bonding and hydrophobic interactions between the sidechains of residues Phe368 and Tyr472 and the benzene ring of conjugated bilirubin play a synergistic role during its catalytic process. Their total binding free energy (∆Gbind) values were calculated to be as high as −65.05 ± 12.66 and −86.70 ± 17.18 kJ/mol, respectively. These results suggest that CpGUS possesses high binding and catalytic hydrolysis properties for both pNPG and conjugated bilirubin. Full article
(This article belongs to the Section Molecular Microbiology and Immunology)
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18 pages, 10646 KiB  
Article
Overexpression of the Glycyrrhiza uralensis Phenylalanine Ammonia-Lyase Gene GuPAL1 Promotes Flavonoid Accumulation in Arabidopsis thaliana
by Xifeng Chen, Chao Jiang, Mengqian Long, Xiangxiang Hu, Shouhao Xu, Haotong Huo, Ruixin Shi, Qing Xu, Shuangquan Xie, Zihan Li, Haitao Shen, Fei Wang, Guanghui Xiao, Quanliang Xie, Shandang Shi and Hongbin Li
Int. J. Mol. Sci. 2025, 26(9), 4073; https://doi.org/10.3390/ijms26094073 - 25 Apr 2025
Cited by 1 | Viewed by 603
Abstract
Phenylalanine ammonia-lyase (PAL) serves as a pivotal regulatory enzyme at the initial branching point of the phenylpropanoid pathway, exerting a profound influence on downstream reactions essential for flavonoid biosynthesis. Glycyrrhiza species are important medicinal plants and provide plenty of roots as raw materials [...] Read more.
Phenylalanine ammonia-lyase (PAL) serves as a pivotal regulatory enzyme at the initial branching point of the phenylpropanoid pathway, exerting a profound influence on downstream reactions essential for flavonoid biosynthesis. Glycyrrhiza species are important medicinal plants and provide plenty of roots as raw materials for further utilization, with the components of glycyrrhizic acid and flavonoids as two major active ingredients. However, functional studies of the PAL genes in the medicinal Glycyrrhiza species remain limited. In this study, we identified seven PAL family genes from each of the three medicinal Glycyrrhiza species, Glycyrrhiza uralensis Fisch., G. inflata Bat., and G. glabra L., and comprehensively analyzed their phylogenetic relationships, gene structures, motif distributions, and promoter cis-elements. Gene expression profiling revealed that PAL1 is highly expressed in roots and significantly induced by drought and salt stresses. We further selected G. uralensis GuPAL1 for functional investigation in Arabidopsis. GuPAL1-overexpression lines (GuPAL1-OE) demonstrated significant enhancements in plant growth, flavonoid accumulation, and hormone levels in Arabidopsis thaliana. Conversely, the Atpal1 mutant plants displayed marked reductions in these traits, while the transgenic lines of GuPAL1-OE in the Atpal1 mutant (Atpal1/GuPAL1) recovered to the normal phenotypes similar to wild type (WT). Transcriptomic analysis of the GuPAL1-OE plants compared to WT demonstrated that several key genes in the phenylpropanoid and flavonoid metabolic pathways (4CL, CCoAOMT, CAD, POD, F3H, FLS) were significantly enriched, suggesting that GuPAL1 may promote plant growth and flavonoid biosynthesis by regulating diverse cellular functions, metabolic pathways, and associated gene expressions. These findings highlight the functional importance of GuPAL1 in flavonoid biosynthesis, and provide valuable insights into the molecular mechanisms underlying the medicinal properties of Glycyrrhiza species. Full article
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12 pages, 2521 KiB  
Brief Report
Expression of the Nicotiana benthamiana Retrozyme 1 (NbRZ1) Genomic Locus
by Alexander A. Lezzhov, Anastasia K. Atabekova, Denis A. Chergintsev, Andrey G. Solovyev and Sergey Y. Morozov
Plants 2025, 14(8), 1205; https://doi.org/10.3390/plants14081205 - 14 Apr 2025
Viewed by 534
Abstract
Retrozymes are a class of non-autonomous plant retrotransposons that have long terminal repeats (LTRs) containing hammerhead ribozymes (HHRs) that facilitate the circularization of the retrozyme RNA. The LTR of Nicotiana benthamiana retrozyme 1 (NbRZ1) has been shown to contain a promoter that directs [...] Read more.
Retrozymes are a class of non-autonomous plant retrotransposons that have long terminal repeats (LTRs) containing hammerhead ribozymes (HHRs) that facilitate the circularization of the retrozyme RNA. The LTR of Nicotiana benthamiana retrozyme 1 (NbRZ1) has been shown to contain a promoter that directs transcription of this retroelement. In this study, we identified the transcription start site of the promoter contained in the LTR of NbRZ1 and mapped the promoter region essential for its transcriptional activity. Using transgenic Arabidopsis thaliana plants carrying the GUS gene under the control of the NbRZ1 LTR, the NbRZ1 transcript was demonstrated to potentially encode a protein targeted for proteasomal degradation in the plant cell. Overexpression of this protein in plants using a viral expression vector was found to cause severe necrosis. The data presented suggest a tight regulation of the expression of the NbRZ1-encoded polypeptide in plants and its potential functional importance, although further research is needed to determine whether circular and/or linear retrozyme RNA forms can be translated in plants. Full article
(This article belongs to the Special Issue Recent Advances in Plant Genetics and Genomics)
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