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Khalvandi M, Aghaie P, Siosemardeh A, Hosseini SJ, Ghorbanpour M, Reiahisamani N, Amerian M. Genome-wide study of UDP-glycosyltransferases gene family in Cannabis sativa. 3 Biotech 2024; 14:183. [PMID: 39050981 PMCID: PMC11263533 DOI: 10.1007/s13205-024-04025-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2024] [Accepted: 07/14/2024] [Indexed: 07/27/2024] Open
Abstract
The research focused on analyzing the UGT gene family in Cannabis sativa, which plays a crucial role in the plant's metabolism and glycosylation of secondary metabolites. The study identified 125 UGTs using conserved plant secondary product glycosyltransferase (PSPG) motif amino acid sequences. These UGT genes were categorized into 17 groups (A-Q) through phylogenetic analysis, showing their distribution across 10 chromosomes in C. sativa. The expansion of the CsUGT gene family was attributed to tandem and duplication events, as suggested by gene duplication analysis. Furthermore, the study found various cis-acting regulatory elements related to phytohormones and stress responses in CsUGT promoter regions. Subcellular localization analysis revealed that CsUGT is present in the cytoplasm, chloroplast, and nucleus. The study revealed that CsUGT plays a significant role in various biological processes, cellular components, and molecular functions as highlighted by Gene Ontology analysis. Additionally, the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that some CsUGTs are associated with the biosynthesis of secondary metabolites. This research provides valuable insights into the genomic organization, evolutionary history, and potential regulatory mechanisms of UGT genes in C. sativa. It lays the foundation for further exploration of their specific biological roles and potential applications in the plant's metabolism and stress responses. These findings contribute to a better understanding of the UGT gene family and its relevance to the metabolic pathways in C. sativa. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-024-04025-3.
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Affiliation(s)
- Masoumeh Khalvandi
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Kurdistan, Sanandaj, Iran
| | - Peyman Aghaie
- Department of Biology, Payame Noor University, Tehran, Iran
| | - Adel Siosemardeh
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Kurdistan, Sanandaj, Iran
| | | | - Mansour Ghorbanpour
- Department of Medicinal Plants, Faculty of Agriculture and Natural Resources, Arak University, Arak 38156-8-8349, Iran
| | | | - Mohammadreza Amerian
- Department of Agronomy, Faculty of Agriculture, Shahrood University of Technology, Shahrood, Iran
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Fu H, Guo C, Peng J, Shao F, Sheng S, Wang S. Transcriptomic Insights and Cytochrome P450 Gene Analysis in Kadsura coccinea for Lignan Biosynthesis. Genes (Basel) 2024; 15:270. [PMID: 38540329 PMCID: PMC10969973 DOI: 10.3390/genes15030270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 02/17/2024] [Accepted: 02/19/2024] [Indexed: 06/15/2024] Open
Abstract
Kadsura coccinea is a medicinal plant from the Schisandraceae family that is native to China and has great pharmacological potential due to its lignans. However, there are significant knowledge gaps regarding the genetic and molecular mechanisms of lignans. We used transcriptome sequencing technology to analyze root, stem, and leaf samples, focusing on the identification and phylogenetic analysis of Cytochrome P450 (CYP) genes. High-quality data containing 158,385 transcripts and 68,978 unigenes were obtained. In addition, 36,293 unigenes in at least one database, and 23,335 across five databases (Nr, KEGG, KOG, TrEMBL, and SwissProt) were successfully annotated. The KEGG pathway classification and annotation of these unigenes identified 10,825 categorized into major metabolic pathways, notably phenylpropanoid biosynthesis, which is essential for lignan synthesis. A key focus was the identification and phylogenetic analysis of 233 Cytochrome P450 (CYP) genes, revealing their distribution across 38 families in eight clans, with roots showing specific CYP gene expression patterns indicative of their role in lignan biosynthesis. Sequence alignment identified 22 homologous single genes of these CYPs, with 6 homologous genes of CYP719As and 1 of CYP81Qs highly expressed in roots. Our study significantly advances the understanding of the biosynthesis of dibenzocyclooctadiene lignans, offering valuable insights for future pharmacological research and development.
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Affiliation(s)
- Hanyu Fu
- College of Forestry, Central South University of Forestry & Technology, 498 South Shaoshan Road, Changsha 410004, China; (H.F.); (C.G.); (J.P.); (F.S.)
| | - Chuan Guo
- College of Forestry, Central South University of Forestry & Technology, 498 South Shaoshan Road, Changsha 410004, China; (H.F.); (C.G.); (J.P.); (F.S.)
- Yuelushan Laboratory, Qiushi Building, Hunan Agricultural University, Furong District, Changsha 410128, China
- The Belt and Road International Union Research Center for Tropical Arid Non-Wood Forest in Hunan Province, 498 South Shaoshan Road, Changsha 410004, China
| | - Jiqing Peng
- College of Forestry, Central South University of Forestry & Technology, 498 South Shaoshan Road, Changsha 410004, China; (H.F.); (C.G.); (J.P.); (F.S.)
- Yuelushan Laboratory, Qiushi Building, Hunan Agricultural University, Furong District, Changsha 410128, China
- The Belt and Road International Union Research Center for Tropical Arid Non-Wood Forest in Hunan Province, 498 South Shaoshan Road, Changsha 410004, China
| | - Fengxia Shao
- College of Forestry, Central South University of Forestry & Technology, 498 South Shaoshan Road, Changsha 410004, China; (H.F.); (C.G.); (J.P.); (F.S.)
- Yuelushan Laboratory, Qiushi Building, Hunan Agricultural University, Furong District, Changsha 410128, China
- The Belt and Road International Union Research Center for Tropical Arid Non-Wood Forest in Hunan Province, 498 South Shaoshan Road, Changsha 410004, China
| | - Song Sheng
- Yuelushan Laboratory, Qiushi Building, Hunan Agricultural University, Furong District, Changsha 410128, China
| | - Sen Wang
- College of Forestry, Central South University of Forestry & Technology, 498 South Shaoshan Road, Changsha 410004, China; (H.F.); (C.G.); (J.P.); (F.S.)
- The Belt and Road International Union Research Center for Tropical Arid Non-Wood Forest in Hunan Province, 498 South Shaoshan Road, Changsha 410004, China
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Zhang X, Wang X, Pan L, Guo W, Li Y, Wang W. Genome-wide identification and expression analysis of MADS-box transcription factors reveal their involvement in sex determination of hardy rubber tree ( Eucommia ulmoides oliv.). Front Genet 2023; 14:1138703. [PMID: 36896236 PMCID: PMC9988917 DOI: 10.3389/fgene.2023.1138703] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 02/06/2023] [Indexed: 02/23/2023] Open
Abstract
Eucommia ulmoides is a famous rubber-producing and medicinal tree species that produces unisexual flowers on separate individuals from the earliest stage of stamen/pistil primordium formation. To explore the genetic regulation pathway of sex in E. ulmoides, comprehensive genome-wide analyses and tissue-/sex-specific transcriptome comparisons of MADS-box transcription factors were performed for the first time in this work. Quantitative real-time PCR technique was employed to further validate the expression of genes that are assigned to floral organ ABCDE model. A total of 66 non-redundant E. ulmoides MADS-box (EuMADS) genes were identified, they were classified into Type I (M-type, 17 genes) and Type II (MIKC, 49 genes). Complex protein-motif composition, exon-intron structure and phytohormone-response cis-elements were detected in MIKC-EuMADS genes. Furthermore, 24 differentially-expressed EuMADS genes (DEGs) between male and female flowers, and two DEGs between male and female leaves were revealed. Amongst the 14 floral organ ABCDE model-related genes, there were 6 (A/B/C/E-class) and 5 (A/D/E-class) genes displayed male- and female-biased expression respectively. In particular, one B-class gene EuMADS39 and one A-class gene EuMADS65 were almost exclusively expressed in male trees, no matter in flower or leaf tissues. Collectively, these results suggested a critical role of MADS-box transcription factors in sex determination of E. ulmoides, which is conducive to decoding the molecular regulation mechanism of sex in E. ulmoides.
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Affiliation(s)
- Xianzhi Zhang
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Xinyi Wang
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Linsi Pan
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Wei Guo
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Yongquan Li
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Wencai Wang
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, China
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Genome Wide Analysis of Family-1 UDP Glycosyltransferases in Populus trichocarpa Specifies Abiotic Stress Responsive Glycosylation Mechanisms. Genes (Basel) 2022; 13:genes13091640. [PMID: 36140806 PMCID: PMC9498546 DOI: 10.3390/genes13091640] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 08/22/2022] [Accepted: 08/25/2022] [Indexed: 11/21/2022] Open
Abstract
Populus trichocarpa (Black cottonwood) is a dominant timber-yielding tree that has become a notable model plant for genome-level insights in forest trees. The efficient transport and solubility of various glycoside-associated compounds is linked to Family-1 UDP-glycosyltransferase (EC 2.4.1.x; UGTs) enzymes. These glycosyltransferase enzymes play a vital role in diverse plant functions, such as regulation of hormonal homeostasis, growth and development (seed, flower, fiber, root, etc.), xenobiotic detoxification, stress response (salt, drought, and oxidative), and biosynthesis of secondary metabolites. Here, we report a genome-wide analysis of the P. trichocarpa genome that identified 191 putative UGTs distributed across all chromosomes (with the exception of chromosome 20) based on 44 conserved plant secondary product glycosyltransferase (PSPG) motif amino acid sequences. Phylogenetic analysis of the 191 Populus UGTs together with 22 referenced UGTs from Arabidopsis and maize clustered the putative UGTs into 16 major groups (A–P). Whole-genome duplication events were the dominant pattern of duplication among UGTs in Populus. A well-conserved intron insertion was detected in most intron-containing UGTs across eight examined eudicots, including Populus. Most of the UGT genes were found preferentially expressed in leaf and root tissues in general. The regulation of putative UGT expression in response to drought, salt and heat stress was observed based on microarray and available RNA sequencing datasets. Up- and down-regulated UGT expression models were designed, based on transcripts per kilobase million values, confirmed their maximally varied expression under drought, salt and heat stresses. Co-expression networking of putative UGTs indicated their maximum co-expression with cytochrome P450 genes involved in triterpenoid biosynthesis. Our results provide an important resource for the identification of functional UGT genes to manipulate abiotic stress responsive glycosylation in Populus.
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Chandra S, Leon RG. Genome-Wide Evolutionary Analysis of Putative Non-Specific Herbicide Resistance Genes and Compilation of Core Promoters between Monocots and Dicots. Genes (Basel) 2022; 13:genes13071171. [PMID: 35885954 PMCID: PMC9316059 DOI: 10.3390/genes13071171] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 06/24/2022] [Accepted: 06/25/2022] [Indexed: 02/06/2023] Open
Abstract
Herbicides are key weed-control tools, but their repeated use across large areas has favored the evolution of herbicide resistance. Although target-site has been the most prevalent and studied type of resistance, non-target-site resistance (NTSR) is increasing. However, the genetic factors involved in NTSR are widely unknown. In this study, four gene groups encoding putative NTSR enzymes, namely, cytochrome-P450, glutathione-S-transferase (GST), uridine 5'-diphospho-glucuronosyltransferase (UDPGT), and nitronate monooxygenase (NMO) were analyzed. The monocot and dicot gene sequences were downloaded from publicly available databases. Phylogenetic trees revealed that most of the CYP450 resistance-related sequences belong to CYP81 (5), and in GST, most of the resistance sequences belonged to GSTU18 (9) and GSTF6 (8) groups. In addition, the study of upstream promoter sequences of these NTSR genes revealed stress-related cis-regulatory motifs, as well as eight transcription factor binding sites (TFBS) were identified. The discovered TFBS were commonly present in both monocots and dicots, and the identified motifs are known to play key roles in countering abiotic stress. Further, we predicted the 3D structure for the resistant CYP450 and GST protein and identified the substrate recognition site through the homology approach. Our description of putative NTSR enzymes may be used to develop innovative weed control techniques to delay the evolution of NTSR.
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Affiliation(s)
- Saket Chandra
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC 27695, USA;
| | - Ramon G. Leon
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC 27695, USA;
- Genetic Engineering and Society Center, Center for Environmental Farming Systems, North Carolina State University, Raleigh, NC 27695, USA
- Correspondence: ; Tel.: +1-919-515-5328
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Network Pharmacology-Based Prediction and Verification of the Potential Targets of Pinoresinol Diglucoside for OA Treatment. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2022; 2022:9733742. [PMID: 35469160 PMCID: PMC9034917 DOI: 10.1155/2022/9733742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 03/16/2022] [Accepted: 03/17/2022] [Indexed: 12/02/2022]
Abstract
Objective This study aimed to explore the effects and related mechanisms of pinoresinol diglucoside (PDG) on osteoarthritis (OA) via a combination of pharmacology and animal experiments. Methods Traditional Chinese Medicine Database and Analysis Platform (TCMSP) Drugbank, Online Mendelian Inheritance in Man, and GeneCards databases were used to predict the putative targets of PGD against OA. A protein protein interaction (PPI) network was constructed in STING database to analyze the interaction network of these targets. Enrichment analysis was performed with DAVID database. The OA model was built by anterior cruciate ligament transection and then injected with PDG for 5 weeks. Hematoxylin and eosin (HE) staining and safranin-fixed green staining were used to evaluate the pathological change. ELISA was applied to measure the serum levels of interleukin-1β (IL-1β), interleukin-6 (IL-6), and tumor necrosis factor-α (TNF-α). Immunohistochemistry was employed to detect the protein levels of kinase B (AKT), BAX, Bcl2, matrix metalloproteinase-1 (MMP-1), tissue inhibitor of metalloproteinases 1 (TIMP-1), and phosphatidylinositol 3 kinase (PI3K) in knee cartilage tissues. Results Seventy-one key targets were identified, including AKT1, epidermal growth factor receptor, SRC, estrogen receptor 1 (ESR1), and MMP9. Enrichment analysis revealed a series of pathway related to cancer, PI3K-Akt signaling pathway, and proteoglycans in cancer. Animal experiments showed that PDG alleviated the abnormal histomorphological changes of OA; suppressed TIPM, serum IL-1β, IL-6, and TNF-α levels, and PI3K and AKT activation; and increased MMP-1 expression and Bcl2/Bax ratio. Conclusion PDG has a cartilage-protecting effect associated with PI3K/AKT signaling pathway in rabbit with OA and therefore might serve as a potential agent for the treatment of this disease.
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Deng P, Xie X, Long F, Zhang L, Li Y, Zhao Z, Yang S, Wang Y, Fan R, Li Z. Trait Variations and Probability Grading Index System on Leaf-Related Traits of Eucommia ulmoides Oliver Germplasm. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10112280. [PMID: 34834643 PMCID: PMC8620490 DOI: 10.3390/plants10112280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 10/14/2021] [Accepted: 10/19/2021] [Indexed: 05/14/2023]
Abstract
Eucommia ulmoides Oliver (EUO), an economic tree grown specifically in China, is widely used in various fields. To satisfy the requirements of industrial development, superior varieties need to be selected for different uses. However, there is no unified standard for breeders to reference. In this study, leaf-related traits were classified by a probability grading method. The results indicated there were significant differences between different planting models for the studied traits, and the traits in the Arbor forest model showed more abundant variation. Compared with genotype, the planting model accounted for relatively bigger variance, indicating that the standard should be divided according to planting models. Furthermore, the optimum planting model for different traits would be obtained by analyzing the variation range. Association analyses were conducted among traits to select the crucial evaluation indexes. The indexes were divided into three grades in different planting models. The evaluation system on leaf-related traits of EUO germplasm was established preliminarily, which considered planting models and stability across years for the first time. It can be treated as a reference to identify and evaluate EUO germplasm resources. Additionally, the study served as an example for the classification of quantitative traits in other economically important perennial plants.
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Affiliation(s)
- Peng Deng
- College of Forestry, Northwest A&F University, Xianyang 712100, China; (P.D.); (X.X.); (F.L.); (L.Z.); (Y.L.); (Y.W.); (R.F.)
| | - Xiangchen Xie
- College of Forestry, Northwest A&F University, Xianyang 712100, China; (P.D.); (X.X.); (F.L.); (L.Z.); (Y.L.); (Y.W.); (R.F.)
| | - Feiyu Long
- College of Forestry, Northwest A&F University, Xianyang 712100, China; (P.D.); (X.X.); (F.L.); (L.Z.); (Y.L.); (Y.W.); (R.F.)
| | - Liang Zhang
- College of Forestry, Northwest A&F University, Xianyang 712100, China; (P.D.); (X.X.); (F.L.); (L.Z.); (Y.L.); (Y.W.); (R.F.)
| | - Yonghang Li
- College of Forestry, Northwest A&F University, Xianyang 712100, China; (P.D.); (X.X.); (F.L.); (L.Z.); (Y.L.); (Y.W.); (R.F.)
| | - Zhangxu Zhao
- College of Economics and Management, Northwest A&F University, Xianyang 712100, China;
| | - Shiyao Yang
- College of Life Sciences, Northwest A&F University, Xianyang 712100, China;
| | - Yiran Wang
- College of Forestry, Northwest A&F University, Xianyang 712100, China; (P.D.); (X.X.); (F.L.); (L.Z.); (Y.L.); (Y.W.); (R.F.)
| | - Ruishen Fan
- College of Forestry, Northwest A&F University, Xianyang 712100, China; (P.D.); (X.X.); (F.L.); (L.Z.); (Y.L.); (Y.W.); (R.F.)
| | - Zhouqi Li
- College of Forestry, Northwest A&F University, Xianyang 712100, China; (P.D.); (X.X.); (F.L.); (L.Z.); (Y.L.); (Y.W.); (R.F.)
- Correspondence:
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