scholarly journals Comparative transcriptome and metabolome analyses provide new insights into the molecular mechanisms underlying taproot thickening in Panax notoginseng

2019 ◽  
Author(s):  
Xue-Jiao Li ◽  
Jian-Li Yang ◽  
Bing Hao ◽  
Ying-Chun Lu ◽  
Zhi-Long Qian ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Panax Notoginseng ◽  
Chinese Medicinal Herb ◽  
Primary Metabolite ◽  
Developmental Factors ◽  
Complex Biological Process ◽  
Phenylpropanoid Biosynthesis ◽  
Coordinated Expression ◽  
Major Storage Protein

Abstract Background Taproot thickening is a complex biological process and depends on the coordinated expression of the genes controlled by both environmental and developmental factors. Panax notoginseng is an important Chinese medicinal herb characterized by enlarged taproot as the main organ of saponin accumulation. However, little is known about the molecular mechanism of taproot enlargement. Results A total of 29957 DETs were identified during thickening process of P. notoginseng taproot. GO and KEGG pathway enrichment revealed that DETs associated wthith “plant hormone signal transduction”, “starch and sucrose metabolism”, and “phenylpropanoid biosynthesis” were predominantly enriched. Furher functional analysis by integrating DETs expression profiling, endogenous hormone and primary metabolite identified some critical genes (e.g., RNase-like major storage protein, DA1-related protein, Starch branching enzyme I) and primary metabolites (e.g., Sucrose, Glucose, Fructose Malate and Arginine) potentially controlling taproot thickening, and highlighted that hormones crosstalk, transcriptional regulation, homeostasis regulation of sugar and starch, and cell wall metabolism play an important role during thickening process of P. notoginseng taproot. Conclusion These results provide molecular regulatory network of taproot thickening in P. notoginseng and facilitate the characterization of genes responsible for taproot formation in root medicinal plants or crops.

scholarly journals Comparative transcriptome and metabolome analyses provide new insights into the molecular mechanisms underlying taproot thickening in Panax notoginseng

2019 ◽  
Author(s):  
Xue-Jiao Li ◽  
Jian-Li Yang ◽  
Bing Hao ◽  
Ying-Chun Lu ◽  
Zhi-Long Qian ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Panax Notoginseng ◽  
Chinese Medicinal Herb ◽  
Primary Metabolite ◽  
Developmental Factors ◽  
Complex Biological Process ◽  
Phenylpropanoid Biosynthesis ◽  
Coordinated Expression ◽  
Major Storage Protein

Abstract Background Taproot thickening is a complex biological process and depends on the coordinated expression of the genes controlled by both environmental and developmental factors. Panax notoginseng is an important Chinese medicinal herb characterized by enlarged taproot as the main organ of saponin accumulation. However, little is known about the molecular mechanism of taproot enlargement. Results A total of 29957 DETs were identified during thickening process of P. notoginseng taproot. GO and KEGG pathway enrichment revealed that DETs associated wthith “plant hormone signal transduction”, “starch and sucrose metabolism”, and “phenylpropanoid biosynthesis” were predominantly enriched. Furher functional analysis by integrating DETs expression profiling, endogenous hormone and primary metabolite identified some critical genes (e.g., RNase-like major storage protein, DA1-related protein, Starch branching enzyme I) and primary metabolites (e.g., Sucrose, Glucose, Fructose Malate and Arginine) potentially controlling taproot thickening, and highlighted that hormones crosstalk, transcriptional regulation, homeostasis regulation of sugar and starch, and cell wall metabolism play an important role during thickening process of P. notoginseng taproot. Conclusion These results provide molecular regulatory network of taproot thickening in P. notoginseng and facilitate the characterization of genes responsible for taproot formation in root medicinal plants or crops.

scholarly journals Comparative transcriptome and metabolome analyses provide new insights into the molecular mechanisms underlying taproot thickening in Panax notoginseng

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Xue-Jiao Li ◽  
Jian-Li Yang ◽  
Bing Hao ◽  
Ying-Chun Lu ◽  
Zhi-Long Qian ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Panax Notoginseng ◽  
Chinese Medicinal Herb ◽  
Developmental Factors ◽  
Expression Of Genes ◽  
Complex Biological Process ◽  
Phenylpropanoid Biosynthesis ◽  
Coordinated Expression ◽  
Major Storage Protein

Abstract Background Taproot thickening is a complex biological process that is dependent on the coordinated expression of genes controlled by both environmental and developmental factors. Panax notoginseng is an important Chinese medicinal herb that is characterized by an enlarged taproot as the main organ of saponin accumulation. However, the molecular mechanisms of taproot enlargement are poorly understood. Results A total of 29,957 differentially expressed genes (DEGs) were identified during the thickening process in the taproots of P. notoginseng. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment revealed that DEGs associated with “plant hormone signal transduction,” “starch and sucrose metabolism,” and “phenylpropanoid biosynthesis” were predominantly enriched. Further analysis identified some critical genes (e.g., RNase-like major storage protein, DA1-related protein, and Starch branching enzyme I) and metabolites (e.g., sucrose, glucose, fructose, malate, and arginine) that potentially control taproot thickening. Several aspects including hormone crosstalk, transcriptional regulation, homeostatic regulation between sugar and starch, and cell wall metabolism, were identified as important for the thickening process in the taproot of P. notoginseng. Conclusion The results provide a molecular regulatory network of taproot thickening in P. notoginseng and facilitate the further characterization of the genes responsible for taproot formation in root medicinal plants or crops.

scholarly journals Comparative transcriptome and metabolome analyses provide new insights into the molecular mechanism underlying taproot thickening in Panax notoginseng

2019 ◽  
Author(s):  
Xue-Jiao Li ◽  
Jian-Li Yang ◽  
Ying-Chun Lu ◽  
Zhi-Long Qian ◽  
Ying Li ◽  
...  
Keyword(s):  
Molecular Mechanism ◽  
Panax Notoginseng ◽  
Chinese Medicinal Herb ◽  
Primary Metabolite ◽  
Developmental Factors ◽  
Complex Biological Process ◽  
Phenylpropanoid Biosynthesis ◽  
Coordinated Expression ◽  
Major Storage Protein

Abstract Background Taproot thickening is a complex biological process and depends on the coordinated expression of the genes controlled by both environmental and developmental factors. Panax notoginseng is an important Chinese medicinal herb characterized by enlarged taproot as the main organ of saponin accumulation. However, little is known about the molecular mechanism of taproot enlargement. Results A total of 29957 DETs were identified during thickening process of P. notoginseng taproot. GO and KEGG pathway enrichment revealed that DETs associated wthith “plant hormone signal transduction”, “starch and sucrose metabolism”, and “phenylpropanoid biosynthesis” were predominantly enriched. Furher functional analysis by integrating DETs expression profiling, endogenous hormone and primary metabolite identified some critical genes (e.g., RNase-like major storage protein, DA1-related protein, Starch branching enzyme I) and primary metabolites (e.g., Sucrose, Glucose, Fructose Malate and Arginine) potentially controlling taproot thickening, and highlighted that hormones crosstalk, transcriptional regulation, homeostasis regulation of sugar and starch, and cell wall metabolism play an important role during thickening process of P. notoginseng taproot. Conclusion These results provide molecular regulatory network of taproot thickening in P. notoginseng and facilitate the characterization of genes responsible for taproot formation in root medicinal plants or crops.

scholarly journals Genetic mapping and transcriptomic characterization of a new fuzzless-tufted cottonseed mutant

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Qian-Hao Zhu ◽  
Warwick Stiller ◽  
Philippe Moncuquet ◽  
Stuart Gordon ◽  
Yuman Yuan ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Agronomic Traits ◽  
Gene Families ◽  
Mutant Phenotype ◽  
Wild Type ◽  
Calcium Dependent ◽  
Dependent Protein ◽  
Flanking Region ◽  
Comparative Transcriptomic Analysis

Abstract Fiber mutants are unique and valuable resources for understanding the genetic and molecular mechanisms controlling initiation and development of cotton fibers that are extremely elongated single epidermal cells protruding from the seed coat of cottonseeds. In this study, we reported a new fuzzless-tufted cotton mutant (Gossypium hirsutum) and showed that fuzzless-tufted near-isogenic lines (NILs) had similar agronomic traits and a higher ginning efficiency compared to their recurrent parents with normal fuzzy seeds. Genetic analysis revealed that the mutant phenotype is determined by a single incomplete dominant locus, designated N5. The mutation was fine mapped to an approximately 250-kb interval containing 33 annotated genes using a combination of bulked segregant sequencing, SNP chip genotyping, and fine mapping. Comparative transcriptomic analysis using 0–6 days post-anthesis (dpa) ovules from NILs segregating for the phenotypes of fuzzless-tufted (mutant) and normal fuzzy cottonseeds (wild-type) uncovered candidate genes responsible for the mutant phenotype. It also revealed that the flanking region of the N5 locus is enriched with differentially expressed genes (DEGs) between the mutant and wild-type. Several of those DEGs are members of the gene families with demonstrated roles in cell initiation and elongation, such as calcium-dependent protein kinase and expansin. The transcriptome landscape of the mutant was significantly reprogrammed in the 6 dpa ovules and, to a less extent, in the 0 dpa ovules, but not in the 2 and 4 dpa ovules. At both 0 and 6 dpa, the reprogrammed mutant transcriptome was mainly associated with cell wall modifications and transmembrane transportation, while transcription factor activity was significantly altered in the 6 dpa mutant ovules. These results imply a similar molecular basis for initiation of lint and fuzz fibers despite certain differences.

scholarly journals A Concerted Action of UBA5 C-Terminal Unstructured Regions Is Important for Transfer of Activated UFM1 to UFC1

2021 ◽  
Vol 22 (14) ◽  
pp. 7390
Author(s):  
Nicole Wesch ◽  
Frank Löhr ◽  
Natalia Rogova ◽  
Volker Dötsch ◽  
Vladimir V. Rogov
Keyword(s):  
Cellular Localization ◽  
Molecular Mechanisms ◽  
Biochemical Characterization ◽  
Effective Interaction ◽  
Regulatory Region ◽  
Titration Calorimetry ◽  
Enzymatic Reactions ◽  
Cellular Processes ◽  
Mechanism Of Interaction

Ubiquitin fold modifier 1 (UFM1) is a member of the ubiquitin-like protein family. UFM1 undergoes a cascade of enzymatic reactions including activation by UBA5 (E1), transfer to UFC1 (E2) and selective conjugation to a number of target proteins via UFL1 (E3) enzymes. Despite the importance of ufmylation in a variety of cellular processes and its role in the pathogenicity of many human diseases, the molecular mechanisms of the ufmylation cascade remains unclear. In this study we focused on the biophysical and biochemical characterization of the interaction between UBA5 and UFC1. We explored the hypothesis that the unstructured C-terminal region of UBA5 serves as a regulatory region, controlling cellular localization of the elements of the ufmylation cascade and effective interaction between them. We found that the last 20 residues in UBA5 are pivotal for binding to UFC1 and can accelerate the transfer of UFM1 to UFC1. We solved the structure of a complex of UFC1 and a peptide spanning the last 20 residues of UBA5 by NMR spectroscopy. This structure in combination with additional NMR titration and isothermal titration calorimetry experiments revealed the mechanism of interaction and confirmed the importance of the C-terminal unstructured region in UBA5 for the ufmylation cascade.

scholarly journals High-resolution view of HIV-1 reverse transcriptase initiation complexes and inhibition by NNRTI drugs

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Betty Ha ◽  
Kevin P. Larsen ◽  
Jingji Zhang ◽  
Ziao Fu ◽  
Elizabeth Montabana ◽  
...  
Keyword(s):  
Reverse Transcriptase ◽  
Viral Entry ◽  
Reverse Transcription ◽  
Molecular Mechanisms ◽  
Dissociation Kinetics ◽  
Structural Mechanism ◽  
Medium Resolution ◽  
Kinetics Of ◽  
Hiv 1

AbstractReverse transcription of the HIV-1 viral RNA genome (vRNA) is an integral step in virus replication. Upon viral entry, HIV-1 reverse transcriptase (RT) initiates from a host tRNALys3 primer bound to the vRNA genome and is the target of key antivirals, such as non-nucleoside reverse transcriptase inhibitors (NNRTIs). Initiation proceeds slowly with discrete pausing events along the vRNA template. Despite prior medium-resolution structural characterization of reverse transcriptase initiation complexes (RTICs), higher-resolution structures of the RTIC are needed to understand the molecular mechanisms that underlie initiation. Here we report cryo-EM structures of the core RTIC, RTIC–nevirapine, and RTIC–efavirenz complexes at 2.8, 3.1, and 2.9 Å, respectively. In combination with biochemical studies, these data suggest a basis for rapid dissociation kinetics of RT from the vRNA–tRNALys3 initiation complex and reveal a specific structural mechanism of nucleic acid conformational stabilization during initiation. Finally, our results show that NNRTIs inhibit the RTIC and exacerbate discrete pausing during early reverse transcription.

scholarly journals Hemolysis in the spleen drives erythrocyte turnover

Blood ◽  
2020 ◽  
Author(s):  
Thomas robert leon Klei ◽  
Jill Jasmine Dalimot ◽  
Benjamin Nota ◽  
Martijn Veldthuis ◽  
Erik Mul ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Matrix Proteins ◽  
Human Spleen ◽  
Erythrocyte Adhesion ◽  
Subsequent Degradation ◽  
Macrophage Subpopulations ◽  
Senescent Erythrocytes ◽  
Red Pulp

Red pulp macrophages of the spleen mediate turnover of billions of senescent erythrocytes per day. However, the molecular mechanisms involved in sequestration of senescent erythrocytes, their recognition and their subsequent degradation by red pulp macrophages remain unclear. In this study we provide evidence that the splenic environment is of substantial importance in facilitating erythrocyte turnover through induction of hemolysis. Upon isolating human spleen red pulp macrophages we noted a substantial lack of macrophages that were in the process of phagocytosing intact erythrocytes. Detailed characterization of erythrocyte and macrophage subpopulations from human spleen tissue led to the identification of erythrocytes that are devoid of hemoglobin, so-called erythrocyte ghosts. By in vivo imaging and transfusion experiments we further confirmed that senescent erythrocytes that are retained in the spleen are subject to hemolysis. Additionally, we show that erythrocyte adhesion molecules, which are specifically activated on aged erythrocytes, cause senescent erythrocytes to interact with extracellular matrix proteins that are exposed within the splenic architecture. Such adhesion molecule-driven retention of senescent erythrocytes, under low shear conditions, was found to result in steady shrinkage of the cell and ultimately resulted in hemolysis. In contrast to intact senescent erythrocytes, the remnant erythrocyte ghost shells were prone to recognition and breakdown by red pulp macrophages. These data identify hemolysis as a key event in the turnover of senescent erythrocytes, which alters our current understanding of how erythrocyte degradation is regulated.

scholarly journals Analysis of saponins detoxification genes in Ilyonectria mors-panacis G3B inducing root rot of Panax notoginseng by RNA-Seq

2021 ◽  
Author(s):  
Guohong Zeng ◽  
Jin Li ◽  
Yuxiu Ma ◽  
Qian Pu ◽  
Tian Xiao ◽  
...  
Keyword(s):  
Root Rot ◽  
Molecular Mechanisms ◽  
Management Strategies ◽  
Panax Notoginseng ◽  
Glycoside Hydrolases ◽  
Rna Seq ◽  
Host Interaction ◽  
Excellent Starting Point ◽  
Starting Point ◽  
Genes Encoding

AbstractSaponins are kinds of antifungal compounds produced by Panax notoginseng to resist invasion by pathogens. Ilyonectria mors-panacis G3B was the dominant pathogen inducing root rot of P. notoginseng, and the abilities to detoxify saponins were the key to infect P. notoginseng successfully. To research the molecular mechanisms of detoxifying saponins in I. mors-panacis G3B, we used high-throughput RNA-Seq to identify 557 and 1519 differential expression genes (DEGs) in I. mors-panacis G3B with saponins treatments for 4H (Hours) and 12H (Hours) compared with no saponins treatments, respectively. Among these DEGs, we found 93 genes which were simultaneously highly expressed in I. mors-panacis G3B with saponins treatments for 4H and 12H, they mainly belong to genes encoding transporters, glycoside hydrolases, oxidation–reduction enzymes, transcription factors and so on. In addition, there were 21 putative PHI (Pathogen–Host Interaction) genes out of those 93 up-regulated genes. In this report, we analyzed virulence-associated genes in I. mors-panacis G3B which may be related to detoxifying saponins to infect P. notoginseng successfully. They provided an excellent starting point for in-depth study on pathogenicity of I. mors-panacis G3B and developed appropriate root rot disease management strategies in the future.

scholarly journals Integrated Transcriptomic and Un-Targeted Metabolomics Analysis Reveals Mulberry Fruit (Morus atropurpurea) in Response to Sclerotiniose Pathogen Ciboria shiraiana Infection

2020 ◽  
Vol 21 (5) ◽  
pp. 1789 ◽  
Author(s):  
Lijun Bao ◽  
Hongpeng Gao ◽  
Zelin Zheng ◽  
Xiaoxiao Zhao ◽  
Minjuan Zhang ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Early Stage ◽  
Metabolite Profile ◽  
Northwest China ◽  
Targeted Metabolomics ◽  
Mulberry Fruit ◽  
Phenylpropanoid Biosynthesis ◽  
Mapman Analysis ◽  
Mulberry Fruits ◽  
Prevention Methods

Mulberry sclerotiniose caused by Ciboria shiraiana is a devastating disease of mulberry (Morus alba L.) fruit in Northwest China. At present, no disease-resistant varieties are used in production, as the molecular mechanisms of this disease are not well understood. In this study, to explore new prevention methods and provide direction for molecular breeding, transcriptomic sequencing and un-targeted metabolomics were performed on healthy (CK), early-stage diseased (HB1), and middle-stage diseased (HB2) mulberry fruits. Functional annotation, gene ontology, a Kyoto encyclopedia of genes and genomes (KEGG) analysis, and a Mapman analysis of the differentially expressed genes revealed differential regulation of genes related to plant hormone signal transduction, transcription factors, and phenylpropanoid biosynthesis. A correspondence between the transcript pattern and metabolite profile was observed in the phenylpropanoid biosynthesis pathway. It should be noted that the log2 ratio of eugenol (isoeugenol) in HB1 and HB2 are 85 times and 23 times higher than CK, respectively. Our study shows that phenylpropanoid biosynthesis may play an essential role in response to sclerotiniose pathogen infection and eugenol(isoeugenol) enrichment in mulberry fruit, which may provide a novel method for mulberry sclerotiniose control.

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