scholarly journals Transcriptional reprogramming strategies and miRNA-mediated regulation networks of Taxus media induced into callus cells from tissues

2020 ◽  
Author(s):  
Ying Chen ◽  
Meng Zhang ◽  
Xiaofei Jin ◽  
Haoran Tao ◽  
Yamin Wang ◽  
...  
Keyword(s):  
Secondary Metabolites ◽  
Cost Effective ◽  
Environment Friendly ◽  
Taxus Media ◽  
Taxol Biosynthesis ◽  
Defense Systems ◽  
Transcriptional Reprogramming ◽  
Expression Of Genes ◽  
Phenylpropanoid Biosynthesis ◽  
Plant Pathogen Interaction

Abstract Background Taxus cells are a potential sustainable and environment-friendly source of taxol, but they have low survival ratios and slow grow rates. Despite these limitations, Taxus callus cells induced through 6 months of culture contain more taxol than their parent tissues. In this work, we utilized 6-month-old Taxus media calli to investigate their regulatory mechanisms of taxol biosynthesis by applying multiomics technologies. Our results provide insights into the adaptation strategies of T. media by transcriptional reprogramming when induced into calli from parent tissues. Results Seven out of 12 known taxol, most of flavonoid and phenylpropanoid biosynthesis genes were significantly upregulated in callus cells relative to that in the parent tissue, thus indicating that secondary metabolism is significantly strengthened. The expression of genes involved in pathways metabolizing biological materials, such as amino acids and sugars, also dramatically increased because all nutrients are supplied from the medium. The expression level of 94.1% genes involved in photosynthesis significantly decreased. These results reveal that callus cells undergo transcriptional reprogramming and transition into heterotrophs. Interestingly, common defense and immune activities, such as “plant–pathogen interaction” and salicylic acid- and jasmonic acid-signaling transduction, were repressed in calli. Thus, it’s an intelligent adaption strategy to use secondary metabolites as a cost-effective defense system. MiRNA- and degradome-sequencing results showed the involvement of a precise regulatory network in the miRNA-mediated transcriptional reprogramming of calli. MiRNAs act as direct regulators to enhance the metabolism of biological substances and repress defense activities. Given that only 17 genes of secondary metabolite biosynthesis were effectively regulated, miRNAs are likely to play intermediate roles in the biosynthesis of secondary metabolites by regulating transcriptional factors (TFs), such as ERF, WRKY, and SPL. Conclusion Our results suggest that increasing the biosynthesis of taxol and other secondary metabolites is an active regulatory measure of calli to adapt to heterotrophic culture, and this alteration mainly involved direct and indirect miRNA-induced transcriptional reprogramming. These results expand our understanding of the relationships among the metabolism of biological substances, the biosynthesis of secondary metabolites, and defense systems. They also provide a series of candidate miRNAs and transcription factors for taxol biosynthesis.

scholarly journals Transcriptional reprogramming strategies and miRNA-mediated regulation networks of Taxus media induced into callus cells from tissues

2020 ◽  
Author(s):  
Ying Chen ◽  
Meng Zhang ◽  
Xiaofei Jin ◽  
Haoran Tao ◽  
Yamin Wang ◽  
...  
Keyword(s):  
Secondary Metabolites ◽  
Cost Effective ◽  
Environment Friendly ◽  
Taxus Media ◽  
Taxol Biosynthesis ◽  
Defense Systems ◽  
Transcriptional Reprogramming ◽  
Expression Of Genes ◽  
Phenylpropanoid Biosynthesis ◽  
Plant Pathogen Interaction

Abstract Background Taxus cells are a potential sustainable and environment-friendly source of taxol, but they have low survival ratios and slow grow rates. Despite these limitations, Taxus callus cells induced through 6 months of culture contain more taxol than their parent tissues. In this work, we utilized 6-month-old Taxus media calli to investigate their regulatory mechanisms of taxol biosynthesis by applying multiomics technologies. Our results provide insights into the adaptation strategies of T. media by transcriptional reprogramming when induced into calli from parent tissues. Results Seven out of 12 known taxol, most of flavonoid and phenylpropanoid biosynthesis genes were significantly upregulated in callus cells relative to that in the parent tissue, thus indicating that secondary metabolism is significantly strengthened. The expression of genes involved in pathways metabolizing biological materials, such as amino acids and sugars, also dramatically increased because all nutrients are supplied from the medium. The expression level of 94.1% genes involved in photosynthesis significantly decreased. These results reveal that callus cells undergo transcriptional reprogramming and transition into heterotrophs. Interestingly, common defense and immune activities, such as “plant–pathogen interaction” and salicylic acid- and jasmonic acid-signaling transduction, were repressed in calli. Thus, it’s an intelligent adaption strategy to use secondary metabolites as a cost-effective defense system. MiRNA- and degradome-sequencing results showed the involvement of a precise regulatory network in the miRNA-mediated transcriptional reprogramming of calli. MiRNAs act as direct regulators to enhance the metabolism of biological substances and repress defense activities. Given that only 17 genes of secondary metabolite biosynthesis were effectively regulated, miRNAs are likely to play intermediate roles in the biosynthesis of secondary metabolites by regulating transcriptional factors (TFs), such as ERF, WRKY, and SPL. Conclusion Our results suggest that increasing the biosynthesis of taxol and other secondary metabolites is an active regulatory measure of calli to adapt to heterotrophic culture, and this alteration mainly involved direct and indirect miRNA-induced transcriptional reprogramming. These results expand our understanding of the relationships among the metabolism of biological substances, the biosynthesis of secondary metabolites, and defense systems. They also provide a series of candidate miRNAs and transcription factors for taxol biosynthesis.

scholarly journals Metabolome and transcriptome analysis reveals the molecular profiles underlying the ginseng response to rusty root symptoms

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Xingbo Bian ◽  
Yan Zhao ◽  
Shengyuan Xiao ◽  
He Yang ◽  
Yongzhong Han ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Molecular Mechanisms ◽  
Plant Hormone ◽  
Soil Microbiology ◽  
Mechanism Model ◽  
Expression Of Genes ◽  
Phenylpropanoid Biosynthesis ◽  
Plant Pathogen Interaction ◽  
Molecular Profiles

Abstract Background Ginseng rusty root symptoms (GRS) is one of the primary diseases of ginseng. This disease leads to a severe decline in the quality of ginseng. It has been shown that the occurrence of GRS is associated with soil environmental degradation, which may involve changes in soil microbiology and physicochemical properties. Results In this study, GRS and healthy ginseng (HG) samples were used as experimental materials for comparative analysis of transcriptome and metabolome. Compared with those in HG samples, 949 metabolites and 9451 genes were significantly changed at the metabolic and transcriptional levels in diseased samples. The diseased tissues’ metabolic patterns changed, and the accumulation of various organic acids, alkaloids, alcohols and phenols in diseased tissues increased significantly. There were significant differences in the expression of genes involved in plant hormone signal transduction, phenylpropanoid biosynthesis, the peroxidase pathway, and the plant-pathogen interaction pathway. Conclusion The current study involved a comparative metabolome and transcriptome analysis of GRS and HG samples. Based on the findings at the transcriptional and metabolic levels, a mechanism model of the ginseng response to GRS was established. Our results provide new insights into ginseng’s response to GRS, which will reveal the potential molecular mechanisms of this disease in ginseng.

An efficient biotreatment process for polyvinyl alcohol containing textile wastewater

2013 ◽  
Vol 8 (3-4) ◽  
pp. 469-478 ◽  
Author(s):  
Sandip S. Magdum ◽  
Gauri P. Minde ◽  
Upendra S. Adhyapak ◽  
V. Kalyanraman
Keyword(s):  
Polyvinyl Alcohol ◽  
Process Optimization ◽  
Textile Wastewater ◽  
Cost Effective ◽  
Chemical Oxidation ◽  
High Rate ◽  
Microbial Consortia ◽  
Environment Friendly ◽  
Candida Sp ◽  
Textile Wastewater Treatment

The aim of this work was to optimize the biodegradation of polyvinyl alcohol (PVA) containing actual textile wastewater for a sustainable treatment solution. The isolated microbial consortia of effective PVA degrader namely Candida Sp. and Pseudomonas Sp., which were responsible for symbiotic degradation of chemical oxidation demand (COD) and PVA from desizing wastewater. In the process optimization, the maximum aeration was essential to achieve a high degradation rate, where as stirring enhances further degradation and foam control. Batch experiments concluded with the need of 16 lpm/l and 150 rpm of air and stirring speed respectively for high rate of COD and PVA degradation. Optimized process leads to 2 days of hydraulic retention time (HRT) with 85–90% PVA degradation. Continuous study also confirmed above treatment process optimization with 85.02% of COD and 90.3% of PVA degradation of effluent with 2 days HRT. This study gives environment friendly and cost effective solution for PVA containing textile wastewater treatment.

Antimicrobial properties of actively purified secondary metabolites isolated from different marine organisms

2020 ◽  
Vol 21 ◽  
Author(s):  
Nilushi Indika Bamunu Arachchige ◽  
Fazlurrahman Khan ◽  
Young-Mog Kim
Keyword(s):  
Secondary Metabolites ◽  
Pathogenic Bacteria ◽  
Antimicrobial Agents ◽  
Bacterial Species ◽  
Antimicrobial Properties ◽  
Antimicrobial Effect ◽  
Cost Effective ◽  
Resistance Mechanisms ◽  
Marine Organisms ◽  
Antimicrobial Compounds

Background: The treatment of infection caused by pathogenic bacteria becomes one of the serious concerns globally. The failure in the treatment was found due to the exhibition of multiple resistance mechanisms against the antimicrobial agents. Emergence of resistant bacterial species has also been observed due to prolong treatment using conventional antibiotics. To combat these problems, several alternative strategies have been employed using biological and chemically synthesized compounds as antibacterial agents. Marine organisms considered as one of the potential sources for the isolation of bioactive compounds due to the easily available, cost-effective, and eco-friendly. Methods: The online search methodology was adapted for the collection of information related to the antimicrobial properties of marine-derived compounds. These compound has been isolated and purified by different purification techniques, and their structure also characterized. Furthermore, the antibacterial activities have been reported by using broth microdilution as well as disc diffusion assays. Results: The present review paper describes the antimicrobial effect of diverse secondary metabolites which are isolated and purified from the different marine organisms. The structural elucidation of each secondary metabolite has also been done in the present paper, which will help for the in silico designing of the novel and potent antimicrobial compounds. Conclusion: A thorough literature search has been made and summarizes the list of antimicrobial compounds that are isolated from both prokaryotic and eukaryotic marine organisms. The information obtained from the present paper will be helpful for the application of marine compounds as antimicrobial agents against different antibiotic-resistant human pathogenic bacteria.

scholarly journals Proteomic and Transcriptomic Analyses Provide Novel Insights into the Crucial Roles of Host-Induced Carbohydrate Metabolism Enzymes in Xanthomonas oryzae pv. oryzae Virulence and Rice-Xoo Interaction

Rice ◽  
2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Guichun Wu ◽  
Yuqiang Zhang ◽  
Bo Wang ◽  
Kaihuai Li ◽  
Yuanlai Lou ◽  
...  
Keyword(s):  
Gene Expression ◽  
Signal Transduction ◽  
Amino Acids ◽  
Secondary Metabolites ◽  
Carbohydrate Metabolism ◽  
Virulence Factors ◽  
Global Gene Expression ◽  
Xanthomonas Oryzae ◽  
Oxidation Reduction ◽  
Phenylpropanoid Biosynthesis

Abstract Background Xanthomonas oryzae pv. oryzae (Xoo) causes bacterial leaf blight, a devastating rice disease. The Xoo-rice interaction, wherein wide ranging host- and pathogen-derived proteins and genes wage molecular arms race, is a research hotspot. Hence, the identification of novel rice-induced Xoo virulence factors and characterization of their roles affecting rice global gene expression profiles will provide an integrated and better understanding of Xoo-rice interactions from the molecular perspective. Results Using comparative proteomics and an in vitro interaction system, we revealed that 5 protein spots from Xoo exhibited significantly different expression patterns (|fold change| > 1.5) at 3, 6, 12 h after susceptible rice leaf extract (RLX) treatment. MALDI-TOF MS analysis and pathogenicity tests showed that 4 host-induced proteins, including phosphohexose mutase, inositol monophosphatase, arginase and septum site-determining protein, affected Xoo virulence. Among them, mutants of two host-induced carbohydrate metabolism enzyme-encoding genes, ΔxanA and Δimp, elicited enhanced defense responses and nearly abolished Xoo virulence in rice. To decipher rice differentially expressed genes (DEGs) associated with xanA and imp, transcriptomic responses of ΔxanA-treated and Δimp-treated susceptible rice were compared to those in rice treated with PXO99A at 1 and 3 dpi. A total of 1521 and 227 DEGs were identified for PXO99A vs Δimp at 1 and 3 dpi, while for PXO99A vs ΔxanA, there were 131 and 106 DEGs, respectively. GO, KEGG and MapMan analyses revealed that the DEGs for PXO99A vs Δimp were mainly involved in photosynthesis, signal transduction, transcription, oxidation-reduction, hydrogen peroxide catabolism, ion transport, phenylpropanoid biosynthesis and metabolism of carbohydrates, lipids, amino acids, secondary metabolites, hormones, and nucleotides, while the DEGs from PXO99A vs ΔxanA were predominantly associated with photosynthesis, signal transduction, oxidation-reduction, phenylpropanoid biosynthesis, cytochrome P450 and metabolism of carbohydrates, lipids, amino acids, secondary metabolites and hormones. Although most pathways were associated with both the Δimp and ΔxanA treatments, the underlying genes were not the same. Conclusion Our study identified two novel host-induced virulence factors XanA and Imp in Xoo, and revealed their roles in global gene expression in susceptible rice. These results provide valuable insights into the molecular mechanisms of pathogen infection strategies and plant immunity.

Transcriptome-wide analysis of AP2/ERF transcription factors involved in regulating Taxol biosynthesis in Taxus × media

2021 ◽  
Vol 171 ◽  
pp. 113972
Author(s):  
Kaikai Zhang ◽  
Luyuan Jiang ◽  
Xu Wang ◽  
Hua Han ◽  
Duanfen Chen ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Taxus Media ◽  
Taxol Biosynthesis ◽  
Erf Transcription Factors

scholarly journals Effects of Laccaria bicolor on Gene Expression of Populus trichocarpa Root under Poplar Canker Stress

2021 ◽  
Vol 7 (12) ◽  
pp. 1024
Author(s):  
Fengxin Dong ◽  
Yihan Wang ◽  
Ming Tang
Keyword(s):  
Gene Expression ◽  
Disease Resistance ◽  
Plant Disease Resistance ◽  
Mycorrhizal Fungi ◽  
Populus Trichocarpa ◽  
Gene Expression Pattern ◽  
Oxygen Metabolism ◽  
Resistance Response ◽  
Expression Of Genes ◽  
Plant Pathogen Interaction

Poplars can be harmed by poplar canker. Inoculation with mycorrhizal fungi can improve the resistance of poplars to canker, but the molecular mechanism is still unclear. In this study, an aseptic inoculation system of L. bicolor–P. trichocarpa–B. dothidea was constructed, and transcriptome analysis was performed to investigate regulation by L. bicolor of the expression of genes in the roots of P. trichocarpa during the onset of B. dothidea infection, and a total of 3022 differentially expressed genes (DEGs) were identified. Weighted correlation network analysis (WGCNA) was performed on these DEGs, and 661 genes’ expressions were considered to be affected by inoculation with L. bicolor and B. dothidea. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses showed that these 661 DEGs were involved in multiple pathways such as signal transduction, reactive oxygen metabolism, and plant-pathogen interaction. Inoculation with L. bicolor changed the gene expression pattern of the roots, evidencing its involvement in the disease resistance response of P. trichocarpa. This research reveals the mechanism of L. bicolor in inducing resistance to canker of P. trichocarpa at the molecular level and provides a theoretical basis for the practical application of mycorrhizal fungi to improve plant disease resistance.

scholarly journals Recent Advances in Enzymes for the Bioremediation of Pollutants

2021 ◽  
Vol 2021 ◽  
pp. 1-12
Author(s):  
Seyyed Mojtaba Mousavi ◽  
Seyyed Alireza Hashemi ◽  
Seyed Mohammad Iman Moezzi ◽  
Navid Ravan ◽  
Ahmad Gholami ◽  
...  
Keyword(s):  
Ion Exchange ◽  
Azo Dyes ◽  
Membrane Filtration ◽  
Cost Effective ◽  
Physicochemical Characteristics ◽  
Pollutant Removal ◽  
Inorganic Pollutants ◽  
Environment Friendly ◽  
Different Types ◽  
Biological Methods

Nowadays, pollution of the environment is a huge problem for humans and other organisms’ health. Conventional methods of pollutant removal like membrane filtration or ion exchange are not efficient enough to lower the number of pollutants to standard levels. Biological methods, because of their higher efficiency and biocompatibility, are preferred for the remediation of pollutants. These cost-effective and environment-friendly methods of reducing pollutants are called bioremediation. In bioremediation methods, enzymes play the most crucial role. Enzymes can remedy different types of organic and inorganic pollutants, including PAHs, azo dyes, polymers, organocyanides, lead, chromium, and mercury. Different enzymes isolated from various species have been used for the bioremediation of pollutants. Discovering new enzymes and new subtypes with specific physicochemical characteristics would be a promising way to find more efficient and cost-effective tools for the remediation of pollutants.

Biological Synthesis of Silver Nanoparticles and their Biomedical Activity: A Review

2021 ◽  
Vol 09 ◽  
Author(s):  
Sarvat Zafar ◽  
Aiman Zafar ◽  
Fakhra Jabeen ◽  
Miad Ali Siddiq
Keyword(s):  
Silver Nanoparticles ◽  
Large Scale ◽  
Scale Up ◽  
Cost Effective ◽  
Biological Properties ◽  
Single Step ◽  
Biological Synthesis ◽  
Nanosized Particles ◽  
Environment Friendly ◽  
Physical And Chemical

: Nanotechnology studies the various phenomena of physio-chemical procedures and biological properties for the generation of nanosized particles, and their rising challenges in the various sectors, like medicine, engineering, agriculture, electronic, and environmental studies. The nanosized particles exhibit good anti-microbial, anti-inflammatory, cytotoxic, drug delivery, anti-parasitic, anti-coagulant and catalytic properties because of their unique dimensions with large surface area, chemical stability and higher binding density for the accumulation of various bio-constituents on their surfaces. Biological approaches for the synthesis of silver nanoparticles (AgNPs) have been reviewed because it is an easy and single-step protocol and a viable substitute for the synthetic chemical-based procedures. Physical and chemical approaches for the production of AgNPs are also mentioned herein. Biological synthesis has drawn attention because it is cost-effective, faster, non-pathogenic, environment-friendly, easy to scale-up for large-scale synthesis, and having no demand for usage of high pressure, energy, temperature, or noxious chemical ingredients, and safe for human therapeutic use. Therefore, the collaboration of nanomaterials with bio-green approaches could extend the utilization of biological and cytological properties compatible with AgNPs. In this perspective, there is an immediate need to develop ecofriendly and biocompatible techniques, which strengthen efficacy against microbes and minimize toxicity for human cells. The present study introduces the biological synthesis of silver nanoparticles, and their potential biomedical applications have also been reviewed.

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.

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