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1.
Science ; 384(6701): 1220-1227, 2024 Jun 14.
Artigo em Inglês | MEDLINE | ID: mdl-38753766

RESUMO

Developing vehicles that efficiently deliver genes throughout the human central nervous system (CNS) will broaden the range of treatable genetic diseases. We engineered an adeno-associated virus (AAV) capsid, BI-hTFR1, that binds human transferrin receptor (TfR1), a protein expressed on the blood-brain barrier. BI-hTFR1 was actively transported across human brain endothelial cells and, relative to AAV9, provided 40 to 50 times greater reporter expression in the CNS of human TFRC knockin mice. The enhanced tropism was CNS-specific and absent in wild-type mice. When used to deliver GBA1, mutations of which cause Gaucher disease and are linked to Parkinson's disease, BI-hTFR1 substantially increased brain and cerebrospinal fluid glucocerebrosidase activity compared with AAV9. These findings establish BI-hTFR1 as a potential vector for human CNS gene therapy.


Assuntos
Antígenos CD , Encéfalo , Capsídeo , Técnicas de Transferência de Genes , Vetores Genéticos , Glucosilceramidase , Receptores da Transferrina , Animais , Humanos , Camundongos , Antígenos CD/metabolismo , Antígenos CD/genética , Barreira Hematoencefálica/metabolismo , Encéfalo/metabolismo , Capsídeo/metabolismo , Proteínas do Capsídeo/metabolismo , Proteínas do Capsídeo/genética , Dependovirus , Células Endoteliais/metabolismo , Técnicas de Introdução de Genes , Terapia Genética , Receptores da Transferrina/metabolismo , Receptores da Transferrina/genética , Glucosilceramidase/genética , Doença de Gaucher/genética , Doença de Gaucher/terapia , Doença de Parkinson/genética , Doença de Parkinson/terapia
2.
BMC Plant Biol ; 24(1): 473, 2024 May 30.
Artigo em Inglês | MEDLINE | ID: mdl-38811869

RESUMO

BACKGROUND: Carbon nano sol (CNS) can markedly affect the plant growth and development. However, few systematic analyses have been conducted on the underlying regulatory mechanisms in plants, including tobacco (Nicotiana tabacum L.). RESULTS: Integrated analyses of phenome, ionome, transcriptome, and metabolome were performed in this study to elucidate the physiological and molecular mechanisms underlying the CNS-promoting growth of tobacco plants. We found that 0.3% CNS, facilitating the shoot and root growth of tobacco plants, significantly increased shoot potassium concentrations. Antioxidant, metabolite, and phytohormone profiles showed that 0.3% CNS obviously reduced reactive oxygen species production and increased antioxidant enzyme activity and auxin accumulation. Comparative transcriptomics revealed that the GO and KEGG terms involving responses to oxidative stress, DNA binding, and photosynthesis were highly enriched in response to exogenous CNS application. Differential expression profiling showed that NtNPF7.3/NtNRT1.5, potentially involved in potassium/auxin transport, was significantly upregulated under the 0.3% CNS treatment. High-resolution metabolic fingerprints showed that 141 and 163 metabolites, some of which were proposed as growth regulators, were differentially accumulated in the roots and shoots under the 0.3% CNS treatment, respectively. CONCLUSIONS: Taken together, this study revealed the physiological and molecular mechanism underlying CNS-mediated growth promotion in tobacco plants, and these findings provide potential support for improving plant growth through the use of CNS.


Assuntos
Carbono , Metabolômica , Nicotiana , Reguladores de Crescimento de Plantas , Transcriptoma , Nicotiana/genética , Nicotiana/metabolismo , Nicotiana/crescimento & desenvolvimento , Carbono/metabolismo , Reguladores de Crescimento de Plantas/metabolismo , Perfilação da Expressão Gênica , Metaboloma , Raízes de Plantas/metabolismo , Raízes de Plantas/crescimento & desenvolvimento , Raízes de Plantas/genética , Brotos de Planta/metabolismo , Brotos de Planta/crescimento & desenvolvimento , Brotos de Planta/genética
3.
Plant Physiol Biochem ; 207: 108413, 2024 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-38330776

RESUMO

Ethylene responsive factor (ERF) is a plant-specific transcription factor that plays a pivotal regulatory role in various stress responses. Although the genome of tobacco harbors 375 ER F genes, the functional roles of the majority of these genes remain unknown. Expression pattern analysis revealed that NtERF283 was induced by water deficit and salt stresses and mainly expressed in the roots and leaves. Subcellular localization and transcriptional activity assays confirmed that NtERF283 was localized in the nucleus and exhibited transcriptional activity. In comparison to the wild-type (WT), the NtERF283-overexpressing transgenic plants (OE) exhibited enhanced water deficit tolerance, whereas the knockout mutant erf283 displayed contrasting phenotypes. Transcriptional analysis demonstrated that several oxidative stress response genes were significantly altered in OE plants under water deficit conditions. 3,3'-diaminobenzidine (DAB) and nitroblue tetrazolium (NBT) staining showed that erf283 accumulated a higher level of reactive oxygen species (ROS) compared to the WT under water deficit conditions. Conversely, OE plants displayed the least amount of ROS accumulation. Furthermore, the activities of POD and SOD were higher in OE plants and lower in erf283, suggesting that NtERF283 enhanced the capacity to effectively eliminate ROS, consequently enhancing water deficit tolerance in tobacco. These findings strongly indicate the significance of NtERF283 in promoting tobacco water deficit tolerance through the activation of the antioxidant system.


Assuntos
Antioxidantes , Água , Antioxidantes/metabolismo , Espécies Reativas de Oxigênio/metabolismo , Água/metabolismo , Estresse Oxidativo , Plantas Geneticamente Modificadas/metabolismo , Nicotiana/genética , Regulação da Expressão Gênica de Plantas , Proteínas de Plantas/metabolismo , Estresse Fisiológico/genética
4.
BMC Plant Biol ; 23(1): 646, 2023 Dec 15.
Artigo em Inglês | MEDLINE | ID: mdl-38097981

RESUMO

BACKGROUND: Long noncoding RNAs (lncRNAs) have been shown to play important roles in the response of plants to various abiotic stresses, including drought, heat and salt stress. However, the identification and characterization of genome-wide salt-responsive lncRNAs in tobacco (Nicotiana tabacum L.) have been limited. Therefore, this study aimed to identify tobacco lncRNAs in roots and leaves in response to different durations of salt stress treatment. RESULTS: A total of 5,831 lncRNAs were discovered, with 2,428 classified as differentially expressed lncRNAs (DElncRNAs) in response to salt stress. Among these, only 214 DElncRNAs were shared between the 2,147 DElncRNAs in roots and the 495 DElncRNAs in leaves. KEGG pathway enrichment analysis revealed that these DElncRNAs were primarily associated with pathways involved in starch and sucrose metabolism in roots and cysteine and methionine metabolism pathway in leaves. Furthermore, weighted gene co-expression network analysis (WGCNA) identified 15 co-expression modules, with four modules strongly linked to salt stress across different treatment durations (MEsalmon, MElightgreen, MEgreenyellow and MEdarkred). Additionally, an lncRNA-miRNA-mRNA network was constructed, incorporating several known salt-associated miRNAs such as miR156, miR169 and miR396. CONCLUSIONS: This study enhances our understanding of the role of lncRNAs in the response of tobacco to salt stress. It provides valuable information on co-expression networks of lncRNA and mRNAs, as well as networks of lncRNAs-miRNAs-mRNAs. These findings identify important candidate lncRNAs that warrant further investigation in the study of plant-environment interactions.


Assuntos
MicroRNAs , RNA Longo não Codificante , Nicotiana/genética , RNA Longo não Codificante/genética , RNA Longo não Codificante/metabolismo , MicroRNAs/genética , Regulação da Expressão Gênica de Plantas , Plantas Geneticamente Modificadas/genética , Estresse Salino , RNA Mensageiro/genética , Redes Reguladoras de Genes
5.
Funct Integr Genomics ; 23(3): 272, 2023 Aug 12.
Artigo em Inglês | MEDLINE | ID: mdl-37568053

RESUMO

Plants release a mixture of volatile compounds when subjects to environmental stress, allowing them to transmit information to neighboring plants. Here, we find that Nicotiana benthamiana plants infected with tobacco mosaic virus (TMV) induces defense responses in neighboring congeners. Analytical screening of volatiles from N. benthamiana at 7 days post inoculation (dpi) using an optimized SPME-GC-MS method showed that TMV triggers the release of several volatiles, such as (E)-2-octenal, 6-methyl-5-hepten-2-one, and geranylacetone. Exposure to (E)-2-octenal enhances the resistance of N. benthamiana plants to TMV and triggers the immune system with upregulation of pathogenesis-related genes, such as NbPR1a, NbPR1b, NbPR2, and NbNPR1, which are related to TMV resistance. Furthermore, (E)-2-octenal upregulates jasmonic acid (JA) that levels up to 400-fold in recipient N. benthamiana plants and significantly affects the expression pattern of key genes in the JA/ET signaling pathway, such as NbMYC2, NbERF1, and NbPDF1.2, while the salicylic acid (SA) level is not significantly affected. Our results show for the first time that the volatile (E)-2-octenal primes the JA/ET pathway and then activates immune responses, ultimately leading to enhanced TMV resistance in adjacent N. benthamiana plants. These findings provide new insights into the role of airborne compounds in virus-induced interplant interactions.


Assuntos
Nicotiana , Vírus do Mosaico do Tabaco , Humanos , Nicotiana/genética , Nicotiana/metabolismo , Vírus do Mosaico do Tabaco/metabolismo , Ácido Salicílico/metabolismo , Ácido Salicílico/farmacologia , Doenças das Plantas/genética
6.
PLoS Biol ; 21(7): e3002112, 2023 07.
Artigo em Inglês | MEDLINE | ID: mdl-37467291

RESUMO

Viruses have evolved the ability to bind and enter cells through interactions with a wide variety of cell macromolecules. We engineered peptide-modified adeno-associated virus (AAV) capsids that transduce the brain through the introduction of de novo interactions with 2 proteins expressed on the mouse blood-brain barrier (BBB), LY6A or LY6C1. The in vivo tropisms of these capsids are predictable as they are dependent on the cell- and strain-specific expression of their target protein. This approach generated hundreds of capsids with dramatically enhanced central nervous system (CNS) tropisms within a single round of screening in vitro and secondary validation in vivo thereby reducing the use of animals in comparison to conventional multi-round in vivo selections. The reproducible and quantitative data derived via this method enabled both saturation mutagenesis and machine learning (ML)-guided exploration of the capsid sequence space. Notably, during our validation process, we determined that nearly all published AAV capsids that were selected for their ability to cross the BBB in mice leverage either the LY6A or LY6C1 protein, which are not present in primates. This work demonstrates that AAV capsids can be directly targeted to specific proteins to generate potent gene delivery vectors with known mechanisms of action and predictable tropisms.


Assuntos
Barreira Hematoencefálica , Capsídeo , Camundongos , Animais , Barreira Hematoencefálica/metabolismo , Capsídeo/metabolismo , Vetores Genéticos , Sistema Nervoso Central/metabolismo , Proteínas do Capsídeo/genética , Proteínas do Capsídeo/metabolismo , Dependovirus/genética , Dependovirus/metabolismo
7.
Pest Manag Sci ; 79(9): 3342-3353, 2023 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-37132116

RESUMO

BACKGROUND: The green peach aphid (Myzus persicae Sulzer) is a harmful agricultural pest that causes severe crop damage by directly feeding or indirectly vectoring viruses. 1,8-cineole synthase (CINS) is a multiproduct enzyme that synthesizes monoterpenes, with 1,8-cineole dominating the volatile organic compound profile. However, the relationship between aphid preference and CINS remains elusive. RESULTS: Here, we present evidence that SoCINS, a protein from garden sage (Salvia officinalis), enhanced aphid repellence and increased trichome density in transgenic tobacco. Our results demonstrated that overexpression of SoCINS (SoCINS-OE) led to the emission of 1,8-cineole at a level of up to 181.5 ng per g fresh leaf. Subcellular localization assay showed that SoCINS localized to chloroplasts. A Y-tube olfactometer assay and free-choice assays revealed that SoCINS-OE plants had a repellent effect on aphids, without incurring developmental or fecundity-related penalties. Intriguingly, the SoCINS-OE plants displayed an altered trichome morphology, showing increases in trichome density and in the relative proportion of glandular trichomes, as well as enlarged glandular cells. We also found that SoCINS-OE plants had significantly higher jasmonic acid (JA) levels than wild-type plants. Furthermore, application of 1,8-cineole elicited increased JA content and trichome density. CONCLUSION: Our results demonstrate that SoCINS-OE plants have a repellent effect on aphids, and suggest an apparent link between 1,8-cineole, JA and trichome density. This study presents a viable and sustainable approach for aphid management by engineering the expression of 1,8-cineole synthase gene in plants, and underscores the potential usefulness of monoterpene synthase for pest control. © 2023 Society of Chemical Industry.


Assuntos
Afídeos , Nicotiana , Animais , Nicotiana/genética , Nicotiana/metabolismo , Engenharia Metabólica , Afídeos/genética , Afídeos/metabolismo , Eucaliptol , Tricomas/genética
8.
Anal Chem ; 95(2): 638-649, 2023 01 17.
Artigo em Inglês | MEDLINE | ID: mdl-36599407

RESUMO

Data-dependent acquisition (DDA) mode in ultra-high-performance liquid chromatography-high-resolution mass spectrometry (UHPLC-HRMS) can provide massive amounts of MS1 and MS/MS information of compounds in untargeted metabolomics and can thus facilitate compound identification greatly. In this work, we developed a new platform called AntDAS-DDA for the automatic processing of UHPLC-HRMS data sets acquired under the DDA mode. Several algorithms, including extracted ion chromatogram extraction, feature extraction, MS/MS spectrum construction, fragment ion identification, and MS1 spectrum construction, were developed within the platform. The performance of AntDAS-DDA was investigated comprehensively with a mixture of standard and complex plant data sets. Results suggested that features in complex sample matrices can be extracted effectively, and the constructed MS1 and MS/MS spectra can benefit in compound identification greatly. The efficiency of compound identification can be improved by about 20%. AntDAS-DDA can take full advantage of MS/MS information in multiple sample analyses and provide more MS/MS spectra than single sample analysis. A comparison with advanced data analysis tools indicated that AntDAS-DDA may be used as an alternative for routine UHPLC-HRMS-based untargeted metabolomics. AntDAS-DDA is freely available at http://www.pmdb.org.cn/antdasdda.


Assuntos
Metabolômica , Espectrometria de Massas em Tandem , Espectrometria de Massas em Tandem/métodos , Metabolômica/métodos , Cromatografia Líquida de Alta Pressão/métodos , Íons , Análise de Dados
9.
Environ Res ; 216(Pt 4): 114848, 2023 01 01.
Artigo em Inglês | MEDLINE | ID: mdl-36403441

RESUMO

Root-knot nematode (RKN) disease is a destructive soil disease that affects crop health and causes huge losses in crop production. To explore the relationships between soil environments, rhizobacterial communities, and plant health, rhizosphere bacterial communities were analyzed using metagenomic sequencing in tobacco samples with different grades of RKN disease. The results showed that the community structure and function of the plant rhizosphere were significantly correlated to the RKN disease. RKN density and urease content were key factors affecting the rhizosphere bacterial community. Urease accelerated the catabolism of urea and led to the production of high concentrations of ammonia, which directly suppressed the development of RKNs or by improving the nutritional and growth status of microorganisms that were antagonistic to RKNs. Further experiments showed that the suppression role of ammonia should be attributed to the direct inhibition of NH3. The bacterial members that were positively correlated with RKN density, contained many plant cell wall degrading enzymes, which might destroy plant cell walls and promote the colonization of RKN in tobacco roots. The analysis of metatranscriptome and metabolism demonstrated the role of these cell wall degrading enzymes. This study offers a comprehensive insight into the relationships between RKNs, bacteria, and soil environmental factors and provides new ideas for the biological control of RKNs.


Assuntos
Microbiota , Tylenchoidea , Animais , Tylenchoidea/fisiologia , Nicotiana , Rizosfera , Amônia , Urease/metabolismo , Doenças das Plantas , Raízes de Plantas/metabolismo , Bactérias/genética , Solo
10.
bioRxiv ; 2023 Dec 22.
Artigo em Inglês | MEDLINE | ID: mdl-38187643

RESUMO

Developing vehicles that efficiently deliver genes throughout the human central nervous system (CNS) will broaden the range of treatable genetic diseases. We engineered an AAV capsid, BI-hTFR1, that binds human Transferrin Receptor (TfR1), a protein expressed on the blood-brain barrier (BBB). BI-hTFR1 was actively transported across a human brain endothelial cell layer and, relative to AAV9, provided 40-50 times greater reporter expression in the CNS of human TFRC knock-in mice. The enhanced tropism was CNS-specific and absent in wild type mice. When used to deliver GBA1, mutations of which cause Gaucher disease and are linked to Parkinson's disease, BI-hTFR1 substantially increased brain and cerebrospinal fluid glucocerebrosidase activity compared to AAV9. These findings establish BI-hTFR1 as a promising vector for human CNS gene therapy.

11.
Zhonghua Nan Ke Xue ; 29(12): 963-972, 2023 Dec.
Artigo em Chinês | MEDLINE | ID: mdl-38639947

RESUMO

OBJECTIVE: Explore the effects of Astragaloside IV and Scorpion Venom Peptide on the activity, migration, apoptosis, cell cycle, autophagy, and the expression of proteins related to the PI3K/AKT signaling pathway in prostate cancer cells. METHODS: The human prostate cancer cell lines LNCaP and PC-3 were randomly divided into blank control group, Astragaloside IV group, Scorpion Venom Peptide group, Astragaloside IV-Scorpion Venom Peptide group, and rapamycin (positive drug group). After corresponding drug treatments for 24 hours, logarithmic growth phase tumor cells were collected for testing. Cell proliferation was assessed using a Cell Counting Kit-8 (CCK-8) assay, Transwell assay, apoptosis assay, cell cycle assay, and immunofluorescence analysis were performed to detect the activity and migration capacity of prostate cancer cells in each group, as well as their effects on apoptosis, cell cycle, and the autophagy target LC3. Western blot analysis was employed to measure the protein expression levels of p-PI3K, p-Akt, p-mTOR, Beclin1, LC3, and P62. RESULTS: Compared to the blank control group, the Astragaloside IV-Scorpion Venom Peptide group exhibited a significant decrease in the activity of prostate cancer cells (P<0.05) and a reduction in the cell invasion ability (migration capacity) (P<0.05). The early apoptosis rate (LR), late apoptosis rate (UR), and total apoptosis rate all increased (P<0.05). The proportion of cells in the G1 phase increased (P<0.05), while the proportion in the G2+S phase decreased (P<0.05). The immunofluorescence expression of LC3 significantly increased (P<0.05). The expression of LC3Ⅱ and Beclin1 proteins in prostate cancer cells LNCaP and PC-3 was upregulated (P<0.05), while the expression of P62, p-PI3K, p-AKT, and p-mTOR proteins was downregulated (P<0.05).Astragaloside IV-Scorpion Venom Peptide is superior to the Astragaloside IV group or Scorpion Venom Peptide group alone in inhibiting the activity and migration capacity of prostate cancer cells, suppressing cell mitosis, promoting early apoptosis, upregulating the expression level of LC3, and inhibiting the PI3K/AKT pathway while promoting autophagy (P<0.05). CONCLUSION: The mechanism by which Astragaloside IV-Scorpion Venom Peptide inhibits the proliferation and migration of prostate cancer cells, suppresses cell mitosis, promotes early apoptosis, and enhances autophagy may be related to the inhibition of the PI3K/AKT pathway.


Assuntos
Neoplasias da Próstata , Saponinas , Venenos de Escorpião , Triterpenos , Humanos , Masculino , Apoptose , Autofagia , Proteína Beclina-1/metabolismo , Linhagem Celular Tumoral , Proliferação de Células , Fosfatidilinositol 3-Quinases/metabolismo , Proteínas Proto-Oncogênicas c-akt/metabolismo , Saponinas/farmacologia , Venenos de Escorpião/farmacologia , Transdução de Sinais , Serina-Treonina Quinases TOR/metabolismo , Triterpenos/farmacologia
12.
Front Plant Sci ; 13: 999403, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-36311086

RESUMO

Proteins of the Nitrate Transporter 1/Peptide Transporter (NPF) family transport a diverse variety of substrates, such as nitrate, peptides, hormones and chloride. In this study, a systematic analysis of the tobacco (Nicotiana tabacum) NPF family was performed in the cultivated 'K326'. In total, 143 NtNPF genes were identified and phylogenetically classified into eight subfamilies, NPF1 to NPF8, based on the classification of NPF families in other plant species. The chromosomal locations and structures of the NtNPF genes were analyzed. The expression profiles of NtNPF genes under NaCl stress were analyzed to screen the possible NPF genes involving in chloride regulation in tobacco. Most NtNPF6 genes responded to salt stress in the roots and leaves. The expression of NtNPF6.13 was significantly down-regulated after salt stress for 12h. The chloride content was reduced in the roots of ntnpf6.13 mutant. These findings support the participation of NtNPF6.13 in chloride uptake. Several other NtNPF genes that play potential roles in chloride metabolism of tobacco require further study.

13.
Nat Cardiovasc Res ; 1(4): 389-400, 2022 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-35571675

RESUMO

Endothelial cells have a crucial role in nervous system function, and mounting evidence points to endothelial impairment as a major contributor to a wide range of neurological diseases. However, tools to genetically interrogate these cells in vivo remain limited. Here, we describe AAV-BI30, a capsid that specifically and efficiently transduces endothelial cells throughout the central nervous system. At relatively low systemic doses, this vector transduces the majority of arterial, capillary, and venous endothelial cells in the brain, retina, and spinal cord vasculature of adult C57BL/6 mice. Furthermore, we show that AAV-BI30 robustly transduces endothelial cells in multiple mouse strains and rats in vivo and human brain microvascular endothelial cells in vitro. Finally, we demonstrate AAV-BI30's capacity to achieve efficient and endothelial-specific Cre-mediated gene manipulation in the central nervous system. This combination of attributes makes AAV-BI30 uniquely well-suited to address outstanding research questions in neurovascular biology and aid the development of therapeutics to remediate endothelial dysfunction in disease.

14.
Anal Chim Acta ; 1193: 339393, 2022 Feb 08.
Artigo em Inglês | MEDLINE | ID: mdl-35058006

RESUMO

Substantial deviations in retention times among samples pose a great challenge for the accurate screening and identifying of metabolites by ultrahigh-performance liquid chromatography high-resolution mass spectrometry (UHPLC-HRMS). In this study, a coarse-to-refined time-shift correction methodology was proposed to efficiently address this problem. Metabolites producing multiple fragment ions were automatically selected as landmarks to generate pseudo-mass spectra for a coarse time-shift correction. Refined peak alignment for extracted ion chromatograms was then performed by using a moving window-based multiple-peak alignment strategy. Based on this novel coarse-to-refined time-shift correction methodology, a new comprehensive UHPLC-HRMS data analysis platform was developed for UHPLC-HRMS-based metabolomics. Original datasets were employed as inputs to automatically extract and register features in the dataset and to distinguish fragment ions from metabolites for chemometric analysis. Its performance was further evaluated using complex datasets, and the results suggest that the new platform can satisfactorily resolve the time-shift problem and is comparable with commonly used UHPLC-HRMS data analysis tools such as XCMS Online, MS-DIAL, Mzmine2, and Progenesis QI. The new platform can be downloaded from: http://www.pmdb.org.cn/antdas2tsc.


Assuntos
Quimiometria , Análise de Dados , Cromatografia Líquida de Alta Pressão , Cromatografia Líquida , Espectrometria de Massas
15.
FEBS Open Bio ; 12(1): 231-249, 2022 01.
Artigo em Inglês | MEDLINE | ID: mdl-34792288

RESUMO

Exposure to extended periods of darkness is a common source of abiotic stress that significantly affects plant growth and development. To understand how Nicotiana benthamiana responds to dark stress, the proteomes and metabolomes of leaves treated with darkness were studied. In total, 5763 proteins and 165 primary metabolites were identified following dark treatment. Additionally, the expression of autophagy-related gene (ATG) proteins was transiently upregulated. Weighted gene coexpression network analysis (WGCNA) was utilized to find the protein modules associated with the response to dark stress. A total of four coexpression modules were obtained. The results indicated that heat-shock protein (HSP70), SnRK1-interacting protein 1, 2A phosphatase-associated protein of 46 kDa (Tap46), and glutamate dehydrogenase (GDH) might play crucial roles in N. benthamiana's response to dark stress. Furthermore, a protein-protein interaction (PPI) network was constructed and top-degreed proteins were predicted to identify potential key factors in the response to dark stress. These proteins include isopropylmalate isomerase (IPMI), eukaryotic elongation factor 5A (ELF5A), and ribosomal protein 5A (RPS5A). Finally, metabolic analysis suggested that some amino acids and sugars were involved in the dark-responsive pathways. Thus, these results provide a new avenue for understanding the defensive mechanism against dark stress at the protein and metabolic levels in N. benthamiana.


Assuntos
Metabolômica , Nicotiana , Proteômica , Redes Reguladoras de Genes , Metaboloma , Folhas de Planta/metabolismo , Proteoma , Nicotiana/genética , Nicotiana/metabolismo
16.
BMC Plant Biol ; 21(1): 299, 2021 Jun 29.
Artigo em Inglês | MEDLINE | ID: mdl-34187357

RESUMO

BACKGROUND: Cigar wrapper leaves are the most important raw material of cigars. Studying the genomic information of cigar tobacco is conducive to improving cigar quality from the perspective of genetic breeding. However, no reference genome or full-length transcripts at the genome-wide scale have been reported for cigar tobacco. In particular, anion channels/transporters are of high interest for their potential application in regulating the chloride content of cigar tobacco growing on coastal lands, which usually results in relatively high Cl- accumulation, which is unfavorable. Here, the PacBio platform and NGS technology were combined to generate a full-length transcriptome of cigar tobacco used for cigar wrappers. RESULTS: High-quality RNA isolated from the roots, leaves and stems of cigar tobacco were subjected to both the PacBio platform and NGS. From PacBio, a total of 11,652,432 subreads (19-Gb) were generated, with an average read length of 1,608 bp. After corrections were performed in conjunction with the NGS reads, we ultimately identified 1,695,064 open reading frames including 21,486 full-length ORFs and 7,342 genes encoding transcription factors from 55 TF families, together with 2,230 genes encoding long non-coding RNAs. Members of gene families related to anion channels/transporters, including members of the SLAC and CLC families, were identified and characterized. CONCLUSIONS: The full-length transcriptome of cigar tobacco was obtained, annotated, and analyzed, providing a valuable genetic resource for future studies in cigar tobacco.


Assuntos
Proteínas de Transporte de Ânions/genética , Genoma de Planta/genética , Canais Iônicos/genética , Nicotiana/genética , Proteínas de Plantas/genética , Produtos do Tabaco , Transcriptoma/genética , Proteínas de Transporte de Ânions/metabolismo , Canais Iônicos/metabolismo , Filogenia , Proteínas de Plantas/metabolismo , RNA Longo não Codificante/genética , RNA de Plantas/genética , Nicotiana/metabolismo , Fatores de Transcrição/genética
17.
J Sep Sci ; 43(14): 2794-2803, 2020 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-32386337

RESUMO

There are numerous articles published for geographical discrimination of tea. However, few research works focused on the authentication and traceability of Westlake Longjing green tea from the first- and second-grade producing regions because the tea trees are planted in a limited growing zone with identical cultivate condition. In this work, a comprehensive analytical strategy was proposed by ultrahigh performance liquid chromatography-quadrupole time-of-flight mass spectrometry-based untargeted metabolomics coupled with chemometrics. The automatic untargeted data analysis strategy was introduced to screen metabolites that expressed significantly among different regions. Chromatographic features of metabolites can be automatically and efficiently extracted and registered. Meanwhile, those that were valuable for geographical origin discrimination were screened based on statistical analysis and contents in samples. Metabolite identification was performed based on high-resolution mass values and tandem mass spectra of screened peaks. Twenty metabolites were identified, based on which the two-way encoding partial least squares discrimination analysis was built for geographical origin prediction. Monte Caro simulation results indicated that prediction accuracy was up to 99%. Our strategy can be applicable for practical applications in the quality control of Westlake Longjing green tea.


Assuntos
Metabolômica , Chá/química , Chá/metabolismo , Cromatografia Líquida de Alta Pressão , Geografia , Espectrometria de Massas , Simulação de Dinâmica Molecular , Método de Monte Carlo , Fatores de Tempo
18.
DNA Res ; 27(2)2020 Apr 01.
Artigo em Inglês | MEDLINE | ID: mdl-32324848

RESUMO

Tobacco (Nicotiana tabacum) is one of the most widely cultivated commercial non-food crops with significant social and economic impacts. Here we profiled transcriptome and metabolome from 54 tobacco samples (2-3 replicates; n = 151 in total) collected from three varieties (i.e. genetic factor), three locations (i.e. environmental factor), and six developmental stages (i.e. developmental process). We identified 3,405 differentially expressed (DE) genes (DEGs) and 371 DE metabolites, respectively. We used quantitative real-time PCR to validate 20 DEGs, and confirmed 18/20 (90%) DEGs between three locations and 16/20 (80%) with the same trend across developmental stages. We then constructed nine co-expression gene modules and four co-expression metabolite modules , and defined seven de novo regulatory networks, including nicotine- and carotenoid-related regulatory networks. A novel two-way Pearson correlation approach was further proposed to integrate co-expression gene and metabolite modules to identify joint gene-metabolite relations. Finally, we further integrated DE and network results to prioritize genes by its functional importance and identified a top-ranked novel gene, LOC107773232, as a potential regulator involved in the carotenoid metabolism pathway. Thus, the results and systems-biology approaches provide a new avenue to understand the molecular mechanisms underlying complex genetic and environmental perturbations in tobacco.


Assuntos
Variação Biológica da População , Redes Reguladoras de Genes , Variação Genética , Metaboloma , Nicotiana/genética , Transcriptoma , Carotenoides/metabolismo , Genes de Plantas , Genômica/métodos , Nicotiana/metabolismo
19.
J Pharm Pharmacol ; 72(5): 748-760, 2020 May.
Artigo em Inglês | MEDLINE | ID: mdl-32128823

RESUMO

OBJECTIVES: As a traditional Chinese medicine (TCM), Huangqi Jianzhong Tang (HQJZ) has a good efficacy in treating chronic atrophic gastritis (CAG). Our objective was to determine its mechanism based on the urine comprehensive metabolome. METHODS: In the study, a metabolomic approach was applied to reveal the efficacy of HQJZ on the constructed CAG rats coupled with proton nuclear magnetic resonance (1 H NMR) and ultra-performance liquid chromatography/quadrupole time-of-flight mass spectrometry (UPLC-Q/TOF MS). KEY FINDINGS: The results showed the regulatory effect of HQJZ on urinary metabolism disorder in CAG rats was similar to the positive drug teprenone. Nineteen and 16 potential biomarkers related to CAG were detected by NMR and UPLC-Q/TOF MS, respectively. Thirty-two urine metabolites were significantly regulated by HQJZ treatment. Combined with MetPA and partial least square regression analysis (PLS-RA), three metabolic pathways of valine, leucine and isoleucine, TCA cycle, and glycine, serine and threonine metabolism were the most relevant pathways for HQJZ treatment. CONCLUSIONS: The main mechanism of HQJZ might be due to the balance of energy consumption, inflammatory inhibition, improvement of the immune system and oxidative stress on the constructed CAG rats. These findings provided comprehensive metabolic information of TCM by parallel measurements by LC-MS and NMR.


Assuntos
Medicamentos de Ervas Chinesas/farmacologia , Gastrite Atrófica/tratamento farmacológico , Gastrite Atrófica/urina , Animais , Astragalus propinquus , Biomarcadores/metabolismo , Biomarcadores/urina , Cromatografia Líquida , Medicamentos de Ervas Chinesas/uso terapêutico , Gastrite Atrófica/metabolismo , Masculino , Espectrometria de Massas , Redes e Vias Metabólicas/efeitos dos fármacos , Metaboloma/efeitos dos fármacos , Metabolômica , Espectroscopia de Prótons por Ressonância Magnética , Ratos , Ratos Sprague-Dawley , Análise de Regressão
20.
mBio ; 10(4)2019 08 20.
Artigo em Inglês | MEDLINE | ID: mdl-31431550

RESUMO

The blast fungus initiates infection using a heavily melanized, dome-shaped infection structure known as the appressorium, which forcibly ruptures the cuticle to enter the rice leaf tissue. How this process takes place remains not fully understood. Here, we used untargeted metabolomics analyses to profile the metabolome of developing appressoria and identified significant changes in six key metabolic pathways, including early sphingolipid biosynthesis. Analyses employing small molecule inhibitors, gene disruption, or genetic and chemical complementation demonstrated that ceramide compounds of the sphingolipid biosynthesis pathway are essential for normal appressorial development controlled by mitosis. In addition, ceramide was found to act upstream from the protein kinase C-mediated cell wall integrity pathway during appressorium repolarization and pathogenicity in rice blast. Further discovery of the sphingolipid biosynthesis pathway revealed that glucosylceramide (GlcCer) synthesized by ceramide is the key substance affecting the pathogenicity of Magnaporthe oryzae Our results provide new insights into the chemical moieties involved in the infection-related signaling networks, thereby revealing a potential target for the development of novel control agents against the major disease of rice and other cereals.IMPORTANCE Our untargeted analysis of metabolomics throughout the course of pathogenic development gave us an unprecedented high-resolution view of major shifts in metabolism that occur in the topmost fungal pathogen that infects rice, wheat, barley, and millet. Guided by these metabolic insights, we demonstrated their practical application by using two different small-molecule inhibitors of sphingolipid biosynthesis enzymes to successfully block the pathogenicity of M. oryzae Our study thus defines the sphingolipid biosynthesis pathway as a key step and potential target that can be exploited for the development of antifungal agents. Furthermore, future investigations that exploit such important metabolic intermediates will further deepen our basic understanding of the molecular mechanisms underlying the establishment of fungal blast disease in important cereal crops.


Assuntos
Magnaporthe/metabolismo , Metabolômica , Morfogênese/fisiologia , Transdução de Sinais/fisiologia , Esfingolipídeos/análise , Esfingolipídeos/biossíntese , Antifúngicos/farmacologia , Vias Biossintéticas/efeitos dos fármacos , Vias Biossintéticas/fisiologia , Parede Celular/metabolismo , Grão Comestível/microbiologia , Proteínas Fúngicas/genética , Proteínas Fúngicas/metabolismo , Deleção de Genes , Regulação Fúngica da Expressão Gênica , Genes Fúngicos/genética , Glucosilceramidas/metabolismo , Magnaporthe/citologia , Magnaporthe/genética , Magnaporthe/patogenicidade , Proteínas de Membrana/genética , Proteínas de Membrana/metabolismo , Metaboloma , Mitose , Oryza/microbiologia , Fenótipo , Doenças das Plantas/microbiologia , Poaceae , Proteína Quinase C/metabolismo , Transdução de Sinais/efeitos dos fármacos , Esfingolipídeos/genética , Transcriptoma , Virulência
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