scholarly journals Metabolic networks of the Nicotiana genus in the spotlight: content, progress and outlook

2020 ◽  
Author(s):  
Hartmut Foerster ◽  
James N D Battey ◽  
Nicolas Sierro ◽  
Nikolai V Ivanov ◽  
Lukas A Mueller
Keyword(s):  
Nicotiana Tabacum ◽  
Metabolic Pathway ◽  
Nicotiana Benthamiana ◽  
Metabolic Networks ◽  
External Database ◽  
Related Data ◽  
Current Content ◽  
Species Specific ◽  
Solanaceae Family

Abstract Manually curated metabolic databases residing at the Sol Genomics Network comprise two taxon-specific databases for the Solanaceae family, i.e. SolanaCyc and the genus Nicotiana, i.e. NicotianaCyc as well as six species-specific databases for Nicotiana tabacum TN90, N. tabacum K326, Nicotiana benthamiana, N. sylvestris, N. tomentosiformis and N. attenuata. New pathways were created through the extraction, examination and verification of related data from the literature and the aid of external database guided by an expert-led curation process. Here we describe the curation progress that has been achieved in these databases since the first release version 1.0 in 2016, the curation flow and the curation process using the example metabolic pathway for cholesterol in plants. The current content of our databases comprises 266 pathways and 36 superpathways in SolanaCyc and 143 pathways plus 21 superpathways in NicotianaCyc, manually curated and validated specifically for the Solanaceae family and Nicotiana genus, respectively. The curated data have been propagated to the respective Nicotiana-specific databases, which resulted in the enrichment and more accurate presentation of their metabolic networks. The quality and coverage in those databases have been compared with related external databases and discussed in terms of literature support and metabolic content.

scholarly journals A Draft Genome Sequence of Nicotiana benthamiana to Enhance Molecular Plant-Microbe Biology Research

2012 ◽  
Vol 25 (12) ◽  
pp. 1523-1530 ◽  
Author(s):  
Aureliano Bombarely ◽  
Hernan G. Rosli ◽  
Julia Vrebalov ◽  
Peter Moffett ◽  
Lukas A. Mueller ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Nicotiana Benthamiana ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Virus Induced Gene Silencing ◽  
Transient Protein Expression ◽  
Mitogen Activated Protein ◽  
Microbe Interactions ◽  
Solanaceae Family ◽  
Biology Research

Nicotiana benthamiana is a widely used model plant species for the study of fundamental questions in molecular plant-microbe interactions and other areas of plant biology. This popularity derives from its well-characterized susceptibility to diverse pathogens and, especially, its amenability to virus-induced gene silencing and transient protein expression methods. Here, we report the generation of a 63-fold coverage draft genome sequence of N. benthamiana and its availability on the Sol Genomics Network for both BLAST searches and for downloading to local servers. The estimated genome size of N. benthamiana is 3 Gb (gigabases). The current assembly consists of approximately 141,000 scaffolds, spanning 2.6 Gb with 50% of the genome sequence contained within scaffolds >89 kilobases. Of the approximately 16,000 N. benthamiana unigenes available in GenBank, >90% are represented in the assembly. The usefulness of the sequence was demonstrated by the retrieval of N. benthamiana orthologs for 24 immunity-associated genes from other species including Ago2, Ago7, Bak1, Bik1, Crt1, Fls2, Pto, Prf, Rar1, and mitogen-activated protein kinases. The sequence will also be useful for comparative genomics in the Solanaceae family as shown here by the discovery of microsynteny between N. benthamiana and tomato in the region encompassing the Pto and Prf genes.

scholarly journals N-1-naphthylphthalamic acid stimulates tomato hypocotyl elongation, elevates ethylene levels and alters metabolic homeostasis

2018 ◽  
Author(s):  
Sapana Nongmaithem ◽  
Sameera Devulapalli ◽  
Yellamaraju Sreelakshmi ◽  
Rameshwar Sharma
Keyword(s):  
Butyric Acid ◽  
Metabolic Networks ◽  
Higher Plants ◽  
Red Light ◽  
Hypocotyl Elongation ◽  
Stimulated Emission ◽  
Ethylene Action ◽  
Naphthylphthalamic Acid ◽  
Exogenous Ethylene ◽  
Species Specific

One sentence summaryN-1-naphthylphthalamic acid (NPA) treatment stimulates tomato hypocotyl elongation likely by elevating ethylene emission and lowering indole-3-butyric acid levels in the seedlings.AbstractIn higher plants, phytohormone indole-3-acetic acid is characteristically transported from the apex towards the base of the plant, termed as polar auxin transport (PAT). Among the inhibitors blocking PAT, N-1-naphthylphthalamic acid (NPA) that targets ABCB transporters is most commonly used. NPA-treated light-grown Arabidopsis seedlings show severe inhibition of hypocotyl and root elongation. In light-grown tomato seedlings, NPA inhibited root growth, but contrary to Arabidopsis stimulated hypocotyl elongation. The NPA-stimulation of hypocotyl elongation was milder in blue, red, and far-red light-grown seedlings. The NPA-treatment stimulated emission of ethylene from the seedlings. The scrubbing of ethylene by mercuric perchlorate reduced NPA-stimulated hypocotyl elongation. NPA action on hypocotyl elongation was antagonized by 1-methylcyclopropene, an inhibitor of ethylene action. NPA-treated seedlings had reduced levels of indole-3-butyric acid and higher levels of zeatin in the shoots. NPA did not alter indole-3-acetic levels in shoots. The analysis of metabolic networks indicated that NPA-treatment induced moderate shifts in the networks compared to exogenous ethylene that induced a drastic shift in metabolic networks. Our results indicate that in addition to ethylene, NPA-stimulated hypocotyl elongation in tomato may also involve zeatin and indole-3-butyric acid. Our results indicate that NPA-mediated physiological responses may vary in a species-specific fashion.

scholarly journals SERRATE, a miRNA biogenesis factor, affects viroid infection in Nicotiana benthamiana and Nicotiana tabacum

Virology ◽  
2019 ◽  
Vol 528 ◽  
pp. 164-175 ◽  
Author(s):  
Nikoleta Kryovrysanaki ◽  
Anastasios Alexiadis ◽  
Alexandra M. Grigoriadou ◽  
Konstantina Katsarou ◽  
Kriton Kalantidis
Keyword(s):  
Nicotiana Tabacum ◽  
Nicotiana Benthamiana ◽  
Mirna Biogenesis ◽  
Viroid Infection

BIOSYNTHETIC POTENTIALS FROM SPECIES-SPECIFIC METABOLIC NETWORKS

2008 ◽  
Author(s):  
GEORG BASLER ◽  
ZORAN NIKOLOSKI ◽  
OLIVER EBENHÖH ◽  
THOMAS HANDORF
Keyword(s):  
Metabolic Networks ◽  
Species Specific

scholarly journals Genome-Wide microRNA Profiling Using Oligonucleotide Microarray Reveals Regulatory Networks of microRNAs in Nicotiana benthamiana During Beet Necrotic Yellow Vein Virus Infection

Viruses ◽  
2020 ◽  
Vol 12 (3) ◽  
pp. 310 ◽  
Author(s):  
Junying Liu ◽  
Huiyan Fan ◽  
Ying Wang ◽  
Chenggui Han ◽  
Xianbing Wang ◽  
...  
Keyword(s):  
Nicotiana Benthamiana ◽  
Regulatory Networks ◽  
Target Genes ◽  
Tobacco Rattle Virus ◽  
Yellow Vein ◽  
Differentially Expressed ◽  
Virus Induced Gene Silencing ◽  
Developmental Defects ◽  
Differentially Expressed Mirnas ◽  
Species Specific

Beet necrotic yellow vein virus (BNYVV) infections induce stunting and leaf curling, as well as root and floral developmental defects and leaf senescence in Nicotiana benthamiana. A microarray analysis with probes capable of detecting 1596 candidate microRNAs (miRNAs) was conducted to investigate differentially expressed miRNAs and their targets upon BNYVV infection of N. benthamiana plants. Eight species-specific miRNAs of N. benthamiana were identified. Comprehensive characterization of the N. benthamiana microRNA profile in response to the BNYVV infection revealed that 129 miRNAs were altered, including four species-specific miRNAs. The targets of the differentially expressed miRNAs were predicted accordingly. The expressions of miR164, 160, and 393 were up-regulated by BNYVV infection, and those of their target genes, NAC21/22, ARF17/18, and TIR, were down-regulated. GRF1, which is a target of miR396, was also down-regulated. Further genetic analysis of GRF1, by Tobacco rattle virus-induced gene silencing, assay confirmed the involvement of GRF1 in the symptom development during BNYVV infection. BNYVV infection also induced the up-regulation of miR168 and miR398. The miR398 was predicted to target umecyanin, and silencing of umecyanin could enhance plant resistance against viruses, suggesting the activation of primary defense response to BNYVV infection in N. benthamiana. These results provide a global profile of miRNA changes induced by BNYVV infection and enhance our understanding of the mechanisms underlying BNYVV pathogenesis.

scholarly journals The biosynthetic pathway of the nonsugar, high-intensity sweetener mogroside V from Siraitia grosvenorii

2016 ◽  
Vol 113 (47) ◽  
pp. E7619-E7628 ◽  
Author(s):  
Maxim Itkin ◽  
Rachel Davidovich-Rikanati ◽  
Shahar Cohen ◽  
Vitaly Portnoy ◽  
Adi Doron-Faigenboim ◽  
...  
Keyword(s):  
Metabolic Pathway ◽  
Biosynthetic Pathway ◽  
Genomic Organization ◽  
Expression Patterns ◽  
Functional Expression ◽  
Docking Studies ◽  
Gene Clustering ◽  
Siraitia Grosvenorii ◽  
Coordinated Expression ◽  
Species Specific

The consumption of sweeteners, natural as well as synthetic sugars, is implicated in an array of modern-day health problems. Therefore, natural nonsugar sweeteners are of increasing interest. We identify here the biosynthetic pathway of the sweet triterpenoid glycoside mogroside V, which has a sweetening strength of 250 times that of sucrose and is derived from mature fruit of luo-han-guo (Siraitia grosvenorii, monk fruit). A whole-genome sequencing of Siraitia, leading to a preliminary draft of the genome, was combined with an extensive transcriptomic analysis of developing fruit. A functional expression survey of nearly 200 candidate genes identified the members of the five enzyme families responsible for the synthesis of mogroside V: squalene epoxidases, triterpenoid synthases, epoxide hydrolases, cytochrome P450s, and UDP-glucosyltransferases. Protein modeling and docking studies corroborated the experimentally proven functional enzyme activities and indicated the order of the metabolic steps in the pathway. A comparison of the genomic organization and expression patterns of these Siraitia genes with the orthologs of other Cucurbitaceae implicates a strikingly coordinated expression of the pathway in the evolution of this species-specific and valuable metabolic pathway. The genomic organization of the pathway genes, syntenously preserved among the Cucurbitaceae, indicates, on the other hand, that gene clustering cannot account for this novel secondary metabolic pathway.

scholarly journals RNA-Dependent RNA Polymerase 1 from Nicotiana tabacum Suppresses RNA Silencing and Enhances Viral Infection in Nicotiana benthamiana

2010 ◽  
Vol 22 (4) ◽  
pp. 1358-1372 ◽  
Author(s):  
Xiao-Bao Ying ◽  
Li Dong ◽  
Hui Zhu ◽  
Cheng-Guo Duan ◽  
Quan-Sheng Du ◽  
...  
Keyword(s):  
Nicotiana Tabacum ◽  
Rna Polymerase ◽  
Viral Infection ◽  
Nicotiana Benthamiana ◽  
Rna Silencing ◽  
Rna Dependent Rna Polymerase ◽  
Rna Polymerase 1

Cocksfoot mottle virus P1 suppresses RNA silencing in Nicotiana benthamiana and Nicotiana tabacum

2007 ◽  
Vol 123 (1) ◽  
pp. 95-99 ◽  
Author(s):  
Cecilia Sarmiento ◽  
Eva Gomez ◽  
Merike Meier ◽  
Tony A. Kavanagh ◽  
Erkki Truve
Keyword(s):  
Nicotiana Tabacum ◽  
Nicotiana Benthamiana ◽  
Rna Silencing ◽  
Mottle Virus ◽  
Cocksfoot Mottle Virus
Sign in / Sign up

Export Citation Format

Share Document