scholarly journals Advanced Engineering of Lipid Metabolism in Nicotiana benthamiana Using a Draft Genome and the V2 Viral Silencing-Suppressor Protein

PLoS ONE ◽  
2012 ◽  
Vol 7 (12) ◽  
pp. e52717 ◽  
Author(s):  
Fatima Naim ◽  
Kenlee Nakasugi ◽  
Ross N. Crowhurst ◽  
Elena Hilario ◽  
Alexander B. Zwart ◽  
...  
Keyword(s):  
Lipid Metabolism ◽  
Nicotiana Benthamiana ◽  
Draft Genome ◽  
Silencing Suppressor ◽  
Viral Silencing Suppressor

scholarly journals Expression analysis of host defense responses against the 8K (KDa) cysteine-rich viral silencing suppressor protein in Nicotiana benthamiana

Plant Omics ◽  
2018 ◽  
Vol 11 (02) ◽  
pp. 113-119
Author(s):  
Aminallah Tahmasebi ◽  
◽  
Alireza Afsharifar ◽  
Ahmad Heydari ◽  
Mohammad Mehrabadi ◽  
...  
Keyword(s):  
Expression Analysis ◽  
Host Defense ◽  
Nicotiana Benthamiana ◽  
Defense Responses ◽  
Silencing Suppressor ◽  
Viral Silencing Suppressor

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 High-level HIV-1 Nef transient expression in Nicotiana benthamiana using the P19 gene silencing suppressor protein of Artichoke Mottled Crinckle Virus

2009 ◽  
Vol 9 (1) ◽  
pp. 96 ◽  
Author(s):  
Raffaele Lombardi ◽  
Patrizia Circelli ◽  
Maria Villani ◽  
Giampaolo Buriani ◽  
Luca Nardi ◽  
...  
Keyword(s):  
Gene Silencing ◽  
Transient Expression ◽  
Nicotiana Benthamiana ◽  
Silencing Suppressor ◽  
High Level ◽  
Hiv 1

scholarly journals A homology-guided, genome-based proteome for improved proteomics in the alloploid Nicotiana benthamiana

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Jiorgos Kourelis ◽  
Farnusch Kaschani ◽  
Friederike M. Grosse-Holz ◽  
Felix Homma ◽  
Markus Kaiser ◽  
...  
Keyword(s):  
Nicotiana Benthamiana ◽  
Draft Genome ◽  
Model Organism ◽  
Functional Annotations ◽  
Draft Genome Assembly ◽  
Extracellular Proteome ◽  
Protein Encoding ◽  
Gene Models ◽  
Genome Assemblies ◽  
Encoding Genes

Abstract Background Nicotiana benthamiana is an important model organism of the Solanaceae (Nightshade) family. Several draft assemblies of the N. benthamiana genome have been generated, but many of the gene-models in these draft assemblies appear incorrect. Results Here we present an improved proteome based on the Niben1.0.1 draft genome assembly guided by gene models from other Nicotiana species. Due to the fragmented nature of the Niben1.0.1 draft genome, many protein-encoding genes are missing or partial. We complement these missing proteins by similarly annotating other draft genome assemblies. This approach overcomes problems caused by mis-annotated exon-intron boundaries and mis-assigned short read transcripts to homeologs in polyploid genomes. With an estimated 98.1% completeness; only 53,411 protein-encoding genes; and improved protein lengths and functional annotations, this new predicted proteome is better in assigning spectra than the preceding proteome annotations. This dataset is more sensitive and accurate in proteomics applications, clarifying the detection by activity-based proteomics of proteins that were previously predicted to be inactive. Phylogenetic analysis of the subtilase family of hydrolases reveal inactivation of likely homeologs, associated with a contraction of the functional genome in this alloploid plant species. Finally, we use this new proteome annotation to characterize the extracellular proteome as compared to a total leaf proteome, which highlights the enrichment of hydrolases in the apoplast. Conclusions This proteome annotation provides the community working with Nicotiana benthamiana with an important new resource for functional proteomics.

Small RNA profiles of wild-type and silencing suppressor-deficient tomato spotted wilt virus infected Nicotiana benthamiana

2015 ◽  
Vol 208 ◽  
pp. 30-38 ◽  
Author(s):  
Paolo Margaria ◽  
Laura Miozzi ◽  
Cristina Rosa ◽  
Michael J. Axtell ◽  
Hanu R. Pappu ◽  
...  
Keyword(s):  
Small Rna ◽  
Nicotiana Benthamiana ◽  
Tomato Spotted Wilt Virus ◽  
Silencing Suppressor ◽  
Wild Type ◽  
Tomato Spotted Wilt ◽  
Wilt Virus

scholarly journals Apple chlorotic leaf spot virus 50 kDa movement protein acts as a suppressor of systemic silencing without interfering with local silencing in Nicotiana benthamiana

2007 ◽  
Vol 88 (1) ◽  
pp. 316-324 ◽  
Author(s):  
Hajime Yaegashi ◽  
Tsubasa Takahashi ◽  
Masamichi Isogai ◽  
Takashi Kobori ◽  
Satoshi Ohki ◽  
...  
Keyword(s):  
Leaf Spot ◽  
Nicotiana Benthamiana ◽  
Rna Silencing ◽  
Fluorescent Protein ◽  
Movement Protein ◽  
Silencing Suppressor ◽  
Spot Virus ◽  
Double Stranded Rna ◽  
Chlorotic Leaf ◽  
Green Fluorescent

Apple chlorotic leaf spot virus (ACLSV) is the type species of the genus Trichovirus and its single-stranded, plus-sense RNA genome encodes a 216 kDa protein (P216) involved in replication, a 50 kDa movement protein (P50) and a 21 kDa coat protein (CP). In this study, it was investigated whether these proteins might have RNA silencing-suppressor activities by Agrobacterium-mediated transient assay in the green fluorescent protein-expressing Nicotiana benthamiana line 16c. The results indicated that none of these proteins could suppress local silencing in infiltrated leaves. However, systemic silencing in upper leaves induced by both single- and double-stranded RNA could be suppressed by P50, but not by a frame-shift mutant of P50, P216 or CP. Moreover, when P50 was expressed separately from where silencing signals were generated in a leaf, systemic silencing in upper leaves was inhibited. Collectively, our data indicate that P50 acts as a suppressor of systemic silencing without interfering with local silencing, probably by inhibiting the movement of silencing signals.

scholarly journals Turnip Mosaic Virus Counteracts Selective Autophagy of the Viral Silencing Suppressor HCpro

2017 ◽  
Vol 176 (1) ◽  
pp. 649-662 ◽  
Author(s):  
Anders Hafrén ◽  
Suayib Üstün ◽  
Anton Hochmuth ◽  
Steingrim Svenning ◽  
Terje Johansen ◽  
...  
Keyword(s):  
Mosaic Virus ◽  
Turnip Mosaic Virus ◽  
Silencing Suppressor ◽  
Selective Autophagy ◽  
Viral Silencing Suppressor

scholarly journals Homology-guided re-annotation improves the gene models of the alloploid Nicotiana benthamiana

2018 ◽  
Author(s):  
Jiorgos Kourelis ◽  
Farnusch Kaschani ◽  
Friederike M. Grosse-Holz ◽  
Felix Homma ◽  
Markus Kaiser ◽  
...  
Keyword(s):  
Nicotiana Benthamiana ◽  
Gene Annotation ◽  
Draft Genome ◽  
Model Organism ◽  
Extracellular Proteins ◽  
Functional Annotations ◽  
Draft Genome Assembly ◽  
Protein Encoding ◽  
Gene Models ◽  
Encoding Genes

Nicotiana benthamiana is an important model organism of the Solanaceae (Nightshade) family. Several draft assemblies of the N. benthamiana genome have been generated, but many of the gene-models in these draft assemblies appear incorrect. Here we present an improved re-annotation of the Niben1.0.1 draft genome assembly guided by gene models from other Nicotiana species. This approach overcomes problems caused by mis-annotated exon-intron boundaries and mis-assigned short read transcripts to homeologs in polyploid genomes. With an estimated 98.1% completeness; only 53,411 protein-encoding genes; and improved protein lengths and functional annotations, this new predicted proteome is better than the preceding proteome annotations. This dataset is more sensitive and accurate in proteomics applications, clarifying the detection by activity-based proteomics of proteins that were previously mis-annotated to be inactive. Phylogenetic analysis of the subtilase family of hydrolases reveal a pseudogenisation of likely homeologs, associated with a contraction of the functional genome in this alloploid plant species. We use this gene annotation to assign extracellular proteins in comparison to a total leaf proteome, to display the enrichment of hydrolases in the apoplast.

Sign in / Sign up

Export Citation Format

Share Document