ArticleBMC genomics2019
A homology-guided, genome-based proteome for improved proteomics in the alloploid Nicotiana benthamiana.
Article in BMC genomics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 50 papers.
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50 citing papers in PubMed, 83 citations in OpenAlex.
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- Proximity Labelling-Based Proteomics Identifies Antiviral Host Factors Associated With the Potexvirus Replicase.Molecular plant pathology · 2026Article
- 4D-DIA proteomics reveals distinct proteolytic landscapes induced by mechanical stress, Agrobacterium, and a viral capsid precursor.PloS one · 2026Article
- Bamboo mosaic virus-induced metabolic reprogramming engages mitochondrial function to regulate redox homeostasis and defense responses in Nicotiana benthamiana.BMC plant biology · 2025Article
- Review
- Untargeted Proteomics Identifies Plant Substrates of the Bacterial-Derived ADP-Ribosyltransferase AvrRpm1.Plant direct · 2025Article
- Toward simple, rapid, and deep plant proteome analysis with an in-cell proteomics strategy.bioRxiv : the preprint server for biology · 2025Article
- Pupylation-Based Proximity Labeling Unravels a Comprehensive Protein and Phosphoprotein Interactome of the Arabidopsis TOR Complex.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Genomic diversity of mcr-carrying plasmids and the role of type IV secretion systems in IncI2 plasmids conjugation.Communications biology · 2025Article
- Pupylation-based proximity labeling reveals regulatory factors in cellulose biosynthesis in Arabidopsis.Nature communications · 2025Article
- The disordered effector RipAO of Ralstonia solanacearum destabilizes microtubule networks in Nicotiana benthamiana cells.Molecules and cells · 2025Article
- XopM, An FFAT Motif-Containing Type III Effector Protein From Xanthomonas, Suppresses MTI Responses at the Plant Plasma Membrane.Molecular plant pathology · 2024Article
- Subtilase SBT5.2 inactivates flagellin immunogenicity in the plant apoplast.Nature communications · 2024Article
- Extracellular plant subtilases dampen cold-shock peptide elicitor levels.Nature plants · 2024Article
- The proteome of Nicotiana benthamiana is shaped by extensive protein processing.The New phytologist · 2024Article
- Posttranslational regulation of photosynthetic activity via the TOR kinase in plants.Science advances · 2024Article
- Specific members of the TOPLESS family are susceptibility genes for Fusarium wilt in tomato and Arabidopsis.Plant biotechnology journal · 2024Article
- Characterization of Phytaspase Proteolytic Activity Using Fluorogenic Peptide Substrates.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Importin α2 participates in RNA interference against bamboo mosaic virus accumulation in Nicotiana benthamiana via NbAGO10a-mediated small RNA clearance.Molecular plant pathology · 2024Article
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Authors and funding
6 authors at 2 institutions in 2 countries.
Funding
Abstract
backgroundNicotiana 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.
resultsHere 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.
conclusionsThis proteome annotation provides the community working with Nicotiana benthamiana with an important new resource for functional proteomics.
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