Ribosome profiles and riboproteomes of healthy and Potato virus A- and Agrobacterium-infected Nicotiana benthamiana plants.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:30375150", "kind": "science-record", "revision": 6, "content_hash": "sha256:b02ff606bb818f2c13325478981b6f15dc4ddda76e6918e527f93fff1e77b6a8", "created_at": "2026-11-01T15:40:38Z", "updated_at": "2026-11-01T21:21:44Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Ribosome profiles and riboproteomes of healthy and Potato virus A- and Agrobacterium-infected Nicotiana benthamiana plants.", "doi": "10.1111/mpp.12764", "pmid": "30375150", "authors": ["Katri Eskelin", "Markku Varjosalo", "Janne Ravantti", "Kristiina Mäkinen"], "journal": "Molecular plant pathology", "year": 2019, "abstract": "Nicotiana benthamiana is an important model plant for plant-microbe interaction studies. Here, we compared ribosome profiles and riboproteomes of healthy and infected N. benthamiana plants. We affinity purified ribosomes from transgenic leaves expressing a FLAG-tagged ribosomal large subunit protein RPL18B of Arabidopsis thaliana. Purifications were prepared from healthy plants and plants that had been infiltrated with Agrobacterium tumefaciens carrying infectious cDNA of Potato virus A (PVA) or firefly luciferase gene, referred to here as PVA- or Agrobacterium-infected plants, respectively. Plants encode a number of paralogous ribosomal proteins (r-proteins). The N. benthamiana riboproteome revealed approximately 6600 r-protein hits representing 424 distinct r-proteins that were members of 71 of the expected 81 r-protein families. Data are available via ProteomeXchange with identifier PXD011602. The data indicated that N. benthamiana ribosomes are heterogeneous in their r-protein composition. In PVA-infected plants, the number of identified r-protein paralogues was lower than in Agrobacterium-infected or healthy plants. A. tumefaciens proteins did not associate with ribosomes, whereas ribosomes from PVA-infected plants co-purified with viral cylindrical inclusion protein and helper component proteinase, reinforcing their possible role in protein synthesis during virus infection. In addition, viral NIa protease-VPg, RNA polymerase NIb and coat protein were occasionally detected. Infection did not affect the proportions of ribosomal subunits or the monosome to polysome ratio, suggesting that no overall alteration in translational activity took place on infection with these pathogens. The riboproteomic data of healthy and pathogen-infected N. benthamiana will be useful for studies on the specific use of r-protein paralogues to control translation in infected plants.", "claims": [{"id": "claim-method", "statement": "For peptide identification, a false discovery rate (FDR) < 0.05 was used.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30375150", "locator": "sections[23] \"MS and data analysis\" paragraph 4", "quote": "For peptide identification, a false discovery rate (FDR) < 0.05 was used."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data are available via ProteomeXchange with identifier PXD011602.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30375150", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Data are available via ProteomeXchange with identifier PXD011602."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:30375150"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:PXD011602"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:PXD011602"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:30375150", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1111/mpp.12764", "sha256": "sha256:7014254960ce9b655dbb51a0687e81bb29c8d3d93edb3593c6528c64b51482f4", "bytes": 93430, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1111/mpp.12764", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6637900", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD011602", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=PXD011602", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD011602", "version": null, "note": "Data are available via ProteomeXchange with identifier PXD011602.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data are available via ProteomeXchange with identifier PXD011602.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "LC-MSMS of RIBOPROTEOMES OF HEALTHY, POTATO VIRUS A- AND AGROBACTERIUM -INFECTED NICOTIANA BENTHAMIANA PLANTS", "resolution_checked_at": "2026-10-31T18:35:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:30375150:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:2b1b40d62071a38a17556e33541883001a4d2e9dc40cea391ae122e8b55f74c9", "bytes": 1151, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[1]#mpp12764-tbl-0001", "version": null, "note": "Summary of riboproteome mass spectrometry (MS) data. Median values, averages and range are shown for sequence coverage (%), number of identified peptides and peptide matching scores (PSM). Data include r‐proteins (ribosomal proteins), P‐proteins and RACK (ribosome‐associated receptor for activating C kinase) having PSM values above 1.", "structure": {"pmcid": "PMC6637900", "section_index": 10, "section_title": "Total number of r‐protein paralogues incorporated into N. benthamiana ribosomes is the lowest in PVA‐infected samples", "row_count": 12, "column_count": 4}, "table": {"label": "Table 1", "caption": "Summary of riboproteome mass spectrometry (MS) data. Median values, averages and range are shown for sequence coverage (%), number of identified peptides and peptide matching scores (PSM). Data include r‐proteins (ribosomal proteins), P‐proteins and RACK (ribosome‐associated receptor for activating C kinase) having PSM values above 1.", "rows": [["", "Mock", "Agrobacterium‐infected", "Potato virus A‐infected"], ["Total number of r‐protein hits", "2272", "2360", "1923"], ["Unique r‐protein hits", "417", "421", "384"], ["Median coverage (%)", "18.7", "18.8", "16.7"], ["Average coverage (%)", "20.4", "20.8", "18.4"], ["Coverage range (%)", "3.0–77.9", "3.0–92.0", "1.8–72.6"], ["Median number of peptides per protein", "2.0", "2.0", "2.0"], ["Average number of peptides per protein", "2.7", "2.8", "2.4"], ["Number of peptides per protein: range", "1–12", "1–12", "1‐10"], ["Median PSM value", "4.0", "4.0", "3.0"], ["Average PSM value", "5.3", "5.3", "3.9"], ["Range for PSM values", "2–27", "2–32", "2–20"]], "row_count": 12, "column_count": 4, "numeric_cells": 33, "header_rows": 1, "locator": "section[10]/table-wrap[1]#mpp12764-tbl-0001"}}, {"id": "asset:table:pmid:30375150:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:4f6178cab3a84b7711ce5ef3ed83b6ee99718f1bcea601295daab1a3fcb6ef82", "bytes": 835, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[1]#mpp12764-tbl-0002", "version": null, "note": "Identified phosphopeptides. Phosphorylated amino acids marked in lower case.", "structure": {"pmcid": "PMC6637900", "section_index": 13, "section_title": "Identification of novel phosphorylation events in r‐proteins and viral nuclear inclusion protein b (NIb)", "row_count": 9, "column_count": 4}, "table": {"label": "Table 2", "caption": "Identified phosphopeptides. Phosphorylated amino acids marked in lower case.", "rows": [["Peptide sequence", "R‐protein", "Nb protein", "Number of hits"], ["SRLsAASKPSVAA", "RPS6", "NbS00006996g0012", "1"], ["SRLsAASKPSIAA", "RPS6", "NbS00012569g0012, NbS00000439g0011, Nbs00005003g0014, Nbs00002662g0109", "2"], ["KEEKEEsDDDMGFSLFD", "RPP2, RPP3", "NbS00021044g0016, NbS00005878g0110,", "3"], ["KEEPKEEsDDDMGFSLFD", "RPP1", "NbS00042976g0007, NbS00053503g0005", "5"], ["KVEEKEEsDDDMGFSLFD", "RPP2", "NbS00029619g0005, NbS00019361g0011", "1"], ["DyKSFRLFsLSIEDVNDK*", "RPL18", "NbS00020801g0014", "1"], ["SSsGTAPLIDVTQYGYFK", "RPL27a", "NbS00010663g0005", "1"], ["RFYAWVLEQsPyNALATTGLAPyIAESALK", "PVA NIb", "", "1"]], "row_count": 9, "column_count": 4, "numeric_cells": 17, "header_rows": 1, "locator": "section[13]/table-wrap[1]#mpp12764-tbl-0002"}}, {"id": "asset:table:pmid:30375150:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:7cb801dd6117cef1d22ec796caa505f9d9a870a21a4bce8628995b07e1431fae", "bytes": 591, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[15]/table-wrap[1]#mpp12764-tbl-0003", "version": null, "note": "Potato virus A (PVA) protein hits from affinity‐purified ribosomes at 4 days post‐infection (dpi). Peptide matching scores (PSM) are given.", "structure": {"pmcid": "PMC6637900", "section_index": 15, "section_title": "Unlike PVA proteins, proteins of A. tumefaciens do not associate with N. benthamiana ribosomes", "row_count": 7, "column_count": 5}, "table": {"label": "Table 3", "caption": "Potato virus A (PVA) protein hits from affinity‐purified ribosomes at 4 days post‐infection (dpi). Peptide matching scores (PSM) are given.", "rows": [["", "Purification 3, technical 1", "Purification 3, technical 2", "Purification 4, technical 1", "Purification 4, technical 2"], ["CI", "11", "8", "2", "3"], ["HCPro", "16", "16", "1", "4"], ["NIaPro", "1", "1", "–", "–"], ["VPg", "1", "1", "1", "–"], ["NIb", "2", "2", "–", "–"], ["CP", "1", "1", "1", "1"]], "row_count": 7, "column_count": 5, "numeric_cells": 23, "header_rows": 1, "locator": "section[15]/table-wrap[1]#mpp12764-tbl-0003"}}, {"id": "asset:table:pmid:30375150:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:ac25f2722bd0152b3e8e0e17cbe480754d2abca0a11fb847d872a39436d09866", "bytes": 952, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[16]/table-wrap[1]#mpp12764-tbl-0004", "version": null, "note": "A comparison of the r‐protein paralogues identified from Nicotiana benthamiana and Arabidopsis thaliana.", "structure": {"pmcid": "PMC6637900", "section_index": 16, "section_title": "Discussion", "row_count": 2, "column_count": 4}, "table": {"label": "Table 4", "caption": "A comparison of the r‐protein paralogues identified from Nicotiana benthamiana and Arabidopsis thaliana.", "rows": [["N. benthamiana 40S", "A. thaliana 40S*", "N. benthamiana 60S", "A. thaliana 60S*"], ["RPS3a, RPS3, RPS4, RPS5, RPS6, RPS7, RPS8, RPS10, RPS11, RPS12, RPS14, RPS16, RPS17, RPS24, RPS27 and RACK1", "RPSa, RPS2, RPS3a, RPS3, RPS6, RPS7, RPS10, RPS11, RPS12, RPS14, RPS15a, RPS15, RPS16, RPS19, RPS21, RPS23, RPS24, RPS25, S27a", "RPP0, RPP1, RPP2, RPL3, RPL4, RPL5, RPL6, RPL7, RPL8, RPL9, RPL10, RPL11, RPL12, RPL13, RPL14, RPL15, RPL18, RPL19, RPL21, RPL22, RPL26, RPL27a, RPL27, RPL30, RPL34, RPL35, RPL38", "RPP0, RPP1, RPP2, RPL4, RPL5, RPL6, RPL7, RPL7a, RPL8, RPL10, RPL10a, RPL13a, RPL17, RPL18a, RPL18, RPL19, RPL22, RPL23a, RPL26, RPL27, RPL28, RPL31, RPL32, RPL35, RPL36, RPL37a"]], "row_count": 2, "column_count": 4, "numeric_cells": 8, "header_rows": 1, "locator": "section[16]/table-wrap[1]#mpp12764-tbl-0004"}}], "gaps": ["asset:data:geo:PXD011602 not downloaded", "asset:data:geo:PXD011602 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "False discovery rate (FDR) control, with FDR < 0.05 for peptide identification", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "For peptide identification, a false discovery rate (FDR) < 0.05 was used."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "blocked", "tier": "R4", "blocking_axis": "method", "blocked_on": "method:not_determinable", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (False discovery rate (FDR) control, with FDR < 0.05 for peptide identification), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. 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Summary of riboproteome mass spectrometry (MS) data. Median values, averages and range"], "order_basis": "paper_text_order:3043", "id": "assay:1"}, {"role": "data_generation", "definition_id": "western_blot", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["gels and stained with silver or subjected to Western blotting, as described above. Supplementary Materials", "Click here for additional data file. Fig. S3 Western blot analysis of eIF4E/eIFiso4E and PABP in Agrob"], "order_basis": "paper_text_order:6143", "id": "assay:2"}]}