Prideapplication/xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD065660/parameters.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD065660/checksum.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD065660/proteinGroups.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD065660/evidence.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD065660/0115_CMS_240229-OA-TMTp_FAIMS-TbID_N-4x1000ng_OE480-02.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD065660/0115_CMS_240229-OA-TMTp_FAIMS-TbID_N-4x1000ng_OE480-01.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD065660/0115_CMS_240229-OA-TMTp_FAIMS-TbID_N-4x1000ng_OE480-03.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD065660/0115_CMS_240229-OA-TMTp_FAIMS-TbID_N-4x1000ng_OE480-04.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD065660/Ath_TAIR10_pep_20101214.fastaftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD065660/mzTab.mzTabprimaryOK200mbhattac@iastate.eduChristian Montes SereyData-dependent acquisitionAffinity purification coupled with mass spectrometry proteomicsMass SpectrometryBottom-up proteomicsPhytophthora sojaeMiniturboArabidopsisPss1Nonhost resistanceProtein interactomeProximity labelinghttps://www.ebi.ac.uk/pride/archive/projects/PXD065660SeedlingTen-day-old Arabidopsis seedlings expressing PSS1-miniTurbo, PSS1G119D-miniTurbo, miniTurbo-PSS1, or miniTurbo-PSS1G119D were vertically grown on half-strength Murashige and Skoog (MS) medium and transferred into sterile six-well plates containing water for a 2-day acclimation period. On Day 2, seedlings were inoculated with a P. sojae zoospore suspension (10⁶ zoospores/mL) and incubated in the dark. Mock controls were treated with sterile water. Four hours post-inoculation, biotin (Sigma, USA) was added to a final concentration of 250 µM, and seedlings were incubated for an additional 20 hours in the dark at room temperature (RT). Following labeling, plants were rinsed three times with sterile deionized water (5 minutes each) and blotted dry on filter paper. This experiment was performed nine times. Seedlings from three independent experiments were pooled per replicate, resulting in three biological replicates. Plant tissues were weighed, flash-frozen, and ground in liquid nitrogen using a chilled mortar and pestle. Total protein was extracted using RIPA buffer (50 mM Tris-HCl pH 7.5, 150 mM NaCl, 0.5% or 1% NP-40, 1% sodium deoxycholate, 0.1% SDS, and 1× protease inhibitor cocktail; Roche, USA). The lysates were centrifuged twice at 16,000 × g for 10 minutes at 4 °C. To remove excess free biotin, protein extracts were desalted using PD-10 columns (Sigma, USA) equilibrated with extraction buffer lacking protease inhibitors, following the manufacturer’s instructions. After desalting, 500 µL of 1× protease inhibitor cocktail was added to each sample. Protein concentrations were determined by Bradford assay. Biotinylated proteins were enriched using Dynabeads MyOne Streptavidin C1 beads (Thermo Fisher Scientific, USA). For each 6.5 mg of desalted protein, 200 µL of bead slurry was used. Beads were pre-washed and equilibrated in binding buffer before incubation with the protein extracts. Binding was performed overnight (15 h) at 4 °C on a rotator. The next day, the beads were separated using a magnetic rack and subjected to a stringent wash protocol: once with cold extraction buffer (1 mL, 4 °C), once with 1 M KCl, once with 100 mM Na₂CO₃, once with 2 M urea in 10 mM Tris-HCl (pH 7.5), and six washes with 50 mM Tris-HCl (pH 7.5). Finally, beads were resuspended in 200 µL of 50 mM Tris-HCl (pH 7.5). To verify enrichment of biotinylated proteins, 5% of the bead slurry was boiled at 95 °C for 10 minutes in 50 µL of 2× SDS-PAGE loading buffer containing 20 mM DTT and 2 mM biotin. The eluate was analyzed by western blot. The remaining beads were flash-frozen in liquid nitrogen and stored at –80 °C until LC-MS/MS analysis. Enriched proteins were eluted from streptavidin beads by incubation at 95 °C for 10 minutes in 1× S-Trap lysis buffer (5% SDS, 50 mM TEAB, pH 8.5) supplemented with 12.5 mM biotin. Eluates were processed using S-Trap micro columns (ProtiFi, USA; Cat# C02-micro-80) following the manufacturer's protocol. Protein samples were reduced by 2 mM TCEP and alkylated with 50 mM iodoacetamide (IAA), then digested overnight at 37 °C using 100 ng each of trypsin and Lys-C. Resulting peptides were desalted using Sep-Pak C18 columns (Waters, USA). Peptides were labeled using Tandem Mass Tag (TMT) reagents (Thermo Fisher Scientific, USA) as previously described [29]. Labeling reactions were quenched with 5% hydroxylamine and pooled. Pooled samples were fractionated using the Pierce High pH Reversed-Phase Peptide Fractionation Kit (Thermo Fisher Scientific) per manufacturer instructions. The resulting eight fractions were concatenated to four pooled sets (1+5, 2+6, 3+7, 4+8), dried using a SpeedVac, and reconstituted in 0.1% TFA prepared with Optima™-grade H₂O (Fisher Scientific). For LC-MS/MS analysis, 1.5 µg of peptides from each sample (20 µL injection volume) were analyzed using liquid chromatography coupled to high-field asymmetric waveform ion mobility spectrometry and tandem mass spectrometry (LC-FAIMS-MS/MS). Samples were separated on a Vanquish Neo UHPLC system coupled to an Orbitrap Exploris 480 mass spectrometer using a μPAC Neo 110 cm column (PharmaFluidics). Flow was maintained at 300 nL/min. The EASY-Spray source was connected to a FAIMS Duo Pro interface, operating with compensation voltages of –45 and –65.PrideRaw MS/MS spectra were searched against the Arabidopsis thaliana TAIR10 proteome (Arabidopsis.org) supplemented with a reverse decoy database, common contaminants, and the custom PSS1-miniTurbo sequence. Searches were performed using the Andromeda search engine within MaxQuant (v1.6.7.0). Trypsin/Lys-C specificity was set, allowing up to two missed cleavages. Carbamidomethylation of cysteine was specified as a fixed modification, while methionine oxidation and protein N-terminal acetylation were treated as variable modifications. A minimum peptide length of seven amino acids was required, and identifications were filtered at a 1% FDR at both peptide-spectrum match and protein levels using MaxQuant’s built-in target-decoy approach. Quantitative and statistical analyses were conducted using the TMT-NEAT pipeline. MaxQuant “ProteinGroups” output and a metadata file specifying TMT label assignments were provided as input. Initial processing included trimming and relabeling, and the removal of known contaminants. Data normalization was performed using both sample loading and internal reference normalization to ensure comparability across TMT runsProteomicsMadann K. BhattacharyyaDepartment of Agronomy Iowa State UniversityCOMPLETEArabidopsis Thaliana (mouse-ear Cress)Phytophthora Sojae41869043 Akintayo OF, Montes Serey C, Walley JW, Bhattacharyya MK. Proximity labelling suggests association of the nonhost receptor PSS1 protein with enzymes of multiple defense pathways in Arabidopsis. Front Plant Sci. 2025 16:1701640 10.3389/fpls.2025.1701640chrisfm@iastate.eduIowa State UniversityUnited States10.6019/PXD065660<h4>Introduction</h4><i>PSS1</i> encoding a glycine-rich integral plasma membrane protein plays a pivotal role in nonhost resistance of Arabidopsis against the soybean pathogens, <i>Phytophthora sojae</i> and <i>Fusarium virguliforme</i>. Notably, <i>P. sojae</i> fails to penetrate the wildtype Col-0 ecotype but not the pss1 mutant. To elucidate the molecular basis of <i>PSS1</i>-mediated nonhost immunity, we employed a miniTurbo-based proximity labeling approach.<h4>Methods</h4>The miniTurbo fused to either wild-type PSS1 or its mutant variant, PSS1^G119D, and expressed in the <i>pss1</i> knockout mutant background. Seedlings were challenged with or without <i>P. sojae</i> zoospores and biotinylated proteins were isolated for mass spectrometry analysis. Col-0 and PSS1^G119D lines served as controls to validate labeling specificity and biological relevance.<h4>Results</h4>Prior to infection, spatial proximity between PSS1 and the plasma membrane H(⁺)-ATPase 6 transporter was detected; however, this association was not observed following <i>P. sojae</i> challenge. Several candidate PSS1-associated proteins were predominantly localized to the plastid and cytosol, suggesting a possible redistribution of PSS1 during infection, potentially to facilitate nonhost immunity. PSS1 is also associated with thioglucoside glucohydrolase 1 (TGG1), a key enzyme in glucosinolate (GLS) metabolism, and to coproporphyrinogen III oxidase (LIN2), involved in tetrapyrrole biosynthesis and reactive oxygen species (ROS) production linked to defense-related cell death.<h4>Conclusions</h4>We hypothesize that PSS1 contributes to a positive feedback loop that enhances multiple defense pathways. Based on consistent enrichment and functional relevance, we nominate TGG1, LIN2, and H(⁺)-ATPase 6 as priority candidates for functional validation in the context of PSS1-mediated nonhost immunity.Proximity labelling suggests association of the nonhost receptor PSS1 protein with enzymes of multiple defense pathways in Arabidopsis.Akintayo Oluwatoyosi F OF, Montes Serey Christian C, Walley Justin W JW, Bhattacharyya Madan K MKfalseArabidopsis thaliana PSS1 TurboID N-teminal fusionThe Arabidopsis PSS1 gene, which encodes a glycine-rich protein, plays a pivotal role in nonhost resistance to the soybean oomycete Phytophthora sojae and the fungal pathogen Fusarium virguliforme. To elucidate the molecular basis of PSS1-mediated immunity, we employed miniTurbo-based proximity labeling in stable transgenic Arabidopsis lines expressing miniTurbo fused to either wild-type PSS1 or its nonfunctional mutant variant, PSS1G119D. Seedlings were challenged with or without P. sojae, and biotinylated proteins were isolated and analyzed by mass spectrometry. The resulting PSS1 interactomes revealed several candidate proteins predominantly localized in the plastid and cytosol. Notably, proteins such as LIN2, ATPMEPCRA, and TGG1 were specifically enriched in wild-type PSS1 lines under P. sojae infection, suggesting their potential involvement in PSS1-mediated nonhost resistance. Our findings offer novel insights into immune protein networks and provide a foundational resource for dissecting nonhost immunity mechanisms in 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