{"database":"Pride","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Tabular":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD069025/PXD069025_community_annotated.sdrf.tsv"],"Xlsx":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD069025/20250718_044_AW_6hisYjlC-BsNDH_F2.xlsx","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD069025/20250718_044_AW_6hisYjlC-SaNDH_F2.xlsx","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD069025/SDRF_044_AW.xlsx"],"Raw":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD069025/20250718_044_AW_6hisYjlC-BsNDH_F2.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD069025/20250718_044_AW_6hisYjlC-SaNDH_F2.raw"],"Fasta":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD069025/20250723_6hisYjlC_044_WA.fasta","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD069025/Escherichia_coli_K-12_sp_tr_canonical_TaxID83333.fasta","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD069025/20250723_BsNDH_044_WA.fasta","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD069025/20250723_SaNDH_044_WA.fasta"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"labhead_mail":["magalon@imm.cnrs.fr"],"submitter":["Salomé Sauvage"],"technology_type":["Data-dependent acquisition","Mass Spectrometry","Bottom-up proteomics"],"software":[""],"submitter_keywords":["helical membrane plugin proteins","bacillales","electron transfer chains","Nadh dehydrogenase ; bacillales ; helical membrane plugin proteins ; electron transfer chains","Nadh dehydrogenase","Quinone-reacting oxidoreductase"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD069025"],"sample_protocol":["Culture preparation B. subtilis and its derivatives were cultured overnight at 37 °C in Luria-Bertani (LB) medium. The precultures were diluted to an OD₆₀₀ of 0.05 in CE medium, supplemented with 0.1 mM tryptophan, 30 mM malate, and 0.1 % (w/v) xylose, when specified. The cultures were incubated for 6 h, after which they were diluted to an OD₆₀₀ of 0.1 in CE medium containing 2 % (w/v) xylose, as indicated. For growth monitoring, 100 µL aliquots were incubated in a microplate reader at 37 °C with shaking at 180 rpm for 6 h. For recombinant protein production, B. subtilis, E. coli, and their derivatives were cultured overnight in LB at 37 °C. The precultures were diluted to OD₆₀₀ of 0.05 in LB and grown to 339 mid-exponential phase (OD₆₀₀ = 0.4–0.6). Protein expression was induced with 0.8 % (w/v) xylose (B. subtilis) and 1 mM IPTG (E. coli) for 4 h. The cells were harvested, washed once 341 with 50 mM Tris-HCl (pH 8.0), and stored at -80 °C.  Protein extraction All steps were performed at 4°C using an ÄKTA FPLC system (Cytiva). Frozen cells (B. subtilis and E. coli) were thawed and resuspended in 15 mL 50 mM of Tris-HCl (pH 8), supplemented with a protease inhibitor cocktail (Roche). For B. subtilis, lysozyme (1 mg/mL) and DNase I were added, and the suspension was incubated for 30 min at 37 °C, followed by 347 quenching with 0.5 mM EDTA. Cell disruption was achieved using a French press, and cell debris was removed by centrifugation at 11,000g for 30 min. The resulting supernatant was adjusted to contain 150 mM NaCl and 20 mM imidazole, and loaded onto a 5 mL Ni-NTA column (Cytiva). After washing with a buffer containing 50 mM Tris-HCl, 150 mM NaCl and 20 mM imidazole, a second washing step was performed with 50 mM imidazole, and the protein was eluted using 200 mM imidazole. Imidazole was removed by buffer exchange using a 100 kDa Amicon (Millipore). The purified protein was supplemented with 5 % glycerol, flash frozen in liquid nitrogen, and stored at -80 °C. For size-exclusion chromatography (SEC) purification, 25 µL of YjlC/Ndh (3 mg/mL) and 25 µL of YjlC/SaNdh (4.8 mg/mL) were loaded onto a Superdex 200 5/150 GL (Cytiva) column equilibrated with Tris 50 mM (pH 8) NaCl 150 mM at a flow rate of 0.3 mL.min-1. Fractions 1 to 6 were analyzed by SDS-PAGE. Protein digestion The revealed protein bands were excised and washed three times during 10 min with 50 % ammonium bicarbonate 100 mM/50 % acetonitrile (ACN), before to be dried with 100 % ACN during 15 min. Disulfide bonds were disrupted with 10 mM DTT, 45 min at 56 °C in the dark; and cysteines were alkylated with 55 mM iodoacetamide, 30 min in the dark. Gel bands were then treated with 50 % ammonium bicarbonate 100 mM/50 % ACN (10 min, 2 times) and dried again with 100 % ACN during 15 min. Proteins were digested with Trypsin/LysC protease mix (Promega) with final 0.025 % ProteaseMax (v/v) overnight at 37 °C in ammonium bicarbonate 25 mM. Finally, peptides were extracted with 0.1 % trifluoroacetic acid (TFA) followed by 100 % ACN (5 min each, 2 times) and then dried. NanoLC-MS/MS protein analyses Tryptic peptides were solubilized in H2O with 0.05 % TFA and 2 % ACN, and analyzed on a Q Exactive Plus (Thermo Scientific) mass spectrometer equipped with a nanoEasy Spray source coupled with a Vanquish Neo (Thermo Scientific) liquid chromatography. Peptides were injected onto an enrichment column (C18 Acclaim PepMap RSLC,75 µm × 500 mm, 2 µm, 100 Ǻ, Thermo Scientific). The buffers for the mobile phase were composed of 100 % H2O/0.1 % formic acid (FA) (A) and 80 % ACN/20 % H2O/0.1 % FA (B). The elution gradient duration was 117 min: 2 % to 25 % B from 0 to 90 min, 25 % to 50 % B from 90 to 110 min, and 50 % to 99 % B from 110 to 117 min. The flow rate was 0.3 µL/min. The temperature of the column was set at 40 °C. The maximum injection time was set to 100 ms. The capillary voltage was set to 1.9 kV. The temperature of the capillary was 280 °C. The Data dependent analysis was performed in HCD fragmentation mode of the 10 most intense ions selected (Top 10), with Nitrogen used as the collision gas. The m/z detection range was 350-1,900. The resolution was set to 70,000 for Full MS, and 17,500 for MS/MS fragmentation. All spectra obtained were exported in “.raw” format to identify peptides."],"repository":["Pride"],"quantification_method":["Not available"],"modification":[""],"data_protocol":["For identification :  NDH protein of Bacillus subtilis with His-YjlC expressed in Escherichia coli K12 (TxID=83333) strain correspond to this raw data: 20250718_044_AW_6hisYjlC-BsNDH_F2 NDH protein of Staphylococcus aureus with His-YjlC expressed in Escherichia coli K12 (TxID=83333) strain correspond to this raw data: 20250718_044_AW_6hisYjlC-SaNDH_F2 For His-YjlC, the sequence used corresponded to YjlC with an n-terminal extension consisting of Met-Ala followed by a hexahistidine tag (Met-Ala-His6).  Data were searched by the software Proteome Discoverer 3.0 (Thermo Scientific) and searched against  Escherichia coli K-12 (TxID: 83333, 4516 entries) from NCBI as database, amino acid modifications such carbamidomethylation on cysteine (fixed), oxidation on methionine (variable) and acetylation on protein N-term (variable) were added, and two missed cleavages were allowed. Then, proteins were filtered by a minimum number of Peptide Spectral Match (PSM) of 5."],"omics_type":["Proteomics"],"labhead":["Axel Magalon"],"instrument_platform":[""],"labhead_affiliation":["Laboratoire de Chimie Bacterienne, UMR7283 CNRS-AMU, 31 Chemin Joseph Aiguier, 13009 Marseille, France"],"submission_type":["PARTIAL"],"species":["Escherichia Coli (strain K12)"],"submitter_mail":["salome.sauvage@orange.fr"],"publication":["42315832 Seduk F, Osman R, Garcia PS, Bizien-Jaglin L, Juyoux P, Kosta A, Sauvage S, Maté MJ, Pierrel F, Lebrun R, Schoehn G, Yamaryo-Botté Y, Botté CY, Nicolet Y, Cherrier MV, Walburger A, Magalon A. A Bacillales-specific tubular scaffold essential for NADH dehydrogenase activity. Nat Commun. 2026 17(1):7717 10.1038/s41467-026-74385-2"],"submitter_affiliation":["Proteomics Facility of Institut de Microbiologie de la Méditerranée, CNRS, 31 Chemin Joseph Aiguier, 13009 Marseille"],"submitter_country":["France"],"pubmed_abstract":["Respiratory type II NADH:quinone oxidoreductases (NDH-II) are typically monotopic flavoproteins that make direct contact with the membrane to access the quinone pool. Here, we show that in Bacillus subtilis, one NDH-II, termed Ndh, assembles with the helical membrane plugin (HMP) protein YjlC and forms supramolecular fibers. Genetic and biochemical analyses demonstrate that Ndh and YjlC proteins are essential for NADH oxidation. Cryo-EM analysis reveals that YjlC forms a tubular scaffold onto which multiple Ndh subunits are regularly docked via their C-terminal domain, repurposed from its classical role in direct membrane binding. These fibers can extend up to ~1000 Å, creating a continuous hydrophobic tunnel filled with lipids and quinones, thereby mimicking the membrane environment. Comparative genomics unveils that this partnership arose exclusively within Bacillales through the recruitment of an ancestral HMP originally associated with sulfide:quinone reductases. Together, our findings uncover a lineage-specific structural adaptation in which NDH-II enzymes depend on an HMP scaffold, expanding their functional diversity beyond the classical monotopic paradigm."],"pubmed_title":["A Bacillales-specific tubular scaffold essential for NADH dehydrogenase activity."],"pubmed_authors":["Seduk Farida F, Osman Rayan R, Garcia Pierre Simon PS, Bizien-Jaglin Lilou L, Juyoux Pauline P, Kosta Artemis A, Sauvage Salomé S, Maté Maria J MJ, Pierrel Fabien F, Lebrun Régine R, Schoehn Guy G, Yamaryo-Botté Yoshiki Y, Botté Cyrille Y CY, Nicolet Yvain Y, Cherrier Mickael V MV, Walburger Anne A, Magalon Axel A"],"additional_accession":[]},"is_claimable":false,"name":"A Bacillales-specific tubular scaffold essential for NADH dehydrogenase activity","description":"Respiratory type II NADH:quinone oxidoreductases (NDH-II) are typically monotopic flavoproteins that make direct contact with the membrane to access the quinone pool. Here, we show that in Bacillus subtilis, one NDH-II, termed Ndh, assembles with the helical membrane plugin (HMP) protein YjlC and forms supramolecular fibers. Genetic and biochemical analyses demonstrate that Ndh and YjlC proteins are essential for NADH oxidation. Cryo-EM analysis reveals that YjlC forms a tubular scaffold onto which multiple Ndh subunits are regularly docked via their C-terminal domain, repurposed from its classical role in direct membrane attachment. These fibers can extend up to ~1,000 Å, creating a continuous hydrophobic tunnel filled with lipids and quinones, thereby mimicking the membrane environment. Comparative genomics unveils that this partnership arose exclusively within Bacillales through the recruitment of an ancestral HMP originally associated with sulfide:quinone reductases. Together, our findings uncover a lineage-specific structural adaptation in which NDH-II enzymes depend on an HMP scaffold, expanding their functional diversity beyond the classical monotopic 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