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Cabrera-OreficeData-dependent acquisitionMass SpectrometryBottom-up proteomicsF1fo atp synthaseOxidative phosphorylationMitochondrial supercomplexesOligomeric complex vChlorophycean algaehttps://www.ebi.ac.uk/pride/archive/projects/PXD0753711) Algal strain, growth conditions and mitochondria isolation. P. parva (strain number 198.80 from the Culture Collection of Algae at the University of Göttingen) was grown in liquid mineral Tris-phosphate medium supplemented with sodium acetate (30 mM), and vitamins (biotin 10 %, B12 vitamin 10 %, and B1 vitamin 2 × 10–5 % (w/v)) (pH 7.0). Cells were harvested by centrifugation at 7,000 x g for 10 minutes and stored at -70 °C until use. Sedimented cells were resuspended in SPT buffer (0.3 M sucrose, 4 mM potassium-EDTA, and 20 mM Tris-HCl pH 7.2) and disrupted with a Potter homogenizer. An enriched mitochondrial membrane fraction was obtained by a two-step differential centrifugation as earlier described (Miranda-Astudillo et al., 2018). 2) Complexome profiling 2.1) Native electrophoresis, in-gel digestion and peptide recovery Isolated mitochondria (100 µg) were solubilized with either LM, digitonin or GDN at a ratio of 2 mg detergent to 1 mg protein and resolved by BN-PAGE on a 3–12% acrylamide gradient gel (Wittig et al., 2006). After electrophoresis, the gels were fixed overnight in 50 % methanol, 10 % acetic acid and 100 mM ammonium acetate. It was then stained for 45 min with 0.025 % Coomassie G-250 in 10 % acetic acid, destained in 10% acetic acid, and stored in deionized water allowing the gel to re-swell to its original dimensions. The gels were scanned, and a full real size image was used for the cutting procedure. Each lane was cut into 48 equal slices (upward from the bottom until the top of the gel), diced and transferred to 96-well filter plates (Millipore, MABVN1250) taped over waste collectors (Nunc MaxiSorp plates). Gel pieces were washed repeatedly in 50 % methanol, 50 mM ammonium bicarbonate (ABC) until all blue dye had disappeared. Excess liquid was removed with brief centrifugations (1,000 x g, 20 s) between washes. Cysteines were reduced in 10 mM dithiothreitol, 50 mM ABC for 45 min, and further alkylated with 30 mM chloroacetamide, 50 mM ABC for 30 min in the dark. After a 15 min dehydration step in 50 % methanol, 50 mM ABC and air-drying for 30–45 min at room temperature, 20 µl of a sequencing-grade trypsin solution at 5 ng/µL) in 50 mM ABC, 1 mM CaCl2 were added to each well. The gel pieces were incubated at 4 °C for 20 min and covered with 50 µL of fresh ABC. The proteins were digested overnight at 37 °C. The resultant peptides were collected into clean 96-well PCR microplates after centrifugation at 1,000 x g for 60 sec, followed by a 20 min incubation in 30 % acetonitrile, 3 % formic acid and finally eluted as in the previous step. The combined eluates were vacuum-dried (~3 h) in a Concentrator Plus (Eppendorf) and the peptides were resuspended in 20 µL of 5.0 % acetonitrile, 0.5 % formic acid. Samples were stored at –20 °C until used. 2.2) Nano LC–MS/MS analysis Thawed peptides were thoroughly agitated for ~20 min, and the plates were loaded onto an Ultimate 3000 UHPLC system coupled to an Orbitrap Eclipse Tribrid mass spectrometer (Thermo Fisher Scientific). Prior to electrospraying, 5 µL of peptides from each fraction were concentrated and desalted in a PepMap Neo Trap column (Thermo Fisher Scientific), followed by separation on an Elite Aurora column (1.7 µm C18, 15 cm × 75 µm ID (IonOpticks, Australia) maintained at 60 °C. Peptide elution was performed over 55 min using a linear gradient of solvent A (0.1% formic acid in water) and solvent B (0.1% formic acid in acetonitrile) at a flow rate of 0.3 µL/min, with the gradient programmed as follows: sample loading 0-4 min (2% B); separation 4-5 min (2-5% B), 5-35 min (5-40 %B), and 35-40 min (40-90% B). The column was washed for 8 min at 90% B, then adjusted back to 2% B in 1 min followed by a 6 min re-equilibration at 2% B. MS analysis was performed in positive mode. A NanoFlex source was used for electrospray ionization, applying 2.4 kV, with a source temperature of 275 °C. MS data were acquired in data-dependent acquisition (DDA) mode. Full MS scans were recorded from 375 to 1500 m/z at a resolution of 120,000, with an RF lens setting of 30%. MS1 data were collected in profile mode. The 20 most abundant precursors (charge states 2-7) were selected for MS/MS analysis. Fragmentation was performed using collision-induced dissociation (CID) at 35% collision energy. All other instrument parameters (e.g., AGC, injection times, dynamic exclusion) were set to default.Pride3) Data processing and profile analysis Raw spectra were processed with MaxQuant v2.6.5.0 against three combined databases: the protein sequences from P. parva annotated in UniProt, the transcriptome of P.parva SAG 63-3 (sample MMETSP0052 from the Marine Microbial Eukaryote Transcriptome Sequencing Project) (Mallet and Lee, 2006; Smith et al., 2010) and the mass spectrometry proteomic data obtained from Polytomella sp. SAG 198.80 (with identifier PXD035155 deposited at the ProteomeXchange Consortium) (Lacroux et al., 2022), with a false discovery rate (FDR) threshold of <1%. The following modifications were specified: N-terminal acetylation (+42.01), deamidation of glutamine and asparagine (+0.98), and oxidation of methionine (+15.99) as variable modifications, while carbamidomethylation of cysteines (+57.02) was set as a fixed modification. were removed from the list. A total of 2,921 proteins were identified and annotated using BLAST in Phytozome, the Plant Comparative Genomics portal of the Department of Energy's Joint Genome Institute (https://phytozome-next.jgi.doe.gov/) (Goodstein et al., 2012). Keratins, trypsin, and other common contaminants were not considered. Intensity-based absolute quantification (iBAQ) values were used to reflect protein abundances. Each profile was scaled to its own maximum, sorted by average-linkage hierarchical clustering with centered Pearson distance and displayed as black, yellow, and red heat maps in Microsoft Excel 2019. Further analysis was performed by manual inspection of the obtained profiles, and the iBAQ values were re-normalized within specific apparent molecular mass ranges.ProteomicsProf. Dr. Diego González-HalphenDepartamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico.PARTIALPolytomella Parvaalfredbiomed@gmail.com42209873 Ostolga-Chavarría M, Rico-Luna A, Fuentes-Hernández S, Miranda-Astudillo HV, Cabrera-Orefice A, González-Halphen D. Mitochondrial super complexes in the colorless chlorophycean alga Polytomella parva. J Bioenerg Biomembr. 2026 58(1):11 10.1007/s10863-026-10103-3Institute of Biochemistry, Justus-Liebig-University GiessenGermanyChlorophycean algae of the genera Chlamydomonas and Polytomella share a common photosynthetic ancestor. However, members of the Polytomella lineage have adopted a heterotrophic lifestyle, having lost the photosynthetic apparatus and relying instead on acetate or ethanol as carbon sources, with energy production centered on oxidative phosphorylation (OXPHOS). In this study, we investigated the composition of the mitochondrial supercomplexes of the colorless alga Polytomella parva. Mitochondrial membranes were solubilized using mild detergents such as glycol-diosgenin and digitonin, followed by separation of OXPHOS complexes supramolecular assemblies via Blue Native electrophoresis and Fast Protein Liquid Chromatography (FPLC). Additionally, complexome profiling of solubilized algal mitochondria resolved by Blue Native Gel Electrophoresis was carried out (data are available via ProteomeXchange with identifier PXD075371). The resulting data indicate that the OXPHOS supercomplexes of Polytomella closely resemble those observed in situ in the mitochondria of its green relative Chlamydomonas reinhardtii, as revealed by electron cryo-tomography and subtomogram averaging.Mitochondrial super complexes in the colorless chlorophycean alga Polytomella parva.Ostolga-Chavarría Marcos M, Rico-Luna Anaiza A, Fuentes-Hernández Sergio S, Miranda-Astudillo Héctor V HV, Cabrera-Orefice Alfredo A, González-Halphen Diego DfalseMitochondrial super complexes in the colorless chlorophycean alga Polytomella parvaChlorophycean algae of the genera Chlamydomonas and Polytomella share a common photosynthetic ancestor. However, members of the Polytomella lineage have adopted a heterotrophic lifestyle, having lost the photosynthetic apparatus and relying instead on acetate or ethanol as carbon sources, with energy production centered on oxidative phosphorylation (OXPHOS). In this study, we investigated the composition of the mitochondrial supercomplexes of the colorless alga Polytomella parva. Mitochondrial membranes were solubilized using mild detergents such as glycol-diosgenin and digitonin, followed by separation of OXPHOS complexes supramolecular assemblies via Blue Native electrophoresis and Fast Protein Liquid Chromatography (FPLC). Additionally, complexome profiling of solubilized algal mitochondria resolved by Blue Native Gel Electrophoresis was carried out. The resulting data indicate that the OXPHOS supercomplexes of Polytomella closely resemble those observed in situ in the mitochondria of its green relative Chlamydomonas reinhardtii, as revealed by electron cryo-tomography and subtomogram averaging.2026-06-012026-03-09PXD075371NEWT:6945NEWT:3555NEWT:2NEWT:157546NEWT:35554NEWT:38942NEWT:307972NEWT:32046NEWT:544496NEWT:2042546NEWT:45351NEWT:43179NEWT:4513NEWT:5722NEWT:55153NCBITaxon:10407NEWT:1736309NEWT:309800NEWT:1211601NEWT:876138NEWT:237561NEWT:5833NEWT:6928NEWT:10036NEWT:36745NEWT:1351NEWT:1438992NEWT:2649997NEWT:272563NEWT:224326NCBITaxon:79857NEWT:1096976NEWT:95648NEWT:3885NEWT:3888NEWT:1589NEWT:135622NEWT:6915NEWT:3649NEWT:101510NEWT:3880NEWT:272559NEWT:3641NEWT:383379NEWT:466585NEWT:10029NEWT:1000589NEWT:85963NEWT:85962NEWT:317447NEWT:7955NEWT:7959NEWT:2261NEWT:31156NEWT:398580NEWT:4565NEWT:1264690NEWT:515619NEWT:192875NEWT:34305NEWT:59729NCBITaxon:183674NEWT:224308NEWT:84645NEWT:626528NEWT:139927NEWT:4558NEWT:209285NEWT:1283NEWT:931281NEWT:4550NEWT:1000561NEWT:197NCBITaxon:79824NEWT:4787NCBITaxon:4563NEWT:5755NEWT:44689NEWT:3218NEWT:5759NEWT:1736231NEWT:1270NEWT:2242NEWT:4784NEWT:11320NEWT:360106NEWT:286NEWT:287NEWT:10117NEWT:10239NEWT:10116NEWT:1280NEWT:1735272NEWT:83334NEWT:83332NEWT:44685NEWT:317513NEWT:1148NEWT:580240NEWT:294128NEWT:11676NEWT:55571NEWT:100226NEWT:4530NEWT:4896NEWT:75058NEWT:13616NEWT:1094343NEWT:296543NEWT:1773NEWT:1895NEWT:1182590NEWT:935293NEWT:64152NEWT:4924NEWT:749200NEWT:990346NEWT:145953NEWT:257309NEWT:100816NEWT:263NEWT:230741NEWT:52283NEWT:284812NCBITaxon:1313NEWT:43330NEWT:1603293NEWT:408169NEWT:44544NEWT:4911NEWT:645463NEWT:3702NEWT:129249NEWT:243277NEWT:990119NEWT:408172NEWT:408170NEWT:493760NEWT:260710NEWT:257313NEWT:400772NEWT:3708NEWT:128161NEWT:332648NEWT:106592NEWT:536231NEWT:460519NEWT:1187947NEWT:1432138NEWT:10312NEWT:1424507NCBITaxon:1773NEWT:9598NEWT:8030NEWT:1639NEWT:188229NEWT:3818NEWT:480NEWT:4909NEWT:67767NEWT:432359NEWT:46835NEWT:1182263NEWT:2711NEWT:376686NEWT:95486NEWT:9103NEWT:29159NEWT:253NEWT:10306NCBITaxon:2759NEWT:1233435NEWT:8022NEWT:145943NCBITaxon:4932NEWT:595536NEWT:240906NEWT:593117NEWT:3635NEWT:5811NEWT:235443NEWT:272624NEWT:411483NEWT:884019NEWT:198215NEWT:411490NEWT:983964NEWT:169963NEWT:32644NEWT:499175NEWT:109779NEWT:476272NEWT:3747NEWT:195051NEWT:367830NEWT:1255228NEWT:178616NEWT:410289NEWT:373153NEWT:352472NEWT:357NEWT:360094NEWT:470NEWT:1313NEWT:411469NEWT:84023NEWT:559292NEWT:39491NCBITaxon:5811NEWT:411464NEWT:411460NEWT:2014887NEWT:2762NEWT:1174673NEWT:562NEWT:411470NEWT:33952NEWT:2094720NCBITaxon:2697049NEWT:571256NEWT:28038NEWT:1663NEWT:1423NEWT:4932NEWT:3603NEWT:2759NEWT:3847NEWT:327159NEWT:178876NEWT:327160NEWT:573NEWT:9031NEWT:7091NEWT:241368NEWT:42528NEWT:190802NEWT:9778NEWT:150475NEWT:303NEWT:9417NEWT:7111NEWT:347515NEWT:1216979NEWT:5180NEWT:256737NEWT:115104NEWT:1121114NEWT:663NEWT:1081927NEWT:1238993NEWT:67825NEWT:185579NEWT:941442NEWT:220668NEWT:13076NEWT:1249668NEWT:317NEWT:7227NEWT:7469NEWT:885318NEWT:9402NEWT:415540NEWT:550NEWT:675060NEWT:4081NEWT:334542NEWT:554NEWT:98334NEWT:426428NEWT:7574NEWT:1715256NEWT:7215NEWT:575412NEWT:29204NEWT:2172103NEWT:507601NEWT:643680NCBITaxon:6157NEWT:746360NEWT:6239NEWT:470150NEWT:216257NEWT:102169NEWT:9986NEWT:4054NEWT:73239NEWT:226186NEWT:1268063NEWT:8782NEWT:1263854NEWT:435590NEWT:1902NEWT:160488NEWT:28104NEWT:1908NCBITaxon:2NEWT:985076NEWT:1215323NEWT:52641NEWT:7038NEWT:6192NEWT:28532NCBITaxon:38727NEWT:353152NEWT:2829NEWT:366581NEWT:216599NEWT:216595NEWT:243230NEWT:8355NEWT:9685NEWT:7029NEWT:1080772NEWT:1283300NEWT:6183NEWT:6063NEWT:334747NEWT:61235NEWT:6289NEWT:436486NEWT:6287NEWT:300641NEWT:727NEWT:9796NEWT:725NEWT:170187NEWT:260707NCBITaxon:6191NEWT:1836NEWT:185431NEWT:29760NEWT:260704NEWT:703612NEWT:260705NEWT:80863NEWT:2697049NEWT:105231NEWT:1216981NCBITaxon:6073NEWT:884204NEWT:6279NEWT:1123869NEWT:9544NEWT:7370NEWT:83906NEWT:607699NEWT:6282NEWT:208964NEWT:1134506NEWT:575584NEWT:38783NEWT:8727NEWT:4006NEWT:8726NEWT:6426NEWT:6669NEWT:10090NEWT:4120NEWT:51515NEWT:5693NEWT:8724NEWT:51511NEWT:92867NEWT:8723NEWT:5334NEWT:37334NEWT:382352NCBITaxon:10359NEWT:242619NEWT:632957NEWT:34073NEWT:373995NEWT:5689NEWT:544404NEWT:9925NEWT:8839NEWT:4232NEWT:2758385NEWT:4113NEWT:837NEWT:11298NEWT:171101NEWT:714NEWT:421932NEWT:196627NEWT:5691NEWT:48479NEWT:627025NEWT:1097677NEWT:61674NEWT:1117957NEWT:9913NEWT:4100NEWT:1076NEWT:6763NEWT:803NEWT:29722NEWT:380394NEWT:1692259NEWT:180066NEWT:135588NEWT:1843183NEWT:58002NEWT:326423NEWT:4577NEWT:1416333NEWT:5664NEWT:2157NEWT:1678078NEWT:749906NEWT:418985NEWT:146479NEWT:1911079NEWT:69373NEWT:264203NEWT:1480154NEWT:1274414NEWT:27606NEWT:59202NEWT:9975NEWT:9612NEWT:38865NEWT:51953NEWT:3197NEWT:9615NEWT:10299NEWT:860688NEWT:36329NEWT:1147787NCBITaxon:3044782NEWT:72407NEWT:349741NEWT:9605NEWT:9606NEWT:157295NEWT:641501NEWT:7668NEWT:915099NEWT:74940NEWT:9721NEWT:137221NEWT:1450511NEWT:1143193NEWT:411901NEWT:9838NEWT:105884NCBITaxon:9615NEWT:9839NEWT:58334NEWT:1193501NEWT:3055NEWT:58331NEWT:6326NEWT:6689NEWT:5476NEWT:299767NEWT:1274432NEWT:1274426NEWT:70448NEWT:9825NEWT:1274423NEWT:393765NEWT:698936NEWT:39946NEWT:9823NEWT:9940NEWT:521001NEWT:39947NEWT:1274420NEWT:578458422098730000-0002-2042-3794