MetaboLights

application/xml

ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS8088/m_MTBLS8088_LC-MS_positive_reverse-phase_v2_maf.tsvftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS8088/m_MTBLS8088_LC-MS_MSMS_negative_reverse-phase_v2_maf.tsvftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS8088/m_MTBLS8088_LC-MS_MSMS_positive_reverse-phase_v2_maf.tsvftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS8088/m_MTBLS8088_LC-MS_negative_reverse-phase_v2_maf.tsvftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS8088/a_MTBLS8088_LC-MS_MSMS_positive_reverse-phase.txtftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS8088/s_MTBLS8088.txtftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS8088/a_MTBLS8088_LC-MS_negative_reverse-phase.txtftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS8088/a_MTBLS8088_LC-MS_positive_reverse-phase.txtftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS8088/a_MTBLS8088_LC-MS_MSMS_negative_reverse-phase.txtftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS8088/i_Investigation.txtprimaryOK200ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS8088MS/MS-based metabolite annotationAdditional Auto-MS/MS and All-Ions MS analyses were performed using collision energies ranging from 10 to 40 V to support systematic annotation of phenolic metabolites in Mesotaenium extracts. Metabolite annotation was conducted as follows: molecular formulas of precursor and fragment ions were calculated based on monoisotopic mass; diagnostic fragments were identified through searches in METLIN, KEGG, and PubChem databases, as well as available literature; conjugated metabolite forms were manually predicted based on MS/MS spectral interpretation, considering neutral losses, retention times, and ionization modes and All MS/MS spectra were imported into an in-house compound database and library (Agilent PCDL; Meso_database). Putative metabolite annotations were assigned according to the guidelines of the Metabolomics Standards Initiative (MSI), corresponding primarily to Level 2 identification based on accurate mass and MS/MS fragmentation pattern matching. To facilitate structural interpretation, newly detected metabolites were further classified according to diagnostic fragment similarity and inferred core scaffolds. Four structural classes were defined: Class I – coumarins (C8H6O3, chromen-2-one core); Class II – furanocoumarins (C12H8O5), Class III – biscoumarins (C12H6O6), and Class IV – phenolic benzochromenone-type metabolites (C13H8O5, Trihydroxy-benzo[c]chromen-6-one-like). This fragment-based classification was used to group structurally related metabolites and highlight potentially novel phenolic scaffolds detected in Mesotaenium extracts under UV stress. All annotated metabolites and associated parameters are listed in Table S1 of the paper associated to the study.MetaboLightsPublicLiquid Chromatography MS - negative - reverse-phaseLiquid Chromatography MS - positive - reverse-phaseSamples were analyzed using an ultra-high-performance liquid chromatography (UHPLC) system (1290 Infinity, Agilent Technologies, Santa Clara, CA, USA). A volume of 2 μL was injected onto an Acquity HSS T3 column (1.8 μm, 2.1 × 100 mm; Waters Corporation, Milford, USA) maintained at 40 °C. Metabolites were eluted at a flow rate of 0.5 mL/min using a binary gradient of water (0.1% formic acid) and acetonitrile (0.1% formic acid), as previously described[1]. Ref:[1] Feussner, K., Abreu, I.N., Klein, M. and Feussner, I., 2023. Metabolite fingerprinting: A powerful metabolomics approach for marker identification and functional gene annotation. In Methods in enzymology (Vol. 680, pp. 325-350). Academic Press.Chemodiverse cell system responses to UV in an algal sister of land plants. 10.1016/j.cub.2026.04.015.Cäcilia KunzIlka AbreuDept. Plant Biochemistry, Universität GöttingenDepartment of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goettingen 37077, GermanyWhole Organismmass spectrometry assayCultures were transferred into Eppendorf tubes and lyophilized overnight. 2 tungsten beads were added to each tube, and the material was pulverized using a Mixer Ball Mill MM400 (Retsch). Approximately 5 mg of dried and homogenized algal material was extracted with 500 μL of 70% (v/v) methanol, following the protocol previously described[1]. After centrifugation, 200 μL of the supernatant was transferred to an LC vial and dried using a SpeedVac. Prior to analysis, samples were reconstituted in 20 μL methanol and subsequently diluted with 60 μL Milli-Q H2O. Ref:[1] Kelly, A.A., Fulda, M., Aden, M., Abreu, I.N., Feussner, K. and Feussner, I., 2026. Reducing the Sinapine Levels of Camelina sativa Seeds Through Targeted Genome Editing of REF1. Plant Biotechnology Journal, 24(3), pp.1839-1865.Mesotaenium endlicherianumhttps://www.ebi.ac.uk/metabolights/MTBLS8088Jan de Vries. University of Göttingen. devries.jan@uni-goettingen.de.Ilka Abreu. Christian-Albrechts-Universität zu Kiel. i.abreu@plantnutrition.uni-kiel.de.Tatyana Darienko.Ivo Feussner.Kirstin Feussner.Maike Lorenz.Cäcilia Kunz. caeciliafelicitas.kunz@uni-goettingen.de.Janine Fürst-Jansen.Raw MS data were processed using MassHunter Profinder B.08.00 (Agilent Technologies) employing recursive feature extraction, as previously described[1]. The resulting dataset was normalized to sample dry weight and subjected to statistical analysis using MetaboAnalyst 6.0.63. Ref:[1] Kasper, K., Abreu, I.N., Feussner, K., Zienkiewicz, K., Herrfurth, C., Ischebeck, T., Janz, D., Majcherczyk, A., Schmitt, K., Valerius, O. and Braus, G.H., 2022. Multi-omics analysis of xylem sap uncovers dynamic modulation of poplar defenses by ammonium and nitrate. The Plant Journal, 111(1), pp.282-303.UVTimecaeciliafelicitas.kunz@uni-goettingen.dei.abreu@plantnutrition.uni-kiel.deThe earliest land plants had to dynamically adjust to rapidly changing environmental conditions[1]. We worked with the unicellular, genome-sequenced[2][3] zygnematophyte Mesotaenium endlicherianum SAG 12.97 (Me), one of the closest algal relatives of land plants (Figure 1A of the paper associated to this study). The algae were grown at 80-90 μmol photons m^2/s for 7 d. 24 h before experimental start, they were transferred to the experimental setup, where they were subjected to 50±10 μmol photons m^2/s (Figure 1B of the paper associated to this study). Upon experimental start, ultraviolet (UV) specimens were exposed to 3 h of 1.7-2.9 W m^-2 UV radiation with a peak in the UV-B spectrum (at 311 nm, Figure S1A of the paper associated to this study).  Cultivation of algae on solid mediumFor stock culturing, M. endlicherianum was stored on solid Bold’s Basal Medium (BBM) with vitamins and triple nitrate (3NBBM+ V) according to the recipe described before[4](see also[5][6]) at 15 °C under full-spectrum fluorescent lamps (5-10 μmol photons m^2/s; constant light). Stock cultures between 21 and 28 d were used for the inoculation of experimental plates. For the UV-B exposure experiments, the plates were grown at 80-90 μmol photons m^2/s (Niello LED 300W, 380-740 nm spectrum; Figure S1A) for 7 d with a 16/8 h light/dark cycle, before being transferred to the UV setup location for 24 h acclimation before the experiments. Experimental set-upThe UV setup used the same grow lights as previously described in addition to two UV-B lamps used in conjunction, the UV-B Broadband TL fluorescent tube lamp with a UV-B spectrum of 290 to 315 nm, and the UV-B Narrowband TL fluorescent tube lamp with a UV-B spectrum between 305 and 315 nm, which peaks at 311 nm (lamp wattage: 40 W and 20 W; length: 1213.6 mm and 604 mm respectively, Philips, the Netherlands; spectrum Figure S1A). They produced a UV-B intensity ranging from 1.7-2.9 W m^-2, depending on location of the individual petri dish. The photosynthetically active radiation (PAR) values were 40-50 μmol photons m^2/s and 50-60 μmol photons m^2/s for UV-B and control, respectively. While PAR was applied with the previous 16/8 h light/dark cycle, for UV treated samples UVR was applied for 3 h (Figure 1B) To reduce condensation on the lids of the petri dishes, fans were installed to create air circulation. Temperature and humidity were monitored using a Tempo Disc (BlueMaestro). The temperature and humidity ranged from 17.2 °C to 20.6 °C with an average of 19.2 °C and 29.7 % to 51.3 % with an average of 40.4 %, respectively. 10 min before the experiment started, the micropore tape around all the plates and the lid were removed, to avoid UV-B irradiation being filtered out by the plastic lid, as contamination within the following max. 6 h can be neglected. Sampling was performed as follows: 2 plates at each time point of the experiment were taken out of both settings, Mesotaenium was removed from the cellophane and 1/4 of each plate pooled (depending on setting) for transcriptomics and 3/4 of each plate pooled for metabolite analysis. Pooling was done to balance the varying irradiation intensity. Samples were frozen immediately using liquid N2 and stored at -70 °C, to stop any (non-) enzymatic reaction which would distort the results. The experiments were repeated three times to obtain biological triplicates. Refs:[1] Fürst-Jansen, J.M., de Vries, S. and de Vries, J., 2020. Evo-physio: on stress responses and the earliest land plants. Journal of Experimental Botany, 71(11), pp.3254-3269.[2] Cheng, S., Xian, W., Fu, Y., Marin, B., Keller, J., Wu, T., Sun, W., Li, X., Xu, Y., Zhang, Y.U. and Wittek, S., 2019. Genomes of subaerial Zygnematophyceae provide insights into land plant evolution. Cell, 179(5), pp.1057-1067.[3] Dadras, A., Fürst-Jansen, J.M., Darienko, T., Krone, D., Scholz, P., Sun, S., Herrfurth, C., Rieseberg, T.P., Irisarri, I., Steinkamp, R. and Hansen, M., 2023. Environmental gradients reveal stress hubs pre-dating plant terrestrialization. Nature Plants, 9(9), pp.1419-1438.[4] Schlösser, U.C., 1997. Additions to the culture collection of algae since 1994. Botanica Acta, 110 (5), pp.424-429.[5] HC, B., 1963. Some soil algae from Enchanted Rock and related algal species. Phycological Studies IV. University of Texas Publ. No. 6318, 6318, pp.1-95.[6]Starr, R.C. and Zeikus, J.A., 1993. UTEX--The culture collection of algae at the University of Texas at Austin. Metabolomicsall ions fragmentation DIA alignmentMetabolomicsLevel 2 Metabolite Identification Confidencehigh-resolution mass spectrometrypositive polarityuntargeted analysisnegative ionization polarityAgilent 1290 Infinity HPLCAgilent 6546Agilent 1290 Infinity II UHPLCfingerprintinglevel 2 metabolitestressHigh-resolution massAgilent 6546 LC/Q-TOFQTOF MSUV light regimenNegative modeall ions fragmentationpositive modedata-dependent acquisitionWhole Organismexperimental sampleplant evolutionmolecular responses to UVuntargeted metabolite profilingQTOF-MSagilent 1290Mesotaenium endlicherianumall ions fragmentation DIA alignmentMetabolomicsLevel 2 Metabolite Identification Confidencehigh-resolution mass spectrometrypositive polarityuntargeted analysisnegative ionization polarityAgilent 1290 Infinity HPLCAgilent 6546Agilent 1290 Infinity II UHPLCfingerprintinglevel 2 metabolitestressHigh-resolution massAgilent 6546 LC/Q-TOFQTOF MSUV light regimenNegative modeall ions fragmentationpositive modedata-dependent acquisitionWhole Organismexperimental sampleuntargeted metabolite profilingplant evolutionmolecular responses to UVQTOF-MSagilent 1290Mesotaenium endlicherianumThe analysis was carried on using a a quadrupole time-of-flight mass spectrometer (QTOF-MS; 6546 UHD Accurate-Mass QTOF, Agilent Technologies). High-resolution accurate mass spectra were acquired over a mass range of m/z 80-1700 using an electrospray ionization source operated in both positive and negative ionization modes. L-PhenylalanineSucrosedihydroxycoumarin carboxylate (chromenone-like) O-HexosideLGPL-LPE(18:3)Coumarin (dibenzo-pyrone)_like scaffold Hexose-Hexose acidHydroxy-Methoxypsoralen-like derivativeLGGL-LDGDG(16:2)L-arginineGlutamate-TyrosineCoumarin (dibenzo-pyrone)-like scaffold di-HexoseL-ThreonineN-Acetyl-LL-2;6-diaminoheptanedioateHydroxy Methoxypsoralen-like - Hexose4-GuanidinobutanoateLGPL-LPE(16:1)Methyl 7-deshydroxypyrogallin-4-carboxylate - HexoseHydroxyMethoxypsoralen-like-Hydroxyglutaric AcidHydroxy-Methoxypsoralen-like Hexose - Hexose acidL-LeucineLGGL-LDGDG(18:3)5-METHYLTHIOADENOSINE2-(6'-methylthio)hexylmalateLGPL-LPE(16:2)5'-deoxyadenosinecytidineTAG(52:11)LGPL-LPS(22:0)Trihydroxy-benzo[c]chromen-6-one-like-O-Hexoside- SerineGMPL-ProlineS-adenosyl-L-homocysteineDAG(34:8)TAG(54:14)Trihydroxy-benzo[c]chromen-6-one-like-O-Hexoside - ProlineUnkownDigalloylhamamelofuranoseGlycerophosphocholinephosphocholineacetyl-L-glutamate 5-semialdehydeL-methionineGalactonic acid5-HydroxyectoineN-acetyl-L-glutamate 5-semialdehydeDGTS(32:7)HydroxyMethoxypsoralen-like- C2H4O3Pyroglutamic acidXyluloseTrihydroxy-benzo[c]chromen-6-one-like-O-Hexoside - PhenylalanineL-TryptophanMiraxanthin-VGlcCer(37:3)2-KetovalineLGPL-LPE(24:2)PG(44:3)Trihydroxy-benzo[c]chromen-6-one-like-O-Hexoside - TyrosineL-GlutamineguanosineCholineAsparagineLGGL-LMGDG(16:2)(S)-2-acetolactateL-ValineAdenosinMethyl-beta-D-galactopyranosideL-arginino-succinateTrihydroxy-benzo[c]chromen-6-one-like-O-Hexoside - lysineHydroxy Methoxypsoralen-like - Hexose_glucosaminePsoralen-like HexoseLGPL-LPA(22:0)PI(32:5)Pipecolic acid2-(6 methylthio)hexylmalate4-hydroxysphinganineTrihydroxy-benzo[c]chromen-6-one-like-O-Hexoside- GlutamateLGPL-LPS(18:0)S-lactoyl-glutathioneTyrosineHydroxyquinolLGPL-LPA(28:0)Hydroxy-Methoxypsoralen-like- Hexose-C5H6O5Carnitinehydroxycoumarin carboxylic acid_likeHydroxy Methoxypsoralen-like - Hexose-dimer4-GuanidinobutanalAcetylprolinGABAL-GlutamateTrihydroxy-benzo[c]chromen-6-one-like-O-Hexosideporphobilinogen2-Aminoadipic acidD-Galactitol 1-phosphateglutathioneSerineTrihydroxy-benzo[c]chromen-6-one-like-O-Hexoside- AlanineProtochlorophyllideMGDG(48:7)indole-3-acetyl-valine11-hydoxyundecanamideGlcCer(36:1)Hydroxy-Methoxypsoralen-like malate - C9H10N2O2Uridine 5'-diphosphateGlycero Phosphocoline3-Dihydroxybenzoic acidN-hydroxy-L-tryptophanCer(35:5)Hydroxy-Methoxypsoralen-like di HexoseCoumarin (dibenzo-pyrone)-like - HexoseGlcCer(42:2)diaminopimelate6-Anhydro-beta-D-glucoseAdenosine monophosphateTrihydroxy-benzo[c]chromen-6-one-likeGlyceryl-trimethylhomoserineN-Hydroxy-L-valineNADPE(30:1)GlcCer(33:3DGDG(36:5)uracilfalseChemodiverse cell systems responses to UV in an algal sister of land plantsPlant terrestrialization necessitated overcoming a barrage of stressors. Embryophytes (land plants) use an integrated response network to adjust their molecular physiology in response to terrestrial stressors—one of the important stressors is UV irradiance. The zygnematophytes are the closest streptophyte algal relatives of embryophytes, renowned for their UV resilience and key for inferring the UV response toolkit of the earliest embryophytes. Throughout evolution, specialized metabolism radiated, yielding chemodiverse responses to environmental challenges ranging from UV-shielding flavonoids and coumarins to the polymer lignin of tracheophytes16; homologs of the underpinning core pathway occur in streptophyte algae. Here, we exposed the zygnematophyte Mesotaenium to UV-B irradiation and profiled its physiological, morphological, transcriptomic, and metabolomic features. After UV-B exposure, the cells showed rapid photophysiological responses and progressively growing terminal vacuoles. Our transcriptome data capture dynamic changes in gene expression in (1) core downstream homologs of phenol metabolic enzymes, photophysiological homeostats, and DNA repair factors and (2) upstream components featuring key homologs of kinase-mediated signaling cascades, as well as light quality and abscisic acid-mediated signaling components. To scrutinize the acclimatory chassis, we created a metabolite feature database specifically for the Mesotaenium metabolome. The metabolome displayed pronounced temporal shifts, with several phenolic features that accumulate along the UV-stress–acclimation kinetics. Overall, we capture chemodiverse responses, including various phenolics such as methoxypsoralen-like derivatives and coumarins. We establish an integrated model for UV responses in the closest algal relatives of embryophytes, illuminating the toolkit that allowed the progenitors of embryophytes to move out of a protective water column.2026-07-012026-06-30MTBLS8088