MetaboLightsapplication/xmlftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS12252/m_MTBLS12252_LC-MS_positive_hilic_metabolite_profiling_v2_maf.tsvftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS12252/m_MTBLS12252_LC-MS_negative_hilic_metabolite_profiling_v2_maf.tsvftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS12252/i_Investigation.txtftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS12252/a_MTBLS12252_LC-MS_negative_hilic_metabolite_profiling.txtftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS12252/s_MTBLS12252.txtftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS12252/a_MTBLS12252_LC-MS_positive_hilic_metabolite_profiling.txtftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS12252/FILES/DERIVED_FILES/NEG/ST587_2.mzXMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS12252/FILES/DERIVED_FILES/NEG/ST1271_2.mzXMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS12252/FILES/DERIVED_FILES/POS/ST015_1.mzXMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS12252/FILES/DERIVED_FILES/POS/ST1271_1.mzXMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS12252/FILES/DERIVED_FILES/NEG/ST015_3.mzXMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS12252/FILES/DERIVED_FILES/POS/ST015_2.mzXMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS12252/FILES/DERIVED_FILES/NEG/ST015_1.mzXMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS12252/FILES/DERIVED_FILES/POS/ST587_3.mzXMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS12252/FILES/DERIVED_FILES/POS/ST1271_4.mzXMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS12252/FILES/DERIVED_FILES/NEG/ST1271_3.mzXMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS12252/FILES/DERIVED_FILES/POS/ST015_4.mzXMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS12252/FILES/DERIVED_FILES/POS/ST587_4.mzXMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS12252/FILES/DERIVED_FILES/NEG/ST1271_1.mzXMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS12252/FILES/DERIVED_FILES/NEG/ST015_2.mzXMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS12252/FILES/DERIVED_FILES/POS/ST1271_2.mzXMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS12252/FILES/DERIVED_FILES/NEG/ST015_4.mzXMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS12252/FILES/DERIVED_FILES/NEG/ST587_3.mzXMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS12252/FILES/DERIVED_FILES/POS/ST587_1.mzXMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS12252/FILES/DERIVED_FILES/NEG/ST1271_4.mzXMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS12252/FILES/DERIVED_FILES/POS/ST587_2.mzXMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS12252/FILES/DERIVED_FILES/NEG/ST587_1.mzXMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS12252/FILES/DERIVED_FILES/NEG/ST587_4.mzXMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS12252/FILES/DERIVED_FILES/POS/ST015_3.mzXMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS12252/FILES/DERIVED_FILES/POS/ST1271_3.mzXMLprimaryOK200ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS12252<p>The raw data were converted to the mzXML format using ProteoWizard and processed with an in-house program. which was developed using R and based on XCMS, for peak detection, extraction, alignment and integration. The R package and the BiotreeDB(V3.0) were applied in metabolite identification.</p>MetaboLightsPublicLiquid Chromatography MS - positive - hilicLiquid Chromatography MS - negative - hilic<p>For polar metabolites, LC-MS/MS analyses were performed using an UHPLC system (Vanquish, Thermo Fisher Scientific) with a Waters ACQUITY UPLC BEH Amide (2.1 mm x 100 mm, 1.7 μm) coupled to Orbitrap Exploris 120 mass spectrometer (Orbitrap MS, Thermo). The mobile phase consisted of 25 mmol/L ammonium acetate and 25 ammonia hydroxide in water (pH = 9.75) (A) and acetonitrile (B). The auto-sampler temperature was 4 °C and the injection volume was 2 μL.</p>Reprogramming yeast metabolism for customized starch-rich micro-grain through low-carbon microbial manufacturing.Zhihui ShiTianjin Institute of Industrial Biotechnology, Chinese Academy of SciencesWhole Organismmass spectrometry assay<p>The cell pellets (107 cells) were taken, mixed with 1000 uL of extraction solution (MeOH:ACN:H2O, 2:2:1 (v/v)), the extraction solution contain deuterated internal standards, the mixed solution were vortexed for 30s. Add 2 homogenization beads and homogenize for 4 min (35 Hz), then transferred to an ice-water bath to sonicate for 5 min. (Repeat 3 times) The samples were then allowed to thaw at room temperature and vortexed for 30 s. This freeze–thaw cycle was repeated three times.Then the samples were sonicated for 10 min in 4 °C water bath, and incubated for 1 h at -40 °C to precipitate proteins. The samples were centrifuged at 12000 rpm (RCF=13800(×g), R= 8.6cm) for 15 min at 4 °C. The supernatant was transferred to a fresh glass vial for analysis. The quality control (QC) sample was prepared by mixing an equal aliquot of the supernatant of samples.</p>Yarrowia lipolyticahttps://www.ebi.ac.uk/metabolights/MTBLS12252Wang Guokun. Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences. wanggk@tib.cas.cn.Shi Zhihui. Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences. shizhh@tib.cas.cn.<p>The raw data were converted to the mzXML format using ProteoWizard and processed with an in-house program. which was developed using R and based on XCMS, for peak detection, extraction, alignment and integration. The R package and the BiotreeDB(V3.0) were applied in metabolite identification.</p>strainshizhihui18@mails.ucas.ac.cn<p>Metabolomic samples were prepared by cultivating strains in MMA medium in shake flasks for 36 h. Biological quadruplicates were performed for each strain (ST015, ST587 and ST1271). Cell pellets were collected from 2 mL of culture by centrifugation at 5000 rpm and washed twice with PBS and then rapidly frozen in liquid nitrogen.</p>MetabolomicsMetabolic Engineeringuntargeted metabolitesAgricultureAcetateMicroorganismlignocelluloseMetabolic Engineeringuntargeted metabolitesAgricultureAcetateMicroorganismlignocellulose<p>The Orbitrap Exploris 120 mass spectrometer was used for its ability to acquire MS/MS spectra on information-dependent acquisition (IDA) mode in the control of the acquisition software (Xcalibur, Thermo). In this mode, the acquisition software continuously evaluates the full scan MS spectrum. The ESI source conditions were set as following: sheath gas flow rate as 50 Arb, Aux gas flow rate as 15 Arb, capillary temperature 320 °C, full MS resolution as 60000, MS/MS resolution as 15000, collision energy: SNCE 20/30/40, spray voltage as 3.8 kV (positive) or -3.4 kV (negative), respectively.</p>falseReprogramming yeast metabolism for customized starch-rich micro-grain through low-carbon microbial manufacturing<p>Starch is a primary food ingredient and bulk industrial feedstock. Producing starch through fermentation-based low-carbon microbial manufacturing serves as an arable land-independent and carbon-neutral/negative approach, while the efficiency of this route is highly dependent on the starch producer. We reconfigure the oleaginous yeast as an efficient cell factory for starch-rich micro-grain production by rewiring the starch biosynthesis and gluconeogenesis pathways and regulating cell morphology. With the CO2 electro-synthesized acetate as the substrate, the strain accumulates starch up to 47.18% of the dry cell weight. Through the cultivation of the micro-grain in fed-batch bioreactors, starch was produced at 19.30 g/L, 29.60% starch content, and spatial-temporal productivity (243.7 g/m2/d), approximately 50-fold higher than that of crop cultivation and an order of magnitude higher rate (160.83 mg/L/h) than the starch production in other microbes. We validated that the starch composition and starch-protein ratio in the micro-grain can be modulated by strain and process engineering. More surprisingly, we found that the engineered artificial strains adopted a cellular resources reallocation strategy to ensure high-level starch production in micro-grain, and could facilitate a highly efficient straw/cellulose-to-starch conversion. Our work lays the foundation for understanding the global cellular machinery for starch biosynthesis and enables a superior-to-nature high-level production of starch with customized composition, aiding the development of efficient and low-carbon production of nutritional resources.</p>2025-03-032025-02-23MTBLS12252