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KramerMass SpectrometryShotgun proteomicsNot availableSynechocystis sp. pcc 6803LcmseProteomicshttp://www.ebi.ac.uk/pride/archive/projects/PXD001619Sampling from the PBRs for protein analysis was performed as follows: 10 ml of cell suspension from the vessel were harvested via a sampling port with a syringe into a 15 ml tube (on ice) that already contained 5 ml of ice-cold 50 mM ammonium bicarbonate (Fluka BioUltra >99.5 %). For samples from the dark period the tubes were thoroughly covered with aluminium foil. Cells were pelleted by centrifugation at 6000 rpm at 4 °C for 10 min. centrifuge). The supernatant was discarded completely and cells were re-suspended in 1 ml of ice-cold 50 mM ammonium bicarbonate and frozen rapidly in liquid N2 and stored at -20 °C. Prior to the opening by sonication, the cell suspension was supplemented with 0.1 % (w/v) Rapigest SF (Waters). Cell lysis was performed by 1 round of sonication with a micro-tip (duration for 5 min, output strength of 5, and a 50 % duty cycle by a probe-sonicator (Branson) on melting ice. Cell debris was pelleted by centrifugation at 14000 rpm at 4 °C for 30 min (in a pre-chilled table top-centrifuge). The protein content of the supernatant, containing the soluble fraction of the crude cell free extract, was immediately determined by a BCA assay using bovine serum albumin as the standard according to the manufacturers protocol (Pierce). Lysates were brought to same concentrations (0.5 mg/ml) by diluting with 0.1 % Rapigest SF in 50 mM ammonium bicarbonate. Subsequently, samples were reduced with 5 mM dithiothreitol (Sigma-Aldrich) at 60 °C for 30 min and alkylated with 15 mM iodoacetamide (Sigma-Aldrich) at ambient temperature in the dark for 30 min. Proteolytic digestion was initiated by addition of modified trypsin gold grade (Promega, Madison WI) at a 1:50 protease:protein (ratio by weight), followed by overnight incubation at 37 °C. Following digestion, breakdown of the acid-labile detergent (Rapigest SF) was induced by the addition of 1 % trifluoroacetic acid to achieve a pH<2 and subsequent incubation at 37 °C for 45 min. The peptide solutions were centrifuged at 13,000 rpm for 10 min and supernatant was collected. Prior to analyses a protein digest MassPREP Protein Digestion Standard (Waters Corporation) was added, at 1:1 dilution to the sample (50 fmol/µl alcohol dehydrogenase (ADH1) and enolase (ENO) from Saccharomyces cerevisiae). Nanoscale LC separations of tryptic peptides were performed with a NanoAcquity system (Waters Corporation). Samples were loaded onto a Symmetry C18 5 µm, 2 cm x 180 µm trap column (Waters Corporation) at a flow rate of 5 µl/min prior to separation on a Bridged Ethyl Hybrid C18 1.7 µm, 25 cm x 75 µm analytical reversed phase column (Waters Corporation) by application of a 90 minute gradient from 1 % acetonitrile, 0.1 % formic acid to 40 % acetonitrile, 0.1 % formic acid at a column flow rate of 0.300 µl/min. Analysis of eluting tryptic peptides was performed using a Synapt G2 quadrupole time of flight mass spectrometer (Waters Corporation, Manchester, UK) equipped with a nanolockspray source (Waters Corporation) fitted with a pico-tip emitter (New Objective, Woburn, MA). Operated values: around 3 kV capillary voltage, cone voltage of 40 eV, a source temperature of 90 °C and TOF-voltage set at 7 kV. The collision gas used was argon, maintained at a constant pressure of 2.0x10-3 mbar in the collision cell. The lock mass, [Glu1]-Fibrinopeptide B, was delivered from the auxiliary pump of the NanoAcquity system at a concentration of 100 fmol/µl at 0.5 µl/min to the reference sprayer of the nanolockspray source which was sampled every 120 seconds. The data were post-acquisition lock-mass corrected using the monoisotopic mass of the doubly charged precursor of [Glu1]-Fibrinopeptide B. Accurate mass precursor and fragment ion LC-MS data were collected in data independent LCMSE mode of acquisition [14, 15]. Samples of the two Bioreactors, each sampled over 2 days at five time-points (total of 20 samples) were injected twice (technical replicates) to ascertain the reproducibility of the mass spectrometric analysis.PrideMS1 intensity based label-free quantification methodiodoacetamide derivatized residuemonohydroxylated residueContinuum LC-MS data were processed using ProteinLynx GlobalSERVER version 2.5 (PLGS 2.5, Waters Corporation). Parameter settings: digest reagent trypsin, allow 1 ‘missed cleavage’, search tolerances automatic, typically 5 ppm for precursor and 15 ppm for product ions, fixed modification cysteine carbamidomethylation, and variable modification methionine oxidation. Protein identifications were obtained searching the entries of a Synechocystis proteome database (UniProt), with ADH1 and ENO1 of S. cerevisiae appended as internal standard to address technical variation and allow for absolute quantitation of protein amounts. Estimation of false-positive identification rates was done by searching a randomized version of the abovementioned human protein database generated within PLGS 2.5. HI3 peptide quantitation was used to quantify fmoles (label free absolute quantitation) of each protein measured by use of the known amounts of the added Massprep standards [16]. Data were exported as csv-files and fmoles determined by HI3 peptide quantitation were normalized by summed fmoles determined for each LC-MS run to adjust for variability in sample content and instrument performance. A protein was required to be detected a minimum of 9 (out of 40) injections to be regarded as reliably identified and quantified, which lead to identification of 357 Synechocystis proteins with a false discovery rate of <1% as determined by the number of identifications from the randomized database (data not shown). As the data acquired needed to reflect the protein profile over the whole time series to probe the diurnal rhythm of Synechocystis, we applied a second round of selection criteria: i.e. proteins needed to be detected over all time points measured, and be detected in both technical replicates for both the PBRs. This provided a list of 176 proteins for which the normalized fmoles (nfmol) are shown in Supplemental material table S1.ProteomicsJ.M.F.G. AertsSynapt G2 MSPARTIALClinical Proteomics Facility, Medical Biochemistry, Academic Medical Center, University of AmsterdamSynechocystis Sp. Pcc 680327208121 Angermayr SA, van Alphen P, Hasdemir D, Kramer G, Iqbal M, van Grondelle W, Hoefsloot HC, Choi YH, Hellingwerf KJ. Culturing Synechocystis sp. Strain PCC 6803 with N2 and CO2 in a Diel Regime Reveals Multiphase Glycogen Dynamics with Low Maintenance Costs. Appl Environ Microbiol. 2016 Jun 30;82(14):4180-9. Print 2016 Jul 15 10.1128/AEM.00256-16gertjan.kramer@dkfz-heidelberg.deTechnicalBiologicalProteomics of Stem Cells and Cancer.University Clinic Heidelberg.German Cancer Research Center.Im Neuenheimer Feld 581Heidelberg, Germany.Germany<h4>Unlabelled</h4>Investigating the physiology of cyanobacteria cultured under a diel light regime is relevant for a better understanding of the resulting growth characteristics and for specific biotechnological applications that are foreseen for these photosynthetic organisms. Here, we present the results of a multiomics study of the model cyanobacterium Synechocystis sp. strain PCC 6803, cultured in a lab-scale photobioreactor in physiological conditions relevant for large-scale culturing. The culture was sparged with N2 and CO2, leading to an anoxic environment during the dark period. Growth followed the availability of light. Metabolite analysis performed with (1)H nuclear magnetic resonance analysis showed that amino acids involved in nitrogen and sulfur assimilation showed elevated levels in the light. Most protein levels, analyzed through mass spectrometry, remained rather stable. However, several high-light-response proteins and stress-response proteins showed distinct changes at the onset of the light period. Microarray-based transcript analysis found common patterns of ∼56% of the transcriptome following the diel regime. These oscillating transcripts could be grouped coarsely into genes that were upregulated and downregulated in the dark period. The accumulated glycogen was degraded in the anaerobic environment in the dark. A small part was degraded gradually, reflecting basic maintenance requirements of the cells in darkness. Surprisingly, the largest part was degraded rapidly in a short time span at the end of the dark period. This degradation could allow rapid formation of metabolic intermediates at the end of the dark period, preparing the cells for the resumption of growth at the start of the light period.<h4>Importance</h4>Industrial-scale biotechnological applications are anticipated for cyanobacteria. We simulated large-scale high-cell-density culturing of Synechocystis sp. PCC 6803 under a diel light regime in a lab-scale photobioreactor. In BG-11 medium, Synechocystis grew only in the light. Metabolite analysis grouped the collected samples according to the light and dark conditions. Proteome analysis suggested that the majority of enzyme-activity regulation was not hierarchical but rather occurred through enzyme activity regulation. An abrupt light-on condition induced high-light-stress proteins. Transcript analysis showed distinct patterns for the light and dark periods. Glycogen gradually accumulated in the light and was rapidly consumed in the last quarter of the dark period. This suggests that the circadian clock primed the cellular machinery for immediate resumption of growth in the light.Culturing Synechocystis sp. Strain PCC 6803 with N2 and CO2 in a Diel Regime Reveals Multiphase Glycogen Dynamics with Low Maintenance Costs.Angermayr S Andreas SA, van Alphen Pascal P, Hasdemir Dicle D, Kramer Gertjan G, Iqbal Muzamal M, van Grondelle Wilmar W, Hoefsloot Huub C HC, Choi Young Hae YH, Hellingwerf Klaas J KJAdh-1e, sodium salt, Fermentors, single-organism catabolic process, CPD photolyase activity, ammonium formate, PLIP, 13C-labeled, IL1BC, MeCN, cadmium salt, PhrB photolyase activity, Eno2, fond, CASP-1, FEZL, chronic obstructive pulmonary disease (COPD), magnesium formate, CycEI, Apaf-1, mg/ml, ENOA, zinc salt, Type 2A-interacting protein, Long Term, Bca, 5730420M11Rik, dmTAF[[II]]230, Trifluoroacetate, Fermentor, Polypeptides, protein polypeptide chains, M(3L)i, T22F8_160, cobalt(II) formate dihydrate, ATGPR7, CH3-C#N, Alcohol:NAD+ oxidoreductase, B1, Chronic irreversible airway obstruction, 1, GRP8, 2, GRP7, 3, AGM4, NUP96, outer pigmented layer of retina, Adh-1t, Alcohol-NAD+, Il1bc, rounded, epithelium, WMS, HTATIP, nup154, ASD2, (R*, bca, DmelCG17654, CG11940, SET, ostium, Adh-3e, TFIID TAF250, hac-1, cel, Al, catabolism, M, phosphatase 2A inhibitor I2PP2A, ADH1, chemical analysis., CAFL - Chronic airflow limitation, composition, proteins, Saccharomyces uvarum var. melibiosus, IL-1BC, SUPPRESSOR OF AUXIN RESISTANCE 3, AI047805, Pico, DmelCG4299, set, pigment epithelium of retina, decreased, cPLA2, Alcohol-NAD+ Oxidoreductase, column, disease (COPD), anatomical tube, scientific observation, 2-phosphoglycerate dehydratase, sample, D1, pigmented retina epithelium, Argon-40, Mycoderma cerevisiae, D9, Acz, TIP, M(3)RpS17, BEST:LD15491, nickel salt, SGS, dTAF[[II]]230, chronic obstructive lung disease [Ambiguous], Degradations, Caspase-1 subunit p10, cobalt (+2) salt, acid, anon-53Fa, TAF200, Longterm Effect, l(2)SH0173, tip, Cyc E, ANAC091, Alcohol Dehydrogenase (NAD+), Yeast Alcohol Dehydrogenase, DmelCG7788, ACMICD, Fibrinopeptides B, CHRONIC OBSTRUCTIVE AIRWAY DIS, ADH-AA, Baker's Yeasts, Putative MAPK-activating protein PM10, sodium (4:1:1) salt, BG:DS07108.3, Dm1, magnesium salt, Saccharomyces diastaticus, M(3)i(55), dipyrimidine photolyase (photosensitive), AI194826, TIP60, Airflow Obstruction, l(2)05206, CG6829, dark/hac-1/dapaf-1, GLYCINE-RICH PROTEIN 8, Chronic Obstructive Airways Disease, rpS17, Acid, Chronic obstructive lung disease, aluminio, breakdown, HLA-DR-associated protein II, DI-2, LY57, content, I-2Dm, Protein Digestions, proportionality, formate, fmol, rate, cromium (+3), inhibitor of granzyme A-activated DNase, study protocol, beta Trypsin, I-2PP1, Fibrinogen beta chain, eno, TAF-IBETA, F2G1.4, Taf250, OBSTRUCTIVE PULMONARY DISEASE (COPD), duct, Drice, ammonium (4:1) salt, TAF-Ibeta, methyl cyanide, DRICE, tlp, lead (+2) salt, TIP41, Brewer's Yeast, TAF230, Cleland Reagent, cycline, nickel formate dihydrate, lead formate, Effects, Dehydrogenase, DrIce, DrICE, DmcyclinE, aluminum salt, CAO - Chronic airflow obstruction, Pierce, 4-dimercapto-, CHRONIC OBSTRUCTIVE PULM DIS, precursor, Chronic obstructive pulmonary disease NOS, R*)-, protein-containing complex, body system, Saccharomyces italicus, and RNA binding 1, CG7826, ESA1, deoxyribodipyrimidine photolyase activity, stratum pigmentosum retinae, Chronic obstructive pulmonary disease finding, cdi7, period, PULMONARY DISEASE (COPD), cyclinE, M(3)i, TOF, Ly57, CG7835, Cdi7, CDI7, CG42273, system, ZNF312, Cesium Trifluoroacetate, proportion, anatomical systems, dTAF[[II]]250, 2310061K05Rik, thallium (+1) salt, Longterm, cell, PCE-2, beta-Trypsin, rubidium salt, F23A5.3, 2pp2a, DmelCG11940, Long-Term, DmcycE, l(3)dtOA4, methanoic acid, study assay, Alcohol Dehydrogenase I, CG10574, Solution, S. cerevisiae, dTAF250, Melting, DmelCG4579, ms(2)zk, S cerevisiae, 2PP2A, Caspase-1 subunit p20, ATGRP7, ATGRP8, NEC, M(3)i[55], dSET, dSet, Chronic, peptidos, aluminium, Saeure, T18, PTHB1, measuring, dark/dapaf-1/hac-1, mKIAA0559, constant, foramen, 1-(14)C-labeled, chronic obstructive airways disease NOS, degradation, caspase 3, dApaf-1, BcDNA:LD21772, COAD, 2-phospho-D-glycerate hydro-lyase, Clelands Reagent, BG:DS00004.13, potassium formate, CE-2, copper (+2) salt, compositionality, COLD - Chronic obstructive lung disease, acetonitrile, Digestions, Cell, chronic, dTAF230, polypeptide, APAF1, l(2)k02514, native protein, Temperatures, DmCycE, Proteolyses, Hac-1, I-2PP2A, C18, cupric formate, chemical analysis, Long Term Effects, Dm I-2, TAF[[II]]250/230, BcDNA:RE44119, MFS1, (COPD), chronic airway obstruction, chronic obstructive, aluminum formate, dJ142L7.2, CAL - Chronic airflow limitation, Cleland's, Saccharomyces oviformis, Taf[[II]]250, AU020952, RPE, lithium formate, l(2)k02602, underdeveloped, Saeuren, M(3)q, GR-RBP7, GR-RBP8, CG4579, Dark/Dapaf-1/HAC1, IL-1 beta-converting enzyme, ethanenitrile, Interleukin-1 beta-converting enzyme, retinal pigment epithelium, anon-EST:Posey48, Longterm Effects, ME-IV, p. pigmentosa retinae, plan specification, Cleland's Reagent, D-CycE, ZFP312, opening, chronic obstructive lung disease (disorder), structure, quotient, M(3L)i[55], deoxyribonucleate pyrimidine dimer lyase (photosensitive), Baker's Yeast, 13Al, chronic obstructive pulmonary disease, Hac-1/Dark, multicellular organismal catabolic process, Nup32D, TAPETUM 1, Rps17, IPP2A2, T22F8.160, NCMe, determination, and rna binding 2, Chronic Airflow Obstructions, DmelCG6829, RPS17, zinc formate, CG7788, crice, lead salt, protein, pigmented epithelium, composed of, extracted material, peptide, M(3)67, ammonium tetraformate, sampling, Ccne, ClvPrd, peptido, dJ69E11.3, Detergents, chronic obstructive airways disease NOS (disorder), Min, Apaf1, Chronic Obstructive Pulmonary Disease (COPD), protein aggregate, ARK, present in fewer numbers in organism, Adh3-e, Effect, DmelCG42273, Oxidoreductase, COLD (chronic obstructive lung disease), peptides, NEC in ICD9CM_2006, aluminum, TAF-I, TACHD, l(3)67BDo, pigmented retina, hypoplasia, ASD, arc, min, mAPC, Baker, copper, BcDNA:LP01106, ark, free, Protein Degradation, T1, DNA cyclobutane dipyrimidine photolyase activity, Chronic airflow limitation, anon-WO0153538.76, IGAAD, lithium salt, Sputolysin, DmelCG10574, ICE, GLYCINE RICH PROTEIN 7, Saccharomyces capensis, trifluoro-, Baker's, dApaf1, Lyw-57, blood capillary, brewer's yeast, glycine-rich RNA-binding protein 8, Adh-1-t, GPHYSD2, CHRONIC OBSTRUCTIVE PULMONARY DISEASE, ostia, ammonium (2:1) salt, Long-Term Effects, ratio, CHRONIC, phapii, PRE, Tube, obstructive lung disease, Alcohol, ice, iCE, D-Apaf-1, drice, ZC2HC5, deoxyribonucleic cyclobutane dipyrimidine photolyase activity, detergent, Dmel_CG7826, M(3)67C, StF-IT-1, HTATIP1, TAFII-250, foramina, pigmented retinal epithelium, TAF250/230, br37, Airflow Obstructions, pulmonary disease (COPD), TUBE, SLP65, any method, Ly-57, Alcohol Dehydrogenase II, TAFII250, retinal pigment, Cleland, weight, Aluminium, drIce, drICE, Digestion, low temperature, CHRONIC OBSTRUCTIVE, chronic obstructive pulmonary disease and allied conditions, Chronic airway disease, NOS, nickel (+2) salt, retinal pigment layer, Dmel_CG7835, Acetic acid, COPD NOS, CHRONIC OBSTRUCTIVE LUNG DIS, Mnb, MNB, parent ion, Chronic airway obstruction, SLP-65, Yeast, ammonium salt, cold, BASH, retinal pigmented epithelium, Xylella fastidiosa str. Temecula1, acide, Sonications, P45, Rp S17, Trifluoroacetic, cobaltous formate, acids, 3-Butanediol, hac1, acido, CT32526, CG4299, MASS, AW124434, CG17603, TAF[[II]], organ system, dapaf-1S, Chronic Airflow Obstruction, phr A photolyase activity, apaf-1, dapaf-1L, l35Dd, DNA-photoreactivating enzyme, precursor ion, Cesium, SR3-5, COPD - Chronic obstructive pulmonary disease, Acetamide, copper salt, chronic obstructive airways disease, p45, Polypeptide, obstructive pulmonary disease (COPD), Fibrinopeptide B, i2pp2a, COLD, chronic obstructive lung disease, time, ALCOHOL DEHYDROGENASE, d230, Dapaf-1/HAC-1, DISEASE (COPD), Reagent, Degradation, cesium salt, Brewer's, FBN, baker's yeast, dTAFII250, cycE, circadian rhythm, photoreactivating enzyme activity, EfW1, l(2)br37, PHAPII, CYCLE, formic acid, Dark/Hac-1/dApaf1, Argon 40, Cold, method, Hac1, M(3)S33, potassium salt, Dark/Hac-1/dApaf-1, Pulmonary Disease, TAPETUM1, polypeptide chain, reduced, template-activating factor I, dmTAF1, Taf230, subnumerary, Adh-1, ECTOL1, 14C-labeled, Arabidopsis NAC domain containing protein 91, method used in an experiment, zk, stratum pigmentosa retinae, tiny, Pro-Mega, TAF250, Taf200, Cold Temperatures, l(2)10432, MOS3, CYCE, deoxyribocyclobutadipyrimidine pyrimidine-lyase activity, PRECOCIOUS, DmelCG3938, CyclE, ipp2a2, dapaf-1, uniform, 3938, Minute, Taf1p, dapaf, dark, Adh1tl, decreased number, calcium formate, Chronic Obstructive, Protein Degradations, Xylella fastidiosa (strain Temecula1 / ATCC 700964), OCTD, l(2)k05007, Table, dm-cycE, TA1, Candida robusta, 10^[-6], DmelCG3922, Suspension, DARK, taf-ibeta, liquid, cromium (+3) salt, Long-Term Effect, l(2)01501, TAF, dArk, Dapaf-1, FEZ, F23A5_3, 2-iodo-, Yeast Alcohol, sodium formate, Alcohol NAD+ Oxidoreductase, BLNK-S, COPD, small, COAD - Chronic obstructive airways disease, DYRK1, data, TAF[[II]]250, nickel formate, 3H-labeled, Alcohol Dehydrogenase, Saccharomyces cerevisiae 'var. diastaticus', protein complex, not elsewhere classified, igaad, strontium formate, l(3)84Ab, apaf1, Protein Digestion, strontium salt, PULM DIS CHRONIC OBSTRUCTIVE, Peptide, Chronic obstructive pulmonary disease finding (finding), stratum pigmentosum (retina), MODIFIER OF SNC1, capillary vessel, natural protein, p230, Protein, AI551343, deoxyribonucleic photolyase activity, Adh1-t, ADC1, I2PP2A, TFIID, Bioreactor, Dyrk1, CES2A1, GLYCINE-RICH RNA-BINDING PROTEIN 7, Dark, CyeE, connected anatomical system, Adh1-e, Dark/Apaf-I, ACETONITRILE, cyanomethane, WMS2, CG17654, chronic obstructive airway disease, Temperature, VSD1, jog, nup32D, TAF[[II]]230, photolyase activity, Dops, CC1, l(2)35Dd, Tripcellim, TAF[II]250, dApaf-1/DARK/HAC-1, sample population, chromic formate, CG3922, Interleukin-1 beta convertase, Trypure, dSET/TAF-Ibeta, sample collection, 2610030F17Rik, DmelCG17603, Pressures, concentration, Liver regeneration-related protein LRRG036|LRRG043|LRRG189, SSKS, 3.4.22.36, TCV-interacting protein, calcium salt, cold (chronic obstructive lung disease), Peptid, round, assay, Chronic Obstructive Lung Disease, AA407739, CG3938, dAPAF-1, Baker Yeast, TAF1CRYG4, me75, adrenal medullary paraganglioma, cou, chromaffin paraganglioma of the adrenal gland, Maintenances., animal starch, WURCS=2.0/1, adrenal gland Chromaffinoma, adrenal medullary pheochromocytoma, CTRCT4, Tl3, Tl2, ecotype, D17Mit170, T1, strain, adrenal gland pheochromocytoma, adrenal gland chromaffin paraganglioma, CACA, liver starch, Glycogen, photoreceptor PCC, Lr, pheochromocytoma, adrenal pheochromocytoma, cry-g-D, glycogen, Intraadrenal paraganglioma, CCA3, adrenal gland paraganglioma, Bra, CCP, PCC, cultivar, 4, Low, 3/[a2122h-1a_1-5]/1-1-1-1/a4-b1_b4-c1_b6-d1, pheochromocytoma (adrenal)Adh-1e, criteria, Cysteine Hydrochloride, 2-amino-4-(methylsulfanyl)butanoic acid, ion, eno1l1, Eno1, False, Effects, selection process, Addresses, instrument configuration, number, L Isomer, baker's yeast, Gene, Eno-1, protein, precursor, guidelines, protein-containing complex, composed of, Saccharomyces italicus, Long Term, peptide, period, Polypeptides, L-Isomer Methionine, protein polypeptide chains, eno1, Methionine, ClvPrd, peptido, polypeptide chain, Adh-1, Injection, Plgs, Gene Products, L-Methionine, Half-Cystine, MPB1, Adh-1t, protein aggregate, rounded, Adh3-e, Injectables, Effect, Pedameth, proportion, Adh-3e, F, reactivo, PPH, peptides, Longterm, iones, L Cysteine, M, beta-Trypsin, human protein, ADH1, enolase 1, composition, proteins, Adh1tl, number of, Long-Term, ions, Saccharomyces uvarum var. melibiosus, free, S. cerevisiae, Injectable, MBP-1, 2-amino-4-(methylthio)butanoic acid, Candida robusta, 10^[-6], pph, Saccharomyces capensis, ppm, sample, has or lacks parts of type, mbp-1, peptidos, s, eno1a, Mycoderma cerevisiae, variability of a physical quality, Long-Term Effect, eno1b, Half Cystine, brewer's yeast, Adh-1-t, metionina, Racemethionine, Long-Term Effects, reagents, ratio, data, NNE, Nne, Zinc Cysteinate, DL-Methionine, Saccharomyces cerevisiae 'var. diastaticus', AI447866, protein complex, Proteins, 2-Amino-4-(methylthio)butyric acid, Longterm Effect, total expressed protein, extra or missing physical or functional parts, compositionality, L-Isomer, not genetically inherited, Table., Peptide, mereological quality, ADH-AA, polypeptide, nne, native protein, AL022784, Ionen, natural protein, Saccharomyces diastaticus, Protein, Long Term Effects, Adh1-t, ADC1, Methionin, AI194826, methionine, Hmet, Adh1-e, reactif, Met, Data Base, parent ion, F2P9_10, Saccharomyces oviformis, mpb1, instrument, content, F2P9.10, proportionality, Tripcellim, reagent, rate, L-Cysteine, EG433182, SPBPB8B6.07c, beta Trypsin, sample population, Longterm Effects, Protein Gene Products, Trypure, Gene Proteins, 1110030K05Rik, CSV, precursor ion, Ion, Gm5506, structure, cardinality, alpha-amino-gamma-methylmercaptobutyric acid, quotient, twenty-four hour rhythm, Peptid, HSP48, round, Polypeptide, diurnal rhythm, Liquimeth, 0610008I15, Proteomes, time, ENO1L1Hac-1/Dark, scale tissue, nucleocytoplasm, determination, DmelCG6829, Mbp1, Visible Light, Aphanocapsa sp. N-1, protein, Apaf-1, Long Term, qr, dmTAF[[II]]230, Background, protein polypeptide chains, gamma., Cultural, hnu, Magnetic Resonance Imaging, Impacts, 4, Apaf1, Analysis, Environmental Impacts, protein aggregate, myd, ARK, Effect, foton, multicellular organismal biosynthetic process, Mass Spectrum Analysis, ethnicity, single-organism biosynthetic process, hac-1, TFIID TAF250, Analyses, availability, cel, rya-r44F, anabolism, plant peltate hair, KAT13D, arc, Mbp-1, WURCS=2.0/1, present in organism, proteins, mKIAA0334, ark, T1, retention, Rya-R44F, Environmental Impact, reaction, g, dehydrated, CG10844, dya, NMR, Synechocystis sp. (ATCC 27184), dApaf1, Long-Term Effects, intracellular, gamma, close to, dTAF[[II]]230, Radiation, D-Apaf-1, gyltl1b-b, anon-53Fa, TAF200, Longterm Effect, l(2)SH0173, Light, TAFII-250, TAF250/230, XClock, Spectrum Analysis, results, Spectroscopy, Cultural Background, TAFII250, LIGHT, Cultures, weight, MDDGA6, mKIAA0609, qtr, internal to cell, Synechocystis sp. PCC6803, END, CG6829, dark/hac-1/dapaf-1, Visible Radiations, fg, Visible Radiation, gyltl1b, HVEML, maintenance of localization, RyR, mdc1d, expanded, Spectrometry, hac1, CG17603, TAF[[II]], Aphanocapsa sp. (strain N-1), dapaf-1S, MDC1D, apaf-1, dapaf-1L, light quantum, enr, enlarged, Taf250, RYR, Ryr, SR3-5, Magnetic resonance imaging, time, TAF230, big, Beliefs, d230, Synechocystis 6803, Dapaf-1/HAC-1, ryr, Effects, peltate hair, Gene, dTAFII250, biosynthesis, Spectrum Analyses, Illumination, 5330400M04Rik, protein-containing complex, EfW1, froggy, metabolite levels, Gyltl1a, Ly113, Dark/Hac-1/dApaf1, period, clk, large, Hac1, Dark/Hac-1/dApaf-1, polypeptide chain, dmTAF1, Taf230, RyRs, Mass, Gene Products, light, 3/[a2122h-1a_1-5]/1-1-1-1/a4-b1_b4-c1_b6-d1, Mass Spectroscopy, Backgrounds, TAF250, bHLHe8, protoplasm, study, Taf200, dTAF[[II]]250, protoplast, formation, Longterm, cell, MDDGB6, Lichtquant, dapaf-1, animal starch, Cultural Relativisms, Taf1p, dapaf, dark, Visible, Long-Term, synthesis, BPFD#36, dTAF250, Glycogen, Synechocystis sp. (strain PCC 6803), DARK, glycogen, great, photon, Customs, scale (sensu Metazoa), DmelCG10844, Long-Term Effect, TR2, Photobioreactor, culture, dArk, TAF, Dapaf-1, HHT1, dark/dapaf-1/hac-1, TAF[[II]]250, DRR, Synechocystis PCC6803, DRY, protein complex, dApaf-1, Proteins, l(3)84Ab, apaf1, BG:DS00004.13, Cultural Backgrounds, CD258, Cell, Belief, Impact, dTAF230, near to, Environmental, metabolite traits, APAF1, native protein, natural protein, Hac-1, dry, p230, chemical analysis, Long Term Effects, Protein, TAF[[II]]250/230, TFIID, Dark, scales, Dark/Apaf-I, Mass Spectrum Analyses, Radiations, Taf[[II]]250, Mass Spectrum, l(2)k00424, TAF[[II]]230, scale, dRyR, distinct, storage, HVEM-L, Synechocystis sp. (PCC 6803), Photoradiation, Dark/Dapaf-1/HAC1, TAF[II]250, dApaf-1/DARK/HAC-1, LTg, Longterm Effects, Protein Gene Products, Gene Proteins, Xclk, liver starch, l(2)k04913, DmelCG17603, Photoradiations, Biomasses, approaches, vicinity of, Synechocystis sp.PCC6803, Environments, Relativisms, assay, sequestering, Relativism, ORW1, Cultural Relativism, dAPAF-1, Synechocystis sp. ATCC 27184, TAF1, Rya-r76CDsingle-organism catabolic process, adrenal medullary paraganglioma, NK-2, Materials, dhc64C, nk-2, Visible Light, growth and development, Profiles, sulfur, Apaf-1, Long Term, dmTAF[[II]]230, pheochromocytoma, gamma., dhc64c, responsivity, hnu, Cultural, cDhc64C, Magnetic Resonance Imaging, 4, Analysis, myd, Dhc, DHC, ethnicity, amino acids, hac-1, azufre, TFIID TAF250, Analyses, cel, catabolism, anabolism, plant peltate hair, N, HDC16822, KAT13D, S, Mbp-1, Age of onset, WURCS=2.0/1, present in organism, proteins, elevated, ecotype, Signatures, dhc, CD, density, Expression Signature, CCA3, Synechocystis sp. (ATCC 27184), Homo sapiens disease, DmAAF34715, accumulated, dTAF[[II]]230, Radiation, VND, Vnd, anon-53Fa, Dhc46C, TAF200, Longterm Effect, l(2)SH0173, Light, Fs(3)Sz18, XClock, Spectrum Analysis, INSDC_feature:misc_RNA, alpha-amino carboxylic acids, Cultural Background, LIGHT, Cultures, Stickstoff, mKIAA0609, Expression Signatures, PCC, Blue Green Bacteria, Sulfur-16, DHC64C, Synechocystis sp. PCC6803, Expression Profile, END, CG6829, blue-green bacteria, dark/hac-1/dapaf-1, fg, Acid, breakdown, HVEML, Amino acids, cDhc, expanded, Spectrometry, Dhc64, Aphanocapsa sp. (strain N-1), MDC1D, light quantum, nitrogen, Su(Gl)77, enr, Taf250, Material, Blue-Green Algae, Dm-NK2, HMW MAP, Acids, Blue Green, TAF230, big, Synechocystis 6803, Effects, peltate hair, secondary metabolites, biosynthesis, 5330400M04Rik, l(1)GA100, Ly113, blue-green algae, period, CACA, Cdhc, clk, large, Oxyphotobacteria, adrenal pheochromocytoma, Intraadrenal paraganglioma, DmelCG7507, Gene Products, Darknesses, disease or disorder, Dhc64c, 3/[a2122h-1a_1-5]/1-1-1-1/a4-b1_b4-c1_b6-d1, Backgrounds, dTAF[[II]]250, Longterm, cell, Lichtquant, MDDGB6, Profile, Elemental sulfur, Cultural Relativisms, Long-Term, Bacteria, l(1)GA122, synthesis, adrenal gland pheochromocytoma, Sulfur 16, dTAF250, Algae, Lab, photon, Customs, Nkx2, scale (sensu Metazoa), TR2, Photobioreactor, high elevation, Fs(3)Lab, dark/dapaf-1/hac-1, Cyanophyceae, degradation, lab, dApaf-1, Proteins, disorders, function, alpha-amino acids, BG:DS00004.13, Cultural Backgrounds, CD258, Cell, CG7507, dTAF230, APAF1, Hac-1, Blue-Green Bacteria, l(1)VA208, chemical analysis, Gene Expression Signatures, Long Term Effects, Cyanophycota, TAF[[II]]250/230, vnd/NK-2, condition, Dynein, scales, Mass Spectrum Analyses, Taf[[II]]250, underdeveloped, HVEM-L, Oxygenic photosynthetic bacteria, postnatal growth, metabolite, Dark/Dapaf-1/HAC1, azote, Understanding, Longterm Effects, Gene Proteins, Xclk, liver starch, Photoradiations, Gene Expression Profiles, adrenal gland paraganglioma, Relativisms, regulation, Relativism, Cultural Relativism, General activity, Synechocystis sp. ATCC 27184, Hac-1/Dark, multicellular organismal catabolic process, scale tissue, Activity, determination, Feature, DmelCG6829, postnatal development, Aminosaeure, Mbp1, Amino acid, Gene Expression Profile, NK2, atado, Aphanocapsa sp. N-1, qr, Readability, Background, primary metabolites, diseases, Fs(3)Laborc, theion, Impacts, diseases and disorders, Apaf1, Environmental Impacts, Schwefel, ARK, Effect, foton, multicellular organismal biosynthetic process, Mass Spectrum Analysis, single-organism biosynthetic process, human disease, availability, hypoplasia, arc, adrenal gland Chromaffinoma, CG12352, mKIAA0334, EG:118B3.1, ark, T1, Environmental Impact, soufre, Transcriptomes, NMR, dApaf1, l(1)RC24, Long-Term Effects, gamma, pheochromocytoma (adrenal), l(1)EA142, D-Apaf-1, gyltl1b-b, Aminokarbonsaeure, Expression Profiles, TAFII-250, TAF250/230, results, Spectroscopy, Gene Expression, shortened, Blue-Green, TAFII250, l(1)VE769, Dm vnd, MDDGA6, l(1)EC6, qtr, Genetic Materials, cultivar, Genetic Material, Transcriptome Profiles, Visible Radiations, Amino Acid, Visible Radiation, gyltl1b, Blue Green Algae, growth pattern, non-developmental growth, 16S, mdc1d, common, hac1, Features, CG17603, TAF[[II]], dapaf-1S, disease, apaf-1, sulphur, dapaf-1L, enlarged, SR3-5, metabolites, microarray, Cistron, Magnetic resonance imaging, 7N, short, time, Proteomes, protein levels, other disease, Beliefs, d230, Dapaf-1/HAC-1, Transcriptome Profile, Aminocarbonsaeure, l(3)64Ca, Gene, dTAFII250, cyanophytes, Cyanobacteria, alpha-amino acid, Spectrum Analyses, EfW1, froggy, Gyltl1a, Dark/Hac-1/dApaf1, adrenal gland chromaffin paraganglioma, dNK-2, Hac1, Dark/Hac-1/dApaf-1, reduced, dmTAF1, Taf230, Mass, light, tiny, Cyanophyta, Mass Spectroscopy, TAF250, bHLHe8, study, reactivity, Taf200, Genetic, formation, dapaf-1, stubby, animal starch, Taf1p, adrenal medullary pheochromocytoma, dapaf, cyanobacteria, Visible, CTRCT4, dark, EC6, Maintenances, non-neoplastic, BPFD#36, Glycogen, Synechocystis sp. (strain PCC 6803), DARK, glycogen, CG6172, great, DmelCG12352, disorder, Long-Term Effect, Characteristics, culture, dArk, TAF, Dapaf-1, HHT1, span, small, TAF[[II]]250, Synechocystis PCC6803, Transcriptome, total expressed protein, l(3)84Ab, apaf1, enzyme activity, medical condition, Cistrons, strain, Belief, Impact, development, Environmental, photoreceptor PCC, Characteristic, l(1)1Bf, cry-g-D, p230, Protein, TFIID, Gene Expression Signature, Dark, DmelCG6172, Dark/Apaf-I, Radiations, CRYG4, Mass Spectrum, TAF[[II]]230, scale, distinct, chromaffin paraganglioma of the adrenal gland, Synechocystis sp. (PCC 6803), Photoradiation, TAF[II]250, Amino, Age symptoms begin, dApaf-1/DARK/HAC-1, FCP-A, LTg, nitrogeno, Protein Gene Products, requirements, DmelCG17603, Synechocystis sp.PCC6803, Environments, CCP, assay, response, Signature, ORW1, growth, dAPAF-1, TAF1Synechocystis PCC6803, Synechocystis 6803, cycline, DmcyclinE, fond, Proteins, FBN, Gene, cycE, function, Profiles, Aphanocapsa sp. N-1, CycEI, Cyc E, br37, l(2)br37, CYCLE, ACMICD, cdi7, l(2)k02514, Ccne, DmCycE, cyclinE, BG:DS07108.3, ECTOL1, Protein, Gene Products, Cdi7, CDI7, MFS1, CyeE, l(2)05206, Synechocystis sp. PCC6803, Metabolic Profile, WMS, WMS2, Metabolic Profiles, CYCE, l(2)k02602, Metabolic, Metabolomes, DmelCG3938, Profile, CyclE, Synechocystis sp. (PCC 6803), l(2)35Dd, 3938, proteins, MASS, DmcycE, Aphanocapsa sp. (strain N-1), SSKS., Protein Gene Products, OCTD, l(2)k05007, Gene Proteins, D-CycE, dm-cycE, l35Dd, Synechocystis sp. (strain PCC 6803), Synechocystis sp.PCC6803, Synechocystis sp. (ATCC 27184), GPHYSD2, CG3938, Synechocystis sp. ATCC 27184, SGS271trueDynamics of the physiology, metabolome and proteins during the circadian cycle of Synechocystis sp. PCC 6803 under culturing conditions relevant for mass culturingHere, we present the results of a study of the model cyanobacterium Synechocystis sp. PCC 6803, cultured in a lab-scale photobioreactor simulating physiological conditions present during large-scale culturing. The culture is flushed with N2 and CO2 without additional O2. This leads to an anoxic environment during the dark period. A circadian illumination regime of 12 h light/12 h dark is applied. We show that formation of biomass strictly follows the availability of light. The storage compound glycogen reached a maximum level of ~40 % of the cells gram dry weight already before the end of the light period. The subsequent consumption of glycogen during the dark period essentially only started in the last quarter of the dark period, which suggests anticipatory effects, possibly governed by the circadian clock, in order to prepare the cellular machinery for efficient energy usage. Most intracellular metabolite levels, as determined by Nuclear Magnetic Resonance analysis, from samples close to the transition points of light, change only mildly. Nevertheless, a distinct metabolic profile is evident from the cells sampled at different time points. Likewise, protein analysis by mass spectrometry shows moderate dynamics for the majority of the identified proteins. Both analyses suggest that in order to change the flux through a metabolic network the relative amounts of the metabolites and proteins do not need to change drastically, at least for the time points close to the change of the light regime.2016-09-272014-12-16PXD00161928065516460991804982953585111454224942024527872842188090368093270429330845811363336351524260119834300662758385NCBITaxon:128068888561896111430118726355557114526236493461364031952065126957366649274670738538836411354615821582310665688954762721123294422291180992323122586365458333460792519365914320597129386558195851149315242592637371250232NCBITaxon:127211195774818661488584310430024513586722175543740816918045426683429531945305861266835149822505814963674452158554528113208147956410039237514636942049433208964208963445974137979138712728384400667453293529367156759388036478434716052165994048321659721659545501315282693042165915627161696833218321729204277944762376454317203094980197525556978159509439843948840479NCBITaxon:2157525338551531051067439899037122857759515205968762262311210884555588845587077918178081736309431794571698936160488409859NCBITaxon:37162104782679401505907148364320421061320491381693630355543204663263331199456545351102541110321745921612926420128867641002642036945694101676341021076127735152486713165823925472793342814613584301417298760917463345774449167547604893212873567568403013506219172651813019411192943936711041131023932025559863258278839659104759347495109716049016529983552566317585439801102432608663102459808757417555183201964471452680457966313670190832331156114155355104219325552113834397634981812359871069955529NCBITaxon:47518502983354761136157414654771800665564843376771441379299767982510216998238976484074137351155711089725482444474153NCBITaxon:50557899698441000364653493341471474935480194675129911435974127647313708632654787656589363983532215958936698381920111067757727103481985234878026555447946409860995861571871766859919157295137221171101292921076878349741986020280914884063342492342351523359859886559746499870392021110729433117113936352721598741908503711708271170828418235024145113969293190219782247463604614712374940237593972328758172253256648905079452659600131972211915853101774208588596NCBITaxon:615750521028307989515586411051989972375059576131720002634196102641088878176179212190659407121906772275885815689964975151950582873757244NCBITaxon:22023717NCBITaxon:17036122019998570506050617476792745062724915961533355418400524643213686150596487844612286662941786661347515363291018194301086731018510184NCBITaxon:1763573039635586331492862876705801321650852718481865368595105135553482260710185687294296110091416333NCBITaxon:619184023210007348824123363630710470058127187878645159812894555663577553470951451225786425011449447260704NCBITaxon:13356262607052607076584574054163677483167233150561007133705654195NCBITaxon:305550445791399878168119011928752829126806315327341478281055524NCBITaxon:9606135858469008111167815022830519302836728593008529005NCBITaxon:5693826883064017946991510118499435258759131515901448242838111394422584416041937047592721204414370860423281677285035158199011951953267386370137024924053608838581622488186156227748817562615835583715333760572671193501998086119350216787910857913711371272407190650371475917262981288057125627457572709030903113335503728142433747924910078711082NCBITaxon:96157243359463318586260799141262200298492670NCBITaxon:126371928124921252830385683856959116926610065813735237561275045426662551519788135663837506442233600941293497905463224535247214012575151164990851515143899237453747445446415243235937605920222887051580595536555088157932716029385157811497863389229382894535936479437509173NCBITaxon:685441275422511775299159010901341673871589552101296610306129671585158451584937659393432715910022637673388990461423451287689591198332966467041464792936576164280341160221641331599280382803536909108917688149894621812141080348179392287889295027113133295282829445686174934681911265269972273218903821076012471904007271597369978281143114020641198108713554774365814245072295337969820423212422312916321803347087145372091645733215358157546992877702020603281143193382935508332912922114864374572526499972830357390871830872672710379085507176299707678926837041557372921405329412816078395639243142626548982273775611559620732208659588273555169360533079725518113549143213715974953502611595561432138406072587814144733521509493349194963401614334728005936046316461046603815184547448500356709747777195124017484185560133575554792042741580536076994688103762014887100594120037582890931643542826885007123038399001389464940838283594144242322197857742171598921409212205853939621157781154756929793244704749906604162103591905158114452749907312987779913112273170187546991103589915NCBITaxon:37296103609833418710491130798133679531640729946710340157865826453033373306383011306413992530642363650591169654788546981121162034317652616103372861299404458620734011535711195296526117455311147161338654131316634305521323120179836025323731276125523299351299385057316317642619794011513458445772678728623219334151346186208621160791392227983516811961255228149539322323116761757312108077213487999948861856962814084341033517787996321849620994887321392488209711533820961153392095330439375569927612686266447NCBITaxon:26970493398624369411031219588320509202906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