PAXDBapplication/xmlhttp://pax-db.org/downloads/latest/datasets/bioprojects-abundance-files-v4.0.zipprimary200OK0000ProteomicsChristian von Mering272623https://pax-db.org/dataset/272623/3365734308mering@imls.uzh.chUniversity of ZurichPAXDBFor the rescaling, the datasets are first parsed or processed such that the data reflect proportional abundances of whole protein molecules (i.e. proportionality to counts of complete, individual protein molecules, not to molecular weights, protein volumes, or digested peptides). In the case of spectral counting data protein. The proportional abundances are rescaled linearly to add up to one million; this means the abundance of each protein of interest is finally expressed in (parts per million,) relative to all other proteins in a sample. For a given protein abundance dataset, we then compute the absolute log abundance ratios of all pairs of proteins annotated to be functionally linked. The median of these absolute log abundance ratios represents an indirect quality metric: the closer it is to zero, the better (i.e. the more there is consistency between abundance values and functional annotations such as protein complexes or pathways). We then compute a background expectation for this metric, by permuting the abundance values in a given dataset randomly, and recomputing the median log abundance ratios. The permutation is repeated several times, yielding a distribution of medians. The actually observed median is then expressed as a Z-score distance to the random distribution ofmedians—this distance is termed the interaction consistency score.Protein turnover plays an important role in cell metabolism by regulating metabolic fluxes. Furthermore, the energy costs for protein turnover have been estimated to account for up to a third of the total energy production during cell replication and hence may represent a major limiting factor in achieving either higher biomass or production yields. This work aimed to measure the specific growth rate (μ)-dependent abundance and turnover rate of individual proteins, estimate the ATP cost for protein production and turnover, and compare this with the total energy balance and other maintenance costs. The lactic acid bacteria model organism Lactococcus lactis was used to measure protein turnover rates at μ = 0.1 and 0.5 h(-1) in chemostat experiments. Individual turnover rates were measured for ~75% of the total proteome. On average, protein turnover increased by sevenfold with a fivefold increase in growth rate, whilst biomass yield increased by 35%. The median turnover rates found were higher than the specific growth rate of the bacterium, which suggests relatively high energy consumption for protein turnover. We found that protein turnover costs alone account for 38 and 47% of the total energy produced at μ = 0.1 and 0.5 h(-1), respectively, and gene ontology groups Energy metabolism and Translation dominated synthesis costs at both growth rates studied. These results reflect the complexity of metabolic changes that occur in response to changes in environmental conditions, and signify the trade-off between biomass yield and the need to produce ATP for maintenance processes.Protein turnover forms one of the highest maintenance costs in Lactococcus lactis.Lahtvee Petri-Jaan PJ, Seiman Andrus A, Arike Liisa L, Adamberg Kaarel K, Vilu Raivo RAdd, DmelCG43443, ADD, ADD-87, Hts-RC, data, AU023367, Data Set, protein complex, supply, Proteins, Ovhts, Gene, HtsRC, CG9325, protein, neutral molecular compounds, protein-containing complex, Dmel_CG9325, Xt, Peptide, 1B1, add, Polypeptides, anon-EST:Posey9, protein polypeptide chains, native protein, peptido, htsRC, GLI3-190, natural protein, polypeptide chain, Add-hts, Protein, CG43443, Gene Products, l(2)k14523, Dmel_CG34197, l(2)00634, median, Ovhts-RC, background, supply and distribution, protein aggregate, all_pairs, molecule, Bph, molecula, Random selection by shearing, oligonucleotide random primer, proportion, HTS-R1, HTS, Hts, molecules, peptides, l(2)k06121, adducin, GLI3FL, distribution, AI854843, proportionality, add-like, HTS-RC, rate, proteins, Molekuel, Pdn, sample population, introduction, Protein Gene Products, Gene Proteins, Adducin, RANDOM, 10^[-6], ppm, sample, supply., quotient, Peptid, peptidos, Polypeptide, Attention Deficit Hyperactivity Disorder, l(2)01103, EST D, CG34197, HtsF, ratioProtein Gene Products, Forms, Gene Proteins, Bacterium lactis, protein polypeptide chains, native protein, natural protein, polypeptide chain, protein complex, Protein, Gene Products, Proteins, Gene, Lactococcus lactis subsp. lactis, proteins, protein, Bacterium lacti, protein aggregate, protein-containing complex, Maintenances, Lactococcus lactis (Lohnis) Schleifer et al. 1986, Streptococcus lactis.organism, bacteria, whole body, multi-cellular organism, whole organism, animal, body, Koerper, fungi.biochemical pathways, protein translation, Striadyne, Metabolic Process, Gene Ontology Projects, Adenosine Triphosphate, Metabolisms, postnatal development, Metabolic Concepts, Bioenergetics, growth and development, protein, dmTAF[[II]]230, protein polypeptide chains, Roles, Toxicity and JNK inducer, Concepts, Project, Metabolism Concept, Expenditure, protein aggregate, Phenomenon, animal, H4atp, multicellular organismal biosynthetic process, average, increased, single-organism biosynthetic process, Chromium Adenosine Triphosphate, TFIID TAF250, cel, catabolism, anabolism, proteins, metabolic process resulting in cell growth, Estimated, ATPsyn b, CrATP, Cr(H2O)4 ATP, Role Concepts, biotransformation, Catabolism, ATP, Chromium Ammonium Salt, ATPsyn-&bgr, protein anabolism, dTAF[[II]]230, protein biosynthetic process, anatomical protrusion, ATPsyn-b, PLATEST, Process, metabolism resulting in cell growth, TAJ-alpha, TAF200, TAFII-250, TAF250/230, results, organism, TAFII250, Role Concept, Manganese Salt, Role, protein formation, Magnesium Salt, secretion, Ontology Projects, spine., median, Adenosine 5'-triphosphate, CG11154, Gene Ontologies, Ontology, ADENOSINE-5'-TRIPHOSPHATE, whole organism, Ontologies, Projects, growth pattern, non-developmental growth, TROY, CG17603, TAF[[II]], Adenosine triphosphate, CaATP, Energy Metabolisms, Taf250, protein synthesis, SR3-5, Koerper, MgATP, Proteomes, Platelets, TAF230, accessory, d230, multi-cellular organism, Magnesium Adenosine Triphosphate, Processes, ATP-MgCl2, Gene, dTAFII250, biosynthesis, Metabolic Processes, IB, protein-containing complex, EfW1, supernumerary, Gene Ontology Project, Adenylpyrophosphate, Gene Ontology, protrusion, polypeptide chain, dmTAF1, Taf230, Metabolism, ATP-synbeta, Gene Products, Bacterium lacti, Metabolism Phenomena, TAF250, Taf200, dTAF[[II]]250, DmelCG11154, formation, cell, beta-ATPase, ATP MgCl2, Metabolic Concept, Energy, Taf1p, Expenditures, Maintenances, Lactococcus lactis (Lohnis) Schleifer et al. 1986, synthesis, dTAF250, Chromium Salt, ATPasebeta, MnATP, ATPase beta, species, TAF, ATPB, TAJ, TRADE, TAF[[II]]250, degradation, protein complex, Lactic Acid Bacteria, body, synthesize, Streptococcus lactis, Proteins, Magnesium Chloride, total expressed protein, l(3)84Ab, whole body, BG:DS00004.13, Adenosine 5'-(tetrahydrogen triphosphate), Cell, Concept, dTAF230, Metabolic Phenomena, ATP-syn-B, Bacterium lactis, development, Metabolism Concepts, Atriphos, ML-1, native protein, natural protein, p230, Protein, Phenomena, TAF[[II]]250/230, TFIID, protein biosynthesis, metabolism, Metabolic Phenomenon, Energy Expenditure, Taf[[II]]250, Ontology Project, multicellular organism metabolic process, Manganese Adenosine Triphosphate, TAF[[II]]230, biodegradation, Metabolic, increased number, postnatal growth, Energy Expenditures, TAF[II]250, Bioenergetic, Protein Gene Products, Gene Proteins, present in greater numbers in organism, single-organism metabolic process, DmelCG17603, Biomasses, ATPIB, Lactococcus lactis subsp. lactis, growth, Calcium Salt, TAF1, Anabolism0falseL.lactis - Whole organism, SC (Lahtvee,microbiology,2014)abundance based on Spectral counting, Interaction consistency score: 11.2, Coverage: 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