PAXDBapplication/xmlhttp://pax-db.org/downloads/latest/datasets/bioprojects-abundance-files-v4.0.zipprimaryOK2000000ProteomicsChristian von Mering272620https://pax-db.org/dataset/272620/1693104356mering@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.Nutrient adaptation is key in limiting environments for the promotion of microbial growth and survival. In microbial systems, iron is an essential component for many cellular processes, and bioavailability varies greatly among different conditions. In the bacterium, <i>Klebsiella pneumoniae</i>, the impact of iron limitation is known to alter transcriptional expression of iron-acquisition pathways and influence secretion of iron-binding siderophores, however, a comprehensive view of iron limitation at the protein level remains to be defined. Here, we apply a mass-spectrometry-based quantitative proteomics strategy to profile the global impact of iron limitation on the cellular proteome and extracellular environment (secretome) of <i>K. pneumoniae</i>. Our data define the impact of iron on proteins involved in transcriptional regulation and emphasize the modulation of a vast array of proteins associated with iron acquisition, transport, and binding. We also identify proteins in the extracellular environment associated with conventional and non-conventional modes of secretion, as well as vesicle release. In particular, we demonstrate a new role for Lon protease in promoting iron homeostasis outside of the cell. Characterization of a Lon protease mutant in <i>K. pneumoniae</i> validates roles in bacterial growth, cell division, and virulence, and uncovers novel degradation candidates of Lon protease associated with improved iron utilization strategies in the absence of the enzyme. Overall, we provide evidence of unique connections between Lon and iron in a bacterial system and suggest a new role for Lon protease in the extracellular environment during nutrient limitation.Iron Limitation in <i>Klebsiella pneumoniae</i> Defines New Roles for Lon Protease in Homeostasis and Degradation by Quantitative Proteomics.Muselius Benjamin B, Sukumaran Arjun A, Yeung Jason J, Geddes-McAlister Jennifer JAdd, 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, ratioAutoregulation, biochemical pathways, Peptidomics., single-organism catabolic process, multicellular organismal catabolic process, cellular breakdown, Bacillus pneumoniae, Bacterium pneumoniae crouposae, Klebsiella pneumoniae aerogenes, degradation, number, fer, LonHS, CG8798, PIM1, presence, cellular catabolism, 'Klebsiella aerogenes' (Kruse) Taylor et al. 1956, DLag1, DLAG1, count in organism, Prss15, LONP, DmelCG8798, Iron 56, PRSS15, positive regulation of homeostatic process, Lon, LON, cellular degradation, secretion, 26Fe, Klebsiella rhinoscleromatis, regulation of homeostatic process, l(1)G0061, breakdown of molecule, ferrum, hierro, DmelCG3576, breakdown, biodegradation, Iron, lon, breakdown of chemical, catabolism, Dlag1, Iron-56, 1200017E13Rik, inhibition of homeostatic process, Lag1, Fe, l(1)G0365, breakdown of substance, Eisen, activation of homeostatic process, Hyalococcus pneumoniae, lag1, l(1)G0489, CG3576, negative regulation of homeostatic process, homeostasis, biotransformation, hLON, iron, anon-WO0118547.350, CG15898Koerper., organism, whole body, multi-cellular organism, whole organism, animal, bodybiochemical pathways, single-organism catabolic process, multicellular organismal catabolic process, Bacillus pneumoniae, acquisition by organism of nutrients from host via siderophores, postnatal development, nutrients., iron acquisition by symbiont from host heme, Phases, growth and development, protein, infectivity, Divisions, Social Controls, dmTAF[[II]]230, solute:solute exchange, protein polypeptide chains, DmelCG8798, Secretome, Roles, Concepts, Impacts, cellular degradation, 26Fe, Environmental Impacts, protein aggregate, Nutrient, Formal Social Controls, IKKg, WMS, KEY, Key, viral infection, iron homeostasis, M Phases, TFIID TAF250, cel, catabolism, M, Bodily, proteins, Social, Division Phase, Environmental Impact, Secretion, Hyalococcus pneumoniae, Secretions, Role Concepts, biotransformation, GPHYSD2, Siderochromes, SGS, dTAF[[II]]230, anatomical protrusion, Bacterium pneumoniae crouposae, external secretion, TAF200, CG8798, TAFII-250, TAF250/230, Cell Divisions, ACMICD, DLag1, exocrine gland fluid/secretion, DLAG1, Bodily Secretion, DmIKKgamma, TAFII250, Prss15, LONP, Iron 56, Role Concept, PRSS15, single-organism transport, dIKK, Kenny, membrane-enclosed vesicle, Role, Pathogenicity, secretion, heme acquisition, absence, breakdown, death rate, growth pattern, Iron, non-developmental growth, IKK-gamma, Control, Protein Secretomes, Dlag1, MASS, Controls, 1200017E13Rik, CG17603, Lag1, TAF[[II]], Fe, organ system, l(1)G0365, Eisen, DmelCG16910, Taf250, spine, SR3-5, lag1, l(1)G0489, Biocatalyst, microarray, small molecule transport, iron, E430016J11Rik, exocrine gland secretion, Regulation, CG15898, Proteomes, TAF230, Regulations, d230, exocrine gland fluid, exocrine gland fluid or secretion, Peptidomics, Biocatalysts, number, FBN, Gene, LonHS, dTAFII250, PIM1, protein-containing complex, Ximpact, EfW1, presence, body system, dIKK-gamma, cellular catabolism, 'Klebsiella aerogenes' (Kruse) Taylor et al. 1956, protrusion, polypeptide chain, Lon, LON, dmTAF1, ECTOL1, Taf230, DmIKK-gamma, Gene Products, system, dmIKKgamma, IKK[[gamma]], TAF250, hierro, Taf200, anatomical systems, dTAF[[II]]250, Cell Division Phase, lon, breakdown of chemical, cell, ligand, nutrients, absent from organism, Siderophore, Taf1p, Cell Division, Division, OCTD, dTAF250, secreted substance, Enzyme, IKK, bodily secretion, time of survival, CG3576, TAF, anon-WO0118547.350, membrane-bounded vesicle, Macronutrient, cellular breakdown, nutrient, data, TAF[[II]]250, Secretomes, Klebsiella pneumoniae aerogenes, degradation, Formal Social Control, protein complex, Proteins, fer, total expressed protein, l(3)84Ab, BG:DS00004.13, impact-a, Cell, Impact, Concept, dTAF230, Macronutrients, development, Environmental, IKKgamma, count in organism, survival, native protein, natural protein, Social Control, p230, Protein, TAF[[II]]250/230, TFIID, MFS1, Klebsiella rhinoscleromatis, connected anatomical system, l(1)G0061, M Phase, WMS2, breakdown of molecule, Taf[[II]]250, Phase, ferrum, DmelCG3576, TAF[[II]]230, biodegradation, Dmikkgamma, postnatal growth, TAF[II]250, Iron-56, CG16910, Protein Gene Products, Gene Proteins, extracellular, breakdown of substance, DmelCG17603, SSKS, Environments, Protein Secretome, hLON, regulation, virulence, acquisition by symbiont of nutrients from host via siderophores, growth, RWDD5, TAF10falseKpneumoniae - Whole organism, iBAQ (Museliusetal,frontmicrobiol2020)abundance based on iBAQ, Interaction consistency score: 13.2, Coverage: 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