PAXDBapplication/xmlhttp://pax-db.org/downloads/latest/datasets/bioprojects-abundance-files-v4.0.zipprimaryOK2000000ProteomicsChristian von Mering309800https://pax-db.org/dataset/309800/1357931706mering@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.The membrane protease LonB is an essential protein in the archaeon Haloferax volcanii and globally impacts its physiology. However, natural substrates of the archaeal Lon protease have not been identified. The whole proteome turnover was examined in a H. volcanii LonB mutant under reduced and physiological protease levels. LC-MS/MS combined with stable isotope labeling was applied for the identification/quantitation of membrane and cytoplasm proteins. Differential synthesis and degradation rates were evidenced for 414 proteins in response to Lon expression. A total of 58 proteins involved in diverse cellular processes showed a degradation pattern (none/very little degradation in the absence of Lon and increased degradation in the presence of Lon) consistent with a LonB substrate, which was further substantiated for several of these candidates by pull-down assays. The most notable was phytoene synthase (PSY), the rate-limiting enzyme in carotenoid biosynthesis. The rapid degradation of PSY upon LonB induction in addition to the remarkable stabilization of this protein and hyperpigmentation phenotype in the Lon mutant strongly suggest that PSY is a LonB substrate. This work identifies for the first time candidate targets of the archaeal Lon protease and establishes proteolysis by Lon as a novel post-translational regulatory mechanism of carotenogenesis.LonB Protease Is a Novel Regulator of Carotenogenesis Controlling Degradation of Phytoene Synthase in Haloferax volcanii.Cerletti Micaela M, Paggi Roberto R, Troetschel Christian C, Ferrari María Celeste MC, Guevara Carina Ramallo CR, Albaum Stefan S, Poetsch Ansgar A, De Castro Rosana 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, ratioHDC07747, DMU42699, DmelCG42865, CG42865, TRH, Trh, Dmel_CG13885, l(3)10512, CG13885., bHLHe13, 3.1, CG6883, BP1081, Dmel_CG6883biochemical pathways, single-organism catabolic process, multicellular organismal catabolic process, cellular breakdown, Controlling, (15-cis)-isomer, breakdown, 11', reference sample, biodegradation, degradation, breakdown of chemical, all-trans-phytoene, catabolism, 7', cellular catabolism, 11, 12, breakdown of substance, 12'-octahydro-psi, (all-E)-, trans-phytoene, Halobacterium volcanii., psi-carotene, 8', (cis)-isomer, cellular degradation, biotransformation, secretion, 7, 8, regulator, phytoene, 15-cis-phytoene, Controlled, breakdown of moleculeds2, l(2)k04603, multi-cellular organism, Dm01335, whole organism, T28P16.15, body, CG5920, T28P16_15, sop, whole body, 7-11HD, anon-EST:Posey202, CG5925, desat-2, DELTA 9 DESATURASE, dS2, Desat2, organism, DmelCG5920, Fad, DmelCG5925, Koerper, desat, Rp S2, animal, desat2/Fad, ADS2, l(2)03848, 16:0delta9 desaturase 2, 2018., S2liquid chromatography tandem mass spectroscopy, biochemical pathways, single-organism catabolic process, multicellular organismal catabolic process, carotenoid synthesis, Ghrfr, 11', Effects, Biocatalysts, Degradation, number, Gene, LonHS, protein, biosynthesis, PIM1, protein-containing complex, Isotope-Coded Affinity, Hypermelanosis, supernumerary, presence, cellular catabolism, carotenoid formation, Long Term, LC-MS-MS, Protoplasm, protrusion, 11, 12, Membrane Tissues, protein polypeptide chains, DmelCG8798, polypeptide chain, reduced, Lon, LON, integral component of membrane, LC-MSMS, Gene Products, cellular degradation, tiny, Isotopically-Coded Affinity, 7, protein aggregate, 8, Effect, Isotopically-Coded Affinity Tagging, 15-cis-phytoene, multicellular organismal biosynthetic process, increased, single-organism biosynthetic process, LCMSMS, pattern, lon, ATP-dependent proteolysis, formation, breakdown of chemical, all-trans-phytoene, Longterm, Tissues, catabolism, distribution, anabolism, absent from organism, membrane region, Tissue, hypoplasia, Lag1., proteins, Long-Term, Protein Degradations, Protein Degradation, synthesis, Enzyme, Stable, (all-E)-, psi-carotene, Isotope-Coded Affinity Tagging, region of membrane, CG3576, biotransformation, Long-Term Effect, Tagging, anon-WO0118547.350, Long-Term Effects, Stable Isotope Labeling, small, LC-MS2, Membrane Tissue, cellular breakdown, membrane, carotenoid biosynthesis, Archaebacteria, Archaeobacteria, (15-cis)-isomer, Degradations, anatomical protrusion, degradation, protein complex, synthesize, Cytoplasms, Proteins, LC-MS/MS, Longterm Effect, integral to membrane, total expressed protein, CG8798, lit, function, membranous organ component, Protein Digestion, Labeling, Digestions, Hypermelanoses, DLag1, DLAG1, Isotope, count in organism, LC/MS/MS, Prss15, LONP, 12'-octahydro-psi, native protein, PRSS15, natural protein, Halobacterium volcanii, Proteolyses, Stable Isotope, trans-phytoene, Digestion, Protein, Long Term Effects, whole membrane, (cis)-isomer, secretion, l(1)G0061, Archebacteria, Isotope Coded Affinity Tagging, phytoene, breakdown of molecule, little, transmembrane, membrane of organ, absence, DmelCG3576, breakdown, biodegradation, underdeveloped, increased number, Protein Digestions, 7', Dlag1, Isotope Labeling, Membrane, 1200017E13Rik, Lag1, Affinity Tagging, Isotopically-Coded, Longterm Effects, carotenoid anabolism, Protein Gene Products, l(1)G0365, Gene Proteins, present in greater numbers in organism, Phenotypes, breakdown of substance, spine, liquid chromatography-tandem mass spectroscopy, lag1, l(1)G0489, Protoplasms, 8', Biocatalyst, Archaeon, Isotope-Coded, liquid chromatography tandem mass spectrometry, hLON, CG15898, Proteomes, accessory0falseHvolcanii DS2 - Whole organism, SC (Cerlettietal,j.proteomeres.2018)abundance based on Spectral counting, Interaction consistency score: 3.1, Coverage: 13135793170629411617D4GUH5_HALVDD4GZL6_HALVDD4GR98_HALVDD4GSW1_HALVDD4GT81_HALVDD4GZG3_HALVDD4GVS6_HALVDD4GRV6_HALVDD4GWZ7_HALVDD4GYY0_HALVDD4GTA4_HALVDD4GUM8_HALVDD4GZT6_HALVDD4GSH9_HALVDRADA_HALVDD4GTN7_HALVDD4GSX4_HALVDD4GP49_HALVDD4GZX6_HALVDD4GYN8_HALVDD4GZC3_HALVDPYREL_HALVDD4GTR7_HALVDNUOCD_HALVDD4GTZ2_HALVDD4GQH8_HALVDD4GPY2_HALVDD4GTW5_HALVDD4GPT4_HALVDD4GQ14_HALVDD4GTI4_HALVDD4GRN6_HALVDD4GXP5_HALVDD4GPU2_HALVDD4GP04_HALVDQ1XBW1_HALVDD4GQR2_HALVDD4GQ22_HALVDD4GW81_HALVDD4GWT1_HALVDD4GXG7_HALVDD4GT46_HALVDD4GS68_HALVDD4GTB2_HALVDD4GUM3_HALVDAGLG_HALVDD4GZ06_HALVDD4GUI3_HALVDD4GRB6_HALVDD4GYP9_HALVDAGL6_HALVDGLN1A_HALVDD4GTJ2_HALVDD4GUK7_HALVDD4GUW2_HALVDD4GQ94_HALVDTHS2_HALVDD4GYS6_HALVDVATC_HALVDRL1_HALVDNREA_HALVDD4GYH9_HALVDD4GPA0_HALVDD4GSQ2_HALVDD4GT62_HALVDD4GYW1_HALVDD4H0D0_HALVDD4GXG2_HALVDD4GWH6_HALVDD4GWN2_HALVDD4GUN6_HALVDD4GTG3_HALVDD4GPI0_HALVDAGLB_HALVDD4GRM3_HALVDD4GT33_HALVDD4GTY6_HALVDD4GZI2_HALVDD4GUB6_HALVDD4GRK7_HALVDD4GYP4_HALVDD4GUW4_HALVDD4GW92_HALVDD4GVX2_HALVDD4GY36_HALVDVATE_HALVDD4GPT6_HALVDD4GSP2_HALVDD4GRT7_HALVDD4GVZ5_HALVDD4GQR9_HALVDD4GR74_HALVDCAS6_HALVDD4GXX3_HALVDD4GSZ5_HALVDD4GQU9_HALVDD4GWS5_HALVDD4GV57_HALVDD4GRW2_HALVDD4GTZ0_HALVDD4GTR9_HALVDD4GT20_HALVDD4GW44_HALVDD4GTY1_HALVDD4H037_HALVDD4GVK1_HALVDD4GQG0_HALVDD4GTX6_HALVDD4H042_HALVDD4GW94_HALVDD4GXM1_HALVDD4GSF0_HALVDD4GZQ4_HALVDD4GRZ1_HALVDD4GYN3_HALVDD4GU45_HALVDD4GPT9_HALVDD4GW65_HALVDD4GYF3_HALVDD4GTQ2_HALVDD4GVZ8_HALVDD4GST9_HALVDD4GT59_HALVDD4GYQ0_HALVDPAN2_HALVDD4GTX8_HALVDD4GVP4_HALVDD4GUV9_HALVDD4GXB4_HALVDD4GUM1_HALVDTHTR_HALVDD4GV18_HALVDD4GY92_HALVDD4GUK5_HALVDD4GWM1_HALVDD4GX41_HALVDD4GWS1_HALVDD4H050_HALVDD4GZE0_HALVDD4GVG3_HALVDD4GUQ5_HALVDD4GTD4_HALVDD4GYS8_HALVDD4H056_HALVDD4GZY6_HALVDD4GVF6_HALVDD4GV80_HALVDD4GWG6_HALVDD4GXH2_HALVDD4GYP0_HALVDD4H049_HALVDD4GUF8_HALVDD4GUD8_HALVDD4GSN1_HALVDD4GZU0_HALVDD4GZ02_HALVDD4GRI5_HALVDD4GVB6_HALVDD4GZ62_HALVDD4GQ85_HALVDFTSZ1_HALVDD4GZY7_HALVDD4GQK7_HALVDD4GUG0_HALVDD4GTS8_HALVDD4GU21_HALVDD4GWM6_HALVDD4GYY9_HALVDD4GUA4_HALVDD4GU54_HALVDD4GTD5_HALVDD4H0E1_HALVDD4GZP8_HALVDD4GTY7_HALVDD4GYJ6_HALVDD4GW68_HALVDD4GX33_HALVDD4GYI3_HALVDD4GVF5_HALVDD4GXG9_HALVDD4GV19_HALVDD4GW22_HALVDD4GPF8_HALVDURIC_HALVDD4H064_HALVDGLPA1_HALVDDPM1L_HALVDD4GWY1_HALVDD4GRX8_HALVDD4GXR7_HALVDD4GX79_HALVDD4GRH8_HALVDD4GZ07_HALVDD4GWF9_HALVDTHS3_HALVDD4GXW9_HALVDD4GYP1_HALVDD4GTE0_HALVDRL11_HALVDD4GWX0_HALVDFTSZ2_HALVDD4GWR8_HALVDD4GX38_HALVDD4GX40_HALVDD4GW85_HALVDD4GPU9_HALVDD4GRI1_HALVDD4GT52_HALVDD4GYI9_HALVDD4GQG3_HALVDD4GR87_HALVDD4GYD4_HALVDD4GV09_HALVDD4GVG4_HALVDD4GTZ3_HALVDD4GYC9_HALVDD4GTT9_HALVDGLPK_HALVDD4GT00_HALVDD4GZJ5_HALVDD4GSN8_HALVDD4GTJ3_HALVDCETZ6_HALVDD4GTZ6_HALVDD4GP72_HALVDD4GXY4_HALVDD4GTJ6_HALVDRAD50_HALVDD4GUK6_HALVDD4H055_HALVDALF_HALVDD4GW84_HALVDD4GX92_HALVDD4GTT8_HALVDD4GZV0_HALVDPSA2_HALVDD4GVV8_HALVDD4GW78_HALVDD4GZ03_HALVDD4GSN7_HALVDD4GS94_HALVDD4GVF8_HALVDD4GYI6_HALVDD4GZF1_HALVDD4H061_HALVDD4GY50_HALVDDACZ_HALVDD4GUU7_HALVDD4GWX3_HALVDD4GTZ5_HALVDPSA1_HALVDD4GW83_HALVDD4GTJ4_HALVDD4GXC6_HALVDD4GTU3_HALVDD4GYZ2_HALVDD4GV21_HALVDD4GSU1_HALVDD4GQV8_HALVDD4GVU6_HALVDD4GVQ6_HALVDD4GSF9_HALVDD4GVH3_HALVDTHS1_HALVDD4GUK8_HALVDCSG_HALVDD4GP51_HALVDD4GVK0_HALVDD4GVT3_HALVDD4GSJ9_HALVDD4GUM2_HALVDD4GPA1_HALVDD4GTY5_HALVDD4GWK9_HALVDD4GX17_HALVDD4GUV5_HALVDD4GWZ1_HALVDD4GSR4_HALVDD4GXV5_HALVDD4GZ85_HALVDPSB_HALVDSRP54_HALVDD4GX49_HALVDD4GWX7_HALVDD4GXI7_HALVDD4GX09_HALVDD4GRE2_HALVDD4GVZ4_HALVDD4GZX7_HALVDD4GTV1_HALVDQ1XBW2_HALVDD4GTE5_HALVDD4H019_HALVDD4GPB9_HALVDD4GZY3_HALVDD4GPJ9_HALVDD4GQX9_HALVDD4GQ21_HALVDD4GYP3_HALVDD4GZ00_HALVDD4GV30_HALVDD4GTB8_HALVDIDH_HALVDD4GTY0_HALVDD4GSN9_HALVDD4GVD8_HALVDD4GUG8_HALVDD4GZY8_HALVDD4GTU0_HALVDD4GTZ1_HALVDD4GYI4_HALVDD4GWM8_HALVDSECF_HALVDPAN1_HALVDD4GXY9_HALVDD4GWD2_HALVDD4GSG5_HALVDD4GVJ7_HALVDAGL7_HALVDD4GWL5_HALVDAGLP_HALVDD4GXW6_HALVDD4GS27_HALVDD4GWI5_HALVDD4GR09_HALVDD4GWY3_HALVDD4GVN2_HALVDD4GZV8_HALVDD4GS24_HALVDD4GXM0_HALVDD4GYF4_HALVDD4GS85_HALVDD4GWG2_HALVDD4GPA8_HALVDD4GTX9_HALVDD4GPH0_HALVDD4GZT5_HALVDD4GTV3_HALVDD4GYB7_HALVDD4GQ10_HALVDD4GYJ7_HALVDD4GZ37_HALVDD4GZA5_HALVDD4GUE0_HALVDD4GUT6_HALVDD4GYR9_HALVDANTRB_HALVDD4GVZ7_HALVDD4GWS6_HALVDD4GX82_HALVDFTSY_HALVDD4GQP7_HALVDD4GWA3_HALVDD4GWY5_HALVDD4GZB1_HALVDD4GYU6_HALVDD4GPB6_HALVDSECD_HALVDCAS8B_HALVDD4GVE6_HALVDD4GSM4_HALVDD4GWS7_HALVDD4GRR2_HALVDCETZ1_HALVDD4GVC3_HALVDD4H0F7_HALVDD4GX81_HALVDD4GZI5_HALVDD4H067_HALVDCAS5_HALVDD4GYF2_HALVDD4GTS6_HALVDD4GQ40_HALVDRL18_HALVDD4GWP9_HALVDD4GUL6_HALVDD4GYB5_HALVDD4GUI5_HALVDD4GVT6_HALVDD4GS66_HALVDD4GSE9_HALVDD4GSX1_HALVDGGR_HALVDD4GT91_HALVDAGL10_HALVDD4GVS3_HALVDD4GYU8_HALVDD4GUS5_HALVDDNLJ_HALVDD4GSV7_HALVDD4GU42_HALVDD4GZY1_HALVDD4GYN0_HALVDD4GWE6_HALVDD4GRA5_HALVDD4GV60_HALVDD4GXF2_HALVDD4GT09_HALVDD4GZS0_HALVDVATA_HALVDD4GQ97_HALVDD4H090_HALVDD4GRZ3_HALVDD4GRL3_HALVDD4GWI6_HALVDD4GP47_HALVDD4GVZ6_HALVDD4GYC2_HALVDD4GVH6_HALVDD4GUY6_HALVDD4GV86_HALVDD4GWT4_HALVDD4GPY5_HALVDD4GSA3_HALVDD4GVY4_HALVDD4H035_HALVDD4GYB0_HALVDCAS7_HALVDD4GTX4_HALVDD4GP86_HALVDD4GYF6_HALVDD4GSL7_HALVDD4GVJ5_HALVDD4GWJ9_HALVDD4GTL4_HALVDD4GQZ0_HALVDD4H036_HALVDD4GSE8_HALVDMDH_HALVDD4GWZ3_HALVDD4GTX5_HALVDD4GV93_HALVDD4GPZ2_HALVDD4GY71_HALVDD4GXF1_HALVDD4GR08_HALVDD4GY77_HALVDD4GZG5_HALVDFLGA1_HALVDD4GWU7_HALVDD4GY09_HALVDTBP2_HALVDQ1XBW3_HALVDD4GTQ6_HALVDD4GS18_HALVDVATB_HALVDD4GU86_HALVDD4GZ34_HALVDD4GYR4_HALVDD4GYQ4_HALVDD4GT78_HALVDD4GSB2_HALVDD4GYW4_HALVDD4GPT3_HALVDD4GTN0_HALVDD4GP88_HALVDD4GT25_HALVDD4GY23_HALVDD4GVU2_HALVDD4GQ46_HALVDD4GVY5_HALVDLEUC_HALVDD4GSW0_HALVDD4GZR5_HALVDD4GX65_HALVDD4GTG8_HALVDD4GUC3_HALVDD4GVS7_HALVDD4GW47_HALVDD4GU90_HALVDD4GTX0_HALVDD4GPD3_HALVDD4GT75_HALVDD4GP38_HALVDD4GPN3_HALVDD4GUG9_HALVDD4GPC8_HALVDD4GS65_HALVDD4GR03_HALVDD4GZX5_HALVDD4GXP9_HALVDD4GY19_HALVDD4GTR6_HALVDD4H082_HALVDD4GSQ3_HALVDD4GU28_HALVDD4GUD0_HALVDSECY_HALVDD4GXQ1_HALVDD4GZY0_HALVDD4GUS3_HALVDD4GS21_HALVDD4GZX4_HALVDD4GVY7_HALVDD4GTB5_HALVDD4GQ51_HALVDD4GUH7_HALVDD4GS14_HALVDD4GYW3_HALVDD4GRU7_HALVDD4GYV8_HALVDD4GSF6_HALVDD4GU40_HALVDD4GU29_HALVDD4GVJ1_HALVDD4GW49_HALVDD4GZ32_HALVDD4GVY6_HALVDD4GZS2_HALVDD4GVI6_HALVDD4GXE9_HALVDD4GVT4_HALVDD4GWE4_HALVDD4GV96_HALVDD4GUI1_HALVDD4GX64_HALVDD4GZC2_HALVDD4GYQ7_HALVD