GPMDB00135OtherPeebo K, et al.InstrumentNot AvailableNot availableEnterobacteria_phage_13a_uid30603, Enterobacteria_phage_933w_uid14043, Enterobacteria_phage_alpha3_uid14570, Enterobacteria_phage_ba14_uid30599, Enterobacteria_phage_bp_4795_uid14287, Enterobacteria_phage_bz13_uid14635, Enterobacteria_phage_cdti_uid19737, Enterobacteria_phage_ecods1_uid30601, Enterobacteria_phage_eps7_uid29287, Enterobacteria_phage_epsilon15_uid14285, Enterobacteria_phage_es18_uid15174, Enterobacteria_phage_felix_01_uid14323, Enterobacteria_phage_fels_2_uid32273, Enterobacteria_phage_fi_sensu_lato_uid15459, Enterobacteria_phage_g4_sensu_lato_uid14318, Enterobacteria_phage_hk022_uid14048, Enterobacteria_phage_hk620_uid14115, Enterobacteria_phage_hk97_uid14592, Enterobacteria_phage_i2_2_uid14572, Enterobacteria_phage_id18_sensu_lato_uid16628, Enterobacteria_phage_id2_moscow_id_2001_uid16591, Enterobacteria_phage_if1_uid14039, Enterobacteria_phage_ike_uid14627, Enterobacteria_phage_ime08_uid50177, Enterobacteria_phage_jk06_uid15569, Enterobacteria_phage_js10_uid38265, Enterobacteria_phage_js98_uid27983, Enterobacteria_phage_jse_uid38263, Enterobacteria_phage_k1e_uid16228, Enterobacteria_phage_k1f_uid15880, Enterobacteria_phage_k1_5_uid17059, Enterobacteria_phage_lambda_uid14204, Enterobacteria_phage_m13_uid14549, Enterobacteria_phage_min27_uid29143, Enterobacteria_phage_ms2_uid14659, Enterobacteria_phage_mu_uid14105, Enterobacteria_phage_n15_uid14086, Enterobacteria_phage_n4_uid18511, Enterobacteria_phage_p1_uid14493, Enterobacteria_phage_p22_uid14478, Enterobacteria_phage_p2_uid14035, Enterobacteria_phage_p4_uid14414, Enterobacteria_phage_phi1_uid20789, Enterobacteria_phage_phieco32_uid28729, Enterobacteria_phage_phiecom_gj1_uid27979, Enterobacteria_phage_phip27_uid14599, Enterobacteria_phage_phiv10_uid16381, Enterobacteria_phage_phix174_sensu_lato_uid14015, Enterobacteria_phage_prd1_uid14062, Enterobacteria_phage_psp3_uid14345, Enterobacteria_phage_rb14_uid37825, Enterobacteria_phage_rb16_uid51699, Enterobacteria_phage_rb32_uid17997, Enterobacteria_phage_rb43_uid15417, Enterobacteria_phage_rb49_uid14301, Enterobacteria_phage_rb51_uid37819, Enterobacteria_phage_rb69_uid15141, Enterobacteria_phage_rtp_uid16178, Enterobacteria_phage_sf6_uid14498, Enterobacteria_phage_sfv_uid14162, Enterobacteria_phage_sp6_uid14291, Enterobacteria_phage_ssl_2009a_uid34919, Enterobacteria_phage_st104_uid14499, Enterobacteria_phage_st64t_uid14230, Enterobacteria_phage_st_1_uid38669, Enterobacteria_phage_t1_uid14496, Enterobacteria_phage_t3_uid14336, Enterobacteria_phage_t4_uid14044, Enterobacteria_phage_t5_uid15143, Enterobacteria_phage_t7_uid14460, Enterobacteria_phage_tls_uid19775, Enterobacteria_phage_vt2_sakai_uid14480, Enterobacteria_phage_wa13_sensu_lato_uid16595, Enterobacteria_phage_wv8_uid38281, Enterobacteria_phage_yyz_2008_uid32231, Enterobacteriophage_qbeta_uid15479, Escherichia_coli_k_12_substr__dh10b, Escherichia_coli_k_12_substr__mg1655karl@tftak.eu25712329Tallinn University of Technology, Department of Chemistryhttp://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320007849http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320007845http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320007846http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320007847http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320007848http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320007863http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320007841http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320007842http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320007864http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320007843http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320007844http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320007860http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320007861http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320007862http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320007840http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320007839http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320007856http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320007857http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320007858http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320007859http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320007852http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320007853http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320007855http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320007850http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320007851Not availableGPMDBCells usually respond to changing growth conditions with a change in the specific growth rate (μ) and adjustment of their proteome to adapt and maintain metabolic efficiency. Description of the principles behind proteome resource allocation is important for understanding metabolic regulation in response to changing μ. Thus, we analysed the proteome resource allocation dynamics of Escherichia coli into different metabolic processes in response to changing μ. E. coli was grown on minimal and defined rich media in steady state continuous cultures at different μ and characterised combining two LC-MS/MS-based proteomics methods: stable isotope labelling by amino acids in cell culture (SILAC) and intensity based label-free absolute quantification. We detected slowly growing cells investing more proteome resources in energy generation and carbohydrate transport and metabolism whereas for achieving faster growth cells needed to devote most resources to translation and processes closely related to the protein synthesis pipeline. Furthermore, down-regulation of energy generation and carbohydrate metabolism proteins with faster growth displayed very similar expression dynamics with the global transcriptional regulator CRP (cyclic AMP receptor protein), pointing to a dominant protein resource allocating role of this protein. Our data also suggest that acetate overflow may be the result of global proteome resource optimisation as cells saved proteome resources by switching from fully respiratory to respiro-fermentative growth. The presented results give a quantitative overview of how E. coli adjusts its proteome to achieve faster growth and in future could contribute to the design of more efficient cell factories through proteome optimisation.Proteome reallocation in Escherichia coli with increasing specific growth rate.Peebo Karl K,Valgepea Kaspar K,Maser Andres A,Nahku Ranno R,Adamberg Kaarel K,Vilu Raivo R,Peebo Karl K, Valgepea Kaspar K, Maser Andres A, Nahku Ranno R, Adamberg Kaarel K, Vilu Raivo RAlkalescens-Dispar Group, Eschericia coli, Enteroaggregative Escherichia coli, Diffusely Adherent Escherichia coli, Bacterium coli, Bacterium coli commune, Escherichia/Shigella coli, Enteroinvasive E. coli, Diffusely Adherent E. coli, Bacillus coli, Escherchia coli, bacterium E3, E coli, Enteroinvasive Escherichia coli, Enterococcus coli, EAggEC, Proteomes, Enteroaggregative E. coli, E. coli.LC-MS2, liquid chromatography tandem mass spectroscopy, biochemical pathways, projections, incorporation, protein translation, sugar transport, data, protein anabolism, Metabolic Process, protein biosynthetic process, anatomical protrusion, degradation, Process, mol, Processes, lamellae, anatomical process, metabolism resulting in cell growth, number, LC-MS/MS, Metabolic Concepts, lamina, flanges, Sialic acid-binding Ig-like lectin 1, Metabolic Processes, presence, process of organ, Cell, LC-MS-MS, Concept, Metabolic Phenomena, protrusion, lamella, Metabolism Concepts, protein synthesis., count in organism, LC/MS/MS, count, uninterrupted, Metabolism, LC-MSMS, Phenomena, shelf, protein formation, smooth ER, Concepts, protein biosynthesis, Metabolism Concept, Phenomenon, metabolism, Metabolism Phenomena, flange, organ process, Metabolic Phenomenon, SER, mobilization, multicellular organism metabolic process, LCMSMS, Siglec-1, biodegradation, Metabolic, growth pattern, catabolism, non-developmental growth, shelves, Metabolic Concept, metabolic process resulting in cell growth, ridges, Sheep erythrocyte receptor, projection, ridge, turnover, process, processes, single-organism metabolic process, protein synthesis, spine, liquid chromatography-tandem mass spectroscopy, papilla, liquid chromatography tandem mass spectrometry, biotransformation, processus, quantitative, laminae, Catabolism, Proteomes, CD169, presence or absence in organism, AnabolismAlkalescens-Dispar Group, Eschericia coli, Enteroaggregative Escherichia coli, Diffusely Adherent Escherichia coli, Bacterium coli, Bacterium coli commune, Escherichia/Shigella coli, Enteroinvasive E. coli, Diffusely Adherent E. coli, Bacillus coli, Escherchia coli, bacterium E3, E coli, Enteroinvasive Escherichia coli, Enterococcus coli, EAggEC, Proteomes, Enteroaggregative E. coli, E. coli.projections, liquid chromatography tandem mass spectroscopy, biochemical pathways, protein translation, sugar transport, Metabolic Process, Allocation of Resources, Aminosaeure, Metabolic Concepts, ethanoate, bacterium E3, Downregulation, Productivity, Readability, uninterrupted, Roles, Method, responsivity, Concepts, 3, Enterococcus coli, Metabolism Concept, Phenomenon, LCMSMS, amino acids, Escherichia/Shigella coli, catabolism, D1S181E, cAMP, HEL-141, Catabolite, E coli, AW743261, metabolic process resulting in cell growth, proteins, procedures, Gene Activator, free, E. coli, CH3-COO(-), Eschericia coli, Enteroaggregative Escherichia coli, Activators, Catabolic Gene, Methodological Studies, papilla, Role Concepts, biotransformation, Resource Allocations, Catabolism, LC-MS2, incorporation, protein anabolism, anatomical protrusion, protein biosynthetic process, Epididymis luminal protein 141, Process, CRP4, 4)/p-1/fC2H3O2/q-1, Aminokarbonsaeure, CRP2, metabolism resulting in cell growth, CRP1, ACETATE ION, lamina, LC-MS/MS, cAMP Receptor Proteins, flanges, Efficiency, Procedure, Enteroaggregative E. coli, results, Role Concept, count, Receptor Down-Regulation, Diffusely Adherent E. coli, InChI=1/C2H4O2/c1-2(3)4/h1H3, Proteomes., shelf, protein formation, Activator Protein, Role, CSRP, Resources Allocation, regulator, Ethanoat, Receptor Protein, Allocations, Diffusely Adherent Escherichia coli, Ab1-341, carbohydrate metabolism, Catabolite Regulator Proteins, Enteroinvasive E. coli, Catabolite Activator, growth pattern, non-developmental growth, shelves, cAMP Receptor Protein, Methodological, Catabolic Gene Activators, Receptor Proteins, projection, Methodological Study, ridge, turnover, protein synthesis, spine, liquid chromatography-tandem mass spectroscopy, Acids, Catabolite Activator Protein, Proteomes, Aa1249, Ba2-693, Allocative, Cysteine-rich protein 1, Procedures, lamellae, Processes, Aminocarbonsaeure, number, Gene, InChIKey=QTBSBXVTEAMEQO-KSORUIRRCC, Metabolic Processes, Catabolite Gene Activator Protein, process of organ, presence, Allocative Efficiency, LC-MS-MS, protrusion, (H, lamella, Catabolic, Azetat, CYRP, Metabolism, Escherchia coli, LC-MSMS, single-organism carbohydrate metabolic process, ESP1, Studies, Gene Products, Regulator Protein, Enteroinvasive Escherichia coli, Gene Activators, Metabolism Phenomena, reactivity, multicellular organismal carbohydrate metabolic process, Activator Proteins, cell, Metabolic Concept, Activator, labeling, Cyclic AMP Receptor Proteins, ridges, Ac1-114, Catabolite Regulator, Study, Catabolite Gene Activator Proteins, 0610010I23Rik, Regulator Proteins, AI255847, laminae, Catabolite Regulator Protein, Alkalescens-Dispar Group, cAMP Receptor, data, Bacterium coli, degradation, C2H3O2, anatomical process, Proteins, ion(1-), EAggEC, Cell, Down Regulation, Concept, Metabolic Phenomena, polypeptide, Metabolism Concepts, count in organism, LC/MS/MS, Down-Regulation, Resource, Ac1262, Catabolic Gene Activator, Bacillus coli, Down-Regulation (Physiology), Protein, Phenomena, protein biosynthesis, CC([O-])=O, techniques, metabolism, flange, organ process, Metabolic Phenomenon, Crp, CRP, mobilization, multicellular organism metabolic process, biodegradation, Metabolic, Hlp, Allocation, Ab2-196, Understanding, Amino, Carbohydrate, Protein Gene Products, Catabolite Activator Proteins, process, processes, Gene Proteins, single-organism metabolic process, Bacterium coli commune, Ac2-069, MeCO2 anion, processus, liquid chromatography tandem mass spectrometry, regulation, Receptor, response, quantitative, acetic acid, PTX1, methodology, C77570, Anabolism, presence or absence in organism1305http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320007851dbgap_ncbi~0patentfamilies~0rfam~0merops~0complex-portal~0uniprot~0wormbaseparasite~0embl-covid19~0reactome~0emdb~0wgs_masters~0ebiweb_resources~0opentargets_genetics~0biomodels_all~0ipd-mhc~0ebiweb_teams~0taxonomy~0genome_assembly~0sc-experiments~0ebiweb_people~0enzymeportal_enzymes~0ipd-nhkir~0cellosaurus~0pdbe~0chebi~0patentproteins~0interpro7~0uniref~0chembl~0pdbekb~0gpcrdb~0hgnc~0sc-genes~0intact~0rhea~0ebiweb_training~0alphafold~0imgt-hla~0patentnucleotides~0ensemblroot~0eva_studies~0non-coding~0europepmc~0pubmed~1identifiers_registry~0pdbechem~0hpa-covid19~0eva-variants-covid19~0biosamples~0gwas_catalog~0biotools~0tls_masters~0mesh~0coding~0sra~0opentargets~0efo~0embl-pathogen~0project~0pride~1human_diseases~0geo_datasets~0embl~0treefam~0uniparc~0ols~0dgva~0intenz~0go~0tsa_masters~0biosamples-covid19~0ebiweb_corporate~0omim~0lrg~0earlycause-molecular-sequences~0ipd-kir~0empiar~0rnacentral~0orcid_data_claims~0gpmdb~2lineage-covid19~0metagenomics~0pfam~0pride archive~1varsite~00Resource Reanalysis0.00.00.0040098704503392970.01.0falseProteome reallocation in Escherichia coli with increasing specific growth rateData from ProteomeXchange, PXD ID: PXD001594. File: 130326_01_Orbi1_SK_SER_G250_T295_Piimhappe_BT_projekt_proov_F201_S2_P9.mzml. Published as part of Mol Biosyst. 2015 Feb 25 . From ProteomeXchange: {{i}} E. coli was grown on minimal and defined rich media in steady state continuous cultures at different mu and characterised by absolute quantitative LC-MS/MS based proteomics. We detected slowly growing cells investing more proteome resources in energy generation and carbohydrate transport and metabolism whereas for achieving faster growth cells needed to devote most resources to translation and processes closely related to the protein synthesis pipeline. {{/i}}2015-02-28GPM3232000785125712329PXD001594PXD001594