Prideapplication/xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/11/PXD010845/mqpar.xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/11/PXD010845/4.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/11/PXD010845/5.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/11/PXD010845/2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/11/PXD010845/7.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/11/PXD010845/8.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/11/PXD010845/9.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/11/PXD010845/3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/11/PXD010845/10.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/11/PXD010845/1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/11/PXD010845/6.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/11/PXD010845/search.zipprimaryOK200liuxiaoxiang413@126.comxiaonan fuMass SpectrometryShotgun proteomicsNot availableRegulonRposTranscriptomeProteomePseudomonas fluorescenshttp://www.ebi.ac.uk/pride/archive/projects/PXD010845Whole BodyBacterial strains and culture conditions Wild-type P. fluorescens strain UK4 and the rpoS in-frame deletion mutant (Liu et al., 2018) were grown aerobically at 28°C with shaking at 220 rpm in Nutrient Broth (NB) medium, and growth was monitored spectrophotometrically at OD600. Cultures were grown in triplicate and the bacterial cells at stationary-phase (OD600 ≈ 1.5) were harvested by centrifugation at 7,000 g for 10 min and were frozen in liquid nitrogen prior to RNA and protein isolation. Illumina library preparation and RNA-seq Three biological repeats were prepared for the wild type strain and the rpoS mutant. The total RNA was isolated using RNeasy Plant Mini Kit (Qiagen, Germany) and was treated with RNase-Free DNase Set (Qiagen, Germany) to remove the contaminating DNA. The concentration and quality were determined using a NanoDrop spectrophotometer (Thermo, USA) and Agilent 2100 Bioanalyzer (Agilent, USA). Then, rRNA from the total RNAs was removed using a Ribo-Zero Magnetic Kit (Epicentre, USA) for Gram-Negative bacteria per the manufacturer’s protocol. Fragmentation buffer was added to cleave the mRNA into short fragments. Strand-specific RNA sequencing libraries were prepared by following a modified deoxy-UTP (dUTP) strand-marking protocol described previously [63]. Briefly, first strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (NEB, USA). Double-stranded cDNA was subsequently synthesized with dUTP incorporation into the second strand. Illumina TruSeq adaptors were ligated to the ends of the cDNA fragments and amplified according to the manufacturer’s instructions (Illumina, USA). In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, USA). Then the dUTP-marked strand was selectively degraded with USER enzyme (NEB, USA) and the remaining strand was amplified to generate a cDNA library suitable for sequencing. Following validation with the Agilent Bioanalyzer 2100 system (Agilent, USA), the cDNA library was sequenced on a flow cell using high-throughput 150-bp pair-end mode on an Illumina HiSeq 4000 platform (Illumina, USA).PrideNot availableNo PTMs are included in the datasetProteomics data processing The resulting MS/MS data was processed using MaxQuant with integrated Andromeda search engine (v.1.5.2.8). Tandem mass spectra were searched against the genome database of P. fluorescens UK4 containing 5321 proteins in Genbank (http://www.pseudomonas.com/). Trypsin/P was specified as cleavage enzyme allowing up to 2 missing cleavages. Mass error was set to 10 ppm for precursor ions and 0.02 Da for fragment ions. Carbamidomethyl on Cys was specified as fixed modification, while oxidation on Met and Acetylation on protein N-term were specified as variable modifications. For protein quantitation, Protein quantitative ratios were weighted and normalized relative to the median ratio in Mascot (http://www.matrixscience.com). Only proteins with significant quantitative ratios between the two strains (p < 0.05) and with fold changes >1.2 or <0.83 were considered to be differentially expressed.ProteomicsXiaoxiang LiuQ ExactiveSchool of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, Hangzhou, Zhejiang 310053, P.R.ChinaPARTIALPseudomonas Fluorescens2016460649@qq.com30787912 Liu X, Xu J, Zhu J, Du P, Sun A. Combined Transcriptome and Proteome Analysis of RpoS Regulon Reveals Its Role in Spoilage Potential of Pseudomonas fluorescens. Front Microbiol. 2019 10:94 10.3389/fmicb.2019.00094Biologicalzhejiang scientific technology universitiyChinaMicrobial contamination is considered the main cause of food spoilage. <i>Pseudomonas fluorescens</i> is a typical spoilage bacterium contributing to a large extent to the spoilage process of proteinaceous foods. RpoS is known as an alternative sigma factor controlling stress resistance and virulence in many pathogens. Our previous work revealed that RpoS contributes to the spoilage activities of <i>P</i>. <i>fluorescens</i> by regulating resistance to different stress conditions, extracellular acylated homoserine lactone (AHL) levels, extracellular protease and total volatile basic nitrogen (TVB-N) production. However, RpoS-dependent genes in <i>P</i>. <i>fluorescens</i> remained undefined. RNA-seq transcriptomics analysis combined with quantitative proteomics analysis based on multiplexed isobaric tandem mass tag (TMT) labeling was performed in the <i>P</i>. <i>fluorescens</i> wild-type strain UK4 and its derivative carrying an <i>rpoS</i> mutation. A total of 375 differentially expressed coding sequences (DECs) and 212 differentially expressed proteins (DEPs) were identified. The DECs were further verified by qRT-PCR. The combined transcriptome and proteome analyses revealed the involvement of this regulator in several cellular processes, mainly including polysaccharide metabolism, intracellular secretion, extracellular structures, cell wall biogenesis, stress responses, and amino acid and biogenic amine metabolism, which may contribute to the biofilm formation, stress resistance, and spoilage activities of <i>P</i>. <i>fluorescens</i>. Moreover, we indeed observed that RpoS contributed to the production of the macrocolony biofilm's matrix. Our results provide insights into the regulatory network of RpoS and expand the knowledge about the role of RpoS in the functioning of <i>P. fluorescens</i> in food spoilage.Combined Transcriptome and Proteome Analysis of RpoS Regulon Reveals Its Role in Spoilage Potential of <i>Pseudomonas fluorescens</i>.Liu Xiaoxiang X, Xu Jun J, Zhu Junli J, Du Peng P, Sun Aihua AHERV-K(III) Pol protein, Ribonucleic, IPP2A2, nebb, RNA Sequence Determination, CG10718, Sequence Determination, Pflanze, postnatal development, RNA Sequence, A4, ribosomal RNA, growth and development, protein, Xkl-1, viridiplantae, Integrase, 5730420M11Rik, Background, protein polypeptide chains, KL receptor activity, Gsfsco1, cDNA library construction, Cultural, sl(2)ry, SCO5, Min, SCO1, Analysis, protein aggregate, Gsfsow3, HERV-K_19p13.11 provirus ancestral Pol protein, Gsfsco5, CG18546, Non Polyadenylated, DmelCG42273, RNA Gene Products, SOW3, D2Bwg0749e, RT, SET, ethnicity, thymus nucleic acid, Analyses, HERV-K_1q23.3 provirus ancestral Pol protein, TAF-I, Determination, N, phosphatase 2A inhibitor I2PP2A, complementary DNA, klp38B, min, nucleic acid library preparation, 5031412I06Rik, mAPC, proteins, purification, W, Sequence Determinations, ecotype, free, AI047805, DmelCG4299, isolation and purification, set, IGAAD, HERV-K_11q22.1 provirus ancestral Pol protein, DmelCG10574, DNAse, mitotic nuclear envelope breakdown, Bs, s, Double-Stranded DNA, Strains, deoxyribonucleic acids, KLP 38B, DNAn, Sl, phapii, KIF14, total RNA extract, HERV-K_5q33.3 provirus ancestral Pol protein, ribose nucleic acid, ribonucleic acids, Dmel_CG7826, StF-IT-1, RNA-seq, Tr-kit, Double-Stranded, anon-WO03070958.3, tio, Determinations, (Deoxyribonucleotide)n+m, shortened, PBT, HERV-K107 Pol protein, Cultural Background, Cultures, Dm1, Stickstoff, mitotic nuclear envelope degradation, Ribonukleinsaeure, HERV-K_19q11 provirus ancestral Pol protein, kl1-A, pentosenucleic acids, 5133400F09Rik, cultivar, Ribonucleic acids, HiSeq 4000., KIT, desoxyribose nucleic acid, END, Dmel_CG7835, Mnb, MNB, tyrosine-protein kinase Kit, Acid, pbt, oligonucleotide random primer, HLA-DR-associated protein II, protein_coding_transcript, growth pattern, DI-2, HERV-K_3q27.2 provirus ancestral Pol protein, non-developmental growth, Dutp, I-2Dm, Plant, HERV-K110 Pol protein, kit, CG4299, inhibitor of granzyme A-activated DNase, AW124434, study protocol, I-2PP1, organ system, Reverse transcriptase, NEB177D, DMDA, nitrogen, TAF-IBETA, HERV-K(C19) Pol protein, ds DNA, 2018, Mot, TAF-Ibeta, HERV-K_8p23.1 provirus ancestral Pol protein, DNA, 7N, short, HERV-K(HML-2.HOM) Pol protein, Strains and Sprains, i2pp2a, HERV-K_1q22 provirus ancestral Pol protein, krk1, mitotic nuclear envelope catabolism, HERV-K10 Pol protein, Beliefs, DNS, 38B.12, Ribonuclease H, (Deoxyribonucleotide)n, 38B.10, DmKlp38B, SCF receptor activity, protein-containing complex, body system, TYPE, DmelCG10718, CG7826, PHAPII, Deoxyribonucleic acids, KLP-38B, Buffer, DAGA4, method, HERV-K115 Pol protein, IN, local NEB, polypeptide chain, scfr, template-activating factor I, Deoxyribonucleic Acid, isolation, method used in an experiment, Klp38B, CG7835, Gene Products, CG42273, Whole Transcriptome Shotgun Sequencing, system, HERV-K18 Pol protein, MAM, Sprains, SCG3, SCFR, l(2)k00802, Backgrounds, plantae, KLP38B, flow_cell, Fdc, anatomical systems, HERV-K(C1a) Pol protein, nutrients, ipp2a2, nucleic acid library construction, stubby, 2pp2a, Double Stranded, messenger RNA, Cultural Relativisms, Deoxyribonucleic acid, NEM2, CG10574, Sequencing, ribosomal ribonucleic acid, Non-Polyadenylated RNA, template RNA, dUTPase, RANDOM, 2PP2A, RNA Sequence Analyses, taf-ibeta, Neb, NEB, HERV-K_7p22.1 provirus ancestral Pol protein, dSET, dSet, Gram Negative Bacteria, Customs, RNA Sequencing, liquid, (Deoxyribonucleotide)m, culture, RNase H, HHT1, Sequence Analyses, nutrient, proto-oncogene c-Kit, DYRK1, RNA, protein complex, RNA Sequence Determinations, DNAn+1, Sprain, mitotic nuclear envelope disassembly, igaad, DmelCG31211, RNS, Cultural Backgrounds, nuclear envelope breakdown, cDNA, buffer, Cell, LGMD2C, HERV-K102 Pol protein, Belief, strain, oligonucleotide primer, development, l(2)03552, HERV-K108 Pol protein, native protein, INSDC_feature:rRNA, natural protein, I-2PP2A, KIT ligand receptor activity, yeast nucleic acid, Protein, Dm I-2, Strain, I2PP2A, INSDC_feature:mRNA, Dyrk1, 3.1.26.4, ds-DNA, connected anatomical system, Library, XKrk1, Random selection by shearing, AU020952, ribonucleic acid, c-KIT, l(2)k07614, DMDA1, mRNA, library construction, Non Polyadenylated RNA, CC1, postnatal growth, Non-Polyadenylated, Magnetic, INSDC_qualifier:unknown, HERV-K(C7) Pol protein, azote, Ribonucleic Acid, HERV-K113 Pol protein, CD117, CG14732, ME-IV, nitrogeno, plan specification, dSET/TAF-Ibeta, c-kit, 2610030F17Rik, Klp38, C-Kit, DEL, concentration, Dm0332, Ssm, RNA Sequence Analysis, SCARMD2, xkl-1, Desoxyribonukleinsaeure, Relativisms, Relativism, sl(2)ry3, ORW1, Cultural Relativism, AA407739, growth, 2.7.7.49Transcriptome, determination, Transcriptome Profile, Profile, Expression Profiles, Bacterium fluorescens, Gene Expression Profile, total expressed protein, Gene, Regulons, Profiles, Signatures, Concept, Gene Expression, Bacillus fluorescens, Bacterium fluorescen, Role Concept, Bacillus fluorescens liquefaciens, Expression Signature, Roles, Gene Expression Profiles, Expression Signatures, Gene Expression Signatures, chemical analysis, Role Concepts, Transcriptomes, Role, Concepts, Gene Expression Signature, assay, Signature, Liquidomonas fluorescens., Expression Profile, Proteomes, Transcriptome ProfilesIPP2A2, Pseudomona, 2-amino-4-(methylsulfanyl)butanoic acid, ion, Hgfr, Peptidomics, AW549739, Ass-1, number, cleavage, FBN, 5730555F13Rik, Gene, Flavimonas, protein, precursor, protein-containing complex, presence, PHAPII, 5730420M11Rik, protein polypeptide chains, HGF, Methionine, template-activating factor I, polypeptide chain, HGFR, ECTOL1, Gene Products, fold, F15E12.6, nom. rejic. Opin. 6 (not "Chlorobacterium" Lauterborn 1916), RCCP2, protein aggregate, Sprains, WMS, C79691, Search Engines, SET, F15E12_6, proportion, Genomes, TAF-I, MUB3_18, "Chlorobacterium" Guillebeau 1890, scatter factor receptor, iones, M, phosphatase 2A inhibitor I2PP2A, ipp2a2, Acetylations, 2pp2a, proteins, MUB3.18, ions, CG10574, AUTS9, OCTD, DmelCG4299, Lccp, ASS, mKIAA0989, set, IGAAD, data processing, 2PP2A, 2-amino-4-(methylthio)butanoic acid, 10^[-6], DmelCG10574, taf-ibeta, ppm, dSET, dSet, Strains, AI838057, RG7MT1, GPHYSD2, metionina, AA408052., Racemethionine, SGS, ratio, phapii, Chryseomonas, data, proto-oncogene c-Met, DL-Methionine, PRO, protein complex, Proteins, acetylation, Sprain, igaad, 2-Amino-4-(methylthio)butyric acid, StF-IT-1, Search, 9130215G10Rik, CYS, Engine, Loefflerella, ACMICD, RNA similarity group I, count in organism, native protein, Ionen, natural protein, I-2PP2A, Protein, Dm I-2, Liquidomonas, I2PP2A, Strain, MFS1, Methionin, median, methionine, Hmet, and GLY protein 2, WMS2, Data Base, ATCMPG1, MET, Met, ATCMPG2, parent ion, HGF receptor, HGF/SF receptor, and GLY protein 1, HLA-DR-associated protein II, DI-2, I-2Dm, tyrosine-protein kinase Met, proportionality, rate, MASCOT, MASS, CG4299, inhibitor of granzyme A-activated DNase, hCMT1c, c-Met, Protein Gene Products, I-2PP1, Gene Proteins, data analysis, dSET/TAF-Ibeta, 2610030F17Rik, TAF-IBETA, precursor ion, Ion, SSKS, alpha-amino-gamma-methylmercaptobutyric acid, quotient, TAF-Ibeta, Par4, quantitative, variable, AA407739, i2pp2a, 5730455C01Rik, Strains and Sprains, SF receptor, presence or absence in organismextent, projections, multicellular organismal polysaccharide metabolic process, Materials, nucleocytoplasm, acute necrotizing hemorrhagic leukoencephalitis, determination, Mbp1, A4, Gene Expression Profile, Profiles, Liquidomonas fluorescens, infectivity, Mutations, dmTAF[[II]]230, Bacillus fluorescens, qRT-PCR, Roles, Concepts, myd, R-717, WMS, ammoniac, viral infection, dermoid cyst with malignant transformation, TFIID TAF250, cel, N, Mbp-1, Bodily, virus process, proteins, W, ecotype, Signatures, retention, Des1, sals, DES1, ACE, AMMONIA, Secretion, DEGS-1, Expression Signature, papilla, Secretions, spirit of hartshorn, Role Concepts, Transcriptomes, v, GPHYSD2, xCYP26, intracellular, SGS, br31, bus, Mdes, MLD, dTAF[[II]]230, anatomical protrusion, gyltl1b-b, completeness, RT-rt PCR, external secretion, homoserine lactone hydrochloride, Expression Profiles, lamina, TAF200, flanges, RNA-seq, TAFII-250, TAF250/230, mdfw, results, ACMICD, Gene Expression, exocrine gland fluid/secretion, Bodily Secretion, S-adenosyl-L-methionine:thiol S-methyltransferase activity, TAFII250, Role Concept, Stickstoff, MDDGA6, mKIAA0609, Expression Signatures, shelf, Pathogenicity, Role, Genetic Materials, secretion, cultivar, internal to cell, W., regulator, Expression Profile, Genetic Material, PCR, Transcriptome Profiles, fg, AA536663, gyltl1b, maintenance of localization, shelves, mdc1d, expanded, MASS, Race, CG17603, projection, TAF[[II]], ridge, MDC1D, homoserine lactone, race, nitrogen, DMDA, Bacillus fluorescens liquefaciens, nmf181, enr, enlarged, Taf250, spine, Material, SR3-5, Ammonia, Cistron, 7N, RACE, TMT, exocrine gland secretion, Des-1, Proteomes, TAF230, big, degs, Ahl, AHL, d230, ammonia, exocrine gland fluid, Peptidomics, Transcriptome Profile, exocrine gland fluid or secretion, lamellae, amoniaco, number, FBN, Gene, FADS7, dTAFII250, l(2)br31, EfW1, process of organ, presence, TYPE, froggy, Gyltl1a, protrusion, DAGA4, lamella, large, ahl, dmTAF1, ECTOL1, Taf230, glycan metabolism, resistance, Gene Products, Whole Transcriptome Shotgun Sequencing, DEGS, Carrying, MAM, SCG3, acute haemorrhagic leucoencephalitis of Weston Hurst, TAF250, protoplasm, anon-EST:fe3D10, homoserine lactone hydrobromide, l34Eb, Taf200, 4930542A03Rik, dTAF[[II]]250, pattern, Genetic, protoplast, distribution, cell, MDDGB6, DmelCG8827, Profile, Bacterium fluorescens, ANCE, Taf1p, labeling, ridges, Leukoencephalitis, OCTD, BPFD#36, ance, dTAF250, (S)-isomer, secreted substance, Bacterium fluorescen, bodily secretion, time of survival, great, Degs, AnCE, azane, acute hemorrhagic leukoencephalitis, l(2)34Eb, TAF, laminae, thiol methyltransferase activity, Weston-Hurst syndrome, ahl1, acute hemorrhagic encephalomyelitis, TAF[[II]]250, Transcriptome, glycan metabolic process, nmf252, anatomical process, Proteins, Ammoniak, XCYP26A1, total expressed protein, l(3)84Ab, BG:DS00004.13, Cistrons, Cell, LGMD2C, strain, Concept, dTAF230, count in organism, survival, p230, chemical analysis, Protein, Gene Expression Signatures, TAF[[II]]250/230, Acute Hemorrhagic, TFIID, MFS1, bob, Gene Expression Signature, background, NH3, [NH3], Foods, flange, organ process, WMS2, teratoma with malignant transformation, Taf[[II]]250, TAF[[II]]230, USH1D, DMDA1, storage, nmf112, polysaccharide metabolism, cyp26, BG:DS08220.3, TAF[II]250, azote, introduction, nitrogeno, Protein Gene Products, processes, process, extracellular, Gene Proteins, DmelCG17603, RRT-PCR, Gene Expression Profiles, SSKS, SCARMD2, processus, Ethnicity, virulence, assay, sequestering, quantitative, Signature, AHLE, CG8827, presence or absence in organism, TAF1extent, projections, multicellular organismal polysaccharide metabolic process, Materials, nucleocytoplasm, acute necrotizing hemorrhagic leukoencephalitis, determination, Aminosaeure, Sigma Element, Mbp1, A4, Gene Expression Profile, Amino acid, Profiles, Liquidomonas fluorescens, infectivity, Mutations, Bacillus fluorescens, Initiation Factor, qRT-PCR, Roles, Concepts, myd, Minor Sigma Factor, viral infection, amino acids, reference sample, dermoid cyst with malignant transformation, Subunit, N, Mbp-1, Bodily, virus process, proteins, W, ecotype, Signatures, sals, Secretion, Expression Signature, papilla, Secretions, Role Concepts, Transcriptomes, v, intracellular, RNA Polymerase Sigma Factor H, bus, biogenic amine metabolism, anatomical protrusion, gyltl1b-b, completeness, RT-rt PCR, external secretion, Aminokarbonsaeure, homoserine lactone hydrochloride, Expression Profiles, lamina, flanges, RNA-seq, mdfw, alpha-amino carboxylic acids, results, Sigma Initiation, Gene Expression, exocrine gland fluid/secretion, Bodily Secretion, S-adenosyl-L-methionine:thiol S-methyltransferase activity, Role Concept, Stickstoff, MDDGA6, mKIAA0609, Expression Signatures, shelf, Pathogenicity, Role, Genetic Materials, secretion, cultivar, internal to cell, Biofilm, regulator, Expression Profile, Genetic Material, Transcriptome Profiles, fg, Sigma Factor, Amino Acid, Acid, Epistemology, gyltl1b, Sigma, Amino acids, shelves, mdc1d, expanded, Foods., projection, ridge, MDC1D, homoserine lactone, nitrogen, DMDA, Bacillus fluorescens liquefaciens, nmf181, enr, enlarged, spine, Material, Cistron, Acids, 7N, TMT, exocrine gland secretion, Proteomes, big, cell wall assembly, Ahl, AHL, exocrine gland fluid, Peptidomics, Transcriptome Profile, exocrine gland fluid or secretion, lamellae, number, Aminocarbonsaeure, Gene, Sigma Subunit, alpha-amino acid, process of organ, presence, TYPE, froggy, Gyltl1a, protrusion, DAGA4, lamella, large, ahl, glycan metabolism, resistance, Gene Products, Whole Transcriptome Shotgun Sequencing, Carrying, MAM, SCG3, acute haemorrhagic leucoencephalitis of Weston Hurst, protoplasm, homoserine lactone hydrobromide, 4930542A03Rik, Genetic, protoplast, MDDGB6, Profile, Bacterium fluorescens, labeling, ridges, Leukoencephalitis, BPFD#36, (S)-isomer, secreted substance, Bacterium fluorescen, bodily secretion, great, acute hemorrhagic leukoencephalitis, laminae, thiol methyltransferase activity, Controlled, Weston-Hurst syndrome, ahl1, Controlling, acute hemorrhagic encephalomyelitis, Transcriptome, glycan metabolic process, nmf252, anatomical process, Proteins, total expressed protein, Factor, alpha-amino acids, Sigma Initiation Factor, Cistrons, LGMD2C, strain, Concept, count in organism, chemical analysis, Protein, Gene Expression Signatures, Acute Hemorrhagic, bob, Gene Expression Signature, Foods, flange, organ process, teratoma with malignant transformation, USH1D, DMDA1, nmf112, polysaccharide metabolism, azote, Amino, nitrogeno, Protein Gene Products, processes, process, extracellular, Gene Proteins, RRT-PCR, Gene Expression Profiles, SCARMD2, processus, virulence, assay, quantitative, Signature, Minor, AHLE, presence or absence in organismTranscriptome, determination, Transcriptome Profile, Profile, Expression Profiles, Bacterium fluorescens, Gene Expression Profile, total expressed protein, Gene, Regulons, Profiles, Signatures, Gene Expression, Bacillus fluorescens, Bacterium fluorescen, Bacillus fluorescens liquefaciens, Expression Signature, Gene Expression Profiles, Expression Signatures, Gene Expression Signatures, chemical analysis, Transcriptomes, Gene Expression Signature, assay, Signature, Liquidomonas fluorescens., Expression Profile, Proteomes, Transcriptome ProfilesfalseCombining transcriptome and proteome analysis to identify and characterize the RpoS regulon in Pseudomonas fluorescensBackground: Microorganisms are the major cause of food spoilage during storage, processing and distribution. Pseudomonas fluorescens is a typical spoilage bacterium that contributes to a large extent to the spoilage process of proteinaceous food. RpoS is considered an important global regulator involved in stress survival and virulence in many pathogens. Our previous work revealed that RpoS contributed to the spoilage activities of P. fluorescens by regulating resistance to different stress conditions, extracellular acylated homoserine lactone (AHL) levels, extracellular protease and total volatile basic nitrogen (TVB-N) production. However, RpoS-dependent genes in P. fluorescens remained undefined. Results: RNA-seq transcriptomics analysis combined with quantitative proteomics analysis basing on multiplexed isobaric tandem mass tag (TMT) labeling was performed for the P. fluorescens wild-type strain UK4 and its derivative carrying a rpoS mutation. A total of 375 differentially expressed genes (DEGs) and 212 differentially expressed proteins (DEPs) were identified in these two backgrounds. The DGEs were further verified by qRT-PCR tests, and the genes directly regulated by RpoS were confirmed by 5’-RACE-PCR sequencing. The combining transcriptome and proteome analysis revealed a role of this regulator in several cellular processes, including polysaccharide metabolism, intracellular secretion and extracellular structures, cell well biogenesis, stress responses, ammonia and biogenic amine production, which may contribute to biofilm formation, stress resistance and spoilage activities of P. fluorescens. Moreover, in this work we indeed observed that RpoS contributed to the production of the macrocolony biofilm’s 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