Prideapplication/xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/02/PXD006643/P16279.prot.xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/02/PXD006643/P16279.pep.xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/02/PXD006643/P16279_3_F2_160815184730.raw.mzXMLprimaryOK200002270yunbiopride@foxmail.comJie YuMass SpectrometryShotgun proteomicsNot availableLactobacillus casei str. zhanglace of glucoseLactobacillus casei str. zhang ;lace of glucosehttp://www.ebi.ac.uk/pride/archive/projects/PXD006643Cell CultureStrains and culture conditions The baseline strain L. casei Zhang for experimental evolution was obtained from the Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, China. It has been deposited in the China General Microbiological Culture Collection Center with the deposit number CGMCC No. 1697. For propagation, L. casei Zhang was grown in de Mann-Rogosa-Sharpe (MRS) broth at 37°C. Experimental design and statistical rationale Proteomic profiling of L. casei Zhang evolved in glucose-limited medium (medium L) or normal medium (medium N) was performed on day 1 and after 1000, 2000, 3000, 4000, 5000, 6000, 7000, and 8000 generations. The day 1 expression profiles (Ancestor-N-P1 or Ancestor-L-P1) were used as the baseline profiles for each evolved population. TMT quantitative proteomics analysis was performed using a high-resolution mass spectrometer. Data screening was performed with a false discovery rate (FDR) of <0.01 to obtain highly viable qualitative results. Genomic re-sequencing was also conducted followed by data filtering and variant calling. Experimental evolution The laboratory evolution experiments were based on the standard protocol reported previouslyPrideTMT6plex-126 reporter+balance reagent acylated residueNot availableTMT quantitative proteomics analysis was performed using a high-resolution mass spectrometer, Q Exactive (Thermo Scientific), to obtain the original map file (.raw file). Proteome Discoverer 1.4 software [20] (Thermo Scientific) was used to convert the original map file generated by Q Exactive into an .mgf file, and the data were submitted to the MASCOT2.2 server for database retrieval via built-in software tools. Then, using Proteome Discoverer 1.4, the library file (.Dat file) on the MASCOT server was introduced back to the software, followed by data screening with a false discovery rate (FDR) of <0.01 to obtain highly viable qualitative results. The protein sequence was qualitatively analyzed by combining the protein database NCBI_Lactobacillus_casei_Zhang_5461_20160928.fasta (total number of sequences: 5461; download time: 2016-09-28). Mascot 2.2 was used for database searching and quantitative analysis. In the quantitative analysis process, Proteome Discoverer 1.4 was used to extract the ion peak intensity of the peptide, and the quantitative values were normalized [NCBI refseq protein ID and GI conversion were performed using the NCBI online tool; according to the refseq protein ID, uniprot was used to obtain Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation and the corresponding gene symbol]. According to the GenBank file at https://www.ncbi.nhm/niuccore/NC_021224.2, the NCBI refseq protein ID information for the gene locus tag was obtained, which can associate the protein data with the re-sequenced genome data. For the convenience of gene annotation, the corresponding Entrez gene IDs of the proteins were used for further bioinformatics analysis. First, one-way analysis of variance (ANOVA) was performed for bacteria grown in medium N (N group) and medium L (L group) to screen for proteins with larger intergroup differences than intragroup differences. The significantly differentially expressed proteins between the N and L groups of the same generation were screened using a t-test, and FDR < 0.05 was the threshold of screening. The L group-specific proteins were illustrated using a Venn diagram. To obtain an overview of the biological functions of the proteins, GO analysis [19] was performed using the software program Blast2GO [18], and KEGG annotation was performed using the KEGG database (http://geneontology.org/) [21]. The hypergeometric test method was used to perform GO and KEGG enrichment analysis of differentially expressed proteins using R language. Enrichment results with FDR < 0.05 were considered significant. Genomic re-sequencing, assembly, and annotation Genomic DNA isolated from each sample of each generation was used to generate the genomic DNA library using the Illumina TruSeq™ DNA Sample Prep Kit [22] following the manufacturer’s protocol (Illumina Inc., San Diego, CA, USA). L. casei Zhang generations 1000 and 2000 in the L and N groups were sequenced using the Illumina Miseq platform [23], and the other generations were sequenced using the Illumina Hiseq platform [24]. Sequencing assembly referred to ftp://ftp.ensemblgenomes.org/pub/bacteria/release-33/fasta/bacteria_14_collection/lactobacillus_casei_str_zhang/dna/Lactobacillus_casei_str_zhang.ASM1924v3.dna.chromosome.Chromosome.fa.gz. Genome annotation was performed using ftp://ftp.ensemblgenomes.org/pub/bacteria/release-33/gff3/bacteria_14_collection/lactobacillus_casei_str_zhang/Lactobacillus_casei_str_zhang.ASM1924v3.33.chromosome.Chromosome.gff3.gz.ProteomicsJie YuLTQ Orbitrap ElitePARTIALKey Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University.Lactobacillus Casei Str. Zhang29405720 Yu J, Hui W, Cao C, Pan L, Zhang H, Zhang W. Integrative genomic and proteomic analysis of response of Lactobacillus casei Zhang to glucose restriction. J Proteome Res. 2018 10.1021/acs.jproteome.7b0088643439408@qq.comBiologicalKey Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University.ChinaNutrient starvation is an important survival challenge for bacteria during industrial production of functional foods. As next-generation sequencing technology has greatly advanced, we performed proteomic and genomic analysis to investigate the response of Lactobacillus casei Zhang to a glucose-restricted environment. L. casei Zhang strains were permitted to evolve in glucose-restricted or normal medium from a common ancestor over a 3 year period, and they were sampled at 1000, 2000, 3000, 4000, 5000, 6000, 7000, and 8000 generations and subjected to proteomic and genomic analyses. Genomic resequencing data revealed different point mutations and other mutational events in each selected generation of L. casei Zhang under glucose restriction stress. The differentially expressed proteins induced by glucose restriction were mostly related to fructose and mannose metabolism, carbohydrate metabolic processes, lyase activity, and amino-acid-transporting ATPase activity. Integrative proteomic and genomic analysis revealed that the mutations protected L. casei Zhang against glucose starvation by regulating other cellular carbohydrate, fatty acid, and amino acid catabolism; phosphoenolpyruvate system pathway activation; glycogen synthesis; ATP consumption; pyruvate metabolism; and general stress-response protein expression. The results help reveal the mechanisms of adapting to glucose starvation and provide new strategies for enhancing the industrial utility of L. casei Zhang.Integrative Genomic and Proteomic Analysis of the Response of Lactobacillus casei Zhang to Glucose Restriction.Yu Jie J, Hui Wenyan W, Cao Chenxia C, Pan Lin L, Zhang Heping H, Zhang Wenyi Wgluco-hexose, Beliefs, Activity, experimental, determination, Laboratory, Glucose, Peptidomics, False, Glukose, Training, number, Monohydrate, (DL)-Isomer, Literacy Program, Normalcies, presence, School-Age, Background, method, HP1, Workshops, Cultural, Dextrose, HNP-1, Sprains, Sinkiang, Backgrounds, Normalities, average, School-Age Populations, ethnicity, proportion, methods, F, dermoid cyst with malignant transformation, teaching, experimental section, Literacy, Mros, MRS, Educational Activity, SPG70, Cultural Relativisms, number of, Melkersson syndrome, experimental design, Population, Workshop, ecotype, DL-glucose, glucose, DEFA2, method used in an experiment., Educational, curriculum, has or lacks parts of type, Customs, Training Programs, Strains, culture, School Age Population, Anhydrous, thiol methyltransferase activity, ratio, Individual Health, data, (beta-D)-Isomer, HP-1, Melkersson's syndrome (disorder), Sprain, extra or missing physical or functional parts, Normalcy, Cultural Backgrounds, People's Republic of China, results, Belief, strain, Programs, METRS, Manchuria, mereological quality, Program, count in organism, Cultural Background, Inner Mongolia, S-adenosyl-L-methionine:thiol S-methyltransferase activity, Cultures, Melkersson's syndrome, School Age, chemical analysis, Strain, cultivar, laboratory, Individual, (alpha-D)-Isomer, Training Program, teratoma with malignant transformation, D-Glucose, Populations, Mainland China, training, Cheilitis granulomatosa of Mescher-Melkersson-Rosenthal, Normality, Engineerings, cheilitis Granulomatosa, cheilitis granulomatosa of Mescher-Melkersson-Rosenthal, proportionality, rate, Educational Activities, study protocol, School Age Populations, Anhydrous Dextrose, experimental procedures, Activities, plan specification, Biotechnologies, Melkersson-Rosenthal syndrome, Health, Literacy Programs, D Glucose, cardinality, Melkersson-Rosenthal Syndrome, quotient, Relativisms, DEF1, MTRNS, School-Age Population, assay, quantitative, Relativism, variable, Cultural Relativism, Glucose Monohydrate, Strains and Sprains, TMT, Cheilitis granulomatosa of Miescher-Melkersson-Rosenthal (disorder), presence or absence in organism, Glcgluco-hexose, reactivity, D-Glucose, Lactobacillus casei, Bacillus casei a, Lactobacterium casei, (beta-D)-Isomer, Glucose, Bacterium casei a, Glukose, Glc., Monohydrate, (DL)-Isomer, Streptobacterium casei, Caseobacterium vulgare, Lactobacillus casei subsp. casei, DL-glucose, Anhydrous Dextrose, glucose, D Glucose, responsivity, Dextrose, proteomic analysis, Bacillus a, Lactobacillus casei casei, response, (alpha-D)-Isomer, Glucose Monohydrate, Anhydrousprojections, type 2, Materials, Raw, ion, H105E3, Long Term, Polypeptides, protein polypeptide chains, KL receptor activity, SCO5, 2, SCO1, Software Engineering, Analysis, DA transporter, Gsfsow3, C79691, adenomas, L-methionine aminopeptidase activity, thymus nucleic acid, 2810441M03Rik, F, Genomes, Analyses, DmelCG14026, Kitl, ANOVA, proteins, W, number of, Mast cell growth factor, Lccp, Bacteria <bacteria>, Solute carrier family 6 member 3, Variance Analysis, Prokaryotae, sample, Bs, Procaryotae, DmAAF34715, NK/GPI, Gpi, anatomical protrusion, MYH-associated polyposis, Longterm Effect, somatomedin, IBP1, Software Tools, Computer Applications, PBT, Computer Applications Software, shelf, Ontology Projects, prokaryotes, NK|GPI, desoxyribose nucleic acid, TKV, Tkv, MUTYH-associated polyposis, MUTYH-related AFAP, RUTBC3, pbt, Ontology, Software Applications, Projects, Source Software, Stem cell factor, proportionality, rate, MASCOT, INSDC_feature:gene, STAT5, study protocol, projection, ridge, Atkv, stem cell factor, Applications, Chromosome, Material, multiple colorectal, ds DNA, Variance Analyses, MUTYH-related attenuated familial polyposis coli, DNA, TMT, PEP, Gb, Bglap-rs1, Prokaryota, Computer Software Applications, krk1, Clo, DNS, (Deoxyribonucleotide)n, Peptidomics, False, Effects, Slf, SLF, lamellae, number, NAT13P, protein-containing complex, process of organ, Gene Ontology Project, Gene Ontology, period, lamella, Deoxyribonucleic Acid, Gene Products, Pgi, nat13, MAP, Application, Open Source Softwares, SIDS, proportion, Longterm, Gpi-1r, Software Application, Gpi-1s, familial adenomatous polyposis 2, Phi, Gpi-1t, Open Source Software, Double Stranded, Deoxyribonucleic acid, Long-Term, ions, Dtfr, Computer Software Application, mKIAA0989, Con, Tools, kv, blz, peptidos, dtfr, (Deoxyribonucleotide)m, laminae, proto-oncogene c-Kit, bacteria, STK-A, grupo, hematopoietic growth factor KL, anatomical process, DNAn+1, mak3, Proteins, D10Wsu136e, Brk25D, MF, Amf, Tool, polypeptide, prophase chromosome, native protein, KIT ligand receptor activity, MUTYH-related attenuated FAP, chemical analysis, Long Term Effects, Bpa, Brk25D2, Brk25D1, Library, organ process, NK, XKrk1, Ontology Project, Col4a-1, interphase chromosome, Ntup1, CD117, primary structure of sequence macromolecule, Longterm Effects, plan specification, Computer Programs, processes, Gene Proteins, Applications Softwares, C-Kit, prokaryote, Ssm, MGF, Mgf, quotient, Desoxyribonukleinsaeure, xkl-1, MAP syndrome, PE, quantitative, AI450383, Mak3, l(2)04415, MAK3, Atr25D, AI747449, Bru, Gene Ontology Projects, PKDYS, determination, methionine aminopeptidase activity, Languages, PreP, Str, Somatomedin-C, atado, protein, Xkl-1, AA410010, extracted material, contrasted, peptide, Gsfsco1, ClvPrd, peptido, Pop, str, Project, protein aggregate, Gpi-1, Effect, Gsfsco5, Computer Program, peptidase M activity, SOW3, Svc, rabGAPLP, Eubacteria, dermoid cyst with malignant transformation, peptides, Nlk, Open, somatomedin-C, Computer Programs and Programming, SF, RabGAP-5, chromatid, CG12352, hNAT5, hSAN, RUSC3, IGF1, papilla, Mechano growth factor, Double-Stranded DNA, Soluble KIT ligand, deoxyribonucleic acids, DNAn, Sl, Long-Term Effects, Mak3p, ratio, IGF-I, steel factor, NAT13, lamina, autosomal recessive familial adenomatous polyposis, Maps, flanges, Tr-kit, extra or missing physical or functional parts, Double-Stranded, Ids, Nat13, Thermo Scientific, Source Softwares, results, sKITLG, Programs, (Deoxyribonucleotide)n+m, Program, MP-1, S-adenosyl-L-methionine:thiol S-methyltransferase activity, 5830400N10Rik, mOC-X, Ionen, mechano growth factor, Computer Applications Softwares, kl1-A, Genetic Materials, Softwares, KIT, Igf-1, Genetic Material, autosomal recessive, tyrosine-protein kinase Kit, Gene Ontologies, SHEP7, ORG, Org, Ontologies, Dialects, mast cell growth factor, shelves, Gpi1-r, Gpi1-s, AI047692, mKIAA1104, kit, Gpi1-t, RABGAP5, Kitlg, KL-1, spine, MP1, KITLG, Cistron, Polypeptide, time, 2600005K24Rik, pub, Gruppe, Gpi1s, tkv1, MPS2, nat5, AW549739, AI461847, SCF receptor activity, Gene, FPH2, NAT5P, eubacteria, Computer, presence, Deoxyribonucleic acids, gDNA, protrusion, method, polypeptide chain, scfr, method used in an experiment, Del(8)44H, SCFR, familial adenomatous polyposis, Fdc, Genetic, iones, tkva, ridges, Monera, autosomal recessive multiple colorectal adenomas, Paralactobacillus, grupos, DmelCG12352, has or lacks parts of type, Nat5, NAT5, Long-Term Effect, fungi, TKV1, DAT, thiol methyltransferase activity, span, Applications Software, MUTYH-related attenuated familial adenomatous polyposis, Open Source, data, DAT1, Encyclopedias, interphase chromosome., MUTYH-Associated Polyposis, Computer Software, protein complex, Cistrons, Peptide, group, mereological quality, count in organism, AW112078, Illumina MiSeq, Software Tool, natural protein, Protein, l(2)25Da, sequence, ds-DNA, CG14026, Software, Dat1, flange, Data Base, teratoma with malignant transformation, San, SAN, c-KIT, Variance, Engineering, Rest, 2310012C15Rik, Dialect, MYH-Associated Polyposis, sample population, Protein Gene Products, san, process, c-kit, Ion, XAP104, c-Kit ligand, cardinality, processus, Peptid, assay, SCF, groupe, FAP2, presence or absence in organism, colorectal adenomatous polyposisprojections, multicellular organismal catabolic process, single-organism catabolic process, Lactobacterium casei, determination, Bacterium casei a, Glukose, Aminosaeure, Amino acid, Monohydrate, hydrates de carbone, protein, (DL)-Isomer, Streptobacterium casei, glucide, carbohydrates, Mutations, protein polypeptide chains, Levulosa Mein, responsivity, glucido, Dextrose, Impacts, Environmental Impacts, protein aggregate, average, arabino-Hexulose, Kohlenhydrate, Eubacteria, amino acids, mannose metabolism, catabolism, proteins, Fruktose, Fruchtzucker, Lactobacillus casei subsp. casei, DL-glucose, glucose, Environmental Impact, ATPsyn b, Bacteria <bacteria>, Prokaryotae, papilla, Procaryotae, Strains, pyruvate metabolism, ATP, ATPsyn-&bgr, Levulose, Levulosa, anatomical protrusion, ATPsyn-b, Levulosado Vitulia, Aminokarbonsaeure, Arts, lamina, flanges, saccharides, Normalcy, alpha-amino carboxylic acids, results, Levulosado Braun, glycogen synthesis, shelf, precocious, prokaryotes, Individual, (alpha-D)-Isomer, activation, Kohlenhydrat, saccharidum, CG11154, glycogen anabolism, D-Glucose, Amino Acid, Acid, Industrial, breakdown, Industrial Arts, Amino acids, Levulosa Baxter, glycogen formation, shelves, common, carbohidratos, projection, ridge, early, amino acid-importing ATPase activity, organ system, carbohidrato, Health, fructose, D Glucose, spine, Fructose, Lactobacillus casei casei, Acids, a carbohydrate, glucidos, Glucose Monohydrate, Strains and Sprains, time, Levulosa Braun, Prokaryota, Levulosado Bieffe Medit, gluco-hexose, advanced, 2-Propenoic acid, Fru, Fleboplast, glycogen biosynthesis, Glucose, lamellae, Plast Apyr Levulosa Mein, carbohydrate, Aminocarbonsaeure, saccharide, Gene, eubacteria, alpha-amino acid, IB, protein-containing complex, Normalcies, pyruvate dehydrogenase bypass, Caseobacterium vulgare, process of organ, body system, protrusion, period, lamella, amino acid ABC transporter, polypeptide chain, Apir Levulosa, ATP-synbeta, Gene Products, Fleboplast Levulosa, system, Sprains, Normalities, reactivity, Lactobacillus casei, anatomical systems, DmelCG11154, nutrients, other lyase activity, beta-ATPase, Levulosa Grifols, ridges, Monera, ATPasebeta, time of survival, ATPase beta, fungi, laminae, Anhydrous, ATPB, Individual Health, nutrient, bacteria, data, Bacillus casei a, (beta-D)-Isomer, ATP-dependent amino acid transmembrane transporter activity, degradation, protein complex, anatomical process, Sprain, Proteins, Point Mutations, ion(1-), alpha-amino acids, 2-(phosphonooxy)-, Impact, ATP-syn-B, Environmental, survival, Apir, ML-1, native protein, natural protein, chemical analysis, Protein, Strain, arabino-hex-2-ulose, connected anatomical system, glucides, Foods, Mutation, flange, organ process, Normality, amino acid-transporting ATPase activity, Glc., Amino, Carbohydrate, Anhydrous Dextrose, Levulosa Ife, Probiotic, Protein Gene Products, Gene Proteins, processes, process, prokaryote, Point, ATPIB, Bacillus a, Environments, processus, assay, response, Levulosa Ibys, amino acid-exporting ATPase activity, Glcprojections, multicellular organismal catabolic process, single-organism catabolic process, Lactobacterium casei, determination, Bacterium casei a, Glukose, Aminosaeure, adenosinetriphosphatase activity, Amino acid, Monohydrate, hydrates de carbone, protein, (DL)-Isomer, Streptobacterium casei, glucide, carbohydrates, Mutations, protein polypeptide chains, Levulosa Mein, ATP hydrolysis-dependent activity, responsivity, glucido, Dextrose, Impacts, Environmental Impacts, protein aggregate, average, arabino-Hexulose, (Ca2+ + Mg2+)-ATPase, Kohlenhydrate, Eubacteria, amino acids, catabolism, proteins, Fruktose, Fruchtzucker, Lactobacillus casei subsp. casei, DL-glucose, glucose, Environmental Impact, ATPsyn b, Bacteria <bacteria>, Prokaryotae, papilla, Procaryotae, Strains, pyruvate metabolism, ATP, ATPsyn-&bgr, Levulose, Levulosa, anatomical protrusion, ATPsyn-b, Levulosado Vitulia, ATP hydrolase activity, Aminokarbonsaeure, Arts, acid, lamina, flanges, saccharides, Normalcy, alpha-amino carboxylic acids, results, Levulosado Braun, glycogen synthesis, ATPase-dependent activity, shelf, precocious, prokaryotes, Individual, (alpha-D)-Isomer, activation, Kohlenhydrat, saccharidum, CG11154, ATP phosphohydrolase activity, glycogen anabolism, D-Glucose, Acid, Amino Acid, Industrial, breakdown, Industrial Arts, Amino acids, Levulosa Baxter, glycogen formation, acide, shelves, acids, common, SV40 T-antigen, acido, carbohidratos, projection, ridge, early, organ system, carbohidrato, Health, fructose, D Glucose, spine, Fructose, Lactobacillus casei casei, Acids, a carbohydrate, glucidos, Glucose Monohydrate, Strains and Sprains, time, Levulosa Braun, Prokaryota, Levulosado Bieffe Medit, gluco-hexose, advanced, 2-Propenoic acid, Fru, Fleboplast, glycogen biosynthesis, Glucose, lamellae, Plast Apyr Levulosa Mein, carbohydrate, Aminocarbonsaeure, saccharide, Gene, eubacteria, alpha-amino acid, IB, protein-containing complex, Normalcies, pyruvate dehydrogenase bypass, Caseobacterium vulgare, process of organ, body system, protrusion, period, lamella, polypeptide chain, Apir Levulosa, Metabolism, ATP monophosphatase activity, ATP-synbeta, Gene Products, Fleboplast Levulosa, system, Sprains, adenosine triphosphatase activity, Normalities, reactivity, Lactobacillus casei, complex V (mitochondrial electron transport), anatomical systems, DmelCG11154, nutrients, other lyase activity, beta-ATPase, Levulosa Grifols, ATPase activity, ridges, Monera, ATPasebeta, time of survival, ATPase beta, fungi, laminae, Saeure, Anhydrous, ATPB, Individual Health, nutrient, bacteria, data, Bacillus casei a, (beta-D)-Isomer, degradation, protein complex, anatomical process, adenosine 5'-triphosphatase activity, Sprain, Proteins, Point Mutations, ion(1-), alpha-amino acids, 2-(phosphonooxy)-, Impact, ATP-syn-B, Environmental, survival, Apir, ML-1, native protein, natural protein, chemical analysis, Protein, HCO3--ATPase, Strain, arabino-hex-2-ulose, connected anatomical system, glucides, Foods, Mutation, flange, coupled, organ process, Normality, Saeuren, Glc., Amino, Carbohydrate, Anhydrous Dextrose, Levulosa Ife, Protein Gene Products, Gene Proteins, processes, process, prokaryote, Point, ATPIB, Bacillus a, Environments, processus, assay, response, Levulosa Ibys, GlcAtr25D, gluco-hexose, AI747449, tkv1, STK-A, Bacillus casei a, Lactobacterium casei, (beta-D)-Isomer, determination, Glucose, Bacterium casei a, Glukose, Str, Brk25D, Monohydrate, (DL)-Isomer, Streptobacterium casei, H105E3, Caseobacterium vulgare, responsivity, chemical analysis, Dextrose, str, l(2)25Da, Bpa, Brk25D2, Brk25D1, (alpha-D)-Isomer, CG14026, TKV, Tkv, reactivity, D-Glucose, Lactobacillus casei, DmelCG14026, Glc., tkva, Dtfr, Lactobacillus casei subsp. casei, DL-glucose, Anhydrous Dextrose, Atkv, glucose, D Glucose, kv, XAP104, Bacillus a, Lactobacillus casei casei, dtfr, assay, TKV1, response, l(2)04415, Glucose Monohydrate, Anhydrous227trueIntegrative genomic and proteomic analysis of response of Lactobacillus casei str. Zhang to glucose limitationNutrient starvation is an important survival challenge for bacteria during industrial production of functional foods. Lactobacilli are increasingly being used as probiotics in functional foods. As next-generation sequencing technology has greatly advanced, we performed integrative proteomic and genomic analysis to investigate the response of Lactobacillus casei Zhang to a glucose-restricted environment. L. casei Zhang strains were permitted to evolve in glucose-limited or normal medium from a common ancestor over a 3-year period, and they were sampled after 1000, 2000, 3000, 4000, 5000, 6000, 7000, and 8000 generations and subjected to proteomic and genomic analyses. Genomic resequencing data revealed different point mutations and other mutational events in each generation of L. casei Zhang under glucose limitation stress. The proteins expressed differentially under glucose limitation were found to be significantly related to fructose and mannose metabolism, carbohydrate metabolic processes, lyase activity, and amino acid-transporting ATPase activity. The integrative proteomic and genomic analysis revealed that the mutations protected L. casei Zhang against glucose starvation by regulating other cellular carbohydrate, fatty acid, and amino acid catabolism; phosphoenolpyruvate system pathway activation; glycogen synthesis; ATP consumption; pyruvate metabolism; and general stress response protein expression. The results help reveal the mechanisms of adapting to glucose starvation and provide new strategies for enhancing the industrial utility of L. casei Zhang.2018-02-082017-06-01PXD0066434466449917558258038804333029535851114512067811080612461962461972842188090320637522995811363350906836351524260275838538791187947398007186801NCBITaxon:1280572307688881114301187263555571468351452627412583649117571508472746707364113546138855821803582329031388869152167786889539978447512951398704351123294126246942229692812397713311809933995232310343043654813583334607925198183659219813143205971293818826826558194762149363295726373719222212502321979116938197912NCBITaxon:12721119577412478186613283882813955843451358672217554372949140816918045416193426683413903634530586112041623264460711210411706127443210859561496367469412831666943694559729452811320810039241065837514633087936944784475174206542208964317447127020896344597413797912838411946694006671454587932993529320101981264690410661145755121659940483392512165972165954550131528269731606212133128312821280339523218108323217825252920435315227794428112454349825741948147871720309498019752555536231439841356742951053948824261914548140479NCBITaxon:215711506215515312924398990371228577829965975320596876231935163098005888455869781817808173630943179566069893616048856614098591047825664162425150590711870234821187053204913816936306386323555432046632226186633129945658606884535151262321721921745921612956717136044100160235870026420369456941016763410210761277351131658215048023925472793321604281461002913584303578617463313252911187002157641809699756654577444915666675476044524676756191726518130194111929439633664113633672175111764510239870932025NCBITaxon:4055932582359092788396523652649821787074982163472565691569387224982116544872056973474951666905108944835525663661410NCBITaxon:4932871556891758543102459808108944475741755518100058945268087322875351908323311561263730069303911415542193255521872587268723872487298727123598755529NCBITaxon:475154762422314146547730551800664417725564843376771581419198822445299767446982510216998231174673897641041051155744689444474153NCBITaxon:5055796016776744685100036487529600NCBITaxon:58116534911822637082483341475480557841946751299114578458359741276473194439137086326547876569835566369838192011164034624136810893161001428099612NCBITaxon:548681NCBITaxon:582054641498523077479464098609958652283637379196627290587668960596061572951372218759446708756227086266596417110133548330903497412982998603878348106267566430615127936543194747033424947223598596108961588655974649987039202111072878272154078211908503757075298351170828206189257771480418985487350247158779627300251563041190252867463604614796469644375939491146247274612874601134506253256648452659197221963819155263858859652639NCBITaxon:6157505210283071105172375059576131302409720002634196105264110909469407722774694163485689961123869497515NCBITaxon:2NCBITaxon:135231703612506174767927450627249159615384005257313246432136861505962697968666299034694171344346360347515363296440421018194301086731018510976063558633149616128628724620096692729435133813216968583551865368595968912801726071018568729411009118696141633316780781186941436183NCBITaxon:6191118698840231719475932118691443906NCBITaxon:102982100071257118348824387279694836419080218787870384766425731055347095145122578656870861822607046183260705260707NCBITaxon:7803906NCBITaxon:1502451516658457702921158612184519307920928520131974707856100713370565295076192126385454195NCBITaxon:3055504457391538337991399878168192875NCBITaxon:10239NCBITaxon:7142829126806315327341478281309570547044830064175158592381055524159084128108228233446900815025754122810451930174830085210977970671356225833136185509924NCBITaxon:56938268830640527796179469958334240906151015151034809NCBITaxon:631240674482428130767070876138370475927237082816772850351581990119519533702492405360888175626158355833376021267192853217735726711935018464517729980861678791774373711104905637121534813714121532395767690147266470913170475712562745790311333550372885962859634792491308126387121203511082332648373153214693NCBITaxon:9615383235946331858626079914126220029813141313493760833344926701311111497019281239655833325283010184138569591110065812375612750454266625515197887492003750360094129349715300910766204114903524725175014012573983649908515151438992NCBITaxon:1155237453988374744544641521399275931179286643235983906288705158059553611945993271602938511497861603293338922853422999810894535936457428412754121536024271831627713512251179948875058NCBITaxon:10407242715502779167971816738713491306274158955210103065027802915954126291586600255158493765327159570210022633889423451287689135588675512930945146479203124216413328038280351928434369093581539858089462108034817939211825902878892950274560990690174934681927256322732189038292867572279011247190400727NCBITaxon:5796537457114311233523562114020641198108713554771424507229533796983555222212916347087141045775126216115429315754613962242139213907702020603281857323114319338293550833292307411292211481640278489616010677252649997574472758024055071762992512296833536658192683214053576229412816078395763206672400540296543282312273777729818431832246596205755499229575757592845939360533079725518113549706671436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