#METABOLOMICS WORKBENCH araskind_20150604_9310291_mwtab.txt DATATRACK_ID:269 STUDY_ID:ST000173 ANALYSIS_ID:AN000267 PROJECT_ID:PR000150 VERSION 1 CREATED_ON 2016-09-17 #PROJECT PR:PROJECT_TITLE Evolutionary-genomics approach for elucidating and improving complex phenotypes PR:PROJECT_SUMMARY Genome evolution and engineering to study isobutanol tolerance in E. coli PR:INSTITUTE University of Michigan PR:DEPARTMENT Chemical Engineering PR:LABORATORY Lin Lab PR:LAST_NAME Lin PR:FIRST_NAME Nina PR:ADDRESS Ann Arbor, MI PR:EMAIL ninalin@umich.edu PR:PHONE 734-647-8026 #STUDY ST:STUDY_TITLE WT and iButOH tolerant E. coli ST:STUDY_TYPE Comparative metabolomics study of WT and iButOH tolerant E. coli ST:STUDY_SUMMARY This study aims to elucidate metabolic mechanisms of tolerance to isobutanol in ST:STUDY_SUMMARY coli. Two strains are utilized: WT parental strain EcHW24, and isobutanol ST:STUDY_SUMMARY strain 38-20-4 created via multiplex genome engineering. The metabolic response ST:STUDY_SUMMARY growth with isobutanol (0.7% w/v) and without (0% w/v) on NG50 minimal media ST:STUDY_SUMMARY be compared for each strain. 3 replicates for each strain/iButOH concentration ST:STUDY_SUMMARY been submitted, excpet for WT/0.7%; we have observed high growth phenotype ST:STUDY_SUMMARY for this combination, and have corresponding submitted 5x replicates. Strain ST:STUDY_SUMMARY contains mutations in the TCA cycle (gltA SNP) and amino acid metabolism ST:STUDY_SUMMARY indels in glnE, gltD, and tnaA), thus our hypothesis is that tolerance arises ST:STUDY_SUMMARY rewiring of TCA cycle and amino acid metabolism, possibly resulting in ST:STUDY_SUMMARY intracellular ratio of glutamine:glutamate ST:INSTITUTE University of Michigan ST:DEPARTMENT Biomedical Research Core Facilities ST:LABORATORY Metabolomics core ST:LAST_NAME Kachman ST:FIRST_NAME Maureen ST:ADDRESS 6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714 ST:EMAIL mkachman@umich.edu ST:PHONE - ST:NUM_GROUPS 4 ST:TOTAL_SUBJECTS 14 #SUBJECT SU:SUBJECT_TYPE Cells SU:SUBJECT_SPECIES Escherichia coli SU:TAXONOMY_ID 562 #SUBJECT_SAMPLE_FACTORS: SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Additional sample data SUBJECT_SAMPLE_FACTORS SU0003750 S00014363 Strain:iButOH tol mutant | iButOH concentration:0.7% (w/v) SUBJECT_SAMPLE_FACTORS SU0003750 S00014364 Strain:iButOH tol mutant | iButOH concentration:0.7% (w/v) SUBJECT_SAMPLE_FACTORS SU0003750 S00014365 Strain:iButOH tol mutant | iButOH concentration:0.7% (w/v) SUBJECT_SAMPLE_FACTORS SU0003751 S00014369 Strain:iButOH tol mutant | iButOH concentration:0% (w/v) SUBJECT_SAMPLE_FACTORS SU0003751 S00014370 Strain:iButOH tol mutant | iButOH concentration:0% (w/v) SUBJECT_SAMPLE_FACTORS SU0003751 S00014371 Strain:iButOH tol mutant | iButOH concentration:0% (w/v) SUBJECT_SAMPLE_FACTORS SU0003749 S00014358 Strain:WT | iButOH concentration:0.7% (w/v) SUBJECT_SAMPLE_FACTORS SU0003749 S00014359 Strain:WT | iButOH concentration:0.7% (w/v) SUBJECT_SAMPLE_FACTORS SU0003749 S00014360 Strain:WT | iButOH concentration:0.7% (w/v) SUBJECT_SAMPLE_FACTORS SU0003749 S00014361 Strain:WT | iButOH concentration:0.7% (w/v) SUBJECT_SAMPLE_FACTORS SU0003749 S00014362 Strain:WT | iButOH concentration:0.7% (w/v) SUBJECT_SAMPLE_FACTORS SU0003750 S00014366 Strain:WT | iButOH concentration:0% (w/v) SUBJECT_SAMPLE_FACTORS SU0003750 S00014367 Strain:WT | iButOH concentration:0% (w/v) SUBJECT_SAMPLE_FACTORS SU0003750 S00014368 Strain:WT | iButOH concentration:0% (w/v) #COLLECTION CO:COLLECTION_SUMMARY - CO:SAMPLE_TYPE Cells #TREATMENT TR:TREATMENT_SUMMARY - #SAMPLEPREP SP:SAMPLEPREP_SUMMARY - SP:SAMPLEPREP_PROTOCOL_FILENAME Gly-TCA-nucleotides_analysis_protocol-2015-03-09.docx #CHROMATOGRAPHY CH:CHROMATOGRAPHY_TYPE HILIC CH:INSTRUMENT_NAME Agilent 1260 CH:COLUMN_NAME Phenomenex Luna NH2 (150 x 1mm, 3um) CH:METHODS_ID AQM020 CH:METHODS_FILENAME QTOF-002-HILIC-35min-1mm-No_Insert.m.zip #ANALYSIS AN:ANALYSIS_TYPE MS AN:LABORATORY_NAME MRC2 (University of Michigan) AN:ACQUISITION_PARAMETERS_FILE QTOF-002-HILIC-35min-1mm-No_Insert.m.zip AN:PROCESSING_PARAMETERS_FILE EX00268-MassHunterQuant-GlyTCA-LCMS-DataAnalysis-Method.m.zip #MS MS:MS_COMMENTS - MS:INSTRUMENT_NAME Agilent 6520 QTOF MS:INSTRUMENT_TYPE QTOF MS:MS_TYPE ESI MS:ION_MODE NEGATIVE #MS_METABOLITE_DATA MS_METABOLITE_DATA:UNITS pmol/µg protein MS_METABOLITE_DATA_START Samples S00014363 S00014364 S00014365 S00014369 S00014370 S00014371 S00014358 S00014359 S00014360 S00014361 S00014362 S00014366 S00014367 S00014368 Factors Strain:iButOH tol mutant | iButOH concentration:0.7% (w/v) Strain:iButOH tol mutant | iButOH concentration:0.7% (w/v) Strain:iButOH tol mutant | iButOH concentration:0.7% (w/v) Strain:iButOH tol mutant | iButOH concentration:0% (w/v) Strain:iButOH tol mutant | iButOH concentration:0% (w/v) Strain:iButOH tol mutant | iButOH concentration:0% (w/v) Strain:WT | iButOH concentration:0.7% (w/v) Strain:WT | iButOH concentration:0.7% (w/v) Strain:WT | iButOH concentration:0.7% (w/v) Strain:WT | iButOH concentration:0.7% (w/v) Strain:WT | iButOH concentration:0.7% (w/v) Strain:WT | iButOH concentration:0% (w/v) Strain:WT | iButOH concentration:0% (w/v) Strain:WT | iButOH concentration:0% (w/v) 2 or 3-phosphoglycerate_2PG/3PG 14.6231 15.0675 19.9326 23.9388 27.6402 21.1007 18.2216 17.2047 15.0237 3.9067 21.4089 18.1798 39.5745 11.3409 6-Phosphogluconate 13.9444 17.2882 23.6233 19.9348 23.8832 19.8617 18.4697 16.8741 13.8920 35.6731 23.1444 19.7346 35.6786 12.2426 Acetyl-CoA 101.2717 69.9782 30.3327 28.6623 83.8354 19.0556 19.4181 15.2324 25.4247 11.2779 20.5402 10.2365 34.7388 19.7278 ADP 59.8609 45.4350 32.6725 47.3993 53.9194 46.9707 56.5382 40.7714 48.9466 32.1336 42.5048 33.1767 82.6093 32.4458 AMP 468.6528 640.0592 548.2236 179.3753 131.6597 190.7570 510.0472 224.7394 303.2559 360.6920 276.3876 162.2454 273.2725 116.0689 ATP 31.5363 18.7255 16.1269 197.8798 184.2821 176.2550 46.6419 31.3991 35.4084 18.9544 32.7698 95.5592 396.0803 84.9824 Citrate or Isocitrate 31.7825 19.8295 34.4473 64.1118 337.4923 64.0393 54.1606 43.3294 43.7871 39.4770 53.8658 60.4637 146.6198 27.6021 flavin adenine dinucleotide 7.4301 6.2109 3.5280 2.9901 7.2957 2.3115 6.7033 5.1204 5.8737 3.8732 5.4551 0.8256 4.7134 1.0834 Fructose 1_6-bisphosphate 191.8273 168.0143 65.8361 1062.8595 1811.5182 803.5714 57.4799 32.9218 42.9384 99.1063 50.5504 333.0973 691.6452 207.9252 Glucose 6-phosphate or fructose-6-phosphate 32.1766 24.9929 22.9404 31.7818 125.5306 39.5274 47.5659 34.1695 43.7118 24.2825 33.7526 61.5747 142.3570 23.9117 Malate 15.9873 4.2361 9.6528 73.0902 23.7694 97.9414 68.5973 50.3800 66.3604 38.9266 90.7737 138.2056 205.1752 41.5968 Nicotinamide Adenine Dinucleotide oxidized 38.7360 26.4255 20.1809 46.5887 77.1859 45.4301 33.1771 24.6665 32.1135 13.8631 24.9433 48.3238 102.1010 23.4921 nicotinamide adenine dinucleotide phosphate oxidized 51.5576 43.0065 35.7741 34.8033 41.1653 38.7304 32.1572 30.8799 25.5053 23.4901 28.7286 30.7262 66.3856 18.1886 nicotinamide adenine dinucleotide phosphate reduced 0.0000 0.0000 0.0000 0.0000 0.0000 1.1191 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 Nicotinamide Adenine Dinucleotide reduced 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 Phosphoenolpyruvate 4.9730 0.0000 0.0000 0.0000 11.8220 0.0000 4.8906 0.0000 2.6533 0.0000 0.0000 0.0000 0.0000 0.0000 Sucrose 32.0448 39.1860 36.0973 41.0328 121.4753 39.2094 51.4235 27.0913 47.0851 50.9168 38.9965 30.7294 63.9595 19.6622 MS_METABOLITE_DATA_END #METABOLITES METABOLITES_START metabolite_name moverz_quant ri ri_type pubchem_id inchi_key kegg_id other_id other_id_type 2 or 3-phosphoglycerate_2PG/3PG 724 2PG/3PG UM_Target_ID 6-Phosphogluconate 91493 6PG UM_Target_ID Acetyl-CoA 444493 aCoA UM_Target_ID ADP 6022 ADP UM_Target_ID AMP 6083 AMP UM_Target_ID ATP 5957 ATP UM_Target_ID Citrate or Isocitrate 311 CIT/ICIT UM_Target_ID flavin adenine dinucleotide 46906035 FAD UM_Target_ID Fructose 1,6-bisphosphate 21125049 FBP UM_Target_ID Glucose 6-phosphate or fructose-6-phosphate 5958 G6P/F6P UM_Target_ID Malate 525 MAL UM_Target_ID Nicotinamide Adenine Dinucleotide oxidized 15938971 NAD UM_Target_ID nicotinamide adenine dinucleotide phosphate oxidized 15938972 NADP UM_Target_ID nicotinamide adenine dinucleotide phosphate reduced 22833512 NADPH UM_Target_ID Nicotinamide Adenine Dinucleotide reduced 439153 NADH UM_Target_ID Phosphoenolpyruvate 1005 PEP UM_Target_ID Sucrose 5988 SUC UM_Target_ID METABOLITES_END #END