JBEI - Tyrosine pathway engineering proteomic data

JBEI - Tyrosine pathway engineering proteomic data
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LINCS_P100_DIA_Plate97_annotated_minimized_2020-06-29_18-13-03.sky.zip2020-06-29 15:20:4490961922,76490
BSA-QC_68fmol_Jun2020_Impact-II_minPanorama_2020-06-28_22-05-23.sky.zip2020-06-28 22:10:23131402165
19_8_27_LARP1_Kinase_Reaction_2020-06-18_10-51-35.sky.zip2020-06-24 21:25:59264762373
Phospho_CDK2_Silencing_Experiment_Human_2020-06-23_16-21-00.sky.zip2020-06-24 21:25:5911921636
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Sky0 ACE2 TMPRSS2 cell lines_2020-06-18_16-55-27.sky.zip2020-06-18 13:38:456252919732
LINCS_P100_DIA_Plate96_annotated_minimized_2020-06-11_19-02-30.sky.zip2020-06-11 16:24:3290961922,76493
AMBPb_2020-06-01_14-39-27.sky.zip2020-06-11 15:34:1311261
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AMBPc_2020-06-02_12-38-26.sky.zip2020-06-11 15:34:1311262
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IGHA1b_2020-06-03_16-47-13.sky.zip2020-06-11 15:34:13112101
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LYZ_2020-06-04_15-26-23.sky.zip2020-06-11 15:34:13112460
LYZb_2020-06-04_18-12-30.sky.zip2020-06-11 15:34:13112412
SERPINF1_2020-06-05_12-55-50.sky.zip2020-06-11 15:34:13112669
SERPINF1b_2020-06-05_16-03-56.sky.zip2020-06-11 15:34:1311262
Sky1 Synthetic SARS-CoV2 proteome library_2020-05-30_00-33-22.sky.zip2020-06-09 13:21:56121431351,2121
Sky3 52 patients nano PRM-MS2 raw_2020-05-30_00-38-21.sky.zip2020-06-09 13:20:236345734055
Sky4 5 positive patients nano PRM-MS2 refined_2020-05-30_00-52-02.sky.zip2020-06-09 13:20:22634492945
Sky6 11 positive patients micro PRM-MS2 refined_2020-05-30_00-19-04.sky.zip2020-06-09 13:11:206345527311
Sky5 91 patients micro PRM-MS2 raw_2020-05-30_00-57-41.sky.zip2020-06-09 13:11:206345527391
Sky2 Dilution series SARS Cov2 nano and microflow_2020-05-30_00-30-29.sky.zip2020-06-09 13:04:536345737118
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20191031_Cdc55AID_PRM_l2_manual3_2020-05-13_10-32-35.sky.zip2020-06-02 20:16:492627542064
20191031_Cdc55AID_PRM_l3_manual3_2020-05-13_11-25-38.sky.zip2020-06-02 20:16:492424481824
STORI_COHORT_2020-06-02_14-14-43.sky.zip2020-06-02 05:16:2773154154616102
Intra-day QC_2020-06-02_14-13-40.sky.zip2020-06-02 05:14:01731541546166
Inter-day QC_2020-06-02_14-12-41.sky.zip2020-06-02 05:13:11731541546165
Instrumental set-up QC_2020-06-02_14-10-53.sky.zip2020-06-02 05:11:30731541546165
MRM-C26-CT_2020-05-26_10-19-25.sky.zip2020-05-26 01:26:17217715461713
MRM-BaF-CT_2020-05-26_10-12-57.sky.zip2020-05-26 01:17:00217815662512
ARMeD_NEDP1_2019-11-02_13-41-15.sky.zip2020-05-25 20:17:53751481622,58918
Batch1412_2020-05-12_15-21-49.sky.zip2020-05-19 20:17:272141254
Batch1553_2020-05-12_15-28-16.sky.zip2020-05-19 20:17:272141263
Batch1508_2020-05-12_15-31-44.sky.zip2020-05-19 20:17:272151639
Batch1015_2020-05-12_15-39-40.sky.zip2020-05-19 20:17:272151631
Batch1134_2020-05-12_15-41-42.sky.zip2020-05-19 20:17:272141235
Batch1139_2020-05-12_15-45-12.sky.zip2020-05-19 20:17:272141238
Batch1039_2020-05-12_15-46-04.sky.zip2020-05-19 20:17:272141265
Batch1039b_2020-05-12_15-47-09.sky.zip2020-05-19 20:17:272141211
Batch1135_2020-05-12_15-49-04.sky.zip2020-05-19 20:17:262141264
Batch1553rep_2020-05-12_15-50-08.sky.zip2020-05-19 20:17:262141213
Batch1059_2020-05-12_15-51-24.sky.zip2020-05-19 20:17:262041284
Batch 1143_2020-05-12_15-53-25.sky.zip2020-05-19 20:17:262141265
Precision_2020-05-18_19-01-24.sky.zip2020-05-19 20:17:262141219
PRM_60min_2020-05-12_18-57-21.sky.zip2020-05-19 20:16:45417201228
PRM_9min_2020-05-18_21-07-56.sky.zip2020-05-19 20:16:44299668
PRM_9min_2020-05-19_07-53-44.sky.zip2020-05-19 20:16:10299668
LINCS_P100_DIA_Plate29_annotated_minimized_2020-05-18_18-50-11.sky.zip2020-05-18 15:59:1690961921,02896
DIAassayLibrary_Gasac-Gill_Rev2_2020-05-15_18-31-25.sky.zip2020-05-15 19:31:421,6914,7464,87926,1230
DIAassayLibrary_Gasac-Gill_Rev1_2020-05-15_17-01-05.sky.zip2020-05-15 17:38:291,5075,0745,10425,3220
Inflammatory_peptides_2020-05-13_13-35-09.sky.zip2020-05-13 10:58:1317494921860
Manually_filtered_peptides_2020-05-13_08-27-56.sky.zip2020-05-13 05:51:586253,2053,20513,12660
Prefiltering_CSF_document_2020-05-12_09-28-28.sky.zip2020-05-12 07:21:051,2225,9545,95422,91166
ResponseCurve-EGFR-LTQLGTFEDHFLSLQR_2020-01-28_09-46-19.sky.zip2020-05-11 16:35:09112434
ResponseCurve-CCND1-AYPDANLLNDR_2020-01-28_09-46-04.sky.zip2020-05-11 16:35:09112644
ResponseCurve-FOLH1-TYSVSFDSLFSAVK_2020-01-28_09-46-45.sky.zip2020-05-11 16:35:09112638
ResponseCurve-MUC1-DISEMFLQIYK_2020-01-28_09-47-16.sky.zip2020-05-11 16:35:09112428
ResponseCurve-PSA-LSEPAETDAVK_2020-01-28_09-47-42.sky.zip2020-05-11 16:35:09112644
ResponseCurve-SPINK1-QTSILIQK_2020-01-28_09-48-12.sky.zip2020-05-11 16:35:09112632
ResponseCurve-MMP9-LGLGADVAQVTGALR_2020-01-28_09-47-01.sky.zip2020-05-11 16:35:09112643
ResponseCurve-NCOA2-LLQDSSSPVDLAK_2020-01-28_09-47-28.sky.zip2020-05-11 16:35:09112442
ResponseCurve-SPRC-LEAGDHPVELLAR_2020-01-28_09-48-25.sky.zip2020-05-11 16:35:09112442
ResponseCurve-TGFB1-GGEIEGFR_2020-01-28_09-48-56.sky.zip2020-05-11 16:35:09112436
ResponseCurve-VEGFA-FMDVYQR_2020-01-28_09-49-13.sky.zip2020-05-11 16:35:09112433
ResponseCurve-CAMKK2-SLSAPGNLLTK_2020-01-28_09-45-49.sky.zip2020-05-11 16:35:09112442
ResponseCurve-ERG_pan-VIVPADPTLWSTDHVR_2020-01-28_09-46-32.sky.zip2020-05-11 16:35:09112643
ResponseCurve-SMAD4-YCQYAFDLK_2020-01-28_09-47-57.sky.zip2020-05-11 16:35:09112444
ResponseCurve-TFF3-VDCGYPHVTPK_2020-01-28_09-48-41.sky.zip2020-05-11 16:35:09112444
ResponseCurve-ANXA2-GLGTDEDSLIEIICSR_2020-01-28_09-49-31.sky.zip2020-05-11 16:35:09112441
CPDR-FFPE-ID-1193_2020-01-29_12-44-32.sky.zip2020-05-11 16:23:121616328224
CPDR-FFPE-ID-859_2020-01-29_12-41-32.sky.zip2020-05-11 16:23:121616328423
CPDR-FFPE-ID-1250_2020-01-29_12-41-18.sky.zip2020-05-11 16:23:121616328229
CPDR-FFPE-ID-1376_2020-01-29_14-56-40.sky.zip2020-05-11 16:23:121616328027
CPDR-FFPE-ID-1689_2020-01-29_12-40-48.sky.zip2020-05-11 16:23:121616328425
CPDR-FFPE-ID-636_2020-01-28_13-43-56.sky.zip2020-05-11 16:23:121616328632
CPDR-FFPE-ID-779_2020-01-28_13-41-34.sky.zip2020-05-11 16:23:121616328225
CPDR-FFPE-ID-850_2020-01-29_12-24-07.sky.zip2020-05-11 16:23:121616328223
CPDR-FFPE-ID-613_2020-01-28_13-47-05.sky.zip2020-05-11 16:23:121616328218
CPDR-FFPE-ID-623_2020-01-28_13-43-21.sky.zip2020-05-11 16:23:121616328244
CPDR-FFPE-ID-607_2020-01-28_13-42-17.sky.zip2020-05-11 16:23:121616328230
CPDR-FFPE-ID-573_2020-01-28_13-40-55.sky.zip2020-05-11 16:23:121616328415
CPDR-FFPE-ID-440_2020-01-28_13-27-00.sky.zip2020-05-11 16:23:121616328021
CPDR-FFPE-ID-497_2020-01-28_11-16-43.sky.zip2020-05-11 16:23:121616328430
CPDR-FFPE-ID-428_2020-01-28_11-16-26.sky.zip2020-05-11 16:23:121616328424
CPDR-FFPE-ID-1380_2020-01-29_14-57-50.sky.zip2020-05-11 16:23:121616328227
CPDR-FFPE-ID-1030_2020-01-29_14-49-38.sky.zip2020-05-11 16:23:121616328028
CPDR-FFPE-ID-726_2020-01-29_14-42-29.sky.zip2020-05-11 16:23:121616328229
CPDR-FFPE-ID-1217_2020-01-29_14-53-36.sky.zip2020-05-11 16:23:121616328224
CPDR-FFPE-ID-1059_2020-01-29_14-51-26.sky.zip2020-05-11 16:23:121616328425
CPDR-FFPE-ID-837_2020-01-29_14-45-59.sky.zip2020-05-11 16:23:121616328422
CPDR-FFPE-ID-835_2020-01-29_14-45-16.sky.zip2020-05-11 16:23:111616328428
CPDR-FFPE-ID-675_2020-01-29_14-30-10.sky.zip2020-05-11 16:23:111616328428
CPDR-FFPE-ID-659_2020-01-29_13-41-39.sky.zip2020-05-11 16:23:111616328224
CPDR-FFPE-ID-808_2020-01-29_12-41-02.sky.zip2020-05-11 16:23:111616328235
CPDR-FFPE-ID-1442_2020-01-29_12-40-36.sky.zip2020-05-11 16:23:111616328422
Modular Engineering of L-Tyrosine Production in Escherichia coli

  • Organism: Escherichia coli
  • Instrument: AB Sciex 4000 Q-trap
  • SpikeIn: No
Abstract
Efficient biosynthesis of L-tyrosine from glucose is necessary to make biological production economically viable. To this end, we designed and constructed a modular biosynthetic pathway for L-tyrosine production in E. coli MG1655 by encoding the enzymes for converting erythrose-4-phosphate (E4P) and phosphoenolpyruvate (PEP) to L-tyrosine on two plasmids. Rational engineering to improve L-tyrosine production and to identify pathway bottlenecks was directed by targeted proteomics and metabolite profiling. The bottlenecks in the pathway were relieved by modifications in plasmid copy numbers, promoter strength, gene codon usage, and the placement of genes in operons. One major bottleneck was due to the bifunctional activities of quinate/shikimate dehydrogenase (YdiB), which caused accumulation of the intermediates dehydroquinate (DHQ) and dehydroshikimate (DHS) and the side product quinate; this bottleneck was relieved by replacing YdiB with its paralog AroE, resulting in the production of over 700 mg/liter of shikimate. Another bottleneck in shikimate production, due to low expression of the dehydroquinate synthase (AroB), was alleviated by optimizing the first 15 codons of the gene. Shikimate conversion to L-tyrosine was improved by replacing the shikimate kinase AroK with its isozyme, AroL, which effectively consumed all intermediates formed in the first half of the pathway. Guided by the protein and metabolite measurements, the best producer, consisting of two medium-copy-number, dual-operon plasmids, was optimized to produce >2 g/liter L-tyrosine at 80% of the theoretical yield. This work demonstrates the utility of targeted proteomics and metabolite profiling in pathway construction and optimization, which should be applicable to other metabolic pathways.
Created on 6/11/18, 2:54 PM