JBEI - Mitch Thompson

JBEI - Mitch Thompson
Clustergrammer Heatmap
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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
STORI_COHORT_2020-05-26_09-26-46.sky.zip2020-05-26 00:28:3173154154616102
Intra-day QC_2020-05-26_09-25-29.sky.zip2020-05-26 00:26:00731541546166
Inter-day QC_2020-05-26_09-23-53.sky.zip2020-05-26 00:24:21731541546165
Instrumental set-up QC_2020-05-26_09-21-49.sky.zip2020-05-26 00:22:31731541546165
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
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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
CPDR-FFPE-ID-928_2020-01-29_12-40-07.sky.zip2020-05-11 16:23:111616328225
CPDR-FFPE-ID-939_2020-01-29_12-39-50.sky.zip2020-05-11 16:23:111616328437
CPDR-FFPE-ID-1530_2020-01-29_12-38-39.sky.zip2020-05-11 16:23:111616328226
CPDR-FFPE-ID-796_2020-01-29_12-35-45.sky.zip2020-05-11 16:23:111616328429
CPDR-FFPE-ID-1090_2020-01-29_12-35-31.sky.zip2020-05-11 16:23:111616328427
CPDR-FFPE-ID-816_2020-01-29_12-35-04.sky.zip2020-05-11 16:23:111616328228
CPDR-FFPE-ID-831_2020-01-29_12-33-40.sky.zip2020-05-11 16:23:111616328239
CPDR-FFPE-ID-846_2020-01-29_12-34-49.sky.zip2020-05-11 16:23:111616328426
CPDR-FFPE-ID-1177_2020-01-29_12-34-34.sky.zip2020-05-11 16:23:111616328233
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CPDR-FFPE-ID-1502_2020-01-29_12-33-53.sky.zip2020-05-11 16:23:111616327831
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CPDR-FFPE-ID-698_2020-01-29_12-26-45.sky.zip2020-05-11 16:23:111616328228
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CPDR-FFPE-ID-776_2020-01-29_12-44-15.sky.zip2020-05-11 16:23:111616328024
CPDR-FFPE-ID-1350_2020-01-29_12-40-21.sky.zip2020-05-11 16:23:101616328225
CPDR-FFPE-ID-1660_2020-01-29_12-39-36.sky.zip2020-05-11 16:23:101616328436
CPDR-FFPE-ID-804_2020-01-29_12-39-10.sky.zip2020-05-11 16:23:101616328223
CPDR-FFPE-ID-995_2020-01-29_12-38-23.sky.zip2020-05-11 16:23:101616328422
CPDR-FFPE-ID-1423_2020-01-29_12-38-07.sky.zip2020-05-11 16:23:101616328024
CPDR-FFPE-ID-1552_2020-01-29_12-36-56.sky.zip2020-05-11 16:23:101616328224
CPDR-FFPE-ID-1137_2020-01-29_12-36-39.sky.zip2020-05-11 16:23:101616328026
CPDR-FFPE-ID-1147_2020-01-29_12-35-59.sky.zip2020-05-11 16:23:101616328462
CPDR-FFPE-ID-1103_2020-01-29_12-32-17.sky.zip2020-05-11 16:23:101616328235
CPDR-FFPE-ID-656_2020-01-29_12-30-34.sky.zip2020-05-11 16:23:101616328227
CPDR-FFPE-ID-651_2020-01-29_12-22-55.sky.zip2020-05-11 16:23:101616328421
CPDR-FFPE-ID-1145_2020-01-29_12-22-42.sky.zip2020-05-11 16:23:101616328421
CPDR-FFPE-ID-736_2020-01-29_12-22-25.sky.zip2020-05-11 16:23:101616328230
Massively parallel fitness profiling reveals multiple novel enzymes in Pseudomonas putida lysine metabolism

  • Organism: Pseudomonas putida KT2440
  • Instrument: 6460 Triple Quadrupole LC/MS
  • SpikeIn: No
  • Keywords: targeted proteomics
  • Lab head: Chris Petzold
Abstract
The lysine metabolism of Pseudomonas putida can produce multiple important commodity chemicals and is implicated in rhizosphere colonization. However, despite intensive study, the biochemical and genetic links between lysine metabolism and central metabolism remains unresolved in P. putida. Here, we leverage Random Barcode Transposon Sequencing (RB-TnSeq), a genome-wide assay measuring the fitness of thousands of genes in parallel, to identify multiple novel enzymes and regulators in both L- and D-lysine metabolism. We first describe three pathway enzymes that catabolize 2-aminoadipate (2AA) to 2-ketoglutarate (2KG) connecting D-lysine to the TCA cycle. One of these enzymes, PP_5260, contains a DUF1338 domain, a family without previously described biological function. We demonstrate PP_5260 converts 2-oxoadipate (2OA) to 2-hydroxyglutarate (2HG), a novel biochemical reaction. We expand on recent work showing that the glutarate hydroxylase CsiD can co-utilize 2OA and 2KG. We further show glutarate metabolism is locally regulated by two independent glutarate responsive transcription factors, and that cellular abundance of D- and L-lysine pathway proteins are highly sensitive to pathway specific substrates. This work demonstrates the utility of RB-TnSeq of discovering novel metabolic pathways in even well-studied bacterial species.
Experiment Description
Targeted proteomics - more information is available in the paper reference.
Created on 10/12/18, 11:31 AM