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Aerobic catabolism of isobutylene by Mycolicibacterium sp. ELW1 requires plasmid-borne ibc genes

ABSTRACT: Shotgun proteomic analysis was performed on batch cultures of strain Mycolicibacterium sp. ELW1 grown on IB (10%, v/v, gas phase) or fructose (final concentration ~10 mM) in MSM media. Cells grown to ~mid log phase in a dark shaking incubator (150 rpm; at 30C). Bacterial pellets (sample sizes IB-grown: n=3 and fructose-grown: n=3) were submitted to the UC Davis Proteomics Core Facility for protein extraction, digestion, and liquid chromatography tandem mass spectrometry (LC-MS/MS) using a timsTOF HT/EvoSep. Raw data files along with the differential expression analysis are provided. The results (.sne file) can be found at https://doi.org/10.5281/zenodo.16985746.

INSTRUMENT(S): timsTOF HT

ORGANISM(S): Mycolicibacterium Sp. Elw1

SUBMITTER: Michael Hyman

PROVIDER: MSV000100012 | MassIVE | Mon Nov 24 17:46:00 GMT 2025

REPOSITORIES: MassIVE

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Project description:Study of the possible existence of a replication fork trap in Vibrio cholerae. 1- FX85: EPV50(WT) grown in M9 minimal medium supplemented with 0.4 % fructose to exponential phase (0.2 OD 650 nm). 2- FX86: EPV50(WT) grown in M9 minimal medium supplemented with 0.4 % fructose to stationary phase (long overnight). 3- FX288: EGV140 (oriL3) grown in M9 minimal medium supplemented with 0.4 % fructose to exponential phase (0.2 OD 650 nm). 4- FX289:EGV140 (oriL3) grown in M9 minimal medium supplemented with 0.4 % fructose to stationary phase (long overnight). 5- FX290: EGV111 (oriR4) grown in M9 minimal medium supplemented with 0.4 % fructose to exponential phase (0.2 OD 650 nm). 6- FX291:EGV111 (oriR4) grown in M9 minimal medium supplemented with 0.4 % fructose to stationary phase (long overnight). 7- FX355:EPV50 (WT) grown in LB medium to exponential phase (0.2 OD 650nm) 8- FX356:EPV50 (WT) grown in LB medium to stationary phase (overnight) 9- FX286:EGV140 (oriL3) grown in LB medium to exponential phase (0.2 OD 650nm) 10- FX287:EGV140 (oriL3) grown in LB medium to stationary phase (overnight) 11- FX292:EGV111 (oriR4) grown in LB medium to exponential phase (0.2 OD 650nm) 12- FX49: MCH1 (WT monochromosome) grown in M9 minimal medium supplemented with 0.4 % fructose to exponential phase (0.2 OD 650 nm). 13- FX48: MCH1 (WT monochromosome) grown in M9 minimal medium supplemented with 0.4 % fructose to stationary phase (long overnight). 14- FX11: EGV369 (oriL3 monochromosome) grown in M9 minimal medium supplemented with 0.4 % fructose to exponential phase (0.2 OD 650 nm). 15- FX12: EGV366 (oriR4 monochromosome) grown in M9 minimal medium supplemented with 0.4 % fructose to exponential phase (0.2 OD 650 nm). 16- FX296 EPV50 M9 Exp 17- FX294 EPV50 M9 Stat 18-FX316 EGV140 M9 Exp 19- FX315 EGV111 M9 Exp 20-FX318 MCH1 M9 Exp 21- FX317 MCH1 M9 Stat 22- FX320 EGV369 M9 Exp 23- FX319 EGV366 M9 Exp Chromosomal DNA was extracted using the Sigma GenElute bacterial genomic DNA kit. 5 μg of DNA were used to generate a genomic library according to Illumina's protocol. The libraries and the sequencing were performed by the High-throughput Sequencing facility of the I2BC (http://www.i2bc.paris-saclay.fr/spip.php?article399〈=en,CNRS, Gif-sur-Yvette, France). Genomic DNA libraries were made with the ‘Nextera DNA library preparation kit’ (Illumina) following the manufacturer’s recommendations. Library quality was assessed on an Agilent Bioanalyzer 2100, using an Agilent High Sensitivity DNA Kit (Agilent technologies). Libraries were pooled in equimolar proportions. 75 bp single reads were generated on an Illumina MiSeq instrument, using a MiSeq Reagent kit V2 (500 cycles) (Illumina), with an expected depth of 217X. Reads were aligned on the in silico reconstituted genome of the cognate strain using BWA software. An in-lab written MATLAB-based script was used to perform marker frequency analysis. Data were normalized by dividing uniquely mapping sequence reads by the total number of reads. Enrichment of uniquely mapping sequence reads in 1 kb non-overlapping windows were calculated and plotted against the chromosomal coordinates.

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Aerobic catabolism of isobutylene by Mycolicibacterium sp. ELW1 requires plasmid-borne ibc genes

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