DOI: 10.5281/zenodo.16985746
title: Aerobic catabolism of isobutylene by Mycolicibacterium sp. ELW1 requires plasmid-borne ibc genes

description: Folder: UC Davis Proteomics Data.zip

File: 20240401_140048_Hyman_Mycobacterium.sne

Proteomics data results and differential expression analysis for isobutylene-grown (IB) vs fructose-grown (f) cells of Mycolicibacterium sp. ELW1. Data Independent Acquisition LC-MS/MS Proteomic Profiling and differential expression analysis was performed by the UC Davis Proteomics Core Facility on biological replicates in triplicate using a timsTOF HT/EvoSep. Peptide identification used protein IDs for both CP032155.1 and CP032156.1 and the NZ_CP032155.1 and NZ_CP032156.1 GenBank entries for the Mycobacterium sp. ELW1 reference genome. This .sne file can be opened and used with the free software, Biognosys Spectronaut Viewer (PC only). User must request a free viewer license: Viewers for Biognosys Data - Biognosys. 

Variables

IB = isobutylene-grown cells

f = fructose-grown cells

Sample names

03272024-60spd-MH-f1_S3-A1_1_4336.htrms = fructose-grown sample 1

03272024-60spd-MH-f2_S3-B1_1_4341.htrms = fructose-grown sample 2

03272024-60spd-MH-f4_S3-C1_1_4338.htrms = fructose-grown sample 4

03272024-60spd-MH-IB1_S3-D1_1_4340.htrms = isobutylen-grown sample 1

03272024-60spd-MH-IB2_S3-E1_1_4337.htrms = isobutylen-grown sample 2

03272024-60spd-MH-IB4_S3-F1_1_4339.htrms = isobutylen-grown sample 4

 

File: Proteomic-Transcriptomic_Differential_Expression_Analysis_results_in_IB_vs_Fructose-grown_cells_of_ELW1.xlsx

The file contains four sheets:

Proteomic Full DE analysis: the results of the differential expression analysis (also available in the .sne file listed above) as performed by UC Davis Proteomics Core Facility using Spectronaut v18.6.231227.55695 (Biognosys Schlieren, Switzerland) and the directDIA workflow. The analysis was performed for isobutylene-grown (IB) vs fructose-grown (f) cells of Mycolicibacterium sp. ELW1. Peptide identification used protein IDs for both CP032155.1 and CP032156.1 and the NZ_CP032155.1 and NZ_CP032156.1 GenBank entries for the Mycobacterium sp. ELW1 reference genome. The differential expression analysis output can be viewed on this sheet. 

RNAseq Full DE analysis: the results of RNAseq differential expression analysis performed by the NC State University Genomic Sciences Laboratory (GSL) (Raleigh, NC) using an Illumina® NovaSeq 6000 and the subsequent differential expression analysis performed using CLC Genomics Workbench v23.0.4 (QIAGEN). The analysis was performed for isobutylene-grown (IB) vs fructose-grown (f) cells of Mycolicibacterium sp. ELW1 (IB-grown cells n=4, fructose-grown cells n=5). Transcripts were mapped to the NZ_CP032155.1 and NZ_CP032156.1 GenBank entries for the Mycobacterium sp. ELW1 reference genome and then analysis was performed using the Differential Expression in Two Groups tool from the RNA-Seq and Small RNA Analysis modules. The differential expression analysis output can be viewed on this sheet. 

Upregulated genes (Chromosome): Author curated listed of upregulated proteins and transcripts observed from the Proteomic Full DE analysis and the RNAseq Full DE analysis results from the Mycolicibacterium sp. ELW1 chromsome.

Upregulated genes (Plasmid): Author curated listed of upregulated proteins and transcripts observed from the Proteomic Full DE analysis and the RNAseq Full DE analysis results from the Mycolicibacterium sp. ELW1 megaplasmid, pELW1-1.
description: Isobutylene (2-methylpropene; IB) is the simplest branched alkene and is used industrially to produce a wide range of products ranging from fuel oxygenates to automobile tires. Only members of the Mycobacteriaceae family, including Mycolicibacterium sp. ELW1, are known to aerobically catabolize IB as a sole carbon and energy source. A multi-omics approach established two gene clusters on a large catabolic plasmid, pELW1-1, carried by Mycolicibacterium sp. ELW1. These two clusters separately contain the predicted genes necessary for the catabolism of IB to 2-hydroxyisobutyrate (2-HIBA) (cluster 1) and the biosynthesis of cobalamin and the further cobalamin-dependent transformation of 2-HIBA to acetyl-CoA (cluster 2). Curing strain ELW1 of pELW1-1 resulted in the loss of the ability of ELW1 to grow on IB and downstream metabolites including isobutylene oxide (IBO), 2-methyl-1,2-propanediol (MPD), and 2-hydroxyisobutyric acid (2-HIBA). Activity-based labeling (ABL), growth, and activity assays, combined with transcriptomic and proteomic analyses, confirmed the large catabolic plasmid is necessary for IB catabolism and that the plasmid-borne ibc genes are strongly induced during growth on IB.