Dataset Information

Quantitative Mass Spectrometry Reveals Plasticity of Metabolic Networks in Mycobacterium smegmatis

ABSTRACT: Carbon metabolism in Mycobacterium smegmatis was analysed using reverse-phase chromatography coupled to orbitrap high-resolution mass spectrometer using trypsin digestion. MS/MS files were searched against the Mycobacterium smegmatis strain MC2-155 database Release 1 - July 2010 ) by MaxQuant software (version 1.3.0.5). Mass spectra were searched with an initial mass tolerance of 7 ppm in MS mode and 0.5 Da in MS/MS mode. Up to two missed cleavages were allowed. Carbamidomethylation was set as a fixed modification, whereas oxidation (M), acetylation (Protein N-term) and Phospho (S, T, Y) were considered as variable modifications. Minimum required peptide length was set to seven amino acids and at least two (unique + razor) peptides were required for protein identification. A cut-off was fixed at 1% FDR at the peptide and protein level. Reverse and contaminants sequences were removed and proteins with a Posterior Error Probability (PEP) lower than 0.1 were accepted for further data treatment. Protein quantification was performed with razor and unique peptides, using only unmodified, oxidated (M) and acetylated (Protein N-term) peptides. A minimum of two ratio counts was required to quantify proteins.

INSTRUMENT(S): LTQ Orbitrap Elite

ORGANISM(S): Mycobacterium Smegmatis (strain Atcc 700084 / Mc(2)155)

SUBMITTER: Romain Hamelin

LAB HEAD: Moniatte

PROVIDER: PXD000253 | Pride | 2014-07-09

REPOSITORIES: Pride

ACCESS DATA

Dataset's files

Source:

Items per page:

1 - 5 of 25

Publications

Quantitative mass spectrometry reveals plasticity of metabolic networks in Mycobacterium smegmatis.

Chopra Tarun T Hamelin Romain R Armand Florence F Chiappe Diego D Moniatte Marc M McKinney John D JD

Molecular & cellular proteomics : MCP 20140705 11

Mycobacterium tuberculosis has a remarkable ability to persist within the human host as a clinically inapparent or chronically active infection. Fatty acids are thought to be an important carbon source used by the bacteria during long term infection. Catabolism of fatty acids requires reprogramming of metabolic networks, and enzymes central to this reprogramming have been targeted for drug discovery. Mycobacterium smegmatis, a nonpathogenic relative of M. tuberculosis, is often used as a model s ...[more]

PMID: 24997995

Similar Datasets

Project description:Total transcriptome analyses were carried out to investigate changes in transcript patterns in the Mycobacterium smegmatis wild type strain SMR5 due to nitrogen starvation and to expand the knowledge about the role of the two transcriptional regulators of nitrogen metabolism, namely GlnR and AmtR, in these processes. A first experiment revealed enhanced transcript levels of 284 genes and reduced transcripts of 231 genes in the wild type under nitrogen starvation compared to nitrogen surplus. When glnR deletion strain MH1 was compared to the wild type under nitrogen starvation, decreased transcript levels of 125 genes were detected, indicating that these are activated by GlnR due to nitrogen limitation. Comparing amtR deletion strain YL1 to the wild type under nitrogen starvation, enhanced transcript levels of 2 genes were found, indicating that they are repressed by AmtR under nitrogen surplus. A comparison of YL1 and wild type under surplus, as well as a comparison of YL1 under nitrogen surplus and starvation and of MH1 under nitrogen surplus and starvation were carried out as additional control experiments. It can be concluded that GlnR is the master regulator of nitrogen control in M. smegmatis and that AmtR fulfills only a small, subordinate role in the regulation of an operon. This SuperSeries is composed of the following subset Series: GSE30033: Mycobacterium smegmatis - Comparison of glnR deletion strain MH1 under nitrogen surplus and starvation GSE30231: Mycobacterium smegmatis - Comparison of wild type SMR5 and amtR deletion strain YL1 under nitrogen starvation GSE30232: Mycobacterium smegmatis - Comparison of amtR deletion strain YL1 under nitrogen surplus and starvation GSE30233: Mycobacterium smegmatis - Comparison of wild type SMR5 under nitrogen surplus and starvation GSE30234: Mycobacterium smegmatis - Comparison of wild type SMR5 and glnR deletion strain MH1 under nitrogen starvation GSE30235: Mycobacterium smegmatis - Comparison of wild type SMR5 and amtR deletion strain YL1 under nitrogen surplus Refer to individual Series

			Action	DRS
	MS_A_R1_11.raw	Raw
	MS_A_R1_2.raw	Raw
	MS_A_R1_4.raw	Raw
	MS_A_R1_5.raw	Raw
	MS_A_R1_6.raw	Raw