Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Proteomics data for Mycolicibacterium smegmatis mutants of the riboflavin biosynthetic pathway

ABSTRACT: This dataset contains raw DIA data for the proteome of wild-type and riboflavin biosynthetic pathway gene deletion mutants of Mycolicibacterium smegmatis (Msm). These strains were generated to investigate the essentiality of the riboflavin biosynthetic pathway, the source of metabolic antigens recognized by mucosal-associated invariant T (MAIT) cells, and the impact of elevated riboflavin on the proteome of Msm.

INSTRUMENT(S):

ORGANISM(S): Mycobacterium Tuberculosis H37rv

SUBMITTER: Nurudeen Oketade

LAB HEAD: Karen Dobos

PROVIDER: PXD068360 | Pride | 2025-12-15

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	Blank_Slot1-1_1_4183.d.zip	Other
	Blank_Slot1-1_1_4243.d.zip	Other
	Blank_Slot1-1_2_4116.d.zip	Other
	Blank_Slot1-1_2_4162.d.zip	Other
	Msm_Sample_Annotation.csv	Csv

Items per page:

1 - 5 of 122

Similar Datasets

Proteomics data for Mycobacterium tuberculosis mutants of the riboflavin biosynthetic pathway

Project description:Project Description This dataset contains raw DIA data for the proteome of wild-type and riboflavin biosynthetic pathway gene deletion mutants of Mycobacterium tuberculosis (Mtb). These strains were generated to investigate the essentiality of the riboflavin biosynthetic pathway, the source of metabolic antigens recognized by mucosal-associated invariant T (MAIT) cells, and the impact of elevated riboflavin on the proteome of Mtb.

2025-12-15 | PXD068335 | Pride

RNA-seq of Mycobacterium smegmatis mc2-155 SMR5 wild-type vs. a pafBC deletion strain under different growth/stress conditions

Project description:The goal of the experiment is to obtain a differential gene expression profile for Mycobacterium smegmatis mc2-155 SMR5 (Msm) wild-type in comparison to a pafBC deletion strain (MSMEG_3888 and MSMEG_3889). In addition, the gene expression is to be analyzed with respect to different growth/stress conditions. Four groups were etablished: (1) Msm wild-type under standard conditions (2) Msm delta-pafBC under standard conditions (3) Msm wild-type treated with mitomycin C (4) Msm delta-pafBC treated with mitomycin C.

2018-06-17 | E-MTAB-6497 | biostudies-arrayexpress

Evolution of an outbreak of meningococcal disease among men who have sex with men

Project description:Neisseria meningitidis (meningococcus) is usually transmitted via respiratory droplets, whereas its close relative, the gonococcus is sexually transmitted. Invasive meningococcal disease due to isolates of serogroup C increased in Europe and the United States among men who have sex with men (MSM). These isolates were also recovered from cases of urethritis suggesting sexual transmission. Genome sequencing of representative strains revealed that isolates from MSM and urethritis cases belonged to a unique clade within clonal complex11. Proteome analysis showed expression of nitrite reductase by these isolates, enabling anaerobic growth as in gonococci. Invasive isolates from MSM, but not urethritis isolates expressed functional human factor H (hfH) binding protein associated with enhanced survival in transgenic mice expressing hfH, a complement regulatory protein. Our data provide a unique example of meningococcal evolution with adaptation to sexual transmissibility, initially associated with low virulence but with subsequent fHbp-associated invasiveness. Implications for vaccination strategies are discussed.

2016-05-18 | PXD001498 | Pride

Integrated omics studies delineate the formation and dynamics of lipid droplets in Rhodococcus opacus PD630 for biofuel feedstock

Project description:Purpose: To delineate mechanisms underlying lipid storage in LDs, we compared the transcriptomes of cells cultivated under three lipid-accumulating conditions. Methods: PD630 mRNA profiles of 3 different conditions (normal condition and LDs acculation conditions) were generated by deep sequencing, using Solid platform. The sequence reads were mapped by using Bowtie followed by Cufflinks. Results: Most genes were either expressed under all three conditions (6,759 genes) or under at least one condition (7,770 genes), but 1,177 genes were not expressed under any of these conditions. We observed a marked response 3 h after cells were transferred from NB to MSM; 56.99% of the genes were up-regulated and 30.32% were down-regulated, with 21.15% being up-regulated more than 2-fold and 9.36% being down-regulated more than 2-fold Conclusions: Genes in category J (translation, ribosomal structure and biogenesis) were significantly up-regulated (p-value 5.05E-20, two-tailed Chi-square test), while genes in category K (transcription), G (carbohydrate transport and metabolism) and C (energy production and conversion) were down-regulated (p-values: 6.0E-07, 8.08E-06 and 4.56E-05, respectively, two-tailed Chi-square test). Increased expression of ribosomal proteins is consistent with number of genes (56.99%) up-regulated in the MSM3 treatment. This decrease in energy production and conversion is consistent with inhibition of cell division and lipid accumulation in MSM. PD630 mRNA profiles of 3 different conditions (normal condition and LDs acculation conditions) were generated by deep sequencing, using Solid platform.

2013-11-04 | E-GEOD-42381 | biostudies-arrayexpress

Transcriptomics and Real-Time PCR analysis reveals a cross-modulatory effect between riboflavin and iron and outlines common and specific responses to riboflavin biosynthesis and uptake in Vibrio cholerae

Project description:Riboflavin-derived molecules such as flavin mononucleotide and flavin adenine dinucleotide comprise the most important redox coenzymes all across life kingdoms. Vibrio cholerae, a pandemic diarrheagenic bacterium, is able to synthesize riboflavin through the riboflavin biosynthetic pathway (RBP) and to internalize exogenous riboflavin using the RibN importer. This bacterium thrives in different environments such as estuarine waters and the human intestinal tract. The presence of two independent riboflavin supply pathways in this species may be related to the variable riboflavin availability and requirements across different niches. In order to gain insights into the role of the riboflavin provision pathways in the physiology of V. cholerae, we analyzed the bacterial transcriptomics response to extracellular riboflavin and to the deletions of ribD (RBP-deficient strain) or ribN. Notably, many genes responding to riboflavin have been previously reported to belong to the iron regulon. Real time PCR analysis confirmed this effect and further documented that reciprocally, iron regulates RBP and ribN genes in a riboflavin-dependent way. A subset of genes were responding to both ribD and ribN deletions. Nonetheless, a group of genes was specifically affected in the ∆ribD strain, on which the functional terms protein folding and oxidation reduction process were enriched. Also, a subset of genes was affected specifically in the ∆ribN strain, on which the cytochrome complex assembly functional term was enriched. Results indicate that iron and riboflavin interrelate to regulate its respective provision genes and suggest that both common and specific effects of biosynthesized and internalized riboflavin exist.

2018-02-21 | GSE107538 | GEO

Transcription profiling of liver from sticklebacks exposed to copper, dibezanthracene or ethinyl-estradiol

Project description:Stickleback were exposed to Cu, DbA (Dibezanthracene), EE2 (Ethinyl-estradiol) or relevant controls. Liver tissue from individual fish exposed to different doses were arrayed versus a common reference.

2009-07-10 | E-MAXD-42 | biostudies-arrayexpress

Comprehensive Proteomic Analysis of Nitrogen Starved Mycobacterium smegmatis Δpup Reveals the Impact of Pupylation on Nitrogen Stress Response

Project description:Mycobacterium smegmatis is a soil bacterium exposed to continuously environmental changes of nitrogen availability. As member of Actinobacteria, it possesses an ubiquitin-like post-translational modification pathway called pupylation. The pathway starts when a small protein called Pup is attached to a lysine of a specific cellular target. Then the Pup-modified protein is degraded by the proteasome, as it was shown that Pup acts as degradation signal. Recent studies showed the role of pupylation in Mycobacterium smegmatis for survival under nitrogen starvation by supplying recycled amino acids. The present study is an investigation of the influence of Mycobacterium smegmatis Pup protein on the whole proteome in absence of nitrogen sources. Therefore a pup deletion mutant was generated. Applying stable isotope dimethyl labelling, low impact of the pupylation on proteome was revealed immediately after exposure to growth medium lacking nitrogen. In contrast, post 24 h of nitrogen starvation, Msm pup deletion strain showed several proteins with significant changes in abundance. Noteworthy, key proteins involved in nitrogen assimilation were significantly affected in Msm Δpup. Furthermore, we label-free quantified pupylated proteins of nitrogen starved Msm for a more extensive understanding of pupylation role in surviving and overcoming the lack of nitrogen.

2016-08-11 | PXD003229 | Pride

Transcription profiling of Stickleback liver exposed to Cu, DbA (Dibezanthracene), EE2 (Ethinyl-estradiol) or relevant controls

Project description:Stickleback were exposed to Cu, DbA (Dibezanthracene), EE2 (Ethinyl-estradiol) or relevant controls. Pooled liver tissue from treatment groups exposed to different doses were arrayed versus a common reference.

2009-07-10 | E-MAXD-43 | biostudies-arrayexpress

Gene expression in livers and thymi of uninjected or MegaFasL-injected C57BL/6 and MSM/Ms mice

Project description:Here we examine the expression of genes in unstimulated or following intraperitoneal injection with MegaFasL in MSM/Ms and C57BL/6 mouse livers and thymi This dataset is from two groups of 2 mice (1 MSM/Ms [MSM] and 1 C57BL/6 [B6] mouse) - either untreated (#1-#4) or injected intraperitoneally with 1.5ug of MegaFasL (#5-#8). Each group has four (4) samples - one liver (L) and one thymus (T) sample from each mouse. The liver and thymi were harvested from the same mouse. Unstimulated samples: 1_S1 = B6 T, 2_S=MSM T, 3_S3=B6 L, 4_S4=MSM L; MegaFasL-injected samples: 5_S1=B6 T, 6_S2=MSM T, 7_S3=B6 L, 8_S4=MSM L.

2015-09-04 | E-GEOD-72454 | biostudies-arrayexpress

Expression data from liver of male mouse at 10-week-old

Project description:To investigate mouse intersubspecific divergence of transcriptional regulation between C57BL/6J (B6) and Japanese wild-derived MSM/Ms strains, we performed transcriptome analysis by microarray on liver from B6 and MSM, and B6-ChrNMSM chromosome substitution strain panel, which carries MSM-derived chromosome or chromosomal segment on the B6 host.

2023-03-31 | GSE72825 | GEO