Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Mass spectrometry-based analysis of Mycobacterial single-colony proteome

ABSTRACT: Here as an attempt to explore bacterial single-colony proteomics, we describe a quantitative mass spectrometry-based protocol to isolate and analyse the proteome of a single mycobacterial colony from 7H10 media. Tryptic peptides are evaluated with high performance liquid chromatography coupled with a hybrid quadrupole mass filter Orbitrap analyser (Q Exactive) and raw data analysed using the MaxQuant Suite and downstream analysis using Perseus software . A total of 7805 unique peptides and 1387 proteins were identified

INSTRUMENT(S): Q Exactive HF

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

SUBMITTER: john Iradukunda

LAB HEAD: Jonathan Blackburn

PROVIDER: PXD018168 | Pride | 2021-03-11

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Publications

Mass Spectrometry-Based Analysis of Mycobacterial Single-Colony Proteome.

Iradukunda John J Ganief Tariq T Blackburn Jonathan M JM Soares Nelson C NC

Methods in molecular biology (Clifton, N.J.) 20210101

Mass spectrometry-based single-cell proteomic analysis has recently gained momentum and is now an emerging area with established protocols and promising results. Traditional proteomic studies, especially involving bacteria, have been limited to suspension cultures with large protein yields. Such studies, however, remain population centered with the uniqueness of individual responses to environmental challenges becoming diluted. To enable bacterial single-colony proteomics, we describe a quantita ...[more]

PMID: 33687715

Similar Datasets

Trichodesmium single colony metaproteomes field station Tricolim_19

Project description:Metaproteomes of individual Trichodesmium colonies collected from a single location in the Carribbean sea (65.22W, 17.02N) at 17:00 local time. Some colonies were associated with auto-fluorescent mineral particles. Their proteomes were analyzed individually to investigate the effect of the minerals on colony physiology.

2021-07-05 | PXD016330 | Pride

Identification of a complex genetic network involved in Saccharomyces cerevisiae colony morphology

Project description:When grown on solid substrates, different microorganisms often form colonies with very specific morphologies. Whereas the pioneers of microbiology often used colony morphology to discriminate between species and strains, the phenomenon has not received much recent attention. In this study, we use a genome-wide assay in the model yeast Saccharomyces cerevisiae to identify all genes that affect colony morphology. We show that several major signaling cascades, including the MAPK, TORC, SNF1 and RIM101 pathways play a role, indicating that morphological changes are a reaction to changing environments. Other genes that affect colony morphology are involved in protein sorting and epigenetic regulation. Interestingly, the screen reveals only few genes that are likely to play a direct role in establishing colony morphology, one notable exception being FLO11, a gene encoding a cell-surface adhesin that has already been implicated in colony morphology, biofilm formation, and invasive and pseudohyphal growth. Using a series of modified promoters to tune FLO11 expression, we confirm the central role of Flo11 and show that differences in FLO11 expression result in distinct colony morphologies. Together, our results provide a first comprehensive looks at the complex genetic network that underlies the diversity in the morphologies of yeast colonies. Microarrays were used to measure gene expression between WT and FLO11 mutants in both liquid and solid medium to assess which genes induce altered colony morphology through FLO11.

2012-04-27 | E-GEOD-36151 | biostudies-arrayexpress

Single colony sequencing

Project description:Single colony sequencing

| PRJEB17864 | ENA

Quantitative Mass Spectrometry Reveals Plasticity of Metabolic Networks in Mycobacterium smegmatis

Project description: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.

2014-07-09 | PXD000253 | Pride

Expression profiling of various colony phenotypes of wild Saccharomyces cerevisiae strain

Project description:Transcriptome comparison of cells from 4 and 7 day-old microcolonies of wild Saccharomyces cerevisiae BR-F strain, 4 and 7 day-old microcolonies of feral BR-RF strain and 4- and 7 day-old microcolonies of domesticated BR-S strain. All colonies grown on solid complex media with glycerol as carbon source. The aim of the study was to identify genes required for fluffy (structured) colony formation as well as the genes specific for certain phenotypic variant. BR-F is wild strain isolated from natural habitat and forms structured colonies when grown on media with non-fermentable carbon source. BR-S strain arose by phenotypic switch from the original wild BR-F strain during the cultivation of BR-F strain under rich and favourable conditions (process of so-called domestication), forms smooth colonies. BR-RF strain is derived from the domesticated BR-S strain under adverse conditions and restores the formation of structured colonies and other properties of original wild BR-F strain. Comparison of transcriptomes of cells from BR-F colonies vs cells from BR-RF colonies (see samples BR-FxBR-RF...), comparison of transcriptomes of cells from BR-F colonies vs cells from BR-S colonies (see samples BR-FxBR-S...) and comparison of transcriptomes of cells from BR-RF colonies vs cells from BR-S colonies (see samples BR-RFxBR-S...). Comparison of each couple performed with 4 day-old colonies and with 7 day-old colonies. 2 biological replicates for each time point from total 3 technical replicates (for first biological replicate see ...rep1, ...rep2 files, second biological replicate ...rep3 file). Dye-swap was performed between first two replicates (...rep1, ...rep2). In total six samples for each couple. Spotted ORFs microarray slides contain double genome of S. cerevisiae.

2014-02-19 | E-GEOD-40625 | biostudies-arrayexpress

Transcription profiling of brains from honey bee soldiers of different subspecies and host colony environment

Project description:Expression profiling of soldiers brains as a function of individual genotype (AHB/EHB) and environment (AHB/EHB host colony)

2009-07-01 | E-TABM-607 | biostudies-arrayexpress

Anopheles funestus FANG colony RNAseq

Project description:Anopheles funestus FANG colony RNAseq

| PRJEB10294 | ENA

Comparison between the proteome of Escherichia coli single colony and during liquid culture

Project description:Most of the proteomic studies done so far uses bacterial cells harvested from liquid culture media. However it is widely accepted that many important determinants associated with virulence and host cell adhesion are exclusively expressed during growth on solid media. As an attempt to complement previous studies, in this study we compare the proteome coverage of Escherichia coli K12 from a single colony on solid media with those at different growth phases in liquid culture; i.e. early log, mid log, early - and late stationary growth phases. A total of 2044 protein groups covering approximately 47% of the total proteome were identified across all studied conditions; 1650 number of proteins identified from single colonies and 1679 proteins from liquid cultured cells. Label-free quantitative analysis revealed that single colony proteome in a solid agar differs largely from that in liquid culture. The presence of the Suf-operon, involved in iron mobilisation and swarming motility were associated exclusively with single colony profiles. Whereas proteins involved in motility such as MotA, MotB, fliH, flip, fliD and fliJ were associated exclusively to cells grown in liquid culture. The data presented here provide a valuable resource for understanding the role of key proteins within microenvironments surrounding E.coli single colonies.

2021-09-09 | PXD019140 | Pride

Proteomics profiling of xanthomonas retroflexus colony variants

Project description:Plasmid conjugation is a key facilitator of horizontal gene transfer. Since plasmids often carry antibiotic resistance genes, they are crucial drivers of the world-wide rise of antibiotic resistance among pathogens. In natural, engineered and clinical environments, bacteria often grow in protective biofilms. Therefore, a better understanding of plasmid transfer in biofilms is needed. Our aim was to investigate plasmid transfer in a biofilm adapted wrinkly colony mutant of Xanthomonas retroflexus (XRw) with enhanced matrix production and reduced motility. We found that XRw biofilms had an increased uptake of the broad host-range IncP-1ϵ plasmid pKJK5 compared to the wild type. Proteomics revealed fewer flagellum associated proteins in XRw, suggesting that flagella were responsible for reducing plasmid uptake. This was confirmed by the higher plasmid uptake of non-flagellated ∆fliM mutants of X. retroflexus wild type and wrinkly mutant. Moreover, testing several flagella mutants of Pseudomonas putida suggested that the flagella effect was more general. We identified seven mechanisms with the potential to explain the flagella effect and simulated them in an individual-based model. Two mechanisms could thus be eliminated (increased distances between cells and increased lag times due to flagella). Another mechanism identified as viable in the modelling was eliminated by further experiments. Four additional proposed mechanisms have a reduced probability of plasmid transfer in common. Our findings highlight the important yet complex effects of flagella during bacterial conjugation in biofilms.

2024-01-26 | PXD040461 | Pride

Genomic binding profile of TAL1 in human Endothelial Colony-Forming Cells

Project description:Endothelial colony-forming cells (ECFCs) have been reported as promising cells for regenerative medicine thanks to their angiorepair properties. Transcription factors are primary determinants of the functional capacity of the cells and TAL1 has been shown as a critical regulator of endothelial lineage in both development and adult life. However, only few (three) TAL1 targets have been identified so far in mouse and human endothelial cells. This ChIP-seq experiment was designed to identify genome binding/occupancy of TAL1 by ChIP and high throughput sequencing in primary human endothelial stem/progenitor cells. TAL1 ChIP and IgG ChIP (negative control) were performed in crosslinked ECFCs derived from human umbilical cord blood.

2014-05-06 | E-GEOD-44442 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data