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ProteomicsLabel-free shotgun proteomics of M. hyopneumoniae and M. feriruminatoris
Mycoplasmas are wall-less parasitic bacteria possessing extremely small genomes. Despite this, growth rates differ among mycoplasma species with doubling times ranging from only 0.5h to 16h. Here, we analyzed the whole proteomes of M. hyopneumoniae and M. feriruminatoris and performed a comparative ...
ORGANISM(S): Mycoplasma hyopneumoniae (strain 232) Mycoplasma feriruminatoris 
2021-08-23 | PXD025422 | Pride
M. hyopneumoniae M. feriruminatoris 
ProteomicsProteome wide measurements of protein half-lives in Mycoplasma pneumoniae
We obtained proteome wide measurements of protein half-lives in M. pneumoniae by performing pulse-chase experiments following SILAC methods. We estimated degradation rates of individual proteins by measuring the increase in light protein compared to heavy protein labeling along the growth curve.
ORGANISM(S): Mycoplasma pneumoniae (strain ATCC 29342 / M129) 
2020-11-24 | PXD016386 | Pride
Degradation rates Protein half-life Silac 
MetabolomicsLongitudinal multi-omics reveals subset-specific mechanisms underlying irritable bowel syndrome

The gut microbiome has been implicated in multiple human chronic gastrointestinal (GI) disorders. Determining its mechanistic role in disease has been difficult due to apparent disconnects between animal and human studies and lack of an integrated multi-omics view of disease-specific physiologica...

2020-09-08 | MTBLS1396 | MetaboLights
ProteomicsLabel-free shotgun proteomics of Lon and FtsH conditional mutants of Mycoplasma pneumoniae under depleting and inducing conditions
Using Mycoplasma pneumoniae as a model organism, we conditionally depleted the two essential ATP-dependent proteases (Lon and FtsH) of this bacterium, by engineering three strains carrying a Lon and/or FtsH inducible expression locus. An integrative comparative study combining label-free shotgun pro...
ORGANISM(S): Mycoplasma pneumoniae (strain ATCC 29342 / M129) 
2020-11-24 | PXD016343 | Pride
Protease Mycoplasma pneumoniae Protein homeostasis Degradation 
ProteomicsLabel-free shotgun proteomics of Triton X-100 insoluble fractions of Lon and FtsH conditional mutants of Mycoplasma pneumoniae under depleting and inducing conditions
Using Mycoplasma pneumoniae as a model organism, we conditionally depleted the two essential ATP-dependent proteases (Lon and FtsH) of this bacterium, by engineering strains carrying a Lon and/or FtsH inducible expression locus. An integrative comparative study combining label-free shotgun proteomic...
ORGANISM(S): Mycoplasma pneumoniae (strain ATCC 29342 / M129) 
2020-11-24 | PXD021506 | Pride
Protease Mycoplasma pneumoniae Protein homeostasis Degradation Insoluble fraction 
ProteomicsLabel-free shotgun proteomics of tmRNA substrates enriched by immunoprecipitation
We used a combination of genetic and proteomic approaches to characterize tmRNA (ssrA) activity in the genome-reduced bacterium Mycoplasma pneumoniae. For this, we generated tmRNA mutants encoding a tag resistant to proteolysis. Endogenous protein tagging by the mutant tmRNA gene (ssrAmk) was then e...
ORGANISM(S): Mycoplasma pneumoniae (strain ATCC 29342 / M129) 
2021-08-23 | PXD023973 | Pride
Trans-translation Ribosome stalling Mycoplasma pneumoniae Protein degradation Tmrna 
ProteomicsAbsolute protein quantification of Mycoplasma pneumoniae proteome by combining selected reaction monitoring of a reduced set of labeled peptides and label-free shotgun mass spectrometry.
We quantified the protein abundances of Mycoplasma pneumoniae (Mpn), a genome-reduced organism, by combining selected reaction monitoring of a reduced set of labeled peptides and label-free shotgun mass spectrometry. A set of 77 labeled peptides were synthesized and used as internal standard peptide...
ORGANISM(S): Mycoplasma pneumoniae (strain ATCC 29342 / M129) 
2023-08-31 | PXD035159 | Pride
Mycoplasma pneumoniae Absolute quantification Label-free Selected reaction monitoring 
TranscriptomicsRibosome profiling of the genome-reduced bacterium Mycoplasma pneumoniae
In order to study quantitatively the translation efficiency in the genome-reduced bacterium Mycoplasma pneumoniae, we performed ribosome profiling (ribo-seq) in standard growth conditions. We first tested whether the ribosome profiling method could be applied to M. pneumoniae and assessed the qualit...
ORGANISM(S): Escherichia coli K-12 
2023-07-01 | E-MTAB-11935 | biostudies-arrayexpress
TranscriptomicstRNAs quantification by hydro-tRNA-seq in the genome-reduced bacterium Mycoplasma pneumoniae
We measured abundances of tRNAs by means of hydro-tRNA-seq (Gogakos et al., 2017), a method based on partial alkaline RNA hydrolysis that generates fragments suitable for sequencing, in the genome-reduced bacterium Mycoplasma pneumoniae.
ORGANISM(S): Mycoplasma pneumoniae M129 
2023-06-29 | E-MTAB-11930 | biostudies-arrayexpress
TranscriptomicsRNA-seq differential expression analysis of tmRNA (ssrA) mutants in the genome-reduced bacterium Mycoplasma pneumoniae
We used a combination of genetic and proteomic approaches to characterize tmRNA (ssrA) activity in the genome-reduced bacterium Mycoplasma pneumoniae. For this, we generated tmRNA mutants encoding a tag resistant to proteolysis. Endogenous protein tagging by the mutant tmRNA gene (ssrAmk) was then e...
ORGANISM(S): Mycoplasma pneumoniae 
2021-08-09 | E-MTAB-10111 | biostudies-arrayexpress
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