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ProteomicsMapping the tRNA Modification Landscape of Bartonella henselae Houston I and Bartonella quintana Toulouse
Transfer RNA (tRNA) modifications play a crucial role in maintaining translational fidelity and efficiency, and they may function as regulatory elements in stress response and virulence. Despite their pivotal roles, a comprehensive mapping of tRNA modifications and their associated synthesis genes i...
ORGANISM(S): Bartonella henselae (strain ATCC 49882 / Houston 1) (Rochalimaea henselae) Bartonella quintana str. Toulouse 
2024-01-23 | PXD048805 | Pride
Trna modification Intracellular pathogens Mass spectrometry Next-generation sequencing. 
ProteomicsA comprehensive portrait of tissue-, age- and sex-specific DNA modifications in rodents and humans
DNA damage causes genomic instability underlying many diseases, with traditional analytical approaches providing minimal insight into the spectrum of DNA lesions in vivo. Here we used untargeted chromatography-coupled tandem mass spectrometry-based adductomics (LC-MS/MS) to define the landscape of D...
ORGANISM(S): Homo sapiens (Human) Rattus norvegicus (Rat) 
2023-09-12 | PXD045311 | Pride
Adductomics Strp mrm 
ProteomicsArsenic toxicity is regulated by queuine availability and oxidation-induced reprogramming of the human tRNA epitranscriptome
Cells respond to environmental stress by regulating gene expression at the level of both transcription and translation. The ~50 modified ribonucleotides of the human epitranscriptome contribute to the latter, with mounting evidence that dynamic regulation of tRNA wobble modifications leads to select...
ORGANISM(S): Homo sapiens (Human) 
2022-08-27 | PXD030726 | Pride
Human hepg2 arsenic epitranascriptome proteome 
ProteomicsTemporal dynamics and metagenomics of phosphorothioate epigenomes in the human gut microbiome
Epigenetic regulation of gene expression and host defense is well established in microbial communities, with dozens of DNA modifications comprising the epigenomes of prokaryotes and bacteriophage. Phosphorothioation (PT) of DNA, in which a chemically-reactive sulfur atom replaces a non-bridging oxyg...
ORGANISM(S): Escherichia coli 
2025-03-03 | PXD051389 | Pride
Lc-ms/ms Phosphorothioate epigenetic modification Human gut microbiome Mouse gut microbiome 
ProteomicsEnterohemorrhagic Escherichia coli O157:H7 responds to norepinephrine gradients by tRNA reprogramming and codon-biased translation of virulence genes
We grew Escherichia coli O157:H7 strain EDL933 in low glucose DMEM and exposed it to 0 and 50 micromolar norepinephrine. After 5 hr of growth (37C, shaking 180rpm), cells were pelleted. Protein was then extracted and prepared for TMT-tagged proteomics to analyze for differential protein expression.
ORGANISM(S): Escherichia coli 
2026-04-17 | PXD068911 | Pride
Virulence Translational regulation Trna Ehec o157:h7 
TranscriptomicsProfiling of N6-Adenosine (m6A) Methylation in Arabidopsis thaliana wild-type and fip37-4 LEC1:FIP37
N6-methyladenosine (m6A) represents the most prevalent internal modification on messenger RNA, and requires a multicomponent m6A methyltransferase complex in mammals. How their plant counterparts determine the global m6A modification landscape and its molecular link to plant development remain elusi...
ORGANISM(S): Arabidopsis thaliana 
2016-07-25 | E-GEOD-75506 | biostudies-arrayexpress
TranscriptomicsRNA-seq profiles of Arabidopsis thaliana wild-type and fip37-4 LEC1:FIP37
N6-methyladenosine (m6A) represents the most prevalent internal modification on messenger RNA, and requires a multicomponent m6A methyltransferase complex in mammals. How their plant counterparts determine the global m6A modification landscape and its molecular link to plant development remain elusi...
ORGANISM(S): Arabidopsis thaliana 
2016-07-25 | E-GEOD-75507 | biostudies-arrayexpress
ProteomicstRNA modification profile of PA14 transposon insertion mutant library
Transfer RNA (tRNA) modifications have emerged as critical posttranscriptional regulators of gene expression that impact diverse biological and disease processes. While there is extensive knowledge about the enzymes installing the dozens of tRNA modifications – the tRNA epitranscriptome – very littl...
ORGANISM(S): Pseudomonas aeruginosa (strain UCBPP-PA14) 
2025-08-04 | PXD053297 | Pride
Trna modification Ucbpp-pa14 Mrm Lcms 
ProteomicsCohesin is involved in transcriptional repression of invasion-related genes
The most virulent human malaria parasite, Plasmodium falciparum, has a complex life cycle between its human host and mosquito vector. Each stage is driven by a specific transcriptional program, but with a relatively high ratio of genes to specific transcription factors, it is unclear how genes are a...
ORGANISM(S): Homo sapiens (Human) 
2023-10-04 | PXD035225 | Pride
Plasmodium Smc3 Cohesin 
ProteomicstRNA modification reprogramming of Plasmodium falciparum as a feature of artemisinin resistance
Artemisinin (ART)-resistant Plasmodium falciparum (Pf) threatens global malaria control. Resistance, driven by mutations in Pfk13, is multifaceted but quiescence plays a central role. Epigenetic regulation may contribute, given that only a percentage of parasites survive a pulse of the active drug m...
ORGANISM(S): Plasmodium falciparum 
2024-06-22 | PXD043747 | Pride
Plasmodium Artemisinin Rna modification 
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