PXD038324 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Transcriptomic, proteomic and functional consequences of codon usage bias in human cells |
Description | Differences in codon frequency between genomes, genes, or positions along a gene, modulate transcription and translation efficiency, leading to phenotypic and functional differences. Integrative studies quantifying the phenotypic consequences of codon usage bias at different molecular and cellular levels in human cells are lacking. Here, we present a multiscale analysis of the effects of synonymous codon recoding during heterologous gene expression in human cells. Six synonymous versions of an antibiotic resistance gene were generated, fused to a fluorescent reporter, and independently expressed in HEK293 cells. Multiscale phenotype was analysed by means of: quantitative transcriptome and proteome assessment, as proxies for gene expression; cellular fluorescence, as a proxy for single-cell level expression; and real-time cell proliferation in absence or presence of antibiotic, as a proxy for the cell fitness. We show that differences in codon usage bias strongly impact the molecular and cellular phenotype: (i) they result in large differences in mRNA and in protein levels, as well in mRNA-to-protein ratio; (ii) they introduce unpredicted splicing events; (iii) they lead to reproducible phenotypic heterogeneity; and (iv) they lead to a trade-off between the benefit of antibiotic resistance and the burden of heterologous expression. In human cells in culture, codon usage bias modulates gene expression by modifying mRNA availability and suitability for translation, leading to differences in protein levels and eventually eliciting functional phenotypic changes. |
HostingRepository | PRIDE |
AnnounceDate | 2024-10-22 |
AnnouncementXML | Submission_2024-10-22_06:42:39.277.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Functional Proteomics Platform FPP |
SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: 9606; |
ModificationList | acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue |
Instrument | Q Exactive HF |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2022-11-23 04:45:28 | ID requested | |
1 | 2024-05-24 02:43:19 | announced | |
⏵ 2 | 2024-10-22 06:42:40 | announced | 2024-10-22: Updated project metadata. |
Publication List
10.1002/pro.4576; |
Picard MAL, Leblay F, Cassan C, Willemsen A, Daron J, Bauffe F, Decourcelle M, Demange A, Bravo IG, Transcriptomic, proteomic, and functional consequences of codon usage bias in human cells during heterologous gene expression. Protein Sci, 32(3):e4576(2023) [pubmed] |
Keyword List
submitter keyword: culture, mass spectrometry,HEK-293 |
Contact List
Ignacio G. Bravo |
contact affiliation | Laboratory MIVEGEC (CNRS IRD University Montpellier), French National Center for Scientific Research (CNRS), Montpellier, France |
contact email | ignacio.bravo@cnrs.fr |
lab head | |
Functional Proteomics Platform FPP |
contact affiliation | FPP CNRS |
contact email | contact@fpp.cnrs.fr |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD038324
- Label: PRIDE project
- Name: Transcriptomic, proteomic and functional consequences of codon usage bias in human cells