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- Title
Proteome allocation is linked to transcriptional regulation through a modularized transcriptome.
- Authors
Patel, Arjun; McGrosso, Dominic; Hefner, Ying; Campeau, Anaamika; Sastry, Anand V.; Maurya, Svetlana; Rychel, Kevin; Gonzalez, David J.; Palsson, Bernhard O.
- Abstract
It has proved challenging to quantitatively relate the proteome to the transcriptome on a per-gene basis. Recent advances in data analytics have enabled a biologically meaningful modularization of the bacterial transcriptome. We thus investigate whether matched datasets of transcriptomes and proteomes from bacteria under diverse conditions can be modularized in the same way to reveal novel relationships between their compositions. We find that; (1) the modules of the proteome and the transcriptome are comprised of a similar list of gene products, (2) the modules in the proteome often represent combinations of modules from the transcriptome, (3) known transcriptional and post-translational regulation is reflected in differences between two sets of modules, allowing for knowledge-mapping when interpreting module functions, and (4) through statistical modeling, absolute proteome allocation can be inferred from the transcriptome alone. Quantitative and knowledge-based relationships can thus be found at the genome-scale between the proteome and transcriptome in bacteria. Here, the authors suggest that bacterial proteomes and transcriptomes can be modularized similarly, revealing previously uncharacterized relationships and opening up the possibility of predicting proteome allocation from transcriptomic data.
- Subjects
GENETIC transcription regulation; TRANSCRIPTOMES; NON-monogamous relationships; MODULAR design; STATISTICAL models
- Publication
Nature Communications, 2024, Vol 15, Issue 1, p1
- ISSN
2041-1723
- Publication type
Article
- DOI
10.1038/s41467-024-49231-y