PXD055700
PXD055700 is an original dataset announced via ProteomeXchange.
Dataset Summary
| Title | Using conserved protein to mRNA ratios across kingdoms to enhance microbial functional predictions |
| Description | Understanding the biology of native microbial communities is hindered by the lack of robust functional data for the microbes within these communities. Quantifying mRNA levels via transcriptomics to infer function has proven successful in these communities. However, this requires the ability to accurately predict protein levels, which are the primary functional units, from mRNA levels. While a positive correlation exists between mRNA and protein levels, for certain genes, mRNA is not a predictor of protein. To address this challenge, studies have quantified the protein-to-RNA (PTR) ratios of all genes, including those in which mRNA levels are not predictive of protein levels. These data enabled the calculation of RNA-to-protein (RTP) conversion factors for some of these genes that, when applied to mRNA levels, enhance the predictivity for protein levels. Despite the potential of RTP conversion factors, their calculation requires extensive datasets, which are costly and not available for most microbes. Here, we generated and analyzed comprehensive datasets from seven bacterial strains and one archaeon and identified orthologous genes in which mRNA was not predictive of protein but had consistent PTR ratios. Calculation and application of conversion factors for these genes improved protein prediction from mRNA, even when the conversion factors were derived from distantly-related bacteria. RTP conversion factors derived from bacteria also improved protein predictivity from mRNA in an archaeon, indicating that this approach is robust across domains of life. Ultimately, this approach improves protein prediction from mRNA without the need for paired transcriptomic/proteomic data from a microbe of interest. |
| HostingRepository | MassIVE |
| AnnounceDate | 2024-09-07 |
| AnnouncementXML | Submission_2024-09-07_10:50:09.270.xml |
| DigitalObjectIdentifier | |
| ReviewLevel | Non peer-reviewed dataset |
| DatasetOrigin | Original dataset |
| RepositorySupport | Unsupported dataset by repository |
| PrimarySubmitter | Mengshi |
| SpeciesList | scientific name: Porphyromonas gingivalis ATCC 33277; NCBI TaxID: 431947; scientific name: Streptococcus gordonii str. Challis substr. CH1; NCBI TaxID: 467705; scientific name: Aggregatibacter actinomycetemcomitans; NCBI TaxID: 714; scientific name: Aggregatibacter actinomycetemcomitans Y4; NCBI TaxID: 1035194; scientific name: Sulfolobus islandicus M.16.4; NCBI TaxID: 426118; scientific name: Staphylococcus aureus subsp. aureus USA300; NCBI TaxID: 367830; |
| ModificationList | TMTpro |
| Instrument | Dionex instrument model |
Dataset History
| Revision | Datetime | Status | ChangeLog Entry |
|---|---|---|---|
| 0 | 2024-09-07 10:14:24 | ID requested | |
| ⏵ 1 | 2024-09-07 10:50:09 | announced |
Publication List
| no publication |
Keyword List
| submitter keyword: Pseudomonas aeruginosa, RNA to protein ratio, transcriptomics, proteome, translation |
Contact List
| Marvin Whiteley | |
|---|---|
| contact affiliation | Georgia Institute of Technology |
| contact email | mwhiteley3@gatech.edu |
| lab head | |
| Mengshi | |
| contact affiliation | Georgia Institute of Technology |
| contact email | mengshi0928@gmail.com |
| dataset submitter | |
Full Dataset Link List
| MassIVE dataset URI |
| Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://massive.ucsd.edu/v08/MSV000095802/ |
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