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| Status |
Public on Nov 22, 2020 |
| Title |
A global data-driven census of Salmonella small proteins and their potential functions in bacterial virulence |
| Organism |
Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344 |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Small proteins are an emerging class of gene products with diverse roles in bacterial physiology. However, a full understanding of their importance has been hampered by insufficient genome annotations and a lack of characterization in microbes other than Escherichia coli. Here, we have taken an integrative approach to accelerate the discovery of small proteins and their putative virulence-associated functions in Salmonella Typhimurium. We merged the annotated small proteome of Salmonella with new small proteins predicted with in silico and experimental approaches. We then exploited existing and newly generated global datasets that provide information on small open reading frame expression during infection of epithelial cells (dual RNA-seq), contribution to bacterial fitness inside macrophages (TraDIS), and potential engagement in molecular interactions (Grad-seq). This integrative approach suggested a new role for the small protein MgrB beyond its known function in regulating PhoQ. We demonstrated a virulence and motility defect of a Salmonella ΔmgrB mutant and revealed an effect of MgrB in regulating the Salmonella transcriptome and proteome under infection-relevant conditions. Overall, our study highlights the power of interpreting available “omics” datasets with a focus on small proteins, and may serve as a blueprint for a data integration-based survey of small proteins in diverse bacteria.
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| Overall design |
Salmonella cells (WT or delta_mgrB) were grown in minimal medium. Total RNA was extracted and sequenced for two biological replicates.
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| Contributor(s) |
Venturini E |
| Citation(s) |
37223003 |
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Elisa Venturini, Sarah L Svensson, Sandra Maaß, Rick Gelhausen, Florian Eggenhofer, Lei Li, Amy K Cain, Julian Parkhill, Dörte Becher, Rolf Backofen, Lars Barquist, Cynthia M Sharma, Alexander J Westermann, and Jörg Vogel. A global data-driven census of Salmonella small proteins and their potential functions in bacterial virulence. microLife, Volume 1, Issue 1, July 2020, uqaa002, doi:10.1093/femsml/uqaa002
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| Submission date |
May 06, 2020 |
| Last update date |
Aug 11, 2023 |
| Contact name |
Jörg Vogel |
| E-mail(s) |
[email protected]
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| Organization name |
Institute for Molecular Infection Biology
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| Street address |
Josef-Schneider-Straße 2
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| City |
Würzburg |
| ZIP/Postal code |
97080 |
| Country |
Germany |
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| Platforms (1) |
| GPL20056 |
Illumina NextSeq 500 (Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344) |
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| Samples (4)
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| Relations |
| BioProject |
PRJNA630582 |
| SRA |
SRP260186 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE149928_SPI2_mgrB.xlsx |
410.8 Kb |
(ftp)(http) |
XLSX |
| GSE149928_mgrB_RPKM_SPI2.txt.gz |
72.7 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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