A global data-driven census of Salmonella small proteins and their potential functions in bacterial virulence
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ABSTRACT:
ORGANISM(S): Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344
PROVIDER: GSE149893 | GEO | 2020/11/17
REPOSITORIES: GEO
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Project description: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.
2020-11-20 | GSE149580 | GEO
Project description: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.
2020-11-22 | GSE149928 | GEO
Project description: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.
2020-12-07 | PXD018754 | Pride
Project description:A global data-driven census of Salmonella small proteins and their potential functions in bacterial virulence
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Project description:A global data-driven census of Salmonella small proteins and their potential functions in bacterial virulence
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Project description:A global data-driven census of Salmonella small proteins and their potential functions in bacterial virulence
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Project description:Three translatomic approaches were applied to the foodborne pathogen Campylobacter jejuni to identify translated open reading frames, start codons, and stop codons and reveal novel small proteins
2024-05-23 | GSE208756 | GEO
Project description:FinO-domain proteins such as ProQ of the model pathogen Salmonella enterica have emerged as a new class of major RNA-binding proteins in bacteria. ProQ has been shown to target hundreds of transcripts including mRNAs from many virulence regions but its role, if any, in bacterial pathogenesis has not been studied. Here, using a Dual RNA-seq approach to profile ProQ-dependent gene expression changes as Salmonella infects human cells, we reveal dysregulation of bacterial motility, chemotaxis and virulence genes which is accompanied by altered mitogen-activated protein kinase signaling in the host. Comparison with Hfq, Salmonella’s other major RNA chaperone, reinforces the notion that these two global RNA binding proteins work in parallel to ensure full virulence. Of newly discovered infection-associated ProQ-bound small noncoding RNAs, we show that STnc540 represses a virulence-related magnesium transporter mRNA in a ProQ-dependent manner. Together, this comprehensive study uncovers the relevance of ProQ for Salmonella infection and highlights the importance of RNA-binding proteins in regulating bacterial virulence programs.
2018-11-28 | GSE117255 | GEO
Project description:FinO-domain proteins such as ProQ of the model pathogen Salmonella enterica have emerged as a new class of major RNA-binding proteins in bacteria. ProQ has been shown to target hundreds of transcripts including mRNAs from many virulence regions but its role, if any, in bacterial pathogenesis has not been studied. Here, using a Dual RNA-seq approach to profile ProQ-dependent gene expression changes as Salmonella infects human cells, we reveal dysregulation of bacterial motility, chemotaxis and virulence genes which is accompanied by altered mitogen-activated protein kinase signaling in the host. Comparison with Hfq, Salmonella’s other major RNA chaperone, reinforces the notion that these two global RNA binding proteins work in parallel to ensure full virulence. Of newly discovered infection-associated ProQ-bound small noncoding RNAs, we show that STnc540 represses a virulence-related magnesium transporter mRNA in a ProQ-dependent manner. Together, this comprehensive study uncovers the relevance of ProQ for Salmonella infection and highlights the importance of RNA-binding proteins in regulating bacterial virulence programs.
2018-11-28 | GSE117252 | GEO
Project description:Bacterial genomes serve as a blueprint in all aspects of biological research, and therefore accurate annotation is of paramount importance. However, increasing evidence suggests annotated bacterial genomes have missed many, if not all, small genes encoding proteins ≤60 amino acids. To uncover unannotated small genes in Salmonella enterica, we used a genomic technique ‘ribosome profiling’ that provides a snapshot of all mRNAs being translated (translatome). For comprehensive identification of the small genes, we obtained Salmonella translatomes in four different growth conditions including Luria-Bertani medium, MOPS rich defined medium, N-minimal medium with low Mg2+ (10 μM), and N-minimal medium at pH 5.7, respectively. Ribosome profiling data were analysed in combination with in silico predicted putative open reading frames and transcriptome profiles. As a result, we uncovered 127 previously unannotated genes, the majority of which were small genes encoding proteins ≤50 amino acids. We validated expression by western blot of the identified unannotated small genes, the smallest of which is 7-amino acid long. Because some unannotated small genes identified in this study are only expressed in the infection-relevant low Mg2+ conditions, they are likely involved in cellular processes required for Salmonella virulence. Our findings suggest that currently sequenced bacterial genomes are likely under-annotated with regard to small genes and need to be revised.
2017-03-09 | GSE87871 | GEO