The Small Toxic <italic toggle="yes">Salmonella</italic> Protein TimP Targets the Cytoplasmic Membrane and Is Repressed by the Small RNA TimR
ABSTRACT Small proteins are gaining increased attention due to their important functions in major biological processes throughout the domains of life. However, their small size and low sequence conservation make them difficult to identify. It is therefore not surprising that enterobacterial ryfA has...
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| Format: | Article |
| Language: | English |
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American Society for Microbiology
2020-12-01
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| Series: | mBio |
| Subjects: | |
| Online Access: | https://journals.asm.org/doi/10.1128/mBio.01659-20 |
| _version_ | 1818751070984208384 |
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| author | Liis Andresen Yolanda Martínez-Burgo Josefin Nilsson Zangelin Alisa Rizvanovic Erik Holmqvist |
| author_facet | Liis Andresen Yolanda Martínez-Burgo Josefin Nilsson Zangelin Alisa Rizvanovic Erik Holmqvist |
| author_sort | Liis Andresen |
| collection | DOAJ |
| description | ABSTRACT Small proteins are gaining increased attention due to their important functions in major biological processes throughout the domains of life. However, their small size and low sequence conservation make them difficult to identify. It is therefore not surprising that enterobacterial ryfA has escaped identification as a small protein coding gene for nearly 2 decades. Since its identification in 2001, ryfA has been thought to encode a noncoding RNA and has been implicated in biofilm formation in Escherichia coli and pathogenesis in Shigella dysenteriae. Although a recent ribosome profiling study suggested ryfA to be translated, the corresponding protein product was not detected. In this study, we provide evidence that ryfA encodes a small toxic inner membrane protein, TimP, overexpression of which causes cytoplasmic membrane leakage. TimP carries an N-terminal signal sequence, indicating that its membrane localization is Sec-dependent. Expression of TimP is repressed by the small RNA (sRNA) TimR, which base pairs with the timP mRNA to inhibit its translation. In contrast to overexpression, endogenous expression of TimP upon timR deletion permits cell growth, possibly indicating a toxicity-independent function in the bacterial membrane. IMPORTANCE Next-generation sequencing (NGS) has enabled the revelation of a vast number of genomes from organisms spanning all domains of life. To reduce complexity when new genome sequences are annotated, open reading frames (ORFs) shorter than 50 codons in length are generally omitted. However, it has recently become evident that this procedure sorts away ORFs encoding small proteins of high biological significance. For instance, tailored small protein identification approaches have shown that bacteria encode numerous small proteins with important physiological functions. As the number of predicted small ORFs increase, it becomes important to characterize the corresponding proteins. In this study, we discovered a conserved but previously overlooked small enterobacterial protein. We show that this protein, which we dubbed TimP, is a potent toxin that inhibits bacterial growth by targeting the cell membrane. Toxicity is relieved by a small regulatory RNA, which binds the toxin mRNA to inhibit toxin synthesis. |
| first_indexed | 2024-12-18T04:29:44Z |
| format | Article |
| id | doaj.art-a0c0f1e79fa04ba6bb0d2af3606e71c7 |
| institution | Directory Open Access Journal |
| issn | 2150-7511 |
| language | English |
| last_indexed | 2024-12-18T04:29:44Z |
| publishDate | 2020-12-01 |
| publisher | American Society for Microbiology |
| record_format | Article |
| series | mBio |
| spelling | doaj.art-a0c0f1e79fa04ba6bb0d2af3606e71c72022-12-21T21:21:01ZengAmerican Society for MicrobiologymBio2150-75112020-12-0111610.1128/mBio.01659-20The Small Toxic <italic toggle="yes">Salmonella</italic> Protein TimP Targets the Cytoplasmic Membrane and Is Repressed by the Small RNA TimRLiis Andresen0Yolanda Martínez-Burgo1Josefin Nilsson Zangelin2Alisa Rizvanovic3Erik Holmqvist4Department of Cell and Molecular Biology, Biomedical Centre, Uppsala University, Uppsala, SwedenDepartment of Cell and Molecular Biology, Biomedical Centre, Uppsala University, Uppsala, SwedenDepartment of Cell and Molecular Biology, Biomedical Centre, Uppsala University, Uppsala, SwedenDepartment of Cell and Molecular Biology, Biomedical Centre, Uppsala University, Uppsala, SwedenDepartment of Cell and Molecular Biology, Biomedical Centre, Uppsala University, Uppsala, SwedenABSTRACT Small proteins are gaining increased attention due to their important functions in major biological processes throughout the domains of life. However, their small size and low sequence conservation make them difficult to identify. It is therefore not surprising that enterobacterial ryfA has escaped identification as a small protein coding gene for nearly 2 decades. Since its identification in 2001, ryfA has been thought to encode a noncoding RNA and has been implicated in biofilm formation in Escherichia coli and pathogenesis in Shigella dysenteriae. Although a recent ribosome profiling study suggested ryfA to be translated, the corresponding protein product was not detected. In this study, we provide evidence that ryfA encodes a small toxic inner membrane protein, TimP, overexpression of which causes cytoplasmic membrane leakage. TimP carries an N-terminal signal sequence, indicating that its membrane localization is Sec-dependent. Expression of TimP is repressed by the small RNA (sRNA) TimR, which base pairs with the timP mRNA to inhibit its translation. In contrast to overexpression, endogenous expression of TimP upon timR deletion permits cell growth, possibly indicating a toxicity-independent function in the bacterial membrane. IMPORTANCE Next-generation sequencing (NGS) has enabled the revelation of a vast number of genomes from organisms spanning all domains of life. To reduce complexity when new genome sequences are annotated, open reading frames (ORFs) shorter than 50 codons in length are generally omitted. However, it has recently become evident that this procedure sorts away ORFs encoding small proteins of high biological significance. For instance, tailored small protein identification approaches have shown that bacteria encode numerous small proteins with important physiological functions. As the number of predicted small ORFs increase, it becomes important to characterize the corresponding proteins. In this study, we discovered a conserved but previously overlooked small enterobacterial protein. We show that this protein, which we dubbed TimP, is a potent toxin that inhibits bacterial growth by targeting the cell membrane. Toxicity is relieved by a small regulatory RNA, which binds the toxin mRNA to inhibit toxin synthesis.https://journals.asm.org/doi/10.1128/mBio.01659-20small proteintoxin-antitoxinTA systemsRNAgrowth inhibitionryfA |
| spellingShingle | Liis Andresen Yolanda Martínez-Burgo Josefin Nilsson Zangelin Alisa Rizvanovic Erik Holmqvist The Small Toxic <italic toggle="yes">Salmonella</italic> Protein TimP Targets the Cytoplasmic Membrane and Is Repressed by the Small RNA TimR mBio small protein toxin-antitoxin TA system sRNA growth inhibition ryfA |
| title | The Small Toxic <italic toggle="yes">Salmonella</italic> Protein TimP Targets the Cytoplasmic Membrane and Is Repressed by the Small RNA TimR |
| title_full | The Small Toxic <italic toggle="yes">Salmonella</italic> Protein TimP Targets the Cytoplasmic Membrane and Is Repressed by the Small RNA TimR |
| title_fullStr | The Small Toxic <italic toggle="yes">Salmonella</italic> Protein TimP Targets the Cytoplasmic Membrane and Is Repressed by the Small RNA TimR |
| title_full_unstemmed | The Small Toxic <italic toggle="yes">Salmonella</italic> Protein TimP Targets the Cytoplasmic Membrane and Is Repressed by the Small RNA TimR |
| title_short | The Small Toxic <italic toggle="yes">Salmonella</italic> Protein TimP Targets the Cytoplasmic Membrane and Is Repressed by the Small RNA TimR |
| title_sort | small toxic italic toggle yes salmonella italic protein timp targets the cytoplasmic membrane and is repressed by the small rna timr |
| topic | small protein toxin-antitoxin TA system sRNA growth inhibition ryfA |
| url | https://journals.asm.org/doi/10.1128/mBio.01659-20 |
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