Early posttranscriptional response to tetracycline exposure in a gram-negative soil bacterium reveals unexpected attenuation mechanism of a DUF1127 gene
The gram-negative, soil-dwelling plant symbiont Sinorhizobium meliloti shares its free-living habitat with antibiotic producers. To learn about early steps of its adaptation to antibiotics, we analysed transcriptome changes after 10 min exposure to subinhibitory amount of tetracycline (Tc). RNA-seq...
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| Format: | Article |
| Language: | English |
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Taylor & Francis Group
2025-12-01
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| Series: | RNA Biology |
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| Online Access: | https://www.tandfonline.com/doi/10.1080/15476286.2025.2521887 |
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| author | Jennifer A. F. Kothe Till Sauerwein Theresa Dietz Robina Scheuer Muhammad Elhossary Susanne Barth-Weber Jan Wähling Konrad U. Förstner Elena Evguenieva-Hackenberg |
| author_facet | Jennifer A. F. Kothe Till Sauerwein Theresa Dietz Robina Scheuer Muhammad Elhossary Susanne Barth-Weber Jan Wähling Konrad U. Förstner Elena Evguenieva-Hackenberg |
| author_sort | Jennifer A. F. Kothe |
| collection | DOAJ |
| description | The gram-negative, soil-dwelling plant symbiont Sinorhizobium meliloti shares its free-living habitat with antibiotic producers. To learn about early steps of its adaptation to antibiotics, we analysed transcriptome changes after 10 min exposure to subinhibitory amount of tetracycline (Tc). RNA-seq revealed 297 differentially expressed genes. Besides ten upregulated ribosomal genes, there was no recognizable functional pattern in the observed changes. However, polar differential expression pattern was observed: Mostly, upregulated genes were first and downregulated genes downstream in operons. Furthermore, we detected mRNA stabilization upon Tc exposure for several up- and down-regulated genes. Thus, mRNA stabilization contributed to increased mRNA levels, but for downstream genes its effect was probably counteracted by premature transcriptional termination caused by disrupted coupling between transcription and translation. Using reporter constructs, we found that a DUF1127 gene, showing highest mRNA increase, is controlled by transcription attenuation depending on the translation of an upstream ORF (uORF). Our data suggest the following model: The attenuation strongly depends on the accessibility of C-rich codons at the beginning of the uORF. The accessibility is guaranteed by translation of the uORF, and is possible in a time window after a ribosome moves downstream and before a next ribosome occupies the ribosomal binding site (RBS). The accessibility is blocked either by impaired translation initiation or, in the absence of ribosome binding, by base-pairing between the RBS and the C-rich codons. We propose that this is used by bacteria to monitor ribosome availability and translation efficiency, and to ensure reciprocal expression of the DUF1127 gene. |
| format | Article |
| id | doaj-art-9e604e607f1c46f793fdbc99caacf1bf |
| institution | Kabale University |
| issn | 1547-6286 1555-8584 |
| language | English |
| publishDate | 2025-12-01 |
| publisher | Taylor & Francis Group |
| record_format | Article |
| series | RNA Biology |
| spelling | doaj-art-9e604e607f1c46f793fdbc99caacf1bf2025-08-20T03:28:26ZengTaylor & Francis GroupRNA Biology1547-62861555-85842025-12-0122111610.1080/15476286.2025.2521887Early posttranscriptional response to tetracycline exposure in a gram-negative soil bacterium reveals unexpected attenuation mechanism of a DUF1127 geneJennifer A. F. Kothe0Till Sauerwein1Theresa Dietz2Robina Scheuer3Muhammad Elhossary4Susanne Barth-Weber5Jan Wähling6Konrad U. Förstner7Elena Evguenieva-Hackenberg8Institute of Microbiology and Molecular Biology, Justus Liebig University, Giessen, GermanyZB MED - Information Centre for Life Sciences, Cologne, GermanyInstitute of Microbiology and Molecular Biology, Justus Liebig University, Giessen, GermanyInstitute of Microbiology and Molecular Biology, Justus Liebig University, Giessen, GermanyZB MED - Information Centre for Life Sciences, Cologne, GermanyInstitute of Microbiology and Molecular Biology, Justus Liebig University, Giessen, GermanyInstitute of Microbiology and Molecular Biology, Justus Liebig University, Giessen, GermanyZB MED - Information Centre for Life Sciences, Cologne, GermanyInstitute of Microbiology and Molecular Biology, Justus Liebig University, Giessen, GermanyThe gram-negative, soil-dwelling plant symbiont Sinorhizobium meliloti shares its free-living habitat with antibiotic producers. To learn about early steps of its adaptation to antibiotics, we analysed transcriptome changes after 10 min exposure to subinhibitory amount of tetracycline (Tc). RNA-seq revealed 297 differentially expressed genes. Besides ten upregulated ribosomal genes, there was no recognizable functional pattern in the observed changes. However, polar differential expression pattern was observed: Mostly, upregulated genes were first and downregulated genes downstream in operons. Furthermore, we detected mRNA stabilization upon Tc exposure for several up- and down-regulated genes. Thus, mRNA stabilization contributed to increased mRNA levels, but for downstream genes its effect was probably counteracted by premature transcriptional termination caused by disrupted coupling between transcription and translation. Using reporter constructs, we found that a DUF1127 gene, showing highest mRNA increase, is controlled by transcription attenuation depending on the translation of an upstream ORF (uORF). Our data suggest the following model: The attenuation strongly depends on the accessibility of C-rich codons at the beginning of the uORF. The accessibility is guaranteed by translation of the uORF, and is possible in a time window after a ribosome moves downstream and before a next ribosome occupies the ribosomal binding site (RBS). The accessibility is blocked either by impaired translation initiation or, in the absence of ribosome binding, by base-pairing between the RBS and the C-rich codons. We propose that this is used by bacteria to monitor ribosome availability and translation efficiency, and to ensure reciprocal expression of the DUF1127 gene.https://www.tandfonline.com/doi/10.1080/15476286.2025.2521887BacteriaSinorhizobiumantibiotic exposuretranscription attenuationupstream ORFsmall genes |
| spellingShingle | Jennifer A. F. Kothe Till Sauerwein Theresa Dietz Robina Scheuer Muhammad Elhossary Susanne Barth-Weber Jan Wähling Konrad U. Förstner Elena Evguenieva-Hackenberg Early posttranscriptional response to tetracycline exposure in a gram-negative soil bacterium reveals unexpected attenuation mechanism of a DUF1127 gene RNA Biology Bacteria Sinorhizobium antibiotic exposure transcription attenuation upstream ORF small genes |
| title | Early posttranscriptional response to tetracycline exposure in a gram-negative soil bacterium reveals unexpected attenuation mechanism of a DUF1127 gene |
| title_full | Early posttranscriptional response to tetracycline exposure in a gram-negative soil bacterium reveals unexpected attenuation mechanism of a DUF1127 gene |
| title_fullStr | Early posttranscriptional response to tetracycline exposure in a gram-negative soil bacterium reveals unexpected attenuation mechanism of a DUF1127 gene |
| title_full_unstemmed | Early posttranscriptional response to tetracycline exposure in a gram-negative soil bacterium reveals unexpected attenuation mechanism of a DUF1127 gene |
| title_short | Early posttranscriptional response to tetracycline exposure in a gram-negative soil bacterium reveals unexpected attenuation mechanism of a DUF1127 gene |
| title_sort | early posttranscriptional response to tetracycline exposure in a gram negative soil bacterium reveals unexpected attenuation mechanism of a duf1127 gene |
| topic | Bacteria Sinorhizobium antibiotic exposure transcription attenuation upstream ORF small genes |
| url | https://www.tandfonline.com/doi/10.1080/15476286.2025.2521887 |
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