Ribosome profiling reveals downregulation of UMP biosynthesis as the major early response to phage infection
ABSTRACTBacteria have evolved diverse defense mechanisms to counter bacteriophage attacks. Genetic programs activated upon infection characterize phage–host molecular interactions and ultimately determine the outcome of the infection. In this study, we applied ribosome profiling to monitor protein s...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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American Society for Microbiology
2024-04-01
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| Series: | Microbiology Spectrum |
| Subjects: | |
| Online Access: | https://journals.asm.org/doi/10.1128/spectrum.03989-23 |
| _version_ | 1797228844196823040 |
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| author | Patrick B. F. O’Connor Jennifer Mahony Eoghan Casey Pavel V. Baranov Douwe van Sinderen Martina M. Yordanova |
| author_facet | Patrick B. F. O’Connor Jennifer Mahony Eoghan Casey Pavel V. Baranov Douwe van Sinderen Martina M. Yordanova |
| author_sort | Patrick B. F. O’Connor |
| collection | DOAJ |
| description | ABSTRACTBacteria have evolved diverse defense mechanisms to counter bacteriophage attacks. Genetic programs activated upon infection characterize phage–host molecular interactions and ultimately determine the outcome of the infection. In this study, we applied ribosome profiling to monitor protein synthesis during the early stages of sk1 bacteriophage infection in Lactococcus cremoris. Our analysis revealed major changes in gene expression within 5 minutes of sk1 infection. Notably, we observed a specific and severe downregulation of several pyr operons which encode enzymes required for uridine monophosphate biosynthesis. Consistent with previous findings, this is likely an attempt of the host to starve the phage of nucleotides it requires for propagation. We also observed a gene expression response that we expect to benefit the phage. This included the upregulation of 40 ribosome proteins that likely increased the host’s translational capacity, concurrent with a downregulation of genes that promote translational fidelity (lepA and raiA). In addition to the characterization of host–phage gene expression responses, the obtained ribosome profiling data enabled us to identify two putative recoding events as well as dozens of loci currently annotated as pseudogenes that are actively translated. Furthermore, our study elucidated alterations in the dynamics of the translation process, as indicated by time-dependent changes in the metagene profile, suggesting global shifts in translation rates upon infection. Additionally, we observed consistent modifications in the ribosome profiles of individual genes, which were apparent as early as 2 minutes post-infection. The study emphasizes our ability to capture rapid alterations of gene expression during phage infection through ribosome profiling.IMPORTANCEThe ribosome profiling technology has provided invaluable insights for understanding cellular translation and eukaryotic viral infections. However, its potential for investigating host–phage interactions remains largely untapped. Here, we applied ribosome profiling to Lactococcus cremoris cultures infected with sk1, a major infectious agent in dairy fermentation processes. This revealed a profound downregulation of genes involved in pyrimidine nucleotide synthesis at an early stage of phage infection, suggesting an anti-phage program aimed at restricting nucleotide availability and, consequently, phage propagation. This is consistent with recent findings and contributes to our growing appreciation for the role of nucleotide limitation as an anti-viral strategy. In addition to capturing rapid alterations in gene expression levels, we identified translation occurring outside annotated regions, as well as signatures of non-standard translation mechanisms. The gene profiles revealed specific changes in ribosomal densities upon infection, reflecting alterations in the dynamics of the translation process. |
| first_indexed | 2024-04-24T15:03:09Z |
| format | Article |
| id | doaj.art-686b9e90ff334a5f9f68107dec1dc818 |
| institution | Directory Open Access Journal |
| issn | 2165-0497 |
| language | English |
| last_indexed | 2024-04-24T15:03:09Z |
| publishDate | 2024-04-01 |
| publisher | American Society for Microbiology |
| record_format | Article |
| series | Microbiology Spectrum |
| spelling | doaj.art-686b9e90ff334a5f9f68107dec1dc8182024-04-02T14:16:19ZengAmerican Society for MicrobiologyMicrobiology Spectrum2165-04972024-04-0112410.1128/spectrum.03989-23Ribosome profiling reveals downregulation of UMP biosynthesis as the major early response to phage infectionPatrick B. F. O’Connor0Jennifer Mahony1Eoghan Casey2Pavel V. Baranov3Douwe van Sinderen4Martina M. Yordanova5School of Biochemistry and Cell Biology, University College Cork, Cork, IrelandSchool of Microbiology and APC Microbiome Ireland, University College Cork, Cork, IrelandSchool of Microbiology and APC Microbiome Ireland, University College Cork, Cork, IrelandSchool of Biochemistry and Cell Biology, University College Cork, Cork, IrelandSchool of Microbiology and APC Microbiome Ireland, University College Cork, Cork, IrelandSchool of Biochemistry and Cell Biology, University College Cork, Cork, IrelandABSTRACTBacteria have evolved diverse defense mechanisms to counter bacteriophage attacks. Genetic programs activated upon infection characterize phage–host molecular interactions and ultimately determine the outcome of the infection. In this study, we applied ribosome profiling to monitor protein synthesis during the early stages of sk1 bacteriophage infection in Lactococcus cremoris. Our analysis revealed major changes in gene expression within 5 minutes of sk1 infection. Notably, we observed a specific and severe downregulation of several pyr operons which encode enzymes required for uridine monophosphate biosynthesis. Consistent with previous findings, this is likely an attempt of the host to starve the phage of nucleotides it requires for propagation. We also observed a gene expression response that we expect to benefit the phage. This included the upregulation of 40 ribosome proteins that likely increased the host’s translational capacity, concurrent with a downregulation of genes that promote translational fidelity (lepA and raiA). In addition to the characterization of host–phage gene expression responses, the obtained ribosome profiling data enabled us to identify two putative recoding events as well as dozens of loci currently annotated as pseudogenes that are actively translated. Furthermore, our study elucidated alterations in the dynamics of the translation process, as indicated by time-dependent changes in the metagene profile, suggesting global shifts in translation rates upon infection. Additionally, we observed consistent modifications in the ribosome profiles of individual genes, which were apparent as early as 2 minutes post-infection. The study emphasizes our ability to capture rapid alterations of gene expression during phage infection through ribosome profiling.IMPORTANCEThe ribosome profiling technology has provided invaluable insights for understanding cellular translation and eukaryotic viral infections. However, its potential for investigating host–phage interactions remains largely untapped. Here, we applied ribosome profiling to Lactococcus cremoris cultures infected with sk1, a major infectious agent in dairy fermentation processes. This revealed a profound downregulation of genes involved in pyrimidine nucleotide synthesis at an early stage of phage infection, suggesting an anti-phage program aimed at restricting nucleotide availability and, consequently, phage propagation. This is consistent with recent findings and contributes to our growing appreciation for the role of nucleotide limitation as an anti-viral strategy. In addition to capturing rapid alterations in gene expression levels, we identified translation occurring outside annotated regions, as well as signatures of non-standard translation mechanisms. The gene profiles revealed specific changes in ribosomal densities upon infection, reflecting alterations in the dynamics of the translation process.https://journals.asm.org/doi/10.1128/spectrum.03989-23ribosome profilingmRNA translationanti-phage response |
| spellingShingle | Patrick B. F. O’Connor Jennifer Mahony Eoghan Casey Pavel V. Baranov Douwe van Sinderen Martina M. Yordanova Ribosome profiling reveals downregulation of UMP biosynthesis as the major early response to phage infection Microbiology Spectrum ribosome profiling mRNA translation anti-phage response |
| title | Ribosome profiling reveals downregulation of UMP biosynthesis as the major early response to phage infection |
| title_full | Ribosome profiling reveals downregulation of UMP biosynthesis as the major early response to phage infection |
| title_fullStr | Ribosome profiling reveals downregulation of UMP biosynthesis as the major early response to phage infection |
| title_full_unstemmed | Ribosome profiling reveals downregulation of UMP biosynthesis as the major early response to phage infection |
| title_short | Ribosome profiling reveals downregulation of UMP biosynthesis as the major early response to phage infection |
| title_sort | ribosome profiling reveals downregulation of ump biosynthesis as the major early response to phage infection |
| topic | ribosome profiling mRNA translation anti-phage response |
| url | https://journals.asm.org/doi/10.1128/spectrum.03989-23 |
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