O'Connor et al. 2024 (PRJNA970321)

General Details

Title Ribosome profiling experiment characterising early response of Lactococcus Lactis infected in sk1 bacteriophage
Organism
Number of Samples 12
Release Date 2023/05/08 00:00
Sequencing Types
Protocol Details

Study Links

Repository Details

SRA SRP436568
ENA SRP436568
GEO GSE231968
BioProject PRJNA970321

Publication

Title
Authors O'Connor PBF, Mahony J, Casey E, Baranov PV, van Sinderen D, Yordanova MM
Journal Microbiology spectrum
Publication Date 2024 Apr 2
Abstract Bacteria 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. The 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.
PMC PMC10986495
PMID 38451091
DOI
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)
SRR24474755 PRJNA970321 Lactococcus lactis NA_bacteria Ribo-Seq 0.0
SRR24474754 PRJNA970321 Lactococcus lactis NA_bacteria Ribo-Seq 0.0
SRR24474753 PRJNA970321 Lactococcus lactis NA_bacteria Ribo-Seq 0.0
SRR24474752 PRJNA970321 Lactococcus lactis NA_bacteria Ribo-Seq 0.0
SRR24474751 PRJNA970321 Lactococcus lactis NA_bacteria Ribo-Seq 0.0
SRR24474750 PRJNA970321 Lactococcus lactis NA_bacteria Ribo-Seq 0.0
SRR24474749 PRJNA970321 Lactococcus lactis NA_bacteria Ribo-Seq 0.0
SRR24474748 PRJNA970321 Lactococcus lactis NA_bacteria Ribo-Seq 0.0
SRR24474747 PRJNA970321 Lactococcus lactis NA_bacteria Ribo-Seq 0.0
SRR24474746 PRJNA970321 Lactococcus lactis NA_bacteria Ribo-Seq 0.0
SRR24474745 PRJNA970321 Lactococcus lactis NA_bacteria Ribo-Seq 0.0
SRR24474744 PRJNA970321 Lactococcus lactis NA_bacteria Ribo-Seq 0.0
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)

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