Limits...
Decay-Initiating Endoribonucleolytic Cleavage by RNase Y Is Kept under Tight Control via Sequence Preference and Sub-cellular Localisation.

Khemici V, Prados J, Linder P, Redder P - PLoS Genet. (2015)

Bottom Line: We have obtained a global picture of Staphylococcus aureus RNase Y sequence specificity using RNA-seq and the novel transcriptome-wide EMOTE method.Ninety-nine endoribonucleolytic sites produced in vivo were precisely mapped, notably inside six out of seven genes whose half-lives increase the most in an RNase Y deletion mutant, and additionally in three separate transcripts encoding degradation ribonucleases, including RNase Y itself, suggesting a regulatory network.We show that RNase Y is required to initiate the major degradation pathway of about a hundred transcripts that are inaccessible to other ribonucleases, but is prevented from promiscuous activity by membrane confinement and sequence preference for guanosines.

View Article: PubMed Central - PubMed

Affiliation: Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Switzerland.

ABSTRACT
Bacteria depend on efficient RNA turnover, both during homeostasis and when rapidly altering gene expression in response to changes. Nevertheless, remarkably few details are known about the rate-limiting steps in targeting and decay of RNA. The membrane-anchored endoribonuclease RNase Y is a virulence factor in Gram-positive pathogens. We have obtained a global picture of Staphylococcus aureus RNase Y sequence specificity using RNA-seq and the novel transcriptome-wide EMOTE method. Ninety-nine endoribonucleolytic sites produced in vivo were precisely mapped, notably inside six out of seven genes whose half-lives increase the most in an RNase Y deletion mutant, and additionally in three separate transcripts encoding degradation ribonucleases, including RNase Y itself, suggesting a regulatory network. We show that RNase Y is required to initiate the major degradation pathway of about a hundred transcripts that are inaccessible to other ribonucleases, but is prevented from promiscuous activity by membrane confinement and sequence preference for guanosines.

No MeSH data available.


Related in: MedlinePlus

Correlation between changes in half-lives and steady-state levels.The change between WT and ΔY in the half-life of each ORF was estimated using a smallest-difference model, and the same was done for the steady-state levels of the ORFs. The fold-change in half-life is plotted on the x-axis and the fold-change in steady-state level on the y-axis. Each grey circle represents an ORF transcript where sufficient data was available (1464 in all), and the names of ORFs discussed in this study are underlined. Red X's show which ORFs contain an identified RNase Y cleavage, and blue +'s show the ORFs where an RNase Y site was identified within 200 nt of an ORF.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4608709&req=5

pgen.1005577.g001: Correlation between changes in half-lives and steady-state levels.The change between WT and ΔY in the half-life of each ORF was estimated using a smallest-difference model, and the same was done for the steady-state levels of the ORFs. The fold-change in half-life is plotted on the x-axis and the fold-change in steady-state level on the y-axis. Each grey circle represents an ORF transcript where sufficient data was available (1464 in all), and the names of ORFs discussed in this study are underlined. Red X's show which ORFs contain an identified RNase Y cleavage, and blue +'s show the ORFs where an RNase Y site was identified within 200 nt of an ORF.

Mentions: Only 248 ORF RNAs are strongly affected by the RNase Y deletion, whereas 160 ORFs increase in stability just below the conservative 2 fold cut-off used throughout this study (summarised in Table 1, see also S1 Table for a full list). There was an overall good correlation between increased RNA stability and increase in steady-state levels as shown in Fig 1. The ORFs that were significantly affected in both steady-state and half-life levels (upper right quadrant in Fig 1) comprise 50 ORFs encoding several ribosomal proteins, housekeeping genes, chaperones, as well as the virulence regulators sarA, sarR, agrA and agrC. The correlation is nevertheless not absolute and some ORFs that accumulate are not stabilised, presumably due to indirect effects of the ΔY mutation. There are even seven ORF RNAs that decrease in abundance, notably the >8 fold lower expression of the spa transcript, which encodes the antibody-binding Protein A (Fig 1). However spa is negatively regulated by the agr quorum-sensing system [26] whose transcript is stabilised and accumulate in the ΔY mutant (see above), providing a logical explanation and a perfect example of an indirect effect.


Decay-Initiating Endoribonucleolytic Cleavage by RNase Y Is Kept under Tight Control via Sequence Preference and Sub-cellular Localisation.

Khemici V, Prados J, Linder P, Redder P - PLoS Genet. (2015)

Correlation between changes in half-lives and steady-state levels.The change between WT and ΔY in the half-life of each ORF was estimated using a smallest-difference model, and the same was done for the steady-state levels of the ORFs. The fold-change in half-life is plotted on the x-axis and the fold-change in steady-state level on the y-axis. Each grey circle represents an ORF transcript where sufficient data was available (1464 in all), and the names of ORFs discussed in this study are underlined. Red X's show which ORFs contain an identified RNase Y cleavage, and blue +'s show the ORFs where an RNase Y site was identified within 200 nt of an ORF.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4608709&req=5

pgen.1005577.g001: Correlation between changes in half-lives and steady-state levels.The change between WT and ΔY in the half-life of each ORF was estimated using a smallest-difference model, and the same was done for the steady-state levels of the ORFs. The fold-change in half-life is plotted on the x-axis and the fold-change in steady-state level on the y-axis. Each grey circle represents an ORF transcript where sufficient data was available (1464 in all), and the names of ORFs discussed in this study are underlined. Red X's show which ORFs contain an identified RNase Y cleavage, and blue +'s show the ORFs where an RNase Y site was identified within 200 nt of an ORF.
Mentions: Only 248 ORF RNAs are strongly affected by the RNase Y deletion, whereas 160 ORFs increase in stability just below the conservative 2 fold cut-off used throughout this study (summarised in Table 1, see also S1 Table for a full list). There was an overall good correlation between increased RNA stability and increase in steady-state levels as shown in Fig 1. The ORFs that were significantly affected in both steady-state and half-life levels (upper right quadrant in Fig 1) comprise 50 ORFs encoding several ribosomal proteins, housekeeping genes, chaperones, as well as the virulence regulators sarA, sarR, agrA and agrC. The correlation is nevertheless not absolute and some ORFs that accumulate are not stabilised, presumably due to indirect effects of the ΔY mutation. There are even seven ORF RNAs that decrease in abundance, notably the >8 fold lower expression of the spa transcript, which encodes the antibody-binding Protein A (Fig 1). However spa is negatively regulated by the agr quorum-sensing system [26] whose transcript is stabilised and accumulate in the ΔY mutant (see above), providing a logical explanation and a perfect example of an indirect effect.

Bottom Line: We have obtained a global picture of Staphylococcus aureus RNase Y sequence specificity using RNA-seq and the novel transcriptome-wide EMOTE method.Ninety-nine endoribonucleolytic sites produced in vivo were precisely mapped, notably inside six out of seven genes whose half-lives increase the most in an RNase Y deletion mutant, and additionally in three separate transcripts encoding degradation ribonucleases, including RNase Y itself, suggesting a regulatory network.We show that RNase Y is required to initiate the major degradation pathway of about a hundred transcripts that are inaccessible to other ribonucleases, but is prevented from promiscuous activity by membrane confinement and sequence preference for guanosines.

View Article: PubMed Central - PubMed

Affiliation: Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Switzerland.

ABSTRACT
Bacteria depend on efficient RNA turnover, both during homeostasis and when rapidly altering gene expression in response to changes. Nevertheless, remarkably few details are known about the rate-limiting steps in targeting and decay of RNA. The membrane-anchored endoribonuclease RNase Y is a virulence factor in Gram-positive pathogens. We have obtained a global picture of Staphylococcus aureus RNase Y sequence specificity using RNA-seq and the novel transcriptome-wide EMOTE method. Ninety-nine endoribonucleolytic sites produced in vivo were precisely mapped, notably inside six out of seven genes whose half-lives increase the most in an RNase Y deletion mutant, and additionally in three separate transcripts encoding degradation ribonucleases, including RNase Y itself, suggesting a regulatory network. We show that RNase Y is required to initiate the major degradation pathway of about a hundred transcripts that are inaccessible to other ribonucleases, but is prevented from promiscuous activity by membrane confinement and sequence preference for guanosines.

No MeSH data available.


Related in: MedlinePlus