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Yeast Ssd1 is a non-enzymatic member of the RNase II family with an alternative RNA recognition site

Ssd1, a conserved fungal RNA-binding protein, is important in stress responses, cell division and virulence. Ssd1 is closely related to Dis3L2 of the RNase II family of nucleases, but lacks catalytic activity and likely suppresses translation of bound mRNAs. Previous studies identified RNA motifs en...

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Autores principales: Bayne, Rosemary A, Jayachandran, Uma, Kasprowicz, Aleksandra, Bresson, Stefan, Tollervey, David, Wallace, Edward W J, Cook, Atlanta G
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8934651/
https://www.ncbi.nlm.nih.gov/pubmed/34302485
http://dx.doi.org/10.1093/nar/gkab615
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author Bayne, Rosemary A
Jayachandran, Uma
Kasprowicz, Aleksandra
Bresson, Stefan
Tollervey, David
Wallace, Edward W J
Cook, Atlanta G
author_facet Bayne, Rosemary A
Jayachandran, Uma
Kasprowicz, Aleksandra
Bresson, Stefan
Tollervey, David
Wallace, Edward W J
Cook, Atlanta G
author_sort Bayne, Rosemary A
collection PubMed
description Ssd1, a conserved fungal RNA-binding protein, is important in stress responses, cell division and virulence. Ssd1 is closely related to Dis3L2 of the RNase II family of nucleases, but lacks catalytic activity and likely suppresses translation of bound mRNAs. Previous studies identified RNA motifs enriched in Ssd1-associated transcripts, yet the sequence requirements for Ssd1 binding are not defined. Here, we identify precise binding sites of Ssd1 on RNA using in vivo cross-linking and cDNA analysis. These sites are enriched in 5′ untranslated regions of a subset of mRNAs encoding cell wall proteins. We identified a conserved bipartite motif that binds Ssd1 with high affinity in vitro. Active RNase II enzymes have a characteristic, internal RNA binding path; the Ssd1 crystal structure at 1.9 Å resolution shows that remnants of regulatory sequences block this path. Instead, RNA binding activity has relocated to a conserved patch on the surface of the protein. Structure-guided mutations of this surface prevent Ssd1 from binding RNA in vitro and phenocopy Ssd1 deletion in vivo. These studies provide a new framework for understanding the function of a pleiotropic post-transcriptional regulator of gene expression and give insights into the evolution of regulatory and binding elements in the RNase II family.
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spelling pubmed-89346512022-03-21 Yeast Ssd1 is a non-enzymatic member of the RNase II family with an alternative RNA recognition site Bayne, Rosemary A Jayachandran, Uma Kasprowicz, Aleksandra Bresson, Stefan Tollervey, David Wallace, Edward W J Cook, Atlanta G Nucleic Acids Res Structural Biology Ssd1, a conserved fungal RNA-binding protein, is important in stress responses, cell division and virulence. Ssd1 is closely related to Dis3L2 of the RNase II family of nucleases, but lacks catalytic activity and likely suppresses translation of bound mRNAs. Previous studies identified RNA motifs enriched in Ssd1-associated transcripts, yet the sequence requirements for Ssd1 binding are not defined. Here, we identify precise binding sites of Ssd1 on RNA using in vivo cross-linking and cDNA analysis. These sites are enriched in 5′ untranslated regions of a subset of mRNAs encoding cell wall proteins. We identified a conserved bipartite motif that binds Ssd1 with high affinity in vitro. Active RNase II enzymes have a characteristic, internal RNA binding path; the Ssd1 crystal structure at 1.9 Å resolution shows that remnants of regulatory sequences block this path. Instead, RNA binding activity has relocated to a conserved patch on the surface of the protein. Structure-guided mutations of this surface prevent Ssd1 from binding RNA in vitro and phenocopy Ssd1 deletion in vivo. These studies provide a new framework for understanding the function of a pleiotropic post-transcriptional regulator of gene expression and give insights into the evolution of regulatory and binding elements in the RNase II family. Oxford University Press 2021-07-24 /pmc/articles/PMC8934651/ /pubmed/34302485 http://dx.doi.org/10.1093/nar/gkab615 Text en © The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Structural Biology
Bayne, Rosemary A
Jayachandran, Uma
Kasprowicz, Aleksandra
Bresson, Stefan
Tollervey, David
Wallace, Edward W J
Cook, Atlanta G
Yeast Ssd1 is a non-enzymatic member of the RNase II family with an alternative RNA recognition site
title Yeast Ssd1 is a non-enzymatic member of the RNase II family with an alternative RNA recognition site
title_full Yeast Ssd1 is a non-enzymatic member of the RNase II family with an alternative RNA recognition site
title_fullStr Yeast Ssd1 is a non-enzymatic member of the RNase II family with an alternative RNA recognition site
title_full_unstemmed Yeast Ssd1 is a non-enzymatic member of the RNase II family with an alternative RNA recognition site
title_short Yeast Ssd1 is a non-enzymatic member of the RNase II family with an alternative RNA recognition site
title_sort yeast ssd1 is a non-enzymatic member of the rnase ii family with an alternative rna recognition site
topic Structural Biology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8934651/
https://www.ncbi.nlm.nih.gov/pubmed/34302485
http://dx.doi.org/10.1093/nar/gkab615
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