Diverse roles of assembly factors revealed by structures of late nuclear pre-60S ribosomes

The cryo-electron microscopy structures of yeast nucleoplasmic pre-60S ribosomal particles give insight into the function of multiple assembly factors in ribosome biogenesis. Dissecting ribosomal biogenesis in the nucleus The ribosome is one of the largest macromolecular complexes in the eukarotic c...

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Veröffentlicht in:Nature (London) Jg. 534; H. 7605; S. 133 - 137
Hauptverfasser: Wu, Shan, Tutuncuoglu, Beril, Yan, Kaige, Brown, Hailey, Zhang, Yixiao, Tan, Dan, Gamalinda, Michael, Yuan, Yi, Li, Zhifei, Jakovljevic, Jelena, Ma, Chengying, Lei, Jianlin, Dong, Meng-Qiu, Woolford, John L., Gao, Ning
Format: Journal Article
Sprache:Englisch
Veröffentlicht: London Nature Publishing Group UK 02.06.2016
Nature Publishing Group
Schlagworte:
101/28
101/58
45/70
45/90
631/337/1910
631/337/574/1789
631/45/500
631/535/1258/1259
631/80/389/2052
Active Transport, Cell Nucleus
Base Sequence
Catalytic Domain
Cell Nucleus - chemistry
Cell Nucleus - metabolism
Cell Nucleus - ultrastructure
Cryoelectron Microscopy
Cytological research
Cytoplasm - metabolism
DNA, Ribosomal Spacer - chemistry
DNA, Ribosomal Spacer - genetics
DNA, Ribosomal Spacer - metabolism
DNA, Ribosomal Spacer - ultrastructure
Genetic research
GTP Phosphohydrolases - chemistry
GTP Phosphohydrolases - metabolism
GTP Phosphohydrolases - ultrastructure
GTP-Binding Proteins - chemistry
GTP-Binding Proteins - metabolism
GTP-Binding Proteins - ultrastructure
Humanities and Social Sciences
letter
Models, Molecular
Molecular Sequence Data
Molecular structure
multidisciplinary
Nuclear Proteins - chemistry
Nuclear Proteins - metabolism
Nuclear Proteins - ultrastructure
Nucleolus organizer region
Polypeptides
Protein Binding
Protein research
Protein synthesis
Proteins
Ribonucleic acid
Ribonucleoproteins - chemistry
Ribonucleoproteins - metabolism
Ribonucleoproteins - ultrastructure
Ribosomal Proteins - chemistry
Ribosomal Proteins - isolation & purification
Ribosomal Proteins - metabolism
Ribosomal Proteins - ultrastructure
Ribosome Subunits, Large, Eukaryotic - chemistry
Ribosome Subunits, Large, Eukaryotic - metabolism
Ribosome Subunits, Large, Eukaryotic - ultrastructure
Ribosomes
RNA
RNA, Fungal - genetics
RNA, Fungal - metabolism
RNA, Fungal - ultrastructure
RNA, Ribosomal - genetics
RNA, Ribosomal - metabolism
RNA, Ribosomal - ultrastructure
Rotation
Saccharomyces cerevisiae - chemistry
Saccharomyces cerevisiae - cytology
Saccharomyces cerevisiae - metabolism
Saccharomyces cerevisiae - ultrastructure
Saccharomyces cerevisiae Proteins - chemistry
Saccharomyces cerevisiae Proteins - isolation & purification
Saccharomyces cerevisiae Proteins - metabolism
Saccharomyces cerevisiae Proteins - ultrastructure
Science
Yeasts
United States
China
ISSN:0028-0836, 1476-4687
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Abstract The cryo-electron microscopy structures of yeast nucleoplasmic pre-60S ribosomal particles give insight into the function of multiple assembly factors in ribosome biogenesis. Dissecting ribosomal biogenesis in the nucleus The ribosome is one of the largest macromolecular complexes in the eukarotic cell and its biogenesis is a highly complex process, involving hundreds of assembly factors, including many GTPases, ATPases and kinases. To gain insight into the function of these factors, Ning Gao and colleagues used cryo-electron microscopy to characterize structures of several nuclear pre-60S particles. Their data localize more than twenty assembly factors, which are particularly concentrated in two regions. The series of structures outlines three remodelling events that occur to the particle before it is transported to the cytoplasm. Ribosome biogenesis is a highly complex process in eukaryotes, involving temporally and spatially regulated ribosomal protein (r-protein) binding and ribosomal RNA remodelling events in the nucleolus, nucleoplasm and cytoplasm 1 , 2 . Hundreds of assembly factors, organized into sequential functional groups 3 , 4 , facilitate and guide the maturation process into productive assembly branches in and across different cellular compartments. However, the precise mechanisms by which these assembly factors function are largely unknown. Here we use cryo-electron microscopy to characterize the structures of yeast nucleoplasmic pre-60S particles affinity-purified using the epitope-tagged assembly factor Nog2. Our data pinpoint the locations and determine the structures of over 20 assembly factors, which are enriched in two areas: an arc region extending from the central protuberance to the polypeptide tunnel exit, and the domain including the internal transcribed spacer 2 (ITS2) that separates 5.8S and 25S ribosomal RNAs. In particular, two regulatory GTPases, Nog2 and Nog1, act as hub proteins to interact with multiple, distant assembly factors and functional ribosomal RNA elements, manifesting their critical roles in structural remodelling checkpoints and nuclear export. Moreover, our snapshots of compositionally and structurally different pre-60S intermediates provide essential mechanistic details for three major remodelling events before nuclear export: rotation of the 5S ribonucleoprotein, construction of the active centre and ITS2 removal. The rich structural information in our structures provides a framework to dissect molecular roles of diverse assembly factors in eukaryotic ribosome assembly.
AbstractList The cryo-electron microscopy structures of yeast nucleoplasmic pre-60S ribosomal particles give insight into the function of multiple assembly factors in ribosome biogenesis.
Ribosome biogenesis is a highly complex process in eukaryotes, involving temporally and spatially regulated ribosomal protein (r-protein) binding and ribosomal RNA remodelling events in the nucleolus, nucleoplasm and cytoplasm^sup 1,2^. Hundreds of assembly factors, organized into sequential functional groups^sup 3,4^, facilitate and guide the maturation process into productive assembly branches in and across different cellular compartments. However, the precise mechanisms by which these assembly factors function are largely unknown. Here we use cryo-electron microscopy to characterize the structures of yeast nucleoplasmic pre-60S particles affinity-purified using the epitope-tagged assembly factor Nog2. Our data pinpoint the locations and determine the structures of over 20 assembly factors, which are enriched in two areas: an arc region extending from the central protuberance to the polypeptide tunnel exit, and the domain including the internal transcribed spacer 2 (ITS2) that separates 5.8S and 25S ribosomal RNAs. In particular, two regulatory GTPases, Nog2 and Nog1, act as hub proteins to interact with multiple, distant assembly factors and functional ribosomal RNA elements, manifesting their critical roles in structural remodelling checkpoints and nuclear export. Moreover, our snapshots of compositionally and structurally different pre-60S intermediates provide essential mechanistic details for three major remodelling events before nuclear export: rotation of the 5S ribonucleoprotein, construction of the active centre and ITS2 removal. The rich structural information in our structures provides a framework to dissect molecular roles of diverse assembly factors in eukaryotic ribosome assembly.
The cryo-electron microscopy structures of yeast nucleoplasmic pre-60S ribosomal particles give insight into the function of multiple assembly factors in ribosome biogenesis. Dissecting ribosomal biogenesis in the nucleus The ribosome is one of the largest macromolecular complexes in the eukarotic cell and its biogenesis is a highly complex process, involving hundreds of assembly factors, including many GTPases, ATPases and kinases. To gain insight into the function of these factors, Ning Gao and colleagues used cryo-electron microscopy to characterize structures of several nuclear pre-60S particles. Their data localize more than twenty assembly factors, which are particularly concentrated in two regions. The series of structures outlines three remodelling events that occur to the particle before it is transported to the cytoplasm. Ribosome biogenesis is a highly complex process in eukaryotes, involving temporally and spatially regulated ribosomal protein (r-protein) binding and ribosomal RNA remodelling events in the nucleolus, nucleoplasm and cytoplasm 1 , 2 . Hundreds of assembly factors, organized into sequential functional groups 3 , 4 , facilitate and guide the maturation process into productive assembly branches in and across different cellular compartments. However, the precise mechanisms by which these assembly factors function are largely unknown. Here we use cryo-electron microscopy to characterize the structures of yeast nucleoplasmic pre-60S particles affinity-purified using the epitope-tagged assembly factor Nog2. Our data pinpoint the locations and determine the structures of over 20 assembly factors, which are enriched in two areas: an arc region extending from the central protuberance to the polypeptide tunnel exit, and the domain including the internal transcribed spacer 2 (ITS2) that separates 5.8S and 25S ribosomal RNAs. In particular, two regulatory GTPases, Nog2 and Nog1, act as hub proteins to interact with multiple, distant assembly factors and functional ribosomal RNA elements, manifesting their critical roles in structural remodelling checkpoints and nuclear export. Moreover, our snapshots of compositionally and structurally different pre-60S intermediates provide essential mechanistic details for three major remodelling events before nuclear export: rotation of the 5S ribonucleoprotein, construction of the active centre and ITS2 removal. The rich structural information in our structures provides a framework to dissect molecular roles of diverse assembly factors in eukaryotic ribosome assembly.
Ribosome biogenesis is a highly complex process in eukaryotes, involving temporally and spatially regulated ribosomal protein (r-protein) binding and ribosomal RNA remodelling events in the nucleolus, nucleoplasm and cytoplasm. Hundreds of assembly factors, organized into sequential functional groups, facilitate and guide the maturation process into productive assembly branches in and across different cellular compartments. However, the precise mechanisms by which these assembly factors function are largely unknown. Here we use cryo-electron microscopy to characterize the structures of yeast nucleoplasmic pre-60S particles affinity-purified using the epitope-tagged assembly factor Nog2. Our data pinpoint the locations and determine the structures of over 20 assembly factors, which are enriched in two areas: an arc region extending from the central protuberance to the polypeptide tunnel exit, and the domain including the internal transcribed spacer 2 (ITS2) that separates 5.8S and 25S ribosomal RNAs. In particular, two regulatory GTPases, Nog2 and Nog1, act as hub proteins to interact with multiple, distant assembly factors and functional ribosomal RNA elements, manifesting their critical roles in structural remodelling checkpoints and nuclear export. Moreover, our snapshots of compositionally and structurally different pre-60S intermediates provide essential mechanistic details for three major remodelling events before nuclear export: rotation of the 5S ribonucleoprotein, construction of the active centre and ITS2 removal. The rich structural information in our structures provides a framework to dissect molecular roles of diverse assembly factors in eukaryotic ribosome assembly.
Ribosome biogenesis is a highly complex process in eukaryotes, involving temporally and spatially regulated ribosomal protein (r-protein) binding and ribosomal RNA remodelling events in the nucleolus, nucleoplasm and cytoplasm1,2. Hundreds of assembly factors, organized into sequential functional groups3,4, facilitate and guide the maturation process into productive assembly branches in and across different cellular compartments. However, the precise mechanisms by which these assembly factors function are largely unknown. Here we use cryo-electron microscopy to characterize the structures of yeast nucleoplasmic pre-60S particles affinity-purified using the epitope-tagged assembly factor Nog2. Our data pinpoint the locations and determine the structures of over 20 assembly factors, which are enriched in two areas: an arc region extending from the central protuberance to the polypeptide tunnel exit, and the domain including the internal transcribed spacer 2 (ITS2) that separates 5.8S and 25S ribosomal RNAs. In particular, two regulatory GTPases, Nog2 and Nog1, act as hub proteins to interact with multiple, distant assembly factors and functional ribosomal RNA elements, manifesting their critical roles in structural remodelling checkpoints and nuclear export. Moreover, our snapshots of compositionally and structurally different pre-60S intermediates provide essential mechanistic details for three major remodelling events before nuclear export: rotation of the 5S ribonucleoprotein, construction of the active centre and ITS2 removal. The rich structural information in our structures provides a framework to dissect molecular roles of diverse assembly factors in eukaryotic ribosome assembly.
Audience Academic
Author Gao, Ning
Brown, Hailey
Yan, Kaige
Lei, Jianlin
Yuan, Yi
Wu, Shan
Jakovljevic, Jelena
Gamalinda, Michael
Woolford, John L.
Tan, Dan
Tutuncuoglu, Beril
Li, Zhifei
Zhang, Yixiao
Dong, Meng-Qiu
Ma, Chengying
AuthorAffiliation 2 Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
1 Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
4 National Institute of Biological Sciences, Beijing 102206, China
3 Graduate Program in Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
AuthorAffiliation_xml – name: 3 Graduate Program in Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
– name: 4 National Institute of Biological Sciences, Beijing 102206, China
– name: 2 Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
– name: 1 Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
Author_xml – sequence: 1
  givenname: Shan
  surname: Wu
  fullname: Wu, Shan
  organization: Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University
– sequence: 2
  givenname: Beril
  surname: Tutuncuoglu
  fullname: Tutuncuoglu, Beril
  organization: Department of Biological Sciences, Carnegie Mellon University
– sequence: 3
  givenname: Kaige
  surname: Yan
  fullname: Yan, Kaige
  organization: Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University
– sequence: 4
  givenname: Hailey
  surname: Brown
  fullname: Brown, Hailey
  organization: Department of Biological Sciences, Carnegie Mellon University
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  givenname: Yixiao
  surname: Zhang
  fullname: Zhang, Yixiao
  organization: Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University
– sequence: 6
  givenname: Dan
  surname: Tan
  fullname: Tan, Dan
  organization: Graduate Program in Chinese Academy of Medical Sciences and Peking Union Medical College, National Institute of Biological Sciences
– sequence: 7
  givenname: Michael
  surname: Gamalinda
  fullname: Gamalinda, Michael
  organization: Department of Biological Sciences, Carnegie Mellon University
– sequence: 8
  givenname: Yi
  surname: Yuan
  fullname: Yuan, Yi
  organization: Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University
– sequence: 9
  givenname: Zhifei
  surname: Li
  fullname: Li, Zhifei
  organization: Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University
– sequence: 10
  givenname: Jelena
  surname: Jakovljevic
  fullname: Jakovljevic, Jelena
  organization: Department of Biological Sciences, Carnegie Mellon University
– sequence: 11
  givenname: Chengying
  surname: Ma
  fullname: Ma, Chengying
  organization: Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University
– sequence: 12
  givenname: Jianlin
  surname: Lei
  fullname: Lei, Jianlin
  organization: Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University
– sequence: 13
  givenname: Meng-Qiu
  surname: Dong
  fullname: Dong, Meng-Qiu
  organization: Graduate Program in Chinese Academy of Medical Sciences and Peking Union Medical College, National Institute of Biological Sciences
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  givenname: John L.
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  email: jw17@andrew.cmu.edu
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  givenname: Ning
  surname: Gao
  fullname: Gao, Ning
  email: ninggao@tsinghua.edu.cn
  organization: Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University
BackLink https://www.ncbi.nlm.nih.gov/pubmed/27251291$$D View this record in MEDLINE/PubMed
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Snippet The cryo-electron microscopy structures of yeast nucleoplasmic pre-60S ribosomal particles give insight into the function of multiple assembly factors in...
Ribosome biogenesis is a highly complex process in eukaryotes, involving temporally and spatially regulated ribosomal protein (r-protein) binding and ribosomal...
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631/337/574/1789
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631/535/1258/1259
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Active Transport, Cell Nucleus
Base Sequence
Catalytic Domain
Cell Nucleus - chemistry
Cell Nucleus - metabolism
Cell Nucleus - ultrastructure
Cryoelectron Microscopy
Cytological research
Cytoplasm - metabolism
DNA, Ribosomal Spacer - chemistry
DNA, Ribosomal Spacer - genetics
DNA, Ribosomal Spacer - metabolism
DNA, Ribosomal Spacer - ultrastructure
Genetic research
GTP Phosphohydrolases - chemistry
GTP Phosphohydrolases - metabolism
GTP Phosphohydrolases - ultrastructure
GTP-Binding Proteins - chemistry
GTP-Binding Proteins - metabolism
GTP-Binding Proteins - ultrastructure
Humanities and Social Sciences
letter
Models, Molecular
Molecular Sequence Data
Molecular structure
multidisciplinary
Nuclear Proteins - chemistry
Nuclear Proteins - metabolism
Nuclear Proteins - ultrastructure
Nucleolus organizer region
Polypeptides
Protein Binding
Protein research
Protein synthesis
Proteins
Ribonucleic acid
Ribonucleoproteins - chemistry
Ribonucleoproteins - metabolism
Ribonucleoproteins - ultrastructure
Ribosomal Proteins - chemistry
Ribosomal Proteins - isolation & purification
Ribosomal Proteins - metabolism
Ribosomal Proteins - ultrastructure
Ribosome Subunits, Large, Eukaryotic - chemistry
Ribosome Subunits, Large, Eukaryotic - metabolism
Ribosome Subunits, Large, Eukaryotic - ultrastructure
Ribosomes
RNA
RNA, Fungal - genetics
RNA, Fungal - metabolism
RNA, Fungal - ultrastructure
RNA, Ribosomal - genetics
RNA, Ribosomal - metabolism
RNA, Ribosomal - ultrastructure
Rotation
Saccharomyces cerevisiae - chemistry
Saccharomyces cerevisiae - cytology
Saccharomyces cerevisiae - metabolism
Saccharomyces cerevisiae - ultrastructure
Saccharomyces cerevisiae Proteins - chemistry
Saccharomyces cerevisiae Proteins - isolation & purification
Saccharomyces cerevisiae Proteins - metabolism
Saccharomyces cerevisiae Proteins - ultrastructure
Science
Yeasts
Title Diverse roles of assembly factors revealed by structures of late nuclear pre-60S ribosomes
URI https://link.springer.com/article/10.1038/nature17942
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