Landscape of nuclear transport receptor cargo specificity

Nuclear transport receptors (NTRs) recognize localization signals of cargos to facilitate their passage across the central channel of nuclear pore complexes (NPCs). About 30 different NTRs constitute different transport pathways in humans and bind to a multitude of different cargos. The exact cargo...

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Published inMolecular systems biology Vol. 13; no. 12; pp. 962 - n/a
Main Authors Mackmull, Marie‐Therese, Klaus, Bernd, Heinze, Ivonne, Chokkalingam, Manopriya, Beyer, Andreas, Russell, Robert B, Ori, Alessandro, Beck, Martin
Format Journal Article
LanguageEnglish
Published London Nature Publishing Group UK 01.12.2017
EMBO Press
John Wiley and Sons Inc
Springer Nature
Subjects
Active Transport, Cell Nucleus
Biotin
Biotinylation
Cargo
Cell Nucleus - metabolism
EMBO17
EMBO26
EMBO31
Gene Ontology
Humans
interaction network
Interfaces
Localization
Mass spectrometry
Mass spectroscopy
Mutation - genetics
Nuclear Localization Signals
nuclear pore complex
Nuclear transport
Peptide mapping
Peptides
Peptides - metabolism
Protein Binding
Protein Subunits - metabolism
Protein transport
Proteome - metabolism
Proteomes
proteomics
proximity ligation
Receptors
Receptors, Cytoplasmic and Nuclear - metabolism
Redundancy
Reproducibility of Results
RNA, Small Interfering - metabolism
Statistics as Topic
Subcellular Fractions - metabolism
Transport
protein transport
nuclear pore complex
interaction network
proteomics
proximity ligation
Online AccessGet full text

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Abstract Nuclear transport receptors (NTRs) recognize localization signals of cargos to facilitate their passage across the central channel of nuclear pore complexes (NPCs). About 30 different NTRs constitute different transport pathways in humans and bind to a multitude of different cargos. The exact cargo spectrum of the majority of NTRs, their specificity and even the extent to which active nucleocytoplasmic transport contributes to protein localization remains understudied because of the transient nature of these interactions and the wide dynamic range of cargo concentrations. To systematically map cargo–NTR relationships in situ , we used proximity ligation coupled to mass spectrometry (BioID). We systematically fused the engineered biotin ligase BirA* to 16 NTRs. We estimate that a considerable fraction of the human proteome is subject to active nuclear transport. We quantified the specificity and redundancy in NTR interactions and identified transport pathways for cargos. We extended the BioID method by the direct identification of biotinylation sites. This approach enabled us to identify interaction interfaces and to discriminate direct versus piggyback transport mechanisms. Data are available via ProteomeXchange with identifier PXD007976. Synopsis This study provides a comprehensive overview of the nuclear transport receptor (NTR) interactome and quantifies the specificity and redundancy of interactions. The BioID method is extended to directly identify biotinylation sites. NTRs transport functionally related cargos. Multiple members of protein complexes are identified suggesting that they are often transported as fully assembled entities. The direct identification of biotinylated peptides enables mapping of potential interaction sites of NTRs. A statistical framework is introduced that allows quantifying interaction specificity. Graphical Abstract This study provides a comprehensive overview of the nuclear transport receptor (NTR) interactome and quantifies the specificity and redundancy of interactions. The BioID method is extended to directly identify biotinylation sites.
AbstractList Abstract Nuclear transport receptors (NTRs) recognize localization signals of cargos to facilitate their passage across the central channel of nuclear pore complexes (NPCs). About 30 different NTRs constitute different transport pathways in humans and bind to a multitude of different cargos. The exact cargo spectrum of the majority of NTRs, their specificity and even the extent to which active nucleocytoplasmic transport contributes to protein localization remains understudied because of the transient nature of these interactions and the wide dynamic range of cargo concentrations. To systematically map cargo–NTR relationships in situ, we used proximity ligation coupled to mass spectrometry (BioID). We systematically fused the engineered biotin ligase BirA* to 16 NTRs. We estimate that a considerable fraction of the human proteome is subject to active nuclear transport. We quantified the specificity and redundancy in NTR interactions and identified transport pathways for cargos. We extended the BioID method by the direct identification of biotinylation sites. This approach enabled us to identify interaction interfaces and to discriminate direct versus piggyback transport mechanisms. Data are available via ProteomeXchange with identifier PXD007976.
Nuclear transport receptors (NTRs) recognize localization signals of cargos to facilitate their passage across the central channel of nuclear pore complexes (NPCs). About 30 different NTRs constitute different transport pathways in humans and bind to a multitude of different cargos. The exact cargo spectrum of the majority of NTRs, their specificity and even the extent to which active nucleocytoplasmic transport contributes to protein localization remains understudied because of the transient nature of these interactions and the wide dynamic range of cargo concentrations. To systematically map cargo-NTR relationships , we used proximity ligation coupled to mass spectrometry (BioID). We systematically fused the engineered biotin ligase BirA* to 16 NTRs. We estimate that a considerable fraction of the human proteome is subject to active nuclear transport. We quantified the specificity and redundancy in NTR interactions and identified transport pathways for cargos. We extended the BioID method by the direct identification of biotinylation sites. This approach enabled us to identify interaction interfaces and to discriminate direct versus piggyback transport mechanisms. Data are available via ProteomeXchange with identifier PXD007976.
Nuclear transport receptors (NTRs) recognize localization signals of cargos to facilitate their passage across the central channel of nuclear pore complexes (NPCs). About 30 different NTRs constitute different transport pathways in humans and bind to a multitude of different cargos. The exact cargo spectrum of the majority of NTRs, their specificity and even the extent to which active nucleocytoplasmic transport contributes to protein localization remains understudied because of the transient nature of these interactions and the wide dynamic range of cargo concentrations. To systematically map cargo–NTR relationships in situ, we used proximity ligation coupled to mass spectrometry (BioID). We systematically fused the engineered biotin ligase BirA* to 16 NTRs. We estimate that a considerable fraction of the human proteome is subject to active nuclear transport. We quantified the specificity and redundancy in NTR interactions and identified transport pathways for cargos. We extended the BioID method by the direct identification of biotinylation sites. This approach enabled us to identify interaction interfaces and to discriminate direct versus piggyback transport mechanisms. Data are available via ProteomeXchange with identifier PXD007976. Synopsis This study provides a comprehensive overview of the nuclear transport receptor (NTR) interactome and quantifies the specificity and redundancy of interactions. The BioID method is extended to directly identify biotinylation sites. NTRs transport functionally related cargos. Multiple members of protein complexes are identified suggesting that they are often transported as fully assembled entities. The direct identification of biotinylated peptides enables mapping of potential interaction sites of NTRs. A statistical framework is introduced that allows quantifying interaction specificity. This study provides a comprehensive overview of the nuclear transport receptor (NTR) interactome and quantifies the specificity and redundancy of interactions. The BioID method is extended to directly identify biotinylation sites.
Nuclear transport receptors (NTRs) recognize localization signals of cargos to facilitate their passage across the central channel of nuclear pore complexes (NPCs). About 30 different NTRs constitute different transport pathways in humans and bind to a multitude of different cargos. The exact cargo spectrum of the majority of NTRs, their specificity and even the extent to which active nucleocytoplasmic transport contributes to protein localization remains understudied because of the transient nature of these interactions and the wide dynamic range of cargo concentrations. To systematically map cargo-NTR relationships in situ, we used proximity ligation coupled to mass spectrometry (BioID). We systematically fused the engineered biotin ligase BirA* to 16 NTRs. We estimate that a considerable fraction of the human proteome is subject to active nuclear transport. We quantified the specificity and redundancy in NTR interactions and identified transport pathways for cargos. We extended the BioID method by the direct identification of biotinylation sites. This approach enabled us to identify interaction interfaces and to discriminate direct versus piggyback transport mechanisms. Data are available via ProteomeXchange with identifier PXD007976.Nuclear transport receptors (NTRs) recognize localization signals of cargos to facilitate their passage across the central channel of nuclear pore complexes (NPCs). About 30 different NTRs constitute different transport pathways in humans and bind to a multitude of different cargos. The exact cargo spectrum of the majority of NTRs, their specificity and even the extent to which active nucleocytoplasmic transport contributes to protein localization remains understudied because of the transient nature of these interactions and the wide dynamic range of cargo concentrations. To systematically map cargo-NTR relationships in situ, we used proximity ligation coupled to mass spectrometry (BioID). We systematically fused the engineered biotin ligase BirA* to 16 NTRs. We estimate that a considerable fraction of the human proteome is subject to active nuclear transport. We quantified the specificity and redundancy in NTR interactions and identified transport pathways for cargos. We extended the BioID method by the direct identification of biotinylation sites. This approach enabled us to identify interaction interfaces and to discriminate direct versus piggyback transport mechanisms. Data are available via ProteomeXchange with identifier PXD007976.
Nuclear transport receptors ( NTR s) recognize localization signals of cargos to facilitate their passage across the central channel of nuclear pore complexes ( NPC s). About 30 different NTR s constitute different transport pathways in humans and bind to a multitude of different cargos. The exact cargo spectrum of the majority of NTR s, their specificity and even the extent to which active nucleocytoplasmic transport contributes to protein localization remains understudied because of the transient nature of these interactions and the wide dynamic range of cargo concentrations. To systematically map cargo– NTR relationships in situ , we used proximity ligation coupled to mass spectrometry (Bio ID ). We systematically fused the engineered biotin ligase BirA* to 16 NTR s. We estimate that a considerable fraction of the human proteome is subject to active nuclear transport. We quantified the specificity and redundancy in NTR interactions and identified transport pathways for cargos. We extended the Bio ID method by the direct identification of biotinylation sites. This approach enabled us to identify interaction interfaces and to discriminate direct versus piggyback transport mechanisms. Data are available via ProteomeXchange with identifier PXD 007976.
Nuclear transport receptors (NTRs) recognize localization signals of cargos to facilitate their passage across the central channel of nuclear pore complexes (NPCs). About 30 different NTRs constitute different transport pathways in humans and bind to a multitude of different cargos. The exact cargo spectrum of the majority of NTRs, their specificity and even the extent to which active nucleocytoplasmic transport contributes to protein localization remains understudied because of the transient nature of these interactions and the wide dynamic range of cargo concentrations. To systematically map cargo–NTR relationships in situ, we used proximity ligation coupled to mass spectrometry (BioID). We systematically fused the engineered biotin ligase BirA* to 16 NTRs. We estimate that a considerable fraction of the human proteome is subject to active nuclear transport. We quantified the specificity and redundancy in NTR interactions and identified transport pathways for cargos. We extended the BioID method by the direct identification of biotinylation sites. This approach enabled us to identify interaction interfaces and to discriminate direct versus piggyback transport mechanisms. Data are available via ProteomeXchange with identifier PXD007976.
Nuclear transport receptors (NTRs) recognize localization signals of cargos to facilitate their passage across the central channel of nuclear pore complexes (NPCs). About 30 different NTRs constitute different transport pathways in humans and bind to a multitude of different cargos. The exact cargo spectrum of the majority of NTRs, their specificity and even the extent to which active nucleocytoplasmic transport contributes to protein localization remains understudied because of the transient nature of these interactions and the wide dynamic range of cargo concentrations. To systematically map cargo–NTR relationships in situ , we used proximity ligation coupled to mass spectrometry (BioID). We systematically fused the engineered biotin ligase BirA* to 16 NTRs. We estimate that a considerable fraction of the human proteome is subject to active nuclear transport. We quantified the specificity and redundancy in NTR interactions and identified transport pathways for cargos. We extended the BioID method by the direct identification of biotinylation sites. This approach enabled us to identify interaction interfaces and to discriminate direct versus piggyback transport mechanisms. Data are available via ProteomeXchange with identifier PXD007976. Synopsis This study provides a comprehensive overview of the nuclear transport receptor (NTR) interactome and quantifies the specificity and redundancy of interactions. The BioID method is extended to directly identify biotinylation sites. NTRs transport functionally related cargos. Multiple members of protein complexes are identified suggesting that they are often transported as fully assembled entities. The direct identification of biotinylated peptides enables mapping of potential interaction sites of NTRs. A statistical framework is introduced that allows quantifying interaction specificity. Graphical Abstract This study provides a comprehensive overview of the nuclear transport receptor (NTR) interactome and quantifies the specificity and redundancy of interactions. The BioID method is extended to directly identify biotinylation sites.
Author Ori, Alessandro
Klaus, Bernd
Chokkalingam, Manopriya
Heinze, Ivonne
Mackmull, Marie‐Therese
Beyer, Andreas
Russell, Robert B
Beck, Martin
AuthorAffiliation 5 Center for Molecular Medicine Cologne University of Cologne Cologne Germany
1 Structural and Computational Biology Unit European Molecular Biology Laboratory Heidelberg Germany
7 Cell Biology and Biophysics Unit European Molecular Biology Laboratory Heidelberg Germany
2 Centre for Statistical Data Analysis European Molecular Biology Laboratory Heidelberg Germany
4 Cellular Networks and Systems Biology CECAD University of Cologne Cologne Germany
6 Heidelberg University Biochemistry Centre & Bioquant Heidelberg Germany
3 Leibniz Institute on Aging Fritz Lipmann Institute (FLI) Jena Germany
AuthorAffiliation_xml – name: 2 Centre for Statistical Data Analysis European Molecular Biology Laboratory Heidelberg Germany
– name: 3 Leibniz Institute on Aging Fritz Lipmann Institute (FLI) Jena Germany
– name: 4 Cellular Networks and Systems Biology CECAD University of Cologne Cologne Germany
– name: 1 Structural and Computational Biology Unit European Molecular Biology Laboratory Heidelberg Germany
– name: 7 Cell Biology and Biophysics Unit European Molecular Biology Laboratory Heidelberg Germany
– name: 6 Heidelberg University Biochemistry Centre & Bioquant Heidelberg Germany
– name: 5 Center for Molecular Medicine Cologne University of Cologne Cologne Germany
Author_xml – sequence: 1
  givenname: Marie‐Therese
  orcidid: 0000-0003-2928-1144
  surname: Mackmull
  fullname: Mackmull, Marie‐Therese
  organization: Structural and Computational Biology Unit, European Molecular Biology Laboratory
– sequence: 2
  givenname: Bernd
  surname: Klaus
  fullname: Klaus, Bernd
  organization: Centre for Statistical Data Analysis, European Molecular Biology Laboratory
– sequence: 3
  givenname: Ivonne
  surname: Heinze
  fullname: Heinze, Ivonne
  organization: Leibniz Institute on Aging, Fritz Lipmann Institute (FLI)
– sequence: 4
  givenname: Manopriya
  surname: Chokkalingam
  fullname: Chokkalingam, Manopriya
  organization: Cellular Networks and Systems Biology, CECAD, University of Cologne
– sequence: 5
  givenname: Andreas
  orcidid: 0000-0002-3891-2123
  surname: Beyer
  fullname: Beyer, Andreas
  organization: Cellular Networks and Systems Biology, CECAD, University of Cologne, Center for Molecular Medicine Cologne, University of Cologne
– sequence: 6
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  surname: Russell
  fullname: Russell, Robert B
  organization: Heidelberg University Biochemistry Centre & Bioquant
– sequence: 7
  givenname: Alessandro
  orcidid: 0000-0002-3046-0871
  surname: Ori
  fullname: Ori, Alessandro
  email: alessandro.ori@leibniz-fli.de
  organization: Leibniz Institute on Aging, Fritz Lipmann Institute (FLI)
– sequence: 8
  givenname: Martin
  orcidid: 0000-0002-7397-1321
  surname: Beck
  fullname: Beck, Martin
  email: martin.beck@embl.de
  organization: Structural and Computational Biology Unit, European Molecular Biology Laboratory, Cell Biology and Biophysics Unit, European Molecular Biology Laboratory
BackLink https://www.ncbi.nlm.nih.gov/pubmed/29254951$$D View this record in MEDLINE/PubMed
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Copyright European Molecular Biology Laboratory. Published under the terms of the CC BY 4.0 license 2017
2017 European Molecular Biology Laboratory. Published under the terms of the CC BY 4.0 license
2017 European Molecular Biology Laboratory. Published under the terms of the CC BY 4.0 license.
2017. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.
Copyright_xml – notice: European Molecular Biology Laboratory. Published under the terms of the CC BY 4.0 license 2017
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– notice: 2017 European Molecular Biology Laboratory. Published under the terms of the CC BY 4.0 license.
– notice: 2017. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.
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Issue 12
Keywords protein transport
nuclear pore complex
interaction network
proteomics
proximity ligation
Language English
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http://creativecommons.org/licenses/by/4.0
2017 European Molecular Biology Laboratory. Published under the terms of the CC BY 4.0 license.
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Snippet Nuclear transport receptors (NTRs) recognize localization signals of cargos to facilitate their passage across the central channel of nuclear pore complexes...
Nuclear transport receptors ( NTR s) recognize localization signals of cargos to facilitate their passage across the central channel of nuclear pore complexes...
Abstract Nuclear transport receptors (NTRs) recognize localization signals of cargos to facilitate their passage across the central channel of nuclear pore...
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SourceType Open Website
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StartPage 962
SubjectTerms Active Transport, Cell Nucleus
Biotin
Biotinylation
Cargo
Cell Nucleus - metabolism
EMBO17
EMBO26
EMBO31
Gene Ontology
Humans
interaction network
Interfaces
Localization
Mass spectrometry
Mass spectroscopy
Mutation - genetics
Nuclear Localization Signals
nuclear pore complex
Nuclear transport
Peptide mapping
Peptides
Peptides - metabolism
Protein Binding
Protein Subunits - metabolism
Protein transport
Proteome - metabolism
Proteomes
proteomics
proximity ligation
Receptors
Receptors, Cytoplasmic and Nuclear - metabolism
Redundancy
Reproducibility of Results
RNA, Small Interfering - metabolism
Statistics as Topic
Subcellular Fractions - metabolism
Transport
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Title Landscape of nuclear transport receptor cargo specificity
URI https://link.springer.com/article/10.15252/msb.20177608
https://onlinelibrary.wiley.com/doi/abs/10.15252%2Fmsb.20177608
https://www.ncbi.nlm.nih.gov/pubmed/29254951
https://www.proquest.com/docview/1979476887
https://www.proquest.com/docview/1978726852
https://pubmed.ncbi.nlm.nih.gov/PMC5740495
https://doaj.org/article/3a9c1083fbbe4327afbf2c62b03c4d64
Volume 13
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