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Steiner A, Favre S, Mack M, Hausharter A, Pillet B, Hafner J, Mitterer V, Kressler D, Pertschy B, Zierler I. Dissecting the Nuclear Import of the Ribosomal Protein Rps2 (uS5). Biomolecules 2023; 13:1127. [PMID: 37509163 PMCID: PMC10377357 DOI: 10.3390/biom13071127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 07/06/2023] [Accepted: 07/12/2023] [Indexed: 07/30/2023] Open
Abstract
The ribosome is assembled in a complex process mainly taking place in the nucleus. Consequently, newly synthesized ribosomal proteins have to travel from the cytoplasm into the nucleus, where they are incorporated into nascent ribosomal subunits. In this study, we set out to investigate the mechanism mediating nuclear import of the small subunit ribosomal protein Rps2. We demonstrate that an internal region in Rps2, ranging from amino acids 76 to 145, is sufficient to target a 3xyEGFP reporter to the nucleus. The importin-β Pse1 interacts with this Rps2 region and is involved in its import, with Rps2 residues arginine 95, arginine 97, and lysine 99 being important determinants for both Pse1 binding and nuclear localization. Moreover, our data reveal a second import mechanism involving the N-terminal region of Rps2, which depends on the presence of basic residues within amino acids 10 to 28. This Rps2 segment overlaps with the binding site of the dedicated chaperone Tsr4; however, the nuclear import of Rps2 via the internal as well as the N-terminal nuclear-targeting element does not depend on Tsr4. Taken together, our study has unveiled hitherto undescribed nuclear import signals, showcasing the versatility of the mechanisms coordinating the nuclear import of ribosomal proteins.
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Affiliation(s)
- Andreas Steiner
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50, 8010 Graz, Austria; (A.S.); (M.M.); (V.M.)
- BioTechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria
| | - Sébastien Favre
- Unit of Biochemistry, Department of Biology, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland; (S.F.); (B.P.); (D.K.)
| | - Maximilian Mack
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50, 8010 Graz, Austria; (A.S.); (M.M.); (V.M.)
- BioTechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria
| | - Annika Hausharter
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50, 8010 Graz, Austria; (A.S.); (M.M.); (V.M.)
| | - Benjamin Pillet
- Unit of Biochemistry, Department of Biology, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland; (S.F.); (B.P.); (D.K.)
| | - Jutta Hafner
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50, 8010 Graz, Austria; (A.S.); (M.M.); (V.M.)
- BioTechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria
| | - Valentin Mitterer
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50, 8010 Graz, Austria; (A.S.); (M.M.); (V.M.)
- BioTechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria
| | - Dieter Kressler
- Unit of Biochemistry, Department of Biology, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland; (S.F.); (B.P.); (D.K.)
| | - Brigitte Pertschy
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50, 8010 Graz, Austria; (A.S.); (M.M.); (V.M.)
- BioTechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria
| | - Ingrid Zierler
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50, 8010 Graz, Austria; (A.S.); (M.M.); (V.M.)
- BioTechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria
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Wing CE, Fung HYJ, Chook YM. Karyopherin-mediated nucleocytoplasmic transport. Nat Rev Mol Cell Biol 2022; 23:307-328. [PMID: 35058649 PMCID: PMC10101760 DOI: 10.1038/s41580-021-00446-7] [Citation(s) in RCA: 117] [Impact Index Per Article: 58.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/09/2021] [Indexed: 12/25/2022]
Abstract
Efficient and regulated nucleocytoplasmic trafficking of macromolecules to the correct subcellular compartment is critical for proper functions of the eukaryotic cell. The majority of the macromolecular traffic across the nuclear pores is mediated by the Karyopherin-β (or Kap) family of nuclear transport receptors. Work over more than two decades has shed considerable light on how the different Kap family members bring their respective cargoes into the nucleus or the cytoplasm in efficient and highly regulated manners. In this Review, we overview the main features and established functions of Kap family members, describe how Kaps recognize their cargoes and discuss the different ways in which these Kap-cargo interactions can be regulated, highlighting new findings and open questions. We also describe current knowledge of the import and export of the components of three large gene expression machines - the core replisome, RNA polymerase II and the ribosome - pointing out the questions that persist about how such large macromolecular complexes are trafficked to serve their function in a designated subcellular location.
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Kimura M, Imai K, Morinaka Y, Hosono-Sakuma Y, Horton P, Imamoto N. Distinct mutations in importin-β family nucleocytoplasmic transport receptors transportin-SR and importin-13 affect specific cargo binding. Sci Rep 2021; 11:15649. [PMID: 34341383 PMCID: PMC8329185 DOI: 10.1038/s41598-021-94948-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 07/20/2021] [Indexed: 01/25/2023] Open
Abstract
Importin-(Imp)β family nucleocytoplasmic transport receptors (NTRs) are supposed to bind to their cargoes through interaction between a confined interface on an NTR and a nuclear localization or export signal (NLS/NES) on a cargo. Although consensus NLS/NES sequence motifs have been defined for cargoes of some NTRs, many experimentally identified cargoes of those NTRs lack those motifs, and consensus NLSs/NESs have been reported for only a few NTRs. Crystal structures of NTR-cargo complexes have exemplified 3D structure-dependent binding of cargoes lacking a consensus NLS/NES to different sites on an NTR. Since only a limited number of NTR-cargo interactions have been studied, whether most cargoes lacking a consensus NLS/NES bind to the same confined interface or to various sites on an NTR is still unclear. Addressing this issue, we generated four mutants of transportin-(Trn)SR, of which many cargoes lack a consensus NLS, and eight mutants of Imp13, where no consensus NLS has been defined, and we analyzed their binding to as many as 40 cargo candidates that we previously identified by a nuclear import reaction-based method. The cargoes bind differently to the NTR mutants, suggesting that positions on an NTR contribute differently to the binding of respective cargoes.
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Affiliation(s)
- Makoto Kimura
- Cellular Dynamics Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan.
| | - Kenichiro Imai
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan.
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan.
| | - Yuriko Morinaka
- Cellular Dynamics Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan
| | - Yoshiko Hosono-Sakuma
- Cellular Dynamics Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan
| | - Paul Horton
- Department of Computer Science and Information Engineering, National Cheng Kung University, Tainan City, Taiwan
| | - Naoko Imamoto
- Cellular Dynamics Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan.
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Swale C, Da Costa B, Sedano L, Garzoni F, McCarthy AA, Berger I, Bieniossek C, Ruigrok RWH, Delmas B, Crépin T. X-ray Structure of the Human Karyopherin RanBP5, an Essential Factor for Influenza Polymerase Nuclear Trafficking. J Mol Biol 2020; 432:3353-3359. [PMID: 32222384 DOI: 10.1016/j.jmb.2020.03.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 03/16/2020] [Accepted: 03/22/2020] [Indexed: 12/15/2022]
Abstract
Here, we describe the crystal structures of two distinct isoforms of ligand-free human karyopherin RanBP5 and investigate its global propensity to interact with influenza A virus polymerase. Our results confirm the general architecture and mechanism of the IMB3 karyopherin-β subfamily whilst also highlighting differences with the yeast orthologue Kap121p. Moreover, our results provide insight into the structural flexibility of β-importins in the unbound state. Based on docking of a nuclear localisation sequence, point mutations were designed, which suppress influenza PA-PB1 subcomplex binding to RanBP5 in a binary protein complementation assay.
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Affiliation(s)
- Christopher Swale
- Institut de Biologie Structurale (IBS), University Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France; EMBL Grenoble Outstation, 71 Avenue des Martyrs, BP181, F-38042 Grenoble Cedex 9, France
| | - Bruno Da Costa
- Virologie et Immunologie Moléculaires, INRA, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Laura Sedano
- Virologie et Immunologie Moléculaires, INRA, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Frédéric Garzoni
- EMBL Grenoble Outstation, 71 Avenue des Martyrs, BP181, F-38042 Grenoble Cedex 9, France
| | - Andrew A McCarthy
- EMBL Grenoble Outstation, 71 Avenue des Martyrs, BP181, F-38042 Grenoble Cedex 9, France
| | - Imre Berger
- EMBL Grenoble Outstation, 71 Avenue des Martyrs, BP181, F-38042 Grenoble Cedex 9, France; Max Planck Centre for Minimal Biology, University of Bristol, Clifton BS8 1TD, United Kingdom
| | - Christoph Bieniossek
- Roche Innovation Centre, Basel, Switzerland F. Hoffmann-La Roche AG, Grenzacherstrasse 124, CH-4070 Basel, Switzerland
| | - Rob W H Ruigrok
- Institut de Biologie Structurale (IBS), University Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | - Bernard Delmas
- Virologie et Immunologie Moléculaires, INRA, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Thibaut Crépin
- Institut de Biologie Structurale (IBS), University Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France.
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Kimura M, Morinaka Y, Imai K, Kose S, Horton P, Imamoto N. Extensive cargo identification reveals distinct biological roles of the 12 importin pathways. eLife 2017; 6:e21184. [PMID: 28117667 PMCID: PMC5305215 DOI: 10.7554/elife.21184] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 01/17/2017] [Indexed: 12/31/2022] Open
Abstract
Vast numbers of proteins are transported into and out of the nuclei by approximately 20 species of importin-β family nucleocytoplasmic transport receptors. However, the significance of the multiple parallel transport pathways that the receptors constitute is poorly understood because only limited numbers of cargo proteins have been reported. Here, we identified cargo proteins specific to the 12 species of human import receptors with a high-throughput method that employs stable isotope labeling with amino acids in cell culture, an in vitro reconstituted transport system, and quantitative mass spectrometry. The identified cargoes illuminated the manner of cargo allocation to the receptors. The redundancies of the receptors vary widely depending on the cargo protein. Cargoes of the same receptor are functionally related to one another, and the predominant protein groups in the cargo cohorts differ among the receptors. Thus, the receptors are linked to distinct biological processes by the nature of their cargoes.
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Affiliation(s)
| | | | - Kenichiro Imai
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
| | - Shingo Kose
- Cellular Dynamics Laboratory, RIKEN, Wako, Japan
| | - Paul Horton
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
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Hirano H, Kobayashi J, Matsuura Y. Structures of the Karyopherins Kap121p and Kap60p Bound to the Nuclear Pore-Targeting Domain of the SUMO Protease Ulp1p. J Mol Biol 2016; 429:249-260. [PMID: 27939291 DOI: 10.1016/j.jmb.2016.11.029] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 11/25/2016] [Accepted: 11/29/2016] [Indexed: 01/23/2023]
Abstract
The budding yeast small ubiquitin-like modifier (SUMO) protease Ulp1p catalyzes both the processing of newly synthesized SUMO to its mature form and the deconjugation of SUMO from target proteins, thereby regulating a wide range of cellular processes including cell division, DNA repair, DNA replication, transcription, and mRNA quality control. Ulp1p is localized primarily at the nuclear pore complex (NPC) through interactions involving the karyopherins Kap121p and Kap95p-Kap60p heterodimer and a subset of nuclear pore-associated proteins. The sequestration of Ulp1p at the nuclear periphery is crucial for the proper control of protein desumoylation. To gain insights into the role of the karyopherins in regulating the localization of Ulp1p, we have determined the crystal structures of Kap121p and Kap60p bound to the N-terminal non-catalytic domain of Ulp1p that is necessary and sufficient for NPC targeting. Contrary to a previous proposal that Ulp1p is tethered to the transport channel of the NPC through unconventional interactions with the karyopherins, our structures reveal that Ulp1p has canonical nuclear localization signals (NLSs): (1) an isoleucine-lysine-NLS (residues 51-55) that binds to the NLS-binding site of Kap121p, and (2) a classical bipartite NLS (residues 154-172) that binds to the major and minor NLS-binding sites of Kap60p. Ulp1p also binds Kap95p directly, and the Ulp1p-Kap95p binding is enhanced by the importin-β-binding domain of Kap60p. GTP-bound Gsp1p (the yeast Ran ortholog) and the exportin Cse1p cooperate to release Ulp1p from the karyopherins, indicating that the stable sequestration of Ulp1p to the NPC would require a karyopherin-independent mechanism to anchor Ulp1p at the NPC.
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Affiliation(s)
- Hidemi Hirano
- Division of Biological Science, Graduate School of Science, Nagoya University, 464-8602, Japan; Structural Biology Research Center, Graduate School of Science, Nagoya University, 464-8602, Japan
| | - Junya Kobayashi
- Division of Biological Science, Graduate School of Science, Nagoya University, 464-8602, Japan
| | - Yoshiyuki Matsuura
- Division of Biological Science, Graduate School of Science, Nagoya University, 464-8602, Japan; Structural Biology Research Center, Graduate School of Science, Nagoya University, 464-8602, Japan.
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Fung HYJ, Fu SC, Brautigam CA, Chook YM. Structural determinants of nuclear export signal orientation in binding to exportin CRM1. eLife 2015; 4:e10034. [PMID: 26349033 PMCID: PMC4596688 DOI: 10.7554/elife.10034] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2015] [Accepted: 09/08/2015] [Indexed: 12/03/2022] Open
Abstract
The Chromosome Region of Maintenance 1 (CRM1) protein mediates nuclear export of hundreds of proteins through recognition of their nuclear export signals (NESs), which are highly variable in sequence and structure. The plasticity of the CRM1-NES interaction is not well understood, as there are many NES sequences that seem incompatible with structures of the NES-bound CRM1 groove. Crystal structures of CRM1 bound to two different NESs with unusual sequences showed the NES peptides binding the CRM1 groove in the opposite orientation (minus) to that of previously studied NESs (plus). Comparison of minus and plus NESs identified structural and sequence determinants for NES orientation. The binding of NESs to CRM1 in both orientations results in a large expansion in NES consensus patterns and therefore a corresponding expansion of potential NESs in the proteome.
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Affiliation(s)
- Ho Yee Joyce Fung
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Szu-Chin Fu
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Chad A Brautigam
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, United States
| | - Yuh Min Chook
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, United States
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