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Fung HYJ, Neisman AB, Bernardes NE, Jiou J, Chook YM. Nap1 and Kap114 co-chaperone H2A-H2B and facilitate targeted histone release in the nucleus. bioRxiv 2024:2023.05.09.539987. [PMID: 37214964 PMCID: PMC10197623 DOI: 10.1101/2023.05.09.539987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Core histones are synthesized and processed in the cytoplasm before transport into the nucleus for assembly into nucleosomes; however, they must also be chaperoned as free histones are toxic. The importin Kap114 binds and transports histone H2A-H2B into the yeast nucleus, where RanGTP facilitates H2A-H2B release. Kap114 and H2A-H2B also bind the Nap1 histone chaperone, which is found in both the cytoplasm and the nucleus, but how Nap1 and Kap114 cooperate in H2A-H2B processing and nucleosome assembly has been unclear. To understand these mechanisms, we used biochemical and structural analyses to reveal how Nap1, Kap114, H2A-H2B and RanGTP interact. We show that Kap114, H2A-H2B and a Nap1 dimer (Nap1 2 ) assemble into a 1:1:1 ternary complex. Cryogenic electron microscopy revealed two distinct Kap114/Nap1 2 /H2A-H2B structures: one of H2A-H2B sandwiched between Nap1 2 and Kap114, and another in which Nap1 2 bound to the Kap114·H2A-H2B complex without contacting H2A-H2B. Another Nap1 2 ·H2A-H2B·Kap114·Ran GTP structure reveals the nuclear complex. Mutagenesis revealed shared critical interfaces in all three structures. Consistent with structural findings, DNA competition experiments demonstrated that Kap114 and Nap1 2 together chaperone H2A-H2B better than either protein alone. When RanGTP is present, Kap114's chaperoning activity diminishes. However, the presence of Nap1 2 within the Nap1 2 ·H2A-H2B·Kap114·Ran GTP quaternary complex restores its ability to chaperone H2A-H2B. This complex effectively deposits H2A-H2B into nucleosomes. Together, these findings suggest that Kap114 and Nap12 provide a sheltered path from cytoplasm to nucleus, facilitating the transfer of H2A-H2B from Kap114 to Nap1 2 , ultimately directing its specific deposition into nucleosomes.
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Humphreys JM, Teixeira LR, Akella R, He H, Kannangara AR, Sekulski K, Pleinis J, Liwocha J, Jiou J, Servage KA, Orth K, Joachimiak L, Rizo J, Cobb MH, Brautigam CA, Rodan AR, Goldsmith EJ. Hydrostatic Pressure Sensing by WNK kinases. Mol Biol Cell 2023; 34:ar109. [PMID: 37585288 PMCID: PMC10559305 DOI: 10.1091/mbc.e23-03-0113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 08/10/2023] [Accepted: 08/10/2023] [Indexed: 08/18/2023] Open
Abstract
Previous study has demonstrated that the WNK kinases 1 and 3 are direct osmosensors consistent with their established role in cell-volume control. WNK kinases may also be regulated by hydrostatic pressure. Hydrostatic pressure applied to cells in culture with N2 gas or to Drosophila Malpighian tubules by centrifugation induces phosphorylation of downstream effectors of endogenous WNKs. In vitro, the autophosphorylation and activity of the unphosphorylated kinase domain of WNK3 (uWNK3) is enhanced to a lesser extent than in cells by 190 kPa applied with N2 gas. Hydrostatic pressure measurably alters the structure of uWNK3. Data from size exclusion chromatography in line with multi-angle light scattering (SEC-MALS), SEC alone at different back pressures, analytical ultracentrifugation (AUC), NMR, and chemical crosslinking indicate a change in oligomeric structure in the presence of hydrostatic pressure from a WNK3 dimer to a monomer. The effects on the structure are related to those seen with osmolytes. Potential mechanisms of hydrostatic pressure activation of uWNK3 and the relationships of pressure activation to WNK osmosensing are discussed.
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Affiliation(s)
- John M. Humphreys
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Liliana R. Teixeira
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Radha Akella
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Haixia He
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Ashari R. Kannangara
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Kamil Sekulski
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - John Pleinis
- Department of Internal Medicine, Division of Nephrology and Hypertension and Department of Human Genetics, University of Utah, Salt Lake City UT 84112
| | - Joanna Liwocha
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Jenny Jiou
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Kelly A. Servage
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Kim Orth
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Lukasz Joachimiak
- Center for Alzheimer’s and Neurodegenerative Diseases, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Josep Rizo
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Melanie H. Cobb
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Chad A. Brautigam
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX 75390
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Aylin R. Rodan
- Department of Internal Medicine, Division of Nephrology and Hypertension and Department of Human Genetics, University of Utah, Salt Lake City UT 84112
| | - Elizabeth J. Goldsmith
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX 75390
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Shaffer JM, Jiou J, Tripathi K, Olaluwoye OS, Fung HYJ, Chook YM, D'Arcy S. Molecular basis of RanGTP-activated release of Histones H2A-H2B from Importin-9. Structure 2023; 31:903-911.e3. [PMID: 37379840 PMCID: PMC10527638 DOI: 10.1016/j.str.2023.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 05/22/2023] [Accepted: 06/02/2023] [Indexed: 06/30/2023]
Abstract
Imp9 is the primary importin for shuttling H2A-H2B from the cytoplasm to the nucleus. It employs an unusual mechanism where the binding of RanGTP is insufficient to release H2A-H2B. The resulting stable RanGTP·Imp9·H2A-H2B complex gains nucleosome assembly activity with H2A-H2B able to be deposited into an assembling nucleosome in vitro. Using hydrogen-deuterium exchange coupled with mass spectrometry (HDX), we show that Imp9 stabilizes H2A-H2B beyond the direct-binding site, like other histone chaperones. HDX also shows that binding of RanGTP releases H2A-H2B contacts at Imp9 HEAT repeats 4-5, but not 18-19. DNA- and histone-binding surfaces of H2A-H2B are exposed in the ternary complex, facilitating nucleosome assembly. We also reveal that RanGTP has a weaker affinity for Imp9 when H2A-H2B is bound. Imp9 thus provides a connection between the nuclear import of H2A-H2B and its deposition into chromatin.
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Affiliation(s)
- Joy M Shaffer
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson 75080, USA
| | - Jenny Jiou
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas 75390, USA
| | - Kiran Tripathi
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson 75080, USA
| | - Oladimeji S Olaluwoye
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson 75080, USA
| | - Ho Yee Joyce Fung
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas 75390, USA
| | - Yuh Min Chook
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas 75390, USA
| | - Sheena D'Arcy
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson 75080, USA.
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4
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Jiou J, Shaffer JM, Bernades NE, Fung HYJ, Kikumoto Dias J, D’Arcy S, Chook YM. Mechanism of RanGTP priming H2A-H2B release from Kap114 in an atypical RanGTP•Kap114•H2A-H2B complex. Proc Natl Acad Sci U S A 2023; 120:e2301199120. [PMID: 37450495 PMCID: PMC10629556 DOI: 10.1073/pnas.2301199120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 06/08/2023] [Indexed: 07/18/2023] Open
Abstract
Previously, we showed that the nuclear import receptor Importin-9 wraps around the H2A-H2B core to chaperone and transport it from the cytoplasm to the nucleus. However, unlike most nuclear import systems where RanGTP dissociates cargoes from their importins, RanGTP binds stably to the Importin-9•H2A-H2B complex, and formation of the ternary RanGTP•Importin-9•H2A-H2B complex facilitates H2A-H2B release to the assembling nucleosome. It was unclear how RanGTP and the cargo H2A-H2B can bind simultaneously to an importin, and how interactions of the three components position H2A-H2B for release. Here, we show cryo-EM structures of Importin-9•RanGTP and of its yeast homolog Kap114, including Kap114•RanGTP, Kap114•H2A-H2B, and RanGTP•Kap114•H2A-H2B, to explain how the conserved Kap114 binds H2A-H2B and RanGTP simultaneously and how the GTPase primes histone transfer to the nucleosome. In the ternary complex, RanGTP binds to the N-terminal repeats of Kap114 in the same manner as in the Kap114/Importin-9•RanGTP complex, and H2A-H2B binds via its acidic patch to the Kap114 C-terminal repeats much like in the Kap114/Importin-9•H2A-H2B complex. Ran binds to a different conformation of Kap114 in the ternary RanGTP•Kap114•H2A-H2B complex. Here, Kap114 no longer contacts the H2A-H2B surface proximal to the H2A docking domain that drives nucleosome assembly, positioning it for transfer to the assembling nucleosome or to dedicated H2A-H2B chaperones in the nucleus.
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Affiliation(s)
- Jenny Jiou
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX75390
| | - Joy M. Shaffer
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, TX75080
| | - Natalia E. Bernades
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX75390
| | - Ho Yee Joyce Fung
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX75390
| | - Juliana Kikumoto Dias
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, TX75080
| | - Sheena D’Arcy
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, TX75080
| | - Yuh Min Chook
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX75390
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5
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Shaffer JM, Jiou J, Tripathi K, Olaluwoye OS, Fung HYJ, Chook YM, D’Arcy S. Molecular basis of RanGTP-activated nucleosome assembly with Histones H2A-H2B bound to Importin-9. bioRxiv 2023:2023.01.27.525896. [PMID: 36747879 PMCID: PMC9901172 DOI: 10.1101/2023.01.27.525896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Padavannil et al. 2019 show that Importin-9 (Imp9) transports Histones H2A-H2B from the cytoplasm to the nucleus using a non-canonical mechanism whereby binding of a GTP-bound Ran GTPase (RanGTP) fails to evict the H2A-H2B cargo. Instead, a stable complex forms, comprised of equimolar RanGTP, Imp9, and H2A-H2B. Unlike the binary Imp9•H2A-H2B complex, this RanGTP•Imp9•H2A-H2B ternary complex can release H2A-H2B to an assembling nucleosome. Here, we define the molecular basis for this RanGTP-activated nucleosome assembly by Imp9. We use hydrogen-deuterium exchange coupled with mass spectrometry and compare the dynamics and interfaces of the RanGTP•Imp9•H2A-H2B ternary complex to those in the Imp9•H2A-H2B or Imp9•RanGTP binary complexes. Our data are consistent with the Imp9•H2A-H2B structure by Padavannil et al. 2019 showing that Imp9 HEAT repeats 4-5 and 18-19 contact H2A-H2B, as well as many homologous importin•RanGTP structures showing that importin HEAT repeats 1 and 3, and the h8 loop, contact RanGTP. We show that Imp9 stabilizes H2A-H2B beyond the direct binding site, similar to other histone chaperones. Importantly, we reveal that binding of RanGTP releases H2A-H2B interaction at Imp9 HEAT repeats 4-5, but not 18-19. This exposes DNA- and histone-binding surfaces of H2A-H2B, thereby facilitating nucleosome assembly. We also reveal that RanGTP has a weaker affinity for Imp9 when H2A-H2B is bound. This may ensure that H2A-H2B is only released in high RanGTP concentrations near chromatin. We delineate the molecular link between the nuclear import of H2A-H2B and its deposition into chromatin by Imp9. Significance Imp9 is the primary importin for shuttling H2A-H2B from the cytoplasm to the nucleus. It employs an unusual mechanism where the binding of RanGTP alone is insufficient to release H2A-H2B. The resulting stable RanGTP•Imp9•H2A-H2B complex gains nucleosome assembly activity as H2A-H2B can be deposited onto an assembling nucleosome. We show that H2A-H2B is allosterically stabilized via interactions with both N- and C-terminal portions of Imp9, reinforcing its chaperone-like behavior. RanGTP binding causes H2A-H2B release from the N-terminal portion of Imp9 only. The newly-exposed H2A-H2B surfaces can interact with DNA or H3-H4 in nucleosome assembly. Imp9 thus plays a multi-faceted role in histone import, storage, and deposition regulated by RanGTP, controlling histone supply in the nucleus and to chromatin.
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Affiliation(s)
- Joy M. Shaffer
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, United States, 75080
| | - Jenny Jiou
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, United States, 75390
| | - Kiran Tripathi
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, United States, 75080
| | - Oladimeji S. Olaluwoye
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, United States, 75080
| | - Ho Yee Joyce Fung
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, United States, 75390
| | - Yuh Min Chook
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, United States, 75390
| | - Sheena D’Arcy
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, United States, 75080
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6
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Akella R, Drozdz MA, Humphreys JM, Jiou J, Durbacz MZ, Mohammed ZJ, He H, Liwocha J, Sekulski K, Goldsmith EJ. A Phosphorylated Intermediate in the Activation of WNK Kinases. Biochemistry 2020; 59:1747-1755. [PMID: 32314908 PMCID: PMC7914002 DOI: 10.1021/acs.biochem.0c00146] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
WNK kinases autoactivate by autophosphorylation. Crystallography of the kinase domain of WNK1 phosphorylated on the primary activating site (pWNK1) in the presence of AMP-PNP reveals a well-ordered but inactive configuration. This new pWNK1 structure features specific and unique interactions of the phosphoserine, less hydration, and smaller cavities compared with those of unphosphorylated WNK1 (uWNK1). Because WNKs are activated by osmotic stress in cells, we addressed whether the structure was influenced directly by osmotic pressure. pWNK1 crystals formed in PEG3350 were soaked in the osmolyte sucrose. Suc-WNK1 crystals maintained X-ray diffraction, but the lattice constants and pWNK1 structure changed. Differences were found in the activation loop and helix C, common switch loci in kinase activation. On the basis of these structural changes, we tested for effects on in vitro activity of two WNKs, pWNK1 and pWNK3. The osmolyte PEG400 enhanced ATPase activity. Our data suggest multistage activation of WNKs.
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Affiliation(s)
- Radha Akella
- Department of Biophysics, The University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390-8816, USA
| | - Mateusz A. Drozdz
- Department of Biophysics, The University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390-8816, USA
| | - John M. Humphreys
- Department of Biophysics, The University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390-8816, USA
| | - Jenny Jiou
- Department of Biophysics, The University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390-8816, USA
| | - Mateusz Z. Durbacz
- Faculty of Agronomy and Bioengineering, University of Life Sciences, Wojska Polskiego 28, 60-624 Poznan, Poland
| | - Zuhair J. Mohammed
- Biomedical Engineering, University of Texas at Dallas, Richardson, TX 75080
| | - Haixia He
- Department of Biophysics, The University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390-8816, USA
| | - Joanna Liwocha
- Department of Molecular Machines and Signaling, Max Planck Institute for Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Kamil Sekulski
- Department of Biophysics, The University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390-8816, USA
| | - Elizabeth J. Goldsmith
- Department of Biophysics, The University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390-8816, USA
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7
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Tomchick DR, Sreelatha A, Yee SS, Lopez VA, Park BC, Kinch LN, Pilch S, Servage KA, Zhang J, Jiou J, Karasiewicz-Urbańska M, Łobocka M, Grishin NV, Orth K, Kucharczyk R, Pawłowski K, Tagliabracci VS. Protein AMPylation by an evolutionarily conserved pseudokinase. Acta Crystallogr A Found Adv 2019. [DOI: 10.1107/s0108767319096922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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8
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Padavannil A, Sarkar P, Kim SJ, Cagatay T, Jiou J, Brautigam CA, Tomchick DR, Sali A, D'Arcy S, Chook YM. Importin-9 wraps around the H2A-H2B core to act as nuclear importer and histone chaperone. eLife 2019; 8:e43630. [PMID: 30855230 PMCID: PMC6453568 DOI: 10.7554/elife.43630] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 03/09/2019] [Indexed: 01/29/2023] Open
Abstract
We report the crystal structure of nuclear import receptor Importin-9 bound to its cargo, the histones H2A-H2B. Importin-9 wraps around the core, globular region of H2A-H2B to form an extensive interface. The nature of this interface coupled with quantitative analysis of deletion mutants of H2A-H2B suggests that the NLS-like sequences in the H2A-H2B tails play a minor role in import. Importin-9•H2A-H2B is reminiscent of interactions between histones and histone chaperones in that it precludes H2A-H2B interactions with DNA and H3-H4 as seen in the nucleosome. Like many histone chaperones, which prevent inappropriate non-nucleosomal interactions, Importin-9 also sequesters H2A-H2B from DNA. Importin-9 appears to act as a storage chaperone for H2A-H2B while escorting it to the nucleus. Surprisingly, RanGTP does not dissociate Importin-9•H2A-H2B but assembles into a RanGTP•Importin-9•H2A-H2B complex. The presence of Ran in the complex, however, modulates Imp9-H2A-H2B interactions to facilitate its dissociation by DNA and assembly into a nucleosome.
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Affiliation(s)
- Abhilash Padavannil
- Department of PharmacologyUniversity of Texas Southwestern Medical CenterDallasUnited States
| | - Prithwijit Sarkar
- Department of Biological SciencesUniversity of Texas at DallasRichardsonUnited States
| | - Seung Joong Kim
- Department of PhysicsKorea Advanced Institute of Science and Technology (KAIST)DaejeonKorea
| | - Tolga Cagatay
- Department of PharmacologyUniversity of Texas Southwestern Medical CenterDallasUnited States
| | - Jenny Jiou
- Department of PharmacologyUniversity of Texas Southwestern Medical CenterDallasUnited States
| | - Chad A Brautigam
- Department of BiophysicsUniversity of Texas Southwestern Medical CenterDallasUnited States
| | - Diana R Tomchick
- Department of BiophysicsUniversity of Texas Southwestern Medical CenterDallasUnited States
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative BiosciencesUniversity of California, San FranciscoSan FranciscoUnited States
- Department of Pharmaceutical Chemistry, California Institute for Quantitative BiosciencesUniversity of California, San FranciscoSan FranciscoUnited states
| | - Sheena D'Arcy
- Department of Chemistry and BiochemistryUniversity of Texas at DallasRichardsonUnited States
| | - Yuh Min Chook
- Department of PharmacologyUniversity of Texas Southwestern Medical CenterDallasUnited States
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9
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Yoshizawa T, Ali R, Jiou J, Fung HYJ, Burke KA, Kim SJ, Lin Y, Peeples WB, Saltzberg D, Soniat M, Baumhardt JM, Oldenbourg R, Sali A, Fawzi NL, Rosen MK, Chook YM. Nuclear Import Receptor Inhibits Phase Separation of FUS through Binding to Multiple Sites. Cell 2019; 173:693-705.e22. [PMID: 29677513 DOI: 10.1016/j.cell.2018.03.003] [Citation(s) in RCA: 210] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 11/29/2017] [Accepted: 02/28/2018] [Indexed: 01/04/2023]
Abstract
Liquid-liquid phase separation (LLPS) is believed to underlie formation of biomolecular condensates, cellular compartments that concentrate macromolecules without surrounding membranes. Physical mechanisms that control condensate formation/dissolution are poorly understood. The RNA-binding protein fused in sarcoma (FUS) undergoes LLPS in vitro and associates with condensates in cells. We show that the importin karyopherin-β2/transportin-1 inhibits LLPS of FUS. This activity depends on tight binding of karyopherin-β2 to the C-terminal proline-tyrosine nuclear localization signal (PY-NLS) of FUS. Nuclear magnetic resonance (NMR) analyses reveal weak interactions of karyopherin-β2 with sequence elements and structural domains distributed throughout the entirety of FUS. Biochemical analyses demonstrate that most of these same regions also contribute to LLPS of FUS. The data lead to a model where high-affinity binding of karyopherin-β2 to the FUS PY-NLS tethers the proteins together, allowing multiple, distributed weak intermolecular contacts to disrupt FUS self-association, blocking LLPS. Karyopherin-β2 may act analogously to control condensates in diverse cellular contexts.
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Affiliation(s)
- Takuya Yoshizawa
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Rustam Ali
- Department of Biophysics and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jenny Jiou
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ho Yee Joyce Fung
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Kathleen A Burke
- Department of Molecular Pharmacology, Physiology and Biotechnology, Brown University, Providence, RI 02912, USA
| | - Seung Joong Kim
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Yuan Lin
- Department of Biophysics and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Howard Hughes Medical Institute (HHMI) Summer Institute, Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - William B Peeples
- Department of Biophysics and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Howard Hughes Medical Institute (HHMI) Summer Institute, Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - Daniel Saltzberg
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Michael Soniat
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jordan M Baumhardt
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Rudolf Oldenbourg
- Marine Biological Laboratories, 7 MBL Street, Woods Hole, MA 02543, USA
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Nicolas L Fawzi
- Department of Molecular Pharmacology, Physiology and Biotechnology, Brown University, Providence, RI 02912, USA
| | - Michael K Rosen
- Department of Biophysics and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Howard Hughes Medical Institute (HHMI) Summer Institute, Marine Biological Laboratory, Woods Hole, MA 02543, USA.
| | - Yuh Min Chook
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Howard Hughes Medical Institute (HHMI) Summer Institute, Marine Biological Laboratory, Woods Hole, MA 02543, USA.
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10
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Sreelatha A, Yee SS, Lopez VA, Park BC, Kinch LN, Pilch S, Servage KA, Zhang J, Jiou J, Karasiewicz-Urbańska M, Łobocka M, Grishin NV, Orth K, Kucharczyk R, Pawłowski K, Tomchick DR, Tagliabracci VS. Protein AMPylation by an Evolutionarily Conserved Pseudokinase. Cell 2018; 175:809-821.e19. [PMID: 30270044 DOI: 10.1016/j.cell.2018.08.046] [Citation(s) in RCA: 115] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 07/19/2018] [Accepted: 08/17/2018] [Indexed: 02/06/2023]
Abstract
Approximately 10% of human protein kinases are believed to be inactive and named pseudokinases because they lack residues required for catalysis. Here, we show that the highly conserved pseudokinase selenoprotein-O (SelO) transfers AMP from ATP to Ser, Thr, and Tyr residues on protein substrates (AMPylation), uncovering a previously unrecognized activity for a member of the protein kinase superfamily. The crystal structure of a SelO homolog reveals a protein kinase-like fold with ATP flipped in the active site, thus providing a structural basis for catalysis. SelO pseudokinases localize to the mitochondria and AMPylate proteins involved in redox homeostasis. Consequently, SelO activity is necessary for the proper cellular response to oxidative stress. Our results suggest that AMPylation may be a more widespread post-translational modification than previously appreciated and that pseudokinases should be analyzed for alternative transferase activities.
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Affiliation(s)
- Anju Sreelatha
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Samantha S Yee
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Victor A Lopez
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Brenden C Park
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Lisa N Kinch
- Howard Hughes Medical Institute, Dallas, TX 75390, USA
| | - Sylwia Pilch
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw 02-106, Poland
| | - Kelly A Servage
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Junmei Zhang
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jenny Jiou
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | | | - Małgorzata Łobocka
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw 02-106, Poland; Faculty of Agriculture and Biology, Warsaw University of Life Sciences, Warsaw 02-776, Poland
| | - Nick V Grishin
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Howard Hughes Medical Institute, Dallas, TX 75390, USA; Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Kim Orth
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Howard Hughes Medical Institute, Dallas, TX 75390, USA; Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Roza Kucharczyk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw 02-106, Poland
| | - Krzysztof Pawłowski
- Faculty of Agriculture and Biology, Warsaw University of Life Sciences, Warsaw 02-776, Poland
| | - Diana R Tomchick
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Vincent S Tagliabracci
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA; Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.
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Goldsmith EJ, Akella R, Jiou J. Structural basis for activation of WNK kinases by hydrostatic pressure. Acta Crystallogr A Found Adv 2017. [DOI: 10.1107/s0108767317096945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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