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Valentino IM, Llivicota-Guaman JG, Dao TP, Mulvey EO, Lehman AM, Galagedera SKK, Mallon EL, Castañeda CA, Kraut DA. Phase separation of polyubiquitinated proteins in UBQLN2 condensates controls substrate fate. Proc Natl Acad Sci U S A 2024; 121:e2405964121. [PMID: 39121161 DOI: 10.1073/pnas.2405964121] [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: 03/22/2024] [Accepted: 06/26/2024] [Indexed: 08/11/2024] Open
Abstract
Ubiquitination is one of the most common posttranslational modifications in eukaryotic cells. Depending on the architecture of polyubiquitin chains, substrate proteins can meet different cellular fates, but our understanding of how chain linkage controls protein fate remains limited. UBL-UBA shuttle proteins, such as UBQLN2, bind to ubiquitinated proteins and to the proteasome or other protein quality control machinery elements and play a role in substrate fate determination. Under physiological conditions, UBQLN2 forms biomolecular condensates through phase separation, a physicochemical phenomenon in which multivalent interactions drive the formation of a macromolecule-rich dense phase. Ubiquitin and polyubiquitin chains modulate UBQLN2's phase separation in a linkage-dependent manner, suggesting a possible link to substrate fate determination, but polyubiquitinated substrates have not been examined directly. Using sedimentation assays and microscopy we show that polyubiquitinated substrates induce UBQLN2 phase separation and incorporate into the resulting condensates. This substrate effect is strongest with K63-linked substrates, intermediate with mixed-linkage substrates, and weakest with K48-linked substrates. Proteasomes can be recruited to these condensates, but proteasome activity toward K63-linked and mixed linkage substrates is inhibited in condensates. Substrates are also protected from deubiquitinases by UBQLN2-induced phase separation. Our results suggest that phase separation could regulate the fate of ubiquitinated substrates in a chain-linkage-dependent manner, thus serving as an interpreter of the ubiquitin code.
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Affiliation(s)
| | | | - Thuy P Dao
- Department of Biology, Department of Chemistry, Bioinspired Institute, Interdisciplinary Neuroscience Program, Syracuse University, Syracuse, NY 13244
| | - Erin O Mulvey
- Department of Chemistry, Villanova University, Villanova, PA 19085
| | - Andrew M Lehman
- Department of Chemistry, Villanova University, Villanova, PA 19085
| | - Sarasi K K Galagedera
- Department of Biology, Department of Chemistry, Bioinspired Institute, Interdisciplinary Neuroscience Program, Syracuse University, Syracuse, NY 13244
| | - Erica L Mallon
- Department of Chemistry, Villanova University, Villanova, PA 19085
| | - Carlos A Castañeda
- Department of Biology, Department of Chemistry, Bioinspired Institute, Interdisciplinary Neuroscience Program, Syracuse University, Syracuse, NY 13244
| | - Daniel A Kraut
- Department of Chemistry, Villanova University, Villanova, PA 19085
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Onwunma J, Binsabaan S, Allen SP, Sankaran B, Wohlever ML. The structural and biophysical basis of substrate binding to the hydrophobic groove in Ubiquilin Sti1 domains. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.10.602902. [PMID: 39026758 PMCID: PMC11257586 DOI: 10.1101/2024.07.10.602902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Ubiquilins are a family of cytosolic proteins that ferry ubiquitinated substrates to the proteasome for degradation. Recent work has demonstrated that Ubiquilins can also act as molecular chaperones, utilizing internal Sti1 domains to directly bind to hydrophobic sequences. Ubiquilins are associated with several neurodegenerative diseases with point mutations in UBQLN2 causing dominant, X-linked Amyotrophic Lateral Sclerosis (ALS). The molecular basis of Ubiquilin chaperone activity and how ALS mutations in the Sti1 domains affect Ubiquilin activity are poorly understood. This study presents the first crystal structure of the Sti1 domain from a fungal Ubiquilin homolog bound to a transmembrane domain (TMD). The structure reveals that two Sti1 domains form a head-to-head dimer, creating a hydrophobic cavity that accommodates two TMDs. Mapping the UBQLN2 sequence onto the structure shows that several ALS mutations are predicted to disrupt the hydrophobic groove. Using a newly developed competitive binding assay, we show that Ubiquilins preferentially bind to hydrophobic substrates with low helical propensity, motifs that are enriched in both substrates and in Ubiquilins. This study provides insights into the molecular and structural basis for Ubiquilin substrate binding, with broad implications for the role of the Sti1 domain in phase separation and ALS.
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Affiliation(s)
- Joan Onwunma
- Previously at University of Toledo, Department of Chemistry & Biochemistry
| | | | - Shawn P Allen
- Previously at University of Toledo, Department of Chemistry & Biochemistry
- University of Pittsburgh, Department of Cell Biology
| | - Banumathi Sankaran
- Lawrence Berkley National Lab, Berkeley Center for Structural Biology, Molecular Biophysics and Integrated Bioimaging
| | - Matthew L Wohlever
- Previously at University of Toledo, Department of Chemistry & Biochemistry
- University of Pittsburgh, Department of Cell Biology
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Valentino IM, Llivicota-Guaman JG, Dao TP, Mulvey EO, Lehman AM, Galagedera SKK, Mallon EL, Castañeda CA, Kraut DA. Phase separation of polyubiquitinated proteins in UBQLN2 condensates controls substrate fate. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.15.585243. [PMID: 38559018 PMCID: PMC10980000 DOI: 10.1101/2024.03.15.585243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Ubiquitination is one of the most common post-translational modifications in eukaryotic cells. Depending on the architecture of polyubiquitin chains, substrate proteins can meet different cellular fates, but our understanding of how chain linkage controls protein fate remains limited. UBL-UBA shuttle proteins, such as UBQLN2, bind to ubiquitinated proteins and to the proteasome or other protein quality control machinery elements and play a role in substrate fate determination. Under physiological conditions, UBQLN2 forms biomolecular condensates through phase separation, a physicochemical phenomenon in which multivalent interactions drive the formation of a macromolecule-rich dense phase. Ubiquitin and polyubiquitin chains modulate UBQLN2's phase separation in a linkage-dependent manner, suggesting a possible link to substrate fate determination, but polyubiquitinated substrates have not been examined directly. Using sedimentation assays and microscopy we show that polyubiquitinated substrates induce UBQLN2 phase separation and incorporate into the resulting condensates. This substrate effect is strongest with K63-linked substrates, intermediate with mixed-linkage substrates, and weakest with K48-linked substrates. Proteasomes can be recruited to these condensates, but proteasome activity towards K63-linked and mixed linkage substrates is inhibited in condensates. Substrates are also protected from deubiquitinases by UBQLN2-induced phase separation. Our results suggest that phase separation could regulate the fate of ubiquitinated substrates in a chain-linkage dependent manner, thus serving as an interpreter of the ubiquitin code.
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Affiliation(s)
| | | | - Thuy P. Dao
- Department of Biology, Department of Chemistry, Bioinspired Institute, Interdisciplinary Neuroscience Program, Syracuse University, Syracuse, NY 13244
| | - Erin O. Mulvey
- Department of Chemistry, Villanova University, Villanova, PA 19085
| | - Andrew M. Lehman
- Department of Chemistry, Villanova University, Villanova, PA 19085
| | - Sarasi K. K. Galagedera
- Department of Biology, Department of Chemistry, Bioinspired Institute, Interdisciplinary Neuroscience Program, Syracuse University, Syracuse, NY 13244
| | - Erica L. Mallon
- Department of Chemistry, Villanova University, Villanova, PA 19085
| | - Carlos A. Castañeda
- Department of Biology, Department of Chemistry, Bioinspired Institute, Interdisciplinary Neuroscience Program, Syracuse University, Syracuse, NY 13244
| | - Daniel A. Kraut
- Department of Chemistry, Villanova University, Villanova, PA 19085
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Debelouchina GT, Lasker K, Mukhopadhyay S. Emerging biophysical principles of macromolecular phase separation. Biophys J 2024; 123:E1-E3. [PMID: 38761796 PMCID: PMC11163286 DOI: 10.1016/j.bpj.2024.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 05/01/2024] [Accepted: 05/01/2024] [Indexed: 05/20/2024] Open
Affiliation(s)
- Galia T Debelouchina
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California.
| | - Keren Lasker
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California.
| | - Samrat Mukhopadhyay
- Centre for Protein Science, Design and Engineering, Department of Biological Sciences, and Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India.
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Liao J, Yeong V, Obermeyer AC. Charge-Patterned Disordered Peptides Tune Intracellular Phase Separation in Bacteria. ACS Synth Biol 2024; 13:598-612. [PMID: 38308651 DOI: 10.1021/acssynbio.3c00564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2024]
Abstract
Subcellular phase-separated compartments, known as biomolecular condensates, play an important role in the spatiotemporal organization of cells. To understand the sequence-determinants of phase separation in bacteria, we engineered protein-based condensates in Escherichia coli using electrostatic interactions as the main driving force. Minimal cationic disordered peptides were used to supercharge negative, neutral, and positive globular model proteins, enabling their phase separation with anionic biomacromolecules in the cell. The phase behavior was governed by the interaction strength between the cationic proteins and anionic biopolymers, in addition to the protein concentration. The interaction strength primarily depended on the overall net charge of the protein, but the distribution of charge between the globular and disordered domains also had an impact. Notably, the protein charge distribution between domains could tune mesoscale attributes such as the size, number, and subcellular localization of condensates within E. coli cells. The length and charge density of the disordered peptides had significant effects on protein expression levels, ultimately influencing the formation of condensates. Taken together, charge-patterned disordered peptides provide a platform for understanding the molecular grammar underlying phase separation in bacteria.
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Affiliation(s)
- Jane Liao
- Department of Chemical Engineering, Columbia University, New York, New York 10027, United States
| | - Vivian Yeong
- Department of Chemical Engineering, Columbia University, New York, New York 10027, United States
| | - Allie C Obermeyer
- Department of Chemical Engineering, Columbia University, New York, New York 10027, United States
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