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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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2
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Li C, Hao B, Yang H, Wang K, Fan L, Xiao W. Protein aggregation and biomolecular condensation in hypoxic environments (Review). Int J Mol Med 2024; 53:33. [PMID: 38362920 PMCID: PMC10903932 DOI: 10.3892/ijmm.2024.5357] [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] [Received: 11/08/2023] [Accepted: 01/15/2024] [Indexed: 02/17/2024] Open
Abstract
Due to molecular forces, biomacromolecules assemble into liquid condensates or solid aggregates, and their corresponding formation and dissolution processes are controlled. Protein homeostasis is disrupted by increasing age or environmental stress, leading to irreversible protein aggregation. Hypoxic pressure is an important factor in this process, and uncontrolled protein aggregation has been widely observed in hypoxia‑related conditions such as neurodegenerative disease, cardiovascular disease, hypoxic brain injury and cancer. Biomolecular condensates are also high‑order complexes assembled from macromolecules. Although they exist in different phase from protein aggregates, they are in dynamic balance under certain conditions, and their activation or assembly are considered as important regulatory processes in cell survival with hypoxic pressure. Therefore, a better understanding of the relationship between hypoxic stress, protein aggregation and biomolecular condensation will bring marked benefits in the clinical treatment of various diseases. The aim of the present review was to summarize the underlying mechanisms of aggregate assembly and dissolution induced by hypoxic conditions, and address recent breakthroughs in understanding the role of aggregates in hypoxic‑related diseases, given the hypotheses that hypoxia induces macromolecular assemblage changes from a liquid to a solid phase, and that adenosine triphosphate depletion and ATP‑driven inactivation of multiple protein chaperones play important roles among the process. Moreover, it is anticipated that an improved understanding of the adaptation in hypoxic environments could extend the overall survival of patients and provide new strategies for hypoxic‑related diseases.
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Affiliation(s)
- Chaoqun Li
- School of Exercise and Health, Shanghai University of Sport, Shanghai 200438, P.R. China
- Institute of Energy Metabolism and Health, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, P.R. China
| | - Bingjie Hao
- Institute of Energy Metabolism and Health, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, P.R. China
| | - Haiguang Yang
- Institute of Energy Metabolism and Health, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, P.R. China
| | - Kai Wang
- Institute of Energy Metabolism and Health, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, P.R. China
| | - Lihong Fan
- School of Exercise and Health, Shanghai University of Sport, Shanghai 200438, P.R. China
- Institute of Energy Metabolism and Health, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, P.R. China
| | - Weihua Xiao
- School of Exercise and Health, Shanghai University of Sport, Shanghai 200438, P.R. China
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3
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Ramirez DA, Hough LE, Shirts MR. Coiled-coil domains are sufficient to drive liquid-liquid phase separation in protein models. Biophys J 2024; 123:703-717. [PMID: 38356260 PMCID: PMC10995412 DOI: 10.1016/j.bpj.2024.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 12/09/2023] [Accepted: 02/09/2024] [Indexed: 02/16/2024] Open
Abstract
Liquid-liquid phase separation (LLPS) is thought to be a main driving force in the formation of membraneless organelles. Examples of such organelles include the centrosome, central spindle, and stress granules. Recently, it has been shown that coiled-coil (CC) proteins, such as the centrosomal proteins pericentrin, spd-5, and centrosomin, might be capable of LLPS. CC domains have physical features that could make them the drivers of LLPS, but it is unknown if they play a direct role in the process. We developed a coarse-grained simulation framework for investigating the LLPS propensity of CC proteins, in which interactions that support LLPS arise solely from CC domains. We show, using this framework, that the physical features of CC domains are sufficient to drive LLPS of proteins. The framework is specifically designed to investigate how the number of CC domains, as well as the multimerization state of CC domains, can affect LLPS. We show that small model proteins with as few as two CC domains can phase separate. Increasing the number of CC domains up to four per protein can somewhat increase LLPS propensity. We demonstrate that trimer-forming and tetramer-forming CC domains have a dramatically higher LLPS propensity than dimer-forming coils, which shows that multimerization state has a greater effect on LLPS than the number of CC domains per protein. These data support the hypothesis of CC domains as drivers of protein LLPS, and have implications in future studies to identify the LLPS-driving regions of centrosomal and central spindle proteins.
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Affiliation(s)
- Dominique A Ramirez
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado
| | - Loren E Hough
- Department of Physics and BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado
| | - Michael R Shirts
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado.
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4
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Waite KA, Vontz G, Lee SY, Roelofs J. Proteasome condensate formation is driven by multivalent interactions with shuttle factors and ubiquitin chains. Proc Natl Acad Sci U S A 2024; 121:e2310756121. [PMID: 38408252 DOI: 10.1073/pnas.2310756121] [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: 06/26/2023] [Accepted: 01/26/2024] [Indexed: 02/28/2024] Open
Abstract
Stress conditions can cause the relocalization of proteasomes to condensates in yeast and mammalian cells. The interactions that facilitate the formation of proteasome condensates, however, are unclear. Here, we show that the formation of proteasome condensates in yeast depends on ubiquitin chains together with the proteasome shuttle factors Rad23 and Dsk2. These shuttle factors colocalize to these condensates. Strains deleted for the third shuttle factor gene, DDI1, show proteasome condensates in the absence of cellular stress, consistent with the accumulation of substrates with long K48-linked ubiquitin chains that accumulate in this mutant. We propose a model where the long K48-linked ubiquitin chains function as a scaffold for the ubiquitin-binding domains of the shuttle factors and the proteasome, allowing for the multivalent interactions that further drive condensate formation. Indeed, we determined different intrinsic ubiquitin receptors of the proteasome-Rpn1, Rpn10, and Rpn13-and the Ubl domains of Rad23 and Dsk2 are critical under different condensate-inducing conditions. In all, our data support a model where the cellular accumulation of substrates with long ubiquitin chains, potentially due to reduced cellular energy, allows for proteasome condensate formation. This suggests that proteasome condensates are not simply for proteasome storage, but function to sequester soluble ubiquitinated substrates together with inactive proteasomes.
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Affiliation(s)
- Kenrick A Waite
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160
| | - Gabrielle Vontz
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160
| | - Stella Y Lee
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160
| | - Jeroen Roelofs
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160
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5
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Galagedera SKK, Dao TP, Enos SE, Chaudhuri A, Schmit JD, Castañeda CA. Polyubiquitin ligand-induced phase transitions are optimized by spacing between ubiquitin units. Proc Natl Acad Sci U S A 2023; 120:e2306638120. [PMID: 37824531 PMCID: PMC10589717 DOI: 10.1073/pnas.2306638120] [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: 04/25/2023] [Accepted: 09/01/2023] [Indexed: 10/14/2023] Open
Abstract
Biomolecular condensates form via multivalent interactions among key macromolecules and are regulated through ligand binding and/or posttranslational modifications. One such modification is ubiquitination, the covalent addition of ubiquitin (Ub) or polyubiquitin chains to target macromolecules. Specific interactions between polyubiquitin chains and partner proteins, including hHR23B, NEMO, and UBQLN2, regulate condensate assembly or disassembly. Here, we used a library of designed polyubiquitin hubs and UBQLN2 as model systems for determining the driving forces of ligand-mediated phase transitions. Perturbations to either the UBQLN2-binding surface of Ub or the spacing between Ub units reduce the ability of hubs to modulate UBQLN2 phase behavior. By developing an analytical model based on polyphasic linkage principles that accurately described the effects of different hubs on UBQLN2 phase separation, we determined that introduction of Ub to UBQLN2 condensates incurs a significant inclusion energetic penalty. This penalty antagonizes the ability of polyUb hubs to scaffold multiple UBQLN2 molecules and cooperatively amplify phase separation. The extent to which polyubiquitin hubs promote UBQLN2 phase separation is encoded in the spacings between Ub units. This spacing is modulated by chains of different linkages and designed chains of different architectures, thus illustrating how the ubiquitin code regulates functionality via the emergent properties of the condensate. The spacing in naturally occurring linear polyubiquitin chains is already optimized to promote phase separation with UBQLN2. We expect our findings to extend to other condensates, emphasizing the importance of ligand properties, including concentration, valency, affinity, and spacing between binding sites in studies and designs of condensates.
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Affiliation(s)
- Sarasi K. K. Galagedera
- Department of Biology, Syracuse University, Syracuse, NY13244
- Department of Chemistry, Syracuse University, Syracuse, NY13244
| | - Thuy P. Dao
- Department of Biology, Syracuse University, Syracuse, NY13244
- Department of Chemistry, Syracuse University, Syracuse, NY13244
| | - Suzanne E. Enos
- Department of Biology, Syracuse University, Syracuse, NY13244
- Department of Chemistry, Syracuse University, Syracuse, NY13244
| | - Antara Chaudhuri
- Department of Biology, Syracuse University, Syracuse, NY13244
- Department of Chemistry, Syracuse University, Syracuse, NY13244
| | - Jeremy D. Schmit
- Department of Physics, Kansas State University, Manhattan, KS66506
| | - Carlos A. Castañeda
- Department of Biology, Syracuse University, Syracuse, NY13244
- Department of Chemistry, Syracuse University, Syracuse, NY13244
- Interdisciplinary Neuroscience Program, Syracuse University, Syracuse, NY13244
- BioInspired Institute, Syracuse University, Syracuse, NY13244
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6
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Qin C, Wang YL, Zhou JY, Shi J, Zhao WW, Zhu YX, Bai SM, Feng LL, Bie SY, Zeng B, Zheng J, Zeng GD, Feng WX, Wan XB, Fan XJ. RAP80 phase separation at DNA double-strand break promotes BRCA1 recruitment. Nucleic Acids Res 2023; 51:9733-9747. [PMID: 37638744 PMCID: PMC10570032 DOI: 10.1093/nar/gkad686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 07/29/2023] [Accepted: 08/17/2023] [Indexed: 08/29/2023] Open
Abstract
RAP80 has been characterized as a component of the BRCA1-A complex and is responsible for the recruitment of BRCA1 to DNA double-strand breaks (DSBs). However, we and others found that the recruitment of RAP80 and BRCA1 were not absolutely temporally synchronized, indicating that other mechanisms, apart from physical interaction, might be implicated. Recently, liquid-liquid phase separation (LLPS) has been characterized as a novel mechanism for the organization of key signaling molecules to drive their particular cellular functions. Here, we characterized that RAP80 LLPS at DSB was required for RAP80-mediated BRCA1 recruitment. Both cellular and in vitro experiments showed that RAP80 phase separated at DSB, which was ascribed to a highly disordered region (IDR) at its N-terminal. Meanwhile, the Lys63-linked poly-ubiquitin chains that quickly formed after DSBs occur, strongly enhanced RAP80 phase separation and were responsible for the induction of RAP80 condensation at the DSB site. Most importantly, abolishing the condensation of RAP80 significantly suppressed the formation of BRCA1 foci, encovering a pivotal role of RAP80 condensates in BRCA1 recruitment and radiosensitivity. Together, our study disclosed a new mechanism underlying RAP80-mediated BRCA1 recruitment, which provided new insight into the role of phase separation in DSB repair.
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Affiliation(s)
- Caolitao Qin
- Henan Provincial Key Laboratory of Radiation Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
- Department of Radiation Oncology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, P.R. China
- GuangDong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, P.R. China
| | - Yun-Long Wang
- Henan Provincial Key Laboratory of Radiation Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
- Department of Radiation Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
- Department of Radiation Oncology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, P.R. China
| | - Jin-Ying Zhou
- Henan Provincial Key Laboratory of Radiation Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
- Department of Radiation Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
| | - Jie Shi
- Department of Radiation Oncology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, P.R. China
- GuangDong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, P.R. China
| | - Wan-Wen Zhao
- Department of Radiation Oncology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, P.R. China
- GuangDong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, P.R. China
| | - Ya-Xi Zhu
- GuangDong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, P.R. China
- Department of Pathology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, P.R. China
| | - Shao-Mei Bai
- GuangDong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, P.R. China
- Department of Pathology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, P.R. China
| | - Li-Li Feng
- Department of Radiation Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
- Department of Radiation Oncology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, P.R. China
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong 510655, P.R. China
| | - Shu-Ying Bie
- Henan Provincial Key Laboratory of Radiation Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
- GuangDong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, P.R. China
- Department of Pathology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, P.R. China
| | - Bing Zeng
- GuangDong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, P.R. China
- Department of Gastroenterology, Hernia and Abdominal Wall Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, P.R. China
| | - Jian Zheng
- Department of Radiation Oncology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, P.R. China
- GuangDong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, P.R. China
| | - Guang-Dong Zeng
- Department of Radiation Oncology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, P.R. China
- GuangDong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, P.R. China
| | - Wei-Xing Feng
- Department of Radiation Oncology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, P.R. China
- GuangDong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, P.R. China
| | - Xiang-Bo Wan
- Henan Provincial Key Laboratory of Radiation Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
- Department of Radiation Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
- Department of Radiation Oncology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, P.R. China
| | - Xin-Juan Fan
- Henan Provincial Key Laboratory of Radiation Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
- GuangDong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, P.R. China
- Department of Pathology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, P.R. China
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7
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Sinzger-D’Angelo M, Startceva S, Koeppl H. Bye bye, linearity, bye: quantification of the mean for linear CRNs in a random environment. J Math Biol 2023; 87:43. [PMID: 37573263 PMCID: PMC10423146 DOI: 10.1007/s00285-023-01973-x] [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: 08/26/2022] [Revised: 07/04/2023] [Accepted: 07/22/2023] [Indexed: 08/14/2023]
Abstract
Molecular reactions within a cell are inherently stochastic, and cells often differ in morphological properties or interact with a heterogeneous environment. Consequently, cell populations exhibit heterogeneity both due to these intrinsic and extrinsic causes. Although state-of-the-art studies that focus on dissecting this heterogeneity use single-cell measurements, the bulk data that shows only the mean expression levels is still in routine use. The fingerprint of the heterogeneity is present also in bulk data, despite being hidden from direct measurement. In particular, this heterogeneity can affect the mean expression levels via bimolecular interactions with low-abundant environment species. We make this statement rigorous for the class of linear reaction systems that are embedded in a discrete state Markov environment. The analytic expression that we provide for the stationary mean depends on the reaction rate constants of the linear subsystem, as well as the generator and stationary distribution of the Markov environment. We demonstrate the effect of the environment on the stationary mean. Namely, we show how the heterogeneous case deviates from the quasi-steady state (Q.SS) case when the embedded system is fast compared to the environment.
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Affiliation(s)
- Mark Sinzger-D’Angelo
- Electrical Engineering and Information Technology, Technische Universität Darmstadt, Darmstadt, Germany
- Centre for Synthetic Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | - Sofia Startceva
- Electrical Engineering and Information Technology, Technische Universität Darmstadt, Darmstadt, Germany
- Centre for Synthetic Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | - Heinz Koeppl
- Electrical Engineering and Information Technology, Technische Universität Darmstadt, Darmstadt, Germany
- Centre for Synthetic Biology, Technische Universität Darmstadt, Darmstadt, Germany
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8
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Liu Z, Qin Z, Liu Y, Xia X, He L, Chen N, Hu X, Peng X. Liquid‒liquid phase separation: roles and implications in future cancer treatment. Int J Biol Sci 2023; 19:4139-4156. [PMID: 37705755 PMCID: PMC10496506 DOI: 10.7150/ijbs.81521] [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] [Received: 12/04/2022] [Accepted: 07/23/2023] [Indexed: 09/15/2023] Open
Abstract
Liquid‒liquid phase separation (LLPS) is a phenomenon driven by weak interactions between biomolecules, such as proteins and nucleic acids, that leads to the formation of distinct liquid-like condensates. Through LLPS, membraneless condensates are formed, selectively concentrating specific proteins while excluding other molecules to maintain normal cellular functions. Emerging evidence shows that cancer-related mutations cause aberrant condensate assembly, resulting in disrupted signal transduction, impaired DNA repair, and abnormal chromatin organization and eventually contributing to tumorigenesis. The objective of this review is to summarize recent advancements in understanding the potential implications of LLPS in the contexts of cancer progression and therapeutic interventions. By interfering with LLPS, it may be possible to restore normal cellular processes and inhibit tumor progression. The underlying mechanisms and potential drug targets associated with LLPS in cancer are discussed, shedding light on promising opportunities for novel therapeutic interventions.
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Affiliation(s)
- Zheran Liu
- Department of Biotherapy and National Clinical Research Center for Geriatrics, Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Zijian Qin
- Department of Biotherapy and National Clinical Research Center for Geriatrics, Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Yingtong Liu
- Chengdu University of Traditional Chinese Medicine, Chengdu 610041, Sichuan, China
| | - Xi Xia
- Shanghai ETERN Biopharma Co., Ltd., Shanghai, China
| | - Ling He
- Department of Biotherapy and National Clinical Research Center for Geriatrics, Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Na Chen
- School of Pharmacy, Chengdu Medical College, Xindu Avenue No 783, Chengdu, 610500, Sichuan Province, China
| | - Xiaolin Hu
- West China School of Nursing, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Xingchen Peng
- Department of Biotherapy and National Clinical Research Center for Geriatrics, Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
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9
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Ramirez DA, Hough LE, Shirts MR. Coiled-coil domains are sufficient to drive liquid-liquid phase separation of proteins in molecular models. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.31.543124. [PMID: 37398035 PMCID: PMC10312653 DOI: 10.1101/2023.05.31.543124] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Liquid-liquid phase separation (LLPS) is thought to be a main driving force in the formation of membraneless organelles. Examples of such organelles include the centrosome, central spindle, and stress granules. Recently, it has been shown that coiled-coil (CC) proteins, such as the centrosomal proteins pericentrin, spd-5, and centrosomin, might be capable of LLPS. CC domains have physical features that could make them the drivers of LLPS, but it is unknown if they play a direct role in the process. We developed a coarse-grained simulation framework for investigating the LLPS propensity of CC proteins, in which interactions which support LLPS arise solely from CC domains. We show, using this framework, that the physical features of CC domains are sufficient to drive LLPS of proteins. The framework is specifically designed to investigate how the number of CC domains, as well as multimerization state of CC domains, can affect LLPS. We show that small model proteins with as few as two CC domains can phase separate. Increasing the number of CC domains up to four per protein can somewhat increase LLPS propensity. We demonstrate that trimer-forming and tetramer-forming CC domains have a dramatically higher LLPS propensity than dimer-forming coils, which shows that multimerization state has a greater effect on LLPS than the number of CC domains per protein. These data support the hypothesis of CC domains as drivers of protein LLPS, and has implications in future studies to identify the LLPS-driving regions of centrosomal and central spindle proteins.
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Affiliation(s)
| | - Loren E. Hough
- Department of Physics and BioFrontiers Institute, University of Colorado Boulder, Boulder CO, 80309
| | - Michael R. Shirts
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder CO, 80309
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10
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Ouyang X, Wang X, Li P, Huang Q, Zhou L, Li J, Gao L, Sun Q, Chai F, Guo S, Zhou Z, Liu X, Dai L, Cheng W, Ren H. Bacterial effector restricts liquid-liquid phase separation of ZPR1 to antagonize host UPR ER. Cell Rep 2023; 42:112700. [PMID: 37379216 DOI: 10.1016/j.celrep.2023.112700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 04/29/2023] [Accepted: 06/09/2023] [Indexed: 06/30/2023] Open
Abstract
How pathogens manipulate host UPRER to mediate immune evasion is largely unknown. Here, we identify the host zinc finger protein ZPR1 as an interacting partner of the enteropathogenic E. coli (EPEC) effector NleE using proximity-enabled protein crosslinking. We show that ZPR1 assembles via liquid-liquid phase separation (LLPS) in vitro and regulates CHOP-mediated UPRER at the transcriptional level. Interestingly, in vitro studies show that the ZPR1 binding ability with K63-ubiquitin chains, which promotes LLPS of ZPR1, is disrupted by NleE. Further analyses indicate that EPEC restricts host UPRER pathways at the transcription level in a NleE-ZPR1 cascade-dependent manner. Together, our study reveals the mechanism by which EPEC interferes with CHOP-UPRER via regulating ZPR1 to help pathogens escape host defense.
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Affiliation(s)
- Xiaoxiao Ouyang
- Department of Pulmonary and Critical Care, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Xueyun Wang
- Department of Pulmonary and Critical Care, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Pan Li
- Department of Pulmonary and Critical Care, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Qin Huang
- Department of Pulmonary and Critical Care, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Li Zhou
- Department of Pulmonary and Critical Care, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Jingxiang Li
- Department of Pulmonary and Critical Care, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Li Gao
- Department of General Practice and National Clinical Research Center for Geriatrics, State Key Laboratory of Biotherapy, West China Hospital, and Sichuan University, Chengdu 610041, China
| | - Qi Sun
- Department of Pulmonary and Critical Care, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Fangni Chai
- Department of Pulmonary and Critical Care, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Shupan Guo
- Department of Pulmonary and Critical Care, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Zhihui Zhou
- Department of Pulmonary and Critical Care, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Xin Liu
- Department of Pulmonary and Critical Care, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Lunzhi Dai
- Department of General Practice and National Clinical Research Center for Geriatrics, State Key Laboratory of Biotherapy, West China Hospital, and Sichuan University, Chengdu 610041, China
| | - Wei Cheng
- Department of Pulmonary and Critical Care, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China; Collaborative Innovation Center of Biotherapy, Sichuan University West China Hospital, Chengdu, Sichuan 610041, China
| | - Haiyan Ren
- Department of Pulmonary and Critical Care, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China; Collaborative Innovation Center of Biotherapy, Sichuan University West China Hospital, Chengdu, Sichuan 610041, China.
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11
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Waite KA, Vontz G, Lee SY, Roelofs J. Proteasome condensate formation is driven by multivalent interactions with shuttle factors and K48-linked ubiquitin chains. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.25.546446. [PMID: 37425862 PMCID: PMC10326979 DOI: 10.1101/2023.06.25.546446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Stress conditions can cause the relocalization of proteasomes to condensates in yeast and mammalian cells. The interactions that facilitate the formation of proteasome condensates, however, are unclear. Here, we show that the formation of proteasome condensates in yeast depends on long K48-linked ubiquitin chains together with the proteasome shuttle factors Rad23 and Dsk2. These shuttle factors colocalize to these condensates. Strains deleted for the third shuttle factor gene, DDI1 , show proteasome condensates in the absence of cellular stress, consistent with the accumulation of substrates with long K48-linked ubiquitin chains that accumulate in this mutant. We propose a model where the long K48-linked ubiquitin chains function as a scaffold for the ubiquitin binding domains of the shuttle factors and the proteasome, allowing for the multivalent interactions that further drive condensate formation. Indeed, we determined different intrinsic ubiquitin receptors of the proteasome (Rpn1, Rpn10, and Rpn13) are critical under different condensate inducing conditions. In all, our data support a model where the cellular accumulation of substrates with long ubiquitin chains, potentially due to reduced cellular energy, allows for proteasome condensate formation. This suggests that proteasome condensates are not simply for proteasome storage, but function to sequester soluble ubiquitinated substrates together with inactive proteasomes. Significance Stress conditions can cause the relocalization of proteasomes to condensates in yeast as well as mammalian cells. Our work shows that the formation of proteasome condensates in yeast depends on long K48-linked ubiquitin chains, the proteasome binding shuttle factors Rad23 and Dsk2 and proteasome intrinsic ubiquitin receptors. Here, different receptors are critical for different condensate inducers. These results indicate distinct condensates can form with specific functionality. Our identification of key factors involved in the process is crucial for understanding the function of proteasome relocalization to condensates. We propose that cellular accumulation of substrates with long ubiquitin chains results in the formation of condensates comprising those ubiquitinated substrates, proteasomes, and proteasome shuttle factors, where the ubiquitin chains serve as the scaffold for condensate formation.
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12
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Hou XN, Tang C. The pros and cons of ubiquitination on the formation of protein condensates. Acta Biochim Biophys Sin (Shanghai) 2023; 55:1084-1098. [PMID: 37294105 PMCID: PMC10423694 DOI: 10.3724/abbs.2023096] [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] [Received: 12/30/2022] [Accepted: 03/19/2023] [Indexed: 06/10/2023] Open
Abstract
Ubiquitination, a post-translational modification that attaches one or more ubiquitin (Ub) molecules to another protein, plays a crucial role in the phase-separation processes. Ubiquitination can modulate the formation of membrane-less organelles in two ways. First, a scaffold protein drives phase separation, and Ub is recruited to the condensates. Second, Ub actively phase-separates through the interactions with other proteins. Thus, the role of ubiquitination and the resulting polyUb chains ranges from bystanders to active participants in phase separation. Moreover, long polyUb chains may be the primary driving force for phase separation. We further discuss that the different roles can be determined by the lengths and linkages of polyUb chains which provide preorganized and multivalent binding platforms for other client proteins. Together, ubiquitination adds a new layer of regulation for the flow of material and information upon cellular compartmentalization of proteins.
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Affiliation(s)
- Xue-Ni Hou
- Beijing National Laboratory for Molecular SciencesCollege of Chemistry and Molecular EngineeringPeking UniversityBeijing100871China
| | - Chun Tang
- Beijing National Laboratory for Molecular SciencesCollege of Chemistry and Molecular EngineeringPeking UniversityBeijing100871China
- Center for Quantitate BiologyPKU-Tsinghua Center for Life ScienceAcademy for Advanced Interdisciplinary StudiesPeking UniversityBeijing100871China
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13
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Furuhata T, Devadasan Racheal PA, Murayama I, Toyoda U, Okamoto A. One-Pot, Photocontrolled Enzymatic Assembly of the Structure-Defined Heterotypic Polyubiquitin Chain. J Am Chem Soc 2023; 145:11690-11700. [PMID: 37200097 DOI: 10.1021/jacs.3c01912] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Heterotypic polyubiquitins are an emerging class of polyubiquitins that have attracted interest because of their potential diversity of structures and physiological functions. There is an increasing demand for structure-defined synthesis of heterotypic chains to investigate the topological factors underlying the intracellular signals that are characteristically mediated by the heterotypic chain. However, the applicability of chemical and enzymatic polyubiquitin synthesis developed to date has been limited by laborious rounds of ligation and purification or by a lack of modularity of the chain structure with respect to the length and the branch position. Here, we established a one-pot, photocontrolled synthesis of structurally defined heterotypic polyubiquitin chains. We designed ubiquitin derivatives with a photolabile protecting group at a lysine residue used for polymerization. Repetitive cycles of linkage-specific enzymatic elongation and photoinduced deprotection of the protected ubiquitin units enabled stepwise addition of ubiquitins with appropriate functionalities to control the length and branching positions. The positional control of branching was achieved without isolation of intermediates, allowing one-pot synthesis of K63 triubiqutin chains and a K63/K48 heterotypic tetraubiquitin chain with defined branching positions. The present study provides a chemical platform for the efficient construction of long polyubiquitin chains with defined branch structures that will facilitate the understanding of the essential relationships between functions and structures of the heterotypic chain that have hitherto been overlooked.
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Affiliation(s)
- Takafumi Furuhata
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Phebee Angeline Devadasan Racheal
- Department of Advanced Interdisciplinary Studies, Graduate School of Engineering, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Iori Murayama
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Usano Toyoda
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Akimitsu Okamoto
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
- Department of Advanced Interdisciplinary Studies, Graduate School of Engineering, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
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14
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Kampmeyer C, Grønbæk-Thygesen M, Oelerich N, Tatham MH, Cagiada M, Lindorff-Larsen K, Boomsma W, Hofmann K, Hartmann-Petersen R. Lysine deserts prevent adventitious ubiquitylation of ubiquitin-proteasome components. Cell Mol Life Sci 2023; 80:143. [PMID: 37160462 PMCID: PMC10169902 DOI: 10.1007/s00018-023-04782-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 03/15/2023] [Accepted: 04/17/2023] [Indexed: 05/11/2023]
Abstract
In terms of its relative frequency, lysine is a common amino acid in the human proteome. However, by bioinformatics we find hundreds of proteins that contain long and evolutionarily conserved stretches completely devoid of lysine residues. These so-called lysine deserts show a high prevalence in intrinsically disordered proteins with known or predicted functions within the ubiquitin-proteasome system (UPS), including many E3 ubiquitin-protein ligases and UBL domain proteasome substrate shuttles, such as BAG6, RAD23A, UBQLN1 and UBQLN2. We show that introduction of lysine residues into the deserts leads to a striking increase in ubiquitylation of some of these proteins. In case of BAG6, we show that ubiquitylation is catalyzed by the E3 RNF126, while RAD23A is ubiquitylated by E6AP. Despite the elevated ubiquitylation, mutant RAD23A appears stable, but displays a partial loss of function phenotype in fission yeast. In case of UBQLN1 and BAG6, introducing lysine leads to a reduced abundance due to proteasomal degradation of the proteins. For UBQLN1 we show that arginine residues within the lysine depleted region are critical for its ability to form cytosolic speckles/inclusions. We propose that selective pressure to avoid lysine residues may be a common evolutionary mechanism to prevent unwarranted ubiquitylation and/or perhaps other lysine post-translational modifications. This may be particularly relevant for UPS components as they closely and frequently encounter the ubiquitylation machinery and are thus more susceptible to nonspecific ubiquitylation.
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Affiliation(s)
- Caroline Kampmeyer
- Department of Biology, The Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Copenhagen, Denmark
| | - Martin Grønbæk-Thygesen
- Department of Biology, The Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Copenhagen, Denmark
| | - Nicole Oelerich
- Institute for Genetics, University of Cologne, Cologne, Germany
| | - Michael H Tatham
- Centre for Gene Regulation and Expression, Sir James Black Centre, School of Life Sciences, University of Dundee, Dundee, UK
| | - Matteo Cagiada
- Department of Biology, The Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Copenhagen, Denmark
| | - Kresten Lindorff-Larsen
- Department of Biology, The Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Copenhagen, Denmark
| | - Wouter Boomsma
- Department of Computer Science, University of Copenhagen, Copenhagen, Denmark.
| | - Kay Hofmann
- Institute for Genetics, University of Cologne, Cologne, Germany.
| | - Rasmus Hartmann-Petersen
- Department of Biology, The Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Copenhagen, Denmark.
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15
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Galagedera SKK, Dao TP, Enos SE, Chaudhuri A, Schmit JD, Castañeda CA. Decoding optimal ligand design for multicomponent condensates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.13.532222. [PMID: 36993708 PMCID: PMC10054939 DOI: 10.1101/2023.03.13.532222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Biomolecular condensates form via multivalent interactions among key macromolecules and are regulated through ligand binding and/or post-translational modifications. One such modification is ubiquitination, the covalent addition of ubiquitin (Ub) or polyubiquitin chains to target macromolecules for various cellular processes. Specific interactions between polyubiquitin chains and partner proteins, including hHR23B, NEMO, and UBQLN2, regulate condensate assembly or disassembly. Here, we used a library of designed polyubiquitin hubs and UBQLN2 as model systems for determining the driving forces of ligand-mediated phase transitions. Perturbations to the UBQLN2-binding surface of Ub or deviations from the optimal spacing between Ub units reduce the ability of hubs to modulate UBQLN2 phase behavior. By developing an analytical model that accurately described the effects of different hubs on UBQLN2 phase diagrams, we determined that introduction of Ub to UBQLN2 condensates incurs a significant inclusion energetic penalty. This penalty antagonizes the ability of polyUb hubs to scaffold multiple UBQLN2 molecules and cooperatively amplify phase separation. Importantly, the extent to which polyubiquitin hubs can promote UBQLN2 phase separation are encoded in the spacings between Ub units as found for naturally-occurring chains of different linkages and designed chains of different architectures, thus illustrating how the ubiquitin code regulates functionality via the emergent properties of the condensate. We expect our findings to extend to other condensates necessitating the consideration of ligand properties, including concentration, valency, affinity, and spacing between binding sites in studies and designs of condensates.
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Affiliation(s)
| | - Thuy P. Dao
- Departments of Biology and Chemistry, Syracuse University, Syracuse, NY 13244, USA
| | - Suzanne E. Enos
- Departments of Biology and Chemistry, Syracuse University, Syracuse, NY 13244, USA
| | - Antara Chaudhuri
- Departments of Biology and Chemistry, Syracuse University, Syracuse, NY 13244, USA
| | - Jeremy D. Schmit
- Department of Physics, Kansas State University, Manhattan, KS 66506, USA
| | - Carlos A. Castañeda
- Departments of Biology and Chemistry, Syracuse University, Syracuse, NY 13244, USA
- Interdisciplinary Neuroscience Program, Syracuse University, Syracuse, NY 13244, USA
- BioInspired Institute, Syracuse University, Syracuse, NY 13244, USA
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16
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Goel S, Oliva R, Jeganathan S, Bader V, Krause LJ, Kriegler S, Stender ID, Christine CW, Nakamura K, Hoffmann JE, Winter R, Tatzelt J, Winklhofer KF. Linear ubiquitination induces NEMO phase separation to activate NF-κB signaling. Life Sci Alliance 2023; 6:e202201607. [PMID: 36720498 PMCID: PMC9889916 DOI: 10.26508/lsa.202201607] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 01/09/2023] [Accepted: 01/09/2023] [Indexed: 02/02/2023] Open
Abstract
The NF-κB essential modulator NEMO is the core regulatory component of the inhibitor of κB kinase complex, which is a critical checkpoint in canonical NF-κB signaling downstream of innate and adaptive immune receptors. In response to various stimuli, such as TNF or IL-1β, NEMO binds to linear or M1-linked ubiquitin chains generated by LUBAC, promoting its oligomerization and subsequent activation of the associated kinases. Here we show that M1-ubiquitin chains induce phase separation of NEMO and the formation of NEMO assemblies in cells after exposure to IL-1β. Phase separation is promoted by both binding of NEMO to linear ubiquitin chains and covalent linkage of M1-ubiquitin to NEMO and is essential but not sufficient for its phase separation. Supporting the functional relevance of NEMO phase separation in signaling, a pathogenic NEMO mutant, which is impaired in both binding and linkage to linear ubiquitin chains, does not undergo phase separation and is defective in mediating IL-1β-induced NF-κB activation.
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Affiliation(s)
- Simran Goel
- Department Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
| | - Rosario Oliva
- Physical Chemistry I-Biophysical Chemistry, Department of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
| | - Sadasivam Jeganathan
- Department Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
| | - Verian Bader
- Department Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
- Department Biochemistry of Neurodegenerative Diseases, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
| | - Laura J Krause
- Department Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
- RESOLV Cluster of Excellence, Ruhr University Bochum, Bochum, Germany
| | - Simon Kriegler
- Physical Chemistry I-Biophysical Chemistry, Department of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
| | - Isabelle D Stender
- Protein Chemistry Facility, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | | | - Ken Nakamura
- Department of Neurology, UCSF, San Francisco, CA, USA
- Gladstone Institute of Neurological Disease, Gladstone Institutes, San Francisco, CA, USA
| | - Jan-Erik Hoffmann
- Protein Chemistry Facility, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Roland Winter
- Physical Chemistry I-Biophysical Chemistry, Department of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
- RESOLV Cluster of Excellence, Ruhr University Bochum, Bochum, Germany
| | - Jörg Tatzelt
- RESOLV Cluster of Excellence, Ruhr University Bochum, Bochum, Germany
- Department Biochemistry of Neurodegenerative Diseases, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
| | - Konstanze F Winklhofer
- Department Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
- RESOLV Cluster of Excellence, Ruhr University Bochum, Bochum, Germany
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17
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Mohanty P, Kapoor U, Sundaravadivelu Devarajan D, Phan TM, Rizuan A, Mittal J. Principles Governing the Phase Separation of Multidomain Proteins. Biochemistry 2022; 61:2443-2455. [PMID: 35802394 PMCID: PMC9669140 DOI: 10.1021/acs.biochem.2c00210] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
A variety of membraneless organelles, often termed "biological condensates", play an important role in the regulation of cellular processes such as gene transcription, translation, and protein quality control. On the basis of experimental and theoretical investigations, liquid-liquid phase separation (LLPS) has been proposed as a possible mechanism for the origin of biological condensates. LLPS requires multivalent macromolecules that template the formation of long-range, intermolecular interaction networks and results in the formation of condensates with defined composition and material properties. Multivalent interactions driving LLPS exhibit a wide range of modes from highly stereospecific to nonspecific and involve both folded and disordered regions. Multidomain proteins serve as suitable macromolecules for promoting phase separation and achieving disparate functions due to their potential for multivalent interactions and regulation. Here, we aim to highlight the influence of the domain architecture and interdomain interactions on the phase separation of multidomain protein condensates. First, the general principles underlying these interactions are illustrated on the basis of examples of multidomain proteins that are predominantly associated with nucleic acid binding and protein quality control and contain both folded and disordered regions. Next, the examples showcase how LLPS properties of folded and disordered regions can be leveraged to engineer multidomain constructs that form condensates with the desired assembly and functional properties. Finally, we highlight the need for improvements in coarse-grained computational models that can provide molecular-level insights into multidomain protein condensates in conjunction with experimental efforts.
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Affiliation(s)
- Priyesh Mohanty
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843
| | - Utkarsh Kapoor
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843
| | | | - Tien Minh Phan
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843
| | - Azamat Rizuan
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843
| | - Jeetain Mittal
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843
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18
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Crosstalk between Biomolecular Condensates and Proteostasis. Cells 2022; 11:cells11152415. [PMID: 35954258 PMCID: PMC9368065 DOI: 10.3390/cells11152415] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 07/19/2022] [Accepted: 07/21/2022] [Indexed: 12/23/2022] Open
Abstract
Proper homeostasis of the proteome, referred to as proteostasis, is maintained by chaperone-dependent refolding of misfolded proteins and by protein degradation via the ubiquitin-proteasome system and the autophagic machinery. This review will discuss a crosstalk between biomolecular condensates and proteostasis, whereby the crowding of proteostasis factors into macromolecular assemblies is often established by phase separation of membraneless biomolecular condensates. Specifically, ubiquitin and other posttranslational modifications come into play as agents of phase separation, essential for the formation of condensates and for ubiquitin-proteasome system activity. Furthermore, an intriguing connection associates malfunction of the same pathways to the accumulation of misfolded and ubiquitinated proteins in aberrant condensates, the formation of protein aggregates, and finally, to the pathogenesis of neurodegenerative diseases. The crosstalk between biomolecular condensates and proteostasis is an emerging theme in cellular and disease biology and further studies will focus on delineating specific molecular pathways involved in the pathogenesis of amyotrophic lateral sclerosis (ALS) and other neurodegenerative diseases.
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19
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Dao TP, Yang Y, Presti MF, Cosgrove MS, Hopkins JB, Ma W, Loh SN, Castañeda CA. Mechanistic insights into enhancement or inhibition of phase separation by different polyubiquitin chains. EMBO Rep 2022; 23:e55056. [PMID: 35762418 PMCID: PMC9346500 DOI: 10.15252/embr.202255056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 06/06/2022] [Accepted: 06/08/2022] [Indexed: 12/03/2022] Open
Abstract
Ubiquitin‐binding shuttle UBQLN2 mediates crosstalk between proteasomal degradation and autophagy, likely via interactions with K48‐ and K63‐linked polyubiquitin chains, respectively. UBQLN2 comprises self‐associating regions that drive its homotypic liquid–liquid phase separation (LLPS). Specific interactions between one of these regions and ubiquitin inhibit UBQLN2 LLPS. Here, we show that, unlike ubiquitin, the effects of multivalent polyubiquitin chains on UBQLN2 LLPS are highly dependent on chain types. Specifically, K11‐Ub4 and K48‐Ub4 chains generally inhibit UBQLN2 LLPS, whereas K63‐Ub4, M1‐Ub4 chains, and a designed tetrameric ubiquitin construct significantly enhance LLPS. We demonstrate that these opposing effects stem from differences in chain conformations but not in affinities between chains and UBQLN2. Chains with extended conformations and increased accessibility to the ubiquitin‐binding surface promote UBQLN2 LLPS by enabling a switch between homotypic to partially heterotypic LLPS that is driven by both UBQLN2 self‐interactions and interactions between multiple UBQLN2 units with each polyubiquitin chain. Our study provides mechanistic insights into how the structural and conformational properties of polyubiquitin chains contribute to heterotypic LLPS with ubiquitin‐binding shuttles and adaptors.
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Affiliation(s)
- Thuy P Dao
- Departments of Biology and Chemistry Syracuse University Syracuse NY USA
| | - Yiran Yang
- Department of Chemistry Syracuse University Syracuse NY USA
| | - Maria F Presti
- Department of Biochemistry and Molecular Biology SUNY Upstate Medical University Syracuse NY USA
| | - Michael S Cosgrove
- Department of Biochemistry and Molecular Biology SUNY Upstate Medical University Syracuse NY USA
| | - Jesse B Hopkins
- The Biophysics Collaborative Access Team (BioCAT), Department of Biological Sciences Illinois Institute of Technology Chicago IL USA
| | - Weikang Ma
- The Biophysics Collaborative Access Team (BioCAT), Department of Biological Sciences Illinois Institute of Technology Chicago IL USA
| | - Stewart N Loh
- Department of Biochemistry and Molecular Biology SUNY Upstate Medical University Syracuse NY USA
| | - Carlos A Castañeda
- Departments of Biology and Chemistry Syracuse University Syracuse NY USA
- Interdisciplinary Neuroscience Program Syracuse University Syracuse NY USA
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20
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Du M, Ea CK, Fang Y, Chen ZJ. Liquid phase separation of NEMO induced by polyubiquitin chains activates NF-κB. Mol Cell 2022; 82:2415-2426.e5. [PMID: 35477005 PMCID: PMC9402427 DOI: 10.1016/j.molcel.2022.03.037] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 02/03/2022] [Accepted: 03/29/2022] [Indexed: 11/15/2022]
Abstract
The NF-κB essential modulator (NEMO) is a regulatory subunit of the IκB kinase (IKK) complex that phosphorylates the NF-κB inhibitors IκBs. NEMO mediates IKK activation by binding to polyubiquitin chains (polyUb). Here we show that Lys63(K63)-linked or linear polyUb binding to NEMO robustly induced the formation of liquid-like droplets in which IKK was activated. This liquid phase separation of NEMO was driven by multivalent interactions between NEMO and polyUb. Both the NEMO-ubiquitin-binding (NUB) domain and the zinc finger (ZF) domain of NEMO mediated binding to polyUb and contributed to NEMO phase separation and IKK activation in cells. Moreover, NEMO mutations associated with human immunodeficiency impaired its phase separation. These results demonstrate that polyUb activates IKK and NF-κB signaling by promoting the phase separation of NEMO.
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Affiliation(s)
- Mingjian Du
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA; Center for Inflammation Research, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA
| | - Chee-Kwee Ea
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA; Center for Inflammation Research, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA
| | - Yan Fang
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA; Center for Inflammation Research, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA
| | - Zhijian J Chen
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA; Center for Inflammation Research, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA; Howard Hughes Medical Institute, 4000 Jones Bridge Rd., Chevy Chase, MD 20815-6789.
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21
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Mohan HM, Trzeciakiewicz H, Pithadia A, Crowley EV, Pacitto R, Safren N, Trotter B, Zhang C, Zhou X, Zhang Y, Basrur V, Paulson HL, Sharkey LM. RTL8 promotes nuclear localization of UBQLN2 to subnuclear compartments associated with protein quality control. Cell Mol Life Sci 2022; 79:176. [PMID: 35247097 PMCID: PMC9376861 DOI: 10.1007/s00018-022-04170-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 01/17/2022] [Accepted: 01/25/2022] [Indexed: 11/24/2022]
Abstract
The brain-expressed ubiquilins (UBQLNs) 1, 2 and 4 are a family of ubiquitin adaptor proteins that participate broadly in protein quality control (PQC) pathways, including the ubiquitin proteasome system (UPS). One family member, UBQLN2, has been implicated in numerous neurodegenerative diseases including ALS/FTD. UBQLN2 typically resides in the cytoplasm but in disease can translocate to the nucleus, as in Huntington's disease where it promotes the clearance of mutant Huntingtin. How UBQLN2 translocates to the nucleus and clears aberrant nuclear proteins, however, is not well understood. In a mass spectrometry screen to discover UBQLN2 interactors, we identified a family of small (13 kDa), highly homologous uncharacterized proteins, RTL8, and confirmed the interaction between UBQLN2 and RTL8 both in vitro using recombinant proteins and in vivo using mouse brain tissue. Under endogenous and overexpressed conditions, RTL8 localizes to nucleoli. When co-expressed with UBQLN2, RTL8 promotes nuclear translocation of UBQLN2. RTL8 also facilitates UBQLN2's nuclear translocation during heat shock. UBQLN2 and RTL8 colocalize within ubiquitin-enriched subnuclear structures containing PQC components. The robust effect of RTL8 on the nuclear translocation and subnuclear localization of UBQLN2 does not extend to the other brain-expressed ubiquilins, UBQLN1 and UBQLN4. Moreover, compared to UBQLN1 and UBQLN4, UBQLN2 preferentially stabilizes RTL8 levels in human cell lines and in mouse brain, supporting functional heterogeneity among UBQLNs. As a novel UBQLN2 interactor that recruits UBQLN2 to specific nuclear compartments, RTL8 may regulate UBQLN2 function in nuclear protein quality control.
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Affiliation(s)
- Harihar Milaganur Mohan
- Department of Neurology, University of Michigan, Ann Arbor, MI, 48109-2200, USA.,Graduate Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI, 48109-2200, USA
| | | | - Amit Pithadia
- Department of Neurology, University of Michigan, Ann Arbor, MI, 48109-2200, USA
| | - Emily V Crowley
- Department of Neurology, University of Michigan, Ann Arbor, MI, 48109-2200, USA
| | - Regina Pacitto
- Department of Neurology, University of Michigan, Ann Arbor, MI, 48109-2200, USA
| | - Nathaniel Safren
- Department of Neurology, University of Michigan, Ann Arbor, MI, 48109-2200, USA.,Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Bryce Trotter
- Department of Neurology, University of Michigan, Ann Arbor, MI, 48109-2200, USA
| | - Chengxin Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109-2200, USA
| | - Xiaogen Zhou
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109-2200, USA
| | - Yang Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109-2200, USA
| | - Venkatesha Basrur
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Henry L Paulson
- Department of Neurology, University of Michigan, Ann Arbor, MI, 48109-2200, USA. .,Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI, 48109-2200, USA.
| | - Lisa M Sharkey
- Department of Neurology, University of Michigan, Ann Arbor, MI, 48109-2200, USA. .,Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI, 48109-2200, USA.
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22
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Michels JJ, Brzezinski M, Scheidt T, Lemke EA, Parekh SH. Role of Solvent Compatibility in the Phase Behavior of Binary Solutions of Weakly Associating Multivalent Polymers. Biomacromolecules 2022; 23:349-364. [PMID: 34866377 PMCID: PMC8753604 DOI: 10.1021/acs.biomac.1c01301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 11/23/2021] [Indexed: 11/29/2022]
Abstract
Condensate formation of biopolymer solutions, prominently those of various intrinsically disordered proteins (IDPs), is often driven by "sticky" interactions between associating residues, multivalently present along the polymer backbone. Using a ternary mean-field "stickers-and-spacers" model, we demonstrate that if sticker association is of the order of a few times the thermal energy, a delicate balance between specific binding and nonspecific polymer-solvent interactions gives rise to a particularly rich ternary phase behavior under physiological circumstances. For a generic system represented by a solution comprising multiassociative scaffold and client polymers, the difference in solvent compatibility between the polymers modulates the nature of isothermal liquid-liquid phase separation (LLPS) between associative and segregative. The calculations reveal regimes of dualistic phase behavior, where both types of LLPS occur within the same phase diagram, either associated with the presence of multiple miscibility gaps or a flip in the slope of the tie-lines belonging to a single coexistence region.
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Affiliation(s)
- Jasper J. Michels
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Mateusz Brzezinski
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Tom Scheidt
- Institute
for Molecular Biology, Johannes Gutenberg
University, Ackermannweg
4, 55128 Mainz, Germany
| | - Edward A. Lemke
- Institute
for Molecular Biology, Johannes Gutenberg
University, Ackermannweg
4, 55128 Mainz, Germany
| | - Sapun H. Parekh
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
- Department
of Biomedical Engineering, The University
of Texas at Austin, 107
West Dean Keeton Street Stop C0800, Austin, Texas 78712, United States
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23
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Spegg V, Altmeyer M. Biomolecular condensates at sites of DNA damage: More than just a phase. DNA Repair (Amst) 2021; 106:103179. [PMID: 34311273 PMCID: PMC7612016 DOI: 10.1016/j.dnarep.2021.103179] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/08/2021] [Accepted: 07/09/2021] [Indexed: 12/12/2022]
Abstract
Protein recruitment to DNA break sites is an integral part of the DNA damage response (DDR). Elucidation of the hierarchy and temporal order with which DNA damage sensors as well as repair and signaling factors assemble around chromosome breaks has painted a complex picture of tightly regulated macromolecular interactions that build specialized compartments to facilitate repair and maintenance of genome integrity. While many of the underlying interactions, e.g. between repair factors and damage-induced histone marks, can be explained by lock-and-key or induced fit binding models assuming fixed stoichiometries, structurally less well defined interactions, such as the highly dynamic multivalent interactions implicated in phase separation, also participate in the formation of multi-protein assemblies in response to genotoxic stress. Although much remains to be learned about these types of cooperative and highly dynamic interactions and their functional roles, the rapidly growing interest in material properties of biomolecular condensates and in concepts from polymer chemistry and soft matter physics to understand biological processes at different scales holds great promises. Here, we discuss nuclear condensates in the context of genome integrity maintenance, highlighting the cooperative potential between clustered stoichiometric binding and phase separation. Rather than viewing them as opposing scenarios, their combined effects can balance structural specificity with favorable physicochemical properties relevant for the regulation and function of multilayered nuclear condensates.
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Affiliation(s)
- Vincent Spegg
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
| | - Matthias Altmeyer
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland.
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24
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Hecw controls oogenesis and neuronal homeostasis by promoting the liquid state of ribonucleoprotein particles. Nat Commun 2021; 12:5488. [PMID: 34531401 PMCID: PMC8446043 DOI: 10.1038/s41467-021-25809-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 08/31/2021] [Indexed: 01/17/2023] Open
Abstract
Specialised ribonucleoprotein (RNP) granules are a hallmark of polarized cells, like neurons and germ cells. Among their main functions is the spatial and temporal modulation of the activity of specific mRNA transcripts that allow specification of primary embryonic axes. While RNPs composition and role are well established, their regulation is poorly defined. Here, we demonstrate that Hecw, a newly identified Drosophila ubiquitin ligase, is a key modulator of RNPs in oogenesis and neurons. Hecw depletion leads to the formation of enlarged granules that transition from a liquid to a gel-like state. Loss of Hecw activity results in defective oogenesis, premature aging and climbing defects associated with neuronal loss. At the molecular level, reduced ubiquitination of the Fmrp impairs its translational repressor activity, resulting in altered Orb expression in nurse cells and Profilin in neurons. Ribonucleoprotein (RNP) granules are responsible for mRNA transport and local translation required for neuronal and oocyte maturation. Here the authors show that loss of the Drosophila Ub ligase Hecw enlarges RNP granules, leads to a liquid to gel-like transition, and results in defective oogenesis and neuronal loss.
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25
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Yousefi R, Jevdokimenko K, Kluever V, Pacheu-Grau D, Fornasiero EF. Influence of Subcellular Localization and Functional State on Protein Turnover. Cells 2021; 10:cells10071747. [PMID: 34359917 PMCID: PMC8306977 DOI: 10.3390/cells10071747] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 07/02/2021] [Accepted: 07/07/2021] [Indexed: 12/14/2022] Open
Abstract
Protein homeostasis is an equilibrium of paramount importance that maintains cellular performance by preserving an efficient proteome. This equilibrium avoids the accumulation of potentially toxic proteins, which could lead to cellular stress and death. While the regulators of proteostasis are the machineries controlling protein production, folding and degradation, several other factors can influence this process. Here, we have considered two factors influencing protein turnover: the subcellular localization of a protein and its functional state. For this purpose, we used an imaging approach based on the pulse-labeling of 17 representative SNAP-tag constructs for measuring protein lifetimes. With this approach, we obtained precise measurements of protein turnover rates in several subcellular compartments. We also tested a selection of mutants modulating the function of three extensively studied proteins, the Ca2+ sensor calmodulin, the small GTPase Rab5a and the brain creatine kinase (CKB). Finally, we followed up on the increased lifetime observed for the constitutively active Rab5a (Q79L), and we found that its stabilization correlates with enlarged endosomes and increased interaction with membranes. Overall, our data reveal that both changes in protein localization and functional state are key modulators of protein turnover, and protein lifetime fluctuations can be considered to infer changes in cellular behavior.
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Affiliation(s)
- Roya Yousefi
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, 37073 Göttingen, Germany; (R.Y.); (K.J.); (V.K.)
- Department of Cellular Biochemistry, University Medical Center Göttingen, 37073 Göttingen, Germany;
| | - Kristina Jevdokimenko
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, 37073 Göttingen, Germany; (R.Y.); (K.J.); (V.K.)
| | - Verena Kluever
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, 37073 Göttingen, Germany; (R.Y.); (K.J.); (V.K.)
| | - David Pacheu-Grau
- Department of Cellular Biochemistry, University Medical Center Göttingen, 37073 Göttingen, Germany;
| | - Eugenio F. Fornasiero
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, 37073 Göttingen, Germany; (R.Y.); (K.J.); (V.K.)
- Correspondence:
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26
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Zheng T, Galagedera SKK, Castañeda CA. Previously uncharacterized interactions between the folded and intrinsically disordered domains impart asymmetric effects on UBQLN2 phase separation. Protein Sci 2021; 30:1467-1481. [PMID: 34029402 DOI: 10.1002/pro.4128] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 05/20/2021] [Accepted: 05/21/2021] [Indexed: 02/06/2023]
Abstract
Shuttle protein UBQLN2 functions in protein quality control (PQC) by binding to proteasomal receptors and ubiquitinated substrates via its N-terminal ubiquitin-like (UBL) and C-terminal ubiquitin-associated (UBA) domains, respectively. Between these two folded domains are low-complexity STI1-I and STI1-II regions, connected by disordered linkers. The STI1 regions bind other components, such as HSP70, that are important to the PQC functions of UBQLN2. We recently determined that the STI1-II region enables UBQLN2 to undergo liquid-liquid phase separation (LLPS) to form liquid droplets in vitro and biomolecular condensates in cells. However, how the interplay between the folded (UBL/UBA) domains and the intrinsically disordered regions mediates phase separation is largely unknown. Using engineered domain deletion constructs, we found that removing the UBA domain inhibits UBQLN2 LLPS while removing the UBL domain enhances LLPS, suggesting that UBA and UBL domains contribute asymmetrically in modulating UBQLN2 LLPS. To explain these differential effects, we interrogated the interactions that involve the UBA and UBL domains across the entire UBQLN2 molecule using nuclear magnetic resonance spectroscopy. To our surprise, aside from well-studied canonical UBL:UBA interactions, there also exist moderate interactions between the UBL and several disordered regions, including STI1-I and residues 555-570, the latter of which is a known contributor to UBQLN2 LLPS. Our findings are essential for the understanding of both the molecular driving forces of UBQLN2 LLPS and the effects of ligand binding to UBL, UBA, or disordered regions on the phase behavior and physiological functions of UBQLN2.
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Affiliation(s)
- Tongyin Zheng
- Department of Chemistry, Syracuse University, Syracuse, New York, USA
| | | | - Carlos A Castañeda
- Departments of Biology and Chemistry, Syracuse University, Syracuse, New York, USA.,Interdisciplinary Neuroscience Program, Syracuse University, Syracuse, New York, USA.,BioInspired Institute, Syracuse University, Syracuse, New York, USA
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27
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Lei L, Wu Z, Winklhofer KF. Protein quality control by the proteasome and autophagy: A regulatory role of ubiquitin and liquid-liquid phase separation. Matrix Biol 2021; 100-101:9-22. [DOI: 10.1016/j.matbio.2020.11.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 11/20/2020] [Accepted: 11/23/2020] [Indexed: 12/14/2022]
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28
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It's not just a phase; ubiquitination in cytosolic protein quality control. Biochem Soc Trans 2021; 49:365-377. [PMID: 33634825 PMCID: PMC7924994 DOI: 10.1042/bst20200694] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 02/01/2021] [Accepted: 02/02/2021] [Indexed: 02/04/2023]
Abstract
The accumulation of misfolded proteins is associated with numerous degenerative conditions, cancers and genetic diseases. These pathological imbalances in protein homeostasis (termed proteostasis), result from the improper triage and disposal of damaged and defective proteins from the cell. The ubiquitin-proteasome system is a key pathway for the molecular control of misfolded cytosolic proteins, co-opting a cascade of ubiquitin ligases to direct terminally damaged proteins to the proteasome via modification with chains of the small protein, ubiquitin. Despite the evidence for ubiquitination in this critical pathway, the precise complement of ubiquitin ligases and deubiquitinases that modulate this process remains under investigation. Whilst chaperones act as the first line of defence against protein misfolding, the ubiquitination machinery has a pivotal role in targeting terminally defunct cytosolic proteins for destruction. Recent work points to a complex assemblage of chaperones, ubiquitination machinery and subcellular quarantine as components of the cellular arsenal against proteinopathies. In this review, we examine the contribution of these pathways and cellular compartments to the maintenance of the cytosolic proteome. Here we will particularly focus on the ubiquitin code and the critical enzymes which regulate misfolded proteins in the cytosol, the molecular point of origin for many neurodegenerative and genetic diseases.
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