1
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Krakowczyk M, Lenkiewicz AM, Sitarz T, Malinska D, Borrero M, Mussulini BHM, Linke V, Szczepankiewicz AA, Biazik JM, Wydrych A, Nieznanska H, Serwa RA, Chacinska A, Bragoszewski P. OMA1 protease eliminates arrested protein import intermediates upon mitochondrial depolarization. J Cell Biol 2024; 223:e202306051. [PMID: 38530280 PMCID: PMC10964989 DOI: 10.1083/jcb.202306051] [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: 06/16/2023] [Revised: 12/28/2023] [Accepted: 02/16/2024] [Indexed: 03/27/2024] Open
Abstract
Most mitochondrial proteins originate from the cytosol and require transport into the organelle. Such precursor proteins must be unfolded to pass through translocation channels in mitochondrial membranes. Misfolding of transported proteins can result in their arrest and translocation failure. Arrested proteins block further import, disturbing mitochondrial functions and cellular proteostasis. Cellular responses to translocation failure have been defined in yeast. We developed the cell line-based translocase clogging model to discover molecular mechanisms that resolve failed import events in humans. The mechanism we uncover differs significantly from these described in fungi, where ATPase-driven extraction of blocked protein is directly coupled with proteasomal processing. We found human cells to rely primarily on mitochondrial factors to clear translocation channel blockage. The mitochondrial membrane depolarization triggered proteolytic cleavage of the stalled protein, which involved mitochondrial protease OMA1. The cleavage allowed releasing the protein fragment that blocked the translocase. The released fragment was further cleared in the cytosol by VCP/p97 and the proteasome.
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Affiliation(s)
- Magda Krakowczyk
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Anna M. Lenkiewicz
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Tomasz Sitarz
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Dominika Malinska
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Mayra Borrero
- IMol Polish Academy of Sciences, Warsaw, Poland
- ReMedy International Research Agenda Unit, IMol Polish Academy of Sciences, Warsaw, Poland
| | - Ben Hur Marins Mussulini
- IMol Polish Academy of Sciences, Warsaw, Poland
- ReMedy International Research Agenda Unit, IMol Polish Academy of Sciences, Warsaw, Poland
| | - Vanessa Linke
- IMol Polish Academy of Sciences, Warsaw, Poland
- ReMedy International Research Agenda Unit, IMol Polish Academy of Sciences, Warsaw, Poland
| | | | - Joanna M. Biazik
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
- University of New South Wales, Sydney, Australia
| | - Agata Wydrych
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Hanna Nieznanska
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Remigiusz A. Serwa
- IMol Polish Academy of Sciences, Warsaw, Poland
- ReMedy International Research Agenda Unit, IMol Polish Academy of Sciences, Warsaw, Poland
| | - Agnieszka Chacinska
- IMol Polish Academy of Sciences, Warsaw, Poland
- ReMedy International Research Agenda Unit, IMol Polish Academy of Sciences, Warsaw, Poland
| | - Piotr Bragoszewski
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
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2
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Durrieu L, Bush A, Colman-Lerner A. Protocol for FRAP-based estimation of nuclear import and export rates in single yeast cells. STAR Protoc 2024; 5:102876. [PMID: 38349788 PMCID: PMC10876970 DOI: 10.1016/j.xpro.2024.102876] [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: 11/07/2023] [Revised: 12/27/2023] [Accepted: 01/22/2024] [Indexed: 02/15/2024] Open
Abstract
Here, we present a protocol for estimating nuclear transport parameters in single cells. We describe steps for performing four consecutive fluorescence recovery after photobleaching experiments, fitting the obtained data to an ordinary differential equations model, and statistical analysis of the fittings using a specialized R package. This protocol permits the estimation of import and export rates, nuclear or cytosolic fixed fractions, and total number of molecules. For complete details on the use and execution of this protocol, please refer to Durrieu et al.1.
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Affiliation(s)
- Lucía Durrieu
- Institute of Physiology, Molecular Biology and Neurosciences, National Council of Scientific and Technical Research (IFIBYNE- UBA-CONICET), Buenos Aires C1428EGA, Argentina; Department of Physiology, Molecular and Cellular Biology, School of Exact and Natural Sciences, University of Buenos Aires (UBA), Buenos Aires C1428EGA, Argentina.
| | - Alan Bush
- Institute of Physiology, Molecular Biology and Neurosciences, National Council of Scientific and Technical Research (IFIBYNE- UBA-CONICET), Buenos Aires C1428EGA, Argentina
| | - Alejandro Colman-Lerner
- Institute of Physiology, Molecular Biology and Neurosciences, National Council of Scientific and Technical Research (IFIBYNE- UBA-CONICET), Buenos Aires C1428EGA, Argentina; Department of Physiology, Molecular and Cellular Biology, School of Exact and Natural Sciences, University of Buenos Aires (UBA), Buenos Aires C1428EGA, Argentina.
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3
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Renz C, Asimaki E, Meister C, Albanèse V, Petriukov K, Krapoth NC, Wegmann S, Wollscheid HP, Wong RP, Fulzele A, Chen JX, Léon S, Ulrich HD. Ubiquiton-An inducible, linkage-specific polyubiquitylation tool. Mol Cell 2024; 84:386-400.e11. [PMID: 38103558 PMCID: PMC10804999 DOI: 10.1016/j.molcel.2023.11.016] [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: 04/07/2023] [Revised: 09/28/2023] [Accepted: 11/15/2023] [Indexed: 12/19/2023]
Abstract
The posttranslational modifier ubiquitin regulates most cellular processes. Its ability to form polymeric chains of distinct linkages is key to its diverse functionality. Yet, we still lack the experimental tools to induce linkage-specific polyubiquitylation of a protein of interest in cells. Here, we introduce a set of engineered ubiquitin protein ligases and matching ubiquitin acceptor tags for the rapid, inducible linear (M1-), K48-, or K63-linked polyubiquitylation of proteins in yeast and mammalian cells. By applying the so-called "Ubiquiton" system to proteasomal targeting and the endocytic pathway, we validate this tool for soluble cytoplasmic and nuclear as well as chromatin-associated and integral membrane proteins and demonstrate how it can be used to control the localization and stability of its targets. We expect that the Ubiquiton system will serve as a versatile, broadly applicable research tool to explore the signaling functions of polyubiquitin chains in many biological contexts.
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Affiliation(s)
- Christian Renz
- Institute of Molecular Biology (IMB) gGmbH, Ackermannweg 4, 55128 Mainz, Germany
| | - Evrydiki Asimaki
- Institute of Molecular Biology (IMB) gGmbH, Ackermannweg 4, 55128 Mainz, Germany
| | - Cindy Meister
- Institute of Molecular Biology (IMB) gGmbH, Ackermannweg 4, 55128 Mainz, Germany
| | | | - Kirill Petriukov
- Institute of Molecular Biology (IMB) gGmbH, Ackermannweg 4, 55128 Mainz, Germany
| | - Nils C Krapoth
- Institute of Molecular Biology (IMB) gGmbH, Ackermannweg 4, 55128 Mainz, Germany
| | - Sabrina Wegmann
- Institute of Molecular Biology (IMB) gGmbH, Ackermannweg 4, 55128 Mainz, Germany
| | | | - Ronald P Wong
- Institute of Molecular Biology (IMB) gGmbH, Ackermannweg 4, 55128 Mainz, Germany
| | - Amitkumar Fulzele
- Institute of Molecular Biology (IMB) gGmbH, Ackermannweg 4, 55128 Mainz, Germany
| | - Jia-Xuan Chen
- Institute of Molecular Biology (IMB) gGmbH, Ackermannweg 4, 55128 Mainz, Germany
| | - Sébastien Léon
- Université de Paris, CNRS, Institut Jacques Monod, 75013 Paris, France
| | - Helle D Ulrich
- Institute of Molecular Biology (IMB) gGmbH, Ackermannweg 4, 55128 Mainz, Germany.
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4
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Kong KYE, Shankar S, Rühle F, Khmelinskii A. Orphan quality control by an SCF ubiquitin ligase directed to pervasive C-degrons. Nat Commun 2023; 14:8363. [PMID: 38102142 PMCID: PMC10724198 DOI: 10.1038/s41467-023-44096-z] [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: 08/11/2023] [Accepted: 11/30/2023] [Indexed: 12/17/2023] Open
Abstract
Selective protein degradation typically involves substrate recognition via short linear motifs known as degrons. Various degrons can be found at protein termini from bacteria to mammals. While N-degrons have been extensively studied, our understanding of C-degrons is still limited. Towards a comprehensive understanding of eukaryotic C-degron pathways, here we perform an unbiased survey of C-degrons in budding yeast. We identify over 5000 potential C-degrons by stability profiling of random peptide libraries and of the yeast C‑terminome. Combining machine learning, high-throughput mutagenesis and genetic screens reveals that the SCF ubiquitin ligase targets ~40% of degrons using a single F-box substrate receptor Das1. Although sequence-specific, Das1 is highly promiscuous, recognizing a variety of C-degron motifs. By screening for full-length substrates, we implicate SCFDas1 in degradation of orphan protein complex subunits. Altogether, this work highlights the variety of C-degron pathways in eukaryotes and uncovers how an SCF/C-degron pathway of broad specificity contributes to proteostasis.
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Affiliation(s)
| | | | - Frank Rühle
- Institute of Molecular Biology (IMB), Mainz, Germany
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5
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Allen J, Flanagan M, Pathak S, Emenecker S, Emenecker R, Strader L. An Improved Toolkit of Gateway- and Gibson Assembly-Compatible Vectors for Protoplast Transfection and Agrobacterium-Mediated Plant Transformation. RESEARCH SQUARE 2023:rs.3.rs-3558280. [PMID: 37986897 PMCID: PMC10659543 DOI: 10.21203/rs.3.rs-3558280/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Objective Understanding the regulation and function of plant genes is essential for addressing the challenges faced by modern agriculture. Plant transformation, in conjunction with fluorescence microscopy, offers a powerful approach to investigate the dynamic behavior of plant genes and the proteins they encode. We previously developed a set of Gateway-compatible tissue-specific plant transformation vectors. In this paper we aim to expand the toolkit of vectors available for Agrobacterium-mediated plant transformation and protoplast transfection. Results Here, we introduce new Agrobacterium-mediated plant transformation vectors by introducing additional fluorophores to create the pJRA vector series. Additionally, we introduce the pLCS series of vectors, a new set of modular Gateway- and Gibson assembly-compatible vectors designed for protoplast transfection. All described vectors are available from Addgene to serve as a resource for the plant research community.
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6
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Brauns F, Iñigo de la Cruz L, Daalman WKG, de Bruin I, Halatek J, Laan L, Frey E. Redundancy and the role of protein copy numbers in the cell polarization machinery of budding yeast. Nat Commun 2023; 14:6504. [PMID: 37845215 PMCID: PMC10579396 DOI: 10.1038/s41467-023-42100-0] [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: 02/05/2022] [Accepted: 09/26/2023] [Indexed: 10/18/2023] Open
Abstract
How can a self-organized cellular function evolve, adapt to perturbations, and acquire new sub-functions? To make progress in answering these basic questions of evolutionary cell biology, we analyze, as a concrete example, the cell polarity machinery of Saccharomyces cerevisiae. This cellular module exhibits an intriguing resilience: it remains operational under genetic perturbations and recovers quickly and reproducibly from the deletion of one of its key components. Using a combination of modeling, conceptual theory, and experiments, we propose that multiple, redundant self-organization mechanisms coexist within the protein network underlying cell polarization and are responsible for the module's resilience and adaptability. Based on our mechanistic understanding of polarity establishment, we hypothesize that scaffold proteins, by introducing new connections in the existing network, can increase the redundancy of mechanisms and thus increase the evolvability of other network components. Moreover, our work gives a perspective on how a complex, redundant cellular module might have evolved from a more rudimental ancestral form.
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Affiliation(s)
- Fridtjof Brauns
- Arnold Sommerfeld Center for Theoretical Physics and Center for NanoScience, Department of Physics, Ludwig-Maximilians-Universität München, Munich, Germany
- Kavli Institute for Theoretical Physics, University of California Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Leila Iñigo de la Cruz
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands
| | - Werner K-G Daalman
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands
| | - Ilse de Bruin
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands
| | - Jacob Halatek
- Arnold Sommerfeld Center for Theoretical Physics and Center for NanoScience, Department of Physics, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Liedewij Laan
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands.
| | - Erwin Frey
- Arnold Sommerfeld Center for Theoretical Physics and Center for NanoScience, Department of Physics, Ludwig-Maximilians-Universität München, Munich, Germany.
- Max Planck School Matter to Life, Hofgartenstraße 8, D-80539, Munich, Germany.
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7
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Lee D, Zhu Y, Colson L, Wang X, Chen S, Tkacik E, Huang L, Ouyang Q, Goldberg AL, Lu Y. Molecular mechanism for activation of the 26S proteasome by ZFAND5. Mol Cell 2023; 83:2959-2975.e7. [PMID: 37595557 PMCID: PMC10523585 DOI: 10.1016/j.molcel.2023.07.023] [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: 11/07/2022] [Revised: 05/07/2023] [Accepted: 07/24/2023] [Indexed: 08/20/2023]
Abstract
Various hormones, kinases, and stressors (fasting, heat shock) stimulate 26S proteasome activity. To understand how its capacity to degrade ubiquitylated proteins can increase, we studied mouse ZFAND5, which promotes protein degradation during muscle atrophy. Cryo-electron microscopy showed that ZFAND5 induces large conformational changes in the 19S regulatory particle. ZFAND5's AN1 Zn-finger domain interacts with the Rpt5 ATPase and its C terminus with Rpt1 ATPase and Rpn1, a ubiquitin-binding subunit. Upon proteasome binding, ZFAND5 widens the entrance of the substrate translocation channel, yet it associates only transiently with the proteasome. Dissociation of ZFAND5 then stimulates opening of the 20S proteasome gate. Using single-molecule microscopy, we showed that ZFAND5 binds ubiquitylated substrates, prolongs their association with proteasomes, and increases the likelihood that bound substrates undergo degradation, even though ZFAND5 dissociates before substrate deubiquitylation. These changes in proteasome conformation and reaction cycle can explain the accelerated degradation and suggest how other proteasome activators may stimulate proteolysis.
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Affiliation(s)
- Donghoon Lee
- Department of Cell Biology, Harvard Medical School, Boston, MA USA
| | - Yanan Zhu
- Department of Systems Biology, Harvard Medical School, Boston, MA USA; Center for Quantitative Biology, Peking University, Beijing, China; State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing, China
| | - Louis Colson
- Department of Systems Biology, Harvard Medical School, Boston, MA USA
| | - Xiaorong Wang
- School of Medicine, University of California Irvine, Irvine, Irvine, CA USA
| | - Siyi Chen
- Department of Systems Biology, Harvard Medical School, Boston, MA USA
| | - Emre Tkacik
- Department of Systems Biology, Harvard Medical School, Boston, MA USA
| | - Lan Huang
- School of Medicine, University of California Irvine, Irvine, Irvine, CA USA
| | - Qi Ouyang
- Center for Quantitative Biology, Peking University, Beijing, China; State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing, China; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | | | - Ying Lu
- Department of Systems Biology, Harvard Medical School, Boston, MA USA.
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8
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Lee D, Zhu Y, Colson L, Wang X, Chen S, Tkacik E, Huang L, Ouyang Q, Goldberg AL, Lu Y. Molecular mechanisms for activation of the 26S proteasome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.09.540094. [PMID: 37214989 PMCID: PMC10197607 DOI: 10.1101/2023.05.09.540094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Various hormones, kinases, and stressors (fasting, heat shock) stimulate 26S proteasome activity. To understand how its capacity to degrade ubiquitylated protein can increase, we studied ZFAND5, which promotes protein degradation during muscle atrophy. Cryo-electron microscopy showed that ZFAND5 induces large conformational changes in the 19S regulatory particle. ZFAND5's AN1 Zn finger interacts with the Rpt5 ATPase and its C-terminus with Rpt1 ATPase and Rpn1, a ubiquitin-binding subunit. Surprisingly, these C-terminal interactions are sufficient to activate proteolysis. With ZFAND5 bound, entry into the proteasome's protein translocation channel is wider, and ZFAND5 dissociation causes opening of the 20S gate for substrate entry. Using single-molecular microscopy, we showed that ZFAND5 binds ubiquitylated substrates, prolongs their association with proteasomes, and increases the likelihood that bound substrates undergo degradation, even though ZFAND5 dissociates before substrate deubiquitylation. These changes in proteasome conformation and reaction cycle can explain the accelerated degradation and suggest how other proteasome activators may stimulate proteolysis.
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9
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Collins MA, Avery R, Albert FW. Substrate-specific effects of natural genetic variation on proteasome activity. PLoS Genet 2023; 19:e1010734. [PMID: 37126494 PMCID: PMC10174532 DOI: 10.1371/journal.pgen.1010734] [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: 06/14/2022] [Revised: 05/11/2023] [Accepted: 04/04/2023] [Indexed: 05/02/2023] Open
Abstract
Protein degradation is an essential biological process that regulates protein abundance and removes misfolded and damaged proteins from cells. In eukaryotes, most protein degradation occurs through the stepwise actions of two functionally distinct entities, the ubiquitin system and the proteasome. Ubiquitin system enzymes attach ubiquitin to cellular proteins, targeting them for degradation. The proteasome then selectively binds and degrades ubiquitinated substrate proteins. Genetic variation in ubiquitin system genes creates heritable differences in the degradation of their substrates. However, the challenges of measuring the degradative activity of the proteasome independently of the ubiquitin system in large samples have limited our understanding of genetic influences on the proteasome. Here, using the yeast Saccharomyces cerevisiae, we built and characterized reporters that provide high-throughput, ubiquitin system-independent measurements of proteasome activity. Using single-cell measurements of proteasome activity from millions of genetically diverse yeast cells, we mapped 15 loci across the genome that influence proteasomal protein degradation. Twelve of these 15 loci exerted specific effects on the degradation of two distinct proteasome substrates, revealing a high degree of substrate-specificity in the genetics of proteasome activity. Using CRISPR-Cas9-based allelic engineering, we resolved a locus to a causal variant in the promoter of RPT6, a gene that encodes a subunit of the proteasome's 19S regulatory particle. The variant increases RPT6 expression, which we show results in increased proteasome activity. Our results reveal the complex genetic architecture of proteasome activity and suggest that genetic influences on the proteasome may be an important source of variation in the many cellular and organismal traits shaped by protein degradation.
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Affiliation(s)
- Mahlon A. Collins
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Randi Avery
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Frank W. Albert
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
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10
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Reinbold C, Kong KYE, Kats I, Khmelinskii A, Knop M. Multiplexed protein stability (MPS) profiling of terminal degrons using fluorescent timer libraries in Saccharomyces cerevisiae. Methods Enzymol 2023; 686:321-344. [PMID: 37532406 DOI: 10.1016/bs.mie.2023.02.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/04/2023]
Abstract
N-terminal protein sequences and their proteolytic processing and modifications influence the stability and turnover of proteins by creating potential degrons for cellular proteolytic pathways. Understanding the impact of genetic perturbations of components affecting the processing of protein N-termini and thereby their stability, requires methods compatible with proteome-wide studies of many N-termini simultaneously. Tandem fluorescent timers (tFT) allow the in vivo measurement of protein turnover completely independent of protein abundance and can be deployed for proteome-wide studies. Here we present a protocol for Multiplexed Protein Stability (MPS) profiling of tFT-libraries encoding large numbers of different protein N-termini fused to tFT in the yeast Saccharomyces cerevisiae. This protocol includes fluorescence cell sorting based profiling of these libraries using a pooling approach. Analysis of the sorted pools is done by using multiplexed deep sequencing, in order to generate a stability index for each N-terminally peptide fused to the tFT reporter, and to evaluate half-life changes across all species represented in the library.
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Affiliation(s)
- Christian Reinbold
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | | | - Ilia Kats
- Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Michael Knop
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany; Cell Morphogenesis and Signal Transduction, German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, Heidelberg, Germany.
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11
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Abdelbaki A, Ascanelli C, Okoye CN, Akman HB, Janson G, Min M, Marcozzi C, Hagting A, Grant R, De Luca M, Asteriti IA, Guarguaglini G, Paiardini A, Lindon C. Revisiting degron motifs in human AURKA required for its targeting by APC/C FZR1. Life Sci Alliance 2023; 6:6/2/e202201372. [PMID: 36450448 PMCID: PMC9713472 DOI: 10.26508/lsa.202201372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 11/17/2022] [Accepted: 11/18/2022] [Indexed: 12/02/2022] Open
Abstract
Mitotic kinase Aurora A (AURKA) diverges from other kinases in its multiple active conformations that may explain its interphase roles and the limited efficacy of drugs targeting the kinase pocket. Regulation of AURKA activity by the cell is critically dependent on destruction mediated by the anaphase-promoting complex (APC/CFZR1) during mitotic exit and G1 phase and requires an atypical N-terminal degron in AURKA called the "A-box" in addition to a reported canonical D-box degron in the C-terminus. Here, we find that the reported C-terminal D-box of AURKA does not act as a degron and instead mediates essential structural features of the protein. In living cells, the N-terminal intrinsically disordered region of AURKA containing the A-box is sufficient to confer FZR1-dependent mitotic degradation. Both in silico and in cellulo assays predict the QRVL short linear interacting motif of the A-box to be a phospho-regulated D-box. We propose that degradation of full-length AURKA also depends on an intact C-terminal domain because of critical conformational parameters permissive for both activity and mitotic degradation of AURKA.
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Affiliation(s)
- Ahmed Abdelbaki
- Department of Pharmacology, University of Cambridge, Cambridge, UK
| | | | - Cynthia N Okoye
- Department of Pharmacology, University of Cambridge, Cambridge, UK
| | - H Begum Akman
- Department of Pharmacology, University of Cambridge, Cambridge, UK
| | - Giacomo Janson
- Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy
| | - Mingwei Min
- Department of Pharmacology, University of Cambridge, Cambridge, UK
| | - Chiara Marcozzi
- Department of Pharmacology, University of Cambridge, Cambridge, UK
| | - Anja Hagting
- Department of Pharmacology, University of Cambridge, Cambridge, UK
| | - Rhys Grant
- Department of Pharmacology, University of Cambridge, Cambridge, UK
| | - Maria De Luca
- Department of Pharmacology, University of Cambridge, Cambridge, UK
| | - Italia Anna Asteriti
- Institute of Molecular Biology and Pathology, National Research Council of Italy, c/o Sapienza University of Rome, Rome, Italy
| | - Giulia Guarguaglini
- Institute of Molecular Biology and Pathology, National Research Council of Italy, c/o Sapienza University of Rome, Rome, Italy
| | | | - Catherine Lindon
- Department of Pharmacology, University of Cambridge, Cambridge, UK
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12
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Kong KYE, Reinbold C, Knop M, Khmelinskii A. Building yeast libraries to dissect terminal degrons with fluorescent timers. Methods Enzymol 2023. [PMID: 37532405 DOI: 10.1016/bs.mie.2023.02.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
Abstract
Selective degradation of unnecessary or abnormal proteins by the ubiquitin-proteasome system is an essential part of proteostasis. Ubiquitin ligases recognize substrates of selective protein degradation and modify them with polyubiquitin chains, which mark them for proteasomal degradation. Substrate recognition by ubiquitin ligases often involves degradation signals or degrons, which are typically short linear motifs found in intrinsically disordered regions, e.g., at protein termini. However, specificity in selective protein degradation is generally not well understood, as for most ubiquitin ligases no degrons have been identified thus far. To address this limitation, high-throughput mutagenesis approaches, such as multiplexed protein stability (MPS) profiling, have been developed, enabling systematic surveys of degrons in vivo or allowing to define degron motifs recognized by different ubiquitin ligases. In MPS profiling, thousands of short peptides can be assessed in parallel for their ability to trigger degradation of a fluorescent timer reporter. Here, we describe common types of libraries used to identify and dissect degrons located at protein termini using MPS profiling in budding yeast, and provide protocols for their construction.
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13
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Hoang MD, Doan DT, Schmidt M, Kranz H, Kremling A, Heins A. Application of an Escherichia coli triple reporter strain for at-line monitoring of single-cell physiology during L-phenylalanine production. Eng Life Sci 2023; 23:e2100162. [PMID: 36619877 PMCID: PMC9815085 DOI: 10.1002/elsc.202100162] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 01/24/2022] [Accepted: 02/07/2022] [Indexed: 01/11/2023] Open
Abstract
Biotechnological production processes are sustainable approaches for the production of biobased components such as amino acids for food and feed industry. Scale-up from ideal lab-scale bioreactors to large-scale processes is often accompanied by loss in productivity. This may be related to population heterogeneities of cells originating from isogenic cultures that arise due to dynamic non-ideal conditions in the bioreactor. To better understand this phenomenon, deeper insights into single-cell physiologies in bioprocesses are mandatory before scale-up. Here, a triple reporter strain (3RP) was developed by chromosomally integrating the fluorescent proteins mEmerald, CyOFP1, and mTagBFP2 into the L-phenylalanine producing Escherichia coli strain FUS4 (pF81kan) to allow monitoring of growth, oxygen availability, and general stress response of the single cells. Functionality of the 3RP was confirmed in well-mixed lab-scale fed-batch processes with glycerol as carbon source in comparison to the strain without fluorescent proteins, leading to no difference in process performance. Fluorescence levels could successfully reflect the course of related process state variables, revealed population heterogeneities during the transition between different process phases and potentially subpopulations that exhibit superior process performance. Furthermore, indications were found for noise in gene expression as regulation strategy against environmental perturbation.
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Affiliation(s)
- Manh Dat Hoang
- Chair of Biochemical EngineeringDepartment of Energy and Process EngineeringTUM School of Engineering and DesignTechnical University of MunichGarchingGermany
| | - Dieu Thi Doan
- Systems BiotechnologyDepartment of Energy and Process EngineeringTUM School of Engineering and DesignTechnical University of MunichGarchingGermany
| | - Marlen Schmidt
- Gen‐H Genetic Engineering Heidelberg GmbHHeidelbergGermany
| | - Harald Kranz
- Gen‐H Genetic Engineering Heidelberg GmbHHeidelbergGermany
| | - Andreas Kremling
- Systems BiotechnologyDepartment of Energy and Process EngineeringTUM School of Engineering and DesignTechnical University of MunichGarchingGermany
| | - Anna‐Lena Heins
- Chair of Biochemical EngineeringDepartment of Energy and Process EngineeringTUM School of Engineering and DesignTechnical University of MunichGarchingGermany
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14
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Zhang H, Linster E, Wirtz M, Theodoulou FL. Relative Protein Lifetime Measurement in Plants Using Tandem Fluorescent Protein Timers. Methods Mol Biol 2023; 2581:201-220. [PMID: 36413319 DOI: 10.1007/978-1-0716-2784-6_14] [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] [Indexed: 06/16/2023]
Abstract
Targeted protein degradation plays a wide range of important roles in plant growth and development, but analyzing protein turnover in vivo is technically challenging. Until recently, there has been no straightforward methodology for quantifying protein dynamics at subcellular resolution during cellular transitions in plants. A tandem fluorescent protein timer (tFT) is a fusion of two different fluorescent proteins with distinct fluorophore maturation kinetics, which allows estimation of relative protein age from the ratio of fluorescence intensities of the two fluorescent proteins. Here, we describe approaches to use this technology to report relative protein lifetime in both transient and stable plant transformation systems. tFTs enable in vivo, real-time protein lifetime assessment within subcellular compartments and across tissues, permitting the analysis of protein degradation dynamics in response to stresses or developmental cues and in different genetic backgrounds.
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Affiliation(s)
- Hongtao Zhang
- Plant Sciences and the Bioeconomy, Rothamsted Research, Harpenden, UK
| | - Eric Linster
- Centre for Organismal Studies, University of Heidelberg, Heidelberg, Germany
| | - Markus Wirtz
- Centre for Organismal Studies, University of Heidelberg, Heidelberg, Germany
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15
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Goiran T, Eldeeb MA, Zorca CE, Fon EA. Hallmarks and Molecular Tools for the Study of Mitophagy in Parkinson’s Disease. Cells 2022; 11:cells11132097. [PMID: 35805181 PMCID: PMC9265644 DOI: 10.3390/cells11132097] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 06/28/2022] [Accepted: 06/29/2022] [Indexed: 01/27/2023] Open
Abstract
The best-known hallmarks of Parkinson’s disease (PD) are the motor deficits that result from the degeneration of dopaminergic neurons in the substantia nigra. Dopaminergic neurons are thought to be particularly susceptible to mitochondrial dysfunction. As such, for their survival, they rely on the elaborate quality control mechanisms that have evolved in mammalian cells to monitor mitochondrial function and eliminate dysfunctional mitochondria. Mitophagy is a specialized type of autophagy that mediates the selective removal of damaged mitochondria from cells, with the net effect of dampening the toxicity arising from these dysfunctional organelles. Despite an increasing understanding of the molecular mechanisms that regulate the removal of damaged mitochondria, the detailed molecular link to PD pathophysiology is still not entirely clear. Herein, we review the fundamental molecular pathways involved in PINK1/Parkin-mediated and receptor-mediated mitophagy, the evidence for the dysfunction of these pathways in PD, and recently-developed state-of-the art assays for measuring mitophagy in vitro and in vivo.
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16
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Naruse C, Sugihara K, Miyazaki T, Pan X, Sugiyama F, Asano M. A degron system targeting endogenous PD-1 inhibits the growth of tumor cells in mice. NAR Cancer 2022; 4:zcac019. [PMID: 35734392 PMCID: PMC9204894 DOI: 10.1093/narcan/zcac019] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 05/26/2022] [Accepted: 06/03/2022] [Indexed: 11/12/2022] Open
Abstract
Recently, targeted protein degradation systems have been developed using the ubiquitin-proteasome system. Here, we established Programmed cell death-1 (PD-1) knockdown mice as a model system for subjecting endogenous mouse proteins to the small molecule-assisted shutoff (SMASh) degron system. SMASh degron-tagged PD-1-mCherry in Jurkat cells and CD3+ splenocytes were degraded by the NS3/4A protease inhibitors, asunaprevir (ASV) or grazoprevir (GRV). Growth of MC-38 colon adenocarcinoma cells injected in Pdcd1-mCherry-SMASh homozygous knock-in (KI) mice was repressed by ASV or GRV. Moreover, growth of MC-38 cells was suppressed in wild-type mice transplanted with KI bone marrow cells after GRV treatment. This is the first study to use a degron tag targeting an endogenous mouse protein in vivo. Our experimental system using the SMASh degron may be employed for treating diseases and characterizing the cellular functions of essential proteins.
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Affiliation(s)
- Chie Naruse
- Institute of Laboratory Animals, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Kazushi Sugihara
- Institute of Laboratory Animals, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Tatsuhiko Miyazaki
- Department of Pathology, Gifu University Hospital, 1-1 Yanagido, Gifu 501-1104, Japan
| | - Xuchi Pan
- Institute of Laboratory Animals, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Fumihiro Sugiyama
- Laboratory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Masahide Asano
- Institute of Laboratory Animals, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
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17
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Pócsi I, Szigeti ZM, Emri T, Boczonádi I, Vereb G, Szöllősi J. Use of red, far-red, and near-infrared light in imaging of yeasts and filamentous fungi. Appl Microbiol Biotechnol 2022; 106:3895-3912. [PMID: 35599256 PMCID: PMC9200671 DOI: 10.1007/s00253-022-11967-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 05/02/2022] [Accepted: 05/07/2022] [Indexed: 11/30/2022]
Abstract
Abstract While phototoxicity can be a useful therapeutic modality not only for eliminating malignant cells but also in treating fungal infections, mycologists aiming to observe morphological changes or molecular events in fungi, especially when long observation periods or high light fluxes are warranted, encounter problems owed to altered regulatory pathways or even cell death caused by various photosensing mechanisms. Consequently, the ever expanding repertoire of visible fluorescent protein toolboxes and high-resolution microscopy methods designed to investigate fungi in vitro and in vivo need to comply with an additional requirement: to decrease the unwanted side effects of illumination. In addition to optimizing exposure, an obvious solution is red-shifted illumination, which, however, does not come without compromises. This review summarizes the interactions of fungi with light and the various molecular biology and technology approaches developed for exploring their functions on the molecular, cellular, and in vivo microscopic levels, and outlines the progress towards reducing phototoxicity through applying far-red and near-infrared light. Key points • Fungal biological processes alter upon illumination, also under the microscope • Red shifted fluorescent protein toolboxes decrease interference by illumination • Innovations like two-photon, lightsheet, and near IR microscopy reduce phototoxicity
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Affiliation(s)
- István Pócsi
- Department of Molecular Biotechnology and Microbiology, Institute of Biotechnology, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, 4032, Debrecen, Hungary.
| | - Zsuzsa M Szigeti
- Department of Molecular Biotechnology and Microbiology, Institute of Biotechnology, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, 4032, Debrecen, Hungary
| | - Tamás Emri
- Department of Molecular Biotechnology and Microbiology, Institute of Biotechnology, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, 4032, Debrecen, Hungary
| | - Imre Boczonádi
- Department of Molecular Biotechnology and Microbiology, Institute of Biotechnology, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, 4032, Debrecen, Hungary
| | - György Vereb
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, 4032, Debrecen, Hungary.,MTA-DE Cell Biology and Signaling Research Group, Faculty of Medicine, University of Debrecen, Egyetem tér 1, 4032, Debrecen, Hungary.,Faculty of Pharmacy, University of Debrecen, Egyetem tér 1, 4032, Debrecen, Hungary
| | - János Szöllősi
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, 4032, Debrecen, Hungary.,MTA-DE Cell Biology and Signaling Research Group, Faculty of Medicine, University of Debrecen, Egyetem tér 1, 4032, Debrecen, Hungary
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18
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Spike CA, Tsukamoto T, Greenstein D. Ubiquitin ligases and a processive proteasome facilitate protein clearance during the oocyte-to-embryo transition in Caenorhabditis elegans. Genetics 2022; 221:iyac051. [PMID: 35377419 PMCID: PMC9071522 DOI: 10.1093/genetics/iyac051] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 03/27/2022] [Indexed: 02/07/2023] Open
Abstract
The ubiquitin-mediated degradation of oocyte translational regulatory proteins is a conserved feature of the oocyte-to-embryo transition. In the nematode Caenorhabditis elegans, multiple translational regulatory proteins, including the TRIM-NHL RNA-binding protein LIN-41/Trim71 and the Pumilio-family RNA-binding proteins PUF-3 and PUF-11, are degraded during the oocyte-to-embryo transition. Degradation of each protein requires activation of the M-phase cyclin-dependent kinase CDK-1, is largely complete by the end of the first meiotic division and does not require the anaphase-promoting complex. However, only LIN-41 degradation requires the F-box protein SEL-10/FBW7/Cdc4p, the substrate recognition subunit of an SCF-type E3 ubiquitin ligase. This finding suggests that PUF-3 and PUF-11, which localize to LIN-41-containing ribonucleoprotein particles, are independently degraded through the action of other factors and that the oocyte ribonucleoprotein particles are disassembled in a concerted fashion during the oocyte-to-embryo transition. We develop and test the hypothesis that PUF-3 and PUF-11 are targeted for degradation by the proteasome-associated HECT-type ubiquitin ligase ETC-1/UBE3C/Hul5, which is broadly expressed in C. elegans. We find that several GFP-tagged fusion proteins that are degraded during the oocyte-to-embryo transition, including fusions with PUF-3, PUF-11, LIN-41, IFY-1/Securin, and CYB-1/Cyclin B, are incompletely degraded when ETC-1 function is compromised. However, it is the fused GFP moiety that appears to be the critical determinant of this proteolysis defect. These findings are consistent with a conserved role for ETC-1 in promoting proteasome processivity and suggest that proteasomal processivity is an important element of the oocyte-to-embryo transition during which many key oocyte regulatory proteins are rapidly targeted for degradation.
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Affiliation(s)
- Caroline A Spike
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Tatsuya Tsukamoto
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - David Greenstein
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA
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19
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Guerra P, Vuillemenot LA, Rae B, Ladyhina V, Milias-Argeitis A. Systematic In Vivo Characterization of Fluorescent Protein Maturation in Budding Yeast. ACS Synth Biol 2022; 11:1129-1141. [PMID: 35180343 PMCID: PMC8938947 DOI: 10.1021/acssynbio.1c00387] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Fluorescent protein
(FP) maturation can limit the accuracy with
which dynamic intracellular processes are captured and reduce the in vivo brightness of a given FP in fast-dividing cells.
The knowledge of maturation timescales can therefore help users determine
the appropriate FP for each application. However, in vivo maturation rates can greatly deviate from in vitro estimates that are mostly available. In this work, we present the
first systematic study of in vivo maturation for
12 FPs in budding yeast. To overcome the technical limitations of
translation inhibitors commonly used to study FP maturation, we implemented
a new approach based on the optogenetic stimulations of FP expression
in cells grown under constant nutrient conditions. Combining the rapid
and orthogonal induction of FP transcription with a mathematical model
of expression and maturation allowed us to accurately estimate maturation
rates from microscopy data in a minimally invasive manner. Besides
providing a useful resource for the budding yeast community, we present
a new joint experimental and computational approach for characterizing
FP maturation, which is applicable to a wide range of organisms.
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Affiliation(s)
- Paolo Guerra
- Molecular Systems Biology, Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG Groningen, Netherlands
| | - Luc-Alban Vuillemenot
- Molecular Systems Biology, Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG Groningen, Netherlands
| | - Brady Rae
- Molecular Systems Biology, Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG Groningen, Netherlands
| | - Valeriia Ladyhina
- Molecular Systems Biology, Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG Groningen, Netherlands
| | - Andreas Milias-Argeitis
- Molecular Systems Biology, Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG Groningen, Netherlands
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20
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Fung JJ, Blöcher-Juárez K, Khmelinskii A. High-Throughput Analysis of Protein Turnover with Tandem Fluorescent Protein Timers. Methods Mol Biol 2022; 2378:85-100. [PMID: 34985695 DOI: 10.1007/978-1-0716-1732-8_6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Tandem fluorescent protein timers (tFTs) are versatile reporters of protein dynamics. A tFT consists of two fluorescent proteins with different maturation kinetics and provides a ratiometric readout of protein age, which can be exploited to follow intracellular trafficking, inheritance and turnover of tFT-tagged proteins. Here, we detail a protocol for high-throughput analysis of protein turnover with tFTs in yeast using fluorescence measurements of ordered colony arrays. We describe guidelines on optimization of experimental design with regard to the layout of colony arrays, growth conditions, and instrument choice. Combined with semi-automated genetic crossing using synthetic genetic array (SGA) methodology and high-throughput protein tagging with SWAp-Tag (SWAT) libraries, this approach can be used to compare protein turnover across the proteome and to identify regulators of protein turnover genome-wide.
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Affiliation(s)
- Jia Jun Fung
- Institute of Molecular Biology (IMB), Mainz, Germany
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21
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Kats I, Reinbold C, Kschonsak M, Khmelinskii A, Armbruster L, Ruppert T, Knop M. Up-regulation of ubiquitin-proteasome activity upon loss of NatA-dependent N-terminal acetylation. Life Sci Alliance 2021; 5:5/2/e202000730. [PMID: 34764209 PMCID: PMC8605321 DOI: 10.26508/lsa.202000730] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 10/26/2021] [Accepted: 10/27/2021] [Indexed: 11/26/2022] Open
Abstract
Inactivation of N-terminal acetyltransferase A is found to alter Rpn4 as well as E3 ligase abundance, causing up-regulation of Ubiquitin–proteasome activity. In this context, Tom1 is also identified as a novel chain-elongating enzyme of the UFD-pathway. N-terminal acetylation is a prominent protein modification, and inactivation of N-terminal acetyltransferases (NATs) cause protein homeostasis stress. Using multiplexed protein stability profiling with linear ubiquitin fusions as reporters for the activity of the ubiquitin proteasome system, we observed increased ubiquitin proteasome system activity in NatA, but not NatB or NatC mutants. We find several mechanisms contributing to this behavior. First, NatA-mediated acetylation of the N-terminal ubiquitin–independent degron regulates the abundance of Rpn4, the master regulator of the expression of proteasomal genes. Second, the abundance of several E3 ligases involved in degradation of UFD substrates is increased in cells lacking NatA. Finally, we identify the E3 ligase Tom1 as a novel chain-elongating enzyme (E4) involved in the degradation of linear ubiquitin fusions via the formation of branched K11, K29, and K48 ubiquitin chains, independently of the known E4 ligases involved in UFD, leading to enhanced ubiquitination of the UFD substrates.
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Affiliation(s)
- Ilia Kats
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Christian Reinbold
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Marc Kschonsak
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | | | - Laura Armbruster
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Thomas Ruppert
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Michael Knop
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany .,Deutsches Krebsforschungszentrum (DKFZ), DKFZ-ZMBH Alliance, Heidelberg, Germany
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22
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Verweij FJ, Balaj L, Boulanger CM, Carter DRF, Compeer EB, D'Angelo G, El Andaloussi S, Goetz JG, Gross JC, Hyenne V, Krämer-Albers EM, Lai CP, Loyer X, Marki A, Momma S, Nolte-'t Hoen ENM, Pegtel DM, Peinado H, Raposo G, Rilla K, Tahara H, Théry C, van Royen ME, Vandenbroucke RE, Wehman AM, Witwer K, Wu Z, Wubbolts R, van Niel G. The power of imaging to understand extracellular vesicle biology in vivo. Nat Methods 2021; 18:1013-1026. [PMID: 34446922 PMCID: PMC8796660 DOI: 10.1038/s41592-021-01206-3] [Citation(s) in RCA: 165] [Impact Index Per Article: 55.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 05/20/2021] [Indexed: 01/08/2023]
Abstract
Extracellular vesicles (EVs) are nano-sized lipid bilayer vesicles released by virtually every cell type. EVs have diverse biological activities, ranging from roles in development and homeostasis to cancer progression, which has spurred the development of EVs as disease biomarkers and drug nanovehicles. Owing to the small size of EVs, however, most studies have relied on isolation and biochemical analysis of bulk EVs separated from biofluids. Although informative, these approaches do not capture the dynamics of EV release, biodistribution, and other contributions to pathophysiology. Recent advances in live and high-resolution microscopy techniques, combined with innovative EV labeling strategies and reporter systems, provide new tools to study EVs in vivo in their physiological environment and at the single-vesicle level. Here we critically review the latest advances and challenges in EV imaging, and identify urgent, outstanding questions in our quest to unravel EV biology and therapeutic applications.
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Affiliation(s)
- Frederik J Verweij
- Université de Paris, Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM U1266, Paris, France.
- GHU Paris Psychiatrie et Neurosciences, Hôpital Sainte Anne, Paris, France.
| | - Leonora Balaj
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | - David R F Carter
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, UK
- Evox Therapeutics Limited, Oxford Science Park, Oxford, UK
| | - Ewoud B Compeer
- Kennedy Institute of Rheumatology, NDORMS, University of Oxford, Oxford, UK
| | - Gisela D'Angelo
- Institut Curie, PSL Research University, CNRS, UMR144 Cell Biology and Cancer, Paris, France
| | - Samir El Andaloussi
- Evox Therapeutics Limited, Oxford Science Park, Oxford, UK
- Clinical Research Center, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Jacky G Goetz
- INSERM UMR_S1109, Tumor Biomechanics Lab, Université de Strasbourg, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Equipe Labellisée Ligue contre le Cancer, Strasbourg, France
| | | | - Vincent Hyenne
- INSERM UMR_S1109, Tumor Biomechanics Lab, Université de Strasbourg, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Equipe Labellisée Ligue contre le Cancer, Strasbourg, France
- CNRS SNC5055, Strasbourg, France
| | - Eva-Maria Krämer-Albers
- Johannes Gutenberg-Universität Mainz, Institute of Developmental Biology and Neurobiology, Mainz, Germany
| | - Charles P Lai
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, Taiwan
| | - Xavier Loyer
- Université de Paris, PARCC, INSERM, Paris, France
| | - Alex Marki
- La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - Stefan Momma
- Institute of Neurology (Edinger Institute), Goethe-University, Frankfurt am Main, Germany
| | - Esther N M Nolte-'t Hoen
- Department of Biomolecular Health Sciences, Faculty of veterinary medicine, Utrecht University, Utrecht, the Netherlands
| | - D Michiel Pegtel
- Amsterdam UMC, Vrije Universiteit Amsterdam, Pathology, Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - Hector Peinado
- Microenvironment and Metastasis Laboratory, Molecular Oncology Programme, Spanish National Cancer Research Center (CNIO), Madrid, Spain
| | - Graça Raposo
- Institut Curie, PSL Research University, CNRS, UMR144 Cell Biology and Cancer, Paris, France
| | - Kirsi Rilla
- University of Eastern Finland, Institute of Biomedicine, Kuopio, Finland
| | - Hidetoshi Tahara
- Department of Cellular and Molecular Biology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Clotilde Théry
- Institut Curie, PSL Research University, INSERM U932, Immunity and Cancer, Paris, France
| | | | - Roosmarijn E Vandenbroucke
- VIB Center for Inflammation Research and Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Ann M Wehman
- Department of Biological Sciences, University of Denver, Denver, CO, USA
| | - Kenneth Witwer
- Department of Molecular and Comparative Pathobiology and Neurology and the Richman Family Precision Medicine Center of Excellence in Alzheimer's Disease, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Zhiwei Wu
- Center for Public Health Research, Medical School, Nanjing University, Nanjing, China
- State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing, China
- Medical School, Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing, China
| | - Richard Wubbolts
- Department of Biomolecular Health Sciences, Faculty of veterinary medicine, Utrecht University, Utrecht, the Netherlands
| | - Guillaume van Niel
- Université de Paris, Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM U1266, Paris, France.
- GHU Paris Psychiatrie et Neurosciences, Hôpital Sainte Anne, Paris, France.
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23
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Popova B, Galka D, Häffner N, Wang D, Schmitt K, Valerius O, Knop M, Braus GH. α-Synuclein Decreases the Abundance of Proteasome Subunits and Alters Ubiquitin Conjugates in Yeast. Cells 2021; 10:cells10092229. [PMID: 34571878 PMCID: PMC8468666 DOI: 10.3390/cells10092229] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/25/2021] [Accepted: 08/25/2021] [Indexed: 01/18/2023] Open
Abstract
Parkinson’s disease (PD) is the most prevalent movement disorder characterized with loss of dopaminergic neurons in the brain. One of the pathological hallmarks of the disease is accumulation of aggregated α-synuclein (αSyn) in cytoplasmic Lewy body inclusions that indicates significant dysfunction of protein homeostasis in PD. Accumulation is accompanied with highly elevated S129 phosphorylation, suggesting that this posttranslational modification is linked to pathogenicity and altered αSyn inclusion dynamics. To address the role of S129 phosphorylation on protein dynamics further we investigated the wild type and S129A variants using yeast and a tandem fluorescent timer protein reporter approach to monitor protein turnover and stability. Overexpression of both variants leads to inhibited yeast growth. Soluble S129A is more stable and additional Y133F substitution permits αSyn degradation in a phosphorylation-independent manner. Quantitative cellular proteomics revealed significant αSyn-dependent disturbances of the cellular protein homeostasis, which are increased upon S129 phosphorylation. Disturbances are characterized by decreased abundance of the ubiquitin-dependent protein degradation machinery. Biotin proximity labelling revealed that αSyn interacts with the Rpt2 base subunit. Proteasome subunit depletion by reducing the expression of the corresponding genes enhances αSyn toxicity. Our studies demonstrate that turnover of αSyn and depletion of the proteasome pool correlate in a complex relationship between altered proteasome composition and increased αSyn toxicity.
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Affiliation(s)
- Blagovesta Popova
- Department of Molecular Microbiology and Genetics, Institute for Microbiology and Genetics, University of Göttingen, 37077 Göttingen, Germany; (D.G.); (N.H.); (D.W.); (K.S.); (O.V.)
- Correspondence: (B.P.); (G.H.B.)
| | - Dajana Galka
- Department of Molecular Microbiology and Genetics, Institute for Microbiology and Genetics, University of Göttingen, 37077 Göttingen, Germany; (D.G.); (N.H.); (D.W.); (K.S.); (O.V.)
| | - Nicola Häffner
- Department of Molecular Microbiology and Genetics, Institute for Microbiology and Genetics, University of Göttingen, 37077 Göttingen, Germany; (D.G.); (N.H.); (D.W.); (K.S.); (O.V.)
| | - Dan Wang
- Department of Molecular Microbiology and Genetics, Institute for Microbiology and Genetics, University of Göttingen, 37077 Göttingen, Germany; (D.G.); (N.H.); (D.W.); (K.S.); (O.V.)
| | - Kerstin Schmitt
- Department of Molecular Microbiology and Genetics, Institute for Microbiology and Genetics, University of Göttingen, 37077 Göttingen, Germany; (D.G.); (N.H.); (D.W.); (K.S.); (O.V.)
| | - Oliver Valerius
- Department of Molecular Microbiology and Genetics, Institute for Microbiology and Genetics, University of Göttingen, 37077 Göttingen, Germany; (D.G.); (N.H.); (D.W.); (K.S.); (O.V.)
| | - Michael Knop
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, 69120 Heidelberg, Germany;
| | - Gerhard H. Braus
- Department of Molecular Microbiology and Genetics, Institute for Microbiology and Genetics, University of Göttingen, 37077 Göttingen, Germany; (D.G.); (N.H.); (D.W.); (K.S.); (O.V.)
- Correspondence: (B.P.); (G.H.B.)
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24
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Vangalis V, Likhotkin I, Knop M, Typas MA, Papaioannou IA. Starvation-induced cell fusion and heterokaryosis frequently escape imperfect allorecognition systems in an asexual fungal pathogen. BMC Biol 2021; 19:169. [PMID: 34429100 PMCID: PMC8385987 DOI: 10.1186/s12915-021-01101-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Accepted: 07/16/2021] [Indexed: 01/02/2023] Open
Abstract
Background Asexual fungi include important pathogens of plants and other organisms, and their effective management requires understanding of their evolutionary dynamics. Genetic recombination is critical for adaptability and could be achieved via heterokaryosis — the co-existence of genetically different nuclei in a cell resulting from fusion of non-self spores or hyphae — and the parasexual cycle in the absence of sexual reproduction. Fusion between different strains and establishment of viable heterokaryons are believed to be rare due to non-self recognition systems. Here, we investigate the extent and mechanisms of cell fusion and heterokaryosis in the important asexual plant pathogen Verticillium dahliae. Results We used live-cell imaging and genetic complementation assays of tagged V. dahliae strains to analyze the extent of non-self vegetative fusion, heterokaryotic cell fate, and nuclear behavior. An efficient CRISPR/Cas9-mediated system was developed to investigate the involvement of autophagy in heterokaryosis. Under starvation, non-self fusion of germinating spores occurs frequently regardless of the previously assessed vegetative compatibility of the partners. Supposedly “incompatible” fusions often establish viable heterokaryotic cells and mosaic mycelia, where nuclei can engage in fusion or transfer of genetic material. The molecular machinery of autophagy has a protective function against the destruction of “incompatible” heterokaryons. Conclusions We demonstrate an imperfect function of somatic incompatibility systems in V. dahliae. These systems frequently tolerate the establishment of heterokaryons and potentially the initiation of the parasexual cycle even between strains that were previously regarded as “incompatible.” Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01101-5.
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Affiliation(s)
- Vasileios Vangalis
- Department of Genetics and Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Ilya Likhotkin
- Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
| | - Michael Knop
- Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany.,German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Milton A Typas
- Department of Genetics and Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
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25
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Pirhanov A, Bridges CM, Goodwin RA, Guo YS, Furrer J, Shor LM, Gage DJ, Cho YK. Optogenetics in Sinorhizobium meliloti Enables Spatial Control of Exopolysaccharide Production and Biofilm Structure. ACS Synth Biol 2021; 10:345-356. [PMID: 33465305 DOI: 10.1021/acssynbio.0c00498] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Microorganisms play a vital role in shaping the soil environment and enhancing plant growth by interacting with plant root systems. Because of the vast diversity of cell types involved, combined with dynamic and spatial heterogeneity, identifying the causal contribution of a defined factor, such as a microbial exopolysaccharide (EPS), remains elusive. Synthetic approaches that enable orthogonal control of microbial pathways are a promising means to dissect such complexity. Here we report the implementation of a synthetic, light-activated, transcriptional control platform using the blue-light responsive DNA binding protein EL222 in the nitrogen fixing soil bacterium Sinorhizobium meliloti. By fine-tuning the system, we successfully achieved optical control of an EPS production pathway without significant basal expression under noninducing (dark) conditions. Optical control of EPS recapitulated important behaviors such as a mucoid plate phenotype and formation of structured biofilms, enabling spatial control of biofilm structures in S. meliloti. The successful implementation of optically controlled gene expression in S. meliloti enables systematic investigation of how genotype and microenvironmental factors together shape phenotype in situ.
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Affiliation(s)
- Azady Pirhanov
- Department of Biomedical Engineering, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Charles M. Bridges
- Department of Molecular and Cellular Biology, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Reed A. Goodwin
- Department of Molecular and Cellular Biology, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Yi-Syuan Guo
- Department of Chemical and Biomolecular Engineering, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Jessica Furrer
- Department of Computer Science, Physics, and Engineering, Benedict College, Columbia, South Carolina 29204, United States
| | - Leslie M. Shor
- Department of Chemical and Biomolecular Engineering, University of Connecticut, Storrs, Connecticut 06269, United States
- Center for Environmental Sciences and Engineering, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Daniel J. Gage
- Department of Molecular and Cellular Biology, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Yong Ku Cho
- Department of Biomedical Engineering, University of Connecticut, Storrs, Connecticut 06269, United States
- Department of Chemical and Biomolecular Engineering, University of Connecticut, Storrs, Connecticut 06269, United States
- Center for Environmental Sciences and Engineering, University of Connecticut, Storrs, Connecticut 06269, United States
- Institute for Systems Genomics, University of Connecticut, Storrs, Connecticut 06269, United States
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26
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N α-terminal acetylation of proteins by NatA and NatB serves distinct physiological roles in Saccharomyces cerevisiae. Cell Rep 2021; 34:108711. [PMID: 33535049 DOI: 10.1016/j.celrep.2021.108711] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 10/10/2020] [Accepted: 01/09/2021] [Indexed: 11/22/2022] Open
Abstract
N-terminal (Nt) acetylation is a highly prevalent co-translational protein modification in eukaryotes, catalyzed by at least five Nt acetyltransferases (Nats) with differing specificities. Nt acetylation has been implicated in protein quality control, but its broad biological significance remains elusive. We investigate the roles of the two major Nats of S. cerevisiae, NatA and NatB, by performing transcriptome, translatome, and proteome profiling of natAΔ and natBΔ mutants. Our results reveal a range of NatA- and NatB-specific phenotypes. NatA is implicated in systemic adaptation control, because natAΔ mutants display altered expression of transposons, sub-telomeric genes, pheromone response genes, and nuclear genes encoding mitochondrial ribosomal proteins. NatB predominantly affects protein folding, because natBΔ mutants, to a greater extent than natA mutants, accumulate protein aggregates, induce stress responses, and display reduced fitness in the absence of the ribosome-associated chaperone Ssb. These phenotypic differences indicate that controlling Nat activities may serve to elicit distinct cellular responses.
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27
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Zhang S, Greening DW, Hong Y. Recent advances in bioanalytical methods to measure proteome stability in cells. Analyst 2021; 146:2097-2109. [DOI: 10.1039/d0an01547d] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
This review summarizes recent bioanalytical methods for measuring and profiling protein stability in cells on a proteome-wide scale, which can provide insights for proteostasis and associated diseases.
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Affiliation(s)
- Shouxiang Zhang
- Department of Chemistry and Physics
- La Trobe Institute for Molecular Science
- La Trobe University
- Melbourne
- Australia
| | - David W. Greening
- Molecular Proteomics
- Baker Heart and Diabetes Institute
- Melbourne
- Australia
- Department of Biochemistry and Genetics
| | - Yuning Hong
- Department of Chemistry and Physics
- La Trobe Institute for Molecular Science
- La Trobe University
- Melbourne
- Australia
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28
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Štefl M, Herbst K, Rübsam M, Benda A, Knop M. Single-Color Fluorescence Lifetime Cross-Correlation Spectroscopy In Vivo. Biophys J 2020; 119:1359-1370. [PMID: 32919495 DOI: 10.1016/j.bpj.2020.06.039] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 05/29/2020] [Accepted: 06/16/2020] [Indexed: 01/18/2023] Open
Abstract
The ability to quantify protein concentrations and to measure protein interactions in vivo is key information needed for the understanding of complex processes inside cells, but the acquisition of such information from living cells is still demanding. Fluorescence-based methods like two-color fluorescence cross-correlation spectroscopy can provide this information, but measurement precision is hampered by various sources of errors caused by instrumental or optical limitations such as imperfect overlap of detection volumes or detector cross talk. Furthermore, the nature and properties of used fluorescent proteins or fluorescent dyes, such as labeling efficiency, fluorescent protein maturation, photostability, bleaching, and fluorescence brightness can have an impact. Here, we take advantage of previously published fluorescence lifetime correlation spectroscopy which relies on lifetime differences as a mean to discriminate fluorescent proteins with similar spectral properties and to use them for single-color fluorescence lifetime cross-correlation spectroscopy (sc-FLCCS). By using only one excitation and one detection wavelength, this setup avoids all sources of errors resulting from chromatic aberrations and detector cross talk. To establish sc-FLCCS, we first engineered and tested multiple green fluorescent protein (GFP)-like fluorescent proteins for their suitability. This identified a novel, to our knowledge, GFP variant termed short-lifetime monomeric GFP with the so-far shortest lifetime. Monte-Carlo simulations were employed to explore the suitability of different combinations of GFP variants. Two GFPs, Envy and short-lifetime monomeric GFP, were predicted to constitute the best performing couple for sc-FLCCS measurements. We demonstrated application of this GFP pair for measuring protein interactions between the proteasome and interacting proteins and for measuring protein interactions between three partners when combined with a red florescent protein. Together, our findings establish sc-FLCCS as a valid alternative for conventional dual-color fluorescence cross-correlation spectroscopy measurements.
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Affiliation(s)
- Martin Štefl
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), University of Heidelberg, Heidelberg, Germany; J. Heyrovský Institute of Physical Chemistry, The Czech Academy of Sciences, Prague, Czech Republic.
| | - Konrad Herbst
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), University of Heidelberg, Heidelberg, Germany
| | - Marc Rübsam
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), University of Heidelberg, Heidelberg, Germany
| | - Aleš Benda
- IMCF at BIOCEV, Faculty of Science, Charles University, Vestec, Czech Republic
| | - Michael Knop
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), University of Heidelberg, Heidelberg, Germany; Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany.
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29
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Ashmore-Harris C, Iafrate M, Saleem A, Fruhwirth GO. Non-invasive Reporter Gene Imaging of Cell Therapies, including T Cells and Stem Cells. Mol Ther 2020; 28:1392-1416. [PMID: 32243834 PMCID: PMC7264441 DOI: 10.1016/j.ymthe.2020.03.016] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 02/15/2020] [Accepted: 03/18/2020] [Indexed: 12/14/2022] Open
Abstract
Cell therapies represent a rapidly emerging class of new therapeutics. They are intended and developed for the treatment of some of the most prevalent human diseases, including cancer, diabetes, and for regenerative medicine. Currently, they are largely developed without precise assessment of their in vivo distribution, efficacy, or survival either clinically or preclinically. However, it would be highly beneficial for both preclinical cell therapy development and subsequent clinical use to assess these parameters in situ to enable enhancements in efficacy, applicability, and safety. Molecular imaging can be exploited to track cells non-invasively on the whole-body level and can enable monitoring for prolonged periods in a manner compatible with rapidly expanding cell types. In this review, we explain how in vivo imaging can aid the development and clinical translation of cell-based therapeutics. We describe the underlying principles governing non-invasive in vivo long-term cell tracking in the preclinical and clinical settings, including available imaging technologies, reporter genes, and imaging agents as well as pitfalls related to experimental design. Our emphasis is on adoptively transferred T cell and stem cell therapies.
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Affiliation(s)
- Candice Ashmore-Harris
- Imaging Therapy and Cancer Group, Department of Imaging Chemistry and Biology, School of Biomedical Engineering and Imaging Sciences, King's College London, London SE1 7EH, UK; Centre for Stem Cells and Regenerative Medicine, School of Basic and Medical Biosciences, King's College London, London SE1 9RT, UK
| | - Madeleine Iafrate
- Imaging Therapy and Cancer Group, Department of Imaging Chemistry and Biology, School of Biomedical Engineering and Imaging Sciences, King's College London, London SE1 7EH, UK
| | - Adeel Saleem
- Imaging Therapy and Cancer Group, Department of Imaging Chemistry and Biology, School of Biomedical Engineering and Imaging Sciences, King's College London, London SE1 7EH, UK; Peter Gorer Department of Immunobiology, School of Immunology and Microbial Sciences, King's College London, London SE1 9RT, UK; Department of Haematological Medicine, King's College Hospital, London SE5 9RS, UK
| | - Gilbert O Fruhwirth
- Imaging Therapy and Cancer Group, Department of Imaging Chemistry and Biology, School of Biomedical Engineering and Imaging Sciences, King's College London, London SE1 7EH, UK.
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30
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Devarajan S, Meurer M, van Roermund CWT, Chen X, Hettema EH, Kemp S, Knop M, Williams C. Proteasome-dependent protein quality control of the peroxisomal membrane protein Pxa1p. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183342. [PMID: 32416190 DOI: 10.1016/j.bbamem.2020.183342] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 05/02/2020] [Accepted: 05/04/2020] [Indexed: 10/24/2022]
Abstract
Peroxisomes are eukaryotic organelles that function in numerous metabolic pathways and defects in peroxisome function can cause serious developmental brain disorders such as adrenoleukodystrophy (ALD). Peroxisomal membrane proteins (PMPs) play a crucial role in regulating peroxisome function. Therefore, PMP homeostasis is vital for peroxisome function. Recently, we established that certain PMPs are degraded by the Ubiquitin Proteasome System yet little is known about how faulty/non-functional PMPs undergo quality control. Here we have investigated the degradation of Pxa1p, a fatty acid transporter in the yeast Saccharomyces cerevisiae. Pxa1p is a homologue of the human protein ALDP and mutations in ALDP result in the severe disorder ALD. By introducing two corresponding ALDP mutations into Pxa1p (Pxa1MUT), fused to mGFP, we show that Pxa1MUT-mGFP is rapidly degraded from peroxisomes in a proteasome-dependent manner, while wild type Pxa1-mGFP remains relatively stable. Furthermore, we identify a role for the ubiquitin ligase Ufd4p in Pxa1MUT-mGFP degradation. Finally, we establish that inhibiting Pxa1MUT-mGFP degradation results in a partial rescue of Pxa1p activity in cells. Together, our data demonstrate that faulty PMPs can undergo proteasome-dependent quality control. Furthermore, our observations may provide new insights into the role of ALDP degradation in ALD.
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Affiliation(s)
- S Devarajan
- Department of Cell Biochemistry, University of Groningen, the Netherlands
| | - M Meurer
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - C W T van Roermund
- Laboratory Genetic Metabolic Diseases, Amsterdam University Medical Centres, the Netherlands
| | - X Chen
- Department of Cell Biochemistry, University of Groningen, the Netherlands
| | - E H Hettema
- Department of Molecular Biology, University of Sheffield, Sheffield, United Kingdom
| | - S Kemp
- Laboratory Genetic Metabolic Diseases, Amsterdam University Medical Centres, the Netherlands
| | - M Knop
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany; Cell Morphogenesis and Signal Transduction, German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - C Williams
- Department of Cell Biochemistry, University of Groningen, the Netherlands.
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31
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Iafrate M, Fruhwirth GO. How Non-invasive in vivo Cell Tracking Supports the Development and Translation of Cancer Immunotherapies. Front Physiol 2020; 11:154. [PMID: 32327996 PMCID: PMC7152671 DOI: 10.3389/fphys.2020.00154] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 02/12/2020] [Indexed: 12/26/2022] Open
Abstract
Immunotherapy is a relatively new treatment regimen for cancer, and it is based on the modulation of the immune system to battle cancer. Immunotherapies can be classified as either molecular or cell-based immunotherapies, and both types have demonstrated promising results in a growing number of cancers. Indeed, several immunotherapies representing both classes are already approved for clinical use in oncology. While spectacular treatment successes have been reported, particularly for so-called immune checkpoint inhibitors and certain cell-based immunotherapies, they have also been accompanied by a variety of severe, sometimes life-threatening side effects. Furthermore, not all patients respond to immunotherapy. Hence, there is the need for more research to render these promising therapeutics more efficacious, more widely applicable, and safer to use. Whole-body in vivo imaging technologies that can interrogate cancers and/or immunotherapies are highly beneficial tools for immunotherapy development and translation to the clinic. In this review, we explain how in vivo imaging can aid the development of molecular and cell-based anti-cancer immunotherapies. We describe the principles of imaging host T-cells and adoptively transferred therapeutic T-cells as well as the value of traceable cancer cell models in immunotherapy development. Our emphasis is on in vivo cell tracking methodology, including important aspects and caveats specific to immunotherapies. We discuss a variety of associated experimental design aspects including parameters such as cell type, observation times/intervals, and detection sensitivity. The focus is on non-invasive 3D cell tracking on the whole-body level including aspects relevant for both preclinical experimentation and clinical translatability of the underlying methodologies.
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Affiliation(s)
| | - Gilbert O. Fruhwirth
- Imaging Therapy and Cancer Group, Department of Imaging Chemistry and Biology, School of Biomedical Engineering & Imaging Sciences, King’s College London, London, United Kingdom
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32
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Mideksa YG, Fottner M, Braus S, Weiß CAM, Nguyen TA, Meier S, Lang K, Feige MJ. Site-Specific Protein Labeling with Fluorophores as a Tool To Monitor Protein Turnover. Chembiochem 2020; 21:1861-1867. [PMID: 32011787 PMCID: PMC7383901 DOI: 10.1002/cbic.201900651] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Revised: 01/28/2020] [Indexed: 12/30/2022]
Abstract
Proteins that terminally fail to acquire their native structure are detected and degraded by cellular quality control systems. Insights into cellular protein quality control are key to a better understanding of how cells establish and maintain the integrity of their proteome and of how failures in these processes cause human disease. Here we have used genetic code expansion and fast bio‐orthogonal reactions to monitor protein turnover in mammalian cells through a fluorescence‐based assay. We have used immune signaling molecules (interleukins) as model substrates and shown that our approach preserves normal cellular quality control, assembly processes, and protein functionality and works for different proteins and fluorophores. We have further extended our approach to a pulse‐chase type of assay that can provide kinetic insights into cellular protein behavior. Taken together, this study establishes a minimally invasive method to investigate protein turnover in cells as a key determinant of cellular homeostasis.
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Affiliation(s)
- Yonatan G Mideksa
- Center for Integrated Protein Science Munich (CIPSM) at the Department of Chemistry, Technical University of Munich, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Maximilian Fottner
- Center for Integrated Protein Science Munich (CIPSM) at the Department of Chemistry, Technical University of Munich, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Sebastian Braus
- Center for Integrated Protein Science Munich (CIPSM) at the Department of Chemistry, Technical University of Munich, Lichtenbergstrasse 4, 85748, Garching, Germany.,Current address: Institute of Molecular Biology and Biophysics, ETH Zürich, 8093, Zürich, Switzerland
| | - Caroline A M Weiß
- Center for Integrated Protein Science Munich (CIPSM) at the Department of Chemistry, Technical University of Munich, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Tuan-Anh Nguyen
- Center for Integrated Protein Science Munich (CIPSM) at the Department of Chemistry, Technical University of Munich, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Susanne Meier
- Center for Integrated Protein Science Munich (CIPSM) at the Department of Chemistry, Technical University of Munich, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Kathrin Lang
- Center for Integrated Protein Science Munich (CIPSM) at the Department of Chemistry, Technical University of Munich, Lichtenbergstrasse 4, 85748, Garching, Germany.,Institute for Advanced Study, Technical University of Munich, Lichtenbergstr.2a, 85748, Garching, Germany
| | - Matthias J Feige
- Center for Integrated Protein Science Munich (CIPSM) at the Department of Chemistry, Technical University of Munich, Lichtenbergstrasse 4, 85748, Garching, Germany.,Institute for Advanced Study, Technical University of Munich, Lichtenbergstr.2a, 85748, Garching, Germany
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Abstract
Spatially distributed signaling molecules, known as morphogens, provide spatial information during development. A host of different morphogens have now been identified, from subcellular gradients through to morphogens that act across a whole embryo. These gradients form over a wide-range of timescales, from seconds to hours, and their time windows for interpretation are also highly variable; the processes of morphogen gradient formation and interpretation are highly dynamic. The morphogen Bicoid (Bcd), present in the early Drosophila embryo, is essential for setting up the future Drosophila body segments. Due to its accessibility for both genetic perturbations and imaging, this system has provided key insights into how precise patterning can occur within a highly dynamic system. Here, we review the temporal scales of Bcd gradient formation and interpretation. In particular, we discuss the quantitative evidence for different models of Bcd gradient formation, outline the time windows for Bcd interpretation, and describe how Bcd temporally adapts its own ability to be interpreted. The utilization of temporal information in morphogen readout may provide crucial inputs to ensure precise spatial patterning, particularly in rapidly developing systems.
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34
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Lopez‐Barbosa N, Ludwicki MB, DeLisa MP. Proteome editing using engineered proteins that hijack cellular quality control machinery. AIChE J 2019. [DOI: 10.1002/aic.16854] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Natalia Lopez‐Barbosa
- Robert F. Smith School of Chemical and Biomolecular Engineering Cornell University Ithaca New York
| | - Morgan B. Ludwicki
- Robert F. Smith School of Chemical and Biomolecular Engineering Cornell University Ithaca New York
| | - Matthew P. DeLisa
- Robert F. Smith School of Chemical and Biomolecular Engineering Cornell University Ithaca New York
- Nancy E. and Peter C. Meinig School of Biomedical Engineering Cornell University Ithaca New York
- Biochemistry, Molecular and Cell Biology Cornell University Ithaca New York
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35
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Skruzny M, Pohl E, Abella M. FRET Microscopy in Yeast. BIOSENSORS 2019; 9:E122. [PMID: 31614546 PMCID: PMC6956097 DOI: 10.3390/bios9040122] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 09/19/2019] [Accepted: 09/30/2019] [Indexed: 02/06/2023]
Abstract
Förster resonance energy transfer (FRET) microscopy is a powerful fluorescence microscopy method to study the nanoscale organization of multiprotein assemblies in vivo. Moreover, many biochemical and biophysical processes can be followed by employing sophisticated FRET biosensors directly in living cells. Here, we summarize existing FRET experiments and biosensors applied in yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe, two important models of fundamental biomedical research and efficient platforms for analyses of bioactive molecules. We aim to provide a practical guide on suitable FRET techniques, fluorescent proteins, and experimental setups available for successful FRET experiments in yeasts.
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Affiliation(s)
- Michal Skruzny
- Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany.
- LOEWE Center for Synthetic Microbiology (SYNMIKRO), 35043 Marburg, Germany.
| | - Emma Pohl
- Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
- LOEWE Center for Synthetic Microbiology (SYNMIKRO), 35043 Marburg, Germany
| | - Marc Abella
- Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
- LOEWE Center for Synthetic Microbiology (SYNMIKRO), 35043 Marburg, Germany
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36
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Goslin K, Eschen-Lippold L, Naumann C, Linster E, Sorel M, Klecker M, de Marchi R, Kind A, Wirtz M, Lee J, Dissmeyer N, Graciet E. Differential N-end Rule Degradation of RIN4/NOI Fragments Generated by the AvrRpt2 Effector Protease. PLANT PHYSIOLOGY 2019; 180:2272-2289. [PMID: 31227619 PMCID: PMC6670102 DOI: 10.1104/pp.19.00251] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 06/13/2019] [Indexed: 05/29/2023]
Abstract
In plants, the protein RPM1-INTERACTING PROTEIN4 (RIN4) is a central regulator of both pattern-triggered immunity and effector-triggered immunity. RIN4 is targeted by several effectors, including the Pseudomonas syringae protease effector AvrRpt2. Cleavage of RIN4 by AvrRpt2 generates potentially unstable RIN4 fragments, whose degradation leads to the activation of the resistance protein RESISTANT TO P. SYRINGAE2. Hence, identifying the determinants of RIN4 degradation is key to understanding RESISTANT TO P. SYRINGAE2-mediated effector-triggered immunity, as well as virulence functions of AvrRpt2. In addition to RIN4, AvrRpt2 cleaves host proteins from the nitrate-induced (NOI) domain family. Although cleavage of NOI domain proteins by AvrRpt2 may contribute to pattern-triggered immunity regulation, the (in)stability of these proteolytic fragments and the determinants regulating their stability remain unexamined. Notably, a common feature of RIN4, and of many NOI domain protein fragments generated by AvrRpt2 cleavage, is the exposure of a new N-terminal residue that is destabilizing according to the N-end rule. Using antibodies raised against endogenous RIN4, we show that the destabilization of AvrRpt2-cleaved RIN4 fragments is independent of the N-end rule pathway (recently renamed the N-degron pathway). By contrast, several NOI domain protein fragments are genuine substrates of the N-degron pathway. The discovery of this set of substrates considerably expands the number of known proteins targeted for degradation by this ubiquitin-dependent pathway in plants. These results advance our current understanding of the role of AvrRpt2 in promoting bacterial virulence.
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Affiliation(s)
- Kevin Goslin
- Department of Biology, Maynooth University, Maynooth, County Kildare, Ireland
| | - Lennart Eschen-Lippold
- Department of Stress and Developmental Biology, Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany
| | - Christin Naumann
- Independent Junior Research Group on Protein Recognition and Degradation, Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany
- Centre for Organismal Studies Heidelberg, Heidelberg University, 69120 Heidelberg, Germany
| | - Eric Linster
- Centre for Organismal Studies Heidelberg, Heidelberg University, 69120 Heidelberg, Germany
| | - Maud Sorel
- Department of Biology, Maynooth University, Maynooth, County Kildare, Ireland
| | - Maria Klecker
- Independent Junior Research Group on Protein Recognition and Degradation, Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany
- ScienceCampus Halle - Plant-Based Bioeconomy, 06120 Halle (Saale), Germany
| | - Rémi de Marchi
- Department of Biology, Maynooth University, Maynooth, County Kildare, Ireland
| | - Anne Kind
- Department of Biology, Maynooth University, Maynooth, County Kildare, Ireland
| | - Markus Wirtz
- Centre for Organismal Studies Heidelberg, Heidelberg University, 69120 Heidelberg, Germany
| | - Justin Lee
- Department of Stress and Developmental Biology, Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany
| | - Nico Dissmeyer
- Independent Junior Research Group on Protein Recognition and Degradation, Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany
- ScienceCampus Halle - Plant-Based Bioeconomy, 06120 Halle (Saale), Germany
- Institute of Biochemistry and Biotechnology, Martin Luther University of Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Emmanuelle Graciet
- Department of Biology, Maynooth University, Maynooth, County Kildare, Ireland
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37
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Dederer V, Khmelinskii A, Huhn AG, Okreglak V, Knop M, Lemberg MK. Cooperation of mitochondrial and ER factors in quality control of tail-anchored proteins. eLife 2019; 8:45506. [PMID: 31172943 PMCID: PMC6586462 DOI: 10.7554/elife.45506] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 06/06/2019] [Indexed: 01/04/2023] Open
Abstract
Tail-anchored (TA) proteins insert post-translationally into the endoplasmic reticulum (ER), the outer mitochondrial membrane (OMM) and peroxisomes. Whereas the GET pathway controls ER-targeting, no dedicated factors are known for OMM insertion, posing the question of how accuracy is achieved. The mitochondrial AAA-ATPase Msp1 removes mislocalized TA proteins from the OMM, but it is unclear, how Msp1 clients are targeted for degradation. Here we screened for factors involved in degradation of TA proteins mislocalized to mitochondria. We show that the ER-associated degradation (ERAD) E3 ubiquitin ligase Doa10 controls cytoplasmic level of Msp1 clients. Furthermore, we identified the uncharacterized OMM protein Fmp32 and the ectopically expressed subunit of the ER-mitochondria encounter structure (ERMES) complex Gem1 as native clients for Msp1 and Doa10. We propose that productive localization of TA proteins to the OMM is ensured by complex assembly, while orphan subunits are extracted by Msp1 and eventually degraded by Doa10.
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Affiliation(s)
- Verena Dederer
- Centre for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Anton Khmelinskii
- Centre for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany.,Institute of Molecular Biology (IMB), Mainz, Germany
| | - Anna Gesine Huhn
- Centre for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Voytek Okreglak
- Calico Life Sciences LLC, South San Francisco, United States
| | - Michael Knop
- Centre for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany.,Cell Morphogenesis and Signal Transduction, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Marius K Lemberg
- Centre for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
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38
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Zhang H, Linster E, Gannon L, Leemhuis W, Rundle CA, Theodoulou FL, Wirtz M. Tandem Fluorescent Protein Timers for Noninvasive Relative Protein Lifetime Measurement in Plants. PLANT PHYSIOLOGY 2019; 180:718-731. [PMID: 30872425 PMCID: PMC6548237 DOI: 10.1104/pp.19.00051] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 03/08/2019] [Indexed: 05/17/2023]
Abstract
Targeted protein degradation is an important and pervasive regulatory mechanism in plants, required for perception and response to the environment as well as developmental signaling. Despite the significance of this process, relatively few studies have assessed plant protein turnover in a quantitative fashion. Tandem fluorescent protein timers (tFTs) offer a powerful approach for the assessment of in vivo protein turnover in distinct subcellular compartments of single or multiple cells. A tFT is a fusion of two different fluorescent proteins with distinct fluorophore maturation kinetics, which enable protein age to be estimated from the ratio of fluorescence intensities of the two fluorescent proteins. Here, we used short-lived auxin signaling proteins and model N-end rule (N-recognin) pathway reporters to demonstrate the utility of tFTs for studying protein turnover in living plant cells of Arabidopsis (Arabidopsis thaliana) and Nicotiana benthamiana We present transient expression of tFTs as an efficient screen for relative protein lifetime, useful for testing the effects of mutations and different genetic backgrounds on protein stability. This work demonstrates the potential for using stably expressed tFTs to study native protein dynamics with high temporal resolution in response to exogenous or endogenous stimuli.
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Affiliation(s)
- Hongtao Zhang
- Plant Sciences Department, Rothamsted Research, Harpenden AL5 2JQ, United Kingdom
| | - Eric Linster
- Centre for Organismal Studies, University of Heidelberg, Heidelberg 69120, Germany
| | - Lucy Gannon
- Plant Sciences Department, Rothamsted Research, Harpenden AL5 2JQ, United Kingdom
| | - Wiebke Leemhuis
- Centre for Organismal Studies, University of Heidelberg, Heidelberg 69120, Germany
| | - Chelsea A Rundle
- Plant Sciences Department, Rothamsted Research, Harpenden AL5 2JQ, United Kingdom
| | | | - Markus Wirtz
- Centre for Organismal Studies, University of Heidelberg, Heidelberg 69120, Germany
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39
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Larson ER. Timing Is Everything: Tandem Fluorescent Timers Expand Our Understanding of Protein Longevity. PLANT PHYSIOLOGY 2019; 180:699-700. [PMID: 31160525 PMCID: PMC6548245 DOI: 10.1104/pp.19.00444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Affiliation(s)
- Emily R Larson
- University of Bristol, Bristol, BS8 1QU United Kingdom
- ORCID ID: 0000-0002-5498-8152
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40
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Ludwicki MB, Li J, Stephens EA, Roberts RW, Koide S, Hammond PT, DeLisa MP. Broad-Spectrum Proteome Editing with an Engineered Bacterial Ubiquitin Ligase Mimic. ACS CENTRAL SCIENCE 2019; 5:852-866. [PMID: 31139721 PMCID: PMC6535771 DOI: 10.1021/acscentsci.9b00127] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Indexed: 05/03/2023]
Abstract
Manipulation of the ubiquitin-proteasome pathway to achieve targeted silencing of cellular proteins has emerged as a reliable and customizable strategy for remodeling the mammalian proteome. One such approach involves engineering bifunctional proteins called ubiquibodies that are comprised of a synthetic binding protein fused to an E3 ubiquitin ligase, thus enabling post-translational ubiquitination and degradation of a target protein independent of its function. Here, we have designed a panel of new ubiquibodies based on E3 ubiquitin ligase mimics from bacterial pathogens that are capable of effectively interfacing with the mammalian proteasomal degradation machinery for selective removal of proteins of interest. One of these, the Shigella flexneri effector protein IpaH9.8 fused to a fibronectin type III (FN3) monobody that specifically recognizes green fluorescent protein (GFP), was observed to potently eliminate GFP and its spectral derivatives as well as 15 different FP-tagged mammalian proteins that varied in size (27-179 kDa) and subcellular localization (cytoplasm, nucleus, membrane-associated, and transmembrane). To demonstrate therapeutically relevant delivery of ubiquibodies, we leveraged a bioinspired molecular assembly method whereby synthetic mRNA encoding the GFP-specific ubiquibody was coassembled with poly A binding proteins and packaged into nanosized complexes using biocompatible, structurally defined polypolypeptides bearing cationic amine side groups. The resulting nanoplexes delivered ubiquibody mRNA in a manner that caused efficient target depletion in cultured mammalian cells stably expressing GFP as well as in transgenic mice expressing GFP ubiquitously. Overall, our results suggest that IpaH9.8-based ubiquibodies are a highly modular proteome editing technology with the potential for pharmacologically modulating disease-causing proteins.
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Affiliation(s)
- Morgan B. Ludwicki
- Robert F. Smith
School of Chemical and Biomolecular Engineering, Cornell University, 120 Olin Hall, Ithaca, New
York 14853, United
States
| | - Jiahe Li
- Department of Chemical Engineering and Koch Institute for
Integrative Cancer Research, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Erin A. Stephens
- Biochemistry, Molecular and Cell Biology, Cornell University, Ithaca, New York 14853, United States
| | - Richard W. Roberts
- Department
of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Shohei Koide
- Perlmutter Cancer Center, New York University
Langone Medical Center, New York, New York 10016, United States
- Department of Biochemistry and Molecular
Pharmacology, New York University School
of Medicine, New York, New York 10016, United States
| | - Paula T. Hammond
- Department of Chemical Engineering and Koch Institute for
Integrative Cancer Research, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Matthew P. DeLisa
- Robert F. Smith
School of Chemical and Biomolecular Engineering, Cornell University, 120 Olin Hall, Ithaca, New
York 14853, United
States
- Biochemistry, Molecular and Cell Biology, Cornell University, Ithaca, New York 14853, United States
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41
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Toledo PL, Torkko JM, Müller A, Wegbrod C, Sönmez A, Solimena M, Ermácora MR. ICA512 RESP18 homology domain is a protein-condensing factor and insulin fibrillation inhibitor. J Biol Chem 2019; 294:8564-8576. [PMID: 30979722 DOI: 10.1074/jbc.ra119.007607] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 04/09/2019] [Indexed: 12/19/2022] Open
Abstract
Type 1 diabetes islet cell autoantigen 512 (ICA512/IA-2) is a tyrosine phosphatase-like intrinsic membrane protein involved in the biogenesis and turnover of insulin secretory granules (SGs) in pancreatic islet β-cells. Whereas its membrane-proximal and cytoplasmic domains have been functionally and structurally characterized, the role of the ICA512 N-terminal segment named "regulated endocrine-specific protein 18 homology domain" (RESP18HD), which encompasses residues 35-131, remains largely unknown. Here, we show that ICA512 RESP18HD residues 91-131 encode for an intrinsically disordered region (IDR), which in vitro acts as a condensing factor for the reversible aggregation of insulin and other β-cell proteins in a pH and Zn2+-regulated fashion. At variance with what has been shown for other granule cargoes with aggregating properties, the condensing activity of ICA512 RESP18HD is displayed at a pH close to neutral, i.e. in the pH range found in the early secretory pathway, whereas it is resolved at acidic pH and Zn2+ concentrations resembling those present in mature SGs. Moreover, we show that ICA512 RESP18HD residues 35-90, preceding the IDR, inhibit insulin fibrillation in vitro Finally, we found that glucose-stimulated secretion of RESP18HD upon exocytosis of SGs from insulinoma INS-1 cells is associated with cleavage of its IDR, conceivably to prevent its aggregation upon exposure to neutral pH in the extracellular milieu. Taken together, these findings point to ICA512 RESP18HD being a condensing factor for protein sorting and granulogenesis early in the secretory pathway and for prevention of amyloidogenesis.
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Affiliation(s)
- Pamela L Toledo
- Grupo de Biología Estructural y Biotecnología, Universidad Nacional de Quilmes, 1876 Bernal, Buenos Aires, Argentina; IMBICE, CONICET-CIC-Universidad Nacional de La Plata, B1906APO La Plata, Buenos Aires, Argentina
| | - Juha M Torkko
- Grupo de Biología Estructural y Biotecnología, Universidad Nacional de Quilmes, 1876 Bernal, Buenos Aires, Argentina; IMBICE, CONICET-CIC-Universidad Nacional de La Plata, B1906APO La Plata, Buenos Aires, Argentina; Department of Molecular Diabetology, University Hospital and Faculty of Medicine, TU Dresden, 01307 Dresden, Germany; Paul Langerhans Institute Dresden of the Helmholtz Center Munich at the University Hospital and Faculty of Medicine, TU Dresden, 01307 Dresden, Germany; German Center for Diabetes Research (DZD e.V.), 85764 Neuherberg, Germany
| | - Andreas Müller
- Department of Molecular Diabetology, University Hospital and Faculty of Medicine, TU Dresden, 01307 Dresden, Germany; Paul Langerhans Institute Dresden of the Helmholtz Center Munich at the University Hospital and Faculty of Medicine, TU Dresden, 01307 Dresden, Germany; German Center for Diabetes Research (DZD e.V.), 85764 Neuherberg, Germany
| | - Carolin Wegbrod
- Department of Molecular Diabetology, University Hospital and Faculty of Medicine, TU Dresden, 01307 Dresden, Germany; Paul Langerhans Institute Dresden of the Helmholtz Center Munich at the University Hospital and Faculty of Medicine, TU Dresden, 01307 Dresden, Germany; German Center for Diabetes Research (DZD e.V.), 85764 Neuherberg, Germany
| | - Anke Sönmez
- Department of Molecular Diabetology, University Hospital and Faculty of Medicine, TU Dresden, 01307 Dresden, Germany; Paul Langerhans Institute Dresden of the Helmholtz Center Munich at the University Hospital and Faculty of Medicine, TU Dresden, 01307 Dresden, Germany; German Center for Diabetes Research (DZD e.V.), 85764 Neuherberg, Germany
| | - Michele Solimena
- Department of Molecular Diabetology, University Hospital and Faculty of Medicine, TU Dresden, 01307 Dresden, Germany; Paul Langerhans Institute Dresden of the Helmholtz Center Munich at the University Hospital and Faculty of Medicine, TU Dresden, 01307 Dresden, Germany; German Center for Diabetes Research (DZD e.V.), 85764 Neuherberg, Germany; Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany.
| | - Mario R Ermácora
- Grupo de Biología Estructural y Biotecnología, Universidad Nacional de Quilmes, 1876 Bernal, Buenos Aires, Argentina; IMBICE, CONICET-CIC-Universidad Nacional de La Plata, B1906APO La Plata, Buenos Aires, Argentina.
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42
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Kats I, Khmelinskii A, Kschonsak M, Huber F, Knieß RA, Bartosik A, Knop M. Mapping Degradation Signals and Pathways in a Eukaryotic N-terminome. Mol Cell 2019; 70:488-501.e5. [PMID: 29727619 DOI: 10.1016/j.molcel.2018.03.033] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 01/26/2018] [Accepted: 03/27/2018] [Indexed: 01/01/2023]
Abstract
Most eukaryotic proteins are N-terminally acetylated. This modification can be recognized as a signal for selective protein degradation (degron) by the N-end rule pathways. However, the prevalence and specificity of such degrons in the proteome are unclear. Here, by systematically examining how protein turnover is affected by N-terminal sequences, we perform a comprehensive survey of degrons in the yeast N-terminome. We find that approximately 26% of nascent protein N termini encode cryptic degrons. These degrons exhibit high hydrophobicity and are frequently recognized by the E3 ubiquitin ligase Doa10, suggesting a role in protein quality control. In contrast, N-terminal acetylation rarely functions as a degron. Surprisingly, we identify two pathways where N-terminal acetylation has the opposite function and blocks protein degradation through the E3 ubiquitin ligase Ubr1. Our analysis highlights the complexity of N-terminal degrons and argues that hydrophobicity, not N-terminal acetylation, is the predominant feature of N-terminal degrons in nascent proteins.
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Affiliation(s)
- Ilia Kats
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | - Anton Khmelinskii
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | - Marc Kschonsak
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | - Florian Huber
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | - Robert A Knieß
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | - Anna Bartosik
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | - Michael Knop
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany; Deutsches Krebsforschungszentrum (DKFZ), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany.
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43
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Greenwald EC, Mehta S, Zhang J. Genetically Encoded Fluorescent Biosensors Illuminate the Spatiotemporal Regulation of Signaling Networks. Chem Rev 2018; 118:11707-11794. [PMID: 30550275 PMCID: PMC7462118 DOI: 10.1021/acs.chemrev.8b00333] [Citation(s) in RCA: 316] [Impact Index Per Article: 52.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Cellular signaling networks are the foundation which determines the fate and function of cells as they respond to various cues and stimuli. The discovery of fluorescent proteins over 25 years ago enabled the development of a diverse array of genetically encodable fluorescent biosensors that are capable of measuring the spatiotemporal dynamics of signal transduction pathways in live cells. In an effort to encapsulate the breadth over which fluorescent biosensors have expanded, we endeavored to assemble a comprehensive list of published engineered biosensors, and we discuss many of the molecular designs utilized in their development. Then, we review how the high temporal and spatial resolution afforded by fluorescent biosensors has aided our understanding of the spatiotemporal regulation of signaling networks at the cellular and subcellular level. Finally, we highlight some emerging areas of research in both biosensor design and applications that are on the forefront of biosensor development.
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Affiliation(s)
- Eric C Greenwald
- University of California , San Diego, 9500 Gilman Drive, BRFII , La Jolla , CA 92093-0702 , United States
| | - Sohum Mehta
- University of California , San Diego, 9500 Gilman Drive, BRFII , La Jolla , CA 92093-0702 , United States
| | - Jin Zhang
- University of California , San Diego, 9500 Gilman Drive, BRFII , La Jolla , CA 92093-0702 , United States
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44
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Castells-Ballester J, Zatorska E, Meurer M, Neubert P, Metschies A, Knop M, Strahl S. Monitoring Protein Dynamics in Protein O-Mannosyltransferase Mutants In Vivo by Tandem Fluorescent Protein Timers. Molecules 2018; 23:E2622. [PMID: 30322079 PMCID: PMC6222916 DOI: 10.3390/molecules23102622] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 10/05/2018] [Accepted: 10/09/2018] [Indexed: 12/27/2022] Open
Abstract
For proteins entering the secretory pathway, a major factor contributing to maturation and homeostasis is glycosylation. One relevant type of protein glycosylation is O-mannosylation, which is essential and evolutionarily-conserved in fungi, animals, and humans. Our recent proteome-wide study in the eukaryotic model organism Saccharomyces cerevisiae revealed that more than 26% of all proteins entering the secretory pathway receive O-mannosyl glycans. In a first attempt to understand the impact of O-mannosylation on these proteins, we took advantage of a tandem fluorescent timer (tFT) reporter to monitor different aspects of protein dynamics. We analyzed tFT-reporter fusions of 137 unique O-mannosylated proteins, mainly of the secretory pathway and the plasma membrane, in mutants lacking the major protein O-mannosyltransferases Pmt1, Pmt2, or Pmt4. In these three pmtΔ mutants, a total of 39 individual proteins were clearly affected, and Pmt-specific substrate proteins could be identified. We observed that O-mannosylation may cause both enhanced and diminished protein abundance and/or stability when compromised, and verified our findings on the examples of Axl2-tFT and Kre6-tFT fusion proteins. The identified target proteins are a valuable resource towards unraveling the multiple functions of O-mannosylation at the molecular level.
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Affiliation(s)
| | - Ewa Zatorska
- Centre for Organismal Studies (COS), Heidelberg University, 69120 Heidelberg, Germany.
| | - Matthias Meurer
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, 69120 Heidelberg, Germany.
| | - Patrick Neubert
- Centre for Organismal Studies (COS), Heidelberg University, 69120 Heidelberg, Germany.
| | - Anke Metschies
- Centre for Organismal Studies (COS), Heidelberg University, 69120 Heidelberg, Germany.
| | - Michael Knop
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, 69120 Heidelberg, Germany.
- Deutsches Krebsforschungszentrum (DKFZ), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany.
| | - Sabine Strahl
- Centre for Organismal Studies (COS), Heidelberg University, 69120 Heidelberg, Germany.
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45
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Durrieu L, Kirrmaier D, Schneidt T, Kats I, Raghavan S, Hufnagel L, Saunders TE, Knop M. Bicoid gradient formation mechanism and dynamics revealed by protein lifetime analysis. Mol Syst Biol 2018; 14:e8355. [PMID: 30181144 PMCID: PMC6121778 DOI: 10.15252/msb.20188355] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 08/06/2018] [Accepted: 08/07/2018] [Indexed: 01/21/2023] Open
Abstract
Embryogenesis relies on instructions provided by spatially organized signaling molecules known as morphogens. Understanding the principles behind morphogen distribution and how cells interpret locally this information remains a major challenge in developmental biology. Here, we introduce morphogen-age measurements as a novel approach to test models of morphogen gradient formation. Using a tandem fluorescent timer as a protein age sensor, we find a gradient of increasing age of Bicoid along the anterior-posterior axis in the early Drosophila embryo. Quantitative analysis of the protein age distribution across the embryo reveals that the synthesis-diffusion-degradation model is the most likely model underlying Bicoid gradient formation, and rules out other hypotheses for gradient formation. Moreover, we show that the timer can detect transitions in the dynamics associated with syncytial cellularization. Our results provide new insight into Bicoid gradient formation and demonstrate how morphogen-age information can complement knowledge about movement, abundance, and distribution, which should be widely applicable to other systems.
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Affiliation(s)
- Lucia Durrieu
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, University of Heidelberg, Heidelberg, Germany
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Daniel Kirrmaier
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, University of Heidelberg, Heidelberg, Germany
- Deutsches Krebsforschungszentrum (DKFZ) DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Tatjana Schneidt
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Ilia Kats
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, University of Heidelberg, Heidelberg, Germany
| | - Sarada Raghavan
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, University of Heidelberg, Heidelberg, Germany
| | - Lars Hufnagel
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Timothy E Saunders
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Mechanobiology Institute and Department of Biological Sciences, National University of Singapore, Singapore
- Institute of Molecular and Cell Biology, A*Star, Biopolis, Singapore
| | - Michael Knop
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, University of Heidelberg, Heidelberg, Germany
- Deutsches Krebsforschungszentrum (DKFZ) DKFZ-ZMBH Alliance, Heidelberg, Germany
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46
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Alber AB, Paquet ER, Biserni M, Naef F, Suter DM. Single Live Cell Monitoring of Protein Turnover Reveals Intercellular Variability and Cell-Cycle Dependence of Degradation Rates. Mol Cell 2018; 71:1079-1091.e9. [DOI: 10.1016/j.molcel.2018.07.023] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 06/05/2018] [Accepted: 07/20/2018] [Indexed: 11/28/2022]
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47
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Zöller E, Todd Alexander R, Herrmann JM. Proteasomal degradation competes with Mia40-mediated import into mitochondria. BMC Biol 2018; 16:63. [PMID: 29929505 PMCID: PMC6013994 DOI: 10.1186/s12915-018-0537-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Tandem fluorescent protein timers are elegant tools to determine proteolytic stabilities of cytosolic proteins with high spatial and temporal resolution. In a new study published in BMC Biology, Kowalski et al. fused timers to precursors of proteins of the mitochondrial intermembrane space and found that they are under surveillance of the ubiquitin-proteasome system. Ubiquitination at lysine residues of these precursors directly inhibits their translocation into the intermembrane space and targets them for proteasomal degradation.
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Affiliation(s)
- Eva Zöller
- Cell Biology, University of Kaiserslautern, Erwin-Schrödinger-Strasse 13, 67663, Kaiserslautern, Germany
| | - R Todd Alexander
- Department of Pediatrics, University of Alberta, Edmonton, AB, T6G 1C9, Canada
| | - Johannes M Herrmann
- Cell Biology, University of Kaiserslautern, Erwin-Schrödinger-Strasse 13, 67663, Kaiserslautern, Germany.
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48
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Kowalski L, Bragoszewski P, Khmelinskii A, Glow E, Knop M, Chacinska A. Determinants of the cytosolic turnover of mitochondrial intermembrane space proteins. BMC Biol 2018; 16:66. [PMID: 29929515 PMCID: PMC6013907 DOI: 10.1186/s12915-018-0536-1] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 05/25/2018] [Indexed: 12/31/2022] Open
Abstract
Background The proteome of mitochondria comprises mostly proteins that originate as precursors in the cytosol. Before import into the organelle, such proteins are exposed to cytosolic quality control mechanisms. Multiple lines of evidence indicate a significant contribution of the major cytosolic protein degradation machinery, the ubiquitin-proteasome system, to the quality control of mitochondrial proteins. Proteins that are directed to the mitochondrial intermembrane space (IMS) exemplify an entire class of mitochondrial proteins regulated by proteasomal degradation. However, little is known about how these proteins are selected for degradation. Results The present study revealed the heterogeneous cytosolic stability of IMS proteins. Using a screening approach, we found that different cytosolic factors are responsible for the degradation of specific IMS proteins, with no single common factor involved in the degradation of all IMS proteins. We found that the Cox12 protein is rapidly degraded when localized to the cytosol, thus providing a sensitive experimental model. Using Cox12, we found that lysine residues but not conserved cysteine residues are among the degron features important for protein ubiquitination. We observed the redundancy of ubiquitination components, with significant roles of Ubc4 E2 ubiquitin-conjugating enzyme and Rsp5 E3 ubiquitin ligase. The amount of ubiquitinated Cox12 was inversely related to mitochondrial import efficiency. Importantly, we found that precursor protein ubiquitination blocks its import into mitochondria. Conclusions The present study confirms the involvement of ubiquitin-proteasome system in the quality control of mitochondrial IMS proteins in the cytosol. Notably, ubiquitination of IMS proteins prohibits their import into mitochondria. Therefore, ubiquitination directly affects the availability of precursor proteins for organelle biogenesis. Importantly, despite their structural similarities, IMS proteins are not selected for degradation in a uniform way. Instead, specific IMS proteins rely on discrete components of the ubiquitination machinery to mediate their clearance by the proteasome. Electronic supplementary material The online version of this article (10.1186/s12915-018-0536-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lukasz Kowalski
- Centre of New Technologies, University of Warsaw, Warsaw, Poland.,International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Piotr Bragoszewski
- Centre of New Technologies, University of Warsaw, Warsaw, Poland. .,International Institute of Molecular and Cell Biology, Warsaw, Poland.
| | - Anton Khmelinskii
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Heidelberg, Germany.,Institute of Molecular Biology (IMB), Mainz, Germany
| | - Edyta Glow
- International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Michael Knop
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Heidelberg, Germany.,Deutsches Krebsforschungszentrum (DKFZ), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Agnieszka Chacinska
- Centre of New Technologies, University of Warsaw, Warsaw, Poland. .,International Institute of Molecular and Cell Biology, Warsaw, Poland.
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49
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Bonaiuti P, Chiroli E, Gross F, Corno A, Vernieri C, Štefl M, Cosentino Lagomarsino M, Knop M, Ciliberto A. Cells Escape an Operational Mitotic Checkpoint through a Stochastic Process. Curr Biol 2017; 28:28-37.e7. [PMID: 29249657 DOI: 10.1016/j.cub.2017.11.031] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 10/23/2017] [Accepted: 11/13/2017] [Indexed: 11/18/2022]
Abstract
Improperly attached chromosomes activate the mitotic checkpoint that arrests cell division before anaphase. Cells can maintain an arrest for several hours but eventually will resume proliferation, a process we refer to as adaptation. Whether adapting cells bypass an active block or whether the block has to be removed to resume proliferation is not clear. Likewise, it is not known whether all cells of a genetically homogeneous population are equally capable to adapt. Here, we show that the mitotic checkpoint is operational when yeast cells adapt and that each cell has the same propensity to adapt. Our results are consistent with a model of the mitotic checkpoint where adaptation is driven by random fluctuations of APC/CCdc20, the molecular species inhibited by the checkpoint. Our data provide a quantitative framework for understanding how cells overcome a constant stimulus that halts cell cycle progression.
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Affiliation(s)
- Paolo Bonaiuti
- Istituto Firc di Oncologia Molecolare, IFOM, via Adamello 16, 20139 Milan, Italy
| | - Elena Chiroli
- Istituto Firc di Oncologia Molecolare, IFOM, via Adamello 16, 20139 Milan, Italy
| | - Fridolin Gross
- Istituto Firc di Oncologia Molecolare, IFOM, via Adamello 16, 20139 Milan, Italy
| | - Andrea Corno
- Istituto Firc di Oncologia Molecolare, IFOM, via Adamello 16, 20139 Milan, Italy
| | - Claudio Vernieri
- Istituto Firc di Oncologia Molecolare, IFOM, via Adamello 16, 20139 Milan, Italy; Medical Oncology Department, Fondazione IRCCS Istituto Nazionale Tumori, via Venezian 1, 20133 Milan, Italy
| | - Martin Štefl
- DKFZ-ZMBH Alliance, Centre for Molecular Biology (ZMBH), University of Heidelberg, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | - Marco Cosentino Lagomarsino
- Istituto Firc di Oncologia Molecolare, IFOM, via Adamello 16, 20139 Milan, Italy; Sorbonne Universités, UPMC Univ Paris 06, 5 Place Jussieu, 75005 Paris, France; CNRS, UMR 7238 "Biologie Computationnelle et Quantitative," UPMC, Institut de Biologie Paris Seine, 4 Place Jussieu, 75005 Paris, France
| | - Michael Knop
- DKFZ-ZMBH Alliance, Centre for Molecular Biology (ZMBH), University of Heidelberg, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany; DKFZ-ZMBH Alliance, Department of Cell and Tumour Biology, German Cancer Research Centre (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Andrea Ciliberto
- Istituto Firc di Oncologia Molecolare, IFOM, via Adamello 16, 20139 Milan, Italy; Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (IGM-CNR), via Abbiategrasso 207, 27100 Pavia, Italy.
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50
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Cao QY, Jiang R, Liu M, Wan Q, Xu D, Tian J, Huang H, Wen Y, Zhang X, Wei Y. Preparation of AIE-active fluorescent polymeric nanoparticles through a catalyst-free thiol-yne click reaction for bioimaging applications. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2017; 80:411-416. [DOI: 10.1016/j.msec.2017.06.008] [Citation(s) in RCA: 109] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 05/26/2017] [Accepted: 06/15/2017] [Indexed: 01/25/2023]
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