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Murawska GM, Vogel C, Jan M, Lu X, Schild M, Slabicki M, Zou C, Zhanybekova S, Manojkumar M, Petzold G, Kaiser P, Thomä N, Ebert B, Gillingham D. Repurposing the Damage Repair Protein Methyl Guanine Methyl Transferase as a Ligand Inducible Fusion Degron. ACS Chem Biol 2022; 17:24-31. [PMID: 34982531 DOI: 10.1021/acschembio.1c00771] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We successfully repurpose the DNA repair protein methylguanine methyltransferase (MGMT) as an inducible degron for protein fusions. MGMT is a suicide protein that removes alkyl groups from the O6 position of guanine (O6G) and is thereafter quickly degraded by the ubiquitin proteasome pathway (UPP). Starting with MGMT pseudosubstrates (benzylguanine and lomeguatrib), we first demonstrate that these lead to potent MGMT depletion while affecting little else in the proteome. We then show that fusion proteins of MGMT undergo rapid UPP-dependent degradation in response to pseudosubstrates. Mechanistic studies confirm the involvement of the UPP, while revealing that at least two E3 ligase classes can degrade MGMT depending on cell-line and expression type (native or ectopic). We also demonstrate the technique's versatility with two clinically relevant examples: degradation of KRASG12C and a chimeric antigen receptor.
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Affiliation(s)
- Gosia M. Murawska
- Department of Chemistry, University of Basel, 4056 Basel, Switzerland
| | - Caspar Vogel
- Department of Chemistry, University of Basel, 4056 Basel, Switzerland
| | - Max Jan
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, United States
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Xinyan Lu
- Department of Chemistry, University of Basel, 4056 Basel, Switzerland
| | - Matthias Schild
- Department of Chemistry, University of Basel, 4056 Basel, Switzerland
| | - Mikolaj Slabicki
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, United States
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Charles Zou
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, United States
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Saule Zhanybekova
- Department of Chemistry, University of Basel, 4056 Basel, Switzerland
| | - Manisha Manojkumar
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, United States
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Georg Petzold
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Peter Kaiser
- Department of Biological Chemistry, University of California, Irvine, California 92697, United States
| | - Nicolas Thomä
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Benjamin Ebert
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, United States
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Dennis Gillingham
- Department of Chemistry, University of Basel, 4056 Basel, Switzerland
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Joss D, Reznikova K, Pfund B, Niggli N, Murawska GM, Miarzlou DA, Meyer CE, Chimisso V, Baiyoumy A, Rieder P. Christmas Symposium Basel, December 4, 2020. Chimia (Aarau) 2021. [DOI: 10.2533/chimia.2021.112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Yan D, Yadav SR, Paterlini A, Nicolas WJ, Petit JD, Brocard L, Belevich I, Grison MS, Vaten A, Karami L, El-Showk S, Lee JY, Murawska GM, Mortimer J, Knoblauch M, Jokitalo E, Markham JE, Bayer EM, Helariutta Y. Publisher Correction: Sphingolipid biosynthesis modulates plasmodesmal ultrastructure and phloem unloading. Nat Plants 2019; 5:1023. [PMID: 31420590 DOI: 10.1038/s41477-019-0513-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
- Dawei Yan
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK
| | - Shri Ram Yadav
- Helsinki Institute of Life Science/Institute of Biotechnology, University of Helsinki, Helsinki, Finland
- Department of Biotechnology, Indian Institute of Technology, Roorkee, India
| | - Andrea Paterlini
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK
| | - William J Nicolas
- Laboratoire de Biogenèse Membranaire, UMR 5200, CNRS, Université de Bordeaux, Villenave d'Ornon, France
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Jules D Petit
- Laboratoire de Biogenèse Membranaire, UMR 5200, CNRS, Université de Bordeaux, Villenave d'Ornon, France
| | - Lysiane Brocard
- Bordeaux Imaging Centre, Plant Imaging Platform, UMS 3420, INRA-CNRS-INSERM, University of Bordeaux, Villenave-d'Ornon, France
| | - Ilya Belevich
- Helsinki Institute of Life Science/Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Magali S Grison
- Laboratoire de Biogenèse Membranaire, UMR 5200, CNRS, Université de Bordeaux, Villenave d'Ornon, France
| | - Anne Vaten
- Helsinki Institute of Life Science/Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Leila Karami
- Helsinki Institute of Life Science/Institute of Biotechnology, University of Helsinki, Helsinki, Finland
- Department of Horticulture, Faculty of Agriculture and Natural Resources, Persian Gulf University, Bushehr, Iran
| | - Sedeer El-Showk
- Helsinki Institute of Life Science/Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Jung-Youn Lee
- Department of Plant and Soil Sciences, Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA
| | - Gosia M Murawska
- Biosciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Joint Bioenergy Institute, Emeryville, CA, USA
| | - Jenny Mortimer
- Biosciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Joint Bioenergy Institute, Emeryville, CA, USA
| | - Michael Knoblauch
- School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Eija Jokitalo
- Helsinki Institute of Life Science/Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Jennifer E Markham
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Emmanuelle M Bayer
- Laboratoire de Biogenèse Membranaire, UMR 5200, CNRS, Université de Bordeaux, Villenave d'Ornon, France.
| | - Ykä Helariutta
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK.
- Helsinki Institute of Life Science/Institute of Biotechnology, University of Helsinki, Helsinki, Finland.
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Yan D, Yadav SR, Paterlini A, Nicolas WJ, Petit JD, Brocard L, Belevich I, Grison MS, Vaten A, Karami L, El-Showk S, Lee JY, Murawska GM, Mortimer J, Knoblauch M, Jokitalo E, Markham JE, Bayer EM, Helariutta Y. Sphingolipid biosynthesis modulates plasmodesmal ultrastructure and phloem unloading. Nat Plants 2019; 5:604-615. [PMID: 31182845 PMCID: PMC6565433 DOI: 10.1038/s41477-019-0429-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 04/17/2019] [Indexed: 05/18/2023]
Abstract
During phloem unloading, multiple cell-to-cell transport events move organic substances to the root meristem. Although the primary unloading event from the sieve elements to the phloem pole pericycle has been characterized to some extent, little is known about post-sieve element unloading. Here, we report a novel gene, PHLOEM UNLOADING MODULATOR (PLM), in the absence of which plasmodesmata-mediated symplastic transport through the phloem pole pericycle-endodermis interface is specifically enhanced. Increased unloading is attributable to a defect in the formation of the endoplasmic reticulum-plasma membrane tethers during plasmodesmal morphogenesis, resulting in the majority of pores lacking a visible cytoplasmic sleeve. PLM encodes a putative enzyme required for the biosynthesis of sphingolipids with very-long-chain fatty acid. Taken together, our results indicate that post-sieve element unloading involves sphingolipid metabolism, which affects plasmodesmal ultrastructure. They also raise the question of how and why plasmodesmata with no cytoplasmic sleeve facilitate molecular trafficking.
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Affiliation(s)
- Dawei Yan
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK
| | - Shri Ram Yadav
- Helsinki Institute of Life Science/Institute of Biotechnology, University of Helsinki, Helsinki, Finland
- Department of Biotechnology, Indian Institute of Technology, Roorkee, India
| | - Andrea Paterlini
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK
| | - William J Nicolas
- Laboratoire de Biogenèse Membranaire, UMR 5200, CNRS, Université de Bordeaux, Villenave d'Ornon, France
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Jules D Petit
- Laboratoire de Biogenèse Membranaire, UMR 5200, CNRS, Université de Bordeaux, Villenave d'Ornon, France
- Laboratoire de Biophysique Moléculaire aux Interfaces, TERRA Research Centre, GX ABT, Université de Liège, Gembloux, Belgium
| | - Lysiane Brocard
- Bordeaux Imaging Centre, Plant Imaging Platform, UMS 3420, INRA-CNRS-INSERM, University of Bordeaux, Villenave-d'Ornon, France
| | - Ilya Belevich
- Helsinki Institute of Life Science/Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Magali S Grison
- Laboratoire de Biogenèse Membranaire, UMR 5200, CNRS, Université de Bordeaux, Villenave d'Ornon, France
| | - Anne Vaten
- Helsinki Institute of Life Science/Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Leila Karami
- Helsinki Institute of Life Science/Institute of Biotechnology, University of Helsinki, Helsinki, Finland
- Department of Horticulture, Faculty of Agriculture and Natural Resources, Persian Gulf University, Bushehr, Iran
| | - Sedeer El-Showk
- Helsinki Institute of Life Science/Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Jung-Youn Lee
- Department of Plant and Soil Sciences, Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA
| | - Gosia M Murawska
- Biosciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Joint Bioenergy Institute, Emeryville, CA, USA
| | - Jenny Mortimer
- Biosciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Joint Bioenergy Institute, Emeryville, CA, USA
| | - Michael Knoblauch
- School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Eija Jokitalo
- Helsinki Institute of Life Science/Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Jennifer E Markham
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Emmanuelle M Bayer
- Laboratoire de Biogenèse Membranaire, UMR 5200, CNRS, Université de Bordeaux, Villenave d'Ornon, France.
| | - Ykä Helariutta
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK.
- Helsinki Institute of Life Science/Institute of Biotechnology, University of Helsinki, Helsinki, Finland.
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Murawska GM, Poloni C, Simeth NA, Szymanski W, Feringa BL. Cover Feature: Comparative Study of Photoswitchable Zinc‐Finger Domain and AT‐Hook Motif for Light‐Controlled Peptide–DNA Binding (Chem. Eur. J. 19/2019). Chemistry 2019. [DOI: 10.1002/chem.201901008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Gosia M. Murawska
- Centre for Systems ChemistryStratingh Institute for ChemistryUniversity of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Claudia Poloni
- Centre for Systems ChemistryStratingh Institute for ChemistryUniversity of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Nadja A. Simeth
- Centre for Systems ChemistryStratingh Institute for ChemistryUniversity of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Wiktor Szymanski
- Centre for Systems ChemistryStratingh Institute for ChemistryUniversity of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
- Department of RadiologyUniversity of Groningen, University Medical Centre Groningen Hanzeplein 1 9713 GZ Groningen The Netherlands
| | - Ben L. Feringa
- Centre for Systems ChemistryStratingh Institute for ChemistryUniversity of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
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Murawska GM, Poloni C, Simeth NA, Szymanski W, Feringa BL. Comparative Study of Photoswitchable Zinc-Finger Domain and AT-Hook Motif for Light-Controlled Peptide-DNA Binding. Chemistry 2019; 25:4965-4973. [PMID: 30735272 DOI: 10.1002/chem.201900090] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Indexed: 12/20/2022]
Abstract
DNA-peptide interactions are involved in key life processes, including DNA recognition, replication, transcription, repair, organization, and modification. Development of tools that can influence DNA-peptide binding non-invasively with high spatiotemporal precision could aid in determining its role in cells and tissues. Here, the design, synthesis, and study of photocontrolled tools for sequence-specific small peptide-DNA major and minor groove interactions are reported, shedding light on DNA binding by transcriptionally active peptides. In particular, photoswitchable moieties were implemented in the peptide backbone or turn region. In each case, DNA binding was affected by photochemical isomerization, as determined in fluorescent displacement assays on model DNA strands, which provides promising tools for DNA modulation.
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Affiliation(s)
- Gosia M Murawska
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747, AG, Groningen, The Netherlands
| | - Claudia Poloni
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747, AG, Groningen, The Netherlands
| | - Nadja A Simeth
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747, AG, Groningen, The Netherlands
| | - Wiktor Szymanski
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747, AG, Groningen, The Netherlands.,Department of Radiology, University of Groningen, University Medical Centre Groningen, Hanzeplein 1, 9713 GZ, Groningen, The Netherlands
| | - Ben L Feringa
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747, AG, Groningen, The Netherlands
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Fang L, Ishikawa T, Rennie EA, Murawska GM, Lao J, Yan J, Tsai AYL, Baidoo EEK, Xu J, Keasling JD, Demura T, Kawai-Yamada M, Scheller HV, Mortimer JC. Loss of Inositol Phosphorylceramide Sphingolipid Mannosylation Induces Plant Immune Responses and Reduces Cellulose Content in Arabidopsis. Plant Cell 2016; 28:2991-3004. [PMID: 27895225 PMCID: PMC5240734 DOI: 10.1105/tpc.16.00186] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 11/11/2016] [Accepted: 11/22/2016] [Indexed: 05/03/2023]
Abstract
Glycosylinositol phosphorylceramides (GIPCs) are a class of glycosylated sphingolipids found in plants, fungi, and protozoa. These lipids are abundant in the plant plasma membrane, forming ∼25% of total plasma membrane lipids. Little is known about the function of the glycosylated headgroup, but two recent studies have indicated that they play a key role in plant signaling and defense. Here, we show that a member of glycosyltransferase family 64, previously named ECTOPICALLY PARTING CELLS1, is likely a Golgi-localized GIPC-specific mannosyl-transferase, which we renamed GIPC MANNOSYL-TRANSFERASE1 (GMT1). Sphingolipid analysis revealed that the Arabidopsis thaliana gmt1 mutant almost completely lacks mannose-carrying GIPCs. Heterologous expression of GMT1 in Saccharomyces cerevisiae and tobacco (Nicotiana tabacum) cv Bright Yellow 2 resulted in the production of non-native mannosylated GIPCs. gmt1 displays a severe dwarfed phenotype and a constitutive hypersensitive response characterized by elevated salicylic acid and hydrogen peroxide levels, similar to that we previously reported for the Golgi-localized, GIPC-specific, GDP-Man transporter GONST1 (Mortimer et al., 2013). Unexpectedly, we show that gmt1 cell walls have a reduction in cellulose content, although other matrix polysaccharides are unchanged.
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Affiliation(s)
- Lin Fang
- Joint BioEnergy Institute, Emeryville, California 94608
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Toshiki Ishikawa
- Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan
| | - Emilie A Rennie
- Joint BioEnergy Institute, Emeryville, California 94608
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Gosia M Murawska
- Joint BioEnergy Institute, Emeryville, California 94608
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Jeemeng Lao
- Joint BioEnergy Institute, Emeryville, California 94608
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Jingwei Yan
- Joint BioEnergy Institute, Emeryville, California 94608
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Alex Yi-Lin Tsai
- Joint BioEnergy Institute, Emeryville, California 94608
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Edward E K Baidoo
- Joint BioEnergy Institute, Emeryville, California 94608
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Jun Xu
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720
| | - Jay D Keasling
- Joint BioEnergy Institute, Emeryville, California 94608
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California 94720
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720
| | - Taku Demura
- Cellulose Production Research Team, Biomass Engineering Program, Center for Sustainable Resource Science, RIKEN, Yokohama 230-0045, Japan
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 630-0192 Nara, Japan
| | - Maki Kawai-Yamada
- Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan
| | - Henrik V Scheller
- Joint BioEnergy Institute, Emeryville, California 94608
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California 94720
- Plant and Microbial Biology, University of California, Berkeley, California 94720
| | - Jenny C Mortimer
- Joint BioEnergy Institute, Emeryville, California 94608
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California 94720
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720
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