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Wandres M, Aigner D, Kastelic N, Boltengagen A, Rybak-Wolf A, Rajewsky N. Generation and Downstream Analysis of Single-Cell and Single-Nuclei Transcriptomes in Brain Organoids. J Vis Exp 2024. [PMID: 38619271 DOI: 10.3791/66225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/16/2024] Open
Abstract
Over the past decade, single-cell transcriptomics has significantly evolved and become a standard laboratory method for simultaneous analysis of gene expression profiles of individual cells, allowing the capture of cellular diversity. In order to overcome limitations posed by difficult-to-isolate cell types, an alternative approach aiming at recovering single nuclei instead of intact cells can be utilized for sequencing, making transcriptome profiling of individual cells universally applicable. These techniques have become a cornerstone in the study of brain organoids, establishing them as models of the developing human brain. Leveraging the potential of single-cell and single-nucleus transcriptomics in brain organoid research, this protocol presents a step-by-step guide encompassing key procedures such as organoid dissociation, single-cell or nuclei isolation, library preparation and sequencing. By implementing these alternative approaches, researchers can obtain high-quality datasets, enabling the identification of neuronal and non-neuronal cell types, gene expression profiles, and cell lineage trajectories. This facilitates comprehensive investigations into cellular processes and molecular mechanisms shaping brain development.
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Affiliation(s)
- Miriam Wandres
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine (MDC); Institut für Biologie, Humboldt-Universität zu Berlin
| | - Denise Aigner
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine (MDC); Institut für Biologie, Humboldt-Universität zu Berlin
| | - Nicolai Kastelic
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine (MDC); Organoid platform, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine (MDC)
| | - Anastasiya Boltengagen
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine (MDC)
| | - Agnieszka Rybak-Wolf
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine (MDC); Organoid platform, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine (MDC);
| | - Nikolaus Rajewsky
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine (MDC); Institut für Biologie, Humboldt-Universität zu Berlin;
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Galeffi F, Snellings DA, Wetzel-Strong SE, Kastelic N, Bullock J, Gallione CJ, North PE, Marchuk DA. A novel somatic mutation in GNAQ in a capillary malformation provides insight into molecular pathogenesis. Angiogenesis 2022; 25:493-502. [PMID: 35635655 DOI: 10.1007/s10456-022-09841-w] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 05/09/2022] [Indexed: 01/01/2023]
Abstract
Sturge-Weber syndrome (SWS) is a sporadic, congenital, neuro-cutaneous disorder characterized by a mosaic, capillary malformation. SWS and non-syndromic capillary malformations are both caused by a somatic activating mutation in GNAQ encoding the G protein subunit alpha-q protein. The missense mutation R183Q is the sole GNAQ mutation identified thus far in 90% of SWS-associated or isolated capillary malformations. In this study, we sequenced skin biopsies of capillary malformations from 9 patients. We identified the R183Q mutation in nearly all samples, but one sample exhibited a Q209R mutation. This new mutation occurs at the same residue as the constitutively-activating Q209L mutation, commonly seen in tumors. However, Q209R is a rare variant in this gene. To compare the effect of the Q209R mutation on downstream signaling, we performed reporter assays with a GNAQ-responsive reporter co-transfected with either GNAQ WT, R183Q, Q209L, Q209R, or C9X (representing a null allele). Q209L showed the highest reporter activation, with R183Q and Q209R showing significantly lower activation. To determine whether these mutations had similar or different downstream consequences we performed RNA-seq analysis in microvascular endothelial cells (HMEC-1) electroporated with the same GNAQ variants. The R183 and Q209 missense variants caused extensive dysregulation of a broad range of transcripts compared to the WT or null allele, confirming that these are all activating mutations. However, the missense variants exhibited very few differentially expressed genes (DEGs) when compared to each other. These data suggest that these activating GNAQ mutations differ in magnitude of activation but have similar downstream effects.
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Affiliation(s)
- F Galeffi
- Molecular Genetics & Microbiology, Duke University Medical Center, Durham, NC, USA
| | - D A Snellings
- Molecular Genetics & Microbiology, Duke University Medical Center, Durham, NC, USA
| | - S E Wetzel-Strong
- Molecular Genetics & Microbiology, Duke University Medical Center, Durham, NC, USA
| | - N Kastelic
- Molecular Genetics & Microbiology, Duke University Medical Center, Durham, NC, USA
| | - J Bullock
- Molecular Genetics & Microbiology, Duke University Medical Center, Durham, NC, USA
| | - C J Gallione
- Molecular Genetics & Microbiology, Duke University Medical Center, Durham, NC, USA
| | - P E North
- Medical College of Wisconsin, Milwaukee, WI, USA
| | - D A Marchuk
- Molecular Genetics & Microbiology, Duke University Medical Center, Durham, NC, USA.
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Labi V, Peng S, Klironomos F, Munschauer M, Kastelic N, Chakraborty T, Schoeler K, Derudder E, Martella M, Mastrobuoni G, Hernandez-Miranda LR, Lahmann I, Kocks C, Birchmeier C, Kempa S, Quintanilla-Martinez de Fend L, Landthaler M, Rajewsky N, Rajewsky K. Context-specific regulation of cell survival by a miRNA-controlled BIM rheostat. Genes Dev 2019; 33:1673-1687. [PMID: 31699777 PMCID: PMC6942046 DOI: 10.1101/gad.330134.119] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 10/02/2019] [Indexed: 12/13/2022]
Abstract
Knockout of the ubiquitously expressed miRNA-17∼92 cluster in mice produces a lethal developmental lung defect, skeletal abnormalities, and blocked B lymphopoiesis. A shared target of miR-17∼92 miRNAs is the pro-apoptotic protein BIM, central to life-death decisions in mammalian cells. To clarify the contribution of miR-17∼92:Bim interactions to the complex miR-17∼92 knockout phenotype, we used a system of conditional mutagenesis of the nine Bim 3' UTR miR-17∼92 seed matches. Blocking miR-17∼92:Bim interactions early in development phenocopied the lethal lung phenotype of miR-17∼92 ablation and generated a skeletal kinky tail. In the hematopoietic system, instead of causing the predicted B cell developmental block, it produced a selective inability of B cells to resist cellular stress; and prevented B and T cell hyperplasia caused by Bim haploinsufficiency. Thus, the interaction of miR-17∼92 with a single target is essential for life, and BIM regulation by miRNAs serves as a rheostat controlling cell survival in specific physiological contexts.
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Affiliation(s)
- Verena Labi
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin-Buch 13125, Germany
- Program of Cellular and Molecular Medicine, Children's Hospital, and Immune Disease Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
- Division of Developmental Immunology, Biocenter, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Siying Peng
- Program of Cellular and Molecular Medicine, Children's Hospital, and Immune Disease Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Filippos Klironomos
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin-Buch 13125, Germany
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin-Buch 13125, Germany
| | - Mathias Munschauer
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin-Buch 13125, Germany
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin-Buch 13125, Germany
| | - Nicolai Kastelic
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin-Buch 13125, Germany
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin-Buch 13125, Germany
| | - Tirtha Chakraborty
- Program of Cellular and Molecular Medicine, Children's Hospital, and Immune Disease Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Katia Schoeler
- Division of Developmental Immunology, Biocenter, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Emmanuel Derudder
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin-Buch 13125, Germany
- Program of Cellular and Molecular Medicine, Children's Hospital, and Immune Disease Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
- Institute for Biomedical Ageing Research, University of Innsbruck, Innsbruck 6020, Austria
| | - Manuela Martella
- Institute of Pathology and Neuropathology and Comprehensive Cancer Center Tübingen, Eberhard-Karls-University, Tübingen 72076, Germany
| | - Guido Mastrobuoni
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin-Buch 13125, Germany
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin-Buch 13125, Germany
| | - Luis R Hernandez-Miranda
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin-Buch 13125, Germany
| | - Ines Lahmann
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin-Buch 13125, Germany
| | - Christine Kocks
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin-Buch 13125, Germany
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin-Buch 13125, Germany
| | - Carmen Birchmeier
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin-Buch 13125, Germany
| | - Stefan Kempa
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin-Buch 13125, Germany
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin-Buch 13125, Germany
| | | | - Markus Landthaler
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin-Buch 13125, Germany
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin-Buch 13125, Germany
| | - Nikolaus Rajewsky
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin-Buch 13125, Germany
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin-Buch 13125, Germany
| | - Klaus Rajewsky
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin-Buch 13125, Germany
- Program of Cellular and Molecular Medicine, Children's Hospital, and Immune Disease Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
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Rendleman J, Cheng Z, Maity S, Kastelic N, Munschauer M, Allgoewer K, Teo G, Zhang YBM, Lei A, Parker B, Landthaler M, Freeberg L, Kuersten S, Choi H, Vogel C. New insights into the cellular temporal response to proteostatic stress. eLife 2018; 7:39054. [PMID: 30272558 PMCID: PMC6185107 DOI: 10.7554/elife.39054] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 09/28/2018] [Indexed: 12/13/2022] Open
Abstract
Maintaining a healthy proteome involves all layers of gene expression regulation. By quantifying temporal changes of the transcriptome, translatome, proteome, and RNA-protein interactome in cervical cancer cells, we systematically characterize the molecular landscape in response to proteostatic challenges. We identify shared and specific responses to misfolded proteins and to oxidative stress, two conditions that are tightly linked. We reveal new aspects of the unfolded protein response, including many genes that escape global translation shutdown. A subset of these genes supports rerouting of energy production in the mitochondria. We also find that many genes change at multiple levels, in either the same or opposing directions, and at different time points. We highlight a variety of putative regulatory pathways, including the stress-dependent alternative splicing of aminoacyl-tRNA synthetases, and protein-RNA binding within the 3’ untranslated region of molecular chaperones. These results illustrate the potential of this information-rich resource.
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Affiliation(s)
- Justin Rendleman
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, United States
| | - Zhe Cheng
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, United States
| | - Shuvadeep Maity
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, United States
| | - Nicolai Kastelic
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Mathias Munschauer
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Kristina Allgoewer
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, United States
| | - Guoshou Teo
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, United States
| | - Yun Bin Matteo Zhang
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, United States
| | - Amy Lei
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, United States
| | - Brian Parker
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, United States
| | - Markus Landthaler
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany.,Integrative Research Institute for the Life Sciences, Institute of Biology, Humboldt University, Berlin, Germany
| | | | | | - Hyungwon Choi
- National University of Singapore, Singapore.,Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore
| | - Christine Vogel
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, United States
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Imami K, Milek M, Bogdanow B, Yasuda T, Kastelic N, Zauber H, Ishihama Y, Landthaler M, Selbach M. Phosphorylation of the Ribosomal Protein RPL12/uL11 Affects Translation during Mitosis. Mol Cell 2018; 72:84-98.e9. [PMID: 30220558 DOI: 10.1016/j.molcel.2018.08.019] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [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: 11/08/2017] [Revised: 06/09/2018] [Accepted: 08/10/2018] [Indexed: 12/22/2022]
Abstract
Emerging evidence indicates that heterogeneity in ribosome composition can give rise to specialized functions. Until now, research mainly focused on differences in core ribosomal proteins and associated factors. The effect of posttranslational modifications has not been studied systematically. Analyzing ribosome heterogeneity is challenging because individual proteins can be part of different subcomplexes (40S, 60S, 80S, and polysomes). Here we develop polysome proteome profiling to obtain unbiased proteomic maps across ribosomal subcomplexes. Our method combines extensive fractionation by sucrose gradient centrifugation with quantitative mass spectrometry. The high resolution of the profiles allows us to assign proteins to specific subcomplexes. Phosphoproteomics on the fractions reveals that phosphorylation of serine 38 in RPL12/uL11, a known mitotic CDK1 substrate, is strongly depleted in polysomes. Follow-up experiments confirm that RPL12/uL11 phosphorylation regulates the translation of specific subsets of mRNAs during mitosis. Together, our results show that posttranslational modification of ribosomal proteins can regulate translation.
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Affiliation(s)
- Koshi Imami
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Str. 10, 13092 Berlin, Germany; Department of Molecular and Cellular BioAnalysis, Kyoto University, 606-8501 Kyoto, Japan.
| | - Miha Milek
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Str. 10, 13092 Berlin, Germany
| | - Boris Bogdanow
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Str. 10, 13092 Berlin, Germany
| | - Tomoharu Yasuda
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Str. 10, 13092 Berlin, Germany
| | - Nicolai Kastelic
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Str. 10, 13092 Berlin, Germany
| | - Henrik Zauber
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Str. 10, 13092 Berlin, Germany
| | - Yasushi Ishihama
- Department of Molecular and Cellular BioAnalysis, Kyoto University, 606-8501 Kyoto, Japan
| | - Markus Landthaler
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Str. 10, 13092 Berlin, Germany; IRI Life Sciences, Institute für Biologie, Humboldt Universität zu Berlin, Philippstraße 13, 10115 Berlin, Germany
| | - Matthias Selbach
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Str. 10, 13092 Berlin, Germany; Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany.
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6
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Kastelic N, Landthaler M. mRNA interactome capture in mammalian cells. Methods 2017; 126:38-43. [DOI: 10.1016/j.ymeth.2017.07.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Revised: 05/22/2017] [Accepted: 07/08/2017] [Indexed: 01/14/2023] Open
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Kirchner S, Cai Z, Rauscher R, Kastelic N, Anding M, Czech A, Kleizen B, Ostedgaard LS, Braakman I, Sheppard DN, Ignatova Z. Alteration of protein function by a silent polymorphism linked to tRNA abundance. PLoS Biol 2017; 15:e2000779. [PMID: 28510592 PMCID: PMC5433685 DOI: 10.1371/journal.pbio.2000779] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 04/13/2017] [Indexed: 01/22/2023] Open
Abstract
Synonymous single nucleotide polymorphisms (sSNPs) are considered neutral for protein function, as by definition they exchange only codons, not amino acids. We identified an sSNP that modifies the local translation speed of the cystic fibrosis transmembrane conductance regulator (CFTR), leading to detrimental changes to protein stability and function. This sSNP introduces a codon pairing to a low-abundance tRNA that is particularly rare in human bronchial epithelia, but not in other human tissues, suggesting tissue-specific effects of this sSNP. Up-regulation of the tRNA cognate to the mutated codon counteracts the effects of the sSNP and rescues protein conformation and function. Our results highlight the wide-ranging impact of sSNPs, which invert the programmed local speed of mRNA translation and provide direct evidence for the central role of cellular tRNA levels in mediating the actions of sSNPs in a tissue-specific manner. Synonymous single nucleotide polymorphisms (sSNPs) occur at high frequency in the human genome and are associated with ~50 diseases in humans; the responsible molecular mechanisms remain enigmatic. Here, we investigate the impact of the common sSNP, T2562G, on cystic fibrosis transmembrane conductance regulator (CFTR). Although this sSNP, by itself, does not cause cystic fibrosis (CF), it is prevalent in patients with CFTR-related disorders. T2562G sSNP modifies the local translation speed at the Thr854 codon, leading to changes in CFTR stability and channel function. This sSNP introduces a codon pairing to a low-abundance tRNA, which is particularly rare in human bronchial epithelia, but not in other human tissues, suggesting a tissue-specific effect of this sSNP. Enhancement of the cellular concentration of the tRNA cognate to the mutant ACG codon rescues the stability and conduction defects of T2562G-CFTR. These findings reveal an unanticipated mechanism—inverting the programmed local speed of mRNA translation in a tRNA-dependent manner—for sSNP-associated diseases.
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Affiliation(s)
- Sebastian Kirchner
- Biochemistry, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Zhiwei Cai
- School of Physiology, Pharmacology and Neuroscience, University of Bristol, Bristol, United Kingdom
| | - Robert Rauscher
- Institute for Biochemistry and Molecular Biology, Department of Chemistry, University of Hamburg, Hamburg, Germany
| | - Nicolai Kastelic
- Biochemistry, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Melanie Anding
- Biochemistry, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Andreas Czech
- Institute for Biochemistry and Molecular Biology, Department of Chemistry, University of Hamburg, Hamburg, Germany
| | - Bertrand Kleizen
- Cellular Protein Chemistry, Department of Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
| | - Lynda S. Ostedgaard
- Department of Internal Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Ineke Braakman
- Cellular Protein Chemistry, Department of Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
| | - David N. Sheppard
- School of Physiology, Pharmacology and Neuroscience, University of Bristol, Bristol, United Kingdom
- * E-mail: (ZI); (DNS)
| | - Zoya Ignatova
- Biochemistry, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Institute for Biochemistry and Molecular Biology, Department of Chemistry, University of Hamburg, Hamburg, Germany
- * E-mail: (ZI); (DNS)
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