Juri Rappsilber

Juri Rappsilber
Technische Universität Berlin | TUB · Institute of Biotechnology

About

699
Publications
104,529
Reads
How we measure 'reads'
A 'read' is counted each time someone views a publication summary (such as the title, abstract, and list of authors), clicks on a figure, or views or downloads the full-text. Learn more
38,019
Citations
Additional affiliations
March 2017 - July 2017
Kyoto University
Position
  • Researcher
October 2011 - present
Technische Universität Berlin
Position
  • Professor (Full)
November 2008 - December 2008
University of Copenhagen
Position
  • Researcher

Publications

Publications (699)
Article
Full-text available
Background HuR/ELAV1, a ubiquitous RNA-binding protein, belongs to the RNA-binding protein family and is crucial for stabilizing and regulating the translation of various mRNA targets, influencing gene expression. Elevated HuR levels are associated with multiple disorders, including cancer and neurodegenerative diseases. Despite the identification...
Article
Full-text available
In vitro transcription (IVT) is a technology of vital importance that facilitated the production of mRNA therapeutics and drove numerous breakthroughs in RNA biology. T7 polymerase-produced RNAs can begin with either 5′-triphosphate guanosine (5′-pppG) or 5′-triphosphate adenosine (5′-pppA), generating potential agonists for the RIG-I/type I interf...
Article
Genomes are organised into DNA loops by the Structural Maintenance of Chromosomes (SMC) proteins. SMCs establish functional chromosomal sub-domains for DNA repair, gene expression and chromosome segregation, but how SMC activity is specifically targeted is unclear. Here, we define the molecular mechanism targeting the condensin SMC complex to speci...
Preprint
Full-text available
It has been shown that integrating peptide property predictions such as fragment intensity into the scoring process of peptide spectrum match can greatly increase the number of confidently identified peptides compared to using traditional scoring methods. Here, we introduce Prosit-XL, a robust and accurate fragment intensity predictor covering the...
Article
Protein synthesis begins with the formation of a ribosome-messenger RNA (mRNA) complex. In bacteria, the small ribosomal subunit (30 S ) is recruited to many mRNAs through base pairing with the Shine-Dalgarno (SD) sequence and RNA binding by ribosomal protein bS1. Translation can initiate on nascent mRNAs, and RNA polymerase (RNAP) can promote the...
Article
The Complex Portal (www.ebi.ac.uk/complexportal) is a manually curated reference database for molecular complexes. It is a unifying web resource linking aggregated data on composition, topology and the function of macromolecular complexes from 28 species. In addition to significantly extending the number of manually curated complexes, we have massi...
Article
Full-text available
Understanding the mechanisms of synaptic plasticity is crucial for elucidating how the brain adapts to internal and external stimuli. A key objective of plasticity is maintaining physiological activity states during perturbations by adjusting synaptic transmission through negative feedback mechanisms. However, identifying and characterizing novel m...
Article
Full-text available
[NiFe]-hydrogenases catalyze the reversible activation of H2 using a unique NiFe(CN)2CO metal site, which is assembled by a sophisticated multiprotein machinery. The [4Fe–4S] cluster-containing HypCD complex, which possesses an ATPase activity with a hitherto unknown function, serves as the hub for the assembly of the Fe(CN)2CO subfragment. HypCD i...
Preprint
Full-text available
mRNA decay is a major determinant of gene regulation that is controlled through shortening of mRNA poly(A) tails by the Ccr4-Not complex. The specificity of deadenylation can be mediated through RNA adaptors - RNA-binding proteins that tether substrate mRNAs to Ccr4-Not in a regulated and context-specific manner. Interaction with Ccr4-Not is mediat...
Article
Full-text available
The PIWI-interacting RNA (piRNA) pathway guides the DNA methylation of young, active transposons during germline development in male mice¹. piRNAs tether the PIWI protein MIWI2 (PIWIL4) to the nascent transposon transcript, resulting in DNA methylation through SPOCD1 (refs. 2–5). Transposon methylation requires great precision: every copy needs to...
Article
Full-text available
Scarcity of structural and evolutionary information on protein complexes poses a challenge to deep learning-based structure modelling. We integrate experimental distance restraints obtained by crosslinking mass spectrometry (MS) into AlphaFold-Multimer, by extending AlphaLink to protein complexes. Integrating crosslinking MS data substantially impr...
Article
Accurate chromosome segregation requires the attachment of microtubules to centromeres, epigenetically defined by the enrichment of CENP-A nucleosomes. During DNA replication, CENP-A nucleosomes undergo dilution. To preserve centromere identity, correct amounts of CENP-A must be restored in a cell cycle–controlled manner orchestrated by the Mis18 c...
Article
Full-text available
The inhibitor of κB (IκB) kinase (IKK) is a central regulator of NF-κB signaling. All IKK complexes contain hetero- or homodimers of the catalytic IKKβ and/or IKKα subunits. Here, we identify a YDDΦxΦ motif, which is conserved in substrates of canonical (IκBα, IκBβ) and alternative (p100) NF-κB pathways, and which mediates docking to catalytic IKK...
Preprint
Proteins are comprised of structured domains and dynamic regions, and both are essential for biological function. However, studying dynamic regions is challenging using most structural biology methods, including crosslinking mass spectrometry. Here, we dramatically improve the usefulness of distance restraints from crosslinking MS by taking advanta...
Preprint
Full-text available
Complexes of nuclear factors 45 and 90 (NF45-NF90) play a multitude of roles in co- and post-transcriptional RNA processing, including regulating adenosine-to-inosine editing, cassette exon and back splicing, and splicing fidelity. NF45-NF90 complexes recognise dsRNA and, in human cells, primarily interact with inverted Alu repeats (AluIRs) that ar...
Article
Crosslinking mass spectrometry is a powerful tool to study protein-protein interactions under native or near-native conditions in complex mixtures. Through novel search controls, we show how biassing results towards likely correct proteins can subtly undermine error estimation of crosslinks, with significant consequences. Without adjustments to add...
Article
The mzIdentML data format, originally developed by the Proteomics Standards Initiative in 2011, is the open XML data standard for peptide and protein identification results coming from mass spectrometry. We present mzIdentML version 1.3.0, which introduces new functionality and support for additional use cases. First of all, a new mechanism for enc...
Article
Despite the ever-growing research interest in polyhydroxyalkanoates (PHAs) as green plastic alternatives, our understanding of the regulatory mechanisms governing PHA synthesis, storage, and degradation in the model organism Ralstonia eutropha remains limited. Given its importance for central carbon metabolism, PHA homeostasis is probably controlle...
Article
The centromere, defined by the enrichment of CENP-A (a Histone H3 variant) containing nucleosomes, is a specialised chromosomal locus that acts as a microtubule attachment site. To preserve centromere identity, CENP-A levels must be maintained through active CENP-A loading during the cell cycle. A central player mediating this process is the Mis18...
Preprint
[NiFe]-hydrogenases catalyze the reversible activation of H2 using a unique NiFe(CN)2CO metal site, which is assembled by a sophisticated multi-protein machinery. The [4Fe–4S]-cluster-containing HypCD complex, which possesses an ATPase activity with an hitherto unknown function, serves as the hub for the assembly of the Fe(CN)2CO sub-fragment. HypC...
Article
Full-text available
tRNA modifications affect ribosomal elongation speed and co-translational folding dynamics. The Elongator complex is responsible for introducing 5-carboxymethyl at wobble uridine bases (cm⁵U34) in eukaryotic tRNAs. However, the structure and function of human Elongator remain poorly understood. In this study, we present a series of cryo-EM structur...
Article
Full-text available
Background The proliferation antigen Ki-67 has been widely used in clinical settings for cancer staging for many years, but investigations on its biological functions have lagged. Recently, Ki-67 has been shown to regulate both the composition of the chromosome periphery and chromosome behaviour in mitosis as well as to play a role in heterochromat...
Article
Full-text available
Microtubule (MT) filaments, composed of α/β-tubulin dimers, are fundamental to cellular architecture, function and organismal development. They are nucleated from MT organizing centers by the evolutionarily conserved γ-tubulin ring complex (γTuRC). However, the molecular mechanism of nucleation remains elusive. Here we used cryo-electron tomography...
Article
Full-text available
Adaptation to a change of environment is an essential process for survival, in particular for parasitic organisms exposed to a wide range of hosts. Such adaptations include rapid control of gene expression through the formation of membraneless organelles composed of poly-A RNA and proteins. The African trypanosome Trypanosoma brucei is exquisitely...
Preprint
Full-text available
Faithful chromosome segregation requires packaging of the genome on both global and local scales. Condensin plays a crucial role at pericentromeres to resist spindle forces and ensure the bioriented attachment of kinetochores to microtubules in mitosis. Here we demonstrate that budding yeast condensin is recruited to pericentromeres through a direc...
Preprint
Full-text available
Protein synthesis begins with the formation of a ribosome-mRNA complex. In bacteria, the 30S ribosomal subunit is recruited to many mRNAs through base pairing with the Shine Dalgarno (SD) sequence and RNA binding by ribosomal protein bS1. Translation can initiate on nascent mRNAs and RNA polymerase (RNAP) can promote recruitment of the pioneering 3...
Preprint
Full-text available
Accurate chromosome segregation requires the attachment of spindle microtubules to centromeres, which are epigenetically defined by the enrichment of CENP-A nucleosomes. During DNA replication, existing CENP-A nucleosomes undergo dilution as they get redistributed among the two DNA strands. To preserve centromere identity, CENP-A levels must be res...
Preprint
Full-text available
The interferon (IFN) response is crucial for antiviral activity, but its overstimulation can lead to a wide range of autoimmune disorders. The cytoplasmic pattern recognition receptor RIG-I detects viral RNAs and endogenous polymerase III transcripts carrying a 5′-triphosphate (5′- ppp) or 5′-diphosphate (5′-pp) moiety, triggering an IFN immune res...
Preprint
Full-text available
Crosslinking mass spectrometry is a powerful tool for studying protein-protein interactions under native or near native conditions in complex mixtures. By help of novel search controls, we show that measures that aim to improve the number of identifications based on heuristic considerations can undermine error estimation in non-obvious ways. The re...
Preprint
Full-text available
The centromere, defined by the enrichment of CENP-A (a Histone H3 variant) containing nucleosomes, is a specialised chromosomal locus that acts as a microtubule attachment site. To preserve centromere identity, CENP-A levels must be maintained through active CENP-A loading during the cell cycle. A central player mediating this process is the Mis18...
Preprint
Full-text available
Adaptation to a change of environment is an essential process for survival, in particular for parasitic organisms exposed to a wide range of hosts. Such adaptations include rapid control of gene expression through the formation of membraneless organelles composed of poly-A RNA and proteins. The African trypanosome Trypanosoma brucei is exquisitely...
Article
Cross-linking mass spectrometry (MS) is currently transitioning from a routine tool in structural biology to enabling structural systems biology. MS-cleavable cross-linkers could substantially reduce the associated search space expansion by allowing a MS³-based approach for identifying cross-linked peptides. However, MS² (MS/MS)-based approaches cu...
Preprint
The mzIdentML file format, originally developed by the Proteomics Standards Initiative in 2011, is the open XML data standard for peptide and protein identification results coming from mass spectrometry. We present mzIdentML version 1.3.0, which introduces new functionality and support for additional use cases. First of all, a new mechanism for enc...
Article
Condensin is a structural maintenance of chromosomes (SMC) complex family member thought to build mitotic chromosomes by DNA loop extrusion. However, condensin variants unable to extrude loops, yet proficient in chromosome formation, were recently described. Here, we explore how condensin might alternatively build chromosomes. Using bulk biochemica...
Preprint
Full-text available
Sphingolipids are important structural components of membranes. Additionally, simple sphingolipids such as sphingosine are highly bioactive and participate in complex subcellular signaling. Sphingolipid deregulation is associated with many severe diseases including diabetes, Parkinson's and cancer. Here, we focus on how sphingosine, generated from...
Article
Full-text available
Translation affects messenger RNA stability and, in yeast, this is mediated by the Ccr4–Not deadenylation complex. The details of this process in mammals remain unclear. Here, we use cryogenic electron microscopy (cryo-EM) and crosslinking mass spectrometry to show that mammalian CCR4–NOT specifically recognizes ribosomes that are stalled during tr...
Article
Full-text available
Despite billions of years of evolution, there have been only minor changes in the number and types of proteinogenic amino acids and the standard genetic code with codon assignments across the three domains of life. The rigidity of the genetic code sets it apart from other aspects of organismal evolution, giving rise to key questions about its origi...
Article
Crosslinking mass spectrometry provides pivotal information on the structure and interaction of proteins. MS-cleavable crosslinkers are regarded as a cornerstone for the analysis of complex mixtures. Yet they fragment under similar conditions as peptides, leading to mixed fragmentation spectra of the crosslinker and peptide. This hampers selecting...
Preprint
Full-text available
Using orthogonal translation systems (OTSs) is the most efficient way to produce unnatural proteins by adding non-canonical amino acids (ncAAs) to the genetic code. In the quest to expand substrate specificity the conventional approach begins with a (hyper-)stable enzyme capable of withstanding the structural changes resulting from necessary mutati...
Preprint
CENP-A chromatin specifies mammalian centromere identity, and its chaperone HJURP replenishes CENP-A when recruited by the Mis18 complex (Mis18C) via M18BP/KNL2 to CENP-C at kinetochores during interphase. However, the Mis18C recruitment mechanism remains unresolved in species lacking M18BP1, such as fission yeast. Fission yeast centromeres cluster...
Preprint
Full-text available
Scarcity of structural and evolutionary information on protein complexes poses a challenge to deep learning-based structure modelling. We integrated experimental distance restraints obtained by crosslinking mass spectrometry (MS) into AlphaFold-Multimer, by extending AlphaLink to protein complexes. Integrating crosslinking MS data substantially imp...
Preprint
Full-text available
Orthogonal translation systems (OTSs) are the most expedient way to generate unnatural proteins by adding non-canonical amino acids (ncAAs) to the genetic code. Diversifying substrate specificity typically starts from a stable enzyme that is capable to withstand the structure-perturbing effects of the required mutations. We here take a radically di...
Article
Full-text available
The oxoglutarate dehydrogenase complex (OGDHc) participates in the tricarboxylic acid cycle and, in a multi-step reaction, decarboxylates α-ketoglutarate, transfers succinyl to CoA, and reduces NAD+. Due to its pivotal role in metabolism, OGDHc enzymatic components have been studied in isolation; however, their interactions within the endogenous OG...
Article
Full-text available
The chromosomal cohesin complex establishes sister chromatid cohesion during S phase, which forms the basis for faithful segregation of DNA replication products during cell divisions. Cohesion establishment is defective in the absence of either of three non-essential Saccharomyces cerevisiae replication fork components Tof1-Csm3 and Mrc1. Here, we...
Article
Crosslinking mass spectrometry captures protein structures in solution. The crosslinks reveal spatial proximities as distance restraints, but do not easily reveal which of these restraints derive from the same protein conformation. This superposition can be reduced by photo-crosslinking, and adding information from protein structure models, or quan...
Preprint
Background: The proliferation antigen Ki-67 has been widely used in clinical settings for cancer staging for many years but investigations on its biological functions have lagged. Recently, Ki-67 was shown to regulate both the composition of the chromosome periphery and chromosome behaviour in mitosis as well as to play a role in heterochromatin or...
Article
Full-text available
Newly made mRNAs are processed and packaged into mature ribonucleoprotein complexes (mRNPs) and are recognized by the essential transcription–export complex (TREX) for nuclear export1,2. However, the mechanisms of mRNP recognition and three-dimensional mRNP organization are poorly understood³. Here we report cryo-electron microscopy and tomography...
Article
Full-text available
While AlphaFold2 can predict accurate protein structures from the primary sequence, challenges remain for proteins that undergo conformational changes or for which few homologous sequences are known. Here we introduce AlphaLink, a modified version of the AlphaFold2 algorithm that incorporates experimental distance restraint information into its net...
Article
Full-text available
Operons are transcriptional modules that allow bacteria to adapt to environmental changes by coordinately expressing the relevant set of genes. In humans, biological pathways and their regulation are more complex. If and how human cells coordinate the expression of entire biological processes is unclear. Here, we capture 31 higher-order co-regulati...
Article
Full-text available
A multitude of histone chaperones are required to support histones from their biosynthesis until DNA deposition. They cooperate through the formation of histone co-chaperone complexes, but the crosstalk between nucleosome assembly pathways remains enigmatic. Using exploratory interactomics, we define the interplay between human histone H3-H4 chaper...
Article
Full-text available
Accurately modeling the structures of proteins and their complexes using artificial intelligence is revolutionizing molecular biology. Experimental data enable a candidate-based approach to systematically model novel protein assemblies. Here, we use a combination of in-cell crosslinking mass spectrometry and co-fractionation mass spectrometry (CoFr...
Article
Full-text available
Artificial metalloenzymes (ArMs) enrich bioorthogonal chemistry with new-to-nature reactions while limiting metal deactivation and toxicity. This enables biomedical applications such as activating therapeutics in situ. However, while combination therapies are becoming widespread anticancer treatments, dual catalysis by ArMs has not yet been shown....
Article
Full-text available
Human cytomegalovirus (CMV) is a ubiquitously distributed pathogen whose rodent counterparts such as mouse and rat CMV serve as common infection models. Here, we conducted global proteome profiling of rat CMV-infected cells and uncovered a pronounced loss of the transcription factor STAT2, which is crucial for antiviral interferon signalling. Via d...
Article
Full-text available
Background Mouse models that overexpress human mutant Tau (P301S and P301L) are commonly used in preclinical studies of Alzheimer’s Disease (AD) and while several drugs showed therapeutic effects in these mice, they were ineffective in humans. This leads to the question to which extent the murine models reflect human Tau pathology on the molecular...
Preprint
Full-text available
Crosslinking MS is currently transitioning from a routine tool in structural biology to enabling structural systems biology. MS-cleavable crosslinkers could substantially reduce the associated search space expansion by allowing an MS3-based approach for identifying crosslinked peptides. However, MS2-based approaches currently outperform approaches...
Article
Full-text available
Transfer RNA (tRNA) molecules are essential to decode messenger RNA codons during protein synthesis. All known tRNAs are heavily modified at multiple positions through post-transcriptional addition of chemical groups. Modifications in the tRNA anticodons are directly influencing ribosome decoding and dynamics during translation elongation and are c...
Article
Full-text available
The mechanisms of coordinated changes in proteome composition and their relevance for the differentiation of neutrophil granulocytes are not well studied. Here, we discover two novel human genetic defects in SRPRA and SRP19, constituents of the mammalian co-translational targeting machinery and characterize their role in neutrophil granulocyte diff...
Preprint
Full-text available
Cell-free systems display tremendous potential for biotechnological applications, complementing in vitro reconstituted enzymatic processes and traditional expression systems. However, they often represent "black boxes" without much insight into their components. Here, we characterize a thermophilic cell-free system that produces succinyl-CoA and di...
Preprint
Full-text available
Motivation: The quality of biological data crucially affects progress in science. This quality can be improved with better measurement devices, more sophisticated experimental designs, or repetitious measurements. Each of these options is associated with substantial costs. We present a simple computational tool as an alternative. This algorithmic t...
Preprint
Full-text available
A multitude of histone chaperones are required to protect histones after their biosynthesis until DNA deposition. They cooperate through the formation of co-chaperone complexes, but the crosstalk between nucleosome assembly pathways remains enigmatic. Using explorative interactomics approaches, we characterize the organization of the histone H3–H4...
Article
Full-text available
DNA interstrand cross-links are tumor-inducing lesions that block DNA replication and transcription. When cross-links are detected at stalled replication forks, ATR kinase phosphorylates FANCI, which stimulates monoubiquitination of the FANCD2–FANCI clamp by the Fanconi anemia core complex. Monoubiquitinated FANCD2–FANCI is locked onto DNA and recr...
Conference Paper
Full-text available
It can be challenging to effectively impart higher education content to students. We experienced such difficulty in a lecture series with invited senior scientists presenting their area of Biotech research. Instead of a vivid exchange with the expert, we observed limited and restrained student contributions. In qualitative interviews with these stu...
Conference Paper
Full-text available
Listening to scientific presentations and reading scientific literature are core activities of any scientist, and frequent components of students' curricula. When employing these activities in teaching, finding the right balance between student instruction and autonomous learning is important for best learning outcomes and teachers’ workload. We he...
Article
Full-text available
Epe1 histone demethylase restricts H3K9-methylation-dependent heterochromatin, preventing it from spreading over, and silencing, gene-containing regions in fission yeast. External stress induces an adaptive response allowing heterochromatin island formation that confers resistance on surviving wild-type lineages. Here we investigate the mechanism b...
Preprint
Full-text available
Accurately modeling the structures of proteins and their complexes using artificial intelligence is currently revolutionizing molecular biology. Experimental data enable a candidate-based approach to systematically model novel protein assemblies. Here, we use a combination of in-cell crosslinking mass spectrometry, co-fractionation mass spectrometr...