A5067878753- RNA and protein synthesis mechanisms
- RNA Research and Splicing
- RNA modifications and cancer
- DNA Repair Mechanisms
- CRISPR and Genetic Engineering
- Genomics and Chromatin Dynamics
- Mitochondrial Function and Pathology
- Bacteriophages and microbial interactions
- Bacterial Genetics and Biotechnology
- Molecular Biology Techniques and Applications
- Advanced Proteomics Techniques and Applications
- Mass Spectrometry Techniques and Applications
- Chromosomal and Genetic Variations
- Metabolism and Genetic Disorders
- Synthesis and Properties of Aromatic Compounds
- Endometrial and Cervical Cancer Treatments
- Genetic factors in colorectal cancer
- Insect symbiosis and bacterial influences
- Carbohydrate Chemistry and Synthesis
- Click Chemistry and Applications
- Ovarian cancer diagnosis and treatment
- DNA and Nucleic Acid Chemistry
- Enzyme Structure and Function
- Genomics and Phylogenetic Studies
- Protein Structure and Dynamics
Universitätsmedizin Göttingen
2016-2025
Max Planck Institute for Multidisciplinary Sciences
2022-2025
University of Göttingen
2016-2025
Max Planck Institute for the Study of Religious and Ethnic Diversity
2024
Max Planck Institute for Biophysical Chemistry
2016-2021
University of Tübingen
2016
Abstract Transcription-coupled DNA repair removes bulky lesions from the genome 1,2 and protects cells against ultraviolet (UV) irradiation 3 . begins when RNA polymerase II (Pol II) stalls at a lesion recruits Cockayne syndrome protein CSB, E3 ubiquitin ligase, CRL4 CSA UV-stimulated scaffold A (UVSSA) Here we provide five high-resolution structures of Pol transcription complexes containing human transcription-coupled factors elongation PAF1 complex (PAF) SPT6. Together with biochemical...
Abstract During transcription-coupled DNA repair (TCR), RNA polymerase II (Pol II) transitions from a transcriptionally active state to an arrested that allows for removal of lesions. This transition requires site-specific ubiquitylation Pol by the CRL4 CSA ubiquitin ligase, process is facilitated ELOF1 in unknown way. Using cryogenic electron microscopy, biochemical assays and cell biology approaches, we found serves as adaptor stably position UVSSA on II, leading ligase neddylation...
Abstract Nucleotide excision repair (NER) is the major DNA pathway that removes UV-induced and bulky lesions. There currently no structure of NER intermediates, which form around large multisubunit transcription factor IIH (TFIIH). Here we report cryo-EM an intermediate containing TFIIH XPA. Compared to its conformation, rearranged such ATPase subunits XPB XPD bind double- single-stranded DNA, consistent with their translocase helicase activities, respectively. XPA releases inhibitory kinase...
Abstract Histone H3 trimethylation of lysine 9 (H3K9me3) and proteins the heterochromatin protein 1 (HP1) family are hallmarks heterochromatin, a state compacted DNA essential for genome stability long-term transcriptional silencing. The mechanisms by which H3K9me3 HP1 contribute to chromatin condensation have been speculative controversial. Here we demonstrate that human HP1β is prototypic exemplifying most basal binding effects. These caused dimeric dynamic interaction with highly enriched...
Abstract Protein–DNA interactions are key to the functionality and stability of genome. Identification mapping protein–DNA interaction interfaces sites is crucial for understanding DNA-dependent processes. Here, we present a workflow that allows mass spectrometric (MS) identification proteins in direct contact with DNA reconstituted native chromatin after cross-linking by ultraviolet (UV) light. Our approach enables determination at amino-acid level. With example chromatin-associated protein...
Ferlins, ancient membrane proteins with a unique architecture, are central to multiple essential, Ca 2+ -dependent vesicle fusion processes. Despite numerous functional studies and their link burdening human diseases, mechanistic understanding of how these multi-C 2 domain interact lipid membranes promote remodeling is currently lacking. Here, we elucidate the near-complete cryo-electron microscopy structures myoferlin dysferlin in lipid-bound states. We show that ferlins adopt compact,...
CRISPR-Cas is a sophisticated defence system used by bacteria and archaea to fend off invaders. systems vary in their Cas protein composition have therefore been divided into different classes types. Type I of shown contain the small Cas11 as part interference complex known Cascade. Here we show for first time that an archaeal type I-B also contains homolog Cas11. The Cas11b protein, encoded cas8b gene Haloferax volcanii, represents case internal in-frame translation protein. Translation...
Modern mass spectrometry setups used in today's proteomics studies generate vast amounts of raw data, calling for highly efficient data processing and analysis tools. Software analyzing these is either monolithic (easy to use, but sometimes too rigid) or workflow-driven customize, complex). Thermo Proteome Discoverer (PD) a powerful software which, our eyes, achieves good trade-off between flexibility usability. Here, we present two open-source plugins PD providing additional functionality:...
The regulation of thymocyte development by RNA-binding proteins (RBPs) is largely unexplored. We identify 642 RBPs in the thymus and focus on Arpp21, which shows selective dynamic expression early thymocytes. Arpp21 downregulated response to T cell receptor (TCR) Ca2+ signals. Downregulation requires Stim1/Stim2 CaMK4 involves protein phosphorylation, polyubiquitination proteasomal degradation. directly binds RNA through its R3H domain, with a preference for uridine-rich motifs, promoting...
In protein-RNA cross-linking mass spectrometry, UV or chemical introduces stable bonds between amino acids and nucleic in complexes that are then analyzed detected spectra. This analytical tool delivers valuable information about RNA-protein interactions RNA docking sites proteins, both vitro vivo. The identification of cross-linked peptides with oligonucleotides different length leads to a combinatorial increase search space. We demonstrate the peptide retention time prediction tasks can be...
Abstract Even though Bacillus subtilis is one of the most studied organisms, no function has been identified for about 20% its proteins. Among these unknown proteins are several RNA- and ribosome-binding suggesting that they exert functions in cellular information processing. In this work, we have investigated RNA-binding protein YlxR. This widely conserved bacteria strongly constitutively expressed B. an important function. We RNA subunit essential RNase P as binding partner The main...
Abstract Activating signal co-integrator 1 complex (ASCC) subunit 3 (ASCC3) supports diverse genome maintenance and gene expression processes, contains tandem Ski2-like NTPase/helicase cassettes crucial for these functions. Presently, the molecular mechanisms underlying ASCC3 helicase activity regulation remain unresolved. We present cryogenic electron microscopy, DNA-protein cross-linking/mass spectrometry as well in vitro cellular functional analyses of ASCC3-TRIP4 sub-module ASCC. Unlike...
ABSTRACT UV (ultra-violet) crosslinking with mass spectrometry (XL-MS) has been established for identifying RNA-and DNA-binding proteins along their domains and amino acids involved. Here, we explore chemical XL-MS RNA-protein, DNA-protein, nucleotide-protein complexes in vitro vivo . We introduce a specialized nucleotide-protein-crosslink search engine, NuXL, robust fast identification of such crosslinks at acid resolution. Chemical complements by generating different crosslink species,...
Abstract In Eukaryotes, tRNAs, 5S RNA and U6 are transcribed by polymerase (Pol) III. Human Pol III is composed of 17 subunits. Three specific subunits form a stable ternary subcomplex (RPC62-RPC39-RPC32α/β) being involved in pre-initiation complex formation. No paralogues for this have been found Pols I or II, but hRPC62 was shown to be structurally related the general II transcription factor hTFIIEα. Here we show that these structural homologies extend functional similarities. as well...
CRISPR-Cas is a sophisticated defence system used by bacteria and archaea to fend off invaders. systems vary in their Cas protein composition have therefore been divided into different classes types. Type I of shown contain the small Cas11 as part interference complex. Here we show for first time that an archaeal type also contains protein. In addition, internal in-frame translation The Cas11b from Haloferax volcanii I-B encoded cas8b gene. Translation initiation at methionine open reading...
Abstract Genomes are constantly threatened by DNA damage, but cells can remove a large variety of lesions nucleotide excision repair (NER) 1 . Mutations in NER factors compromise cellular fitness and cause human diseases such as Xeroderma pigmentosum (XP), Cockayne syndrome trichothiodystrophy 2,3 The machinery is built around the multisubunit transcription factor IIH (TFIIH), which opens bubble, scans for lesion, coordinates damaged single strand fragment 1,4 TFIIH consists kinase module...
The molecular classification of endometrial cancer developed by Cancer Genome Atlas project (TCGA, 2013) is currently actively used in gynecological oncology. According to it, carcinoma divided into four subtypes:
Abstract Activating signal co-integrator complex (ASCC) supports diverse genome maintenance and gene expression processes. Its ASCC3 subunit is an unconventional nucleic acid helicase, harboring tandem Ski2-like NTPase/helicase cassettes crucial for ASCC functions. Presently, the molecular mechanisms underlying helicase activity regulation remain unresolved. Here, we present cryogenic electron microscopy, DNA-protein cross-linking/mass spectrometry as well in vitro cellular functional...
ABSTRACT Even though Bacillus subtilis is one of the most studied organisms, no function has been identified for about 20% its proteins. Among these unknown proteins are several RNA- and ribosome-binding suggesting that they exert functions in cellular information processing. In this work, we have investigated RNA-binding protein YlxR. This widely conserved bacteria strongly constitutively expressed B. an important function. We RNA subunit essential RNase P as binding partner The main...