A5021926700- RNA and protein synthesis mechanisms
- RNA Research and Splicing
- RNA modifications and cancer
- Parvovirus B19 Infection Studies
- Viral Infections and Immunology Research
- Plant and animal studies
- Insect and Arachnid Ecology and Behavior
- RNA Interference and Gene Delivery
- Insect and Pesticide Research
- Genomics and Chromatin Dynamics
- Bacteriophages and microbial interactions
- Chemical Synthesis and Analysis
- Plant Virus Research Studies
- Peptidase Inhibition and Analysis
- Respiratory viral infections research
National Cancer Institute
2021-2024
Center for Cancer Research
2021-2024
Max Planck Institute for Developmental Biology
2019-2021
Central European Institute of Technology
2016-2019
Central European Institute of Technology – Masaryk University
2016-2019
Developing an effective mRNA therapeutic often requires maximizing protein output per delivered molecule. We previously found that coding sequence (CDS) design can substantially affect output, with variants containing more optimal codons and higher secondary structure yielding the highest outputs due to their slow rates of decay. Here, we demonstrate CDS-dependent differences in translation initiation elongation lead translation- deadenylation-dependent decay rates, thus explaining effect...
CCR4-NOT is a conserved multiprotein complex which regulates eukaryotic gene expression principally via shortening of poly(A) tails messenger RNA or deadenylation. Here, we reconstitute complete, recombinant human complex. Our reconstitution strategy permits strict compositional control to test mechanistic hypotheses with purified component variants. more active and selective for than the isolated exonucleases, CCR4a CAF1, have distinct deadenylation profiles in vitro. The exonucleases...
Pumilio paralogs, PUM1 and PUM2, are sequence-specific RNA-binding proteins that essential for vertebrate development neurological functions. PUM1&2 negatively regulate gene expression by accelerating degradation of specific mRNAs. Here, we determined the repression mechanism impact human on transcriptome. We identified subunits CCR4-NOT (CNOT) deadenylase complex required stable interaction with to elicit CNOT-dependent repression. Isoform-level RNA sequencing revealed broad coregulation...
Abstract Viruses from the genus Enterovirus are important human pathogens. Receptor binding or exposure to acidic pH in endosomes converts enterovirus particles an activated state that is required for genome release. However, mechanism of uncoating not well understood. Here, we use cryo-electron microscopy visualize virions echovirus 18 process We discover exit RNA particle results a loss one, two, three adjacent capsid-protein pentamers. The opening capsid, which more than 120 Å diameter,...
Pumilio is an RNA-binding protein that represses a network of mRNAs to control embryogenesis, stem cell fate, fertility and neurological functions in Drosophila. We sought identify the mechanism Pumilio-mediated repression find it accelerates degradation target mRNAs, mediated by three N-terminal Repression Domains (RDs), which are unique orthologs. show repressive activities RDs depend on specific subunits Ccr4-Not (CNOT) deadenylase complex. Depletion Pop2, Not1, Not2, or Not3 alleviates...
Abstract XRN1 is the major cytoplasmic exoribonuclease in eukaryotes, which degrades deadenylated and decapped mRNAs last step of 5′–3′ mRNA decay pathway. Metazoan interacts with decapping factors coupling final stages decay. Here, we reveal a direct interaction between CCR4–NOT deadenylase complex mediated by low-complexity region XRN1, term ‘C-terminal interacting region’ or CIR. The CIR represses reporter deadenylation human cells when overexpressed inhibits isolated CAF1 activity vitro....
Abstract Shortening of messenger RNA poly(A) tails, or deadenylation, is a rate-limiting step in mRNA decay and highly regulated during gene expression. The incorporation non-adenosines ‘mixed tailing’, has been observed vertebrates viruses. Here, to quantitate the effect mixed we mathematically modeled deadenylation reactions at single-nucleotide resolution using an vitro system reconstituted with complete human CCR4–NOT complex. Applying this model, assessed disrupting impact single...
Abstract The CCR4-NOT complex acts as a central player in the control of mRNA turnover and mediates accelerated degradation upon HDAC inhibition. Here, we explored acetylation-induced changes composition by purification endogenously tagged scaffold subunit NOT1 identified RNF219 an acetylation-regulated cofactor. We demonstrate that is active RING-type E3 ligase which stably associates with via NOT9 through short linear motif (SLiM) embedded within C-terminal low-complexity region RNF219. By...
The western honeybee (Apis mellifera) is the most important commercial insect pollinator. However, bees are under pressure from habitat loss, environmental stress, and pathogens, including viruses that can cause lethal epidemics. Slow bee paralysis virus (SBPV) belongs to Iflaviridae family of nonenveloped single-stranded RNA viruses. Here we present structure SBPV virion determined two crystal forms resolutions 3.4 Å 2.6 Å. overall resembles picornaviruses, with three major capsid proteins...
Abstract Pumilio paralogs, PUM1 and PUM2, are sequence-specific RNA-binding proteins that essential for vertebrate development neurological functions. PUM1&2 negatively regulate gene expression by accelerating degradation of specific mRNAs. Here, we determined the repression mechanism impact human on transcriptome. We identified subunits CCR4-NOT (CNOT) deadenylase complex required stable interaction with to elicit CNOT-dependent repression. Isoform-level RNA sequencing revealed broad...
ABSTRACT Pumilio is an RNA-binding protein that represses a network of mRNAs to control embryogenesis, stem cell fate, fertility, and neurological functions in Drosophila . We sought identify the mechanism Pumilio-mediated repression find it accelerates degradation target mRNAs, mediated by three N-terminal Repression Domains (RDs), which are unique orthologs. show repressive activities RDs depend on specific subunits Ccr4-Not (CNOT) deadenylase complex. Depletion Pop2, Not1, Not2, or Not3...
Abstract NOT1, NOT10, and NOT11 form a conserved module in the CCR4-NOT complex, critical for post-transcriptional regulation eukaryotes, but how this contributes to functions of remains poorly understood. Here, we present cryo-EM structures human chicken NOT1:NOT10:NOT11 ternary complexes sub-3 Å resolution, revealing an evolutionarily conserved, flexible structure. Through biochemical dissection studies, which include Drosophila orthologs, show that assembly is hierarchical, with binding...