A5056632664- RNA and protein synthesis mechanisms
- Bacterial Genetics and Biotechnology
- Bacteriophages and microbial interactions
- RNA modifications and cancer
- Enzyme Structure and Function
- Genomics and Phylogenetic Studies
- Tuberculosis Research and Epidemiology
- Molecular Biology Techniques and Applications
- DNA and Nucleic Acid Chemistry
- RNA Research and Splicing
- Genomics and Chromatin Dynamics
- Genetics, Bioinformatics, and Biomedical Research
- Total Knee Arthroplasty Outcomes
- DNA Repair Mechanisms
- Mycobacterium research and diagnosis
- Orthopaedic implants and arthroplasty
- Photosynthetic Processes and Mechanisms
- Biochemical and Molecular Research
- Medical Imaging Techniques and Applications
- Bioinformatics and Genomic Networks
- Machine Learning in Bioinformatics
- Radiopharmaceutical Chemistry and Applications
- CRISPR and Genetic Engineering
- Interdisciplinary Research and Collaboration
- Cancer therapeutics and mechanisms
Pennsylvania State University
2016-2025
Universidad del Noreste
2024
Fujita Health University Hospital
2024
Fukushima Medical University Hospital
2020-2024
Eunice Kennedy Shriver National Institute of Child Health and Human Development
2013
National Institutes of Health
2013
Fred Hutch Cancer Center
2012
Yale University
2012
Radboud University Nijmegen
2012
Nikon (Japan)
2008-2009
The crystal structure of Thermus aquaticus RNA polymerase holoenzyme (α 2 ββ′ωσ A ) complexed with a fork-junction promoter DNA fragment has been determined by fitting high-resolution x-ray structures individual components into 6.5-angstrom resolution map. lies across one face the holoenzyme, completely outside active site channel. All sequence-specific contacts core elements are mediated σ subunit. universally conserved tryptophan is ideally positioned to stack on exposed base pair at...
The crystal structure of the initiating form Thermus aquaticus RNA polymerase, containing core polymerase (α 2 ββ′ω) and promoter specificity σ subunit, has been determined at 4 angstrom resolution. Important structural features their roles in positioning within initiation complex are delineated, as well role played by modulating opening active-site channel. two carboxyl-terminal domains separated 45 angstroms on surface but linked an extended loop. loop winds near active site, where it may...
Abstract SARS-CoV-2 proteases Mpro and PLpro are promising targets for antiviral drug development. In this study, we present an screening strategy involving a novel in-cell protease assay, biochemical activity assessments, as well structural determinations rapid identification of inhibitors with low cytotoxicity. We identified eight compounds anti-SARS-CoV-2 from library 64 repurposed drugs modeled at active sites by in silico docking. demonstrate that Sitagliptin Daclatasvir inhibit PLpro,...
Journal Article Differential regulation by ppGpp versus pppGpp in Escherichia coli Get access Undine Mechold, Mechold 1Laboratory of Molecular Genetics, Eunice Kennedy Shriver National Institute Child Health and Human Development, Institutes Health, Bethesda, MD 20892, USA 2Department Biochemistry Biology, The Center for RNA Pennsylvania State University, University Park, PA 16802, Search other works this author on: Oxford Academic PubMed Google Scholar Katarzyna Potrykus, Potrykus Helen...
Escherichia coli RNA polymerase (RNAP) is the most studied bacterial RNAP and has been used as model for screening evaluating potential RNAP-targeting antibiotics. However, x-ray crystal structure of E. limited to individual domains. Here, I report σ(70) holoenzyme, which shows σ region 1.1 (σ1.1) α subunit C-terminal domain first time in context an intact RNAP. σ1.1 positioned at DNA-binding channel completely blocks DNA entry active site. The reveals that contains a basic patch on its...
Spt4/5 in archaea and eukaryote its bacterial homolog NusG is the only elongation factor conserved all three domains of life plays many key roles cotranscriptional regulation recruiting other factors to elongating RNA polymerase. Here, we present crystal structure as well polymerase-Spt4/5 complex using cryoelectron microscopy reconstruction single particle analysis. The binds middle polymerase claw encloses DNA, reminiscent DNA clamp ring helicases. transcription model reveals that an...
DksA and ppGpp are the central players in stringent response mediate a complete reprogramming of transcriptome. A major component is reduction ribosome synthesis, which accomplished by synergistic action bound to RNA polymerase (RNAP) inhibiting transcription rRNAs. Here, we report X-ray crystal structures Escherichia coli RNAP complex with alone ppGpp. The show that accesses template strand at active site downstream DNA binding simultaneously reveal allosteric effector reshapes RNAP–DksA...
DNA polymerase θ (Polθ) is a unique polymerase-helicase fusion protein that promotes microhomology-mediated end-joining (MMEJ) of double-strand breaks (DSBs). How full-length human Polθ performs MMEJ at the molecular level remains unknown. Using biochemical approach, we find helicase essential for long ssDNA overhangs which model resected DSBs. Remarkably, requires attachment, but not disordered central domain, and occurs independently ATPase activity. single-particle microscopy biophysical...
Since 1967, Rifampin (RMP, a Rifamycin) has been used as first line antibiotic treatment for tuberculosis (TB), and it remains the cornerstone of current short-term TB treatment. Increased occurrence Rifamycin-resistant (RIFR ) TB, ∼41% which results from RpoB S531L mutation in RNA polymerase (RNAP), become growing problem worldwide. In this study, we determined X-ray crystal structures Escherichia coli RNAPs containing most clinically important two other frequently observed RIFR mutants,...
Abstract Ribosomal RNA (rRNA) is most highly expressed in rapidly growing bacteria and drastically downregulated under stress conditions by the global transcriptional regulator DksA alarmone ppGpp. Here, we determined cryo-electron microscopy structures of Escherichia coli polymerase (RNAP) σ 70 holoenzyme during rRNA promoter recognition with without DksA/ppGpp. RNAP contacts UP element using dimerized α subunit carboxyl-terminal domains scrunches template DNA finger β’ lid to select...
Argonaute proteins are programmable nucleases that have defense and regulatory functions in both eukaryotes prokaryotes. All known prokaryotic Argonautes (pAgos) characterized so far act on DNA targets. Here, we describe a new class of pAgos uniquely use guides to process RNA The biochemical structural analysis Pseudooceanicola lipolyticus pAgo (PliAgo) reveals an unusual organization the guide binding pocket does not rely divalent cations canonical set contacts for 5'-end interactions....
NusG is a transcription elongation factor that stimulates pausing in Gram+ bacteria including B. subtilis by sequence-specific interaction with conserved pause-inducing − 11 TTNTTT −6 motif found the non-template DNA (ntDNA) strand within bubble. To reveal structural basis of NusG-dependent pausing, we determined cryo-EM structure paused complex (PTC) containing RNA polymerase (RNAP), NusG, and ntDNA strand. The rearranges bubble positioning three consecutive T residues cleft between β-lobe...
Rifampicin resistance, a defining attribute of multidrug-resistant tuberculosis, is conferred by mutations in the β subunit RNA polymerase. Sequencing rifampicin-resistant (RIF-R) clinical isolates Mycobacterium tuberculosis revealed, addition to RIF-R mutations, enrichment potential compensatory around double-psi β-barrel domain β' comprising catalytic site and exit tunnel for newly synthesized RNA. Sequential introduction resistance allele followed isogenic smegmatis showed that these...
Keeping gene transcription in check Transcription of all genes is carried out by RNA polymerase (RNAP). The enzyme thus a pivotal regulation point for many cell and developmental processes. In bacteria, sigma factors play vital role regulation, with σ54 being critical stress response genes. Yang et al. determined the x-ray crystal structure RNAP bound to σ54, as well promoter DNA. initial inhibited state RNAP-σ54 complex, blocks template DNA from entering active site downstream channel....
First step of gene expression is transcribing the genetic information stored in DNA to RNA by transcription machinery including polymerase (RNAP). In Escherichia coli, a primary σ70 factor forms RNAP holoenzyme express housekeeping genes. The contains large insertion between conserved regions 1.2 and 2.1, σ non-conserved region (σNCR), but its function remains be elucidated. this study, we determined cryo-EM structures E. coli complex with promoter (open complex, RPo) at 4.2 5.75 Å...