A5082712375- RNA and protein synthesis mechanisms
- RNA modifications and cancer
- RNA Research and Splicing
- Viral Infections and Immunology Research
- Plant Virus Research Studies
- Mosquito-borne diseases and control
- Bacteriophages and microbial interactions
- Viral Infections and Vectors
- Earthquake Detection and Analysis
- Methane Hydrates and Related Phenomena
- Seismic Waves and Analysis
- CRISPR and Genetic Engineering
- RNA regulation and disease
- Cancer-related molecular mechanisms research
- Hepatitis C virus research
- Viral gastroenteritis research and epidemiology
- Animal Virus Infections Studies
- Animal Disease Management and Epidemiology
- HIV Research and Treatment
- Plant and Fungal Interactions Research
- Advanced Electron Microscopy Techniques and Applications
- Insect symbiosis and bacterial influences
- interferon and immune responses
- Advanced biosensing and bioanalysis techniques
- Virology and Viral Diseases
University of Colorado Anschutz Medical Campus
2005-2025
New York Structural Biology Center
2023-2025
University of Colorado Denver
2015-2024
Howard Hughes Medical Institute
2001-2023
The Medical Center of Aurora
2015-2023
Denver School of Nursing
2022
Molecular Biology Consortium
2020
Yale University
1999-2018
Indiana University School of Medicine
2015
University of Colorado Cancer Center
2013
Flaviviruses are emerging human pathogens and worldwide health threats. During infection, pathogenic subgenomic flaviviral RNAs (sfRNAs) produced by resisting degradation the 5'→3' host cell exonuclease Xrn1 through an unknown RNA structure-based mechanism. Here, we present crystal structure of a complete Xrn1-resistant RNA, which contains interwoven pseudoknots within compact that depends on highly conserved nucleotides. The RNA's three-dimensional topology creates ringlike conformation,...
Zika virus uses a convoluted RNA fold to produce noncoding RNAs associated with pathogenesis.
Dengue virus is a growing global health threat. and other flaviviruses commandeer the host cell’s RNA degradation machinery to generate small flaviviral (sfRNA), noncoding that induces cytopathicity pathogenesis. Host cell exonuclease Xrn1 likely loads on 5′ end of viral genomic degrades processively through ∼10 kB RNA, halting near 3′ RNA. The surviving sfRNA. We interrogated architecture complete 2 sfRNA, identifying five independently-folded structures, two which quantitatively confer...
Recent events have pushed RNA research into the spotlight. Continued discoveries of with unexpected diverse functions in healthy and diseased cells, such as role both source countermeasure to a severe acute respiratory syndrome coronavirus 2 infection, are igniting new passion for understanding this functionally structurally versatile molecule. Although structure is key function, many foundational characteristics misunderstood, default state often thought depicted single floppy strand. The...
Many viruses and certain cellular mRNAs initiate protein synthesis from a highly structured RNA sequence in the 5' untranslated region, called internal ribosome entry site (IRES). In hepatitis C virus (HCV), IRES functionally replaces several large initiation factor proteins by directly recruiting 43S particle. Using quantitative binding assays, modification interference of binding, chemical enzymatic footprinting experiments, we show that three independently folded tertiary structural...
Hepatitis C virus (HCV) contains an internal ribosome entry site (IRES) located in the 5' untranslated region of genomic RNA that drives cap-independent initiation translation viral message. The approximate secondary structure and minimum functional length HCV IRES are known, extensive mutagenesis has established nearly all structural domains critical for activity. However, presence tertiary fold its relevance have not been established. Using chemical enzymatic probes solution, we show...
In bacterial translational initiation, three initiation factors (IFs 1–3) enable the selection of initiator tRNA and start codon in P site 30S ribosomal subunit. Here, we report 11 single-particle cryo-electron microscopy (cryoEM) reconstructions complex subunit with tRNA, mRNA, IFs 1–3, representing different steps along pathway. IF1 provides key anchoring points for IF2 IF3, thereby enhancing their activities. positions a domain an extended conformation appropriate capturing...
Flaviviruses such as Yellow fever, Dengue, West Nile, and Zika generate disease-linked viral noncoding RNAs called subgenomic flavivirus RNAs. Subgenomic result when the 5'-3' progression of cellular exoribonuclease Xrn1 is blocked by RNA elements Xrn1-resistant located within genome's 3'-untranslated region that operate without protein co-factors. Here, we show can halt diverse exoribonucleases, revealing a mechanism in which they act general mechanical blocks 'brace' against an enzyme's...
Significance Folded RNA elements are essential for diverse biological processes. Recently discovered examples include viral xrRNAs, which co-opt the cellular decay machinery within a novel noncoding production pathway. Here we characterize an xrRNA with no apparent evolutionary link or sequence homology to those described previously. Our results show that xrRNAs authentic class of functional RNAs have arisen independently in different contexts, suggesting they may be widespread. The detailed...
Functional RNAs fold through complex pathways that can contain misfolded “kinetic traps.” A complete model of RNA folding requires understanding the formation these states, but they are difficult to characterize because their transient and potentially conformationally dynamic nature. We used cryo–electron microscopy (cryo-EM) visualize a long-lived state in pathway Tetrahymena thermophila group I intron, paradigmatic structure-function system. The structure revealed how this forms...
Giardia lamblia is a deeply branching protist and human pathogen. Its unusual biology presents the opportunity to explore conserved fundamental molecular mechanisms. We determined structure of G. 80S ribosome bound tRNA, mRNA, antibiotic emetine by cryo-electron microscopy, an overall resolution 2.49 Å. The reveals rapidly evolving protein nucleotide regions, differences in peptide exit tunnel, likely altered quality control pathways. Examination translation initiation factor binding sites...
Canonical cap-dependent translation initiation requires a large number of protein factors that act in stepwise assembly process. In contrast, internal ribosomal entry sites (IRESs) are cis-acting RNAs some cases completely supplant these by recruiting and activating the ribosome using single structured RNA. Here we present crystal structures ribosome-binding domain from Dicistroviridae intergenic region IRES at 3.1 angstrom resolution, providing view prefolded architecture an all-RNA...
RNA biochemical or structural studies often require an sample that is chemically pure, and most protocols for its in vitro production use denaturing polyacrylamide gel electrophoresis to achieve this. Unfortunately, many RNAs do not quantitatively refold into active conformation after denaturation, creating significant problems downstream characterization use. In addition, this traditional purification method amenable demanding high-throughput production. Recently, we presented the first...