A5089592562- RNA and protein synthesis mechanisms
- Genomics and Phylogenetic Studies
- RNA modifications and cancer
- Bacterial Genetics and Biotechnology
- DNA and Nucleic Acid Chemistry
- RNA Research and Splicing
- Bacteriophages and microbial interactions
- Epigenetics and DNA Methylation
- Genomics and Chromatin Dynamics
- Plant Virus Research Studies
- Microbial Community Ecology and Physiology
- RNA regulation and disease
- Enzyme Structure and Function
The Ohio State University
2019-2023
Whereas DNA viruses are known to be abundant, diverse, and commonly key ecosystem players, RNA insufficiently studied outside disease settings. In this study, we analyzed ≈28 terabases of Global Ocean sequences expand Earth's virus catalogs their taxonomy, investigate evolutionary origins, assess marine biogeography from pole pole. Using new approaches optimize discovery classification, identified that necessitate substantive revisions taxonomy (doubling phyla adding >50% classes)...
Genomic studies have indicated that certain bacterial lineages such as the Bacteroidetes lack Shine-Dalgarno (SD) sequences, and yet with few exceptions ribosomes of these organisms carry canonical anti-SD (ASD) sequence. Here, we show purified from Flavobacterium johnsoniae, a representative Bacteroidetes, fail to recognize SD sequence mRNA in vitro. A cryo-electron microscopy structure complete 70S ribosome F. johnsoniae at 2.8 Å resolution reveals ASD is sequestered by ribosomal proteins...
Single nucleotide polymorphisms are widely associated with disease, but the ways in which they cause altered phenotypes often unclear, especially when appear non-coding regions. One way could disease is by affecting crucial RNA-protein interactions. While it clear that changing a protein binding motif will alter binding, has been shown single can affect RNA secondary structure, and here we show interactions from outside motifs through structure. By using modified version of Vienna Package...
In all cells, initiation of translation is tuned by intrinsic features the mRNA. Here, we analyze in Flavobacterium johnsoniae, a representative Bacteroidetes. Members this phylum naturally lack Shine-Dalgarno (SD) sequences their mRNA, and yet ribosomes retain conserved anti-SD sequence. Translation mRNA secondary structure identities several key nucleotides upstream start codon. Positive determinants include adenine at position -3, reminiscent Kozak sequence Eukarya. Comparative analysis...
Ribosomes of Bacteroidia (formerly Bacteroidetes) fail to recognize Shine-Dalgarno (SD) sequences even though they harbor the anti-SD (ASD) 16S rRNA. Inhibition SD-ASD pairing is due sequestration 3' tail rRNA in a pocket formed by bS21, bS18, and bS6 on 30S platform. Interestingly, many Flavobacteriales, gene encoding rpsU, contains an extended SD sequence. In this work, we present genetic biochemical evidence that bS21 synthesis Flavobacterium johnsoniae autoregulated via subpopulation...
Abstract Nucleosomes, the fundamental organizing units of eukaryotic genomes, contain ∼146 base pairs DNA wrapped around a histone H3–H4 tetramer and two H2A–H2B dimers. Converting nucleosomes into hexasomes by removal dimer is an important regulatory event, but its regulation functional consequences are not well-understood. To investigate influence on accessibility, we used property Widom-601 Nucleosome Positioning Sequence (NPS) to form homogeneously oriented in vitro. We find that...
The anti-Shine-Dalgarno (ASD) sequence of 16S rRNA is highly conserved across Bacteria, and yet usage Shine-Dalgarno (SD) sequences in mRNA varies dramatically, depending on the lineage. Here, we compared effects ASD mutagenesis Escherichia coli, a Gammaproteobacteria which commonly employs SD sequences, Flavobacterium johnsoniae, Bacteroidia rarely does. In E. 30S subunits carrying any single substitution at positions 1,535-1,539 confer dominant negative phenotypes, whereas with mutations...
In most bacteria, the three ribosomal RNAs (rRNAs) are encoded together in each of several near-identical operons. As soon as nascent precursor rRNA emerges from RNA polymerase, ribosome assembly begins. This process entails protein binding, folding, modification, and processing. model organisms Escherichia coli Bacillus subtilis, processing results similar mature rRNAs, despite substantial differences cohort RNAses involved. A recent study Flavobacterium johnsoniae, a member phylum...
Abstract Motivation RNA-binding proteins are fundamental to many cellular processes. Double-stranded (dsRBPs) in particular crucial for RNA interference, mRNA elongation, A-to-I editing, host defense, splicing and a multitude of other important mechanisms. Since dsRBPs require double-stranded bind, their binding affinity depends on the competition among all possible secondary structures target molecule. Here, we introduce quantitative model that allows calculation effective any given...