A5068706881- RNA and protein synthesis mechanisms
- RNA modifications and cancer
- Bacterial Genetics and Biotechnology
- Genomics and Phylogenetic Studies
- Cancer-related gene regulation
- Bacteriophages and microbial interactions
- Veterinary medicine and infectious diseases
- Peptidase Inhibition and Analysis
- RNA Research and Splicing
- Epigenetics and DNA Methylation
- Molecular Biology Techniques and Applications
- Toxin Mechanisms and Immunotoxins
- Enzyme Structure and Function
- Viral Infections and Immunology Research
- Microbial Community Ecology and Physiology
- interferon and immune responses
- Monoclonal and Polyclonal Antibodies Research
- Antimicrobial Resistance in Staphylococcus
- Bacillus and Francisella bacterial research
- Viral gastroenteritis research and epidemiology
- Antimicrobial Peptides and Activities
- Chemical Reactions and Isotopes
- Antibiotic Resistance in Bacteria
- Microbial Metabolic Engineering and Bioproduction
- Mass Spectrometry Techniques and Applications
University of Rhode Island
2016-2024
Brown University
2008-2018
University of Houston
2015
John Brown University
1995-2014
Whitehead Institute for Biomedical Research
2001
Massachusetts Institute of Technology
2001
Howard Hughes Medical Institute
2001
Johns Hopkins University
2001
University of California, Santa Cruz
2001
On the basis of recent atomic-resolution x-ray structure 50S ribosomal subunit, residues A2451 and G2447 23S rRNA were proposed to participate directly in ribosome-catalyzed peptide bond formation. We have examined peptidyltransferase protein synthesis activities ribosomes carrying mutations at these nucleotides. In Escherichia coli , pure mutant ribosome populations either G2447A or G2447C maintained cell viability. vitro supported a rate comparable that wild-type ribosomes. single-turnover...
All organisms incorporate post-transcriptional modifications into ribosomal RNA, influencing ribosome assembly and function in ways that are poorly understood. The most highly conserved modification is the dimethylation of two adenosines near 3′ end small subunit rRNA. Lack these methylations due to deficiency KsgA methyltransferase stimulates translational errors during both initiation elongation phases protein synthesis confers resistance antibiotic kasugamycin. Here, we present X-ray...
The ribosome decodes mRNA by monitoring the geometry of codon–anticodon base-pairing using a set universally conserved 16S rRNA nucleotides within conformationally dynamic decoding site. By applying single-molecule FRET and X-ray crystallography, we have determined that conditional-lethal, streptomycin-dependence mutations in ribosomal protein S12 interfere with tRNA selection allowing conformational distortions site impair GTPase activation EF-Tu during process. Distortions are reversed...
ABSTRACT Thermus thermophilus is an extremely thermophilic bacterium that widely used as a model thermophile, in large part due to its amenability genetic manipulation. Here we describe system for the introduction of genomic point mutations or deletions using counterselectable marker consisting conditionally lethal mutant allele pheS encoding phenylalanyl-tRNA synthetase α-subunit. Mutant PheS with A294G amino acid substitution renders cells sensitive phenylalanine analog p...
A protocol has been developed that allows protein identifications using available DNA-based or sequences from a reference strain of bacterial species to be extended strains for which no prior sequence information exists. The is predicated on careful isolation specific sub-cellular group proteins. In this study, ribosomal proteins were chosen due their high relative abundance and similarity in copy number per cell. After proteins, MALDI-MS used acquire accurate molecular weights. An iterative...
Journal Article Mutations in the peptidyl transferase region of E.coli 23S rRNA affecting translational accuracy Get access Steven T. Gregory, Gregory Section Biochemistry, Box G, Brown UniversityProvidence, Rl 02912, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Kathy R. Lieberman, Lieberman Albert E. Dahlberg Nucleic Acids Research, Volume 22, Issue 3, 11 February 1994, Pages 279–284, https://doi.org/10.1093/nar/22.3.279 Published: 1994 history...
ABSTRACT Structural studies of the ribosome have benefited greatly from use organisms adapted to extreme environments. However, little is known about mechanisms by which ribosomes or other ribonucleoprotein complexes functioning under conditions, and it unclear what degree mutant phenotypes extremophiles will resemble those their counterparts more moderate It conceivable that mutations affecting thermophilic ribosomes, for instance, be influenced structural adaptations specific a existence....
High-resolution ribosome structures determined by X-ray crystallography have provided important insights into the mechanism of translation. Such studies thus far relied on large crystals kept at cryogenic temperatures to reduce radiation damage. Here, application serial femtosecond (SFX) using an free-electron laser (XFEL) obtain diffraction data from microcrystals in liquid suspension ambient temperature is described. 30S ribosomal subunit diffracted beyond 6 Å resolution, demonstrating...
Abstract Enterococcus faecalis is a gram-positive organism responsible for serious infections in humans, but as with many bacterial pathogens, resistance has rendered number of commonly used antibiotics ineffective. Here, we report the cryo-EM structure E. 70S ribosome to global resolution 2.8 Å. Structural differences are clustered peripheral and solvent exposed regions when compared Escherichia coli , whereas functional centres, including antibiotic binding sites, similar other ribosomes....
IF3 is essential for ensuring the fidelity of initiation step translation in bacterial cells. Mutations at residues R99 and R131 C-terminal domain factor have previously been shown to increase from noncanonical GUA codon. Here we show that these mutant forms fail discriminate against many different non-AUG codons. They also enhance activity tRNAs carrying changes three consecutive G-C pairs are conserved anticodon stem initiator tRNAs. In addition, mutants stimulate initiations leaderless...
The ribosomal protein L11 in bacteria is posttranslationally trimethylated at multiple amino acid positions by the methyltransferase PrmA, product of prmA gene. role methylation ribosome function or assembly has yet to be determined, although deletion Escherichia coli no apparent phenotype. We have constructed a mutant extreme thermophile Thermus thermophilus which gene been disrupted with htk encoding heat-stable kanamycin adenyltransferase. This shows growth defects, indicating that T....
The Escherichia coli rluD gene encodes a pseudouridine synthase responsible for the (Ψ) modifications at positions 1911, 1915, and 1917 in helix 69 of 23S rRNA. It has been reported that deletion K-12 strains E. is associated with extremely slow growth, increased readthrough stop codons, defects 50S ribosomal subunit assembly 30S-50S association. Suppressor mutations prfB prfC genes encoding release factor 2 (RF2) RF3 restore wild type-growth rate also correct have now isolated. These...
Ribosomal proteins S4 and S5 participate in the decoding assembly processes on ribosome interaction with specific antibiotic inhibitors of translation. Many characterized mutations affecting these decrease accuracy translation, leading to a ribosomal-ambiguity phenotype. Structural analyses ribosomal complexes indicate that tRNA selection pathway involves transition between closed open conformations 30S subunit requires disruption interface proteins. In agreement this observation, several...
Codon recognition by aminoacyl-tRNA on the ribosome triggers a process leading to GTP hydrolysis elongation factor Tu (EF-Tu) and release of into A site ribosome. The nature this signal is largely unknown. Here, we present genetic evidence that specific set direct interactions between ribosomal protein S12 aminoacyl-tRNA, together with contacts 16S rRNA, provide pathway for signaling codon EF-Tu. Three novel amino acid substitutions, H76R, R37C, K53E in Thermus thermophilus S12, confer...
The structural basis for the streptomycin dependence phenotype of ribosomal protein S12 mutants is poorly understood. Here we describe application site-directed mutagenesis and gene replacement Thermus thermophilus rpsL to assess importance side chain identity tertiary interactions as phenotypic determinants drug-dependent mutants.