A5001420469- RNA modifications and cancer
- RNA and protein synthesis mechanisms
- DNA Repair Mechanisms
- DNA and Nucleic Acid Chemistry
- RNA Research and Splicing
- Carcinogens and Genotoxicity Assessment
- Advanced biosensing and bioanalysis techniques
- Epigenetics and DNA Methylation
- Bacteriophages and microbial interactions
- Genomics and Phylogenetic Studies
- CRISPR and Genetic Engineering
- Microbial Community Ecology and Physiology
- Molecular Biology Techniques and Applications
- Bacterial Genetics and Biotechnology
- Streptococcal Infections and Treatments
- Cancer-related molecular mechanisms research
- Chemical Analysis and Environmental Impact
- PARP inhibition in cancer therapy
- Antimicrobial Resistance in Staphylococcus
- Amino Acid Enzymes and Metabolism
- Neonatal and Maternal Infections
- Antibiotic Resistance in Bacteria
- Folate and B Vitamins Research
- Metalloenzymes and iron-sulfur proteins
- Fungal and yeast genetics research
Massachusetts Institute of Technology
2014-2025
Center for Environmental Health
2008-2025
Harvard University
2002-2005
Parsons (United States)
2005
University of Rochester
1996-2002
Rockefeller University
1992-1993
Howard Hughes Medical Institute
1993
Decades of study have revealed more than 100 ribonucleoside structures incorporated as post-transcriptional modifications mainly in tRNA and rRNA, yet the larger functional dynamics this conserved system are unclear. To end, we developed a highly precise mass spectrometric method to quantify Saccharomyces cerevisiae. Our approach several novel biosynthetic pathways for RNA led discovery signature changes spectrum damage response mechanistically different toxicants. This is illustrated with...
Phosphorothioate (PT) modification of DNA, with sulfur replacing a nonbridging phosphate oxygen, was recently discovered as product the dnd genes found in bacteria and archaea. Given our limited understanding biological function PT modifications, including sequence context, genomic frequencies, relationships to diversity gene clusters, we undertook quantitative study modifications prokaryotic genomes using liquid chromatography-coupled tandem quadrupole mass spectrometry approach. The...
Cells respond to stress by controlling gene expression at several levels, with little known about the role of translation. Here, we demonstrate a coordinated translational response system involving stress-specific reprogramming tRNA wobble modifications that leads selective translation codon-biased mRNAs representing different classes critical proteins. In budding yeast exposed four oxidants and five alkylating agents, modification patterns accurately distinguished among chemically similar...
DNA damage and epigenetic marks are well established to have profound influences on genome stability cell phenotype, yet there few technologies obtain high-resolution genomic maps of the many types chemical modifications DNA. Here we present Nick-seq for quantitative, sensitive, accurate mapping at single-nucleotide resolution across genomes. Pre-existing breaks first blocked then converted enzymatically or chemically strand-breaks both 3'-extension by nick-translation produce...
Oxidized abasic residues in DNA constitute a major class of radiation and oxidative damage. Free radical attack on the nucleotidyl C-1′ carbon yields 2-deoxyribonolactone (dL) as significant lesion. Although dL are efficiently incised by main human endonuclease enzyme Ape1, we show here that subsequent excision polymerase β is impaired at compared with unmodified sites. This inhibition accompanied accumulation protein-DNA cross-link not observed reactions sites, although similar form can be...
Bacteria respond to environmental stresses using a variety of signaling and gene expression pathways, with translational mechanisms being the least well understood. Here, we identified tRNA methyltransferase in Pseudomonas aeruginosa PA14, trmJ, which confers resistance oxidative stress. Analysis from trmJ mutant revealed that TrmJ catalyzes formation Cm, Um, and, unexpectedly, Am. Defined vitro analyses tRNAMet(CAU) tRNATrp(CCA) are substrates for Cm formation, tRNAGln(UUG), tRNAPro(UGG),...
Two pathways for completion of DNA base excision repair (BER) have recently emerged. In one, called short patch BER, only the damaged nucleotide is replaced, whereas in second, known as long monobasic lesion removed along with additional downstream nucleotides. Flap endonuclease 1, which preferentially cleaves unannealed 5′-flap structures DNA, has been shown to play a crucial role mode repair. This nuclease will efficiently release 5′-terminal abasic lesions part an intact oligonucleotide...
The oxidation of 2-deoxyribose in DNA has emerged as a critical determinant the cellular toxicity oxidative damage to DNA, with each carbon producing unique spectrum electrophilic products. We have developed and validated an isotope-dilution gas chromatography-coupled mass spectrometry (GC−MS) method for rigorous quantification two major products: 2-deoxyribonolactone abasic site 1′-oxidation nucleoside 5′-aldehyde 5′-oxidation chemistry. entails elimination these products...
Prokaryotes protect their genomes from foreign DNA with a diversity of defence mechanisms, including widespread restriction-modification (R-M) system involving phosphorothioate (PT) modification the backbone. Unlike classical R-M systems, highly partial PT consensus motifs in bacterial suggests an unusual mechanism PT-dependent restriction. In Salmonella enterica, is mediated by four genes dptB-E, while restriction involves additional three dptF-H. Here, we performed series studies to...
Epigenetic regulation of gene expression and host defense is well established in microbial communities, with dozens DNA modifications comprising the epigenomes prokaryotes bacteriophage. Phosphorothioation (PT) DNA, which a chemically reactive sulfur atom replaces non-bridging oxygen sugar-phosphate backbone, catalyzed by dnd ssp families widespread bacteria archaea. However, little known about role PTs or other epigenetic human microbiome. Here we optimized applied fecal extraction, mass...
In this report, we perform structure validation of recently reported RNA phosphorothioate (PT) modifications, a new set epitranscriptome marks found in bacteria and eukaryotes including humans. By comparing synthetic PT-containing diribonucleotides with native species hydrolysates by high-resolution mass spectrometry (MS), metabolic stable isotope labeling, PT-specific iodine-desulfurization, disprove the existence PTs from E. coli, S. cerevisiae, human cell lines, mouse brain. Furthermore,...
Multidrug-resistant P. aeruginosa infections pose a serious public health threat due to the rise in antimicrobial resistance. Phage therapy has emerged as promising alternative. However, evolved various mechanisms thwart phage attacks, making it crucial decipher these resistance develop effective therapeutic strategies. In this study, we conducted forward-genetic screen of PA14 non-redundant transposon library (PA14NR) identify dominant-negative mutants displaying phage-resistant phenotypes....
Repair of abasic lesions, one the most common types damage found in DNA, is crucial to an organism's well-being. Studies vitro indicate that after apurinic-apyrimidinic endonuclease cleaves immediately upstream a baseless site, removal 5′-terminal sugar-phosphate residue achieved by deoxyribophosphodiesterase activity, enzyme-mediated β-elimination reaction, or endonucleolytic cleavage downstream sugar. Synthesis and ligation complete repair.Eukaryotic RAD2 homolog 1 (RTH1) nuclease, genetic...
DNA sequence context has emerged as a critical determinant of the location and quantity nucleobase damage caused by many oxidizing agents. However, complexity 2-deoxyribose strong oxidants such ionizing radiation Fenton chemistry Fe2+-EDTA/H2O2 poses challenge to defining effects on in DNA. To address this problem, we developed gel-based method that allows quantification oxidized exploiting Escherichia coli exonuclease III remove fragments containing direct strand breaks abasic sites. The...
Modifications found in the Anticodon Stem Loop (ASL) of tRNAs play important roles regulating translational speed and accuracy. Threonylcarbamoyl adenosine (t6A37) 5-methoxycarbonyl methyl-2-thiouridine (mcm5s2U34) are critical ASL modifications that have been linked to several human diseases. The model yeast Saccharomyces cerevisiae is viable despite absence both modifications, growth however greatly impaired. major observed consequence a subsequent increase protein aggregates aberrant...
Epigenetic regulation of gene expression and host defense is well established in microbial communities, with dozens DNA modifications comprising the epigenomes prokaryotes bacteriophage. Phosphorothioation (PT) DNA, which a chemically-reactive sulfur atom replaces non-bridging oxygen sugar-phosphate backbone, catalyzed by