49 research outputs found

    A Quantitative Systems Approach Reveals Dynamic Control of tRNA Modifications during Cellular Stress

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    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 of this conserved system are unclear. To this end, we developed a highly precise mass spectrometric method to quantify tRNA modifications in Saccharomyces cerevisiae. Our approach revealed several novel biosynthetic pathways for RNA modifications and led to the discovery of signature changes in the spectrum of tRNA modifications in the damage response to mechanistically different toxicants. This is illustrated with the RNA modifications Cm, m[superscript 5]C, and m[superscript 2][subscript 2]G, which increase following hydrogen peroxide exposure but decrease or are unaffected by exposure to methylmethane sulfonate, arsenite, and hypochlorite. Cytotoxic hypersensitivity to hydrogen peroxide is conferred by loss of enzymes catalyzing the formation of Cm, m[superscript 5]C, and m[superscript 2][subscript 2]G, which demonstrates that tRNA modifications are critical features of the cellular stress response. The results of our study support a general model of dynamic control of tRNA modifications in cellular response pathways and add to the growing repertoire of mechanisms controlling translational responses in cells.National Institute of Environmental Health Sciences (ES002109)National Institute of Environmental Health Sciences (ES017010)National Institute of Environmental Health Sciences (ES015037)National Cancer Institute (U.S.) (CA026731)National Center for Research Resources (U.S.) (RR023783)Singapore-MIT Alliance for Research and Technolog

    Structural elements of an NRPS cyclization domain and its intermodule docking domain

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    Epothilones are thiazole-containing natural products with anticancer activity that are biosynthesized by polyketide synthase (PKS)-nonribosomal peptide synthetase (NRPS) enzymes EpoA–F. A cyclization domain of EpoB (Cy) assembles the thiazole functionality from an acetyl group and L-cysteine via condensation, cyclization, and dehydration. The PKS carrier protein of EpoA contributes the acetyl moiety, guided by a docking domain, whereas an NRPS EpoB carrier protein contributes L-cysteine. To visualize the structure of a cyclization domain with an accompanying docking domain, we solved a 2.03-Å resolution structure of this bidomain EpoB unit, comprising residues M1-Q497 (62 kDa) of the 160-kDa EpoB protein. We find that the N-terminal docking domain is connected to the V-shaped Cy domain by a 20-residue linker but otherwise makes no contacts to Cy. Molecular dynamic simulations and additional crystal structures reveal a high degree of flexibility for this docking domain, emphasizing the modular nature of the components of PKS-NRPS hybrid systems. These structures further reveal two 20-Å-long channels that run from distant sites on the Cy domain to the active site at the core of the enzyme, allowing two carrier proteins to dock with Cy and deliver their substrates simultaneously. Through mutagenesis and activity assays, catalytic residues N335 and D449 have been identified. Surprisingly, these residues do not map to the location of the conserved HHxxxDG motif in the structurally homologous NRPS condensation (C) domain. Thus, although both C and Cy domains have the same basic fold, their active sites appear distinct

    Structural elements of an NRPS cyclization domain and its intermodule docking domain

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    Epothilones are thiazole-containing natural products with anticancer activity that are biosynthesized by polyketide synthase (PKS)-nonribosomal peptide synthetase (NRPS) enzymes EpoA-F. A cyclization domain of EpoB (Cy) assembles the thiazole functionality from an acetyl group and l-cysteine via condensation, cyclization, and dehydration. The PKS carrier protein of EpoA contributes the acetyl moiety, guided by a docking domain, whereas an NRPS EpoB carrier protein contributes l-cysteine. To visualize the structure of a cyclization domain with an accompanying docking domain, we solved a 2.03-A resolution structure of this bidomain EpoB unit, comprising residues M1-Q497 (62 kDa) of the 160-kDa EpoB protein. We find that the N-terminal docking domain is connected to the V-shaped Cy domain by a 20-residue linker but otherwise makes no contacts to Cy. Molecular dynamic simulations and additional crystal structures reveal a high degree of flexibility for this docking domain, emphasizing the modular nature of the components of PKS-NRPS hybrid systems. These structures further reveal two 20-A-long channels that run from distant sites on the Cy domain to the active site at the core of the enzyme, allowing two carrier proteins to dock with Cy and deliver their substrates simultaneously. Through mutagenesis and activity assays, catalytic residues N335 and D449 have been identified. Surprisingly, these residues do not map to the location of the conserved HHxxxDG motif in the structurally homologous NRPS condensation (C) domain. Thus, although both C and Cy domains have the same basic fold, their active sites appear distinct

    N 6 -Formyllysine as a Biomarker of Formaldehyde Exposure: Formation and Loss of N 6 -Formyllysine in Nasal Epithelium in Long-Term, Low-Dose Inhalation Studies in Rats

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    Exposure to both endogenous and exogenous formaldehyde has been established to be carcinogenic, likely by virtue of forming nucleic acid and proteins adducts such as N6-formyllysine. To better assess N6-formyllysine as a biomarker of formaldehyde exposure, we studied accumulation of N6-formyllysine adducts in tissues of rats exposed by inhalation to 2 ppm [13C2H2]-formaldehyde for 7, 14, 21, and 28 days (6 h/day) and investigated adduct loss over a 7-day postexposure period using liquid chromatography-coupled tandem mass spectrometry. Our results showed formation of exogenous adducts in nasal epithelium and to some extent in trachea but not in distant tissues of lung, bone marrow, or white blood cells, with a 2-fold increase over endogenous N6-formyllysine over a 3-week exposure period. Postexposure analyses indicated a biexponential decay of N6-formyllysine in proteins extracted from different cellular compartments, with half-lives of ∼25 and ∼182 h for the fast and slow phases, respectively, in cytoplasmic proteins. These results parallel the behavior of DNA adducts and DNA-protein cross-links, with protein adducts cleared faster than DNA-protein cross-links, and point to the potential utility of N6-formyllysine protein adducts as biomarkers of formaldehyde

    Measurement of Oxygenated Polycyclic Aromatic Hydrocarbons Associated with a Size-Segregated Urban Aerosol

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    Size-segregated atmospheric particles were collected in Boston, MA, using a micro-orifice impactor. The samples were analyzed for oxygenated polycyclic aromatic hydrocarbons (OPAH) using gas chromatography/mass spectrometry. Seven PAH ketones (1-acenaphthenone, 9-fluorenone, 11H-benzo[a]fluoren-11-one, 7H-benzo[c]fluoren-7-one, 11H-benzo[b]fluoren-11-one, benzanthrone, and 6H-benzo[cd]pyrene-6-one), four PAH diones (1,4-naphthoquinone, phenanthrenequinone, 5,12-naphthacenequinone, and benzo[a]pyrene-6,12-dione), and one PAH dicarboxylic acid anhydride (naphthalic anhydride) were identified. Seven additional compounds with mass spectra typical of OPAH were tentatively identified. OPAH were generally distributed among aerosol size fractions based on molecular weight. Compounds with molecular weights between 168 and 208 were ap proximately evenly distributed between the fine (aerodynamic diameter, D_p, 2 μm) particles. OPAH with molecular weights of 248 and greater were associated primarily with the fine aerosol fraction. Most OPAH were distributed with particle size in a broad, unimodal hump similar to the the distributions observed for PAH in the same samples. These results suggest that OPAH are initially associated with fine particles after formation by either combustion or gas phase photooxidation and then partition to larger particles by vaporization and sorption. Two OPAH were distributed in bimodal distributions with peaks at D_p ≈ 2 μm and D_p ≈ 2 μm. These bimodal distributions may be indicative of sorption behavior different from PAH and other OPAH

    Measurement of Oxygenated Polycyclic Aromatic Hydrocarbons Associated with a Size-Segregated Urban Aerosol

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    Size-segregated atmospheric particles were collected in Boston, MA, using a micro-orifice impactor. The samples were analyzed for oxygenated polycyclic aromatic hydrocarbons (OPAH) using gas chromatography/mass spectrometry. Seven PAH ketones (1-acenaphthenone, 9-fluorenone, 11H-benzo[a]fluoren-11-one, 7H-benzo[c]fluoren-7-one, 11H-benzo[b]fluoren-11-one, benzanthrone, and 6H-benzo[cd]pyrene-6-one), four PAH diones (1,4-naphthoquinone, phenanthrenequinone, 5,12-naphthacenequinone, and benzo[a]pyrene-6,12-dione), and one PAH dicarboxylic acid anhydride (naphthalic anhydride) were identified. Seven additional compounds with mass spectra typical of OPAH were tentatively identified. OPAH were generally distributed among aerosol size fractions based on molecular weight. Compounds with molecular weights between 168 and 208 were ap proximately evenly distributed between the fine (aerodynamic diameter, D_p, 2 μm) particles. OPAH with molecular weights of 248 and greater were associated primarily with the fine aerosol fraction. Most OPAH were distributed with particle size in a broad, unimodal hump similar to the the distributions observed for PAH in the same samples. These results suggest that OPAH are initially associated with fine particles after formation by either combustion or gas phase photooxidation and then partition to larger particles by vaporization and sorption. Two OPAH were distributed in bimodal distributions with peaks at D_p ≈ 2 μm and D_p ≈ 2 μm. These bimodal distributions may be indicative of sorption behavior different from PAH and other OPAH

    Dosimetry of N 6 -Formyllysine Adducts Following [ 13 C 2 H 2 ]-Formaldehyde Exposures in Rats

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    With formaldehyde as the major source of endogenous N6-formyllysine protein adducts, we quantified endogenous and exogenous N6-formyllysine in the nasal epithelium of rats exposed by inhalation to 0.7, 2, 5.8, and 9.1 ppm [13C2H2]-formaldehyde using liquid chromatography-coupled tandem mass spectrometry. Exogenous N6-formyllysine was detected in the nasal epithelium, with concentration-dependent formation in total as well as fractionated (cytoplasmic, membrane, nuclear) proteins, but was not detected in the lung, liver, or bone marrow. Endogenous adducts dominated at all exposure conditions, with a 6 h 9.1 ppm formaldehyde exposure resulting in one-third of the total load of N6-formyllysine being derived from exogenous sources. The results parallel previous studies of formaldehyde-induced DNA adducts

    Measurement of C_(24)H_(14) Polycyclic Aromatic Hydrocarbons Associated with a Size-Segregated Urban Aerosol

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    Six-ring C_(24)H_(14) (MW 302) polycyclic aromatic hydrocarbons (PAH), some of which are potent mutagens, are present in urban aerosols. Size-segregated atmospheric aerosol samples from Boston, MA, were analyzed for C_(24)H_(14) PAH by gas chromatography/mass spectrometry. Eleven peaks were found with mass to charge ratios of 302; of these, eight were identified using authentic standards. Five of the peaks were quantified. For each of these five, the distributions with respect to particle size were bimodal with the majority of the mass associated with accumulation mode particles (0.3−1.0 μm) and a smaller fraction of the mass associated with ultrafine mode particles (0.09−0.14 μm). These distribu tions are similar to those observed for PAH of molecular weight 252−278 in the same sample but different from those of benzo[ghi]perylene (MW 276) and coronene (MW 300), which were associated to a greater degree with ultrafine particles. The data suggest that C_(24)H_(14) PAH repartition to larger particles by vaporization and sorption more rapidly than do benzo[ghi]perylene and coronene. The total concentration of C_(24)H_(14) PAH (1.5 ng/m^3) was comparable to that of benzo[a]pyrene in the same sample. Because of their mutagenicities, C_(24)H_(14) PAH may make a contribution to the genotoxicity of urban aerosols comparable to that of benzo[a]pyrene

    Measurement of C_(24)H_(14) Polycyclic Aromatic Hydrocarbons Associated with a Size-Segregated Urban Aerosol

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    Six-ring C_(24)H_(14) (MW 302) polycyclic aromatic hydrocarbons (PAH), some of which are potent mutagens, are present in urban aerosols. Size-segregated atmospheric aerosol samples from Boston, MA, were analyzed for C_(24)H_(14) PAH by gas chromatography/mass spectrometry. Eleven peaks were found with mass to charge ratios of 302; of these, eight were identified using authentic standards. Five of the peaks were quantified. For each of these five, the distributions with respect to particle size were bimodal with the majority of the mass associated with accumulation mode particles (0.3−1.0 μm) and a smaller fraction of the mass associated with ultrafine mode particles (0.09−0.14 μm). These distribu tions are similar to those observed for PAH of molecular weight 252−278 in the same sample but different from those of benzo[ghi]perylene (MW 276) and coronene (MW 300), which were associated to a greater degree with ultrafine particles. The data suggest that C_(24)H_(14) PAH repartition to larger particles by vaporization and sorption more rapidly than do benzo[ghi]perylene and coronene. The total concentration of C_(24)H_(14) PAH (1.5 ng/m^3) was comparable to that of benzo[a]pyrene in the same sample. Because of their mutagenicities, C_(24)H_(14) PAH may make a contribution to the genotoxicity of urban aerosols comparable to that of benzo[a]pyrene

    Quantitative Analysis of Histone Modifications: Formaldehyde Is a Source of Pathological N6-Formyllysine That Is Refractory to Histone Deacetylases

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    Aberrant protein modifications play an important role in the pathophysiology of many human diseases, in terms of both dysfunction of physiological modifications and the formation of pathological modifications by reaction of proteins with endogenous electrophiles. Recent studies have identified a chemical homolog of lysine acetylation, N[superscript 6]-formyllysine, as an abundant modification of histone and chromatin proteins, one possible source of which is the reaction of lysine with 3′-formylphosphate residues from DNA oxidation. Using a new liquid chromatography-coupled to tandem mass spectrometry method to quantify all N[superscript 6]-methyl-, -acetyl- and -formyl-lysine modifications, we now report that endogenous formaldehyde is a major source of N[superscript 6]-formyllysine and that this adduct is widespread among cellular proteins in all compartments. N[superscript 6]-formyllysine was evenly distributed among different classes of histone proteins from human TK6 cells at 1–4 modifications per 10[superscript 4] lysines, which contrasted strongly with lysine acetylation and mono-, di-, and tri-methylation levels of 1.5-380, 5-870, 0-1400, and 0-390 per 10[superscript 4] lysines, respectively. While isotope labeling studies revealed that lysine demethylation is not a source of N[superscript 6]-formyllysine in histones, formaldehyde exposure was observed to cause a dose-dependent increase in N[superscript 6]-formyllysine, with use of [[superscript 13]C,[superscript 2]H[subscript 2]]-formaldehyde revealing unchanged levels of adducts derived from endogenous sources. Inhibitors of class I and class II histone deacetylases did not affect the levels of N[superscript 6]-formyllysine in TK6 cells, and the class III histone deacetylase, SIRT1, had minimal activity (<10%) with a peptide substrate containing the formyl adduct. These data suggest that N[superscript 6]-formyllysine is refractory to removal by histone deacetylases, which supports the idea that this abundant protein modification could interfere with normal regulation of gene expression if it arises at conserved sites of physiological protein secondary modification
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