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, m5C, and m2 2G, 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, m5C, and m2 2G, 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.

Phosphorothioate (PT) modification of DNA, with sulfur replacing a nonbridging phosphate oxygen, was recently discovered as a product of the dnd genes found in bacteria and archaea. Given our limited understanding of the biological function of PT modifications, including sequence context, genomic frequencies, and relationships to the diversity of dnd gene clusters, we undertook a quantitative study of PT modifications in prokaryotic genomes using a liquid chromatography-coupled tandem quadrupole mass spectrometry approach. The results revealed a diversity of unique PT sequence contexts and three discrete genomic frequencies in a wide range of bacteria. Metagenomic analyses of PT modifications revealed unique ecological distributions, and a phylogenetic comparison of dnd genes and PT sequence contexts strongly supports the horizontal transfer of dnd genes. These results are consistent with the involvement of PT modifications in a type of restriction-modification system with wide distribution in prokaryotes.DNA modification | bioanalytical chemistry | sulfur P hosphorothioate (PT) modification of DNA, in which sulfur replaces a nonbridging phosphate oxygen, was originally developed as an artificial means to stabilize oligodeoxynucleotides against nuclease degradation (1). However, we recently discovered that the dnd gene products incorporate sulfur into the DNA backbone as a PT in a sequence-and stereo-specific manner (2). Beginning with the original observation in Streptomyces lividans 1326 that the five-gene dnd cluster (dndA-E) caused DNA degradation during electrophoresis (3), the presence of dnd genes has been established in dozens of different bacteria and archaea (4). An emerging picture of Dnd protein function reveals that DndA acts as a cysteine desulfurase and assembles DndC as a 4Fe-4S cluster protein (5). DndC possesses ATP pyrophosphatase activity and is predicted to have PAPS reductase activity, whereas DndB has homology to a group of transcriptional regulators (4, 6). A DndD homologue in Pseudomonas fluorescens Pf0-1, SpfD, has ATPase activity possibly related to DNA structure alteration or nicking during PT incorporation (7).This progress in defining the biochemistry of PT modifications belies a lack of understanding of the biological function of PT modifications, such as the variety of sequence contexts, the distribution of modifications across prokaryotic genomes, and the relationship of PT sequence contexts to the diversity of known dnd gene clusters (4). We have approached this problem with a highly quantitative study of PT modifications in prokaryotic genomes using a liquid chromatography-coupled tandem quadrupole mass spectrometry (LC-MS/MS) approach. The results reveal a diversity of quantized PT sequence contexts consistent with a role for PT modifications as part of a restrictionmodification system. Results and DiscussionDevelopment of a Sensitive Method to Quantify PT Modifications in Bacterial Genomes. We approached the problem of defining the biological function of PT modifications by q...

Bacterial phosphorothioate (PT) DNA modifications are incorporated by Dnd proteins A-E and often function with DndF-H as a restriction-modification (R-M) system, as in Escherichia coli B7A. However, bacteria such as Vibrio cyclitrophicus FF75 lack dndF-H, which points to other PT functions. To better understand PT biology, we report two novel, orthogonal technologies to map PTs across the genomes of B7A and FF75 with >90% agreement: real-time (SMRT) sequencing and deep sequencing of iodine-induced cleavage at PT (ICDS). In B7A, we detect PT on both strands of GpsAAC/GpsTTC motifs, but with only 18% of 40,701 possible sites modified. In contrast, PT in FF75 occurs as a single-strand modification at CpsCA, again with only 14% of 160,541 sites modified. Single-molecule analysis indicates that modification could be partial at any particular genomic site even with active restriction by DndF-H, with direct interaction of modification proteins with GAAC/GTTC sites demonstrated with oligonucleotides. These results point to highly unusual target selection by PT modification proteins and rule out known R-M mechanisms.

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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 a significant lesion. Although dL residues are efficiently incised by the main human abasic endonuclease enzyme Ape1, we show here that subsequent excision by human DNA polymerase ␤ is impaired at dL compared with unmodified abasic sites. This inhibition is accompanied by accumulation of a protein-DNA cross-link not observed in reactions of polymerase ␤ with unmodified abasic sites, although a similar form can be trapped by reduction with sodium borohydride. The formation of the stably cross-linked species with dL depends on the polymerase lysine 72 residue, which forms a Schiff base with the C-1 aldehyde during excision of an unmodified abasic site. In the case of a dL residue, attack on the lactone C-1 by lysine 72 proceeds more slowly and evidently produces an amide linkage, which resists further processing. Consequently dL residues may not be readily repaired by "shortpatch" base excision repair but instead function as suicide substrates in the formation of protein-DNA crosslinks that may require alternative modes of repair.Mutagenesis and disruption of the cell cycle caused by DNA damage is counteracted by DNA repair systems. In the base excision repair pathway (1-3), DNA glycosylases eliminate damaged bases to generate abasic (AP) 1 sites, which are also formed in large numbers by spontaneous depurination (2). In either case, AP sites are incised by an AP endonuclease to allow subsequent DNA repair synthesis and excision of the abasic residue. In mammalian cells, incision is carried out by the major AP endonuclease Ape1 protein (also called Apex, Hap1, or Ref1), while the excision step for regular abasic residues is thought to be mainly carried out by DNA polymerase ␤ (Pol␤) using a ␤-elimination mechanism. A distinct branch of the base excision pathway involves strand displacement repair synthesis and excision of the displaced, damaged strand by the FEN1 nuclease (4 -6). Still another variation is potentiated by the initial DNA glycosylase (7) because some of these enzymes carry out a second reaction to cleave at the abasic site by ␤- elimination (1, 3). The resulting 3Ј-blocked products must then be removed by an enzyme such as Ape1 before repair synthesis can proceed (1).Base excision repair acts on a wide variety of deaminated, alkylated, or oxidized bases (2, 3). However, oxidative damage to DNA also produces various modified abasic residues that may complicate the repair scenario (1). For example, free radical attack forms strand breaks with fragmentary or oxidized products of deoxyribose; when these are present at the 3Ј terminus, removal by Ape1 may be the rate-limiting repair step (8, 9). Oxidized abasic residues without direct strand breakage (10) include 2-deoxypentos-4-ulose residues (a major lesion produced by the antitumor drug bleomycin) and 2-deoxyribonolactone (dL) residues (formed by diverse oxidative agents). 2-D...

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 stress response system involving stress-specific reprogramming of tRNA wobble modifications that leads to selective translation of codon-biased mRNAs representing different classes of critical response proteins. In budding yeast exposed to four oxidants and five alkylating agents, tRNA modification patterns accurately distinguished among chemically similar stressors, with 14 modified ribonucleosides forming the basis for a data-driven model that predicts toxicant chemistry with >80% sensitivity and specificity. tRNA modification subpatterns also distinguish SN1 from SN2 alkylating agents, with SN2-induced increases in m3C in tRNA mechanistically linked to selective translation of threonine-rich membrane proteins from genes enriched with ACC and ACT degenerate codons for threonine. These results establish tRNA modifications as predictive biomarkers of exposure and illustrate a novel regulatory mechanism for translational control of cell stress response.

Genomic modification with sulfur as phosphorothioate (PT) is widespread among prokaryotes, including human pathogens. Apart from its physiological functions, the redox and nucleophilic properties of PT sulfur suggest effects on bacterial fitness in stressful environments. Here we show that PTs are dynamic and labile DNA modifications that cause genomic instability during oxidative stress. Using coupled isotopic labeling-mass spectrometry, we observed sulfur replacement in PTs at a rate of ~2%/h in unstressed Escherichia coli and Salmonella enterica. While PT levels were unaffected by exposure to hydrogen peroxide (H2O2) or hypochlorous acid (HOCl), PT turnover increased to 3.8–10%/h for HOCl and was unchanged for H2O2, consistent with repair of HOCl-induced sulfur damage. PT-dependent HOCl sensitivity extended to cytotoxicity and DNA strand-breaks, which occurred at orders-of-magnitude lower doses of HOCl than H2O2. The genotoxicity of HOCl in PT-containing bacteria suggests reduced fitness in competition with HOCl-producing organisms and during human infections.

Repair of abasic lesions, one of the most common types of damage found in DNA, is crucial to an organism's well-being. Studies in vitro indicate that after apurinic-apyrimidinic endonuclease cleaves immediately upstream of a baseless site, removal of the 5-terminal sugar-phosphate residue is achieved by deoxyribophosphodiesterase activity, an enzyme-mediated ␤-elimination reaction, or by endonucleolytic cleavage downstream of the baseless sugar. Synthesis and ligation complete repair.Eukaryotic RAD2 homolog 1 (RTH1) nuclease, by genetic and biochemical evidence, is involved in repair of modified DNA. Efficient endonucleolytic cleavage by RTH1 nuclease has been demonstrated for annealed primers that have unannealed 5-tails. In vivo, such substrate structures could result from repair-related strand displacement synthesis. Using 5-tailed substrates, we examined the ability of human RTH1 nuclease to efficiently remove 5-terminal abasic residues. A series of upstream primers were used to increasingly displace an otherwise annealed downstream primer containing a 5-terminal deoxyribose-5-phosphate. Until displacement of the first annealed nucleotide, substrates resisted cleavage. With further displacement, efficient cleavage occurred at the 3-end of the tail. Therefore, in combination with strand displacement activity, RTH1 nucleases may serve as an important alternative to other pathways in repair of abasic sites in DNA.Abasic lesions occur in DNA for several reasons, including spontaneous depurination (1), release of the base from a damaged sugar residue, or enzymatic removal of an inappropriate (e.g. uracil) or damaged (e.g. alkylated, deaminated, or oxidized) base by specialized glycosylases (2). Timely repair of abasic lesions is necessary, since during replication the lesion could lead to potentially lethal or mutagenic substitutions (3).Repair of an abasic site is predominantly initiated by an apurinic-apyrimidinic (AP) 1 endonuclease that cleaves immediately upstream of the baseless sugar, creating a 3Ј-hydroxyl terminus and a 5Ј-deoxyribose-5-phosphate terminus (4, 5). The next step, removal of the baseless sugar from the downstream strand, likely occurs by one of three distinct mechanisms.One mechanism involves removal of 5Ј-terminal sugar-phosphate residues by a Mg 2ϩ -dependent hydrolytic reaction, which releases 2-deoxyribose-5-phosphate. The activity responsible for this reaction, deoxyribophosphodiesterase (dRpase), was discovered in Escherichia coli (6). It was later shown to result from cleavage by either exonuclease I (7, 8) or the RecJ protein (9). The product of the RecJ gene was previously identified as a single strand-specific 5Ј-to 3Ј-exonuclease (10). Nonetheless, enzymes with dRpase activity have no associated double strand-specific 5Ј-to 3Ј-exonuclease function, so only a 1-nucleotide gap is produced after removal of the baseless sugar. A DNA polymerase fills in the single gap, and then a DNA ligase fuses the nick. There is support for this pathway, known as base excision repair. It has been s...