Agricultural weeds are the most important biotic constraints to global crop production, and chief among these is weedy rice. Despite increasing yield losses from weedy rice in recent years worldwide, the genetic basis of weediness evolution remains unclear. Using whole-genome sequence analyses, we examined the origins and adaptation of Japanese weedy rice. We find evidence for a weed origin from tropical japonica crop ancestry, which has not previously been documented in surveys of weedy rice worldwide. We further show that adaptation occurs largely through different genetic mechanisms between independently-evolved temperate japonica- and tropical japonica-derived strains; most genomic signatures of positive selection are unique within weed types. In addition, some weedy rice strains have evolved through hybridization between weedy and cultivated rice with adaptive introgression from the crop. Surprisingly, introgression from cultivated rice confers not only crop-like adaptive traits (such as shorter plant height, facilitating crop mimicry) but also weedy-like traits (such as seed dormancy). These findings reveal how hybridization with cultivated rice can promote persistence and proliferation of weedy rice.

Two types of aspartyl-tRNA synthetase exist: the discriminating enzyme (D-AspRS) forms only Asp-tRNA Asp , while the nondiscriminating one (ND-AspRS) also synthesizes Asp-tRNA Asn , a required intermediate in protein synthesis in many organisms (but not in Escherichia coli). On the basis of the E. coli trpA34 missense mutant transformed with heterologous ND-aspS genes, we developed a system with which to measure the in vivo formation of Asp-tRNA Asn and its acceptance by elongation factor EF-Tu. While large amounts of Asp-tRNA Asn are detrimental to E. coli, smaller amounts support protein synthesis and allow the formation of up to 38% of the wild-type level of missense-suppressed tryptophan synthetase.Aspartyl-tRNA synthetase (AspRS) exists in two different forms with respect to tRNA recognition (7). The discriminating enzyme (D-AspRS) recognizes only tRNA Asp , while the nondiscriminating one (ND-AspRS) also recognizes tRNA Asn and therefore forms both Asp-tRNA Asn and Asp-tRNA Asp . Most bacteria and archaea lack asparaginyl-tRNA synthetase and are unable to synthesize Asn-tRNA Asn by direct acylation of tRNA. These organisms rely on the ND-AspRS to produce the misacylated Asp-tRNA Asn , which is then converted by a tRNA-dependent amidotransferase to the correctly acylated Asn-tRNA Asn (1,4,5,19). Thus, the ND-AspRS is essential in organisms that form Asn-tRNA by transamidation.The primary sequence distinguishes two general groups of AspRS. There is a predominantly bacterial type of AspRS that is about 580 amino acids, in addition to a shorter archaealeukaryotic type of about 430 amino acids. In vitro data have made clear that discriminating and nondiscriminating enzymes exist in both groups (16,20). The determinants in the protein sequence responsible for tRNA discrimination are not known.The two AspRS types are usually separated in nature. Genome analyses of bacteria and archaea have revealed that the presence of the ND-AspRS is always accompanied by the occurrence of the heterotrimeric GatCAB amidotransferase, an enzyme capable of converting the misacylated Asp-tRNA Asn to Asn-tRNA Asn (2,5,19). Presumably, this is to avoid introducing the misacylated Asp-tRNA Asn into an organism's translational apparatus and potentially endangering protein synthesis. This reasoning is supported by the fact that the heterologous expression of ND-AspRS or ND-GluRS in Escherichia coli, which lacks GatCAB, is highly toxic to the cell, especially when the synthetase genes are overexpressed (15). However, some organisms (e.g., Deinococcus radiodurans and Thermus thermophilus) contain a D-AspRS in addition to an ND-AspRS and a GatCAB amidotransferase (1,3,5,9).We wanted to observe how E. coli copes with in vivo mischarging effected by the ND-AspRS, as this organism is unable to eliminate the toxic Asp-tRNA Asn . Therefore, we developed an approach that would, in fact, require E. coli to be dependent on the presence of mischarged Asp-tRNA Asn for growth. To this aim, we used missense suppression of a specific mutation in the trp...

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ABSTRACT:Prasugrel, a novel thienopyridine antiplatelet agent, undergoes rapid hydrolysis in vivo to a thiolactone, R-95913, which is further converted to its thiol-containing, pharmacologically active metabolite, R-138727, by oxidation via cytochromes P450 (P450). We trapped a sulfenic acid metabolite as a mixed disulfide with 2-nitro-5-thiobenzoic acid in an incubation mixture containing the thiolactone R-95913, expressed CYP3A4, and NADPH. Further experiments investigated one possible mechanism for the conversion of the sulfenic acid to the active thiol metabolite in vitro. A mixed disulfide form of R-138727 with glutathione was found to be a possible precursor of R-138727 in vitro when glutathione was present. The rate constant for the reduction of the glutathione conjugate of R-138727 to R-138727 was increased by addition of human liver cytosol to the human liver microsomes. Thus, one possible mechanism for the ultimate formation of R-138727 in vitro can be through formation of a sulfenic acid mediated by P450s followed possibly by a glutathione conjugation to a mixed disulfide and reduction of the disulfide to the active metabolite R-138727. Prasugrel [Effient (Eli Lilly and Company, Indianapolis, IN) in the United States and Efient (Eli Lilly and Company) in the EuropeanUnion], clopidogrel [Plavix (Sanofi-Aventis, Paris, France)/Iscover (Bristol-Myers Squibb, New York, NY)], and ticlopidine (Ticlid; Sanofi-Aventis) are thienopyridine antiplatelet agents. Prasugrel has been shown to reduce the rate of thrombotic cardiovascular events and stent thrombosis in patients with acute coronary syndrome that are undergoing percutaneous coronary intervention (Wiviott et al., 2007) (Effient package insert). The thienopyridines are prodrugs that are converted in vivo to their pharmacologically active metabolites that possess a thiol group via a corresponding thiolactone metabolite (Farid et al., 2010). However, with the exception of an oxidation step catalyzed by cytochrome P450 (Savi et al., 1994;Rehmel et al., 2006), the mechanism for the active metabolite formation from thienopyridines remained unknown until recently reported for ticlopidine and clopidogrel (Dansette et al., 2009). In the case of prasugrel, the active metabolite R-138727 was not detected when the thiolactone metabolite R-95913 was incubated with liver homogenates or microsomes in the absence of cofactors, but it was detected when NADPH and a reducing agent such as glutathione were added to the system (Kazui et al., 2000). A sulfenic acid, which is a likely intermediate for the activation of prasugrel, reacts readily with a thiol compound, typically glutathione in vivo, to yield a disulfide metabolite (Decker et al., 1991;Kassahun et al., 2001;Reddy et al., 2005;Dansette et al., 2009). The formed disulfide can be further reduced to provide a thiolcontaining compound. The objective of this study is to investigate the involvement of a sulfenic acid and a glutathione conjugate of R-138727 in the in vitro production of prasugrel's active metabolite (R-1...

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Nanostructured ZnO particles present in skin-care cosmetics and UVB/UVA sunscreen products generate strong oxidizing species (free radicals) when illuminated with UV radiation that can damages human skin and the horny layer. Damage to DNA by ZnO and other pigmentary ingredients in sunscreen formulations under artificial and solar UV exposure has been examined by Agarose gel electrophoresis using pUC 18 DNA plasmids (2686 base-pairs). Initial photoinduced oxidative damage done to DNA plasmids have been probed by nicking assays under in vitro conditions for ZnO. The effects of nanosize ZnO and CeO 2 particles, and the newly developed CaO-doped and SiO 2-coated CeO 2 pigment are compared when subjected to artificial (75-W Hg-lamp) and solar UV radiation. Supercoiled DNA plasmids undergo one nick to produce the relaxed form, followed by a second nick yielding the linear form of the plasmids. The DNA constituents deoxyadenosine-5'-monophosphate (dAMP), guanosine-5'monophosphate (GMP) and cytidine-5'-monophosphate (CMP) have been examined to assess the photooxidative damage done to these nucleotides under photocatalytic conditions using the cosmetic/sunscreen ZnO pigment. Adsorption of the nucleotide through the phosphate on the positively charged ZnO surface, followed by attack of the ribose/phosphate backbone by photogenerated •OH (and/or •OOH) radicals on the ZnO surface lead to the degradation of the dAMP's ribose moiety and subsequently to decomposition of the adenine base residue. About 90% mineralization of the ribose/phosphate backbone occurred as evidenced by formation of H 2 PO 4 ions after only 30 min of UV irradiation. The nitrogen atoms of the adenine base were converted to NO 3 and NH 4 + ions. About 45% of the organic carbons constituting the dAMP ribose backbone was mineralized to CO 2 within 8 h of UV irradiation occurring through formation of carboxylic acid intermediates (succinic, acetic and formic), with 85% of the remaining nucleobase ultimately mineralized after 48 h of UV irradiation. Similar occurrences were seen for the GMP and CMP