A Non-canonical Transferred DNA Insertion at the BRI 1 Locus in Arabidopsis thaliana

Agrobacterium-mediated transformation is widely used in transgenic plant englnserlng and has been proven to be a powerful tool for insertional mutagenesis of the plant genome.The transferred DNA (T-DNA) from Agrobacterlum is Integrated into the plant genome through illegitimate recombination between the T-DNA and the plant DNA.Contrasting to the canonical insertion,here we report on a locus showing a complex mutation associated with T-DNA insertion at the BRI 1 gene in Arabidopsis thaliana.We obtained a mutant line,named salade for its phenotype of dwarf stature and proliferating rosette,Molecular charactedzation of this mutant revealed that in addition to T-DNA a non.T.DNA-Iocalized transposon from bacteda was inserted in the Arabidopsis genome and that a region of more than 11.5 kb of the Arebidopsis genome was deleted at the insertion site.The deleted region contains the brassinosteroid receptor gene BRI 1 and the transcdption factor gene WRKY13.Our finding reveals non-canonical T-DNA insertion,implicating horizontal gene transfer and cautioning the use of T-DNA as mutagen in transgenic research.     

A Model for DNA Sequence Evolution within Transposable Element Families

A quantitative model is proposed for the expected degree of relationship between copies of a family of transposable elements in a finite population of hosts. Special cases of the model (in which the process of homogenization of element copies either is or is not limited by transposition rate) are presented and illustrated, using data on mobile sequences from different species. It is shown that transposition will be expected, in large populations, to result in only a rather distant relationship between transposable elements at different genomic sites. Possible inadequacies of the model are suggested and quantified.     

Somatic Excision of the Ac Transposable Element in Transgenic Arabidopsis thaliana after 5-Azacytidine Treatment

We have introduced the maize Ac transposable element in Arabidopsisthaliana and found that after three selfing generations, theelement is immobile and extensively methylated. Moreover, thenopaline synthase (nos) gene present on the same transferredT-DNA, was active early after transformation and regeneration,but inactive in most of the S1 progeny. We used 5-azacytidine(5AzaC) to determine whether a reduction in the methylationwould affect both Ac transposition and expression of the nosgene. After treatment with 5AzaC doses from 0.3 mM to 1.0 mM,approximately 25% of the plants produced detectable amountsof nopaline, indicating that the nos gene was reactivated. Usingthe polymerase chain reaction (PCR) to detect the empty donorsite left by Ac transposition, we demonstrated that 5AzaC alsoactivates Ac excision in the transgenic plants. Approximately13% of the 5AzaC treated plants (doses from 0.1 mM to 1.0 mM)were shown to have empty donor sites due to Ac excision. Noneof the plants cultivated in the absence of 5AzaC showed evidencefor Ac transposition or reactivation of the nos gene. Furtheranalysis using Southern blot indicate that some de-methylationocurred in the genome of individual plants. These results mayrepresent demethylation in few cells during development whichmay be sufficient to reactivate in these cells the expressionof the nos and Ac transposase transgenes, the latter promotingAc transposition in somatic cells. (Received July 16, 1996; Accepted January 8, 1997)     

The Contribution of Transposable Elements to Expressed Coding Sequence in Arabidopsis thaliana

The goal of this study was to assess the extent to which transposable elements (TEs) have contributed to protein-coding regions in Arabidopsis thaliana. To do this, we first characterized the extent of chimeric TE-gene constructs. We compared a genome-wide TE database to genomic sequences, annotated coding regions, and EST data. The comparison revealed that 7.8% of expressed genes contained a region with close similarity to a known TE sequence. Some groups of TEs, such as helitrons, were underrepresented in exons relative to their genome-wide distribution; in contrast, Copia-like and En/Spm-like sequences were overrepresented in exons. These 7.8% percent of genes were enriched for some GO-based functions, particularly kinase activity, and lacking in other functions, notably structural molecule activity. We also examined gene family evolution for these genes. Gene family information helped clarify whether the sequence similarity between TE and gene was due to a TE contributing to the gene or, instead, the TE co-opting a portion of the gene. Most (66%) of these genes were not easily assigned to a gene family, and for these we could not infer the direction of the relationship between TE and gene. For the remainder, where appropriate, we built phylogenetic trees to infer the direction of the TE-gene relationship by parsimony. By this method, we verified examples where TEs contributed to expressed proteins. Our results are undoubtedly conservative but suggest that TEs may have contributed small protein segments to as many as 1.2% of all expressed, annotated A. thaliana genes. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

重金属诱导拟南芥原生质体DNA 损伤的单细胞凝胶电泳检测

以拟南芥原生质体为实验体系, 研究不同浓度的3种重金属离子对拟南芥原生质体的毒性和DNA损伤的差异。结果表明, 用1-5 mmol.L-1的Zn2+、Cd2+ 和Cu2+分别处理的拟南芥原生质体, 2 小时内活力逐渐下降, 并表现出明显的浓度依赖性;与相同浓度的Cd2+ 和Cu2+ 相比, Zn2+对拟南芥原生质体活力的影响程度较小, 表现出较低的毒性。单细胞凝胶电泳检测发现,用0.1-0.8 mmol .L-1的Zn2+、Cd2+ 和Cu2+ 分别处理拟南芥原生质体30 分钟, 以OTM值表示的原生质体DNA损伤量随重金属离子浓度的增加而递增; 相同浓度(0.5 mmol.L-1)的3种重金属离子相比, Zn2+对原生质体的遗传毒性明显低于Cu2+ 和Cd2+。综合原生质体活力和DNA损伤的单细胞凝胶电泳检测结果, 发现Zn2+对拟南芥原生质体的遗传毒性较低, 而Cd2+ 和Cu2+的遗传毒性较高。本研究建立的拟南芥原生质体实验体系, 结合运用单细胞凝胶电泳技术, 能够快速、灵敏地检测重金属对植物细胞的遗传毒性。     

重金属诱导拟南芥原生质体DNA损伤的单细胞凝胶电泳检测

以拟南芥原生质体为实验体系,研究不同浓度的3种重金属离子对拟南芥原生质体的毒性和DNA损伤的差异。结果表明,用1-5mmol·L^-1的Zn^2＋、Cd^2＋和Cu^2＋分别处理的拟南芥原生质体,2小时内活力逐渐下降,并表现出明显的浓度依赖性：与相同浓度的Cd^2＋和Cu^2＋相比,Zn^2＋对拟南芥原生质体活力的影响程度较小,表现出较低的毒性。单细胞凝胶电泳检测发现,用0．1-0．8mmol·L^-1的Zn^2＋、Cd^2＋和Cu^2＋分别处理拟南芥原生质体30分钟,以OTM值表示的原生质体DNA损伤量随重金属离子浓度的增加而递增：相同浓度（0．5mmol·L^-1）的3种重金属离子相比,Zn^2＋对原生质体的遗传毒性明显低于Cu^2＋和Cd^2＋。综合原生质体活力和DNA损伤的单细胞凝胶电泳检测结果,发现ZnO^2＋对拟南芥原生质体的遗传毒性较低,而CdO^2＋和Cu^2＋的遗传毒性较高。本研究建立的拟南芥原生质体实验体系,结合运用单细胞凝胶电泳技术,能够快速、灵敏地检测重金属对植物细胞的遗传毒性。     

Evidence for Base Excision Repair of Oxidative DNA Damage in Chloroplasts of Arabidopsis thaliana

Chloroplasts are the sites of photosynthesis in plants, and they contain their own multicopy, requisite genome. Chloroplasts are also major sites for production of reactive oxygen species, which can damage essential components of the chloroplast, including the chloroplast genome. Compared with mitochondria in animals, relatively little is known about the potential to repair oxidative DNA damage in chloroplasts. Here we provide evidence of DNA glycosylase-lyase/endonuclease activity involved in base excision repair of oxidized pyrimidines in chloroplast protein extracts of Arabidopsis thaliana. Three base excision repair components (two endonuclease III homologs and an apurinic/apyrimidinic endonuclease) that might account for this activity were identified by bioinformatics. Transient expression of protein-green fluorescent protein fusions showed that all three are targeted to the chloroplast and co-localized with chloroplast DNA in nucleoids. The glycosylase-lyase/endonuclease activity of one of the endonuclease III homologs, AtNTH2, which had not previously been characterized, was confirmed in vitro. T-DNA insertions in each of these genes were identified, and the physiological and biochemical phenotypes of the single, double, and triple mutants were analyzed. This mutant analysis revealed the presence of a third glycosylase activity and potentially another pathway for repair of oxidative DNA damage in chloroplasts.Reactive oxygen species (ROS)² are inevitable by-products of metabolism in all aerobic organisms (1). Plants and algae are especially prone to photo-oxidative stress because of ROS generated during oxygenic photosynthesis. Several types of ROS are generated at various sites in the photosynthetic electron transport chain in chloroplasts, and their production is enhanced by such factors as excess or varying light intensities and extremes of temperature, drought, nutrient deficiencies, and herbicides (2). These ROS can damage many chloroplast constituents, including lipids, proteins, pigments, and the multicopy genome.Plants have evolved numerous mechanisms to deal with photo-oxidative stress, including dissipation of excess light energy, synthesis of antioxidant molecules and scavenging enzymes, and targeted repair (2). DNA repair of oxidized bases, such as thymine glycol (TG) or 8-oxoguanine, can be hypothesized as an important element of chloroplast photoprotection. Although there is considerable overlap in both the types of DNA lesions caused by different insults and the targeting of different DNA repair mechanisms, base excision repair (BER) is considered to be the main repair pathway for oxidative DNA damage, at least in the nucleus and mitochondrion (3, 4).BER repairs single damaged bases (because of oxidation, deamination, alkylation, etc.) in DNA by removing them, breaking the phosphodiester backbone, excising the sugar residue at the abasic site, and filling the gap (reviewed in Refs. 5, 6). BER begins with a DNA glycosylase or glycosylase-lyase. There are many types of glycosylases in any given organism and across taxa, and they are distinguishable by their substrate specificity, whether they are monofunctional (glycosylase activity only) or bifunctional (glycosylase plus apurinic/apyrimidinic (AP) lyase activities; see below), by the phylogenetic family in which they reside, and/or by conserved structural characteristics (reviewed in Refs. 6–8). The glycosylases involved in BER of oxidative DNA damage can be roughly divided into those that target either oxidized purines or oxidized pyrimidines (4, 9). For example, TG is a common type of oxidized pyrimidine, which is removed primarily by endonuclease III (Nth), endonuclease VIII (Nei), or their homologs (10). TG is only poorly mutagenic, but it strongly blocks polymerases, inducing cell cycle arrest and potentially cell death if it is not removed.After an appropriate glycosylase cleaves the N-glycosyl bond attaching a damaged base to deoxyribose, leaving an abasic site, the sugar-phosphate backbone is nicked. Bifunctional glycosylases also have an AP lyase activity that cleaves on the 3′ side of the AP site. However, the site still requires the function of a separate AP endonuclease that cuts on the 5′ side of the AP site to remove the 3′-deoxyribose residue at the nick site (11) before repair can continue. In the case of a monofunctional glycosylase, an AP endonuclease nicks the strand on the 5′ side of the AP site. Escherichia coli has two unrelated AP endonucleases, exonuclease III (Xth) and endonuclease IV (Nfo). In humans Ape1/Ref-1 is an Xth homolog, and in yeast Apn1p is an Nfo homolog (5, 12). Following generation of the AP site and nicking of the backbone, the gap is filled by a polymerase in either a short or long patch and then sealed by a ligase.BER of oxidative DNA lesions such TG has been studied intensively in E. coli, yeast, and mammals, whereas comparatively little is known about BER in plants. For example, only two genes involved in BER of oxidized pyrimidines have been characterized previously in the model plant Arabidopsis thaliana (13, 14), and their localization within the plant cell is unknown. An Nth homolog in Arabidopsis, AtNTH1 (At2g31450), has the expected bifunctional glycosylase-lyase activity in vitro (14). The ARP gene (At2g41460) in Arabidopsis encodes an enzyme with AP endonuclease activity (13).Here we present the results of experiments conducted to address whether there is BER of oxidized pyrimidines in the Arabidopsis chloroplast. Chloroplast protein extracts were assayed for glycosylase-lyase/endonuclease activity. The chloroplast localization of ARP, AtNTH1, and AtNTH2, a second Arabidopsis homolog of Nth, was tested experimentally, and the predicted activity of AtNTH2 was confirmed in vitro. In addition, an analysis of T-DNA insertion mutants affecting each of these three BER genes was performed.     

拟南芥神经酰胺酶基因对氧化胁迫的响应

以拟南芥哥伦比亚生态型（Col）和神经酰胺酶突变体为实验材料,通过对突变体的一系列生理生化指标的测定,来研究拟南芥神经酰胺酶基因（AtCER）对H2O2的响应。利用PCR和Northern blot获得了9个AtCER纯合单突变体。不同浓度H2O2处理野生型和突变体后,发现突变体对H2O2的反应比野生型更加敏感。H2O2处理后突变体叶片出现比野生型更严重的黄化现象和坏死斑点,总叶绿素含量也比野生型下降的更快,电导率测定也发现突变体比野生型的电导率增加得更多。抗氧化酶活性的分析结果发现H2O2处理后,突变体的抗氧化酶活性比野生型提高了1．5～3倍。上述研究结果说明AtCER参与了H2O2诱导的氧化胁迫反应。     

The MAPK Pathway Signals Telomerase Modulation in Response to Isothiocyanate-Induced DNA Damage of Human Liver Cancer Cells

4-methylthiobutyl isothiocyanate (MTBITC), an aliphatic, sulphuric compound from Brassica vegetables, possesses in vitro and in vivo antitumor activity. Recently we demonstrated the potent growth inhibitory potential of the DNA damaging agent MTBITC in human liver cancer cells. Here we now show that MTBITC down regulates telomerase which sensitizes cells to apoptosis induction. This is mediated by MAPK activation but independent from production of reactive oxygen species (ROS). Within one hour, MTBITC induced DNA damage in cancer cells correlating to a transient increase in hTERT mRNA expression which then turned into telomerase suppression, evident at mRNA as well as enzyme activity level. To clarify the role of MAPK for telomerase regulation, liver cancer cells were pre-treated with MAPK-specific inhibitors prior to MTBITC exposure. This clearly showed that transient elevation of hTERT mRNA expression was predominantly mediated by the MAPK family member JNK. In contrast, activated ERK1/2 and P38, but not JNK, signalled to telomerase abrogation and consequent apoptosis induction. DNA damage by MTBITC was also strongly abolished by MAPK inhibition. Oxidative stress, as analysed by DCF fluorescence assay, electron spin resonance spectroscopy and formation of 4-hydroxynonenal was found as not relevant for this process. Furthermore, N-acetylcysteine pre-treatment did not impact MTBITC-induced telomerase suppression or depolarization of the mitochondrial membrane potential as marker for apoptosis. Our data therefore imply that upon DNA damage by MTBITC, MAPK are essential for telomerase regulation and consequent growth impairment in liver tumor cells and this detail probably plays an important role in understanding the potential chemotherapeutic efficacy of ITC.     

A DNA Damage Response System Associated with the phosphoCTD of Elongating RNA Polymerase II

RNA polymerase II translocates across much of the genome and since it can be blocked by many kinds of DNA lesions, detects DNA damage proficiently; it thereby contributes to DNA repair and to normal levels of DNA damage resistance. However, the components and mechanisms that respond to polymerase blockage are largely unknown, except in the case of UV-induced damage that is corrected by nucleotide excision repair. Because elongating RNAPII carries with it numerous proteins that bind to its hyperphosphorylated CTD, we tested for effects of interfering with this binding. We find that expressing a decoy CTD-carrying protein in the nucleus, but not in the cytoplasm, leads to reduced DNA damage resistance. Likewise, inducing aberrant phosphorylation of the CTD, by deleting CTK1, reduces damage resistance and also alters rates of homologous recombination-mediated repair. In line with these results, extant data sets reveal a remarkable, highly significant overlap between phosphoCTD-associating protein genes and DNA damage-resistance genes. For one well-known phosphoCTD-associating protein, the histone methyltransferase Set2, we demonstrate a role in DNA damage resistance, and we show that this role requires the phosphoCTD binding ability of Set2; surprisingly, Set2’s role in damage resistance does not depend on its catalytic activity. To explain all of these observations, we posit the existence of a CTD-Associated DNA damage Response (CAR) system, organized around the phosphoCTD of elongating RNAPII and comprising a subset of phosphoCTD-associating proteins.     

拟南芥prr5突变体对ABA的响应

以拟南芥为材料,统计PRRs （pseudo-response regulators）突变体 prr5及其野生型经ABA处理后的萌发率、根长和NaCl处理后的萌发率,并采用实时定量PCR方法,对不同浓度ABA处理的拟南芥幼苗中的PRR5基因表达进行分析.结果表明：prr5突变体对ABA弱敏感,其种子萌发率比野生型显著或极显著增高,主根比野生型长,且PRR5基因表达受ABA抑制.同时,NaCl处理后,prr5的萌发率比野生型极显著增高.因此,推测prr5可能为ABA信号通路相关基因.     

Profiling of RNA ribose methylation in Arabidopsis thaliana

Eukaryotic rRNAs and snRNAs are decorated with abundant 2′-O-methylated nucleotides (Nm) that are predominantly synthesized by box C/D snoRNA-guided enzymes. In the model plant Arabidopsis thaliana, C/D snoRNAs have been well categorized, but there is a lack of systematic mapping of Nm. Here, we applied RiboMeth-seq to profile Nm in cytoplasmic, chloroplast and mitochondrial rRNAs and snRNAs. We identified 111 Nm in cytoplasmic rRNAs and 19 Nm in snRNAs and assigned guide for majority of the detected sites using an updated snoRNA list. At least four sites are directed by guides with multiple specificities as shown in yeast. We found that C/D snoRNAs frequently form extra pairs with nearby sequences of methylation sites, potentially facilitating the substrate binding. Chloroplast and mitochondrial rRNAs contain five almost identical methylation sites, including two novel sites mediating ribosomal subunit joining. Deletion of FIB1 or FIB2 gene reduced the accumulation of C/D snoRNA and rRNA methylation with FIB1 playing a bigger role in methylation. Our data reveal the comprehensive 2′-O-methylation maps for Arabidopsis rRNAs and snRNAs and would facilitate study of their function and biosynthesis.