Target‐Activated DNA Polymerase Activity for Sensitive RNase H Activity Assay

Herein, the ribonuclease H (RNase H) activity assay based on the target‐activated DNA polymerase activity is described. In this method, a detection probe composed of two functional sequences, a binding site for DNA polymerase and a catalytic substrate for RNase H, serves as a key component. The detection probe, at its initial state, suppresses the DNA polymerase activity, but it becomes destabilized by RNase H, which specifically hydrolyzes RNA in RNA/DNA hybrid duplexes. As a result, DNA polymerase recovers its activity and initiates multiple primer extension reactions in a separate TaqMan probe‐based signal transduction module, leading to a significantly enhanced fluorescence “turn‐on” signal. This assay can detect RNase H activity as low as 0.016 U mL^?1 under optimized conditions. Furthermore, its potential use for evaluating RNase H inhibitors, which have been considered potential therapeutic agents against acquired immune deficiency syndrome (AIDS), is successfully explored. In summary, this approach is quite promising for the sensitive and accurate determination of enzyme activity and inhibitor screening.     

Activity, stability, and structure of metagenome-derived LC11-RNase H1, a homolog of Sulfolobus tokodaii RNase H1

Metagenome‐derived LC11‐RNase H1 is a homolog of Sulfolobus tokodaii RNase H1 (Sto‐RNase H1). It lacks a C‐terminal tail, which is responsible for hyperstabilization of Sto‐RNase H1. Sto‐RNase H1 is characterized by its ability to cleave not only an RNA/DNA hybrid but also a double‐stranded RNA (dsRNA). To examine whether LC11‐RNase H1 also exhibits both RNase H and dsRNase activities, LC11‐RNase H1 was overproduced in Escherichia coli, purified, and characterized. LC11‐RNase H1 exhibited RNase H activity with similar metal ion preference, optimum pH, and cleavage mode of substrate with those of Sto‐RNase H1. However, LC11‐RNase H1 did not exhibit dsRNase activity at any condition examined. LC11‐RNase H1 was less stable than Sto‐RNases H1 and its derivative lacking the C‐terminal tail (Sto‐RNase H1ΔC6) by 37 and 13°C in T_m, respectively. To understand the structural bases for these differences, the crystal structure of LC11‐RNase H1 was determined at 1.4 Å resolution. The LC11‐RNase H1 structure is highly similar to the Sto‐RNase H1 structure. However, LC11‐RNase H1 has two grooves on protein surface, one containing the active site and the other containing DNA‐phosphate binding pocket, while Sto‐RNase H1 has one groove containing the active site. In addition, LC11‐RNase H1 contains more cavities and buried charged residues than Sto‐RNase H1. We propose that LC11‐RNase H1 does not exhibit dsRNase activity because dsRNA cannot fit to the two grooves on protein surface and that LC11‐RNase H1 is less stable than Sto‐RNase H1ΔC6 because of the increase in cavity volume and number of buried charged residues.     

RNase H eliminates R‐loops that disrupt DNA replication but is nonessential for efficient DSB repair

In Saccharomyces cerevisiae, genome stability depends on RNases H1 and H2, which remove ribonucleotides from DNA and eliminate RNA–DNA hybrids (R‐loops). In Schizosaccharomyces pombe, RNase H enzymes were reported to process RNA–DNA hybrids produced at a double‐strand break (DSB) generated by I‐PpoI meganuclease. However, it is unclear if RNase H is generally required for efficient DSB repair in fission yeast, or whether it has other genome protection roles. Here, we show that S. pombe rnh1? rnh201? cells, which lack the RNase H enzymes, accumulate R‐loops and activate DNA damage checkpoints. Their viability requires critical DSB repair proteins and Mus81, which resolves DNA junctions formed during repair of broken replication forks. “Dirty” DSBs generated by ionizing radiation, as well as a “clean” DSB at a broken replication fork, are efficiently repaired in the absence of RNase H. RNA–DNA hybrids are not detected at a reparable DSB formed by fork collapse. We conclude that unprocessed R‐loops collapse replication forks in rnh1? rnh201? cells, but RNase H is not generally required for efficient DSB repair.     

Directed RNase H Cleavage of Nascent Transcripts Causes Transcription Termination

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High-Resolution Mapping of Two Types of Spontaneous Mitotic Gene Conversion Events in Saccharomyces cerevisiae

Gene conversions and crossovers are related products of the repair of double-stranded DNA breaks by homologous recombination. Most previous studies of mitotic gene conversion events have been restricted to measuring conversion tracts that are <5 kb. Using a genetic assay in which the lengths of very long gene conversion tracts can be measured, we detected two types of conversions: those with a median size of ∼6 kb and those with a median size of >50 kb. The unusually long tracts are initiated at a naturally occurring recombination hotspot formed by two inverted Ty elements. We suggest that these long gene conversion events may be generated by a mechanism (break-induced replication or repair of a double-stranded DNA gap) different from the short conversion tracts that likely reflect heteroduplex formation followed by DNA mismatch repair. Both the short and long mitotic conversion tracts are considerably longer than those observed in meiosis. Since mitotic crossovers in a diploid can result in a heterozygous recessive deleterious mutation becoming homozygous, it has been suggested that the repair of DNA breaks by mitotic recombination involves gene conversion events that are unassociated with crossing over. In contrast to this prediction, we found that ∼40% of the conversion tracts are associated with crossovers. Spontaneous mitotic crossover events in yeast are frequent enough to be an important factor in genome evolution.     

Design,synthesis and biological evaluation of 3-hydroxyquinazoline-2,4(1H,3H)-diones as dual inhibitors of HIV-1 reverse transcriptase-associated RNase H and integrase

A novel series of 3-hydroxyquinazoline-2,4(1H,3H)-diones derivatives has been designed and synthesized. Their biochemical characterization revealed that most of the compounds were effective inhibitors of HIV-1 RNase H activity at sub to low micromolar concentrations. Among them, II-4 was the most potent in enzymatic assays, showing an IC₅₀ value of 0.41 ± 0.13 μM, almost five times lower than the IC₅₀ obtained with β-thujaplicinol. In addition, II-4 was also effective in inhibiting HIV-1 IN strand transfer activity (IC₅₀ = 0.85 ± 0.18 μM) but less potent than raltegravir (IC₅₀ = 71 ± 14 nM). Despite its relatively low cytotoxicity, the efficiency of II-4 in cell culture was limited by its poor membrane permeability. Nevertheless, structure-activity relationships and molecular modeling studies confirmed the importance of tested 3-hydroxyquinazoline-2,4(1H,3H)-diones as useful leads for further optimization.     

食管鳞癌MLH1基因改变及其与微卫星不稳定的关系

MLH1是位于3p21．3上的一个DNA错配修复基因,其异常与多种肿瘤相关。为探索食管鳞癌中MLH1基因改变及其与微卫星不稳定(MSI)的关联情况,采用微卫星分析和RT—PCR方法检测了14个微卫星标志在食管癌中的状况及MLH1转录水平的表达,发现35％的食管癌出现至少一个微卫星的不稳定,66．7％的肿瘤在MLH1基因内标志D3S1611位点表现为杂合性丢失,但是MLH1没有明显的mRNA表达下调。MSI与食管癌分期、分级、淋巴结转移、患者年龄和性别等参数及MLH1基因杂合性丢失(LOH)之间无统计学意义的相关性。这些结果表明：食管癌中MLH1存在较高频率的等位基因丢失,但其mRNA表达水平并无明显异常;所测微卫星标志的不稳定是食管癌的频发事件,与MLH1基因LOH不存在必然联系。     

The role of double-strand break-induced allelic homologous recombination in somatic plant cells

During meiosis, homologous recombination occurs between allelic sequences. To evaluate the biological significance of such a pathway in somatic cells, we used transgenic tobacco plants with a restriction site for the rare cutting endonuclease I-SceI within a negative selectable marker gene. These plants were crossed with two tobacco lines containing, in allelic position, either a deletion or an insertion within the marker gene that rendered both marker gene and restriction site inactive. After the double-strand break induction, we selected for repair events resulting in a loss of marker gene function. This loss was mostly due to deletions. We were also able to detect double strand break-induced allelic recombination in which the break was repaired by a faithful copying process from the homologue carrying the shortened transgene. The estimated frequency indicates that homologous recombination in somatic cells between allelic sites appears to occur at the same order of magnitude as between ectopic sites, and is thus far too infrequent to act as major repair pathway. As somatic changes can be transferred to the germ line, the prevalence of intrachromatid rearrangements over allelic recombination might be an indirect prerequisite for the enhanced genome plasticity postulated for plants.     

中国人胃癌KAI1基因表达及遗传不稳定性

采用Envision免疫组织化学,Leica-Qwin计算机图像分析,石蜡包埋组织抽提DNA,PCR-单链构象多态性(SSCP)和常规银染等方法,对56例石蜡包埋胃癌标本及其相应的正常组织,进行KAI1蛋白表达水平的研究和D1S1344、D11S1326位点微卫星不稳定(MSI)、杂合性缺失(LOH)的检测,为揭示KAI1基因作用机制和肿瘤转移机制提供实验依据。实验中,胃癌KAI1蛋白阳性检出率为55.4%(31/56):随着癌组织浸润程度的进展,其阳性率呈降低趋势(P<0.01);在无淋巴结转移的肿瘤组织KAI1蛋白表达率为83.9%,显著高于淋巴结转移肿瘤组织的20.0%;在肿瘤结节转移(tumor node metastasis,TNM)Ⅰ Ⅱ期,KAI1蛋白阳性率为82.8%,明显高于TNMⅢ Ⅳ期的25.9%(P<0.01)。56例胃癌D11S1326、D11S1344位点的SSCP分析中,均未出现MSI或LOH。实验结果提示,KAI1蛋白表达与胃癌组织浸润、淋巴结转移及恶性进展密切相关。在胃癌的发生发展中,KAI1基因未见遗传不稳定性改变。     

裂殖酵母Pap1应答H2O2氧化胁迫的机制

转录因子Pap1是裂殖酵母(Schizosaccharomyces pombe)应答H2O2氧化胁迫反应中的关键调控因子.高浓度的H2O2激活蛋白激酶Sty1途径清除过量的H2O2,使H2O2降至较低浓度再活化Pap1;低浓度的则直接氧化活化Pap1,导致Pap1快速向细胞核内运输从而激活Pap1相关基因的表达.本文综述了裂殖酵母中转录因子Pap1在不同浓度H2O2胁迫下的激活途径,以及蛋白激酶Sty1对Pap1激活的重要作用     

Conserved quantitative stability/flexibility relationships (QSFR) in an orthologous RNase H pair

Many reports qualitatively describe conserved stability and flexibility profiles across protein families, but biophysical modeling schemes have not been available to robustly quantify both. Here we investigate an orthologous RNase H pair by using a minimal distance constraint model (DCM). The DCM is an all atom microscopic model [Jacobs and Dallakyan, Biophys J 2005;88(2):903-915] that accurately reproduces heat capacity measurements [Livesay et al., FEBS Lett 2004;576(3):468-476], and is unique in its ability to harmoniously calculate thermodynamic stability and flexibility in practical computing times. Consequently, quantified stability/flexibility relationships (QSFR) can be determined using the DCM. For the first time, a comparative QSFR analysis is performed, serving as a paradigm study to illustrate the utility of a QSFR analysis for elucidating evolutionarily conserved stability and flexibility profiles. Despite global conservation of QSFR profiles, distinct enthalpy-entropy compensation mechanisms are identified between the RNase H pair. In both cases, local flexibility metrics parallel H/D exchange experiments by correctly identifying the folding core and several flexible regions. Remarkably, at appropriately shifted temperatures (e.g., melting temperature), these differences lead to a global conservation in Landau free energy landscapes, which directly relate thermodynamic stability to global flexibility. Using ensemble-based sampling within free energy basins, rigidly, and flexibly correlated regions are quantified through cooperativity correlation plots. Five conserved flexible regions are identified within the structures of the orthologous pair. Evolutionary conservation of these flexibly correlated regions is strongly suggestive of their catalytic importance. Conclusions made herein are demonstrated to be robust with respect to the DCM parameterization.     

A Single Mutation at Residue 25 Populates the Folding Intermediate of E. coli RNase H and Reveals a Highly Dynamic Partially Folded Ensemble

Understanding the nature of partially folded intermediates transiently populated during protein folding is important for understanding both protein folding and misfolding. These ephemeral species, however, often elude direct experimental characterization. The well-characterized protein ribonuclease H (RNase H) from Escherichia coli populates an on-pathway intermediate identified in both bulk studies and single-molecule mechanical unfolding experiments. Here, we set out to trap the transient intermediate of RNase H at equilibrium by selectively destabilizing the region of the protein known to be unfolded in this species. Surprisingly, a single change at Ile25 (I25A) resulted in the equilibrium population of the intermediate under near-native conditions. The intermediate was undetectable in a series of heteronuclear single quantum coherences, revealing the dynamic nature of this partially unfolded form on the timescale of NMR detection. This result is in contrast to studies in which the structures of trapped intermediates are solved by NMR, indicating that they are well packed and native-like. The dynamic nature of the RNase H intermediate may be important for its role as an on-pathway, productive species that promotes efficient folding.