Coexpression of Escherichia coli RNase III in silkworm cells improves the efficiency of RNA interference induced by long hairpin dsRNAs

Abstract Long hairpin dsRNA transcribed from chromosomal DNA can induce RNA interference in Bombyx mori cells, although its gene silencing efficiency is lower than that of exogenously introduced double‐stranded RNAs (dsRNAs). To solve this problem, we monitored the nuclear cytoplasmic translocation of the transcribed hairpin dsRNA and analyzed the processing efficiency into mature small interfering RNA (siRNA). Northern blot analysis revealed that the transcribed hairpin dsRNAs were spliced and transported into the cytoplasm, but were not effectively diced into siRNAs. Interestingly, RNAi with hairpin dsRNAs from genome‐integrated IR transgene was stimulated by the coexpression of Escherichia coli RNase III, although this exogenous enzyme seemed to bring about nonspecific cleavage of cellular mRNA.     

大肠杆菌trpBA基因的克隆表达

目的:提高大肠杆菌中色氨酸合成酶的表达量和表达活性。方法:利用PCR方法从大肠杆菌K-12的基因组中直接克隆出紧密连锁trpB和trpA基因(简称trpBA),并将其连接到原核表达载体pet22b( )中,得到重组质粒pet22b( )-trp-BA,转化大肠杆菌BL21,IPTG诱导重组蛋白表达,表达产物经SDS-PAGE分析并用比色法测定其活性。结果:凝胶电泳可见PCR扩增产物大小约为2kb,SDS-PAGE鉴定目的蛋白的Mr分别约为29000和44000,色氨酸合成酶α、β亚基分别得到了高效表达,色氨酸合成酶活性提高到对照菌的3.7倍。结论:成功构建了重组质粒pet22b( )-trpBA,色氨酸合成酶的表达量和表达活性在大肠杆菌中得到了提高,为高产色氨酸基因工程菌的构建奠定基础。     

The rne gene is the structural gene for the processing endoribonuclease RNase E of Escherichia coli.

Summary Using T7 RNA polymerase and specific constructs derived from 5S rRNA and RNA I genes, we generated substrates for the RNA processing enzyme RNase E. Using these substrates we have shown that a 3.2 kb DNA fragment that complements the rne-3071 mutation can express RNase E activity. We also found that T7 RNA polymerase terminates within the 5S rRNA gene.     

A peptide from Tetrahymena disrupts subunit organization of E. coli RNA polymerase.

Incubation of the E. coli RNA polymerase with a polypeptide factor from the protozoan Tetrahymena reduces the affinity of the holoenzyme for DNA. SDS-polyacrylamide gel electrophoresis of the peptide-treated RNA polymerase showed that the band pattern of the polymerase subunits was strongly altered. The three large subunits, beta', beta and sigma, disappear and a high number of rapidly migrating bands appeared. However, a brief heat treatment of the samples almost restored the original RNA polymerase subunit composition, and in addition a high molecular weight protein band approximately 240 kDa appeared. It is suggested that the Tetrahymena peptide specifically binds to the RNA polymerase and changes the structures of the large subunits.     

Small RNA interactome of pathogenic E. coli revealed through crosslinking of RNase E

RNA sequencing studies have identified hundreds of non‐coding RNAs in bacteria, including regulatory small RNA (sRNA). However, our understanding of sRNA function has lagged behind their identification due to a lack of tools for the high‐throughput analysis of RNA–RNA interactions in bacteria. Here we demonstrate that in vivo sRNA–mRNA duplexes can be recovered using UV‐crosslinking, ligation and sequencing of hybrids (CLASH). Many sRNAs recruit the endoribonuclease, RNase E, to facilitate processing of mRNAs. We were able to recover base‐paired sRNA–mRNA duplexes in association with RNase E, allowing proximity‐dependent ligation and sequencing of cognate sRNA–mRNA pairs as chimeric reads. We verified that this approach captures bona fide sRNA–mRNA interactions. Clustering analyses identified novel sRNA seed regions and sets of potentially co‐regulated target mRNAs. We identified multiple mRNA targets for the pathotype‐specific sRNA Esr41, which was shown to regulate colicin sensitivity and iron transport in E. coli. Numerous sRNA interactions were also identified with non‐coding RNAs, including sRNAs and tRNAs, demonstrating the high complexity of the sRNA interactome.     

Structures of the two 3D domain-swapped RNase A trimers

When concentrated in mildly acidic solutions, bovine pancreatic ribonuclease (RNase A) forms long-lived oligomers including two types of dimer, two types of trimer, and higher oligomers. In previous crystallographic work, we found that the major dimeric component forms by a swapping of the C-terminal beta-strands between the monomers, and that the minor dimeric component forms by swapping the N-terminal alpha-helices of the monomers. On the basis of these structures, we proposed that a linear RNase A trimer can form from a central molecule that simultaneously swaps its N-terminal helix with a second RNase A molecule and its C-terminal strand with a third molecule. Studies by dissociation are consistent with this model for the major trimeric component: the major trimer dissociates into both the major and the minor dimers, as well as monomers. In contrast, the minor trimer component dissociates into the monomer and the major dimer. This suggests that the minor trimer is cyclic, formed from three monomers that swap their C-terminal beta-strands into identical molecules. These conclusions are supported by cross-linking of lysyl residues, showing that the major trimer swaps its N-terminal helix, and the minor trimer does not. We verified by X-ray crystallography the proposed cyclic structure for the minor trimer, with swapping of the C-terminal beta-strands. This study thus expands the variety of domain-swapped oligomers by revealing the first example of a protein that can form both a linear and a cyclic domain-swapped oligomer. These structures permit interpretation of the enzymatic activities of the RNase A oligomers on double-stranded RNA.     

Effects of injecting cadherin gene dsRNA on growth and development in diamondback moth Plutella xylostella (Lep.: Plutellidae)

Two laboratory diamondback moth (DBM) strains were used to study the effects of injecting cadherin gene double‐stranded RNA (dsRNA) on the growth and development of Plutella xylostella (L.). Specifically, the susceptible strain named DBM.1Ac‐S and the low resistant strain DBM.1Ac‐R selected with Cry1Ac toxin were studied. The third larvae of the two strains were injected dsRNA of cadherin gene and their corresponding controls, DBM.1Ac‐RH and DBM.1Ac‐SH, were both injected diethypyrocarbonate (DEPC)‐treated water respectively. The basic biological properties such as death rate, hatching ratio, fecundity, weight of pupa and eclosion rate of the strains mentioned above were likewise studied. Meanwhile, the length and width of the egg and pupa were also measured. The results showed that the cadherin gene dsRNA injection resulted in a significant increase of the death rate and sex ratio. On the other hand, hatching ratio, fecundity, weight of pupa, eclosion rate and adult longevity for male and female of treatments decreased compared to their corresponding controls. As such, there was no significant difference on the length of egg and pupa in between treatments and the corresponding controls. However, their width increased inversely with their corresponding controls. Hence, the results suggest that cadherin gene dsRNA injection retarded the larval growth and development of P. xylostella. Also, these results can help reveal the function of cadherin gene through the RNA interference technique.     

大豆蚜Kazal型丝氨酸蛋白酶抑制剂基因AgKaSPI对蜡蚧刺束梗孢菌侵染的表达响应

[目的]探究Kazal型丝氨酸蛋白酶抑制剂KaSPI在大豆蚜Aphis glycines的生长发育、消化和免疫防御等过程中的作用.[方法]基于大豆蚜转录组数据PCR克隆大豆蚜Kazal型丝氨酸蛋白酶抑制剂基因cDNA序列;qRT-PCR分别检测AgKaSPI在大豆蚜1-4龄若虫和成虫以及蜡蚧刺束梗孢菌Akanthomy...     

Hypochlorous acid generates N epsilon-(carboxymethyl)lysine from Amadori products

Since the accumulation of N^ε-(carboxymethyl)lysine (CML), a major antigenic advanced glycation end product, is implicated in tissue disorders in hyperglycemia and inflammation, the identification of the pathway of CML formation will provide important information regarding the development of potential therapeutic strategies for these complications. The present study was designed to measure the effect of hypochlorous acid (HOCl) on CML formation from Amadori products. The incubation of glycated human serum albumin (glycated-HSA), a model of Amadori products, with HOCl led to CML formation, and an increasing HOCl concentration and decreasing pH, which mimics the formation of these products in inflammatory lesions. CML formation was also observed when glycated-HSA was incubated with activated neutrophils, and was completely inhibited in the presence of an HOCl scavenger. These data demonstrated that HOCl-mediated CML formation from Amadori products plays a role in CML formation and tissue damage at sites of inflammation.     

Expression of exo‐inulinase gene from Aspergillus niger 12 in E. coli strain Rosetta‐gami B (DE3) and its characterization

Inulin is a linear carbohydrate polymer of fructose subunits (2‐60) with terminal glucose units, produced as carbon storage in selected plants. It cannot directly be taken up by most microorganisms due to its large size, unless prior hydrolysis through inulinase enzymes occurs. The hydrolyzed inulin can be taken up by microbes and/or recovered and used industrially for the production of high fructose syrup, inulo‐oligosaccharides, biofuel, and nutraceuticals. Cell‐free enzymatic hydrolysis would be desirable for industrial applications, hence the recombinant expression, purification and characterization of an Aspergillus niger derived exo‐inulinase was investigated in this study. The eukaroyototic exo‐inulinase of Aspergillus niger 12 has been expressed, for the first time, in an E. coli strain [Rosetta‐gami B (DE3)]. The molecular weight of recombinant exo‐inulinase was estimated to be ～81 kDa. The values of K_m and V_max of the recombinant exo‐inulinase toward inulin were 5.3 ± 1.1 mM and 402.1 ± 53.1 µmol min^?1 mg^?1 protein, respectively. Towards sucrose the corresponding values were 12.20 ± 1.6 mM and 902.8 ± 40.2 µmol min^?1 mg^?1 protein towards sucrose. The S/I ratio was 2.24 ± 0.7, which is in the range of native inulinase. The optimum temperature and pH of the recombinant exo‐inulinase towards inulin was 55°C and 5.0, while they were 50°C and 5.5 towards sucrose. The recombinant exo‐inulinase activity towards inulin was enhanced by Cu²⁺ and reduced by Fe²⁺, while its activity towards sucrose was enhanced by Co²⁺ and reduced by Zn²⁺. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:629–637, 2016     

草鱼呼肠孤病毒RNA聚合酶基因功能区在原核细胞中的表达

草鱼呼肠孤病毒(grass carp reovirus)为我国分离、鉴定的第一株水生动物病毒.1983年,我国首次报道引起爆发性草鱼出血病的病原为草鱼出血病病毒[1,2],其后相继进行了系统的病毒形态学、生物学、生物化学及分子生物学特性等研究[3-8].自1979年Meyers T R等报道从水生动物中分离出第一株呼肠孤样病毒,迄今国际上已分离鉴定40余种水生呼肠孤病毒(aquareovirus).在这些分离株中,大多数毒株不能引起寄主的病理反应或仅表现出较弱的致病性.然而研究认为,GCRV为水生呼肠孤病毒中致病力最强的毒株[9].可见,以GCRV为模型,研究水生呼肠孤病毒的复制与致病机理具有一定的理论及实际意义.我们在对GCRV反应核心及体外转录研究中,已证实GCRV RNA聚合酶在病毒粒子中的存在及其位置[5];GCRV序列测定及定位结果显示,GCRV-VP2多肽为该病毒RNA聚合酶(RNA dependent RNA polymerase RdRp)[6,7].为了探讨草鱼呼肠孤病毒的侵染与宿主的相关性及复制机制,我们首次进行了该病毒RNA聚合酶基因(GCRV-RdRp)功能区序列在原核细胞中的表达研究,并得到高效表达融合蛋白.这一结果将为该酶的活性及特性分析提供实验依据.下面报道本研究结果.     

The RNase E/G-type endoribonuclease of higher plants is located in the chloroplast and cleaves RNA similarly to the E. coli enzyme

RNase E is an endoribonuclease that has been studied primarily in Escherichia coli, where it is prominently involved in the processing and degradation of RNA. Homologs of bacterial RNase E are encoded in the nuclear genome of higher plants. RNA degradation in the chloroplast, an organelle that originated from a prokaryote similar to cyanobacteria, occurs via the polyadenylation-assisted degradation pathway. In E. coli, this process is probably initiated with the removal of 5'-end phosphates followed by endonucleolytic cleavage by RNase E. The plant homolog has been proposed to function in a similar way in the chloroplast. Here we show that RNase E of Arabidopsis is located in the soluble fraction of the chloroplast as a high molecular weight complex. In order to characterize its endonucleolytic activity, Arabidopsis RNase E was expressed in bacteria and analyzed. Similar to its E. coli counterpart, the endonucleolytic activity of the Arabidopsis enzyme depends on the number of phosphates at the 5' end, is inhibited by structured RNA, and preferentially cleaves A/U-rich sequences. The enzyme forms an oligomeric complex of approximately 680 kDa. The chloroplast localization and the similarity in the two enzymes' characteristics suggest that plant RNase E participates in the initial endonucleolytic cleavage of the polyadenylation-stimulated RNA degradation process in the chloroplast, perhaps in collaboration with the two other chloroplast endonucleases, RNase J and CSP41.     

Verotoxin-producing Escherichia coli (VTEC), enteropathogenic E. coli (EPEC) and necrotoxigenic E. coli (NTEC) isolated from healthy cattle in Spain

AIMS: To determine the prevalence and characteristics of verotoxigenic Escherichia coli (VTEC), enteropathogenic E. coli (EPEC) and necrotoxigenic E. coli (NTEC) in healthy cattle. METHODS AND RESULTS: Faecal samples from 412 healthy cattle were screened for the presence of VTEC, EPEC and NTEC. Four isolates from each sample were studied. VTEC, EPEC and NTEC were isolated in 8.7%, 8.2% and 9.9% of the animals, respectively. VTEC and NTEC were isolated more frequently from calves and heifers than from adults. Seventy (4.2%), 69 (4.2%) and 74 (4.5%) of the 1648 E. coli isolates were VTEC, EPEC and NTEC, respectively. Seventeen (24.3%) of the VTEC strains were eae-positive. Thirty-six (51.4%) of VTEC strains belonged to E. coli serogroups associated with haemorrhagic colitis and haemolytic uraemic syndrome in humans. The serogroups most prevalent among the EPEC strains were O10, O26, O71, O145 and O156. CONCLUSIONS: Healthy cattle are a reservoir of VTEC, EPEC and NTEC. SIGNIFICANCE AND IMPACT OF THE STUDY: Although most of the VTEC strains were eae-negative, a high percentage of VTEC strains belonged to serogroups associated with severe disease in humans.     

Structure of the nuclease domain of ribonuclease III from M. tuberculosis at 2.1 A

RNase III enzymes are a highly conserved family of proteins that specifically cleave double-stranded (ds)RNA. These proteins are involved in a diverse group of functions, including ribosomal RNA processing, mRNA maturation and decay, snRNA and snoRNA processing, and RNA interference. Here we report the crystal structure of the nuclease domain of RNase III from the pathogen Mycobacterium tuberculosis. Although globally similar to other RNase III folds, this structure has some features not observed in previously reported models. These include the presence of an additional metal ion near the catalytic site, as well as conserved secondary structural elements that are proposed to have functional roles in the recognition of dsRNAs.     

储存条件对表达马铃薯甲虫腺苷高半胱氨酸水解酶基因dsRNA的大肠杆菌生物活性的影响

【目的】将RNA干扰应用于害虫防治领域,通过饲喂表达ds RNA的转基因植物或表达ds RNA的细菌,可沉默特定基因进而控制害虫,为农业害虫防治开辟一个新领域。而表达ds RNA的细菌能否有效储存是决定此项技术实际应用的关键。【方法】用﹣20℃冻存的表达马铃薯甲虫腺苷高半胱氨酸水解酶(SAHase)ds RNA的大肠杆菌E.coli,饲喂马铃薯甲虫Leptinotarsa decemlineata(Say)2龄幼虫,检测不同时间储存、灭活与否的活性变化,明确其储存条件。【结果】大肠杆菌﹣20℃储存24 h后生物活性优于新鲜菌,储存48 h后效果减弱,而载体大肠杆菌是否灭活对活性影响不大。【结论】ds RNA大肠杆菌发酵液在﹣20℃条件下可以短暂储存。