RNase E action at a distance: degradation of target mRNAs mediated by an Hfq-binding small RNA in bacteria

A major class of bacterial small RNAs (sRNAs), along with RNA-binding protein Hfq and endoribonuclease RNase E, acts on target mRNAs through base-pairing, leading to translational repression and rapid degradation of the mRNAs. In this issue of Genes & Development, Prévost and colleagues (pp. 385-396) demonstrate by using the well-characterized sRNA RyhB that RNase E cleavage at sites distal from the pairing region triggers degradation of target mRNAs. The study has provided an important insight into the initial events of sRNA-induced degradation of target mRNAs.     

Characterization of a chlorella virus PBCV-1 encoded ribonuclease III

Sequence analysis of the 330-kb genome of chlorella virus PBCV-1 revealed an open reading frame, A464R, which encodes a protein with 30-35% amino acid identity to ribonuclease III (RNase III) from many bacteria. The a464r gene was cloned and the protein was expressed in Escherichia coli using the chitin-binding intein system. The recombinant PBCV-1 RNase III cleaves model dsRNA substrates, in a Mg(2+)-dependent manner, into a defined set of products. The substrate cleavage specificity overlaps, but is nonidentical to that of E. coli RNase III. The a464r gene is expressed very early during PBCV-1 infection, within 5-10 min p.i. The RNase III protein appears at 15 min p.i. and disappears by 120 min p.i. The a464r gene is highly conserved among the chlorella viruses. Phylogenetic analyses indicate that the PBCV enzyme is most closely related to Mycoplasma pneumoniae RNase III.     

Mammalian homologue of E. coli ras-like GTPase (ERA) is a possible apoptosis regulator with RNA binding activity

BACKGROUND: ERA (Escherichia coli Ras-like protein) is an E. coli GTP binding protein that is essential for proliferation. A DNA database search suggests that homologous sequences with ERA exist in various organisms including human, mouse, Drosophila, Caenorhabditis elegans and Antirrhinum majus. However, the physiological function of eukaryotic ERA-like proteins is not known. RESULTS: We have cloned cDNAs encoding the entire coding region of a human homologue (H-ERA) and a mouse homologue (M-ERA) of ERA. The mammalian homologue of ERA consists of a typical GTPase/GTP-binding domain and a putative K homology (KH) domain, which is known as an RNA binding domain. We performed transfection experiments with wild-type H-ERA or various H-ERA mutants. H-ERA possessing the amino acid substitution mutation into the GTPase domain induced apoptosis of HeLa cells, which was blocked by Bcl-2 expression. Deletion of the C-terminus, which contains a part of the KH domain, alleviated apoptosis by the H-ERA mutant, suggesting the importance of this domain in the function of H-ERA. We have also shown the RNA binding activity of H-ERA by pull-down experiments using RNA homopolymer immobilized on beads or recombinant H-ERA proteins. CONCLUSION: Our data suggest that H-ERA plays an important role in the regulation of apoptotic signalling with its GTPase/GTP binding domain.     

A case of renal crisis in a Korean scleroderma patient with anti-RNA polymerase I and III antibodies

Scleroderma (SSc) renal crisis has been reported to be associated with anti-RNA polymerase I and III (RNAP I/III) antibodies in Caucasians and the Japanese. However, no report is available for Korean SSc patients. Here, we describe the case of a 65-yr-old female SSc patient who developed renal crisis and whose serum contained anti-RNAP I/III antibodies. She was finally diagnosed as having diffuse cutaneous SSc based on skin thickening proximal to the elbows and knees. Sudden hypertension, oliguria, and pulmonary edema were features of her renal crisis. Despite the use of captopril and adequate blood pressure control, her renal function deteriorated. Subsequent renal biopsy findings showed severe fibrinoid necrosis with luminal obliteration in interlobar arteries and arterioles consistent with SSc renal crisis. Serum anti-RNAP I/III antibodies were detected by radioimmunoprecipitation. This is the first report of a renal crisis in a Korean SSc patient with RNAP I/III antibodies.     

Targeted decay of a regulatory small RNA by an adaptor protein for RNase E and counteraction by an anti-adaptor RNA

Bacterial small RNAs (sRNAs) are well established to regulate diverse cellular processes, but how they themselves are regulated is less understood. Recently, we identified a regulatory circuit wherein the GlmY and GlmZ sRNAs of Escherichia coli act hierarchically to activate mRNA glmS, which encodes glucosamine-6-phosphate (GlcN6P) synthase. Although the two sRNAs are highly similar, only GlmZ is a direct activator that base-pairs with the glmS mRNA, aided by protein Hfq. GlmY, however, does not bind Hfq and activates glmS indirectly by protecting GlmZ from RNA cleavage. This complex regulation feedback controls the levels of GlmS protein in response to its product, GlcN6P, a key metabolite in cell wall biosynthesis. Here, we reveal the molecular basis for the regulated turnover of GlmZ, identifying RapZ (RNase adaptor protein for sRNA GlmZ; formerly YhbJ) as a novel type of RNA-binding protein that recruits the major endoribonuclease RNase E to GlmZ. This involves direct interaction of RapZ with the catalytic domain of RNase E. GlmY binds RapZ through a secondary structure shared by both sRNAs and therefore acts by molecular mimicry as a specific decoy for RapZ. Thus, in analogy to regulated proteolysis, RapZ is an adaptor, and GlmY is an anti-adaptor in regulated turnover of a regulatory small RNA.     

人TPO全长分子在大肠杆菌中的表达及其活性分析

利用反转录－ＰＣＲ从人胎肝中获得编码血小板生成素（ｈＴＰＯ）全长ｃＤＮＡ，在大肠杆菌中表达了人ＴＰＯ全长分子。电镜观察结果，目的蛋白在菌体内以包涵体形式存在，表达量约占菌体总蛋白的２７％；表达产物经初步纯化后，与ＣＯＳ－７细胞中表达的人ＴＰＯ３５３个氨基酸全长分子分别做ＢＡＬＢ／ｃ小鼠体内活性分析，结果表明，原核与真核系统表达的ＴＰＯ均具有明显促进血小板生成的作用。这为进一步研究ＴＰＯ的糖基化与其生物学活性及半衰期关系打下基础。     

影响人干细胞因子基因高效表达的因素探讨

目的；分析SD序列长度，基因起始码ATG和终止码TAA上下游处RNA的二级结构及密码子偏性等影响表达效率的主要因素，以期实现重组人干细胞因子在原核细菌中高效表达。方法，分析并修改编码人SCF氨基酸的密码子，分段合成改造后的基因，PCR一次性完成拼接，将基因克隆到pBV-220载体 上，诱导表达。结果：天然人SCF基因在pBV-220载体的表达占菌体总蛋白的9．5％，基因改造后SCF占菌体总蛋白的27％，表达的蛋白能够为SCF的单克隆抗体所识别，初步纯化的SCF蛋白纯度大于80％，能够促进Mo7e细胞的增殖活性，结论：密码子偏性是影响SCF在原核细菌中高效表达的主要因素，通过改变密码子偏性能过实现高效表达。     

在翻译水平上提高人干扰素α1基因的原核表达

目的　根据翻译起始调控的定量理论及利用翻译增强子序列 ,提高人干扰素α1型变种IFN α1C基因的原核表达。方法　采用“步移式”聚合酶链反应 (PCR) ,对IFN α1C基因 5′端核苷酸序列进行三种不同程度的碱基突变 ,使IFN α1C在pBV2 2 0载体中形成的翻译起始区域 (TIR)的二级结构自由能 (△G)逐渐降低 ,同时 ,采用PCR技术 ,将翻译增强子cDNA序列引入pBV2 2 0中的SD序列上游 ,构建一种新型载体pBVE。结果　三种IFN α1C改造基因的表达量均有所提高 ,而且随△G从原有的 - 5 0 2 4 1.6J mol降至 - 2 2 190 .0J mol(绝对值 ,下同 ) ,其表达量有逐渐升高趋势 ,最高可达 2 .4 3×10 8U L ,约为IFN α1C母体的 13倍。选用IFN α1C及其三种改造基因为报导基因 ,结果显示以pBVE为载体的抗病毒活性比在pBV2 2 0中增强了 2～ 5倍。结论　含有翻译增强子的pBVE为一种新型原核高效表达载体。翻译调控的定量关系理论 ,可有效地运用于提高IFN α1C基因在大肠埃希菌中的表达。     

计算机辅助设计使重组ricin—A链在E.coli中的高效表达

基于对螺旋区随机堆积的ＲＮＡ二级结构的预测和密码子偏性计算，建立了ｐＢＶ２２０载体中外源基因高效表达的判别模型。该模型认为，外源基因的表达水平，与其５′端３０３９区域，以及３′端３０３９区域的二级结构自由能具有显著的统计学意义；其次与３′端９ｂｐ的局部密码子偏性相关。据此模型，我们设计了用于克隆表达ｒｉｃｉｎＡ链的引物。将ＰＣＲ扩增的基因克隆入ｐＢＶ２２０载体中，在ＤＨ５α宿主中获得了高效表达（表达水平在２０％以上），而且在ｐＥｘＳｅｃＩ载体系统中亦获得了高效表达。     

金黄色葡萄球菌核酸酶在大肠杆菌中的表达及其活性分析

目的:构建金黄色葡萄球菌核酸酶(SN)基因的原核表达载体,研究其在大肠杆菌中的表达,并制备兔抗SN抗体。方法:从质粒pPLCSN中扩增SN基因片段,插入表达载体pLEX后转化大肠杆菌GI724,以色氨酸诱导表达。以表达的重组蛋白免疫日本大耳白兔制备抗SN抗体,用Westernblot分析兔抗SN抗体的特异性。结果:重组表达载体pLEXSN在大肠杆菌中获得表达,表达的可溶性蛋白占菌体蛋白总量的37%,具有良好的生物学活性。制备的兔抗SN抗体能够特异识别SN。结论:成功地在大肠杆菌中表达具有生物学活性的SN,并制备了兔抗SN抗体,为进一步探讨其作为抗病毒因子应用于病毒性疾病的治疗奠定了基础。     

Modulating RssB activity: IraP, a novel regulator of sigma(S) stability in Escherichia coli

The sigma(S) subunit of Escherichia coli RNA polymerase regulates the expression of stationary phase and stress response genes. sigma(S) is highly unstable in exponentially growing cells, whereas its stability increases dramatically upon starvation or under certain stress conditions. The degradation of sigma(S) is controlled by the phosphorylatable adaptor protein RssB and the ClpXP protease. RssB specifically directs sigma(S) to ClpXP. An unanswered question is how RssB-mediated degradation of sigma(S) is blocked by conditions such as glucose or phosphate starvation. We report here the identification and characterization of a new regulator of sigma(S) stability, IraP (inhibitor of RssB activity during phosphate starvation), that stabilizes sigma(S) both in vivo and in vitro. Deletion of iraP interferes with sigma(S) stabilization during phosphate starvation, but not during carbon starvation, and has a partial effect in stationary phase and nitrogen starvation. IraP interferes with RssB-dependent degradation of sigma(S) through a direct protein-protein interaction with RssB. A point mutant of IraP was isolated and found to be defective both for inhibition of sigma(S) degradation and interaction with RssB. Our results reveal a novel mechanism of regulation of sigma(S) stability through the regulation of RssB activity and identify IraP as a member of a new class of regulators, the anti-adaptor proteins.     

新型人白细胞介素-13在大肠杆菌中的表达及生物活性分析

目的 :在大肠杆菌中表达人白细胞介素 13的新型拼接体蛋白。方法 :用植物凝集素 (PHA)和刀豆凝集素 (ConA)共刺激人Jurkat细胞 ,通过半巢式RT PCR扩增在 98位缺失Gln、不含信号肽的人IL 13新拼接体基因 ,并克隆入 pBV2 2 0 ,构建 pBVIL 13表达载体 ,经温度诱导后在大肠杆菌DH5α中表达新型人IL 13蛋白。表达产物经S 2 0 0纯化、复性后 ,用TF 1细胞进行MTT比色测定其活性。结果 :成功地分离了人IL 13新拼接体基因 ,并在大肠杆菌中表达。分离纯化的新型IL 13蛋白 ,其比活性为 1.6× 10 6U/mg。结论 :获得具有生物学活性的新型人IL 13细胞因子 ,为用其治疗肿瘤和脓毒症提供了新的手段     

人内皮抑素在大肠杆菌中的高效表达及活性研究

目的:表达人内皮抑素蛋白,制备多克隆抗体,检测其生物学活性。方法:采用PCR法扩增人内皮抑素基因,构建pGEX-ES融合表达载体,IPTG(异丙基硫代-β-D半乳糖苷)诱导表达。初步纯化的内皮抑素包含体蛋白制备兔多克隆抗体,Western-blot检测其在小鼠肝、肾等的表达。亲和纯化的内皮抑素蛋白用内皮细胞抑制实验检测其生物学活性。结果:诱导表达的人内皮抑素蛋白经凝血酶酶切后,分子量约为 20kD,具有抑制内皮细胞生长的活性。制备的多克隆抗体检测出内皮抑素在小鼠肝、肾等组织的表达。结论:人内皮抑素的成功表达及抗体制备为抗血管生成治疗实体瘤的研究及检测奠定实验基础.     

E. coli CNF1 toxin: a two-in-one system for host-cell invasion

The cytotoxic necrotizing factor-1 (CNF1), a bacterial toxin of uropathogenic bacteria (UPEC), hijacks cellular Rho proteins of the Ras GTPase super-family. Recently, we have made three important findings. First, we have established that, following Rho protein activation by deamidation, these cellular proteins are ubiquitylated and degraded by the proteasome. Second, the low level of activated Rho proteins which results from the dual molecular mechanism of action of CNF1 (Rho protein activation followed by their degradation), confers high invasive properties to UPECs. Finally, we have reported that ubiquitylation and degradation of Rac is lost in HEp-2 carcinoma cells, thereby suggesting a possible link between Rho protein ubiquitylation and tumor progression.     

E. coli and colorectal cancer: a complex relationship that deserves a critical mindset

To the multiple factors that may eventually result in colorectal cancer (CRC), strains of E. coli have now been added, in particular strains producing colibactin from their polyketide synthesis (pks) locus. The evidence and mechanistic explanations for this unfortunate effect of what is in most cases a harmless commensal are discussed in the first part of this review. In the second part, observations are presented and discussed that do not fit with the hypothesis that colibactin-producing E. coli produce CRC. The last part of this review is reserved for an alternative explanation of the function of this enigmatic colibactin, a toxin that has not yet been isolated. It is hypothesized that E. coli preferentially colonizes cancerous lesions as an effect rather than a cause and that colibactin production provides a selective advantage to compete with other bacteria.