Understanding the interaction of hepatitis C virus with host DEAD-box RNA helicases

The current therapeutic regimen to combat chronic hepatitis C is not optimal due to substantial side effects and the failure of a significant proportion of patients to achieve a sustained virological response. Recently developed direct-acting antivirals targeting hepatitis C virus (HCV) enzymes reportedly increase the virologic response to therapy but may lead to a selection of drug-resistant variants. Besides direct-acting antivirals, another promising class of HCV drugs in development include host targeting agents that are responsible for interfering with the host factors crucial for the viral life cycle. A family of host proteins known as DEAD-box RNA helicases, characterized by nine conserved motifs, is known to play an important role in RNA metabolism. Several members of this family such as DDX3, DDX5 and DDX6 have been shown to play a role in HCV replication and this review will summarize our current knowledge on their interaction with HCV. As chronic hepatitis C is one of the leading causes of hepatocellular carcinoma, the involvement of DEAD-box RNA helicases in the development of HCC will also be highlighted. Continuing research on the interaction of host DEAD-box proteins with HCV and the contribution to viral replication and pathogenesis could be the panacea for the development of novel therapeutics against HCV.

RNA解旋酶DEAD-box蛋白家族与肿瘤的相关性研究

RNA解旋酶DEAD-box蛋白家族是RNA解旋酶中最大的家族,是基因表达的重要调控因子,在RNA代谢的多个方面发挥作用。RNA解旋酶DEAD-box蛋白家族既在RNA代谢中具有重要作用,又与人类细胞中基因组的不稳定性直接相关。而基因组的不稳定性是癌症克隆进化的驱动因素,能够促进癌症的发生发展。该文对RNA解旋酶DEAD-box蛋白家族与肿瘤发生发展的相关性做一综述。

Identification of the DEAD-box RNA helicase family members in grapevine reveals that VviDEADRH25a confers tolerance to drought stress

Grapevine growing areas are increasingly affected by drought,which has greatly limited global wine production and quality.DEAD-box is one of the largest subfamilies of the RNA helicase family,and its members play key roles in the growth and development of plants and their stress responses.Previous studies have shown the potential of DEAD-box genes in the drought stress responses of Arabidopsis and tomato,rice,and other crop species.However,information about DEAD-box genes in grapevine remains limited.In this report,a total of 40 DEAD-box genes were identified in grapevine and their protein sequence characteristics and gene structures were analyzed.By comparing the expression profiles of VviDEADRHs in response to drought stress in different grapevine varieties,nine candidate genes(VviDEADRH10c,-13,-22,-25a,-25b,-33,-34,-36,and-39)were screened based on expression profiling data.Combined with qRTPCR results,Vvi DEADRH25a was selected for functional verification.Heterologous overexpression of Vvi DEADRH25a in Arabidopsis showed the transgenic plants were more sensitive to drought stress than the control.Both electrolyte permeability and malondialdehyde content were significantly increased in transgenic plants,whereas the chlorophyll content and superoxide dismutase(SOD),peroxidase(POD),catalase(CAT),and ascorbate peroxidase(APX)enzyme activities were significantly decreased.Furthermore,VviDEADRH25a-overexpressing plants showed down-regulated expression levels of several drought stress-related marker genes,namely At COR15a,At RD29A,At ERD15,and At P5CS1,which indicated that they participated in the drought stress response.In summary,this study provides new insights into the structure,evolution,and participation of DEAD-box RNA helicase genes in the response to drought stress in grapevines.

DEAD-box解旋酶21对猪传染性胃肠炎病毒复制的调控作用

旨在探究DEAD-box解旋酶21(DDX21)对猪传染性胃肠炎病毒(TGEV)复制的调控作用。首先通过蛋白免疫印迹(Western Blot)分析了TGEV感染对DDX21表达的影响;进一步构建了猪DDX21真核表达质粒以及建立稳定敲低DDX21的PK-15细胞系,运用荧光定量PCR(RT-qPCR)、蛋白免疫印迹、间接免疫荧光(IFA)和半数细胞培养物感染量(TCID 50)探究外源过表达DDX21及敲低DDX21对TGEV体外复制的调控作用;构建一系列DDX21截短突变体真核表达质粒,鉴定了DDX21调控TGEV增殖的关键功能域。Western Blot分析显示,在TGEV WH-1株感染早期,PK-15细胞内源性DDX21蛋白的表达水平显著上调;RT-qPCR、Western Blot、IFA和TCID 50试验显示,超表达DDX21可以显著提高TGEV N基因的mRNA水平、N蛋白的表达及病毒滴度,且呈剂量依赖性,其601-784 aa区域是其影响TGEV复制的关键;与阴性对照相比,在相应DDX21敲低细胞系中TGEV的增殖显著被抑制,而回补试验逆转了DDX21敲低细胞系中TGEV的滴度。该研究首次揭示了猪DDX21对TGEV增殖的促进作用并鉴定了其调控TGEV复制的关键结构域,为今后研究DDX21蛋白的功能及TGEV的致病机理提供了理论依据。

Rig-I蛋白C端Helicase结构域的原核表达、纯化及其多克隆抗体制备

目的:为Rig-I蛋白结构与模式识别功能的深入研究提供灵敏、高效的免疫学检测试剂。方法:PCR法克隆小鼠Rig-I基因Helicase区编码序列(726～2240bp,编码241～746位氨基酸),构建带组氨酸标签的原核表达载体pET15b-mRig-I-H,阳性克隆经酶切、测序鉴定后转化E.coliBL21进行诱导表达。目的蛋白电泳分离并割胶纯化后免疫家兔制备抗血清。抗血清用ELISA、Western blot、细胞免疫荧光方法进行鉴定。结果:目的蛋白在大肠杆菌中获得了高效表达,制备的抗Rig-I抗体效价达到1∶100000,Western blot、细胞免疫荧光结果显示该抗体能够有效地对细胞内Rig-I蛋白的表达水平进行检测。结论:成功地对mRig-I-H进行了原核表达、纯化,抗mRig-I-H的多克隆抗体具有较高的特异性,为进一步研究Rig-I尤其是Helicase区的结构与功能奠定了坚实的基础。

Post-transcriptional regulation of DEAD-box RNA helicases in hematopoietic malignancies

Hematopoiesis represents a meticulously regulated and dynamic biological process.Genetic aberrations affecting blood cells,induced by various factors,frequently give rise to hematological tumors.These instances are often accompanied by a multitude of abnormal post-transcriptional regulatory events,including RNA alternative splicing,RNA localization,RNA degradation,and storage.Notably,post-transcriptional regulation plays a pivotal role in preserving hematopoietic homeostasis.The DEAD-Box RNA helicase genes emerge as crucial post-transcriptional regulatory factors,intricately involved in sustaining normal hematopoiesis through diverse mechanisms such as RNA alternative splicing,RNA modification,and ribosome assembly.This review consolidates the existing knowledge on the role of DEAD-box RNA helicases in regulating normal hematopoiesis and underscores the pathogenicity of mutant DEADBox RNA helicases in malignant hematopoiesis.Emphasis is placed on elucidating both the positive and negative contributions of DEAD-box RNA helicases within the hematopoietic system.

Effects of Mercury on the Structure and Activity of BLM642-1290 Recombinant Helicase

Objective Bloom’s syndrome is an autosomal recessive disorder characterized by genomic instability and a predisposition to many cancers. Mutations of the BLM gene （encoding a BLM helicase） may form a structure of the etiology of this disease. As a global pollutant, mercury poses a major threat to human health. The current study was conducted to elucidate the effects of Hg^2＋ on the structure and activity of BLM642‐1290 recombinant helicase, and to further explore the molecular mechanisms of mercury toxicity to the DNA helicase. Methods The effects of Hg^2＋ on biological activity and structure of BLM642‐1290 recombinant helicase were determined by fluorescence polarized, ultraviolet spectroscopic, and free‐phosphorus assay technologies, respectively. Results The helicase activity, the DNA‐binding activity, and the ATPase activity of BLM642‐1290 recombinant helicase were inhibited by Hg^2＋ treatment. The LMCT （ligand‐to‐metal charge transition） peaks of the helicase were enhanced with the increase of the Hg^2＋ level. The LMCT peaks of the same concentration of helicase gradually increased over time. Conclusions The biological activity of BLM642‐1290 recombinant helicase is inhibited by Hg^2＋ treatment. The conformation of the helicase is significantly altered by Hg^2＋ . There exist two binding sites between Hg^2＋ and the helicase, which are located in the amino acid residues 1063‐1066 and 940‐944 of the helicase, respectively.

鸭RIG-Ⅰ蛋白C端helicase结构域和RD结构域的原核表达及其单克隆抗体的制备

利用PCR技术将鸭维甲酸诱导基因Ⅰ(RIG-Ⅰ)helicase区和RD区部分编码序列分别进行扩增,并分别命名为c、d段;克隆到p ET30a原核表达载体,构建了重组原核表达质粒p ET30a-c和p ET30a-d,通过转化BL21(DE3)感受态菌、IPTG诱导、镍柱纯化表达蛋白,将纯化的c、d蛋白免疫小鼠制备单克隆抗体(m Ab),采用ELISA、Western blot和间接免疫荧光试验对单克隆抗体进行鉴定分析。获得鼠抗鸭RIG-Ⅰ单克隆抗体有14株与原核分段表达的c、d蛋白有良好的反应性,其中3株与真核表达的RIG-Ⅰ蛋白有良好的反应性。制备的鼠抗鸭RIG-Ⅰ单克隆抗体为RIG-Ⅰ在抗病毒天然免疫信号转导途径的研究奠定了基础。

Potent in vitro Interference of Fleroxacin in DNA-binding,Unwinding and ATPase Activities of Bloom Helicase

Objective To study the effect of fleroxacin （FLRX） on biological properties of Bloom （BLM） helicase catalytic core （BLM 642-2290 helicase） in vitro and the molecular mechanism of interaction between the two molecules. Methods DNA-binding and unwinding activities of BLM 642-1290 helicase were assayed by fluorescence polarization and gel retardation assay under conditions that the helicase was subjected to different concentrations of FLRX. Effect of FLRX on helicase ATPase activity was analyzed by phosphorus-free assay based on a colorimetric estimation of ATP hydrolysis-produced inorganic phosphate. Molecular mechanism of interaction between the two molecules was assayed by ultraviolet and fluorescence spectra. Results The DNA unwinding and ATPase activities of BLM 642-1290 helicase were inhibited whereas the DNA-binding activity was promoted in vitro. A BLM-FLRX complex was formed through one binding site, electrostatic and hydrophobic interaction force. Moreover, the intrinsic fluorescence of the helicase was quenched by FLRX as a result of non-radioactive energy transfer. The biological activity of helicase was affected by FLRX, which may be through an allosteric mechanism and stabilization of enzyme conformation in low helicase activity state, disruption of the coupling of ATP hydrolysis to unwinding, and blocking helicase translocation on DNA strands. Conclusion FLRX may affect the biological activities and conformation of BLM 642-1290 helicase, and DNA helicase may be used as a promising drug target for some diseases.

Structural elucidation of SARS-CoV-2 vital proteins: Computational methods reveal potential drug candidates against main protease, Nsp12 polymerase and Nsp13 helicase

Recently emerged SARS-CoV-2 caused a major outbreak of coronavirus disease 2019(COVID-19)and instigated a widespread fear,threatening global health safety.To date,no licensed antiviral drugs or vaccines are available against COVID-19 although several clinical trials are under way to test possible therapies.During this urgent situation,computational drug discovery methods provide an alternative to tiresome high-throughput screening,particularly in the hit-to-lead-optimization stage.Identification of small molecules that specifically target viral replication apparatus has indicated the highest potential towards antiviral drug discovery.In this work,we present potential compounds that specifically target SARS-CoV-2 vital proteins,including the main protease,Nsp12 RNA polymerase and Nsp13 helicase.An integrative virtual screening and molecular dynamics simulations approach has facilitated the identification of potential binding modes and favourable molecular interaction profile of corresponding compounds.Moreover,the identification of structurally important binding site residues in conserved motifs located inside the active site highlights relative importance of ligand binding based on residual energy decomposition analysis.Although the current study lacks experimental validation,the structural information obtained from this computational study has paved way for the design of targeted inhibitors to combat COVID-19 outbreak.

Heat shock protein 90 promotes RNA helicase DDX5 accumulation and exacerbates hepatocellular carcinoma by inhibiting autophagy

Objective:Hepatocellular carcinoma(HCC),the main type of liver cancer,has a high morbidity and mortality,and a poor prognosis.RNA helicase DDX5,which acts as a transcriptional co-regulator,is overexpressed in most malignant tumors and promotes cancer cell growth.Heat shock protein 90(HSP90)is an important molecular chaperone in the conformational maturation and stabilization of numerous proteins involved in cell growth or survival.Methods:DDX5 m RNA and protein expression in surgically resected HCC tissues from 24 Asian patients were detected by quantitative real-time PCR and Western blot,respectively.The interaction of DDX5-HSP90 was determined by molecular docking,immunoprecipitation,and laser scanning confocal microscopy.The autophagy signal was detected by Western blot.The cell functions and signaling pathways of DDX5 were determined in 2 HCC cell lines.Two different murine HCC xenograft models were used to determine the function of DDX5 and the therapeutic effect of an HSP90 inhibitor.Results:HSP90 interacted directly with DDX5 and inhibited DDX5 protein degradation in the AMPK/ULK1-regulated autophagy pathway.The subsequent accumulation of DDX5 protein induced the malignant phenotype of HCC by activating theβ-catenin signaling pathway.The silencing of DDX5 or treatment with HSP90 inhibitor both blocked in vivo tumor growth in a murine HCC xenograft model.High levels of HSP90 and DDX5 protein were associated with poor prognoses.Conclusions:HSP90 interacted with DDX5 protein and subsequently protected DDX5 protein from AMPK/ULK1-regulated autophagic degradation.DDX5 and HSP90 are therefore potential therapeutic targets for HCC.

P68 RNA helicase is a nucleocytoplasmic shuttling protein

P68 RNA helicase is a prototypical DEAD box RNA helicase. The protein plays a very important role in early organ development and maturation. Consistent with the function of the protein in transcriptional regulation and pre-mRNA splicing, p68 was found to predominately localize in the cell nucleus. However, recent experiments demon- strate a transient cytoplasmic localization of the protein. We report here that p68 shuttles between the nucleus and the cytoplasm. The nucleocytoplasmic shuttling of p68 is mediated by two nuclear localization signal and two nuclear exporting signal sequence elements. Our experiments reveal that p68 shuttles via a classical RanGTPase-dependent pathway.

Functional analysis of helicase and three tandem HRDC domains of RecQ in Deinococcus radiodurans

RecQ is a highly conserved helicase necessary for maintaining genome stability in all organisms. Genome comparison showed that a homologue of RecQ in Deinococcus radiodurans designated as DR1289 is a member of RecQ family with unusual domain arrangement: a helicase domain, an RecQ C-terminal domain, and surprisingly three HRDC domain repeats, whose func-tion, however, remains obscure currently. Using an insertion deletion, we discovered that the DRRecQ mutation causes an increase in gamma radiation, hydroxyurea and mitomycine C and UV sensitivity. Using the shuttle plasmid pRADK, we complemented various domains of the D. radiodurans RecQ (DRRecQ) to the mutant in vivo. Results suggested that both the helicase and helicase-and-RNase-D-C-terminal (HRDC) domains are essential for complementing several phenotypes. The complementation and biochemical function of DRRecQ variants with different domains truncated in vitro suggested that both the helicase and three HRDC domains are necessary for RecQ functions in D. radiodurans, while three HRDC domains have a synergistic effect on the whole function. Our finding leads to the hypothesis that the RecF recombination pathway is likely a primary path of double strand break repair in this well-known radioresistant organism.

Functional interplay among the flavivirus NS3 protease, helicase, and cofactors

Flaviviruses are positive-sense RNA viruses, and many are important human pathogens. Nonstructural protein 2B and 3 of the flaviviruses(NS2BNS3) form an endoplasmic reticulum(ER) membrane-associated hetero-dimeric complex through the NS2B transmembrane region. The NS2BNS3 complex is multifunctional. The N-terminal region of NS3, and its cofactor NS2B fold into a protease that is responsible for viral polyprotein processing, and the C-terminal domain of NS3 possesses NTPase/RNA helicase activities and is involved in viral RNA replication and virus particle formation. In addition, NS2BNS3 complex has also been shown to modulate viral pathogenesis and the host immune response. Because of the essential functions that the NS2BNS3 complex plays in the flavivirus life cycle, it is an attractive target for antiviral development. This review focuses on the recent biochemical and structural advances of NS2BNS3 and provides a brief update on the current status of drug development targeting this viral protein complex.

Chromodomain-helicase-DNA binding protein 5, 7 and pronecrotic mixed lineage kinase domain-like protein serve as potential prognostic biomarkers in patients with resected pancreatic adenocarcinomas

Pancreatic cancer is one of the deadliest cancers with a very poor prognosis. Recently, there has been a significant increase in research directed towards identifying potential biomarkers that can be used to diagnose and provide prognostic information for pancreatic cancer. These markers can be used clinically to optimize and personalize therapy for individual patients. In this review, we focused on 3 biomarkers involved in the DNA damage response pathway and the necroptosis pathway: Chromodomainhelicase-DNA binding protein 5, chromodomain-helicaseDNA binding protein 7, and mixed lineage kinase domain-like protein. The aim of this article is to review present literature provided for these biomarkers and current studies in which their effectiveness as prognostic biomarkers are analyzed in order to determine their future use as biomarkers in clinical medicine. Based on the data presented, these biomarkers warrant further investigation,and should be validated in future studies.

RNA helicase DDX20 as a surrogate marker of statin activity in invasive breast cancer

OBJECTIVE To evaluate if RNA helicase DDX20,highly expressed in triple negative breast cancer(TNBC)cells,could serve as a surrogate marker for simvastatin treatment response.METHODS We first assessed correlation between 17 mevalonate pathway-related genes and expression of DDX20 in a cohort of 1325 breast cancer tumors.TNBC cells,MDA-MB-231,were then treated with simvastatin and mevalonate pathway intermediates to assess the alteration in DDX20 expression.In the mouse model,MDA-MB-231 cells were injected to tail veins of mice,groups of 8mice each were injected intraperioneally with vehicle or simvastatin 25mg·kg-1 3times a week for 6weeks.The number of metastatic colonies formed was quantified and immunohistochemical(IHC)staining of DDX20 was carried out in the lung tissues.RESULTS Among the 17 genes evaluated,positive correlation with DDX20 expression was observed in eight of them,with HMGCR having the highest correlation.Our in vitro experiments show exposure of breast cancer cells to simvastatin lead to a Rho-dependent decrease in gene expression of DDX20,leading to decreased tumor proliferation in a mevalonate pathway-dependent manner.Conversely,ectopic overexpression of DDX20 significantly abrogated the anti-metastatic activity of simvastatin.A similar observation is seen in the mouse model,where simvastatin-injected mice show significantly fewer visible lung metastases compared to placebo-fed mice.IHC staining on these lung tissues showed decreased DDX20 expression in simvastatin-injected group,corroborating our observations in vitro.CONCLUSION DDX20 is a potential surrogate marker for simvastatin treatment response in breast cancer and a long term implication of our findings is the possibility of an effective combinatorial therapeutic intervention using statins(to suppress DDX20 gene expression)and a suitable firstline agent″for the kill″of invasive breast cancer.

Helicase activity and substrate specificity of RecQ5β

RecQ5β is an essential DNA helicase in humans, playing important roles in DNA replication, repair, recombination and transcription. The unwinding activity and substrate specificity of RecQ5β is still elusive. Here, we used stopped-flow kinetic method to measure the unwinding and dissociation kinetics of RecQ5β with several kinds of DNA substrates, and found that RecQ5β could well unwind ss/ds DNA, forked DNA and Holiday junction, but was compromised in unwinding blunt DNA and G-quadruplex. Rec5β has the preferred unwinding specificity for certain DNA substrates containing the junction point, which may improve the binding affinity and unwinding activity of RecQ5β. Moreover, from a comparison with the truncated RecQ5β～（1-467）, we discovered that the C-terminal domain might strongly influence the unwinding activity and binding affinity of RecQ5β. These results may shed light on the physiological functions and working mechanisms of RecQ5β helicase.

Computational biology approach to uncover hepatitis C virus helicase operation

Hepatitis C virus(HCV)helicase is a molecular motor that splits nucleic acid duplex structures during viral replication,therefore representing a promising target for antiviral treatment.Hence,a detailed understanding of the mechanism by which it operates would facilitate the development of efficient drug-assisted therapies aiming to inhibit helicase activity.Despite extensive investigations performed in the past,a thorough understanding of the activity of this important protein was lacking since the underlying internal conformational motions could not be resolved.Here we review investigations that have been previously performed by us for HCV helicase.Using methods of structure-based computational modelling it became possible to follow entire operation cycles of this motor protein in structurally resolved simulations and uncover the mechanism by which it moves along the nucleic acid and accomplishes strand separation.We also discuss observations from that study in the light of recent experimental studies that confirm our findings.

基于公共数据库筛选淋巴特异性解旋酶过表达肺腺癌细胞的差异微小RNA及其关键基因对预后的影响

目的 分析淋巴特异性解旋酶(LSH)在肺腺癌PC9细胞过表达后微小RNA(miRNA)的表达差异,并预测其潜在调控基因。方法 采用高通量测序技术检测LSH过表达的PC9细胞系中的总miRNA,并筛选核质比有差异的候选miRNA,采用实时荧光定量聚合酶链反应(PCR)对候选miRNA的核质比进行验证,应用生物信息学方法对调控基因进行京都基因与基因组百科全书(KEGG)富集分析及基因本位(GO)功能富集分析,构建蛋白质-蛋白质相互作用(PPI)网络对miRNA核靶点进行筛选,利用癌症基因组图谱(TCGA)数据库探究候选靶基因对肺腺癌患者预后的影响。结果 通过对LSH过表达PC9细胞进行测序及基因差异分析,共筛选出5个核质比差异的miRNA:hsa-miRNA-30e-5p、hsa-miRNA-378i、hsa-miRNA-378f、hsa-miRNA-423-5p、hsa-miRNA-4284,其中核内miRNA-4284增加最为显著。经KEGG与GO富集分析发现这些miRNA可能通过结合靶基因参与了RAS信号通路的调控。通过PPI网络及肺癌预后预测发现,差异miRNA可下调CXC趋化因子受体4(CXCR4)表达,增加肺腺癌患者的死亡风险。结论 LSH过表达的肺腺癌PC9细胞核和细胞质中出现多个显著差异表达的miRNA,以核内miRNA-4248变化最为明显,生物信息学分析发现差异miRNA可能通过下调CXCR4的表达增加肺腺癌患者的死亡风险。

猪肺炎支原体解螺旋酶RuvA的原核表达、多克隆抗体制备及活性鉴定

猪肺炎支原体的持续性感染问题频发,同源重组介导的抗原变异扮演重要角色。解螺旋酶RuvA调节霍利迪连接体变构是参与同源重组的关键步骤。鉴于此,本研究旨在原核表达猪肺炎支原体解螺旋酶RuvA重组蛋白,鉴定其DNA结合活性并制备多克隆抗体。试验通过分子克隆构建原核表达质粒pET21a-RuvA,经诱导表达和纯化获得RuvA M hp重组蛋白;免疫家兔制备抗RuvA M hp多克隆抗体,再利用间接ELISA和Western blot试验进行效价测定和特异性验证;利用凝胶迁移试验结合表面等离子共振技术分析RuvA M hp的DNA结合活性;利用凝胶迁移试验结合Western blot试验鉴定RuvA M hp的寡聚特性。结果显示:原核表达的RuvA M hp重组蛋白约为26 ku;制备的抗RuvA M hp多克隆抗体效价为1∶256000,且具有良好的特异性;RuvA M hp具有较强的DNA结合活性,对霍利迪连接体的亲和力高达624.4 pmol·L^(-1)(K D),并且主要以八聚体形式与其形成稳定复合物。通过RuvA M hp的原核表达、多克隆抗体制备及活性鉴定,为后续探索RuvA调解同源重组介导猪肺炎支原体抗原变异的分子机制奠定了基础。