细胞内部核糖体进入位点研究进展

细胞内部核糖体进入位点(IRES)mRNA5’端非编码区的一段特殊的序列,它允许核糖体不从mRNA的5’到3’端阅读而直接在此序列处结合mRNA并起始翻译。本综述了IRES的发现、IRES的识别及细胞IRES的特征、作用机理、生物学意义及其生物学应用等方面的研究进展。     

雌激素受体2（ESR2）mRNA 5′非翻译区内部核糖体进入位点活性的鉴定与分析

真核生物除了传统的帽依赖型翻译机制外,还存在内部核糖体进入位点（internal ribosome entry site, IRES）介导的翻译机制。雌激素受体2（estrogen receptor 2, ESR2）是雌激素受体家族成员之一,其编码的蛋白质在许多肿瘤中发挥重要的作用。ESR2蛋白的异常表达会导致众多肿瘤的发生,但其蛋白质翻译水平的调控机制至今仍不清楚。研究发现,在药物刺激的条件下,乳腺癌细胞MCF7/WT中ESR2蛋白的表达提高,但是其转录水平基本未见发生改变。猜测ESR2 mRNA 5′非翻译区（5′ untranslated region, 5′ UTR）具有IRES活性。为了验证ESR2 mRNA 5′ UTR是否具有IRES元件,将ESR2 mRNA 5′ UTR插入到双顺反子报告基因载体（pRF）中,构建pRL-ESR2-FL重组质粒载体,将其瞬时转染到HEK293细胞。结果发现,ESR2 mRNA 5′ UTR有假定的IRES活性。并且通过3个排除实验验证了ESR2 IRES活性与其5′ UTR中的内部潜在启动子（P<0.0001）、内部剪切位点以及核糖体通读无关。进一步对其序列进行截短研究发现,ESR2 IRES活性发挥的关键区域是3′端的439～468 nt,且ESR2 IRES最大活性的发挥依赖于5′ UTR序列的完整性。并且发现,ESR2 IRES活性的发挥不但需要特定的一级核酸序列,还要有稳定的二级茎环结构。此研究有望为ESR2蛋白调控的相关疾病提供新的药物治疗靶点。     

脑心肌炎病毒(EMCV)的内部核糖体进入位点活性的研究

脑心肌炎病毒(Encephalomyocarditis virus ,EMCV)的内部核糖体进入位点(internal ribosomal entry site ,IRES)已被广泛运用于蛋白的表达中,如应用于Clontech 公司推出的pIRES2 质粒对增强型绿色荧光蛋白(EGFP)的表达。但是由于对EMCV的IRES了解还不够深入而在利用EMCV的IRES进行基因表达过程中经常会遇到问题,很有必要对其进行更深入的研究。以红绿色荧光蛋白基因作为报告基因,通过分子克隆、荧光显微镜、荧光分光光度计、Western blot等分子细胞生物学手段,对EMCV的IRES末端序列与其活性的关系进行了深入研究。研究发现EMCV的IRES末端序列对其IRES的活性影响极大,而人们常用的报告基因EGFP本身也可能存在IRES。     

RNA病毒翻译调控元件—内部核糖体进入位点(IRES)

真核生物大多数蛋白质合成采用了依赖帽子结构的翻译起始方式.但一组缺乏帽子构的RNA病毒的蛋白质合成起始是依赖其5′端非翻译区（untranslated region,UTR）翻译调控的顺式作用元件——内部核糖体进入位点（internal ribosome entry site, IRES）.它 们能够在一些反式作用因子的辅助下,招募核糖体小亚基到病毒mRNA的翻译起始位点.前,依赖IRES元件翻译起始的RNA病毒在哺乳动物,无脊椎动物及植物中均有发现.因此,对RNA病毒IRES元件的深入研究,不仅有助于阐明相关疾病的发生机理,而且为工业应用和疾病治疗提供借鉴意义.本文对RNA病毒IRES元件发现、分类、结构与功能等作了综述.     

IRES介导的非帽依赖翻译调控研究进展

内部核糖体进入位点(Internal ribosome entry site, IRES)是一种存在于RNA内部的特殊功能元件,其可在不依赖5’端帽子结构的情况下直接招募核糖体启动蛋白翻译,已被发现与多种细胞过程密切相关。近来,越来越多的证据表明IRES在环形RNA翻译调控中扮演着极其重要的角色,由此IRES引起人们的极大关注。本文针对目前真核细胞中IRES介导的翻译调控机制进行了综述,并对IRES元件相关生物信息学工具进行了总结。     

基于FMDV IRES的双顺反子载体的构建及体外表达分析

利用RT-PCR扩增出口蹄疫病毒小核糖体进入位点（IRES）序列,并定向克隆进pcDNA3.1(+)载体,构建成双顺反子真核表达载体。为了验证该载体是否能够转录出双顺反子mRNA,在IRES起始密码（ATG）下游正确插入增强型的绿色荧光蛋白基因（egfp）,把重组质粒转染BHK-21细胞,培养20～48 h,在紫外显微镜下观察,能够看到典型的绿色荧光,表明载体能够体能够利用FMDV的IRES能够介导非帽依赖性表达外源基因。并通过流式细胞仪,与同样是CMV启动转录egfp的pGFPN1质粒在细胞中的表达的水平进行了比较。该载体的成功构建为体外表达双基因、双顺反子逆转录载体构建以及相关应用奠定基础,并有作为基因疫苗和标记定位基因治疗载体的潜力。     

HCV内部核糖体进入位点(IRES)结构域Ⅲ中连接点的位置对其三级结构形成的影响

丙型肝炎病毒(HCV)结构含有一个内部核糖体进入位点(IRES);该位点是一段高度保守序列,坐落于mRNA的5'-非翻译区域(5'-UTR).目前,对IRES的三级结构及相关功能研究较少.本实验通过聚丙烯酰胺凝胶电泳和放射显影技术,研究在不同离子浓度、不同RNA浓度条件下,IRES结构域Ⅲ的连接点(junction)在不同位置时对结构域Ⅲ形成的影响,以及不同的结构域Ⅱ与结构域Ⅲ的相互作用关系.实验结果表明,HCV的IRES结构域Ⅲ连接点位置对结构域Ⅲ的形成至关重要,连接点位置不同,则结构域Ⅲ形成的结构不同.因此,在HCV的疫苗和相关药物设计中,可以针对结构域Ⅲ连接点进行研究,使之成为疫苗或药物作用靶点.     

转录激活因子1(ATF1)内部核糖体进入位点的鉴定及活性分析

蛋白质翻译起始通常有两种机制,一是依赖帽结构的翻译,另一种是依赖5′非翻译区的内部核糖体进入位点(IRES).在后一种方式中,在某些IRES反式作用因子,如La蛋白、多聚嘧啶串结合蛋白1等的参与下,直接招募核糖体小亚基到mRNA的翻译起始位点,启始翻译.研究发现,参与细胞生长、分化、细胞周期进程、凋亡和压力调控的相关蛋白中通常含有IRES元件.基于功能,我们提出假说：转录激活因子1(ATF1)的5′-UTR可能具有IRES活性.为验证假说,首先构建了含全长ATF1 5′-UTR的双荧光素酶报告质粒|质粒转染结合报告酶活性分析显示,ATF1 5′-UTR在Bel7402、HCT-8和HEK293细胞中表现出不同的IRES活性|而此IRES活性与5′-UTR中的隐藏启动子无关.同时还发现,ATF1 5′-UTR在NIH3T3细胞中却没有IRES活性.与此结果相一致,Western印迹检测ATF1在这几种细胞系中的表达.结果显示,Bel7402、HCT 8和HEK293中ATF1蛋白质表达水平较高,而在NIH3T3中却极低. ATF1 5′-UTR的系列5′-删除突变及报告酶分析证明,ATF1 5′-UTR的完整性对其IRES活性大小发挥重要作用|其中5′端的204 bp序列对其IRES活性贡献较大. RNA-蛋白免疫共沉淀实验揭示,ATF1 5′-UTR可与La和PTBP1蛋白结合|抑制La和PTBP1蛋白质的表达,并可减低HEK293细胞中ATF1蛋白质表达水平.这些结果提示,La和PTBP1蛋白（两种ITAFs）为ATF1 5′-UTR发挥IRES活性所必需.总之,上述结果证明,ATF1 5′-UTR具有IRES活性,其活性发挥依赖与La和PTBP1蛋白的结合.上述发现为进一步研究La和PTBP1表达及亚细胞定位对ATF1 IRES调控机制的影响奠定了基础.     

内部核糖体进入位点（IRES）调控细胞血清饥饿应激条件下PRDM13的翻译

PRDM13是锌指蛋白转录抑制因子（positive regulatory domain zinc finger protein,PRDM) 家族中的一员,其在细胞分化、肿瘤的发生和恶性转化中起着重要的作用。而对于PRDM13 基因侧翼序列是否含有内部核糖体进入位点(internal ribosome entry site, IRES）及其功能所知甚少。本研究对PRDM13 5′端的非翻译区（5′UTR）进行IRES结构与功能分析,探索其在细胞血清饥饿应激条件下对PRDM13翻译的影响。实验发现,在血清饥饿的条件下,肝癌细胞Bel7402/WT中PRDM13的蛋白质水平增加,但是其mRNA水平基本没有变化。将PRDM13 5′UTR的序列插入双顺反子的报告载体(pRL-FL)中,并且将构建的载体(pRL-PRDM13-FL）转染进细胞中,结果显示,PRDM13 5′UTR含有IRES,且发现PRDM13 5′UTR中的105 nt（53～157）对其IRES的功能至关重要。在帽依赖的翻译（cap-dependent translation）机制被抑制时,IRES这种机制可有效维持PRDM13蛋白合成。本研究提供了在细胞压力条件下调节PRDM13蛋白合成的一种新的解释。     

病毒IRES的结构及IRES介导的蛋白质翻译研究进展

核糖体进入位点(internal ribosome entry sites,IRES)常见于许多正链RNA病毒基因组以及部分细胞基因.在营养缺乏、内质网应激、缺氧和病毒感染等不利条件下,细胞翻译也能够从经典的帽子依赖型翻译转换为依赖于IRES的翻译机制.事实上,自IRES被发现以来,其相关的翻译机制调控被认为是病毒感染...     

Translational efficiency of EMCV IRES in bicistronic vectors is dependent upon IRES sequence and gene location

The internal ribosomal entry site (IRES)from encephalomyocarditis virus (EMCV) is a popular RNA element used widely in experimental and pharmaceutical applications to express proteins in eukaryotic cells or cell-free extracts. Inclusion of the wild-type element in monocistronic or bicistronic messenger RNAs (mRNAs) confers a high level of cap-independent translation activity to appropriately configured cistrons. The history of this element and the experimental consequences of sequence derivations inherent to commercial IRES vectors are less well known. Compared head-to-head with dual-luciferase reporter constructs, a native EMCV IRES in a bicistronic configuration directed 8- to 10-fold more protein than a similarly configured pIRES vector. It also produced nearly twice as much protein as pCITE-1, an early monocistronic iteration, harboring a suboptimal A7 sequence in a crucial structural motif The results indicate that investigators should be aware of and carefully report the sequence of their IRES in any comparative study. The preferred IRES (viral bases 273-845) and the minimum IRES (viral bases 400-836) for optimum activity are illustrated.     

Identification of the TXNIP IRES and characterization of the impact of regulatory IRES trans-acting factors

Translation is a tightly regulated process and is predominantly controlled at the level of its initiation. Translation initiation mostly occurs in a cap-dependent manner. Under stress conditions when cap-dependent translation is hampered, internal ribosome entry sites (IRESes) allow for cap-independent translation of certain mRNAs. IRES-dependent translation is commonly regulated by RNA-interacting proteins, known as IRES trans-acting factors (ITAFs). In the present study, we found the 5′ untranslated region (UTR) of the thioredoxin-interacting protein (TXNIP) mRNA to be bound by the ITAF hnRNPA1. Upon verification of an IRES element within the 5′UTR of TXNIP, we determined additional interacting proteins, which predominantly appeared to interact with the IRES-regulatory second half of the 5′UTR. Amongst these PTB emerged as an inhibitory ITAF, whereas FBP3 and GEMIN5 appeared to contain TXNIP IRES-enhancing properties. In summary, we identified and characterized a novel IRES within the 5′UTR of TXNIP, which is regulated by the ITAFs PTB, FBP3, and GEMIN5.     

Functional and Structural Analysis of Maize Hsp101 IRES

Maize heat shock protein of 101 KDa (HSP101) is essential for thermotolerance induction in this plant. The mRNA encoding this protein harbors an IRES element in the 5′UTR that mediates cap-independent translation initiation. In the current work it is demonstrated that hsp101 IRES comprises the entire 5′UTR sequence (150 nts), since deletion of 17 nucleotides from the 5′ end decreased translation efficiency by 87% compared to the control sequence. RNA structure analysis of maize hsp101 IRES revealed the presence of three stem-loops toward its 5′ end, whereas the remainder sequence contains a great proportion of unpaired nucleotides. Furthermore, HSP90 protein was identified by mass spectrometry as the protein preferentially associated with the maize hsp101 IRES. In addition, it has been found that eIFiso4G rather than eIF4G initiation factor mediates translation of the maize hsp101 mRNA.     

NRF IRES activity is mediated by RNA binding protein JKTBP1 and a 14-nt RNA element

The mRNA of human NF-kappaB repressing factor (NRF) contains a long 5'-untranslated region (UTR) that directs ribosomes to the downstream start codon by a cap-independent mechanism. Comparison of the nucleotide (nt) sequences of human and mouse NRF mRNAs reveals a high degree of identity throughout a fragment of 150 nt proximal to the start codon. Here, we show that this region constitutes a minimal internal ribosome entry segment (IRES) module. Enzymatic RNA structure analysis reveals a secondary structure model of the NRF IRES module. Point mutation analysis of the module determines a short, 14-nt RNA element (nt 640-653) as a mediator of IRES function. Purification of IRES binding cellular proteins and subsequent ESI/MS/MS sequence analysis led to identification of the RNA-binding protein, JKTBP1. EMSA experiments show that JKTBP1 binds upstream to the 14-nt RNA element in the NRF IRES module (nt 579-639). Over-expression of JKTBP1 significantly enhances activity of the NRF IRES module in dicistronic constructs. Moreover, siRNA experiments demonstrate that down-regulation of endogenous JKTBP1 decreases NRF IRES activity and the level of endogenous NRF protein. The data of this study show that JKTBP1 and the 14-nt element act independently to mediate NRF IRES activity.     

Viral IRES Prediction System - a Web Server for Prediction of the IRES Secondary Structure In Silico

The internal ribosomal entry site (IRES) functions as cap-independent translation initiation sites in eukaryotic cells. IRES elements have been applied as useful tools for bi-cistronic expression vectors. Current RNA structure prediction programs are unable to predict precisely the potential IRES element. We have designed a viral IRES prediction system (VIPS) to perform the IRES secondary structure prediction. In order to obtain better results for the IRES prediction, the VIPS can evaluate and predict for all four different groups of IRESs with a higher accuracy. RNA secondary structure prediction, comparison, and pseudoknot prediction programs were implemented to form the three-stage procedure for the VIPS. The backbone of VIPS includes: the RNAL fold program, aimed to predict local RNA secondary structures by minimum free energy method; the RNA Align program, intended to compare predicted structures; and pknotsRG program, used to calculate the pseudoknot structure. VIPS was evaluated by using UTR database, IRES database and Virus database, and the accuracy rate of VIPS was assessed as 98.53%, 90.80%, 82.36% and 80.41% for IRES groups 1, 2, 3, and 4, respectively. This advance useful search approach for IRES structures will facilitate IRES related studies. The VIPS on-line website service is available at http://140.135.61.250/vips/.     

Structural features of the Seneca Valley virus internal ribosome entry site (IRES) element: a picornavirus with a pestivirus-like IRES

The RNA genome of Seneca Valley virus (SVV), a recently identified picornavirus, contains an internal ribosome entry site (IRES) element which has structural and functional similarity to that from classical swine fever virus (CSFV) and hepatitis C virus, members of the Flaviviridae. The SVV IRES has an absolute requirement for the presence of a short region of virus-coding sequence to allow it to function either in cells or in rabbit reticulocyte lysate. The IRES activity does not require the translation initiation factor eIF4A or intact eIF4G. The predicted secondary structure indicates that the SVV IRES is more closely related to the CSFV IRES, including the presence of a bipartite IIId domain. Mutagenesis of the SVV IRES, coupled to functional assays, support the core elements of the IRES structure model, but surprisingly, deletion of the conserved IIId(2) domain had no effect on IRES activity, including 40S and eIF3 binding. This is the first example of a picornavirus IRES that is most closely related to the CSFV IRES and suggests the possibility of multiple, independent recombination events between the genomes of the Picornaviridae and Flaviviridae to give rise to similar IRES elements.     

A selection system for functional internal ribosome entry site (IRES) elements: analysis of the requirement for a conserved GNRA tetraloop in the encephalomyocarditis virus IRES.

Picornavirus internal ribosome entry site (IRES) elements direct cap-independent internal initiation of protein synthesis within mammalian cells. These RNA elements (about 450 nt) contain extensive secondary structure including a hairpin loop with a conserved GNRA motif. Such loops are important in RNA-RNA and RNA-protein interactions. Plasmids that express dicistronic mRNAs of the structure GUS/IRES/HOOK have been constructed. The HOOK sequence encodes a cell-surface-targeted protein (sFv); the translation of this open reading frame within mammalian cells from these dicistronic mRNAs requires a functional IRES element. Cells that express the sFv can be selected from nonexpressing cells. A pool of up to 256 mutant encephalomyocarditis virus IRES elements was generated by converting the wild-type hairpin loop sequence (GCGA) to NNNN. Following transfection of this pool of mutants into COS-7 cells, plasmids were recovered from selected sFv-expressing cells. These DNAs were amplified in Escherichia coli and transfected again into COS-7 cells for further cycles to enrich for plasmids encoding functional IRES elements. The sequence of individual selected IRES elements was determined. All functional IRES elements had a tetraloop with a 3' terminal A residue. Optimal IRES activity, assayed in vitro and within cells, was obtained from plasmids encoding an IRES with the hairpin loop sequence fitting a RNRA consensus. In contrast, IRES elements containing YCYA tetraloops were severely defective.