A mechanical explanation of RNA pseudoknot function in programmed ribosomal frameshifting

The triplet-based genetic code requires that translating ribosomes maintain the reading frame of a messenger RNA faithfully to ensure correct protein synthesis. However, in programmed -1 ribosomal frameshifting, a specific subversion of frame maintenance takes place, wherein the ribosome is forced to shift one nucleotide backwards into an overlapping reading frame and to translate an entirely new sequence of amino acids. This process is indispensable in the replication of numerous viral pathogens, including HIV and the coronavirus associated with severe acute respiratory syndrome, and is also exploited in the expression of several cellular genes. Frameshifting is promoted by an mRNA signal composed of two essential elements: a heptanucleotide 'slippery' sequence and an adjacent mRNA secondary structure, most often an mRNA pseudoknot. How these components operate together to manipulate the ribosome is unknown. Here we describe the observation of a ribosome-mRNA pseudoknot complex that is stalled in the process of -1 frameshifting. Cryoelectron microscopic imaging of purified mammalian 80S ribosomes from rabbit reticulocytes paused at a coronavirus pseudoknot reveals an intermediate of the frameshifting process. From this it can be seen how the pseudoknot interacts with the ribosome to block the mRNA entrance channel, compromising the translocation process and leading to a spring-like deformation of the P-site transfer RNA. In addition, we identify movements of the likely eukaryotic ribosomal helicase and confirm a direct interaction between the translocase eEF2 and the P-site tRNA. Together, the structural changes provide a mechanical explanation of how the pseudoknot manipulates the ribosome into a different reading frame.     

Pol of gag-pol fusion protein required for encapsidation of viral RNA of yeast L-A virus.

Double-stranded RNA viruses have an RNA-dependent RNA polymerase activity associated with the viral particles which is indispensable for their replication cycle. Using the yeast L-A double-stranded RNA virus we have investigated the mechanism by which the virus encapsidates its genomic RNA and RNA polymerase. The L-A gag gene encodes the principal viral coat protein and the overlapping pol gene is expressed as a gag-pol fusion protein which is formed by a -1 ribosomal frameshift. Here we show that Gag alone is sufficient for virus particle formation, but that it fails to package the viral single-stranded RNA genome. Encapsidation of the viral RNA requires only a part of the Pol region (the N-terminal quarter), which is presumably distinct from the RNA polymerase domain. Given that the Pol region has single-stranded RNA-binding activity, these results are consistent with our L-A virus encapsidation model: the Pol region of the fusion protein binds specifically to the viral genome (+) strand, and the N-terminal gag-encoded region primes polymerization of Gag to form the capsid, thus ensuring the packaging of both the viral genome and the RNA polymerase.     

Leaky +1 and -1 frameshift mutations at the same site in a yeast mitochondrial gene

Two mutations in a mitochondrial structural gene, which cause leaky premature polypeptide chain termination and leaky growth, are +1 and -1 frameshifts in the same run of five T residues. The partial restoration of reading frame is probably due to ribosomal frameshifting at this site, and may be promoted by the unique structure of the yeast mitochondrial t RNAPhe.     

Cardioviral internal ribosomal entry site is functional in a genetically engineered dicistronic poliovirus.

High mutation rates have driven RNA viruses to shorten their genomes to the minimum possible size. Mammalian (+)-strand RNA viruses and retroviruses have responded by reducing the number of cis-acting regulatory elements, a constraint that has led to the emergence of the polyprotein. Poliovirus is a (+)-stranded picornavirus whose polyprotein, encoded by an open reading frame spanning most of the viral RNA, is processed by virus-encoded proteinases. Despite their genetic austerity, picornaviruses have retained long 5' untranslated regions, which harbour cis-acting elements that promote initiation of translation independently of the uncapped 5' end of the viral messenger RNA. These elements are termed 'internal ribosomal entry sites' and are formed from highly structured RNA segments of at least 400 nucleotides. How these elements function is not known, but special RNA-binding proteins may be involved. The ribosome or its 40S subunit probably binds at or near a YnXmAUG motif (where Y is a pyrimidine and X is a purine) at the 3' border of the internal ribosomal entry site, which either provides the initiating codon or enables the ribosome to translocate to one downstream (E.W. et al., submitted). Initiation from most eukaryotic messenger RNAs usually occurs by ribosomal recognition of the 5' and subsequent scanning to the AUG codon. Here we describe a genetic strategy for the dissection of polyproteins which proves that an internal ribosomal entry site element can initiate translation independently of the 5' end.     

牛泡沫病毒LTR的反式激活因子靶序列研究

牛泡沫病毒（ＢＦＶ）是反转录病毒科泡沫病毒属成员之一．其基因组除编码ｇａｇ,ｐｏｌ,ｅｎｖ三个结构基因外,在ｅｎｖ和３＇ＬＴＲ之间有２个ＯＲＦ（ＯＲＦ－１和ＯＲＦ－２）,编码自身的反式激活因子Ｔａｓ等调节蛋白．本研究利用我们实验室分离鉴定的ＢＦＶ３０２６中国毒株［１２］为材料,克隆Ｏｒｆ－１基因,构建ｐＢＦＶＯＲＦ－１表达质粒,通过带有ｌｕｃ基因的ＬＴＲ系列缺失质粒与ｐＢＦＶＯＲＦ－１共转染,瞬时表达分析结果将ＢＦＶＬＴＲ上Ｔａｓ应答元件（ＴＲＥ）定位于－９８３／－６６８（ＴＲＥＩ）,－４７０／－１４０（ＴＲＥＩ）和ＲＵ５区．其中ＴＲＥＩ、ＴＲＥＩＩ为正调控区域,ＲＵ５为负调控区域,并进一步证明ＲＵ５在异源启动子（ＢＩＶＬＴＲ）上具有抑制其下游基因表达的功能．这些结果表明ＢＦＶＴａｓ作用机理与慢病毒（Ｔａｔ）,致瘤病毒（Ｔａｘ）等均不相同     

Cloning of a gene that is rearranged in patients with choroideraemia

Choroideraemia (tapetochoroidal dystrophy, TCD), a common form of X-linked blindness, is characterized by progressive dystrophy of the choroid, retinal pigment epithelium and retina. Previous studies have assigned the TCD gene to a small segment of the Xq21 band. By making use of reverse genetics strategies we have isolated eight overlapping complementary DNA clones from the same chromosomal region. The corresponding gene is expressed in retina, choroid and retinal pigment epithelium. The cDNAs encompass an open reading frame of 948 base pairs that is structurally altered in eight TCD patients with deletions, and in a female patient with a balanced translocation involving Xq21. These findings provide strong evidence that we have cloned the gene underlying choroideraemia. Elucidation of its function should provide new insights into the molecular mechanisms responsible for this disorder and other hereditary retinopathies.     

A structural model for the retroviral proteases

In many retroviruses the 5' end of the pol gene codes for a protease vital for the processing of the gag polyprotein into the separate core proteins. In some viruses this protease is encoded at the 3' end of the gag gene, or between the gag and pol genes in a different reading frame to either. A sequence, Asp-Thr-Gly, which is conserved in retroviral proteases is also conserved in the active sites of aspartic proteases, an observation which has led to the suggestion that the retroviral proteases could belong to this family. We have examined the sequences of the aspartic and retroviral protease families, using pattern-recognition, structure prediction and molecular modelling techniques, and conclude that the viral protease sequences probably correspond to a single domain of an aspartic protease and may function in a dimeric form. We have constructed a model of the pol-protease of human immunodeficiency virus 1 (HIV-1) to test this hypothesis.     

小拟南芥几丁质酶基因cDNA的克隆与序列分析

通过合成1对特异引物，应用RT-PCR技术从小拟南芥总RNA中经反转录克隆出几丁质酶基因，该cDNA基因全长985bp，含有1个963bp的开放阅读框(ORF)，编码321个氨基酸，推测分子量为35．53kD，序列同源性分析表明，该基因与拟南芥几丁质酶基因有93％的同源性。     

生物信息学技术克隆并分析新基因STRF7

为进一步研究信号转导相关的新基因片段BE644250,采用生物信息学方法克隆基全长cDNA,并分析了其ORF,电子表达谱,染色体定位等,之后对全长序列进行了实验验证。电子延伸（contig)获得了729bp的延伸产物,含一个典型的74aa的ORF,命名为STRF7。与已知蛋白无明显同源性,部分地相似于人的源框蛋白CDX－4和酵母的转录调节子ADR6,属一新发现的基因;RT－PCR从IL－6刺激后的U937中克隆了STRF7基因,基序列与电子延伸结果安全一致,进一步的分析显示STRF7在多种组织中表达并定位于第6号染色体上,上述结果显示,STRF7是一个新基因,编码含74aa的蛋白,并且是一个潜在的转录因子。