3′-半分子5′-末端双链结构阻止tRNA连接酶酶促反应

用定点突变技术将不同核苷酸引入酵母苯丙氨酸tRNA反密码子环32,37和38位.体外转录制备tRNA前体,其32,37和38位的核苷酸与野生型tRNA前体相应位点的核苷酸不同.用纯化的酵母tRNA内切酶和tRNA连接酶对这些tR-NA前体进行剪接加工.结果说明,这些位点的核苷酸不仅影响tRNA内切酶对tR-NA前体的酶切效率,而且3’-半分子5’-末端双链结构阻止tRNA连接酶将相应的tRNA半分子连接成整分子tRNA.     

与内含子相邻的核苷酸是tRNA内切酶的识别特征

含有内含子的tRNA前体必须经过剪接反应加工成熟.顺序比较指出与内含子顺序相邻的核苷酸有一定的特异性.用寡核苷酸定点突变技术改变这2个位点的核苷酸,确定这些tRNA前体的剪接效率.结果如下:当37位和38位都是嘌呤核苷酸时,tRNA内切酶能够有效地酶切酵母 tRNA~(phe)前体;如果其中的 1个位点变成嘧啶核苷酸,但另1个位点的核苷酸是野生型的嘌呤核苷酸,tRNA前体的酶切效率将降低.如果2个位点的核苷酸都发生变异,其中1个是嘧啶核苷酸,另1个是变异的嘌呤核苷酸,tRNA前体的酶切效率就会进一步降低.如果2个位点都是嘧啶核苷酸,tRNA前体就难以为tRNA内切酶酶切了.由此提出,与内含子相邻的核苷酸也是tRNA由切酶识别的结构特征.tRNA前体的37位和38位核苷酸的改变可能影响剪接位点之间的距离或它们的精细结构,从而影响tRNA内切酶酶切的效率.     

tRNase Z核酸内切酶的研究进展

tRNase Z是一种核酸内切酶,许多细菌、大多数真核生物以及所有的古细菌的tRNA3’末端加工过程都是由核酸内切酶tRNase Z催化的。tRNase Z能催化缺乏CCA的tRNA前体生成末尾带有核苷酸识别的3’-OH和5’磷酸尾巴的成熟tRNA。这对于CCA序列的添加、tRNA的氨酰化和蛋白质的合成十分重要。tRNase Z属于metallo-β-lactamases(MBL)超家族,存在短(tRNase ZS)和长(tRNase ZL)两种形式,具有tRNA 3’末端加工、引导定位蛋白、加工rRNA、与Rex2P的相互作用、调节细胞分化与分裂等功能。预期对tRNaseZ的功能和属性不断深入研究将会对AIDS和前列腺癌的治疗具有潜在和实际的推动作用。     

tRNA衍生片段和tRNA半分子的生物学功能及其在疾病发生中的作用

tRNA衍生片段(tRNA-derived RNA fragment,t RF)和tRNA半分子(tRNA halves,ti RNA)由成熟tRNA或其前体tRNA在不同位点特异性剪切产生,它们是一类广泛存在于原核生物和真核生物转录组中的非编码小RNA分子.t RF主要有tRF-5、tRF-3和tRF-1等3亚类,分别来自成熟tRNA的D环至反密码环茎区间切割至5′端、T环开始至3′端和前体tRNA的3′端尾部,其长度为14~30个核苷酸(nucleotide,nt).ti RNA主要有5′ti RNA和3′ti RNA等2亚类,是在成熟tRNA反密码子环处切割分别产生,其长度为29~50 nt.t RF和ti RNA具有多种生物学功能,既可以在应激反应中作为信号分子,又可以作为基因表达的调节者.它们与人类多种疾病(如肿瘤、神经退行性疾病、代谢性疾病和传染病等)的发生密切相关,有希望成为疾病诊断的新型标志物.本文就t RF和ti RNA的分类、生物学功能以及与人类疾病的关系作一综述.     

RtcB功能的研究进展

RtcB是后生动物中一种重要的RNA连接酶,能完成2′,3′-环磷酸酯和5′-羟基末端的连接。在tRNA的成熟和XBP1 mRNA的剪接中起着重要的作用。它可以连接tRNA成熟过程中产生的2′,3′-环磷酸末端和5′-羟基末端,从而产生成熟的tRNA。另外,可以连接XBP1前体mRNA产生成熟的XBP1 mRNA,调节UPR反应,从而维持内质网稳态。另外,RtcB对动物胚胎发育和抗体分泌具有重要调节作用,并且与多种神经性疾病的发生密切相关。本文将对RtcB的发现、连接酶功能以及生理功能进行综述,为以后更好地研究其功能及相关机制打下基础。     

氨酰tRNA合成酶的分子网络和功能

氨酰tRNA合成酶是生命进化过程中最早出现的一类蛋白质,氨酰tRNA合成酶帮助氨基酸转移到相应的tRNA上,进而参与蛋白质的合成保证了生命体的严谨性和多样性.随着后基因组时代的到来,氨酰tRNA合成酶的结构和功能成为新的研究热点.结构生物学和生物信息学的研究结果表明,氨酰tRNA合成酶在真核生物体内以多聚复合物的形式行使功能,形成复杂的分子网络体系.最新的实验证据显示,氨酰tRNA合成酶不但是蛋白质合成过程中一类最重要的酶,而且参与了转录、翻译水平的调控、RNA剪接、信号传导和免疫应答等众多生命活动.     

人类线粒体tRNA生物合成与线粒体疾病

线粒体是普遍存在于真核细胞中的一类细胞器.每个线粒体含有多个拷贝的闭合环状双链DNA. 人类线粒体DNA (mitochondrial DNA, mtDNA)共编码22种线粒体tRNA(mitochondrial tRNA,mt tRNA), 2种rRNA 及13种多肽.mt tRNA独特的结构特点决定了它们与具有典型三叶草结构的细胞质 tRNA不同.编码mt tRNA的基因突变频率较高,这可能是引起线粒体功能障碍的主要原因之一. 同时 ,这与很多病理现象相关.目前发现,大量与mt tRNA生物代谢和功能相关的核因子包括加工内切酶、 tRNA修饰酶和氨酰-tRNA合成酶.这些核因子的异常导致了疾病相关的tRNA致病突变.由此可见mt tRNA功能对于线粒体活性的重要性.     

真核生物核酸外切体(exosome)的研究进展

RNA的加工和降解是调控基因时空表达的重要步骤,在调节生物体的生长和发育过程中起着至关重要的作用.几乎所有的RNA都是从一条长的前体加工处理而来,形成成熟的RNA发挥功能,之后进行降解.RNA的降解需要5′-3′核酸外切酶、3′-5′核酸外切酶及核酸内切酶的参与.在真核细胞中,部分3′-5′核酸外切酶所进行的RNA降解依赖于一种称为核酸外切体(exosome)的复合物.该复合物由9个核心蛋白亚基组成,已有的证据表明,其广泛参与了动物、酵母及植物体中多种RNA的加工和降解过程.本文综述了真核生物中核酸外切体的研究进展,讨论了该复合体在RNA加工降解过程中的作用机制.     

真核细胞tRNA的降解

tRNA在蛋白质合成过程中起着关键性的作用,不但为三联密码子翻译成氨基酸提供了接合体,而且为将氨基酸运送到核糖体提供了运送载体.在真核细胞中,tRNA前体必须经过广泛的加工修饰,成为成熟的tRNA分子才能充分发挥生物学功能.以往对tRNA的研究主要集中于tRNA的结构、功能、加工和成熟上,却很少关注tRNA分子的降解.最近研究发现tRNA的降解在tRNA的生成、加工和功能发挥上同样起着重要作用.     

十字花科黑腐病菌中存在tRNA衍生片段(tRF)的证据

tRNA衍生片段(tRNA-derived fragment,tRF)是一种由内切核糖核酸酶将初级tRNA(primary tRNA)或成熟tRNA分子剪切后形成的长度为14～30 nt(核苷酸)的稳定的RNA片段.研究表明,tRF广泛存在于各种真核生物中,它们既可以作为信号分子,又可以作为基因表达的调控因子,在细胞的...     

Arabidopsis Encodes Four tRNase Z Enzymes

Functional transfer RNA (tRNA) molecules are a prerequisite for protein biosynthesis. Several processing steps are required to generate the mature functional tRNA from precursor molecules. Two of the early processing steps involve cleavage at the tRNA 5′ end and the tRNA 3′ end. While processing at the tRNA 5′ end is performed by RNase P, cleavage at the 3′ end is catalyzed by the endonuclease tRNase Z. In eukaryotes, tRNase Z enzymes are found in two versions: a short form of about 250 to 300 amino acids and a long form of about 700 to 900 amino acids. All eukaryotic genomes analyzed to date encode at least one long tRNase Z protein. Of those, Arabidopsis (Arabidopsis thaliana) is the only organism that encodes four tRNase Z proteins, two short forms and two long forms. We show here that the four proteins are distributed to different subcellular compartments in the plant cell: the nucleus, the cytoplasm, the mitochondrion, and the chloroplast. One tRNase Z is present only in the cytoplasm, one protein is found exclusively in mitochondria, while the third one has dual locations: nucleus and mitochondria. None of these three tRNase Z proteins is essential. The fourth tRNase Z protein is present in chloroplasts, and deletion of its gene results in an embryo-lethal phenotype. In vitro analysis with the recombinant proteins showed that all four tRNase Z enzymes have tRNA 3′ processing activity. In addition, the mitochondrial tRNase Z proteins cleave tRNA-like elements that serve as processing signals in mitochondrial mRNA maturation.     

Structural characterization of the catalytic subunit of a novel RNA splicing endonuclease

The RNA splicing endonuclease is responsible for recognition and excision of nuclear tRNA and all archaeal introns. Despite the conserved RNA cleavage chemistry and a similar enzyme assembly, currently known splicing endonuclease families have limited RNA specificity. Different from previously characterized splicing endonucleases in Archaea, the splicing endonuclease from archaeum Sulfolobus solfataricus was found to contain two different subunits and accept a broader range of substrates. Here, we report a crystal structure of the catalytic subunit of the S.solfataricus endonuclease at 3.1 angstroms resolution. The structure, together with analytical ultracentrifugation analysis, identifies the catalytic subunit as an inactive but stable homodimer, thus suggesting the possibility of two modes of functional assembly for the active enzyme.     

tRNA 3' end maturation in archaea has eukaryotic features: the RNase Z from Haloferax volcanii

Here, we report the first characterization and partial purification of an archaeal tRNA 3' processing activity, the RNase Z from Haloferax volcanii. The activity identified here is an endonuclease, which cleaves tRNA precursors 3' to the discriminator. Thus tRNA 3' processing in archaea resembles the eukaryotic 3' processing pathway. The archaeal RNase Z has a KCl optimum at 5mM, which is in contrast to the intracellular KCl concentration being as high as 4M KCl.The archaeal RNase Z does process 5' extended and intron-containing pretRNAs but with a much lower efficiency than 5' matured, intronless pretRNAs. At least in vitro there is thus no defined order for 5' and 3' processing and splicing. A heterologous precursor tRNA is cleaved efficiently by the archaeal RNase Z. Experiments with precursors containing mutated tRNAs revealed that removal of the anticodon arm reduces cleavage efficiency only slightly, while removal of D and T arm reduces processing effciency drastically, even down to complete inhibition. Comparison with its nuclear and mitochondrial homologs revealed that the substrate specificity of the archaeal RNase Z is narrower than that of the nuclear RNase Z but broader than that of the mitochondrial RNase Z.     

Crystal structure of the tRNA 3' processing endoribonuclease tRNase Z from Thermotoga maritima

The maturation of the tRNA 3' end is catalyzed by a tRNA 3' processing endoribonuclease named tRNase Z (RNase Z or 3'-tRNase) in eukaryotes, Archaea, and some bacteria. The tRNase Z generally cuts the 3' extra sequence from the precursor tRNA after the discriminator nucleotide. In contrast, Thermotoga maritima tRNase Z cleaves the precursor tRNA precisely after the CCA sequence. In this study, we determined the crystal structure of T. maritima tRNase Z at 2.6-A resolution. The tRNase Z has a four-layer alphabeta/betaalpha sandwich fold, which is classified as a metallo-beta-lactamase fold, and forms a dimer. The active site is located at one edge of the beta-sandwich and is composed of conserved motifs. Based on the structure, we constructed a docking model with the tRNAs that suggests how tRNase Z may recognize the substrate tRNAs.     

Partitioning of the Nuclear and Mitochondrial tRNA 3′-End Processing Activities between Two different Proteins in Schizosaccharomyces pombe

tRNase Z is an essential endonuclease responsible for tRNA 3′-end maturation. tRNase Z exists in a short form (tRNase Z^S) and a long form (tRNase Z^L). Prokaryotes have only tRNase Z^S, whereas eukaryotes can have both forms of tRNase Z. Most eukaryotes characterized thus far, including Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, and humans, contain only one tRNase Z^L gene encoding both nuclear and mitochondrial forms of tRNase Z^L. In contrast, Schizosaccharomyces pombe contains two essential tRNase Z^L genes (trz1 and trz2) encoding two tRNase Z^L proteins, which are targeted to the nucleus and mitochondria, respectively. Trz1 protein levels are notably higher than Trz2 protein levels. Here, using temperature-sensitive mutants of trz1 and trz2, we provide in vivo evidence that trz1 and trz2 are involved in nuclear and mitochondrial tRNA 3′-end processing, respectively. In addition, trz2 is also involved in generation of the 5′-ends of other mitochondrial RNAs, whose 5′-ends coincide with the 3′-end of tRNA. Thus, our results provide a rare example showing partitioning of the nuclear and mitochondrial tRNase Z^L activities between two different proteins in S. pombe. The evolution of two tRNase Z^L genes and their differential expression in fission yeast may avoid toxic off-target effects.     

Naturally occurring mutations in human mitochondrial pre-tRNASer(UCN) can affect the transfer ribonuclease Z cleavage site, processing kinetics, and substrate secondary structure

tRNAs are transcribed as precursors with a 5' end leader and a 3' end trailer. The 5' end leader is processed by RNase P, and in most organisms in all three kingdoms, transfer ribonuclease (tRNase) Z can endonucleolytically remove the 3' end trailer. Long ((L)) and short ((S)) forms of the tRNase Z gene are present in the human genome. tRNase Z(L) processes a nuclear-encoded pre-tRNA approximately 1600-fold more efficiently than tRNase Z(S) and is predicted to have a strong mitochondrial transport signal. tRNase Z(L) could, thus, process both nuclear- and mitochondrially encoded pre-tRNAs. More than 150 pathogenesis-associated mutations have been found in the mitochondrial genome, most of them in the 22 mitochondrially encoded tRNAs. All the mutations investigated in human mitochondrial tRNA(Ser(UCN)) affect processing efficiency, and some affect the cleavage site and secondary structure. These changes could affect tRNase Z processing of mutant pre-tRNAs, perhaps contributing to mitochondrial disease.     

Analysis of the functional modules of the tRNA 3' endonuclease (tRNase Z)

tRNA 3' processing is one of the essential steps during tRNA maturation. The tRNA 3'-processing endonuclease tRNase Z was only recently isolated, and its functional domains have not been identified so far. We performed an extensive mutational study to identify amino acids and regions involved in dimerization, tRNA binding, and catalytic activity. 29 deletion and point variants of the tRNase Z enzyme were generated. According to the results obtained, variants can be sorted into five different classes. The first class still had wild type activity in all three respects. Members of the second and third class still formed dimers and bound tRNAs but had reduced catalytic activity (class two) or no catalytic activity (class three). The fourth class still formed dimers but did not bind the tRNA and did not process precursors. Since this class still formed dimers, it seems that the amino acids mutated in these variants are important for RNA binding. The fifth class did not have any activity anymore. Several conserved amino acids could be mutated without or with little loss of activity.     

Two archaeal tRNase Z enzymes: similar but different

The endoribonuclease tRNase Z plays an essential role in tRNA metabolism by removal of the 3' trailer element of precursor RNAs. To investigate tRNA processing in archaea, we identified and expressed the tRNase Z from Haloferax volcanii, a halophilic archaeon. The recombinant enzyme is a homodimer and efficiently processes precursor tRNAs. Although the protein is active in vivo at 2-4 M KCl, it is inhibited by high KCl concentrations in vitro, whereas 2-3 M (NH(4))(2)SO(4) do not inhibit tRNA processing. Analysis of the metal content of the metal depleted tRNase Z revealed that it still contains 0.4 Zn(2+) ions per dimer. In addition tRNase Z requires Mn(2+) ions for processing activity. We compared the halophilic tRNase Z to the homologous one from Pyrococcus furiosus, a thermophilic archaeon. Although both enzymes have 46% sequence similarity, they differ in their optimal reaction conditions. Both archaeal tRNase Z proteins process mitochondrial pre-tRNAs. Only the thermophilic tRNase Z shows in addition activity toward intron containing pre-tRNAs, 5' extended precursors, the phosphodiester bis(p-nitrophenyl)phosphate (bpNPP) and the glyoxalase II substrate S-D: -lactoylglutathion (SLG).