游仆虫重组核糖体蛋白L11与肽链释放因子的体外相互作用分析

核糖体蛋白L11(ribosome protein L11)是一种高度保守的蛋白质．为研究真核生物的核糖体蛋白L11的功能,从八肋游仆虫（Euplotes octocarinatus）大核基因组中克隆到核糖体蛋白L11基因,构建了重组表达质粒pGEX-6p1-L11,通过谷胱甘肽-Sepharose 4B亲和层析,纯化了重组融合蛋白GST-L11．Pull down 分析显示,八肋游仆虫的核糖体蛋白L11与第一类肽链释放因子eRF1a可以在体外相互作用．这一结果提示,与原核生物一样,低等真核生物的核糖体蛋白L11在肽链终止过程中可能起一定的作用．     

八肋游仆虫酸性核糖体磷酸化蛋白P1有2个亚型

真核生物酸性核糖体磷酸化蛋白(P0、P1、P2)位于核糖体60S大亚基上,它们在核糖体上共同组成一个向外侧凸出的五聚体的柄状复合物［P0·(P1·P2)2］,该复合物在蛋白质合成延伸过程中起着重要作用．为了探讨单细胞真核生物核糖体柄状复合物的组成形式及在蛋白质合成中的作用,对八肋游仆虫（Euplotes octocarinatus）的P1进行了研究．通过生物信息学方法,分析八肋游仆虫基因组及转录组数据,找到2个酸性核糖体蛋白P1基因,从DNA 和cDNA中都扩增到这2个P1基因,表明八肋游仆虫酸性核糖体磷酸化蛋白P1确实存在2个亚型. 将2个基因克隆后分别构建重组表达质粒pET28a-P1A和pGEX-6P-1-P1B,在大肠杆菌BL21中获得高效表达.经镍柱和GST柱亲和层析后,获得较高纯度的八肋游仆虫酸性核糖体蛋白EoP1A和EoP1B,表达产物经Western印迹检测为阳性．Pull-down分析了EoP1A和EoP1B之间的相互作用．结果表明,游仆虫酸性核糖体磷酸化蛋白P1的2个亚型EoP1A和EoP1B之间存在相互作用.     

八肋游仆虫氨酰-tRNA合成酶基因序列分析

氨酰-tRNA合成酶 (aminoacyl-tRNA synthetase, aaRS) 是蛋白质生物合成中的关键酶,能够催化特定的氨基酸和相应tRNA结合。为了研究八肋游仆虫氨酰 tRNA合成酶(Euplotes octocarinatus aminoacyl-tRNA synthetase, EoaaRS)基因的种类、数目、结构及起源,本研究利用生物信息学方法,对八肋游仆虫大核基因组编码的aaRS进行了系统分析。结果表明,八肋游仆虫大核基因组共包含45个aaRS基因,可编码20种不同的aaRS蛋白。其中,EoGlnRS和EoAlaRS仅由1个基因编码,其余EoaaRS均由多个基因编码。亚细胞定位分析显示,仅8个EoaaRS具有线粒体导肽,对应于6种EoaaRS。此外,基于核酸序列分析显示,多个EoaaRS在翻译过程中需要发生编程性核糖体移码,才能形成结构完整的蛋白质产物。结构域分析表明,部分EoaaRS存在特殊结构域,暗示其可能具有氨酰化以外的新功能。进化分析揭示,2个EoGlyRS起源于古菌,而2个EoLysRS起源于细菌。本研究为后续探讨低等真核生物aaRS的结构与功能奠定了基础。     

八肋游仆虫氨酰-tRNA合成酶基因序列分析北大核心CSCD

氨酰-tRNA合成酶(aminoacyl-tRNA synthetase,aaRS)是蛋白质生物合成中的关键酶,能够催化特定的氨基酸和相应tRNA结合。为了研究八肋游仆虫氨酰-tRNA合成酶(Euplotes octocarinatus aminoacyl-tRNA synthetase,EoaaRS)基因的种类、数目、结构及起源,本研究利用生物信息学方法,对八肋游仆虫大核基因组编码的aaRS进行了系统分析。结果表明,八肋游仆虫大核基因组共包含45个aaRS基因,可编码20种不同的aaRS蛋白。其中,Eo GlnRS和Eo AlaRS仅由1个基因编码,其余EoaaRS均由多个基因编码。亚细胞定位分析显示,仅8个EoaaRS具有线粒体导肽,对应于6种EoaaRS。此外,基于核酸序列分析显示,多个EoaaRS在翻译过程中需要发生编程性核糖体移码,才能形成结构完整的蛋白质产物。结构域分析表明,部分EoaaRS存在特殊结构域,暗示其可能具有氨酰化以外的新功能。进化分析揭示,2个Eo GlyRS起源于古菌,而2个Eo LysRS起源于细菌。本研究为后续探讨低等真核生物aaRS的结构与功能奠定了基础。     

滑动序列对游仆虫中识别+1位和+2位编程性核糖体移码具有关键作用

编程性核糖体移码(programmed ribosomal frameshifting,PRF)广泛存在于生命进化谱系的各个分支,是一种翻译水平上的基因表达调控方式。单细胞真核生物游仆虫(Euplotes)中不仅PRF基因比例高,而且移码类型有+1和+2位两种。本研究从基因组水平对八肋游仆虫(E.octocarinatus)中的+2 PRF基因进行了鉴定,比较分析+1及+2 PRF基因中可能的调控元件。为了探讨游仆虫中滑动序列对移码类型的影响,克隆了八肋游仆虫的+1 PRF基因——η微管蛋白基因,将其构建到含绿色荧光蛋白报告基因的游仆虫大核人工染色体中,转染游仆虫细胞,通过检测GFP的表达来确定不同滑动序列突变体对应的移码类型。结果表明,滑动序列的改变能使游仆虫+1 PRF转变为+2 PRF,且这种移码类型的改变与滑动序列第1个密码子编码何种氨基酸无关。本研究揭示了滑动序列对游仆虫中识别+1和+2位的编程性核糖体移码具有关键作用。     

八肋游仆虫微管蛋白基因家族的鉴定及进化分析

为了系统分析八肋游仆虫(Euplotes octocarinatus)微管蛋白基因家族, 从八肋游仆虫大核基因组中共鉴定得到20个微管蛋白基因, 基于同源比对及系统进化分析, 将其归入α、β、γ、δ、ε及η六个微管蛋白亚家族; 多序列比对及Western blot结果显示八肋游仆虫η微管蛋白基因在翻译过程中需发生一次+1位编程性核糖体移码, 其移码位点为AAA-TAA; 所有自由生纤毛虫都含有多个α和β微管蛋白基因亚型, 可能用于组成不同的微管结构。研究为后续深入探讨八肋游仆虫微管蛋白的生物学功能及微管多样性奠定了基础。     

肽链释放因子和核糖体蛋白L11在八肋游仆虫细胞中的定位

原生动物纤毛虫是一类单细胞真核生物,其蛋白质合成终止过程中密码子使用的特殊性使其成为研究蛋白质合成终止机制的一个经典模型。为了能够有效地分析生物大分子在该细胞中的功能作用位点,本研究根据该生物染色体结构的特征,构建了含有红色荧光蛋白基因的大核人工染色体EoMAC_R,并与之前构建的含绿色荧光蛋白基因的大核染色体EoMAC_G一起,对蛋白质合成终止有关的3个重要因子核糖体大亚基蛋白L11、多肽链释放因子eRF1和eRF3在八肋游仆虫细胞中进行了荧光共定位分析。结果显示,在八肋游仆虫细胞中,蛋白质翻译过程主要位于"C"形大核内侧区域。构建的人工染色体能够作为一种有效的工具,对目的蛋白质在八肋游仆虫细胞中进行定位分析。     

八肋游仆虫eRF3 C端的76个氨基酸对于释放因子eRF1a的结合不是必需的

以八肋游仆虫第二类肽链释放因子eRF3基因为模板,用PCR的方法获得eRF3的C端(eRF3C)和C端缺失76个氨基酸的突变体eRF3Ct片段,并构建重组表达质粒pGEX-6p-1-eRF3C和pGEX-6p-1-eRF3Ct,转入大肠杆菌BL21(DE3)中获得了可溶性表达。通过Glutathione Sepharose 4B柱亲和层析纯化,重组蛋白GST-eRF3C和GST-eRF3Ct获得纯化。Western blotting分析表明获得的蛋白为目的蛋白。PreScission酶切割后得到eRF3C和eRF3Ct蛋白。体外pull down分析显示eRF3C和eRF3Ct均能与八肋游仆虫第一类释放因子eRF1a相互作用,这表明八肋游仆虫eRF3 C端的76个氨基酸对于释放因子eRF1a的结合不是必需的。     

八肋游仆虫含绿色荧光蛋白基因的大核人工染色体的构建

为研究八肋游仆虫(Euplotes octocarinatus)相关基因的功能,构建了八肋游仆虫大核人工染色体(macronuclear artificial chromosome of E. octocarinatus,EoMAC-G),其两端为克隆自八肋游仆虫大核β2-微管蛋白基因的5′和3′非编码区和两侧的端粒序列,中间为多克隆位点和密码子优化后的增强型绿色荧光蛋白(enhanced green fluorescence protein, EGFP-Eo) 报道基因. 用脂质体转染方法将携带有EoMAC－G的pBTub-Tel载体转入八肋游仆虫大核,分析EGFP-Eo基因在八肋游仆虫细胞中的表达. 荧光显微镜观察发现,EGFP-Eo产生的荧光均匀分布于八肋游仆虫细胞质中. 在细胞进行有丝分裂的情况下,荧 光可持续20 d以上. 相比pEGFP-N1质粒转化的游仆虫,人工染色体中的EGFP-Eo基因表达的荧光亮度强、稳定且持续时间长. Western 杂交分析进一步证实,外源EGFP-Eo基因在细胞中过量表达. 通过细菌喂食法进行纤毛虫RNA干扰实验,抑制了外源EGFP-Eo基因在八肋游仆虫细胞中的表达. 利用构建的人工染色体不仅可以在八肋游仆虫细胞内表达外源基因,对目的蛋白质进行活细胞实时动态的定位分析,还可通过RNA干扰的方法调控外源基因在纤毛虫细胞中的表达,便于进一步分析目的蛋白质的功能.     

八肋游仆虫组织蛋白酶B基因家族的分子克隆及序列分析

组织蛋白酶B (cathepsin B, CTSB)是一种主要存在于溶酶体中的半胱氨酸蛋白水解酶,广泛存在于各种生物中。为了研究八肋游仆虫组织蛋白酶B (Euplotes octocarinatus Cathepsin B, EoCTSB)基因的序列、结构和功能,本研究利用生物信息学方法,对八肋游仆虫组织蛋白酶B基因进行了系统分析。利用相似性搜索及系统进化分析,共鉴定得到6个EoCTSBs基因。转录组数据及3′RACE分析结果表明这6个基因均具有转录活性。通过与其他真核生物的组织蛋白酶B比较,结果显示,6种EoCTSBs均含有保守的肽链内切酶催化活性位点,但都缺失封闭环结构,因此推测它们都没有外肽酶活性;仅EoCTSB-6的S2亚位为酸性氨基酸残基,暗示其具有催化特异性底物Z-Arg-Arg-AMC水解的活性。本研究为后续深入探讨EoCTSB的生物学功能提供理论依据。     

Cold-shock induced high-yield protein production in Escherichia coli

Overexpression of proteins in Escherichia coli at low temperature improves their solubility and stability. Here, we apply the unique features of the cspA gene to develop a series of expression vectors, termed pCold vectors, that drive the high expression of cloned genes upon induction by cold-shock. Several proteins were produced with very high yields, including E. coli EnvZ ATP-binding domain (EnvZ-B) and Xenopus laevis calmodulin (CaM). The pCold vector system can also be used to selectively enrich target proteins with isotopes to study their properties in cell lysates using NMR spectroscopy. We have cloned 38 genes from a range of prokaryotic and eukaryotic organisms into both pCold and pET14 (ref. 3) systems, and found that pCold vectors are highly complementary to the widely used pET vectors.     

The scc spirochetal coiled-coil protein forms helix-like filaments and binds to nucleic acids generating nucleoprotein structures

The analysis of the genome of Leptospira spp., a group of bacteria of the phylum of spirochetes with several unique evolutionary and morphological features, has allowed the identification of a gene encoding a coiled-coil protein, called Scc, which is completely unrelated to any other eukaryotic or prokaryotic protein. Since coiled-coil proteins are often key elements of the cytoskeleton, we analyzed the protein Scc, which is a 24-kDa protein composed of a N-terminal coiled-coil domain, a proline-rich intermediate domain, and an acidic tail. The gene scc is located in an operon which also contains the genes encoding the initiation factor IF3 and the two ribosomal proteins L20 and L35. In this study, we showed that the presence of the coiled-coil domain was responsible for the polymerization of Scc in helix-like structures, in an ATP-independent manner, in both Escherichia coli living cells and in vitro. Analysis of the Scc polymers by electron microscopy showed filaments with a width of 6 to 10 nm, similar to that of eukaryotic intermediate filaments. Scc was also found to bind both RNA and double-stranded DNA without detectable sequence specificity. By electron microscopy, we showed that Scc polymer assembly was affected by the presence of nucleic acids, giving rise to rod-shaped structures with a width ranging from 45 to 155 nm. Finally, Leptospira biflexa cells depleted in Scc form small colonies, but the morphology of their helicoidal cell body was not affected. These results provide the first insight into a unique DNA binding filament-forming coiled-coil protein that could play an important role in the subcellular architecture of the spirochetal microorganism.     

Supernumerary proteins of mitochondrial ribosomes

Background

Messenger RNAs encoded by mitochondrial genomes are translated on mitochondrial ribosomes that have unique structure and protein composition compared to prokaryotic and cytoplasmic ribosomes. Mitochondrial ribosomes are a patchwork of core proteins that share homology with prokaryotic ribosomal proteins and new, supernumerary proteins that can be unique to different organisms. In mammals, there are specific supernumerary ribosomal proteins that are not present in other eukaryotes.

Scope of review

Here we discuss the roles of supernumerary proteins in the regulation of mitochondrial gene expression and compare them among different eukaryotic systems. Furthermore, we consider if differences in the structure and organization of mitochondrial genomes may have contributed to the acquisition of mitochondrial ribosomal proteins with new functions.

Major conclusions

The distinct and diverse compositions of mitochondrial ribosomes illustrate the high evolutionary divergence found between mitochondrial genetic systems.

General significance

Elucidating the role of the organism-specific supernumerary proteins may provide a window into the regulation of mitochondrial gene expression through evolution in response to distinct evolutionary paths taken by mitochondria in different organisms. This article is part of a Special Issue entitled Frontiers of Mitochondrial Research.     

Analysis of micronuclear, macronuclear and cDNA sequences encoding the regulatory subunit of cAMP-dependent protein kinase of Euplotes octocarinatus: evidence for a ribosomal frameshift

We have isolated and characterized the micronuclear gene encoding the regulatory subunit of cAMP-dependent protein kinase of the ciliated protozoan Euplotes octocarinatus, as well as its macronuclear version and the corresponding cDNA. Analyses of the sequences revealed that the micronuclear gene contains one small 69-bp internal eliminated sequence (IES) that is removed during macronuclear development. The IES is located in the 5'-noncoding region of the micronuclear gene and is flanked by a pair of tetranucleotide 5'-TACA-3' direct repeats. The macronuclear DNA molecule carrying this gene is approximately 1400 bp long and is amplified to about 2000 copies per macronucleus. Sequence analysis suggests that the expression of this gene requires a +1 ribosomal frameshift. The deduced protein shares 31% identity with the cAMP-dependent protein kinase type I regulatory subunit of Homo sapiens, and 53% identity with the regulatory subunit R44 of one of the two cAMP-dependent protein kinases of Paramecium. In addition, it contains two highly conserved cAMP binding sites in the C-terminal domain. The putative autophosphorylation site ARTSV of the regulatory subunit of E. octocarinatus is similar to that of the regulatory subunit R44 of Paramecium but distinct from the consensus motif RRXSZ of other eukaryotic regulatory subunits of cAMP-dependent protein kinases.     

Conservation of ribosomal protein gene ordering in 16 complete genomes

The organization of ribosomal proteins in 16 prokaryotic genomes was studied as an example of comparative genome analyses of gene systems. Hypothetical ribosomal protein-containing operons were constructed. These operons also contained putative genes and other non-ribosomal genes. The correspondences among these genes across different organisms were clarified by sequence homology computations. In this way a cross tabulation of 70 ribosomal proteins genes was constructed. On average, these were organized into 9-14 operons in each genome. There were also 25 non-ribosomal or putative genes in these mainly ribosomal protein operons. Hence the table contains 95 genes in total. It was found that: (i) the conservation of the block of about 20 r-proteins in the L3 and L4 operons across almost the entire eubacteria and ar-chaebacteria is remarkable; (ii) some operons only belong to eubacteria or archaebacte-ria; (iii) although the ribosomal protein operons are highly conserved within domain, there are fine variat