Functional Interaction between Ribosomal Protein L6 and RbgA during Ribosome Assembly

RbgA is an essential GTPase that participates in the assembly of the large ribosomal subunit in Bacillus subtilis and its homologs are implicated in mitochondrial and eukaryotic large subunit assembly. How RbgA functions in this process is still poorly understood. To gain insight into the function of RbgA we isolated suppressor mutations that partially restored the growth of an RbgA mutation (RbgA-F6A) that caused a severe growth defect. Analysis of these suppressors identified mutations in rplF, encoding ribosomal protein L6. The suppressor strains all accumulated a novel ribosome intermediate that migrates at 44S in sucrose gradients. All of the mutations cluster in a region of L6 that is in close contact with helix 97 of the 23S rRNA. In vitro maturation assays indicate that the L6 substitutions allow the defective RbgA-F6A protein to function more effectively in ribosome maturation. Our results suggest that RbgA functions to properly position L6 on the ribosome, prior to the incorporation of L16 and other late assembly proteins.     

Release Factor One Is Nonessential in Escherichia coli

Recoding a stop codon to an amino acid may afford orthogonal genetic systems for biosynthesizing new protein and organism properties. Although reassignment of stop codons has been found in extant organisms, a model organism is lacking to investigate the reassignment process and to direct code evolution. Complete reassignment of a stop codon is precluded by release factors (RFs), which recognize stop codons to terminate translation. Here we discovered that RF1 could be unconditionally knocked out from various Escherichia coli stains, demonstrating that the reportedly essential RF1 is generally dispensable for the E. coli species. The apparent essentiality of RF1 was found to be caused by the inefficiency of a mutant RF2 in terminating all UAA stop codons; a wild type RF2 was sufficient for RF1 knockout. The RF1-knockout strains were autonomous and unambiguously reassigned UAG to encode natural or unnatural amino acids (Uaas) at multiple sites, affording a previously unavailable model for studying code evolution and a unique host for exploiting Uaas to evolve new biological functions.     

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．     

Mutations in the Escherichia coli23S rRNA Increase the Rate of Peptidyl-tRNA Dissociation from the Ribosome

We have studied in vivothe phenotypes of 23S rRNA mutations G2582A, G2582U, G2583C, and U2584C, which are located at the A site of Escherichia coli50S ribosomal subunit. All mutant rRNAs incorporated into 50S ribosomal subunits. Upon sucrose gradient fractionation of cell lysates, 23S rRNAs mutated at G2582 to A and G2583 to C accumulated in the 50S and 70S fractions and were underrepresented in the polysome fraction. Induction of 23S rRNAs mutated at G2582 and G2583 lead to a drastic reduction in cell growth. In addition, mutations G2582A and G2583C reduced to one-third the total protein synthesis but not the RNA synthesis. Finally, we show that 23S rRNA mutations G2582A, G2582U, and G2583C cause a significant increase in peptidyl-tRNA drop-off from ribosomes, thereby reducing translational processivity. The results clearly show that tRNA–23S rRNA interaction has an essential role in maintaining the processivity of translation.     

凋亡诱导因子与非受体酪氨酸激酶c-Abl的相互作用

目的:研究凋亡诱导因子(apoptosis-inducingfactor,AIF)与非受体酪氨酸激酶c-Abl的相互作用及其功能。方法:应用免疫共沉淀法研究蛋白质的相互作用;用抗磷酸化酪氨酸抗体研究蛋白质的体内磷酸化;与GFP质粒共转染研究蛋白在细胞内的表达量。结果:AIF与c-Abl在细胞内能形成复合物;AIF可以被c-Abl磷酸化,且c-Abl能提高AIF的表达量。结论:AIF与c-Abl具有相互作用;AIF可以被c-Abl磷酸化,且c-Abl能提高AIF的表达量。     

The Role of Release Factors in the Hydrolysis of Ester Bond in Peptidyl-tRNA

Biochemistry (Moscow) - Class I release factors (RFs) recognize stop codons in the sequences of mRNAs and are required for the hydrolysis of peptidyl-tRNA in the ribosomal P site during the final...     

拟南芥转录因子HB22与CRY1相互作用研究

通过酵母双杂交的方法,从拟南芥转录因子库中筛选出了6个与CRY1相互作用的转录因子.为了测定其中的HB22与CRY1相互作用的强度,采用了ONPG与CPRG两种方法对其β-半乳糖苷酶活性进行了分析.结果显示在蓝光光强为50μmol/m2s,孵育时间为4 h的情况下,蓝光与暗处理情况下的β-半乳糖苷酶活性比值分别为1.668和2.18.进一步设置蓝光处理时间及光强梯度实验数据显示,在蓝光光强为50μmol/m2s孵育时间为3 h时,二者相互作用强度达到最高.说明HB22与CRY1的相互作用具有蓝光响应.对蓝光处理不同时间的野生型col-4与cry1缺失突变体的材料进行HB22基因的定量PCR分析,发现拟南芥cry1缺失突变体中该基因的表达量比野生型中高,在蓝光处理2 h时,缺失突变体中表达量为野生型中的6倍左右.说明CRY1可能介导蓝光抑制HB22基因表达.     

Short-Range Functional Interaction Between Connexin35 and Neighboring Chemical Synapses

Auditory afferents terminating as mixed, electrical, and chemical, synapses on the goldfish Mauthner cells constitute an ideal experimental model to study the properties of gap junctions in the nervous system as well as to explore possible functional interactions with the other major form of interneuronal communication—chemically mediated synapses. By combining confocal microscopy and freeze-fracture replica immunogold labeling (FRIL), we found that gap junctions at these synapses contain connexin35 (Cx35), the fish ortholog of the neuron-specific human and mouse connexin36 (Cx36). Conductance of gap junction channels at these endings is known to be dynamically modulated by the activity of their co-localized chemically mediated glutamatergic synapses. By using simultaneous pre- and postsynaptic recordings at these single terminals, we demonstrate that such functional interaction takes place in the same ending, within a few micrometers. Accordingly, we also found evidence by confocal and FRIL double-immunogold labeling that the NR1 subunit of the NMDA glutamate receptor, proposed to be a key regulatory element, is present at postsynaptic densities closely associated with gap junction plaques containing Cx35. Given the widespread distribution of Cx35- and Cx36-mediated electrical synapses and glutamatergic synapses, our data suggest that the local functional interactions observed at these identifiable junctions may also apply to other electrical synapses, including those in mammalian brain.     

A Computer Modeling Study of the Interaction Between Tissue Factor Pathway Inhibitor and Blood Coagulation Factor Xa

Activation of blood coagulation factor X to factor Xa (FXa) is inhibited by tissue factor pathway inhibitor (TFPI). The second Kunitz-type inhibitory domain (K2) of TFPI binds a catalytic domain of FXa, whereas the first domain (K1) does not. We analyzed computer models of complexes of FXa with K1 or K2, which were made using a crystal structure of FXa. Favorable hydrophobic interaction was observed in the complex of FXa with K2. Furthermore, we constructed a tertiary structure of FXa using CHIMERA to assess the accuracy of a homology modeling method. The isolated model structure of FXa agreed well with the crystal structure, but analyses of complexes of this structure with K1 or K2 revealed that the models of complexes could not provide clear evidence of greater binding ability to K2 because of the positional difference of a few side chains interacting with the inhibitor.     

GTP-independent tRNA Delivery to the Ribosomal P-site by a Novel Eukaryotic Translation Factor

During translation, aminoacyl-tRNAs are delivered to the ribosome by specialized GTPases called translation factors. Here, we report the tRNA binding to the P-site of 40 S ribosomes by a novel GTP-independent factor eIF2D isolated from mammalian cells. The binding of tRNA_i^Met occurs after the AUG codon finds its position in the P-site of 40 S ribosomes, the situation that takes place during initiation complex formation on the hepatitis C virus internal ribosome entry site or on some other specific RNAs (leaderless mRNA and A-rich mRNAs with relaxed scanning dependence). Its activity in tRNA binding with 40 S subunits does not require the presence of the aminoacyl moiety. Moreover, the factor possesses the unique ability to deliver non-Met (elongator) tRNAs into the P-site of the 40 S subunit. The corresponding gene is found in all eukaryotes and includes an SUI1 domain present also in translation initiation factor eIF1. The versatility of translation initiation strategies in eukaryotes is discussed.     

植物DREB转录因子与植物激素的相互作用

DREB是植物中重要的转录因子,调控一系列非生物胁迫相关基因的表达,增强植物抵抗环境胁迫的能力.同时,当植物受到逆境胁迫时,植物体内的酶和激素都会发生变化,从而影响一系列的生理活动或生化变化来产生抵御胁迫的适应能力.近些年来,研究者们发现DREB与植物激素之间关系密切,从植物激素角度入手研究DREB的功能逐渐成为热点.就逆境胁迫下DREB转录因子与激素之间的相互作用进行阐述.     

用BIAcore系统研究西妥昔单克隆抗体与表皮生长因子受体的结合

目的：应用基于表面等离子体共振技术的BIAcore3000系统研究国产西妥昔单克隆抗体（cetuximab）C225与可溶性重组人表皮生长因子受体（EGFR）的结合能力,并与国外已上市的西妥昔单抗Erbitux相比较。方法：在CM5传感器芯片上设置2个通道,一个氨基偶联重组人EGFR作为检测通道,另一个不固定EGFR作为空白参比通道;以HBS溶液作为工作液,流速为10μL／min;活化与封闭芯片;再以10μL／min的流速分别以梯度浓度进样C225和Erbitux,每个浓度级别检测2次;获得结合动态图谱,拟合处理后用软件模块进行参数计算。结果：C225与可溶性重组人EGFR的结合动力学常数K^为4．00×10^8L／mol,KD为2．50×10^-9mol／L;而Erbitux与可溶性重组人EGFR的结合动力学常数KA为4．25×10^8L／mol,KD为2．35×10^-9mol／L。结论：在与可溶性重组人EGFR的结合能力上,C225与Erbitux有相似的结合动力学特性。     

人类Grx3蛋白与转录因子p65相互作用的研究

巯基氧化还原酶在生物体的系统内担当着非常重要的角色,其主要介导的是巯基和二硫键之间的相互转化的反应。人类Grx3蛋白作为一种巯基氧化还原酶在谷氧还蛋白系统中有着非常重要的作用。已有的研究表明,Grx3蛋白对NF-κB信号通路的活性有十分显著的影响。p65(RELA)是人类机体内十分重要的一种蛋白质,其在NF-κB信号通路有着重要的调控作用,几乎调控着NF-κB信号通路中的所有下游反应。通过大肠杆菌提纯表达的p65与Grx3在体外条件下进行偶联实验,为p65与Grx3存在相互作用提供了强有力的证据,同时也为Grx3蛋白对NF-κB信号通路的影响机制提供了一个可能的解释。     

Distinct Roles for Release Factor 1 and Release Factor 2 in Translational Quality Control

In bacteria, stop codons are recognized by two similar class 1 release factors, release factor 1 (RF1) and release factor 2 (RF2). Normally, during termination, the class 2 release factor 3 (RF3), a GTPase, functions downstream of peptide release where it accelerates the dissociation of RF1/RF2 prior to ribosome recycling. In addition to their canonical function in termination, both classes of release factor are also involved in a post peptidyl transfer quality control (post PT QC) mechanism where the termination factors recognize mismatched (i.e. error-containing) ribosome complexes and promote premature termination. Here, using a well defined in vitro system, we explored the role of release factors in canonical termination and post PT QC. As reported previously, during canonical termination, RF1 and RF2 recognize stop codons in a similar manner, and RF3 accelerates their rate of dissociation. During post PT QC, only RF2 (and not RF1) effectively binds to mismatched ribosome complexes; and whereas the addition of RF3 to RF2 increased its rate of release on mismatched complexes, the addition of RF3 to RF1 inhibited its rate of release but increased the rate of peptidyl-tRNA dissociation. Our data strongly suggest that RF2, in addition to its primary role in peptide release, functions as the principle factor for post PT QC.     

一种金针菇核糖体失活蛋白的分离纯化研究

获得一种为研究其他菌类核糖体失活蛋白的对照品,并论述一种金针菇核糖体失活蛋白的分离纯化及其活性的研究结果。实验中采用了DEAE和CM-离子交换纤维素与Bio-Gel 100柱层析方法。从1 000 g新鲜金针菇中得到5.58 mg的核糖体失活蛋白-Velutin,并证明其具有明显的抑制蛋白质的翻译作用,同时简要介绍了它的应用及展望。分离纯化到具有活性的Velutin,分子量为13.8 ku。     

Genetic Analysis of the Ribosome Biogenesis Factor Ltv1 of Saccharomyces cerevisiae

Ribosome biogenesis has been studied extensively in the yeast Saccharomyces cerevisiae. Yeast Ltv1 is a conserved 40S-associated biogenesis factor that has been proposed to function in small subunit nuclear export. Here we show that Ltv1 has a canonical leucine-rich nuclear export signal (NES) at its extreme C terminus that is both necessary for Crm1 interaction and Ltv1 export. The C terminus of Ltv1 can substitute for the NES in the 60S-export adapter Nmd3, demonstrating that it is a functional NES. Overexpression of an Ltv1 lacking its NES (Ltv1∆C13) was strongly dominant negative and resulted in the nuclear accumulation of RpS3-GFP; however, export of the pre-40S was not affected. In addition, expression of endogenous levels of Ltv1∆C protein complemented both the slow-growth phenotype and the 40S biogenesis defect of an ltv1 deletion mutant. Thus, if Ltv1 is a nuclear export adapter for the pre-40S subunit, its function must be fully redundant with additional export factors. The dominant negative phenotype of Ltv1∆NES overexpression was suppressed by co-overexpressing RpS3 and its chaperone, Yar1, or by deletion of the RpS3-binding site in Ltv1∆NES, suggesting that titration of RpS3 by Ltv1∆NES is deleterious in yeast. The dominant-negative phenotype did not correlate with a decrease in 40S levels but rather with a reduction in the polysome-to-monosome ratio, indicating reduced rates of translation. We suggest that titration of RpS3 by excess nuclear Ltv1 interferes with 40S function or with a nonribosomal function of RpS3.     

The Role of L1 Stalk-tRNA Interaction in the Ribosome Elongation Cycle

The ribosomal L1 stalk is a mobile structure implicated in directing tRNA movement during translocation through the ribosome. This article investigates three aspects of L1 stalk-tRNA interaction. First, by combining data from cryo electron microscopy, X-ray crystallography, and molecular dynamics simulations through the molecular dynamics flexible fitting method, we obtained atomic models of different tRNAs occupying the hybrid P/E state interacting with the L1 stalk. These models confirm the assignment of fluorescence resonance energy transfer states from previous single-molecule investigations of L1 stalk dynamics. Second, the models reconcile how initiator tRNA^fMet interacts less strongly with the L1 stalk compared to elongator tRNA^Phe, as seen in previous single-molecule experiments. Third, results from a simulation of the entire ribosome in which the L1 stalk is moved from a half-closed conformation to its open conformation are found to support the hypothesis that L1 stalk opening is involved in tRNA release from the ribosome.     

Binding Interaction between Tet(M) and the Ribosome: Requirements for Binding

Tet(M) protein interacts with the protein biosynthesis machinery to render this process resistant to tetracycline by a mechanism which involves release of the antibiotic from the ribosome in a reaction dependent on GTP hydrolysis. To clarify this resistance mechanism further, the interaction of Tet(M) with the ribosome has been examined by using a gel filtration assay with radioactively labelled Tet(M) protein. The presence of GTP and 5′-guanylyl imido diphosphate, but not GDP, promoted Tet(M)-ribosome complex formation. Furthermore, thiostrepton, which inhibits the activities of elongation factor G (EF-G) and EF-Tu by binding to the ribosome, blocks stable Tet(M)-ribosome complex formation. Direct competition experiments show that Tet(M) and EF-G bind to overlapping sites on the ribosome.