基于古菌酪氨酰tRNA合成酶非天然氨基酸插入的研究进展

构筑蛋白质的编码信息存在于高度保守的密码子表中,而生物体仅利用20种天然氨基酸,就能排列组合出不同的蛋白质来行使多种生物学功能。通过合成生物学的飞速发展,使得在蛋白质合成中可控地引入非天然氨基酸成为可能。这极大地拓展了蛋白质的结构和功能,并为生物学工具的开发和生物生理过程的研究提供了便利。具有活性基团的非天然氨基酸可以广泛地应用于蛋白质结构研究、蛋白质功能调控以及新型生物材料构建和医药研发等诸多领域。基因密码子拓展技术利用正交翻译系统,通过重新分配密码子改造中心法则,可以在蛋白质的指定位点引入非天然氨基酸。系统地介绍了目前提升密码子拓展技术插入非天然氨基酸效率的方法,包括tRNA以及氨酰tRNA合成酶的各种突变方法和翻译辅助因子的改造。汇总了利用古细菌酪氨酰tRNA合成酶插入的非天然氨基酸和突变位点并总结了密码子拓展技术在生物医药领域的前沿进展。最后讨论了该项技术目前所面临的挑战,如可利用的密码子数量不多、正交翻译系统的种类有限和非天然氨基酸多插效率低下。希望能够帮助研究者建立适合的非天然氨基酸插入方法并推动密码子拓展技术进一步发展。     

四膜虫eRF1识别终止密码子的功能结构域

原生动物的一些纤毛虫中终止密码子发生重分配现象,将1个或2个终止密码子翻译为氨基酸.目前对这一现象的发生机制仍无合理解释．近年来,对蛋白质合成终止过程中肽链释放因子(eukaryotic polypeptide release factor, eRF)结构和功能的深入研究,为揭示终止密码子的重分配机制提供了重要的线索．本实验以具有终止密码子识别特异性的四膜虫Tt-eRF1为研究对象,将其中与密码子识别有关的GTx、NIKS和Y-C-F关键模体(motif) 引入识别通用终止密码子的酵母Sc=eRF1中,构建成各种嵌合体eRF1．利用双荧光素酶报告系统和细胞活性实验,分析关键模体及其周边的氨基酸对eRF1识别终止密码子性质的影响．结果表明,GTx和NIKS模体一定程度上决定eRF1识别终止密码子第1位碱基U和第2位碱基A;Y-C-F模体决定eRF1识别终止密码子UGA的第2位碱基G．模体内及其相邻氨基酸定点突变分析进一步支持以上结果．本研究推测,eRF1在进化过程中一些关键模体结构的改变决定其识别终止密码子的特异性,只能识别3个终止密码子中的1个或2个．随后,由于tRNA基因的突变产生阻抑性tRNA,促成终止密码子在原生动物纤毛虫中的重新分配．     

A型流感病毒NS1基因密码子去优化改造引起病毒毒力减弱

根据A型流感病毒密码子使用偏嗜性,选取稀有密码子对A/Puerto Rico/8/34(H1N1)病毒NS1基因内部110个氨基酸区域进行密码子同义突变改造,并全基因合成NS基因,利用反向遗传操作技术拯救出含有密码子去优化NS1基因的重组病毒(deoNS)。体外细胞噬斑形成实验和病毒生长曲线证明该病毒在MDCK细胞内的感染和复制能力比野生型病毒低约1000倍;BALB/c小鼠体内致病力实验证明deoNS病毒不能引起小鼠发病和死亡,该病毒在小鼠肺内的复制滴度比野生型病毒低100～1000倍。本研究探索了通过基因组密码子去优化改造途径降低A型流感病毒毒力的可行性,首次证明流感病毒NS1基因密码子去优化同义突变可以降低病毒毒力,为流感减毒活疫苗的研究提供了新的思路。     

无细胞体系非天然蛋白质合成研究进展

无细胞非天然蛋白质合成作为蛋白质研究的新兴手段,已成功用于表征蛋白质分子间、蛋白质与核酸分子间相互作用等基础科学研究及医药蛋白、蛋白质材料等工业生产领域。无细胞非天然蛋白质合成系统不需维持细胞的生长,无细胞膜阻碍,可依据研究目的添加基因元件或化学物质从而增强工程设计和过程调控的自由性;也可赋予蛋白质新的特性、结构及功能,如可实现蛋白翻译后修饰、反应手柄引入、生物物理探针及多聚蛋白质合成等。文中系统地综述了目前应用于无细胞蛋白质合成系统中的非天然氨基酸嵌入方法,包括全局抑制及基于正交翻译体系的终止密码子抑制、移码抑制、有义密码子再分配和非天然碱基等方法的研究进展,及非天然氨基酸在蛋白质修饰、生物物理探针、酶工程、蛋白质材料以及医药蛋白质生产等领域的应用进展,并分析了该体系的发展前景及广泛工业化应用的机遇与挑战。     

表达人乳头瘤病毒58型L1、L2壳蛋白的非复制型重组痘苗病毒疫苗株的构建

采用PCR定点突变方法,对HPV581L1基因中痘苗病毒早期基因转录终止信号TTTTTNT结构进行修饰,并保留氨基酸不变.选用非复制型重组痘苗病毒为载体,将修饰的L1基因1.5kb和L2基因1.4kb分别插入痘苗病毒表达载体pJSD的7.5k和H6早期启动子之后,使之与非复制型重组痘苗病毒在TK区重组.经单斑筛选纯化,获得共表达HPV58L1、L2晚期蛋白的非复制型重组痘苗病毒疫苗实验株.该病毒在CEF细胞上连续传至第15代,经斑点杂交分析,重组痘苗病毒基因组中有L1和L2基因插入;经Western blot检测,重组病毒能稳定表达HPV581L1及L2蛋白.此结果为HPV58型非复制型重组痘苗病毒疫苗人用株的研究打下了基础.     

马传染性贫血病毒弱毒疫苗株跨膜蛋白截短突变对其体外复制特性影响

马传染性贫血病毒(EIAV)减毒疫苗是世界首例慢病毒疫苗,但其作用机理尚不明了.研究发现,EIAV疫苗株EIAVFDDV12的跨膜蛋白gp45在马体内发生高频率261W位点翻译终止突变,使该蛋白质C端出现154个氨基酸的截短.为了探讨该截短对EIAV疫苗株生物学特性的作用,以EIAV弱毒疫苗株感染性克隆为骨干,构建了gp45截短型感染性病毒株,检测该截短突变对EIAV疫苗株在体外培养的马外周血单核细胞由来的巨噬细胞(MDM)、驴MDM和驴胎皮细胞(FDD)中的复制.实验结果表明,gp45截短型毒株在马和驴MDM中复制能力比未截短型毒株显著降低(P<0.01),特别是在马MDM中此差异更明显.相反,截短型毒株在FDD中的复制能力则显著高于未截短型毒株(P<0.01).此外,结果显示gp45截短型毒株在马MDM中的低水平复制降低了EIAV对其靶细胞诱导的凋亡.以上结果提示,EIAV疫苗的gp45截短型毒株是适应在体外FDD细胞中传代致弱的变异,该变异导致疫苗株在EIAV体内主要靶细胞巨噬细胞中复制能力的降低,导致毒力进一步减弱.     

丙型肝炎病毒F蛋白缺失对病毒复制及感染性的影响

探索了F蛋白缺失及核心蛋白(Core)二级结构改变对丙型肝炎病毒(HCV)复制和感染性的影响．利用定点突变方法,将J6JFH1的核心基因引进5个终止密码子以中断F蛋白的表达,从而获得F蛋白缺失的病毒复制子J6JFH1/ΔF．体外制备RNA转录体,并电穿孔转染Huh7.5.1细胞,采用免疫荧光、实时荧光定量PCR方法以及病毒感染等方法,观察F蛋白缺失对病毒复制、蛋白质表达及转染细胞上清感染性病毒颗粒产生的影响．在此基础上,构建5个单一突变病毒体,对HCV核心蛋白进行二级结构分析,观察核心蛋白二级结构对HCV复制和翻译的影响．结果显示,转染48 h后,J6JFH1/ΔF与野生型J6JFH1相比,J6JFH1/ΔF转染阳性细胞数明显降低,细胞内HCV RNA 水平降低约95%,J6JFH1/ΔF转染后不同时间点细胞上清中HCV RNA拷贝数和病毒颗粒也明显降低．5个单一突变体不影响核心基因二级结构,病毒在细胞内复制和感染性与野生型水平一致．J6JFH1/ΔF所产生的改变可能是由于5处突变导致核心基因二级结构改变而造成的．结果说明,HCV F蛋白缺失不影响病毒的复制翻译及病毒颗粒的包装释放,核心蛋白二级结构的改变对病毒复制和翻译则产生较大影响．     

麻疹病毒F基因测序及其进化关系的初步分析

研究麻疹病毒疫苗株S191毒种及其传代的病毒溶血素F(Haemolysin,HL)基因稳定性;对该序列一些重要位点的氨基酸进行比较,推测其功能结构及生物学活性变化;同时对该基因与M蛋白基因之间的非编码序列进行比对分析。利用RT-PCR方法扩增S191减毒株MeV23、26、27代及一株流行株YunnanLC-10的F基因,测序后进行比对分析。S191传代病毒F基因序列之间核苷酸同源性为99.8%,氨基酸同源性为99.5%～99.6%;S191疫苗株与流行株之间核苷酸序列同源性达95.2%;疫苗株与流行株1003nt的非编码区序列同源性为85.0%。S191传代病毒F基因具有较高遗传稳定性,关键功能位点氨基酸未发生传代改变;1003nt非编码区序列变异速度较快。     

基因工程疫苗的病毒载体

病毒基因工程疫苗是以活病毒为载体将一段外源基因导入机体细胞内,并使外源基因维持较高水平的表达。通过使用复制型或复制缺陷型载体能使表达的抗原诱生机体产生相应的体液抗体,并能引起机体产生细胞介导的免疫反应及粘膜免疫反应。本文主要介绍有可能用于基因工程疫苗的DNA及RNA病毒载体构建及其应用。     

微生物tRNA与密码子系统应用研究进展*

tRNA作为生命中心法则中翻译过程的重要参与分子,其种类、丰度都会对蛋白质的正常合成产生巨大影响。近年来通过对微生物tRNA的结构功能以及合成修饰过程的解析获得诸多启发,开展密码子扩展的研究,实现将非天然氨基酸引入特定位置从而获得新功能蛋白。同时,通过化学合成微生物基因组开展的密码子重编码工作将释放更多的密码子与tRNA用于更加广泛的密码子扩展研究。对微生物tRNA与密码子系统在合成生物学中的最新应用研究进展进行了综述,并讨论其未来的发展趋势。     

A new generation of HIV vaccines

WHO estimates that currently there are 40 million individuals living with HIV and there are 16000 new infections daily, worldwide. The best strategy to control the AIDS epidemic would be the development of an effective vaccine. New strategies for vaccine development have gained momentum over the past decade, some of which show greater promise in macaque models than did earlier protein-subunit or recombinant-canarypox strategies. These new vaccines include DNA vaccines and live viral vectors, and have been based on the generation of high levels of antiviral T cells. These vaccines do not prevent infection, but rather control virus replication with a rapid expansion and then contraction of antiviral T cells in response to the challenge infection. These recent vaccine successes in macaques raise hope that a vaccine can be developed that will successfully limit both the development of AIDS and viral transmission.     

Evolved orthogonal ribosomes enhance the efficiency of synthetic genetic code expansion

In vivo incorporation of unnatural amino acids by amber codon suppression is limited by release factor-1-mediated peptide chain termination. Orthogonal ribosome-mRNA pairs function in parallel with, but independent of, natural ribosomes and mRNAs. Here we show that an evolved orthogonal ribosome (ribo-X) improves tRNA(CUA)-dependent decoding of amber codons placed in orthogonal mRNA. By combining ribo-X, orthogonal mRNAs and orthogonal aminoacyl-tRNA synthetase/tRNA pairs in Escherichia coli, we increase the efficiency of site-specific unnatural amino acid incorporation from approximately 20% to >60% on a single amber codon and from <1% to >20% on two amber codons. We hypothesize that these increases result from a decreased functional interaction of the orthogonal ribosome with release factor-1. This technology should minimize the functional and phenotypic effects of truncated proteins in experiments that use unnatural amino acid incorporation to probe protein function in vivo.     

Protective Vaccine-Induced CD4+ T Cell-Independent B Cell Responses against Rabies Infection

A major goal in rabies virus (RV) research is to develop a single-dose postexposure prophylaxis (PEP) that would simplify vaccination protocols, reduce costs associated with rabies prevention in humans, and save lives. Live replication-deficient RV-based vaccines are emerging as promising single-dose vaccines to replace currently licensed inactivated RV-based vaccines. Nonetheless, little is known about how effective B cells develop in response to live RV-based vaccination. Understanding this fundamental property of rabies immunology may help in developing a single-dose RV vaccine. Typically, vaccines induce B cells secreting high-affinity, class-switched antibodies during germinal center (GC) reactions; however, there is a lag time between vaccination and the generation of GC B cells. In this report, we show that RV-specific antibodies are detected in mice immunized with live but not inactivated RV-based vaccines before B cells displaying a GC B cell phenotype (B220⁺GL7^hiCD95^hi) are formed, indicating a potential role for T cell-independent and early extrafollicular T cell-dependent antibody responses in the protection against RV infection. Using two mouse models of CD4⁺ T cell deficiency, we show that B cells secreting virus-neutralizing antibodies (VNAs) are induced via T cell-independent mechanisms within 4 days postimmunization with a replication-deficient RV-based vaccine. Importantly, mice that are completely devoid of T cells (B6.129P2-Tcrβ^tm1Mom Tcrδ^tm1Mom/J) show protection against pathogenic challenge shortly after immunization with a live replication-deficient RV-based vaccine. We show that vaccines that can exploit early pathways of B cell activation and development may hold the key for the development of a single-dose RV vaccine wherein the rapid induction of VNA is critical.     

Genetic Incorporation of Unnatural Amino Acids into Proteins in Mycobacterium tuberculosis

New tools are needed to study the intracellular pathogen Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), to facilitate new drug discovery and vaccine development. We have developed methodology to genetically incorporate unnatural amino acids into proteins in Mycobacterium smegmatis, BCG and Mtb, grown both extracellularly in culture and inside host cells. Orthogonal mutant tRNA^Tyr/tyrosyl-tRNA synthetase pairs derived from Methanococcus jannaschii and evolved in Escherichia coli incorporate a variety of unnatural amino acids (including photocrosslinking, chemically reactive, heavy atom containing, and immunogenic amino acids) into proteins in response to the amber nonsense codon. By taking advantage of the fidelity and suppression efficiency of the MjtRNA/pIpaRS pair in mycobacteria, we are also able to use p-iodophenylalanine to induce the expression of proteins in mycobacteria both extracellularly in culture and inside of mammalian host cells. This provides a new approach to regulate the expression of reporter genes or mycobacteria endogenous genes of interest. The establishment of the unnatural amino acid expression system in Mtb, an intracellular pathogen, should facilitate studies of TB biology and vaccine development.     

Inactivated or live-attenuated bivalent vaccines that confer protection against rabies and Ebola viruses

The search for a safe and efficacious vaccine for Ebola virus continues, as no current vaccine candidate is nearing licensure. We have developed (i) replication-competent, (ii) replication-deficient, and (iii) chemically inactivated rabies virus (RABV) vaccines expressing Zaire Ebola virus (ZEBOV) glycoprotein (GP) by a reverse genetics system based on the SAD B19 RABV wildlife vaccine. ZEBOV GP is efficiently expressed by these vaccine candidates and is incorporated into virions. The vaccine candidates were avirulent after inoculation of adult mice, and viruses with a deletion in the RABV glycoprotein had greatly reduced neurovirulence after intracerebral inoculation in suckling mice. Immunization with live or inactivated RABV vaccines expressing ZEBOV GP induced humoral immunity against each virus and conferred protection from both lethal RABV and EBOV challenge in mice. The bivalent RABV/ZEBOV vaccines described here have several distinct advantages that may speed the development of inactivated vaccines for use in humans and potentially live or inactivated vaccines for use in nonhuman primates at risk of EBOV infection in endemic areas.     

体外转录的自我复制型mRNA疫苗研究进展*

自我复制型mRNA是一种灵活的疫苗平台,该平台的开发基于甲病毒表达载体,其中复制必需基因得以完整保留,而结构蛋白基因则被来自病原的抗原基因替换。由于避免了病原培养、毒力返强和现存免疫的干扰,使其成为疫苗快速设计的理想平台。大量研究数据显示,此类疫苗可应用在人、小鼠、兔、猪、禽甚至鱼类体内诱导体液免疫和细胞免疫。过去,自我复制mRNA疫苗的研究采用重组单载体的模式,基因组骨架来源于辛德毕斯病毒、塞姆利基森林病毒和委内瑞拉马脑炎病毒。现在,反式复制型RNA和核酸修饰的反式复制型RNA作为下一代技术平台被寄予厚望。对基于甲病毒表达载体的mRNA疫苗技术的研究进展进行概述,重点介绍针对以流感病毒、新型冠状病毒和寨卡病毒等为代表的自我复制型mRNA疫苗研究现状,并探讨了该技术平台的未来发展方向。     

A Pandemic Influenza H1N1 Live Vaccine Based on Modified Vaccinia Ankara Is Highly Immunogenic and Protects Mice in Active and Passive Immunizations

Background

The development of novel influenza vaccines inducing a broad immune response is an important objective. The aim of this study was to evaluate live vaccines which induce both strong humoral and cell-mediated immune responses against the novel human pandemic H1N1 influenza virus, and to show protection in a lethal animal challenge model.

Methodology/Principal Findings

For this purpose, the hemagglutinin (HA) and neuraminidase (NA) genes of the influenza A/California/07/2009 (H1N1) strain (CA/07) were inserted into the replication-deficient modified vaccinia Ankara (MVA) virus - a safe poxviral live vector – resulting in MVA-H1-Ca and MVA-N1-Ca vectors. These live vaccines, together with an inactivated whole virus vaccine, were assessed in a lung infection model using immune competent Balb/c mice, and in a lethal challenge model using severe combined immunodeficient (SCID) mice after passive serum transfer from immunized mice. Balb/c mice vaccinated with the MVA-H1-Ca virus or the inactivated vaccine were fully protected from lung infection after challenge with the influenza H1N1 wild-type strain, while the neuraminidase virus MVA-N1-Ca induced only partial protection. The live vaccines were already protective after a single dose and induced substantial amounts of neutralizing antibodies and of interferon-γ-secreting (IFN-γ) CD4- and CD8 T-cells in lungs and spleens. In the lungs, a rapid increase of HA-specific CD4- and CD8 T cells was observed in vaccinated mice shortly after challenge with influenza swine flu virus, which probably contributes to the strong inhibition of pulmonary viral replication observed. In addition, passive transfer of antisera raised in MVA-H1-Ca vaccinated immune-competent mice protected SCID mice from lethal challenge with the CA/07 wild-type virus.

Conclusions/Significance

The non-replicating MVA-based H1N1 live vaccines induce a broad protective immune response and are promising vaccine candidates for pandemic influenza.     

Site-specific labeling of proteins with NMR-active unnatural amino acids

A large number of amino acids other than the canonical amino acids can now be easily incorporated in vivo into proteins at genetically encoded positions. The technology requires an orthogonal tRNA/aminoacyl-tRNA synthetase pair specific for the unnatural amino acid that is added to the media while a TAG amber or frame shift codon specifies the incorporation site in the protein to be studied. These unnatural amino acids can be isotopically labeled and provide unique opportunities for site-specific labeling of proteins for NMR studies. In this perspective, we discuss these opportunities including new photocaged unnatural amino acids, outline usage of metal chelating and spin-labeled unnatural amino acids and expand the approach to in-cell NMR experiments.