5'UTR中AUG的分布及其对翻译起始的影响

以细菌和古菌基因组5’UTR序列作为研究对象,分析在5’UTR的3个不同阅读框架中三联体AUG的分布,发现无论是细菌还是古菌基因组都在阅读框1中有非常明显的AUG缺失（depletion）。AUG的缺失表明在起始密码子上游的AUG很可能会对基因的翻译起始产生影响。分析得知：绝大部分的AUG都是以uORF（upstream open readingframe）的形式出现的,uAUG（upstreamAUG）的数量很少,特别是在阅读框1中,而且在细菌基因组的阅读框1中uAUG较多地出现在了含有SD序列的基因上游。比较发现,uAUG引导的序列在同义密码子使用上的偏好性较真正的编码序列差,这可能表明细菌和古菌在同义密码子使用上的偏好性也是决定基因准确地翻译起始的重要因素之一。     

5’UTR中AUG的分布及其对翻译起始的影响

以细菌和古菌基因组5′ UTR序列作为研究对象,分析在5′ UTR 的3个不同阅读框架中三联体AUG的分布,发现无论是细菌还是古菌基因组都在阅读框1中有非常明显的AUG缺失(depletion)。AUG的缺失表明在起始密码子上游的AUG很可能会对基因的翻译起始产生影响。分析得知：绝大部分的AUG都是以uORF(upstream open reading frame)的形式出现的,uAUG(upstream AUG)的数量很少,特别是在阅读框1中,而且在细菌基因组的阅读框1中uAUG较多地出现在了含有SD序列的基因上游。比较发现,uAUG引导的序列在同义密码子使用上的偏好性较真正的编码序列差,这可能表明细菌和古菌在同义密码子使用上的偏好性也是决定基因准确地翻译起始的重要因素之一。     

嗜热毛壳菌基因组密码子偏好性研究

嗜热毛壳菌具有强大的木质纤维素降解能力,将其开发为优异的重组蛋白表达宿主有着广阔的应用前景。蛋白表达宿主的密码子偏好性对重组蛋白的表达水平具有重大影响。为确定嗜热毛壳菌中密码子的使用模式及影响因素,本研究以6 897条CDS序列为对象,对其进行密码子偏好性分析。结果显示,嗜热毛壳菌中GC3的平均含量为66.2%,高于GC1(59.1%)和GC2(45.6%)的平均含量。Effective number of codon(ENC)分析与中性绘图分析结果显示,自然选择是影响嗜热毛壳菌密码子偏好性的主要因素。相关性分析结果显示,芳香族氨基酸比例与GC1含量及蛋白疏水水平呈极显著相关,说明密码子第一位的碱基组成对氨基酸是否具有芳香性影响较大。此外,在嗜热毛壳菌使用频率较高的密码子中,有24个以G/C末端结尾的密码子,进一步确定了23个高表达优越密码子和1个高表达最优密码子(CGC)。通过与其他模式真菌的密码子偏好性进行比较发现：与嗜热毛壳菌在密码子使用频率上差异较小的为嗜热毁丝菌、粗糙脉孢霉,有显著差异的为酿酒酵母。本研究为在嗜热毛壳菌中异源表达重组蛋白提供了目标基因密码子优化的理论依据,为嗜...     

巨枝叶绿体基因组密码子偏好性分析

该文针对巨桉叶绿体基因组序列,选取其中长于300 nt且以AUG为起始密码子的43个非重复基因作为研究对象,采用CodonW1.4.2软件分析巨桉叶绿体基因组的密码子使用偏好性。结果表明:第3位密码子的平均GC含量为27.97%; ENC的变化范围为39.49～61.00,平均为47.04; RSCU1的密码子有31个,其中29个以A/U结尾;中性分析显示,GC12与GC3无显著相关;回归分析未达到显著性水平; ENCplot分析发现,大部分基因落在曲线上或附近;对应分析表明第1轴的贡献率为17.68%,第2轴的贡献率为11.49%,第3轴、第4轴的贡献率分别为8.00%和5.76%,前4轴累计贡献率达42.93%,第1轴与GC、ENC、CAI达到极显著相关。上述分析结果表明,巨桉叶绿体基因组的密码子偏好较弱,密码子第3位偏好以A或U结尾,选择和突变在巨桉叶绿体基因组密码子偏好中起相对均衡的作用,最终确定UUG、CUU、GUU、UCC、UCA、ACA、UAU、UAA、CAU、AAU、AGA和GGA 12个高频高表达密码子为最优密码子。这为转化叶绿体基因密码子优化,提高表达效率和改良巨桉目标性状奠定了坚实基础。     

鸡基因组差异表达基因翻译起始密码子上下游序列的比较研究

翻译起始调控是基因表达调控的一个关键步骤之一。本文以鸡为研究材料,比较研究了鸡基因组高表达基因和低表达基因翻译起始密码子上下游的碱基序列差异,旨在寻找影响鸡基因表达水平的特异性调控位点。全部3 020个单剪接基因完整的mRNA序列及有详细注释的5＇UTRs序列从Ensembl下载。编写计算机程序,读取每个基因mRNA起始密码子上下游各位点的碱基。研究发现,起始密码子上游-3、-2位点可能是鸡基因组基因表达起始密码子正确识别的关键位点。起始密码子上下游的碱基组成分析发现,高表达基因和低表达基因起始密码子的上游均倾向使用（G＋C）,高表达基因的使用偏倚尤为强烈。序列差异比较发现,高表达基因在-9、-6、-3、＋4位点显著偏向G,在-1、-2、-4、-5位点显著偏向C。低表达基因起始密码子上游使用A、U的频率显著高于低表达基因。在-19位点强烈偏向A,在＋1、＋11、＋14位点强烈偏向U。     

金针菇高表达基因的密码子偏好性及特征分析

为探究金针菇的密码子偏好性,挖掘高表达基因的特征信息,以金针菇基因组及转录组数据为材料,分析金针菇的密码子偏好性及其影响因素,并对发育阶段高表达基因进行功能注释和顺式元件分析。分析表明,金针菇高表达基因表现出较强的密码子偏好性,且其偏好密码子多以胞嘧啶(C)结尾,此外在高表达基因中存在6种氨基酸的最优密码子较为保守。在进化过程中,金针菇高表达基因密码子偏好性受到自然选择压力的影响较大。功能注释分类表明,高表达基因多为核糖体通路相关的基因,与蛋白质翻译和生物合成相关。顺式元件分析表明,高表达基因启动子区域大多存在MeJA响应元件、ABA响应元件、光响应元件及MYB转录因子结合元件。研究结果可为提高金针菇异源表达效率和挖掘强启动子提供理论基础和思路。     

拟密码子适应指数方法的设计及应用

密码子适应指数(codon adaptation index,CAI)测量的是生物体内某个基因所用密码子与高表达基因所用密码子的相符合程度,是反映密码子偏好性的一个重要指标。文章根据拟氨基酸编码方法首次提出拟密码子适应指数(quasi-codon adaptation index,Q-CAI)。首先,通过氨基酸编码方法,得到密码子使用具有偏好性,并运用MATLAB分析其碱基组成,发现醋酸菌、大肠杆菌和双歧杆菌的密码子偏好使用c/g结尾,GC整体含量也比较高。随后,利用CAI模型方法进一步证明密码子具有偏好性。最后,利用文中提出的Q-CAI方法,得到醋酸菌、大肠杆菌和酵母菌所有序列的Q-CAI运算结果,发现它们都比CAI运算结果数值更高、更明显,而且双歧杆菌、枯草杆菌和链球菌的Q-CAI运算结果也普遍比CAI运算结果数值高,说明Q-CAI方法能更有效地评价密码子偏好性。文中所使用的6个单细胞物种的90条序列是从NCBI中下载,分析结果说明了Q-CAI方法比CAI方法更具有优越性,是衡量密码子偏好性的有效方法,对研究物种的基因突变有重要参考意义。     

Mx基因稀有密码子和mRNA结构及大肠杆菌表达 优化

通过对稀有密码子和mRNA翻译起始区二级结构的分析, 构建了4种重组表达菌株BL21(DE3)/pET-Mx, Rosseta(DE3)/pET-Mx, BL21(DE3)/pGEX-Mx和Rosseta(DE3)/pGEX-Mx, 在大肠杆菌中进行Mx基因的表达, Rosseta(DE3)/pET-Mx和Rosseta(DE3)/pGEX-Mx重组表达菌中都获得了表达, Western blotting检测到了特异的75 kDa表达产物。实验结果证明稀有密码子和mRNA翻译起始区二级结构对Mx 蛋白表达都有影响, 选择适用于稀有密码子表达的菌株Rosetta(DE3)有利于Mx蛋白的表达, 同时翻译起始区二级结构能值较低的表达载体pGEX-Mx获得的表达量明显增高。实验中首次获得了重组表达鸡全长Mx蛋白的大肠杆菌重组菌。     

茶树CBF1基因密码子使用特性分析

转录因子CBF(C-repeat-binding factor)广泛存在于各种植物中, 是植物抗逆过程中一个重要的调节因子。文章运用CHIPS、CUSP和CodonW在线程序对茶树(Camellia sinensis)CBF1基因(CsCBF1)序列进行分析, 并与茶树基因、模式植物基因组和其他植物CBF基因进行比较, 对了解CsCBF1基因密码子使用特性, 并为其选择合适的表达系统具有重要意义。结果表明：CsCBF1基因与70个茶树基因对密码子的使用有明显的差异, CsCBF1基因偏好使用以G/C结尾的密码子, 而筛选的70个茶树基因偏好使用以A/T结尾的密码子。在密码子使用频率上, CsCBF1基因与拟南芥(Arabidopsis thaliana)、烟草(Nicotiana tobacum)的差异小于与小麦(Triticum aestivum)、玉米(Zea mays)的差异; 因此, 拟南芥、烟草更适合作为CsCBF1基因的外源表达宿主。通过分析40种植物CBF基因编码特点可知大部分CBF基因偏好使用以G/C结尾的密码子, 这可能与基因的特殊功能有关。     

黑莓RuTT12-1基因密码子偏好性分析

MATE家族(multidrug and toxin efflux)成员TT12(TRANSPARENT TESTA 12)广泛存在于植物当中,是植物花青素苷和原花青素由细胞质转运至中央液泡过程中一个重要的转运蛋白。文章利用CUSP和Codon W在线程序对黑莓(Rubus spp.)TT12基因(Ru TT12-1)序列进行分析,并与模式植物基因组和其他植物TT12基因进行比较,对了解Ru TT12-1基因的密码子使用特性,并根据其特性选择合适的表达系统具有重要的意义。结果表明:Ru TT12-1基因表达量不高,偏好使用以A/T结尾的密码子,且7种最优密码子也均以A/T结尾。在密码子的使用频率上,Ru TT12-1基因与拟南芥(Arabidopsis thaliana)、烟草(Nicotiana tobacum)的差异小于和玉米(Zea mays)、小麦(Triticum aestivum)的差异,因此拟南芥和烟草更适合作为该基因的异源表达宿主。通过与35种植物TT12基因密码子偏好系数对比分析,大部分TT12基因偏爱使用以A/T结尾的密码子,这可能与其的功能有关。     

T淋巴瘤侵袭转移诱导因子1的结构与功能

T淋巴瘤侵袭转移诱导因子1(T-lymphoma invasion and metastasis inducing factor 1，Tiam1)是Ras相关的C3肉毒素底物1(Ras-Related C3 botulinum toxin substrate 1，Rac1)的特异性鸟苷酸交换因子(guanine nucleotide ex-change factor，GEF)。在细胞外信号刺激下Tiam1可以促进Rac1从无活性的GDP结合状态向有活性的GTP结合状态转换，有活性的Rac1-GTP与不同的下游效应分子相互作用，从而影响多种细胞事件。     

Expression of glutamate transporters in human and rat retina and rat optic nerve

l-Glutamate is the major excitatory transmitter in the vertebrate retina and plays a central role in the transmission of the various retinal neurons. Glutamate is removed from the extracellular space by at least five different glutamate transporters. The cellular distribution of these has been studied so far mainly using immunocytochemistry. In the present study non-radioactive in situ hybridisation using complementary RNA probes was applied in order to identify the cell types of rat retina and optic nerve expressing generic GLT1, GLT1 variant (GLT1v or GLT1B), GLAST and EAAC1. The results were compared with immunocytochemical data achieved using affinity-purified antibodies against transporter peptides. In the immunohistochemical studies the human retina was included. The study showed that in the rat retina GLT1v and EAAC1 were coexpressed in various cell types, i.e. photoreceptor, bipolar, horizontal, amacrine, ganglion and Müller cells, whereas GLAST was only detected in Müller cells and astrocytes. In the rat optic nerve GLT1v and EAAC1 were preferentially expressed in oligodendrocytes, whereas GLAST was revealed to be present mainly in astrocytes. Generic GLT1 could not be detected in the retina or optic nerve. The cellular distribution of glutamate transporters (only immunocytochemistry) in the human retina was very similar to that of the rat retina. Remarkable results of our studies were that generic GLT1 was not detectable in the rat (and human) retina and that GLT1v and EAAC1 were demonstrable in most cell types of the retina (including photoreceptor cells and their terminals).     

Molecular dialogues between viruses and receptor-like kinases in plants

Receptor-like kinases (RLKs) play a prominent role in the interaction between plants and extracellular pathogens. Intriguingly, in the past few years several studies have demonstrated that a number of RLKs influence plant susceptibility to viruses and, in some cases, interact with viral proteins. In this review, we will summarize and discuss recent advances suggesting a direct role for RLKs in plant–virus interactions.     

Association of SULT1A1 and UGT1A1 polymorphisms with breast cancer risk and phenotypes in Russian women

Estrogens are critical for breast cancer initiation and development. Sulfotransferase 1A1 (SULT1A1) and UDP-glucuronosyltransferase 1A1 (UGT1A1) conjugate and inactivate both estrogens and their metabolites, thus preventing estrogen-mediated mitosis and mutagenesis. SULT1A1 and UGT1A1 are both polymorphic, and different alleles encode functionally different allozymes. We hypothesize that low-activity alleles SULT1A1*2 and UGT1A1*28 are associated with higher risk for breast cancer and more severe breast tumor phenotypes. We performed a case-control study, which included 119 women of Russian ancestry with breast cancer and 121 age-matched Russian female controls. We used PCR followed by pyrosequencing to determine the SULT1A1 and UGT1A1 genotypes. Allele UGT1A1*28 was present at a higher frequency than the wild-type UGT1A1*1 allele in breast cancer patients as compared to controls (P = 0.002, OR = 1.79, CI 1.23–2.63). Consistently, the frequency of genotypes that contain allele UGT1A1*28 in the homozygous or the heterozygous state was greater in breast cancer patients as compared with the frequency of the wild-type UGT1A1*1/*1 genotype (P = 0.003, OR = 4.00, CI 1.49–11.11 and P = 0.014, OR = 2.04, CI 1.14–3.57, respectively). Individuals carrying allele UGT1A1*28 in the homo-or heterozygous state had larger breast tumors (>2 cm) as compared to the group with high-activity genotypes (P = 0.011, IR = 3.44, CI 1.42–8.36). No association was observed between any of the SULT1A1 genotypes and breast cancer risk or phenotypes. Our data suggest that UGT1A1, but not SULT1A1, genotypes are important for breast cancer risk and phenotype in Russian women. Published in Russian in Molekulyarnaya Biologiya, 2006, Vol. 40, No. 2, pp. 263–270. The article was translated by the authors.     

细胞色素P450 1A1基因多态性与我国某些肿瘤遗传易感性

近年来有关细胞色素P450基因多态性与肿瘤遗传易感性的研究正日益吸引越来越多的关注,本文对我国近年来有关细胞色素P450 1A1(CYP1Al)基因多态性与几种肿瘤遗传易感性的研究进行探讨,推测我国几种高发病率肿瘤的发生与我国CYP1A1基因多态分布状况有关,以此为进一步研究CYP1A1与肿瘤的关系作参考。     

Growth reference charts and the nutritional status of Indian children

We evaluate the growth performance of Indian children of age 0-3 using data from the 1998-1999 National Family and Health Survey, making use of the new child growth standards developed by the World Health Organization’ Multicentre Growth Reference Study. We find that the new charts lead to an increase of 4.2 million in the estimated number of stunted children, and an increase of 2.3 million in the estimated number of wasted children. The estimated number of underweight children decreases instead by 2.1 million. We also use data on ethnic Indians living in the United Kingdom to provide evidence on the height genetic potential of Indians. We find that children of Indian ethnicity who live in the UK have anthropometric outcomes comparable to those in commonly used growth standards and that the height of ethnic South Asian in the sample is negatively related with the amount of time spent outside the United Kingdom.     

Some novel flavin-nicotinamide biscoenzymes and their reactivities

The present study was undertaken to investigate flavin-nicotinamide reactions and interactions. A series of novel flavin-nicotinamide biscoenzymes have been synthesized by a general three-step procedure. The structures of these compounds were confirmed by nuclear magnetic resonance spectra, absorption spectra and elemental analysis. These compounds consist of short linear hydrocarbon chains interconnecting the N-1 of nicotinamide and the N-10 of the 7,8-dimethyl-isoalloxazine ring. The compounds were reduced with sodium dithionite (Na₂S₂O₄) and the flavin portion was reoxidized with ferricyanide. Re-reduction of the flavin portion by the nicotinamide portion of the molecule was followed anaerobically at 442 nm. When the interconnecting hydrocarbon chain was unsaturated, a second order reaction was observed with a rate equal to that of lumiflavin and 1-propyl-1,4-dihydronicotinamide (NprNicH₂) under the same conditions. When the two halves of the biscoenzymes were connected by saturated three- and four-carbon chains, the expected unimolecular reaction was not observed. Instead, the reduced biscoenzyme, after separation from excess sodium dithionite, was shown to have a strong absorption at 298 nm. This absorption is characteristic of hydration of dihydronicotinamides at the 5,6-double bond.In further studies, the C₃-biscoenzyme exhibited an absorption at 600 nm due to a complex between the reduced flavin and oxidized nicotinamide portions of the molecule. Absorbance at 600 nm increased linearly with the C₃-biscoenzyme concentration, clearly indicating that this is an intramolecular complex. When the C₃-biscoenzyme was at 0°C in 60–75% dimethylformamide buffer solution, no absorption at 600 nm was observed. When excess dithionite was removed, the spectrum under these conditions showed definite peaks at 297 and 357 nm. These respective peaks were attributed to hydrated dihydronicotinamide and dihydronicotinamide species present in the reaction mixture.The reduced flavin was postulated to be a catalyst for the hydration of dihydronicotinamide. This hypothesis was tested by incubating 1-propyl-1,4-dihydronicotinamide alone and with several concentrations of reduced riboflavin under basic anaerobic conditions. The results show that the reduced flavin increases the rate of disappearance of the dihydronicotinamide species and that the product shows an absorption near 298 nm. These results indicate that a reduced form of the flavin nucleus catalyzes the hydration of dihydronicotinamides.