Quantifying Selection against Synonymous Mutations in HIV-1 env Evolution

Intrapatient evolution of human immunodeficiency virus type 1 (HIV-1) is driven by the adaptive immune system resulting in rapid change of HIV-1 proteins. When cytotoxic CD8⁺ T cells or neutralizing antibodies target a new epitope, the virus often escapes via nonsynonymous mutations that impair recognition. Synonymous mutations do not affect this interplay and are often assumed to be neutral. We test this assumption by tracking synonymous mutations in longitudinal intrapatient data from the C2-V5 part of the env gene. We find that most synonymous variants are lost even though they often reach high frequencies in the viral population, suggesting a cost to the virus. Using published data from SHAPE (selective 2′-hydroxyl acylation analyzed by primer extension) assays, we find that synonymous mutations that disrupt base pairs in RNA stems flanking the variable loops of gp120 are more likely to be lost than other synonymous changes: these RNA hairpins might be important for HIV-1. Computational modeling indicates that, to be consistent with the data, a large fraction of synonymous mutations in this genomic region need to be deleterious with a cost on the order of 0.002 per day. This weak selection against synonymous substitutions does not result in a strong pattern of conservation in cross-sectional data but slows down the rate of evolution considerably. Our findings are consistent with the notion that large-scale patterns of RNA structure are functionally relevant, whereas the precise base pairing pattern is not.     

Equivalent Mutations in the Eight Subunits of the Chaperonin CCT Produce Dramatically Different Cellular and Gene Expression Phenotypes

The eukaryotic cytoplasmic chaperonin-containing TCP-1 (CCT) is a complex formed by two back-to-back stacked hetero-octameric rings that assists the folding of actins, tubulins, and other proteins in an ATP-dependent manner. Here, we tested the significance of the hetero-oligomeric nature of CCT in its function by introducing, in each of the eight subunits in turn, an identical mutation at a position that is conserved in all the subunits and is involved in ATP hydrolysis, in order to establish the extent of ‘individuality’ of the various subunits. Our results show that these identical mutations lead to dramatically different phenotypes. For example, Saccharomyces cerevisiae yeast cells with the mutation in subunit CCT2 display heat sensitivity and cold sensitivity for growth, have an excess of actin patches, and are the only strain here generated that is pseudo-diploid. By contrast, cells with the mutation in subunit CCT7 are the only ones to accumulate juxtanuclear protein aggregates that may reflect an impaired stress response in this strain. System-level analysis of the strains using RNA microarrays reveals connections between CCT and several cellular networks, including ribosome biogenesis and TOR2, that help to explain the phenotypic variability observed.     

Genetic Architecture of Physiological Phenotypes: Empirical Evidence for Coadapted Gene Complexes

Physiological phenotypes are the result of the coordinated functionof many genes, some of which may be differentiated between conspecificpopulations. Within any one population, natural selection willfavor evolution of a coadapted set of alleles which optimizesphysiological performance and reproductive success. The existenceof such coadapted gene complexes may be assessed by assayingphenotypes of interpopulation hybrids: inferior performanceof hybrids suggests that the allelic combinations present inthe parental populations are coadapted. This approach has beenused to examine the genetic architecture of physiological traitsin the copepod Tigriopus californicus, a species characterizedby sharp genetic differentiation of populations. Developmentaltime and response to osmotic stress both show pronounced F₂hybrid breakdown, a result consistent with genetic coadaptationwithin populations. To better understand the biochemical andmolecular mechanisms underlying hybrid breakdown, we are investigatinga specific biochemical phenotype, the activity of the enzymecytochrome c oxidase (COX). COX (encoded by multiple nuclearand mitochondrial genes) catalyzes the oxidation of cytochromec (encoded by a nuclear gene). Two approaches are being usedto address the extent of coadaptation (both among nuclear genesand between nuclear and mitochondrial genes) underlying COXfunction: (1) studies of the DNA (and inferred amino acid) sequencesof component genes among populations in search of coordinatepatterns of amino acid substitution across loci, and (2) directstudies of COX function in interpopulation hybrids and backcrosses.These approaches provide evidence for the existence of nuclear/nuclearand/or nuclear/mitochondrial coadaptation within natural populationsof T. californicus.     

siRNA抑制HIV-1基因表达的研究

RNA干扰(RNAinterfering,RNAi)现象是动植物体内的一种序列特异性的、转录后基因沉默的过程.在哺乳动物细胞中,19～25个核苷酸长短的双链siRNA(smallinterferingRNA)可有效地抑制基因表达.利用pBS/H1SP载体,它表达的双链RNA的转录产物可以用来抑制特异性HIV-1基因的表达.在siRNA实验中,为了比较由H1启动子转录的siRNA在细胞内的作用,使用以绿色荧光蛋白(EGFP)为报告基因的载体——pEGFP-C1质粒,在荧光显微镜下,很容易地看到EGFP在细胞中表达.将HIV-1siRNA表达载体与表达相应EGFP-HIV融合基因的质粒,共转染人胚肾293细胞,结果表明,和对照质控载体相比,转染了pHIV-siRNA质粒的细胞中EGFP-HIV的表达得到显著抑制.通过该途径,筛选出能抑制HIV-1基因表达的有效siRNA.此外,还在同一载体上表达两种或三种siRNA,分别针对不同的HIV基因,获得了良好的抑制效果.     

Phenotypic Interactions among Mutations in a Thermus thermophilus 16S rRNA Gene Detected with Genetic Selections and Experimental Evolution

During protein synthesis, the ribosome undergoes conformational transitions between functional states, requiring communication between distant structural elements of the ribosome. Despite advances in ribosome structural biology, identifying the protein and rRNA residues governing these transitions remains a significant challenge. Such residues can potentially be identified genetically, given the predicted deleterious effects of mutations stabilizing the ribosome in discrete conformations and the expected ameliorating effects of second-site compensatory mutations. In this study, we employed genetic selections and experimental evolution to identify interacting mutations in the ribosome of the thermophilic bacterium Thermus thermophilus. By direct genetic selections, we identified mutations in 16S rRNA conferring a streptomycin dependence phenotype and from these derived second-site suppressor mutations relieving dependence. Using experimental evolution of streptomycin-independent pseudorevertants, we identified additional compensating mutations. Similar mutations could be evolved from slow-growing streptomycin-resistant mutants. While some mutations arose close to the site of the original mutation in the three-dimensional structure of the 30S ribosomal subunit and probably act directly by compensating for local structural distortions, the locations of others are consistent with long-range communication between specific structural elements within the ribosome.     

Molecular Characterization of Ambiguous Mutations in HIV-1 Polymerase Gene: Implications for Monitoring HIV Infection Status and Drug Resistance

Detection of recent HIV infections is a prerequisite for reliable estimations of transmitted HIV drug resistance (t-HIVDR) and incidence. However, accurately identifying recent HIV infection is challenging due partially to the limitations of current serological tests. Ambiguous nucleotides are newly emerged mutations in quasispecies, and accumulate by time of viral infection. We utilized ambiguous mutations to establish a measurement for detecting recent HIV infection and monitoring early HIVDR development. Ambiguous nucleotides were extracted from HIV-1 pol-gene sequences in the datasets of recent (HIVDR threshold surveys [HIVDR-TS] in 7 countries; n=416) and established infections (1 HIVDR monitoring survey at baseline; n=271). An ambiguous mutation index of 2.04×10^-3 nts/site was detected in HIV-1 recent infections which is equivalent to the HIV-1 substitution rate (2×10^-3 nts/site/year) reported before. However, significantly higher index (14.41×10^-3 nts/site) was revealed with established infections. Using this substitution rate, 75.2% subjects in HIVDR-TS with the exception of the Vietnam dataset and 3.3% those in HIVDR-baseline were classified as recent infection within one year. We also calculated mutation scores at amino acid level at HIVDR sites based on ambiguous or fitted mutations. The overall mutation scores caused by ambiguous mutations increased (0.54×10^-23.48×10^-2/DR-site) whereas those caused by fitted mutations remained stable (7.50-7.89×10^-2/DR-site) in both recent and established infections, indicating that t-HIVDR exists in drug-naïve populations regardless of infection status in which new HIVDR continues to emerge. Our findings suggest that characterization of ambiguous mutations in HIV may serve as an additional tool to differentiate recent from established infections and to monitor HIVDR emergence.     

中国株HIV-1核心蛋白真核表达载体的构建与表达

运用限制性内切酶XbaⅠ、SalⅠ对pKSGAG进行双酶切,获得HIV-1 gag基因,并与真核表达载体pCI-neo连接,构建含有中国流行株HIV-1 核心蛋白真核表达载体pCI-neoGAG.经XbaⅠ/SalⅠ双酶切及测序鉴定证实,成功地构建了HIV-1 核心蛋白真核表达载体pCI-neoGAG.通过脂质体将pCI-neoGAG转染入p815细胞,G418筛选4周后,使用间接免疫荧光方法检测表达产物.结果表明所构建的HIV-1 核心蛋白真核表达载体能在p815细胞中高效表达,为下一步进行HIV-1 DNA疫苗研究奠定了基础.     

中国株HIV-1核心蛋白真核表达载体的构建与表达

运用限制性内切酶XbaⅠ、SalⅠ对pKSGAG进行双酶切,获得HIV-lgag基因,并与真核表达载体pCI—neo连接,构建含有中国流行株HIV-1核心蛋白真核表达载体pCI—neoGAG。经XbaⅠ／SalⅠ双酶切及测序鉴定证实,成功地构建了HIV-1核心蛋白真核表达载体pCI-neoGAG。通过脂质体将pCI—neoGAG转染入p815细胞,G418筛选4周后,使用间接免疫荧光方法检测表达产物。结果表明所构建的HIV-1核心蛋白真核表达载体能在p815细胞中高效表达,为下一步进行HIV-1 DNA疫苗研究奠定了基础。     

Silencing of HIV-1 Gene Expression by Sirnas in Transduced Cells

The RNA interference (RNAi) phenomenon is a recently observed process in which the introduction of a double-stranded RNA (dsRNA) into cells causes the specific degradation of an mRNA containing the same sequence. To study dsRNA-mediated gene interference targeted to the env gene (NL4-3: 7490-7508) in HIV-1 infected cells, we constructed tandem-type and hairpin-type siRNA expression vectors, which were under the control of two U6 promoters. We also constructed lentiviral-based siRNA expression vectors for further assessment of their antiviral activity in transduced cells. At both the transient plasmid and lentiviral-mediated RNA expression levels, the siRNA encoding the env fragment exhibited sequence-specific suppression of target gene expression and strongly inhibited (≥90%) HIV-1 infection in the cells, as compared to the antisense RNA expression vector. Targeting the HIV-1 env gene with siRNAs encoding the env gene fragment (7490–7508) might be an effective strategy for gene therapy applications in HIV-1/AIDS treatment and management.     

Negative Dominant Mutations of the uidR Gene in ESCHERICHIA COLI: Genetic Proof for a Cooperative Regulation of uidA Expression

The uidA gene is the first gene involved in the hexuronide-hexuronate pathway in Escherichia coli K-12 and is under the dual control of the uidR and uxuR encoded repressors. Point mutations affecting the uidR regulatory gene were sought to investigate the regulation of uidA. When the uidR mutant allele was on a multicopy plasmid and the wild-type allele was on the chromosome, some of the mutant phenotypes were dominant to the wild-type phenotype, indicating that the active form of the UidR repressor is multimeric. We have demonstrated that expression of the mutant phenotype is dependent on gene dosage. The dominance of the uidR allele was also sensitive to the presence of the wild-type uxuR allele in the cell. This behavior probably results from UidR-UxuR repressor interactions. A mechanism is proposed: we suggest that the UidR and UxuR repressors interact after their binding to the operator site of uidA; the binding of one regulatory molecule may facilitate the binding of the other one in a cooperative process.     

Both Decrease in ACL1 Gene Expression and Increase in ICL1 Gene Expression in Marine-Derived Yeast Yarrowia lipolytica Expressing INU1 Gene Enhance Citric Acid Production from Inulin

In this study, some of the ATP-citrate lyase genes (ACL1) were deleted and the copy number of the iso-citrate lyase gene (ICL1) was increased in the marine-derived yeast Yarrowia lipolytica SWJ-1b displaying the recombinant inulinase. It was found that lipid content and iso-citric acid in the transformant 30 obtained were greatly reduced and citric acid production was greatly enhanced. It was also found that the ACL1 gene expression and ATP-citrate lyase activity in the transformant 30 were declined and the ICL1 gene expression and iso-citrate lyase activity were promoted. During the 2-l fermentation, 84.0 g/l of citric acid and 1.8 g/l of iso-citric acid in the fermented medium were attained from 10.0 % of inulin by the transformant 30 within 214 h. The results showed that only 0.36 % of the residual reducing sugar and 1.0 % of the residual total sugar were left in the fermented medium, suggesting that 89.6 % of the total sugar was used for citric acid production and cell growth by the transformant 30.     

用两步MS-PCR结合ELISA检测HIV-1逆转录酶基因的耐药性突变

高效抗逆转录病毒治疗法（HAART）的推广使用有效地抑制了HIV-1病毒的传播和艾滋病（AIDS）的发病率、死亡率。近年来,HIV-1逆转录酶基因突变所导致的耐药性成为了HAART的治疗失败的主要原因,耐药性突变的检测对于指导病人用药以及新药开发具有重要意义。本工作发展了一种检测HIV-1逆转录酶基因耐药性突变的新方法。采用两步MS-PCR方法检测HIV-1 B亚型野生型和耐药突变型逆转录酶基因突变,检测点包括M41L、K70R、K103N、Y181C和T215,并在两步MS-PCR基础上,设计比野生型引物长的突变型引物,结合微孔板杂交ELISA呈色技术检测各点突变。结果显示,简化的两步MS-PCR能保持灵敏度和特异性高的优点,ELISA的阳性结果与阴性结果的比值（P/N）达到要求,两步MS-PCR结合ELISA方法灵敏度高,操作简单、结果直观、成本低、相对耗时短且能进行高通量检测,其无论在HIV-1耐药性突变及其它的点突变检测中具有较好的临床应用前景。