PLOD3基因3′调控区的人类特异突变改变miR-124a对PLOD3的调控

microRNAs(miRNAs)是一类在转录后水平调控基因表达的不编码蛋白质的小RNA(长度20—24个碱基)。其中,miR-124a是一个在哺乳动物中枢神经系统高度表达的miRNA,在神经前体细胞向神经元分化的过程中起着举足轻重的作用。由于miRNAs特异性地识别靶基因的3′端调控区(3′UTR)的靶序列,因此,在人类起源过程中基因3′UTR的单核苷酸序列变异有可能导致miRNA调控的改变。通过靶基因预测和3′UTR区在哺乳动物代表物种间的同源序列比较,我们发现miR-124a的靶基因中有一个基因(PLOD3)3′UTR的靶位点中存在人类特异突变位点。利用体外报告基因系统,发现PLOD3基因3′UTR靶位点中所含的一个人类特异的突变导致miR-124a对PLOD3的调控效率降低。研究表明,miRNAs靶基因3′UTR的序列变异具有功能效应,它有可能是人类中枢神经系统在起源和演化中发挥关键作用的重要遗传机制之一。     

Kit基因无义突变导致W-3Bao小鼠显性白斑形成

Kit(W)基因是一种原癌基因,在小鼠中该基因位于第5号染色体距着丝粒约42 cM处,其编码的蛋白质是具有酪氨酸激酶活性的干细胞生长因子受体,为酪氨酸激酶受体信号通路的跨膜分子。在人类及小鼠,kit及其配体kitl突变都可能引起不同程度的贫血、肥大细胞减少、毛色变白和生育能力下降或丧失等症状(Rajaraman et al.,2002;Broudy,1997;Rajaraman et al.,2003;Kapur et al.,1999),同源的kit基因突变在猪及禽类都表现为显性的白色斑点(邓素华等,2000)。在先前的研究中,本课题组通过ENU诱变获得6种白斑突变小鼠,通过连锁分析法以微卫星为连锁标…     

Divergent microsatellite evolution in the human and chimpanzee lineages

Comparison of the complete human genome sequence to one of its closest relatives, the chimpanzee genome, provides a unique opportunity for exploring recent evolutionary events affecting the microsatellites in these species. A simple assumption on microsatellite distribution is that the total length of perfect repeats is constant compared to that of imperfect ones regardless of the repeat sequence. In this paper, we show that this is valid for most of the chimpanzee genome but not for a number of human chromosomes. Our results suggest accelerated evolution of microsatellites in the human genome relative to the chimpanzee lineage.     

The evolution of development in Streptomyces analysed by genome comparisons

There is considerable information about the genetic control of the processes by which mycelial Streptomyces bacteria form spore-bearing aerial hyphae. The recent acquisition of genome sequences for 16 species of actinobacteria, including two streptomycetes, makes it possible to try to reconstruct the evolution of Streptomyces differentiation by a comparative genomic approach, and to place the results in the context of current views on the evolution of bacteria. Most of the developmental genes evaluated are found only in actinobacteria that form sporulating aerial hyphae, with several being peculiar to streptomycetes. Only four (whiA, whiB, whiD, crgA) are generally present in nondifferentiating actinobacteria, and only two (whiA, whiG) are found in other bacteria, where they are widespread. Thus, the evolution of Streptomyces development has probably involved the stepwise acquisition of laterally transferred DNA, each successive acquisition giving rise either to regulatory changes that affect the conditions under which development is initiated, or to changes in cellular structure or morphology.     

A novel Werner Syndrome mutation: pharmacological treatment by read-through of nonsense mutations and epigenetic therapies

Werner Syndrome (WS) is a rare inherited disease characterized by premature aging and increased propensity for cancer. Mutations in the WRN gene can be of several types, including nonsense mutations, leading to a truncated protein form. WRN is a RecQ family member with both helicase and exonuclease activities, and it participates in several cell metabolic pathways, including DNA replication, DNA repair, and telomere maintenance. Here, we reported a novel homozygous WS mutation (c.3767 C > G) in 2 Argentinian brothers, which resulted in a stop codon and a truncated protein (p.S1256X). We also observed increased WRN promoter methylation in the cells of patients and decreased messenger WRN RNA (WRN mRNA) expression. Finally, we showed that the read-through of nonsense mutation pharmacologic treatment with both aminoglycosides (AGs) and ataluren (PTC-124) in these cells restores full-length protein expression and WRN functionality.     

The distribution of fitness effects of new beneficial mutations in Pseudomonas fluorescens

Theoretical studies of adaptation emphasize the importance of understanding the distribution of fitness effects (DFE) of new mutations. We report the isolation of 100 adaptive mutants—without the biasing influence of natural selection—from an ancestral genotype whose fitness in the niche occupied by the derived type is extremely low. The fitness of each derived genotype was determined relative to a single reference type and the fitness effects found to conform to a normal distribution. When fitness was measured in a different environment, the rank order changed, but not the shape of the distribution. We argue that, even with detailed knowledge of the genetic architecture underpinning the adaptive types (as is the case here), the DFEs remain unpredictable, and we discuss the possibility that general explanations for the shape of the DFE might not be possible in the absence of organism-specific biological details.     

Rates of genome evolution and branching order from whole genome analysis

Accurate estimation of any phylogeny is important as a framework for evolutionary analysis of form and function at all levels of organization from sequence to whole organism. Using alignments of nonrepetitive components of opossum, human, mouse, rat, and dog genomes we evaluated two alternative tree topologies for eutherian evolution. We show with very high confidence that there is a basal split between rodents (as represented by the mouse and rat) and a branch joining primates (as represented by humans) and carnivores (as represented by dogs), consistent with some but not the most widely accepted mammalian phylogenies. The result was robust to substitution model choice with equivalent inference returned from a spectrum of models ranging from a general time reversible model, a model that treated nucleotides as either purines and pyrimidines, and variants of these that incorporated rate heterogeneity among sites. By determining this particular branching order we are able to show that the rate of molecular evolution is almost identical in rodent and carnivore lineages and that sequences evolve approximately 11%-14% faster in these lineages than in the primate lineage. In addition by applying the chicken as outgroup the analyses suggested that the rate of evolution in all eutherian lineages is approximately 30% slower than in the opossum lineage. This pattern of relative rates is inconsistent with the hypothesis that generation time is an important determinant of substitution rates and, by implication, mutation rates. Possible factors causing rate differences between the lineages include differences in DNA repair and replication enzymology, and shifts in nucleotide pools. Our analysis demonstrates the importance of using multiple sequences from across the genome to estimate phylogeny and relative evolutionary rate in order to reduce the influence of distorting local effects evident even in relatively long sequences.     

A method for molecular phylogeny construction by direct use of nucleotide sequence data

Summary A method for molecular phylogeny construction is newly developed. The method, called the stepwise ancestral sequence method, estimates molecular phylogenetic trees and ancestral sequences simultaneously on the basis of parsimony and sequence homology. For simplicity the emphasis is placed more on parsiomony than on sequence homology in the present study, though both are certainly important. Because parsimony alone will sometimes generate plural candidate trees, the method retains not one but five candidates from which one can then single out the final tree taking other criteria into account.The properties and performance of the method are then examined by simulating an evolving gene along a model phylogenetic tree. The estimated trees are found to lie in a narrow range of the parsimony criteria used in the present study. Thus, other criteria such as biological evidence and likelihood are necessary to single out the correct tree among them, with biological evidence taking precedence over any other criterion. The computer simulation also reveals that the method satisfactorily estimates both tree topology and ancestral sequences, at least for the evolutionary model used in the present study.     

转座因子和宿主基因组的进化

转座因子主要是一些“自在”或“无功能”的DNA,其对宿主进化无关紧要的观点受到了质疑。新近的报道指出,它们有增强宿主基因组自身进化,对环境变化作出反应的潜在能力,很可能是遗传多样性的主要源泉。     

Mammalian gene evolution: Nucleotide sequence divergence between mouse and rat

As a paradigm of mammalian gene evolution, the nature and extent of DNA sequence divergence between homologous protein-coding genes from mouse and rat have been investigated. The data set examined includes 363 genes totalling 411 kilobases, making this by far the largest comparison conducted between a single pair of species. Mouse and rat genes are on average 93.4% identical in nucleotide sequence and 93.9% identical in amino acid sequence. Individual genes vary substantially in the extent of nonsynonymous nucleotide substitution, as expected from protein evolution studies; here the variation is characterized. The extent of synonymous (or silent) substitution also varies considerably among genes, though the coefficient of variation is about four times smaller than for nonsynonymous substitutions. A small number of genes mapped to the X-chromosome have a slower rate of molecular evolution than average, as predicted if molecular evolution is male-driven. Base composition at silent sites varies from 33% to 95% G + C in different genes; mouse and rat homologues differ on average by only 1.7% in silent-site G + C, but it is shown that this is not necessarily due to any selective constraint on their base composition. Synonymous substitution rates and silent site base composition appear to be related (genes at intermediate G + C have on average higher rates), but the relationship is not as strong as in our earlier analyses. Rates of synonymous and nonsynonymous substitution are correlated, apparently because of an excess of substitutions involving adjacent pairs of nucleotides. Several factors suggest that synonymous codon usage in rodent genes is not subject to selection.     

Models of natural mutations including site heterogeneity

New computational models of natural site mutations are developed that account for the different selective pressures acting on different locations in the protein. The number of adjustable parameters is greatly reduced by basing the models on the underlying physical-chemical properties of the amino acids. This allows us to use our method on small data sets built of specific protein types. We demonstrate that with this approach we can represent the evolutionary patterns in HIV envelope proteins far better than with more traditional methods. Proteins 32:289–295, 1998. © 1998 Wiley-Liss, Inc.     

In vivo somatic microsatellite mutations identified in non-malignant human tissue

Microsatellite instability (MSI) has been described in cancer cells and in vitro cell lines, and meiotic changes in repeat length have also been documented. We report the novel observation of somatic microsatellite mutation (SMM) in normal human somatic cells in vivo, detected while genotyping 5,767 prenatal samples (4,640 amniotic fluid samples and 1,127 chorionic villus biopsies) as a diagnostic test for exclusion of trisomy 13, 18 or 21. Quantitative fluorescence-PCR using a multiplex of 12 primer pairs, for four loci on each of the three chromosomes, was followed by fragment analysis on a capillary-based genetic analyser. Forty-seven (4.2%) chorionic villus samples and six (0.1%) amniotic fluid samples showed allelic mosaicism, interpreted as SMM. In four cases, analysis of parental blood samples confirmed the presence of a de novo allele. SMM was detected at all but two of the 12 loci tested, and the incidence of mutation increased with repeat length. Detection of SMM in chorionic villus samples may imply less rigorous correction of replication errors in these extra-embryonic tissues, and is likely to have been facilitated by clonal expansion in the small samples of tissue tested. The presence of the same phenomenon in six amniotic fluid samples would imply that in these pregnancies, the instability event had occurred early in embryogenesis. The results suggest that defective proof reading during DNA replication may be more common in non-malignant human somatic tissue than previously recognised.     

Relation between protein stability, evolution and structure, as probed by carboxylic acid mutations

Native proteins are marginally stable. Low thermodynamic stability may actually be advantageous, although the accumulation of neutral, destabilizing mutations may have also contributed to it. In any case, once marginal stability has been reached, it appears plausible that mutations at non-constrained positions become fixed in the course of evolution (due to random drift) with frequencies that roughly reflect the mutation effects on stability ("pseudo-equilibrium hypothesis"). We have found that all glutamate-->aspartate mutations in wild-type Escherichia coli thioredoxin are destabilizing, as well as most of the aspartate-->glutamate mutations. Furthermore, the effect of these mutations on thioredoxin thermodynamic stability shows a robust correlation with the frequencies of occurrence of the involved residues in several-hundred sequence alignments derived from a BLAST search. These results provide direct and quantitative experimental evidence for the pseudo-equilibrium hypothesis and should have general consequences for the interpretation of mutation effects on protein stability, as they suggest that residue environments in proteins may be optimized for stabilizing interactions to a remarkable degree of specificity. We also provide evidence that such stabilizing interactions may be detected in sequence alignments, and briefly discuss the implications of this possibility for the derivation of structural information (on native and denatured states) from comparative sequence analyses.     

Molecular characterization and sequence analysis of human astroviruses circulating in Hungary

Human astroviruses (HAstVs) are major pathogens in viral gastroenteritis worldwide. Twenty-five HAstV strains were detected from stool specimens of children hospitalized for acute gastroenteritis in Budapest, Hungary, between 1995 and 1999. Sequence analysis was performed at the 3' end of the capsid gene to determine genotypic diversity of HAstVs circulating in Hungary. Five different genotypes of HAstVs were identified: HAstV-1 was predominant, followed by types 5, 8, 3 and 4. Two different subtypes of HAstV-1 were detected, but only one at a time in the community. This is the first report on the genetic diversity of HAstVs in Hungary and Central/Eastern Europe.