植物莽草酸途径EPSPS蛋白的分子进化和基因结构分析

EPSPS既是植物、微生物和真菌等生物芳香族氨基酸生物合成途径——莽草酸途径中的关键酶,也是除草剂草甘膦的靶标酶。EPSPS的克隆能为草甘膦抗性转基因作物的研发提供候选基因。该研究运用比较基因组学方法,通过对41种不同植物的43条EPSPS蛋白序列进行进化分析,取得主要结果如下:(1)不同植物EPSPS蛋白的相似性很高,且具有相同的结构域、保守基序和保守位点,但是其叶绿体转运肽序列差异显著;(2)系统发育分析表明,EPSPS基因按照双子叶植物纲和单子叶植物纲分为2个大的分支,各个小的分支又按照植物的种属亲缘关系进行分支和聚类;(3)基因结构分析表明,植物EPSPS基因基本都含有8个外显子和7个内含子,且所对应外显子的长度相当,而内含子的长度差异很大,说明在植物基因组进化过程中造成EPSPS基因结构差异的主要因素是内含子的改变。研究结果将为揭示植物EPSPS蛋白的结构功能提供参考。     

Partial structure of the gene for chicken cartilage proteoglycan core protein

A genomic DNA fragment (gCORE-1), encoding a portion of the cartilage proteoglycan core protein, has been isolated from a phage library using cDNA as a probe. The genomic insert is about 17 kilobase pairs; two BamHI fragments of the insert (1.3 and 4.8 kilobase pairs) contain most of the hybridizable sequences found in the cDNA. Sequence analysis of these fragments shows that they contain a total of five exons that encompass 216 amino acid residues, all of which are identical to those of the corresponding cDNA sequence. Three of the exons, which are adjacent to one another, are very similar to the corresponding exons in the gene of a rat hepatic lectin as well as to an exon in the gene of human pulmonary surfactant-associated protein. There is a strong degree of conservation of amino acid sequences encoded in the three genes, although there is no similarity between their introns. The sizes of the five exons in gCORE-1, except for one (which is indeterminate because only a partial cDNA sequence is available), are less than 184 base pairs, whereas the sizes of the introns range from 218 to greater than 2629 base pairs. Four of the introns interrupt an exon codon at either their donor or acceptor sites, between the first and second nucleotides. Only one intron does not split a codon. Intron and exon boundary sites are in agreement with known consensus sequences for introns. The dispersed distribution and relatively small size of the exons, if representative of the entire gene, suggest that the complete gene which codes for the core protein may be quite sizable.     

Isolation and characterization of the mouse CD8 beta-chain (Ly-3) genes. Absence of an intervening sequence between V- and J-like gene segments

We have isolated and determined the nucleotide sequence and genomic organization of the genes encoding Ly-3.1 and Ly-3.2. These genes span approximately 14 kb on chromosome 6 and consist of six exons and five introns. The exons correlate roughly with the putative functional domains, namely, a leader exon, a variable and joining region-like exon, a hinge region-like exon, a transmembrane exon, and two intracytoplasmic exons. There is no intervening sequence between V- and J-like gene segments, indicating that rearrangement is not necessary for the expression of the Ly-3 gene. In the 5'-flanking region there is no "TATA" box nor "CAAT" box; however, three "GC" boxes are located upstream of the ATG initiator codon. There are short stretches of sequence homologous to 5'-flanking sequences of the Ly-2 gene. In addition, the sequences CTCTGTGGCA at -748 exhibits homology to the enhancer core sequence of the human Ig H chain and TCR genes. Comparison of the nucleotide sequence corresponding to the extracellular portion between Ly-3.1 and Ly-3.2 revealed a single base difference which results in an amino acid substitution. Therefore it is likely that this amino acid difference is responsible for the previously defined Ly-3 allotypes.     

Cloning and characterization of the carp prolactin gene

A carp genomic DNA clone containing the carp prolactin (Prl) gene was isolated with carp Prl cDNA as a probe. The organization of the carp Prl gene was determined by restriction nuclease mapping and nucleotide sequencing. The Prl gene comprises approx. 2.8 kilobasepairs (kb) of DNA including the 5'-flanking region, five exons, four introns and the 3'-flanking region. Analysis of the 5'-flanking region reveals (1) the sequence TATATAAT at positions -38 to -31 upstream from the cap site which was found to be a guanine residue, and (2) the palindrome, CTCATTGCATATACAAATGAG at positions -79 to -59. The carp Prl gene matches with the reported cDNA except for one difference in coding region and five in the 3'-flanking region, while the encoded amino acid sequences are identical. The arrangement of exons and introns is very similar to that seen in carp GH as well as mammalian Prl, which, however, have much longer introns.     

Characterization of the major histocompatibility complex class II genes in miiuy croaker

Major histocompatibility complex (MHC) has a central role in the adaptive immune system by presenting foreign peptide to the T-cell receptor. In order to study the molecular function and genomic characteristic of class II genes in teleost, the full lengths of MHC class IIA and IIB cDNA and genomic sequence were cloned from miiuy croaker (Miichthys miiuy). As in other teleost, four exons and three introns were identified in miiuy croaker class IIA gene; but the difference is that six exons and five introns were identified in the miiuy croaker class IIB gene. The deduced amino acid sequence of class IIA and class IIB had 26.3-85.7% and 11.0-88.8% identity with those of mammal and teleost, respectively. Real-time quantitative RT-PCR demonstrated that the MHC class IIA and IIB were ubiquitously expressed in ten normal tissues; expression levels of MHC genes were found first upregulated and then downregulated, and finally by a recovery to normal level throughout the pathogenic bacteria infection process. In addition, we report on the underlying mechanism that maintains sequences diversity among many fish species. A series of site-model tests implemented in the CODEML program revealed that positive Darwinian selection is likely the cause of the molecular evolution in the fish MHC class II genes.     

cDNA structure, alternative splicing and exon-intron organization of the predisposing tuberous sclerosis (Tsc2) gene of the Eker rat model.

The Eker rat hereditary renal carcinoma (RC) is an excellent example of a Mendelian dominant predisposition to a specific cancer in an experimental animal. We recently reported that a germline insertion in the rat homologue of the human tuberous sclerosis gene (TSC2) gives rise to the dominantly inherited cancer in the Eker rat model. We now describe the entire cDNA (5375 bp without exons 25 and 31) and genomic structure of the rat Tsc2 gene. The deduced amino acid sequence (1743 amino acids) shows 92% identity to the human counterpart. Surprisingly, there are a great many (> or = 41) coding exons with small sized introns spanning only approximately 35 kb of genomic DNA. Two alternative splicing events [involving exons 25 (129 bp) and 31 (69 bp)] make for a complex diversity of the Tsc2 product. The present determination of the Tsc2 gene and establishment of strong conservation between the rat and man provide clues for assessing unknown gene functions apart from that already predicted from the GTPase activating proteins (GAP3) homologous domain and for future analysis of intragenic mutations in tumors using methods such as PCR-SSCP and for insights into diverse phenotypes between species.     

一步法RT-PCR克隆水稻线粒体磷转运蛋白基因及其序列特征分析

以水稻广亲和品种Cpslo17幼穗为材料,用一步法RT—PCR（逆转录聚合酶链式反应）克隆了一个长度为1118bp的编码线粒体磷转运蛋白的OsMPT基因。序列分析表明其包含了基因完整的编码序列,编码由368个氨基酸组成的线粒体磷转运蛋白,它与玉米、大豆、Lotus japonicus、Betula pendula、拟南芥的线粒体磷转运蛋白氨基酸序列相似率分别为93．5％,85．6％,83．8％,83．7％,81．1％。氨基酸疏水谱分析显示它有线粒体磷转运蛋白家族高度保守的6个跨膜结构域。水稻线粒体磷转运蛋白N端富含精氨酸（Arginine）、丙氨酸（Alanine）和丝氨酸（Serine）。iPSORT预测其蛋白N端具有定位于线粒体的信号肽序列,进一步分析表明此编码区段有6个外显子和5个内含子。RT—PCR结果表明,OsMPT基因在水稻两个亚种粳稻和籼稻的叶片中均有表达,在Cpslo17营养器官和生殖器官中都有高水平表达。水稻线粒体磷转运蛋白的克隆和表达分析将为研究其结构和生物学功能奠定基础。     

Comparative evolutionary rates of introns and exons in murine rodents

Analysis of DNA sequences of 132 introns and 140 exons from 42 pairs of orthologous genes of mouse and rat was used to compare patterns of evolutionary change between introns and exons. The mean of the absolute difference in length (measured in base pairs) between the two species was nearly five times as high in the case of introns as in the case of exons. The average rate of nucleotide substitution in introns was very similar to the rate of synonymous substitution in exons, and both were about three times the rate of substitution at nonsynonymous sites in exons. G+C content of introns and exons of the same gene were correlated; but mean G+C content at the third positions of exons was significantly higher than that of introns or positions 1–2 of exons from the same gene. G+C content was conserved over evolutionary time, as indicated by strong correlations between mouse and rat; but the change in G+C content was greatest at position 3 of exons, intermediate in introns, and lowest at positions 1–2 in introns. Received: 23 December 1996 / Accepted: 1 April 1997     

The rabbit muscle phosphofructokinase gene. Implications for protein structure, function, and tissue specificity

Sequence homologies between bacterial and rabbit muscle phosphofructokinases and between the amino- and carboxyl-terminal halves of the latter suggest that the mammalian enzyme evolved from a prokaryotic progenitor by gene duplication and divergence (Poorman, R. A., Randolph, A., Kemp, R. G., and Heinrikson, R. L. (1984) Nature 309, 467-469). We have isolated the gene for the rabbit enzyme and determined the nucleotide sequence for all the exons and most of the introns. This represents the first eukaryotic phosphofructokinase gene ever sequenced. The cloned gene is 17 kilobase pairs long. The coding sequence for 780 amino acids is split into 22 exons ranging in size from 15 to 63 codons. Sequence analysis shows that 75% of the bases at the third position of the codons in these exons are either G or C. Exons XV and XVI code for the 30 amino acid residues which were left unidentified in the published primary structure for this enzyme. When overlaid on the structure of the protein, most of the introns are located between or near the ends of the secondary structural elements but not at analogous positions in the two protein-coding halves of the gene.     

Structure, sequence, and polymorphism of the Lyt-2 T cell differentiation antigen gene

We have determined the nucleotide sequence and genomic organization of the mouse Lyt-2 T lymphocyte differentiation antigen gene. This gene consists of five exons and four introns, and the organization roughly parallels the protein domains. Alternative splicing to include or exclude exon IV (encoding part of the cytoplasmic tail) results in two forms of mRNA and accounts for the difference in size between the alpha- and alpha'-chains of Lyt-2. The gene structure provides further evidence for the evolutionary relationship between Lyt-2 and immunoglobulin genes. Comparison of the nucleotide sequence of the Lyt-2.1 and Lyt-2.2 alleles shows a high degree of conservation, but indicates that a single nucleotide change and consequent amino acid substitution in the variable region-like domain accounts for the serologic difference between these two alleles.     

Structural organization and complete sequence of the human alpha-N-acetylgalactosaminidase gene: homology with the alpha-galactosidase A gene provides evidence for evolution from a common ancestral gene.

Human alpha-N-acetylgalactosaminidase (alpha-GalNAc; EC 3.2.1.49), the lysosomal glycohydrolase that cleaves alpha-N-acetylgalactosaminyl moieties in glycoconjugates, is encoded by a gene localized to chromosome 22q13----qter. The deficient activity of this enzyme results in Schindler disease, an autosomal recessive disorder characterized by the increased urinary excretion of glycopeptides and oligosaccharides containing alpha-N-acetylgalactosaminyl moieties. Recently, the 3.6-kb full-length alpha-GalNAc cDNA sequence was isolated and found to have remarkable nucleotide and predicted amino acid homology (55.8 and 46.9%, respectively) with the human alpha-galactosidase A (alpha-Gal A) cDNA. To investigate the possible evolutionary relatedness of the two glycosidases, the alpha-GalNAc chromosomal gene was isolated and characterized. Screening of a human genomic DNA cosmid library resulted in the identification of a clone, gAGB-1, with an approximately 35-kb insert that contained the entire alpha-GalNAc gene. A single approximately 15-kb EcoRI fragment of gAGB-1, which contained the complete 3.6-kb cDNA sequence, was digested and the subcloned fragments were sequenced in both orientations. The 13,709-bp alpha-GalNAc gene had nine exons ranging from 95 to 2028 bp and intronic sequences of 304 to 2684 bp. All exon/intron junctions conformed to the GT/AG consensus rule. Analysis of 1.4 kb of 5' flanking sequence revealed three Sp1 and two CAAT-like promoter elements. This region was GC-rich (56%), but no HTF island was identified. The gene contained six Alu-repetitive elements, all in the reverse orientation. Comparison of the structural organization of the alpha-GalNAc and the alpha-Gal A genes revealed that all six alpha-Gal A introns were identically positioned in the homologous alpha-GalNAc exonic sequence. Two additional introns, 1 and 8, were identfied in the alpha-GalNAc gene. The predicted amino acid sequences of alpha-GalNAc exons 2 through 7 and those of corresponding alpha-Gal A exons 1 through 6 were 46.2 to 62.7% identical. In contrast, there was little, if any, similarity between the deduced amino acid sequences of alpha-Gal A exon 7 and alpha-GalNAc exons 8 and 9. The remarkable amino acid identity and the identical exonic interruption by six introns of the alpha-GalNAc and alpha-Gal A genes suggest that this region in both genes is evolutionarily related and arose through duplication and divergence from a common ancestral gene.     

猪CAPN1基因部分外显子及3′UTR区的SNPs检测

以野猪、民猪和大白猪为研究对象, 根据网上公布的序列设计了7对引物, 采用测序、PCR-SSCP和PCR-RFLP方法对CAPN1基因的部分外显子和3′UTR区进行了单核苷酸多态性检测和基因型分析, 探讨CAPN1基因多态性与瘦肉率和嫩度的关系。研究发现11个SNPs, 其中5个位于外显子, 4个位于内含子, 2个位于3′UTR区, 外显子中的突变有一处是错义突变, 导致了蛋白质多肽链第260位氨基酸发生了M/V的替代。群体遗传学分析表明, 在所检测的各多态位点上, 野猪、民猪、大白猪3个品种间不同基因型的分布都存在着极显著的差异(P<0.01), 而野猪和民猪之间各基因型的分布差异不显著(P>0.05), 民猪和大白猪之间各基因型的分布存在着极显著的差异(P<0.01)。结合品种特性分析表明, P4、P6引物和3′ UTR区HinfⅠ位点所检测的不同基因型和瘦肉率具有一定的相关性。     

苹果酸度相关基因MdPH1的克隆、表达及亚细胞定位分析

以苹果属（Malus）植物沧江海棠（M.ombrophila Hand.-Mazz）的果实为材料,对其发育过程中苹果酸的含量进行测定,并结合转录组测序的方法筛选控制果实酸度的候选基因。结果显示：MdPH1候选基因的编码区包含2829 bp,编码942个氨基酸;基因组序列全长为4269 bp,包含8个外显子和7个内含子。对10份苹果种质资源中PH1基因序列的分析结果表明,该基因序列中存在22个单核苷酸多态性（SNP）,其中13个位于内含子区,9个位于外显子区;位于最后一个外显子上SNP（G/A）的变异导致了编码氨基酸从缬氨酸变为异亮氨酸。MdPH1蛋白包含8个跨膜结构域,其中蛋白N端包含3个跨膜结构域,C端包含5个跨膜结构域。系统进化分析结果显示,苹果中的PH家族成员与梨（Pyrus communis L.）中的PH家族成员聚集成一簇。组织特异性表达结果发现,MdPH1基因在苹果果实中的表达量最高,其次是叶、花和根,茎中表达量最低。亚细胞定位分析表明MdPH1蛋白定位于液泡膜上。