Multiple Inter-Kingdom Horizontal Gene Transfers in the Evolution of the Phosphoenolpyruvate Carboxylase Gene Family

Pepcase is a gene encoding phosphoenolpyruvate carboxylase that exists in bacteria, archaea and plants,playing an important role in plant metabolism and development. Most plants have two or more pepcase genes belonging to two gene sub-families, while only one gene exists in other organisms. Previous research categorized one plant pepcase gene as plant-type pepcase (PTPC) while the other as bacteria-type pepcase (BTPC) because of its similarity with the pepcase gene found in bacteria. Phylogenetic reconstruction showed that PTPC is the ancestral lineage of plant pepcase, and that all bacteria, protistpepcase and BTPC in plants are derived from a lineage of pepcase closely related with PTPC in algae. However, their phylogeny contradicts the species tree and traditional chronology of organism evolution. Because the diversification of bacteria occurred much earlier than the origin of plants, presumably all bacterialpepcase derived from the ancestral PTPC of algal plants after divergingfrom the ancestor of vascular plant PTPC. To solve this contradiction, we reconstructed the phylogeny of pepcase gene family. Our result showed that both PTPC and BTPC are derived from an ancestral lineage of gamma-proteobacteriapepcases, possibly via an ancient inter-kingdom horizontal gene transfer (HGT) from bacteria to the eukaryotic common ancestor of plants, protists and cellular slime mold. Our phylogenetic analysis also found 48other pepcase genes originated from inter-kingdom HGTs. These results imply that inter-kingdom HGTs played important roles in the evolution of the pepcase gene family and furthermore that HGTsare a more frequent evolutionary event than previouslythought.     

绵羊Cytb基因序列多态性及系统进化研究

以8个中国地方绵羊品种和1个外来品种的20个个体为研究对象,通过对Cytb基因的全序列测定,结果表明：绵羊的单倍型多样性为97．1％。所有序列的平均碱基组成为27．1％T,28．5％C,31．4％A及13．0％G,G＋C含量为41．5％,核苷酸多样性为0．602％。在所有序列中共检测到43个变异位点,其中包括40处转换和3处颠换。Fu’S中性检验表明差异不显著（0．10〉P〉0．05）,说明绵羊群体未发生群体扩张事件。NJ、ME及UPGMA聚类结果均表明,我国绵羊可分为3个单倍型组,这提示我国绵羊有3个母系起源。     

Empirical Relationship between Intra-Purine and Intra-Pyrimidine Differences in Conserved Gene Sequences

DNA sequences seen in the normal character-based representation appear to have a formidable mixing of the four nucleotides without any apparent order. Nucleotide frequencies and distributions in the sequences have been studied extensively, since the simple rule given by Chargaff almost a century ago that equates the total number of purines to the pyrimidines in a duplex DNA sequence. While it is difficult to trace any relationship between the bases from studies in the character representation of a DNA sequence, graphical representations may provide a clue. These novel representations of DNA sequences have been useful in providing an overview of base distribution and composition of the sequences and providing insights into many hidden structures. We report here our observation based on a graphical representation that the intra-purine and intra-pyrimidine differences in sequences of conserved genes generally follow a quadratic distribution relationship and show that this may have arisen from mutations in the sequences over evolutionary time scales. From this hitherto undescribed relationship for the gene sequences considered in this report we hypothesize that such relationships may be characteristic of these sequences and therefore could become a barrier to large scale sequence alterations that override such characteristics, perhaps through some monitoring process inbuilt in the DNA sequences. Such relationship also raises the possibility of intron sequences playing an important role in maintaining the characteristics and could be indicative of possible intron-late phenomena.     

miR396基因家族的进化及功能分析

MicroRNA(miRNA)是由约22个核苷酸组成的内源性非编码小分子RNA,广泛存在于真核细胞中,通过与靶基因的互补配对在转录后水平对基因表达进行调控,导致mRNA的降解或翻译抑制。本文通过对目前miRBase中收录的miR396家族进行生物信息学分析发现,该家族在植物界中高度保守,它们可能起源于较为古老的物种,经历长期复杂的进化过程而保留了下来;靶基因预测结果显示生长调控因子GRF为其主要靶标;启动子分析表明, miR396编码基因的上游存在光、温度、激素、厌氧、干旱及病害等胁迫响应相关的顺式作用元件,它们可与转录因子结合,参与多种胁迫应答反应。本文可为全面深入研究miRNA的作用机制奠定基础。     

Analysis of the Genetic Diversity and the Phylogenetic Evolution of Chinese Sheep Based on Cyt b Gene Sequences

The complete sequences of Cyt b gene from 20 individuals belonging to eight Chinese indigenous sheep breeds and one foreign breed were studied. The results showed that the hapolotype diversity of Chinese sheep breeds was 97.1%. The mean nucleotide composition of all the sequences was 27.1% T, 28.5% C, 31.4% A, and 13.0% G. The nucleotide diversity was 0.602%. A total of 43 mutation sites were detected, including 40 transitions and 3 transversions. Fu's test of selective neutrality showed that the sheep populations had no population demographic expansion (0.10 > P > 0.05). The different clustering methods, namely neighbor-joining, minimum evolution, and unweighted pair group method with arithmetic means, all showed a similar result, which indicated that Chinese local sheep had three maternal resources.     

Evolution of the Hedgehog Gene Family

Effective intercellular communication is an important feature in the development of multicellular organisms. Secreted hedgehog (hh) protein is essential for both long- and short-range cellular signaling required for body pattern formation in animals. In a molecular evolutionary study, we find that the vertebrate homologs of the Drosophila hh gene arose by two gene duplications: the first gave rise to Desert hh, whereas the second produced the Indian and Sonic hh genes. Both duplications occurred before the emergence of vertebrates and probably before the evolution of chordates. The amino-terminal fragment of the hh precursor, crucial in long- and short-range intercellular communication, evolves two to four times slower than the carboxyl-terminal fragment in both Drosophila hh and its vertebrate homologues, suggesting conservation of mechanism of hh action in animals. A majority of amino acid substitutions in the amino- and carboxyl-terminal fragments are conservative, but the carboxyl-terminal domain has undergone extensive insertion-deletion events while maintaining its autocleavage protease activity. Our results point to similarity of evolutionary constraints among sites of Drosophila and vertebrate hh homologs and suggest some future directions for understanding the role of hh genes in the evolution of developmental complexity in animals.     

Evolution of the Vertebrate Resistin Gene Family

Resistin (encoded by Retn) was previously identified in rodents as a hormone associated with diabetes; however human resistin is instead linked to inflammation. Resistin is a member of a small gene family that includes the resistin-like peptides (encoded by Retnl genes) in mammals. Genomic searches of available genome sequences of diverse vertebrates and phylogenetic analyses were conducted to determine the size and origin of the resistin-like gene family. Genes encoding peptides similar to resistin were found in Mammalia, Sauria, Amphibia, and Actinistia (coelacanth, a lobe-finned fish), but not in Aves or fish from Actinopterygii, Chondrichthyes, or Agnatha. Retnl originated by duplication and transposition from Retn on the early mammalian lineage after divergence of the platypus, but before the placental and marsupial mammal divergence. The resistin-like gene family illustrates an instance where the locus of origin of duplicated genes can be identified, with Retn continuing to reside at this location. Mammalian species typically have a single copy Retn gene, but are much more variable in their numbers of Retnl genes, ranging from 0 to 9. Since Retn is located at the locus of origin, thus likely retained the ancestral expression pattern, largely maintained its copy number, and did not display accelerated evolution, we suggest that it is more likely to have maintained an ancestral function, while Retnl, which transposed to a new location, displays accelerated evolution, and shows greater variability in gene number, including gene loss, likely evolved new, but potentially lineage-specific, functions.     

Evolution of the Growth Hormone Gene Family

SYNOPSIS. Growth hormone, prolactin and chorionic somatomammotropin(placental lactogen) area family of hormones that are relatedby function, immunochemistry and structure. Because of the structuralsimilarities between these hormones, it was proposed that thecorresponding genes were derived from a common precursor geneby duplication and sequence divergence. Comparisons of the mRNAsequences and chromosomal genes for these hormones from severalspecies provide additional support for the model of their commonancestry and indications of how the precursor genewas formed.The diversification of these three genes has involved changesin codon choices thataffect the overall G-C content of the genes,alterations in the sizes of introns with conservedexon-intronboundaries and concerted evolutionary mechanisms with duplicatedgrowth hormone andhorionic somatomammotropin genes in humans.The precursor gene appears to have evolved by the fourfold duplicationof one exon element and the separate insertion of an exon encodinga different protein domain. Finally, there also appears to havebeen the separate insertion of sequences containing a promoterelement and a potential glucocorticoid regulatory element.     

Molecular and Genetic Analysis of the Snf7 Gene in Saccharomyces Cerevisiae

Mutations in the SNF7 gene of Saccharomyces cerevisiae prevent full derepression of the SUC2 (invertase) gene in response to glucose limitation. We report the molecular cloning of the SNF7 gene by complementation. Sequence analysis predicts that the gene product is a 27-kDa acidic protein. Disruption of the chromosomal locus causes a fewfold decrease in invertase derepression, a growth defect on raffinose, temperature-sensitive growth on glucose, and a sporulation defect in homozygous diploids. Genetic analysis of the interactions of the snf7 null mutation with ssn6 and spt6/ssn20 suppressor mutations distinguished SNF7 from the SNF2, SNF5 and SNF6 genes. The snf7 mutation also behaved differently from mutations in SNF1 and SNF4 in that snf7 ssn6 double mutants displayed a synthetic phenotype of severe temperature sensitivity for growth. We also mapped SNF7 to the right arm of chromosome XII near the centromere.     

吉富罗非鱼雌雄群体遗传差异的SSR分析

为探讨吉富罗非鱼(genetic improvement of farmed tilapia,GIFT)雌、雄群体间的遗传差异,本研究对国家级广西南宁罗非鱼良种场雌、雄吉富罗非鱼进行了遗传差异分析。研究结果表明,选取的11对SSR引物中有10对能获得稳定的目的条带;每个SSR基因座的等位基因数在2～4个之间,雌性罗非鱼的平均等位基因(Na)2.9个,稍高于雄性的2.8个;雌、雄吉富罗非鱼平均观察杂合度(HO)分别为0.4183和0.4154,多态信息含量(PIC)分别为0.4048和0.3932,属中度多态;雌雄个体间的遗传距离和相似性指数分别为0.0908和0.9132。此外,SSR基因座PRL-SO2在雄鱼中偏离Hardy Weinberg平衡(P0.005)。上述结果表明,吉富罗非鱼雌、雄群体的SSR多态性基本相同,推测这两者基因组间的差异较小。     

Let-7a 下调 k-Ras 和 c-Myc 癌基因的表达抑制肾癌细胞增殖

摘要 目的： MicroRNA 是近年发现的一类单链小分子 RNA, 对它的研究已成为一个新的热点。最近的研究发现, 1et-7a 在细胞内 影响着基因的表达调控,在疾病发生中起着及极重要的作用, 尤其是在肿瘤的发展过程中, let-7a 扮演着不可替代的角色。本文主 要研究 let-7a 在肾癌细胞株中的表达情况及其调控的靶基因、 抑制细胞增殖的机制,对探索肾癌的致病基因, 寻求肾癌新的治疗 途径有重要意义。 方法： 应用化学合成的 let-7a 拟物（ mimics ）用脂质体 Lipofectamine 2000 在体外瞬时转染 786-O 和 Caki-1 肾 癌细胞株, 转染 48 小时后采用荧光定量 RT-PCR 的方法检测 let-7a 及 c-Myc、 k-Ras mRNA 的表达情况, Western blot 检测这两株 肾癌细胞转染了 let-7a mimics 后 c-Myc 及 k-Ras 蛋白的表达变化;转染 let-7a mimics 后分别在 24、 48、 72 小时三个时间点用 CCK-8 试剂盒检测对肾癌细胞株增殖的影响。 结果： 786-O 和 Caki-1 肾癌细胞株中 let-7a 的表达量明显低于正常肾小管上皮细胞 株 HK-2 （P<0.05 ） ; 转染了 let-7amimics 的 786-O 和 Caki-1 肾癌细胞株, RT-PCR 及 Western blot 结果显示 c-Myc、 k-Ras 在基因及 蛋白的表达水平明显下调 （P<0.05 ） ; CCK-8 检测结果显示转染了 let-7a mimics 的肾癌细胞株细胞增殖能力明显明显受到抑制, 与 阴性对照组比较差异有统计学意义 （P<0.05 ）。结论： Let-7a 在在肿瘤细胞与正常细胞中存在明显差异, let-7a 通过调控 c-Myc、 k-Ras 的表达能抑制肾癌细胞增殖。 Let-7a mimics 可以抑制肾癌细胞的增殖,因此上调 Let-7a 的表达有可能成为肾癌基因治疗的 一种有效治疗手段。     

Let-7a下调k-Ras和c-Myc癌基因的表达抑制肾癌细胞增殖

目的：MicroRNA 是近年发现的一类单链小分子RNA,对它的研究已成为一个新的热点。最近的研究发现,1et-7a 在细胞内影响着基因的表达调控,在疾病发生中起着及极重要的作用,尤其是在肿瘤的发展过程中,let-7a扮演着不可替代的角色。本文主要研究let-7a 在肾癌细胞株中的表达情况及其调控的靶基因、抑制细胞增殖的机制,对探索肾癌的致病基因,寻求肾癌新的治疗途径有重要意义。方法：应用化学合成的let-7a 模拟物（mimics）用脂质体Lipofectamine 2000 在体外瞬时转染786-O 和Caki-1肾癌细胞株,转染48 小时后采用荧光定量RT-PCR的方法检测let-7a 及c-Myc、k-Ras mRNA的表达情况,Western blot 检测这两株肾癌细胞转染了let-7a mimics 后c-Myc 及k-Ras 蛋白的表达变化;转染let-7a mimics 后分别在24、48、72 小时三个时间点用CCK-8 试剂盒检测对肾癌细胞株增殖的影响。结果：786-O 和Caki-1 肾癌细胞株中let-7a 的表达量明显低于正常肾小管上皮细胞株HK-2（P〈0.05）; 转染了let-7amimics的786-O 和Caki-1 肾癌细胞株,RT-PCR 及Western blot 结果显示c-Myc、k-Ras 在基因及蛋白的表达水平明显下调（P〈0.05）;CCK-8 检测结果显示转染了let-7a mimics的肾癌细胞株细胞增殖能力明显明显受到抑制,与阴性对照组比较差异有统计学意义（P〈0.05）。结论：Let-7a 在在肿瘤细胞与正常细胞中存在明显差异,let-7a 通过调控c-Myc、k-Ras的表达能抑制肾癌细胞增殖。Let-7a mimics 可以抑制肾癌细胞的增殖,因此上调Let-7a 的表达有可能成为肾癌基因治疗的一种有效治疗手段。     

Evolution of the Metazoan-Specific Importin α Gene Family

Importin αs are import receptors for nuclear localization signal-containing proteins. Most animal importin αs assort into α1, α2, and α3 groups. Studies in Drosophila melanogaster, Caenorhabditis elegans, and mouse suggest that the animal importin α gene family evolved from ancestral plant-like genes to serve paralog-specific roles in gametogenesis. To explore this hypothesis we extended the phylogenetic analysis of the importin α gene family to nonbilateral animals and investigated whether animal-like genes occur in premetazoan taxa. Maximum likelihood analysis suggests that animal-like importin α genes occur in the Choanoflaggelate Monosiga brevicollis and the amoebozoan Dictyostelium; however, both of these results are caused by long-branch attraction effects. The absence of animal-like α genes in premetazoan taxa is consistent with the hypothesis that they duplicated and then specialized to function in animal gametogenesis. The gene structures of the importin αs provide insight into how the animal importin α gene family may have evolved from the most likely ancestral gene. Interestingly, animal α1s are more similar to plant and fungal α1-like sequences than they are to animal α2s or α3s. We show that animal α1 genes share most of their introns with plant α1-like genes, and α2s and α3s share many more intron positions with each other than with the α1s. Together, phylogenetics and gene structure analysis suggests a parsimonious path for the evolution of the mammalian importin α gene family from an ancestral α1-like progenitor. Finally, these results establish a rational basis for a unified nomenclature of the importin α gene family.     

Rapid Evolution of the Sequences and Gene Repertoires of Secreted Proteins in Bacteria

Proteins secreted to the extracellular environment or to the periphery of the cell envelope, the secretome, play essential roles in foraging, antagonistic and mutualistic interactions. We hypothesize that arms races, genetic conflicts and varying selective pressures should lead to the rapid change of sequences and gene repertoires of the secretome. The analysis of 42 bacterial pan-genomes shows that secreted, and especially extracellular proteins, are predominantly encoded in the accessory genome, i.e. among genes not ubiquitous within the clade. Genes encoding outer membrane proteins might engage more frequently in intra-chromosomal gene conversion because they are more often in multi-genic families. The gene sequences encoding the secretome evolve faster than the rest of the genome and in particular at non-synonymous positions. Cell wall proteins in Firmicutes evolve particularly fast when compared with outer membrane proteins of Proteobacteria. Virulence factors are over-represented in the secretome, notably in outer membrane proteins, but cell localization explains more of the variance in substitution rates and gene repertoires than sequence homology to known virulence factors. Accordingly, the repertoires and sequences of the genes encoding the secretome change fast in the clades of obligatory and facultative pathogens and also in the clades of mutualists and free-living bacteria. Our study shows that cell localization shapes genome evolution. In agreement with our hypothesis, the repertoires and the sequences of genes encoding secreted proteins evolve fast. The particularly rapid change of extracellular proteins suggests that these public goods are key players in bacterial adaptation.