Different recombination site specificity of two developmentally regulated genome rearrangements

In the absence of a combined nitrogen source, such as ammonia, approximately every tenth vegetative cell along filaments of the cyanobacterium Anabaena develops into a heterocyst, a terminally differentiated cell that is morphologically and biochemically specialized for nitrogen fixation. At least two specific DNA rearrangements involving the nitrogen-fixation (nif) genes occur during heterocyst differentiation, one within the nifD gene and the other near the nifS gene. The two rearrangements have several properties in common. Both occur quantitatively in all heterocyst genomes, both occur at approximately the same developmental time, late in the process of heterocyst differentiation, and both result from site-specific recombination between short repeated DNA sequences. We report here the nucleotide sequences found at the site of recombination near the nifS gene. These sequences differ from those found previously for the nifD rearrangement, suggesting that the two rearrangements are catalysed by different enzymes and may be regulated independently. We also show that the nifS gene is transcribed only from rearranged genomes.     

Transmembrane structure and function of dctPQM encoding C4－dicarboxylate transport proteins from nitrogen－fixing P. stutzeri A1501

C4-dicarboxylate transport proteins of diazotroph Pseudomonas stutzeri were encoded by dctPQM genes. Nucleotide sequence analysis indicated that dctP, dctQ,and dctM grouped together. Its nucleotide and amino acid sequence shared high homology with that of dctP gene encoding periplasmic C4-dicarboxylate-binding protein and dctQM genes encoding C4-dicarboxylate transport proteins from the free-living nitrogen-fixing Aotobacter vinelandii.Structural analysis showed that DctP of P. stutzeri did not include membrane-spanning regions, and DctQ and DctM contained 5 and 12 transmembrane segments, respectively.The fragment containing the complete dctPQM genes was cloned into the Tn5 transposon region of suicide mobilization plasmid pSZ2L The resultant plasmid was named pSZY6.By triparental mating, Tn5 transposon carrying the dctPQM genes inserted into the genome of the wild type strain A1501,randomly. The recombinant strain A-142 which harboured an extra copy of dctPQM genes was constructed and identified by PCR amplification of npt II gene. When A-142 was grown in minimal medium with different concentrations (20,10 and 5mmol/L) of C4-dicarboxylates succinate, malate, or fumarate as the sole carbon source, the rate of nitrogen fixation assayed by acetylene reduction was significantly higher than that of the wild-type strain A150L This result was established that an extra copy of dctPQM genes could increase the activity of nitrogen fixation of P. stutzeri strain A1501.     

鱼腥藻PCC 7120染色体上relBE同源基因的克隆及表达

为研究鱼腥藻PCC7120染色体上与relBE同源的基因asl4561和asl4562表达产物的毒素-抗毒素作用,从鱼腥藻细胞中提取总基因组DNA,设计特异引物PCR扩增目的基因asl4561和asl4562,与T载体连接后经XhoI和EcoR I双酶切并与表达载体pET28a（＋）连接,由IPTG诱导表达,并在IPTG浓度和诱导时间上对asl4561基因的表达条件进行了优化.琼脂糖凝胶电泳显示扩增出了264bp的asl4561基因和213bp的asl4562基因,SDS-PAGE检测表明成功表达出15.65kD和13.55kD的两蛋白,当诱导温度28℃、IPTG浓度0.4 mmol/L、诱导时间6h时,asl4561基因表达蛋白在细菌裂解液上清中表达量最大.     

鱼腥藻PCC7120α质粒上的parD/E同源基因all7155/asl7156的克隆及表达

为研究鱼腥藻PCC7120质粒上毒素抗毒素系统的蛋白质性质和相互作用,根据NCBI中PCC7120的α质粒上的all7155和asl7156基因数据,通过降落PCR克隆了目的基因(all7155/336 bp,asl7156/258 bp).将目的基因片段连接至p MD18-T构建了克隆载体,蓝白斑筛选了阳性克隆,经双酶切纯化后将目的基因连接至表达载体p ET30a(+),并转入表达菌BL21中,测序后证实构建成功,并利用IPTG诱导进行了表达.通过NCBI的BLAST蛋白比对,发现了all7155和asl7156与已知的Par D/E毒素抗毒素系统同源,可通过对此基因的克隆,表达和蛋白性质来进一步认识Par D/E系统.     

Comparative chromosome mapping of a conserved homoeo box region in mouse and human

Specific genes are assumed to regulate pattern formation in the mammalian embryo, but as yet none has been identified unequivocally. It is possible that such genes in mammals may be identified by virtue of a conserved coding sequence, because many of the Drosophila melanogaster homoeotic and segmentation genes, which have crucial roles in the regulation of segmental pattern formation during embryonic development, contain a 180-base pair (bp) DNA sequence, the homoeo box, and that sequences homologous to the Drosophila homoeo box are also present in 6-10 copies in higher animals, including mammals. Although the assumption that the homoeo box identifies genes responsible for pattern formation in mammals remains to be validated, it is a particularly attractive hypothesis given the strong conservation of homoeo boxes over vast evolutionary distances. Here we report the localization of a human homoeo box region, previously cloned and shown to contain two homoeo boxes within a sequence of 5-kilobases (kb), to the long arm of chromosome 17. We show that two single-copy homoeo box-flanking probes derived from this region strongly hybridize to single-copy restriction fragments in mouse genomic DNA and that these conserved homoeo box-flanking sequences map to mouse chromosome 11. This may be significant as several genes that map to chromosome 17 in human also map to chromosome 11 in the mouse, implying that a segment of mouse chromosome 11 is homologous to a region of human chromosome 17. Taken together, these data suggest that the homoeo box region detected with our probes is highly conserved in human and mouse.     

人肿瘤坏死因子α在鱼腥藻7120中的表达

通过三亲结合转移方式,将含人肿瘤坏死因子α（ＴＮＦ－α）ｃＤＮＡ和ｐｓｂＡ启动子的鱼腥藻－大肠杆菌穿梭质粒ＰＤＣ－ＴＮＦ导入单细胞丝状鱼腹藻７１２０中。     

The Medicago genome provides insight into the evolution of rhizobial symbioses

Legumes (Fabaceae or Leguminosae) are unique among cultivated plants for their ability to carry out endosymbiotic nitrogen fixation with rhizobial bacteria, a process that takes place in a specialized structure known as the nodule. Legumes belong to one of the two main groups of eurosids, the Fabidae, which includes most species capable of endosymbiotic nitrogen fixation. Legumes comprise several evolutionary lineages derived from a common ancestor 60 million years ago (Myr ago). Papilionoids are the largest clade, dating nearly to the origin of legumes and containing most cultivated species. Medicago truncatula is a long-established model for the study of legume biology. Here we describe the draft sequence of the M. truncatula euchromatin based on a recently completed BAC assembly supplemented with Illumina shotgun sequence, together capturing ～94% of all M. truncatula genes. A whole-genome duplication (WGD) approximately 58 Myr ago had a major role in shaping the M. truncatula genome and thereby contributed to the evolution of endosymbiotic nitrogen fixation. Subsequent to the WGD, the M. truncatula genome experienced higher levels of rearrangement than two other sequenced legumes, Glycine max and Lotus japonicus. M. truncatula is a close relative of alfalfa (Medicago sativa), a widely cultivated crop with limited genomics tools and complex autotetraploid genetics. As such, the M. truncatula genome sequence provides significant opportunities to expand alfalfa's genomic toolbox.     

Initial sequence of the chimpanzee genome and comparison with the human genome

Here we present a draft genome sequence of the common chimpanzee (Pan troglodytes). Through comparison with the human genome, we have generated a largely complete catalogue of the genetic differences that have accumulated since the human and chimpanzee species diverged from our common ancestor, constituting approximately thirty-five million single-nucleotide changes, five million insertion/deletion events, and various chromosomal rearrangements. We use this catalogue to explore the magnitude and regional variation of mutational forces shaping these two genomes, and the strength of positive and negative selection acting on their genes. In particular, we find that the patterns of evolution in human and chimpanzee protein-coding genes are highly correlated and dominated by the fixation of neutral and slightly deleterious alleles. We also use the chimpanzee genome as an outgroup to investigate human population genetics and identify signatures of selective sweeps in recent human evolution.     

稀土元素镧对满江红鱼腥藻的生理影响

对稀土元素镧（Ｌａ）对满江红鱼腥藻（Ａｎａｂａｅｎａ ａｚｏｌｌａｅ）的生理影响和满江红鱼腥藻对镧的富集作用进行了研究。结果显示低浓度镧对满江红鱼腥藻生长表现出促进作用,高浓度则表现出抑制作用。镧对满江红鱼腥藻的叶绿素ａ的合成、光事放氧活性也有影响,同样表现为低浓度促进,高浓度抑制。满江红鱼腥藻对镧的富集作用可能与其光合作用电子传递和能量合成有关。     

固定化藻类对污水中磷的净化能力研究

采用海藻酸钙凝胶包埋固定藻类,对人工污水进行静态模拟净化试验,研究了蛋白核小球藻、突变衣藻、鱼腥藻和双对栅藻在固定和悬浮状态下对污水中磷的净化效率以及藻类的生长特性。结果表明：固定化藻细胞比悬浮态藻细胞具有生长更趋于稳定、藻类的活性保持时间更长的优势。4种藻类中,小球藻和鱼腥藻在污水中的生长状况更好,较适宜采用海藻酸钙凝胶包埋固定化技术。在固定状态下,蛋白核小球藻、突变衣藻、鱼腥藻和双对栅藻对磷的去除率在第3天达到最大值,分别为39.8%、28.3%、33.0%和30.7%。因此,小球藻更适用于去除污水中的磷,是较为优良的除磷藻种。     

转人粒细胞集落刺激因子(hG-CSF)基因的鱼腥藻的构建

本研究目的是构建转G-CSF基因的工程鱼腥藻Anabaena sp..首先将b型G-CSF克隆于中间载体pRL 439和穿梭表达载体pDC-8上.通过三亲接合转移将穿梭表达载体pDCG-CSF转入鱼腥藻内.通过PCR扩增的方法在转基因鱼腥藻中检测到G-CSF基因的存在.     

豆科植物-根瘤菌共生固氮的分子机理

与豆科植物－根瘤菌共生固氮有关的基因涉及根瘤菌基因和宿主基因，根瘤菌基因有结瘤基因（nodD,nodAB-CIJ和hsn基因），根瘤菌细胞表面结构基因（exs,lps和ndv基因）和固氮基因（nif和fix基因）；宿主基因主要是结瘤素基因（ENOD和NOD基因）。根瘤菌结瘤基因表达后诱导产生结瘤因子。在根瘤发育过程中，这些基因在根瘤菌与植物之间进行着信息交换，并且具有不同的表达水平。结瘤因子和植物激素对它们进行着调节。     

Second proteasome-related gene in the human MHC class II region

Antgen processing involves the generation of peptides from cytosolic proteins and their transport into the endoplasmic reticulum where they associate with major histocompatibility complex (MHC) class I molecules. Two genes have been identified in the MHC class II region, RING4 and RING11 in humans, which are believed to encode the peptide transport proteins. Attention is now focused on how the transporters are provided with peptides. The proteasome, a large complex of subunits with multiple proteolytic activities, is a candidate for this function. Recently we reported a proteasome-related sequence, RING10, mapping between the transporter genes. Here we describe a second human proteasome-like gene, RING12, immediately centromeric of the RING4 locus. Therefore RING12, 4, 10 and 11 form a tightly linked cluster of interferon-inducible genes within the MHC with an essential role in antigen processing.     

A general method for site-directed mutagenesis in prokaryotes

The genetic analysis of genes from prokaryotic species for which experimental genetic systems have not yet been developed is often limited by the difficulty of producing mutations in those genes. We report here a general technique applicable to Gram-negative prokaryotes for site-directed mutagenesis of cloned DNA fragments which we have applied to the study of the symbiotic nitrogen fixation genes of Rhizobium meliloti. In particular, we mutagenized cloned R. meliloti restriction fragments in Escherichia coli with transposon Tn5 and then replaced the wild-type parental DNA sequences with the mutant DNA sequences in the R. meliloti genome. Using this method we show that an R. meliloti DNA restriction fragment, cloned previously on the basis of homology to Klebsiella pneumoniae nif genes, contains gene(s) essential for symbiotic nitrogen fixation. In addition, we use this method to construct a physical genetic map of a subset of the R. meliloti nif genes.     

王锦蛇(Elaphe carinata)Sox基因保守区的克隆及测序

参照人SRY基因HMG-box保守区序列设计一对兼并引物,PCR扩增了王锦蛇的Sox基因,采用SSCP技术筛选阳性克隆,并对其进行了测序.结果在雌雄个体中共筛选出4个Sox基因,其中一个为雌性独有,显示出性别差异性;4个Sox基因DNA序列及编码的氨基酸序列与人相应SOX基因的相似性分别为91%、91%、92%、91%和96%、98%、96%、96%,显示出高度的保守性.实验结果为王锦蛇的性别决定机制研究提供了分子资料.     

分子进化中性理论的进展

中性理论与达尔文的自然选择进化论有明显的差别。中性论认为在分子水平上覆盖着多数的进化改变，是在连续产生突变时，由于选择中性（即选择相等），使突变得到随机的固定（即小群体内，样本的随机漂变）。还认为在分子水平上，大多数的种内变异（如蛋白质和ＤＮＡ多态）是选择中性或近于中性，它们能够保持在种内是由于突变的产生和随机消失之间的平衡引起的。近年来，ＤＮＡ顺序的研究资料，都有力地支持中性论，如鼠的拟球蛋白基因、鼹鼠的αＡ－晶状体蛋白、流行性感冒Ａ病毒基因，果蝇的核和线粒体基因等。所以，从地球上生命的历史来看，中性进化的改变至少在数量上已超过达尔文自然选择进化的改变。     

Proteorhodopsin in the ubiquitous marine bacterium SAR11

Proteorhodopsins are light-dependent proton pumps that are predicted to have an important role in the ecology of the oceans by supplying energy for microbial metabolism. Proteorhodopsin genes were first discovered through the cloning and sequencing of large genomic DNA fragments from seawater. They were later shown to be widely distributed, phylogenetically diverse, and active in the oceans. Proteorhodopsin genes have not been found in cultured bacteria, and on the basis of environmental sequence data, it has not yet been possible to reconstruct the genomes of uncultured bacterial strains that have proteorhodopsin genes. Although the metabolic effect of proteorhodopsins is uncertain, they are thought to function in cells for which the primary mode of metabolism is the heterotrophic assimilation of dissolved organic carbon. Here we report that SAR11 strain HTCC1062 ('Pelagibacter ubique'), the first cultivated member of the extraordinarily abundant SAR11 clade, expresses a proteorhodopsin gene when cultured in autoclaved seawater and in its natural environment, the ocean. The Pelagibacter proteorhodopsin functions as a light-dependent proton pump. The gene is expressed by cells grown in either diurnal light or in darkness, and there is no difference between the growth rates or cell yields of cultures grown in light or darkness.     

苦荞蛋白磷酸酶2C家族的鉴定及表达分析

为了研究苦荞蛋白磷酸酶2C(PP2C)家族的成员和分类,及后续探究其在苦荞生长发育中的功能,本文利用生物信息学方法对苦荞PP2C家族进行鉴定、分类,并对其基因结构、保守基序、分子进化等进行分析.结果表明,苦荞PP2C家族有81个成员,划分为A-K的11个亚族,并且在同亚族中序列特征相似,而不同亚族间序列特征有一定差异;苦荞PP2C家族有14次基因重复事件.此外,qRT-PCR分析结果表明其A亚族基因在苦荞根、茎、叶、花、果中均有表达,除FtPP2C44外的8个基因在苦荞花、果中表达量较高;在苦荞幼苗中,除FtPP2C08外的8个基因均受ABA诱导表达量上调.上述结果揭示了苦荞PP2C家族的成员组成、序列特征、扩增和其A亚族基因的组织表达模式及受ABA诱导表达情况.