The methylated component of the Neurospora crassa genome

Cytosine methylation is common, but not ubiquitous, in eukaryotes. Mammals and the fungus Neurospora crassa have about 2-3% of cytosines methylated. In mammals, methylation is almost exclusively in the under-represented CpG dinucleotides, and most CpGs are methylated whereas in Neurospora, methylation is not preferentially in CpG dinucleotides and the bulk of the genome is unmethylated. DNA methylation is essential in mammals but is dispensable in Neurospora, making this simple eukaryote a favoured organism in which to study methylation. Recent studies indicate that DNA methylation in Neurospora depends on one DNA methyltransferase, DIM-2 (ref. 6), directed by a histone H3 methyltransferase, DIM-5 (ref. 7), but little is known about its cellular and evolutionary functions. As only four methylated sequences have been reported previously in N. crassa, we used methyl-binding-domain agarose chromatography to isolate the methylated component of the genome. DNA sequence analysis shows that the methylated component of the genome consists almost exclusively of relics of transposons that were subject to repeat-induced point mutation--a genome defence system that mutates duplicated sequences.     

粗糙脉孢菌及其在发酵工业中的应用研究

粗糙脉孢菌（Neurospora crassa）是一种多细胞丝状真菌,也是一种重要的真核模式生物,它在现代遗传学、生物化学和分子生物学研究领域具有重要的地位。本文介绍了粗糙脉孢菌的生理特性及其分子生物学研究概况,重点阐述了粗糙脉孢菌在发酵工业生产应用中的研究进展。     

真菌中DNA重复序列诱导点突变的研究进展

1987年,由Selker等在粗糙脉孢菌中首次发现重复序列诱导点突变(repeat-induced point mutation,RIP).在重复序列诱导点突变过程中,搜寻前减数分裂组织单倍体核中DNA的重复序列,然后发生众多的碱基C到T的突变,产生富碱基T+A片段,从而使重复序列中的G-C碱基对发生转换突变成为A-T碱基对.此外,发生RIP的序列多集中在着丝粒区域,主要是转座子甲基化后的遗迹.移动转座子是真核生物基因组进化的主要驱动力.对于真菌,重复序列诱导点突变(RIP)在减数分裂过程中通过突变多拷贝DNA,能最大限度地减少转座子的影响,因此对RIP的研究在一定程度上能有助于了解基因组进化的真谛.综述了重复序列诱导点突变的产生机制,以及真菌中重复序列诱导点突变的研究进展.     

Copper metallothionein, a copper-binding protein from Neurospora crassa

Copper is an essential constituent of many proteins which participate in biologically important reactions. In contrast to iron, where different metal storage and transport proteins have been extensively characterised, the existence of copper proteins serving such functions is still a matter of controversy. Studies on the biosynthesis of tyrosinase from Neurospora crassa with respect to the copper status of this fungus have shown that this organism accumulates copper with the concomitant synthesis of a small molecular weight copper-binding protein. This protein is now shown to have a striking sequence homology to the zinc- and cadmium-containing metallothioneins from vertebrates. Growth experiments suggest that this molecule fulfills several important physiological functions in this organism such as copper storage, copper detoxification and provision of copper for tyrosinase.     

蜡状芽孢杆菌ATCC 10987基因组蛋白质编码基因的重新注释与分析

蜡状芽胞杆菌ATCC 10987对于细菌比较基因组学的研究有重要意义.但其染色体中基因的数目被RefSeq注释为5 603个,这个注释是有疑问的.本文采用Zcurve和Glimmer程序联合打分的方法来识别其蛋白质编码基因.为保证预测结果的可靠性,对联合判别附加预测的基因使用了BLAST方法进行数据库同源性搜索.结果,蜡状芽胞杆菌ATCC 10987基因组中的蛋白质编码基因的数目被重新确定为5 180个.这个数目明显低于原始注释的数目,并且一些指标表明新的注释更为可信.这些相对正确的基因集合为该细菌亲缘物种的深入研究提供了基础.     

利用基因打靶技术研制人类疾病小鼠模型

宏伟的人类基因组计划的顺利实施使人类真正进入了功能基因组学研究的新时代 ,与日俱增的大量遗传信息正对生物医学的研究方式和医疗模式产生巨大的影响。发展和应用针对全基因组或全系统的高通量、大规模的整体实验手段 ,利用结构基因组学提供的信息和材料研究基因的功能将成为这个时代生物医学研究的主要特征。基因功能是在由细胞组成的多层次的复杂生命体中实现的 ,因此 ,功能基因组学的研究将会在极大程度上依赖于对模式生物的研究。小鼠作为被研究的脊椎动物 ,尤其具备作为哺乳动物的模式生物具有独特的优势 :首先小鼠是具有较短世代周…     

Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus

Aspergillus fumigatus is exceptional among microorganisms in being both a primary and opportunistic pathogen as well as a major allergen. Its conidia production is prolific, and so human respiratory tract exposure is almost constant. A. fumigatus is isolated from human habitats and vegetable compost heaps. In immunocompromised individuals, the incidence of invasive infection can be as high as 50% and the mortality rate is often about 50% (ref. 2). The interaction of A. fumigatus and other airborne fungi with the immune system is increasingly linked to severe asthma and sinusitis. Although the burden of invasive disease caused by A. fumigatus is substantial, the basic biology of the organism is mostly obscure. Here we show the complete 29.4-megabase genome sequence of the clinical isolate Af293, which consists of eight chromosomes containing 9,926 predicted genes. Microarray analysis revealed temperature-dependent expression of distinct sets of genes, as well as 700 A. fumigatus genes not present or significantly diverged in the closely related sexual species Neosartorya fischeri, many of which may have roles in the pathogenicity phenotype. The Af293 genome sequence provides an unparalleled resource for the future understanding of this remarkable fungus.     

Neurospora NADP-glutamate dehydrogenases and its expression in E. coli and transgenic plants

Genes of NADP-glutamate dehydrogenase (NADP-GDH) were cloned from Neurospora intermedia (Ni), N. crassa (Nc), and N. sitophila (Ns). The sequences showed a high degree of homology at the cDNA and protein level. The three GDH genes were cloned into pET30a and expressed in E. coli. The activity assay of purified GDH showed that the Ni-GDH had a higher activity and affinity to ammonia than Ns-GDH, and Nc-GDH. The K_m value of Ni-GDH ranges from 0.3 to 0.45 mmol/L. Ni-gdh gene was transformed to Nicotiana bethamiana plants. The transformed plants grew much better in low nitrogen media than the only ROKII vector transformed control.     

丝状真菌直接转化纤维素生成酒精的研究

本文对 4株Neurosporacrassa和 4株Fusariumoxysporum菌的纤维素酶生产以及它们直接转化纤维素生成酒精的能力进行了研究 ,筛选出 1株酒精产量较高的菌株 (N .crassaAS 3.16 0 2 ) ,并对该菌株的生长、纤维素酶生产和转化纤维素生成酒精的过程进行了初步的研究 .结果表明 :N .crassaAS 3.16 0 2具有较好的直接转化纤维素生产酒精的能力 ,经过初步优化后 ,酒精产量和转化率分别达到 6 .7g L和 33.5 % .     

Genome sequence of the human malaria parasite Plasmodium falciparum

The parasite Plasmodium falciparum is responsible for hundreds of millions of cases of malaria, and kills more than one million African children annually. Here we report an analysis of the genome sequence of P. falciparum clone 3D7. The 23-megabase nuclear genome consists of 14 chromosomes, encodes about 5,300 genes, and is the most (A + T)-rich genome sequenced to date. Genes involved in antigenic variation are concentrated in the subtelomeric regions of the chromosomes. Compared to the genomes of free-living eukaryotic microbes, the genome of this intracellular parasite encodes fewer enzymes and transporters, but a large proportion of genes are devoted to immune evasion and host-parasite interactions. Many nuclear-encoded proteins are targeted to the apicoplast, an organelle involved in fatty-acid and isoprenoid metabolism. The genome sequence provides the foundation for future studies of this organism, and is being exploited in the search for new drugs and vaccines to fight malaria.     

稻瘟病菌中己糖载体蛋白的生物信息学分析

己糖载体蛋白是一种重要的糖载体蛋白,主要用于己糖的摄取和运输。本文通过生物信息学的方法,研究发现稻瘟病菌有67个可能的己糖载体蛋白。其中,MGG 06203、MGG 03620、MGG 15700、MGG 00040、MGG 13651、MGG 05946的氨基酸序列分别与Neurosporacrassa、Aspergillusnidulans和Colletrotrichumgramini-cola中已鉴定出的己糖载体蛋白高度同源。此外,稻瘟病菌不同的己糖载体蛋白基因在附着胞形成的各个阶段表达量存在很大的差异,尤其是其中有25个基因在稻瘟病菌侵染水稻48 h后有明显上调表达,表明它们可能参与了稻瘟病菌的致病过程。     

A histone H3 methyltransferase controls DNA methylation in Neurospora crassa.

DNA methylation is involved in epigenetic processes such as X-chromosome inactivation, imprinting and silencing of transposons. We have demonstrated previously that dim-2 encodes a DNA methyltransferase that is responsible for all known cytosine methylation in Neurospora crassa. Here we report that another Neurospora gene, dim-5, is required for DNA methylation, as well as for normal growth and full fertility. We mapped dim-5 and identified it by transformation with a candidate gene. The mutant has a nonsense mutation in a SET domain of a gene related to histone methyltransferases that are involved in heterochromatin formation in other organisms. Transformation of a wild-type strain with a segment of dim-5 reactivated a silenced hph gene, apparently by 'quelling' of dim-5. We demonstrate that recombinant DIM-5 protein specifically methylates histone H3 and that replacement of lysine 9 in histone H3 with either a leucine or an arginine phenocopies the dim-5 mutation. We conclude that DNA methylation depends on histone methylation.     

Independent transfer of mitochondrial plasmids in Neurospora crassa

In the ascomycete fungus Neurospora, the distribution of homologous mitochondrial plasmid DNAs in different species and among mitochondrial types of N. crassa suggests that these molecules have moved between lineages of clonally propagated mtDNA. Here we report direct evidence for independent inheritance of mitochondrial plasmids by sexual reproduction which may help explain the distribution of these molecules among mitochondrial lineages.     

Malaria research in the post-genomic era

For many pathogens the availability of genome sequence, permitting genome-dependent methods of research, can partially substitute for powerful forward genetic methods (genome-independent) that have advanced model organism research for decades. In 2002 the genome sequence of Plasmodium falciparum, the parasite causing the most severe type of human malaria, was completed, eliminating many of the barriers to performing state-of-the-art molecular biological research on malaria parasites. Although new, licensed therapies may not yet have resulted from genome-dependent experiments, they have produced a wealth of new observations about the basic biology of malaria parasites, and it is likely that these will eventually lead to new therapeutic approaches. This review will focus on the basic research discoveries that have depended, in part, on the availability of the Plasmodium genome sequences.     

Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii

Species of malaria parasite that infect rodents have long been used as models for malaria disease research. Here we report the whole-genome shotgun sequence of one species, Plasmodium yoelii yoelii, and comparative studies with the genome of the human malaria parasite Plasmodium falciparum clone 3D7. A synteny map of 2,212 P. y. yoelii contiguous DNA sequences (contigs) aligned to 14 P. falciparum chromosomes reveals marked conservation of gene synteny within the body of each chromosome. Of about 5,300 P. falciparum genes, more than 3,300 P. y. yoelii orthologues of predominantly metabolic function were identified. Over 800 copies of a variant antigen gene located in subtelomeric regions were found. This is the first genome sequence of a model eukaryotic parasite, and it provides insight into the use of such systems in the modelling of Plasmodium biology and disease.     

酿酒酵母基因组的研究进展

酿酒酵母(Saccharomyces cerevisiae)是第一个完成全基因组测序工作的真核生物,目前在结构基因组学、功能基因组学、模式生物、最小基因组、比较基因组学等方面的研究已经获得了重大的进展,为人类更深入地研究高等生物基因组打下了坚实的基础。本文将从这几个方面着手对酿酒酵母基因组的研究进展进行综述。     

杜仲内生真菌的分离鉴定及其抑菌活性研究

从药用植物杜仲中分离到41株内生真菌,综合运用形态特征和分子生物学技术,明确其分类地位,分别属于粗糙脉孢霉(Neurospora crassa)、曲霉属(Aspergillus)、小菌核属(Sclerotium)、盾壳霉属(Coniothyrium)、离蠕孢属(Bipolaris)、白僵菌属(Beauveria)6个属,并进行抗植物病原真菌活性检测,结果表明48.8%的内生真菌对植物病原菌有生长抑制作用,除1株白僵菌属菌株外对G+、G-细菌均有明显的抑菌作用.