后生动物起源与进化的分子系统学研究进展

后生动物的起源与进化问题一直是动物学、古生物学和进化生物学研究的重要课题,传统上,对其系统发生和亲缘关系的探讨主要是基于比较形态学和比较胚胎学的证据,然而,随着分子遗传学和分子发育生物学的不断进展及其在相关研究领域的普遍运用,从遗传基础和发育机理上追踪动物各分类群间的系统发生关系已经成为可能。本文就近年来后生动物高级分类群（主要为“门”一级）的分子系统发生研究及其研究中存在的一些问题作了较为系统的综述,同时就后生动物系统发生研究的前景作了展望。     

Topological domains in mammalian genomes identified by analysis of chromatin interactions

The spatial organization of the genome is intimately linked to its biological function, yet our understanding of higher order genomic structure is coarse, fragmented and incomplete. In the nucleus of eukaryotic cells, interphase chromosomes occupy distinct chromosome territories, and numerous models have been proposed for how chromosomes fold within chromosome territories. These models, however, provide only few mechanistic details about the relationship between higher order chromatin structure and genome function. Recent advances in genomic technologies have led to rapid advances in the study of three-dimensional genome organization. In particular, Hi-C has been introduced as a method for identifying higher order chromatin interactions genome wide. Here we investigate the three-dimensional organization of the human and mouse genomes in embryonic stem cells and terminally differentiated cell types at unprecedented resolution. We identify large, megabase-sized local chromatin interaction domains, which we term 'topological domains', as a pervasive structural feature of the genome organization. These domains correlate with regions of the genome that constrain the spread of heterochromatin. The domains are stable across different cell types and highly conserved across species, indicating that topological domains are an inherent property of mammalian genomes. Finally, we find that the boundaries of topological domains are enriched for the insulator binding protein CTCF, housekeeping genes, transfer RNAs and short interspersed element (SINE) retrotransposons, indicating that these factors may have a role in establishing the topological domain structure of the genome.     

Sequence and analysis of chromosome 2 of Dictyostelium discoideum

The genome of the lower eukaryote Dictyostelium discoideum comprises six chromosomes. Here we report the sequence of the largest, chromosome 2, which at 8 megabases (Mb) represents about 25% of the genome. Despite an A + T content of nearly 80%, the chromosome codes for 2,799 predicted protein coding genes and 73 transfer RNA genes. This gene density, about 1 gene per 2.6 kilobases (kb), is surpassed only by Saccharomyces cerevisiae (one per 2 kb) and is similar to that of Schizosaccharomyces pombe (one per 2.5 kb). If we assume that the other chromosomes have a similar gene density, we can expect around 11,000 genes in the D. discoideum genome. A significant number of the genes show higher similarities to genes of vertebrates than to those of other fully sequenced eukaryotes. This analysis strengthens the view that the evolutionary position of D. discoideum is located before the branching of metazoa and fungi but after the divergence of the plant kingdom, placing it close to the base of metazoan evolution.     

短胸大刀螳的化学组成及分析

对短胸大刀螳(Tenodera bravicollisBeier)成虫的化学成分进行了系统的测定.结果表明,短胸大刀螳新鲜样品主要组成为水,其含量为69.0% .干物质的主要成分是蛋白质.粗蛋白、粗脂肪、总糖和灰分分别为64.44% 、11.26% 、1.03% 和4.48% .必需氨基酸含量为28.19% .必需氨基酸占总氨基酸的43.89% ,苏氨酸为其限制性氨基酸,其氨基酸得分为94.1.脂肪中不饱和脂肪酸含量非常丰富,达86.52% .此外还含有大量的矿物质和6 种必需微量元素.因此,短胸大刀螳是一种药食同源的天然食物资源.     

Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions

The architecture of human chromosomes in interphase nuclei is still largely unknown. Microscopy studies have indicated that specific regions of chromosomes are located in close proximity to the nuclear lamina (NL). This has led to the idea that certain genomic elements may be attached to the NL, which may contribute to the spatial organization of chromosomes inside the nucleus. However, sequences in the human genome that interact with the NL in vivo have not been identified. Here we construct a high-resolution map of the interaction sites of the entire genome with NL components in human fibroblasts. This map shows that genome-lamina interactions occur through more than 1,300 sharply defined large domains 0.1-10 megabases in size. These lamina-associated domains (LADs) are typified by low gene-expression levels, indicating that LADs represent a repressive chromatin environment. The borders of LADs are demarcated by the insulator protein CTCF, by promoters that are oriented away from LADs, or by CpG islands, suggesting possible mechanisms of LAD confinement. Taken together, these results demonstrate that the human genome is divided into large, discrete domains that are units of chromosome organization within the nucleus.     

生物圈演化事件与地球圈层演化的相关性问题

讨论了地史中主要生物类型出现、生物爆发和显生宙５次大的生物集群绝灭等生物圈演化事件与地球圈层演化的关系。这些生物圈事件包括生命起源与无核生物的发展、原核生物和真核生物的出现、后生动物的出现、带壳后生动物的出现、寒武纪早期的生物大爆发事件以及晚奥陶世、晚泥盆世、晚二叠世、晚三叠世和白垩纪末期的生物集群绝灭事件。在讨论显生宙５次大的生物集群绝灭的可能原因时,把地内原因与地外原因结合起来,阐述了地史中生物圈演化事件与地球圈层演化事件乃至地外事件之间的耦合效应。但是目前还难以识别事件形成的初因,需要进行高精度的地层学方面的研究来解决     

The genome sequence of the rice blast fungus Magnaporthe grisea

Magnaporthe grisea is the most destructive pathogen of rice worldwide and the principal model organism for elucidating the molecular basis of fungal disease of plants. Here, we report the draft sequence of the M. grisea genome. Analysis of the gene set provides an insight into the adaptations required by a fungus to cause disease. The genome encodes a large and diverse set of secreted proteins, including those defined by unusual carbohydrate-binding domains. This fungus also possesses an expanded family of G-protein-coupled receptors, several new virulence-associated genes and large suites of enzymes involved in secondary metabolism. Consistent with a role in fungal pathogenesis, the expression of several of these genes is upregulated during the early stages of infection-related development. The M. grisea genome has been subject to invasion and proliferation of active transposable elements, reflecting the clonal nature of this fungus imposed by widespread rice cultivation.     

Image reconstructions of helical assemblies of the HIV-1 CA protein

The type 1 human immunodeficiency virus (HIV-1) contains a conical capsid comprising approximately 1,500 CA protein subunits, which organizes the viral RNA genome for uncoating and replication in a new host cell. In vitro, CA spontaneously assembles into helical tubes and cones that resemble authentic viral capsids. Here we describe electron cryo-microscopy and image reconstructions of CA tubes from six different helical families. In spite of their polymorphism, all tubes are composed of hexameric rings of CA arranged with approximate local p6 lattice symmetry. Crystal structures of the two CA domains were 'docked' into the reconstructed density, which showed that the amino-terminal domains form the hexameric rings and the carboxy-terminal dimerization domains connect each ring to six neighbours. We propose a molecular model for the HIV-1 capsid that follows the principles of a fullerene cone, in which the body of the cone is composed of curved hexagonal arrays of CA rings and the ends are closed by inclusion of 12 pentagonal 'defects'.     

The protein Aly links pre-messenger-RNA splicing to nuclear export in metazoans

In metazoans, most pre-messenger RNAs contain introns that are removed by splicing. The spliced mRNAs are then exported to the cytoplasm. Recent studies showed that splicing promotes efficient mRNA export, but the mechanism for coupling these two processes is not known. Here we show that Aly, the metazoan homologue of the yeast mRNA export factor Yralp (ref. 2), is recruited to messenger ribonucleoprotein (mRNP) complexes generated by splicing. In contrast, Aly does not associate with mRNPs assembled on identical mRNAs that already have no introns or with heterogenous nuclear RNP (hnRNP) complexes. Aly is recruited during spliceosome assembly, and then becomes tightly associated with the spliced mRNP. Aly shuttles between the nucleus and cytoplasm, and excess recombinant Aly increases both the rate and efficiency of mRNA export in vivo. Consistent with its splicing-dependent recruitment, Aly co-localizes with splicing factors in the nucleus. We conclude that splicing is required for efficient mRNA export as a result of coupling between the splicing and the mRNA export machineries.     

The Phaeodactylum genome reveals the evolutionary history of diatom genomes

Diatoms are photosynthetic secondary endosymbionts found throughout marine and freshwater environments, and are believed to be responsible for around one-fifth of the primary productivity on Earth. The genome sequence of the marine centric diatom Thalassiosira pseudonana was recently reported, revealing a wealth of information about diatom biology. Here we report the complete genome sequence of the pennate diatom Phaeodactylum tricornutum and compare it with that of T. pseudonana to clarify evolutionary origins, functional significance and ubiquity of these features throughout diatoms. In spite of the fact that the pennate and centric lineages have only been diverging for 90 million years, their genome structures are dramatically different and a substantial fraction of genes ( approximately 40%) are not shared by these representatives of the two lineages. Analysis of molecular divergence compared with yeasts and metazoans reveals rapid rates of gene diversification in diatoms. Contributing factors include selective gene family expansions, differential losses and gains of genes and introns, and differential mobilization of transposable elements. Most significantly, we document the presence of hundreds of genes from bacteria. More than 300 of these gene transfers are found in both diatoms, attesting to their ancient origins, and many are likely to provide novel possibilities for metabolite management and for perception of environmental signals. These findings go a long way towards explaining the incredible diversity and success of the diatoms in contemporary oceans.     

The evolution of the marine phosphate reservoir

Phosphorus is a biolimiting nutrient that has an important role in regulating the burial of organic matter and the redox state of the ocean-atmosphere system. The ratio of phosphorus to iron in iron-oxide-rich sedimentary rocks can be used to track dissolved phosphate concentrations if the dissolved silica concentration of sea water is estimated. Here we present iron and phosphorus concentration ratios from distal hydrothermal sediments and iron formations through time to study the evolution of the marine phosphate reservoir. The data suggest that phosphate concentrations have been relatively constant over the Phanerozoic eon, the past 542 million years (Myr) of Earth's history. In contrast, phosphate concentrations seem to have been elevated in Precambrian oceans. Specifically, there is a peak in phosphorus-to-iron ratios in Neoproterozoic iron formations dating from ～750 to ～635?Myr ago, indicating unusually high dissolved phosphate concentrations in the aftermath of widespread, low-latitude 'snowball Earth' glaciations. An enhanced postglacial phosphate flux would have caused high rates of primary productivity and organic carbon burial and a transition to more oxidizing conditions in the ocean and atmosphere. The snowball Earth glaciations and Neoproterozoic oxidation are both suggested as triggers for the evolution and radiation of metazoans. We propose that these two factors are intimately linked; a glacially induced nutrient surplus could have led to an increase in atmospheric oxygen, paving the way for the rise of metazoan life.     

Drosophila Spire is an actin nucleation factor

The actin cytoskeleton is essential for many cellular functions including shape determination, intracellular transport and locomotion. Previous work has identified two factors--the Arp2/3 complex and the formin family of proteins--that nucleate new actin filaments via different mechanisms. Here we show that the Drosophila protein Spire represents a third class of actin nucleation factor. In vitro, Spire nucleates new filaments at a rate that is similar to that of the formin family of proteins but slower than in the activated Arp2/3 complex, and it remains associated with the slow-growing pointed end of the new filament. Spire contains a cluster of four WASP homology 2 (WH2) domains, each of which binds an actin monomer. Maximal nucleation activity requires all four WH2 domains along with an additional actin-binding motif, conserved among Spire proteins. Spire itself is conserved among metazoans and, together with the formin Cappuccino, is required for axis specification in oocytes and embryos, suggesting that multiple actin nucleation factors collaborate to construct essential cytoskeletal structures.     

自由生活线虫的研究进展

近年来自由生活线虫作为生物学研究的模式动物日益受到重视,尤其是新新华美小杆线虫因其易保存、生活周期短、基因组小等原因被广泛应用于生物学研究的各个领域.本文就新华美小杆线虫在发育生物学、基因和分子生物学方面与其它后生物的相似性和同源性以及转基因线虫在毒力学方面的应用进行综述,旨在表明新华美小杆线虫将成为理想的模式动物为生命科学研究开辟一个广阔的前景.     

Evolution and metabolic significance of the urea cycle in photosynthetic diatoms

Diatoms dominate the biomass of phytoplankton in nutrient-rich conditions and form the basis of some of the world's most productive marine food webs. The diatom nuclear genome contains genes with bacterial and plastid origins as well as genes of the secondary endosymbiotic host (the exosymbiont), yet little is known about the relative contribution of each gene group to diatom metabolism. Here we show that the exosymbiont-derived ornithine-urea cycle, which is similar to that of metazoans but is absent in green algae and plants, facilitates rapid recovery from prolonged nitrogen limitation. RNA-interference-mediated knockdown of a mitochondrial carbamoyl phosphate synthase impairs the response of nitrogen-limited diatoms to nitrogen addition. Metabolomic analyses indicate that intermediates in the ornithine-urea cycle are particularly depleted and that both the tricarboxylic acid cycle and the glutamine synthetase/glutamate synthase cycles are linked directly with the ornithine-urea cycle. Several other depleted metabolites are generated from ornithine-urea cycle intermediates by the products of genes laterally acquired from bacteria. This metabolic coupling of bacterial- and exosymbiont-derived proteins seems to be fundamental to diatom physiology because the compounds affected include the major diatom osmolyte proline and the precursors for long-chain polyamines required for silica precipitation during cell wall formation. So far, the ornithine-urea cycle is only known for its essential role in the removal of fixed nitrogen in metazoans. In diatoms, this cycle serves as a distribution and repackaging hub for inorganic carbon and nitrogen and contributes significantly to the metabolic response of diatoms to episodic nitrogen availability. The diatom ornithine-urea cycle therefore represents a key pathway for anaplerotic carbon fixation into nitrogenous compounds that are essential for diatom growth and for the contribution of diatoms to marine productivity.     

Tetraradial symmetry in early poriferans

Here is currently little consensus on the branching order and phyletic status of the oldest metazoan groups, but sponges are widely believed to be the earliest- branching living metazoans. Porifera are thought to have diverged before the emergence of developmental charac- ters typical of Eumetazoa, such as well-defined symmetry; extant sponges show radial symmetry of indeterminate high order, or none, combined with polarisation along the axis. In contrast, other early-branching phyla include bilateral and tetraradial （Cnidaria） and biradial （Cte- nophora） symmetry, or none （Placozoa）. A variety of prismatic early fossil sponges had shown here where the shared symmetry has been overlooked, and also describe structural tetraradial symmetry in Cambrian sponges from South China. Based on this study, this symmetry is likely to have been a primitive feature of sponges, and that the earliest-known fossil sponges were highly organised, cel- lularly integrated individuals whose body form was under strict genetic control.     

Conservation between yeast and man of a protein associated with U5 small nuclear ribonucleoprotein

The process of nuclear pre-messenger RNA splicing is similar in Saccharomyces cerevisiae and metazoan cells in that the two-step mechanism is identical and the reaction occurs in a large ribonucleoprotein complex, the spliceosome. Little is known, however, about the degree of conservation of splicing factors other than of the small nuclear RNAs (snRNAs). Yeast counterparts of the metazoan spliceosomal snRNAs (U1, U2, U4, U5 and U6) have been identified but, with the exception of U6, the yeast snRNAs are larger and sequence similarity is limited to short regions. By using antibodies against the yeast PRP8 protein, a pre-mRNA splicing factor of relative molecular mass 280,000 (Mr280K) stably associated with U5 small nuclear ribonucleoproteins (snRNPs), we have now identified an immunologically related protein in HeLa cell nuclear extracts. The HeLa cell protein has an Mr greater than 200K and is associated with purified 20S U5 snRNPs. This is the first report of phylogenetic conservation between yeast and man of a protein splicing factor.     

贵州新元古代瓮安生物群中动物胚胎化石研究进展

 瓮安生物群指产出于贵州瓮安磷矿地区新元古代埃迪卡拉纪陡山沱组（635~551Ma）上磷矿段的一个特殊磷酸盐化微体化石组合,主要由多细胞藻类、大型带刺疑源类和处于不同发育阶段的多种后生动物胚胎组成,并包括少量可能的后生动物幼虫和成体化石。瓮安生物群作为迄今为止世界上最古老的前寒武纪后生动物化石群,为探索后生动物的起源和早期演化历程提供了独一无二的实证记录。10余年来,瓮安生物群中动物胚胎化石的研究取得多项突破性进展,已确认至少5种不同卵裂方式的动物胚胎化石,胚胎化石分类从单纯的形态学分类向生物学分类转变,为揭示瓮安生物群中动物多样性提供了更多线索。同时,相关研究更新了繁盛于埃迪卡拉纪大型带刺疑源类生物属性的传统认识,并将之与有表面装饰的动物休眠卵（滞育胚胎）化石相联系。同步辐射X射线显微CT技术的应用成功解决了胚胎化石三维无损成像难题,为古胚胎学的发展带来了新的机遇。