Linearly concatenated cyclobutane lipids form a dense bacterial membrane

Lipid membranes are essential to the functioning of cells, enabling the existence of concentration gradients of ions and metabolites. Microbial membrane lipids can contain three-, five-, six- and even seven-membered aliphatic rings, but four-membered aliphatic cyclobutane rings have never been observed. Here we report the discovery of cyclobutane rings in the dominant membrane lipids of two anaerobic ammonium-oxidizing (anammox) bacteria. These lipids contain up to five linearly fused cyclobutane moieties with cis ring junctions. Such 'ladderane' molecules are unprecedented in nature but are known as promising building blocks in optoelectronics. The ladderane lipids occur in the membrane of the anammoxosome, the dedicated intracytoplasmic compartment where anammox catabolism takes place. They give rise to an exceptionally dense membrane, a tight barrier against diffusion. We propose that such a membrane is required to maintain concentration gradients during the exceptionally slow anammox metabolism and to protect the remainder of the cell from the toxic anammox intermediates. Our results further illustrate that microbial membrane lipid structures are far more diverse than previously recognized.     

Molecular mechanism of anaerobic ammonium oxidation

Two distinct microbial processes, denitrification and anaerobic ammonium oxidation (anammox), are responsible for the release of fixed nitrogen as dinitrogen gas (N(2)) to the atmosphere. Denitrification has been studied for over 100 years and its intermediates and enzymes are well known. Even though anammox is a key biogeochemical process of equal importance, its molecular mechanism is unknown, but it was proposed to proceed through hydrazine (N(2)H(4)). Here we show that N(2)H(4) is produced from the anammox substrates ammonium and nitrite and that nitric oxide (NO) is the direct precursor of N(2)H(4). We resolved the genes and proteins central to anammox metabolism and purified the key enzymes that catalyse N(2)H(4) synthesis and its oxidation to N(2). These results present a new biochemical reaction forging an N-N bond and fill a lacuna in our understanding of the biochemical synthesis of the N(2) in the atmosphere. Furthermore, they reinforce the role of nitric oxide in the evolution of the nitrogen cycle.     

Anaerobic ammonium oxidation by anammox bacteria in the Black Sea

The availability of fixed inorganic nitrogen (nitrate, nitrite and ammonium) limits primary productivity in many oceanic regions. The conversion of nitrate to N2 by heterotrophic bacteria (denitrification) is believed to be the only important sink for fixed inorganic nitrogen in the ocean. Here we provide evidence for bacteria that anaerobically oxidize ammonium with nitrite to N2 in the world's largest anoxic basin, the Black Sea. Phylogenetic analysis of 16S ribosomal RNA gene sequences shows that these bacteria are related to members of the order Planctomycetales performing the anammox (anaerobic ammonium oxidation) process in ammonium-removing bioreactors. Nutrient profiles, fluorescently labelled RNA probes, 15N tracer experiments and the distribution of specific 'ladderane' membrane lipids indicate that ammonium diffusing upwards from the anoxic deep water is consumed by anammox bacteria below the oxic zone. This is the first time that anammox bacteria have been identified and directly linked to the removal of fixed inorganic nitrogen in the environment. The widespread occurrence of ammonium consumption in suboxic marine settings indicates that anammox might be important in the oceanic nitrogen cycle.     

沸石载体恢复受饥饿影响厌氧氨氧化菌的性能研究

利用沸石良好的吸氨能力和微生物载体功能,将受饥饿影响的厌氧氨氧化菌在含沸石的反应器内进行活性恢复,研究沸石对长期饥饿影响下厌氧氨氧化菌恢复过程中菌群活性及结构的影响.结果表明,经过82天的运行,沸石反应器和对照反应器(无沸石添加)内厌氧氨氧化菌均获得恢复.沸石反应器的脱氮效率从第59天开始与对照反应器拉开差距,运行第8...     

Using the Acropora digitifera genome to understand coral responses to environmental change

Despite the enormous ecological and economic importance of coral reefs, the keystone organisms in their establishment, the scleractinian corals, increasingly face a range of anthropogenic challenges including ocean acidification and seawater temperature rise. To understand better the molecular mechanisms underlying coral biology, here we decoded the approximately 420-megabase genome of Acropora digitifera using next-generation sequencing technology. This genome contains approximately 23,700 gene models. Molecular phylogenetics indicate that the coral and the sea anemone Nematostella vectensis diverged approximately 500 million years ago, considerably earlier than the time over which modern corals are represented in the fossil record (～240 million years ago). Despite the long evolutionary history of the endosymbiosis, no evidence was found for horizontal transfer of genes from symbiont to host. However, unlike several other corals, Acropora seems to lack an enzyme essential for cysteine biosynthesis, implying dependency of this coral on its symbionts for this amino acid. Corals inhabit environments where they are frequently exposed to high levels of solar radiation, and analysis of the Acropora genome data indicates that the coral host can independently carry out de novo synthesis of mycosporine-like amino acids, which are potent ultraviolet-protective compounds. In addition, the coral innate immunity repertoire is notably more complex than that of the sea anemone, indicating that some of these genes may have roles in symbiosis or coloniality. A number of genes with putative roles in calcification were identified, and several of these are restricted to corals. The coral genome provides a platform for understanding the molecular basis of symbiosis and responses to environmental changes.     

Genome-wide phenotype analysis in ES cells by regulated disruption of Bloom's syndrome gene

The chief limitation of phenotype-based genetic screening in mammalian systems is the diploid nature of the genome. Cells deficient in the Bloom's syndrome gene (Blm) show an increased rate of loss of heterozygosity. Here we have used a tetracycline-regulated Blm allele (Blm(tet)) to introduce bi-allelic mutations across the genome in mouse embryonic stem (ES) cells. Transient loss of Blm expression induces homologous recombination not only between sister chromatids but also between homologous chromosomes. We considered that the phenotype of ES cells bearing bi-allelic mutations would be maintained after withdrawal of the tetracycline analogue doxycycline. Indeed, a combination of N-ethyl-N-nitrosourea mutagenesis and transient loss of Blm expression enabled us to generate an ES cell library with genome-wide bi-allelic mutations. The library was evaluated by screening for mutants of glycosylphosphatidylinositol-anchor biosynthesis, which involves at least 23 genes distributed throughout the genome. Mutants derived from 12 different genes were obtained and two unknown mutants were simultaneously isolated. Our results indicate that phenotype-based genetic screening with Blm(tet) is very efficient and raises possibilities for identifying gene functions in ES cells.     

The genome sequence of the food-borne pathogen Campylobacter jejuni reveals hypervariable sequences

Campylobacter jejuni, from the delta-epsilon group of proteobacteria, is a microaerophilic, Gram-negative, flagellate, spiral bacterium-properties it shares with the related gastric pathogen Helicobacter pylori. It is the leading cause of bacterial food-borne diarrhoeal disease throughout the world. In addition, infection with C. jejuni is the most frequent antecedent to a form of neuromuscular paralysis known as Guillain-Barré syndrome. Here we report the genome sequence of C. jejuni NCTC11168. C. jejuni has a circular chromosome of 1,641,481 base pairs (30.6% G+C) which is predicted to encode 1,654 proteins and 54 stable RNA species. The genome is unusual in that there are virtually no insertion sequences or phage-associated sequences and very few repeat sequences. One of the most striking findings in the genome was the presence of hypervariable sequences. These short homopolymeric runs of nucleotides were commonly found in genes encoding the biosynthesis or modification of surface structures, or in closely linked genes of unknown function. The apparently high rate of variation of these homopolymeric tracts may be important in the survival strategy of C. jejuni.     

铁对厌氧氨氧化过程及其微生物群落的影响

从电子传递机制、微生物活动和影响因子等角度出发,综述铁对厌氧氨氧化过程的影响。结果表明,不同价态的铁作为电子受体或电子供体生成厌氧氨氧化底物促进反应,且产生铁氨氧化(Feammox)、硝酸盐依赖型亚铁氧化反应(nitrate-dependent ferrous iron oxidation,NAFO)等不同反应。同时铁元素对厌氧氨氧化过程中功能微生物富集、血红素含量提升及颗粒化过程均有促进作用,从而明显提升对厌氧氨氧化工艺的处理效果。并总结了最佳的铁投加状态,铁元素加强厌氧氨氧化过程中的最适温度、pH值,为后续的铁元素加强厌氧氨氧化过程的研究提供参考。     

棉铃虫性信息素合成激活肽基因的检测

性信息素合成激活肽是调节昆虫性信息素合成的神经肽．根据昆虫性信息素合成激活肽的氨基酸序列保守性,合成若干引物,以棉铃虫基因组ＤＮＡ为模板,用ＰＣＲ方法得到单一的扩增条带．ＲＴＰＣＲ方法从棉铃虫咽下神经结中检测出性信息素合成激活肽基因在棉铃虫基因组中不仅存在,而且表达．     

Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp. APS

Almost all aphid species (Homoptera, Insecta) have 60-80 huge cells called bacteriocytes, within which are round-shaped bacteria that are designated Buchnera. These bacteria are maternally transmitted to eggs and embryos through host generations, and the mutualism between the host and the bacteria is so obligate that neither can reproduce independently. Buchnera is a close relative of Escherichia coli, but it contains more than 100 genomic copies per cell, and its genome size is only a seventh of that of E. coli. Here we report the complete genome sequence of Buchnera sp. strain APS, which is composed of one 640,681-base-pair chromosome and two small plasmids. There are genes for the biosyntheses of amino acids essential for the hosts in the genome, but those for non-essential amino acids are missing, indicating complementarity and syntrophy between the host and the symbiont. In addition, Buchnera lacks genes for the biosynthesis of cell-surface components, including lipopolysaccharides and phospholipids, regulator genes and genes involved in defence of the cell. These results indicate that Buchnera is completely symbiotic and viable only in its limited niche, the bacteriocyte.     

A physical map of the human genome

The human genome is by far the largest genome to be sequenced, and its size and complexity present many challenges for sequence assembly. The International Human Genome Sequencing Consortium constructed a map of the whole genome to enable the selection of clones for sequencing and for the accurate assembly of the genome sequence. Here we report the construction of the whole-genome bacterial artificial chromosome (BAC) map and its integration with previous landmark maps and information from mapping efforts focused on specific chromosomal regions. We also describe the integration of sequence data with the map.     

长江下游厌氧氨氧化细菌标记基因相对丰度及影响因素

为探索河流系统中厌氧氨氧化细菌的分布情况, 于2014年春秋两季采集长江下游6个断面的水体和沉积物样品, 通过宏基因组测序方法, 根据优化序列与自建厌氧氨氧化细菌标记基因hzsA, hzsB, hzsC, hdh数据集的比对结果, 计算各基因相对丰度。结果表明, 水体溶解氧浓度较高导致厌氧氨氧化细菌标记基因丰度极低, 而沉积物中各基因相对丰度较高, 平均值分别为4.540×10^-10, 4.939×10^-10, 4.333×10^-10和2.859×10^-10。随着温度升高, 秋季沉积物中各基因相对丰度显著高于春季。大通、南京和徐六泾沉积物中各基因相对丰度较高, 这与人类活动扰动的增强以及入海口盐度升高有关。物种分类鉴定结果表明, 长江下游沉积物中厌氧氨氧化细菌在属水平上以Candidatus Brocadia和Candidatus Jettenia为主。厌氧氨氧化细菌标记基因相对丰度与NO₂^--N,NO₃^--N和NH₄⁺-N等理化因子相关, 并且, 由于NO₂^--N浓度远远低于NH₄⁺-N, 因此NO₂^--N浓度是长江下游沉积物中厌氧氨氧化细菌生长的限制性因子。     

2类氨氧化菌的生态特性及其应用研究进展

氮素作为组成生物体的重要元素，一直以其独特的方式在自然界中循环。经典氮循环理论认为细菌的好氧氨氧化是氧化氨氮的唯一途径，然而，随着生物技术的发展，新的氮循环途径被不断发现，其中的古菌好氧氨氧化以及厌氧氨氧化过程，由于其突出的生态及工程应用重要性，成为学术界的研究热点。本文主要综述了氮循环新途径中的厌氧氨氧化以及古菌好氧氨氧化过程的发现及研究现状，并进一步探讨了这两类氨氧化菌的研究及应用前景。     

The ring of life provides evidence for a genome fusion origin of eukaryotes

Genomes hold within them the record of the evolution of life on Earth. But genome fusions and horizontal gene transfer seem to have obscured sufficiently the gene sequence record such that it is difficult to reconstruct the phylogenetic tree of life. Here we determine the general outline of the tree using complete genome data from representative prokaryotes and eukaryotes and a new genome analysis method that makes it possible to reconstruct ancient genome fusions and phylogenetic trees. Our analyses indicate that the eukaryotic genome resulted from a fusion of two diverse prokaryotic genomes, and therefore at the deepest levels linking prokaryotes and eukaryotes, the tree of life is actually a ring of life. One fusion partner branches from deep within an ancient photosynthetic clade, and the other is related to the archaeal prokaryotes. The eubacterial organism is either a proteobacterium, or a member of a larger photosynthetic clade that includes the Cyanobacteria and the Proteobacteria.     

Initial sequencing and analysis of the human genome

The human genome holds an extraordinary trove of information about human development, physiology, medicine and evolution. Here we report the results of an international collaboration to produce and make freely available a draft sequence of the human genome. We also present an initial analysis of the data, describing some of the insights that can be gleaned from the sequence.     

联氨在金属纳米粉制备中的行为研究

通过ＵＶ、ＸＲＤ和化学分析方法研究了联氨在同Ｆｅ（ＩＩ） 、Ｃｏ（ＩＩ） 、Ｎｉ（ＩＩ） 反应制备金属纳米粉的行为． 认为在乙醇－ 水体系中， 水合肼还原Ｃｏ（ＩＩ） 、Ｎｉ（ＩＩ） 的反应是经过配合催化， 还原Ｆｅ（ＩＩ） 的反应是经过表面催化和高压诱导． 用水合肼对钴、镍纳米粉进行铁的包覆， 以及有钴、镍存在下的岐化分解都是表面催化．     

Enzymic activation and transfer of fatty acids as acyl-adenylates in mycobacteria

The metabolic repertoire in nature is augmented by generating hybrid metabolites from a limited set of gene products. In mycobacteria, several unique complex lipids are produced by the combined action of fatty acid synthases and polyketide synthases (PKSs), although it is not clear how the covalently sequestered biosynthetic intermediates are transferred from one enzymatic complex to another. Here we show that some of the 36 annotated fadD genes, located adjacent to the PKS genes in the Mycobacterium tuberculosis genome, constitute a new class of long-chain fatty acyl-AMP ligases (FAALs). These proteins activate long-chain fatty acids as acyl-adenylates, which are then transferred to the multifunctional PKSs for further chain extension. This mode of activation and transfer of fatty acids is contrary to the previously described universal mechanism involving the formation of acyl-coenzyme A thioesters. Similar mechanisms may operate in the biosynthesis of other lipid-containing metabolites and could have implications in engineering novel hybrid products.