·Nature系列期刊导读·

·Nature系列期刊导读·

新型转基因水稻既高产又环保

来自中国、美国和瑞典的联合课题组，首次成功研发出了第一种转基因水稻，可以同时减少甲烷释放量和提高稻谷颗粒淀粉含量。其中的关键基因是大麦中的糖信号分子(sugar signalling in barley 2，SUSIBA2)。SUSIBA2是一种只存在于植物的转录因子，参与调节糖分子诱导的基因表达，因而可能参与了能量分子从合成到固定下来的信号通路。过量表达SUSIBA2可以导致植物更高的淀粉合成水平和沉积量，并且减少甲烷的释放量。因此，SUSIBA2转基因水稻的安全性验证如果能够通过的话，那么对于人类的可持续发展将具有重要意义。

研究发现新技术可显著提高基因编辑准确性

近日，研究人员开发了一种新技术可以显著提高科学家们靶向特定错误基因，对其进行“编辑”，用健康DNA替换损伤的遗传密码。在这项研究中，研究人员开发了一种方法能够降低基因编辑工具酶的脱靶效应，他们将这种方法命名为DB-PACE(DNA-binding phage-assisted continuous evolution)，利用这种方法能够大大提高核酸酶的DNA结合能力和切割特异性。研究人员将这一系统应用于TALEN技术，大大提高了TALEN技术的DNA切割特异性，这表明DB-PACE系统可作为提高基因编辑精准性的多用途方法在基因组工程领域发挥重要功能。

论文链接: Basil PHubbard，etal..Continuous directed evolution of DNA-binding proteins to improve TALEN specificity.

Nature Methods，DOI:10.1038/nmeth.3515.Published online:10 August，2015.

Abstract:Nucleases containing programmable DNA-binding domains can alter the genomes of model organisms and have the potential to become human therapeutics.Here we present DNA-binding phage-assisted continuous evolution(DB-PACE)as a general approach for the laboratory evolution of DNA-binding activity and specificity.We used this system to generate transcription activator-like effectors nucleases (TALENs)with broadly improved DNA cleavage specificity，establishing DB-PACE as a versatile approach for improving the accuracy of genome-editing agents.

翻转酶机制被揭示

脂质穿过膜双层的转位(被称为翻转)是维持脂质非对称性所必需的，也是信号传导和囊泡形成等过程所要求的。嵌入在膜中的脂质(含有大型极性头基)的翻转是缓慢的，从能量角度来讲也是不利的。这一过程由翻转酶催化，其机制目前尚不知道。研究者获得了ABC transporter PglK的X-射线晶体结构，该物质在Campylobacter jejuni中，在向内和向外的状态下帮助“脂联寡糖”(LLO)的翻转。这些结构和随后的生物化学实验支持一个不同寻常的机制，在其中LLO的“聚戊烯基”尾巴仍然部分嵌入在脂质双层中，“焦磷酸盐-寡糖”头基在ATP被水解之后翻转到了向外的空腔内。

论文链接: Perez C，et al..Structure and mechanism of an active lipid-linked oligosaccharide flippase.

Nature.2015，524(7566):433-438.DOI:10.1038/nature14953.Published online:12 August，2015.

Abstract:The flipping of membrane-embedded lipids containing large，polar head groups is slow and energetically unfavourable，and is therefore catalysed by flippases，the mechanisms of which are unknown.A prominent example of a flipping reaction is the translocation of lipid-linked oligosaccharides that serve as donors in N-linked protein glycosylation.In Campylobacter jejuni，this process is catalysed by the ABC transporter PglK.Here we present a mechanism of PglK-catalysed lipid-linked oligosaccharide flipping based on crystal structures in distinct states，a newly devised in vitro flipping assay，and in vivo studies.PglK can adopt inward-and outward-facing conformations in vitro，but only outward-facing states are required for flipping.While the pyrophosphate-oligosaccharide head group of lipid-linked oligosaccharides enters the translocation cavity and interacts with positively charged side chains，the lipidic polyprenyl tail binds and activates the transporter but remains exposed to the lipid bilayer during the reaction.The proposed mechanism is distinct from the classical alternating-accessmodel applied to other transporters.

研究发现细菌对抗抗生素的秘密武器

一些细菌能够将磷酸化合物转化为磷酸盐促进其生长，它们进化出一套由14个蛋白质组成的体系，有5种酶会在细胞内形成一个叫做C-P裂解酶的复合体，能够催化磷酸化合物转化的五步化学反应中的两步。科学家们通过研究确定了C-P裂解酶复合体的精确分子结构，首次揭秘了细菌这一秘密武器的工作机制。通过这项研究可以更新人们对细菌在极端环境下如何存活以及如何分解特定抗生素的认识，该成果还可用于水净化技术的开发，以移除饮用水中的杀虫剂污染，以及避免细菌产生抗生素抵抗。

论文链接: Paulina Seweryn，et al..Structural insights into the bacterial carbon-phosphorus lyasemachinery.

Nature，2015，525(7567):68-72.DOI:10.1038/nature14683.Published online:17 Aug，2015.

Abstract:Phosphorus is required for all life and microorganisms can extract it from their environment through severalmetabolic pathways. When phosphate is in limited supply，some bacteria are able to use phosphonate compounds，which require specialized enzymaticmachinery to break the stable carbon-phosphorus(C-P)bond.Despite its importance，the details of how thismachinery catabolizes phosphonates remain unknown.Herewe determine the crystal structure of the 240-kilodalton Escherichia coli C-P lyase core complex(PhnG-PhnH-PhnI-PhnJ；PhnGHIJ)，and show that it is a two-fold symmetric hetero-octamer comprising an intertwined network of subunits with unexpected selfhomologies.It contains two potential active sites that probably couple phosphonate compounds to ATP and subsequently hydrolyse the C-P bond.Wemap the binding site of PhnK on the complex using electron microscopy，and show that it binds to a conserved insertion domain of PhnJ.Our results provide a structural basis for understanding microbial phosphonate breakdown.

真核生物中原核生物基因的来源被揭示

多年来，人们一直认为真核生物基因组中所见的原核生物基因是在一个原核细胞器的内共生之后到达那里的。但最近的研究证据表明，在真核生物之间以及在原核生物和真核生物之间也存在实质性的横向基因转移。对细菌、古菌和真核生物基因组所做的这项分析，没有发现连续横向基因转移对真核基因内容的演化具有可以检测得到的累积影响的证据。相反，真核生物是在广泛的差异基因(differential gene)丢失之后、在相对于线粒体和质体起源的两次“演化涌入”事件中获得其原核生物基因的。

论文链接: Ku C，et al..Endosymbiotic origin and differential loss of eukaryotic genes.

Nature，2015，524(7566):427-432.DOI:10.1038/nature14963.Published online:19 August，2015.

Abstract:Chloroplasts arose from cyanobacteria，mitochondria arose from proteobacteria.Both organelles have conserved their prokaryotic biochemistry，but their genomes are reduced，and most organelle proteins are encoded in the nucleus.Endosymbiotic theory posits that bacterial genes in eukaryotic genomes entered the eukaryotic lineage via organelle ancestors.It predicts episodic influx of prokaryotic genes into the eukaryotic lineage，with acquisition corresponding to endosymbiotic events.Eukaryotic genome sequences，however，increasingly implicate lateral gene transfer，both from prokaryotes to eukaryotes and among eukaryotes，as a source of gene content variation in eukaryotic genomes，which predicts continuous，lineage-specific acquisition of prokaryotic genes in divergent eukaryotic groups.Here we discriminate between these two alternatives by clustering and phylogenetic analysis of eukaryotic gene families having prokaryotic homologues.Our results indicate(1)that gene transfer from bacteria to eukaryotes is episodic，as revealed by gene distributions，and coincides with major evolutionary transitions at the origin of chloroplasts and mitochondria；(2)that gene inheritance in eukaryotes is vertical，as revealed by extensive topological comparison，sparse gene distributions stemming from differential loss；and(3)that continuous，lineage-specific lateral gene transfer，although it sometimes occurs，does not contribute to long-term gene content evolution in eukaryotic genomes.

科学家利用单细胞mRNA测序发现罕见细胞类型

近日，来自荷兰的科学家利用一种新的计算方法结合转录组测序发现了小肠中一些罕见的细胞类型。由于目前可用的计算方法只能对一些丰度较高的细胞类型进行确定，因此研究人员开发了一种叫做RaceID的算法，利用这种计算方法发现Reg4是一种罕见的肠内分泌细胞的新标记基因，同时还发现了一些新的细胞亚型。这项研究通过开发一种算法分析转录组测序结果，能够在复杂的单细胞群体中发现一些罕见的细胞类型及其特定标记基因，对于了解正常的和疾病状态下的组织生物学具有重要意义。

论文链接: Dominic Grün，et al..Single-cellmessenger RNA sequencing reveals rare intestinal cell types.

Nature，DOI:10.1038/nature14966.Published online:19 August，2015.

Abstract:Understanding the development and function of an organ requires the characterization of all of its cell types.Traditional methods for visualizing and isolating subpopulations of cells are based on messenger RNA or protein expression of only a few known marker genes.The unequivocal identification of a specific marker gene，however，poses amajor challenge，particularly if this cell type is rare.Identifying rare cell types，such as stem cells，short-lived progenitors，cancer stem cells，or circulating tumour cells，is crucial to acquire a better understanding of normal or diseased tissue biology.To address this challenge we first sequenced the transcriptome of hundreds of randomly selected cells from mouse intestinal organoids1，cultured self-organizing epithelial structures that contain all cell lineages of the mammalian intestine.Organoid buds，like intestinal crypts，harbour stem cells that continuously differentiate into a variety of cell types，occurring at widely different abundances2.Since available computational methods can only resolve more abundant cell types，we developed RaceID，an algorithm for rare cell type identification in complex populations of single cells.We demonstrate that this algorithm can resolve cell types represented by only a single cell in a population of randomly sampled organoid cells.We use thisalgorithm to identify Reg4 as a novel marker for enteroendocrine cells，a rare population of hormone-producing intestinal cells3.Next，we use Reg4 expression to enrich for these rare cells and investigate the heterogeneity within this population.RaceID confirmed the existence of known enteroendocrine lineages，and moreover discovered novel subtypes，which we subsequently validated in vivo.Having validated RaceID we then applied the algorithm to ex vivoisolated Lgr5-positive stem cellsand their directprogeny.We find that Lgr5-positive cells representa homogenousabundant population ofstem cellsmixed with a rare population of Lgr5-positive secretory cells.We envision broad applicability of ourmethod for discovering rare cell types and the correspondingmarker genes in healthy and diseased organs.

研究揭示线粒体基因缺陷改造新策略

最近，一项研究称，线粒体mtDNA突变可以通过遗传获得的方式来纠正，正常代谢功能可以通过多能干细胞来恢复。利用线粒体DNA突变患者皮肤中的成纤维细胞，通过细胞因子介导的重编程(iPS细胞)和体细胞核转移(SCNT)这两种方法，科学家可以获得相关的多能干细胞，最后可以恢复这些细胞线粒体的正常代谢功能。这种针对携带线粒体突变细胞，得到多能干细胞或者诱导多能干细胞的方法，有望用于针对下一代的基因改造，使得女性患者的后代免遭这种线粒体突变带来的疾病的困扰。

论文链接: Ma H，et al..Metabolic rescue in pluripotent cells from patients with mtDNA disease.

Nature，2015，524(7564):234-238.DOI:10.1038/nature14546.Published online:15 July，2015.

Abstract:Mitochondria have amajor role in energy production via oxidative phosphorylation1，which is dependenton the expression of critical genes encoded by mitochondrial(mt)DNA.Mutations in mtDNA can cause fatal or severely debilitating disorders with limited treatment options2.Clinical manifestations vary based on mutation type and heteroplasmy(that is，the relative levels of mutant and wild-typemtDNA within each cell)3，4.Here we generated genetically corrected pluripotent stem cells(PSCs)from patients with mtDNA disease.Multiple induced pluripotent stem(iPS)cell lines were derived from patients with common heteroplasmic mutations including 3243A＞G，causing mitochondrial encephalomyopathy and stroke-like episodes(MELAS)5，and 8993T＞G and 13513G＞A，implicated in Leigh syndrome. Isogenic MELAS and Leigh syndrome iPS cell lines were generated containing exclusively wild-type ormutantmtDNA through spontaneous segregation of heteroplasmic mtDNA in proliferating fibroblasts.Furthermore，somatic cell nuclear transfer(SCNT)enabled replacement of mutantmtDNA from homoplasmic 8993T＞G fibroblasts to generate corrected Leigh-NT1 PSCs.Although Leigh-NT1 PSCs contained donor oocyte wild-typemtDNA(human haplotype D4a)that differed from Leigh syndrome patienthaplotype(F1a)ata total of47 nucleotide sites，Leigh-NT1 cells displayed transcriptomic profiles similar to those in embryo-derived PSCs carrying wild-type mtDNA，indicative of normal nuclear-to-mitochondrial interactions.Moreover，genetically rescued patient PSCs displayed normalmetabolic function compared to impaired oxygen consumption and ATP production observed in mutant cells.We conclude that both reprogramming approaches offer complementary strategies for derivation of PSCs containing exclusively wild-type mtDNA，through spontaneous segregation of heteroplasmic mtDNA in individual iPS cell lines ormitochondrial replacement by SCNT in homoplasmic mtDNA-based disease.

研究揭示章鱼的进化

科学家们针对12种不同类型的章鱼组织的进行了基因图谱的检测。研究人员发现章鱼基因组竟然堪比人类，并且含有更多的蛋白质编码基因(约3.3万个)。研究小组发现基因组的增长集中在两个基因家族的急剧扩张与数百个新基因重复序列的引入。分析还发现了上百个其他基因为章鱼所特有的，并在特定组织高表达。

论文链接: Caroline B A，et al..The octopus genome and the evolution of cephalopod neural and morphological novelties.

Nature，2015，524(7564):220-224.DOI:10.1038/nature14668.

Abstract:Coleoid cephalopods(octopus，squid and cuttlefish)are active，resourceful predators with a rich behavioural repertoire1.They have the largest nervous systems among the invertebrates2 and present other striking morphological innovations including camera-like eyes，prehensile arms，a highly derived early embryogenesis and a remarkably sophisticated adaptive colouration system1，3.To investigate the molecular bases of cephalopod brain and body innovations，we sequenced the genome and multiple transcriptomes of the California two-spot octopus，Octopus bimaculoides.We found no evidence for hypothesized whole-genome duplications in the octopus lineage4，5，6.The core developmental and neuronal gene repertoire of the octopus is broadly similar to that found across invertebrate bilaterians，except for massive expansions in two gene families previously thought to be uniquely enlarged in vertebrates:the protocadherins，which regulate neuronal development，and the C2H2 superfamily of zinc-finger transcription factors.Extensive messenger RNA editing generates transcript and protein diversity in genes involved in neural excitability，as previously described7，as well as in genes participating in a broad range of other cellular functions.We identified hundreds of cephalopod-specific genes，many of which showed elevated expression levels in such specialized structures as the skin，the suckers and the nervous system.Finally，we found evidence for large-scale genomic rearrangements that are closely associated with transposable element expansions.Our analysis suggests that substantial expansion of a handful of gene families，along with extensive remodelling of genome linkage and repetitive content，played a critical role in the evolution of cephalopod morphological innovations，including their large and complex nervous systems.

线粒体功能障碍相关的蛋白运输

线粒体功能障碍和细胞蛋白平衡失败是很多疾病和与年龄相关的病变的特征。受损的线粒体会通过各种机制(包括能量剥夺)导致细胞死亡。最近的研究发现了另外一种机制:来自胞质核糖体的线粒体蛋白的低效运输。研究者们发现，线粒体损伤会阻断核编码的蛋白向线粒体内的运输，通过触发胞质中“线粒体前体过度积累压力”(mPOS)的通道造成细胞退化。

论文链接: Wang XW，et al..A cytosolic network suppressingmitochondria-mediated proteostatic stress and cell death.

Nature，2015，524(7566):481-484.DOI:10.1038/nature14859.Published online:20 July，2015.

Abstract:Mitochondria are multifunctional organelles whose dysfunction leads to neuromuscular degeneration and ageing.The multifunctionality poses a great challenge for understanding the mechanismsby which mitochondrial dysfunction causes specific pathologies.Among the leading mitochondrial mediators of cell death are energy depletion，free radical production，defects in iron-sulfur cluster biosynthesis，the release of pro-apoptotic and non-cell-autonomous signalling molecules，and altered stress signalling.Here we identify a new pathway of mitochondria-mediated cell death in yeast.This pathway was named mitochondrial precursor over-accumulation stress(mPOS)，and is characterized by aberrant accumulation of mitochondrial precursors in the cytosol.mPOS can be triggered by clinically relevant mitochondrial damage that is not limited to the core machineries of protein import.We also discover a large network of genes that suppress mPOS，by modulating ribosomal biogenesis，messenger RNA decapping，transcript-specific translation，protein chaperoning and turnover.In response to mPOS，several ribosome-associated proteins were upregulated，including Gis2 and Nog2，which promote cap-independent translation and inhibit the nuclear exportof the60S ribosomalsubunit，respectively.Gis2 and Nog2 upregulation promotes cellsurvival，whichmay be partof a feedback loop that attenuatesmPOS.Our data indicate thatmitochondrial dysfunction contributes directly to cytosolic proteostatic stress，and provide an explanation for the association between these two hallmarks of degenerative diseases and ageing.The results are relevant to understanding diseases(for example，spinocerebellar ataxia，amyotrophic lateral sclerosis and myotonic dystrophy)that involve mutations within the anti-degenerative network.

论文链接: Su J，et al..Expression of barley SUSIBA2 transcription factor yields high-starch low-methane rice.

Atmospheric methane is the second most important greenhouse gas after carbon dioxide，and is responsible for about 20%of the global warming effect since pre-industrial times.Rice paddies are the largest anthropogenic methane source and produce 7～17%of atmospheric methane.Warm waterlogged soil and exuded nutrients from rice roots provide ideal conditions formethanogenesis in paddies with annual methane emissions of 25～100 million tonnes.This scenariowill be exacerbated by an expansion in rice cultivation needed tomeet the escalating demand for food in the coming decades.There is an urgentneed to establish sustainable technologies for increasing rice production while reducing methane fluxes from rice paddies.However，ongoing efforts for methane mitigation in rice paddies are mainly based on farming practices and measures that are difficult to implement.Despite proposed strategies to increase rice productivity and reduce methane emissions，no high-starch low-methane-emission rice has been developed.Here we show that the addition of a single transcription factor gene，barleySUSIBA2(refs 7，8)，conferred a shift of carbon flux to SUSIBA2 rice，favouring the allocation of photosynthates to aboveground biomass over allocation to roots.The altered allocation resulted in an increased biomass and starch content in the seeds and stems，and suppressed methanogenesis，possibly through a reduction in root exudates.Three-year field trials in China demonstrated that the cultivation of SUSIBA2 rice was associated with a significant reduction in methane emissions and a decrease in rhizospheric methanogen levels.SUSIBA2 rice offers a sustainablemeans of providing increased starch content for food production while reducing greenhouse gas emissions from rice cultivation.Approaches to increase rice productivity and reducemethane emissions as seen in SUSIBA2 ricemay be particularly beneficial in a future climate with rising temperatures resulting in increased methane emissions from paddies.

re，2015，523(7562):602-606.

10.1038/nature14673.Published online:22 July，2015.