·Nature系列期刊導讀·

·Nature系列期刊導讀·

新型轉(zhuǎn)基因水稻既高產(chǎn)又環(huán)保

來自中國、美國和瑞典的聯(lián)合課題組，首次成功研發(fā)出了第一種轉(zhuǎn)基因水稻，可以同時減少甲烷釋放量和提高稻谷顆粒淀粉含量。其中的關鍵基因是大麥中的糖信號分子(sugar signalling in barley 2，SUSIBA2)。SUSIBA2是一種只存在于植物的轉(zhuǎn)錄因子，參與調(diào)節(jié)糖分子誘導的基因表達，因而可能參與了能量分子從合成到固定下來的信號通路。過量表達SUSIBA2可以導致植物更高的淀粉合成水平和沉積量，并且減少甲烷的釋放量。因此，SUSIBA2轉(zhuǎn)基因水稻的安全性驗證如果能夠通過的話，那么對于人類的可持續(xù)發(fā)展將具有重要意義。

研究發(fā)現(xiàn)新技術可顯著提高基因編輯準確性

近日，研究人員開發(fā)了一種新技術可以顯著提高科學家們靶向特定錯誤基因，對其進行“編輯”，用健康DNA替換損傷的遺傳密碼。在這項研究中，研究人員開發(fā)了一種方法能夠降低基因編輯工具酶的脫靶效應，他們將這種方法命名為DB-PACE(DNA-binding phage-assisted continuous evolution)，利用這種方法能夠大大提高核酸酶的DNA結(jié)合能力和切割特異性。研究人員將這一系統(tǒng)應用于TALEN技術，大大提高了TALEN技術的DNA切割特異性，這表明DB-PACE系統(tǒng)可作為提高基因編輯精準性的多用途方法在基因組工程領域發(fā)揮重要功能。

論文鏈接: 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.

翻轉(zhuǎn)酶機制被揭示

脂質(zhì)穿過膜雙層的轉(zhuǎn)位(被稱為翻轉(zhuǎn))是維持脂質(zhì)非對稱性所必需的，也是信號傳導和囊泡形成等過程所要求的。嵌入在膜中的脂質(zhì)(含有大型極性頭基)的翻轉(zhuǎn)是緩慢的，從能量角度來講也是不利的。這一過程由翻轉(zhuǎn)酶催化，其機制目前尚不知道。研究者獲得了ABC transporter PglK的X-射線晶體結(jié)構(gòu)，該物質(zhì)在Campylobacter jejuni中，在向內(nèi)和向外的狀態(tài)下幫助“脂聯(lián)寡糖”(LLO)的翻轉(zhuǎn)。這些結(jié)構(gòu)和隨后的生物化學實驗支持一個不同尋常的機制，在其中LLO的“聚戊烯基”尾巴仍然部分嵌入在脂質(zhì)雙層中，“焦磷酸鹽-寡糖”頭基在ATP被水解之后翻轉(zhuǎn)到了向外的空腔內(nèi)。

論文鏈接: 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.

研究發(fā)現(xiàn)細菌對抗抗生素的秘密武器

一些細菌能夠?qū)⒘姿峄衔镛D(zhuǎn)化為磷酸鹽促進其生長，它們進化出一套由14個蛋白質(zhì)組成的體系，有5種酶會在細胞內(nèi)形成一個叫做C-P裂解酶的復合體，能夠催化磷酸化合物轉(zhuǎn)化的五步化學反應中的兩步?？茖W家們通過研究確定了C-P裂解酶復合體的精確分子結(jié)構(gòu)，首次揭秘了細菌這一秘密武器的工作機制。通過這項研究可以更新人們對細菌在極端環(huán)境下如何存活以及如何分解特定抗生素的認識，該成果還可用于水凈化技術的開發(fā)，以移除飲用水中的殺蟲劑污染，以及避免細菌產(chǎn)生抗生素抵抗。

論文鏈接: 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來源被揭示

多年來，人們一直認為真核生物基因組中所見的原核生物基因是在一個原核細胞器的內(nèi)共生之后到達那里的。但最近的研究證據(jù)表明，在真核生物之間以及在原核生物和真核生物之間也存在實質(zhì)性的橫向基因轉(zhuǎn)移。對細菌、古菌和真核生物基因組所做的這項分析，沒有發(fā)現(xiàn)連續(xù)橫向基因轉(zhuǎn)移對真核基因內(nèi)容的演化具有可以檢測得到的累積影響的證據(jù)。相反，真核生物是在廣泛的差異基因(differential gene)丟失之后、在相對于線粒體和質(zhì)體起源的兩次“演化涌入”事件中獲得其原核生物基因的。

論文鏈接: 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.

科學家利用單細胞mRNA測序發(fā)現(xiàn)罕見細胞類型

近日，來自荷蘭的科學家利用一種新的計算方法結(jié)合轉(zhuǎn)錄組測序發(fā)現(xiàn)了小腸中一些罕見的細胞類型。由于目前可用的計算方法只能對一些豐度較高的細胞類型進行確定，因此研究人員開發(fā)了一種叫做RaceID的算法，利用這種計算方法發(fā)現(xiàn)Reg4是一種罕見的腸內(nèi)分泌細胞的新標記基因，同時還發(fā)現(xiàn)了一些新的細胞亞型。這項研究通過開發(fā)一種算法分析轉(zhuǎn)錄組測序結(jié)果，能夠在復雜的單細胞群體中發(fā)現(xiàn)一些罕見的細胞類型及其特定標記基因，對于了解正常的和疾病狀態(tài)下的組織生物學具有重要意義。

論文鏈接: 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.

研究揭示線粒體基因缺陷改造新策略

最近，一項研究稱，線粒體mtDNA突變可以通過遺傳獲得的方式來糾正，正常代謝功能可以通過多能干細胞來恢復。利用線粒體DNA突變患者皮膚中的成纖維細胞，通過細胞因子介導的重編程(iPS細胞)和體細胞核轉(zhuǎn)移(SCNT)這兩種方法，科學家可以獲得相關的多能干細胞，最后可以恢復這些細胞線粒體的正常代謝功能。這種針對攜帶線粒體突變細胞，得到多能干細胞或者誘導多能干細胞的方法，有望用于針對下一代的基因改造，使得女性患者的后代免遭這種線粒體突變帶來的疾病的困擾。

論文鏈接: 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.

研究揭示章魚的進化

科學家們針對12種不同類型的章魚組織的進行了基因圖譜的檢測。研究人員發(fā)現(xiàn)章魚基因組竟然堪比人類，并且含有更多的蛋白質(zhì)編碼基因(約3.3萬個)。研究小組發(fā)現(xiàn)基因組的增長集中在兩個基因家族的急劇擴張與數(shù)百個新基因重復序列的引入。分析還發(fā)現(xiàn)了上百個其他基因為章魚所特有的，并在特定組織高表達。

論文鏈接: 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.

線粒體功能障礙相關的蛋白運輸

線粒體功能障礙和細胞蛋白平衡失敗是很多疾病和與年齡相關的病變的特征。受損的線粒體會通過各種機制(包括能量剝奪)導致細胞死亡。最近的研究發(fā)現(xiàn)了另外一種機制:來自胞質(zhì)核糖體的線粒體蛋白的低效運輸。研究者們發(fā)現(xiàn)，線粒體損傷會阻斷核編碼的蛋白向線粒體內(nèi)的運輸，通過觸發(fā)胞質(zhì)中“線粒體前體過度積累壓力”(mPOS)的通道造成細胞退化。

論文鏈接: 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.

論文鏈接: 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.