·Nature導(dǎo)讀·

解析花蜜的進(jìn)化之謎

植物生產(chǎn)和分泌花蜜的過程仍然未知。研究人員對三種不同的開花植物(擬南芥、蕪菁和野生煙草)的研究發(fā)現(xiàn)，糖轉(zhuǎn)運蛋白SWEET9在三種植物中負(fù)責(zé)介導(dǎo)花蜜分泌的過程，將糖轉(zhuǎn)運到蜜腺的細(xì)胞外區(qū)域，是花蜜合成和分泌中的關(guān)鍵元件。SWEET9還可能對于開花植物的進(jìn)化至關(guān)重要，出現(xiàn)在開花植物進(jìn)化的早期。

論文鏈接:Lin I W，et al..Nectar secretion requires sucrose phosphate synthases and the sugar transporter SWEET9.

Angiosperms developed floral nectaries that reward pollinating insects.Although nectar function and composition have been characterized，the mechanism of nectar secretion has remained unclear.Here we identify SWEET9 as a nectary-specific sugar transporter in three eudicot species:Arabidopsis thaliana，Brassica rapa(extrastaminal nectaries)and Nicotiana attenuata(gynoecial nectaries).We show that SWEET9 is essential for nectar production and can function as an efflux transporter.We also show that sucrose phosphate synthase genes，encoding key enzymes for sucrose biosynthesis，are highly expressed in nectaries and that their expression is also essential for nectar secretion.Together these data are consistent with a model in which sucrose is synthesized in the nectary parenchyma and subsequently secreted into the extracellular space via SWEET9，where sucrose is hydrolysed by an apoplasmic invertase to produce a mixture of sucrose，glucose and fructose.The recruitment of SWEET9 for sucrose export may have been a key innovation，and could have coincided with the evolution of core eudicots and contributed to the evolution of nectar secretion to reward pollinators.

蝴蝶翅膀圖案多樣化的基因控制

蝴蝶翅膀的擬態(tài)是自然選擇的一種典型范例。有證據(jù)表明，燕尾蝶基因組中存在一個控制擬態(tài)的區(qū)域，鑒于擬態(tài)的復(fù)雜性，通常認(rèn)為蝴蝶翅膀的擬態(tài)圖案應(yīng)該是多個基因共同作用的結(jié)果，而該研究發(fā)現(xiàn)，控制性別分化的doublesex基因單獨承擔(dān)了這項工作。單個基因能夠控制如此復(fù)雜的機(jī)能的原因可能在于控制doublesex表達(dá)時機(jī)和地點的非編碼DNA可能起到了重要作用，并且，doublesex是一個可激活其他基因的轉(zhuǎn)錄因子，其差異性可能是翅膀圖案多樣化的原因。

論文鏈接:Kunte K，et al..doublesex is a mimicry supergene.

Nature，doi:10.1038/nature13112.Published online:05 March，2014.Abstract:One of the most striking examples of sexual dimorphism is sex-limited mimicry in butterflies，a phenomenon in which one sex—usually the female—mimics a toxic model species，whereas the other sex displays a different wing pattern1.Sex-limited mimicry is phylogenetically widespread in the swallowtail butterfly genus Papilio，in which it is often associated with female mimetic polymorphism.In multiple polymorphic species，the entire wing pattern phenotype is controlled by a single Mendelian‘supergene’.Although theoretical work has explored the evolutionary dynamics of supergene mimicry，there are almost no empirical data that address the critical issue of what a mimicry supergene actually is at a functional level.Using an integrative approach combining genetic and association mapping，transcriptome and genome sequencing，and gene expression analyses，we show that a single gene，doublesex，controls supergene mimicry in Papilio polytes.This is in contrast to the long-held view that supergenes are likely to be controlled by a tightly linked cluster of loci.Analysis of gene expression and DNA sequence variation indicates that isoform expression differences contribute to the functional differences between dsx mimicry alleles，and protein sequence evolution may also have a role.Our results combine elements from different hypotheses for the identity of supergenes，showing that a single gene can switch the entire wing pattern among mimicry phenotypes but may require multiple，tightly linked mutations to do so.

細(xì)菌IV型分泌系統(tǒng)與細(xì)菌抗生素耐藥性

細(xì)菌IV型分泌系統(tǒng)能夠在細(xì)胞間分配遺傳物質(zhì)，如，抗生素抗性基因，該機(jī)制直接導(dǎo)致了抗生素耐藥性傳播。它還在引發(fā)潰瘍、百日咳、軍團(tuán)病一類嚴(yán)重肺炎的感染毒素分泌過程起至關(guān)重要的作用。研究人員重建了大腸桿菌的IV型分泌系統(tǒng)，從分子結(jié)構(gòu)和分泌機(jī)制等方面揭示出IV型分泌系統(tǒng)與其他的細(xì)菌分泌系統(tǒng)的顯著差異。

論文鏈接:Low H H，et al..Structure of a type IV secretion system.

Nature，doi:10.1038/nature13081.Published online:09 March，2014.

Abstract:Bacterial type IV secretion systems translocate virulence factors into eukaryotic cells，distribute genetic material between bacteria and have shown potential as a tool for the genetic modification of human cells.Given the complex choreography of the substrate through the secretion apparatus，the molecular mechanism of the type IV secretion system has proved difficult to dissect in the absence of structural data for the entire machinery.Here we use electron microscopy to reconstruct the type IV secretion system encoded by the Escherichia coli R388 conjugative plasmid.We show that eight proteins assemble in an intricate stoichiometric relationship to form an approximately 3 megadalton nanomachine that spans the entire cell envelope.The structure comprises an outer membrane-associated core complex connected by a central stalk to a substantial inner membrane complex that is dominated by a battery of 12 VirB4 ATPase subunits organized as side-by-side hexameric barrels.Our results show a secretion system with markedly different architecture，and consequently mechanism，to other known bacterial secretion systems.

RNAi通路的關(guān)鍵酶在細(xì)菌中起防止DNA入侵的作用

RNA干涉(RNAi)在真核細(xì)胞中可以通過一個過程來保護(hù)細(xì)胞不受外來“小單鏈RNA”(ssRNAs)的影響。在這個過程中，被主體編碼的短RNA結(jié)合同源RNA目標(biāo)，并介導(dǎo)它們的降解。Argonaute(Ago)是真核細(xì)胞中由RNA引導(dǎo)的RNAi通路的一個關(guān)鍵酶。研究發(fā)現(xiàn)，原核生物的Ago(來自細(xì)菌Thermus thermophilus)保護(hù)細(xì)胞不受DNA而不是RNA入侵。在本研究中，Ago被加載了miRNA(與來自質(zhì)體DNA的miRNA相似)，后者結(jié)合并掀開互補(bǔ)的DNA鏈。

論文鏈接:Swarts D C，et al..DNA-guided DNA interference by a prokaryotic Argonaute.

Nature，2014，507(7491)，258 －261.doi:10.1038/nature12971.

Abstract:RNA interference is widely distributed in eukaryotes and has a variety of functions，including antiviral defence and gene regulation.All RNA interference pathways use small single-stranded RNA(ssRNA)molecules that guide proteins of the Argonaute(Ago)family to complementary ssRNA targets:RNA-guided RNA interference.The role of prokaryotic Ago variants has remained elusive，although bioinformatics analysis has suggested their involvement in host defence.Here we demonstrate that Ago of the bacterium Thermus thermophilus(TtAgo)acts as a barrier for the uptake and propagation of foreign DNA.In vivo，TtAgo is loaded with 5'-phosphorylated DNA guides，13～25 nucleotides in length，that are mostly plasmid derived and have a strong bias for a 5'-end deoxycytidine.These small interfering DNAs guide TtAgo to cleave complementary DNA strands.Hence，despite structural homology to its eukaryotic counterparts，TtAgo functions in host defence by DNA-guided DNA interference.

Cas9-RNA“審查”DNA的機(jī)制

基于CRISPR/Cas9的DNA靶向技術(shù)成為合成生物學(xué)和基因組工程領(lǐng)域的一個領(lǐng)先工具。該研究報告了利用單分子和宏觀生化實驗來揭示RNA引導(dǎo)的Cas9如何識別基因組DNA并查找特定的切割位點。結(jié)果顯示，一個很短的三核苷酸protospacer adjacent motif(PAM)，在將Cas9-RNA復(fù)合物向潛在DNA靶點上招募中以及在激活核酸酶催化活性中起作用。競爭測定法實驗證據(jù)表明，DNA鏈的分離和RNA-DNA異源雙鏈體的形成開始于PAM，并朝向靶序列的遠(yuǎn)末端進(jìn)行。

論文鏈接:Sternberg S H，et al..DNA interrogation by the CRISPR RNA-guided endonuclease Cas9.

Nature，2014，507(7490)，62 －67.doi:10.1038/nature13011.

Abstract:The clustered regularly interspaced short palindromic repeats(CRISPR)-associated enzyme Cas9 is an RNA-guided endonuclease that uses RNA-DNA base-pairing to target foreign DNA in bacteria.Cas9-guide RNA complexes are also effective genome engineering agents in animals and plants.Here we use single-molecule and bulk biochemical experiments to determine how Cas9-RNA interrogates DNA to find specific cleavage sites.We show that both binding and cleavage of DNA by Cas9-RNA require recognition of a short trinucleotide protospacer adjacent motif(PAM).Non-target DNA binding affinity scales with PAM density，and sequences fully complementary to the guide RNA but lacking a nearby PAM are ignored by Cas9-RNA.Competition assays provide evidence that DNA strand separation and RNA-DNA heteroduplex formation initiate at the PAM and proceed directionally towards the distal end of the target sequence.Furthermore，PAM interactions trigger Cas9 catalytic activity.These results reveal how Cas9 uses PAM recognition to quickly identify potential target sites while scanning large DNA molecules，and to regulate scission of double-stranded DNA.

肺換氣相關(guān)細(xì)胞的“兼性”干細(xì)胞功能

肺換氣發(fā)生在結(jié)構(gòu)精妙的肺泡囊中，其內(nèi)壁有兩種上皮細(xì)胞類型:鱗狀1-型肺泡細(xì)胞(AT1細(xì)胞)和骰狀2-型肺泡細(xì)胞(AT2細(xì)胞)。前者介導(dǎo)換氣，后者分泌防止肺泡在呼吸過程中崩潰的表面活性劑。采用肺泡標(biāo)記物、遺傳世系追蹤和克隆分析來在小鼠整個生命周期中對肺泡祖細(xì)胞進(jìn)行活體識別，發(fā)現(xiàn)AT1和AT2細(xì)胞是在發(fā)育過程中從一種“雙潛力”祖細(xì)胞形成的。在出生后，成熟AT2細(xì)胞起“兼性”干細(xì)胞的作用，形成再生肺泡的慢慢增大的單克隆位點。有致癌作用的Kras(G12D)突變永久性地激發(fā)AT2自我更新，劫持這種“兼性”干細(xì)胞功能來啟動肺癌。

論文鏈接:Desa T J，et al..Alveolar progenitor and stem cells in lung development，renewal and cancer.

Nature，2014，507(7491)，190 －194.doi:10.1038/nature12930.

Abstract:Alveoli are gas-exchange sacs lined by squamous alveolar type(AT)1 cells and cuboidal，surfactant-secreting AT2 cells.Classical studies suggested that AT1 arise from AT2 cells，but recent studies propose other sources.Here we use molecular markers，lineage tracing and clonal analysis to map alveolar progenitors throughout the mouse lifespan.We show that，during development，AT1 and AT2 cells arise directly from a bipotent progenitor，whereas after birth new AT1 cells derive from rare，self-renewing，long-lived，mature AT2 cells that produce slowly expanding clonal foci of alveolar renewal.This stem-cell function is broadly activated by AT1 injury，and AT2 self-renewal is selectively induced by EGFR(epidermal growth factor receptor)ligands in vitro and oncogenic Kras(G12D)in vivo，efficiently generating multifocal，clonal adenomas.Thus，there is a switch after birth，when AT2 cells function as stem cells that contribute to alveolar renewal，repair and cancer.We propose that local signals regulate AT2 stem-cell activity:a signal transduced by EGFR-KRAS controls self-renewal and is hijacked during oncogenesis，whereas another signal controls reprogrammi ng to AT1 fate.

RNA毒性積累是導(dǎo)致C9orf72引發(fā)ALS和FTD兩種疾病的原因

C9orf72六核苷酸重復(fù)擴(kuò)張已被發(fā)現(xiàn)是造成“肌萎縮側(cè)索硬化”(ALS)和“額顳癡呆”(FTD)這兩種疾病的原因。正常的C9orf72含有多達(dá)25個重復(fù)片段，而患病者的該基因則會含有數(shù)千個。研究人員在新研究中找出了六核苷酸重復(fù)擴(kuò)增(HRE)結(jié)構(gòu)多態(tài)性導(dǎo)致ALS/FTD的病理分子機(jī)制。轉(zhuǎn)錄的C9orf72六核苷酸重復(fù)片段被發(fā)現(xiàn)以一種依賴于構(gòu)形的方式與特定的核糖核蛋白如核仁蛋白相結(jié)合。因此，核仁蛋白被錯誤局部化，并且在功能上受損，導(dǎo)致“核仁應(yīng)激”。RNA毒性的增加在ALS/FTD兩種疾病中是造成與C9orf72相關(guān)病理的原因。

論文鏈接:Haeusler A R，et al..C9orf72 nucleotide repeat structures initiate molecular cascades of disease.

Nature，2014，507(7491)，195 －200.doi:10.1038/nature13124.

Abstract:A hexanucleotide repeat expansion(HRE)，(GGGGCC)n，in C9orf72 is the most common genetic cause of the neurodegenerative diseases amyotrophic lateral sclerosis(ALS)and frontotemporal dementia(FTD).Here we identify a molecular mechanism by which structural polymorphism of the HRE leads to ALS/FTD pathology and defects.The HRE forms DNA and RNA G-quadruplexes with distinct structures and promotes RNA·DNA hybrids(R-loops).The structural polymorphism causes a repeat-length-dependent accumulation of transcripts aborted in the HRE region.These transcribed repeats bind to ribonucleoproteins in a conformation-dependent manner.Specifically，nucleolin，an essential nucleolar protein，preferentially binds the HRE G-quadruplex，and patient cells show evidence of nucleolar stress.Our results demonstrate that distinct C9orf72 HRE structural polymorphism at both DNA and RNA levels initiates molecular cascades leading to ALS/FTD pathologies，and provide the basis for a mechanistic model for repeat-associated neurodegenerative dise ases.

可應(yīng)用于疫苗研發(fā)的蛋白設(shè)計方法

在一項采用計算蛋白設(shè)計方法來生成人“呼吸道合胞體病毒”(RSV)疫苗的新穎候選藥物的研究中，準(zhǔn)確模仿一個RSV抗原表位結(jié)構(gòu)的人造蛋白支架，被發(fā)現(xiàn)能在恒河猴身上誘導(dǎo)產(chǎn)生中和RSV的有效抗體。此研究所用的蛋白設(shè)計方法，即，表位集中和支架為基礎(chǔ)的疫苗的設(shè)計，進(jìn)一步加以開發(fā)可用于多種其他目標(biāo)的疫苗，包括抗原性高度可變的病原體，例如，人免疫缺陷病毒和流感。

論文鏈接:Correia B E，et al..Proof of principle for epitope-focused vaccine design.

Nature，507(7491)，201 －206.doi:10.1038/nature12966.

Abstract:Vaccines prevent infectious disease largely by inducing protective neutralizing antibodies against vulnerable epitopes.Several major pathogens have resisted traditional vaccine development，although vulnerable epitopes targeted by neutralizing antibodies have been identified for several such cases.Hence，new vaccine design methods to induce epitope-specific neutralizing antibodies are needed.Here we show，with a neutralization epitope from respiratory syncytial virus，that computational protein design can generate small，thermally and conformationally stable protein scaffolds that accurately mimic the viral epitope structure and induce potent neutralizing antibodies.These scaffolds represent promising leads for the research and development of a human respiratory syncytial virus vaccine needed to protect infants，young children and the elderly.More generally，the results provide proof of principle for epitope-focused and scaffold-based vaccine design，and encourage the evaluation and further development of these strategies for a variety of other vaccine targets，including antigenically highly variable pathogens such as human immunodeficiency virus and infl uenza.

首次全面揭示食管鱗癌基因組異常改變

食管癌是中國高發(fā)的惡性腫瘤。目前，食管癌發(fā)生和發(fā)展的機(jī)制尚不明了，臨床治療缺乏特異性的分子靶點和有效的治療藥物。研究人員通過高通量測序、比較基因組雜交芯片分析、生物學(xué)功能和臨床驗證研究，全面系統(tǒng)揭示了食管鱗癌的遺傳突變背景，發(fā)現(xiàn)了與食管鱗癌發(fā)生發(fā)展進(jìn)程和臨床預(yù)后相關(guān)的基因。

論文鏈接:Song Y M，et al..Identification of genomic alterations in oesophageal squamous cell cancer.

Nature，doi:10.1038/nature13176.Published online:16 March，2014.

Abstract:Oesophageal cancer is one of the most aggressive cancers and is the sixth leading cause of cancer death worldwide.Approximately 70%of global oesophageal cancer cases occur in China，with oesophageal squamous cell carcinoma(ESCC)being the histopathological form in the vast majority of cases(＞90%).Currently，there are limited clinical approaches for the early diagnosis and treatment of ESCC，resulting in a 10%five-year survival rate for patients.However，the full repertoire of genomic events leading to the pathogenesis of ESCC remains unclear.Here we describe a comprehensive genomic analysis of 158 ESCC cases，as part of the International Cancer Genome Consortium research project.We conducted whole-genome sequencing in 17 ESCC cases and whole-exome sequencing in 71 cases，of which 53 cases，plus an additional 70 ESCC cases not used in the whole-genome and whole-exome sequencing，were subjected to array comparative genomic hybridization analysis.We identified eight significantly mutated genes，of which six are well known tumour-associated genes(TP53，RB1，CDKN2A，PIK3CA，NOTCH1，NFE2L2)，and two have not previously been described in ESCC(ADAM29 and FAM135B).Notably，F(xiàn)AM135B is identified as a novel cancer-implicated gene as assayed for its ability to promote malignancy of ESCC cells.Additionally，MIR548K，a microRNA encoded in the amplified 11q13.3 ～ 13.4 region，is characterized as a novel oncogene，and functional assays demonstrate that MIR548K enhances malignant phenotypes of ESCC cells.Moreover，we have found that several important histone regulator genes(MLL2(also called KMT2D)，ASH1L，MLL3(KMT2C)，SETD1B，CREBBP and EP300)are frequently altered in ESCC.Pathway assessment reveals that somatic aberrations are mainly involved in the Wnt，cell cycle and Notch pathways.Genomic analyses suggest that ESCC and head and neck squamous cell carcinoma share some common pathogenic mechanisms，and ESCC development is associated with alcohol drinking.This study has explored novel biological markers and tumorigenic pathways that would greatly improve therapeutic strategies for ESCC.