小立碗藓萜类物质的合成酶基因分析及其UPLC-QTOF检测

根据基因组信息和KEGG数据库分析小立碗藓基因组中合成萜类物质的基因,比较小立碗藓与酵母和拟南芥合成萜类物质基因的氨基酸序列同源性同时利用UPLC-QTOF分析小立碗藓中物质组成,来分析小立碗藓基因组中萜类物质合成的基因及小立碗藓中存在的萜类物质。与酵母相比,小立碗藓两条萜类次生代谢途径完整,途径中的基因及氨基酸丰富性更高,提示可以合成更丰富的前体物质如FPP,GPP等;小立碗藓与拟南芥的序列相似性较高,萜类背景简单。UPLC-QTOF分析检测到小立碗藓中次生代谢物质主要是芳香族化合物及各类生物碱,一种萜类物质ent-16beta-Methoxy-19-kauranoic acid。小立碗藓中本身具有合成萜类前体物质和二萜的基因,检测到少量萜类物质,适合作为萜类活性物质异源合成的底盘细胞。     

小立碗藓LysM型类受体激酶基因家族生物信息学分析

植物LysM型类受体激酶(lysin motif receptor-like kinase,LYKs)是植物中发现的一类重要的RLK,在植物生长发育、抵御逆境胁迫等方面具有不可忽视的作用,是植物中基因功能的研究热点。为更好地了解小立碗藓中的LYK基因,该文利用生物信息学的方法对小立碗藓(Physcomitrella patens) LysM型类受体激酶基因家族成员进行鉴定及分析。通过分析小立碗藓LYK家族成员的基本物理信息、基因结构、染色体定位及系统发生关系,初步探讨了其LYK基因结构、进化与功能间的联系。结果表明:(1)小立碗藓中共有21个LYK基因,其氨基酸序列大小在625～755 aa之间,分子量为69.54～82.02 kDa,等电点在5.98～7.78之间。(2)将小立碗藓所有LYK蛋白与3种典型模式植物(水稻、拟南芥和蒺藜苜蓿)的LYK蛋白共同构建系统进化树,所有LYK蛋白被分为4个亚组(LYK-I、LYK-Ⅱ、LYR-I和LYR-Ⅱ)。小立碗藓各亚组内成员的基因结构、保守域特征显示出较为相似的特征,由此推测其可能具有相同或相似的功能。(3)染色体定位发现21个LYK基因集中分布于4条染色体上并出现小型基因簇,这可能与基因功能相联系。该文分析了小立碗藓LysM型类受体蛋白激酶基因家族的基本信息,可为后续深入研究其LYK基因家族成员的生理生化功能奠定基础。     

植物分子生物学研究极具前景的模式系统——小立碗藓

小立碗藓作为植物分子生物学研究极具前景的模式系统已日益受到人们的重视,它的生活史周期短,易于培养,转基因植株易于分析,核基因组容易和外源DNA 发生同源重组,这些特点使它成为研究基因功能的良好材料。一些成功的基因敲除和基因破坏已经在小立碗藓中实现,这些基因的功能也通过小立碗藓转化植株的特点得以证实。小立碗藓标签突变文库已经建立,其应用为小立碗藓基因的进一步研究打下了基础。关于小立碗藓的ESTs 数据库已经建立,已有67 000 条ESTs 信息。     

植物分子生物学研究极具前景的模式系统--小立碗藓

小立碗藓作为植物分子生物学研究极具前景的模式系统已日益受到人们的重视,它的生活史周期短,易于培养,转基因植株易于分析,核基因组容易和外源DNA发生同源重组,这些特点使它成为研究基因功能的良好材料.一些成功的基因敲除和基因破坏已经在小立碗藓中实现,这些基因的功能也通过小立碗藓转化植株的特点得以证实.小立碗藓标签突变文库已经建立,其应用为小立碗藓基因的进一步研究打下了基础.关于小立碗藓的ESTs数据库已经建立,已有67 000条ESTs信息.     

小立碗藓扩展蛋白基因家族的鉴定与生物信息学分析

扩展蛋白(Expansins,EXP)是一类基因家族,几乎参与了植物发育的全过程,从种子萌发到果实成熟都有扩展蛋白的参与。该研究利用生物信息学的方法对小立碗藓(Physcomitrella patens) Expansin基因家族成员进行鉴定,分析了其基因结构、染色体定位以及系统发生关系。结果表明:小立碗藓基因组中含有Expansin A(EXPA) 32个、Expansin-like A(EXLA) 6个,并未发现Expansin-like B(EXLB)及Expansin B(EXPB)。扩展蛋白氨基酸序列长度在228～290 aa之间,编码蛋白质具有两个保守的结构域Pollen_allerg_1和DPBB_1。蛋白质亚细胞定位预测结果表明:运用CELLO在线工具预测发现小立碗藓中约4/5的EXP家族基因定位于细胞外;而Euk-mPLoc预测结果则显示小立碗藓EXP基因家族成员全定位于细胞外。基因结构分析表明,小立碗藓中约68%Expansin基因有含有1～3个内含子。以上结果可为深入研究小立碗藓扩展蛋白基因的分子进化与生物学功能奠定基础。     

MIR166基因家族在陆生植物中的进化模式分析

MicroRNA（miRNA）是一类广泛存在于真核生物中的具有转录后水平调控功能的内源非编码小分子RNA。在植物中．miRNA通过对靶基因的剪切或沉默来实现对植物生命活动的调控,它是基因表达调控网络的重要组成部分。miR165／166（miR166）是陆生植物中最为古老的MIRNA家族之一,它通过对3型同源异域型-亮氨酸拉链（1id—ZIPⅢ）等靶标的调控,在植物的众多发育时期起着关键的调控作用。本文分析了MIR166基因在陆生植物中的进化关系,并对MIR166在基部陆生植物小立碗藓（Physcomitrella patens）中的复制及进化进行了研究。此外,HD—ZIPⅢ蛋白是植物中重要的一类转录因子,miR166对HD-ZIP Ⅲ基因的调控作用在陆地植物保守的存在,本文对HD—ZIP Ⅲ基因和miR166在进化中的相互作用进行了初步的探讨。     

小立碗藓愈伤组织诱导和培养

小立碗藓已经成为植物功能基因组学的模式系统,其材料的大量培养是所有工作的基础.文章探讨了小立碗藓愈伤组织诱导和组织培养的基本条件,并观察了小立碗藓愈伤组织的亚显微结构.     

小立碗藓属在中国的记录

本文作者在湖南张家界采得小立碗藓属植物,经扫描电镜显示,其孢子具多数柱状疣的特征与小立碗藓加利福尼亚亚种相一致,可确定它为P．patens(Hedw．)B．S．G．subsp．californica(Crum et Anderson)Tan。此为小立碗藓属植物在我国的首次记录。     

基于HMM的齿肋赤藓VOZ转录因子的预测与分析

VOZ(Vascular plant One Zinc finger protein)作为与植物的进化与发育密切相关的基因,在极端耐旱荒漠苔藓植物齿肋赤藓(Syntrichia caninervis)中对VOZ基因进行挖掘和分析有利于更好的揭示VOZ基因的进化关系,且可作为抗逆基因进行更为深入的分子生物学研究。在VOZ转录因子蛋白中VOZ-domain是一个保守的DNA结合结构功能域,利用VOZ-domain多序列联配构建隐马尔可夫模型序列谱能够很好的进行家族成员的识别和预测。利用拟南芥、小立碗藓和水稻等植物已知的转录因子序列信息构建HMM序列谱模型,对荒漠苔藓齿肋赤藓转录组进行比对搜索。最终得到一条新的齿肋赤藓VOZ转录因子ScVOZ1(NCBI/EBI检索号:HG764415),序列长度为1 495 bp,具有完整的VOZ-domain结构域。生物信息学分析表明其具有转录调控功能和核定位潜能。多序列比对、进化和保守基序分析表明,ScVOZ1蛋白序列与小立碗藓VOZ家族和拟南芥AtVOZ1相似度较高。本研究为进一步研究ScVOZ1基因的功能以及其进化起源奠定了基础。     

有前景的模式植物小立碗藓的研究新进展

小立碗藓是在分子生物学研究方面有广阔应用前景的模式植物。该文主要综述了有关小立碗藓在功能基因组学、进化和适应性及植物生理等方面最新的研究进展。     

Common functions for diverse small RNAs of land plants

Endogenous small RNAs, including microRNAs (miRNAs) and short interfering RNAs (siRNAs), are critical components of plant gene regulation. Some abundant miRNAs involved in developmental control are conserved between anciently diverged plants, while many other less-abundant miRNAs appear to have recently emerged in the Arabidopsis thaliana lineage. Using large-scale sequencing of small RNAs, we extended the known diversity of miRNAs in basal plants to include 88 confidently annotated miRNA families in the moss Physcomitrella patens and 44 in the lycopod Selaginella moellendorffii. Cleavage of 29 targets directed by 14 distinct P. patens miRNA families and a trans-acting siRNA (ta-siRNA) was experimentally confirmed. Despite a core set of 12 miRNA families also expressed in angiosperms, weakly expressed and apparently lineage-specific miRNAs accounted for the majority of miRNA diversity in both species. Nevertheless, the molecular functions of several of these lineage-specific small RNAs matched those of angiosperms, despite dissimilarities in the small RNA sequences themselves, including small RNAs that mediated negative feedback regulation of the miRNA pathway and miR390-dependent ta-siRNAs that guided the cleavage of AUXIN RESPONSE FACTOR mRNAs. Diverse, lineage-specific, small RNAs can therefore perform common biological functions in plants.     

Computational analysis of drought stress-associated miRNAs and miRNA co-regulation network in Physcomitrella patens

miRNAs are non-coding small RNAs that involve diverse biological processes. Until now, little is known about their roles in plant drought resistance. Physcomitrella patens is highly tolerant to drought; however, it is not clear about the basic biology of the traits that contribute P. patens this important character. In this work, we discovered 16 drought stress-associated miRNA (DsAmR) families in P. patens through computational analysis. Due to the possible discrepancy of expression periods and tissue distributions between potential DsAmRs and their targeting genes, and the existence of false positive results in computational identification, the prediction results should be examined with further experimental validation. We also constructed an miRNA co-regulation network, and identified two network hubs, miR902a-5p and miR414, which may play important roles in regulating drought-resistance traits. We distributed our results through an online database named ppt-miRBase, which can be accessed at http://bioinfor.cnu.edu.cn/ppt_miRBase/index.php. Our methods in finding DsAmR and miRNA co-regulation network showed a new direction for identifying miRNA functions.     

Analyses of a Glycine max Degradome Library Identify microRNA Targets and MicroRNAs that Trigger Secondary SiRNA Biogenesis

Plant microRNAs (miRNAs) regulate gene expression mainly by guiding cleavage of target mRNAs. In this study, a degradome library constructed from different soybean (Glycine max (L.) Merr.) tissues was deep-sequenced. 428 potential targets of small interfering RNAs and 25 novel miRNA families were identified. A total of 211 potential miRNA targets, including 174 conserved miRNA targets and 37 soybean-specific miRNA targets, were identified. Among them, 121 targets were first discovered in soybean. The signature distribution of soybean primary miRNAs (pri-miRNAs) showed that most pri-miRNAs had the characteristic pattern of Dicer processing. The biogenesis of TAS3 small interfering RNAs (siRNAs) was conserved in soybean, and nine Auxin Response Factors were identified as TAS3 siRNA targets. Twenty-three miRNA targets produced secondary small interfering RNAs (siRNAs) in soybean. These targets were guided by five miRNAs: gma-miR393, gma-miR1508, gma-miR1510, gma-miR1514, and novel-11. Multiple targets of these secondary siRNAs were detected. These 23 miRNA targets may be the putative novel TAS genes in soybean. Global identification of miRNA targets and potential novel TAS genes will contribute to research on the functions of miRNAs in soybean.     

Identification and Characterization of ABA-Responsive MicroRNAs in Rice

MicroRNAs(miRNAs) are endogenous non-coding small RNAs that silence genes through mRNA degradation or translational inhibition.The phytohormone abscisic acid(ABA) is essential for plant development and adaptation to abiotic and biotic stresses.In Arabidopsis,miRNAs are implicated in ABA functions.However,ABA-responsive miRNAs have not been systematically studied in rice.Here high throughput sequencing of small RNAs revealed that 107 miRNAs were differentially expressed in the rice ABA deficient mutant,Osabal.Of these,13 were confirmed by stem-loop RT-PCR.Among them,miR1425-5P,miR169 a,miR169n,miR390-5P,miR397 a and miR397 b were up-regulated,but miR162 b reduced in expression in Osabal.The targets of these 13 miRNAs were predicted and validated by gene expression profiling.Interestingly,the expression levels of these miRNAs and their targets were regulated by ABA.Cleavage sites were detected on 7 of the miRNA targets by 5'-Rapid Amplification of cDNA Ends(5'-RACE).Finally,miR162 b and its target OsTREl were shown to affect rice resistance to drought stress,suggesting that miR162 b increases resistance to drought by targeting OsTREl.Our work provides important information for further characterization and functional analysis of ABA-responsive miRNAs in rice.