揭开拟南芥基因组序列的奥秘

拟南芥植物的个体较小,生活周期短,很适于根农杆菌的转化,因此被认为是特别适合在实验室中进行遗传操作的模式植物。１９８７年,在美国密歇根州立大学召开的第三届国际拟南芥大会上,人们再次确认了这种植物的模式植物地位。由于拟南芥基因组较小,约１２０兆碱基对,而玉米和小麦的碱基对则大得多,前者约为２５００兆,后者１６０００兆。因此,拟南芥应是测定基因组序列最为理想的材料。另外,更为重要的是,尽管拟南芥的基因组没有在高等植物上普遍存在的大量DNA重复区,但它们却包含了植物发育、代谢、环境信号反应和抗病性等所…     

拟南芥PHD-finger蛋白家族的全基因组分析

PHD—finger蛋白是一类广泛存在于真核生物中,在基因转录和染色质状态调控方面有重要作用的锌指蛋白。目前在动物中对PHD—finger蛋白的结构和功能方面的研究较为广泛和深入,而在植物中仅有少数PHD—finger蛋白的功能被阐明。通过SMART和Pfam等数据库分析,我们发现拟南芥中共有70个PHD-finger蛋白,其中大部分PHD—tinger蛋白的功能未知。本文通过生物信息学分析获得拟南芥PHD-tinger家族较为全面的信息,包括基因结构、染色体定位、基因表达、蛋白结构域、系统进化关系等,为深入研究PHD-finger家族蛋白的结构与功能提供了参考。     

拟南芥中MATE基因家族的研究进展

多药和有毒化合物排出家族（Multidrug and Toxic Compound Extrusion, MATE）是一个新的次级转运蛋白家族,此类转运蛋白对氨基葡糖、阳离子染料、多种抗生素和药物有转运作用。拟南芥中的MATE基因家族是一个多基因家族,大概由56个成员构成,本文综述了拟南芥中MATE家族基因的研究进展,包括3个方面：第一是拟南芥中MATE家族成员的构成及主要特征;第二描述了转运蛋白的主要功能;第三分析了其功能多样的大致原因。此外,还展望了此家族研究的一些前景。     

拟南芥F-box蛋白家族的功能研究进展

F-box蛋白是一类含有F-box基序、在泛素介导的蛋白质水解过程中具有底物识别特性的蛋白质。该文对国内外近年来有关F-box家族在拟南芥中的数量、种类以及在生长发育、细胞信号转导、生物及非生物逆境胁迫等多种生理过程中的作用等方面的研究进展进行综述,以期促进该家族基因在拟南芥和其他重要农作物中的功能研究,尽快描绘出该家族在植物中的代谢网络图谱。     

拟南芥泛素家族的全基因组分析

泛素家族是一类含有保守性泛素结构域的蛋白质统称,主要通过ATP依赖性的泛素-蛋白水解酶复合体通路选择性降解细胞蛋白的各种生理活动。本研究基于HMM模型,已知泛素氨基酸序列作为训练集,搜索拟南芥信息资源数据库并鉴定AtUBQ家族成员,然后对这些基因编码的蛋白质序列进行基因结构分析、染色体定位、多序列联配、系统发育树构建和组织差异表达分析。结果表明,AtUBQ家族中共有13个推定的AtUBQ基因,命名为AtUBQ01~AtUBQ13,均属无内含子基因且结构基本相同,非均匀分布于拟南芥5条染色体;AtUBQ家族可划分为A、B和C3个亚家族,其中76.92%的基因编码蛋白质属于A亚家族;EST搜索发现除AtUBQ02和AtUBQ07基因无EST数据支持外,余下的AtUBQ基因在拟南芥根、芽和叶等7个组织中呈现差异表达,仅见AtUBQ08和AtUBQ10基因在上述7个组织中均表达,而AtUBQ03基因仅表达于叶中。本研究结果可为进一步开展该家族的生物学功能和分子进化机制的研究提供基础资料。     

拟南芥MATE家族成员DTX18表达调控

拟南芥多药物和有毒化合物排出家族(MATE)属次级转运蛋白家族, 此类转运蛋白与解毒内源的次生代谢物和外源的有毒化合物有关.通过 PCR 的方法从拟南芥基因组中扩增到该家族成员DTX18的启动子序列,构建重组质粒后,通过农杆菌介导的方法获得转基因植物.GUS 组织化学染色发现此基因的表达受到伤害和茉莉酸甲酯(MJ)诱导.同时结合半定量 PCR 的方法检测该基因在伤害及 MJ 处理下转录本丰度的变化,进一步证实了此结果.另外,此基因在突变体coi1,ein2中的表达量明显降低,这一点揭示了此基因表达的调控机制,即与植物激素JA/ET的信号传导密切相关.     

拟南芥MATE家族基因DTX12的表达模式分析

拟南芥多药物和有毒化合物排出家族属次级转运蛋白家族,此类转运蛋白与解毒内源的次生代谢物和外源的有毒化合物有关。通过PCR的方法从拟南芥基因组中扩增到该家族成员DTX12的启动子序列,构建双元载体pBI101.2-ProDTX12-GUS,通过农杆菌介导的方法转化拟南芥,然后对转基因植株用GUS底物进行组织化学显色分析。同时,通过半定量RT-PCR的方法,进一步验证了DTX12在不同组织中的表达情况。结果表明该基因在成熟的花器官的花药中和幼苗的根尖特异表达,另外,在子叶的尖端也有少量的表达。由于DTX12编码的是一个具有转运有毒化合物功能的蛋白,推测其功能可能是转运与细胞分裂或生长有关的次生代谢物。     

DEAD-box基因家族在拟南芥生长发育中的作用

在RNA代谢过程中,需要许多蛋白和核酸的参与,其中一类蛋白就是RNA解旋酶。RNA解旋酶通过水解ATP获得能量来参与RNA代谢的多个方面,包括核内转录、pre-mRNA的剪切、核糖体发生、核质运输、蛋白质翻译、RNA降解、细胞器内基因的表达。DEAD-box蛋白家族是RNA解旋酶中最大的亚家族,它具有9个保守结构域,因motifyⅡ的保守氨基酸序列Asp-Glu-Ala-Asp(DEAD)而命名。该家族在酵母、拟南芥(Arabidopsis thaliana Heynh.)和人类基因组中都有较多的家庭成员。近年来,研究者对拟南芥DEAD-box蛋白家族的结构和功能进行了一些研究,本文着重总结DEAD-box基因家族对拟南芥生长发育的影响。     

拟南芥DNA全序列测定与分析完成

在 2 0 0 0年 1 2月 1 4日英国出版的ＮＡＴＵＲＥ杂志上 (Ｖｏｌ.4 0 8:796～ 81 5) ,发表了植物分子遗传研究的模式开花植物拟南芥 1 1 5.4Ｍｂ的全序列图谱 ,原文的中文译名为“开花植物拟南芥的基因组序列分析”。拟南芥ＤＮＡ全长 1 2 5Ｍｂ ,只剩下 1 0Ｍｂ的中心着丝区ＤＮＡ ,因为多重复序列所含基因很少 ,还未全测出。拟南芥全基因组ＤＮＡ包含 2 5498个功能基因组及其所对应的 1 1 0 0 0个蛋白质家族。这是人类首次全部破译出一种高等植物的全基因序列 ,是在分子水平上向植物生命奥秘探索的又一里程碑式的工作。拟南芥植物基因组…     

拟南芥过氧化物酶序列与功能的生物信息学分析

植物过氧化物酶(POD)属于多基因家族,不仅是植物体内清除活性氧自由基的重要酶类之一,而且参与多种生理生化过程,在维系植物生长发育过程中发挥重要的作用。采用生物信息学方法对拟南芥过氧化物酶家族的73个基因编码的蛋白质序列的结构和功能进行了分析,其中包含氨基酸的数量、等电点、跨膜结构域、信号肽、二级结构组成及磷酸化位点等,并用Mega4.0软件构建了去除信号肽前后的系统进化树,旨在了解其结构特征。对已经进行功能研究的成员进行结构分析,以此来揭示结构与功能之间的联系,为植物抵御氧化胁迫方面研究提供理论基础。     

Prediction of drought-resistant genes in Arabidopsis thaliana using SVM-RFE

Background

Identifying genes with essential roles in resisting environmental stress rates high in agronomic importance. Although massive DNA microarray gene expression data have been generated for plants, current computational approaches underutilize these data for studying genotype-trait relationships. Some advanced gene identification methods have been explored for human diseases, but typically these methods have not been converted into publicly available software tools and cannot be applied to plants for identifying genes with agronomic traits.

Methodology

In this study, we used 22 sets of Arabidopsis thaliana gene expression data from GEO to predict the key genes involved in water tolerance. We applied an SVM-RFE (Support Vector Machine-Recursive Feature Elimination) feature selection method for the prediction. To address small sample sizes, we developed a modified approach for SVM-RFE by using bootstrapping and leave-one-out cross-validation. We also expanded our study to predict genes involved in water susceptibility.

Conclusions

We analyzed the top 10 genes predicted to be involved in water tolerance. Seven of them are connected to known biological processes in drought resistance. We also analyzed the top 100 genes in terms of their biological functions. Our study shows that the SVM-RFE method is a highly promising method in analyzing plant microarray data for studying genotype-phenotype relationships. The software is freely available with source code at http://ccst.jlu.edu.cn/JCSB/RFET/.     

拟南芥基因组中新的microRNA预测及分析

MicroRNA（miRNA）是一类存在于动植物体内、长度为21～25nt的内源性小RNA,对生物体的转录后基因调控起着关键作用,但一些低丰度的miRNA和组织特异性miRNA往往很难发现。为了系统识别拟南芥基因组中新的非同源miRNA,首先基于已报道的拟南芥miRNA的特征,从全基因组范围中筛选出453条可能的miRNA前体;其次,为了进一步对上述miRNA前体进行筛选,利用人的miRNA前体数据构建了支持向量机模型GenomicSVM,该模型对人测试集的敏感性和特异性分别为86.3％和98．1％（30个人miRNA前体和1000个阴性miRNA前体）,对拟南芥测试集的正确率为93．6％（78个miRNA前体）;最后,利用GenomicSVM预测上述453条miRNA前体序列,得到了37条候选的新的拟南芥miRNA前体,为进一步的miRNA实验发现研究提供了指导。     

Prediction of protein-protein interactions between Ralstonia solanacearum and Arabidopsis thaliana

Ralstonia solanacearum is a devastating bacterial pathogen that has an unusually wide host range. R. solanacearum, together with Arabidopsis thaliana, has become a model system for studying the molecular basis of plant-pathogen interactions. Protein-protein interactions (PPIs) play a critical role in the infection process, and some PPIs can initiate a plant defense response. However, experimental investigations have rarely addressed such PPIs. Using two computational methods, the interolog and the domain-based methods, we predicted 3,074 potential PPIs between 119 R. solanacearum and 1,442 A. thaliana proteins. Interestingly, we found that the potential pathogen-targeted proteins are more important in the A. thaliana PPI network. To facilitate further studies, all predicted PPI data were compiled into a database server called PPIRA (http://protein.cau.edu.cn/ppira/). We hope that our work will provide new insights for future research addressing the pathogenesis of R. solanacearum.     

Functional bioinformatics for Arabidopsis thaliana

MOTIVATION: The genome of Arabidopsis thaliana, which has the best understood plant genome, still has approximately one-third of its genes with no functional annotation at all from either MIPS or TAIR. We have applied our Data Mining Prediction (DMP) method to the problem of predicting the functional classes of these protein sequences. This method is based on using a hybrid machine-learning/data-mining method to identify patterns in the bioinformatic data about sequences that are predictive of function. We use data about sequence, predicted secondary structure, predicted structural domain, InterPro patterns, sequence similarity profile and expressions data. RESULTS: We predicted the functional class of a high percentage of the Arabidopsis genes with currently unknown function. These predictions are interpretable and have good test accuracies. We describe in detail seven of the rules produced.     

Functional bioinformatics for Arabidopsis thaliana

The authors would     

An Autoinhibitory Domain Confers Redox Regulation to Maize Glycerate Kinase

Glycerate 3-kinase (GLYK) is the terminal enzyme of the photorespiratory cycle in plants and many cyanobacteria. For several C₄ plants, notably grasses of the NADP-malic enzyme (ME) subtype, redox regulation of GLYK has been reported, but the responsible molecular mechanism is not known. We have analyzed the enzyme from the NADP-ME C₄ plant maize (Zea mays) and found that maize GLYK, in contrast to the enzyme from C₃ plants and a dicotyledonous NADP-ME C₄ plant, harbors a short carboxy-terminal extension. In its oxidized (night) form, a disulfide bridge is formed between the two cysteine residues present in this extra domain, and GLYK activity becomes inhibited. Cleavage of this bond by thioredoxin f produces the fully active thiol form, releasing autoinhibition. Fusion of the maize GLYK redox-regulatory domain to GLYK from C₃ plants confers redox regulation to these otherwise unregulated enzymes. It appears that redox regulation of GLYK could be an exclusive feature of monocotyledonous C₄ plants of the NADP-ME type, in which linear electron transport occurs only in the mesophyll chloroplasts. Hence, we suggest that GLYK, in addition to its function in photorespiration, provides glycerate 3-phosphate for the accelerated production of triose phosphate and its export from the mesophyll. This could facilitate the activation of redox-regulated Calvin cycle enzymes and the buildup of Calvin cycle intermediates in the bundle sheath of these particular C₄ plants during the dark/light transition.Glycerate kinases are important enzymes of primary metabolism in all organisms. Glycerate 2-kinases are involved in the degradation of Glc and other metabolic pathways in animals and bacteria (Guo et al., 2006; Kehrer et al., 2007) but have not been reported for plants. Instead, a glycerate 3-kinase (GLYK) occurs in plant chloroplasts and many cyanobacteria, where it produces glycerate 3-phosphate (3PGA) from glycerate in the last step of the photorespiratory C₂ cycle (Boldt et al., 2005; Bartsch et al., 2008). This pathway is an indispensable auxiliary component of the photosynthetic CO₂ assimilation network in cyanobacteria and plants (Eisenhut et al., 2008), and its operation is most evident in higher plants with the C₃ pathway of photosynthesis. Although it was long known that photorespiration also occurs in C₄ plants (Osmond and Harris, 1971), the indispensability of this pathway for the survival of plants of this particular photosynthetic type in normal air was proven only recently (Dever et al., 1995; Zelitch et al., 2009).Based on differences in the bundle sheath-located decarboxylation step of their CO₂ concentration cycle, C₄ plants are separated into the three subgroups of NADP-malic enzyme (ME), NAD-ME, and phosphoenolpyruvate carboxykinase types (Kanai and Edwards, 1999). Biochemical studies have shown that most enzymes of the photorespiratory cycle occur with highest activities in the bundle sheath of C₄ plants (Woo and Osmond, 1977; Ohnishi and Kanai, 1983). GLYK is an exception from this rule, since it occurs exclusively in the mesophyll of C₄ plants, irrespective of their C₄ photosynthetic subtype (Osmond and Harris, 1971; Usuda and Edwards, 1980a). Hence, photorespiratory glycerate is produced in the bundle sheath but phosphorylated to 3PGA in the mesophyll of all C₄ plants (Usuda and Edwards, 1980b). Another study reported thiol-dependent regulation of GLYK in several C₄ plants, and it was proposed that GLYK, in addition to its function in the final step of photorespiration, could also serve as part of the intercellular transport system for 3PGA (Kleczkowski and Randall, 1986).Thiol-dependent activation is a well-known feature of several Calvin cycle enzymes, and thioredoxins (Trxs) are important components of this process (for review, see Buchanan and Balmer, 2005; Meyer et al., 2009). On the other hand, knowledge about the regulation of photorespiratory enzymes is scarce. We found that GLYK (ZmGLYK) from the C₄ plant maize (Zea mays), in contrast to GLYKs from most other plants, carries a small C-terminal extension including two Cys residues that spontaneously combine to form a disulfide under nonreducing conditions, resulting in the inhibition of the enzyme. Cleavage of the disulfide bond by Trx f reestablished full activity. Artificial fusion of this redox-regulatory domain to GLYK from C₃ plants conferred autoinhibition and Trx activation to these otherwise unregulated enzymes.