Computational identification of novel family members of microRNA genes in Arabidopsis thaliana and Oryza sativa

MicroRNAs (miRNAs) are a class of endogenous small RNAs that play important regulatory roles in both animals and plants, miRNA genes have been intensively studied in animals, but not in plants. In this study, we adopted a homology search approach to identify homologs of previously validated plant miRNAs in Arabidopsis thaliana and Oryza sativa. We identified 20 potential miRNA genes in Arabidopsis and 40 in O. sativa, providing a relatively complete enumeration of family members for these miRNAs in plants. In addition, a greater number of Arabidopsis miRNAs (MIR168, MIR159 and MIR172) were found to be conserved in rice. With the novel homologs, most of the miRNAs have closely related fellow miRNAs and the number of paralogs varies in the different miRNA families. Moreover, a probable functional segment highly conserved on the elongated stem of pre-miRNA fold-backs of MIR319 and MIR159 family was identified. These results support a model of variegated miRNA regulation in plants, in which miRNAs with different functional elements on their pre-miRNA fold-backs can differ in their function or regulation, and closely related miRNAs can be diverse in their specificity or competence to downregulate target genes. It appears that the sophisticated regulation of miRNAs can achieve complex biological effects through qualitative and quantitative modulation of gene expression profiles in plants.     

Computational analysis of the glutamate receptor gene family of Arabidopsis thaliana

Ionotropic glutamate receptors (iGluRs) function as glutamate-activated ion channels in rapid synaptic transmission in animals. Arabidopsis thaliana possess 20 glutamate receptor-like genes (AtGLRs) in its genome which are involved in many functions including light signal transduction and calcium homeostasis. However, little is known about the physico-chemical, functional and structural properties of AtGLRs. In this study, glutamate receptor-like genes of A. thaliana have been studied in silico. Exon–intron structures revealed common origin of majority of these genes. The presence of several phosphorylation and myristoilation sites indicate the involvement of AtGLRs in various signaling processes. Gene ontology analysis showed the participation of AtGLRs in various biological processes including different stress responses. In two genes namely AT2G17260 and AT4G35290, presence of RAV1-A binding site motif in the promoter coupled with results from gene ontology annotation indicate their role in stomatal movement through abscisic acid signaling. Expression analysis showed differential expression of several tandemly arranged genes which indicates neo or sub-functionalization. Two genes namely AT5G48400 and AT5G48410 showed significantly more expression in response to Botrytis cinerea infection. Five of these genes have shown G-protein-coupled γ-aminobutyric acid (GABA) receptor activity indicating a possible interaction between AtGLRs and GABA. Structurally, all of them were similar while differences were found regarding electrostatic surfaces as well as surface hydrophobicity. Results of this study provide a comprehensive reference regarding AtGLRs for further analysis regarding the structure, function, and evolution of the glutamate receptors in plants.     

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。     

Genome-wide analysis of lipoxygenase gene family in Arabidopsis and rice

The enzymes called lipoxygenases (LOXs) can dioxygenate unsaturated fatty acids, which leads to lipoperoxidation of biological membranes. This process causes synthesis of signaling molecules and also leads to changes in cellular metabolism. LOXs are known to be involved in apoptotic (programmed cell death) pathway, and biotic and abiotic stress responses in plants. Here, the members of LOX gene family in Arabidopsis and rice are identified. The Arabidopsis and rice genomes encode 6 and 14 LOX proteins, respectively, and interestingly, with more LOX genes in rice. The rice LOXs are validated based on protein alignment studies. This is the first report wherein LOXs are identified in rice which may allow better understanding the initiation, progression and effects of apoptosis, and responses to bitoic and abiotic stresses and signaling cascades in plants.Key words: apoptosis, biotic and abiotic stresses, genomics, jasmonic acid, lipidsLipoxygenases (linoleate:oxygen oxidoreductase, EC 1.13.11.-; LOXs) catalyze the conversion of polyunsaturated fatty acids (lipids) into conjugated hydroperoxides. This process is called hydroperoxidation of lipids. LOXs are monomeric, non-heme and non-sulfur, but iron-containing dioxygenases widely expressed in fungi, animal and plant cells, and are known to be absent in prokaryotes. However, a recent finding suggests the existence of LOX-related genomic sequences in bacteria but not in archaea.¹ The inflammatory conditions in mammals like bronchial asthama, psoriasis and arthritis are a result of LOXs reactions.² Further, several clinical conditions like HIV-1 infection,³ disease of kidneys due to the activation of 5-lipoxygenase,^4,5 aging of the brain due to neuronal 5-lipoxygenase⁶ and atherosclerosis⁷ are mediated by LOXs. In plants, LOXs are involved in response to biotic and abiotic stresses.⁸ They are involved in germination⁹ and also in traumatin and jasmonic acid biochemical pathways.^10,11 Studies on LOX in rice are conducted to develop novel strategies against insect pests¹² in response to wounding and insect attack,¹³ and on rice bran extracts as functional foods and dietary supplements for control of inflammation and joint health.¹⁴ In Arabidopsis, LOXs are studied in response to natural and stress-induced senescence,¹⁵ transition to flowering,¹⁶ regulation of lateral root development and defense response.¹⁷The arachidonic, linoleic and linolenic acids can act as substrates for different LOX isozymes. A hydroperoxy group is added at carbons 5, 12 or 15, when arachidonic acid is the substrate, and so the LOXs are designated as 5-, 12- or 15-lipoxygenases. Sequences are available in the database for plant lipoxygenases (EC:1.13.11.12), mammalian arachidonate 5-lipoxygenase (EC:1.13.11.34), mammalian arachidonate 12-lipoxygenase (EC:1.13.11.31) and mammalian erythroid cell-specific 15-lipoxygenase (EC:1.13.11.33). The prototype member for LOX family, LOX-1 of Glycine max L. (soybean) is a 15-lipoxygenase. The LOX isoforms of soybean (LOX-1, LOX-2, LOX-3a and LOX-3b) are the most characterized of plant LOXs.¹⁸ In addition, five vegetative LOXs (VLX-A, -B, -C, -D, -E) are detected in soybean leaves.¹⁹ The 3-dimensional structure of soybean LOX-1 has been determined.^20,21 LOX-1 was shown to be made of two domains, the N-terminal domain-I which forms a β-barrel of 146 residues, and a C-terminal domain-II of bundle of helices of 693 residues²¹ (Fig. 1). The iron atom was shown to be at the centre of domain-II bound by four coordinating ligands, of which three are histidine residues.²²Open in a separate windowFigure 1Three-dimensional structure of soybean lipoxygenase L-1. The domain I (N-terminal) and domain II (C-terminal) are indicated. The catalytic iron atom is embedded in domain II (PDB ID-1YGE).²¹This article describes identification of LOX genes in Arabidopsis and rice. The Arabidopsis genome encodes for six LOX proteins²³ (www.arabidopsis.org) (

苹果柠檬酸合酶3基因家族成员鉴定及表达分析

柠檬酸合酶(citrate synthase 3, CS3)是细胞代谢途径中的关键酶之一,其活性调节着生物体的物质和能量代谢过程。本研究旨在从苹果全基因组中鉴定CS3基因家族成员,并进行生物信息学和表达模式分析,为研究苹果CS3基因的潜在功能提供理论基础。利用BLASTp基于GDR数据库鉴定苹果CS3家族成员,通过Pfam、SMART、MEGA5.0、clustalx.exe、ExPASy Proteomics Server、MEGAX、SOPMA、MEME和WoLF PSORT等软件分析CS3蛋白序列基本信息、亚细胞定位情况、结构域组成、系统进化关系以及染色体定位情况。利用酸含量的测定和实时荧光定量PCR (real-time fluorescence quantitative polymerase chain reaction, qRT-PCR)技术检测苹果6个CS3的组织表达和诱导表达特性。苹果CS3基因家族包含6个成员,这些CS3蛋白包括473−608个不等的氨基酸残基,等电点分布在7.21−8.82。亚细胞定位结果显示CS3蛋白分别定位在线粒体和叶绿体。系统进化分析可将其分为3类,各亚家族基因数量分别为2个。染色体定位结果显示,CS3基因分布在苹果不同的染色体上。蛋白二级结构以a-螺旋为主,其次是无规则卷曲,b-转角所占比例最小。筛选的6个家族成员在不同苹果组织中均有表达,整体表达趋势从高到低依次为MdCS3.4相对表达含量最高,MdCS3.6次之,其他家族成员相对表达量依次为MdCS3.3>MdCS3.2>MdCS3.1>MdCS3.5。qRT-PCR结果显示,MdCS3.1和MdCS3.3基因在酸含量较低的‘成纪1号’果肉中相对表达量最高,酸含量较高的‘艾斯达’果肉中MdCS3.2和MdCS3.3基因相对表达量最高。因此,本研究对不同苹果品种中CS3基因相对表达量进行了检测,并分析了其在苹果果实酸合成过程中的作用。结果表明,CS3基因在不同苹果品种中的相对表达量存在差异,为后续研究苹果品质形成机制提供了参考。     

Diversity and evolution of MicroRNA gene clusters

microRNA (miRNA) gene clusters are a group of miRNA genes clustered within a proximal distance on a chromosome. Although a large number of miRNA clusters have been uncovered in animal and plant genomes, the functional consequences of this arrangement are still poorly understood. Located in a polycistron, the coexpressed miRNA clusters are pivotal in coordinately regulating multiple processes, including embryonic development, cell cycles and cell differentiation. In this review, based on recent progress, we discuss the genomic diversity of miRNA gene clusters, the coordination of expression and function of the clustered miRNAs, and the evolutionarily adaptive processes with gain and loss of the clustering miRNA genes mediated by duplication and transposition events. Supported by State Key Program of National Natural Science of China(Grant No. 306300130)     

水稻全基因组编码抗病基因同源序列分析

利用模糊搜索的方法,在TIGR水稻日本晴基因组数据库(TIGR Rice Genome Annotation-Release5)中识别出565个编码抗病蛋白质的同源序列;利用识别出565个编码抗病蛋白质序列分别与籼稻基因组数据库进行BLASTP联配,共确定320个对应的等位基因。通过在线生物信息学软件,识别了这565个抗病基因的保守结构域、保守模体和DNA序列内转座子元件,其中有14个抗病基因同源序列注释错误。同时绘出了这些基因的基因组分布,并基于这些基因的同源树分析和基因组物理分布,认为基因的原位和远程复制事件产生了抗病基因的现存分布和多样性,其中转座子在复制过程中扮演了重要角色。这些对抗病机制研究和抗病基因进化研究以及抗病基因的转育具有重要意义。     

基因重复研究进展

基因复制是基因通过不等交换,反转录转座或由全基因组复制等途径产生一个与原基因相似的基因或碱基序列,它与生物体基因组大小的进化、新基因的起源、物种的分化以及基因抗突变的能力大小等都密切相关。本文综述了复制基因的产生和保留机制、选择作用、分化的途径以及复制基因进化速率等方面的相关研究,揭示了基因复制对于生物进化的重要性,以引起大家对该领域的了解与关注。关键词：基因复制;复制基因;不等交换;反转录转座;全基因组复制     

Comprehensive expression analysis of rice phospholipase D gene family during abiotic stresses and development

Phospholipase D is one of the crucial enzymes involved in lipid mediated signaling, triggered during various developmental and physiological processes. Different members of PLD gene family have been known to be induced under different abiotic stresses and during developmental processes in various plant species. In this report, we are presenting a detailed microarray based expression analysis and expression profiles of entire set of PLD genes in rice genome, under three abiotic stresses (salt, cold and drought) and different developmental stages (3-vegetative stages and 11-reproductive stages). Seven and nine PLD genes were identified, which were expressed differentially under abiotic stresses and during reproductive developmental stages, respectively. PLD genes, which were expressed significantly under abiotic stresses exhibited an overlapping expression pattern and were also differentially expressed during developmental stages. Moreover, expression pattern for a set of stress induced genes was validated by real time PCR and it supported the microarray expression data. These findings emphasize the role of PLDs in abiotic stress signaling and development in rice. In addition, expression profiling for duplicated PLD genes revealed a functional divergence between the duplicated genes and signify the role of gene duplication in the evolution of this gene family in rice. This expressional study will provide an important platform in future for the functional characterization of PLDs in crop plants.     

Detecting the undetectable: uncovering duplicated segments in Arabidopsis by comparison with rice

Genome analysis shows that large-scale gene duplications have occurred in fungi, animals and plants, creating genomic regions that show similarity in gene content and order. However, the high frequency of gene loss reduces colinearity resulting in duplicated regions that, in the extreme, no longer share homologous genes. Here, we show that by comparison with an appropriate second genome, such paralogous regions can still be identified.     

高粱磷脂酶D基因家族的鉴定和表达分析

磷脂酶D（PLD）是植物生长和胁迫反应过程中参与膜磷脂分解代谢的关键酶。PLD编码基因在高等植物中构成了一个大的基因家族,但是仍未对高粱PLD基因家族进行深入研究。本研究中,通过全基因组分析,鉴定了15个PLD基因,并分成6个亚组,初步揭示了SbPLDs的基因结构、保守结构域、染色体定位和系统发育关系等信息。基因复制的研究表明,片段复制在高粱PLD基因家族的扩展中发挥了重要作用,SbPLDs在进化过程中经历了强烈的纯化选择。此外,转录组数据表明,受启动子区上游顺式元件调控的PLD家族基因可能在高粱的生长发育中发挥重要作用。通过real-time PCR分析,显示部分SbPLDs参与非生物胁迫和激素途径的潜力。亚细胞定位表明,高粱PLD蛋白在细胞质中富集,可能具有抗逆胁迫的功能。本研究为了解高粱PLD基因的特征提供了理论参考,为研究高粱PLD基因家族的进化提供了新的视角,也为阐明高粱PLD基因家族的功能提供了基础信息。     

MADS-box基因家族基因重复及其功能的多样性

基因的重复(duplication)及其功能的多样性(diversification)为生物体新的形态进化提供了原材料。MADS-box基因在植物(特别是被子植物)的进化过程中发生了大规模的基因重复事件而形成一个多基因家族。MADS-box基因家族的不同成员在植物生长发育过程中起着非常重要的作用,在调控开花时间、决定花分生组织和花器官特征以及调控根、叶、胚珠及果实的发育中起着广泛的作用。探讨MADS-box基因家族的进化历史有助于深入了解基因重复及随后其功能分化的过程和机制。本文综述了MADS-box基因家族基因重复及其功能分化式样的研究进展。     

Genomic analysis and expression investigation of caleosin gene family in Arabidopsis

Caleosin is a common lipid-droplet surface protein, which has the ability to bind calcium. Arabidopsis (Arabidopsis thaliana) is considered a model organism in plant researches. Although there are growing researches about caleosin in the past few years, a systemic analysis of caleosins in Arabidopsis is still scarce. In this study, a comprehensive investigation of caleosins in Arabidopsis was performed by bioinformatics methods. Firstly, eight caleosins in Arabidopsis are divided into two types, L-caleosin and H-caleosin, according to their molecular weights, and these two types of caleosin have many differences in characteristics. Secondly, phylogenetic tree result indicates that L-caleosin may evolve from H-caleosin. Thirdly, duplication pattern analysis shows that segmental and tandem duplication are main reasons for Arabidopsis caleosin expansion with the equal part. Fourthly, the expression profiles of caleosins are also investigated in silico in different organs and under various stresses and hormones. In addition, based on promoter analysis, caleosin may be involved in calcium signal transduction and lipid accumulation. Thus, the classification and expression analysis of caleosin genes in Arabidopsis provide facilities to the research of phylogeny and functions in this gene family.