Microarray and proteomic analysis of brassinosteroid- and gibberellin-regulated gene and protein expression in rice

Brassinosteroid (BR) and gibberellin (GA) are two groups of plant growth regulators essential for normal plant growth and development. To gain insight into the molecular mechanism by which BR and GA regulate the growth and development of plants, especially the monocot plant rice, it is necessary to identify and analyze more genes and proteins that are regulated by them. With the availability of draft sequences of two major types, japonica and indica rice, it has become possible to analyze expression changes of genes and proteins at genome scale. In this review, we summarize rice functional genomic research by using microarray and proteomic approaches and our recent research results focusing on the comparison of cDNA microarray and proteomic analyses of BR- and GA-regulated gene and protein expression in rice. We believe our findings have important implications for understanding the mechanism by which BR and GA regulate the growth and development of rice.     

Molecular cloning and characterization of a novel brassinolide enhanced gene OsBLE1 in Oryza sativa seedlings.

Brassinosteroids (BRs) are plant steroids essential for normal growth and development. To gain insight into the molecular mechanism by which BRs regulate the growth and development of plants, it is necessary to identify and analyze more genes that are regulated by BRs. A novel brassinolide (BL)-enhanced gene designated OsBLE1, which was originally identified by using rice (Oryza sativa L.) cDNA microarray, was cloned and characterized. Its cDNA is 598 bp long, encoding a predicted polypeptide with 81 amino acid residues. Northern blots analysis revealed that OsBLE1 expression began to increase at 6 h and reached its maximum at 12 h after BL treatment. OsBLE1 expression was most responsive to BL in lamina joint in rice seedlings; besides, IAA and GA3 also enhanced its expression. OsBLE1 expressed mainly in active tissues such as vascular bundles and root primordial. Transgenic rice expressing antisense OsBLE1 exhibits various degrees of repressed growth. Results suggest that OsBLE1 might be involved in BL-regulated growth processes in rice seedlings.     

Gibberellin biosynthesis: its regulation by endogenous and environmental signals

The hormone gibberellin (GA) plays an essential role in many aspects of plant growth and development, such as seed germination, stem elongation and flower development. In recent years, exciting progress has been made in understanding how the biosynthesis of this hormone is regulated by endogenous and environmental factors. This has resulted from isolation of genes encoding enzymes involved in GA biosynthesis and metabolism, which also enabled us to manipulate the pathway by modifying the expression of these genes in transgenic plants. In addition, new GA response mutants provided information about how signaling components are involved in feedback regulation of the GA biosynthetic pathway.     

Efficacy of microarray profiling data combined with QTL mapping for the identification of a QTL gene controlling the initial growth rate in rice

Seedling vigor, which is controlled by many quantitative trait loci (QTLs), is one of several important agronomic traits for direct-seedling rice systems. However, isolating these QTL genes is laborious and expensive. Here, we combined QTL mapping and microarray profiling to identify QTL genes for seedling vigor. By performing QTL mapping using 82 backcross inbred lines (BILs) of the Koshihikari (japonica) and Habataki (indica) cultivars for the rice initial growth, we identified two QTLs, early-stage plant development1/2 (qEPD1 and qEPD2), whose Koshihikari alleles promote plant height and/or leaf sheath length. Phenotypic analysis of the two substituted lines carrying the Habataki qEPD1 or qEPD2 allele revealed that qEPD2 functioned more dominantly for the initial growth of rice. From the microarray experiment, 55 and 45 candidate genes were found in the qEPD1 and qEPD2 genomic regions, which are expressed differentially between each substitution line (SL) and Koshihikari. Gibberellin 20 oxidase-2 (OsGA20ox2), which is identical to Semi Dwarf1 (SD1), was included among the 55 candidate genes of qEPD1, whereas its paralog, OsGA20ox1, was included among the 45 candidate genes of qEPD2. Consistently, introduction of the Koshihikari OsGA20ox1 allele into SL(qEPD2) increaseed its plant height and leaf sheath length significantly relative to the introduction of the Habataki OsGA20ox1 allele. Therefore, microarray profiling could be useful for rapidly screening QTL candidate genes. We concluded that OsGA20ox1 and OsGA20ox2 (SD1) function during the initial growth of rice, but OsGA20ox1 plays a dominant role in increasing plant height and leaf sheath length at the initial growth stage.     

能源植物小桐子赤霉素合成代谢及信号转导相关基因的鉴定及序列分析

赤霉素(gibberellin,GA)是一类非常重要的植物激素,在植物种子萌发、茎干伸长、叶片生长、腺毛发育、花粉成熟、开花诱导和果实成熟等生长发育过程中都发挥着重要的作用。GA在一年生草本植物中可以促进开花,而在大多数多年生木本植物中则抑制成花诱导。为了更好地研究赤霉素在木本油料能源植物小桐子(Jatropha curcas)开花调控方面的作用机理,我们对小桐子整个基因组中参与GA合成代谢和信号转导的全部基因进行了鉴定和序列分析。这些基因包括6个多基因家族编码的蛋白,即GA2氧化酶(GA2-oxidase,GA2ox)、GA3氧化酶(GA3-oxidase,GA3ox)、GA20氧化酶(GA20-oxidase,GA20ox)、GID1(GIBBERELLIN INSENSITIVE DWARF1)、DELLAs和F-box蛋白,以及2个单基因编码的蛋白,EL1(EARLY FLOWERING1)和SPY(SPINDLY)。采用拟南芥和水稻中已经鉴定的上述基因编码的蛋白序列在小桐子基因组序列数据库和本实验的小桐子转录组数据库中进行BLASTP分析,找到17个同源蛋白的全长序列,并将其与28个拟南芥的、16个水稻的、24个葡萄的和22个蓖麻的同源蛋白构建系统发育树进行比对分析。结果表明,小桐子中参与赤霉素合成代谢及信号转导的大多数基因与蓖麻和葡萄同源基因的相似度更高。     

赤霉素信号转导与棉纤维的分子发育

赤霉素(Gas)作为一种高效能的植物生长调节物质对棉纤维的分化和发育有着非常重要的影响, 但是, 一直以来有关赤霉素与棉纤维分化和发育的分子机制的研究还很少。文章论述了近年来GA信号组分、转导途径的分子生物学研究进展以及GA与棉纤维分子发育的相关研究成果, 旨在为揭示赤霉素调控棉纤维分化和发育的分子机制以及改善棉纤维品质的棉花育种工作提供新的思路。     

植物赤霉素生物合成和信号传导的分子生物学

赤霉素 (GAs)在植物的种子萌发、茎的伸长和花的发育等许多方面起着非常重要的作用。最近几年 ,对GA生物合成及其信号传导途径相关基因的研究取得了惊人的进展。这些进展促进了对其生物合成及其信号传导途径的认识。GA生物合成相关基因的表达受到多种内源和外源因子的调控 ,其中研究较多的是发育阶段、激素水平和光信号等内源及环境因子的调控。GA信号传导通常处于抑制状态 ,GA信号通过去抑制作用激活该传导途径而促进GA刺激植物生长和发育。     

Evolutionary analysis of three gibberellin oxidase genes in rice, Arabidopsis, and soybean

GAs are plant hormones that play fundamental roles in plant growth and development. GA2ox, GA3ox, and GA20ox are three key enzymes in GA biosynthesis. These enzymes belong to the 2OG-Fe (II) oxygenase superfamily and are independently encoded by different gene families. To date, genome-wide comparative analyses of GA oxidases in plant species have not been thoroughly carried out. In the present work, 61 GA oxidase family genes from rice (Oryza sativa), Arabidopsis, and soybean (Glycine max) were identified and a full study of these genes including phylogenetic tree construction, gene structure, gene family expansion and analysis of functional motifs was performed. Based on phylogeny, most of the GA oxidases were divided into four subgroups that reflected functional classifications. Intron/intron average length of GA oxidase genes in rice analysis revealed that GA oxidase genes in rice experienced substantial evolutionary divergence. Segmental duplication events were mainly found in soybean genome. However, in rice and Arabidopsis, no single expansion pattern exhibited dominance, indicating that GA oxidase genes from these species might have been subjected to a more complex evolutionary mechanism. In addition, special functional motifs were discovered in GA20ox, GA3ox, and GA2ox, which suggested that different functional motifs are associated with differences in protein function. Taken together our results suggest that GA oxidase family genes have undergone divergent evolutionary routes, especially at the monocot-dicot split, with dynamic evolution occurring in Arabidopsis thaliana and soybean.     

高等植物赤霉素代谢及其信号转导通路

赤霉素是一类重要的植物激素,对植物的生长发育,如种子的萌发、茎的延展、叶片的生长、休眠芽的萌发以及植物的花和种子的发育等生理具有重要的调控作用。从1926年被发现至今,阐明了赤霉素代谢机理及调控机制,明确了赤霉素在植物体内的信号转导途径。本文综述了赤霉素的生物合成途径及其平衡的调节;赤霉素受体GID1、DELLA蛋白在赤霉素信号转导途径中的作用及相关研究;泛素介导的DELLA蛋白降解在赤霉素信号转导中的研究进展。     

植物赤霉素生物合成和信号传导的分子生物学

赤霉素(GAs)在植物的种子萌发、茎的伸长和花的发育等许多方面起着非常重要的作用。最近几年,对GA生物合成及其信号传导途径相关基因的研究取得了惊人的进展。这些进展促进了对其生物合成及其信号传导途径的认识。GA生物合成相关基因的表达受到多种内源和外源因子的调控, 其中研究较多的是发育阶段、激素水平和光信号等内源及环境因子的调控。GA信号传导通常处于抑制状态, GA信号通过去抑制作用激活该传导途径而促进GA刺激植物生长和发育。     

受赤霉素调节的拟南芥F-box基因筛选分析

赤霉素(Gibberellins,GAs)作为一种植物激素,对植物的生长发育具有重要调控作用,但其作用机制有待进一步完善。F-box蛋白是SCF复合体的一个亚基,通过特异性识别底物来调控植物的生长发育。本研究采用生物信息学方法,通过分析拟南芥基因芯片数据库提供的数据筛选到38个受GA调节的候选F-box基因,并对其中6个基因进行了实时荧光定量PCR验证。Plant CARE分析显示,其中30个基因的启动子区具有GA响应元件、以及IAA、ABA、光、温度干旱胁迫、或生物钟相关的顺式作用元件。通过分析Bio Grid数据库提供的相互作用对象,发现其中18个候选F-box蛋白与GA2ox1,GA3ox1和GA3ox3具有相互作用关系。基因表达谱分析表明,这些候选F-box基因在拟南芥各个组织器官中都有不同程度的表达,对IAA、ABA、光、温度干旱等胁迫或不同光周期都具有一定的响应。为深入研究GA调控植物生长发育的分子机制提供了重要线索。     

Gibberellic acid in plant: Still a mystery unresolved

Gibberellic acid (GA), a plant hormone stimulating plant growth and development, is a tetracyclic di-terpenoid compound. GAs stimulate seed germination, trigger transitions from meristem to shoot growth, juvenile to adult leaf stage, vegetative to flowering, determines sex expression and grain development along with an interaction of different environmental factors viz., light, temperature and water. The major site of bioactive GA is stamens that influence male flower production and pedicel growth. However, this opens up the question of how female flowers regulate growth and development, since regulatory mechanisms/organs other than those in male flowers are mandatory. Although GAs are thought to act occasionally like paracrine signals do, it is still a mystery to understand the GA biosynthesis and its movement. It has not yet confirmed the appropriate site of bioactive GA in plants or which tissues targeted by bioactive GAs to initiate their action. Presently, it is a great challenge for scientific community to understand the appropriate mechanism of GA movement in plant’s growth, floral development, sex expression, grain development and seed germination. The appropriate elucidation of GA transport mechanism is essential for the survival of plant species and successful crop production.     

A quantitative trait locus GW6 controls rice grain size and yield through the gibberellin pathway

Grain size is one of the essential components determining rice yield and is a target for both domestication and artificial breeding. Gibberellins (GAs) are diterpenoid phytohormones that influence diverse aspects of plant growth and development. Several quantitative trait loci (QTLs) have been identified that control grain size through phytohormone regulation. However, little is known about the role of GAs in the control of grain size. Here we report the cloning and characterization of a QTL, GW6 (GRAIN WIDTH 6), which encodes a GA‐regulated GAST family protein and positively regulates grain width and weight. GW6 is highly expressed in the young panicle and increases grain width by promoting cell expansion in the spikelet hull. Knockout of GW6 exhibits reduced grain size and weight, whereas overexpression of GW6 results in increased grain size and weight. GW6 is induced by GA and its knockout downregulates the expression of GA biosynthesis genes and decreases GA content in the young panicle. We found that a natural variation in the cis element CAAT‐box in the promoter of GW6 is associated with its expression level and grain width and weight. Furthermore, introduction of GW6 to Oryza indica variety HJX74 can lead to a 10.44% increase in rice grain yield, indicating that GW6 has great potential to improve grain yield in rice.     

SDG714 Regulates Specific Gene Expression and Consequently Affects Plant Growth via H3K9 Dimethylation

Histone lysine methylation is known to be involved in the epigenetic regulation of gene expression in all eukaryotes including plants. Here we show that the rice SDG714 is primarily responsible for dimethylation but not trimethylation on histone H3K9 in vivo. Overexpression of YFP-SDG714 in Arabidopsis significantly inhibits plant growth and this inhibition is associated with an enhanced level of H3K9 dimethylation. Our microarray results show that many genes essential for the plant growth and development were downregulated in transgenic Arabidopsis plants overexpressing YFP-SDG714. By chromatin immunoprecipitation analysis, we show that YFP-SDG714 is targeted to specific chromatin regions and dimethylate the H3K9, which is linked with heterochromatinization and the downregulation of genes. Most interestingly, when YFP-SDG714 production is stopped, the inhibited plants can partially restore their growth, suggesting that the perturbation of gene expression caused by YFP-SDG714 is revertible. Taken together, our results point to an important role of SDG714 in H3K9 dimethylation, suppression of gene expression and plant growth, and provide a potential method to regulate gene expression and plant development by an on-off switch of SDG714 expression.     

高等植物赤霉素2-氧化酶基因的克隆、表达及其调控

赤霉素(GA)是一类重要的植物激素,对高等植物整个生命周期的生长发育起关键作用。调控赤霉素生物合成和代谢途径中的关键酶基因的表达可以控制植物体内赤霉素的含量。GA2-氧化酶是调节赤霉素合成和代谢的关键酶之一,使活性GA失活。本文主要对GA2-氧化酶基因的克隆、表达调控及其在植物基因工程中的应用等方面进行综述,为通过基因工程技术调控植物体内活性赤霉素的含量从而得到改良品种提供思路。