水稻线粒体丝氨酸羟甲基转移酶基因的电子克隆

采用基于EST的电子克隆方法得到了一段长1611bp的cDNA序列,以此为信息探针搜索HTGs数据库,找到一个与之高度匹配的基因组DNA序列——OSJNBa0057G07克隆。用FGENESH分析该克隆中的联配区域得到一个包含14个外显子和13个内含子的基因。该基因位于水稻第3染色体物理图谱的136．0～137．6cM区域。推导的ORF编码498个氨基酸,经BLASTP搜索SWISS-PROT数据库和蛋白序列的亚细胞定位显示,该基因编码水稻的线粒体丝氨酸羟甲基转移酶(mSHMT)。该基因受到EST序列的完全支持,其中不乏来自盐胁迫、稻瘟病菌侵染等逆境处理的EST序列,推测该基因与水稻对逆境的应答反应有关。     

In silico analyses of superoxide dismutases (SODs) of rice (Oryza sativa L.)

Superoxide dismutases (SODs), members of the metalloenzymes family are most effective intracellular enzymatic antioxidant in aerobic organisms. These enzymes provide the first line of defense in plants against the toxic effects of elevated levels of reactive oxygen species (ROS) generated during various environmental stresses. The availability of high-throughput computational tools has provided better opportunities to characterize the protein features and determine their function. In the present study an attempt was made to gain an insight into the structure and evolution of subunits of SODs (Cu-Zn, Mn and Fe SODs) of rice. The 3-Dimensional structures of SODs were modeled based on available X-ray crystal structures and further validated. The primary sequence, secondary and tertiary structure analysis revealed Mn and Fe SOD to be structurally homologous while Cu-Zn SOD is un-related to either of them. Comparative structural study also revealed former two were dominated by α-helices followed by β-strands in contrast; Cu-Zn SOD dominated by β-strands. Molecular phylogeny indicated a common evolutionary origin of Mn and Fe SOD while Cu-Zn SOD may have evolved separately.     

Proteomic analysis of rice (Oryza sativa) seeds during germination

Although seed germination is a major subject in plant physiological research, there is still a long way to go to elucidate the mechanism of seed germination. Recently, functional genomic strategies have been applied to study the germination of plant seeds. Here, we conducted a proteomic analysis of seed germination in rice (Oryza sativa indica cv. 9311) - a model monocot. Comparison of 2-DE maps showed that there were 148 proteins displayed differently in the germination process of rice seeds. Among the changed proteins, 63 were down-regulated, 69 were up-regulated (including 20 induced proteins). The down-regulated proteins were mainly storage proteins, such as globulin and glutelin, and proteins associated with seed maturation, such as "early embryogenesis protein" and "late embryogenesis abundant protein", and proteins related to desiccation, such as "abscisic acid-induced protein" and "cold-regulated protein". The degradation of storage proteins mainly happened at the late stage of germination phase II (48 h imbibition), while that of seed maturation and desiccation associated proteins occurred at the early stage of phase II (24 h imbibition). In addition to alpha-amylase, the up-regulated proteins were mainly those involved in glycolysis such as UDP-glucose dehydrogenase, fructokinase, phosphoglucomutase, and pyruvate decarboxylase. The results reflected the possible biochemical and physiological processes of germination of rice seeds.     

水稻水溶性环氧化合物水解酶的生物信息学分析

水溶性环氧化合物水解酶（Soluble Epoxide Hydrolase,SEH）是一组催化环氧化合物水解为相应邻位二醇的酶类,在哺乳动物、植物、昆虫和微生物体内广泛存在。通过BLAST对水稻基因组的蛋白质数据库进行搜索,获得10个水溶性环氧化物水解酶（Soluble Epoxide Hydrolase SEH）sEH蛋白的同源序列。经分析发现这些基因在水稻不同胁迫处理下各个部位都有所表达,而且不同成员之间的表达模式存在较大的差异。水稻sEH蛋白主要参与角质层形成,应激反应,以及病原防御等生理过程,特别在脱毒过程中扮演着重要的角色。对蛋白质多序列联配和三级结构预测结果表明：水溶性环氧化合物水解酶的核心结构域由3个催化残基Asp、His和Asp形成三位一体的催化活性构象。这类基因的表达受抗逆环境诱导,其功能与抗逆性有关,为基因工程抗逆育种提供了参考。     

Molecular cloning and structural analysis of a novel Rac gene osRACB in rice (Oryza sativa L.)

Rac is a subfamily of small GTP-binding protein family. Its molecular weight is between 20 and 30 kilodaltons. As a signal protein, Rac directly or indirectly participates in many physiological processes, such as the regulation of cytoskeleton and the transduction of stress-induced signal. So Rac is also named ?molecular switch? The switch is based on the cycle from a GTP-bound 憃n?to a GDP-bound 憃ff?state[1]. In the superfamily of GTP-binding protein, only heterotrimeric G protein, Ra…     

Molecular Cloning and Expression of a cDNA Encoding Lon Protease from rice (Oryza sativa)

The ATP-dependent Lon protease is a highly conserved enzyme that is present in archeae, eubacteria, and eukaryotes, and plays an important role in intracellular protein degradation. We have isolated a Lon protease gene, OsLon1, from Oryza sativa. The cDNA contained a 2,655 bp ORF. Comparative analysis showed that OsLon1 shared significant similarity with the previously reported Lon proteases from maize, Arabidopsis, human, and bacteria. Tissue expression pattern analysis revealed that OsLon1 was highly expressed in young leaves, mature leaves, and leaf sheaths but only weakly in young roots, mature roots, and young panicles. The OsLon1 gene was successfully expressed in E. coli and the detected protein size, about 120 kDa, matched the expected molecular mass of the His-tagged OsLon1 protein.     

Oxygen dynamics in submerged rice (Oryza sativa)

Complete submergence of plants prevents direct O(2) and CO(2) exchange with air. Underwater photosynthesis can result in marked diurnal changes in O(2) supply to submerged plants. Dynamics in pO(2) had not been measured directly for submerged rice (Oryza sativa), but in an earlier study, radial O(2) loss from roots showed an initial peak following shoot illumination. O(2) dynamics in shoots and roots of submerged rice were monitored during light and dark periods, using O(2) microelectrodes. Tissue sugar concentrations were also measured. On illumination of shoots of submerged rice, pO(2) increased rapidly and then declined slightly to a new quasi-steady state. An initial peak was evident first in the shoots and then in the roots, and was still observed when 20 mol m(-3) glucose was added to the medium to ensure substrate supply in roots. At the new quasi-steady state following illumination, sheath pO(2) was one order of magnitude higher than in darkness, enhancing also pO(2) in roots. The initial peak in pO(2) following illumination of submerged rice was likely to result from high initial rates of net photosynthesis, fuelled by CO(2) accumulated during the dark period. Nevertheless, since sugars decline with time in submerged rice, substrate limitation of respiration could also contribute to morning peaks in pO(2) after longer periods of submergence.     

Systematic analysis of rice (Oryza sativa) metabolic responses to herbivory

Plants defend against attack from herbivores by direct and indirect defence mechanisms mediated by the accumulation of phytoalexins and release of volatile signals, respectively. While the defensive arsenals of some plants, such as tobacco and Arabidopsis are well known, most of rice's (Oryza sativa) defence metabolites and their effectiveness against herbivores remain uncharacterized. Here, we used a non‐biassed metabolomics approach to identify many novel herbivory‐regulated metabolic signatures in rice. Most were up‐regulated by herbivore attack while only a few were suppressed. Two of the most prominent up‐regulated signatures were characterized as phenolamides (PAs), p‐coumaroylputrescine and feruloylputrescine. PAs accumulated in response to attack by both chewing insects, i.e. feeding of the lawn armyworm (Spodoptera mauritia) and the rice skipper (Parnara guttata) larvae, and the attack of the sucking insect, the brown planthopper (Nilaparvata lugens, BPH). In bioassays, BPH insects feeding on 15% sugar solution containing p‐coumaroylputrescine or feruloylputrescine, at concentrations similar to those elicited by heavy BPH attack in rice, had a higher mortality compared to those feeding on sugar diet alone. Our results highlight PAs as a rapidly expanding new group of plant defence metabolites that are elicited by herbivore attack, and deter herbivores in rice and other plants.     

Expression of asparagine synthetase in rice (Oryza sativa) roots in response to nitrogen

The expression of asparagine synthetase (AS; EC 6.3.5.4) in response to externally supplied nitrogen was investigated with respect to enzyme activity and protein levels as detected immunologically in rice ( Oryza sativa ) seedlings. The asparagine content was very low in leaves and roots of nitrogen-starved rice plants but increased significantly after the supply of 1 m M NH₄⁺ to the nutrient solution. While neither AS activity nor AS protein could be detected in leaves and roots prior to the supply of nitrogen, levels became detectable in roots but not in leaves within 12 h of the supply of 1 m M NH₄⁺ or 10 m M glutamine. Other nitrogen compounds, such as nitrate, glutamate, aspartate and asparagine had no effect. Methionine sulfoximine completely inhibited the NH₄⁺-induced accumulation of AS protein but did not affect the glutamine-induced accumulation of the enzyme. The results suggested that glutamine or glutamine-derived metabolites regulate AS expression in rice roots.     

Protein profile of rice (Oryza sativa) seeds

Seeds are the most important plant storage organ and play a central role in the life cycle of plants. Since little is known about the protein composition of rice (Oryza sativa) seeds, in this work we used proteomic methods to obtain a reference map of rice seed proteins and identify important molecules. Overall, 480 reproducible protein spots were detected by two-dimensional electrophoresis on pH 4–7 gels and 302 proteins were identified by MALDI-TOF MS and database searches. Together, these proteins represented 252 gene products and were classified into 12 functional categories, most of which were involved in metabolic pathways. Database searches combined with hydropathy plots and gene ontology analysis showed that most rice seed proteins were hydrophilic and were related to binding, catalytic, cellular or metabolic processes. These results expand our knowledge of the rice proteome and improve our understanding of the cellular biology of rice seeds.     

A chromosome 5-specific repetitive DNA sequence in rice (Oryza sativa L)

Repetitive DNA sequences in the rice genome comprise more than half of the nuclear DNA. The isolation and characterization of these repetitive DNA sequences should lead to a better understanding of rice chromosome structure and genome organization. We report here the characterization and chromosome localization of a chromosome 5-specific repetitive DNA sequence. This repetitive DNA sequence was estimated to have at least 900 copies. DNA sequence analysis of three genomic clones which contain the repeat unit indicated that the DNA sequences have two sub-repeat units of 37 bp and 19 bp, connected by 30-to 90-bp short sequences with high similarity. RFLP mapping and physical mapping by fluorescence in situ hybridization (FISH) indicated that almost all copies of the repetitive DNA sequence are located in the centromeric heterochromatic region of the long arm of chromosome 5. The strategy for cloning such repetitive DNA sequences and their uses in rice genome research are discussed.     

Primary structural features of the 20S proteasome subunits of rice (Oryza sativa)

The 20S proteasome is the proteolytic complex that is involved in removing abnormal proteins, and it also has other diverse biological functions. Its structure comprises 28 subunits arranged in four rings of seven subunits, and exists as a hollow cylinder. The two outer rings and two inner rings form an 7β7β77 structure, and each subunit, and β, exists as seven different types, thus giving 14 kinds of subunits. In this study, we report the primary structures of the 14 proteasomal subunit subfamilies in rice (Oryza sativa), representing the first set for all of the subunits from monocots. Amino acid sequence homology within the rice family (-type: 28.9–42.1%; β-type: 17.2–31.9%) were lower than those between rice subunits and corresponding orthologs from Arabidopsis and yeast (-type: 49.2–94.5%; β-type: 34.8–87.7%). Structural features observed in eukaryotic proteasome subunits, i.e., - or β-type signature at the N-termini, Thr active sites in β1, β2 and β5 subunits, and nuclear localization signal-like sequences in some -type subunits, were shown to be conserved in rice.     

杂草稻落粒粳的抗逆境特性研究

杂草稻落粒粳（Oryza sativa）发生在我国辽宁丹东.落粒粳植株明显高于当地大多数栽培品种,颖果呈中长型,成熟后容易掉粒;果壳稻草色或黄间黑灰色,小穗无芒或有芒,芒长4～12 cm;颖果千粒重235 g,种皮桔红色.落粒粳种子在13～38 ℃条件下的发芽率均大于88%,水层2.5～10 cm处理,落粒粳植株干重减少50%～69%.在幼苗期,落粒粳对无芒稗的各项影响因子均明显大于化感潜力品种I-kung-pao,表明落粒粳无化感作用.落粒粳可以忍耐0.5%的盐碱.     

Isolation and molecular evolutionary analysis of a cytochrome c gene from Oryza sativa (rice)

A cytochrome c gene, OsCc-1, from rice (Oryza sativa) has been isolated and analyzed. The OsCc-1 gene encodes a cytochrome c protein that is typical of higher-plant cytochrome c proteins. OsCc-1 consists of three exons separated by two introns that are 817 and 747 bp in length, respectively. From genomic DNA hybridization analysis, OsCc-1 appears to be one of possibly two cytochrome c genes in several Asian, American, and Indian rice species and varieties surveyed. A single, unique cytochrome c gene appears to be present in one African cultivated rice species. We performed comparative molecular evolutionary analyses of OsCc-1 and other cytochrome c genes. We calculated a unit evolutionary period of 19.4 Myr for cytochrome c DNA sequences, which agrees closely with previous estimates based on protein sequence comparisons.