水稻SBP基因家族的生物信息学分析(英文)

SQUAMOSA PROMOTER BINDING PROTEIN-LIKE(SBP)转录因子家族是植物特有的一类转录因子。本文确定了20水稻基因组上编码的SBP基因。通过分类,染色体定位,保守区确定,亲缘关系,以及水稻SBP家族中的重复基因及该家族成员形成蛋白二聚体的可能性进行分析,其次利用了Affymetrix水稻基因组芯片数据,对所有这些基因的表达谱进行了分析。结果表明,水稻SBP基因在花和种子的发育过程中可能发挥重要作用,而其对环境胁迫却不敏感。这对进一步研究SBP的功能提供了有价值的线索和思路。     

Genome‐wide expression quantitative trait locus studies facilitate isolation of causal genes controlling panicle structure

The morphology of rice (Oryza sativa L.) panicles is an important determinant of grain yield, and elucidation of the genetic control of panicle structure is very important for fulfilling the demand for high yield in breeding programs. In a quantitative trait locus (QTL) study using 82 backcross inbred lines (BILs) derived from Koshihikari and Habataki, 68 QTLs for 25 panicle morphological traits were identified. Gene expression profiling from inflorescence meristems of BILs was obtained. A combination of phenotypic QTL (pQTL) and expression QTL (eQTL) analysis revealed co‐localization between pQTLs and eQTLs, consistent with significant correlations between phenotypic traits and gene expression levels. By combining pQTL and eQTL data, two genes were identified as controlling panicle structure: OsMADS18 modulates the average length of the primary rachis and OsFTL1 has pleiotropic effects on the total number of secondary rachides, number of grains per panicle, plant height and the length of flag leaves. Phenotypes were confirmed in RNA interference knocked‐down plants and overexpressor lines. The combination of pQTL and eQTL analysis could facilitate identification of genes involved in rice panicle formation.     

The pleiotropic ABNORMAL FLOWER AND DWARF1 affects plant height,floral development and grain yield in rice

Moderate plant height and successful establishment of reproductive organs play pivotal roles in rice grain production. The molecular mechanism that controls the two aspects remains unclear in rice. In the present study, we characterized a rice gene, ABNORMAL FLOWER AND DWARF1 (AFD1) that determined plant height, floral development and grain yield. The afd1 mutant showed variable defects including the dwarfism, long panicle, low seed setting and reduced grain yield. In addition, abnormal floral organs were also observed in the afd1 mutant including slender and thick hulls, and hull‐like lodicules. AFD1 encoded a DUF640 domain protein and was expressed in all tested tissues and organs. Subcellular localization showed AFD1‐green fluorescent fusion protein (GFP) was localized in the nucleus. Meantime, our results suggested that AFD1 regulated the expression of cell division and expansion related genes.     

OsPIN5b modulates rice (Oryza sativa) plant architecture and yield by changing auxin homeostasis,transport and distribution

Plant architecture attributes such as tillering, plant height and panicle size are important agronomic traits that determine rice (Oryza sativa) productivity. Here, we report that altered auxin content, transport and distribution affect these traits, and hence rice yield. Overexpression of the auxin efflux carrier‐like gene OsPIN5b causes pleiotropic effects, mainly reducing plant height, leaf and tiller number, shoot and root biomass, seed‐setting rate, panicle length and yield parameters. Conversely, reduced expression of OsPIN5b results in higher tiller number, more vigorous root system, longer panicles and increased yield. We show that OsPIN5b is an endoplasmic reticulum (ER) ‐localized protein that participates in auxin homeostasis, transport and distribution in vivo. This work describes an example of an auxin‐related gene where modulating its expression can simultaneously improve plant architecture and yield potential in rice, and reveals an important effect of hormonal signaling on these traits.     

Direct development of plantlets from immature panicles of rice in vitro

Cultured immature panicles of rice formed plantlets from spikelets without callus or embryoid formation on MS and HE media containing 2 mg/l each of NAA and kinetin. Developmental stage, ploidy of explant and plant growth regulators in the medium are the major factors affecting the frequency of spikelet budding in young panicle culture. It is suggested that spikelet budding occurs by the reversion of floral primordia to vegetative stage or by the formation of adventitious buds from epidermal cells.     

Molecular characterization of an anther-preferential gene from rice

Expression levels of anther-expressed genes in rice were estimated by plaque hybridization. A total of 33 cDNAs, isolated randomly from an anther-enriched cDNA library, were used as probes to hybridize both anther and leaf cDNAs. The expression level of individual cDNA clones was then estimated by counting the number of plaques hybridized to each probe. Based on abundance patterns that appeared in both anther and leaf cDNA libraries, the clones were classified into three groups. This classification showed that the majority of the clones (one group) exhibited expression in both cDNA libraries at almost equal frequency. The other two groups showed either low or no expression in the leaf cDNA library. Among the cDNA clones,RA1003 (detected only in the anther cDNA library) was selected and further characterized at the molecular level. Consistent with the results of the plaque hybridization experiment, northern blot analysis also revealed no gene expression in vegetative organs, leaves, or roots. However, expression was high in the flowers, especially in the anthers. Detailed molecular studies of the gene are also described and discussed here.     

Two amidophosphoribosyltransferase genes of Arabidopsis thaliana expressed in different organs

Amidophosphoribosyltransferase (ATase: EC 2.4.2.14) is a key enzyme in the pathway of purine nucleotide biosynthesis. We have identified several cDNA clones whose amino acid sequences exhibit similarity with the known ATases in a cDNA library of young floral buds of Arabidopsis thaliana. The cDNA clones are derived from two genes homologous with each other. These cDNAs represent the first plant representatives of ATase gene. Structural comparison with ATases of other organisms has revealed that the two genes encode [4Fe-4S] cluster-dependent ATases. Northern blot analysis showed that expression level of the genes is different in three organs; one gene is expressed in flowers and roots, while the other gene is mainly expressed in leaves.     

Identification of genes expressed in the shoot apex ofBrassica campestris during floral transition

The vegetative-to-floral transition ofBrassica campestris cv. Osome was induced by vernalization. Poly(A)+RNA was isolated from the transition shoot apex after 6 weeks of vernalization, the floral apex after 12 weeks of vernalization and the expanded leaves just before vernalization, and cDNAs were synthesized. These cDNAs were used for subtraction and differential screening to select cDNA preferentially present in the transition and floral apices. Nucleotide sequences of the resulting 14 cDNA clones were determined, and northern blot analysis was carried out on six cDNAs. Two cDNA clones which did not show significant similarity to known genes were shown to be preferentially expressed in the floral apex.     

Expressed sequence tags of Chinese cabbage flower bud cDNA.

We randomly selected and partially sequenced cDNA clones from a library of Chinese cabbage (Brassica campestris L. ssp. pekinensis) flower bud cDNAs. Out of 1216 expressed sequence tags (ESTs), 904 cDNA clones were unique or nonredundant. Five hundred eighty-eight clones (48.4%) had sequence homology to functionally defined genes at the peptide level. Only 5 clones encoded known flower-specific proteins. Among the cDNAs with no similarity to known protein sequences (628), 184 clones had significant similarity to nucleotide sequences registered in the databases. Among these 184 clones, 142 exhibited similarities at the nucleotide level only with plant ESTs. Also, sequence similarities were evident between these 142 ESTs and their matching ESTs when compared using the deduced amino acid sequences. Therefore, it is possible that the anonymous ESTs encode plant-specific ubiquitous proteins. Our extensive EST analysis of genes expressed in floral organs not only contributes to the understanding of the dynamics of genome expression patterns in floral organs but also adds data to the repertoire of all genomic genes.     

Over-expression of the rice LRK1 gene improves quantitative yield components

In rice ( Oryza sativa L.), the number of panicles, spikelets per panicle and grain weight are important components of grain yield. These characteristics are controlled by quantitative trait loci (QTLs) and are derived from variation inherent in crops. As a result of the complex genetic basis of these traits, only a few genes involved in their control have been cloned and characterized. We have previously map-cloned a gene cluster including eight leucine-rich repeat receptor-like kinase ( LRK ) genes in Dongxiang wild rice ( Oryza rufipogon Griff.), which increased the grain yield by 16%. In the present study, we characterized the LRK1 gene, which was contained in the donor parent (Dongxiang wild rice) genome and absent from the recurrent parent genome (Guichao2, Oryza sativa L. ssp. indica ). Our data showed that rice LRK1 is a plasma membrane protein expressed constitutively in leaves, young panicles, roots and culms. The over-expression of rice LRK1 results in increased panicles, spikelets per panicle, weight per grain and enhanced cellular proliferation, leading to a 27.09% increase in total grain yield per plant. The increased number of panicles and spikelets per panicle are associated with increased branch number. Our data suggest that rice LRK1 regulates rice branch number by enhancing cellular proliferation. The functional characterization of rice LRK1 facilitates an understanding of the mechanisms involved in cereal crop yield, and may have utility in improving grain yield in cereal crops.     

Transformation of rice with the Arabidopsis floral regulator LEAFY causes early heading

Onset of flowering, or heading date, is an important agronomic trait of cereal crops such as rice and early-heading varieties are required for certain regions in which rice is cultivated. Since the floral control gene LEAFY from Arabidopsis can dramatically accelerate flowering in dictoyledonous plants, the usefulness of LEAFY for manipulating heading date in rice has been tested. Constitutive expression of LEAFY from the cauliflower mosaic virus 35S promoter caused early flowering in transgenic rice, with a heading date that was 26–34 days earlier than that of wild-type plants. Early flowering was accompanied by a small yield penalty and some panicle abnormality. These observations suggest that floral regulatory genes from Arabidopsis are useful tools for heading date improvement in cereal crops.     

水稻叶绿体蛋白质在生长发育过程中的表达研究

在植物中,叶绿体是负责光合作用的细胞器,对叶绿体内的各种生物过程人们已经积累了很多知识,但对叶绿体蛋白质的表达还所知甚少．为了解水稻叶绿体蛋白质在正常生长发育过程中的表达情况,尝试基于抗体的水稻蛋白质组学策略．选取了10个水稻叶绿体基因,利用表达的蛋白质或合成的抗原决定簇片段制备了抗体,用Western blotting检测了相应蛋白质在5个发育时期的根、茎、叶及穗组织中的表达．发现10个蛋白质均在叶片中表达,在根中不表达．与原初反应相关的叶绿素A/B结合蛋白1和2(CAB1和CAB2)、与电子传递相关的放氧增强蛋白1(OEE1)及与活性氧清除相关的过氧还蛋白过氧化物酶(2-CysP)和硫氧还蛋白(Trx)在茎中表达．而在卡尔文循环中发挥作用的Rubisco活化酶(RCA)、甘油醛-3-磷酸脱氢酶(GAPDH)、果糖二磷酸醛缩酶(FBPA)和景天庚酮糖-1, 7-二磷酸酶(SBPase)蛋白质在茎中不表达．在穗中,这些蛋白质的表达时序不同,CAB2和2-CysP在穗发育的全程表达,CAB1和OEE1在中后期表达,而卡尔文循环中的蛋白质只在中期表达．有意思的是,卡尔文循环中的蛋白质表达模式相似,这一结果从蛋白质表达水平支持它们之间的相互衔接关系．此外,实验还揭示了可能的蛋白质修饰、二聚体及不同的转录本现象．将目标基因的表达谱与转录谱进行比较,发现二者间有一定的平行性,但也有明显的区别．以水稻叶绿体蛋白质为对象,直观并相对定量地揭示了它们的表达模式,为阐释其功能提供了信息,也为基于抗体的水稻蛋白质组学策略提供了一个初步数据．     

Identification of three shikimate kinase genes in rice: characterization of their differential expression during panicle development and of the enzymatic activities of the encoded proteins

The shikimate pathway is common to the biosynthesis of the three aromatic amino acids and that of various secondary metabolites in land plants. Shikimate kinase (SK; EC 2.7.1.71) catalyzes the phosphorylation of shikimate to yield shikimate 3-phosphate. In an attempt to elucidate the functional roles of enzymes that participate in the shikimate pathway in rice (Oryza sativa), we have now identified and characterized cDNAs corresponding to three SK genes—OsSK1, OsSK2, and OsSK3—in this monocotyledenous plant. These SK cDNAs encode proteins with different NH₂-terminal regions and with putative mature regions that share sequence similarity with other plant and microbial SK proteins. An in vitro assay of protein import into intact chloroplasts isolated from pea (Pisum sativum) seedlings revealed that the full-length forms of the three rice SK proteins are translocated into chloroplasts and processed, consistent with the assumption that the different NH₂-terminal sequences function as chloroplast transit peptides. The processed forms of all three rice proteins synthesized in vitro manifested SK catalytic activity. Northern blot analysis revealed that the expression of OsSK1 and OsSK2 was induced in rice calli by treatment with the elicitor N-acetylchitoheptaose, and that expression of OsSK1 and OsSK3 was up-regulated specifically during the heading stage of panicle development. These results suggest that differential expression of the three rice SK genes and the accompanying changes in the production of shikimate 3-phosphate may contribute to the defense response and to panicle development in rice.The nucleotide sequences of OsSK1, OsSK2, and OsSK3 cDNAs are available in GenBank under the accession numbers AB188834, AB188835, and AB188836, respectively.     

利用抑制性扣除杂交技术克隆水稻磷饥饿诱导基因

磷素是植物生长所必需的重要元素。在缺磷环境中,植物能够调节自身的形态、生理生化和基因表达水平来适应环境的变化。为研究水稻(Oryzn sativa L.)耐低磷胁迫的分子机理,采用抑制性扣除杂交技术(SSH)构建磷饥饿诱导的水稻根系扣除cDNA文库。通过文库筛选和测序获得18个已知基因和47个功能未知基因。这些基因参与了不同的代谢过程,包括磷吸收和转运、信号传导、蛋白质合成和降解、碳水化合物代谢和胁迫反应。Northern杂交结果表明,在磷饥饿胁迫下这些基因呈现不同的表达模式,并且不同代谢过程中的基因对磷饥饿有着不同的反应。     

Isolation of genes abundantly expressed in rice anthers at the microspore stage

A cDNA library of rice (Oryza sativa L.) has been constructed from anthers at an early stage of pollen development. By differential screening of the library, we have isolated cDNAs of two genes, designated as Osc4 and Osc6, that are abundantly expressed in anthers containing tetrads and uninucleate microspores, but are not expressed in leaves or roots. Expression of Osc4 is absent in mature anthers, while Osc6 is present although the expression decays during pollen maturation. A comparison of the nucleotide and deduced amino acid sequences with those in data banks has not shown significant homology to known molecules.