A survey of the Arabidopsis thaliana mitochondrial phosphoproteome

Plant mitochondria play central roles in cellular energy production, metabolism and stress responses. Recent phosphoproteomic studies in mammalian and yeast mitochondria have presented evidence indicating that protein phosphorylation is a likely regulatory mechanism across a broad range of important mitochondrial processes. This study investigated protein phosphorylation in purified mitochondria from cell suspensions of the model plant Arabidopsis thaliana using affinity enrichment and proteomic tools. Eighteen putative phosphoproteins consisting of mitochondrial metabolic enzymes, HSPs, a protease and several proteins of unknown function were detected on 2‐DE separations of Arabidopsis mitochondrial proteins and affinity‐enriched phosphoproteins using the Pro‐Q Diamond phospho‐specific in‐gel dye. Comparisons with mitochondrial phosphoproteomes of yeast and mouse indicate that these three species share few validated phosphoproteins. Phosphorylation sites for seven of the eighteen mitochondrial proteins were characterized by titanium dioxide enrichment and MS/MS. In the process, 71 phosphopeptides from Arabidopsis proteins which are not present in mitochondria but found as contaminants in various types of mitochondrial preparations were also identified, indicating the low level of phosphorylation of mitochondrial components compared with other cellular components in Arabidopsis. Information gained from this study provides a better understanding of protein phosphorylation at both the subcellular and the cellular level in Arabidopsis.     

Genetic, proteomic and metabolic analysis of the regulation of energy storage in rice seedlings in response to drought

We used proteomic analysis to determine the response of rice plant seedlings to drought-induced stress. The expression of 71 protein spots was significantly altered, and 60 spots were successfully identified. The greatest down-regulated protein functional category was translation. Up-regulated proteins were mainly related to protein folding and assembly. Additionally, many proteins involved in metabolism (e.g. carbohydrate metabolism) also showed differences in expression. cDNA microarray and GC-MS analysis showed 4756 differentially expressed mRNAs and 37 differentially expressed metabolites. Once these data were integrated with the proteomic analysis, we were able to elucidate the metabolic pathways affected by drought-induced stress. These results suggest that increased energy consumption from storage substances occurred during drought. In addition, increased expression of the enzymes involved in anabolic pathways corresponded with an increase in the content of six amino acids. We speculated that energy conversion from carbohydrates and/or fatty acids to amino acids was increased. Analysis of basic metabolism networks allowed us to understand how rice plants adjust to drought conditions.     

Characterisation of magnesium nutrition and interaction of magnesium and potassium in rice

Magnesium (Mg) is known as one of the essential nutrients for higher plants; yet, the preliminary physiological responses of field crops to its deficiency or excess, particularly to its interaction with potassium (K), remain largely unknown. In this study, we observed that Mg deficiency in rice (Oryza sativa) [less than 1.1 mg g^?1 dry weight (DW) in the shoot] resulted in significant reduction in shoot biomass, decrease in total chlorophyll concentration and net photosynthetic rate and reduction in activities of both nitrate reductase [NR; enzyme classification (EC) 1.6.6.1] and glutamine synthetase (EC 6.3.1.2) in the leaves. However, the Mg‐deficient plant contained higher starch in the leaves, and partitioned larger biomass into roots. Excess of Mg (more than 3.0 mg g^?1 DW in the shoot), together with low K supply, suppressed NR activity and decreased concentration of soluble sugar in the leaves. There were great antagonistic and moderately synergistic effects between K and Mg, but the effects of K were much more significant than those of Mg on their uptake and translocation, NR activity and net photosynthetic rate in the leaves. The optimum weight ratio of K to Mg ranged between 22 and 25 in the leaves at tillering stage. Mg deficiency was not compensated for by moderate supply of K but was aggravated by excess supply of K, suggesting specific roles of Mg in both dry matter production and partition of carbon assimilates in rice.     

Novel clues on abiotic stress tolerance emerge from embryo proteome analyses of rice varieties with contrasting stress adaptation

Cereal embryos sustain severe water deficit at the final stage of seed maturation. The molecular mechanisms underlying the acquisition of desiccation tolerance in seed embryos are similar to those displayed during water deficit in vegetative tissues. The genetic variation among six rice genotypes adapted to diverse environmental conditions was analysed at the proteome level to get further clues on the mechanisms leading to water-stress tolerance. MS analysis allowed the identification of 28 proteins involved in stress tolerance (late embryogenesis abundant proteins), nutrient reservoir activity, among other proteins implicated in diverse cellular processes potentially related to the stress response (e.g., mitochondrial import translocase). Hierarchical clustering and multidimensional scaling analyses revealed a close relationship between the stress-sensitive genotypes, whereas the stress-tolerant varieties were more distantly related. Besides qualitative and significant quantitative changes in embryo proteins across the distinct varieties, we also found differences at post-translational level. The results indicated that late embryogenesis abundant Rab21 was more strongly phosphorylated in the embryos of the sensitive varieties than in the embryos of the tolerant ones. We propose that the differences found in the phosphorylation status of Rab21 are related to stress tolerance.     

Genetic analysis of leaffolder resistance in rice

A double haploid(DH)population,which consists of 120 lines derived from anther culture of a typical indica and japonica hybrid'CJ06'/'TN1',was used to investigate the genetic basis for rice leaffolder resistance.Using a constructed molecular linkage map,five QTLs for rolled leaves were detected on chromosomes 1,2,3,4,and 8.The positive alleles from C J06 on chromosomes 3,4,and 8 in-creased the resistance to dee leaffolder,and the alleles from TN1 on chromosomes 1 and 2 also enhanced resistance to leaffolder.The interactions between QTLs were identified and tested,and four conditional interactions were acquired for resistance to rice leaffolder.These loci were located on chromosomes 2,9,10,and 11,respectively.QTL pyramiding indicated that the positive alleles affect resis-tance to leaffolder.The prospective application of this data in rice breeding was also discussed.     

The structure and cytochemistry of the pistil of Hypericum calycinum: the style

Summary A typical style of Hypericum calycinum is solid with a core of transmitting tissue traversing the whole length of the style. This transmitting tissue consists of loosely arranged cells and large intercellular spaces filled with a secretion product. The secretion product is rich in lipids, but poor in proteins and polysaccharides. The intercellular spaces of the transmitting tissue originate partly by a separation of cells as a result of the decomposition of the middle lamella and partly by degeneration of some of the cells of the transmitting tissue. H. calycinum is self-compatible. Both self- and cross-pollinations result in profuse pollen germination on the stigma and pollen tube growth through the style. The data on Hypericum is discussed in relation to information available on other solidstyled systems.     

Genetic analysis of leaffolder resistance in rice

A double haploid(DH)population,which consists of 120 lines derived from anther culture of a typical indica and japonica hybrid 'CJ06'/'TN1',was used to investigate the genetic basis for rice leaffolder resistance.Using a constructed molecular linkage map,five QTLs for rolled leaves were detected on chromosomes 1,2,3,4,and 8.The positive alleles from CJ06 on chromosomes 3,4,and 8 in-creased the resistance to rice leaffolder,and the alleles from TN1 on chromosomes 1 and 2 also enhanced resistance to leaffolde...     

Improvement of rice callus regeneration in the presence of NaCl

The effects of abscisic acid (37.8 μM), polyethylene glycol (5%), proline (10 mM), tryptophan (490 μM) and indoleacetic acid (5.7 μM) on rice callus regeneration were studied at various doses of NaCl (0, 50 and 100 mM) on three month-old mature embryo-derived callus of two japonica (I Kong Pao and Aiwu) and two indica (IR 2153 and Nona Bokra) rice cultivars differing in salinity tolerance. NaCl strongly decreased the regeneration frequency of all cultivars but slightly increased the survival of regenerated plantlets. Tryptophan stimulated regeneration and increased subsequent survival rates of regenerated plantlets in all cultivars at all NaCl doses. Abscisic acid and polyethylene glycol, though not affecting the final regeneration percentages, delayed regeneration and reduced the mean number of plantlets produced per regenerating callus in all cultivars, as well as rooting ability and survival of regenerated plantlets in indica genotypes. Proline had no marked effect on regeneration, whatever the NaCl dose or cultivar, while indoleacetic acid reduced shoot regeneration and increased root regeneration. This revised version was published online in June 2006 with corrections to the Cover Date.     

Protein-protein interactions of tandem affinity purification-tagged protein kinases in rice

Forty-one rice cDNAs encoding protein kinases were fused to the tandem affinity purification (TAP) tag and expressed in transgenic rice plants. The TAP-tagged kinases and interacting proteins were purified from the T1 progeny of the transgenic rice plants and identified by mass spectrometry. Ninety-five percent of the TAP-tagged kinases were recovered. Fifty-six percent of the TAP-tagged kinases were found to interact with other rice proteins. A number of these interactions were consistent with known protein complexes found in other species, validating the TAP-tag method in rice plants. Phosphorylation sites were identified on four of the kinases that interacted with either 14-3-3 proteins or cyclins.     

Isolation and annotation of 10828 putative full length cDNAs from indica rice

Rice has become a model plant for genomic studies of monocot species, because of its relative small ge-nome size (430 Mb), high synteny with other impor-tant crop species such as maize, barley and wheat, the release of draft sequences of both indica[1] and japon-ica[2] genomes, and the near completion of the map-based sequencing of rice genome by the Interna-tional Rice Genome Sequencing Project. Currently, more than 340 Mb of non-overlapping genomic se-quences including completely sequenced…     

Genetic analysis and gene mapping of a rice few-tillering mutant in early backcross populations ( Oryza sativa L.)

A rice mutant,G069, characteristic of few tiller numbers, was found in anther culture progeny from theF ₁ hybrid between anindica-japonica cross, Gui630×02428. The mutant has another two major features: delayed tillering development and yellowing apex and margin on the mature leaves. As a donor parent,G069 was further backcrossed with the recurrent parent,02428, for two turns to develop aBC ₂F₂ population. Genetic analysis in theBC ₂F₂ population showed that the traits of few-tillering and yellowing apex and margin on the mature leaves were controlled by one recessive gene. A pool of equally mixed genomic DNA, from few-tillering individual plants inBC ₂F₂, was constructed to screen polymorphism with simple sequence repeat (SSR) markers in comparison with the02428 genome. One SSR marker and three restriction fragment length polymorphism (RFLP) markers were found possibly linked with the recessive gene. By using these markers, the gene of few-tillering was mapped on chromosome 2 between RFLP marker C424 and S13984 with a genetic distance of 2.4 cM and 0.6 cM, respectively. The gene is designatedft1.     

一个新的水稻叶绿素缺失黄叶突变体的特征及基因分子定位

从粳稻"嘉花1号"60Coγ射线辐照的后代中筛选到一个叶绿素缺失黄叶突变体(yl11),与野生型"嘉花1号"相比该突变体表现为全生育期植株叶片呈黄色,叶绿素含量以及净光合速率明显下降,叶绿体发育不完善,并且伴随着株高等主要农艺性状的变化。遗传分析表明,该突变性状受一对隐性核基因(yl11)控制。该突变体与籼稻"培矮64S"杂交生产的F2、F3群体中的分离出突变体型920个单株作为定位群体,利用SSR和InDel分子标记将yl11基因定位在水稻第11染色体长臂上的MM2199和ID21039分子标记之间,其物理距离约为110kb,目前该区域内没有发现与水稻叶绿素合成/叶绿体发育相关已知功能基因。研究结果为今后对该基因的克隆和功能分析奠定了基础。     

Sodium chloride induced changes in leaf growth, and pigment and protein contents in two rice cultivars

Rice (Oryza sativa L.) seedlings were grown under NaCl stress. The leaf growth of resistant cv. Damodar was less affected than that of the susceptible cv. Jaya. The leaf protein content showed no distinct cultivar or age dependent differences under NaCl salinity. There was a significant increase in chlorophyll (Chl) and carotenoid (Car) contents of 25-d-oldseedlings of both cv. Jaya and cv. Damodar. However, Chl and Car content of 15-d-old seedlings of cv. Jaya decreased and that of cv. Damodar increased, under NaCl stress. This revised version was published online in July 2006 with corrections to the Cover Date.     

水稻OsGRF6的克隆及调控初生根发育功能的初步分析

OsGRF6隶属于GRF家族，参与调控植物的生长发育和调控植物对非生物胁迫的耐受性。为了研究OsGRF6调控水稻初生根发育的分子机制，该研究从水稻品种‘ZH11’中克隆得到转录因子基因OsGRF6，并对其进行了进化树构建，启动子分析，并对OsGRF6-OE和osgrf6进行了基因型分析和qRT-PCR鉴定及水稻表型观察，并通过酵母单杂交检测了OsGRF6的结合基序，进一步通过ChIP-seq和RNA-seq数据分析了OsGRF6下游的候选靶基因。结果显示：（1）OsGRF6含有一个QLQ和一个WRC保守的功能结构域，与拟南芥AtGRF1和AtGRF2以及水稻OsGRF7亲缘关系较近。OsGRF6启动子区域含有多个非生物胁迫和激素响应顺式作用元件。（2）OsGRF6在水稻种子、幼穗和根中表达量较高，而在叶中表达量较低。亚细胞定位显示，OsGRF6定位于细胞核，并且OsGRF6具有转录激活活性。（3）与野生型相比，过表达OsGRF6的转基因材料表现出初生根长度较长，而突变体材料则表现出初生根变短的表型。（4）OsGRF6能与CGGCA基序结合。（5）结合ChIP-seqs和RNA-seqs分析发现，OsGRF6靶基因中包含多个参与调控水稻根发育的基因，如OsARF7，OsARF4等。     

水稻Ds插入淡绿叶突变体的鉴定和遗传分析

Ac/Ds插入突变是水稻基因功能鉴定的有力工具之一。文章从水稻中花11 Ds-T-DNA转化纯合体与Ac-T-DNA 转化纯合体的杂交群体中筛选到一个淡绿叶突变体。该突变体在三叶期由绿苗转为淡绿叶苗, 自然光照下突变体迅速焦枯, 但是在弱光照条件下, 突变体能缓慢生长至开花结实; 突变体光合作用特性研究表明该突变是典型的光抑制突变体。遗传分析表明该突变为Ds插入导致的隐性突变。     

水稻株高基因及其分子生物学研究进展

株高是水稻品种的重要农艺性状之一,植株过高容易引起倒伏而减产。近年来,随着研究手段的改进和水平的提高,在水稻株高基因的发现、定位、克隆及作用机理等方面的研究取得较大进展。本文介绍了国内外在该领域的研究进展概况。