Functional phosphoproteomic profiling of phosphorylation sites in membrane fractions of salt-stressed Arabidopsis thaliana

The in vitro stationary phase proteome of the human pathogen Shigella dysenteriae serotype 1 (SD1) was quantitatively analyzed in Coomassie Blue G250 (CBB)-stained 2D gels. More than four hundred and fifty proteins, of which 271 were associated with distinct gel spots, were identified. In parallel, we employed 2D-LC-MS/MS followed by the label-free computationally modified spectral counting method APEX for absolute protein expression measurements. Of the 4502 genome-predicted SD1 proteins, 1148 proteins were identified with a false positive discovery rate of 5% and quantitated using 2D-LC-MS/MS and APEX. The dynamic range of the APEX method was approximately one order of magnitude higher than that of CBB-stained spot intensity quantitation. A squared Pearson correlation analysis revealed a reasonably good correlation (R ² = 0.67) for protein quantities surveyed by both methods. The correlation was decreased for protein subsets with specific physicochemical properties, such as low M_r values and high hydropathy scores. Stoichiometric ratios of subunits of protein complexes characterized in E. coli were compared with APEX quantitative ratios of orthologous SD1 protein complexes. A high correlation was observed for subunits of soluble cellular protein complexes in several cases, demonstrating versatile applications of the APEX method in quantitative proteomics.     

Insertional mutagenesis in Arabidopsis thaliana

Recently, a number of mutant gene loci in the Arabidopsis thaliana plant genome have been identified through insertional mutagenesis. In this review, we evaluate different methods used for Agrobacterium tumefaciens-mediated T-DNA insertional mutagenesis with regard to their mutation frequencies and conclude that a major breakthrough in the isolation of genes involved in plant development has been acheived. To provide a specific example, we summarize recent progress made in the understanding of flower morphogenesis at the molecular level through the study of homeotic genes obtained via gene tagging. T-DNA gene fusion vectors are being discussed that will allow the isolation of plant regulatory sequences with particular cell or tissue specificity, or that are controlled by specific external stimuli. Finally, we report on the approaches followed to convert the maize transposons Ac/Ds into valuable gene tags for use in a heterologous host such as Arabidopsis.     

The DNA of Arabidopsis thaliana

Summary Arabidopsis thaliana is a small flowering plant of the mustard family. It has a four to five week generation time, can be self- or cross-pollinated and bears as many as 10⁴ seeds per plant. Many visible and biochemical mutations exist and have been mapped by recombination to one of the five chromosomes that comprise the haploid karyotype. With the experiments reported here we demonstrate that Arabidopsis has an extraordinarily small haploid genome size (approximately 7×10⁷ nucleotide pairs) and a low level of cytosine methylation for an angiosperm. In addition, it appears to have little repetitive DNA in its nuclear DNA, in contrast to other higher plants.     

In planta transformation of Arabidopsis thaliana

Transformants of Arabidopsis thaliana can be generated without using tissue culture techniques by cutting primary and secondary inflorescence shoots at their bases and inoculating the wound sites with Agrobacterium tumefaciens suspensions. After three successive inoculations, treated plants are grown to maturity, harvested and the progeny screened for transformants on a selective medium. We have investigated the reproducibility and the overall efficiency of this simple in planta transformation procedure. In addition, we determined the T-DNA copy number and inheritance in the transformants and examined whether transformed progeny recovered from the same Agrobacterium-treated plant represent one or several independent transformation events. Our results indicate that in planta transformation is very reproducible and yields stably transformed seeds in 7–8 weeks. Since it does not employ tissue culture, the in planta procedure may be particularly valuable for transformation of A. thaliana ecotypes and mutants recalcitrant to in vitro regeneration. The transformation frequency was variable and was not affected by lower growth temperature, shorter photoperiod or transformation vector. The majority of treated plants gave rise to only one transformant, but up to nine siblings were obtained from a single parental plant. Molecular analysis suggested that some of the siblings originated from a single transformed cell, while others were descended from multiple, independently transformed germ-line cells. More than 90% of the transformed progeny exhibited Mendelian segregation patterns of NPTII and GUS reporter genes. Of those, 60% contained one functional insert, 16% had two T-DNA inserts and 15% segregated for T-DNA inserts at more than two unlinked loci. The remaining transformants displayed non-Mendelian segregation ratios with a very high proportion of sensitive plants among the progeny. The small numbers of transformants recovered from individual T₁ plants and the fact that none of the T₂ progeny were homozygous for a specific T-DNA insert suggest that transformation occurs late in floral development.National Research Council of Canada Publication No. 38003     

Characterization of two Arabidopsis thaliana fructokinases

Two different fructokinase isoforms of Arabidopsis thaliana have been identified and characterized by non-denaturing electrophoresis followed by activity-staining. The two fructokinases, fructokinase1 (FRK1) and fructokinase2 (FRK2), showed a high specificity for fructose and did not stain when glucose or mannose were used as substrate. Fructose and ATP at high concentrations (above 5 mM) induced a substrate inhibition of the two enzymatic activities. Arabidopsis FRK1 and FRK2 were capable of employing GTP, CTP, UTP and TTP as phosphate donors, although with a significantly lower efficiency than ATP. The two fructokinase activities were also activated by K⁺, at around 10–20 mM, and inhibited by ADP and AMP at concentrations above 10 mM. Finally, FRK1 and FRK2 showed a different expression pattern in the plant, with FRK1 being more abundant in the roots and FRK2 in the shoots. The results demonstrate a simple technique that provides important information about fructokinase activities in the plants and which can be useful for the analysis of Arabidopsis mutants.     

UV-B预处理诱导拟南芥耐旱性的提高

为了解UV-B提高拟南芥(Arabidopsis thaliana)耐旱性的生理机制,将2周龄的野生型拟南芥(WT)和sto突变体幼苗用不同剂量UV-B预处理1周,再用30%PEG模拟干旱处理24 h,对植株的表型进行统计,并测定类黄酮、脯氨酸和MDA含量。结果表明,低剂量UV-B预处理能够提高拟南芥的耐旱性,植株的类黄酮与脯氨酸含量分别提高了20%～40%和50%～65%,细胞膜受损程度降低,从而提高了保水性。低剂量UV-B提高拟南芥耐旱性的效应在sto突变体中消失,证明这种效应在分子机制上可能与STO蛋白相关。     

A two-element Enhancer-Inhibitor transposon system in Arabidopsis thaliana

The Enhancer-Inhibitor (En-I), also known as Suppressor-mutator (Spm-dSpm), transposable element system of maize was modified and introduced into Arabidopsis by Agrobacterium tumefaciens transformation. A stable En/Spm transposase source under control of the CaMV 35S promoter mediated frequent transposition of I/dSpm elements. Transposition occurred continuously throughout plant development over at least seven consecutive plant generations after transformation. New insertions were found at both linked and unlinked positions relative to a transposon donor site. The independent transposition frequency was defined as a transposition parameter, which quantified the rate of unique insertion events and ranged from 7.8% to 29.2% in different populations. An increase as well as a decrease in I/dSpm element copy number was seen at the individual plant level, but not at the population level after several plant generations. The continuous, frequent transposition observed for this transposon system makes it an attractive tool for use in gene tagging in Arabidopsis.     

A highly repeated DNA sequence in Arabidopsis thaliana

Summary Three members of a family of highly repeated DNA sequences from Arabidopsis thaliana have been cloned and characterized. The repeat unit has an average length of 180 bp and is tandemly repeated in arrays longer than 50 kb. This family represents more than one percent of the Arabidopsis genome. Sequence comparisons with tandemly repeated DNA sequences from other Cruciferae species show several regions of homology and a similar length of the repeat unit. Homologies are also found to highly repeated sequences from other plant species. When the sequence CCGG occurs in the repeated DNA, the inner cytosine is generally methylated.     

拟南芥基因密码子偏爱性分析

密码子偏爱性对外源基因的表达强度有一定影响,特别是编码蛋白质N端7～8个氨基酸残基的密码子.通过对拟南芥染色体中26 827个蛋白质对应的基因密码子进行分析,得到了编码氨基酸的61种密码子在拟南芥中的使用频率,并与大肠杆菌和哺乳动物进行了比较,结果表明三者间的密码子偏爱性有较大差异.这一分析结果对于动物基因在植物中的表达,及植物基因在微生物中的表达具有一定指导意义.同时提供了一种直接以XML文档为数据源解析巨型XML格式染色体数据的方法.     

SMB基因与拟南芥细胞脱分化

应用Affymetrix基因芯片技术研究脱分化过程的全基因组表达情况,分析拟南芥叶柄细胞在脱分化过程中的差异表达基因。结果显示:(1)脱分化叶柄有4 222个基因表现出2倍或以上的表达差异,其中1 684个基因表达上调,2 538个基因表达下调。(2)半定量RT-PCR对部分差异表达基因进行验证,进一步筛选出参与拟南芥脱分化候选基因SMB(SOMBRERO)。(3)实时PCR结果表明,野生型叶柄诱导脱分化时,SMB基因表达量随着诱导时间延长而逐渐增加。(4)SMB基因功能缺失突变体smb-3经CIM诱导很难形成愈伤组织;在激素诱导不同时间段,smb-3叶柄没有明显脱分化现象,SMB基因缺失造成拟南芥叶柄脱分化障碍。研究表明,SMB基因参与拟南芥叶柄细胞脱分化过程。     

Responses of Arabidopsis thaliana to bicarbonate-induced iron deficiency

Morpho-physiological and biochemical responses of Arabidopsis thaliana (accession N1438) to bicarbonate-induced iron deficiency were investigated. Plants were grown in cabinet under controlled conditions, in a nutrient solution containing 5 μM Fe, added or not with 10 mM NaHCO₃. After 30 days, bicarbonate-treated plants displayed significantly lower biomass, leaf number and leaf surface area as compared to control plants, and slight yellowing of their younger leaves was observed. Potassium (K⁺) content was not modified by bicarbonate treatment in roots, whereas it was significantly diminished in shoots. Their content in ferrous iron (Fe²⁺) and in leaf total chlorophylls was noticeably lower than in control plants. Root Fe(III)-chelate reductase and phosphoenolpyruvate carboxylase (PEPC) activities were significantly enhanced, but leaf ribulose 1.5-bisphosphate carboxylase (Rubisco) activity was decreased.     

Expression of a yeast polygalacturonase gene in Arabidopsis thaliana

Polygalacturonases are enzymes involved in plant cell wall growth and reorganization. Transgenic Arabidopsis thaliana plants with a Saccharomyces cerevisiae endopolygalacturonase gene (PGU1) were obtained. The yeast gene was properly expressed in the plants as it has been shown by RT-PCR as well as by the increase in the endopolygalacturonase activity. The transgenic plants showed conspicuous malformations in early stages of development probably due to a weak cell adhesion. On the other hand, adult plants exhibited almost no phenotypic differences as compared to the wild type plants, this suggesting the appearance of some mechanisms on the plant side to counteract the effect of the overexpressed polygalacturonase.     

Analysis of naturally occurring late flowering in Arabidopsis thaliana

Summary We have examined the late-flowering behavior of two ecotypes of Arabidopsis thaliana, Sf-2 and Le-0. The late-flowering trait segregates as a single dominant gene in crosses with the early-flowering Columbia ecotype. This gene, which we refer to as FLA, is located at one end of chromosome 4 between RFLP markers 506 and 3843 and is thus distinct from previously mapped genes that affect flowering time. The extreme delay in flowering time caused by the FLA gene can be overcome by vernalization in both the ecotypes in which it occurs naturally and in the Columbia ecotype into which this gene has been introgressed.     

Functional expression of Arabidopsis thaliana sterol glycosyltransferase from stably transformed Drosophila melanogaster S2 cells

Arabidopsis thaliana sterol glycosyltransferase (SGT), UGT80A2, was expressed from stably transformed Drosophila melanogaster Schneider 2 (S2) cells. Recombinant SGT was detected in both intracellular and extracellular fractions with a molecular mass of approximately 76 kDa. Secreted recombinant SGT accounted for approximately 60% of the total recombinant SGT production. Recombinant SGT in the extracellular fractions was purified to homogeneity using a simple one-step Ni-NTA affinity fractionation. Radiometrical assay using uridine diphospho-d-[U-¹⁴C]glucose (UDP-¹⁴C-glucose) as a sugar donor and sterols, β-sitosterol and stigmasterol, as sugar acceptors showed that the purified recombinant SGT contained UDP-glycosyltransferase activity and could attach ¹⁴C-glucose to β-sitosterol and stigmasterol. Recombinant SGT contained higher catalytic activity with β-sitosterol, which was similar to the recombinant SGT produced by a bacterial expression system. The transfer of ¹⁴C-glucose by recombinant SGT was further determined by gas chromatography-mass spectrometry (GC-MS) analysis of cellulase-treated ¹⁴C-glucosetransferred β-sitosterol and stigmasterol reactants.     

花色素苷对拟南芥耐盐性的影响

为探讨花色素苷在盐胁迫中的防御作用及其机制,以模式植物拟南芥(Arabidopsis thaliana)花色素苷合成途径相关基因缺失突变体(DFR基因缺失突变体tt3,CHS基因缺失突变体tt4,CHS、DFR基因双缺失突变体tt3tt4)及其野生型(WT)为材料,采用叶绿素荧光和超氧阴离子(O_2·~–)组织定位等方法,分析了tt3,tt4,tt3tt4和WT对盐胁迫处理的生理响应。结果表明,盐胁迫下3种缺失突变体叶片花色素苷含量的增加显著低于野生型,与WT相比,叶绿素荧光参数Fv/Fm、Yield、ETR、q P和NPQ下降较快,膜渗漏率升高显著,叶片O_2·~–积累程度为tt3tt4tt3/tt4WT。这表明花色素苷在植物抵御盐胁迫过程中起着重要作用,它可能是作为渗透调节剂及抗氧化剂来增强植物的耐盐性。因此,花色素苷含量可以作为筛选耐盐作物的指标。     

拟南芥DNA去甲基化基因RLL4的定位与功能分析

该研究以携带2×35S:LUC报告基因的转基因拟南芥Col-LUC为亲本系,将其种子进行甲基磺酸乙酯(EMS)诱变,在M2代筛选出1株低荧光的候选突变体,命名为rll4(reduced LUC luminescence 4)。遗传学分析表明,rll4突变位点包含1个核基因隐性突变。图位克隆技术定位结果显示,突变基因的位点位于4号染色体2个分子标记CL417-B10M1和CL418-B2M2之间,这2个分子标记分别位于F20D10和F20M13BAC(bacterial artificial chromosome)克隆。酶切PCR(Chop-PCR)结果显示,rll4突变体中基因组DNA的部分位点甲基化显著升高。反转录PCR(RT-PCR)结果显示,rll4突变体中ROS1(REPRESSOR OF SILENCING 1)的表达量并没有明显变化,而一些RNA介导的DNA甲基化(RdDM)过程靶位点的基因表达量有明显下降。研究表明,RLL4位点很可能参与了拟南芥DNA去甲基化过程。     

Evolutionary origins of Brassicaceae specific genes in Arabidopsis thaliana

Background  

All sequenced genomes contain a proportion of lineage-specific genes, which exhibit no sequence similarity to any genes outside the lineage. Despite their prevalence, the origins and functions of most lineage-specific genes remain largely unknown. As more genomes are sequenced opportunities for understanding evolutionary origins and functions of lineage-specific genes are increasing.