Global and Comparative Proteome Analysis of Nitrogen-Stress Responsive Proteins in the Root,Stem and Leaf of <i>Brassica napus</i>

Nitrogen (N) is one of the basic nutrients and signals for plant development and deficiency of it would always limit the productions of crops in the field. Quantitative research on expression of N-stress responsive proteins on a proteome level remains elusive. In order to gain a deep insight into the proteins responding to nitrogen stress in rapeseed (Brassica napus L.), comparative proteomic analysis was performed to investigate changes of protein expression profiles from the root, stem and leaf under different N concentrations, respectively. More than 200 differential abundance proteins (DAPs) were detected and categorized into groups according to annotations, including “binding and catalytic activity”, “involved in primary metabolism and cellular processes”, “stress-response” and so on. Variation in chlorophyll (Chl) content and antioxidant activities further revealed that oxidative stress raised with the increase of N concentration. Bioinformatics analysis based on the expression level of total proteins suggested these DAPs might play important roles in adaptation to N-stress conditions. Generally, these results provides a new aspect into N-stress responding proteins in Brassica plants.     

Analysis of a large number of independent transgenic rice plants produced by the biolistic method

Summary Over 500 independent transgenic rice plants have been obtained by the biolistic method with an average transformation frequency of 9.7% for japonica variety Taipei 309. A tight selection procedure using 50 mg/l of hygromycin B successfully prevented the growth of nontransformed tissues. Analysis of the T0 transgenic rice plants revealed that more than 97% of the transgenic plants were morphologically normal and more than 80% were at least partially fertile. The hyg^r trait was inherited as a dominant trait in a Mendelian manner in 8 out of 11 transgenic events assayed. Thirty-seven out of fifty transgenic plants were estimated to contain no more than five copies of the transgenes. In six out of seven transformation events, unlinked, co-transformed genes co-segregated in the T1 generation. The hyg^r trait has been stably inherited to the T4 generation. No chimerical transgenic plant has been found in an intensive search. Novel phenomena observed in transgenic rice plants are also reported.     

A <Emphasis Type="Italic">pqr2</Emphasis> mutant encodes a defective polyamine transporter and is negatively affected by ABA for paraquat resistance in <Emphasis Type="Italic">Arabidopsis thaliana</Emphasis>

Despite the paraquat-resistant mutants that have been reported in plants, this study identified a novel A. thaliana mutant (pqr2) from an XVE inducible activation library based on its resistance to 2 μM paraquat. The pqr2 mutant exhibited a termination mutation in the exon of AT1G31830/PAR1/PQR2, encoded a polyamine uptake transporter AtPUT2/PAR1/PQR2. The PQR2 mutation could largely reduce superoxide accumulation and cell death in the pqr2 plants under paraquat treatment. Moreover, compared with wild type, the pqr2 mutant exhibited much reduced tolerance to putrescine, a classic polyamine compound, which confirmed that PQR2 encoded a defective polyamine transporter. Notably, co-treated with ABA and paraquat, both pqr2 mutant and wild type exhibited a lethal phenotype from seed germination, but the wild type like pqr2 mutant, could remain paraquat-resistance while co-treated with high dosage of Na₂WO₄, an ABA synthesis inhibitor. Gene expression analysis suggested that ABA signaling should widely regulate paraquat-responsive genes distinctively in wild type and pqr2 mutant. Hence, this study has for the first time reported about ABA negative effect on paraquat-resistance in A. thaliana, providing insight into the ABA signaling involved in the oxidative stress responses induced by paraquat in plants.     

Comparison of the Prognostic Utility of the Diverse Molecular Data among lncRNA,DNA Methylation,microRNA, and mRNA across Five Human Cancers

IntroductionAdvances in high-throughput technologies have generated diverse informative molecular markers for cancer outcome prediction. Long non-coding RNA (lncRNA) and DNA methylation as new classes of promising markers are emerging as key molecules in human cancers; however, the prognostic utility of such diverse molecular data remains to be explored.ResultsUsing the IDFO approach, we obtained good predictive performance of the molecular datasets (bootstrap accuracy: 0.71–0.97) in five cancer types. Impressively, lncRNA was identified as the best prognostic predictor in the validated cohorts of four cancer types, followed by DNA methylation, mRNA, and then microRNA. We found the incorporating of multi-type molecular data showed similar predictive power to single-type molecular data, but with the exception of the lncRNA + DNA methylation combinations in two cancers. Survival analysis of proportional hazard models confirmed a high robustness for lncRNA and DNA methylation as prognosis factors independent of traditional clinical variables.ConclusionOur study provides insight into systematically understanding the prognostic performance of diverse molecular data in both single and aggregate patterns, which may have specific reference to subsequent related studies.     

芒不同基因型愈伤组织诱导及分化的差异

芒(Miscanthus sinensis)具较高的生物学产量, 是一种极具发展前景的纤维素类能源植物。以芒的8种不同基因型幼穗为外植体, 进行了组织培养研究。结果表明, 不同基因型芒在愈伤组织诱导率、胚性愈伤组织诱导率和胚性愈伤组织分化率等方面均存在显著差异。W89和W70均具较高的愈伤组织诱导率, 分别为91.7%和89.1%; W69的外植体几乎全部褐化, 且未能诱导出愈伤组织。W89、W70和W17的胚性愈伤组织分化率较高, 达50%以上。另外, 发现愈伤组织诱导率与细胞壁木质素含量间呈显著的负相关。该研究建立了稳定且有效的再生体系, 并初步确定W89和W70可作为芒组织培养的理想材料, 为芒的遗传转化、定向改良和良种快繁提供了技术支持。     

Terminal alkene formation by the thioesterase of curacin A biosynthesis: structure of a decarboxylating thioesterase

Curacin A is a polyketide synthase (PKS)-non-ribosomal peptide synthetase-derived natural product with potent anticancer properties generated by the marine cyanobacterium Lyngbya majuscula. Type I modular PKS assembly lines typically employ a thioesterase (TE) domain to off-load carboxylic acid or macrolactone products from an adjacent acyl carrier protein (ACP) domain. In a striking departure from this scheme the curacin A PKS employs tandem sulfotransferase and TE domains to form a terminal alkene moiety. Sulfotransferase sulfonation of β-hydroxy-acyl-ACP is followed by TE hydrolysis, decarboxylation, and sulfate elimination (Gu, L., Wang, B., Kulkarni, A., Gehret, J. J., Lloyd, K. R., Gerwick, L., Gerwick, W. H., Wipf, P., Håkansson, K., Smith, J. L., and Sherman, D. H. (2009) J. Am. Chem. Soc. 131, 16033–16035). With low sequence identity to other PKS TEs (<15%), the curacin TE represents a new thioesterase subfamily. The 1.7-Å curacin TE crystal structure reveals how the familiar α/β-hydrolase architecture is adapted to specificity for β-sulfated substrates. A Ser-His-Glu catalytic triad is centered in an open active site cleft between the core domain and a lid subdomain. Unlike TEs from other PKSs, the lid is fixed in an open conformation on one side by dimer contacts of a protruding helix and on the other side by an arginine anchor from the lid into the core. Adjacent to the catalytic triad, another arginine residue is positioned to recognize the substrate β-sulfate group. The essential features of the curacin TE are conserved in sequences of five other putative bacterial ACP-ST-TE tridomains. Formation of a sulfate leaving group as a biosynthetic strategy to facilitate acyl chain decarboxylation is of potential value as a route to hydrocarbon biofuels.     

Genetic Engineering of Energy Crops: A Strategy for Biofuel Production in China

Biomass utilization is increasingly considered as a practical way for sustainable energy supply and long-term environment care around the world.In concerns with food security in China,starch or sugar-based bioethanol and edible-oil-derived biodiesel are harshly restricted for large scale production.However,conversion of lignocellulosic residues from food crops is a potential alternative.Because of its recalcitrance,current biomass process is unacceptably expensive,but genetic breeding of energy crops is a p...     

Genetic Engineering of Energy Crops: A Strategy for Biofuel Production in China Free Access

Biomass utilization is increasingly considered as a practical way for sustainable energy supply and long‐term environment care around the world. In concerns with food security in China, starch or sugar‐based bioethanol and edible‐oil‐derived biodiesel are harshly restricted for large scale production. However, conversion of lignocellulosic residues from food crops is a potential alternative. Because of its recalcitrance, current biomass process is unacceptably expensive, but genetic breeding of energy crops is a promising solution. To meet the need, energy crops are defined with a high yield for both food and biofuel purposes. In this review, main grasses (rice, wheat, maize, sorghum and miscanthus) are evaluated for high biomass production, the principles are discussed on modification of plant cell walls that lead to efficient biomass degradation and conversion, and the related biotechnologies are proposed in terms of energy crop selection.     

The MrCYP52 cytochrome P450 monoxygenase gene of Metarhizium robertsii is important for utilizing insect epicuticular hydrocarbons

Fungal pathogens of plants and insects infect their hosts by direct penetration of the cuticle. Plant and insect cuticles are covered by a hydrocarbon-rich waxy outer layer that represents the first barrier against infection. However, the fungal genes that underlie insect waxy layer degradation have received little attention. Here we characterize the single cytochrome P450 monoxygenase family 52 (MrCYP52) gene of the insect pathogen Metarhizium robertsii, and demonstrate that it encodes an enzyme required for efficient utilization of host hydrocarbons. Expressing a green florescent protein gene under control of the MrCYP52 promoter confirmed that MrCYP52 is up regulated on insect cuticle as well as by artificial media containing decane (C10), extracted cuticle hydrocarbons, and to a lesser extent long chain alkanes. Disrupting MrCYP52 resulted in reduced growth on epicuticular hydrocarbons and delayed developmental processes on insect cuticle, including germination and production of appressoria (infection structures). Extraction of alkanes from cuticle prevented induction of MrCYP52 and reduced growth. Insect bioassays against caterpillars (Galleria mellonella) confirmed that disruption of MrCYP52 significantly reduces virulence. However, MrCYP52 was dispensable for normal germination and appressorial formation in vitro when the fungus was supplied with nitrogenous nutrients. We conclude therefore that MrCYP52 mediates degradation of epicuticular hydrocarbons and these are an important nutrient source, but not a source of chemical signals that trigger infection processes.     

A novel paradigm for potential drug-targets discovery: quantifying relationships of enzymes and cascade interactions of neighboring biological processes to identify drug-targets

Target discovery is the most crucial step in a modern drug discovery development. Our objective in this study is to propose a novel paradigm for a better discrimination of drug-targets and non-drug-targets with minimum disruptive side-effects under a biological pathway context. We introduce a novel metric, namely, "pathway closeness centrality", for each gene that jointly considers the relationships of its neighboring enzymes and cross-talks of biological processes, to evaluate its probability of being a drug-target. This metric could distinguish drug-targets with non-drug-targets. Genes with lower pathway closeness centrality values are prone to play marginal roles in biological processes and have less lethality risk, but appear to have tissue-specific expressions. Compared with traditional metrics, our method outperforms degree, betweenness and bridging centrality under the human pathway context. Analysis of the existing top 20 drugs with the most disruptive side-effects indicates that pathway closeness centrality is an appropriate index to predict the probability of the occurrence of adverse pharmacological effects. Case studies in prostate cancer and type 2 diabetes mellitus indicate that the pathway closeness centrality metric could distinguish likely drug-targets well from human pathways. Thus, our method is a promising tool to aid target identification in drug discovery.