The isolation and characterization of Pik, a rice blast resistance gene which emerged after rice domestication

? The rice-rice blast pathosystem is of great interest, not only because of the damaging potential of rice blast to the rice crop, but also because both the pathogen and its host are experimentally amenable. The rice blast resistance gene Pik, which is one of the five classical alleles located at the Pik locus on the long arm of chromosome 11, confers high and stable resistance to many Chinese rice blast isolates. ? The isolation and functional characterization of Pik were performed in the present study through genetic and genomic approaches. ? A combination of Pik-1 and Pik-2 is required for the expression of Pik resistance. Both Pik-1 and Pik-2 encode coiled-coil nucleotide binding site leucine-rich repeat (NBS-LRR) proteins, and each shares a very high level of protein identity with corresponding proteins encoded by the Pik-m and Pik-p alleles. Pik could be distinguished from other Pik alleles, including Pik-m and Pik-p, by the allele-specific, single-nucleotide polymorphism T1-2944G. ? The coupled genes probably did not evolve as a result of a duplication event, and are far from any NBS-LRR R gene characterized. Pik is a younger allele at the locus that probably emerged after rice domestication.     

A protein complex network of Drosophila melanogaster

Determining the composition of protein complexes is an essential step toward understanding the cell as an integrated system. Using coaffinity purification coupled to mass spectrometry analysis, we examined protein associations involving nearly 5,000 individual, FLAG-HA epitope-tagged Drosophila proteins. Stringent analysis of these data, based on a statistical framework designed to define individual protein-protein interactions, led to the generation of a Drosophila protein interaction map (DPiM) encompassing 556 protein complexes. The high quality of the DPiM and its usefulness as a paradigm for metazoan proteomes are apparent from the recovery of many known complexes, significant enrichment for shared functional attributes, and validation in human cells. The DPiM defines potential novel members for several important protein complexes and assigns functional links to 586 protein-coding genes lacking previous experimental annotation. The DPiM represents, to our knowledge, the largest metazoan protein complex map and provides a valuable resource for analysis of protein complex evolution.     

Improved method for constructing plant amiRNA vectors with blue-white screening and MAGIC

Artificial microRNA (amiRNA) technology is a novel tool in reverse genetic research for discovering or validating gene functions in plants. A convenient cloning strategy has been developed to construct plant amiRNA vectors based on lacO reconstruction and mating-assisted, genetically-integrated cloning (MAGIC). The amiRNA precursor fragment was generated by PCR and inserted into a small donor plasmid through reconstruction of integrated lacO sequence. Blue recombinants were selected on plates containing X-gal and the efficiency of successful clones was 100%. The amiRNA expression cassette was transferred from the donor plasmid to the recipient plasmid p1301-gfp through MAGIC and an amiRNA expression plasmid was created. More than 40 plant amiRNA vectors were generated through this method, one of which was transformed into Arabidopsis thaliana and the target gene was silenced efficiently. The approach will be useful for amiRNA expression vectors construction in plants.     

Structural determinants of caspase-9 inhibition by the vaccinia virus protein, F1L

In multicellular organisms, apoptosis is a powerful method of host defense against viral infection. Apoptosis is mediated by a cascade of caspase-family proteases that commit infected cells to a form of programmed cell death. Therefore, to replicate within host cells, viruses have developed various strategies to inhibit caspase activation. In the mitochondrial cell-death pathway, release of cytochrome c from mitochondria into the cytosol triggers assembly of the oligomeric apoptosome, resulting in dimerization and activation of the apical caspase-9 (C9), and in turn its downstream effector caspases, leading to apoptosis. We previously showed that the vaccinia virus-encoded Bcl-2-like protein, F1L, which suppresses cytochrome c release by binding Bcl-2 family proteins, is also a C9 inhibitor. Here, we identify a novel motif within the flexible N-terminal region of F1L that is necessary and sufficient for interaction with and inhibition of C9. Based on functional studies and mutagenesis, we developed an atomic model of the complex in which F1L inhibits C9 by engaging the active site in the reverse orientation with respect to substrate peptides, in a manner analogous to that of XIAP-mediated inhibition of caspases-3 and -7. These studies offer new insights into the mechanism of apoptosome inhibition by F1L as well as novel probes to understand the molecular bases of apoptosome regulation and turnover. They also suggest how the two distinct functionalities of F1L (inhibition of C9 and suppression of pro-apoptotic Bcl-2 family proteins) may operate in a cellular setting.     

Regulation of cellular levels of Sprouty2 protein by prolyl hydroxylase domain and von Hippel-Lindau proteins

Sprouty (Spry) proteins modulate the actions of receptor tyrosine kinases during development and tumorigenesis. Decreases in cellular levels of Spry, especially Sprouty2 (Spry2), have been implicated in the growth and progression of tumors of the breast, prostate, lung, and liver. During development and tumor growth, cells experience hypoxia. Therefore, we investigated how hypoxia modulates the levels of Spry proteins. Hypoxia elevated the levels of all four expressed Spry isoforms in HeLa cells. Amounts of endogenous Spry2 in LS147T and HEP3B cells were also elevated by hypoxia. Using Spry2 as a prototype, we demonstrate that silencing and expression of prolyl hydroxylase domain proteins (PHD1-3) increase and decrease, respectively, the cellular content of Spry2. Spry2 also preferentially interacted with PHD1-3 and von Hippel-Lindau protein (pVHL) during normoxia but not in hypoxia. Additionally, Spry2 is hydroxylated on Pro residues 18, 144, and 160, and substitution of these residues with Ala enhanced stability of Spry2 and abrogated its interactions with pVHL. Silencing of pVHL increased levels of Spry2 by decreasing its ubiquitylation and degradation and thereby augmented the ability of Spry2 to inhibit FGF-elicited activation of ERK1/2. Thus, prolyl hydroxylase mediated hydroxylation and subsequent pVHL-elicited ubiquitylation of Spry2 target it for degradation and, consequently, provide a novel mechanism of regulating growth factor signaling.     

Prediction of mitochondrial proteins of malaria parasite using bi-profile Bayes feature extraction

Mitochondrial proteins of Plasmodium falciparum are considered as attractive targets for anti-malarial drugs, but the experimental identification of these proteins is a difficult and time-consuming task. Computational prediction of mitochondrial proteins offers an alternative approach. However, the commonly used subcellular location prediction methods are unsuited for P. falciparum mitochondrial proteins whereas the organism and organelle-specific methods were constructed on the basis of a rather small dataset. In this study, a novel dataset termed PfM233, which included 108 mitochondrial and 125 non-mitochondrial proteins with sequence similarity below 25%, was established and the methods for predicting mitochondrial proteins of P. falciparum were described. Both bi-profile Bayes and split amino acid composition were applied to extract the features from the N- and C-terminal sequences of these proteins, which were then used to construct two SVM based classifiers (PfMP-N25 and PfMP-30). Using PfM233 as the dataset, PfMP-N25 and PfMP-30 achieved accuracies (MCCs) of 90.13% (0.80) and 90.99% (0.82). When tested with the commonly used 40 mitochondrial proteins in PfM175 and the 108 mitochondrial proteins in PfM233, these two methods obviously outperformed the existing general, organelle-specific and organism and organelle-specific methods.     

Isolation and characterization of an apple cytosolic malate dehydrogenase gene reveal its function in malate synthesis

Cytosolic NAD-dependent malate dehydrogenase (cyMDH) is an enzyme crucial for malate synthesis in the cytosol. The apple MdcyMDH gene (GenBank Accession No. DQ221207) encoding the cyMDH enzyme in apple was cloned and functionally characterized. The protein was subcellularly localized to the cytoplasm and plasma membrane. Based on kinetic parameters, it mainly catalyzes the reaction from oxalacetic acid (OAA) to malate in vitro. The expression level of MdcyMDH was positively correlated with malate dehydrogenase (MDH) activity throughout fruit development, but not with malate content, especially in the ripening apple fruit. MdcyMDH overexpression contributed to malate accumulation in the apple callus and tomato. Taken together, our results support the involvement of MdcyMDH directly in malate synthesis and indirectly in malate accumulation through the regulation of genes/enzymes associated with malate degradation and transportation, gluconeogenesis and the tricarboxylic acid cycle.     

双酚A诱导雄性中国林蛙肝细胞雌激素受体表达和卵黄蛋白原合成

为探讨双酚A(bisphenol A,BPA)对雄性两栖动物肝细胞中雌激素受体(estrogenreceptor,ER)表达和卵黄蛋白原(vitellogenin,VTG)合成的影响,将中国林蛙(Ranachensinensis)雄性成体分别持续暴露于10-7、10-6、10-5mol/LBPA水体中10、20、30d,设10-9、10-8mol/L雌二醇(E2)为阳性对照。用原位杂交技术检测ERmRNA在肝细胞中的表达定位,用免疫组织化学技术检测肝细胞中ER和VTG蛋白的表达。结果显示,各BPA和E2处理组肝细胞中均有ERmRNA阳性反应,ER和VTG蛋白的表达相对值均显著高于空白对照组。在同一暴露时间,ER和VTG表达值是随着BPA浓度的增加呈增高趋势。在同一BPA浓度,VTG表达值是随暴露时间的延长呈增高趋势,而ER表达值则无显著性变化。这些表明BPA可以通过诱导雄性中国林蛙肝细胞的ER高调导致VTG合成,但其效应远低于E2。     

Three-dimensional structure of Bax-mediated pores in membrane bilayers

B-cell lymphoma 2 (Bcl-2)-associated X protein (Bax) is a member of the Bcl-2 protein family having a pivotal role in triggering cell commitment to apoptosis. Bax is latent and monomeric in the cytosol but transforms into its lethal, mitochondria-embedded oligomeric form in response to cell stress, leading to the release of apoptogenic factors such as cytochrome C. Here, we dissected the structural correlates of Bax membrane insertion while oligomerization is halted. This strategy was enabled through the use of nanometer-scale phospholipid bilayer islands (nanodiscs) the size of which restricts the reconstituted system to single Bax-molecule activity. Using this minimal reconstituted system, we captured structural correlates that precede Bax homo-oligomerization elucidating previously inaccessible steps of the core molecular mechanism by which Bcl-2 family proteins regulate membrane permeabilization. We observe that, in the presence of BH3 interacting domain death agonist (Bid) BH3 peptide, Bax monomers induce the formation of ∼3.5-nm diameter pores and significantly distort the phospholipid bilayer. These pores are compatible with promoting release of ions as well as proteinaceous components, suggesting that membrane-integrated Bax monomers in the presence of Bid BH3 peptides are key functional units for the activation of the cell demolition machinery.