PIF4 and PIF5 Transcription Factors Link Blue Light and Auxin to Regulate the Phototropic Response in Arabidopsis

Both blue light (BL) and auxin are essential for phototropism in Arabidopsis thaliana. However, the mechanisms by which light is molecularly linked to auxin during phototropism remain elusive. Here, we report that PHYTOCHROME INTERACTING FACTOR4 (PIF4) and PIF5 act downstream of the BL sensor PHOTOTROPIN1 (PHOT1) to negatively modulate phototropism in Arabidopsis. We also reveal that PIF4 and PIF5 negatively regulate auxin signaling. Furthermore, we demonstrate that PIF4 directly activates the expression of the AUXIN/INDOLE-3-ACETIC ACID (IAA) genes IAA19 and IAA29 by binding to the G-box (CACGTG) motifs in their promoters. Our genetic assays demonstrate that IAA19 and IAA29, which physically interact with AUXIN RESPONSE FACTOR7 (ARF7), are sufficient for PIF4 to negatively regulate auxin signaling and phototropism. This study identifies a key step of phototropic signaling in Arabidopsis by showing that PIF4 and PIF5 link light and auxin.     

A plant-transformation-competent BIBAC library of ginseng (Panax ginseng C. A. Meyer) for functional genomics research and characterization of genes involved in ginsenoside biosynthesis

Ginseng (Panax ginseng C. A. Mey.) is widely used as a major medicinal herb and as a feedstock for the medicine, beverage, food, cosmetic, etc. industries, in China and several other Asian countries. However, limited research has been accomplished into its genetics, genomics and breeding. To clone, characterize and utilize the genes of economic importance in the species, we have developed a large-insert plant-transformation-competent binary bacterial artificial chromosome (BIBAC) library for Jilin ginseng cv. Damaya. The library contains 141,312 clones, with an average insert size of 110 kb, each likely containing approximately 20–30 genes. The clones of the library have all been arrayed in 384-well microplates and permanently archived. We screened the library and identified BIBAC clones containing nine genes likely involved in the biosynthesis pathway of ginsenosides—the major medicinally effective compounds of ginseng—with approximately four BIBACs per gene. This result further verified the quality of the library and demonstrated its utility in cloning, characterization and utilization of economically important genes in ginseng. Furthermore, since the library is cloned in a plant-transformation-competent BIBAC vector (pCLD04541) that can be directly transformed in a variety of plants via both the Agrobacterium-mediated method and the particle bombardment method, we have also demonstrated the stability of large-insert ginseng DNA BIBACs in different Agrobacterium strains, which is crucial to large-insert BIBAC transformation in plants. Therefore, the Jilin ginseng BIBAC library provides resources and tools useful for functional genomics research, and cloning, characterization and utilization of economically important genes in the species.     

Clinical Investigation on the Beneficial Effects of the Chinese Medicinal Herb Gushen Pian on Sensorineural Deafness and Tinnitus

The objective is to study the therapeutic effects of Gushen Pian on sensorineural deafness according to the Phase II clinical trial protocol, as approved for novel traditional Chinese medicines by Ministry of Health of PRC. This is a double blind study in which 120 patients were allocated randomly into treatment and control groups and an open treatment group (40 cases in each group). Patients in the treatment groups were administrated with Gushen Pian and controls received placebo. Routine examination of blood and urine, hepatic and renal function tests and pure tone audiometry were performed before and after treatment. Clinical symptoms and therapeutic outcomes were compared and evaluated. For double-blind treatment group, the total effective rate of deafness was 42.2 % and total relieved rate of deafness was 4.6 %; for double-blind control group, the total effective rate of deafness was 18.7 % and total relieved rate of deafness was 0 %; for simple treatment group, the total effective rate of deafness was 58.7 % and total relieved rate of deafness was 6.3 %. For double-blind treatment group, the total effective rate of tinnitus was 89.2 % and total relieved rate of tinnitus was 59.5 %; for double-blind control group, the total effective rate of tinnitus was 30.8 % and total relieved rate of tinnitus was 5.1 %; for simple treatment group, the total effective rate of tinnitus was 74.3 % and total relieved rate of tinnitus was 57.1 %. The double-blind treatment showed statistically significant differences from control group. The medication could effectively alleviate aural fullness, dizziness, lassitude of loins and knees, dysphoria with feverish sensation in chest, insomnia, and fatigue, etc. No adverse effect was reported during treatment; no abnormal results were reported in blood, urine, faces, heart function, liver function and kidney function examination. Gushen Pian had beneficial effect on deafness and tinnitus and could effectively alleviate aural fullness, insomnia, etc., without any adverse effects.     

一株产甘露聚糖酶菌株的分离鉴定及酶的纯化与性质

【目的】筛选性能良好的产碱性甘露聚糖酶的菌株,对菌株进行多项分类鉴定,分离纯化所产甘露聚糖酶并进行性质研究。【方法】利用碱性魔芋粉培养基分离纯化产甘露聚糖酶的嗜碱菌,通过形态特征观察、生理生化测定、16S rRNA序列分析等实验确定菌株的分类地位。利用硫酸铵沉淀、阴离子交换层析和分子筛层析得到电泳纯的酶,分析了酶的最适温度、最适pH、温度和pH稳定性、NaCl以及金属离子等的耐受性。【结果】从我国内蒙古碱湖样品中分离得到一株产碱性甘露聚糖酶的菌株HMTS15,经过多项分类鉴定显示其是与Bacillus agaradhaerens DSM 8721不同的新菌株。菌株HMTS15所产的甘露聚糖酶反应的最适pH为10.0,最适温度75℃。【结论】多项分类结果鉴定菌株为Bacillus agaradhaerens HMTS15。该菌株产生的碱性甘露聚糖酶与同类其他来源的酶相比具有更好的热稳定性和pH适应性,有进一步的研究价值。     

Functional mutation of SMAC/DIABLO, encoding a mitochondrial proapoptotic protein, causes human progressive hearing loss DFNA64

SMAC/DIABLO is a mitochondrial proapoptotic protein that is released from mitochondria during apoptosis and counters the inhibitory activities of inhibitor of apoptosis proteins, IAPs. By linkage analysis and candidate screening, we identified a heterozygous SMAC/DIABLO mutation, c.377C>T (p.Ser126Leu, refers to p.Ser71Leu in the mature protein) in a six-generation Chinese kindred characterized by dominant progressive nonsyndromic hearing loss, designated as DFNA64. SMAC/DIABLO is highly expressed in human embryonic ears and is enriched in the developing mouse inner-ear hair cells, suggesting it has a role in the development and homeostasis of hair cells. We used a functional study to demonstrate that the SMAC/DIABLO(S71L) mutant, while retaining the proapoptotic function, triggers significant degradation of both wild-type and mutant SMAC/DIABLO and renders host mitochondria susceptible to calcium-induced loss of the membrane potential. Our work identifies DFNA64 as the human genetic disorder associated with SMAC/DIABLO malfunction and suggests that mutant SMAC/DIABLO(S71L) might cause mitochondrial dysfunction.     

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.