黄萎病菌诱导下野生茄‘托鲁巴姆’SSH文库的构建与分析

由大丽轮枝菌(Verticillium dahliae Kleb.)引起的茄子黄萎病是一种严重的土传病害,但在茄子栽培品种中缺少高抗种质,野生茄‘托鲁巴姆’高抗黄萎病。为探讨野生茄‘托鲁巴姆’抗黄萎病的分子机制,该试验以‘托鲁巴姆’为试材,利用抑制性差减杂交技术,分别以黄萎病菌侵染与未侵染的根系为检测方(tester)和驱动方(driver),构建了1个黄萎病菌诱导下的根器官正向差减cDNA文库。结果表明:(1)随机挑取170个阳性克隆,经测序,共获得109个非冗余EST,其中61个EST与其他植物的抗逆相关基因同源,如几丁质酶、细胞色素P450、过氧化物酶、蛋白酶抑制子等。(2)借助NCBI中的EST序列,经过电子拼接结合RT-PCR验证,克隆了1个通用胁迫蛋白基因———StUSP1。(3)表达分析结果显示,‘托鲁巴姆’受黄萎病菌侵染后,StUSP1在根中上调表达。     

Selection of ceramic fluorapatite‐binding peptides from a phage display combinatorial peptide library: optimum affinity tags for fluorapatite chromatography

Peptide affinity tags have become efficient tools for the purification of recombinant proteins from biological mixtures. The most commonly used ligands in this type of affinity chromatography are immobilized metal ions, proteins, antibodies, and complementary peptides. However, the major bottlenecks of this technique are still related to the ligands, including their low stability, difficulties in immobilization, and leakage into the final products. A model approach is presented here to overcome these bottlenecks by utilizing macroporous ceramic fluorapatite (CFA) as the stationary phase in chromatography and the CFA‐specific short peptides as tags. The CFA chromatographic materials act as both the support matrix and the ligand. Peptides that bind with affinity to CFA were identified from a randomized phage display heptapeptide library. A total of five rounds of phage selection were performed. A common N‐terminal sequence was found in two selected peptides: F4‐2 (KPRSMLH) and F5‐4 (KPRSVSG). The peptide F5‐4, displayed by more than 40% of the phages analyzed in the fifth round of selection, was subjected to further studies. Selectivity of the peptide for the chemical composition and morphology of CFA was assured by the adsorption studies. The dissociation constant, obtained from the F5‐4/CFA adsorption isotherm, was in the micromolar range, and the maximum capacity was 39.4 nmol/mg. The chromatographic behavior of the peptides was characterized on a CFA stationary phase with different buffers. Preferential affinity and specific retention properties suggest the possible application of the phage‐derived peptides as a tag in CFA affinity chromatography for enhancing the selective recovery of proteins. Copyright © 2013 John Wiley & Sons, Ltd.     

Introduction of New Tools for Chemical Biology Research on Microbial Metabolites

Recently, high-throughput screening (HTS) has become the mainstream technique for drug discovery. Compounds that are synthesized by combinatorial chemistry might be more suitable than natural products to apply to HTS, because the purification procedure is a drawback of using natural products. Nevertheless, natural products remain an extremely important source of drugs. To overcome the demerits of natural products, we are constructing the RIKEN Natural Products Depository (NPDepo) that is focused primarily on microbial metabolites. In this review, I describe (i) engineering pathways for biosynthetic gene clusters of microbial metabolites, (ii) construction of fraction libraries of microbial metabolites, and (iii) the development of a new screening system using a chemical array and a protein library produced by GLORIA.     

Guanosine Diphosphate Mannose in Conformational Relation to Other Suger Nucleotides and Phosphates in Solution

Molecular conformational transition of GDPMan and solution conformation of α-d- mannopyranose moiety in Man-l-P and GDPMan were examined in relation to other sugar nucleotides and phosphates. GDPMan and other sugar nucleotides examined revealed changes in the optical rotation in sigmoidal curve in water by addition of urea. The change was reversible without significant decomposition and is attributable to dissociation of an ordered form into a random form. Optical conformational values in 8m urea solution were+116° for GDPMan, +58°~+79° for UDPGlc, +79° for UDPGal, +135°~+143° for UDPGlcNAc, and +138°~ +155° for UDPGIcA.

NMR analysis and periodate oxidation study revealed the ⁴C₁ conformation of α-d-hexopyranose moieties in Man-1-P, Glc-l-P, GDPMan, UDPGlcNAc and UDPGalNAc.     

Subunit Structure of Glucoamylase of Saccharomyces diastaticus

Extracellular glucoamylase produced by a starch-fermenting yeast, Saccharomyces diastaticus 5106-9A, was purified. The enzyme was found to be heterogeneous in molecular weight, ranging from approximately 80K to 66K as estimated by gel filtration, and consisted of two subunits, H and Y. The molecular weight of subunit H was heterogeneous and was determined to be approximately 68K, 59K, and 53K by acrylamide gel electrophoresis in the presence of sodium dodecyl sulfate. The molecular weight of subunit Y was 14K, estimated by the same gel. the molecular weight of the deglycosylated form of subunit H was 41K, suggesting that the heterogeneity of the enzyme was due to glycosyl moieties of subunit H. Subunits H and Y were separated by gel filtration in the presence of sodium dodecyl sulfate. Subunit Y seemed to be hydrophobic, since it was insoluble in an aqueous buffer without detergent.     

Metabolism of O,O-Dipropyl S-[2-(2′-Methyl-1′-piperidinyl)-2-oxo-ethyl] Phosphorodithioate (C 19 490) in Paddy Rice

The fate of O,O-dipropyl S-[2-(2′-methyl-1′-piperidinyl)-2-oxo-ethyl] phosphorodithioate (C 19 490, piperophos) was followed in greenhouse-grown rice after application of 1.6 kg/ha ¹⁴C-labeled C 19 490 into the paddy water. At maturity the shoots contained 2.5 ppm and the hulled grains 0.16 ppm ¹⁴C-C 19 490 equivalents. Small amounts of unchanged C 19 490 were found in the shoots but none in the grains.

The main metabolites found were:- 2-(2′-methyl-1′-piperidiny])-2-oxo-ethane sulfonic acid, 2-(2?-methyl-1?-piperidinyl)-2-oxo-ethanoic acid and a fraction of polar unknown substances. O,O-Dipropyl S-[2-(2?-methyl-1′ -piperidinyl)-2-oxo-ethyl] phosphorothioate, 2-(2?-methyl-1?-piperidinyl)- 1-methyl-sulfinyl-2-oxo-ethane, 2-(2?-methyl-1?-piperidinyl)-1-methyl-sulfonyl-2-oxo- ethane, 2-methyl-piperidine and CO₂ were found in smaller amounts.     

Studies on Abscisic Acid

Methyl α-ionylideneacetates were oxidized with selenium dioxide to a mixture of methyl 3′-keto-β-ionylideneacetates and a small amount of methyl 4′-keto-α-ionylidene-acetates followed by treatment with active manganese dioxide. By a similar oxidation methyl 3′-keto-β-ionylideneacetates were prepared from methyl β-ionylidene acetates. Methyl 4′-keto-α-ionylideneacetates were obtained by oxidation of methyl α-ionylideneacetates with tert-butyl chromate. Dehydrobromination of methyl bromoionylideneacetate, obtained by bromination of methyl 2-trans-α-ionylideneacetate with N-bromosuccinimide, gave a mixture of methyl 2-trans-dehydro-β-ionylideneacetate and methyl 2-cis-dehydro-β-ionylideneacetate. The growth inhibitory activities of these sesquiterpene carboxylic acids and keto esters on rice seedlings were tested.     

Design,construction, and characterization of a second‐generation DARPin library with reduced hydrophobicity

Designed ankyrin repeat proteins (DARPins) are well‐established binding molecules based on a highly stable nonantibody scaffold. Building on 13 crystal structures of DARPin‐target complexes and stability measurements of DARPin mutants, we have generated a new DARPin library containing an extended randomized surface. To counteract the enrichment of unspecific hydrophobic binders during selections against difficult targets containing hydrophobic surfaces such as membrane proteins, the frequency of apolar residues at diversified positions was drastically reduced and substituted by an increased number of tyrosines. Ribosome display selections against two human caspases and membrane transporter AcrB yielded highly enriched pools of unique and strong DARPin binders which were mainly monomeric. We noted a prominent enrichment of tryptophan residues during binder selections. A crystal structure of a representative of this library in complex with caspase‐7 visualizes the key roles of both tryptophans and tyrosines in providing target contacts. These aromatic and polar side chains thus substitute the apolar residues valine, leucine, isoleucine, methionine, and phenylalanine of the original DARPins. Our work describes biophysical and structural analyses required to extend existing binder scaffolds and simplifies an existing protocol for the assembly of highly diverse synthetic binder libraries.     

锌胁迫下小麦SSH文库的构建及初步分析

Zn是植物必需的微量元素,同时也是近年来造成环境污染的重金属元素之一.为了从基因表达水平揭示小麦Zn胁迫响应的分子机制,本研究利用抑制差减杂交(suppression subtractive hybridization,SSH)技术构建了Zn胁迫（0.5 mmol/L,1 mmol/L）下小麦的正反向SSH文库.从正反向文库中随机挑选阳性单克隆,并利用通用引物T7/Sp6对其进行验证. 结果显示,正反库中分别获得307和821个EST序列,其片段长度在200～1 000 bp之间,它们反映了Zn胁迫下特异响应的基因.利用BLASTn和BLASTx将这些EST序列进行比对分析,在正、反库中分别筛选出221和641个uniESTs,其中751个uniESTs被注释（包括正库中193个和反库中558个）.这些序列的功能主要涉及信号转导、抗氧化防御、转录与翻译、物质运输、核糖体结构、能量代谢,以及一些功能未知的基因.