Structure of YciA from Haemophilus influenzae (HI0827), a hexameric broad specificity acyl-coenzyme A thioesterase

The crystal structure of HI0827 from Haemophilus influenzae Rd KW20, initially annotated "hypothetical protein" in sequence databases, exhibits an acyl-coenzyme A (acyl-CoA) thioesterase "hot dog" fold with a trimer of dimers oligomeric association, a novel assembly for this enzyme family. In studies described in the preceding paper [Zhuang, Z., Song, F., Zhao, H., Li, L., Cao, J., Eisenstein, E., Herzberg, O., and Dunaway-Mariano, D. (2008) Biochemistry 47, 2789-2796], HI0827 is shown to be an acyl-CoA thioesterase that acts on a wide range of acyl-CoA compounds. Two substrate binding sites are located across the dimer interface. The binding sites are occupied by two CoA molecules, one with full occupancy and the second only partially occupied. The CoA molecules, acquired from HI0827-expressing Escherichia coli cells, remained tightly bound to the enzyme through the protein purification steps. The difference in CoA occupancies indicates a different substrate affinity for each of the binding sites, which in turn implies that the enzyme might be subject to allosteric regulation. Mutagenesis studies have shown that the replacement of the putative catalytic carboxylate Asp44 with an alanine residue abolishes activity. The impact of this mutation is seen in the crystal structure of D44A HI0827. Whereas the overall fold and assembly of the mutant protein are the same as those of the wild-type enzyme, the CoA ligands are absent. The dimer interface is perturbed, and the channel that accommodates the thioester acyl chain is more open and wider than that observed in the wild-type enzyme. A model of intact substrate bound to wild-type HI0827 provides a structural rationale for the broad substrate range.     

Crystal structure of Saccharomyces cerevisiae 3'-phosphoadenosine-5'-phosphosulfate reductase complexed with adenosine 3',5'-bisphosphate

Most assimilatory bacteria, fungi, and plants species reduce sulfate (in the activated form of APS or PAPS) to produce reduced sulfur. In yeast, PAPS reductase reduces PAPS to sulfite and PAP. Despite the difference in substrate specificity and catalytic cofactor, PAPS reductase is homologous to APS reductase in both sequence and structure, and they are suggested to share the same catalytic mechanism. Metazoans do not possess the sulfate reduction pathway, which makes APS/PAPS reductases potential drug targets for human pathogens. Here, we present the 2.05 A resolution crystal structure of the yeast PAPS reductase binary complex with product PAP bound. The N-terminal region mediates dimeric interactions resulting in a unique homodimer assembly not seen in previous APS/PAPS reductase structures. The "pyrophosphate-binding" sequence (47)TTAFGLTG(54) defines the substrate 3'-phosphate binding pocket. In yeast, Gly54 replaces a conserved aspartate found in APS reductases vacating space and charge to accommodate the 3'-phosphate of PAPS, thus regulating substrate specificity. Also, for the first time, the complete C-terminal catalytic motif (244)ECGIH(248) is revealed in the active site. The catalytic residue Cys245 is ideally positioned for an in-line attack on the beta-sulfate of PAPS. In addition, the side chain of His248 is only 4.2 A from the Sgamma of Cys245 and may serve as a catalytic base to deprotonate the active site cysteine. A hydrophobic sequence (252)RFAQFL(257) at the end of the C-terminus may provide anchoring interactions preventing the tail from swinging away from the active site as seen in other APS/PAPS reductases.     

红曲菌代谢产物中低极性组分的分离及表征

以石油醚∶醋酸乙酯 =4∶1(V/V)作为洗脱剂 ,采用柱层层析粗分离醇溶性红曲菌代谢产物中的低极性组分。经浓缩、结晶除去白色结晶后的浓缩液 ,用正己烷∶醋酸乙酯 =9∶1(V/V)作为展开剂进行薄层层析分离 ,在紫外灯下观察 ,从低极性组分中分离出六个组分 ,分别为 :具荧光组分、两个相隔较近的黄色组分、淡黄色具荧光组分、具浅蓝绿色荧光组分、具荧光组分。各组分的Rf 值分别为 :0 2 9、0 15、0 12、0 0 9、0 0 6、0 0 4。MS测定结果表明 ,Rf 值最大的具荧光组分可能为含有 OH及Br的共轭烯烃或脂肪酮 ,而在紫外灯下呈淡黄色组分为含有 OH的环状化合物。     

TDRD3 promotes DHX9 chromatin recruitment and R-loop resolution

R-loops, which consist of a DNA/RNA hybrid and a displaced single-stranded DNA (ssDNA), are increasingly recognized as critical regulators of chromatin biology. R-loops are particularly enriched at gene promoters, where they play important roles in regulating gene expression. However, the molecular mechanisms that control promoter-associated R-loops remain unclear. The epigenetic ‘reader’ Tudor domain-containing protein 3 (TDRD3), which recognizes methylarginine marks on histones and on the C-terminal domain of RNA polymerase II, was previously shown to recruit DNA topoisomerase 3B (TOP3B) to relax negatively supercoiled DNA and prevent R-loop formation. Here, we further characterize the function of TDRD3 in R-loop metabolism and introduce the DExH-box helicase 9 (DHX9) as a novel interaction partner of the TDRD3/TOP3B complex. TDRD3 directly interacts with DHX9 via its Tudor domain. This interaction is important for recruiting DHX9 to target gene promoters, where it resolves R-loops in a helicase activity-dependent manner to facilitate gene expression. Additionally, TDRD3 also stimulates the helicase activity of DHX9. This stimulation relies on the OB-fold of TDRD3, which likely binds the ssDNA in the R-loop structure. Thus, DHX9 functions together with TOP3B to suppress promoter-associated R-loops. Collectively, these findings reveal new functions of TDRD3 and provide important mechanistic insights into the regulation of R-loop metabolism.     

沙田柚系列遗传关系的RAPD标记研究

采用 RAPD标记技术分析了沙田柚系列 1 2个样品的遗传关系。利用经筛选具多态性的 1 4个 1 0碱基随机引物对 1 2个样品进行 DNA随机扩增 ,获得清晰可重复的位点 99个 ,其中多态性位点 5 8个 ,占 5 8.89% ;在部分样品中检出了特异性 RAPD标记 1 9个 ,占 1 9.1 9% ;通过样品间遗传相似性系数比较与 UPGMA聚类分析 ,并根据历史事实可知 ,广西沙田柚、梅州金柚为沙田柚的无性繁殖系 ,软枝系沙田柚、沙田柚早熟单株为沙田柚的芽变后代 ,梅花早柚、菊花心沙田柚、冬瓜圈沙田柚、段氏柚、垫江沙田柚、古老钱沙田柚为沙田柚的实生变异品系。     

Amplified Fragment Length Polymorphism (AFLP) Provides Molecular Markers for the Identification of Caladium bicolor Cultivars

Caladiums are popular ornamental plants that have not been wellstudied at the molecular level. Identification of species withinthe genus Caladium (Araceae) has been based primarily on morphology.However, the lack of comprehensive references makes identificationof Caladium cultivars extremely difficult. Amplified fragmentlength polymorphism (AFLP) analysis using 17 primer combinationswas carried out on two species of Caladium (C. bicolor and C.schomburgkii), including six cultivars of C. bicolor. Resultsshowed that AFLP can be used to distinguish these two speciesby their unique and different banding patterns. Unweighted PairGroup Method using Arithmetic Averages (UPGMA) permitted clusteranalysis of data from 17 selected primer combinations on sixcultivars of C. bicolor and one cultivar ofC. schomburgkii .It showed that closely related species can clearly be differentiatedand that genetic difference between cultivars can also be established.Unique AFLP molecular markers were detected for all the C. bicolorcultivars used. The use of AFLP has potential for preciselycharacterizing and identifying particular caladium cultivarsas well as for the registration of new cultivars. It will alsobe useful in future breeding programmes and systematics studies.Copyright 1999 Annals of Botany Company Araceae, Caladium species and cultivars, AFLP DNA fingerprinting, diversity, AFLP markers.     

桃儿七传粉生物学特性及其在进化上的意义

对分布于云南中甸县不同居群的桃儿七进行了传粉生物学特性研究,结果如下：（１）首次发现其具有一种适应于自花授粉的传粉机制。即在花尚未开放或刚开放时,雌蕊呈直立状,而一旦花完全开放时,子房柄会发生弯曲,以致整个雌蕊靠向某一花药,从而使柱头与花药贴合实现传粉;当完成传粉后,雌蕊又重新直立,此时受精作用也随之完成。整个传粉、受精过程仅需４￣６ｈ。（２）其生殖节律快,有效率高。从孢子母细胞减数分裂开始到双受     

Directed Transfer of Large DNA Fragments between Streptomyces Species

The biosynthesis of complex natural products in bacteria is invariably encoded within large gene clusters. Although this facilitates the cloning of such gene clusters, their heterologous expression in genetically amenable hosts remains a challenging problem, principally due to the difficulties associated with manipulating large DNA fragments. Here we describe a new method for the directed transfer of a gene cluster from one Streptomyces species to another. The method takes advantage of tra gene-mediated conjugal transfer of chromosomal DNA between actinomycetes. As proof of principle, we demonstrate transfer of the entire ~22-kb actinorhodin gene cluster, and also the high-frequency cotransfer of two loci that are 150 to 200 kb apart, from Streptomyces coelicolor to an engineered derivative of Streptomyces lividans.