Functional Dynamics Revealed by the Structure of the SufBCD Complex,a Novel ATP-binding Cassette (ABC) Protein That Serves as a Scaffold for Iron-Sulfur Cluster Biogenesis

ATP-binding cassette (ABC)-type ATPases are chemomechanical engines involved in diverse biological pathways. Recent genomic information reveals that ABC ATPase domains/subunits act not only in ABC transporters and structural maintenance of chromosome proteins, but also in iron-sulfur (Fe-S) cluster biogenesis. A novel type of ABC protein, the SufBCD complex, functions in the biosynthesis of nascent Fe-S clusters in almost all Eubacteria and Archaea, as well as eukaryotic chloroplasts. In this study, we determined the first crystal structure of the Escherichia coli SufBCD complex, which exhibits the common architecture of ABC proteins: two ABC ATPase components (SufC) with function-specific components (SufB-SufD protomers). Biochemical and physiological analyses based on this structure provided critical insights into Fe-S cluster assembly and revealed a dynamic conformational change driven by ABC ATPase activity. We propose a molecular mechanism for the biogenesis of the Fe-S cluster in the SufBCD complex.     

New chemotypes for cathepsin K inhibitors

Cyano pyrimidine acetylene and cyano pyrimidine t-amine, which belong to a new chemical class, were prepared and tested for inhibitory activities against cathepsin K and the highly homologous cathepsins L and S. The use of novel chemotypes in the development of cathepsin K inhibitors has been demonstrated by derivatives of compounds 1 and 8.     

Quantification of Chloroflexi Eikelboom morphotype 1851 for prediction and control of bulking events in municipal activated sludge plants in Japan

The dominant filamentous bacteria associated with bulking incidents in Japanese activated sludge plants with nutrient removal were identified and their quantitative correlations with sludge settleability were assessed, with the aim of controlling bulking incidents by specifically suppressing bacterial growth. Fluorescence in situ hybridization (FISH) analyses using existing oligonucleotide FISH probes indicated that the presence of Eikelboom type 1851 filamentous bacteria belonging to the phylum Chloroflexi is correlated with biomass settleability in the municipal wastewater treatment plants examined. Real-time quantitative PCR (qPCR) assays developed in this study also showed a linear correlation between type 1851 filament members and sludge settleability, with the exception of some winter samples. The real-time qPCR assays and 16S ribosomal RNA gene amplicon sequencing to reveal the microbial community of activated sludge showed that the abundance of type 1851 at 200 mL g⁻¹ of sludge volume index was estimated to be about 1.9% of the total microbial cells. The abundance of type 1851 served as a bulking indicator in plants where type 1851 was dominant.

     

水稻纹枯病菌营养及寄主资源生态位

由于IPM概念的局限性,有害生物生态调控（EPM）理论和方法的提出发展了IPM,生态位原则是有害生物生态调控（EPM）的重要原则之一,生态位研究为EPM的具体实施提供了依据。应用可持续农业和EPM理论及生态位理论研究了水稻纹枯病的生态位,分析了水稻纹枯病菌氮肥营养生态位和寄主品种资源生态位,结果表明：以相对侵染效率作为指标,在水稻不同生育期,纹枯病的氮肥营养生态位宽度不同,其中以孕穗期的生态位宽度最小,为0.6979,拔节期、抽穗期、灌浆期和乳熟期的生态位宽度分别是0.9741,0.8884,0.7974和0.9815,表明水稻纹枯病在水稻不同生育阶段利用氮肥的效能不同。寄主品种资源生态位宽度在拔节期、孕穗期、抽穗期、乳熟期分别为0.9348,0.7677,0.8875和0.9962。以病情指数为指标,氮肥营养生态位宽度在拔节期、孕穗期、抽穗期、灌浆期和乳熟期分别为0.9379,0.9696,0.6775,0.6729和0.7691。其氮肥营养生态位宽度在拔节期与孕穗期最大,生态位宽度指数接近于1。寄主品种资源生态位宽度在各生育期均接近1,表明寄主品种资源生态位宽度在各生育期是相似的,即说明水长期稻纹枯病菌利用品种资源各状态的选择和利用效能是相似的。     

Purification of Clostridium perfringens enterotoxins by high performance liquid chromatography

Abstract Treatment of Saccharomyces cerevisiae a cells with α-factor partially inhibits mannosylation of the high M _r mannoproteins, although there is an increase in the total amount of these molecules present in the wall. They show a similar mobility in SDS-acrylamide gels to those from untreated mnn2 cells. No other significant effects on wall mannoproteins have been observed, except a decrease in the amount of the 29 kDa species.     

Competition for growth substrates in river water between Escherichia coli and indigenous bacteria illustrated by high-resolution mass spectrometry

Escherichia coli normally cannot grow in the environment. One environmental stress that prevents E. coli growth may be the competition for growth substrates with co-existing micro-organisms. In this study, the growth substrates of E. coli were screened by high-resolution mass spectrometry and compared with those of indigenous bacteria in river water. In an incubation experiment, E. coli multiplied in sterilized river water, but did not multiply when indigenous micro-organisms were present in the water. By analysing dissolved organic matter in the river water before and after E. coli growth, 35 compounds were identified as putative growth substrates of E. coli. Among them, 33 compounds were also identified as putative growth substrates of indigenous bacteria. These results indicate that E. coli and indigenous bacteria compete for organic substrates in river water, which could suppress the growth of E. coli.     

Triazoyl–phenyl linker system enhancing the aqueous solubility of a molecular probe and its efficiency in affinity labeling of a target protein for jasmonate glucoside

In methods employing molecular probes to explore the targets of bioactive small molecules, long or rigid linker moieties are thought to be critical factors for efficient tagging of target protein. We previously reported the synthesis of a jasmonate glucoside probe with a highly rigid linker consisting of a triazoyl–phenyl (TAzP) moiety, and this probe demonstrated effective target tagging. Here we compare the TAzP probe with other rigid or flexible probes with respect to target tagging efficiency, hydrophobic parameters, aqueous solubility, and dihedral angles around the biaryl linkage by a combination of empirical and calculation methods. The rigid biaryl linkage of the TAzP probe has a skewed conformation that influences its aqueous solubility. Such features that include rigidness and good aqueous solubility resulted in highly efficient target tagging. These findings provide a promising guideline toward designing of better linkers for improving molecular probe performance.     

Sunstruck Flavor of Rice Vinegar

It was found that the precursor of the sunstruck flavor was formed in the course of maturing sake cake. A large quantity of yeasts in the sake cake was autolysed and VB₂ was evolved. Like the sunstruck flavor of milk reported by Patton et al. it is thought that, VB₂, a photochemical sensitization substance caused methionine to react photochemically and to evolve the sunstruck flavor 3-(methylthio)-propanal (methional). Organoleptically, vinegar with added methional an vinegar which had evolved the sunstruck flavor had the same odor.     

Characterization of monooxygenase gene diversity in benzene‐amended soils

Aim: To understand soil benzene monooxygenase gene diversity by clone library construction and microarray profiling. Methods and Results: A primer set was designed, and benzene monooxygenase gene diversity was characterized in two benzene‐amended soils. The dominant sequence types in the clone libraries were distinct between the two soils, and both sequences were assigned to novel clusters. Monooxygenase gene richness and diversity increased after benzene degradation. Oligonucleotide probes for microarray analysis were designed to detect a number of sequenced clones and reported monooxygenase genes. The microarray detected several genes that were not detected in the clone libraries of the same samples. Six probes were detected in more than one soil. Conclusions: The primer set designed in this study successfully detected diverse benzene monooxygenase genes. The level of diversity may have increased because the degradation of benzene differed from soil to soil. Microarrays have great potential in the comprehensive detection of gene richness as well as the elucidation of key genes for degradation. Significance and Impact of the Study: This study introduces a new primer set that may be used to identify diverse benzene monooxygenase genes in the environment; moreover, it demonstrates the potential of microarray technology in the profiling of environmental samples.     

Blood group activity of human sucrase from intestinal metaplasia.

Sucrases were purified from human small intestine and from areas of intestinal metaplasia of the stomach mucosa surrounding stomach cancers. The kinetic constants and pH activity profiles of enzyme preparations from the two sources were similar. No blood group activity of sucrase was detectable in preparations from three cases of intestinal metaplasia, but preparations from two other cases showed activity like that of the small intestine. These results indicate that sucrase from areas of intestinal metaplasia has similar enzymatic properties to those of enzyme from the small intestine, but that the antigenic sugar moiety of the enzyme associated with blood group activity varies.