Small stable RNA maturation and turnover in Bacillus subtilis

Stable RNA maturation is a key process in the generation of functional RNAs, and failure to correctly process these RNAs can lead to their elimination through quality control mechanisms. Studies of the maturation pathways of ribosomal RNA and transfer RNA in Bacillus subtilis showed they were radically different from Escherichia coli and led to the identification of new B. subtilis‐specific enzymes. We noticed that, despite their important roles in translation, a number of B. subtilis small stable RNAs still did not have characterised maturation pathways, notably the tmRNA, involved in ribosome rescue, and the RNase P RNA, involved in tRNA maturation. Here, we show that tmRNA is matured by RNase P and RNase Z at its 5′ and 3′ extremities, respectively, whereas the RNase P RNA is matured on its 3′ side by RNase Y. Recent evidence that several RNases are not essential in B. subtilis prompted us to revisit maturation of the scRNA, a component of the signal recognition particle involved in co‐translational insertion of specific proteins into the membrane. We show that RNase Y is also involved in 3′ processing of scRNA. Lastly, we identified some of the enzymes involved in the turnover of these three stable RNAs.     

Proteome analysis for antifungal effects of Bacillus subtilis KB-1122 on Magnaporthe grisea P131

Rice blast, caused by Magnaporthe grisea threatens rice production worldwide. It is important to develop novel and environment-safe strategies to control the fungus. Here we reported that Bacillus subtilis KB-1122 could strikingly inhibit the growth of M. grisea P131 in agar diffusion assays. To further understand the molecular mechanism on the suppressive role of B. subtilis on M. grisea, the antagonist–pathogen interaction of the two strains was studied by using comparative proteome analysis in this report. The cellular and culture supernatant (CSN) proteins were prepared from co-culture and subjected to two-dimensional polyacrylamide gel electrophoresis. Proteome analysis revealed 33 cellular and 18 CSN proteins showing changes upon co-culture respectively. Importantly, down-regulated cellular proteins came from M. grisea, whereas up-regulated proteins derived from B. subtilis. Results suggested that glyceraldehyde-3-phosphate dehydrogenase and serine protein kinase might contribute to antifungal activity of B. subtilis KB-1122. Of CSN proteins identified, the endo-1,4-beta-glucanase (involved in degradation of polysaccharides) was up-regulated consistently at different times of incubation. This suggests that this enzyme plays an important role in the interaction between B. subtilis KB-1122 with M. grisea P131.     

PatternLab for proteomics: a tool for differential shotgun proteomics

Background  

A goal of proteomics is to distinguish between states of a biological system by identifying protein expression differences. Liu et al. demonstrated a method to perform semi-relative protein quantitation in shotgun proteomics data by correlating the number of tandem mass spectra obtained for each protein, or "spectral count", with its abundance in a mixture; however, two issues have remained open: how to normalize spectral counting data and how to efficiently pinpoint differences between profiles. Moreover, Chen et al. recently showed how to increase the number of identified proteins in shotgun proteomics by analyzing samples with different MS-compatible detergents while performing proteolytic digestion. The latter introduced new challenges as seen from the data analysis perspective, since replicate readings are not acquired.     

Review of the Macrophya regia group (Hymenoptera: Tenthredinidae) from China with the descriptions of two new species

The Macrophya regia group is reviewed and five species are recognized from China, among them two new species, M. acutiserrula Li, Liu & Wei sp. nov. and M. frontalis Li, Liu & Zhu sp. nov., and three known species, M. regia Forsius 1930 , M. maculoclypeatina Wei et al. 2003, and M. xiaoi Wei et al. 2003. A key to the Chinese species of the Macrophya regia group are provided.