SPOT-Seq-RNA: Predicting protein-RNA complex structure and RNA-binding function by fold recognition and binding affinity prediction

RNA-binding proteins (RBPs) play key roles in RNA metabolism and post-transcriptional regulation. Computational methods have been developed separately for prediction of RBPs and RNA-binding residues by machine-learning techniques and prediction of protein-RNA complex structures by rigid or semiflexible structure-to-structure docking. Here, we describe a template-based technique called SPOT-Seq-RNA that integrates prediction of RBPs, RNA-binding residues, and protein-RNA complex structures into a single package. This integration is achieved by combining template-based structure-prediction software, SPARKS X, with binding affinity prediction software, DRNA. This tool yields reasonable sensitivity (46 %) and high precision (84 %) for an independent test set of 215 RBPs and 5,766 non-RBPs. SPOT-Seq-RNA is computationally efficient for genome-scale prediction of RBPs and protein-RNA complex structures. Its application to human genome study has revealed a similar sensitivity and ability to uncover hundreds of novel RBPs beyond simple homology. The online server and downloadable version of SPOT-Seq-RNA are available at http://sparks-lab.org/server/SPOT-Seq-RNA/

THUMP from archaeal tRNA:m(2)(2)G10 methyltransferase, a genuine autonomously folding domain

The tRNA:m(2)(2)G10 methyltransferase of Pyrococus abyssi (PAB1283, a member of COG1041) catalyzes the N(2),N(2)-dimethylation of guanosine at position 10 in tRNA. Boundaries of its THUMP (THioUridine synthases, RNA Methyltransferases and Pseudo-uridine synthases)—containing N-terminal domain [1–152] and C-terminal catalytic domain [157–329] were assessed by trypsin limited proteolysis. An inter-domain flexible region of at least six residues was revealed. The N-terminal domain was then produced as a standalone protein (THUMPα) and further characterized. This autonomously folded unit exhibits very low affinity for tRNA. Using protein fold-recognition (FR) methods, we identified the similarity between THUMPα and a putative RNA-recognition module observed in the crystal structure of another THUMP-containing protein (ThiI thiolase of Bacillus anthracis). A comparative model of THUMPα structure was generated, which fulfills experimentally defined restraints, i.e. chemical modification of surface exposed residues assessed by mass spectrometry, and identification of an intramolecular disulfide bridge. A model of the whole PAB1283 enzyme docked onto its tRNA(Asp) substrate suggests that the THUMP module specifically takes support on the co-axially stacked helices of T-arm and acceptor stem of tRNA and, together with the catalytic domain, screw-clamp structured tRNA. We propose that this mode of interactions may be common to other THUMP-containing enzymes that specifically modify nucleotides in the 3D-core of tRNA

Ochrona środowiska w edukacji

In this report we point out the requirement of local communities for environmental education of society that results from accession of Poland to the project titled „Decade for Sustainable Development 2005-2014”. The paper includes results of the surveys carried out among students, teachers and officers of communes that reveal the role of environmental education in schools, communes and universities. The results demonstrate that environmental education should become connected with actions in aid of both natural and social local environments.W pracy wskazano na zapotrzebowanie środowiska lokalnego na edukację środowiskową społeczeństwa, wynikające z przystąpienia Polski do udziału w projekcie Dekada Edukacji dla Zrównoważonego Rozwoju 2005-2014. Praca zawiera wyniki badań ankietowych studentów, nauczycieli i pracowników gmin wskazujące miejsce i rolę edukacji środowiskowej w szkole, gminie oraz na studiach przyrodniczych i pedagogicznych. Wyniki świadczą o konieczności zbliżenia trendów kształcenia przyrodniczego do praktycznych działań na rzecz lokalnego środowiska przyrodniczego i społecznego