DFG-Projekt: Schwerpunktprogramm Selenproteine – Biochemische Grundlagen und klinische Bedeutung – SPP 1087 Projekt: Algorithmic determination of whether a protein’s cysteine residue can be replaced by selenocysteine by silent/similar pointwise mutagenesis in DANN/RNA

The 21st amino-acid selenocysteine is encoded by UGA, a codon that usually terminates the translation of the mRNA by the ribosome. The cotranslational insertion of selenocysteine in bacterial selenoproteins requires a special mRNA element (called SECIS, Selenocysteine Insertion Sequence) after the UGA codon. A problem that remains of active research interest is the characterization of the SECIS-element. A conserved pattern can be described for the natural SECIS-elements in E.coli. For the Gram positive anaerobe E.acidaminophilum that has at least 6 selenoproteins of different functions, no conserved pattern has been found for the corresponding SECIS-elements so far. In this project, a unique approach to characterize SECIS-elements of E.acidaminophilum will be applied by throughly combining bioinformatics methods and corresponding biological experiments. Using a SELEX method, mRNA sequences will be generated that bind to SelB. These sequences will be combined into a consensus motif using bioinformatics methods. This motif can be used in a computer program that allows to assign for any mRNA sequence the probability of being a SECIS-element. To validate the motif found, high scoring RNA sequence will be tested for their capability of binding to SelB, using again SELEX methods.

contact person: Prof. Dr. Rolf Backofen
Email: backofen@informatik.uni-freiburg.de

Start of project: 2002
End of project: 2005

Albert-Ludwigs-University Freiburg
Prof. Dr. Rolf Backofen
Bioinformatik
Prof. Dr. Rolf Backofen
Georges-Köhler-Allee 106
79110 Freiburg
Germany

Phone: +49 (0) 761-203-7461
Fax: +49 (0) 761-203-7462
Email: backofen@informatik.uni-freiburg.de
http://www.bioinf.uni-freiburg.de
Actual Research Report

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DFG-Projekt