RNA-sequence-structure properties and selenocysteine insertion Rolf Backofen
Ludwig Maximilian University, Germany
Selenocysteine (Sec) is a recently discovered 21st amino acid. Selenocysteine is encoded by the nucleotide triplet UGA, which is usually interpreted as a STOP signal. The insertion of selenocysteine requires an additional signal in form of a SECIS-element (Selenocysteine Insertion Sequence). This is an mRNA-motif, which is defined by both sequence-related and structure-related properties.
The bioinformatics problem of interest is to design new selenoproteins (i.e., proteins containing selenocysteine), since seleno variants of proteins are very useful in the structure analysis. The SECIS-element is in the region of the mRNA that is translated into the amino acid sequence. Hence, changes on the level of mRNA made in order to generate a SECIS-element will also modify the amino acid sequence. Thus, one searches for an mRNA that is maximal similar on both levels, and satisfies the constraints imposed by the structure.
We will show that this problem can be solved efficiently (though the problem is NP-complete if arbitrary structural constraints are allowed), given a description of the SECIS-element. We will then discuss various approaches to generate a description of the SECIS-element (and its diversity) based on the available data.