Two distinct SECIS structures capable of directing selenocysteine incorporation in eukaryotes

Translation of UGA as selenocysteine requires specific RNA secondary struct ures in the mRNAs of selenoproteins. These elements differ in sequence, str ucture, and location in the mRNA, that is, coding versus 3' untranslated re gion, in prokaryotes, eukaryotes, and archaea. Analyses of eukaryotic selen ocysteine insertion Sequence (SECIS) elements via computer folding programs , mutagenesis studies, and chemical and enzymatic probing has led to the de rivation of a predicted consensus structural model for these elements. This model consists of a stem-loop or hairpin, with conserved nucleotides in th e loop and in a non-Watson-Crick motif at the base of the stem. However, th e sequences of a number of SECIS elements predict that they would diverge f rom the consensus structure in the loop region. Using site-directed mutagen esis to introduce mutations predicted to either disrupt or restore structur e, or to manipulate loop size or stem length, we show that eukaryotic SECIS elements fall into two distinct classes, termed forms 1 and 2. Form 2 elem ents have additional secondary structures not present in form 1 elements. B y either insertion or deletion of the sequences and structures distinguishi ng the two classes of elements while maintaining appropriate loop size, con version of a form 1 element to a functional form P-like element and of a fo rm 2 to a functional form 1-like element was achieved. These results sugges t commonality of function of the two classes. The information obtained rega rding the existence of two classes of SECIS elements and the tolerances for manipulations of stem length and loop size should facilitate designing RNA molecules for obtaining high-resolution structural information about these elements.