Selenocysteine insertion into archaeal selenopolypeptides is directed through an mRNA structure (the SECIS element) situated in the 3' non-translated region like in eukaryotes. To elucidate the mechanism how this element affects decoding of an in-frame UGA with selenocysteine the open reading frames of the genome of Methanococcus jannaschii were searched for the existence of a homolog to the bacterial specialized translation factor Selb. The product of the open reading frame MJ0495 was identified as the archaeal Selb homolog on the basis of the following characteristics: (1) MJ0495 possesses sequence features characteristic of bacterial Selb; (2) purified MJ0495 displays guanine nucleotide binding properties like Selb; and (3) it preferentially binds selenocysteyl-tRNA(Sec). In contrast to bacterial Selb, however, no binding of MJ0495 protein to the SECIS element of the mRNA was found under the experimental conditions employed which correlates with the fact that MJ0495 lacks the C-terminal domain of the bacterial Selb protein known to bind the SECIS element. It is speculated that in Archaea the functions of bacterial Selb are distributed over at least two proteins, one, serving as the specific translation factor, like MJ0495, and another one, binding to the SECTS which interacts with the ribosorne and primes it to decode UGA. (C) 2000 Academic Press.