Ancient translation factor is essential for tRNA-dependent cysteine biosynthesis in methanogenic archaea

Yuchen Liu, Akiyoshi Nakamura, Yuto Nakazawac, Nozomi Asanoc, Kara A. Forda, Michael J. Hohna, Isao Tanakab, Min Yao, and Dieter Söll

Departments of aMolecular Biophysics and Biochemistry and Chemistry, Yale University, New Haven, CT 06520.

Abstract

Methanogenic archaea lack cysteinyl-tRNA synthetase; they synthesize Cys-tRNA and cysteine in a tRNA-dependent manner. Two enzymes are required: Phosphoseryl-tRNA synthetase (SepRS) forms phosphoseryl-tRNA^Cys (Sep-tRNA^Cys), which is converted to Cys-tRNA^Cys by Sep-tRNA:Cys-tRNA synthase (SepCys). This represents the ancestral pathway of Cys biosynthesis and coding in archaea. Here we report a translation factor, SepCysE, essential for methanococcal Cys biosynthesis; its deletion in Methanococcus maripaludis causes Cys auxotrophy. SepCysE acts as a scaffold for SepRS and SepCysS to form a stable high-affinity complex for tRNA^Cyscausing a 14-fold increase in the initial rate of Cys-tRNACys formation. Based on our crystal structure (2.8-Å resolution) of a SepCysSSepCysE complex, a SepRSSepCysESepCysS structure model suggests that this ternary complex enables substrate channeling of Sep-tRNA^Cys. A phylogenetic analysis suggests coevolution of SepCysE with SepRS and SepCysS in the last universal common ancestral state. Our findings suggest that the tRNA-dependent Cys biosynthesis proceeds in a multienzyme complex without release of the intermediate and this mechanism may have facilitated the addition of Cys to the genetic code.

Keywords: methanogen aminoacyl-tRNA protein complex.