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

• Published in: Proceedings of the National Academy of Sciences - PNAS Vol. 111; no. 29; pp. 10520 - 10525
• Main Authors: Liu, Yuchen, Nakamura, Akiyoshi, Nakazawa, Yuto, Asano, Nozomi, Ford, Kara A., Hohn, Michael J., Tanaka, Isao, Yao, Min, Söll, Dieter
• Format: Journal Article
• Language: English
• Published: United States National Academy of Sciences 22-07-2014; National Acad Sciences
• Subjects: Acetylation; Amino acids; Archaea; Archaea - metabolism; Archaeal Proteins - chemistry; Archaeal Proteins - metabolism; Biological Sciences; Biosynthesis; Conserved Sequence; Crystal structure; Crystallography, X-Ray; Cysteine - biosynthesis; Enzymes; Evolution; Gels; Kinetics; Methanococcus - metabolism; Methanogens; Models, Molecular; Peptide Initiation Factors - chemistry; Peptide Initiation Factors - metabolism; Phylogenetics; Protein Binding; Protein Structure, Tertiary; Ribonucleic acid; RNA; RNA, Transfer, Cys - chemistry; RNA, Transfer, Cys - metabolism; Sulfur; Transfer RNA; protein complex; aminoacyl-tRNA; methanogen
• ISSN: 0027-8424; 1091-6490
• DOI: 10.1073/pnas.1411267111

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 (SepCysS). 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 Cys causing a 14-fold increase in the initial rate of Cys-tRNA Cys formation. Based on our crystal structure (2.8-Å resolution) of a SepCysS·SepCysE complex, a SepRS·SepCysE·SepCysS 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.