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

Proc Natl Acad Sci U S A. 2014 Jul 22;111(29):10520-5. doi: 10.1073/pnas.1411267111. Epub 2014 Jul 7.

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 (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.

Keywords: aminoacyl-tRNA; methanogen; protein complex.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Acetylation
  • Archaea / metabolism*
  • Archaeal Proteins / chemistry
  • Archaeal Proteins / metabolism*
  • Conserved Sequence
  • Crystallography, X-Ray
  • Cysteine / biosynthesis*
  • Kinetics
  • Methanococcus / metabolism*
  • Models, Molecular
  • Peptide Initiation Factors / chemistry
  • Peptide Initiation Factors / metabolism*
  • Protein Binding
  • Protein Structure, Tertiary
  • RNA, Transfer, Cys / chemistry
  • RNA, Transfer, Cys / metabolism*

Substances

  • Archaeal Proteins
  • Peptide Initiation Factors
  • RNA, Transfer, Cys
  • Cysteine

Associated data

  • PDB/3WKR
  • PDB/3WKS