Evidence map›Paper›PMID 25002468›Full record

ArticleProceedings of the National Academy of Sciences of the United States of America2014

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

Yuchen Liu, Akiyoshi Nakamura, Yuto Nakazawa, Nozomi Asano, Kara A Ford, Michael J Hohn, Isao Tanaka, Min Yao, Dieter Söll

Open access · bronzeAbstract read
In one paragraph

Article in Proceedings of the National Academy of Sciences of the United States of America, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.

0numbers the graph read from it
0cells of the map it votes in
12citing papers in PubMed
1.0field-weighted citation impact, top 25% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

12 citing papers in PubMed, 19 citations in OpenAlex.

  1. Crystallographic analysis of the Escherichia coli tRNA seleno-modification enzyme in complex with tRNA.Acta crystallographica. Section F, Structural biology communications · 2025
    Article
  2. Review
  3. Article
  4. Article
  5. Unconventional genetic code systems in archaea.Frontiers in microbiology · 2022
    Review
  6. Article
  7. Article
  8. Why Selenocysteine Is Unique?Frontiers in molecular biosciences · 2020
    Article
  9. Article
  10. Article
  11. Crystallographic analysis of a subcomplex of the transsulfursome with tRNA for Cys-tRNA(Cys) synthesis.Acta crystallographica. Section F, Structural biology communications · 2016
    Article
  12. Structure of the Pseudomonas aeruginosa transamidosome reveals unique aspects of bacterial tRNA-dependent asparagine biosynthesis.Proceedings of the National Academy of Sciences of the United States of America · 2015
    Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

9 authors at 3 institutions in 2 countries.

Yuchen LiuDepartments of Molecular Biophysics and Biochemistry and.
Akiyoshi NakamuraDepartments of Molecular Biophysics and Biochemistry andFaculty of Advanced Life Science and.
Yuto NakazawaGraduate School of Life Sciences, Hokkaido University, Sapporo 060-0810, Japan.
Nozomi AsanoGraduate School of Life Sciences, Hokkaido University, Sapporo 060-0810, Japan.
Kara A FordDepartments of Molecular Biophysics and Biochemistry and.
Michael J HohnDepartments of Molecular Biophysics and Biochemistry and.
Isao TanakaFaculty of Advanced Life Science and.
Min YaoFaculty of Advanced Life Science andGraduate School of Life Sciences, Hokkaido University, Sapporo 060-0810, Japan dieter.soll@yale.edu yao@castor.sci.hokudai.ac.jp.
Dieter SöllDepartments of Molecular Biophysics and Biochemistry andChemistry, Yale University, New Haven, CT 06520; and dieter.soll@yale.edu yao@castor.sci.hokudai.ac.jp.
Advanced Life Science Institute · JPHokkaido University · JPYale University · US

Funding

TRANSFER RNAR01GM022854 · NIGMS · YALE UNIVERSITY · PI SOLL, DIETER · 1985 to 2016
$21.3M
TRANSFER RNAR37GM022854 · NIGMS · YALE UNIVERSITY · PI SOLL, DIETER G · 1991 to 2000
$786k
NIGMS NIH HHS GM22854NIGMS NIH HHS R01 GM022854NIGMS NIH HHS R37 GM022854
6 · The paper itself

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.

Indexed as

AcetylationArchaeaArchaeal ProteinsConserved SequenceCrystallography, X-RayCysteineKineticsMethanococcusModels, MolecularPeptide Initiation FactorsProtein BindingProtein Structure, TertiaryRNA, Transfer, CysArchaeal ProteinsCysteinePeptide Initiation FactorsRNA, Transfer, Cysaminoacyl-tRNAmethanogenprotein complex

Identifiers

PMID25002468
PMCPMC4115501
OpenAlexW2046853951

What OpenQuestion holds

Textmetadata
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.