Evidence map›Paper›PMID 22904325›Full record

ArticleThe Journal of biological chemistry2012

Biosynthesis of 4-thiouridine in tRNA in the methanogenic archaeon Methanococcus maripaludis.

Yuchen Liu, Xiang Zhu, Akiyoshi Nakamura, Ron Orlando, Dieter Söll, William B Whitman

Open access · hybridAbstract read
In one paragraph

Article in The Journal of biological chemistry, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.

0numbers the graph read from it
0cells of the map it votes in
36citing papers in PubMed
1.9field-weighted citation impact, top 15% 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

36 citing papers in PubMed, 57 citations in OpenAlex.

  1. Article
  2. Article
  3. Article
  4. Article
  5. Article
  6. Article
  7. Review
  8. Article
  9. Biosynthesis and Degradation of Sulfur Modifications in tRNAs.International journal of molecular sciences · 2021
    Review
  10. Review
  11. tRNA Modifications as a Readout of S and Fe-S Metabolism.Methods in molecular biology (Clifton, N.J.) · 2021
    Article
  12. Article
  13. Article
  14. Article
  15. Review
  16. Review
  17. Article
  18. Article
  19. Nonredox thiolation in tRNA occurring via sulfur activation by a [4Fe-4S] cluster.Proceedings of the National Academy of Sciences of the United States of America · 2017
    Article
  20. Biochemical and structural characterization of oxygen-sensitive 2-thiouridine synthesis catalyzed by an iron-sulfur protein TtuA.Proceedings of the National Academy of Sciences of the United States of America · 2017
    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

6 authors at 2 institutions in 1 country.

Yuchen LiuDepartment of Microbiology, University of Georgia, Athens, Georgia 30602, USA.
Xiang Zhu
Akiyoshi Nakamura
Ron Orlando
Dieter Söll
William B Whitman
University of Georgia · USYale University · US

Funding

TRANSFER RNAR01GM022854 · NIGMS · YALE UNIVERSITY · PI SOLL, DIETER · 1985 to 2016
$21.3M
ZINC DEFICIENCY &PROTEIN EXPRESSION IN RAT OLFACTORY BULBSP41RR018502 · NCRR · UNIVERSITY OF GEORGIA (UGA) · PI AZADI, PARASTOO · 2003 to 2011
$13.1M
TRANSFER RNAR37GM022854 · NIGMS · YALE UNIVERSITY · PI SOLL, DIETER G · 1991 to 2000
$786k
NCRR NIH HHS P41 RR018502NCRR NIH HHS P41-RR-018502NIGMS NIH HHS GM22854NIGMS NIH HHS R01 GM022854NIGMS NIH HHS R37 GM022854
6 · The paper itself

Abstract

4-Thiouridine (s(4)U) is a conserved modified nucleotide at position 8 of bacterial and archaeal tRNAs and plays a role in protecting cells from near-UV killing. Escherichia coli employs the following two enzymes for its synthesis: the cysteine desulfurase IscS, which forms a Cys persulfide enzyme adduct from free Cys; and ThiI, which adenylates U8 and transfers sulfur from IscS to form s(4)U. The C-terminal rhodanese-like domain (RLD) of ThiI is responsible for the sulfurtransferase activity. The mechanism of s(4)U biosynthesis in archaea is not known as many archaea lack cysteine desulfurase and an RLD of the putative ThiI. Using the methanogenic archaeon Methanococcus maripaludis, we show that deletion of ThiI (MMP1354) abolished the biosynthesis of s(4)U but not of thiamine. MMP1354 complements an Escherichia coli ΔthiI mutant for s(4)U formation, indicating that MMP1354 is sufficient for sulfur incorporation into s(4)U. In the absence of an RLD, MMP1354 uses Cys(265) and Cys(268) located in the PP-loop pyrophosphatase domain to generate persulfide and disulfide intermediates for sulfur transfer. In vitro assays suggest that S(2-) is a physiologically relevant sulfur donor for s(4)U formation catalyzed by MMP1354 (K(m) for Na(2)S is ∼1 mm). Thus, methanogenic archaea developed a strategy for sulfur incorporation into s(4)U that differs from bacteria; this may be an adaptation to life in sulfide-rich environments.

Indexed as

Amino Acid MotifsAmino Acid SequenceBacterial ProteinsCarbon-Sulfur LyasesChromatography, High Pressure LiquidEscherichia coliGenetic Complementation TestMethanococcusModels, BiologicalPeptide FragmentsProtein Structure, TertiaryRNA, ArchaealRNA, TransferSulfidesSulfurtransferasesThiouridineBacterial ProteinsCarbon-Sulfur Lyasescysteine desulfurasePeptide FragmentspersulfidesRNA, ArchaealRNA, TransferSulfidesSulfurtransferasesThiI protein, bacteriaThiouridine

Identifiers

PMID22904325
PMCPMC3481272
OpenAlexW1966709195

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.