Evidence map›Paper›PMID 41196353›Full record

ArticleProceedings of the National Academy of Sciences of the United States of America2025

Methanogenic archaea encoding Pyrrolysine maintain ambiguous amber codon usage.

Katie E Shalvarjian, Grayson L Chadwick, Paloma I Pérez, Philip H Woods, Victoria J Orphan, Dipti D Nayak

Abstract read
In one paragraph

Article in Proceedings of the National Academy of Sciences of the United States of America, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.

0numbers the graph read from it
0cells of the map it votes in
5citing papers in PubMed
–field-weighted citation impact
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

5 citing papers in PubMed.

  1. Article
  2. Article
  3. Article
  4. Article
  5. 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.

Katie E ShalvarjianDepartment of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720.ORCID 0000-0002-4792-8477
Grayson L ChadwickDepartment of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720.ORCID 0000-0003-0700-9350
Paloma I PérezDepartment of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720.ORCID 0000-0003-4802-3538
Philip H WoodsDivision of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125.ORCID 0000-0003-1673-8096
Victoria J OrphanDivision of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125.ORCID 0000-0002-5374-6178
Dipti D NayakDepartment of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720.ORCID 0000-0002-3449-3419

Funding

Adolph C. and Mary Sprague Miller Institute for Basic Research in Science, University of California Berkeley (MIBRS) NAAlfred P. Sloan Foundation (APSF) NAArnold and Mabel Beckman Foundation (AMBF) NAChan Zuckerberg Initiative (CZI) NADavid and Lucile Packard Foundation (PF) NADOE | SC | Basic Energy Sciences (BES) S589706NSF | NSF Graduate Research Fellowship Program (GRFP) Fellow ID: 202299857Simons Foundation (SF) NA
6 · The paper itself

Abstract

Natural genetic code expansion is a phenomenon wherein an additional amino acid is encoded by a stop codon. These nonstandard amino acids are beneficial as they facilitate novel biochemical reactions. However, code expansion leads to ambiguity at the recoded stop codon, which can either be read-through or terminated. Pyrrolysine (Pyl) is encoded by the amber codon (TAG/UAG) and is widespread in archaea, where it is required for methylamine-mediated methanogenesis, an environmentally important metabolism. Mechanisms to conditionally suppress the amber stop codon for Pyl installation during protein synthesis have not been identified. In the model methanogen,

Indexed as

Codon, TerminatorLysineMethanosarcinaGenetic CodeMethaneProtein BiosynthesisCodon, TerminatorLysineMethanepyrrolysinearchaeagenetic codemethanogenPyrrolysine

Identifiers

PMID41196353
PMCPMC12626013

What Socratic holds

Textmetadata
LicenceCC BY-NC-ND
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 Socratic graph.