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Site Specific Lysine Acetylation of Histones for Nucleosome Reconstitution using Genetic Code Expansion in Escherichia coli
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Methanogenic archaea encoding Pyrrolysine maintain ambiguous amber codon usage.

Katie E Shalvarjian1, Grayson L Chadwick2, Paloma I Pérez2

  • 1Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720.

Proceedings of the National Academy of Sciences of the United States of America
|November 6, 2025
PubMed
Summary
This summary is machine-generated.

Genetic code expansion allows pyrrolysine (Pyl) to be encoded by stop codons in archaea. Researchers found that in Methanosarcina acetivorans, the UAG codon dual-encodes stop and Pyl, regulated by cellular demand.

Keywords:
Pyrrolysinearchaeagenetic codemethanogen

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Area of Science:

  • Molecular Biology
  • Biochemistry
  • Genetics

Background:

  • Genetic code expansion introduces nonstandard amino acids by reassigning stop codons.
  • Pyrrolysine (Pyl) is a nonstandard amino acid essential for methanogenesis in some archaea, encoded by the amber stop codon (UAG).
  • Mechanisms for conditional stop codon suppression for Pyl incorporation remain largely unknown.

Purpose of the Study:

  • To investigate the mechanisms of pyrrolysine (Pyl) incorporation during protein synthesis in the archaeon Methanosarcina acetivorans.
  • To understand how the amber stop codon (UAG) is conditionally suppressed for Pyl encoding.
  • To explore the regulation of Pyl biosynthesis and incorporation genes in response to cellular needs.

Main Methods:

  • Utilized Methanosarcina acetivorans as a model organism.
  • Investigated gene expression related to Pyl biosynthesis and incorporation.
  • Analyzed the dual decoding of the UAG codon as both a stop signal and a Pyl codon.

Main Results:

  • Demonstrated that the UAG codon functions dually, serving as both a stop codon and encoding pyrrolysine (Pyl) in M. acetivorans.
  • Observed that the expression of Pyl-related genes is regulated in accordance with the cellular demand for Pyl.
  • Provided evidence for a regulatory mechanism that manages ambiguous stop codon decoding.

Conclusions:

  • The amber stop codon (UAG) exhibits context-dependent dual meaning in M. acetivorans, enabling pyrrolysine incorporation.
  • Gene expression tuning allows archaea to manage ambiguous stop codon decoding based on environmental cues and cellular requirements.
  • This regulatory strategy is crucial for efficient methanogenesis and adaptation in environments where Pyl is essential.