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Widespread stop-codon recoding in bacteriophages may regulate translation of lytic genes
Adair L Borges1,2, Yue Clare Lou1,3, Rohan Sachdeva1,4
1Innovative Genomics Institute, University of California, Berkeley, CA, USA.
Nature Microbiology
|May 26, 2022
Summary
Bacteriophages (viruses that infect bacteria) can alter their genetic code by reassigning stop codons. This genetic adaptation is common in gut phages and may prevent premature protein production.
Area of Science:
- Microbiology
- Genetics
- Virology
Background:
- Bacteriophages (phages) rely on host bacterial translation machinery.
- Some phages exhibit alternative genetic codes with reassigned stop codons, potentially disrupting bacterial translation.
- The prevalence and function of stop-codon recoding in phages are not fully understood.
Purpose of the Study:
- To investigate the occurrence and distribution of stop-codon recoding across diverse phage lineages.
- To explore the potential functional implications of stop-codon recoding in phage biology.
- To understand the evolutionary dynamics of stop-codon recoding in phages.
Main Methods:
- Genome-wide analysis of 9,422 phage genomes.
- Identification and characterization of stop-codon reassignment events.
- Comparative genomics to assess the distribution and over-representation of recoded stop codons in specific gene categories.
Main Results:
- Stop-codon recoding has evolved independently in various phage clades infecting gut bacteria.
- Recoded stop codons are significantly enriched in phage structural and lysis genes.
- Evidence suggests stop-codon recoding can evolve rapidly within closely related phage lineages.
Conclusions:
- Stop-codon recoding is a recurrent adaptive strategy in bacteriophages.
- This genetic innovation may serve to regulate viral protein synthesis, preventing premature production of late-stage proteins.
- The rapid evolution of recoded stop codons highlights their adaptive significance on short evolutionary timescales.
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