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MgCod: Gene Prediction in Phage Genomes with Multiple Genetic Codes.

Aaron Pfennig1, Alexandre Lomsadze2, Mark Borodovsky3

  • 1School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA.

Journal of Molecular Biology
|May 27, 2023
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Summary
This summary is machine-generated.

A new tool, MgCod, identifies viral genomes with unusual stop codon recoding. This discovery reveals dual-coding genes in phages, potentially impacting protein translation and gene expression during infection cycles.

Keywords:
crAssphagesgene predictionmetagenomesmultiple genetic codesstop codon recoding

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Area of Science:

  • Microbiology
  • Bioinformatics
  • Genomics

Background:

  • Massive sequencing has revealed numerous phage genomes with intermittent stop codon recoding.
  • Understanding these recoding events is crucial for deciphering viral genetic information.

Purpose of the Study:

  • To develop a computational tool for identifying genomic regions with distinct stop codon recoding.
  • To analyze viral contigs from human metagenomic data for stop codon recoding patterns.

Main Methods:

  • Development of the MgCod computational tool for simultaneous gene prediction and stop codon recoding identification.
  • Scanning of human metagenomic contigs using MgCod.
  • Analysis of identified viral contigs, including crAssphages.

Main Results:

  • Hundreds of viral contigs with intermittent stop codon recoding were identified in human metagenomic data.
  • Many identified contigs originated from crAssphage genomes.
  • Dual-coding genes, capable of alternative translation, were found clustered in blocks and enriched in early-stage phage genes, contrasting with single-coding late-stage genes.

Conclusions:

  • MgCod effectively identifies stop codon recoding types in novel genomic sequences alongside gene prediction.
  • Intermittent stop codon recoding in phages is linked to distinct gene organization patterns, specifically single-coding and dual-coding strategies.
  • The differential distribution of dual-coded (early-stage) and single-coded (late-stage) genes suggests a role in phage life cycle regulation.