Genome modularization reveals overlapped gene topology is necessary for efficient viral reproduction

Bradley W. Wright, Juanfang Ruan, Mark P. Molloy*, Paul R. Jaschke

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

Abstract

Sequence overlap between two genes is common across all genomes, with viruses having high proportions of these gene overlaps. Genome modularization and refactoring is the process of disrupting natural gene overlaps to separate coding sequences to enable their individual manipulation. The biological function and fitness effects of gene overlaps are not fully understood, and their effects on gene cluster and genome-level refactoring are unknown. The bacteriophage φX174 genome has ∼26% of nucleotides involved in encoding more than one gene. In this study we use an engineered φX174 phage containing a genome with all gene overlaps removed to show that gene overlap is critical to maintaining optimal viral fecundity. Through detailed phenotypic measurements we reveal that genome modularization in φX174 causes virion replication, stability, and attachment deficiencies. Quantitation of the complete phage proteome across an infection cycle reveals 30% of proteins display abnormal expression patterns. Taken together, we have for the first time comprehensively demonstrated that gene modularization severely perturbs the coordinated functioning of a bacteriophage replication cycle. This work highlights the biological importance of gene overlap in natural genomes and that reducing gene overlap disruption should be an integral part of future genome engineering projects.

Original languageEnglish
Pages (from-to)3079-3090
Number of pages12
JournalACS Synthetic Biology
Volume9
Issue number11
DOIs
Publication statusPublished - 20 Nov 2020

Keywords

  • Bacteriophage
  • Genome engineering
  • Proteomics
  • Refactoring
  • Synthetic biology
  • Virus structure

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