Genome Modularization Reveals Overlapped Gene Topology Is Necessary for Efficient Viral Reproduction.

  title={Genome Modularization Reveals Overlapped Gene Topology Is Necessary for Efficient Viral Reproduction.},
  author={Bradley W. Wright and Juanfang Ruan and Mark P. Molloy and Paul R. Jaschke},
  journal={ACS synthetic biology},
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… 

Overlapping genes in natural and engineered genomes

This Review highlights exciting new uses for sequence overlap to control translation, compress synthetic genetic constructs, and protect against mutation.

Creating De Novo Overlapped Genes

This chapter provides a workflow for utilising CAMEOS to create synthetic overlaps between two genes, one essential (infA) and one non-essential (aroB), to protect the non- essential gene from mutation and loss of protein function.

Proteomic and transcriptomic analysis of Microviridae φXI74 infection reveals broad up-regulation of host membrane damage and heat shock responses

The proteomic and transcriptomic pathways differentially regulated during the φX174 infection cycle are revealed, and a coordinated cellular response to membrane damage that results in increased lipoprotein processing and membrane trafficking, likely due to the phage antibiotic-like lysis protein.

Plaque Size Tool: an automated plaque analysis tool for simplifying and standardising bacteriophage plaque morphology measurements

An automated command-line application called Plaque Size Tool (PST) is developed that can detect plaques of different morphology on the images of Petri dishes and measure plaque area and diameter, indicating future results using PST are backwards compatible with prior measurements in the literature.



ΦX174 Attenuation by Whole-Genome Codon Deoptimization

The need to better understand how selection acts on patterns of synonymous codon usage across the genome is highlighted and the recoded bacteriophage ΦX174 provides a convenient system to investigate the genetic determinants of virulence.

Why genes overlap in viruses

It is concluded that gene overlap is unlikely to have evolved as a way of compressing the genome in response to the harmful effect of mutation because RNA viruses, despite having generally higher mutation rates, have less gene overlap on average than DNA viruses of comparable genome length.

Conservation of Gene Cassettes among Diverse Viruses of the Human Gut

Approaches to metagenomic assembly to probe genome structure in a sample of 5.6 Gb of gut viral DNA sequence from six individuals reveal that free-living bacteriophages, while usually dissimilar at the nucleotide level, often have significant similarity at the level of encoded amino acid motifs, gene order, and gene orientation.

The evolution of genome compression and genomic novelty in RNA viruses.

It is suggested that RNA viruses are a good model system for the investigation of general evolutionary relationship between genome attributes such as mutational robustness, mutation rate, and size.

Properties of overlapping genes are conserved across microbial genomes.

It is shown that overlapping genes are a consistent feature across all microbial genomes sequenced to date, have homologs in more microbes than do non-overlapping genes, and are likely more conserved, and the size, phase, and distribution, among other characteristics, of overlap genes are most consistent with the hypothesis that overlaps function in the regulation of gene expression.

Genome rearrangement affects RNA virus adaptability on prostate cancer cells

It is observed that gene order affects phenotypic adaptability (reproductive growth; viral suppression of immune function), especially on PC-3 cells that strongly select against virus infection, and populations derived from the least-fit ancestor adapted fastest, consistent with theory predicting populations with low initial fitness should improve faster in evolutionary time.

Overlapping genes: a window on gene evolvability

It is shown that taking into account the processes leading to the expression of protein-coding genes hold the key to the understanding of overlapping genes structures, and that these structures exhibit high levels of plasticity.

Genome urbanization: clusters of topologically co-regulated genes delineate functional compartments in the genome of Saccharomyces cerevisiae

It is proposed that genome architecture evolves with a core of essential genes occupying a compact genomic ‘old town’, whereas more recently acquired, condition-specific genes tend to be located in a more spacious ‘suburban’ genomic periphery.