Abstract:Sequence overlap between two genes is common across all genomes, with viruses having high proportions of these gene overlaps. 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 cri… Show more
“…While coding potential was retained (Fig. 5a ), this refactoring led to numerous phenotypic defects, including a substantial reduction in burst size and lower attachment efficiency, along with large changes in levels of several essential assembly and replication proteins produced during the infection cycle 139 . Fig.…”
Section: Overlapping Genes In Bioengineeringmentioning
Modern genome-scale methods that identify new genes, such as proteogenomics and ribosome profiling, have revealed, to the surprise of many, that overlap in genes, open reading frames and even coding sequences is widespread and functionally integrated into prokaryotic, eukaryotic and viral genomes. In parallel, the constraints that overlapping regions place on genome sequences and their evolution can be harnessed in bioengineering to build more robust synthetic strains and constructs. With a focus on overlapping protein-coding and RNA-coding genes, this Review examines their discovery, topology and biogenesis in the context of their genome biology. We highlight exciting new uses for sequence overlap to control translation, compress synthetic genetic constructs, and protect against mutation.
“…While coding potential was retained (Fig. 5a ), this refactoring led to numerous phenotypic defects, including a substantial reduction in burst size and lower attachment efficiency, along with large changes in levels of several essential assembly and replication proteins produced during the infection cycle 139 . Fig.…”
Section: Overlapping Genes In Bioengineeringmentioning
Modern genome-scale methods that identify new genes, such as proteogenomics and ribosome profiling, have revealed, to the surprise of many, that overlap in genes, open reading frames and even coding sequences is widespread and functionally integrated into prokaryotic, eukaryotic and viral genomes. In parallel, the constraints that overlapping regions place on genome sequences and their evolution can be harnessed in bioengineering to build more robust synthetic strains and constructs. With a focus on overlapping protein-coding and RNA-coding genes, this Review examines their discovery, topology and biogenesis in the context of their genome biology. We highlight exciting new uses for sequence overlap to control translation, compress synthetic genetic constructs, and protect against mutation.
“…Phage genomes are typically small and highly gene dense, which is likely to limit the overall complexity of their native gene expression programs [33,34]. The phage PhiX, for instance, encodes only 11 essential genes on a genome that spans ≈5,000 base-pairs [35,36].…”
Section: Discussionmentioning
confidence: 99%
“…Our study is motivated by the observation that naturally evolved phages appear to regulate their gene expression via the mechanisms discussed here. Phage genomes are typically small and highly gene dense, which is likely to limit the overall complexity of their native gene expression programs [31][32][33][34]. Even with relatively small genomes, numerous studies have shown that phages are capable of producing complex gene expression dynamics over the course of an infection cycle.…”
Synthetic biology has successfully advanced our ability to design complex, time-varying genetic circuits executing precisely specified gene expression patterns. However, such circuits usually require regulatory genes whose only purpose is to regulate the expression of other genes. When designing very small genetic constructs, such as viral genomes, we may want to avoid introducing such auxiliary gene products. To this end, here we demonstrate that varying only the placement and strengths of promoters, terminators, and RNase cleavage sites in a computational model of a bacteriophage genome is sufficient to achieve solutions to a variety of basic expression patterns. We discover these solutions by computationally evolving genomes to reproduce desired target expression patterns. Our approach shows non-trivial patterns can be evolved, including patterns in which the relative ordering of genes by abundance changes over time. We find that some patterns are easier to evolve than others, and different genomes that express comparable expression patterns may differ in their genetic architecture. Our work opens up a novel avenue to genome engineering via fine-tuning the balance of gene expression and gene degradation rates.
“…Such regions have important biological and evolutionary implications. First, they are associated with virus within-host multiplication, betweenhost transmission, disease severity and strength of host immune response [3][4][5][6]. Second, viruses are subjected to strong selection for maintaining smaller genomes because this (i) reduces the chances for deleterious mutations to become fixed in the virus genome, particularly in viruses with high mutation rates; (ii) improves virus fitness due to faster replication; and (iii) optimizes virion formation due to physical limitations imposed by the capsid size [7][8][9].…”
In RNA viruses, which have high mutation—and fast evolutionary— rates, gene overlapping (i.e., genomic regions that encode more than one protein) is a major factor controlling mutational load and therefore the virus evolvability. Although DNA viruses use host high-fidelity polymerases for their replication, and therefore should have lower mutation rates, it has been shown that some of them have evolutionary rates comparable to those of RNA viruses. Notably, these viruses have large proportions of their genes with at least one overlapping instance. Hence, gene overlapping could be a modulator of virus evolution beyond the RNA world. To test this hypothesis, we use the genus Begomovirus of plant viruses as a model. Through comparative genomic approaches, we show that terminal gene overlapping decreases the rate of virus evolution, which is associated with lower frequency of both synonymous and nonsynonymous mutations. In contrast, terminal overlapping has little effect on the pace of virus evolution. Overall, our analyses support a role for gene overlapping in the evolution of begomoviruses and provide novel information on the factors that shape their genetic diversity.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.
