Abstract
BackgroundViral genomes often contain metabolic genes that were acquired from host genomes (auxiliary genes). It is assumed that these genes are fixed in viral genomes as a result of a selective force, favoring viruses that acquire specific metabolic functions. While many individual auxiliary genes were observed in viral genomes and metagenomes, there is great importance in investigating the abundance of auxiliary genes and metabolic functions in the marine environment towards a better understanding of their role in promoting viral reproduction.ResultsIn this study, we searched for enriched viral auxiliary genes and mapped them to metabolic pathways. To initially identify enriched auxiliary genes, we analyzed metagenomic microbial reads from the Global Ocean Survey (GOS) dataset that were characterized as viral, as well as marine virome and microbiome datasets from the Line Islands. Viral-enriched genes were mapped to a “global metabolism network” that comprises all KEGG metabolic pathways. Our analysis of the viral-enriched pathways revealed that purine and pyrimidine metabolism pathways are among the most enriched pathways. Moreover, many other viral-enriched metabolic pathways were found to be closely associated with the purine and pyrimidine metabolism pathways. Furthermore, we observed that sequential reactions are promoted in pathways having a high proportion of enriched genes. In addition, these enriched genes were found to be of modular nature, participating in several pathways.ConclusionsOur naïve metagenomic analyses strongly support the well-established notion that viral auxiliary genes promote viral replication via both degradation of host DNA and RNA as well as a shift of the host metabolism towards nucleotide biosynthesis, clearly indicating that comparative metagenomics can be used to understand different environments and systems without prior knowledge of pathways involved.
Highlights
Viral genomes often contain metabolic genes that were acquired from host genomes
Detection of viral-enriched host-like metabolic genes In order to define the enriched set of metabolic genes carried in viral genomes, we used the previously published Line Islands metagenomes, including four viral-size fraction and four microbial-size fraction metagenomes, each pair sampled at the same geographical locations [28]
Hypergeometric enrichment analysis was performed for each KEGG Orthologs (KO) in each of the viromes studied to detect ortholog groups that are over-represented in the viral metagenome compared to the entire Global Ocean Survey (GOS) metagenome or to the Line Islands microbiome
Summary
Viral genomes often contain metabolic genes that were acquired from host genomes (auxiliary genes). It is assumed that these genes are fixed in viral genomes as a result of a selective force, favoring viruses that acquire specific metabolic functions. While many individual auxiliary genes were observed in viral genomes and metagenomes, there is great importance in investigating the abundance of auxiliary genes and metabolic functions in the marine environment towards a better understanding of their role in promoting viral reproduction. The high abundance of viruses combined with evidence that viral particles are a major source of planktonic mortality [5,6,7] and horizontal gene transfer [8] demonstrate the immense influence of the virosphere on the ecology and biology of the marine environment. The identification of auxiliary metabolic genes found in viral genomes is enabling a deeper understanding of the functions that increase viral fitness and the mechanism in which these functions are promoted. While increasing viral fitness, newly acquired genes are fixed in the viral genomes at the expense of larger genome sizes, and only the most essential genes are expected to be enriched in the viral genomes
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