Elusive preferred hosts or nucleic acid level selection? A commentary on: Evolutionary interpretations of mycobacteriophage biodiversity and host-range through the analysis of codon usage bias (Esposito et al. 2016)

TL;DR

This paper discusses how mycobacteriophages often do not match their host's codon usage, suggesting their preferred hosts may differ from the hosts where they are isolated, impacting understanding of virus-host evolution.

Contribution

It offers a new perspective on virus-host relationships by analyzing codon usage bias, challenging assumptions about virus adaptation and host specificity.

Findings

Viruses do not always mimic host codon usage patterns.

Mycobacteriophages may prefer hosts different from their isolation source.

Codon usage analysis can reveal elusive virus-host relationships.

Abstract

While confirming the long held view that viruses do not closely imitate the use of their host's codon catalogue, Esposito and coworkers nevertheless consider it surprising that, despite having the ability to infect the same host, many mycobacteriophages share little or no genetic similarity (i.e. similarity in their GC contents and codon utilization patterns). Arguing correctly that efficient translation of a phage's proteins within a host is likely to be optimized by the phage's ability to match the host's codon usage pattern, it is concluded that the preferred host of many mycobacteriophages is not Mycobacterium smegmatis, despite their having been isolated on that organism. Thus, a virus and its elusive preferred hosts would have had similar GC percentages and codon usages, but the same virus could still infect a less-preferred host (Mycobacterium smegmatis), where the virus-host similarity would be less evident. However, there is another evolutionary interpretation.