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)
11 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.
Donald R. Forsdyke, Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, Ontario, Canada K7L3N6
Argument for elusive preferred host
While confirming the long held view that “viruses do not closely imitate the use of the [host’s] … codon catalogue” (Grantham et al., et al.,
M. smegmatis , despite their having been isolated on
M. smegmatis. ” Thus, a virus and its elusive preferred hosts would have had similar GC% and codon usages, but the same virus could still infect a less-preferred host (
M. smegmatis ), where the virus-host similarity would be less evident.
Another evolutionary interpretation
All this rests on the incorrect assumption that efficient translation (protein level selection; Ran et al., in extremis , a virus that ‘needs’ to translate more rapidly is ‘forced’ to encode its own tRNAs tailored to this special need.
Nucleic acid level selection
Grantham himself had noted that α and β globin mRNAs are translated within the same eukaryotic cell yet have different GC% values and codon usage patterns (Grantham et al., widely in genome GC% (and hence in codon usage pattern), whereas viruses with different hosts differed much less in GC% (and hence in codon usage pattern). Other virus-pair examples include the low GC% HIV and the high GC% HTLV1 that are both hosted by CD4 lymphocytes and are likely derived from the same retroviral ancestor (Forsdyke, 2014; Meyer et al. 2016). The GC% differences may themselves be an expression of more fundamental oligonucleotide differences that bar recombination (Brbić et al., et al., et al. (2016), but here the emphasis is on selection on RNA secondary structure rather than at the genome-level (i.e. on
M. smegmatis
DNA).
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