Why do some fungal mitoviruses rarely Trp on UGA?

Read the full article on ScienceDirect.

Mitovirus UGA(Trp) codon usage parallels that of host mitochondria

Text by Max Nibert

Mitoviruses are intriguing because they replicate in mitochondria of their host fungi. In a molecular sense they are also notably simple, each encoding a single protein, the viral RNA-dependent RNA polymerase (RdRp), in its plus-strand RNA genome. In the mitochondria of most fungi (as also in those of vertebrates), both UGG and UGA encode tryptophan (Trp), unlike in the cytosol, where UGA is a stop codon. As might therefore be expected, a typical fungal mitovirus contains a substantial number of UGA codons in its RdRp open reading frame. Some, however, do not. The highlighted Virology article (1) provides original evidence that fungal mitoviruses that lack, or have only a few, UGA codons derive from host fungi in which UGA is strongly disfavored relative to UGG for use as a mitochondrial Trp codon.

How did this finding come to light? While pursuing other work on fungal mitoviruses, I became more aware of the fact that several of them have no UGA codons. This in turn struck me as odd. Some authors have suggested that this might allow these particular mitoviruses to express their RdRps, and perhaps also replicate their genomes, in the fungal cytosol, providing a possible explanation for why they have evolved to lack these codons. For several reasons described in the article, however, I was not convinced by this explanation and set out to explore another possibility, namely, that UGA(Trp) may simply be a rare mitochondrial codon in the fungal hosts of these particular mitoviruses. As also described in the article, the evidence suggests that this is indeed the case.

Are there broader implications of this finding? The fact that UGA(Trp) is a rare mitochondrial codon in some fungi, correlating with a lack of mitochondrially encoded tRNA(Trp)UCA, seems not to have been widely discussed to date. Though I did not perform a systematic literature review, I was able to find only a 2014 article by Hegedusova et al. (2) that also addresses this topic across a range of fungi, identifying UGA(Trp) as a rare mitochondrial codon in some basidiomycetes (but not extending their findings to mitoviruses). Moreover, in the highlighted article, I show that UGA(Trp) is likewise a rare mitochondrial codon in many other, more phylogenetically primitive fungi, including glomeromycetes, suggesting that any mitoviruses of these other fungi are also likely to have no or few UGA codons. Time may tell if this prediction is consistently correct and if it holds any deeper importance for understanding the curious evolution of mitoviruses.

mitoUGA-Fig1 copy

Figure legend

See Fig. 2 in the highlighted article for additional details. Fungal mitovirus UGA(Trp) vs. UGG(Trp) codon usage parallels that of host mitochondria (lower left, UGA rare; upper right, UGA more common). Host fungi: blue, ascomycetes; green, basidiomycetes; orange, glomeromycetes. The fungi represented at lower left have mitochondrially encoded tRNA(Trp)CCA, but not tRNA(Trp)UCA, whereas those at upper right have mitochondrially encoded tRNA(Trp)UCA, usually without but in some species also with tRNA(Trp)CCA (see Table 2 in highlighted article).

Introducing the author


Max Nibert is a Professor of Microbiology & Immunobiology at Harvard Medical School, Boston, MA, USA, and also an active member of the Harvard Ph.D. Program in Virology.

About the research

Mitovirus UGA(Trp) codon usage parallels that of host mitochondria
Max L. Nibert
Virology,  Volume 507, July 2017, Pages 96–100


  1. Nibert ML. 2017. Mitovirus UGA(Trp) codon usage parallels that of host mitochondria. Virology 507:96–100.
  1. Hegedusova E, Brejova B, Tomaska L, Sipiczki M, Nosek J. 2014. Mitochondrial genome of the basidiomycetous yeast Jaminaea angkorensis. Curr Genet 60:49–59.