Co-Evolution of Mitochondrial tRNA Import and Codon Usage Determines Translational Efficiency in the Green Alga Chlamydomonas

Abstract

Mitochondria from diverse phyla, including protozoa, fungi, higher plants, and humans, import tRNAs from the cytosol in order to ensure proper mitochondrial translation. Despite the broad occurrence of this process, our understanding of tRNA import mechanisms is fragmentary, and crucial questions about their regulation remain unanswered. In the unicellular green alga Chlamydomonas, a precise correlation was found between the mitochondrial codon usage and the nature and amount of imported tRNAs. This led to the hypothesis that tRNA import might be a dynamic process able to adapt to the mitochondrial genome content. By manipulating the Chlamydomonas mitochondrial genome, we introduced point mutations in order to modify its codon usage. We find that the codon usage modification results in reduced levels of mitochondrial translation as well as in subsequent decreased levels and activities of respiratory complexes. These effects are linked to the consequential limitations of the pool of tRNAs in mitochondria. This indicates that tRNA mitochondrial import cannot be rapidly regulated in response to a novel genetic context and thus does not appear to be a dynamic process. It rather suggests that the steady-state levels of imported tRNAs in mitochondria result from a co-evolutive adaptation between the tRNA import mechanism and the requirements of the mitochondrial translation machinery.

Codon expansion and systematic transcriptional deletions produce tetra-, pentacoded mitochondrial peptides

“…The distributions of amino acids specifically inserted at stops for tetra-and pentacoded peptides are similar to each other (r = 0.375, one tailed P = 0.057), but not to the amino acid distributions in the known proteomes and the complete tetraand pentacoded peptides (Table 5). This result strengthens the hypothesis that antitermination tRNA(s) with anticodon(s) matching stops (Seligmann 2010a,b;2011a) insert unknown amino acids at stops (Seligmann 2011b(Seligmann ,2012cFaure 2011), including imported cytosolic tRNA(s) (Tassarov and Martin 1996;Schneider et al 2000;Rubio et al 2008;Duchène et al 2009;Schneider 2011;Salinas et al 2012). This issue of amino acid insertions at stops deserves more in depth analyses at an ulterior stage, including consideration of insertions considering codon-anticodon mismatches (Seligmann 2010c(Seligmann , 2011c.…”

Aminoacyl-tRNA synthetase evolution and sectoring of the genetic code

“…Import of tRNA Ile (IAU) is less important, because tRNA Ile (GAU) is encoded in the mitochondria and can suffice to read mRNA codons AUC and AUU. Import of a cytosolic tRNA Gly (GCC) also appears necessary, and cytosolic tRNA Gly (GCC) is imported into mitochondria [31]. Furthermore, mitochondrial-encoded tRNAs are heavily biased toward wobble U rather than C (Figure 8).…”

Experimental Support That Natural Selection Has Shaped the Latitudinal Distribution of Mitochondrial Haplotypes in Australian Drosophila melanogaster

“…In the green alga Chlamydomonas, experimental alteration of mitochondrial codons 305 drastically changes translational efficiency, suggesting that mitochondrial codon usage has been optimised for translation of mitochondrial products (Salinas, et al 2012). In our study, represented by a guanine or cytosine, and conversely those of B1 reveal a GC content of only 20% (Table S6A, Fishers exact test, p = 0.001).…”