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J. Fungi 2018, 4(3), 78; https://doi.org/10.3390/jof4030078

Biological Roles of Protein-Coding Tandem Repeats in the Yeast Candida Albicans

1
Centre for Professional and Continuing Education, Massey University, Palmerston North 4412, New Zealand
2
Institute of Fundamental Sciences, Massey University, Palmerston North 4412, New Zealand
*
Author to whom correspondence should be addressed.
Received: 23 May 2018 / Revised: 16 June 2018 / Accepted: 27 June 2018 / Published: 29 June 2018
(This article belongs to the Special Issue Cell Adhesion in Fungal Life and Pathogenesis)
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Abstract

Tandem repeat (TR) DNA mutates faster than other DNA by insertion and deletion of repeats. Large parts of eukaryotic proteomes are encoded by ORFs containing protein-coding TRs (TR-ORFs, pcTRs) with largely unknown biological consequences. We explored these in the yeast Candida albicans, an opportunistic human pathogen. We found that almost half of C. albicans’ proteins are encoded by TR-ORFs. pcTR frequency differed only moderately between different gene (GO) categories. Bioinformatic predictions of genome-wide mutation rates and clade-specific differences in pcTR allele frequencies indicated that pcTRs (i) significantly increase the genome-wide mutation rate; (ii) significantly impact on fitness and (iii) allow the evolution of selectively advantageous clade-specific protein variants. Synonymous mutations reduced the repetitiveness of many amino acid repeat-encoding pcTRs. A survey, in 58 strains, revealed that in some pcTR regions in which repetitiveness was not significantly diminished by synonymous mutations the habitat predicted which alleles were present, suggesting roles of pcTR mutation in short-term adaptation and pathogenesis. In C. albicans pcTR mutation apparently is an important mechanism for mutational advance and possibly also rapid adaptation, with synonymous mutations providing a mechanism for adjusting mutation rates of individual pcTRs. Analyses of Arabidopsis and human pcTRs showed that the latter also occurs in other eukaryotes. View Full-Text
Keywords: protein coding DNA tandem repeats; mutation rate; proteome evolution; amino acid tandem repeats; Candida albicans; synonymous mutations; Red Queen’s race; contingency genes protein coding DNA tandem repeats; mutation rate; proteome evolution; amino acid tandem repeats; Candida albicans; synonymous mutations; Red Queen’s race; contingency genes
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Wilkins, M.; Zhang, N.; Schmid, J. Biological Roles of Protein-Coding Tandem Repeats in the Yeast Candida Albicans. J. Fungi 2018, 4, 78.

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