Role of Ectopic Gene Conversion in the Evolution of a Candida krusei Pleiotropic Drug Resistance Transporter Family

Abstract

Gene duplications enable the evolution of novel gene function, but strong positive selection is required to preserve advantageous mutations in a population. This is because frequent ectopic gene conversions (EGCs) between highly similar, tandem-duplicated, sequences, can rapidly remove fate-determining mutations by replacing them with the neighboring parent gene sequences. Unfortunately, the high sequence similarities between tandem-duplicated genes severely hamper empirical studies of this important evolutionary process, because deciphering their correct sequences is challenging. In this study, we employed the eukaryotic model organism Saccharomyces cerevisiae to clone and functionally characterize all 30 alleles of an important pair of tandem-duplicated multidrug efflux pump genes, ABC1 and ABC11, from seven strains of the diploid pathogenic yeast Candida krusei. Discovery and functional characterization of their closest ancestor, C. krusei ABC12, helped elucidate the evolutionary history of the entire gene family. Our data support the proposal that the pleiotropic drug resistance (PDR) transporters Abc1p and Abc11p have evolved by concerted evolution for ∼134 MY. While >90% of their sequences remained identical, very strong purifying selection protected six short DNA patches encoding just 18 core amino acid (aa) differences in particular trans membrane span (TMS) regions causing two distinct efflux pump functions. A proline-kink change at the bottom of Abc11p TMS3 was possibly fate determining. Our data also enabled the first empirical estimates for key parameters of eukaryotic gene evolution, they provided rare examples of intron loss, and PDR transporter phylogeny confirmed that C. krusei belongs to a novel, yet unnamed, third major Saccharomycotina lineage.

Contrasting patterns of coding and flanking region evolution in mammalian keratin associated protein-1 genes

“…The role of gene conversion is supported by two key pieces of evidence: 1) unique amino acid tracts that are shared by KAP1 copies within a species, but are unique to that species/group of related species; and 2) the possession of shared nucleotide variants between KRTAP1 gene copies in sheep populations. These results extend previous reports of homogenization via ongoing short-tract gene conversion events in other protein coding genes (Noonan, et al 2004; Lamping, et al 2017).…”

“…Repeats are ubiquitous denizens of eukaryote genomes, where they exist in different forms (coding, non-coding) and organizations (tandem, dispersed). Our results add to the growing list of examples that illustrate how different molecular and evolutionary processes can impinge on repeats to structure their sequences and create distinctive patterns of evolution (Shyue, et al 1994; Noonan, et al 2004; Ganley and Kobayashi 2007; Storz, et al 2007; Hiwatashi, et al 2011; Lamping, et al 2017). However, it is unclear how widespread these sorts of evolutionary dynamics are for eukaryotic gene repeats, largely because the patterns of evolution have not been investigated for the vast majority of multi-gene families.…”

“…These results extend previous reports of homogenization via ongoing short-tract gene conversion events in other protein coding genes (N oonan et al . 2004; L amping et al . 2017).…”

Population genomics shows no distinction between pathogenic Candida krusei and environmental Pichia kudriavzevii: One species, four names

“…There is also uncertainty about the ploidy of the species. The MLST study indicated that isolates are diploid [ 24 ], as did two genome analyses [ 10 , 23 ], but evidence of triploid and aneuploid strains has also been reported [ 26 ].…”

“…Fluconazole resistance in C . krusei is not fully understood but appears to have two causes: its ergosterol synthesis enzyme Erg11 has unusually low affinity for fluconazole, and the drug efflux pumps Abc1 and Abc11 are constitutively expressed [ 26 , 27 ]. Echinocandins such as micafungin are the current drugs of choice for treatment of C .…”