Abstract
Gene duplication and diversification drive the emergence of novel functions during evolution. Because of whole genome duplications, ciliates from the Paramecium aurelia group constitute a remarkable system to study the evolutionary fate of duplicated genes. Paramecium species harbor two types of nuclei: a germline micronucleus (MIC) and a somatic macronucleus (MAC) that forms from the MIC at each sexual cycle. During MAC development, ~45,000 germline Internal Eliminated Sequences (IES) are excised precisely from the genome through a ‘cut-and-close’ mechanism. Here, we have studied the P. tetraurelia paralogs of KU80, which encode a key DNA double-strand break repair factor involved in non-homologous end joining. The three KU80 genes have different transcription patterns, KU80a and KU80b being constitutively expressed, while KU80c is specifically induced during MAC development. Immunofluorescence microscopy and high-throughput DNA sequencing revealed that Ku80c stably anchors the PiggyMac (Pgm) endonuclease in the developing MAC and is essential for IES excision genome-wide, providing a molecular explanation for the previously reported Ku-dependent licensing of DNA cleavage at IES ends. Expressing Ku80a under KU80c transcription signals failed to complement a depletion of endogenous Ku80c, indicating that the two paralogous proteins have distinct properties. Domain-swap experiments identified the α/β domain of Ku80c as the major determinant for its specialized function, while its C-terminal part is required for excision of only a small subset of IESs located in IES-dense regions. We conclude that Ku80c has acquired the ability to license Pgm-dependent DNA cleavage, securing precise DNA elimination during programmed rearrangements. The present study thus provides novel evidence for functional diversification of genes issued from a whole-genome duplication.
Highlights
Gene duplication and diversification have been considered a driving force for the evolution of organisms throughout the tree of life and different gene duplication mechanisms have been described
Cells were submitted to control, PGM, KU70 or KU80c RNAi and the efficiency of each KD was monitored based on the absence of viable progeny with a functional new MAC (S1 Table)
In the absence of pre-extraction, the Pgm nuclear signal decreased moderately in Ku80c- and Ku70-depleted cells (25% and 44% decrease, respectively), whereas it completely vanished from control Pgm-depleted cells, as expected for efficient PGM KD (Fig 1A and 1B), indicating that Ku70/80c are not strictly required for Pgm localization per se in the new developing MAC
Summary
Gene duplication and diversification have been considered a driving force for the evolution of organisms throughout the tree of life (reviewed in [1]) and different gene duplication mechanisms have been described. The Paramecium aurelia group of ciliate species constitutes a remarkable system to study the evolutionary fate of duplicated genes. In these unicellular eukaryotes, at least three successive WGDs have occurred during evolution [5] and numerous gene duplicates from the intermediate and recent WGDs have been retained in extant diploid genomes (~25% and ~50% of pre-duplication genes, respectively) [5,6]. Extensive analyses of Paramecium genomes and gene expression levels have indicated that the vast majority of postWGD gene pairs ( called ohnologs) have likely preserved their original function owing to gene dosage constraints [8] and tend to return to their initial single-copy state over time [5]. Within a pair of ohnologs, progressive dosage unbalance between duplicates is thought to allow pseudogenization and eventual loss of the copy with the lower expression level [9]
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