A germline-limited piggyBac transposase gene is required for precise excision in Tetrahymena genome rearrangement

Abstract

Developmentally programmed genome rearrangement accompanies differentiation of the silent germline micronucleus into the transcriptionally active somatic macronucleus in the ciliated protozoan Tetrahymena thermophila. Internal eliminated sequences (IES) are excised, followed by rejoining of MAC-destined sequences, while fragmentation occurs at conserved chromosome breakage sequences, generating macronuclear chromosomes. Some macronuclear chromosomes, referred to as non-maintained chromosomes (NMC), are lost soon after differentiation. Large NMC contain genes implicated in development-specific roles. One such gene encodes the domesticated piggyBac transposase TPB6, required for heterochromatin-dependent precise excision of IES residing within exons of functionally important genes. These conserved exonic IES determine alternative transcription products in the developing macronucleus; some even contain free-standing genes. Examples of precise loss of some exonic IES in the micronucleus and retention of others in the macronucleus of related species suggest an evolutionary analogy to introns. Our results reveal that germline-limited sequences can encode genes with specific expression patterns and development-related functions, which may be a recurring theme in eukaryotic organisms experiencing programmed genome rearrangement during germline to soma differentiation.

Host–transposon interactions: conflict, cooperation, and cooption

“…In Paramecium, PiggyMac (Pgm) is a piggyBac-derived transposase required for DNA elimination that catalyzes and interacts with five additional related Pgm-like proteins to ensure complete IES targeting (Bétermier and Duharcourt 2014;Bischerour et al 2018). Tetrahymena also uses a suite of related transposase-derived genes (TBP, TBP2, TBP6, and LIA5) to ensure proper genome rearrangement and IES deletion Cheng et al 2016;Feng et al 2017). Although these proteins are all clearly related to piggyBac transposases, they are extremely diverged from each other and share no close similarity to any extant TEs in these species, indicating that they have been fully and possibly independently coopted (Cheng et al 2010;Bétermier and Duharcourt 2014).…”

Genome analyses of the new model protist Euplotes vannus focusing on genome rearrangement and resistance to environmental stressors

“…efficient MAC genome is developed from a zygotic nucleus during sexual reproduction (conjugation) through a series of genome wide rearrangements, including chromosome fragmentation, micronuclear DNA elimination, and DNA amplification (Chalker & Yao, 2011;Chen et al, 2014;Nowacki, Shetty, & Landweber, 2011;Riley & Katz, 2001). However, conflicting models suggest a variety of mechanisms for genome rearrangement within the investigated ciliates (Chen et al, 2014;Feng et al, 2017;Maurer-Alcalá, Knight, & Katz, 2018), Second, the nuclear genetic code in ciliates is diversified and flexible as standard stop codons are often reassigned to amino acids; even stranger, in some ciliates all three standard stop codons can either code for amino acid or terminate translation in a context-dependent manner (Swart, Serra, Petroni, & Nowacki, 2016). More relevant for the current study, euplotid ciliates exhibit widespread programmed ribosomal frameshifting (PRF) at stop codons, 60-fold higher than other organisms, for instance, human, mouse, flies, Caenorhabditis elegans, yeast and Escherichia coli (Wang, Xiong, Wang, Miao, & Liang, 2016).…”

Evolutionary origins and impacts of genome architecture in ciliates

“…Their absence from the somatic genome suggests that these germline‐limited transposases are not domesticated to the same degree as in Paramecium and Tetrahymena . Interestingly, a germline‐limited PiggyBac transposase has been identified in Tetrahymena and is required for precise excision of germline‐limited DNA, whereas the somatic PiggyBac , which is responsible for the bulk of IES excision, does so at variable boundaries . These data from ciliates are yet another example of how TE proteins, regardless of their domestication status, have often been co‐opted into numerous pathways as adaptations to a variety of evolutionary conflicts spanning the tree of life …”

“…41 These data from ciliates are yet another example of how TE proteins, regardless of their domestication status, have often been co-opted into numerous pathways as adaptations to a variety of evolutionary conflicts spanning the tree of life. 37,[41][42][43]…”