MITE infestation accommodated by genome editing in the germline genome of the ciliate Blepharisma

Abstract

During their development following sexual conjugation, ciliates excise numerous internal eliminated sequences (IESs) from a copy of the germline genome to produce the functional somatic genome. Most IESs are thought to have originated from transposons, but the presumed homology is often obscured by sequence decay. To obtain more representative perspectives on the nature of IESs and ciliate genome editing, we assembled 40,000 IESs of Blepharisma stoltei , a species belonging to a lineage (Heterotrichea) that diverged early from those of the intensively studied model ciliate species. About a quarter of IESs were short (<115 bp), largely nonrepetitive, and with a pronounced ~10 bp periodicity in length; the remainder were longer (up to 7 kbp) and nonperiodic and contained abundant interspersed repeats. Contrary to the expectation from current models, the assembled Blepharisma germline genome encodes few transposases. Instead, its most abundant repeat (8,000 copies) is a Miniature Inverted-repeat Transposable Element (MITE), apparently a deletion derivative of a germline-limited Pogo-family transposon. We hypothesize that MITEs are an important source of IESs whose proliferation is eventually self-limiting and that rather than defending the germline genomes against mobile elements, transposase domestication actually facilitates the accumulation of junk DNA.

ISWI1 complex proteins facilitate developmental genome editing inParamecium

“…In the future, it would be worth investigating the expression of PTIWI01/09 and related genome editing genes (e.g., NOWA1/2 and PTCAF1) for knockdowns to observe if their expression changes are similar to those in ICOP1/2-KD. However, it is clear that the IES retention in ICOP1/2-KD is substantially stronger than the PTIWIs (Fig Most IESs are likely remnants of autonomous or non-autonomous transposons (Seah et al 2023;Sellis et al 2021) that decayed beyond recognition with time due to a lack of selection pressure caused by their efficient removal during MAC genome development (Sellis et al 2021). A third of all IESs are 26 to 28 bp in length and are proposed to be short enough to allow the interaction of two PGMs without DNA bending (Arnaiz et al 2012).…”

Nuclear dualism without extensive DNA elimination in the ciliateLoxodes magnus

“…To account for incompletely predicted genes, we performed a translated search (TBLASTN) against the genomes with model ciliate Pgm and TBE-transposase protein sequences. The best hit ( Blepharisma stoltei Pgm 9 to the L. magnus MIC) had an E-value of only 0.12, compared to 10 -33 for an alignment of Paramecium tetraurelia Pgm to the B. stoltei genome that recovered the B. stoltei Pgm. The weak match in L. magnus is hence likely spurious.…”

“…Secondary loss is more parsimonious, because karyorelicts are sister to heterotrichs, 42,66 in which at least one genus ( Blepharisma ) performs extensive genome editing like other ciliates. 9,12 The presence of Dcl genes in Loxodes , homologous to those involved in genome editing in other ciliates, also support secondary loss, whereas the apparent absence of a domesticated excisase is less conclusive, as ciliate excisases come from at least two different families, 12,19,21,67 and so were independently or repeatedly domesticated.…”

“…6,7 IESs are thought to originate from DNA transposons, and the excisases that remove them evolved from DDE-family DNA transposases. [7][8][9][19][20][21][22] Excision is proposed to be guided by development-specific small RNAs of different classes. [23][24][25][26][27] Genome editing removes mobile elements from the MAC, as a result, they are not exposed to natural selection and tend to accumulate in MIC genomes over time.…”

How ciliates got their nuclei

“…But a few models cannot do justice to the richness of ciliate diversity (let alone protists). Ciliates include the majestic trumpet-shaped Stentor , able to regenerate itself from the tiniest cell fragment; Euplotes , which walks on leg-like bundles of coordinated cilia; Loxodes , which senses gravity using a subcellular organelle, not unlike a vertebrate inner ear; Didinium , which can paralyze and engulf prey far larger than itself in one “bite”; and Blepharisma , one of the few microorganisms that can easily be recognized without a microscope by its purple tinge, and the subject of the two papers in this issue from Seah, Singh, Swart, and colleagues ( 1 , 2 ).…”