Evolution of IESs and scrambling in the actin I gene in hypotrichous ciliates

Abstract

Germ-line (micronuclear) genes in hypotrichous ciliates are interrupted by numerous, short, noncoding, AT-rich segments called internal eliminated segments, or IESs. IESs divide a gene into macronuclear destined segments, or MDSs. IESs are excised from micronuclear genes, and the MDSs are spliced when a micronuclear genome is processed into a macronuclear genome after cell mating. In the micronuclear version of the actin I gene intramolecular recombination between IESs during evolution has put MDSs into a scrambled disorder in some but not all hypotrichs. Studies using rDNA sequences to define phylogenetic relationships among eight hypotrichs suggests that evolution of the micronuclear actin I gene proceeds by successive addition of IESs in earlier diverging species, without MDS scrambling. Continued addition of IESs and recombination among IESs in later diverging species produced actin I genes with scrambled MDSs. Subsequent to MDS scrambling, additional IESs were inserted into the more recently evolved species. Thus, IES insertions and gene scrambling occur in a progressive manner during species evolution to produce micronuclear actin I genes of increasing structural complexity.

Figure 1

Structure of micronuclear and macronuclear actin I genes in U. grandis (A), E. mobilis (B), Oxytricha sp. (Misty) (C), S. pustulata (D), and S. lemnae (E). Micronuclear DNA PCR products are indicated by lines above each micronuclear gene. MDSs are blocks and IESs are lines between blocks. Unsequenced regions are indicated by dashed blocks and dashed lines.

Figure 2

Maximum parsimony trees based on the sequence of rDNA (A; ssrDNA–ITSI–5.8S rDNA–ITS2–1400 bp of the large subunit lsrDNA; the first number is the bootstrap value and the second is for quartet puzzling) and the sequence of amino acids in the actin I gene (B).

Figure 3

Evolutionary scheme for the insertion of IESs and the scrambling of MDSs in the micronuclear actin I gene in eight hypotrichs. MDSs are blocks, and IESs are lines between blocks. Regions not sequenced in micronuclear DNA are dashed blocks and lines.