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Template-guided recombination for IES elimination and unscrambling of genes in stichotrichous ciliates
David M Prescott1, A Ehrenfeucht, G Rozenberg
1Department of Molecular, Cellular and Developmental Biology, Howard Hughes Medical Institute, University of Colorado, Campus, Box 347, Boulder, CO 80309-0347, USA. prescotd@spot.colorado.edu
Abstract:
The micronuclear versions of genes in stichotrichous ciliates are interrupted by multiple, short, non-coding DNA segments called internal eliminated segments, or IESs. IESs divide a gene into macronuclear destined segments, or MDSs. In some micronuclear genes MDSs are in a scrambled disorder. During development of a micronucleus into a macronucleus after cell mating the IESs are excised from micronuclear genes and the MDSs are spliced in the sequentially correct order. Pairs of short repeat sequences in the ends of MDSs undergo homologous recombination to excise IESs and splice MDSs. However, the repeat sequences are too short to guide unambiguously their own alignment in preparation for recombination. Based on experiments by others on the distantly related ciliate, Paramecium, we propose a molecular model of template-guided recombination to explain the excision of the 100,000-150,000 IESs and splicing of MDSs, including unscrambling, in the genome of stichotrichous ciliates. The model solves the problem of correct pairing of pointers, precisely identifies MDS-IES junctions, and provides for irreversible recombination.
Insights
Stichotrichous ciliates use template-guided recombination to precisely excise internal eliminated segments (IESs) and splice macronuclear destined segments (MDSs), unscrambling scrambled gene sequences during development.
Area of Science:
- Molecular Biology
- Genetics
- Cell Biology
Background:
- Stichotrichous ciliates possess micronuclear genes interrupted by internal eliminated segments (IESs).
- These IESs divide genes into macronuclear destined segments (MDSs), which can be in a scrambled order.
- During macronuclear development, IESs are excised and MDSs are spliced in the correct sequence.
Purpose of the Study:
- To propose a molecular model for IES excision and MDS splicing in stichotrichous ciliates.
- To explain the unscrambling of scrambled MDSs during macronuclear development.
- To address the challenge of imprecise alignment of short repeat sequences involved in recombination.
Main Methods:
- Development of a molecular model based on template-guided recombination principles.
- Extrapolation of findings from experiments on the related ciliate, Paramecium.
- Analysis of homologous recombination mechanisms at MDS-IES junctions.
Main Results:
- The proposed model explains the precise excision of numerous IESs (100,000-150,000 per genome).
- The model accounts for the sequential splicing of MDSs, including the unscrambling of previously disordered segments.
- The model resolves the issue of ambiguous alignment of short repeat sequences by providing a template-guided pairing mechanism.
Conclusions:
- Template-guided recombination provides a robust mechanism for genome rearrangement in stichotrichous ciliates.
- This process ensures the accurate formation of the macronuclear genome from the micronuclear precursor.
- The model offers insights into the evolution of gene regulation and genome plasticity in ciliates.
