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Chapter 16 : Programmed Genome Rearrangements in

Authors: Meng-chao Yao1, Ju-lan Chao2, Chao-yin Cheng3
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Affiliations: 1: Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan; 2: Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan; 3: Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
Content Type: Monograph
Publication Year: 2015

Category: Clinical Microbiology

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Abstract:

This chapter reviews recent studies on the remarkable phenomenon of programmed DNA rearrangements in ciliated protozoa, focusing primarily on the species . The phenomenon occurs widely among ciliates, a diverse group of single-celled eukaryotes. It varies significantly in mechanistic detail among the species that have been described, chiefly , , , , and . Readers are referred to other chapters in this volume for studies in and . displays perhaps the simplest version of these DNA rearrangements and is the easiest to grow and manipulate in the laboratory, hence offering excellent opportunities for in-depth understanding. Since the publication of ( ), significant progress has brought about fundamental changes in our understanding. Among other things, clear links have now been established between these processes and RNA interference (RNAi) and transposon domestication. This chapter will concentrate on progress made during this period, with a brief summary of earlier work to provide an introduction.

Citation: Yao M, Chao J, Cheng C. 2015. Programmed Genome Rearrangements in , p 349-367. In Craig N, Chandler M, Gellert M, Lambowitz A, Rice P, Sandmeyer S (ed), Mobile DNA III. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.MDNA3-0012-2014
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Programmed Genome Rearrangements in Tetrahymena
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Citation: Yao M, Chao J, Cheng C. 2015. Programmed Genome Rearrangements in , p 349-367. In Craig N, Chandler M, Gellert M, Lambowitz A, Rice P, Sandmeyer S (ed), Mobile DNA III. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.MDNA3-0012-2014
/content/10.1128/9781555819217.chap16.fig16-1
Figure 1
An image of during vegetative growth. The fixed cell was labeled with antibodies against centrin (green) to show basal bodies on the cell cortex and a modified histone (red) to show the micronucleus. The macronucleus and micronucleus were stained with 4′,6-diamidino-2-phenylindole (DAPI; blue). The image was captured using Delta Vision.
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Figure 1

An image of during vegetative growth. The fixed cell was labeled with antibodies against centrin (green) to show basal bodies on the cell cortex and a modified histone (red) to show the micronucleus. The macronucleus and micronucleus were stained with 4′,6-diamidino-2-phenylindole (DAPI; blue). The image was captured using Delta Vision.

Citation: Yao M, Chao J, Cheng C. 2015. Programmed Genome Rearrangements in , p 349-367. In Craig N, Chandler M, Gellert M, Lambowitz A, Rice P, Sandmeyer S (ed), Mobile DNA III. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.MDNA3-0012-2014
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Figure 2
Cytological and molecular events during conjugation. Various cytological events during mating progression (from 0 to 16 hours after cells are mixed) are represented by drawings of cells and nuclei. Expressions of key genes during this process are indicated above and activities of DNA and RNA are indicated below the cells.
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Image of Figure 2
Figure 2

Cytological and molecular events during conjugation. Various cytological events during mating progression (from 0 to 16 hours after cells are mixed) are represented by drawings of cells and nuclei. Expressions of key genes during this process are indicated above and activities of DNA and RNA are indicated below the cells.

Citation: Yao M, Chao J, Cheng C. 2015. Programmed Genome Rearrangements in , p 349-367. In Craig N, Chandler M, Gellert M, Lambowitz A, Rice P, Sandmeyer S (ed), Mobile DNA III. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.MDNA3-0012-2014
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Figure 3
Key steps of programmed DNA deletion in . The steps of programmed DNA deletion are summarized. The earlier two events occur in meiotic nuclei and the later events in developing macronuclei, as indicated by the drawings of cells to the left. Key proteins involved in each step are also indicated.
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Figure 3

Key steps of programmed DNA deletion in . The steps of programmed DNA deletion are summarized. The earlier two events occur in meiotic nuclei and the later events in developing macronuclei, as indicated by the drawings of cells to the left. Key proteins involved in each step are also indicated.

Citation: Yao M, Chao J, Cheng C. 2015. Programmed Genome Rearrangements in , p 349-367. In Craig N, Chandler M, Gellert M, Lambowitz A, Rice P, Sandmeyer S (ed), Mobile DNA III. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.MDNA3-0012-2014
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Figure 4
Localization of key proteins during conjugation. The panels summarize the localization patterns of various proteins in different cellular compartments during conjugation. Genes for the proteins involved are listed to the left, with each row indicating the progression of mating (from left to right). Proteins with similar patterns are shown in the same row. The compartments in which proteins have been detected (using antibodies or peptide tags) are colored.
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Figure 4

Localization of key proteins during conjugation. The panels summarize the localization patterns of various proteins in different cellular compartments during conjugation. Genes for the proteins involved are listed to the left, with each row indicating the progression of mating (from left to right). Proteins with similar patterns are shown in the same row. The compartments in which proteins have been detected (using antibodies or peptide tags) are colored.

Citation: Yao M, Chao J, Cheng C. 2015. Programmed Genome Rearrangements in , p 349-367. In Craig N, Chandler M, Gellert M, Lambowitz A, Rice P, Sandmeyer S (ed), Mobile DNA III. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.MDNA3-0012-2014
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Figure 5
Formation of the Pdd1p aggregates during DNA deletion. The chromodomain protein Pdd1p and other proteins that participate in the formation of the large heterochromatin aggregates are shown. The proteins are guided to IESs through sRNAs and eventually form large aggregates with excised IESs. The left panels show micrographs of mating cells in three successive stages stained with antibodies against Pdd1p (green) and DAPI (blue).
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Figure 5

Formation of the Pdd1p aggregates during DNA deletion. The chromodomain protein Pdd1p and other proteins that participate in the formation of the large heterochromatin aggregates are shown. The proteins are guided to IESs through sRNAs and eventually form large aggregates with excised IESs. The left panels show micrographs of mating cells in three successive stages stained with antibodies against Pdd1p (green) and DAPI (blue).

Citation: Yao M, Chao J, Cheng C. 2015. Programmed Genome Rearrangements in , p 349-367. In Craig N, Chandler M, Gellert M, Lambowitz A, Rice P, Sandmeyer S (ed), Mobile DNA III. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.MDNA3-0012-2014
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Figure 6
Setting deletion boundaries. The cartoon shows a possible heterochromatin structure with associated proteins over the IES to the right and the neighboring euchromatin to the left. The domesticated transposase Tpb2p is targeted to the junction for DNA cutting. In the example represented here, the M-element is shown to have a flanking regulatory sequence (5′-AAAAAGGGGG-3′) that is recognized by Lia3p to set the heterochromatin boundary and specify the cutting site.
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Image of Figure 6
Figure 6

Setting deletion boundaries. The cartoon shows a possible heterochromatin structure with associated proteins over the IES to the right and the neighboring euchromatin to the left. The domesticated transposase Tpb2p is targeted to the junction for DNA cutting. In the example represented here, the M-element is shown to have a flanking regulatory sequence (5′-AAAAAGGGGG-3′) that is recognized by Lia3p to set the heterochromatin boundary and specify the cutting site.

Citation: Yao M, Chao J, Cheng C. 2015. Programmed Genome Rearrangements in , p 349-367. In Craig N, Chandler M, Gellert M, Lambowitz A, Rice P, Sandmeyer S (ed), Mobile DNA III. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.MDNA3-0012-2014
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Figure 7
Mating-type determination through homologous recombination. The top shows a germline configuration of the locus and the bottom shows the corresponding locus in the macronucleus of a mating type VI cell. The connecting lines indicate the two types of rearrangements required: deletion of IESs and removal of the other five mating-type sequences, presumably by recombination between homologous sequences (marked by similarly shaded areas) (modified from 97).
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Image of Figure 7
Figure 7

Mating-type determination through homologous recombination. The top shows a germline configuration of the locus and the bottom shows the corresponding locus in the macronucleus of a mating type VI cell. The connecting lines indicate the two types of rearrangements required: deletion of IESs and removal of the other five mating-type sequences, presumably by recombination between homologous sequences (marked by similarly shaded areas) (modified from 97).

Citation: Yao M, Chao J, Cheng C. 2015. Programmed Genome Rearrangements in , p 349-367. In Craig N, Chandler M, Gellert M, Lambowitz A, Rice P, Sandmeyer S (ed), Mobile DNA III. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.MDNA3-0012-2014
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