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Chapter 33 : Repeat-Induced Point Mutation and Other Genome Defense Mechanisms in Fungi

Author: Eugene Gladyshev1
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Affiliations: 1: Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138
Content Type: Monograph
Publication Year: 2017

Category: Microbial Genetics and Molecular Biology; Environmental Microbiology

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Abstract:

Mobile DNA, comprising both active and decaying copies of transposable elements (TEs), is present in nearly all living organisms. Although fungal genomes tend to be significantly smaller than the genomes of plants and animals, they still can vary dramatically with respect to their TE loads ( ). While TEs have been proposed to provide some beneficial functions to their hosts, e.g., by promoting genetic diversity and accelerating adaptive evolution ( ), their overall impact is considered deleterious ( ). Insertional mutagenesis, gene misexpression, and genome instability represent some well-known examples of the deleterious effects associated with TEs. Importantly, by being able to move between vertical genetic lineages, TEs can still proliferate in a population of sexually reproducing individuals despite causing substantial fitness defects ( ).

Citation: Gladyshev E. 2017. Repeat-Induced Point Mutation and Other Genome Defense Mechanisms in Fungi, p 687-699. In Heitman J, Howlett B, Crous P, Stukenbrock E, James T, Gow N (ed), The Fungal Kingdom. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.FUNK-0042-2017
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Repeat-Induced Point Mutation and Other Genome Defense Mechanisms in Fungi
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Citation: Gladyshev E. 2017. Repeat-Induced Point Mutation and Other Genome Defense Mechanisms in Fungi, p 687-699. In Heitman J, Howlett B, Crous P, Stukenbrock E, James T, Gow N (ed), The Fungal Kingdom. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.FUNK-0042-2017
/content/10.1128/9781555819583.chap33.fig33-1
Figure 1

The structure of motif VI in Masc1/RID proteins is not canonical. The canonical motif VI contains the absolutely conserved NV diad (asparagine-valine). This diad is present in all C5-cytosine methyltransferases except Masc1/RID. The asparagine residue of NV physically interacts with the proline residue of the catalytic triad PCQ (in motif IV) and thus plays a critical role by controlling the positions of these segments with respect to one another in the native structure of the protein. The valine residue of NV is also functionally important, because its substitution for alanine is known to inactivate the catalytic activity of M.HhaI. Yet in all Masc1/RID proteins the NV diad is replaced with either QT (e.g., in RID) or ET (e.g., in Masc1), hinting at the possibility that Masc1/RID proteins might have unique catalytic and/or substrate requirements.

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10.1128/9781555819583/fig33-1.gif
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Figure 1

The structure of motif VI in Masc1/RID proteins is not canonical. The canonical motif VI contains the absolutely conserved NV diad (asparagine-valine). This diad is present in all C5-cytosine methyltransferases except Masc1/RID. The asparagine residue of NV physically interacts with the proline residue of the catalytic triad PCQ (in motif IV) and thus plays a critical role by controlling the positions of these segments with respect to one another in the native structure of the protein. The valine residue of NV is also functionally important, because its substitution for alanine is known to inactivate the catalytic activity of M.HhaI. Yet in all Masc1/RID proteins the NV diad is replaced with either QT (e.g., in RID) or ET (e.g., in Masc1), hinting at the possibility that Masc1/RID proteins might have unique catalytic and/or substrate requirements.

Citation: Gladyshev E. 2017. Repeat-Induced Point Mutation and Other Genome Defense Mechanisms in Fungi, p 687-699. In Heitman J, Howlett B, Crous P, Stukenbrock E, James T, Gow N (ed), The Fungal Kingdom. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.FUNK-0042-2017
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Figure 2

Recognition of interspersed homology during RIP in . This assay detects and quantifies the occurrence of RIP mutations in response to engineered DNA repeats. Instances of DNA homology are created between two short segments of chromosomal DNA, one of which is normally represented by an endogenous sequence, while the sequence and orientation of the other segment can be manipulated as desired. In this situation, the number of RIP mutations provides a very sensitive readout of DNA homology perceived by the recombination-independent mechanism of repeat recognition for RIP. Weak interspersed homology is formed between the endogenous 500-bp segment (blue) and a synthetic DNA segment (green) integrated at a nearby position as the replacement of the () gene. This particular pattern involves 4-bp units of homology spaced with the periodicity of 11 bp and exists between “repeat units” in the inverted orientation. Pairwise sequence comparisons showing all matches of 4 bp long. Two situations are presented: random homology (left panel) and interspersed homology (right panel). No cryptic homology can be seen except the intended pattern of weak interspersed homology (magenta box). The occurrence of mutations induced by weak interspersed homology. Seventy progeny spores from the “XKO” cross ( ), which had been previously found to contain at least one RIP mutation, were reanalyzed by sequencing of an additional 255 bp in the “left” flank of the construct (corresponding to the single-copy coding/translated sequence of ).

10.1128/9781555819583/fig33-2_thmb.gif
10.1128/9781555819583/fig33-2.gif
Image of Figure 2
Figure 2

Recognition of interspersed homology during RIP in . This assay detects and quantifies the occurrence of RIP mutations in response to engineered DNA repeats. Instances of DNA homology are created between two short segments of chromosomal DNA, one of which is normally represented by an endogenous sequence, while the sequence and orientation of the other segment can be manipulated as desired. In this situation, the number of RIP mutations provides a very sensitive readout of DNA homology perceived by the recombination-independent mechanism of repeat recognition for RIP. Weak interspersed homology is formed between the endogenous 500-bp segment (blue) and a synthetic DNA segment (green) integrated at a nearby position as the replacement of the () gene. This particular pattern involves 4-bp units of homology spaced with the periodicity of 11 bp and exists between “repeat units” in the inverted orientation. Pairwise sequence comparisons showing all matches of 4 bp long. Two situations are presented: random homology (left panel) and interspersed homology (right panel). No cryptic homology can be seen except the intended pattern of weak interspersed homology (magenta box). The occurrence of mutations induced by weak interspersed homology. Seventy progeny spores from the “XKO” cross ( ), which had been previously found to contain at least one RIP mutation, were reanalyzed by sequencing of an additional 255 bp in the “left” flank of the construct (corresponding to the single-copy coding/translated sequence of ).

Citation: Gladyshev E. 2017. Repeat-Induced Point Mutation and Other Genome Defense Mechanisms in Fungi, p 687-699. In Heitman J, Howlett B, Crous P, Stukenbrock E, James T, Gow N (ed), The Fungal Kingdom. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.FUNK-0042-2017
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