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Repeat-Induced Point Mutation and the Population Structure of Transposable Elements in Microbotryum Violaceum

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Repeat-Induced Point Mutation and the Population Structure of Transposable Elements in Microbotryum Violaceum Copyright © 2005 by the Genetics Society of America DOI: 10.1534/genetics.105.042564 Repeat-Induced Point Mutation and the Population Structure of Transposable Elements in Microbotryum violaceum Michael E. Hood,*,1 Melanie Katawczik† and Tatiana Giraud‡ *Department of Biology, University of Virginia, Charlottesville, Virginia 22903, †Department of Plant Pathology, North Carolina State University, Raleigh, North Carolina 27695 and ‡Ecologie, Syste´matique et Evolution, Universite´ Paris-Sud, F-91405 Orsay Cedex, France Manuscript received February 25, 2005 Accepted for publication April 12, 2005 ABSTRACT Repeat-induced point mutation (RIP) is a genome defense in fungi that hypermutates repetitive DNA and is suggested to limit the accumulation of transposable elements. The genome of Microbotryum violaceum has a high density of transposable elements compared to other fungi, but there is also evidence of RIP activity. This is the first report of RIP in a basidiomycete and was obtained by sequencing multiple copies of the integrase gene of a copia-type transposable element and the helicase gene of a Helitron-type element. In M. violaceum, the targets for RIP mutations are the cytosine residues of TCG trinucleotide combinations. Although RIP is a linkage-dependent process that tends to increase the variation among repetitive se- quences, a chromosome-specific substructuring was observed in the transposable element population. The observed chromosome-specific patterns are not consistent with RIP, but rather suggest an effect of gene conversion, which is also a linkage-dependent process but results in a homogenization of repeated se- quences. Particular sequences were found more widely distributed within the genome than expected by chance and may reflect the recently active variants. Therefore, sequence variation of transposable elements in M. violaceum appears to be driven by selection for transposition ability in combination with the context- specific forces of the RIP and gene conversion. RANSPOSABLE elements make up a diverse group erally have relatively small genomes that are said to be Tof molecular parasites found in nearly all organ- “streamlined” because they contain little repetitive DNA isms. Their activity can be harmful to the host organism (Kidwell 2002; Selker 2002; Wo¨stemeyer and Krei- because insertion of new copies often disrupts gene bich 2002; Brookfield 2003; Galagan and Selker expression (Wright et al. 2003) and because the similar- 2004). ity between copies at different loci promotes ectopic The mechanistic details and specific protein-DNA in- recombination and destabilizes chromosomes (Charles- teractions involved in target recognition and site-spe- worth et al. 1992; Petrov et al. 2003). Therefore, it is cific mutation are not completely resolved, but the gen- not surprising that parallels are drawn between transpo- eral properties of the RIP process have been well sitional activity and the virulence of conventional para- characterized in several ascomycete species (for reviews sites (Jordan and McDonald 1999). Moreover, the see Selker 2002; Galagan and Selker 2004). RIP in- term “arms race” has been used when there is evidence duces C-to-T mutations in duplicated DNA sequences. that the host genome has evolved mechanisms to defend Cytosine residues of particular nucleotide combinations against transposable elements (Jordan et al. 1999; Lov- are targeted; for example, in Neurospora crassa CA dinu- sin et al. 2001). cleotides are the targets of RIP activity. RIP is known to A genome defense called repeat-induced point mutation occur within haploid nuclei following mating but prior (RIP) is known to occur in ascomycete fungi (reviewed to meiosis (i.e., in the dikaryotic stage that precedes by Selker 2002). RIP is a homology-dependent gene- karyogamy). Cytosine methylation is frequently associ- silencing mechanism that directly mutates multicopy ated with RIP-mutated sequences; however, it remains DNA sequences. RIP has been credited with preventing undetermined whether this is a required step in a deami- transposable element accumulation in fungi, which gen- nation process to yield C-to-T mutations. RIP acts in a pairwise manner on duplicated DNA sequences, such that they not only are altered but also become dissimilar Sequence data from this article have been deposited with the because not all the same cytosine residues are changed EMBL/GenBank Data Libraries under accession nos. AY729078– in both copies. Finally, RIP occurs at a much higher AY729484 and AY939912–AY939923. rate between a pair of duplicated sequences when they 1Corresponding author: Department of Biology, Gilmer Hall, Univer- sity of Virginia, Charlottesville, VA 22903. are located on the same chromosome, and more so E-mail: [email protected] when they are in close linkage as compared to unlinked Genetics 170: 1081–1089 ( July 2005) 1082 M. E. Hood, M. Katawczik and T. Giraud duplications. In addition to inactivating transposable some bands, but one sample (plug 7 of Figure 1A) was in a elements by point mutations, RIP is thought to discour- region where bands are not as well resolved; this extract may therefore have included DNA from multiple chromosomes. age ectopic recombination by decreasing the sequence PCR primers were designed for a retrotransposon fragment similarity between copies at different loci (Cambareri found previously by sequencing random AFLP products from et al. 1991). M. violaceum (Hood 2002; Hood and Antonovics 2004): in- RIP has been studied mostly from a mechanistic per- ternal primers for the retrotransposon sequence were ECA/ Ј spective and as a gene-silencing tool. However, there is MGA700BR.2 forward 5 TGGAACCTGTACGTTGATGG and reverse 5Ј ATTTTCTGACCCGTTTGACG. The sequence is little understanding of how RIP affects the intragenomic in the integrase region of a Ty1/copia-type element, the most “population” of transposable elements or their evolu- common type of transposable element in M. violaceum. The re- tionary history. The homology-dependent and linkage- sulting 367-bp sequence begins approximately with the first dependent nature of RIP may cause the genetic changes histidine of the HHCC motif that characterizes the N terminus in transposable elements to be largely influenced by the of the Psuedoviridae integrase gene (as defined in Peterson- Burch and Voytas 2002). particular genomic or chromosomal contexts in which A separate PCR reaction was conducted with each chromo- they reside. This presents a strong contrast to our para- some-specific sample of DNA that was isolated from the karyo- digm of sequence evolution based on random mutation type gel. The resulting PCR products were then cloned using the clones per chromosome 30ف and may seriously complicate the interpretation of trans- TA cloning kit from Invitrogen and posable element evolution based on their sequence vari- were sequenced using dye termination techniques with an ABI 377 automated DNA sequencer. Sequence alignment was carried ation. out manually in Sequencher (Gene Codes Corporation) and is In this study, we determined the sequence variation available under accession nos. AY729078–AY729484 in the Pop- for transposable elements in the fungus Microbotryum Set section of GenBank (http://www.ncbi.nlm.nih.gov). All devia- violaceum, which is unusual among fungi because this tions from the consensus sequence were confirmed to represent species contains a high density and diversity of transpos- unambiguous base pair signals in the electropherograms. As a test to determine whether evidence of RIP activity is able elements (Hood et al. 2004; Hood 2005). We pro- also present in the sequence variation of the other types of vide evidence of RIP activity in M. violaceum by identi- transposable elements in M. violaceum, PCR primers were de- fying the target site for C-to-T mutations, the first such signed for a Helitron-type sequence (accession no. BZ782234) reported for a basidiomycete. We also compare the se- identified in a previous study (Hood 2005). Helitrons are re- quence variation of element copies within and between cently discovered DNA-based transposable elements that repli- cated by a rolling circle mechanism and are found in a broad the different chromosomes and provide evidence that range of organisms (Kapitonov and Jurka 2001; Poulter et gene-conversion acts in addition to RIP to determine al. 2003). Internal primers for a 301-bp region of BZ782234 the population structure of transposable elements in were 44-forward 5Ј CACGGTGAGTAGCCATTCC and 374- M. violaceum. reverse 5Ј CCGTTTACTGCGTGATCTCC. PCR was con- ducted using whole genomic DNA, 12 products of which were then cloned and sequenced as described above, and sequences are available under accession nos. AY939912–AY939923 in MATERIALS AND METHODS GenBank. M. violaceum (Basidiomycota; formerly Ustilago violacea)isa As a control to confirm that DNA isolated from karyotype gels pathogenic fungus of plants in the Caryophyllaceae. It is com- was chromosome specific, the methods described above were monly studied as a model for disease ecology and fungal genet- replicated with a separate culture of the same fungal strain. ics (Antonovics et al. 2002; Garber and Ruddat 2002, and DNA was isolated as before from chromosome bands corre- references therein). Collections of the fungus from different sponding to plugs 2 and 3 in Figure 1A and were similarly host plants probably represent cryptic species, but the taxon- used for PCR amplification and sequencing of 30 clones per omy of these lineages is not resolved.
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