Trends in Genetics
RIP: the evolutionary cost of genome defense
Section snippets
What is RIP?
RIP is a process that efficiently detects and mutates duplicated sequences 2, 5 (Figure 1). Acting only during the sexual cycle, RIP identifies duplications that are greater than ∼400bp (or ∼1kb in the case of unlinked duplications) [6] and introduces C:G to T:A mutations into both copies of the duplicated sequences. All duplications that share greater than ∼80% nucleotide identity [7] are detected efficiently and in a single passage through the sexual cycle, up to ∼30% of the C:G pairs in
Evolution by gene duplication
One of the most striking characteristics of the N. crassa genome sequence is the almost complete absence of highly similar gene pairs (Figure 2). Of the predicted 10 082 N. crassa protein-coding genes, only six pairs (12 genes) share >80% nucleotide or amino-acid identities in their coding sequences (Figure 2). This value is significant because, as described previously, RIP mutates duplicated sequences that share greater than ∼80% nucleotide similarity. Five of the six pairs of highly similar
RIP and mobile elements
The deactivation of repeated sequences by RIP serves as an effective defense against mobile elements. Early studies revealed clear evidence of inactivation by RIP of both the retrotransposon Tad (transposon from Adiopodoumé) [17] and the DNA-type transposon Punt (putative transposon) [15], consistent with failures to detect transpositions in numerous wild Neurospora strains. An analysis of sequences from the centromeric region of linkage group VII revealed the relics of several additional types
Repeated genes persisting in the face of RIP
Only a few repeated genes are known to survive RIP. The dispersed 5S rRNA and tRNA genes apparently evade RIP because their length is below the threshold for RIP; indeed, the first known natural relic of RIP consists of a tandem duplication of an 800 bp segment that includes a 5S rRNA gene [9]. The only sizeable repetitive sequences that are known to persist in spite of RIP in N. crassa are ∼175 copies [21] of the tandemly arranged, 9 kb rDNA repeats that give rise to the 17S, 5.8S and 25S rRNAs.
Mechanism of RIP
The study of the mechanism of RIP by biochemical approaches is difficult owing to the microscopic ascogenous tissue in which the process takes place. In addition, classical genetic studies of RIP are hampered by the fact that the cells in this tissue contain nuclei from each parent, preventing recognition of recessive defects. As a result, only one component of the molecular machinery for RIP has been reported to date. A candidate-gene approach was used to identify a gene required for RIP
Relationship between RIP and methylation
Methylation in N. crassa appears to be closely related to RIP. Approximately 2% of cytosines in the N. crassa genome are methylated [36] and, as with animals and plants, methylation has been shown to cause gene silencing in this fungus [11]. In contrast to mammals and plants, methylation in N. crassa is not biased towards symmetric (e.g. CpG) sites [34]. DNA methylation is typically heavy but heterogeneous, with every cytosine in the affected region having a >80% chance of being methylated [35]
Phylogenetic distribution
Since its discovery in N. crassa, evidence has accumulated that RIP or similar processes occur in other fungi. Experimental evidence of repeat-induced mutation has been reported in Magnaporthe grisea 43, 44, Podospora anserina [45] and Leptosphaeria maculans [46] (Table 1). In addition, transposons displaying mutations that are consistent with RIP have been identified in various other fungi including several Neurospora species [17], in addition to Fusarium oxysporum 47, 48, 49, Aspergillus
Perspectives and conclusions
The nature of RIP and its impact on the N. crassa genome raise several interesting considerations. Gene duplication has been considered the primary means by which organisms evolve new genes [14]. Although there has been considerable debate over the degree of selection acting on duplicated genes, the frequency with which beneficial mutations are generated, the rate at which new functions evolve and the rate at which duplicated genes are lost 57, 58, gene duplication has nonetheless remained
Acknowledgements
We thank Michael Freitag, Kristina Smith, Sarah Calvo and Bruce Birren for their feedback and comments. This work was supported by NIH grants GM35690 (E.U.S.), HG02045–05 (J.E.G.) and HG02152–03 (J.E.G), and by NSF grants MCB-0131383 (E.U.S.) and 0078148 (J.E.G.).
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