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REVIEW
1 Department of Biochemistry and Cell Biology, Institute for Cell and Developmental Biology, SUNY Stony Brook, Stony Brook, New York 11794-5215, USA; 2 Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey 08854, USA
During meiosis, recombination between homologous chromosomes creates a physical connection that is necessary for proper chromosome segregation at the first meiotic division. For many years, the paradigm used to explain the molecular mechanism of recombination has been the double-strand break repair (DSBR) model (Fig. 1; Szostak et al. 1983
). (The definitions of the acronyms used in this review, in order of their appearance, can be found in Table 1.) One key feature of this model is that recombination is initiated by the formation of programmed DSBs (double-strand breaks). The meiosis-specific protein responsible for catalyzing these breaks is a topoisomerase-like protein called Spo11 (Bergerat et al. 1997
; Keeney et al. 1997
). The identification and functional analysis of Spo11 homologs from a wide variety of organisms, including worms, fruit flies, fission yeast, and mammals, indicates that repair of programmed DSBs is a universal feature of meiotic recombination (Keeney 2001
). A second key feature of the model is the generation of a recombination intermediate called a double Holliday junction (dHJ). Differential resolution of this intermediate was proposed to determine the formation of crossover (CO) versus noncrossover (NCO) chromosomes. Recent advances indicate, however, that the decision of whether a recombination event will result in a CO or NCO chromosome occurs much earlier, soon after DSB formation (Allers and Lichten 2001a
; Hunter and Kleckner 2001
; Clyne et al. 2003
). In addition, studies of a newly discovered endonuclease, Mus81, indicate that, in addition to dHJ resolution, COs may be formed by the processing of non-dHJ intermediates (Heyer et al. 2003
; Osman et al. 2003
). The decision of which crossover pathway to use appears to vary between organisms and may, therefore, be evolutionarily significant (de los Santos et al. 2003
).
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| The double-strand break repair model for meiotic recombination |
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Recent data from the Lichten and Kleckner labs have challenged the idea that both COs and NCO chromosomes are derived from dHJs. For example, mutant conditions exist in which HJs are unresolved and COs are greatly reduced. Nevertheless, the formation of NCO chromosomes is unaffected (Allers and Lichten 2001a
; Clyne et al. 2003
). These results support the argument that repair of DSBs can occur by two separate pathways during budding yeast meiosisa CO pathway that involves the formation of fully mature dHJ intermediates and an NCO pathway that does not (Fig. 2). NCOs are proposed to arise by displacement of the extended invading strand followed by reannealing to the 3'-tail on the other side of the break (synthesis-dependent strand annealing or SDSA; for review, see Paques and Haber 1999
). Kinetic studies of the formation of different recombination intermediates during meiosis in wild-type cells support this view (Allers and Lichten 2001a
; Hunter and Kleckner 2001
).
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| The Mus81* endonuclease functions in DNA metabolism in mitotic and meiotic cells |
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The MUS81/MMS4/EME1 genes were identified independently by several different labs, and mus81/mms4/eme1 mutant phenotypes are consistent with a role in DNA repair (Haber and Heyer 2001
). In mitotic cells, mus81/mms4 mutants exhibit sensitivity to DNA damaging agents such as methylmethane sulfonate (MMS) and camptothecin (CPT), which are believed to stall replication forks and generate DSBs as a result of problems with DNA replication (Prakash and Prakash 1977
; Interthal and Heyer 2000
; Doe et al. 2002
; Bastin-Shanower et al. 2003
). Mus81* is not generally required for DSB repair in vegetative cells, however, as mus81/mms4 mutants are resistant to DSB-producing agents such as ionizing radiation and bleomycin (Prakash and Prakash 1977
; Xiao et al. 1998
; Boddy et al. 2000
; Interthal and Heyer 2000
). Mus81 physically interacts with the budding yeast recombination protein Rad54 and with the fission yeast DNA damage checkpoint kinase Cds1 (Boddy et al. 2000
; Interthal and Heyer 2000
). Mus81 is a nuclear protein and, in human cells, is recruited to sites of UV-induced damage specifically in S phase (Fu and Xiao 2003
; Gao et al. 2003
). These observations are consistent with the idea that Mus81* plays a role in rescuing stalled replication forks. In addition, mus81 and mms4 are synthetically lethal with mutants in SGS1 (RQH1 in fission yeast), a conserved 3'5' DNA helicase known to be required for genome stability (Boddy et al. 2000
; Mullen et al. 2001
). This lethality can be rescued by preventing homologous recombination, suggesting that Mus81* acts on some type of recombination intermediate in mitotic cells (Fabre et al. 2002
; Bastin-Shanower et al. 2003
).
In both fission and budding yeast, mus81/mms4/eme1 mutants have severe meiotic phenotypes. In fission yeast, spore viability is reduced to
1%, with high levels of chromosome missegregation (Boddy et al. 2001
). In budding yeast, depending on temperature and strain background, up to 90%100% of mus81/mms4 diploids arrest in prophase as a result of unprocessed recombination intermediates triggering the meiotic recombination checkpoint (de los Santos et al. 2001
, 2003
). In those rare tetrads that are formed, spore viability is reduced to
40% (Interthal and Heyer 2000
; de los Santos et al. 2003
). In both yeasts, these phenotypes are caused by a failure to repair meiosis-specific DSBs, as defects in meiotic progression and spore viability are rescued by mutations that prevent initiation of recombination (Boddy et al. 2001
; de los Santos et al. 2001
; Kaliraman et al. 2001
). Clearly, Mus81* plays an essential role in meiotic recombination in both S. pombe and S. cerevisiae. The critical question then has been, what is the mechanism of its action?
| Model I: Mus81* cleaves intact HJs |
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In contrast to rMus81*, partially purified preparations of epitope-tagged Mus81* from S. pombe cell extracts (TEV-Mus81*) are active on intact HJs (Boddy et al. 2001
; Gaillard et al. 2003
). It has been suggested that the ability of TEV-Mus81* to cleave intact junctions is caused by the presence of a protein accessory factor or posttranslational modification (Gaillard et al. 2003
). Mus81* partially purified from human cells, however, exhibits the same substrate specificity as the recombinant complexes, making it unlikely that the preference for 3'-flaps and pRFs over HJs exhibited by the bacterially produced enzymes is caused by a lack of a posttranslational modification (Constantinou et al. 2002
). Based on the preference of Mus81* for nicked HJs, it has been proposed that Mus81* cleaves intact junctions by a "nick/counternick" mechanism (Gaillard et al. 2003
). In this case, the first cut by Mus81* is slow and rate-limiting. This nick makes the junction more flexible and a better substrate for Mus81*, and the second cut is proposed therefore to be nearly simultaneous with the first. An alternative explanation for the differences observed between TEV-Mus81* and rMus81, however, could derive from impurities present in the crude TEV-Mus81* fraction. Resolving this paradox, therefore, will require comparison of rMus81/Eme1 from E. coli with highly purified Mus81* from S. pombe cells.
The HJ cleavage observed by Mus81* is nonsymmetrical and therefore leaves flaps and gaps on the HJs that cannot be repaired simply by ligation (Fig. 3E; Boddy et al. 2001
; Constantinou et al. 2002
). Therefore, if Mus81 resolves intact HJs, it does so by a non-RuvC/RusA-like mechanism. The idea that eukaryotic HJ resolution is mechanistically distinct from prokaryotic resolvases, while intriguing, is challenged by the discovery of a canonical RuvC-like activity in human cells. This activity, called Resolvase A, efficiently cuts intact HJs symmetrically to make ligatable, linear, nicked duplexes, is dependent on a branch migration activity, and is biochemically separable from Mus81* (Constantinou et al. 2002
). Taken together, the biochemical data make it unlikely that the in vivo substrate of Mus81 is an intact HJ.
Further evidence that Mus81* is not required to cleave intact HJs comes from meiotic studies using budding yeast (de los Santos et al. 2001
, 2003
). In this organism, dHJs can be directly analyzed (Schwacha and Kleckner 1995
). Whereas HJs would be predicted to accumulate in a resolvase mutant, mms4 exhibited a decrease in the frequency of dHJs during meiosis compared with wild type. In addition, the effect of mms4 on crossing over was, at most, twofold and appears to be dependent on chromosome size. Finally, overexpression of rusA had no effect on the meiotic defects of either mus81 or mms4 in budding yeast (de los Santos et al. 2003
). Therefore Mus81* is not required to generate the bulk of meiotic COs in budding yeast. This fact, coupled with the observation that dHJs are the precursor to the majority of meiotic COs, provides compelling evidence that Mus81* is not resolving intact HJs in budding yeast.
| Model II: Mus81* cleaves 3'-flaps generated by a partial strand displacement and annealing pathway of recombination |
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| Budding yeast has two genetically separable pathways for generating meiotic crossovers |
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40%. Interestingly, the COs that occur in msh4 mutants do not exhibit genetic interference (Novak et al. 2001
20% viable spores, confirming that these genes define two independent pathways for generating crossovers, an MSH4MSH5-dependent interference pathway (designated Class I) and an MUS81MMS4-dependent noninterference pathway (Class II).
The discovery of two different CO pathways in budding yeast may explain why spore viability is decreased to a much lesser extent in budding yeast mus81 diploids compared with fission yeast mus81 mutants (40% vs. <1%). In fission yeast, none of the COs display interference and the gene products required for the Class I pathway (e.g., MSH4 and MSH5) are absent from the S. pombe genome (Munz 1994
; Villeneuve and Hillers 2001
). Therefore, although the MUS81MMS4 pathway accounts for a relatively minor fraction of COs in budding yeast, it is responsible for most, if not all, of the COs in fission yeast (Fig. 5).
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| Model III: Mus81* cleaves D-loops and half-junctions |
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5 nt. Such flaps could isomerize to 3'-flaps and be cleaved by Mus81* or they could be processed by a 5'-flap endonuclease such as Rad27 in budding yeast or Rad2 in fission yeast (Alleva and Doetsch 1998
Model III beautifully reconciles the data between fission yeast and budding yeast. The assumption is that the SEI intermediate is the precursor to recombination in both organisms. In fission yeast, NCOs result from SDSA, whereas COs result almost exclusively from Mus81* cleavage (Fig. 5; Osman et al. 2003
). In budding yeast, NCOs are also derived by SDSA, but COs can be generated by two independent pathways. The Class II, noninterfering COs result from Mus81* cleavage, similar to fission yeast. Whether D-loop cleavage by Mus81* occurs prior to SEC as drawn in Osman et al. (2003
) or after SEC (Fig. 5) is not yet known. For the Class I, interference-dependent COs, the SEC intermediate is matured into a dHJ structure that is then resolved, presumably by an RuvC/RusA-like mechanism, to make COs. If Mus81* cleaves D-loops before SEC, then MSH4MSH5 could act at the step promoting formation of the SEC intermediate. Alternatively, if Mus81* cleaves after SEC, MSH4MSH5 might prevent this cleavage, thereby allowing maturation to dHJs. The MutS homolog, Msh2, is known to bind directly to HJs, so perhaps Msh4Msh5 complexes bind directly to branched junctions as well (Alani et al. 1997
; Marsischky et al. 1999
). Msh4Msh5 is part of the complex of proteins required for interference that includes Zip1, Zip2, and Zip3 (Agarwal and Roeder 2000
). Binding of this complex to the junctions of developing recombination intermediates could create a physical barrier that prevents Mus81* from cutting.
In budding yeast, Class II COs comprise a minority class that is derived independently from Class I COs and NCOs. Therefore, mus81/mms4 mutants would be predicted to exhibit only a small decrease in COs and have no deleterious effects on gene conversion, which is exactly what is observed (de los Santos et al. 2003
). In fission yeast, crossing over occurs primarily, if not entirely, by the Class II pathway. Therefore, by Model III, COs should be greatly reduced (Fig. 5). NCOs occur by SDSA after D-loop formation, and therefore should be unaffected. These predictions are consistent with the fission yeast recombination data (Osman et al. 2003
; Smith et al. 2003
). A strength of Model III, therefore, is that the differences observed in meiotic phenotypes between fission and budding yeast are explained, not by saying that Mus81* cleaves different substrates in the two yeasts, but rather that cleavage of the same substrate has a different relative contribution to the total number of meiotic COs in each yeast.
The rusA suppression of fission yeast mus81 meiotic phenotypes could be explained if SEC intermediates can spontaneously proceed to dHJs, thereby creating excellent substrates for RusA. If this occurs, then fission yeast has no way of normally resolving these dHJs, given the very low spore viability of mus81 mutants. The fact that rusA overexpression is unable to suppress budding yeast mus81 meiotic defects may mean that formation of dHJs cannot proceed spontaneously in S. cerevisiae, but requires the activity of proteins such as Msh4Msh5. Alternatively, the failure of rusA to suppress mus81 budding yeast meiotic phenotypes could be due to the very significant differences in meiotic chromosome behavior exhibited by the two yeasts. During budding yeast meiosis, homologous chromosomes become physically associated by the formation of a meiosis-specific protein-aceous structure called the synaptonemal complex (SC; Roeder 1997
). In contrast, in fission yeast, homologs do not synapse and no SC is formed (Bahler et al. 1993
). The SC may, therefore, prevent RusA from accessing recombination intermediates during budding yeast meiosis. Consistent with this idea, rusA is able to suppress some mus81/mms4 phenotypes in vegetatively growing budding yeast cells where the SC is absent (Bastin-Shanower et al. 2003
; Odagiri et al. 2003
).
| The semantics of resolution |
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| Conclusion |
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One outcome in having two independent ways of generating COs is the ability to modulate interference. Interestingly, mms4 exhibits a stronger phenotype on a small chromosome that displays a lower level of interference than on a large chromosome on which interference is stronger (Kaback et al. 1999
; de los Santos et al. 2003
). Therefore, the degree of interference may be regulated by altering the frequency with which the different CO pathways are used. The two extreme cases are fission yeast, where there is no interference and COs are generated primarily, if not exclusively, by the Class II pathway, and worms, where interference is strong (Hillers and Villeneuve 2003
) and the Class I pathway apparently generates all COs. It is possible that mammals, like budding yeast, use both CO pathways during meiosis. Mammalian chromosomes exhibit interference, and MSH4 and MSH5 are meiosis-specific genes required for the proper execution of meiosis; Mus81* activity has been detected in somatic cells (de Vries et al. 1999
; Broman and Weber 2000
; Kneitz et al. 2000
). However, whether mammals follow the worm paradigm, in which all COs are MSH4/MSH5-dependent, or the budding yeast paradigm, in which a minority of COs are generated by Mus81*, is as yet unknown. The study of this very interesting enzyme has therefore suggested a novel mechanism for generating meiotic COs and may ultimately shed light on how the distribution of COs is regulated in different organisms.
| Acknowledgments |
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| Footnotes |
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3 Corresponding author. E-MAIL brill{at}mbcl.rutgers.edu; FAX (732) 235-4880. ![]()
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