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10.1146/annurev.genet.38.072902.091500
Annu. Rev. Genet. 2004. 38:233–71
doi: 10.1146/annurev.genet.38.072902.091500
c 2004 by Annual Reviews. All rights reserved
Copyright First published online as a Review in Advance on June 21, 2004
RECOMBINATION PROTEINS IN YEAST
Berit Olsen Krogh and Lorraine S. Symington
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Columbia University Medical Center, New York, New York 10032;
email: [email protected]; [email protected]
Key Words double-strand break repair, RAD52 epistasis group, Holliday junction
resolution, replication fork collapse
■ Abstract The process of homologous recombination promotes error-free repair
of double-strand breaks and is essential for meiosis. Central to the process of homologous recombination are the RAD52 group genes (RAD50, RAD51, RAD52, RAD54,
RDH54/TID1, RAD55, RAD57, RAD59, MRE11, and XRS2), most of which were identified by their requirement for the repair of ionizing radiation-induced DNA damage
in Saccharomyces cerevisiae. The Rad52 group proteins are highly conserved among
eukaryotes. Recent studies showing defects in homologous recombination and doublestrand break repair in several human cancer-prone syndromes have emphasized the
importance of this repair pathway in maintaining genome integrity. Herein, we review
recent genetic, biochemical, and structural analyses of the genes and proteins involved
in recombination.
CONTENTS
INTRODUCTION . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
SUBSTRATES AND MECHANISMS OF HOMOLOGOUS
RECOMBINATION . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
The DSBR and SDSA Models . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
One-Ended Strand Invasion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Single-Strand Annealing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Recombination at Stalled or Collapsed Replication Forks . . . . . . . . . . . . . . . . . . . .
DSB FORMATION . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Initiation of Meiotic Recombination . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Initiation of Mitotic Recombination . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
FORMATION OF 3 ssDNA TAILS AT BREAK SITES . . . . . . . . . . . . . . . . . . . . . . .
Properties of the MRX Complex . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Resection of DSBs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
FORMATION OF THE RAD51 NUCLEOPROTEIN FILAMENT . . . . . . . . . . . . . .
Properties of Rad51 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Mediators of Rad51 Filament Assembly . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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Homologous Pairing and Strand Exchange . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Negative Regulation of Recombination by Srs2 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
RAD51-INDEPENDENT RECOMBINATION . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Rad52: a DNA Annealing Protein . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Dmc1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
HOLLIDAY JUNCTION RESOLUTION ACTIVITIES . . . . . . . . . . . . . . . . . . . . . . .
The Mus81-Mms4 (Eme1) Nuclease . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Resolvase A . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Dissolution of dHJs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
NONHOMOLOGOUS END JOINING . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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INTRODUCTION
Recombination refers to the exchange, or transfer, of information between DNA
molecules and is found in all organisms that have been studied in detail. Homologous recombination (HR) involves the interaction of DNA sequences with
perfect, or near-perfect, homology over several hundreds of base pairs. Recombination between sequences with little or no sequence homology is referred to as
nonhomologous recombination or end joining (NHEJ). The process of homologous recombination plays essential roles in the maintenance of genome stability
in prokaryotic and eukaryotic organisms. The primary function of homologous
recombination in mitotic cells is to repair double-strand breaks (DSBs) or singlestrand gaps that form as a result of replication fork collapse, from processing of
spontaneous damage, and from exposure to DNA-damaging agents. Homologous
recombination is also required for telomere maintenance, and consequently, proliferation, in the absence of telomerase. During meiosis, HR is essential to establish
a physical connection between homologous chromosomes to ensure their correct
disjunction at the first meiotic division. In addition, the high frequency of meiotic recombination contributes to diversity by creating new linkage arrangements
between genes, or parts of genes.
Yeast has proved a valuable system for the analysis of recombination in eukaryotes. Much of our understanding of the mechanisms of recombination is based on
organisms, such as Saccharomyces cerevisiae, in which all of the products of
an individual meiosis can be recovered for analysis in the form of asci containing four haploid spores. The analysis of the segregation of heterozygous markers
during meiosis forms the basis for most recombination models. The ability to
manipulate the genome to create well-defined genetic and physical markers has
also contributed to our understanding of the mechanisms of HR. Genetic screens
for mutants with altered rates of recombination, decreased survival in response to
DNA-damaging agents, reduced sporulation, or spore viability have led to the identification of more than 30 genes involved in recombination. The proteins encoded
by the RAD52 epistasis group genes [RAD50, RAD51, RAD52, RAD54, RAD55,
RAD57, RAD59, RDH54 (TID1), MRE11 (RAD58), and XRS2] play direct roles
in HR and are the focus of this review.
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SUBSTRATES AND MECHANISMS OF HOMOLOGOUS
RECOMBINATION
Two types of recombination events have been identified based on the segregation
of heterozygous markers during meiosis: crossing over and gene conversion. Studies in yeast and other fungi have shown that meiotic gene conversion events are
frequently associated with the exchange of flanking markers (79). This association
was thought to be due to alternate resolution of a Holliday junction (HJ) containing intermediate to generate crossover or noncrossover products. However, recent
studies suggest crossover and noncrossover products are generated from different
intermediates in meiotic recombination (7). Several models have been proposed to
explain the molecular mechanisms of recombination (52, 72, 125, 139, 203), and
of these the double-strand-break repair (DSBR) and synthesis-dependent strandannealing (SDSA) models are most consistent with the available genetic data.
The DSBR and SDSA Models
Studies of DSB-induced recombination between plasmid and chromosomal sequences provided the impetus for the DSBR model (144, 145, 203), and subsequent
meiotic studies were in good agreement with its predictions (30, 124, 168, 196). In
this model the initiating event is a DSB (Figure 1). The ends are resected to form
3 single-stranded (ss) tails that are active in strand invasion with a homologous
duplex. Following strand invasion, the 3 end is extended by DNA synthesis. The
D-loop formed by strand invasion is able to pair with the other side of the DSB
(second end capture), and the 3 end of the noninvading strand is also extended by
DNA synthesis. Gap filling and ligation results in the formation of a double Holliday junction (dHJ) intermediate. Random resolution of the two Holliday junctions
is expected to yield equal numbers of crossover and noncrossover products.
The DSBR model adequately explains several features of meiotic recombination. To account for the low levels of associated crossing over observed for mitotic
DSB-induced gene conversion events, the synthesis-dependent strand-annealing
(SDSA) model was proposed (52, 139, 189) (Figure 1). In the SDSA model, one
or both ends of the broken duplex invade the donor and initiate DNA synthesis as envisioned in the DSBR model. For two-ended invasions, both strands are
subsequently displaced and able to anneal through the newly synthesized complementary regions (139). For a one-ended invasion, the elongated invading strand is
displaced after extensive DNA synthesis and pairs with the other side of the break
(52).
One-Ended Strand Invasion
Under some circumstances, a broken chromosome may present only one end for
repair (Figure 2). Collapsed replication forks generate only one end for strand
invasion to restart replication. A one-ended DSB will also be generated when
a telomere becomes uncapped and is degraded (62, 66, 113). The chromosome
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Figure 1 Models for the repair of double-strand breaks. The DSBR and SDSA models
both initiate with invasion of a 3 end (left panel). After priming DNA synthesis,
the second end is captured and a double Holliday junction intermediate is formed
(DSBR). Resolution can occur in either plane at both junctions to generate crossover
or noncrossover products. In the SDSA model, the nascent strand is displaced, pairs
with the other 3 single-stranded tail, and DNA synthesis completes repair. A DSB made
between direct repeats is subject to resection to generate 3 single-stranded tails (right
panel). When complementary sequences are revealed owing to extensive resection,
the single-stranded DNA anneals resulting in deletion of one of the repeats and the
intervening DNA. The 3 tails are removed by the Rad1/10 nuclease and the nicks are
ligated. 3 ends are indicated by arrowheads, newly synthesized DNA is represented
by dashed lines.
end can then invade homologous sequences (sister chromatid or homologue, or
subtelomeric repeats of other chromosomes) and initiate DNA synthesis from the
site of strand invasion to the telomere, templated by the donor duplex. This process
is termed break-induced replication (BIR). Homology-dependent duplication of
an entire chromosome arm to the end of a transformed linearized plasmid has also
been detected in yeast and is presumed to occur by a similar mechanism (43, 134).
BIR can occur at a conventional DSB if the gene conversion pathway is restricted
by mutation of RAD51, or by limiting homology to one side of the break (99, 116).
Single-Strand Annealing
Single-strand annealing (SSA) is restricted to DSBs that occur between direct
repeats (Figure 1). These events have been detected in yeast and animal cells using
artificial direct repeats and could conceivably be important for repair in genomes
of higher eukaryotes that contain many repeated sequences (54, 107, 119). After
formation of the DSB, the ends are resected to produce 3 single-stranded tails,
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Figure 2 One-ended strand invasion. If a telomere becomes uncapped, or the other
side of a DSB is not available for HR, strand invasion can occur and replication proceeds
to the end of the chromosome (BIR).
which can anneal together when resection is sufficient to reveal complementary
single-stranded regions. Single-stranded tails are removed by nucleases and the
resulting gaps/nicks filled in by DNA repair synthesis and ligation. This process
is accompanied by deletion of one of the repeats and the DNA between the direct
repeats and is therefore considered to be mutagenic.
Recombination at Stalled or Collapsed Replication Forks
In yeast, HR efficiently repairs DSBs, but it is not clear if all mitotic recombination
events initiate from DSBs. Single-stranded gaps at stalled replication forks might
also initiate recombination and may occur more frequently than DSBs during
vegetative growth of budding yeast (50). In Escherichia coli, generation of DSBs at
stalled replication forks is thought to occur about once every two to three rounds of
replication (126). In vertebrates, DSBs are thought to occur during every S-phase,
explaining the essential requirement for recombination factors such as RAD51
(183, 214). There are several possible mechanisms for the formation of DSBs
during replication. First, the replication fork could run into a nick on the template
strand, resulting in collapse of the replication fork. Assuming that the nascent
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Figure 3 Role of recombination in restoring collapsed or stalled replication forks.
DSBs made by replication fork collapse, or resolution of a regressed fork, are repaired
by strand invasion restoring the fork. A gap on the lagging strand can be used to pair
with the homologous sister chromatid to allow bypass of the lesion.
strand of the other arm becomes ligated to the template strand of the same polarity,
the broken arm could invade this duplex to restart replication (Figure 3). Second,
the nascent strands at a stalled fork could pair and reverse branch migrate to form
a pseudo-Holliday structure, also known as a regressed fork or chicken foot (71).
This intermediate could then be cleaved by an HJ-specific endonuclease, resulting
in collapse of the fork (170). The collapsed fork would then have to undergo
strand invasion as described above. There is genetic evidence for regressed forks in
E. coli (170), but in yeast, regressed forks have only been observed in hydroxyurea
(HU)-arrested cells in the absence of the S-phase checkpoint kinase Rad53 (111).
If replication stalls because of a lesion present on the leading strand, the fork
could regress such that the lagging strand of the paired nascent strands templates
synthesis of the leading strand (71). The regressed fork could then be resolved by
branch migration to restart replication without strand invasion (Figure 3). Recent
studies in E. coli have shown continued synthesis of the lagging strand when
the leading strand is stalled, providing further support for this template-switching
model (147). Template switching may also function in the repair of polymeraseblocking lesions on the lagging strand. In this case, the single-stranded region could
pair with the parental strand of the sister chromatid and the newly synthesized
leading strand could template synthesis of the stalled lagging strand in order to
bypass the lesion (Figure 3) (50). The template-switching models do not involve a
DSB intermediate, but are likely to require HR proteins for annealing and branch
migration.
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The above models share a number of common features, including formation of
single-stranded DNA at break sites (or gaps), strand invasion or strand annealing,
and resolution of recombination intermediates. Below, we review genetic, molecular, and biochemical studies of the yeast proteins thought to catalyze these steps
of the homologous recombination reaction.
DSB FORMATION
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Initiation of Meiotic Recombination
During meiosis, the Spo11 protein catalyzes DSB formation at 150–200 sites
within the genome to initiate high frequency of recombination (94). Spo11 is a
meiosis-specific protein with sequence similarity to the small subunit (Top6A)
of a type IIB topoisomerase from Sulfolobus shibatae (18, 95). Classical type
II topoisomerases transiently break both strands of duplex DNA by formation
of covalent 5 phosphotyrosyl enzyme-DNA intermediates. Following substrate
topoisomerization, the covalent linkage is resolved and the DNA strands resealed.
Spo11 appears to catalyze only the first of these two steps and in certain mutants
(rad50S, sae2, mre11-S, and mre11-58) remains stably covalently joined to the
5 ends at break sites (5, 95, 123, 138, 158, 209). Tyr-135 is the active site tyrosine
in Spo11 and accordingly, mutation of this residue results in the inability to induce
DSBs in vivo (18, 48). The currently favored model is that Spo11 is removed
from ends by the Mre11-Rad50-Xrs2 (MRX) complex and Sae2, and the resulting
free 5 ends are then available for resection. Spo11 cleaves nonrandomly, but does
not exhibit sequence-specific cleavage. The sites of DSBs coincide with DNase I
hypersensitive sites in chromatin and are generally in the 5 noncoding regions of
genes (17, 65, 232).
Nine other genes, MEI4, MER2/REC107, REC102, REC103/SKI8, REC104,
REC114, MRE11, RAD50, and XRS2, as well as two meiosis-specific RNA splicing factors (Mer1 and Mre2), are required for DSB formation during meiosis (94).
MRE11, RAD50, and XRS2 are members of the RAD52 epistasis group, and are
required for the repair of ionizing radiation (IR)-induced DNA damage in mitotic cells in addition to meiotic DSB formation in S. cerevisiae (4, 202). Mre11
transiently associates with sequences within chromatin that are the sites of Spo11dependent DSBs (23). This association, however, is still observed in the spo11Y135F active site mutant, indicating that Mre11 localization is not dependent on
the presence of DSBs. Mre11 remains associated with DSB sites in strains that
are defective for resection, but still dissociates from chromatin in strains defective
for strand invasion, indicating that it is resection, not repair, that is the signal for
removal of Mre11. The requirement for the MRX complex in DSB formation may
be to ensure that the factors required for processing of Spo11-induced DSBs are
present at the time of cleavage.
The role of the other genes required for DSB formation is poorly understood.
SKI8 is the only other gene, in addition to MRE11, RAD50, and XRS2, that is
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expressed in vegetative cells and because of its well characterized role in RNA
metabolism was thought to function indirectly during meiosis (94). However, Arora
et al. (10) have shown that Ski8 and Spo11 directly interact and that both are
required to recruit other proteins to chromatin, implicating a scaffold function for
Ski8 in assembly of the pre-DSB complex (10).
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Initiation of Mitotic Recombination
Mitotic recombination is initiated by accidental DSBs, single-strand gaps, and
by the induction of specialized endonucleases. The best characterized of these
endonucleases are HO and I-SceI, which have long nonpalindromic recognition
sequences and generate 4-bp staggered cuts with 3 -OH overhangs (36, 98). HO endonuclease cleaves a 24-bp sequence within the mating-type locus MAT, to initiate
gene conversion between the resident MAT allele and one of the two transcriptionally silent HM cassettes (141, 189). The HO endonuclease is normally expressed
at the end of G1 in haploid mother cells, and the protein is highly unstable owing
to the presence of a PEST signal that signals degradation via the ubiquitin –26S
proteosome system (92). The DSB made by HO is repaired using the same factors
required to repair IR-induced DSBs (see below).
The mitochondrial endonuclease I-SceI is encoded by the optional intron of the
21S rRNA gene and is responsible for intron mobility (36). I-SceI recognizes and
cleaves an 18-bp nonsymmetrical sequence within omega− DNA and the omega+
intron is used to template repair resulting in propagation of the intron. The recombination factors within mitochondria that promote repair of the I-SceI-induced
break are unknown. When expressed in the nucleus, I-SceI cleaves its target site
and subsequent repair occurs by the same mechanisms as in other chromosomal
DSBs (156).
FORMATION OF 3 ssDNA TAILS AT BREAK SITES
Properties of the MRX Complex
Repair of DNA double-strand breaks (DSBs) by homologous recombination requires nucleolytic processing of the DNA ends to form invasive 3 ssDNA tails.
In S. cerevisiae, 3 ssDNA regions can be detected that extend hundreds to a few
thousand nucleotides into the sequences flanking meiotic and mitotic DSBs (197,
225, 227). The initial observation that unresected meiotic DSBs accumulate in
rad50S mutants suggested a role for Rad50 and its complex partners Mre11 and
Xrs2 (MRX complex) in processing DSBs during meiosis. Yeast rad50, mre11
and xrs2 null mutants are also extremely sensitive to DNA-damaging agents such
as IR and methyl methane-sulfonate (MMS) (28, 59, 88, 209). Moreover, the null
mutants have slowed resection of HO-induced DSBs at the MAT locus (83, 191,
209). These observations suggested a common role for MRX in processing both
meiotic and mitotic DSBs.
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Structural and functional homologues of the Mre11/Rad50 complex exist in
all domains of life (9). In E. coli, the Rad50/Mre11 homologues SbcC/SbcD
form a large complex with ATP-dependent dsDNA 3 -5 exonuclease and ATPindependent ssDNA endonuclease activities (38, 171). Consistent with the homology to the nuclease subunit SbcD, human and yeast Mre11 have manganesedependent nuclease activities in vitro (149, 207, 208). The nucleolytic repertoire
of Mre11 includes: (a) 3 -5 exonuclease activity on blunt and 3 recessed ends; (b)
endonuclease activity on circular and linear ssDNA, but not on homopolymers;
and (c) endonuclease cleavage of hairpin ends and 3 ssDNA overhangs at the
single-/double-stranded transition. The observation that ssDNA homopolymers
are resistant to cleavage suggests that Mre11 is structure specific and cleaves ssDNA by trapping transient secondary structures that allow the enzyme to cut at
the preferred single-/double-stranded transition. Rad50 and Xrs2 both influence
MRX substrate binding and potentiate the intrinsic nuclease activity of Mre11
(206, 207). The N-terminal region of the 78-kDa Mre11 protein contains five conserved phosphoesterase motifs found in a superfamily of phosphoesterases that
includes di-metal Ser/Thr protein phosphatases and E. coli SbcD (88, 171). The
crystal structure of Pyrococcus furiosus (Pf) Mre11 (res. 1–342) shows a protein
with a two-domain fold. Domain I encompasses the Mre11 active site with seven
residues from the conserved phosphoesterase motifs coordinating two Mn2+ ions.
Domain II forms a cap structure that partially overhangs the active site (76).
S. cerevisiae (Sc) Rad50 is a 153-kDa protein with homology to E. coli SbcC
(5, 162, 171). Both proteins share the modular sequence architecture found in the
structural maintenance of chromosomes (SMC) family of proteins (190). Common
features include N-terminal Walker A and C-terminal Walker B motifs, linked by a
600–900 residue α-helical coiled-coil domain (9). The crystal structure of PfRad50
catalytic domain (cd) (res. 1–152 & 735–882) reveals that the Walker A and B domains assemble into a single globular intramolecular ATP-binding cassette (ABC)
type ATPase domain. The α-helical region linking the two parts of the composite
ATPase domain folds up as a protruding antiparallel coiled-coil (Figure 4) (75,
76, 78). In ScRad50 each coiled-coil extends approximately 60 nm away from the
globular ATPase domain (8). PfRad50 forms homodimers in the presence of ATP
(75, 78). Two nucleotides are bound per dimer, each specifically coordinated in
cis by the Walker A motif of one monomer and in trans by the ABC signature
motif of the other monomer, thereby linking ATP binding with dimer formation
(129). Dimerization creates a DNA-binding interface across the Rad50 dimer that
could explain the ATP stimulated DNA binding observed for both yeast and P. furiosus Rad50 (77, 162). Mre11 binds to the base of the coiled-coil near the Rad50
DNA-binding interface, suggesting the formation of a composite DNA-binding
site within the (Mre11)2/(Rad50) 2 heterotetramer. The model MR-tetramer has
two protruding coiled-coil tails pointing away from a globular head containing an
Mre11 dimer bound to the Rad50 ABC-ATPase dimer (8, 75, 76). A conserved
Cys-X-X-Cys motif at the apex of the coiled-coil forms a molecular zinc-hook,
which allows Rad50 to form intermolecular dimers across the coiled-coil domains
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(75). Each Rad50 coiled-coil contributes two cysteines from the CXXC motif to
form an interlocking metal binding site with one tetrahedrally coordinated Zn2+
ion. The overall structure of the MR complex and intermolecular dimers/multimers
formed through the Rad50 zinc-hook have been observed by electron microscopy
(EM) (8, 75) and scanning force microscopy (SFM) (44, 219). SFM analyses have
also revealed that the HsMR and ScMRX complexes associate with ends of dsDNA molecules and through intermolecular interactions between the extended
coiled-coils and zinc-hooks can tether linear DNA molecules together (34, 44,
219). Juxtaposition of DNA ends may be one of the important functions of MRX
in NHEJ. The flexibility of the Rad50 coiled-coil and the overall length (120 nm) of
a coiled-coil dimer suggests that the MRX complex may in fact be able to connect
sister chromatids during HR (Figure 4). Mutations in the ScRad50 C687YLC690
Figure 4 Models of the Mre112Rad502Xrs21 pentamer and MRX DNA tethering
functions. The terminal CXXC-hooks form an interlocking dimerization interface in the
Rad50 coiled-coils. Intermolecular dimerization between individual complexes allows
MRX to tether DNA ends (bottom) and perhaps tether and align sister chromatids (top).
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motif result in defective MRX complex formation or increased IR sensitivity, underscoring the structural and functional importance of the zinc-hook (75).
The third complex component, Xrs2 in yeast (MRX) or Nbs1 in vertebrates
(MRN), is found only in eukaryotes (31, 88, 215, 220). Xrs2 is part of the complex
through direct interaction with Mre11. Sedimentation analyses and size-exclusion
chromatography suggest a M2R2X1 complex stoichiometry (8, 34, 215). Although
they are thought to be functional analogues, the sequence similarity between Xrs2
and Nbs1 is limited to an N-terminal forkhead-associated (FHA) domain. The FHA
domain is a phosphorylation-dependent protein-protein interaction motif found in
a variety of eukaryotic proteins. The HsMRN and ScMRX complexes play critical
roles in initiation of the intra S-phase checkpoint in response to DNA damage,
and Nbs1/Xrs2 are both phosphorylated as part of the damage signal by kinases
from the ATM family of protein kinases (41, 106, 214a, 233, 236). The checkpoint
function in combination with the DNA tethering and nuclease activities is likely
to contribute to the complexity of phenotypes displayed by mrx mutants.
Resection of DSBs
The predicted nucleolytic activity needed for processing DSBs into 3 ssDNA ends
is a 5 -3 exonuclease. Mre11 is a 3 -5 exonuclease, which leaves a directionality conflict inherently at odds with the involvement of Mre11 in DSB resection.
However, point mutations in the conserved phosphoesterase motifs [D16A, D56N,
H125N, and H213Y (mre11-58S)], which abolish Mre11-nuclease activity in vitro,
result in accumulation of unresected meiotic DSBs and sporulation failure in vivo
(57, 131, 209). The phenotype caused by these mre11-nuclease defective (nd)
alleles is similar to that found for the rad50S mutants, which accumulate unresected DSBs with the meiotic Spo11-transesterase still covalently attached to the
5 DNA end (4, 95, 197). Similar biochemical analyses have not been repeated
for the mre11-nd mutants, but based on the similarity in DSB accumulation and
lack of resection, it is likely that these breaks also contain the covalent Spo11DNA adduct. The directionality paradox notwithstanding, these observations are
evidence of a direct role for the MRX complex and Mre11-nuclease activity in
meiotic DSB processing and Spo11 removal.
Despite the severe meiotic phenotypes associated with mre11-nd alleles, the
majority of these nuclease mutants show only mild-to-intermediate sensitivity to
IR, and mating-type switching and resection of HO-induced DSBs occur with
wild-type kinetics (29, 57, 103, 131). Moreover, the rad50, mre11 and xrs2 null
mutations slow resection of HO-induced DSBs but do not abolish processing (83).
Two alleles of mre11 show sensitivity to IR and MMS comparable to the null allele,
mre11-4 (H241L,H243Y) and mre11-58S (H213Y). Both mutants, however, fail
to interact with Rad50 in two-hybrid or coimmunoprecipitation assays, implying
that for mitotic DSB resection, MRX as a complex is more important than the
catalytic activity of Mre11 (29, 209, 215).
To reconcile the conflicts surrounding the roles of MRX in meiotic versus
mitotic DSB processing, we suggest the following resection models (Figure 5). To
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Figure 5 Model for the roles of the MRX complex in processing of DSBs. For
simplicity, only one side of the DSB is included in this illustration. Resection of DSBs
with modified/blocked ends is initiated by MRX (center). The “clean” ends are then
substrate for continued processing by MRX (center) or by a 5 -3 exonuclease, e.g.,
Exo1 (right). Unmodified DSB ends can be resected directly by a 5 -3 exonuclease,
independent of Mre11-mediated initiation (right) or through DNA unwinding by an
unknown helicase and cleavage by the Mre11 structure-specific endonuclease (center
and left).
solve the nuclease directionality problem, MRX could potentially cooperate with
a helicase to unwind the DNA duplex from the break and Mre11 processing the 5
strand by continuous endonucleolytic cleavage at transient secondary structures.
For meiotic DSBs, resection of the 5 strand would be intrinsic to removal of
Spo11, because the protein is released by the nucleolytic reaction most proximal
to the DSB. It is also possible that Mre11 only acts as the initiating nuclease,
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responsible for removing only a short stretch of DNA attached to the covalent
DNA-(5 -phosphotyrosyl)-Spo11 adduct. Once the terminal adduct is removed, a
5 -3 exonuclease could take over and continue resection. A weak ATP-dependent
DNA-unwinding activity has been associated with the human Rad50/Mre11/Nbs1
complex (150). Perhaps this weak helicase activity is sufficient to unwind a short
stretch of DNA duplex from the Spo11 break site, enough for Mre11 to release
Spo11 by the structure-specific endonuclease activity.
We propose a model for mitotic DSB resection similar to the model for Mre11processing of Spo11-attached meiotic DSBs in which the Mre11-nuclease is specialized to deal with DSBs carrying modified ends that other nucleases are unable
to process. Ionizing radiation as a source of DNA damage often generates DSBs
with modified terminal nucleotides or even protein-DNA adducts. In our model,
these modified DSBs require Mre11 for initial resection or “clean-up.” In contrast,
HO-induced DSBs and other mitotic DSBs with unmodified clean ends would be
direct substrates for processing by a bona fide resection nuclease or other redundant nucleases, even without Mre11 activity. Exo1, a 5 -3 dsDNA exonuclease
and flap-endonuclease, is the only nuclease with an identified role in DSB resection in the absence of MRX (53). The exo1mre11 double mutant has severe
growth defects and increased IR sensitivity compared with mre11 (210). When
expressed from a high-copy-number plasmid, EXO1 partially rescues the mitotic
DNA repair defects of mre11 strains, indicating that Exo1 is capable of some
DSB processing in the absence of MRX (103, 132). In contrast, overexpression of
Exo1 in a mre11-nd strain does not lead to an increase in IR resistance (132). The
incomplete rescue of mre11 by Exo1 and the failure to rescue mre11-nd mutants
support the model that certain DSBs require initial processing by MRX. In addition to a role in initiating DSB resection, the MRX complex may be involved in
recruiting the resection nuclease(s) to the site of damage. The high concentration
of Exo1 needed to ameliorate the mre11 phenotypes could reflect poor recruitment of Exo1 to DSBs in the absence of MRX. This added recruitment function
would explain the relatively mild phenotypes resulting from most mre11-nd alleles
compared with the mre11 and other mre11 mutants that are not proficient for
MRX complex formation. Finally, the observation that mating-type switching in
an exo1mre11-nd double mutant proceeds with wild-type kinetics suggests that
at least one additional nuclease is capable of substituting for Mre11 and Exo1 in
processing unmodified DSBs (132).
Consistent with the idea that Mre11 is a specialized nuclease capable of removing bulky adducts from DNA ends, E. coli SbcC/SbcD efficiently removes
biotin-avidin complexes from the 5 ends of DNA duplexes in vitro (37). Additional support for the Mre11-nuclease processing terminal DNA adducts is found
in the apparent requirement for the MRN complex in removal of the terminal
protein of adenovirus. In early region E4-deleted adenoviruses, newly replicated
genomes fail to package owing to extensive MRX-dependent concatemerization
mediated through nonhomologous end joining (188, 226). No concatemerization
was observed in similar experiments using cells expressing the nuclease-deficient
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Mre11-3 protein (equivalent to the yeast mre11-3 H125L,D126V allele) (188).
These results suggest that the Mre11-nuclease is responsible for initiating viral
concatemerization by removing the terminal protein-DNA adduct.
Sae2, a protein with no known homologues, is a possible fourth member of
the MRX complex based on the similarity in meiotic phenotypes of sae2 null
and rad50S mutants (123, 158). In addition, the sae2 null mutant is epistatic to
and mimics the mitotic phenotypes of nuclease mutant mre11-D56N (160; B.O.
Krogh, E.A. Morgan & L.S. Symington, unpublished data). These results indicate
that in vivo the catalytic activity of MRX is perhaps modulated by, and only fully
functional in, the presence of Sae2.
FORMATION OF THE RAD51 NUCLEOPROTEIN FILAMENT
Properties of Rad51
The 3 ssDNA tails formed by resection are substrates for binding by the Rad51
protein to promote pairing and strand exchange with the homologous duplex.
S. cerevisiae Rad51 is a 43-kDa protein with 30% identity to the catalytic domain of RecA encompassing the Walker A and B motifs for nucleotide binding
and/or hydrolysis, referred to as the ATPase domain (AD) (1, 16, 174). The crystal structures of the human RAD51 AD and full-length P. furiosus Rad51 have
been determined (151, 172) and show similar structural organization to the AD of
RecA protein (187). The PfRad51 N-terminal domain (absent from RecA) forms
a small globular domain that is implicated in DNA binding and is separated from
the AD by a flexible linker (3, 172). The crystal structure of PfRad51 reveals a
double heptameric ring, consistent with ring structures observed by EM (234).
The ATPase domains of PfRad51 are arranged as pie-shaped wedges within the
heptameric ring. Interaction between monomers is mediated by the polymerization
motif (PM) previously defined as the BRC-peptide interaction domain (151, 172).
The ring structure is proposed to be the inactive, or storage, form of Rad51, which
under appropriate conditions is targeted to ssDNA, disassembles, and then binds
to ssDNA as a filament (172).
ScRad51 forms right-handed helical filaments on single- and double-stranded
DNA with structural similarity to those formed by RecA (142, 200). Binding to
ssDNA activates the Rad51 ATPase. Mutation of the conserved lysine residue
within the Walker A box to alanine (Rad51-K191A) abolishes DNA binding and
ATPase activities of ScRad51. When the same lysine residue is substituted with
arginine (Rad51-K191R), the protein retains ATP-dependent DNA binding, but no
significant hydrolysis of ATP. In vivo, the rad51-K191A mutation confers a null
phenotype and is dominant negative in diploids, whereas rad51-K191R mutants are
partially functional for repair and recombination (133, 174, 201). RPA stimulates
binding of Rad51 to ssDNA that contains secondary structures, suggesting that the
role of RPA in presynapsis is to remove secondary structures from ssDNA to allow
formation of a continuous Rad51 nucleoprotein filament (Figure 6). However, RPA
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Figure 6 Model for strand invasion by Rad51 and mediator proteins, Rad52, Rad54
& Rad55/Rad57 (only one side of the DSB is shown). 1) 3 ssDNA tails are produced
by the MRX complex and/or a 5 -3 resection exonuclease. 2) The ssDNA tails are
coated by RPA to eliminate secondary structures. 3) Rad52 recruits Rad51 to the
RPA-ssDNA complex. 4) The Rad51 nucleoprotein filament extends on the ssDNA
mediated by Rad55/Rad57 and RPA is displaced. 5) The Rad51 nucleoprotein filament
locates a homologous DNA donor sequence. 6) Rad54 interacts with Rad51, promotes
chromatin remodeling, DNA unwinding and strand annealing between donor DNA and
the incoming Rad51 nucleoprotein filament.
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has a higher affinity for ssDNA, and in vitro Rad51 only successfully competes
for DNA binding if added to the reaction prior to RPA (199). In vivo, RPA is very
abundant and presumably binds to ssDNA prior to Rad51. This poses a problem
because Rad51 has to replace RPA to form an active filament for strand exchange.
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Mediators of Rad51 Filament Assembly
The severe reduction in Rad51-mediated strand exchange products caused by addition of RPA simultaneously with or prior to Rad51 can be overcome by addition
of Rad52 (140, 175, 198). The 52-kDa Rad52 protein interacts directly with both
RPA and Rad51 and is thought to mediate Rad51 filament assembly by displacing
RPA and simultaneously delivering Rad51 to ssDNA (Figure 6) (182, 194). Mutations that delete the C-terminal region of Rad52, or residues 409–412, responsible
for Rad51 interaction are defective in this mediator function in vitro (100, 175).
Strains that express C-terminal truncations of Rad52 show higher resistance to IR
than rad52 null mutants and are also suppressed by RAD51 present in high copy.
Rad51 localization to sites of DSBs in vivo has been shown by immunofluoresence, chromatin immunoprecipitation (ChIP), and by the use of GFP-Rad51
in live cells (19, 49, 128, 193, 230). Localization of Rad51 to the site of DSBs
requires Rad52, consistent with the biochemical data indicating Rad52 is essential
for loading of Rad51 onto RPA-coated ssDNA (64, 128, 193, 230).
The Rad55 and Rad57 proteins are also implicated as mediators in assembly
of the Rad51 nucleoprotein filament (Figure 6). Rad55 and Rad57 are referred
to as Rad51 paralogs because they share 20%–30% sequence identity to Rad51.
Null mutants of rad55 or rad57 are as sensitive to IR as rad51 mutants at low
temperatures (20◦ C), but the IR sensitivity is significantly suppressed at 30◦ C
(112). This cold sensitivity is thought to be due to the role of Rad55 and Rad57 in
stabilization of the Rad51 nucleoprotein filament. The Rad55 and Rad57 proteins
interact to form a stable heterodimer that binds to ssDNA and exhibits a weak
ATPase activity (68, 87, 199). Mutation of the conserved lysine residue within the
Walker A box to alanine in Rad57 confers only a weak DNA repair defect, whereas
the equivalent mutation in Rad55 confers a severe defect in response to IR (87).
Both RAD55 and RAD57 are required for the formation of Rad51 foci in meiotic
cells, but studies in mitotic cells show only a partial defect in Rad51 localization
to DSBs (63, 64, 128, 193, 230). Using ChIP, Sugawara et al. found a delay in
assembly of the Rad51 filament at an HO-induced DSB, but no pairing between the
3 ssDNA tail and donor sequences, suggesting Rad55 (and presumably Rad57)
could have another function after formation of the Rad51 filament, or that the Rad51
filament is only partially assembled and this is insufficient to support homologous
pairing (193). Overexpression of RAD51 or point mutations within RAD51 that
result in higher affinity of the mutant proteins for DNA suppress the IR sensitivity
of rad55 or rad57 mutants, consistent with a role for these proteins in formation
or stabilization of the Rad51 filament (55, 68, 87). The purified Rad55/Rad57
heterodimer functions as a mediator in the strand-exchange reaction by allowing
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Rad51 to nucleate on ssDNA in the presence of RPA (199). Rad55 interacts with
Rad51, but not with RPA, suggesting that the mediator activity is distinct from that
exerted by Rad52 (68, 87).
The Rad54 protein, a member of the Swi2/Snf2 family of chromatin remodeling
proteins, also functions to facilitate Rad51 binding to ssDNA in the presence of
RPA and to stabilize Rad51 nucleoprotein filaments in vitro (121, 230). However,
the significance of these biochemical studies is unclear because Rad51 foci still
form in response to DSBs, and persist longer, in rad54 mutants (128).
Homologous Pairing and Strand Exchange
Once assembled, the Rad51 nucleoprotein filament is capable of interacting with
a second DNA molecule, either single- or double-stranded DNA, to initiate strand
exchange. Synapsis entails alignment of the nucleoprotein filament with homologous sequences within the second molecule. Although the details of this step of the
reaction have not been well characterized for Rad51, studies with RecA protein
suggest that the homology search is rapid and involves random collisions of the
two molecules. Once homology is found, strand exchange occurs between the two
aligned molecules if one of the partners has a free end to allow stable intertwining
of the complementary strands. The reaction requires ATP, but is also supported by
nonhydrolyzable analogs of ATP. The polarity of strand exchange is 5 to 3 with
respect to the complementary strand of the DNA duplex, opposite to the polarity
observed for RecA (200).
Although the strand transfer assay has been used extensively to characterize
recombinases, the reaction between linear ssDNA and homologous supercoiled
plasmid DNA (D-loop assay) is thought to better mimic the in vivo substrates.
Rad51 and RPA inefficiently promote D-loop formation, but the reaction is greatly
stimulated by the addition of Rad54 or the Rad54-related protein Rdh54 (152, 154).
Both Rad54 and Rdh54 exhibit dsDNA-specific ATPase activity and translocate on
duplex DNA to generate unconstrained negative and positive supercoils (122, 154,
155, 217). These activities are dependent on ATP, and mutation of the conserved lysine within the Walker A box of Rad54 or Rdh54 results in a null phenotype in vivo
(35, 154, 155). The ATPase and translocation activities of Rad54 are stimulated by
Rad51, or by Rad51-ssDNA complexes (122, 217). Rad54 does not stimulate the
pairing activity of RecA, suggesting that the physical interaction between Rad51
and Rad54 is functionally important (35, 86, 122, 217). The strand separation at
unwound regions is expected to facilitate the search for homology between duplex
DNA and the incoming Rad51 nucleoprotein filament and to promote formation
of the nascent joint when homology is located. The ATP-dependent translocation
activity of Rad54 on duplex DNA also functions to displace nucleosomes (and
presumably non-nucleosomal proteins as well) that could be inhibitory to strand
invasion by the Rad51 nucleoprotein filament (6, 84).
Sugawara et al. (193) showed homologous pairing between the MAT and HML
loci in vivo in rad54 mutants, but DNA synthesis to extend the invading 3 end
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was not observed, suggesting that the primary function of Rad54 is postsynaptic
(Figure 6). Rad54 has been shown to promote heteroduplex DNA extension during
strand exchange and to displace Rad51 from duplex DNA (180, 181). Disruption
of Rad51-dsDNA complexes could be important for turnover of Rad51 at the end
of recombination, to uncover the 3 end of paired intermediates to initiate DNA
repair synthesis, or to remove unproductive association of Rad51 with duplex DNA
during presynapsis.
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Negative Regulation of Recombination by Srs2
SRS2 encodes a DNA helicase that is suggested to limit heteroduplex extension
and/or reverse abnormal recombination intermediates (33, 163, 218). Mutations
in SRS2 suppress the UV sensitivity of rad6 and rad18 mutants, and this suppression is thought to occur by channeling lesions from error-prone repair into the
recombinational repair pathway (1, 102, 167). Elevated rates of gene conversion
are observed between direct repeats in srs2 mutants, but in some DSB-induced
recombination assays, the recovery of recombinants is reduced (2, 11). The UV
sensitivity of srs2 diploids is suppressed by homozygous mutations in RAD51,
RAD52, RAD55, and RAD57, suggesting that lethal recombination intermediates
are formed in the absence of srs2 (1). Such intermediates are thought to arise
spontaneously in srs2 rad54 and srs2 sgs1 mutants (61, 97).
In vitro, the Srs2 protein inhibits strand exchange mediated by Rad51 (101,
221). Srs2 inhibits the reaction by displacement of Rad51 from the presynaptic
filament rather than by disruption of joint molecules. The current model is that
Srs2 prevents initiation of inappropriate recombination events presynaptically by
disrupting the Rad51 filament, but Srs2 could also function at later steps in the
removal of Rad51, or by acting on DNA intermediates (81).
RAD51-INDEPENDENT RECOMBINATION
Rad52: a DNA Annealing Protein
The RAD51-dependent pathway for recombination is the most efficient pathway
for gene conversion and is required to repair most DSBs in mitotic cells. However,
in some assays, significant rates of recombination are detected in rad51 mutants,
suggesting an alternate pathway for strand invasion. The alternate pathway requires RAD52 and to some extent, RAD59. Deletion of RAD52 in S. cerevisiae
results in severe defects in gene conversion, SSA, recombination between inverted repeats, and formation of survivors in the absence of telomerase (202). In
contrast, rad51 mutants show no defect in SSA, a five- to tenfold reduction in
the rate of spontaneous recombination between inverted repeats and a defect in
one of the two telomere recombination pathways (82, 161, 213). The rad52-327
allele, encoding a truncated protein lacking the Rad51 interaction domain, promotes RAD51-independent recombination, suggesting that a core activity capable
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of strand invasion is retained in the N-terminal region (212). Intermolecular recombination shows a much greater dependence on RAD51 than intramolecular events,
but even in this context HR events are still detected in rad51 mutants and these
occur at higher rates than those observed in rad52 mutants (15, 43). These observations suggest that Rad52 can promote efficient intramolecular recombination
and a low incidence of intermolecular strand invasion.
Both yeast and human Rad52 are multimeric and form ring structures as visualized by electron microscopy (159, 176, 185). Using both conventional and
scanning transmission electron microscopy, the HsRad52 protein was observed
to form heptameric rings with a strong pinwheel appearance and a central channel (185). Rad52 appears to have two modes of self-association. Assembly of
monomers into rings requires sequences in the conserved N-terminal domain of
Rad52, whereas the formation of higher-order multimers is mediated by the C
terminus (159). Formation of multimers is consistent with genetic studies showing intragenic complementation between N- and C-terminal mutations of rad52
(27). The crystal structure of the N-terminal domain (residues 1–209 or 1–212) of
the HsRad52 protein has been determined and reveals an 11-membered ring (90,
177). The overall structure resembles a mushroom, consisting of a stem containing highly conserved hydrophobic residues and a domed cap. A positively charged
groove was identified under the domed cap and mutational analysis was consistent
with this region comprising a DNA-binding surface (90). One residue identified as
important for DNA binding, Arg55, is equivalent to Arg70 of ScRad52, previously
shown to be important for Rad52 function in vivo (13, 136).
The purified Rad52 protein binds preferentially to single-stranded DNA and
promotes annealing of complementary DNA sequences (135). Rad52-promoted
annealing of long molecules is stimulated by RPA, whereas Rad52 efficiently
anneals oligonucleotides in the absence of RPA (135, 176, 195). The probable role
of RPA in strand annealing is to remove secondary structures from single-stranded
DNA to allow annealing by Rad52. The important function of Rad52 in SSA is to
anneal the complementary single-stranded regions exposed by resection (179).
The human Rad52 protein has been shown to promote the formation of D-loops.
This activity, as well as DNA binding, is retained in a truncated form of the protein
comprising the first 237 residues (89). The formation of D-loops by Rad52 probably
occurs by annealing between the incoming single-stranded DNA and transiently
single-stranded DNA present in the supercoiled plasmid. Because RAD52 is the
only gene known to be essential for RAD51-independent recombination events, it
is assumed that the annealing activity of Rad52 can be used for strand invasion
(116, 161). Presumably, some donor sequences are transiently single-stranded and
can be annealed by Rad52 to ssDNA generated from a resected DSB. Once this
annealing step has occurred, the 3 end could be extended by DNA synthesis to
stabilize the intermediate.
Like Rad51, Rad52 forms discrete foci in response to IR-, HO-, and Spo11induced DSBs and during S-phase of unirradiated cells (64, 109, 128). Surprisingly,
only one or two foci are observed using a Rad52-GFP fusion protein, independent
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of the dose of IR, suggesting that damaged DNA is sequestered at one or two sites
within the nucleus, perhaps at specialized repair centers (108). The formation of
Rad52 foci is independent of Rad51 (128).
The RAD59 gene was identified in a screen for mutants defective for RAD51independent spontaneous mitotic recombination between inverted repeats (14).
The rad59 mutation was shown to cause modest defects in several mitotic recombination assays and moderate sensitivity to IR. RAD59 is important for SSA
between chromosomal direct repeats, especially as the repeat length decreases
(13, 192). This suggests that Rad52 becomes more dependent on Rad59 when the
repeats to be annealed are short, or when short homologies are embedded within
extensive regions of heterology. Consistent with this hypothesis, recent studies
have shown that RAD59 is required for spontaneous recombination between homologous sequences, whereas the RAD51-promoted pathway acts preferentially
on sequences with extensive homology (184).
RAD52 present in more than one copy suppresses the radiation sensitivity of
rad59 mutants, suggesting that the proteins interact and/or have overlapping functions (14). RAD59 encodes a 26-kDa protein with homology to the N terminus of
Rad52, which includes the self-interaction and DNA-binding domains of Rad52.
Rad52 interacts with Rad59 raising the possibility of formation of a heteromeric
Rad52-Rad59 ring (42). Purified Rad59 binds to ss and dsDNA and promotes annealing of complementary ssDNA (42, 153). However, the annealing activity of
Rad59 is not stimulated by RPA and even though the biochemical activities of
the two proteins are similar, Rad59 is unable to substitute for Rad52 in Rad51independent recombination (14, 42). We suggest Rad59 is a stimulatory factor
for Rad52 and is important for recombination between short repeats or when the
activity of Rad52 is compromised.
Dmc1
DMC1 encodes a 334-amino acid polypeptide with significant similarity to RecA
and Rad51, which is expressed only during meiosis (20). Dmc1 is 45% identical
to Rad51 along its entire length, and biochemical studies indicate a higher functional conservation than the other Rad51 paralogs to RecA/Rad51. Both Dmc1 and
Rad51 form foci during meiosis, and the foci indicate significant colocalization of
the two proteins (19). Mutation of DMC1 leads to the accumulation of DSBs in
meiosis and a reduction in the frequency of reciprocal recombinants, as measured
by physical assay (20). RAD51 and DMC1 are both required for high rates of meiotic recombination and have overlapping, but nonidentical, roles in meiosis (173).
Overexpression of RAD51 partially suppresses the recombination and sporulation
defects of dmc1 diploids, consistent with the proteins being partially redundant
(211). Dmc1 is important to direct repair between homologous nonsister chromatids during meiosis, a function shared by three other meiosis-specific proteins,
Hop1, Mek1, and Red1 (169, 223).
HsDmc1 has a weak ATPase activity, binds to ss and dsDNA, and catalyzes
strand exchange between oligucleotides in vitro (105, 120). The yeast Dmc1 protein
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also promotes annealing of complementary ssDNA (74). Dmc1 has been observed
to form octameric rings or helical filaments on DNA by EM (120, 148, 169a).
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HOLLIDAY JUNCTION RESOLUTION ACTIVITIES
The DSBR model predicts the formation of a dHJ intermediate, which must be
resolved for segregation of the recombinant duplexes. Models for the repair of
collapsed replication forks and template switching also predict the requirement
for branch migration and Holliday junction resolution activities.
The Mus81-Mms4 (Eme1) Nuclease
The mus81 and eme1 (mms4 in S. cerevisiae) mutants of Schizosaccharomyces
pombe exhibit meiotic phenotypes consistent with a defect in the resolution of recombination intermediates. mus81 and eme1 mutants produce less than 1% viable
spores and show aberrant segregation of DNA, frequently with the DNA present in
only one spore, suggesting a defect in chromosome segregation (21). Remarkably,
the spore inviability and unequal DNA distribution observed in mus81 mutants is
suppressed by expression of the bacterial HJ resolvase RusA (21). Meiotic crossing over is reduced 20- to 50-fold in mus81 diploids, but gene conversion events
unassociated with crossing over occur at normal, or even higher, frequency than
in wild-type cells (146, 178). Thus, Mus81 and Eme1 are specifically required
to resolve meiotic recombination intermediates to form crossover products in
S. pombe. Mus81 and Mms4/Eme1 were identified in two-hybrid screens by interaction with Rad54 and checkpoint kinases, by sensitivity to MMS, and in a screen
for mutations that cause synthetic lethality with sgs1 (21, 22, 46, 80, 137, 157).
SGS1 encodes a helicase of the RecQ family and is homologous to the human
BLM and WRN helicases, which play important roles in genome stability (12,
60). Mus81 has sequence similarity to the nuclease domain of Rad1, and Mms4
has limited similarity to Rad10, suggesting that they are components of a structurespecific nuclease (21, 137). The Mus81-Mms4/Eme1 heterodimer cleaves a variety
of branched molecules, including simple Y-structures, duplex Y-structures, and Xforms, with a strong preference for duplex Y-structures (21, 91). The activity on
X-form structures is weak, but greatly enhanced if one of the four component
strands is discontinuous in the vicinity of the junction (58, 146).
Doubts over the generality of Mus81-Mms4 as the HJ resolvase have been raised
by genetic studies in S. cerevisiae. In budding yeast, mus81 and mms4 mutants
exhibit a sporulation defect, but genetic and physical studies have shown only a
twofold decrease in crossing over relative to wild type (45, 46). mus81 mutants
exhibit no sensitivity to IR, are proficient for mating-type switching and show no
alteration in the proportion of crossover events during DSBR in mitotic cells (80,
81). The conflicting results are best explained by proposing alternate pathways for
processing meiotic recombination intermediates in these two yeasts (70, 73, 146).
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The substrate specificity and meiotic crossover defect in S. pombe led Osman et al.
(146) to suggest that Mus81-Eme1 cleaves meiotic strand invasion intermediates in
two steps, prior to formation of a dHJ, to yield crossover products (Figure 7). They
propose that single-end invasion intermediates (SEIs) can be resolved by Mus81Eme1 to form crossover products, or dissociate as envisioned by the SDSA model
to form noncrossover products in S. pombe (Figure 7). In budding yeast, a subset of
Figure 7 Resolution of recombination intermediates. A dHJ intermediate can be
resolved by endonucleolytic cleavage of the junctions or dissolved by the combined
actions of BLM (Sgs1) and TOPO IIIα. An unligated strand invasion intermediate
can be resolved in two steps to form crossover products by the Mus81-Mms4/Eme1
endonuclease.
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SEIs is channeled into a pathway to form dHJ intermediates. These are processed
by a bona fide resolvase to form crossover products. This pathway is subject to
crossover interference and regulated by Msh4 and Msh5 (45, 73). The interference pathway and synaptonemal complex are absent from S. pombe (146). The
other SEIs can be processed in the same way as in S. pombe, to form crossover or
noncrossover products by a pathway that is not subject to crossover interference.
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Resolvase A
Biochemical evidence in support for two distinct resolvase activities has come from
characterization of fractionated mammalian cell extracts. Fractionation of HeLa
cell extracts revealed two Holliday junction resolvase activities, one corresponding
to Mus81, and the other to the previously described Resolvase A (39, 40). Resolvase
A shows high specificity for Holliday junctions and the resulting cleavage products
can be ligated (39). In contrast, Mus81 cleaves 3 flap and Y-shaped molecules more
efficiently than intact X-forms and the products of resolution are not ligatable (39).
Resolvase A promotes a concerted branch migration/resolution reaction similar to
that catalyzed by the E. coli RuvABC complex (40). Although the identity of
Resolvase A is currently unknown, recent studies indicate that it is intimately
associated with the Rad51 paralog, RAD51C (110).
Dissolution of dHJs
An alternative mode of resolving dHJ intermediates to form noncrossover products
is through the action of a topoisomerase. Recent biochemical studies provided direct evidence for resolution of dHJ intermediates by the combined action of BLM
and hTOPO IIIα (231). BLM is homologous to S. cerevisiae Sgs1 and was previously shown to exhibit DNA helicase activity to promote branch migration of
Holliday junctions (93). As a type IA topoisomerase, Topo III can make singlestranded incisions in ssDNA and catalyzes decatenation of negatively supercoiled
plasmids. The yeast TOP3 gene was originally identified in a genetic screen for
increased recombination between short repeated sequences (222). The top3 mutant has a severe growth defect, which is suppressed by deletion of SGS1 (60).
Like top3 mutants, sgs1 mutants show elevated rates of mitotic recombination and
hypersensitivity to chemicals that stall replication forks. Mutations in BLM are
causative of the human cancer predisposition syndrome, Bloom’s syndrome (12).
A defining cytological feature of cells from BLM patients is the high rate of sister
chromatid exchange (32). It is unclear whether the elevated rate of recombination
in sgs1 and BLM cell lines is due to increased numbers of recombinogenic lesions
formed by aberrant replication, or if the mutants have altered processing of recombination intermediates. sgs1 mutants do not show sensitivity to IR, suggesting that
Sgs1 is not essential for DSBR. However, recent studies have shown a significant
increase in crossovers during DSBR in sgs1 and top3 mutants (81). This result
was interpreted as a role for Sgs1 and Top3 in resolving dHJ recombination intermediates into noncrossover products. The biochemical studies with the equivalent
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human proteins support this hypothesis (231). Although no resolution activity was
detected on single HJs, the dHJ substrate was efficiently resolved by the combined
activities of BLM and hTOPO IIIα. Presumably, the branch migration activity
of BLM on the constrained substrate creates torsional stress, which activates the
decatenation activity of hTOPO IIIα.This mode of resolution, termed dissolution,
yields only noncrossover products.
In summary, eukaryotic cells resolve recombination intermediates by diverse
mechanisms. Resolution of dHJ intermediates can occur by endonucleolytic cleavage to form crossover or noncrossover products, or by dissolution to form noncrossover products. Single-end strand invasion intermediates can be cleaved to
form crossover products, or dissociated (SDSA model) to form noncrossovers.
The redundancy for this step of the reaction is a plausible explanation for why no
single mutant with the predicted resolution-defective phenotype has been identified
in budding yeast.
NONHOMOLOGOUS END JOINING
Nonhomologous end joining is a major pathway for repair of DSBs in higher
eukaryotes (85). The key components of this pathway in mammals are the DNAdependent protein kinase (DNA-PK), composed of the Ku heterodimer and DNAPK catalytic subunit (DNA-PKcs), and the DNA ligase IV/XRCC4 complex.
Mutations in any of these components result in hypersensitivity to ionizing radiation and in defective V(D)J recombination.
Because the rad52 group mutants are hypersensitive to IR, and haploid yeast
cells in the G1 stage of the cell cycle show high sensitivity to IR, it was originally
thought that yeast cells lack a mammalian-like NHEJ pathway. However, random
integration of linear DNA with no homology to chromosomal sequences occurs
with low frequency during transformation, and haploid yeast cells have an efficient
mechanism for the ligation of plasmids linearized with restriction enzymes when
these molecules are used to transform yeast cells (25, 166). The joining of cohesive ends occurs with high fidelity to restore the original sequence of the plasmid
(25). However, plasmids with blunt ends, or incompatible overhang ends, are poor
substrates for the rejoining pathway. This contrasts with S. pombe and mammalian
cells, which show efficient joining of blunt, cohesive ends and incompatible overhangs (117, 164, 228). Although end joining occurs with high efficiency in haploid
yeast cells, diploids show much lower levels of NHEJ. As described below, this
is because of an essential NHEJ factor that is regulated by mating-type heterozygosity (56, 96, 143, 216). It is assumed that diploids repress NHEJ because a
chromosome homologue is available throughout the cell cycle to template HR,
whereas haploids cannot use the higher fidelity HR pathway during G1.
A heterodimeric protein complex with homology to the mammalian Ku70/Ku80
complex was first identified as a high-affinity DNA end-binding activity in yeast
extracts (51, 127). Mutation of the YKU70 or YKU80 genes does not confer
sensitivity to IR, MMS, or bleomycin, but the mutants are defective in the rejoining
of linear plasmid DNA during transformation, or joining of chromosomal DSBs
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made with EcoRI or HO (24, 25, 104, 115, 127, 130). The end-joined products
recovered from yku70 and yku80 mutants have large deletions and the junctions
usually form at small homologies (1–4 nucleotides) (25). The yku70 and yku80
mutants show temperature-sensitive growth, short telomeres, and are defective
for transcriptional silencing of genes close to telomeres (telomere position effect,
TPE) (26). The Ku70 and Ku80 proteins localize to telomeres in yeast, but in the
presence of DNA damage show a Rad9-dependent relocalization to the sites of
damage (118). Recent studies have shown a direct interaction between Ku70 and
the RNA component of Telomerase, TLC1, and this interaction is important for the
telomere protection function of Ku (186). To date, no candidate for the DNA-PKcs
has been identified in budding or fission yeast. The DNL4 gene encodes an ATPdependent DNA ligase (Ligase IV), which is required for NHEJ in yeast (165,
204, 229). dnl4 mutants are epistatic to yku70 and yku80 for plasmid rejoining but
Figure 8 Repair of DSBs by NHEJ. DSB ends are stabilized and tethered together
by the Ku70/Ku80 heterodimer and the MRX complex. The Ligase IV complex, Dnl4Lif1, is recruited to ligate the ends by interactions to Xrs2. The haploid specific protein,
Nej1, is responsible for nuclear localization of Lif1.
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have normal growth, telomere length, and TPE, suggesting that these functions
of Ku70/Ku80 are independent of their role in NHEJ. As in mammalian cells, an
accessory protein, Lif1, activates and targets Dnl4 to DSBs in yeast (69, 205). The
phenotype of lif1 mutants is indistinguishable from that of dnl4 mutants. Another
factor that interacts with Lif1, Nej1/Lif2, was identified by two-hybrid analysis,
in a genetic screen for NHEJ mutants, and as a haploid-specific gene (56, 96, 143,
216). Diploid MATa/MATα cells that constitutively express NEJ1 are proficient
for NHEJ, indicating that this is the only factor in the pathway regulated by mating
type. Nej1 is required for nuclear localization of Lif1 (216), but it is currently
unknown if this is the only role for Nej1 in NHEJ (Figure 8).
In S. cerevisiae, Rad50, Mre11, and Xrs2 are also required for NHEJ, but these
factors play no role in NHEJ in S. pombe (117, 130). rad50, mre11, and xrs2
mutants are as defective in plasmid end joining as yku70 and yku80 mutants, but
the rare junctions formed usually show no loss of nucleotides (26). The Mre11nuclease activity is only required for end joining if the ends have hairpins, and this
specialized end-joining reaction also requires Sae2 and Pso2, the putative homolog
of the human V(D)J-recombination nuclease, Artemis (235). A chromosomal assay
for joining of incompatible ends revealed a requirement for Mre11 and Dnl4, but
not Yku70, suggesting there are at least two pathways for NHEJ (114). Genetic
and biochemical studies in animal cells also support the existence of another endjoining pathway, independent of that promoted by DNA-PK (67, 224).
The purified MRX complex stimulates intermolecular DNA joining by the
Dnl4/Lif1 complex (34). AFM analysis revealed juxtaposition of DNA ends by the
MRX complex to form linear concatamers, suggesting that the MRX complex can
align DNA molecules for ligation (Figure 4). Xrs2 interacts with Lif1, suggesting
that Xrs2 might function to recruit Dnl4/Lif1 to ends held together by the MRX
complex. Purified DNA-PK has been shown to synapse DNA ends, raising the
possibility that the MRX complex has assumed this role in S. cerevisiae (47).
ACKNOWLEDGMENTS
We are grateful to the members of our laboratory, past and present, for stimulating
discussions. Research performed in our laboratory that is cited in this review
was supported by grants from the National Institutes of Health (GM41784 and
GM54099). B.O.K. was supported by fellowships from the Danish Natural Science
Research Council and The Carlsberg Foundation.
The Annual Review of Genetics is online at http://genet.annualreviews.org
LITERATURE CITED
1. Aboussekhra A, Chanet R, Adjiri A,
Fabre F. 1992. Semidominant suppressors of Srs2 helicase mutations of
Saccharomyces cerevisiae map in the
RAD51 gene, whose sequence predicts
a protein with similarities to procaryotic
RecA proteins. Mol. Cell Biol. 12:3224–
34
15 Oct 2004 19:50
AR
AR230-GE38-08.tex
AR230-GE38-08.sgm
LaTeX2e(2002/01/18)
Annu. Rev. Genet. 2004.38:233-271. Downloaded from arjournals.annualreviews.org
by UNIVERSITY OF SOUTH CAROL on 02/10/05. For personal use only.
RECOMBINATION PROTEINS IN YEAST
2. Aguilera A, Klein HL. 1988. Genetic
control of intrachromosomal recombination in Saccharomyces cerevisiae. I.
Isolation and genetic characterization of
hyper-recombination mutations. Genetics 119:779–90
3. Aihara H, Ito Y, Kurumizaka H,
Yokoyama S, Shibata T. 1999. The Nterminal domain of the human Rad51
protein binds DNA: structure and a DNA
binding surface as revealed by NMR. J.
Mol. Biol. 290:495–504
4. Alani E, Padmore R, Kleckner N. 1990.
Analysis of wild-type and rad50 mutants
of yeast suggests an intimate relationship
between meiotic chromosome synapsis
and recombination. Cell 61:419–36
5. Alani E, Subbiah S, Kleckner N. 1989.
The yeast RAD50 gene encodes a predicted 153-kD protein containing a
purine nucleotide-binding domain and
two large heptad-repeat regions. Genetics 122:47–57
6. Alexeev A, Mazin A, Kowalczykowski
SC. 2003. Rad54 protein possesses
chromatin-remodeling activity stimulated by the Rad51-ssDNA nucleoprotein filament. Nat. Struct. Biol. 10:182–
86
7. Allers T, Lichten M. 2001. Differential
timing and control of noncrossover and
crossover recombination during meiosis.
Cell 106:47–57
8. Anderson DE, Trujillo KM, Sung P, Erickson HP. 2001. Structure of the Rad50·
Mre11 DNA repair complex from Saccharomyces cerevisiae by electron microscopy. J. Biol. Chem. 276:37027–33
9. Aravind L, Walker DR, Koonin EV.
1999. Conserved domains in DNA repair
proteins and evolution of repair systems.
Nucleic Acids Res. 27:1223–42
10. Arora C, Kee K, Maleki S, Keeney S.
2004. Antiviral protein Ski8 is a direct
partner of Spo11 in meiotic DNA break
formation, independent of its cytoplasmic role in RNA metabolism. Mol. Cell
13:549–59
P1: GCE
259
11. Aylon Y, Liefshitz B, Bitan-Banin G, Kupiec M. 2003. Molecular dissection of
mitotic recombination in the yeast Saccharomyces cerevisiae. Mol. Cell Biol.
23:1403–17
12. Bachrati CZ, Hickson ID. 2003. RecQ
helicases: suppressors of tumorigenesis
and premature aging. Biochem. J. 374:
577–606
13. Bai Y, Davis AP, Symington LS. 1999.
A novel allele of RAD52 that causes severe DNA repair and recombination deficiencies only in the absence of RAD51
or RAD59. Genetics 153:1117–30
14. Bai Y, Symington LS. 1996. A Rad52
homolog is required for RAD51independent mitotic recombination in
Saccharomyces cerevisiae. Genes Dev.
10:2025–37
15. Bartsch S, Kang LE, Symington LS.
2000. RAD51 is required for the repair of plasmid double-stranded DNA
gaps from either plasmid or chromosomal templates. Mol. Cell Biol. 20:1194–
205
16. Basile G, Aker M, Mortimer RK. 1992.
Nucleotide sequence and transcriptional
regulation of the yeast recombinational
repair gene RAD51. Mol. Cell Biol. 12:
3235–46
17. Baudat F, Nicolas A. 1997. Clustering
of meiotic double-strand breaks on yeast
chromosome III. Proc. Natl. Acad. Sci.
USA 94:5213–18
18. Bergerat A, de Massy B, Gadelle D,
Varoutas PC, Nicolas A, Forterre P. 1997.
An atypical topoisomerase II from Archaea with implications for meiotic recombination. Nature 386:414–17
19. Bishop DK. 1994. RecA homologs
Dmc1 and Rad51 interact to form multiple nuclear complexes prior to meiotic
chromosome synapsis. Cell 79:1081–
92
20. Bishop DK, Park D, Xu L, Kleckner N.
1992. DMC1: a meiosis-specific yeast
homolog of E. coli recA required for
recombination, synaptonemal complex
15 Oct 2004 19:50
260
21.
Annu. Rev. Genet. 2004.38:233-271. Downloaded from arjournals.annualreviews.org
by UNIVERSITY OF SOUTH CAROL on 02/10/05. For personal use only.
22.
23.
24.
25.
26.
27.
28.
29.
AR
KROGH
AR230-GE38-08.tex
AR230-GE38-08.sgm
LaTeX2e(2002/01/18)
P1: GCE
SYMINGTON
formation, and cell cycle progression.
Cell 69:439–56
Boddy MN, Gaillard PH, McDonald
WH, Shanahan P, Yates JR, 3rd, Russell
P. 2001. Mus81-Eme1 are essential components of a Holliday junction resolvase.
Cell 107:537–48
Boddy MN, Lopez-Girona A, Shanahan
P, Interthal H, Heyer WD, Russell P.
2000. Damage tolerance protein Mus81
associates with the FHA1 domain of
checkpoint kinase Cds1. Mol. Cell Biol.
20:8758–66
Borde V, Lin W, Novikov E, Petrini JH,
Lichten M, Nicolas A. 2004. Association
of Mre11p with double-strand break sites
during yeast meiosis. Mol. Cell. 13:389–
401
Boulton SJ, Jackson SP. 1996. Identification of a Saccharomyces cerevisiae Ku80
homologue: roles in DNA double-strand
break rejoining and in telomeric maintenance. Nucleic Acids Res. 24:4639–48
Boulton SJ, Jackson SP. 1996. Saccharomyces cerevisiae Ku70 potentiates
illegitimate DNA double-strand break
repair and serves as a barrier to errorprone DNA repair pathways. EMBO J.
15:5093–103
Boulton SJ, Jackson SP. 1998. Components of the Ku-dependent nonhomologous end-joining pathway are involved in telomeric length maintenance
and telomeric silencing. EMBO J. 17:
1819–28
Boundy-Mills KL, Livingston DM.
1993. A Saccharomyces cerevisiae
RAD52 allele expressing a C-terminal
truncation protein: activities and intragenic complementation of missense mutations. Genetics 133:39–49
Bressan DA, Baxter BK, Petrini JH.
1999. The Mre11-Rad50-Xrs2 protein
complex facilitates homologous recombination-based double-strand break repair in Saccharomyces cerevisiae. Mol.
Cell Biol. 19:7681–87
Bressan DA, Olivares HA, Nelms BE,
30.
31.
32.
33.
34.
35.
36.
37.
38.
Petrini JH. 1998. Alteration of Nterminal phosphoesterase signature motifs inactivates Saccharomyces cerevisiae Mre11. Genetics 150:591–600
Cao L, Alani E, Kleckner N. 1990.
A pathway for generation and processing of double-strand breaks during meiotic recombination in S. cerevisiae. Cell
61:1089–101
Carney JP, Maser RS, Olivares H, Davis
EM, Le Beau M, et al. 1998. The
hMre11/hRad50 protein complex and
Nijmegen breakage syndrome: linkage
of double-strand break repair to the cellular DNA damage response. Cell 93:477–
86
Chaganti RS, Schonberg S, German J.
1974. A manyfold increase in sister chromatid exchanges in Bloom’s syndrome
lymphocytes. Proc. Natl. Acad. Sci. USA
71:4508–12
Chanet R, Heude M, Adjiri A, Maloisel
L, Fabre F. 1996. Semidominant mutations in the yeast Rad51 protein and their
relationships with the Srs2 helicase. Mol.
Cell Biol. 16:4782–89
Chen L, Trujillo K, Ramos W, Sung
P, Tomkinson AE. 2001. Promotion
of Dnl4-catalyzed DNA end-joining by
the Rad50/Mre11/Xrs2 and Hdf1/Hdf2
complexes. Mol. Cell 8:1105–15
Clever B, Interthal H, Schmuckli-Maurer
J, King J, Sigrist M, Heyer WD. 1997.
Recombinational repair in yeast: functional interactions between Rad51 and
Rad54 proteins. EMBO J. 16:2535–44
Colleaux L, D’Auriol L, Galibert F, Dujon B. 1988. Recognition and cleavage
site of the intron-encoded omega transposase. Proc. Natl. Acad. Sci. USA 85:
6022–26
Connelly JC, de Leau ES, Leach DR.
2003. Nucleolytic processing of a
protein-bound DNA end by the E. coli
SbcCD (MR) complex. DNA Repair
2:795–807
Connelly JC, de Leau ES, Okely
EA, Leach DR. 1997. Overexpression,
15 Oct 2004 19:50
AR
AR230-GE38-08.tex
AR230-GE38-08.sgm
LaTeX2e(2002/01/18)
RECOMBINATION PROTEINS IN YEAST
39.
Annu. Rev. Genet. 2004.38:233-271. Downloaded from arjournals.annualreviews.org
by UNIVERSITY OF SOUTH CAROL on 02/10/05. For personal use only.
40.
41.
42.
43.
44.
45.
46.
47.
48.
purification, and characterization of the
SbcCD protein from Escherichia coli. J.
Biol. Chem. 272:19819–26
Constantinou A, Chen X-B, McGowan
CH, West SC. 2002. Human Holliday
junction resolvases: two activities with
distinct substrate specificities. EMBO J.
21:5577–85
Constantinou A, Davies AA, West SC.
2001. Branch migration and Holliday
junction resolution catalyzed by activities from mammalian cells. Cell 104:
259–68
D’Amours D, Jackson SP. 2001. The
yeast Xrs2 complex functions in S
phase checkpoint regulation. Genes Dev.
15:2238–49
Davis AP, Symington LS. 2001. The
yeast recombinational repair protein
Rad59 interacts with Rad52 and stimulates single-strand annealing. Genetics
159:515–25
Davis AP, Symington LS. 2004. RAD51dependent break-induced replication in
yeast. Mol. Cell Biol. 24:2344–51
de Jager M, van Noort J, van Gent DC,
Dekker C, Kanaar R, Wyman C. 2001.
Human Rad50/Mre11 is a flexible complex that can tether DNA ends. Mol. Cell
8:1129–35
de los Santos T, Hunter N, Lee C, Larkin
B, Loidl J, Hollingsworth NM. 2003.
The Mus81/Mms4 endonuclease acts independently of double-Holliday junction
resolution to promote a distinct subset
of crossovers during meiosis in budding
yeast. Genetics 164:81–94
de los Santos T, Loidl J, Larkin B,
Hollingsworth NM. 2001. A role for
MMS4 in the processing of recombination intermediates during meiosis in Saccharomyces cerevisiae. Genetics 159:
1511–25
DeFazio LG, Stansel RM, Griffith JD,
Chu G. 2002. Synapsis of DNA ends by
DNA-dependent protein kinase. EMBO
J. 21:3192–200
Diaz RL, Alcid AD, Berger JM, Keeney
49.
50.
51.
52.
53.
54.
55.
56.
P1: GCE
261
S. 2002. Identification of residues in
yeast Spo11p critical for meiotic DNA
double-strand break formation. Mol. Cell
Biol. 22:1106–15
Essers J, Houtsmuller AB, van Veelen
L, Paulusma C, Nigg AL, et al. 2002.
Nuclear dynamics of RAD52 group
homologous recombination proteins in
response to DNA damage. EMBO J.
21:2030–37
Fabre F, Chan A, Heyer WD, Gangloff
S. 2002. Alternate pathways involving
Sgs1/Top3, Mus81/ Mms4, and Srs2 prevent formation of toxic recombination
intermediates from single-stranded gaps
created by DNA replication. Proc. Natl.
Acad. Sci. USA 99:16887–92
Feldmann H, Winnacker EL. 1993. A putative homologue of the human autoantigen Ku from Saccharomyces cerevisiae.
J. Biol. Chem. 268:12895–900
Ferguson DO, Holloman WK. 1996. Recombinational repair of gaps in DNA
is asymmetric in Ustilago maydis and
can be explained by a migrating Dloop model. Proc. Natl. Acad. Sci. USA
93:5419–24
Fiorentini P, Huang KN, Tishkoff DX,
Kolodner RD, Symington LS. 1997.
Exonuclease I of Saccharomyces cerevisiae functions in mitotic recombination in vivo and in vitro. Mol. Cell Biol.
17:2764–73
Fishman-Lobell J, Rudin N, Haber
JE. 1992. Two alternative pathways of
double-strand break repair that are kinetically separable and independently
modulated. Mol. Cell Biol. 12:1292–
303
Fortin GS, Symington LS. 2002. Mutations in yeast Rad51 that partially bypass
the requirement for Rad55 and Rad57
in DNA repair by increasing stability
of Rad51/DNA complexes. EMBO J.
21:3160–70
Frank-Vaillant M, Marcand S. 2001.
NHEJ regulation by mating type is exercised through a novel protein, Lif2p,
15 Oct 2004 19:50
262
57.
Annu. Rev. Genet. 2004.38:233-271. Downloaded from arjournals.annualreviews.org
by UNIVERSITY OF SOUTH CAROL on 02/10/05. For personal use only.
58.
59.
60.
61.
62.
63.
64.
65.
AR
KROGH
AR230-GE38-08.tex
AR230-GE38-08.sgm
LaTeX2e(2002/01/18)
P1: GCE
SYMINGTON
essential to the ligase IV pathway. Genes
Dev. 15:3005–12
Furuse M, Nagase Y, Tsubouchi H,
Murakami-Murofushi K, Shibata T, Ohta
K. 1998. Distinct roles of two separable
in vitro activities of yeast Mre11 in mitotic and meiotic recombination. EMBO
J. 17:6412–25
Gaillard PH, Noguchi E, Shanahan P,
Russell P. 2003. The endogenous Mus81Eme1 complex resolves Holliday junctions by a nick and counternick mechanism. Mol. Cell 12:747–59
Game JC, Mortimer RK. 1974. A genetic
study of X-ray sensitive mutants in yeast.
Mutat. Res. 24:281–92
Gangloff S, McDonald JP, Bendixen C,
Arthur L, Rothstein R. 1994. The yeast
type I topoisomerase Top3 interacts with
Sgs1, a DNA helicase homolog: a potential eukaryotic reverse gyrase. Mol. Cell
Biol. 14:8391–98
Gangloff S, Soustelle C, Fabre F. 2000.
Homologous recombination is responsible for cell death in the absence of
the Sgs1 and Srs2 helicases. Nat. Genet.
25:192–94
Garvik B, Carson M, Hartwell L. 1995.
Single-stranded DNA arising at telomeres in cdc13 mutants may constitute a
specific signal for the RAD9 checkpoint.
Mol. Cell Biol. 15:6128–38
Gasior SL, Olivares H, Ear U, Hari DM,
Weichselbaum R, Bishop DK. 2001. Assembly of RecA-like recombinases: distinct roles for mediator proteins in mitosis and meiosis. Proc. Natl. Acad. Sci.
USA 98:8411–18
Gasior SL, Wong AK, Kora Y, Shinohara A, Bishop DK. 1998. Rad52 associates with RPA and functions with rad55
and rad57 to assemble meiotic recombination complexes. Genes Dev. 12:2208–
21
Gerton JL, DeRisi J, Shroff R, Lichten
M, Brown PO, Petes TD. 2000. Inaugural article: global mapping of meiotic
recombination hotspots and coldspots
66.
67.
68.
69.
70.
71.
72.
73.
74.
75.
in the yeast Saccharomyces cerevisiae.
Proc. Natl. Acad. Sci. USA 97:11383–90
Hackett JA, Greider CW. 2003. End resection initiates genomic instability in
the absence of telomerase. Mol. Cell
Biol. 23:8450–61
Han JO, Erskine LA, Purugganan MM,
Stamato TD, Roth DB. 1998. V(D)J
recombination intermediates and nonstandard products in XRCC4-deficient
cells. Nucleic Acids Res. 26:3769–75
Hays SL, Firmenich AA, Berg P. 1995.
Complex formation in yeast doublestrand break repair: participation of
Rad51, Rad52, Rad55, and Rad57 proteins. Proc. Natl. Acad. Sci. USA 92:
6925–29
Herrmann G, Lindahl T, Schar P. 1998.
Saccharomyces cerevisiae LIF1: a function involved in DNA double-strand
break repair related to mammalian
XRCC4. EMBO J. 17:4188–98
Heyer WD, Ehmsen KT, Solinger JA.
2003. Holliday junctions in the eukaryotic nucleus: resolution in sight? Trends
Biochem. Sci. 28:548–57
Higgins NP, Kato K, Strauss B. 1976.
A model for replication repair in mammalian cells. J. Mol. Biol. 101:417–25
Holliday R. 1964. A mechanism for gene
conversion in fungi. Genet. Res. 5:282–
304
Hollingsworth NM, Brill SJ. 2004. The
Mus81 solution to resolution: generating meiotic crossovers without Holliday
junctions. Genes Dev. 18:117–25
Hong EL, Shinohara A, Bishop DK.
2001. Saccharomyces cerevisiae Dmc1
protein promotes renaturation of singlestrand DNA (ssDNA) and assimilation
of ssDNA into homologous super-coiled
duplex DNA. J. Biol. Chem. 276:41906–
12
Hopfner KP, Craig L, Moncalian G,
Zinkel RA, Usui T, et al. 2002. The
Rad50 zinc-hook is a structure joining
Mre11 complexes in DNA recombination and repair. Nature 418:562–66
15 Oct 2004 19:50
AR
AR230-GE38-08.tex
AR230-GE38-08.sgm
LaTeX2e(2002/01/18)
Annu. Rev. Genet. 2004.38:233-271. Downloaded from arjournals.annualreviews.org
by UNIVERSITY OF SOUTH CAROL on 02/10/05. For personal use only.
RECOMBINATION PROTEINS IN YEAST
76. Hopfner KP, Karcher A, Craig L, Woo
TT, Carney JP, Tainer JA. 2001. Structural biochemistry and interaction architecture of the DNA double-strand
break repair Mre11 nuclease and Rad50ATPase. Cell 105:473–85
77. Hopfner KP, Karcher A, Shin D, Fairley C, Tainer JA, Carney JP. 2000.
Mre11 and Rad50 from Pyrococcus furiosus: cloning and biochemical characterization reveal an evolutionarily
conserved multiprotein machine. J. Bacteriol. 182:6036–41
78. Hopfner KP, Karcher A, Shin DS, Craig
L, Arthur LM, et al. 2000. Structural
biology of Rad50 ATPase: ATP-driven
conformational control in DNA doublestrand break repair and the ABC-ATPase
superfamily. Cell 101:789–800
79. Hurst DD, Fogel S, Mortimer RK.
1972. Conversion-associated recombination in yeast (hybrids-meiosis-tetradsmarker loci-models). Proc. Natl. Acad.
Sci. USA 69:101–5
80. Interthal H, Heyer WD. 2000. MUS81
encodes a novel helix-hairpin-helix protein involved in the response to UVand methylation-induced DNA damage
in Saccharomyces cerevisiae. Mol. Gen.
Genet. 263:812–27
81. Ira G, Malkova A, Liberi G, Foiani
M, Haber JE. 2003. Srs2 and Sgs1Top3 suppress crossovers during doublestrand break repair in yeast. Cell 115:
401–11
82. Ivanov EL, Sugawara N, FishmanLobell J, Haber JE. 1996. Genetic
requirements for the single-strand annealing pathway of double-strand break
repair in Saccharomyces cerevisiae. Genetics 142:693–704
83. Ivanov EL, Sugawara N, White CI,
Fabre F, Haber JE. 1994. Mutations
in XRS2 and RAD50 delay but do not
prevent mating-type switching in Saccharomyces cerevisiae. Mol. Cell Biol.
14:3414–25
84. Jaskelioff M, Van Komen S, Krebs JE,
85.
86.
87.
88.
89.
90.
91.
92.
93.
P1: GCE
263
Sung P, Peterson CL. 2003. Rad54p
is a chromatin remodeling enzyme required for heteroduplex DNA joint formation with chromatin. J. Biol. Chem.
278:9212–18
Jeggo PA. 1998. Identification of genes
involved in repair of DNA double-strand
breaks in mammalian cells. Radiat. Res.
150:S80–91
Jiang H, Xie Y, Houston P, Stemke-Hale
K, Mortensen UH, et al. 1996. Direct association between the yeast Rad51 and
Rad54 recombination proteins. J. Biol.
Chem. 271:33181–86
Johnson RD, Symington LS. 1995.
Functional differences and interactions
among the putative RecA homologs
Rad51, Rad55, and Rad57. Mol. Cell
Biol. 15:4843–50
Johzuka K, Ogawa H. 1995. Interaction of Mre11 and Rad50: two proteins
required for DNA repair and meiosisspecific double-strand break formation
in Saccharomyces cerevisiae. Genetics
139:1521–32
Kagawa W, Kurumizaka H, Ikawa S,
Yokoyama S, Shibata T. 2001. Homologous pairing promoted by the human Rad52 protein. J. Biol. Chem. 276:
35201–8
Kagawa W, Kurumizaka H, Ishitani R,
Fukai S, Nureki O, et al. 2002. Crystal
structure of the homologous-pairing domain from the human Rad52 recombinase in the undecameric form. Mol. Cell.
10:359–71
Kaliraman V, Mullen JR, Fricke WM,
Bastin-Shanower SA, Brill SJ. 2001.
Functional overlap between Sgs1-Top3
and the Mms4-Mus81 endonuclease.
Genes Dev. 15:2730–40
Kaplun L, Ivantsiv Y, Kornitzer D, Raveh
D. 2000. Functions of the DNA damage response pathway target Ho endonuclease of yeast for degradation via the
ubiquitin-26S proteasome system. Proc.
Natl. Acad. Sci. USA 97:10077–82
Karow JK, Constantinou A, Li JL, West
15 Oct 2004 19:50
264
94.
Annu. Rev. Genet. 2004.38:233-271. Downloaded from arjournals.annualreviews.org
by UNIVERSITY OF SOUTH CAROL on 02/10/05. For personal use only.
95.
96.
97.
98.
99.
100.
101.
102.
103.
AR
KROGH
AR230-GE38-08.tex
AR230-GE38-08.sgm
LaTeX2e(2002/01/18)
P1: GCE
SYMINGTON
SC, Hickson ID. 2000. The Bloom’s syndrome gene product promotes branch migration of Holliday junctions. Proc. Natl.
Acad. Sci. USA 97:6504–8
Keeney S. 2001. Mechanism and control of meiotic recombination initiation.
Curr. Top. Dev. Biol. 52:1–53
Keeney S, Giroux CN, Kleckner N.
1997. Meiosis-specific DNA doublestrand breaks are catalyzed by Spo11, a
member of a widely conserved protein
family. Cell 88:375–84
Kegel A, Sjostrand JO, Astrom SU.
2001. Nej1p, a cell type-specific regulator of nonhomologous end joining in
yeast. Curr. Biol. 11:1611–17
Klein HL. 2001. Mutations in recombinational repair and in checkpoint control
genes suppress the lethal combination
of srs2 with other DNA repair genes
in Saccharomyces cerevisiae. Genetics
157:557–65
Kostriken R, Heffron F. 1984. The product of the HO gene is a nuclease: purification and characterization of the enzyme.
Cold Spring Harbor Symp. Quant. Biol.
49:89–96
Kraus E, Leung WY, Haber JE. 2001.
Break-induced replication: a review and
an example in budding yeast. Proc. Natl.
Acad. Sci. USA 98:8255–62
Krejci L, Song B, Bussen W, Rothstein
R, Mortensen UH, Sung P. 2002. Interaction with Rad51 is indispensable
for recombination mediator function of
Rad52. J. Biol. Chem. 277:40132–41
Krejci L, Van Komen S, Li Y, Villemain
J, Reddy MS, et al. 2003. DNA helicase
Srs2 disrupts the Rad51 presynaptic filament. Nature 423:305–9
Lawrence CW, Christensen RB. 1979.
Metabolic suppressors of trimethoprim
and ultraviolet light sensitivities of Saccharomyces cerevisiae rad6 mutants. J.
Bacteriol. 139:866–87
Lee S-E, Bressan DA, Petrini JH, Haber
JE. 2002. Complementation between
N-terminal Saccharomyces cerevisiae
104.
105.
106.
107.
108.
109.
110.
111.
112.
113.
mre11 alleles in DNA repair and telomere length maintenance. DNA Repair
1:27–40
Lewis LK, Kirchner JM, Resnick
MA. 1998. Requirement for end-joining
and checkpoint functions, but not
RAD52-mediated recombination, after
EcoRI endonuclease cleavage of Saccharomyces cerevisiae DNA. Mol. Cell Biol.
18:1891–902
Li Z, Golub EI, Gupta R, Radding CM.
1997. Recombination activities of HsDmc1 protein, the meiotic human homolog of RecA protein. Proc. Natl. Acad.
Sci. USA 94:11221–26
Lim DS, Kim ST, Xu B, Maser RS,
Lin J, et al. 2000. ATM phosphorylates
p95/nbs1 in an S-phase checkpoint pathway. Nature 404:613–17
Lin FL, Sperle K, Sternberg N. 1984.
Model for homologous recombination
during transfer of DNA into mouse L
cells: role for DNA ends in the recombination process. Mol. Cell Biol. 4:1020–
34
Lisby M, Mortensen UH, Rothstein R.
2003. Colocalization of multiple DNA
double-strand breaks at a single Rad52
repair centre. Nat. Cell Biol. 5:572–77
Lisby M, Rothstein R, Mortensen UH.
2001. Rad52 forms DNA repair and
recombination centers during S phase.
Proc. Natl. Acad. Sci. USA 98:8276–82
Liu Y, Masson JY, Shah R, O’Regan P,
West SC. 2004. RAD51C is required for
Holliday junction processing in mammalian cells. Science 303:243–46
Lopes M, Cotta-Ramusino C, Pellicioli
A, Liberi G, Plevani P, et al. 2001. The
DNA replication checkpoint response
stabilizes stalled replication forks. Nature 412:557–61
Lovett ST, Mortimer RK. 1987. Characterization of null mutants of the RAD55
gene of Saccharomyces cerevisiae: effects of temperature, osmotic strength
and mating type. Genetics 116:547–53
Lundblad V, Blackburn EH. 1993. An
15 Oct 2004 19:50
AR
AR230-GE38-08.tex
AR230-GE38-08.sgm
LaTeX2e(2002/01/18)
RECOMBINATION PROTEINS IN YEAST
114.
Annu. Rev. Genet. 2004.38:233-271. Downloaded from arjournals.annualreviews.org
by UNIVERSITY OF SOUTH CAROL on 02/10/05. For personal use only.
115.
116.
117.
118.
119.
120.
121.
122.
alternative pathway for yeast telomere
maintenance rescues est1-senescence.
Cell 73:347–60
Ma JL, Kim EM, Haber JE, Lee SE.
2003. Yeast Mre11 and Rad1 proteins
define a Ku-independent mechanism to
repair double-strand breaks lacking overlapping end sequences. Mol. Cell Biol.
23:8820–28
Mages GJ, Feldmann HM, Winnacker
EL. 1996. Involvement of the Saccharomyces cerevisiae HDF1 gene in DNA
double-strand break repair and recombination. J. Biol. Chem. 271:7910–15
Malkova A, Ivanov EL, Haber JE. 1996.
Double-strand break repair in the absence of RAD51 in yeast: a possible
role for break-induced DNA replication.
Proc. Natl. Acad. Sci. USA 93:7131–36
Manolis KG, Nimmo ER, Hartsuiker
E, Carr AM, Jeggo PA, Allshire RC.
2001. Novel functional requirements for
non-homologous DNA end joining in
Schizosaccharomyces pombe. EMBO J.
20:210–21
Martin SG, Laroche T, Suka N, Grunstein M, Gasser SM. 1999. Relocalization of telomeric Ku and SIR proteins in
response to DNA strand breaks in yeast.
Cell 97:621–33
Maryon E, Carroll D. 1991. Characterization of recombination intermediates
from DNA injected into Xenopus laevis
oocytes: evidence for a nonconservative
mechanism of homologous recombination. Mol. Cell Biol. 11:3278–87
Masson JY, Davies AA, Hajibagheri
N, Van Dyck E, Benson FE, et al.
1999. The meiosis-specific recombinase
hDmc1 forms ring structures and interacts with hRad51. EMBO J. 18:6552–60
Mazin AV, Alexeev AA, Kowalczykowski SC. 2003. A novel function
of Rad54 protein. Stabilization of the
Rad51 nucleoprotein filament. J. Biol.
Chem. 278:14029–36
Mazin AV, Bornarth CJ, Solinger JA,
Heyer WD, Kowalczykowski SC. 2000.
123.
124.
125.
126.
127.
128.
129.
130.
131.
P1: GCE
265
Rad54 protein is targeted to pairing loci
by the Rad51 nucleoprotein filament.
Mol. Cell 6:583–92
McKee AH, Kleckner N. 1997. A general method for identifying recessive
diploid-specific mutations in Saccharomyces cerevisiae, its application to the
isolation of mutants blocked at intermediate stages of meiotic prophase and
characterization of a new gene SAE2. Genetics 146:797–816
Merker JD, Dominska M, Petes TD.
2003. Patterns of heteroduplex formation associated with the initiation of meiotic recombination in the yeast Saccharomyces cerevisiae. Genetics 165:47–63
Meselson MS, Radding CM. 1975. A
general model for genetic recombination. Proc. Natl. Acad. Sci. USA 72:358–
61
Michel B, Ehrlich SD, Uzest M. 1997.
DNA double-strand breaks caused by
replication arrest. EMBO J. 16:430–
38
Milne GT, Jin S, Shannon KB, Weaver
DT. 1996. Mutations in two Ku homologs define a DNA end-joining repair
pathway in Saccharomyces cerevisiae.
Mol. Cell Biol. 16:4189–98
Miyazaki T, Bressan DA, Shinohara M,
Haber JE, Shinohara A. 2004. In vivo
assembly and disassembly of Rad51 and
Rad52 complexes during double-strand
break repair. EMBO J. 23:939–49
Moncalian G, Lengsfeld B, Bhaskara V,
Hopfner KP, Karcher A, et al. 2004. The
rad50 signature motif: essential to ATP
binding and biological function. J. Mol.
Biol. 335:937–51
Moore JK, Haber JE. 1996. Cell cycle
and genetic requirements of two pathways of nonhomologous end-joining
repair of double-strand breaks in Saccharomyces cerevisiae. Mol. Cell Biol. 16:
2164–73
Moreau S, Ferguson JR, Symington LS.
1999. The nuclease activity of Mre11 is
required for meiosis but not for mating
15 Oct 2004 19:50
266
132.
Annu. Rev. Genet. 2004.38:233-271. Downloaded from arjournals.annualreviews.org
by UNIVERSITY OF SOUTH CAROL on 02/10/05. For personal use only.
133.
134.
135.
136.
137.
138.
139.
140.
AR
KROGH
AR230-GE38-08.tex
AR230-GE38-08.sgm
LaTeX2e(2002/01/18)
P1: GCE
SYMINGTON
type switching, end joining, or telomere
maintenance. Mol. Cell Biol. 19:556–
66
Moreau S, Morgan EA, Symington LS.
2001. Overlapping functions of the Saccharomyces cerevisiae Mre11, Exo1 and
Rad27 nucleases in DNA metabolism.
Genetics 159:1423–33
Morgan EA, Shah N, Symington LS.
2002. The requirement for ATP hydrolysis by Saccharomyces cerevisiae Rad51
is bypassed by mating-type heterozygosity or RAD54 in high copy. Mol. Cell.
Biol. 22:6336–43
Morrow DM, Connelly C, Hieter P.
1997. “Break copy” duplication: a model
for chromosome fragment formation
in Saccharomyces cerevisiae. Genetics
147:371–82
Mortensen UH, Bendixen C, Sunjevaric
I, Rothstein R. 1996. DNA strand annealing is promoted by the yeast Rad52
protein. Proc. Natl. Acad. Sci. USA 93:
10729–34
Mortensen UH, Erdeniz N, Feng Q,
Rothstein R. 2002. A molecular genetic dissection of the evolutionarily
conserved N terminus of yeast Rad52.
Genetics 161:549–62
Mullen JR, Kaliraman V, Ibrahim SS,
Brill SJ. 2001. Requirement for three
novel protein complexes in the absence
of the Sgs1 DNA helicase in Saccharomyces cerevisiae. Genetics 157:103–
18
Nairz K, Klein F. 1997. mre11S a yeast
mutation that blocks double-strandbreak processing and permits nonhomologous synapsis in meiosis. Genes Dev.
11:2272–90
Nassif N, Penney J, Pal S, Engels WR,
Gloor GB. 1994. Efficient copying of
nonhomologous sequences from ectopic
sites via P-element-induced gap repair.
Mol. Cell Biol. 14:1613–25
New JH, Sugiyama T, Zaitseva E, Kowalczykowski SC. 1998. Rad52 protein
stimulates DNA strand exchange by
141.
142.
143.
144.
145.
146.
147.
148.
149.
150.
151.
Rad51 and replication protein A. Nature
391:407–10
Nickoloff JA, Chen EY, Heffron F. 1986.
A 24-base-pair DNA sequence from the
MAT locus stimulates intergenic recombination in yeast. Proc. Natl. Acad. Sci.
USA 83:7831–35
Ogawa T, Yu X, Shinohara A, Egelman
EH. 1993. Similarity of the yeast RAD51
filament to the bacterial RecA filament.
Science 259:1896–99
Ooi SL, Shoemaker DD, Boeke JD.
2001. A DNA microarray-based genetic
screen for nonhomologous end-joining
mutants in Saccharomyces cerevisiae.
Science 294:2552–56
Orr-Weaver TL, Szostak JW. 1983.
Yeast recombination: the association
between double-strand gap repair and
crossing-over. Proc. Natl. Acad. Sci.
USA 80:4417–21
Orr-Weaver TL, Szostak JW, Rothstein
RJ. 1981. Yeast transformation: a model
system for the study of recombination.
Proc. Natl. Acad. Sci. USA 78:6354–58
Osman F, Dixon J, Doe CL, Whitby MC.
2003. Generating crossovers by resolution of nicked Holliday junctions: a role
for Mus81-Eme1 in meiosis. Mol. Cell
12:761–74
Pages V, Fuchs RP. 2003. Uncoupling of
leading- and lagging-strand DNA replication during lesion bypass in vivo. Science 300:1300–3
Passy SI, Yu X, Li Z, Radding CM, Masson JY, et al. 1999. Human Dmc1 protein
binds DNA as an octameric ring. Proc.
Natl. Acad. Sci. USA 96:10684–88
Paull TT, Gellert M. 1998. The 3 to 5
exonuclease activity of Mre11 facilitates
repair of DNA double-strand breaks.
Mol. Cell 1:969–79
Paull TT, Gellert M. 1999. Nbs1
potentiates ATP-driven DNA unwinding and endonuclease cleavage by the
Mre11/Rad50 complex. Genes Dev. 13:
1276–88
Pellegrini L, Yu DS, Lo T, Anand S, Lee
15 Oct 2004 19:50
AR
AR230-GE38-08.tex
AR230-GE38-08.sgm
LaTeX2e(2002/01/18)
RECOMBINATION PROTEINS IN YEAST
152.
Annu. Rev. Genet. 2004.38:233-271. Downloaded from arjournals.annualreviews.org
by UNIVERSITY OF SOUTH CAROL on 02/10/05. For personal use only.
153.
154.
155.
156.
157.
158.
159.
160.
M, et al. 2002. Insights into DNA recombination from the structure of a RAD51BRCA2 complex. Nature 420:287–93
Petukhova G, Stratton S, Sung P. 1998.
Catalysis of homologous DNA pairing
by yeast Rad51 and Rad54 proteins. Nature 393:91–94
Petukhova G, Stratton SA, Sung P. 1999.
Single-strand DNA binding and annealing activities in the yeast recombination
factor Rad59. J. Biol. Chem. 274:33839–
42
Petukhova G, Sung P, Klein H. 2000.
Promotion of Rad51-dependent D-loop
formation by yeast recombination factor Rdh54/Tid1. Genes Dev. 14:2206–
15
Petukhova G, Van Komen S, Vergano
S, Klein H, Sung P. 1999. Yeast Rad54
promotes Rad51-dependent homologous
DNA pairing via ATP hydrolysis-driven
change in DNA double helix conformation. J. Biol. Chem. 274:29453–62
Plessis A, Perrin A, Haber JE, Dujon B.
1992. Site-specific recombination determined by I-SceI, a mitochondrial group I
intron-encoded endonuclease expressed
in the yeast nucleus. Genetics 130:451–
60
Prakash L, Prakash S. 1977. Isolation and
characterization of MMS-sensitive mutants of Saccharomyces cerevisiae. Genetics 86:33–55
Prinz S, Amon A, Klein F. 1997. Isolation of COM1, a new gene required to
complete meiotic double-strand breakinduced recombination in Saccharomyces cerevisiae. Genetics 146:781–95
Ranatunga W, Jackson D, Lloyd JA,
Forget AL, Knight KL, Borgstahl GE.
2001. Human RAD52 exhibits two
modes of self-association. J. Biol. Chem.
276:15876–80
Rattray AJ, McGill CB, Shafer BK,
Strathern JN. 2001. Fidelity of mitotic double-strand-break repair in Saccharomyces cerevisiae. A role for
sae2/com1. Genetics 158:109–22
P1: GCE
267
161. Rattray AJ, Symington LS. 1994. Use
of a chromosomal inverted repeat to
demonstrate that the RAD51 and RAD52
genes of Saccharomyces cerevisiae have
different roles in mitotic recombination.
Genetics 138:587–95
162. Raymond WE, Kleckner N. 1993.
RAD50 protein of S. cerevisiae exhibits
ATP-dependent DNA binding. Nucleic
Acids Res. 21:3851–56
163. Rong L, Klein HL. 1993. Purification and
characterization of the SRS2 DNA helicase of the yeast Saccharomyces cerevisiae. J. Biol. Chem. 268:1252–59
164. Roth DB, Wilson JH. 1986. Nonhomologous recombination in mammalian cells:
role for short sequence homologies in the
joining reaction. Mol. Cell Biol. 6:4295–
304
165. Schar P, Herrmann G, Daly G, Lindahl T. 1997. A newly identified DNA
ligase of Saccharomyces cerevisiae involved in RAD52-independent repair of
DNA double-strand breaks. Genes Dev.
11:1912–24
166. Schiestl RH, Petes TD. 1991. Integration of DNA fragments by illegitimate
recombination in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 88:
7585–89
167. Schiestl RH, Prakash S, Prakash L. 1990.
The SRS2 suppressor of rad6 mutations
of Saccharomyces cerevisiae acts by
channeling DNA lesions into the RAD52
DNA repair pathway. Genetics 124:817–
31
168. Schwacha A, Kleckner N. 1995. Identification of double Holliday junctions as
intermediates in meiotic recombination.
Cell 83:783–91
169. Schwacha A, Kleckner N. 1997. Interhomolog bias during meiotic recombination: meiotic functions promote a highly
differentiated interhomolog-only pathway. Cell 90:1123–35
169a. Sehorn MG, Sigurdsson S, Bussen
W, Unger VM, Sung P. 2004. Human
meiotic recombinase Dmc1 promotes
15 Oct 2004 19:50
268
170.
Annu. Rev. Genet. 2004.38:233-271. Downloaded from arjournals.annualreviews.org
by UNIVERSITY OF SOUTH CAROL on 02/10/05. For personal use only.
171.
172.
173.
174.
175.
176.
177.
178.
179.
AR
KROGH
AR230-GE38-08.tex
AR230-GE38-08.sgm
LaTeX2e(2002/01/18)
P1: GCE
SYMINGTON
ATP-dependent homologous DNA
strand exchange. Nature 429:433–37
Seigneur M, Bidnenko V, Ehrlich SD,
Michel B. 1998. RuvAB acts at arrested
replication forks. Cell 95:419–30
Sharples GJ, Leach DR. 1995. Structural
and functional similarities between the
SbcCD proteins of Escherichia coli and
the RAD50 and MRE11 (RAD32) recombination and repair proteins of yeast.
Mol. Microbiol. 17:1215–17
Shin DS, Pellegrini L, Daniels DS, Yelent B, Craig L, et al. 2003. Full-length
archaeal Rad51 structure and mutants:
mechanisms for RAD51 assembly and
control by BRCA2. EMBO J. 22:4566–
76
Shinohara A, Gasior S, Ogawa T, Kleckner N, Bishop DK. 1997. Saccharomyces
cerevisiae recA homologues RAD51 and
DMC1 have both distinct and overlapping roles in meiotic recombination.
Genes Cells 2:615–29
Shinohara A, Ogawa H, Ogawa T. 1992.
Rad51 protein involved in repair and recombination in S. cerevisiae is a RecAlike protein. Cell 69:457–70. Erratum.
1992. Cell 71(1):180
Shinohara A, Ogawa T. 1998. Stimulation by Rad52 of yeast Rad51-mediated
recombination. Nature 391:404–7
Shinohara A, Shinohara M, Ohta T, Matsuda S, Ogawa T. 1998. Rad52 forms
ring structures and co-operates with RPA
in single-strand DNA annealing. Genes
Cells 3:145–56
Singleton MR, Wentzell LM, Liu Y, West
SC, Wigley DB. 2002. Structure of the
single-strand annealing domain of human RAD52 protein. Proc. Natl. Acad.
Sci. USA 99:13492–97
Smith GR, Boddy MN, Shanahan P, Russell P. 2003. Fission yeast Mus81.Eme1
Holliday junction resolvase is required
for meiotic crossing over but not for gene
conversion. Genetics 165:2289–93
Smith J, Rothstein R. 1999. An allele
of RFA1 suppresses RAD52-dependent
180.
181.
182.
183.
184.
185.
186.
187.
188.
189.
double-strand break repair in Saccharomyces cerevisiae. Genetics 151:447–
58
Solinger JA, Heyer WD. 2001. Rad54
protein stimulates the postsynaptic phase
of Rad51 protein-mediated DNA strand
exchange. Proc. Natl. Acad. Sci. USA
98:8447–53
Solinger JA, Kiianitsa K, Heyer WD.
2002. Rad54, a Swi2/Snf2-like recombinational repair protein, disassembles Rad51:dsDNA filaments. Mol. Cell
10:1175–88
Song B, Sung P. 2000. Functional interactions among yeast Rad51 recombinase, Rad52 mediator, and replication
protein A in DNA strand exchange. J.
Biol. Chem. 275:15895–904
Sonoda E, Sasaki MS, Buerstedde JM,
Bezzubova O, Shinohara A, et al. 1998.
Rad51-deficient vertebrate cells accumulate chromosomal breaks prior to cell
death. EMBO J. 17:598–608
Spell RM, Jinks-Robertson S. 2003. Role
of mismatch repair in the fidelity of
RAD51- and RAD59-dependent recombination in Saccharomyces cerevisiae.
Genetics 165:1733–44
Stasiak AZ, Larquet E, Stasiak A, Muller
S, Engel A, et al. 2000. The human
Rad52 protein exists as a heptameric
ring. Curr. Biol. 10:337–40
Stellwagen AE, Haimberger ZW, Veatch
JR, Gottschling DE. 2003. Ku interacts
with telomerase RNA to promote telomere addition at native and broken chromosome ends. Genes Dev. 17:2384–95
Story RM, Weber IT, Steitz TA. 1992.
The structure of the E. coli recA protein
monomer and polymer. Nature 355:318–
25
Stracker TH, Carson CT, Weitzman MD.
2002. Adenovirus oncoproteins inactivate the Mre11-Rad50-Nbs1 DNA repair
complex. Nature 418:348–52
Strathern JN, Klar AJ, Hicks JB, Abraham JA, Ivy JM, et al. 1982. Homothallic
switching of yeast mating type cassettes
15 Oct 2004 19:50
AR
AR230-GE38-08.tex
AR230-GE38-08.sgm
LaTeX2e(2002/01/18)
RECOMBINATION PROTEINS IN YEAST
190.
Annu. Rev. Genet. 2004.38:233-271. Downloaded from arjournals.annualreviews.org
by UNIVERSITY OF SOUTH CAROL on 02/10/05. For personal use only.
191.
192.
193.
194.
195.
196.
197.
198.
is initiated by a double-stranded cut in
the MAT locus. Cell 31:183–92
Strunnikov AV, Jessberger R. 1999.
Structural maintenance of chromosomes
(SMC) proteins: conserved molecular
properties for multiple biological functions. Eur. J. Biochem. 263:6–13
Sugawara N, Haber JE. 1992. Characterization of double-strand break-induced
recombination: homology requirements
and single-stranded DNA formation.
Mol. Cell Biol. 12:563–75
Sugawara N, Ira G, Haber JE. 2000.
DNA length dependence of the singlestrand annealing pathway and the role
of Saccharomyces cerevisiae RAD59 in
double-strand break repair. Mol. Cell
Biol. 20:5300–9
Sugawara N, Wang X, Haber JE. 2003. In
vivo roles of Rad52, Rad54, and Rad55
proteins in Rad51-mediated recombination. Mol. Cell 12:209–19
Sugiyama T, Kowalczykowski SC. 2002.
Rad52 protein associates with replication protein A (RPA)-single-stranded
DNA to accelerate Rad51-mediated
displacement of RPA and presynaptic complex formation. J. Biol. Chem.
277:31663–72
Sugiyama T, New JH, Kowalczykowski
SC. 1998. DNA annealing by RAD52
protein is stimulated by specific interaction with the complex of replication
protein A and single-stranded DNA.
Proc. Natl. Acad. Sci. USA 95:6049–
54
Sun H, Treco D, Schultes NP, Szostak
JW. 1989. Double-strand breaks at an initiation site for meiotic gene conversion.
Nature 338:87–90
Sun H, Treco D, Szostak JW. 1991. Extensive 3 -overhanging, single-stranded
DNA associated with the meiosisspecific double-strand breaks at the
ARG4 recombination initiation site. Cell
64:1155–61
Sung P. 1997. Function of yeast Rad52
protein as a mediator between replication
199.
200.
201.
202.
203.
204.
205.
206.
207.
208.
P1: GCE
269
protein A and the Rad51 recombinase. J.
Biol. Chem. 272:28194–97
Sung P. 1997. Yeast Rad55 and Rad57
proteins form a heterodimer that functions with replication protein A to promote DNA strand exchange by Rad51
recombinase. Genes Dev. 11:1111–21
Sung P, Robberson DL. 1995. DNA
strand exchange mediated by a RAD51ssDNA nucleoprotein filament with polarity opposite to that of RecA. Cell
82:453–61
Sung P, Stratton SA. 1996. Yeast Rad51
recombinase mediates polar DNA strand
exchange in the absence of ATP hydrolysis. J. Biol. Chem. 271:27983–86
Symington LS. 2002. Role of RAD52
epistasis group genes in homologous recombination and double-strand break repair. Microbiol. Mol. Biol. Rev. 66:630–
70
Szostak JW, Orr-Weaver TL, Rothstein
RJ, Stahl FW. 1983. The double-strandbreak repair model for recombination.
Cell 33:25–35
Teo SH, Jackson SP. 1997. Identification
of Saccharomyces cerevisiae DNA ligase
IV: involvement in DNA double-strand
break repair. EMBO J. 16:4788–95
Teo SH, Jackson SP. 2000. Lif1p targets the DNA ligase Lig4p to sites of
DNA double-strand breaks. Curr. Biol.
10:165–68
Trujillo KM, Roh DH, Chen L, Van
Komen S, Tomkinson A, Sung P. 2003.
Yeast Xrs2 binds DNA and helps target
Rad50 and Mre11 to DNA ends. J. Biol.
Chem. 278:48957–64
Trujillo KM, Sung P. 2001. DNA
structure-specific nuclease activities in
the Saccharomyces cerevisiae Rad50
Mre11 complex. J. Biol. Chem. 276:
35458–64
Trujillo KM, Yuan SS, Lee EY, Sung P.
1998. Nuclease activities in a complex
of human recombination and DNA repair factors Rad50, Mre11, and p95. J.
Biol. Chem. 273:21447–50
15 Oct 2004 19:50
Annu. Rev. Genet. 2004.38:233-271. Downloaded from arjournals.annualreviews.org
by UNIVERSITY OF SOUTH CAROL on 02/10/05. For personal use only.
270
AR
KROGH
AR230-GE38-08.tex
AR230-GE38-08.sgm
LaTeX2e(2002/01/18)
P1: GCE
SYMINGTON
209. Tsubouchi H, Ogawa H. 1998. A novel
mre11 mutation impairs processing of
double-strand breaks of DNA during
both mitosis and meiosis. Mol. Cell Biol.
18:260–68
210. Tsubouchi H, Ogawa H. 2000. Exo1
roles for repair of DNA double-strand
breaks and meiotic crossing over in Saccharomyces cerevisiae. Mol. Biol. Cell
11:2221–33
211. Tsubouchi H, Roeder GS. 2003. The importance of genetic recombination for fidelity of chromosome pairing in meiosis.
Dev. Cell 5:915–25
212. Tsukamoto M, Yamashita K, Miyazaki
T, Shinohara M, Shinohara A. 2003.
The N-terminal DNA-binding domain
of Rad52 promotes RAD51-independent
recombination in Saccharomyces cerevisiae. Genetics 165:1703–15
213. Tsukamoto Y, Taggart AK, Zakian VA.
2001. The role of the Mre11-Rad50Xrs2 complex in telomerase-mediated
lengthening of Saccharomyces cerevisiae telomeres. Curr. Biol. 11:1328–35
214. Tsuzuki T, Fujii Y, Sakumi K, Tominaga
Y, Nakao K, et al. 1996. Targeted disruption of the Rad51 gene leads to lethality
in embryonic mice. Proc. Natl. Acad. Sci.
USA 93:6236–40
214a. Usui T, Ogawa H, Petrini JH. 2001. A
DNA damage response pathway controlled by Tel1 and the Mre11 complex.
Mol. Cell 7:1255–66
215. Usui T, Ohta T, Oshiumi H, Tomizawa
J, Ogawa H, Ogawa T. 1998. Complex
formation and functional versatility of
Mre11 of budding yeast in recombination. Cell 95:705–16
216. Valencia M, Bentele M, Vaze MB, Herrmann G, Kraus E, et al. 2001. NEJ1
controls non-homologous end joining
in Saccharomyces cerevisiae. Nature
414:666–69
217. Van Komen S, Petukhova G, Sigurdsson S, Stratton S, Sung P. 2000. Superhelicity-driven homologous DNA pairing by yeast recombination factors
218.
219.
220.
221.
222.
223.
224.
225.
226.
Rad51 and Rad54. Mol. Cell. 6:563–
72
Van Komen S, Reddy MS, Krejci L,
Klein H, Sung P. 2003. ATPase and
DNA helicase activities of the Saccharomyces cerevisiae anti-recombinase
Srs2. J. Biol. Chem. 278:44331–37
van Noort J, van Der Heijden T, de
Jager M, Wyman C, Kanaar R, Dekker
C. 2003. The coiled-coil of the human
Rad50 DNA repair protein contains specific segments of increased flexibility.
Proc. Natl. Acad. Sci. USA 100:7581–86
Varon R, Vissinga C, Platzer M, Cerosaletti KM, Chrzanowska KH, et al.
1998. Nibrin, a novel DNA doublestrand break repair protein, is mutated
in Nijmegen breakage syndrome. Cell
93:467–76
Veaute X, Jeusset J, Soustelle C, Kowalczykowski SC, Le Cam E, Fabre F. 2003.
The Srs2 helicase prevents recombination by disrupting Rad51 nucleoprotein
filaments. Nature 423:309–12
Wallis JW, Chrebet G, Brodsky G,
Rolfe M, Rothstein R. 1989. A hyperrecombination mutation in S. cerevisiae
identifies a novel eukaryotic topoisomerase. Cell 58:409–19
Wan L, de los Santos T, Zhang C,
Shokat K, Hollingsworth NM. 2004.
Mek1 kinase activity functions downstream of RED1 in the regulation of meiotic double-strand break repair in budding yeast. Mol. Biol. Cell 15:11–23
Wang H, Perrault AR, Takeda Y, Qin W,
Iliakis G. 2003. Biochemical evidence
for Ku-independent backup pathways of
NHEJ. Nucleic Acids Res. 31:5377–88
Wang X, Haber JE. 2004. Role of
Saccharomyces single-stranded DNAbinding protein RPA in the strand invasion step of double-strand break repair.
PLoS Biol. 2:E21
Weiden MD, Ginsberg HS. 1994. Deletion of the E4 region of the genome
produces adenovirus DNA concatemers.
Proc. Natl. Acad. Sci. USA 91:153–57
15 Oct 2004 19:50
AR
AR230-GE38-08.tex
AR230-GE38-08.sgm
LaTeX2e(2002/01/18)
Annu. Rev. Genet. 2004.38:233-271. Downloaded from arjournals.annualreviews.org
by UNIVERSITY OF SOUTH CAROL on 02/10/05. For personal use only.
RECOMBINATION PROTEINS IN YEAST
227. White CI, Haber JE. 1990. Intermediates of recombination during mating type
switching in Saccharomyces cerevisiae.
EMBO J. 9:663–73
228. Wilson S, Warr N, Taylor DL, Watts FZ.
1999. The role of Schizosaccharomyces
pombe Rad32, the Mre11 homologue,
and other DNA damage response proteins in non-homologous end joining and
telomere length maintenance. Nucleic
Acids Res. 27:2655–61
229. Wilson TE, Grawunder U, Lieber MR.
1997. Yeast DNA ligase IV mediates
non-homologous DNA end joining. Nature 388:495–98
230. Wolner B, van Komen S, Sung P, Peterson CL. 2003. Recruitment of the recombinational repair machinery to a DNA
double-strand break in yeast. Mol. Cell.
12:221–32
231. Wu L, Hickson ID. 2003. The Bloom’s
syndrome helicase suppresses crossing
over during homologous recombination.
Nature 426:870–74
232. Wu TC, Lichten M. 1994. Meiosis-
233.
234.
235.
236.
P1: GCE
271
induced double-strand break sites determined by yeast chromatin structure. Science 263:515–18
Wu X, Ranganathan V, Weisman DS,
Heine WF, Ciccone DN, et al. 2000.
ATM phosphorylation of Nijmegen
breakage syndrome protein is required
in a DNA damage response. Nature
405:477–82
Yang S, Yu X, Seitz EM, Kowalczykowski SC, Egelman EH. 2001. Archaeal RadA protein binds DNA as both
helical filaments and octameric rings. J.
Mol. Biol. 314:1077–85
Yu J, Marshall K, Yamaguchi M, Haber
JE, Weil CF. 2004. Microhomologydependent end joining and repair of
transposon-induced DNA hairpins by
host factors in Saccharomyces cerevisiae. Mol. Cell Biol. 24:1351–64
Zhao S, Renthal W, Lee EY. 2002.
Functional analysis of FHA and BRCT
domains of NBS1 in chromatin association and DNA damage responses.
Nucleic Acids Res. 30:4815–22
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CONTENTS
MOBILE GROUP II INTRONS, Alan M. Lambowitz and Steven Zimmerly
THE GENETICS OF MAIZE EVOLUTION, John Doebley
GENETIC CONTROL OF RETROVIRUS SUSCEPTIBILITY IN MAMMALIAN
CELLS, Stephen P. Goff
LIGHT SIGNAL TRANSDUCTION IN HIGHER PLANTS, Meng Chen,
Joanne Chory, and Christian Fankhauser
1
37
61
87
CHLAMYDOMONAS REINHARDTII IN THE LANDSCAPE OF PIGMENTS,
Arthur R. Grossman, Martin Lohr, and Chung Soon Im
THE GENETICS OF GEOCHEMISTRY, Laura R. Croal, Jeffrey A. Gralnick,
Davin Malasarn, and Dianne K. Newman
CLOSING MITOSIS: THE FUNCTIONS OF THE CDC14 PHOSPHATASE AND
ITS REGULATION, Frank Stegmeier and Angelika Amon
RECOMBINATION PROTEINS IN YEAST, Berit Olsen Krogh
and Lorraine S. Symington
119
175
203
233
DEVELOPMENTAL GENE AMPLIFICATION AND ORIGIN REGULATION,
John Tower
273
THE FUNCTION OF NUCLEAR ARCHITECTURE: A GENETIC APPROACH,
Angela Taddei, Florence Hediger, Frank R. Neumann,
and Susan M. Gasser
305
GENETIC MODELS IN PATHOGENESIS, Elizabeth Pradel
and Jonathan J. Ewbank
347
MELANOCYTES AND THE MICROPHTHALMIA TRANSCRIPTION FACTOR
NETWORK, Eirı́kur Steingrı́msson, Neal G. Copeland,
and Nancy A. Jenkins
EPIGENETIC REGULATION OF CELLULAR MEMORY BY THE POLYCOMB
AND TRITHORAX GROUP PROTEINS, Leonie Ringrose and Renato Paro
REPAIR AND GENETIC CONSEQUENCES OF ENDOGENOUS DNA BASE
DAMAGE IN MAMMALIAN CELLS, Deborah E. Barnes
and Tomas Lindahl
365
413
445
MITOCHONDRIA OF PROTISTS, Michael W. Gray, B. Franz Lang,
and Gertraud Burger
477
v
P1: JRX
October 18, 2004
vi
14:55
Annual Reviews
AR230-FM
CONTENTS
METAGENOMICS: GENOMIC ANALYSIS OF MICROBIAL COMMUNITIES,
Christian S. Riesenfeld, Patrick D. Schloss, and Jo Handelsman
525
GENOMIC IMPRINTING AND KINSHIP: HOW GOOD IS THE EVIDENCE?,
David Haig
553
MECHANISMS OF PATTERN FORMATION IN PLANT EMBRYOGENESIS,
Viola Willemsen and Ben Scheres
Annu. Rev. Genet. 2004.38:233-271. Downloaded from arjournals.annualreviews.org
by UNIVERSITY OF SOUTH CAROL on 02/10/05. For personal use only.
DUPLICATION AND DIVERGENCE: THE EVOLUTION OF NEW GENES
AND OLD IDEAS, John S. Taylor and Jeroen Raes
GENETIC ANALYSES FROM ANCIENT DNA, Svante Pääbo,
Hendrik Poinar, David Serre, Viviane Jaenicke-Despres, Juliane Hebler,
Nadin Rohland, Melanie Kuch, Johannes Krause, Linda Vigilant,
and Michael Hofreiter
587
615
645
PRION GENETICS: NEW RULES FOR A NEW KIND OF GENE,
Reed B. Wickner, Herman K. Edskes, Eric D. Ross, Michael M. Pierce,
Ulrich Baxa, Andreas Brachmann, and Frank Shewmaker
681
PROTEOLYSIS AS A REGULATORY MECHANISM, Michael Ehrmann and
Tim Clausen
709
MECHANISMS OF MAP KINASE SIGNALING SPECIFICITY IN
SACCHAROMYCES CEREVISIAE, Monica A. Schwartz
and Hiten D. Madhani
725
rRNA TRANSCRIPTION IN ESCHERICHIA COLI, Brian J. Paul, Wilma Ross,
Tamas Gaal, and Richard L. Gourse
749
COMPARATIVE GENOMIC STRUCTURE OF PROKARYOTES,
Stephen D. Bentley and Julian Parkhill
771
SPECIES SPECIFICITY IN POLLEN-PISTIL INTERACTIONS,
Robert Swanson, Anna F. Edlund, and Daphne Preuss
793
INTEGRATION OF ADENO-ASSOCIATED VIRUS (AAV) AND
RECOMBINANT AAV VECTORS, Douglas M. McCarty,
Samuel M. Young Jr., and Richard J. Samulski
819
INDEXES
Subject Index
ERRATA
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847