**6. Eukaryotes**

Eukaryotes are capable of several different types of DNA repair process:


well-studied processes. These include mismatch repair (MMR), nucleotide excision repair (NER) and base excision repair (BER) [14]. These processes appear to have arisen in the archaea [59], but are most well understood in the eukaryotes. This option was not available to organisms with ssRNA genomes because the double-stranded state exists only transiently during replication. In any case the enzymes that carry out such repair processes in organisms with DNA genomes are not known to be encoded in the ssRNA virus genomes. Thus this type of mechanism was not likely present during the early evolutionary stages in ssRNA genome containing organisms.


During meiosis homologous chromosomes originating from different parents align intimately with each other. This is followed by transfer of sequence information between homologs, homologous recombination. The main mechanism is SDSA (copy-choice recombination), a central characteristic of meiosis (see Section 6.1). Less frequent homologous recombination by breakage and exchange of chromosomes also occurs during meiosis.

Copy-choice recombination is also an important general mechanism for dealing with DNA damages that block the movement of the DNA polymerase during DNA replication (see Section 6.2).

#### **6.1 Meiotic and mitotic recombination**

The results of numerous studies in a wide range of eukaryotes indicate that during meiosis a variety of DNA damages are repaired by recombinational repair (reviewed in [62]). In somatic cells, mitotic recombination also facilitates DNA repair. Molecular models of recombination have been revised over the years as relevant evidence accumulated. Our current understanding of recombination reflects the work of several groups of investigators that have provided evidence that SDSA is a major mechanism of recombination [11, 63–65]. Furthermore, SDSA is a type of copy-choice mechanism since it involves switching from one template to another during strand synthesis and the return to the original template after a short distance (compare **Figure 5** to **Figure 2**).

**Figure 5** illustrates the series of steps that occur by the meiotic SDSA process in the repair of a double-strand break (DSB) in one chromosome using information

**33**

**Figure 5.**

from an adjacent undamaged homologous chromosome. As shown in the figure, the steps include strand invasion by a broken strand to form a D-loop, the further extension of the strand by DNA synthesis, and then the reassociation of the transferred strand with its original pairing partner. These strand-switching and DNA synthesis events associated with repair of a damage are similar to the copy-choice

*Synthesis-dependent strand annealing (SDSA) in the repair of a double-strand break.*

*Origin of DNA Repair in the RNA World DOI: http://dx.doi.org/10.5772/intechopen.93822* *DNA - Damages and Repair Mechanisms*

ssRNA genomes.

somes also occurs during meiosis.

**6.1 Meiotic and mitotic recombination**

replication (see Section 6.2).

(compare **Figure 5** to **Figure 2**).

stages in ssRNA genome containing organisms.

well-studied processes. These include mismatch repair (MMR), nucleotide excision repair (NER) and base excision repair (BER) [14]. These processes appear to have arisen in the archaea [59], but are most well understood in the eukaryotes. This option was not available to organisms with ssRNA genomes because the double-stranded state exists only transiently during replication. In any case the enzymes that carry out such repair processes in organisms with DNA genomes are not known to be encoded in the ssRNA virus genomes. Thus this type of mechanism was not likely present during the early evolutionary

c.Double-strand damages in double-stranded DNA, such as double-strand breaks, can be repaired without the presence of an homologous template by such processes as non-homologous end joining (NHEJ) and microhomology mediated end joining (MMEJ). These processes depend on the duplex nature of DNA but not on strict homology. NHEJ can be accurate if the ends of the DNA in double-strand breaks do not need processing. However, if the ends need processing before rejoining then mutations are very likely to be introduced [60]. MMEJ is inaccurate and is always associated with a DNA deletion [61]. Thus these processes are inaccurate and generate mutations and are not applicable to

d.Homologous recombinational repair is possible when two templates are present and adjacent. Such repair may occur for various types of DNA damage. For double-strand breaks in mitosis, homologous recombinational repair, either by the less common breakage and exchange mechanism or by the more frequently used SDSA (copy-choice) mechanism [11], are the only accurate forms of repair available. Template switching can occur during mitosis when two sister chromatids are present and adjacent after DNA synthesis and before cell division.

During meiosis homologous chromosomes originating from different parents align intimately with each other. This is followed by transfer of sequence information between homologs, homologous recombination. The main mechanism is SDSA (copy-choice recombination), a central characteristic of meiosis (see Section 6.1). Less frequent homologous recombination by breakage and exchange of chromo-

Copy-choice recombination is also an important general mechanism for dealing with DNA damages that block the movement of the DNA polymerase during DNA

The results of numerous studies in a wide range of eukaryotes indicate that during meiosis a variety of DNA damages are repaired by recombinational repair (reviewed in [62]). In somatic cells, mitotic recombination also facilitates DNA repair. Molecular models of recombination have been revised over the years as relevant evidence accumulated. Our current understanding of recombination reflects the work of several groups of investigators that have provided evidence that SDSA is a major mechanism of recombination [11, 63–65]. Furthermore, SDSA is a type of copy-choice mechanism since it involves switching from one template to another during strand synthesis and the return to the original template after a short distance

**Figure 5** illustrates the series of steps that occur by the meiotic SDSA process in the repair of a double-strand break (DSB) in one chromosome using information

**32**

from an adjacent undamaged homologous chromosome. As shown in the figure, the steps include strand invasion by a broken strand to form a D-loop, the further extension of the strand by DNA synthesis, and then the reassociation of the transferred strand with its original pairing partner. These strand-switching and DNA synthesis events associated with repair of a damage are similar to the copy-choice

recombination described above for ssRNA viruses. Thus a central feature of eukaryotic recombination in meiosis and mitosis, strand-switching copy-choice recombinational repair, may have evolved from the simpler repair-related copy-choice events postulated above for ssRNA protocells based on the known processes in ssRNA viruses. Experimental evidence demonstrating that SDSA is a major recombination pathway in meiosis was presented by McMahill et al. [64].

The process of SDSA can accurately repair genome damage by copying the information lost in a damaged template strand from another intact homologous template strand without the need for physical breakage and exchange of DNA. Evidence bearing on the role of SDSA during meiotic recombination was reviewed by Bernstein et al. [66]. An alternative mechanism for recombinational repair termed the Double-Strand Break Repair (DSBR) model also explains some types of recombination events, but in contrast to SDSA recombination, the DSBR model does require physical breakage and exchange of DNA strands [67]. However,

#### **Figure 6.**

*Bypassing a DNA damage during replication. This mechanism involves reversal of the replication fork, where the newly replicated strands dissociate from their previous templates and anneal to form a cruciform intermediate, known as the "chicken foot" structure. Further replication of the previously blocked strand can then continue, leading to the bypass of the damaged site.*

**35**

*Origin of DNA Repair in the RNA World DOI: http://dx.doi.org/10.5772/intechopen.93822*

elements of copy-choice recombination.

simpler copy-choice processes in ssRNA protocells.

**6.2 DNA replication**

**7. Conclusions**

ribozyme polymerases.

reassortment.

would be similar.

have occurred.

both the SDSA and DSBR models include a step in a which a DNA strand switches at a site of damage from one complementary partner strand to another and then continues synthesis with the new partner as template. Thus both models have

With respect to mitotic recombination in somatic cells, Andersen and Sekelsky [11] reviewed evidence that DSBR is a minor pathway for recombinational repair, and that the SDSA model appears to describe mitotic repair more accurately.

During DNA replication, a DNA damage in a template strand may be present and act as roadblock to the movement of the DNA polymerase as it extends synthesis of a new complementary strand. A blocked replication fork may be accurately bypassed by the mechanism illustrated in **Figure 6** [12, 13]. When movement of the replicative polymerase is blocked by a damage, the polymerase can switch template strands (mediated by a helicase) [12, 13] to form a structure referred to as a "chickenfoot" intermediate. As synthesis of the new strand proceeds along the alternate template it synthesizes the DNA region that is complementary to the damaged site in its original partner strand. The newly forming strand may then unwind and then re-associate with its original partner to continue synthesis along its original track. Polymerase-mediated strand-switching to deal with a damaged template during DNA synthesis appears to be an important general mechanism in eukaryotic cells [64]. This mechanism can be regarded as a type of copy-choice recombinational repair, and it too may have evolved from

Given the copy-choice genomic repair mechanism present in today's ssRNA viruses, it appears that copy choice as a repair process may have emerged as early as 3.5 to 2.5 billion years ago when RNA was apparently the only genetic material. It is possible that the capability for strand-switching was a property of the earliest

In early protocells, the ssRNA genomes may have been segmented, as some ssRNA viruses are in the present day. Two protocells with damaged segmented genomes could have been able to generate undamaged progeny after fusion and then reassortment of segments. Present day ssRNA segmented genome viruses can repair damage in their genomes through both copy choice and segment

The early stages of the evolution of genome repair proposed here are based on known capabilities of extant RNA viruses. Currently it is not known if these RNA viruses are the actual evolutionary descendants of early RNA life forms, or if they arose later. It has only been assumed here that the problem of dealing with damage to an RNA genome arises in the two cases, and that the solutions to this problem

The earliest ssRNAs that formed folded structures that acted as ribozymes can be designated plus (+) strands. Such a ribozyme strand could have had polymerase activity and acted as an RdRp. The progeny ssRNAs that it synthesizes would be complementary to the corresponding parental (+) strands, and can be designated minus (−) strands. During the synthesis of (−) strands template-switching may

both the SDSA and DSBR models include a step in a which a DNA strand switches at a site of damage from one complementary partner strand to another and then continues synthesis with the new partner as template. Thus both models have elements of copy-choice recombination.

With respect to mitotic recombination in somatic cells, Andersen and Sekelsky [11] reviewed evidence that DSBR is a minor pathway for recombinational repair, and that the SDSA model appears to describe mitotic repair more accurately.

### **6.2 DNA replication**

*DNA - Damages and Repair Mechanisms*

recombination described above for ssRNA viruses. Thus a central feature of eukaryotic recombination in meiosis and mitosis, strand-switching copy-choice recombinational repair, may have evolved from the simpler repair-related copy-choice events postulated above for ssRNA protocells based on the known processes in ssRNA viruses. Experimental evidence demonstrating that SDSA is a major recom-

The process of SDSA can accurately repair genome damage by copying the information lost in a damaged template strand from another intact homologous template strand without the need for physical breakage and exchange of DNA. Evidence bearing on the role of SDSA during meiotic recombination was reviewed by Bernstein et al. [66]. An alternative mechanism for recombinational repair termed the Double-Strand Break Repair (DSBR) model also explains some types of recombination events, but in contrast to SDSA recombination, the DSBR model does require physical breakage and exchange of DNA strands [67]. However,

*Bypassing a DNA damage during replication. This mechanism involves reversal of the replication fork, where the newly replicated strands dissociate from their previous templates and anneal to form a cruciform intermediate, known as the "chicken foot" structure. Further replication of the previously blocked strand can* 

bination pathway in meiosis was presented by McMahill et al. [64].

**34**

**Figure 6.**

*then continue, leading to the bypass of the damaged site.*

During DNA replication, a DNA damage in a template strand may be present and act as roadblock to the movement of the DNA polymerase as it extends synthesis of a new complementary strand. A blocked replication fork may be accurately bypassed by the mechanism illustrated in **Figure 6** [12, 13]. When movement of the replicative polymerase is blocked by a damage, the polymerase can switch template strands (mediated by a helicase) [12, 13] to form a structure referred to as a "chickenfoot" intermediate. As synthesis of the new strand proceeds along the alternate template it synthesizes the DNA region that is complementary to the damaged site in its original partner strand. The newly forming strand may then unwind and then re-associate with its original partner to continue synthesis along its original track. Polymerase-mediated strand-switching to deal with a damaged template during DNA synthesis appears to be an important general mechanism in eukaryotic cells [64]. This mechanism can be regarded as a type of copy-choice recombinational repair, and it too may have evolved from simpler copy-choice processes in ssRNA protocells.
