**2. Genome repair in the RNA world**

Since the actual sequence of evolutionary adaptive events in the RNA world that gave rise to genome repair occurred in organisms that are probably long extinct, and it is unlikely that events at the nucleic acid level are preserved in the fossil record, the sequence of evolutionary events proposed here is necessarily speculative. However, the proposed evolutionary sequence is based on the established activities of extant RNA viruses. These activities are reviewed in sections 2.1, 2.2, 3 and 4. Thus it is assumed, as discussed by Bernstein et al. (pgs. 342-345) [8], that the adaptations that extant RNA viruses use to repair genome damage can illuminate how early life in the RNA world also coped with genome damage.

In early protocellular organisms the genome is thought to have consisted of ssRNAs (genes) that formed folded structures with catalyic activity (ribozymes) [16]. If two or more such ssRNAs were present in a protocell they presumably functioned interdependently to promote the viability and reproduction of the protocell. A key ribozyme in early protocellular organisms would likely have been a polymerase that could catalyze RNA replication [4]. A persistent problem for early protocellular organisms would probably have been damage to their ssRNA genomes. The damaging stresses on protocellular organisms likely would have included hydrolytic reactions, exposure to UV light and interaction with reactive chemicals in the environment. For example, Sagan [17] analyzed the flux of solar UV light that penetrated the earth's primitive reducing atmosphere. His analysis indicated that unprotected microorganisms of the type existing today would receive a mean lethal dose at 2600 angstroms within 0.3 seconds and that this vulnerability could have posed a major problem during the early evolution of life. A protocell that has only one copy of each ssRNA (a haploid protocell) would be very vulnerable to damage, since damage to even one base in a ssRNA sequence might be lethal to the protocell by either blocking replication of the ssRNA or interfering with an essential ssRNA ribozyme function [8].

One possible adaptation for dealing with genome damage would be to maintain two or more copies of each ssRNA gene in each protocell, yielding a diploid or polyploid state. Genome redundancy would allow replacement of a damaged gene by an additional replication of an undamaged homologous gene. However, for a simple protocellular organism, the proportion of available resource budgeted to the maintenance of two or more genomes would have been a large portion of its total resource budget. When resources are limited, the protocell's reproductive rate would likely be inversely related to ploidy number. The fitness of the protocell would be diminished by the costs of genome redundancy. Coping with damage to the ssRNA genome while minimizing the costs of genome redundancy would likely have been a fundamental problem in the early evolution of cellular life [8].

When the costs of maintaining genome redundancy verses the costs of genome damage were balanced against each other in a cost–benefit analysis, it was found that under a wide range of conditions the selected strategy would be for each

protocell to be haploid, but to periodically fuse with another haploid protocell to form a transient diploid [18]. This strategy allows the haploid state to be retained to maximize reproductive rate, while the periodic fusions would allow otherwise lethally damaged protocells to be mutually reactivated. Reactivation can occur if at least one undamaged copy of each ssRNA gene is present in the transient diploid and this leads to production of a viable progeny protocell. In order for two (rather than just one) viable progeny protocells to be produced, an extra replication of the gene(s) homologous to damaged gene(s) would have to occur before division of the fused diploid protocell. The process of recovering from potentially lethal damage in one ssRNA genome by reassorting information with another homologous ssRNA genome can be regarded as a primitive form of genome repair [8, 18]. This proposed cycle for coping with genome damage, although hypothetical, is based on the way that ssRNA viruses with segmented RNA genomes deal with genome damage as discussed below in Section 2.1.

The events that contributed to the evolution of genomic repair in ssRNA protocells can also be viewed as an early stage in the evolution of sexual reproduction since these events include the coming together of two genomes from separate parents to generate progeny genomes containing shared genetic information [18].

### **2.1 Recombination in influenza virus and hantavirus**

Influenza virus (Family *Bunyavirales*) is an example of a virus with a segmented ssRNA genome (**Figure 1**). Influenza virus has a genome comprised of eight physically separated ssRNA segments [19]. These eight segments of singlestranded RNA code for seven virion structural proteins and three non-structural proteins. During infection of a host cell by two viruses, recombinant progeny can be formed as the result of exchange of segments of the virus ssRNA, a process termed reassortment [19].

#### **Figure 1.**

*Influenza virus. An enveloped virus with an outer lipid membrane and glycoprotein "spikes." Influenza A or B viruses have eight genome segments inside the virion. https://pixnio.com/science/microscopy-images/ influenza/3-dimensional-model-of-influenza-virus In the public domain.*

**25**

**hantavirus**

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

an adaptive genomic repair process.

played a role in the observed multiplicity reactivation.

tions may have been adaptively beneficial only infrequently.

ment as a mechanism of genome repair [31].

**2.2 Intragenic recombination in segmented ssRNA influenza virus and** 

by template-switching (copy-choice) during viral genome replication [32].

In influenza virus infections, genome segment reassortment is not the only mechanism of recombination. Intragenic homologous recombination can also occur between a pair of homologous viral genes [31]. Homologous recombination occurs

In addition to influenza viruses, ssRNA hantaviruses are also capable of recombination by both segment reassortment and by homologous recombination [33]. In the evolution of repair processes in the RNA world, template-switching (copy-choice) recombination was likely an important advance since it allows two damaged homologous genes to generate an undamaged homolog. However, at present there is insufficient evidence available to determine whether copy-choice recombination emerged before or after the emergence of genome segment reassort-

Upon infection, influenza virus induces a host response involving increased production of reactive oxygen species, and this can damage the virus genome [20]. Consider two individual viruses each with a lethal damage in its genome. If either of these viruses infects a host cell the infection aborts and no progeny viruses are produced. However, if these two damaged viruses infect the same host cell, the multiple infection may lead to reactivation (production of viable progeny). This phenomenon is known as "multiplicity reactivation" and is thought to reflect acts of recombination that allow an undamaged genome to be reconstituted from damaged ones [21]. Multiplicity reactivation has been demonstrated in influenza virus infections after induction of RNA damage by UV-irradiation [22] and ionizing radiation [23]. In these studies, recombination by reassortment of genome segments likely

Hantaviruses (Order *Bunyavirales*; Family *Hantaviridae*), another group of segmented ssRNA viruses, are also able to undergo reassortment [24, 25]. Reovirus (Family *Reoviridae*), a segmented double-stranded RNA virus, can also undergo multiplicity reactivation after its genome is damaged by exposure to UV light [26]. Substantial evidence in model virus systems indicates that multiplicity reactivation is a recombinational repair process for overcoming a variety of types of genome damage (reviewed in [27, 28]). If, under natural conditions, virus survival is ordinarily vulnerable to oxidative or other damage, then multiplicity reactivation likely acts as

Recombination by reassortment is a simple way of restoring an undamaged genome from multiple lethally damaged genomes and thus is a primitive form of genomic repair. Lehman [29] has reviewed evidence supporting the view that recombination is an evolutionary development as ancient as the origins of life. In addition to the role of recombination in genome repair, recombination also has a role in viral evolution by generating new genetic combinations that can be tested by natural selection. An infrequent new genetic combination may be selectively advantageous. However, RNA is very vulnerable to damage. Because of the reactivity of the oxygen and nitrogen atoms of the nucleobases [30], RNA molecules are especially susceptible to certain types of chemical damage from sources such as reactive oxygen species, UV light, and alkylating agents; and the oxygen atoms of the ribose and the phosphodiester backbone are also vulnerable to chemical damage [30]. In early protocells, repair of RNA genome damage likely provided a considerable and immediate selective advantage while new recombinant genetic combina-

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

*DNA - Damages and Repair Mechanisms*

discussed below in Section 2.1.

termed reassortment [19].

**2.1 Recombination in influenza virus and hantavirus**

protocell to be haploid, but to periodically fuse with another haploid protocell to form a transient diploid [18]. This strategy allows the haploid state to be retained to maximize reproductive rate, while the periodic fusions would allow otherwise lethally damaged protocells to be mutually reactivated. Reactivation can occur if at least one undamaged copy of each ssRNA gene is present in the transient diploid and this leads to production of a viable progeny protocell. In order for two (rather than just one) viable progeny protocells to be produced, an extra replication of the gene(s) homologous to damaged gene(s) would have to occur before division of the fused diploid protocell. The process of recovering from potentially lethal damage in one ssRNA genome by reassorting information with another homologous ssRNA genome can be regarded as a primitive form of genome repair [8, 18]. This proposed cycle for coping with genome damage, although hypothetical, is based on the way that ssRNA viruses with segmented RNA genomes deal with genome damage as

The events that contributed to the evolution of genomic repair in ssRNA protocells can also be viewed as an early stage in the evolution of sexual reproduction since these events include the coming together of two genomes from separate parents to generate progeny genomes containing shared genetic information [18].

Influenza virus (Family *Bunyavirales*) is an example of a virus with a segmented ssRNA genome (**Figure 1**). Influenza virus has a genome comprised of eight physically separated ssRNA segments [19]. These eight segments of singlestranded RNA code for seven virion structural proteins and three non-structural proteins. During infection of a host cell by two viruses, recombinant progeny can be formed as the result of exchange of segments of the virus ssRNA, a process

*Influenza virus. An enveloped virus with an outer lipid membrane and glycoprotein "spikes." Influenza A or B viruses have eight genome segments inside the virion. https://pixnio.com/science/microscopy-images/*

*influenza/3-dimensional-model-of-influenza-virus In the public domain.*

**24**

**Figure 1.**

Upon infection, influenza virus induces a host response involving increased production of reactive oxygen species, and this can damage the virus genome [20]. Consider two individual viruses each with a lethal damage in its genome. If either of these viruses infects a host cell the infection aborts and no progeny viruses are produced. However, if these two damaged viruses infect the same host cell, the multiple infection may lead to reactivation (production of viable progeny). This phenomenon is known as "multiplicity reactivation" and is thought to reflect acts of recombination that allow an undamaged genome to be reconstituted from damaged ones [21]. Multiplicity reactivation has been demonstrated in influenza virus infections after induction of RNA damage by UV-irradiation [22] and ionizing radiation [23]. In these studies, recombination by reassortment of genome segments likely played a role in the observed multiplicity reactivation.

Hantaviruses (Order *Bunyavirales*; Family *Hantaviridae*), another group of segmented ssRNA viruses, are also able to undergo reassortment [24, 25]. Reovirus (Family *Reoviridae*), a segmented double-stranded RNA virus, can also undergo multiplicity reactivation after its genome is damaged by exposure to UV light [26]. Substantial evidence in model virus systems indicates that multiplicity reactivation is a recombinational repair process for overcoming a variety of types of genome damage (reviewed in [27, 28]). If, under natural conditions, virus survival is ordinarily vulnerable to oxidative or other damage, then multiplicity reactivation likely acts as an adaptive genomic repair process.

Recombination by reassortment is a simple way of restoring an undamaged genome from multiple lethally damaged genomes and thus is a primitive form of genomic repair. Lehman [29] has reviewed evidence supporting the view that recombination is an evolutionary development as ancient as the origins of life.

In addition to the role of recombination in genome repair, recombination also has a role in viral evolution by generating new genetic combinations that can be tested by natural selection. An infrequent new genetic combination may be selectively advantageous. However, RNA is very vulnerable to damage. Because of the reactivity of the oxygen and nitrogen atoms of the nucleobases [30], RNA molecules are especially susceptible to certain types of chemical damage from sources such as reactive oxygen species, UV light, and alkylating agents; and the oxygen atoms of the ribose and the phosphodiester backbone are also vulnerable to chemical damage [30]. In early protocells, repair of RNA genome damage likely provided a considerable and immediate selective advantage while new recombinant genetic combinations may have been adaptively beneficial only infrequently.

### **2.2 Intragenic recombination in segmented ssRNA influenza virus and hantavirus**

In influenza virus infections, genome segment reassortment is not the only mechanism of recombination. Intragenic homologous recombination can also occur between a pair of homologous viral genes [31]. Homologous recombination occurs by template-switching (copy-choice) during viral genome replication [32].

In addition to influenza viruses, ssRNA hantaviruses are also capable of recombination by both segment reassortment and by homologous recombination [33].

In the evolution of repair processes in the RNA world, template-switching (copy-choice) recombination was likely an important advance since it allows two damaged homologous genes to generate an undamaged homolog. However, at present there is insufficient evidence available to determine whether copy-choice recombination emerged before or after the emergence of genome segment reassortment as a mechanism of genome repair [31].
