Chapter 5 : Genome Instability and DNA Repair

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This chapter describes DNA repair systems that have not been described for species even though orthologues are found at least in the genome databases. A section of the chapter describes the genetic plasticity as it relates to drug resistance. In haploid cells, the rate of spontaneous mutation in the nuclear genome is rather low under laboratory conditions. An additional marker of the genetic instability in is represented by aneuploidies. Aneuploidies are common in laboratory strains of but are especially abundant when those strains have been subjected to genetic manipulations, including several laboratory strains successively derived from CAI-4, or treated with mutagenic agents such as UV light. Genetic instability could be caused by an increase in the rate of mutations in the form of single base substitutions, microinsertions, and microdeletions. These alterations are known to arise from errors during normal DNA replication by polymerases δ and ε and are usually corrected before being fixed by methyl mismatch repair (MMR). It was suggested that has evolved additional DNA repair systems to defend itself against killing by the oxygen radicals generated by macrophages. For an opportunistic pathogen, drug resistance represents an excellent and practical system to correlate phenotypic traits with genomic changes. Azoles are drugs commonly used in clinics. Hypermutable subpopulations are characterized by the presence of secondary mutations unrelated to that selected, which are distributed throughout the genome.

Citation: Larriba G, Calderone R. 2012. Genome Instability and DNA Repair, p 57-74. In Calderone R, Clancy C (ed), and Candidiasis, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817176.ch5
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(A) Mechanism of reciprocal translocations mediated by MRS. MRS, when acting as direct repeats, but not as inverted repeats, may cause chimerical chromosomes. The chimerical chromosomes shown have been found in strain WO-1. (B) Scheme of Chr1 and the genetic system used to determine recombination rates in (for details, see text). doi:10.1128/9781555817176.ch5.f1

Citation: Larriba G, Calderone R. 2012. Genome Instability and DNA Repair, p 57-74. In Calderone R, Clancy C (ed), and Candidiasis, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817176.ch5
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Molecular models for DSBR, SDSA, BIR, and SSA pathways of HR. According to current models, HR events are initiated by the introduction of a DSB in a DNA molecule. The ends of a DSB are resected by nucleases (MRX and Sae2, followed by the exonuclease Exo1 and/or the helicase-topoisomerase complex Sgs1-Top3-Rmi1) that leave 3’ ssDNA overhanging ends ( ) which are first coated by RPA to prevent formation of DNA secondary structures (a). RPA recruits Rad52, which, in turn, displaces RPA, at the time that it interacts with Rad51 and facilitates the formation of a Rad51-ssDNA right-handed helical nucleoprotein filament (b). Other proteins, such as Rad55 and Rad57, may also help in the formation of the filament ( ) (not shown). The Rad51 filament locates a homologous DNA donor and with the help of Rad54 causes chromatin remodeling, DNA unwinding, and strand exchange with the homologous partner ( ) (c). This process generates a displaced strand, which is a substrate for RPA and Rad52, and forms a structure known a D loop (c). Then Rad51 is displaced through the action of Rad54, and the 3’ end of the invading strand becomes a substrate for elongation by DNA polymerases ( ) (d). Synthesis of DNA results in further DNA displacement and binding of RPA and Rad52. BIR may occur when only one end of the DSB has homology to the template or the other end is lost (left column); the homologous end can undergo strand invasion into a homologous or nonhomologous chromosome, forming a replication fork (k); long segments of the template that can extend until the telomere are then replicated, resulting in long tracts of GC (l). The final product contains the undamaged molecule and one of the two molecules resulting from a CO in DSBR (half-CO). When both ends of the DSB have homology to the template, two events can occur. In SDSA the newly synthesized band dissociates from the template and reanneals to the other resected DNA end (i). After DNA synthesis and ligation, the recombined molecules are resolved as non-COs (j). Alternatively, the displaced strand now captures the second resected end and anneals it to the D loop (second-end capture), a process promoted by Rad52 ( ) (e). DNA synthesis from the second end and ligation result in a double Holliday junction (f) which is resolved as either non-COs (g) or COs (h). When a DSB occurs between direct repeats, recombination may take place by SSA (upper right). Resection of the 5’ ends allows annealing of the direct repeats of both DNA molecules; this event is followed by resection of the 3’ overhanging ends by the endonuclease Rad1-Rad10 (see text), DNA synthesis, and ligation. SSA results in the loss of one of the direct repeats and the intervening sequence. doi:10.1128/9781555817176.ch5.f2

Citation: Larriba G, Calderone R. 2012. Genome Instability and DNA Repair, p 57-74. In Calderone R, Clancy C (ed), and Candidiasis, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817176.ch5
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Mechanisms of fluconazole resistance in due to aneuploidies. (Top left) Fluconazole-susceptible (Flu) . Fluconazole (blue star) enters the cell by facilitated diffusion (Mansfield et al., 10th Candida and Candidiasis, 2010, ASM Conferences, Miami, FL). Efflux pumps (green) and (red) excrete fluconazole out of the cell. Sensitive Erg11 (lanosterol demethylase) (blue ellipse) is inhibited by fluconazole, and this results in the synthesis of toxic sterols that destabilize the plasma membrane. (Top right) Flu cell. The asterisk after the Tac1, Mrr1, and Erg11 indicates that the corresponding gene is in homozygosis. Mutated Erg11 that has become Flu is indicated as a hexagon. (Bottom) Schemes of isochromosome i(5L) and a chimerical chromosome ( ). The presence of an extra i(5L) implies an increase in the copy number of both and transcriptional activator . The presence of an extra chimerical chromosome i(5L)-3R implies also an additional increase in the copy number of Other genes related to fluconazole resistance are indicated in chromosomes 4, 6, and 7 (as described in reference ). doi:10.1128/9781555817176.ch5.f3

Citation: Larriba G, Calderone R. 2012. Genome Instability and DNA Repair, p 57-74. In Calderone R, Clancy C (ed), and Candidiasis, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817176.ch5
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Pathways responsible for maintenance of genetic stability

Citation: Larriba G, Calderone R. 2012. Genome Instability and DNA Repair, p 57-74. In Calderone R, Clancy C (ed), and Candidiasis, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817176.ch5

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