17. Mutation, Repair, and Recombination

It has been shown that infectious agents such as viruses often exert a dramatic effect on their host cell's genome architecture. In many cases, viruses induce methylation of host DNA sequences in order to enhance their infectivity. What specific host gene functions would you consider as strong candidates for such methylation by infecting viruses?

Xeroderma pigmentosum (XP) is an autosomal recessive condition characterized by moderate to severe sensitivity to ultraviolet (UV) light. Patients develop multiple skin lesions on UV-exposed skin, and skin cancers often develop as a result. XP is caused by deficient repair of DNA damage from UV exposure.Many genes are known to be involved in repair of UV-induced DNA damage, and several of these genes are implicated in XP. What genetic phenomenon is illustrated by XP?

You have identified five genes in S. cerevisiae that are induced when the yeast are grown in a high-salt (NaCl) medium. To study the potential roles of these genes in acclimation to growth in high-salt conditions, you wish to examine the phenotypes of loss- and gain-of-function alleles of each.How would your answer differ if you were working with tomato plants instead of yeast?

You have identified five genes in S. cerevisiae that are induced when the yeast are grown in a high-salt (NaCl) medium. To study the potential roles of these genes in acclimation to growth in high-salt conditions, you wish to examine the phenotypes of loss- and gain-of-function alleles of each.How will you do this?

The SOS repair genes in E. coli (discussed in Chapter 15) are negatively regulated by the lexA gene product, called the LexA repressor. When a cell's DNA sustains extensive damage, the LexA repressor is inactivated by the recA gene product (RecA), and transcription of the SOS genes is increased dramatically.One of the SOS genes is the uvrA gene. You are a student studying the function of the uvrA gene product in DNA repair. You isolate a mutant strain that shows constitutive expression of the UvrA protein. Naming this mutant strain uvrAᶜ, you construct the diagram shown above in the right-hand column showing the lexA and uvrA operons:Outline a series of genetic experiments that would use partial diploid strains to determine which of the two possible mutations you have isolated.

Describe the 'end-replication problem' in eukaryotes. How is it resolved?

A fellow student considers the issues in Problem 22 and argues that there is a more straightforward, nongenetic experiment that could differentiate between the two types of mutations. The experiment requires no fancy genetics and would allow you to easily assay the products of the other SOS genes. Propose such an experiment.

Many of the gene products involved in DNA synthesis were initially defined by studying mutant E. coli strains that could not synthesize DNA.The dnaQ gene encodes the ε subunit of DNA polymerase. What effect is expected from a mutation in this gene?

Many of the gene products involved in DNA synthesis were initially defined by studying mutant E. coli strains that could not synthesize DNA.The dnaE gene encodes the α subunit of DNA polymerase III. What effect is expected from a mutation in this gene? How could the mutant strain be maintained?

When a double-strand DNA break occurs in a eukaryotic cell, it may be repaired by either nonhomologous end joining or homologous recombination. How do these different repair mechanisms lead to potentially different outcomes?

Ataxia telangiectasia (OMIM 208900) is a human inherited disorder characterized by poor coordination (ataxia), red marks on the face (telangiectasia), increased sensitivity to X-rays and other radiation, and an increased susceptibility to cancer. Recent studies have shown that this disorder occurs as a result of mutation of the ATM gene. Propose a mechanism for how a mutation in the ATM gene leads to the characteristics associated with the disorder. Be sure to relate the symptoms of this disorder to functions of the ATM protein. Further, explain why DNA repair mechanisms cannot correct this problem.

A geneticist searching for mutations uses the restriction endonucleases SmaI and PvuII to search for mutations that eliminate restriction sites. SmaI will not cleave DNA with CpG methylation. It cleaves DNA at the restriction digestion sequence↓5′−CCC GGG−3′3′−GGG CCC−3′↑PvuII is not sensitive to CpG methylation. It cleaves DNA at the restriction sequence↓5′−CAG CTG−3′3′−GTC GAC−5′↑Explain why CpG dinucleotides are hotspots of mutation.

A geneticist searching for mutations uses the restriction endonucleases SmaI and PvuII to search for mutations that eliminate restriction sites. SmaI will not cleave DNA with CpG methylation. It cleaves DNA at the restriction digestion sequence↓5′−CCC GGG−3′3′−GGG CCC−3′↑PvuII is not sensitive to CpG methylation. It cleaves DNA at the restriction sequence↓5′−CAG CTG−3′3′−GTC GAC−5′↑What process is the researcher intending to detect with the use of these restriction enzymes?