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From DNA to Proteins: Transcription and RNA Processing

On November 8, 2009, 31-year-old Tomasa was hiking the Lodi Lake nature trail east of San Francisco with her husband and cousin when they came across some large white mushrooms that looked very much like edible mushrooms that they enjoyed in their native Mexico. They picked the mushrooms and took them home, cooking and consuming them for dinner. Within hours, Tomasa and her family were sick and went to the hospital. They were later transferred to the critical care unit at California Pacific Medical Center in San Francisco, where Tomasa died of liver failure three weeks later. Her husband eventually recovered after a lengthy hospitalization; her cousin required a liver transplant to survive.

The mushrooms consumed by Tomasa and her family were Amanita phalloides, commonly known as the death cap. A single death cap contains enough toxin to kill an adult human. The death rate among those who consume death caps is 22%; among children under the age of 10, it’s more than 50%. Death cap mushrooms appear to be spreading in California, leading to a surge in the number of mushroom poisonings.

Death cap poisoning is insidious. Gastrointestinal symptoms—abdominal pain, cramping, vomiting, diarrhea—begin within 6 to 12 hours of consuming the mushrooms, but these symptoms usually subside within a few hours, and the patient seems to recover. Because of this initial remission, the poisoning is often not taken seriously until it’s too late to pump the stomach and remove the toxin from the body. After a day or two, serious symptoms begin. Cells in the liver die, causing permanent liver damage and death within a few days. There is no effective treatment, other than a liver transplant to replace the damaged organ.

How do death caps kill? Their deadly toxin, contained within the fruiting bodies that produce reproductive spores, is the protein α-amanitin, which consists of a short peptide of eight amino acids that forms a circular loop. α-Amanitin is a potent inhibitor of RNA polymerase II, the enzyme that transcribes protein-encoding genes in eukaryotes. RNA polymerase II binds to genes and synthesizes RNA molecules that are complementary to the DNA template. In the process of transcription, the RNA polymerase moves down the DNA template, adding one nucleotide at a time to the growing RNA chain. α-Amanitin binds to RNA polymerase and jams the moving parts of the enzyme, interfering with its ability to move along the DNA template. In the presence of α-amanitin, RNA synthesis slows from its normal rate of several thousand nucleotides per minute to just a few nucleotides per minute. The results are catastrophic. Without transcription, protein synthesis—­required for cellular function—ceases, and cells die. The liver, where the toxin accumulates, is irreparably damaged and stops functioning. In severe cases, the patient dies.

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Death cap poisoning illustrates the extreme importance of transcription and the central role that RNA polymerase plays in the process. This chapter is about the process of transcription—the first step in the central dogma, the pathway of information transfer from DNA (genotype) to protein (phenotype). Transcription is a complex process that requires precursors to RNA nucleotides, a DNA template, and a number of protein components. As we examine the stages of transcription, try to keep all the details in perspective and focus on understanding how they relate to the overall purpose of transcription: the selective synthesis of an RNA molecule.

This chapter begins with a brief review of RNA structure and a discussion of the different classes of RNA. We then consider the major components required for transcription. Finally, we explore the process of transcription. At several points in the text, we’ll pause to consider some general principles that emerge.