Nobel Prize in Chemistry 2006: Kornberg and the Molecular Basis of Transcription

This note covers the Nobel Prize in Chemistry 2006: why Roger D. Kornberg won it, how a cell copies its DNA instructions into RNA through the process called transcription, how Kornberg built atomic pictures of this process using yeast and X-ray crystallography, how the discovery unfolded over several decades, why it matters for medicine, and quick facts for exams.

What was the Nobel Prize in Chemistry 2006 awarded for?

The Royal Swedish Academy of Sciences gave the Nobel Prize in Chemistry 2006 to Roger D. Kornberg "for his studies of the molecular basis of eukaryotic transcription". That is the official citation, and it names the exact achievement being honoured.

In plain words, Kornberg worked out, at the level of individual atoms, how a cell's machinery reads the genetic instructions written in DNA and copies them into a related molecule called RNA. This copying step is called transcription.

It happens inside every cell that has a proper nucleus, a group of organisms called eukaryotes, which includes yeast, plants, animals and humans.

Without transcription, none of the proteins that build and run a body could be made, because the instructions for making proteins never leave the DNA to reach the protein-making parts of the cell.

Kornberg's pictures showed this copying machine caught in the act, something no one had managed before for a eukaryotic cell.

Who are the laureates?

The 2006 Chemistry prize went to a single laureate, who received the whole prize (a share of 1/1).

Roger D. Kornberg

Roger D. Kornberg was born on 24 April 1947 in St. Louis, Missouri, USA. At the time of the award he was affiliated with Stanford University, Stanford, California, USA, where he held a professorship in medicine.

Kornberg's contribution was to combine careful biochemical preparation of molecules with a picture-making technique called X-ray crystallography to build detailed three-dimensional models of the enzyme that performs transcription in eukaryotic cells, together with the helper molecules that switch the process on and regulate it.

His laboratory produced, from the year 2000 onwards, crystal structures detailed enough to show the position of individual atoms as a new RNA strand was being built.

He was not working alone in a historical sense: his father, Arthur Kornberg, had won the 1959 Nobel Prize in Physiology or Medicine for showing how genetic information passes from one DNA molecule to another when a cell divides.

Roger Kornberg, as a twelve-year-old, had attended that ceremony in Stockholm, and decades later described the next step: how the same genetic information is copied out of DNA into messenger RNA so that it can be used to build proteins.

What problem does transcription solve inside a living cell?

Every cell in the body carries the same genetic information, stored as a sequence of four chemical building blocks in the DNA molecule, usually written with the letters G, C, A and T.

This DNA sits safely inside the cell nucleus, where it is protected but also inactive on its own.

To be useful, the information in a gene has to be copied and carried out of the nucleus to the parts of the cell that actually build proteins.

That copy is made of messenger RNA, and the copying step is transcription. The proteins built from this information then do the real work of the cell and the body.

If transcription stops completely, no new proteins can be made and the organism dies within a few days; this is exactly what happens in poisoning by certain toadstools such as the death cap, whose toxin blocks the key transcription enzyme.

Transcription must also be very accurate: no more than one error in ten thousand characters copied can be tolerated before the cell is harmed.

A second, separate requirement is regulation: different cells in the same body, such as liver cells and blood cells, must switch on different sets of genes even though they all hold the same DNA.

Before Kornberg's work, scientists knew many of the molecules involved in eukaryotic transcription, but had no detailed picture of how the whole system worked together, or why eukaryotic cells needed such a complex system compared with simpler bacteria.

How does RNA polymerase copy DNA into RNA?

The enzyme at the centre of transcription is called RNA polymerase. In eukaryotic cells such as yeast and humans, the particular form responsible for copying genes into messenger RNA is called RNA polymerase II, and in yeast it is built from twelve separate protein subunits.

Kornberg's crystal structures let scientists follow the basic steps of the copying process in order:

1. The DNA double helix opens up at the start of a gene so that one strand can be read as a template, with help from several supporting "general transcription factors" that first recognise where a gene begins.
2. RNA polymerase holds the single DNA strand in the right position inside a narrow channel, so tightly that only the matching RNA building block can fit opposite each DNA letter.
3. A matching RNA building block is added to the growing RNA strand, one letter at a time, each new letter paired correctly with the DNA template beneath it.
4. A small, flexible helical part of the enzyme, described by Kornberg's group as a bridge helix, flips back and forth and pushes the DNA strand forward by one position after each new letter is added.
5. As the RNA strand grows, it is peeled away from the DNA template by a loop inside the enzyme, so that the two original DNA strands can come back together behind the moving polymerase.

This step-wise, highly selective process is why the death cap toxin is so dangerous: it jams the bridge-helix mechanism, so RNA polymerase simply stops moving and transcription ends.

Draw a large blob labelled "RNA polymerase" with a blue strand of DNA running through a groove in it.

Show a short stretch of red RNA strand growing out of one side, with a small green helix near the point where the new RNA letter is being added, representing the bridge helix that pushes the DNA forward.

How did Kornberg capture transcription in action?

To study eukaryotic transcription in detail, Kornberg chose an unusual model organism: ordinary baker's yeast. Yeast is a simple eukaryote, easy to grow in large amounts and easy to modify genetically, unlike mammalian liver cells, which were difficult to work with in the laboratory.

Building a working, test-tube version of yeast transcription took Kornberg's research group about ten years of patient effort, with little that could be published along the way.

Once this system worked, it could supply enough purified RNA polymerase and transcription factors to attempt crystallography: growing orderly crystals of the molecules and firing X-rays at them to calculate, by computer, where every atom sits.

The breakthrough came in 2001, when Kornberg's team solved the structure of a ten-subunit yeast RNA polymerase and also captured it in the middle of building an RNA strand, by deliberately leaving one RNA building block out of the mixture so the process froze at a chosen point.

Along the way, Kornberg's group also discovered an entirely new molecular complex, which they named Mediator, made up of around twenty different proteins.

Mediator acts as a relay: it passes signals from gene-specific activator proteins, bound to DNA regions called enhancers, through to RNA polymerase and the general transcription factors, switching particular genes on in particular tissues.

Draw the enzyme as a large irregular shape with a blue DNA helix threading through it and a red growing RNA strand emerging to one side, marking a pink dot inside for the active site where new letters are joined, and a green ribbon nearby for the bridge helix.

How did the discovery unfold?

Kornberg's work built on nearly five decades of earlier research into how genes are copied, starting with a rat-liver cell nuclei (eukaryotic) RNA polymerase activity in 1959, after which bacterial transcription was worked out in detail first because its enzyme was easier to purify.

Why does this discovery matter?

Transcription sits at the centre of how a single set of genes can produce the enormous variety of cell types in a body.

The same DNA is present in every cell, but Mediator and the enhancers let different genes be switched on in different tissues, which is why liver cells and blood cells look and behave so differently.

Because of this central role, faults in the transcription process are linked, as the awarding committee noted, to illnesses such as cancer, heart disease and various inflammations. Understanding the detailed mechanism gives researchers a map of where such faults can occur.

The work also connects to stem cell research: a stem cell's ability to develop into many different specialised cell types depends on how transcription in that cell is regulated. Learning to control transcription more precisely is described as an important step towards using stem cells safely in medical treatments.

At the time of the prize, Kornberg's laboratory had already begun extending the structural studies to include the general transcription factors and Mediator acting together with RNA polymerase, with the stated aim of building a complete, atom-by-atom picture of the whole transcription machinery in action.

How does this connect to what you study?

School biology lessons on genes usually describe DNA as the molecule that stores hereditary information and proteins as the molecules that carry out cell functions.

Kornberg's work fills in the missing link between these two ideas: the step called transcription, where information moves from DNA to messenger RNA before it reaches the protein-making machinery.

The idea that the same DNA sequence can be used differently in different cells, because of selective transcription, also helps explain basic ideas about cell differentiation, the process by which a single fertilised cell develops into the many different cell types of a body.

Understanding that a single toxin, from a poisonous mushroom, can kill by jamming one specific enzyme also shows how a tiny change at the molecular level can have a dramatic effect on a whole organism, a useful example when thinking about how medicines and poisons act on cells.

Finally, the method Kornberg used, X-ray crystallography, is the same broad technique used to work out the shapes of many other important biological molecules, including enzymes and antibodies, linking this prize to the wider idea of structural biology as a tool for understanding life.

Quick facts for exams

The Nobel Prize in Chemistry 2006 was awarded on 4 October 2006 by the Royal Swedish Academy of Sciences to Roger D. Kornberg of Stanford University, USA, who received the entire prize.

The citation praised his studies of the molecular basis of eukaryotic transcription, the process by which a cell copies the genetic information in DNA into messenger RNA so that proteins can be built.

Kornberg used X-ray crystallography on yeast cells to produce the first atom-level pictures of this process and also discovered the Mediator complex, which switches transcription on in specific tissues. The prize carried an amount of ten million Swedish kronor.

Note: Source. The prize facts in this note are from the Nobel Prize's official site, nobelprize.org.

Glossary

• Transcription — the process of copying the genetic information in a DNA strand into a complementary messenger RNA strand.
• Eukaryote — an organism whose cells have a well-defined nucleus, such as yeast, plants, animals and humans.
• RNA polymerase — the enzyme that reads a DNA template and builds a matching RNA strand during transcription.
• Messenger RNA (mRNA) — the RNA copy of a gene that carries information out of the nucleus to where proteins are built.
• General transcription factors — a set of helper proteins that allow RNA polymerase to find the start of a gene and begin transcription.
• Mediator — a multiprotein complex, discovered by Kornberg's group, that relays activating or repressing signals to RNA polymerase.
• Enhancer — a region of DNA that binds tissue-specific activator proteins, switching on nearby genes in particular cells.
• Bridge helix — a flexible helical part of RNA polymerase that moves the DNA strand forward after each RNA building block is added.
• X-ray crystallography — a technique that uses X-rays passed through a crystal of a molecule to calculate the positions of its atoms.
• Promoter — the specific DNA sequence at the start of a gene where RNA synthesis begins.
• Nucleosome — the basic repeating unit of chromatin, made of DNA wrapped around a cluster of histone proteins.
• Stem cell — a cell that can develop into several different specialised cell types, depending on how its transcription is regulated.

Common errors and misconceptions

• Misconception: Kornberg discovered DNA or RNA for the first time. Correct: DNA and RNA were already known; Kornberg discovered how the copying process, transcription, works in eukaryotic cells at the atomic level.
• Misconception: The prize covers bacterial transcription. Correct: The citation specifically names eukaryotic transcription, the process in cells with a defined nucleus.
• Misconception: Kornberg used human cells for his key structures. Correct: He used baker's yeast as the model organism because it was easier to grow and manipulate.
• Misconception: Mediator is the same as a general transcription factor. Correct: Mediator is a separate complex that relays signals from activator proteins to the general transcription factors and RNA polymerase.
• Misconception: Transcription and translation are the same process. Correct: Transcription copies DNA into RNA; translation, performed later by ribosomes, builds proteins from that RNA.
• Misconception: This was a shared prize. Correct: Roger D. Kornberg received the entire 2006 Chemistry prize alone, a share of 1/1.
• Misconception: Kornberg's father also worked on this exact topic. Correct: Arthur Kornberg's 1959 medicine prize concerned copying DNA into DNA, a different step from Roger Kornberg's work on copying DNA into RNA.

Exam-style questions with model answers

Q1. What is transcription? [2 marks]

1. Transcription is the process by which the genetic information stored in DNA is copied into messenger RNA. This RNA copy then carries that information to where proteins are built, so it can direct protein production in the cell.

Q2. State the exact citation for the 2006 Nobel Prize in Chemistry. [1 mark]

1. "for his studies of the molecular basis of eukaryotic transcription".

Q3. Why did Roger Kornberg choose yeast rather than mammalian cells for his studies? [3 marks]

1. Mammalian liver cells, although they were where RNA polymerase was first found, proved very difficult to work with and purify for structural work.
2. Baker's yeast is also a eukaryote, so its transcription system closely resembles that of mammals, but yeast is far easier to grow in bulk and to modify genetically.
3. This made yeast a practical model organism that could supply enough purified RNA polymerase and transcription factors for crystallography, even though building the working yeast system took about ten years of effort.

Q4. Explain how RNA polymerase selects the correct building block when copying DNA into RNA. [4 marks]

1. RNA polymerase holds the single, opened-up DNA strand inside a narrow channel so that only one RNA building block can physically fit opposite each DNA letter at a time.
2. If the wrong RNA building block does not match the DNA letter at that position, it does not fit the shape of the cavity, much like the wrong piece in an unfinished jigsaw puzzle.
3. Once the correct matching letter is inserted and joined to the growing RNA chain, a flexible bridge helix inside the enzyme flips and pushes the DNA strand forward by one position.
4. This repeated cycle of matching, joining and shifting builds the new RNA strand step by step, keeping the error rate extremely low.

Q5. What is Mediator, and why was its discovery important? [3 marks]

1. Mediator is a large complex of around twenty proteins, discovered by Kornberg's research group while studying yeast transcription.
2. It acts as a relay, carrying activating or repressing signals from DNA-bound, tissue-specific proteins to RNA polymerase and the general transcription factors.
3. Its discovery explained how different genes can be switched on in different tissues even though every cell shares the same DNA, a question earlier research had left unanswered.

Q6. Discuss why Kornberg's structural studies of transcription are considered medically important, with reference to the committee's stated reasons. [6 marks]

1. Transcription is essential for every living cell, since it is the step that converts the fixed instructions in DNA into messenger RNA, which is then used to build the proteins that carry out all cell functions.
2. The awarding committee noted that problems in the transcription process are tied to several human illnesses, among them cancer, heart disease and different kinds of inflammation, so understanding the mechanism in atomic detail opens a path to understanding where these problems occur.
3. The committee also linked transcription regulation to stem cell biology, noting that a stem cell's capacity to develop into specific, functional cell types depends on how its transcription is controlled.
4. Because the interest in using stem cells for medical therapies rests on directing them to become only the wanted cell type, understanding how Mediator, enhancers and general transcription factors regulate transcription was described as a necessary step towards realising that potential.
5. Kornberg's atomic-level pictures of RNA polymerase in action therefore give researchers a structural map on which future work on transcriptional regulation and disease can build.

Q7. Name two general transcription factors that help RNA polymerase II begin transcription at the correct site. [2 marks]

1. TFIIB and TFIIH are two of the general transcription factors that help RNA polymerase II begin transcription at the correct site.

Q8. What happens to an organism if transcription stops completely, and why? [2 marks]

1. If transcription stops, no new proteins can be produced, and the organism dies within a few days, as happens in poisoning by the death cap toadstool.

Key takeaways

• Roger D. Kornberg won the entire Nobel Prize in Chemistry 2006 for mapping the molecular basis of eukaryotic transcription.
• Transcription copies genetic information from DNA into messenger RNA, which is later used to build proteins.
• Kornberg used baker's yeast as a model eukaryote because it was far easier to grow and modify than mammalian cells.
• His laboratory combined biochemistry with X-ray crystallography to build atom-level pictures of RNA polymerase in action.
• A flexible bridge helix inside RNA polymerase pushes the DNA template forward after each RNA letter is added.
• Kornberg's group discovered Mediator, a relay complex that switches on specific genes in specific tissues.
• Faults in transcriptional regulation are linked to cancer, heart disease and inflammation, and to how stem cells develop.
• The breakthrough crystal structures were published in 2001, building on decades of earlier research on bacterial and eukaryotic transcription.

Test yourself

Where and when was Roger D. Kornberg born?

Roger D. Kornberg was born on 24 April 1947 in St. Louis, Missouri, in the United States.

Which university was Kornberg affiliated with when he won the prize?

Kornberg was affiliated with Stanford University in Stanford, California, USA, at the time of the award.

What model organism did Kornberg use for his key experiments?

He used baker's yeast, Saccharomyces cerevisiae, because it was easy to grow in bulk and to modify genetically.

What technique did Kornberg use to see individual atoms in RNA polymerase?

He used X-ray crystallography, which calculates the atomic positions in a molecule from how it scatters X-rays as a crystal.

What is the name of the relay complex Kornberg's group discovered?

They discovered Mediator, a complex of about twenty proteins that passes activating signals to RNA polymerase.

In what year did Kornberg's group publish the breakthrough RNA polymerase II structure?

The breakthrough structures were published in 2001, showing yeast RNA polymerase both alone and while elongating RNA.

Who won the Nobel Prize in Physiology or Medicine in 1959, and how is he connected to Roger Kornberg?

Arthur Kornberg won it in 1959 for studying DNA copying; he was Roger Kornberg's father.

Why can a death cap toadstool be fatal?

Its toxin blocks the transcription enzyme RNA polymerase, stopping protein production so that organs fail within days.