2006 Kornberg Description

2006 Kornberg Description - I n f o r m at I o n for the...

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Unformatted text preview: I n f o r m at I o n for the publIc The Nobel Prize in Chemistry 2006 This year’s Nobel Prize in Chemistry is awarded to Roger D. Kornberg for his fundamental studies concerning how the information stored in the genes is copied, and then transferred to those parts of the cells that produce proteins. Kornberg was the first to create an actual picture of this process at the molecular level, in the important group of organisms called eukaryotes (which, as opposed to bacteria, have well-defined cell nuclei). Mammals like ourselves, as well as ordinary yeast, belong to this group of organisms. Central to life Constant transcription of the genetic information in the DNA is a central process for all living  beings. The DNA-molecule itself lies protected within the cell nuclei. The genetic information  therefore needs to be copied and transformed into what is called messenger-RNA, which carries the information out into the protein-producing parts of the cells. It is the proteins that in  their turn actually construct the organism and its function. If  the  transcription  process  is  interrupted  the  organism  will  soon  die,  since  all  protein-  production in the cells ceases. This is what happens in cases of poisoning  by certain types of toadstools, like the death cap. The toxin in the death  cap blocks the function of a specific enzyme, RNA-polymerase, which plays  a  central  role  in  the  transcription  process.  Within  a  few  days  the  toxin  spreads from the bowels to the liver and kidneys, hence slowly destroying  all these organs. Many illnesses – like cancer, heart disease, and different kinds of inflammation – are also linked to disturbances in the transcription process. Explains variety It is thanks to the flexible transcription system in eukaryotes that such complexity is possible  within this group of organisms. All the cells of the body contain the same genetic information,  but there is great variation between organs in the information that is actually transcribed,  and thereby translated into protein production. Knowledge about  the  transcription  process  is  also  fundamental  for  understanding  how  stem  cells  develop  into  different  kinds  of  specific  cells,  with  well-defined functions in different organs. The interest in stem cells  for therapeutic applications is very largely based on their capacity to  develop into any kind of functional cell in a living organism. Understanding more about how transcription is regulated is therefore one  of  the  necessary  steps,  if  we  want  to  realise  the  full  potential  of  stem cells in medicine. The DNA-molecule is constructed using four different types of building blocks: G, C, A and  T. The RNA is composed of four corresponding types of building blocks. The genetic information written into these molecules is determined by the sequence in which the building blocks  are put together. The genetic code therefore consists of an alphabet with only four letters. The Nobel Prize in Chemistry 2006 • The Royal Swedish Academy of Sciences • www.kva.se  (5) The DNA-molecule is a double helix, with a G on one of the strands always opposing a C on  the other strand, and A in a similar manner opposing T (Watson, Crick and Wilkins were  awarded their famous Nobel Prize in Physiology or Medicine in 962 for this discovery). The  transcription process starts with the DNA-double helix opening up so that a strand of “naked”  building blocks can be used as a template in creating an RNA-strand. The cell contains the  RNA  building  blocks  in  solution.  If  the  transcription  process  functions,  the  RNA  building  block corresponding to a G inserts itself opposite a C on the DNA-strand, the RNA-version of  a T inserts itself opposite an A on the DNA-strand, and vice versa. In this manner, the RNAstrand  is  constructed  in  a  step-wise  process  to  form  a  “negative”  of  the  DNA-strand.  One  fundamental question is how this process works in more detail. The wellbeing of the organism  depends on translation of the correct information into proteins. Not more than one fault in ten  thousand can be tolerated before the organism is impaired. For this reason the mechanism  ensuring that the building blocks of RNA are put together in the right order must be very specific. The key lies in a special enzyme that carefully governs this process: RNA-polymerase. A snapshot of life The  picture  below  showing  RNA-polymerase  in  full  action  was  created  by  Kornberg  as  recently as 200. The big white molecule (which looks like a bundle of wires) is the RNA-polymerase, serving as a support for the DNA-strand (in blue). The polymerase molecule keeps  the DNA-strand in the right position during transcription and creates a minuscule “cavity”, so  small that it will only accept the RNA building block that fits with the opposing DNA building  block exactly. If the wrong RNA building block tries to insert itself into the cavity it simply  does not fit, just as the wrong piece cannot be inserted in a half completed jigsaw puzzle. This  Figure 1. The transcription process as depicted by Roger Kornberg in 2001. RNA-polymerase in white, DNA-helix in blue and the growing RNA-strand in red. 2 (5) The Nobel Prize in Chemistry 2006 • The Royal Swedish Academy of Sciences • www.kva.se leads to the step-wise construction of the RNA-strand (in red). Once a new building block  has been inserted in the right place, the DNA-strand is prompted forward by a small helical  structure (in green) in the polymerase. This spring-like structure flips back and forth thanks  to constant spontaneous changes in shape of the polymerase (this is precisely the mechanism  which is destroyed by the toxin of the death cap, mentioned above). In this manner, the DNAstrand is again and again moved into the right position for a new building block to be added  to the growing RNA-strand. The truly revolutionary aspect of the picture Kornberg  has created is that it captures the process of transcription in full flow. What we see is an RNA-strand being constructed, and hence  the exact positions of the DNA, polymerase and RNA during this process. In an ingenious  manner Kornberg has managed to freeze the construction process of RNA half-way through,  simply by leaving out one of the necessary building blocks from the solution he uses. When  the construction reaches the point where the missing building block should be inserted the  whole process stops. Kornberg has then created crystals of the molecules involved, and “taken  their picture” using X-rays. This picture is of course not an ordinary photo but an image of  the molecules in their crystalline form. Starting with such a picture, a computer can calculate  the real position of atoms in the molecules. The image shown here, has thus been created by  a computer. This  method  of  making  crystals  of  biological  molecules  in  order  to  depict  them  is  a  very  common tool today. Normally, however, we only see pictures of finished complexes and individual molecules. To capture a chemical reaction as it takes place is very difficult, and it is  not enough to be a good crystallographer in order to succeed. What is particular about the  way Kornberg works is that he combines crystallography with very deep biochemical knowledge which makes it possible for him to assume full control of the process he wants to depict.  Besides this detailed picture of the role of RNA-polymerase, he has also contributed several  other important pieces of information concerning the transcription process by studying other  crystals of RNA-polymerase, DNA, RNA and important complexes called general transcription factors. These images make it possible to understand the molecular mechanisms governing the transcription process. Bacteria, mammals and yeast For a long time it was believed that the transcription process in eukaryotes was very similar  to that in bacteria (which unlike eukaryotic cells lack a well-defined nucleus). It has however  become  clear  that  the  process  in  eukaryotes  is  much  more  complex.  RNA-polymerase  was  actually first found in mammalian liver cells, but it proved very difficult to work with these  cells.  Instead,  bacteria  became  the  first  organisms  to  be  studied  in  detail,  since  they  were  much easier to use. In 965 the Nobel Prize in Physiology or Medicine was awarded to Jacques Monod, André  Lwoff and François Jacob, among other things for their description of how transcription in  bacteria works. Besides RNA-polymerase another molecule called sigma factor is necessary  in order for transcription in bacteria to start. This molecules binds to RNA-polymerase and,  through its capacity to recognize special codes in the DNA, it tells where the genetic information starts and where it ends. Without the sigma factor, transcription would never start since  the polymerase on its own does not “know” where on the DNA-strand to start reading. The Nobel Prize in Chemistry 2006 • The Royal Swedish Academy of Sciences • www.kva.se  (5) However, when researchers returned to eukaryotic cells after this discovery no one managed  to  find  the  sigma  factor.  It  gradually  transpired  that  in  eukaryotes  there  are  five  different  molecular complexes which correspond to the single sigma factor in bacteria. All of them are  necessary for transcription to start in our cells. These complexes are called general transcription factors and play an important role in the fine-tuning of transcription in eukaryotes. Finding all these five transcription factors required a great deal of painstaking work, purifying  cell extracts in several steps. By removing one substance at a time from these extracts until  the transcription stopped working, researchers isolated  the substances  that  were necessary  for transcription to take place. When this was done, many were convinced that every part of  the transcription system in eukaryotes had been discovered, just as with bacteria. Even so, the  great variety in shape and function of eukaryotic cells had not been explained. There were as  yet no good answers to questions concerning how certain genes are expressed in blood cells,  others in the cells of the liver, and so on. One of Kornberg’s great contributions at this stage was his development of a new system of  using yeast cells in laboratory work. Ordinary yeast is a eukaryote, just as mammals are. This  makes  it  possible  to  use  yeast  as  a  model  organism  instead  of  cells  from  mammal  organs.  Yeast cells are much easier to manipulate and it is easier to create a homogenous material  to  work  with  using  these  cells.  In  spite  of  this,  Kornberg’s  research  group  spent  ten  years  fine-tuning the system, before it could be used to investigate the transcription process. Many  research groups would have given up much earlier, since several years went by without any  actual results that could be published. But it is this very system, using yeast cells, that has  made it possible for Kornberg to produce RNA-polymerase and general transcription factors  in the adequate form and quantity to create crystals to investigate. The necessary relay Thanks to this system of yeast cells, Kornberg found yet another molecular complex which  turned out to play an important role as a kind of on-off switch for the transcription process in  eukaryotes. The DNA-helix includes parts called  enhancers which bind to specific substances  that are found in different tissues. In this manner transcription of certain genes is stimulated  in certain tissues. In the liver – for instance – there is a specific signalling substance, which  binds to a liver-enhancer in the DNA hence turning on the transcription of a gene close to the  enhancer. In other parts of the body, this liver-specific gene will however never be switched  on because the necessary signalling substance is lacking. Kornberg discovered that this regulation requires the presence of yet another molecular complex, transmitting the signals and  thereby switching the transcription on or off. This “relay”-complex is called Mediator. The great complexity of eukaryotic organisms is actually enabled by the fine interplay between  tissue-specific substances, enhancers in the DNA and  Mediator. The discovery of  Mediator is  therefore a true milestone in the understanding of the transcription process. To be continued Kornberg continues his crystallographic and functional work today, by trying to include ever  larger  parts  of  the  transcription  apparatus  in  his  descriptions.  Hitherto  he  has  shown  the  interplay  between  RNA-polymerase,  DNA  and  the  growing  RNA-strand  and  its  building   (5) The Nobel Prize in Chemistry 2006 • The Royal Swedish Academy of Sciences • www.kva.se blocks. The next step is to include all the general transcription factors and especially Mediator in full action. Kornberg has already taken the first steps in this direction. Crystallography  is  a  particularly  important  tool  in  this  context  because  the  actual  spatial  configuration of the different components in the transcription system plays such a decisive  role. It is very difficult to create an understanding of the process through traditional chemical  methods, which do not tell us anything about the spatial positions of the molecules and atoms.  Many of the components in the process undergo no important chemical changes, we need to  quite physically “see” the molecules and their positions at different stages in the process to  understand how the transcription works. The gradual construction of a functional image of how transcription works ultimately involves  attaining understanding of how the genetic information generates the great variety of living  organisms around us. Knowledge about how this happens in the human body is also of fundamental medical importance. ..................................................................................................................................................... liNKs aNd fuRTheR ReadiNg The Academy’s website, www.kva.se, and http://nobelprize.org have more information on this year’s Prizes, including a web-TV broadcast of the press conference and advanced information mainly intended for the research community. Original scientific articles: Cramer, P., Bushnell, D.A. and Kornberg, R.D. (2001) Structural basis of transcription: RNA polymerase II at 2.8 ångstrom resolution. Science 292, 1863-1876. Gnatt, A.L., Cramer, P., Fu, J., Bushnell, D.A. and Kornberg, R.D. (2001) Structural basis of transcription: An RNA polymerase II elongation complex at 3.3 Å resolution. Science 292, 1876-1882. Bushnell, D.A., Westover, K.D., Davis, R.E. and Kornberg, R.D. (2004) Structural basis of transcription: An RNA polymerase II – TFIIB cocrystal at 4.5 angstroms. Science 303, 983-988. Review article: Boeger, H., Bushnell, D.A., Davis, R., Griesenbeck, J., Lorch, Y., Strattan, J.S., Westover, K.D. and Kornberg, R.D. (2005). Structural basis of eukaryotic gene transcription. FEBS Lett. 579, 899-903. Link: Film of transcription: The Dolan DNA learning center – genes in education. http://www.dnalc.org/home.html. Media showcase; Transcription: DNA codes for mRNA, 3D animation. ...................................................................................................................................................... The lauReaTe Roger D. Kornberg Stanford University School of Medicine Fairchild building, 1st floor 299 Campus Dr. Stanford, California 94 305-5126 USA http://kornberg.stanford.edu/ US citizen. Born 1947 (59) in St Louis, MO, USA. PhD from Stanford University, CA, USA. Mrs. George A. Winzer Professor in Medicine at Stanford University School of Medicine, CA, USA. The Nobel Prize in Chemistry 2006 • The Royal Swedish Academy of Sciences • www.kva.se 5 (5) ...
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