Time for Nobels

This year's Nobel Prize in Chemistry is awarded for work showing how cells essentially produce RNA transcripts of genes. How cells degrade transcripts again by the regulatory process of RNA interference is simultaneously honoured by the Nobel Prize for Physiology or Medicine. By Ralf Neumann

In December 1959 twelve year old Roger witnessed the Stockholm ceremony in which his father Arthur Kornberg together with Spaniard Severo Ochoa received the Nobel Prize in Physiology or Medicine for their insights into how cells replicate their DNA prior to cell division. Forty-seven years later Roger Kornberg from Stanford University, California, will return to Stockholm to be awarded the Nobel prize in Chemistry "for his fundamental studies of the molecular basis of eukaryotic transcription".

Roger Kornberg entered the field when the basic molecular principles of bacterial transcription were already known. The more complex processes of eukaryotic transcription, however, still left certain important aspects hidden in the mist. Subsequently, a conclusive picture of how eukaryotic transcription worked and was regulated on the molecular level was yet to be discovered.

Kornberg set out to burn off this mist in the early seventies. One of his first achievements was in 1974 when he suggested that the basal unit of DNA packaging in chromatin, the nucleosome, is a histone octamer associated with 200 base pairs of DNA - just to ascertain from what the DNA had to be unpacked before it could be transcribed. Kornberg's next "eye opener" came in 1990 when his team discovered a multi-protein complex called Mediator transferring the signals from DNA-binding, gene-specific transcription factors to RNA polymerase II and the general transcription factors. Hence, Kornberg contributed most significantly to the notion that chromatin and Mediator constitute new layers of regulation between the gene-specific transcription factors and RNA polymerase, leading to a much greater complexity of regulation in eukaryotic transcription.

The players of eukaryotic transcription were thus known by the early nineties. However, the play they were performing at the molecular level still remained behind the curtain. Kornberg therefore switched to structural biology. The breakthrough came in 2001 when Kornberg and Co. published two papers back-to-back in Science (vol. 292, 1863-76 and 1876-82) describing the structure of a 10-subunit yeast RNA polymerase at 2.8 Angstršm resolutions as well as an elongating complex consisting of RNA polymerase, template DNA and product RNA. Nearly a dozen more crystal structures of RNA Polymerase have followed from the Kornberg lab to-date describing different functional complexes with DNA, RNA, nucleotides or other proteins. This multitude of data enabled (and is still enabling) a dynamic interpretation of the various processes of "transcription in action" for the very first time.

One might well be thinking there is a degree of irony to this year's Nobel Prizes since it's only a very small step from eukaryotic transcription to the subject of the Prize in Physiology or Medicine. However, just think about what happens to the product of transcription, the RNA transcript: It becomes processed to a messenger RNA (mRNA) and enters the cytoplasm where it is ready for serving as a template for protein synthesis - unless the cell changes its mind and targets the mRNA for degradationÉ

And that is exactly what this year's Noble Prize in Physiology or Medicine focuses on. Andrew Z. Fire from Stanford University, California, and Craig C. Mello from the University of Massachusetts Medical School in Worcester share the Prize for their discovery of how cells can pin pointedly degrade specific mRNAs in order to turn down the expression of the corresponding genes.

When Fire and Mello set out to elucidate the mechanism of what they later called RNA interference (RNAi), a number of specific gene silencing effects had already been described which apparently were initiated by RNA molecules. The researchers suggested that injected RNA molecules (or RNA transcribed from injected DNA molecules) bound mRNAs in a sequence-dependent antisense manner, thereby preventing them from entering the ribosome for protein synthesis.

The results of a 1998 paper by Fire (first author) and Mello (senior author), however, wiped that picture off the board (Nature 391: 806-811). In contrast to previous studies they injected double-stranded RNA (dsRNA) molecules into cells of Caenorhabditis elegans resulting in a much stronger and more specific gene silencing effect compared to single-stranded RNAs. Silencing was specific for an mRNA homologous to the dsRNA, however, at the same time only a handful of dsRNA molecules were sufficient to initiate the complete degradation of the targeted mRNA species. Mello and Fire therefore concluded that the dsRNA molecules triggered a catalytic process rather than binding stochiometrically via antisense sequences to the target mRNAs. Furthermore, they found that this RNA interference (RNAi) is a post-transcriptional and cytoplasmic mechanism, as well as that the dsRNA effect could spread between tissues and even to the progeny.

With this framework at hand, the discovery of the remaining details, eg. identification of the enzymes involved, was formality. Hence, the current picture of the RNAi machinery is as follows: Double-stranded RNA binds to a protein complex, Dicer, which cleaves it into fragments. Another protein complex, RISC, binds these fragments called short interfering RNAs (siRNA). One of the RNA strands is eliminated but the other remains bound to the RISC complex and serves as a probe to detect mRNA molecules. When an mRNA molecule can pair with the RNA fragment on RISC, it is bound to the RISC complex, cleaved and degraded. The gene served by this particular mRNA has thus been silenced.

RNAi is apparently an evolutionarily old process occurring universally among animals, plants and fungi. Its natural role for the cell is regarded to be a kind of "immune system of the genome" actually preventing virus integration or insertion of transposons since many of them create double-stranded RNAs during their "life cycles". Two other aspects about RNAi are apparently even more important. Firstly, with their results Mello and Fire effectively opened up the completely new field of gene regulation by "small RNAs" including for example the discovery of similar regulatory RNAs like microRNAs, pi RNAs or rasiRNAs. In recent years these insights have been blowing lots of fresh air into many fields of biological and biomedical research. And secondly, the mechanism of RNAi simultaneously provided scientists with a very powerful yet simple research tool to suppress the expression of specifically targeted genes in almost all eukaryotic organisms.

As always, one question still remains when the awardees have been announced: Did they deserve their Prizes? No doubts about Kornberg have been raised so far. However, some mumbling can be heard about Mello and Fire. The phenomenon of post-transcriptional gene silencing (cosuppression), which later turned out to be caused by RNAi, had been discovered as early as 1990 by plant researchers, allege some critics. Others claim that in 1993 the groups of Victor Ambros and Gary Ruvkun already described the gene silencing effect of a particular microRNA, another family of small regulatory RNAs whose members in contrast to siRNAs are coded by specific loci in the genome. Fact is, however, that none of them did more than describe the phenomena. As for the underlying mechanisms they were only able to speculate that the RNA molecules might act via anti-sense binding. In exactly that respect was where Mello and Fire proved them wrong and, subsequently paved the way to the real RNAi mechanism.