An Essay on the Prize

The Central Dogma, a theory put forward in 1958 by Francis Crick, is the fundamental concept of life. Three crucial molecules are involved: DNA houses an organism’s genetic blueprint. The DNA genome contains the information required to produce all of an organism’s proteins. Proteins endow cells, tissues, and organisms with their forms and capabilities. Messenger RNA (mRNA) is the intermediate molecule that links DNA to proteins. Particular DNA instructions are converted into individual mRNA molecules to produce specific proteins by a process called gene transcription. Crucially, transcription of specific genes must occur at the correct times and in the correct cellular locations so that the subsets of proteins required for function are only produced when and where they are needed. The gene transcription process has four steps: (1) Initiation; (2) Pausing/Promoter Clearance; (3) Elongation; (4) Termination. In 2006, Roger Kornberg won the Nobel Prize for discoveries concerning how the enzyme called RNA Polymerase converts DNA into mRNA. The work of this year’s Shaw Prize recipients, Eva Nogales and Patrick Cramer, represents the next major leap in our understanding of gene transcription. They pioneered structural biology approaches to enable visualization, at the level of the individual atoms, of the protein machines responsible for gene transcription. They revealed the molecular mechanism underlying each step in gene transcription, and the importance of proper gene transcription to promote health and prevent disease.

Visualizing biology at the atomic level requires determining the structures of the tiny but highly complicated machines that catalyze life processes. Two major approaches are used: x-ray crystallography and the more recently developed technology, cryo-electron microscopy. X-ray crystallography delivers structures of single proteins or small protein complexes that can be crystalized. A familiar crystal is table salt (NaCl) that consists of many microscopic cubes tightly bound together to yield the crystalline form of salt in a shaker. In the case of proteins and small protein complexes, the protein crystals are exposed to an x-ray beam that diffracts in different directions. The diffraction pattern provides precise information about where every atom in the protein or protein complex resides and its relation to every other atom in the protein or protein complex. Thus, the diffraction pattern can be computed into the 3-dimensional structure of the protein or small protein complex. Cryo-electron microscopy is, in essence, a form of molecular photography. Cryo-electron microscopy enables the shapes of flash-frozen protein complexes to be visualized by shooting electrons at the protein complexes and recording the resulting projected images. Thousands of such projections are collected and combined, and the structure of the protein complex is determined by reconstructing its 3-dimensional shape. Cryo-electron microscopy is especially powerful because it enables atomic-resolution structures of complexes that are too large for x-ray crystallography.

Both of this year’s Shaw Prize winners are giants in the structural biology field and both have, for the first time, solved structures of biology’s most central molecular machines: the protein complexes required for gene transcription that make life possible across all organisms, from bacteria to humans. Indeed, in their monumental work, Nogales and Cramer have solved the structures of protein complexes long deemed experimentally intractable. Moreover, their delivery of the structures of complete multi-protein complexes, not the individual protein components in isolation, has driven a transformation in our understanding of gene transcription in health and disease.

Shaw Prize recipient Eva Nogales pioneered cryo-electron microscopy to transform our understanding of the earliest steps in gene transcription. These studies involved the human TFIID recognition and binding of core promoter DNA and the consequent assembly of the transcription pre-initiation complex (PIC). This large and complex molecular machinery, which is required for the launch of the gene transcription process, is scarce, fragile, and extremely flexible, all of which made the structures Nogales captured a Herculean accomplishment. Nogales revealed how TFIID keeps the TATA binding protein (TBP) sequestered until the rest of the complex engages with the promoter sequences and only then deploys TBP for PIC assembly. She showed the stepwise assembly of the PIC, how the PIC is stabilized on the DNA, and how coupling occurs between PIC states to allow transcription initiation.

Shaw Prize recipient Patrick Cramer used x-ray crystallography and cryo-electron microscopy to determine many breathtaking structures capturing the sequential steps of gene transcription. Cramer’s array of structures includes the full PIC, a 46-protein machine that contains crucial players called Mediator and TFIIH. Cramer also solved structures of RNA polymerase II after it initiates synthesis of an mRNA messenger. These structures include the paused elongation complex, the elongation complex in action, the elongation complex together with the nucleosome (nucleosomes are proteins with DNA wrapped around them and the elongation complex must clear them to proceed), the elongation complex with the nucleosome and remodeling factors, and the elongation complex with the pre-mRNA splicing complex (the splicing complex stitches mRNAs together following elongation). Combined, Cramer’s extraordinary structures provide the world’s first “movie” of gene transcription.

Nogales’ and Cramer’s landmark discoveries drove a paradigm shift in our understanding of one of life’s most central processes: gene transcription. They showed how transcription can initiate and proceed, and how transcription is regulated to enable cells to differentiate so that organisms can properly develop and function.

12 November 2023 Hong Kong