Ikerbasque researcher: Nicola Abrescia
Structural studies of large macromolecular complexes and virus particles
Recently, the results of your research have been published, in which the complete enzyme machinery for the RNA polymerase of an organism of the Archaea kingdom has been seen for the first time. What is the function of this polymerase and what is the significance of the discovery of its mechanism?
Gene expression is carried out by multi-subunit RNA polymerase (RNAP) enzymes that transcribe DNA into RNA which in turn is translated into proteins by ribosomes. Transcription can be divided into three major steps: Initiation, Transcription/Elongation, Termination. Initiation and Termination are the less understood processes but relevant in many associate gene disorders. Eukaryotes have three different nuclear RNAPs whilst Archaea and Bacteria have single RNAPs. Archaeal transcription is homologous to that of eukaryotes but initiation is somehow simpler requiring only accessory factors: TFB and TBP. Thus it can serve as model system for eukaryotic initiation. Many Archaea are extremophiles; they live in high salt, acid or temperature environments and appeared billions of years ago when Earth was still a pretty unpleasant place to live. Our recent structure of the complete archaeal RNAP complex (13 subunits; molecular weight ~ 405 kDa) from Sulfolobus shibatae has fully elucidated its architecture and revealed a new subunit whose location and topology suggests its role in the opening of the double strand DNA when transcription initiation starts. Also our RNAP structure has revealed that the enzyme that converts DNA into RNA is staggeringly conserved despite a 2 billion year evolutionary gulf between simple single celled organisms called Sulfolobus and human beings. These findings explore how evolution has shaped our enzyme to accomplish more complex functions.
X ray crystallography technique was used in this research. What is this exactly and what can it be used for?
Crystallography uses X-rays to investigate the three-dimensional structure of biological and synthetic molecules. In our case X-rays hit a relatively small crystal (few microns) composed of the biological macromolecule of interest. The encounter of the X-rays with the ordered array of molecules within the crystal produces diffracted X-rays that are collected on a detector. Multiple diffraction images from the finely rotating crystal are collected for subsequent data processing then the obtained information is deconvoluted into the electron density corresponding to the macromolecule. Finally this electron cloud is interpreted and modelled in terms of the molecule atomic model. X-ray crystallography has been used for years to study the relationship between structure and function of biological molecules important in many cellular processes (think of the famous first diffraction pattern of the B-DNA by Rosalind Franklin!). Nowadays crystallographers and structural biologists tend to focus their attention to protein complexes, the so-called large macromolecular assemblies, because of the understanding that protein-protein cross-talk is in many cases even more important than the structure of an individual protein. For example new frontiers in crystallography have been opened by visualizing lipid-containing viruses as big as 65MDa or full membrane proteins with implications in biomedical research. Similarly crystallography is used routinely to study, screen and design new and better drugs by displaying the atomic details of the interaction of the target molecule with the ligand.
What has accepting the offer from Ikerbasque meant to your professional career?
Becoming a senior Ikerbasque Professor has allowed me to start my own research group whose interest focuses onto the understanding of how large multi-component proteins assemble, function and interact in the cellular context. The commitment of Ikerbasque to foster scientific excellence has been the turning point in my professional career by laying the conditions of a steady but consistent progression as scientist. Indeed the stability of the position is a prerequisite to pursue challenging biological goals but simultaneously the Ikerbasque three-years review process allows keeping scientific competitiveness high. Furthermore accepting the offer from Ikerbasque has meant for my professional career a double pledge for excellence; from one side the opportunity to develop my lines of research and from the other side the responsibility to represent worldwide the efforts that Ikerbasque is putting in creating a strong and productive scientific community.
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