Essential exons, irrelevant introns
Biomolecular NMR experts in Germany have discovered how the U2AF protein facilitates the process of splicing used by cells to make the correct template for RNA transcription and the subsequent expression of proteins.
In order to express a protein, the gene locked in the DNA that codes for the protein must first be transcribed into RNA and shortened in a process known as splicing to the appropriate template. RNA splicing requires various proteins, splicing factors to cooperate, among them U2AF. This protein has two structural modules and binds to the RNA near the boundary between the nucleotide sequence within a gene that is removed by RNA splicing, the seemingly irrelevant introns and the essential exons, the sequences left after splicing; the intron-exon boundary. mRNA is comprised solely of exons.
Many cellular functions involve proteins with multiple domains, these are composed of structurally independent modules that are connected by flexible chemical linkages. Science often knows how a given domain recognizes its target molecule, an oligonucleotide or peptide motif for instance, but the dynamic interactions between multiple domains and what effect recognition of the targets by each component has is not always fully understood.
Pre-messaging
Now, researchers at the Helmholtz Zentrum München, the Technical University of Munich, the European Molecular Biology Laboratory (EMBL) in Heidelberg, Germany and the Centre for Genomic Regulation in Barcelona , Spain, have reported details in the journal Nature of how this process occurs. Their study shows how the U2AF protein allows the pre-messenger-RNA to be spliced to form the templating mRNA.
According to Michael Sattler, Professor of Biomolecular NMR Spectroscopy at the Technische Universität München, the spatial structure of the U2AF protein alternates between a closed and an open conformation. He and his colleagues have found that a matching RNA sequence in the intron causes the U2AF to assume an open conformation, which activates splicing and eventually leads to the removal of the intron. Splicing is an essential part of current understanding of how and why genetic information flows from DNA to RNA to make proteins. NMR data help explain inconsistencies in the X-ray structures of U2AF as well as revealing key information about the conformational changes that take place during the splicing process.
The intron's RNA sequence determines how effectively this conformational change can be triggered meaning that the toggling between the closed and the open form of U2AF occurs through a process of conformational selection. In other words, the RNA binds to a small fraction of the open conformation that already exists even in the absence of RNA. The scientists presume that similar mechanisms - balanced between a closed, inactive and an open, active conformation - play an important role in the regulation of many other signal pathways in the cell.
"We expect that similar mechanisms of multi-domain conformational selection coupled to biological activity operate in many multi-domain proteins that must functionally distinguish degenerate nucleotide or amino acid motifs from similar, nonspecific sequences. As demonstrated here for U2AF65, structural analysis of multiple domains connected by flexible linkers critically depends on the use of solution techniques in a multidisciplinary approach," the team concludes.
"The next step will be to see how and if our observation is influenced by additional factors that bind at the 3' splice site," Sattler told SpectroscopyNOW. He hopes that the results will help researchers to understand the basic mechanisms of alternative splicing regulation, which is a complex process involving a combinatorial fine-tuned balance of different positive and negative regulators. "The molecular interactions that play a role in these processes are potential targets for interfering with small molecules towards drug discovery," he adds, "and this is also a focus of our research in the future."
The views represented in this article are solely those of the author and do not necessarily represent those of John Wiley and Sons, Ltd.
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