How Do Genome and Capsid Fluctuations Determine the Translation Efficiencies of RNA Viruses?

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Many viruses, including animal and plant pathogens, have very simple genomes and life cycles, and yet little is known about how their genes start working once they have infected their host. This project studies plant virus made of a single RNA molecule packaged inside a spherical shell of protein (capsid), and this virus will be investigated using methods and techniques of molecular biology and physics. The main question that will be answered is how virus genome (which is made of RNA instead of DNA) is pulled out of the capsid inside the cell. Programs currently in place between UCLA and Historically Black Colleges and Universities (HBCU), California State University Dominguez Hills (with its 70% population of under-represented minorities), and China (through UCLA's Cross-disciplinary Students in Science and Technology [CSST] program) will enable the participation of diverse undergraduate students in research during the next three summers. The scientific aims of this research are focused on viruses whose genomes are directly translated into protein products in the cytoplasm of infected cells, as opposed to more complicated viruses whose genomes involve DNA replication and transcription and hence need to enter the nucleus of their host cells. The particular hypothesis being tested in this work is the possibility that the viral genome can engage with the ribosomal machinery and have its genes expressed even as the capsid protecting it remains intact. Several single-virus-particle methods will be used in attempts to catch an end of the genome as it fluctuates out of the intact capsid and initiates its gene expression (translation into protein products). State-of-the-art physical techniques, including high-resolution cryoelectron microscopy structure determination, and optical and magnetic "tweezers" capable of manipulating separately both the viral genome and its capsid, will be exploited throughout the project.