Current Projects

The rapid improvements in cryo-EM and accuracy of structure prediction will likely render much of protein structure determination routine. The focus of structural biology has therefore begun to shift to understanding how molecules work together to realize the plethora of biological processes inside cells, tissues and organisms. The Lucas Lab builds new tools to leverage these growing “structureomic” datasets to visualize the spatiotemporal organization, assembly and heterogeneity of ribosomes and other complexes directly in cells and tissues.

Ribosomes are the modular molecular machines that are responsible for faithfully translating the genetic code to produce every cellular protein. Ribosome assembly is the most energy demanding process in a growing cell, consuming more than half of available energy. In yeast >200 ribosome biogenesis factor proteins are required to assemble the 4 rRNAs and ~80 proteins to produce ~2,000 ribosomes per minute. Structures of purified intermediates in the assembly pathway have revealed how some of these 200 biogenesis factors aid assembly. However, in cells, ribosome assembly spans three subcellular compartments, the nucleolus, the nucleus and the cytoplasm. How the detailed molecular arrangements are coordinated in the cell is unclear. We make use of new cryo-EM methods to visualize intermediates of ribosome assembly from the nucleolus to the cytoplasm. Using this approach, we can correlated the detailed molecular structures of intermediates with their subcellular location at high resolution. In this way, we aim to build a spatially resolved molecular model of an entire biological pathway.

Cryo-EM can reveal the atomic details of cells. However, only a few cells are sufficiently thin to image directly. The application of Focused Ion Beam (FIB) milling, a method in common use in materials science, to generate thin sections cryogenically frozen cells was a major development that allowed visualization of the internal architecture of almost any cell. However, how the milling process damages the cellular molecular structure is only beginning to be understood. The Lucas Lab uses 2DTM to quantitatively analyze the damage caused by milling and to identify milling strategies that minimize damage.

Transcription of the genetic code from DNA to RNA is the first step in gene expression. Messenger (m)RNAs carry the genetic code that is translated by the ribosome to protein. mRNAs also contain untranslated regions (UTRs) at their 5' and 3' ends that can extend to thousands of nucleotides, in some cases, many times longer than the translated region. RNA structure in UTRs can regulate mRNA localization, translation and turnover, and therefore affect gene expression. However, the molecular mechanisms by which RNA structure affects gene expression has only been studied for a handful of mRNAs. Identifying mRNA UTR structural elements that affect mRNA localization, translation and turnover and the molecular mechanisms of their action is crucial to understand gene expression and to inform the design of mRNA therapeutics.