Joseph H. Davis

Massive macromolecular complexes are essential in numerous cellular processes, including transcription, translation, splicing, nuclear import/export, metabolism, and degradation. Notably, errors in these assembly and disassembly processes dysregulate cellular homeostasis and have been linked to a variety of diseases.

We are actively working to uncover how these complexes are assembled, disassembled, and degraded, and to learn how environmental stress, mutations, disease, and aging alter the fidelity of these processes. Additionally, we contend that learning the assembly principles of natural macromolecular complexes can guide efforts to build ever larger synthetic molecular machines with applications in metabolic engineering, drug delivery, and materials science.


AUTOPHAGY

Autophagy is a protein, macromolecular complex, and organelle degradation process that requires the assembly of a mixed protein/membrane structure (autophagosome) that targets and delivers substrates for degradation in the lysosome as illustrated below. Elegant genetic screens revealed the identify of ~40 integral genes involved in this process, however the mechanistic details of how autophagosomes assemble are still unclear.

schematic of autophagosome assembly

Interestingly, autophagy was once thought to act nonspecifically, however recent work has found ‘selective’ forms of autophagy specifically targeted at particular organelles, macromolecular complexes, and individual proteins. Notably, the relative importance of selective vs. non-selective autophagy in maintaining proteostasis or in driving pathology is currently underexplored.

The Davis lab is working to uncover autophagosome assembly and maturation pathways, determine the effect of disease-linked mutations on the assembly pathway and to understand how this process might be therapeutically modulated.

KEY QUESTIONS OF INTEREST TO THE DAVIS LAB INCLUDE:

  • What is the order of protein binding in autophagosome assembly and how do mutations in autophagy proteins affect the assembly pathway?
  • How do post-translational modifications affect assembly kinetics?
  • What are the structures of the assembly intermediates required for autophagosome maturation?
  • What is the full complement of selective autophagic substrates and how quickly are these substrates degraded?
  • How do genetic mutations, environmental stress, or organismal aging affect substrate selection and degradation rates?
  • Which receptor proteins select targets for degradation?

   

RIBOSOME BIOGENESIS

Bacterial ribosome biogenesis is a multistep process requiring coordinated synthesis, RNA processing, and folding of three large ribosomal RNAs, and the translation, folding, modification, and binding of ~50 ribosomal proteins. Despite this complexity, the process is rapid and precise (bacteria produce ~100,000 ribosomes/h), and is guided by dozens of essential assembly factors that smooth the energetic landscape, resulting in efficient assembly. We have recently made exciting progress understanding how RNA folding and protein binding are linked through ‘cooperative folding domains’, and how assembly factors guide ribosome biogenesis (read more here).

ribosome biogenesis

THE DAVIS LAB IS NOW ACTIVELY WORKING TO UNDERSTAND

  • What are the structures and compositions of assembly intermediates and how are they ordered along the assembly pathway?
  • How does the cell utilize parallel assembly pathways during times of stress?
  • When and where do assembly factors bind on the ribosomal subunits?
  • How do essential assembly factors work in concert to guide the biogenesis process?

 


Davis JH*, Tan YZ*, Carragher B, Potter CS, Lyumkis D, Williamson JR. Modular assembly of the bacterial large ribosomal subunit. Cell 2016. 167(6):1610-1622.

Davis JH, Williamson JR. Structure and dynamics of bacterial ribosome biogenesisPhilosophical Transactions of the Royal Society B 2017. 10.1098/rstb.2016.0181.

Tan YZ, Baldwin PR, Davis JH, Williamson JR, Potter CS, Carragher B, Lyumkis D. Single-Particle CryoEM Analysis: Addressing Preferred Orientation through TiltingNature Methods 2017. 14(8):793-796.

Stokes JM, Davis JH, Mangat CS, Williamson JR, Britton RA. Discovery of a small molecule that inhibits bacterial ribosome biogenesiseLife 2014. 18(3) e03574.

Jomaa A*, Jain N*, Davis JH*, Williamson JR, Britton RA, Ortega J. Functional domains of the 50S subunit mature late in the assembly processNucleic Acids Research, 2014. 42(5):3419-35.