In this episode Tim chats with Phil Sharp, Nobel laureate, Institute Investigator at MIT and member of the Biology Department as well as the Koch Institute. Phil confronted the question of how large protein complexes assemble inside of cells nearly 30 years ago, but had no way to address it at that time. He tells us why he left the question unanswered, and then returned to it so many years later. Phil encourages us to consider how the physics insights of liquid phase separations can help biologists understand fundamental properties of cells.
This is the first of three episodes in our Living Droplets series. Many important processes inside cells involve huge “supercomplexes” of hundreds to thousands of proteins (and sometimes other things like RNA), that carry out many biochemical processes from gene transcription to nuclear transport to microtubule nucleation. While biologists have learned a lot about their functions, in many cases the factors that caused their formation or dissolution are not understood. These big big complexes often appear as aggregates that are separated from their surroundings but retain properties of a liquid. Inside cells, these appear similar to the way vinegar forms separate droplets inside of olive oil (before you dunk some bread in it). Now interdisciplinary investigations are using some very old physics to explore the physical properties of biological liquids, on which cells rely to make their components work together efficiently.
Papers discussed in this episode:
RNA interference discovery by Andy Fire and Craig Mello. This work demonstrated that double stranded RNA induced potent and specific reduction in expression of a target gene.
RNA interference mechanism paper by Phil Sharp and David Bartel, showing how double stranded RNA is processed inside the cell and then binds to its target sequences in messenger RNA.
Perspective paper published by Cell in 2017 by Phil Sharp’s lab with the labs of Rick Young and Arup Chakraborty, in which they propose that transcription machinery assembles on genes as a phase separated condensate.
Three papers published together in Science in July 2018:
- Demonstration that the activator proteins that coassemble at gene promoters behave as liquids by the labs of Rick Young, Phil Sharp, and Ibrahim Cisse.
- Demonstration using live super-resolution microscopy of the coactivator protein Mediator and RNA polymerase II showing they form stable condensates at gene promoters by the Cisse lab.
- Not mentioned in the interview: Here the labs of Robert Tjian, Xavier Darzacq (from UC Berkeley) and Luke Lavis (from Janelia Research Campus) investigate the protein domains of transcription-related factors that accomplish their liquid-like behaviors inside cells. They show how regions called low-complexity domains coalesce at gene promoters.
Stress granules in yeast. A different context from that shown above is provided by yeast biologist Allan Drummond, also not mentioned in this episode. His lab has found that upon stress by heat or low pH, the cytoplasm inside yeast quickly transitions to a solid. This transition is an adaptive response that is critical for yeast to tolerate these environmental stresses.
“Over Under”, “Allada”
Kevin MacLeod (incompetech.com)
“Time Out” by Florio Time DJ.
Licensed under Creative Commons: By Attribution 3.0
Transcript for this episode: Phil Sharp transcript