Systems Chemistry and Nested Biomolecular Information

The Plant Microbiome as an External Organ

The rhizosphere is the most complex systems on the planet consisting of microbes, fungi, and complex chemical reaction. Thus far, it has been shown that there is a spatial and temporal relationship that exists within the rhizosphere between plant roots and parasites surrounding plant roots, but thus far we do not know how this spatial temporal relationship is established nor how it works. Currently, the Lynn lab is interested in understanding diffusion in space and time within the rhizosphere between plant roots and microbes and how this spatial temporal relationship impacts climate change.

Organizing the Rhizosphere Participants into a Plant Organ

Reaction-Diffusion Dynamics Hypothesis: Reduced quinones and O2 released from the host plant root diffuse into the rhizosphere, react with bacterial phenazines (methylene blue), to create autocatalytic stationary state Turing patterns that define the spatiotemporal ordering of the external organ.

Amphiphiles and 2-step Nucleation of Biomaterials

Prion-like low complexity domains (PLCD) exist as head-to-tail linked amphiphiles, accessing liquid-liquid phase transitions enable spatiotemporal cellular organization critical in division, signaling, and transcriptional regulation.

Intrinsically disordered (IDP) biomolecular condensates are found in ribonucleoprotein bodies, the nucleolus, and as domain of ~40% of all eukaryotic proteins.

RNA/Amyloid Co-assemblies

RNA-A10 templates amyloid assembly of KLVIIAG into well-ordered cross-B peptide leaflets that order into multi-lamellar nanotubes with 50nm IDs.

  • Cooperative templating requires 6 bases and accommodates >8kb,
  • More effective templating with dsDNA/dsRNA/quadDNA,
  • Co-assembly remains dynamic and thermally reversible like ribonuclear particles

Sticker/Spacer Oligomers as Primitive Proteins Capable of Novel Functions