🧬 Week 12: Building Genomes
Global Listener — Anastasia Ntavou | Athens, Greece Project: Mycelium Surfboard (Ganoderma lucidum engineering)
Reflection: Genome-Scale Engineering & the Mycelium Surfboard
This week’s lectures on synthetic genomes — from JCVI-syn3.0 (473 genes) to Sc2.0 — provided important context for the mycelium surfboard project.
Minimal genomes: JCVI-syn3.0 has ~30% genes with unknown function. For G. lucidum (~49 Mb, ~16,000 genes), the complexity is vastly greater — reinforcing why targeted CRISPR knock-in (2 genes) is the right strategy rather than whole-genome redesign.
Recoding: George Church’s 57-codon E. coli inspired a thought: could freed codons in G. lucidum be reassigned to incorporate non-natural amino acids into SC16 for enhanced surface binding? Speculative but scientifically interesting future direction.
CRISPRi for metabolic engineering (recitation): CRISPRi could downregulate competing secretion pathways in G. lucidum, channeling more resources toward SC16 hydrophobin production.
Design principles from genome-scale work applied to this project:
| Principle | Application |
|---|---|
| Modularity | Each gene construct (SC16, LAC2) independently functional |
| Orthogonality | GPD promoter drives constitutive expression without disrupting native regulation |
| Verification | Whole-genome sequencing (Illumina) post-transformation to confirm on-target integration |