SynBERC:Parts

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This is a draft list of research topics that the SynBERC Parts Thrust is considering for support.
Please contribute & edit with impunity.
We need to get the set of topics correct and then organize ourselves (and anybody else who wants) around getting the work done.

Goals

3. Parts engineering

• a. New function
• b. Tune strength, timing
• c. Orthogonal, composable function
• d. Develop general methods for part redesign

Part Families

Transcriptional

• repressors, DNA binding proteins
• terminators
• promoters

Translational

• RBS
• Riboregulators
• mRNA procesing

Degradation

• degrons

Secretion

• Targeting sequences

Sensing/actuating

• protein binding
• small molecule ligand binding
• light sensing
• switches

Assembly

• Protein-protein interactions (orthogonal set)

Phosphorylation logic control

• Kinases
• Phosphatases
• Docking motifs
• phosphorecognition

Chassis parts

• Vectors
• YAC components
• Transposon components

Projected Parts Application to Testbeds

Tumor-killing devices

• Gene expression devices
  • Transcriptional parts
  • Translational parts (riboregulators)
• Post-Translational device
  • Degradation
  • Phosphorylation logic
• Sensing/actuating/signaling devices
  • Sensing/actuating parts
  • Assembly – assembly based logic
  • Riboregulators
  • Phosphorylation logic
  • Cell adhesion, targeting
• Chassis parts

Microbial drug factory

• Gene expression devices
  • Transcriptional parts
  • Translational parts (riboregulators)
• Post-Translational device
  • Degradation
  • Phosphorylation logic
• Biosynthetic devices
  • Engineered metabolic enzymes (malic acid to malic semi-aldehyde)
• Sensing/actuating/signaling devices
  • Sensing/actuating parts
  • Assembly – assembly based logic
  • Riboregulators
  • Phosphorylation logic
  • Transporters
• Chassis parts