SynBERC:Parts

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	**Phosphorylation logic		**Phosphorylation logic
	*Sensing/actuating/signaling devices		*Sensing/actuating/signaling devices
-	**Sensing/actuating parts	+	**Sensing/actuating parts
	**Assembly – assembly based logic		**Assembly – assembly based logic
	**Riboregulators		**Riboregulators
	** Phosphorylation logic		** Phosphorylation logic
-	**Cell adhesion, targeting	+	**Cell adhesion, targeting
	* Chassis parts		* Chassis parts

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Revision as of 15:25, 20 September 2006

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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.

Contents 1 Goals 1.1 1. Parts collection, registry 1.2 2. Parts characterization 1.3 3. Parts engineering 2 Part Families 2.1 Transcriptional 2.2 Translational 2.3 Degradation 2.4 Secretion 2.5 Sensing/actuating 2.6 Assembly 2.7 Phosphorylation logic control 2.8 Biosynthetic enzymes 2.9 Transporters 2.10 Cell adhesion 2.11 Chassis parts 3 Projected Parts Application to Testbeds 3.1 Tumor destroying bacteria 3.2 Microbial drug factory

Goals

1. Parts collection, registry

2. Parts characterization

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

Biosynthetic enzymes

Transporters

Cell adhesion

Chassis parts

• Vectors
• YAC components
• Transposon components

Projected Parts Application to Testbeds

Tumor destroying bacteria

• 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