6. How are we exploiting our knowledge of the bacterial cell?

Question 1

Bioremediation

Answer 1

Bacteria can be used in environmental applications.
Uses mainly microorganisms, plants, or microbial/plant enzymes to detoxify contaminants in the soil and other environments.

Question 2

Bioremediation Examples

Answer 2

Oil spills - hydrocarbon oxidizing bacteria occur naturally.
Pollutants such as pesticides, industrial waste.
Often relatively resistant to natural degradation.
Microbes that can deal with them can often be found (EG Pseudomonas)
Plastic degrading bacteria (Expresses PETase that degrades PET-based plastic)

Question 3

Bacteria in biotechnology.

Answer 3

Nutrient (O2) -> Bacterial cell -> Valuable biomolecules.
Living organisms that produce medically or commercially useful biomolecules.
Main advantage is that cells do the hard work.
Bacterial cultures grow quickly and easily, input materials are cheap and environmentally friendly.
Whereas chemical synthesis can be difficult, laborious and involve expensive and toxic reagents.

Question 4

Genetic modification of bacteria

Answer 4

Cloning and expressing a mammalian gene in bacteria.

Uses a bacterial plasmid (dsDNA), bacterial promoter and ribosome binding sire and Mammalian gene (dsDNA).

Question 5

Genetic modification of bacteria - Method

Answer 5

1. Linearise plasmid vector
2. Ligate gene into plasmid
3. Transform E.coli expressing cells with the plasmid
4. E.coli multiply in fermenter
5. Protein expression is induced
6. Cells are lysed and protein is purified
7. Purified protein now ready for research, medical or commercial use.

Question 6

Recombinant therapeutics

Answer 6

Huge range of actual and potential applications.
Well understood theoretical and practical path to commercialization.
Small scale, high value products.

Question 7

Industrial enzymes

Answer 7

Different commercialization model.

Commodity products - high volume, low cost business.

Question 8

New DNA editing technologies

Answer 8

Allow precise editing of any genome.
Clustered regularly interspaced short palindromic repeats (CRISPR)
Transcription activator like effector nucleases (TALENs)
Zinc-finger Nucleases (ZFNs)

Question 9

Synthetic biology

Answer 9

Design and construction of new biological parts, devices and systems, and the redesign of existing, natural biological systems for useful purposes.

Question 10

Example of Synthetic biology

Answer 10

Bacteria that absorb CO2, make unusual products, engineered living materials etc

Question 11

Biological components

Answer 11

Components should be modular and well characterised.
Can be put together in any order.
Allows complex designs with predictable outputs.
Components represented by symbols.

Question 12

Promoter

Answer 12

Binding site of RNA polymerase, allows gene transcription

Question 13

Ribosome binding site

Answer 13

Ribosome translates RNA into protein

Question 14

Terminator

Answer 14

Ends transcription

Question 15

Lac repressor protein (Lacl)

Answer 15

Prevents transcription unless lactose is present. Lacl is an ‘off’ switch, lactose is an ‘on’ switch.

Question 16

Protein engineering

Answer 16

Engineered proteins add microbial functionality.
Either by rational design or artificial evolution.
Proteins can change the behavior/functionality of bacteria that express them.
Or a new enzyme may allow synthesis of a novel, high value compound by the bacteria.

Question 17

Examples of Protein engineering

Answer 17

Temperature-controlled gene expression.
Gene expression turned on between 40-45°c.

Mutant PETase
Engineered from Ideonella sakaiensis (plastic degrading bacteria)
Mutant of amino acids in active site bind PET in more favourable conformation.
Leads to increased activity of the enzyme

Question 18

Metabolic engineering

Answer 18

Gene circuits and engineered proteins can be combined to alter or create new metabolic processes in bacteria.
Complex, multi-enzyme cascades.
Improve the efficiency of current metabolic processes or allow bacteria to synthesise new compounds.

Question 19

Traditional methanol production

Answer 19

70% produced in mint plants grown mainly by subsistence farmers in India.
30% produced by chemical synthesis.
Production is expensive.

Question 20

Synthetic Biology

Answer 20

The future.
Increasing speed and fidelity of DNA synthesis.
Enhanced assembly methods enabling larger and larger genomes to be assembled.
The discovery and characterisation of new biological parts, improved design processes and predictive algorithms will generate increasingly reliable functional systems.
Vast range of applications.