L6- Functional Genomics

why is bacteria used in the food industry

they generate useful properties such as flavour and texture in food products

why is bacteria used in water treatment facilities

• activated sludge in water treatment plants contain microbes that metabolise organic matter to CO2

• cleaning out waste organic material from the water

• can be reused to ‘seed’ the aeration tank

why is bacteria used in composting

decomposes heterogenous wastes in a controlled, microbially active environment

• can be highly optimised (commercial) or rudimentary (home)

• basic ingredients are carbon (brown waste), nitrogen (green waste), oxygen and water

what is bioremediation

a process to detoxify contaminants in the soil and other environments

• hydrocarbon degrading bacteria occur naturally

how is oil biodegradation by marine microbes an example of bioremediation

they rapidly form spherical biofilms around oil droplets which expedite degradation

how is pesticide dechlorination by Burkholderia an example of bioremediation

• use oxygenase’s to generate TCA intermediates

• can deal with Xenobiotic pollutants (e.g. pesticides, dyes, industrial waste) which are often resistant to natural degradation

how is Ideonella sakaiensis an example of bioremediation

expresses PETase enzyme that hydrolyses and degrades PET-based plastic

what are bacterial cell factories

living organisms that produce medically or commercially useful biomolecules (such as antibiotics, enzymes, drugs, hormones etc.)

what are the advantages of cellular factories

• bacterial cultures grow quickly and easily

• they input materials often cheaply and environmentally friendly

what are antibiotics

secondary metabolites produced naturally by bacteria

• used in cellular factories

• can lead to the discovery of new chemistry (e.g. Teixobactin)

what is vitamin B12

• essential for DNA synthesis and metabolism

• only produced by certain bacteria and archaea

how do you express a mammalian or mutant protein

using recombinant DNA technologies so proteins can be made in large quantities as well as bacterial fermentation

how does genetic modification of bacteria occur

• clone the gene into a vector and transform into E.coli

• generates a microbial ‘factory’

• E.coli factories are grown by large scale fermentation

• expression of the gene of interest is induced

• cells are lysed and the expressed protein is purified for research, commercial or medical use

what are the advantages of recombinant therapeutics

• small scale

• high value products

what are the advantages of recombinant enzymes

• high volume

• low cost commodities

what is synthetic biology

the design and construction of new biological parts, devices and systems, and the re-design of existing, natural biological systems for useful purposes

what are the uses of biological components

• modular and well characterised

• can be put together in any order

• allow complex designs with predictable outcomes

give examples of biological components

• promoter

• terminator

• ribosome binding site

• coding sequence

what are optogenetics

• different wavelengths of light trigger the production of different coloured compounds

• induction of bacterial gene expression in tissue via small molecule signalling

• therapeutic delivery tool

what is temperature controlled gene expression

• gene expression occurs between 40-45 degrees C

• circuits dictate colour response of E.coli

• applications in temperature triggered by therapeutics

what is protein engineering

adding new functions to proteins or improving current functions (either by rational design or artificial evolution)

give an example of protein engineering

engineering PETase from l.sakaiensis (plastic degrading bacteria) by active site mutation leads to increased enzymatic activity

what is metabolic engineering

gene circuits and engineered products can be combined to alter or create new metabolic processes in bacteria

• complex multi-enzyme cascades

describe menthol production as an example of metabolic engineering

naturally 70% produced in mint plants, 30% chemical synthesis

• uses 0.29 million hectares of arable land

• expensive

  instead it can go through metabolic engineering for a 76% purity

what do transcriptomics do

measure gene expression of all genes under any specified condition

what does CRISPR stand for

Clustered Regularly Interspaced Short Palindromic Repeats

what are the advantages of CRISPR

• can be modified to allow precise editing of any genome

• hugely powerful tools with wide ranging applications from synthetic biology to basic research to gene therapy