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images-8.jpegBioBricks and the standardisation of biological components

The use of standardised components is found in all fields of engineering, where it allows the benefits of abstraction, decoupling and insulation from unnecessary detail in the design of complex systems. The ability to construct new DNA sequences has far outpaced our capacity to design the genetic circuits that these might encode. Synthetic Biology promises simplified design using modular standardised DNA components, or BioBricks. 


 

Improved BioBrick components for bioluminescence

iGEM2010 Cambridge Bioluminescence1c.jpg

The Cambridge iGEM2010 team built a set of BioBricks to allow bioluminescence in a wide range of colours which have applications both as reporters for biosensors and as natural light sources. They adopted a number of strategies to extend the use of firefly luciferase: (i) codon optimisation for increased light output, (ii) use of a luciferin regenerating enzyme and (iii) mutagenesis to create a number of different colours. The team also created a BioBrick version of the Vibrio fischeri Lux operon which results in light emission in E. coli without the need for addition of any external substrate. This produces a high light output (as demonstrated by Ben Reeve and Theo Sanderson above!)

   

Bacterial rainbow

 

The Cambridge iGEM2009 team has produced a series of gene expression cassettes that allow in vivo production of a spectrum of pigments in bacteria. More details can be found at http://2009.igem.org/Team:Cambridge/Project/Pigments

Carotenoids: The enzymes required for carotenoid production originally come from Pantoea ananatis, and were available in the registry. These were used to produce orange and red.
Melanin: The tyrosinase required for melanin production originally comes from Rhizobium etli and produces brown.
Violacein: The enzymes required for voilacein production came from Chromobacterium violaceum. The operon can be manipulated to produce violet, green, and blue.

   

Synthetic operon for violacein production

 

The Cambridge iGEM2009 team received sponsorship from DNA2.0 Inc., which allowed them to design and construct a synthetic operon for the biosynthesis of violacein. The operon is 7.5Kb in size, contains 5 genes, and has been submitted to the MIT Registry for Standard Parts in BioBrick format - Part BBa_K274002. Expression of the VioA-E genes results in conversion of L-Tyrosine to an intense violet pigment. Violacein is a hydrophobic compound, and is retained within cells.

   

New BioBrick encoding an improved fluorescent protein

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Green Fluorescent Protein (GFP) offers efficient and convenient means of visualising the dynamic process of gene expression and of obtaining readout of the current state of complex gene regulatory networks - features of major interest for synthetic biology.

Stefan Milde, working in the Haseloff Lab at Cambridge as part of iGEM2008  has constructed BioBrick versions of improved GFP variants and tested their properties (Parts:BBa I746908-I746919). He has compared two recently reported GFP variants to the mut3GFP variant in the Registry of Standard Biological Parts. The two GFP variants chosen were "superfolder GFP", developed and described by Pédelacq et al (2006), which was engineered for improved fluorescence in fusion proteins and P7 GFP ("superfast GFP") which was engineered by Fisher et al (2008) and selected on the basis of its very rapid folding in vitro. Read on for more...

   

The Registry of Standard Parts at MIT 

parts-icon
With BioBrick parts from Cambridge iGEM teams: iGEM2005iGEM2006iGEM2007iGEM2008 and the Haseloff Lab and new Bacillus subtilis strains and key parts 
(http://partsregistry.org/) 
   

In Living Color: Bacterial Pigments as an Untapped Resource in the Classroom and Beyond

Charkoudian LK, Fitzgerald JT, Khosla C, Champlin A (2010) In Living Color: Bacterial Pigments as an Untapped Resource in the Classroom and Beyond. PLoS Biol 8(10)

Recent advances in the study of natural products made by bacteria have laid the foundation for engineering these molecules and for developing cost-effective ways to manufacture them. In our lab, we study a number of natural products that are synthesized by harmless soil bacteria of the Streptomyces genus. Whereas our primary interest in these molecules is due to their antibiotic properties, many of these natural products have distinct colors [1]. (The reasons for why Streptomyces make antibiotics or pigments remain mysterious.) This article is intended to make the case to the scientific and educational communities thatStreptomyces-derived natural products are an untapped source of useful biopigments. By sharing some of our own experiences in harnessing these pigments to create paint and paintings, we also hope to inspire others to explore the potential ofStreptomyces-derived pigments in art, industry, and perhaps most importantly, the classroom.

The pedagogical value of bacterial pigments is highlighted by the wide range of concepts and methods in chemistry, biology, and art that can be introduced to students in this context (see Box 1). Teachers can incorporate bacterial pigments into their lessons while introducing fundamental scientific principles ranging from the physics of color to the chemistry behind paints that fade in sunlight. Painting with living bacteria (Box 2) or extracting pigments from bacterial cultures (Box 3) provides a visual and kinesthetic activity to support key aspects of scientific investigations and methods learned in the classroom. Because the methods to do so are safe, inexpensive, and easily implementable in the everyday world, it is possible to use biopigments as a vehicle to introduce school children to science via art and vice versa. While many of these concepts and techniques are appropriate for the advanced high school or undergraduate classroom, even elementary school children can use bacterial paints prepared by their teacher to create art, an activity that may teach children at a young age that bacteria are a source of valuable materials rather than merely agents of disease.

BactPigments.jpg

   
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