Team:Cambridge/Project/Carotenoid

Colour pigment: Carotenoid

Introduction

Carotenoids are organic pigments naturally present in plants, algae and some bacteria. There are more than 600 carotenoids, which can be categorised into xanthophylls (hydrocarbons containing oxygen element) and carotenes (hydrocarbons containing no oxygen). Carotenoids perform a range of functions, including light energy absorption, protection against photo-damage, acting as antioxidants, and as precursor to other organic compounds. In human, for example, beta-carotene is the precursor to vitamin A.

Part of the carotenoid biosynthesis pathway is shown below (figure adopted from iGEM 2007 Team Edinburgh):

Some of the intermediates in the above pathways are coloured, e.g. lycopene (red), beta-carotene (orange), and zeaxanthin (yellow). The enzymes involved in the biosynthetic pathway are CrtE, CrtB, CrtI, CrtY, and CrtZ. Since our team aims to use different colour pigments as signal output, the above pathway can be incorporated in our design of colour production.

Research by previous igem teams

A few iGEM teams of previous years (e.g. Edinburgh 07, Edinburgh 08, Guelph 08) conducted research in the carotenoid system. We are fortunate to have access to some of their Biobricks in the registry. Here is a summary of the Biobricks available:

The above enzymes all come from Pantoea ananatis (GenBank: D90087.2).

However, we have encountered certain issues during our preliminary research.

• In part K152005, the “CrtE” sequence (which originated from part K152001) contains 3 nucleotides different from the NCBI data base.
• Originally, the registry annotation for K152005 indicated that there was no ribosome binding site before gene CrtI (i.e. “…rbs+CrtB+CrtI+rbs+CrtY…”). After clarification with Team Guelph 08, we were told that it was solely an error in annotation. The registry entry for K152005 has been updated to the sequence in the table above.
• Teams of previous years constructed various composite parts containing two or more enzymes of the synthetic pathways (e.g. CrtEBI, CrtEBIY), but they were not available in the 2009 Distribution Plates.

Action plan of our team

In our project this year, we aim to incorporate the carotenoid biosynthesis pathway in E. coli and produce different coloured pigments. Potential candidates are lycopene (red), beta-carotene (orange), and zeaxanthin (yellow). Since these three compounds are sequential in the biosynthetic pathway, we hope to demonstrate colour changes from red to orange to yellow, by controlling expression of the enzymes involved in conversion.

Our action plan is as follows:

1. Test the activity of K152005 (CrtEBIY).
2. Construct composite biobrick containing CrtE, CrtB and CrtI (i.e. CrtEBI) and test its activity.
3. Transform E. coli with CrtEBI and CrtY. Test if activation of CrtY can cause colour changes in vivo (by converting red lycopene to orange beta-carotene).
4. Characterise our composite biobricks and the colour output.
5. Test compatibility with biobricks from previous iGEM teams and see if we can convert their outputs into pigment production.

·        Test activity of K152005

We wish to test the feasibility of incorporating the carotenoid biosynthetic pathway into E. coli, which does not produce carotenoids naturally. K152005 contains the enzymes for beta-carotene formation, and is a quick way to verify our concept.

We transformed E. coli (TOP10) using K152005 from the 2009 Distribution Plate (Week 2). After incubation for about 3 days, some light yellowish pigmention was visible. The long incubation time may be due to the fact that K152005 does not contain promoter. Although only small amount of yellow pigment was observed (instead of the expected orange colour), this gave us confidence that the carotenoid biosynthetic pathway was working in E. coli.

We will then put K152005 under a strong promoter (R0011, constitutive) to see if stronger colour production can be achieved.

·        Construct composite Biobrick CrtEBI

We wish to produce the first coloured compound in the pathway, lycopene (red), which can then be converted into other colours by subsequent enzymatic reaction.

In order to “pause” at lycopene, we need enzymes CrtE, CrtB and CrtI only. Currently in the registry there is no available Biobrick containing CrtEBI, so we decide to construct our own.

After transforming E. coli with K118014 (rbs+CrtE), K118006 (rbs+CrtB) and K118005 (rbs+CrtI), we construct composite biobrick by ligating the three genes together.

·        Test colour changes by CrtY

·        Characterisation of Biobricks and colour output

·        Test compatibility with other biobricks.