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Team:Macquarie Australia/Project/background
From 2013.igem.org
Photosynthesis
Photosynthesis is the process where light from the sun is converted into chemical energy that can be used by photosynthetic organisms to fuel their growth and metabolism. The process is divided into two differed photosystems; photosystem I and photosystem II. Photosystem II is the first step in capturing energy from the sun in the form of photons, this energy is captured by chlorophyll molecules and then used to energize electrons that split water atoms into hydrogen atoms and oxygen [1]. Photosystem I then further excites electrons from photosystem II and uses them to produce NADPH for carbon fixation where inorganic carbon in the form of carbon dioxide is converted to organic compounds [2].
Photosynthetic organisms such as the single celled algae Chlamydomonas reinhardtii are reliant on this system in order to survive and function.
Mutagenesis
Mutagenesis techniques have been an important tool for scientists to determine the individual functions of the genes. For example, Meinecke et al conducted a study on Chlamydomonas reinhardtii that were chlorophyll deficient. These mutants were found to have a build up of Mg-protoporphyrin IX as a result of mutations in the ChlM gene. The ChlM gene encodes the enzyme Mg-protoporhyrin IX methyltransferase and this buildup of substrate resulted in no production of chlorophyll, suggesting that the ChlM gene was an essential step in the chlorophyll biosynthetic pathway [3].
Whilst it is known how the chlorophyll biosynthetic pathway operates, currently there has been little success in replicating this system synthetically. Hence, this serves as the basis for this research project. If the chlorophyll biosynthetic pathway is successfully created, it will be a world first advancement in this area.
Chlorophyll
Chlorophyll is a photosynthetic pigment differentiated from other tetrapyrroles by the presence of a magnesium ion in its structure [4]. Currently, four types of chlorophyll pigments have been identified including chlorophyll a, b, c and d. Recently a fifth type, chlorophyll f, has been discovered as an accessory pigment in a cyanobacterium [5]. Before the discovery that the cyanobacterium Acaryochloris marina used chlorophyll d as its primary photosynthetic pigment, it was thought that only chlorophyll a was utilised by the photosynthetic reaction centres of all photosynthetic organisms [6]. In this study we are interested in chlorophyll a, as this is one of the main photosynthetic pigments produced in Chlmaydomonas reinhardtii, the organism from which the genes necessary for out project have been sourced [1].
Gibson Assembly
Gibson cloning is a powerful and innovative method of DNA polymer synthesis, devised by DG Gibson et al. in 2009 (Gibson et al., 2009). The technique comprises an isothermal, single-reaction experiment involving the concerted action of a 5’-exonuclease, a DNA polymerase and a DNA ligase. An overview of the Gibson assembly method is provided in Figure 1 below and involves the ligation of DNA oligos, or ‘gBlocks’, of varying size (up to 500 BP each). As can be seen in the figure, gBlocks contain overlapping DNA regions of at least 30 BP which are exposed upon the action of the exonuclease. This facilitates complimentary base pairing between gBlocks. The simultaneous action of a DNA polymerase (preferably with proof-reading activity) and Taq polymerase, respectively, then complete and seal the newly formed conjugate (Gibson et al., 2010, Gibson et al., 2009).
The technique has obvious advantages in terms of time efficiency and simplicity. It involves considerably less labour and steps to complete compared to traditional methods. In particular there are no polymerase cycling assembly; PCR, gel purification; restriction digestion and DNA ligation steps are necessary (Gibson et al., 2010). For these reasons we have chosen to apply this technique to the assembly our BioBricks.
References
1. Nanba O, Satoh K: Isolation of a photosystem II reaction center consisting of D-1 and D-2 polypeptides and cytochrome b-559. Proceedings of the National Academy of Sciences 1987, 84(1):109-112.
2. Silver SC, Niklas J, Du P, Poluektov OG, Tiede DM, Utschig LM: Protein delivery of a ni catalyst to photosystem I for light-driven hydrogen production. Journal of the American Chemical Society 2013, 135(36):13246-13249.
3. Meinecke, L., Alawady, A., Schroda, M., Willows, R., Kobayashi, M. C., Niyogi, K. K., Grimm, B., & Beck, C. F. (2010). Chlorophyll-deficient mutants of Chlamydomonas reinhardtii that accumulate magnesium protoporphyrin IX. Plant molecular biology, 72(6), 643-658. 4. Willows, R.D.(2004)Chlorophylls in Plant Pigments and their Manipulation (Davies, K. ed.),Blackwell Publishing. pp 23-56
5. Chen, M., Li, Y., Birch, D., & Willows, R. D. (2012). A cyanobacterium that contains chlorophyll red-absorbing photopigment. FEBS letters 586,3249-3254!
6. Chen, M., Schliep, M., Willows, R. D., Cai, Z. L., Neilan, B. A., & Scheer, H. (2010). A red-shifted chlorophyll. Science, 329(5997), 1318-1319.\
7. GIBSON, D. G., SMITH, H. O., HUTCHISON III, C. A., VENTER, J. C. & MERRYMAN, C. 2010. Chemical synthesis of the mouse mitochondrial genome. Nature Methods, 7, 901-903.
8. GIBSON, D. G., YOUNG, L., CHUANG, R. Y., VENTER, J. C., HUTCHISON, C. A. & SMITH, H. O. 2009. Enzymatic assembly of DNA molecules up to several hundred kilobases. Nature methods, 6, 343-345.
