The background of biological problems

Figure 1.1 Using synthetic biology to building complex systems

(Channon, K. et al. 2008) 

The left figure is BioBricks project (http://www.biobricks.org/). They aim to produce a wide range of standard ‘parts’, analogous to components in an electronic circuit, which can be added to a host ‘chassis’ to produce novel functions. The right figure is projects such as the Los Alamos ‘protocell’ aim to create an entirely new minimal reproducing machine.

1.1.1 The background of biological problems

The metabolism is an important mechanism of physiologically in all organisms. All of the organisms have primary metabolism, which is a general pathway for synthesis the essential compounds and macromolecular to support growth and essential physiologically. For example, carbohydrates, proteins, fats, and nucleic acids are primary metabolites. In contrast to primary metabolism, the secondary metabolism occurs only in some organism such as plants, fungus, and some microbes (e.g.

Streptomyces coelicolor). Secondary metabolites play a key role in plant survival because they can protect plants from herbivores and microbial infection, as attractants for pollinators and seed-dispersing animals, as allelopathic agents, UV protectants and signal molecules in the formation of nitrogen-fixing root nodules in legumes. They

3 

are also used as dye, fibers, glues, oils, waxes, flavouring agents, drugs and perfumes[3]. For the above reasons given, we consider that the plant secondary metabolites have very important economic and scientific value. Figure 1.2 shows the classification of plant secondary metabolites.

  Figure 1.2 Overview of the plant metabolism involved secondary metabolism There can be classified into eight kind of secondary metabolite involved isoprenoids, complex isoprenoids, alkaloids, complex alkaloids, polyketides, phenylpropanoids, flavonoids, and complex flavonoids show in blue box. Gold box show the primary metabolic. The central metabolic pathways are shown by red box.

1.1.1.2 Phenolic compounds

The definition of phenolic compounds is that they have one or more hydroxyl groups attached to an aromatic ring[4] (see Figure 1.3 (A)). Table 1.1 shows the main phenolic compounds in the natural world. Phenylpropanoids, which are classes of

plant secondary metabolites, are main phenolic compounds in plant (see Figure 1.2).

The major role in nature is to protect plants. Many Chinese medicine research display the ingredient of Chinese herbal medicine are abundant of phenolic compounds[5].

Recently, their effects on human health are respected. The oldest medical is the usage of phenol as an antiseptic. However, the phenolic compound contain aromatic ring that can absorb UV-B radiation from the sum and thus prevent sunburns. The traditional sunscreens contain phenolic compound. In modern medicine, we used phenolic compound in following ways. Isoflavones (Figure 1.3 (B)) have estrogenic activity, which is an important mimicry hormone in women. Another important characteristic for phenol compound is that they have antioxidant properties. Catechin (Figure 1.3 (C)) is a powerful, water soluable polyphenol and antioxidant that exists in green tea. And another important antioxidant is resveratrol (Figure 1.3 (D)), which exists in red wine, grapes and peanuts.

Figure 1.3 Phenolic compounds

5 

(A) The example of phenolic, which have one or more hydroxyl groups attached to an aromatic ring. The (B) (C) (D) are chemical structure of isoflavones, catechin, and resveratrol, respectively.

Table 1.1 Structural skeletons of phenolic and polyphenolic compounds Number of

carbons

Skeleton Classication Example Basic structure

7 C6–C1 Phenolic acids Gallic acid 8 C6–C2 Acetophenones Gallacetophenone 8 C6–C2 Phenylacetic acid p-Hydroxyphenyl

-acetic acid

9 C6–C3

Hydroxycinnamic

acids p-Coumaric acid

9 C6–C3 Coumarins Esculetin

10 C6–C4 Naphthoquinones Juglone

13 C6–C1–C6 Xanthones Mangiferin 14 C6–C2–C6 Stilbenes Resveratol 15 C6–C3–C6 Flavonoids Naringenin

1.1.1.3 Synthetic biology

Synthetic biology is integrated by different field, including biology, chemistry, engineering, and some others field. The biologists have the ability to design the construction of the systems of synthetic biology and provide a direct and compelling method for testing the current understanding of natural biological systems. The chemists are able to create novel molecules and molecular systems, which promote the development of useful diagnostic assays, drugs, and biofuels. The re-writers mean the new genomes encoding natural biological systems. The engineers used the

technology to build up a system that works in genetic engineering and development of foundational technologies. Totally, the synthetic biology makes the design and construction of engineered biological systems easier[6]. Heinemann et al. think the synthetic biology is divided into two parts – design and fabrication. They consider that at the beginning of study synthetic biology, it has to possess the biological knowledge and then the computational tools would help the systems design. When the systems are designed by some knowledge and computational computing, the biological experiment such as cloning and DNA synthesis will implement a novel biological system [7] (see Figure 1.4).

Figure 1.4 Synthetic biology — the systems design and system fabrication (Heinemann, M. and S. Panke, 2006)

1.1.1.4 Suitability species for metabolic engineering

Microbes are well established as effective hosts for the biosynthesis of bio-molecules;

consequently, engineered microbial biological systems represent critical frontier in synthetic biology[8]. Engineered microorganisms are employed in numerous applications, including food additives, pharmaceuticals, fuels, animal feed supplements, cosmetics and polymer materials[9]. For example, Corynebacterium glutamicum and Escherichia coli are used to produce lysine, methionine, valine and

7 

threonine [9-13] which are essential intermediate precursors for antibiotics [14] and biofuels [15].

1.1.1.5 Protein post-translational modifications (PTMs)

If we choose microbes about E. coli or others prokaryote as a metabolic engineering host and the genes object to clone are eukaryote, we may suffer a problem in prokaryote because they do not exist PTMs. PTMs is an extremely important cellular control mechanism because it may alter proteins’ physical and chemical properties folding, conformation distribution, stability, activity, and consequently, their functions[16]. In normal eukaryotic cell, they are more than 200 types of PTMs. Some important about acetylation, methylation, phosphorylation, ubiquitination, and GPI anchor [17] are shown in Figure 1.5.

Figure 1.5 Cellular protein post-translational modifications (Jensen, O.N. et al. 2006)

This figure shows some important post-translational modifications (PTMs) about acetylation, methylation, phosphorylation, ubiquitination, and GPI anchor. In normal cell, they are more than 200 types of PTMs.

Ac, acetyl group; GPI, glycosylphosphatidylinositol; Me, methyl group; P, phosphoryl group; Ub, ubiquitin.