The Metabolic Pathway Modification Biology Essay

Published: Last Edited:

This essay has been submitted by a student. This is not an example of the work written by our professional essay writers.

It was required to develop a yeast-based bioprocess that is able to produce Artemisinin for antimalarial treatment. It was required to utilise Yeast cells with glucose as feedstock because the client already has subsidiaries working with Yeast, as a result it is considered to be cost effective. From bioprocessing point of view, use of Saccharomyces cerevisiae is qualified as the expression system because;

S. cerevesie is characterised by intracellular compartments that ensure the mechanisms required for either secretion or insertion of the host protein in the plasma membrane.

Both A.annua and S. cerevesie use the Mevalonate metabolic Pathway (MVA) to generate IPP and DMAPP. (discussed further below)

S. cerevisiae is favoured over prokaryote because organisms such as E.coli produces toxic and contains pyrogenic cell wall components which effectively undesirable in the production of pharmaceutical or food components (Scheiner-Bobis, 2009)


Artemisinin is a naturally found therapeutic medicine that is highly effective towards multi-drug resistant Plasmodium falciparum. It is extracted from Artemisia annua, commonly known as the sweet wormwood. Artemisinin is a sesquiterpene lactone and contains an unusual peroxide bridge, which is believed to be responsible for the drug's mechanism of action. Only few other natural compounds with such a peroxide bridge are known. (RSC, 2006)

Why Bio synthesis?

Naturally, artemisinin in A. annua ranges from 0.01% to 0.8% of the plant dry weight making artemisinin relatively expensive and difficult to meet the demand of over 100 million courses of artemisinin-based combinational therapies per year. One way to overcome this problem is to synthesise artemisinin chemically using basic organic reagents which is however complex and commercially not viable. (Schmid., Hofhienz., 1983)

Alternatively, biosynthesis of artemisinin or any of its derivatives from microbially sourced artemisinic acid (its immediate precursor) have shown to be cost-effective, high-quality and reliable source of artemisinin. (Acton., Roth., 1992)

metabolic Pathway modification

The Mevalonate pathway was chosen for bioengineering modification as it is used by both A.annua and S.cerevisiae and the key enzymes and the intermediates responsible in production of artemisinic acid.

Biosynthesis of artemisinic acid involves using engineered Saccharomyces cerevisiae to produce high concentration of (preferably more than 100 mg.l-1) of artemisinic acid. It is achieved by converting FPP to amorphadiene which subsequently oxidises by a cytochrome into artemisinic acid.

To ensure the genetic stability; all of these modifications were made by chromosomal integration of the host yeast stain and performed in three steps;

Engineering the farnesyl pyrophosphate (FPP) biosynthetic pathway (MVA) to be overexpressed in order to increase FPP production while decreasing its use for ergosterol

Introducing the amorphadiene synthase gene (ADS) from A.annua to host yeast to convert high FPP production into amorphadiene

Cloning a cytochrome (P450) that performs a three-step oxidation of amorphadiene to artemisinic acid from A.annua and expressing it in the amorphadiene producer (host yeast) (Ro et al., 2006)

S.cerevisiae pathway

A.annua pathway

Saccharomyces cerevisiae

Engineering modification of MVP pathway of S.cerevisiae can be performed by overexpressing the rate determining enzyme, HMGR, which is responsible for FPP conversion to sterol.

According to Ro et al, 2006 over-expressing improves amorphadiene production approximately by fivefolds.

Such modifications, even though improve the amorphadiene production, it however result decline in cell density due to insufficient production of ergosterol. As such, integration of an additional copy of HMGR gene into the S.cerevisaie chromosomal DNA can be achieved to increase amorphadiene production drastically yet preventing decline in cell density. The combined variation result in significantly high amount of amorphadiene and a sesquiterpene production, several folds higher than the yeast engineered with ADS alone. (Jackson et al., 2003)

Similarly, ERG9 gene which encodes for squalene synthase (SQS) can be down-regulated using methionine-repressible promoter (PMET3) allowing the sterol production to be reduced while increasing the FPP conversion to amorphadiene by further twofolds. (Ro et al., 2006)

According to Davies et al., (2005), UPC2 is a global transcription factor that regulates biosynthesis of sterols in S. cerevisiae and has a mild effect on amorphadiene production. Overexpressing semi-dominant mutant allele (upc2-1) enhances the activity of UPC2. Studies have shown that combined variation in ERG9 and upc2-1 further improves amorphadiene production. (Ro et al., 2006)

A. annua

Monooxygenase (P450) is a conserved biosynthetic enzyme and is responsible for amorphadiene oxidation in A. annua. (Bertea et al., 2005) Its corresponding full-length cDNA sequence (CYP71AV1) can be recovered from A. annua DNA and introduced in S. cerevisiae under the control of a strong HXT7 promoter. To have a functional heterologous expression of CYP71AV1; Cytochrome P450 oxidoreductase (CPR) must also be isolated from A. annua. Studies have shown and confirm that structurally authentic artemisinic acid is synthesised by transgenic yeast de novo, when A. annua CPR was used as a redox partner for CYP71AV1.

A similar approach has been taken previously by Eelco Wallaart et al, 2000. Where cDNA clone encoding amorphadiene synthase was isolated from A.annua and expressed in E.coli. The recombinant enzyme demonstrated the conversion of amorphadiene to FDP.

To check whether or not CYP71AV1 catalyses all three oxidation reactions from amorphadiene to artemisinic acid; Ro et al., 2006 performed experimental observations in vitro when microsomes from engineered S. cerevisiae strain expressing CPR and CYP71AV1, were incubated along with pathway intermediates (amorphadiene, artemisinic alcohol and artemisinic aldehyde).

The experiment illustrated high conversion of amorphadiene, artemisinic alcohol and artemisinic aldehyde to the final product artemisinic acid. This demonstrates the ability and functionality of the recombinant cDNA at the C12 position of amorphadiene. (Bertia et al., 2005)

Also, it is worth mentioning the fact that efficient conversion of amorphadiene to artemisinic acid in vivo by recombinant CYP71AV1 indicates its significance as a key contributor to artemisinin biosynthesis.

HmgR Phosphorylation inhibition

During metabolic pathways, HMGR is momentarily down-regulated by means of phosphorylation. In S. cerevisiae, phosphorylation of HMGR occurs at Serine 872 residue by AMP- activated protein kinase. Phosphorylation occurs when energy charge is low in the cell and there is a rise in AMP concentration. However HMGR is the rate determining step enzyme and is responsible for FPP conversion to sterol which subsequently converted to artemisinic acid. As such, HMGR phosphorylation would have detrimental effect in the production rate of artemisinic acid. (Goldstein, Brown, 1990)

To inhibit phosphorylation; site-specific mutagenesis can be performed on DNA sequence of HMGR gene. Serine 872 (AGA) can be replaced with Alanine (CGA). Phosphorylation cannot proceed, and structural conformation of protein will not occur. As such, up-regulation of the artemisinic acid formation pathway can be achieved.

Molecular cloning

The insertion of bioengineered and heterologous genes (taken from A.annua) into S.cervisiae, can be conducted via Molecular cloning which involves cloning of any DNA fragment into a host organism following several mechanistic steps.

A cloning vector such as plasmid is used as a vehicle to artificially carry the genetic material into the host organism. In the case of S.cerevisiae an expression plasmid should be used as it contains an origin of replication which assures the transcription and translation events to occur during transformation. (Brown., 2006)


Genomic DNA that to be cloned is extracted from A.annua and purified from contaminating molecules using simple methods. Polymerase chain reaction or PCR is one of the methods, often used to amplify specific DNA sequences prior to molecular cloning.

The purified genomic DNA along with the modified mevalonate pathway sequence of S.cerevisiae are then treated with restriction endonuclease to generate fragments with ends compatible to those of the expression plasmid. To ensure a cleavage site that is compatible with that of the rDNA ends; both the expression plasmid DNA and rDNAs must be cleaved with the same restriction enzyme. (Russell., Sambrook., 2001)

Once completed, the transformation of S.cerevisiae can be carried out using electroporation which involves the use of high voltage electrical pulses to translocate DNA effectively across the cell membrane. Transformation is rarely 100%, only a small fraction of cells take up exogenous DNA. As a result, artificial genetic selection is used where cells that can actively replicate encoded DNA can be isolated using selectable marker gene.


Immobilisation is a well known technique used in many industrial applications to immobilise biological molecules/ living cells. In pharmaceutical industry, immobilisation usually carried out by entrapment of plant protoplasts, bacteria or enzymes in ionic network. Other methods of immobilisation are gelification, physical adsorption, ionic binding, covalent binding or cross-linking. (Giorno., Drioli., 2000)

One of the examples is the production of ampicillin and amoxicillin by entrapping penicillin Amidase in cellulose triacetate fibres by ionic network formation. This further demonstrates the practicality of entrapment technique and as such it should be implemented for the immobilisation of S.cerevisiae.

Entrapment by ionic network formation

Ionic network formation involves single-step entrapment where gel beads are formed using polysaccharide. Alginate is a linear polysaccharide chain that forms a stable gel in the presence of positively charged ions such as calcium cations.

Gel beads are formed by thoroughly suspending yeast cells in a sodium alginate solution. Yeast-alginate solution is then dripped into a stirred crosslinking calcium chloride solution. Gel bead formation occurs as the yeast-alginate drops come in direct contact with the calcium chloride solution. Once formed, the beads are air dried followed by wash with sterile saline solution to remove excess calcium ions and cells. (Wang., 2009)

Entrapment can be performed by a single-step method, however the preparation usually suffer from heat damage and low mechanical strength. Alternatively, two-step methods may be employed which involves the use of resin and curing agent to create a more porous structure beads with desirable elastic behaviour and improved mechanical properties throughout handling. (Klein., Eng., 1979)

The small diameter beads are generally preferred because of the favourable mass transfer characteristics. The Smaller the beads the higher the surface area to volume ratio, allowing good transport of essential nutrients and are also less fragile upon mild agitation. A suitable approach for production of small and porous beads under controlled conditions is necessary. Studies conducted by Ulku Mehmetoglu (1990) on immobilised S.cerevisiae cells by calcium alginate, suggests that bead size of 0.175cm gives a better rate of reaction and effective diffusion coefficient than bead size of 0.5cm.

Advantages and Disadvantages

Free suspended yeast cells are sensitive to mechanical and fluid shear, as they can cause disruption. Feedstock cannot be transported using conventional pumps without significant loss of viability during pumping. Immobilisation provides solution to such problems as it protects yeast cells from sustained shear with no equipment modification. (Williams., Mavituna., 1992)

Physical separation of cells from the medium means simplicity of medium exchange or nutrient replenishment and product purity. The composition of the culture medium can be readily monitored via an external loop, and the concentrations of O2 or glucose can be adjusted as required. (Tyler et al., 1995)To avoid crabtree effect, the glucose feed should be no greater than 0.1%.

In terms of system stability, entrapment provides a stable colloidal system with beads being suspended in the medium. Assuming that oxygen, glucose and artemisinic acid have no polar interaction contribution; the beads will not flocculate due to their relatively large sizes. But more importantly because of the Ca+2 cross-links forming positively charged surfaces, suppressing Van der Waals attractive forces interacting between beads. On the other hand, repulsive forces become dominant keeping the beads suspended, as shown ---- below. The suspended system is said to high zeta potential, far away from their iso-electric point (iep) where particles carry no net electrical charge and flocculate.

One of the main disadvantages of immobilisation is that high productivity is only achieved by the cells suspended near the surface of the beads. Attempt to obtain the released artemisinic acid from the cells at the centre, is usually done by techniques such as permeabilisation which however decrease cells' viability to an undesirable extend. (Hutabarat, 2001)

Engineering constraints

Cell generation

Asexual reproduction of S.cervisiae is relatively short (about 90 minutes). Attempts to operate the process for extended period mean increase in cell density and physical rupture of the matrix. One way to tackle this problem is to ensure even distribution of cells in the beads. Also, to compensate space and nutrients with the newly born cells; fewer cells should be immobilised per bead initially.

Aeration of Immobilised Cells

Oxygen is a key nutrient in cellular metabolism. Low oxygen concentration affects cell growth and overall product yield, while oxygen in excessive amount can potentially be toxic due to superoxide radicals generation which may affect cells directly or indirectly by oxidising the medium component. Oxygen requirement of living cells varies according to different cell lines and culture conditions. Typical aeration method is sparging, which is bubbling gas directly into the culture medium for liquid volumes >10-100 L. Other methods are usually problematic, although they are able to outperform sparging in some aspects. (Sadettin, 2005)

Bead swelling

Alginate beads consist of hydrophilic polymer chains cross linked with cross-linking agent (Ca+2). The degree of water sorption of a hydrogel is not only determined by chemical composition but also by the physical forces and subsequent elastic responses of the constituent macromolecular chains. Studies conducted by Roy, et al, 2009 have shown that a variation in chemical composition of the network can effectively control the swelling of the hydrophilic macromolecular matrices.

One can use higher amount of alginate to achieve a more compact matrix network. However this gives rise to smaller network pore sizes, affecting diffusional mass transfer of molecules cross the matrix.

Effect of pH and temperature

Alginate beads are said to be structurally stable at pH 4-4.5. Increase in pH affects their structural stability. Beyond pH 7.2, the COOH groups of alginate molecules undergo dissociation which weakens the physical forces between the two polymer chains, leading to bead disintegration and possibly flocculation as the zeta potential is decreased and the system is likely to reach its iep.

Similarly temperature higher than the optimum weakens the cross-links and attributes to the continuous erosion of surface layers of the beads which becomes faster with increasing temperature due to greater solubility at higher temperature.

Mass Transport

The analysis of mass transfer in immobilised cell reactors is of great importance as it dictates the performance in these reactors which is often affected by;

The rate of transport of reactants to and products from the immobilised cell system due to external mass transfer limitations

the rate of transport inside the immobilised cell system due to internal mass transfer limitations

Internal mass transfer

Internal mass transfer occurs by diffusion which is the random motion of molecules that arise from thermal energy transferred by molecular collisions. Diffusion occurs due to concentration gradient and can be described by Fick's first law.

For internal mass balance, beads were modelled as porous catalyst spheres with cells being the active sites. Also, it was assumed that the reaction proceeds according to Michealis Menten kinetics, Ê‹ and that the liquid-film has no contribution at this stage. This gives a second order differential for glucose:

Note: Complete derivations for glucose, oxygen and artemisinic acid is given in the appendix.

Where DEff is the effective diffusion coefficient, dS is the change in concentration of glucose along the bead's radius, r.

Vmax represents the maximum rate achieved by the system at maximum substrate concentrations. Km is the Michaelis constant and represents the substrate concentration at half of Vmax

External mass transfer

Mass transport of nutrients and the removal of products from the bead surface, is usually occurred by convection and is described in terms of a liquid phase mass transfer coefficient ks, lumping convective, and diffusive mass transport in the boundary layer around the bead. As such, the external mass transfer for glucose is given in terms of boundary conditions.


kS - Average mass-transfer coefficient

S0 - Substrate concentrations in the bulk fluid

S* - Substrate concentration at solid-liquid interface.

As the liquid film at the interface was taken into account; the beads were considered as an uncharged, non-porous particle with the entire surface of which is uniformly accessible.

Note: Complete derivations for glucose, oxygen and artemisinic acid is given in the appendix.

Simultaneous mass transfer

Both the internal and external mass transfer resistances are significant and occur simultaneously. To obtain a combined analysis which consider both resistances and provide a dynamic model for substrate/product mass transport; the boundary conditions at each step were change to dimensionless form. While applying dimensionless boundary conditions, simultaneous mass transfer for glucose is given by:

Where, is the Thiele modulus - ratio of the intrinsic chemical reaction rate in the absence of mass transfer limitation to the rate of diffusion through a particle.

Note: Complete derivations for glucose, oxygen and artemisinic acid is given in the appendix.


The studies presented here provide a promising biosynthetic pathway to produce immediate drug precursor artemisinic acid by an engineered yeast strain. The engineering modification was performed in three levels:

Genome- Manipulating HMGR Serine residue with Alanine, introducing amorphadiene synthase gene (ADS) from A.annua to host yeast to convert high FPP production into amorphadiene and introducing a cytochrome to perform three step oxidation to artemisinic acid.

Proteome- inhibition of the down-regulation of HMGR by phosphorylation

Metabolome- overexpressed the biosynthetic MVA pathway to increase FPP production while decreasing its use for ergosterol.

Compared to A. annua, the engineered S. cerevisiae is expected to produce a much higher amount of artemisinic acid which is an immediate precursor of artemisinin, making biosynthesis cost-effective, fast and reliable source of immediate precursor artemisinin.

In terms of yeast cell immobilisation, even though gel bead entrapment suffers from mass transfer limitations; it is still far more practical method of immobilisation than the alternatives. One of the main alternatives is the immobilisation by natural cell floc formation, which although relatively cheaper and outperform entrapment, it still however far more problematic and challenging in terms of process stability, supply of energy mechanically, separation and purification.