Improving recombinant eukaryotic membrane protein yields in Pichia pastoris:the importance of codon optimization and clone selection

In the last 15 years, 80% of all recombinant proteins reported in the literature were produced in the bacterium, Escherichia coli, or the yeast, Pichia pastoris. Nonetheless, developing effective general strategies for producing recombinant eukaryotic membrane proteins in these organisms remains a particular challenge. Using a validated screening procedure together with accurate yield quantitation, we therefore wished to establish the critical steps contributing to high yields of recombinant eukaryotic membrane protein in P. pastoris. Whilst the use of fusion partners to generate chimeric constructs and directed mutagenesis have previously been shown to be effective in bacterial hosts, we conclude that this approach is not transferable to yeast. Rather, codon optimization and the preparation and selection of high-yielding P. pastoris clones are effective strategies for maximizing yields of human aquaporins.

Exceptional overproduction of a functional human membrane protein

Eukaryotic-especially human-membrane protein overproduction remains a major challenge in biochemistry. Heterologously overproduced and purified proteins provide a starting point for further biochemical, biophysical and structural studies, and the lack of sufficient quantities of functional membrane proteins is frequently a bottleneck hindering this. Here, we report exceptionally high production levels of a correctly folded and crystallisable recombinant human integral membrane protein in its active form; human aquaporin 1 (hAQP1) has been heterologously produced in the membranes of the methylotrophic yeast Pichia pastoris. After solubilisation and a two step purification procedure, at least 90 mg hAQP1 per liter of culture is obtained. Water channel activity of this purified hAQP1 was verified by reconstitution into proteoliposomes and performing stopped-flow vesicle shrinkage measurements. Mass spectrometry confirmed the identity of hAQP1 in crude membrane preparations, and also from purified protein reconstituted into proteoliposomes. Furthermore, crystallisation screens yielded diffraction quality crystals of untagged recombinant hAQP1. This study illustrates the power of the yeast P. pastoris as a host to produce exceptionally high yields of a functionally active, human integral membrane protein for subsequent functional and structural characterization. © 2007 Elsevier Inc. All rights reserved.

Developing a scalable model of recombinant protein yield from Pichia pastoris:the influence of culture conditions, biomass and induction regime

Background The optimisation and scale-up of process conditions leading to high yields of recombinant proteins is an enduring bottleneck in the post-genomic sciences. Typical experiments rely on varying selected parameters through repeated rounds of trial-and-error optimisation. To rationalise this, several groups have recently adopted the 'design of experiments' (DoE) approach frequently used in industry. Studies have focused on parameters such as medium composition, nutrient feed rates and induction of expression in shake flasks or bioreactors, as well as oxygen transfer rates in micro-well plates. In this study we wanted to generate a predictive model that described small-scale screens and to test its scalability to bioreactors. Results Here we demonstrate how the use of a DoE approach in a multi-well mini-bioreactor permitted the rapid establishment of high yielding production phase conditions that could be transferred to a 7 L bioreactor. Using green fluorescent protein secreted from Pichia pastoris, we derived a predictive model of protein yield as a function of the three most commonly-varied process parameters: temperature, pH and the percentage of dissolved oxygen in the culture medium. Importantly, when yield was normalised to culture volume and density, the model was scalable from mL to L working volumes. By increasing pre-induction biomass accumulation, model-predicted yields were further improved. Yield improvement was most significant, however, on varying the fed-batch induction regime to minimise methanol accumulation so that the productivity of the culture increased throughout the whole induction period. These findings suggest the importance of matching the rate of protein production with the host metabolism. Conclusion We demonstrate how a rational, stepwise approach to recombinant protein production screens can reduce process development time.

Altering the ribosomal subunit ratio in yeast maximizes recombinant protein yield

Background The production of high yields of recombinant proteins is an enduring bottleneck in the post-genomic sciences that has yet to be addressed in a truly rational manner. Typically eukaryotic protein production experiments have relied on varying expression construct cassettes such as promoters and tags, or culture process parameters such as pH, temperature and aeration to enhance yields. These approaches require repeated rounds of trial-and-error optimization and cannot provide a mechanistic insight into the biology of recombinant protein production. We published an early transcriptome analysis that identified genes implicated in successful membrane protein production experiments in yeast. While there has been a subsequent explosion in such analyses in a range of production organisms, no one has yet exploited the genes identified. The aim of this study was to use the results of our previous comparative transcriptome analysis to engineer improved yeast strains and thereby gain an understanding of the mechanisms involved in high-yielding protein production hosts. Results We show that tuning BMS1 transcript levels in a doxycycline-dependent manner resulted in optimized yields of functional membrane and soluble protein targets. Online flow microcalorimetry demonstrated that there had been a substantial metabolic change to cells cultured under high-yielding conditions, and in particular that high yielding cells were more metabolically efficient. Polysome profiling showed that the key molecular event contributing to this metabolically efficient, high-yielding phenotype is a perturbation of the ratio of 60S to 40S ribosomal subunits from approximately 1:1 to 2:1, and correspondingly of 25S:18S ratios from 2:1 to 3:1. This result is consistent with the role of the gene product of BMS1 in ribosome biogenesis. Conclusion This work demonstrates the power of a rational approach to recombinant protein production by using the results of transcriptome analysis to engineer improved strains, thereby revealing the underlying biological events involved.

Understanding the yeast host cell response to recombinant membrane protein production

Membrane proteins are drug targets for a wide range of diseases. Having access to appropriate samples for further research underpins the pharmaceutical industry's strategy for developing new drugs. This is typically achieved by synthesizing a protein of interest in host cells that can be cultured on a large scale, allowing the isolation of the pure protein in quantities much higher than those found in the protein's native source. Yeast is a popular host as it is a eukaryote with similar synthetic machinery to that of the native human source cells of many proteins of interest, while also being quick, easy and cheap to grow and process. Even in these cells, the production of human membrane proteins can be plagued by low functional yields; we wish to understand why. We have identified molecular mechanisms and culture parameters underpinning high yields and have consolidated our findings to engineer improved yeast host strains. By relieving the bottlenecks to recombinant membrane protein production in yeast, we aim to contribute to the drug discovery pipeline, while providing insight into translational processes.

Organic reactions in ionic liquids:ionic liquids ethylammonium nitrate promoted Knoevenagel condensation of aromatic aldehydes with active methylene compounds

The Knoevenagel condensation of aromatic aldehydes with active methylene compounds proceeded efficiently in a reusable ionic liquid, ethylammonium nitrate, at room temperature in the absence of any catalyst with high yields.

Organic reactions in ionic liquids:Ionic liquid promoted Knoevenagel condensation of aromatic aldehydes with (2-thio)barbituric acid

The Knoevenagel condensation of aromatic aldehydes with (2-thio)barbituric acid proceeded efficiently in reusable ionic liquids, EAN, BmimBF4, and BmimPF6 at room temperature in the absence of any catalyst with high yields.

Hypervalent iodine in synthesis. 90. A mild and efficient method for the iodination of pyrazoles

The combined reagent of iodobenzene diacetate (or polymer-supported iodobenzene diacetate) with iodine was used as an effective iodinating agent of pyrazoles to the corresponding 4-iodopyrazole derivatives at room temperature with high yields.

Hypervalent iodine in synthesis 91: a mild and efficient method for the halogenation of 6-methyluracil derivatives

The combined reagent of iodobenzene diacetate (or polymer-supported iodobenzene diacetate) with iodine or bromine was used as an effective halogenative agent of 6-methyluracil derivatives to the corresponding 5-halo-6-methyluracil derivatives at room temperature with high yields.

Optimising yeast as a host for recombinant protein production (review)

Having access to suitably stable, functional recombinant protein samples underpins diverse academic and industrial research efforts to understand the workings of the cell in health and disease. Synthesising a protein in recombinant host cells typically allows the isolation of the pure protein in quantities much higher than those found in the protein's native source. Yeast is a popular host as it is a eukaryote with similar synthetic machinery to the native human source cells of many proteins of interest, while also being quick, easy, and cheap to grow and process. Even in these cells the production of some proteins can be plagued by low functional yields. We have identified molecular mechanisms and culture parameters underpinning high yields and have consolidated our findings to engineer improved yeast cell factories. In this chapter, we provide an overview of the opportunities available to improve yeast as a host system for recombinant protein production.

Mapping the yeast host cell response to recombinant membrane protein production:relieving the biological bottlenecks

Understanding the structures and functions of membrane proteins is an active area of research within bioscience. Membrane proteins are key players in essential cellular processes such as the uptake of nutrients, the export of waste products, and the way in which cells communicate with their environment. It is therefore not surprising that membrane proteins are targeted by over half of all prescription drugs. Since most membrane proteins are not abundant in their native membranes, it is necessary to produce them in recombinant host cells to enable further structural and functional studies. Unfortunately, achieving the required yields of functional recombinant membrane proteins is still a bottleneck in contemporary bioscience. This has highlighted the need for defined and rational optimization strategies based upon experimental observation rather than relying on trial and error. We have published a transcriptome and subsequent genetic analysis that has identified genes implicated in high-yielding yeast cells. These results have highlighted a role for alterations to a cell's protein synthetic capacity in the production of high yields of recombinant membrane protein: paradoxically, reduced protein synthesis favors higher yields. These results highlight a potential bottleneck at the protein folding or translocation stage of protein production.

Relieving the first bottleneck in the drug discovery pipeline:using array technologies to rationalize membrane protein production

The slow down in the drug discovery pipeline is, in part, owing to a lack of structural and functional information available for new drug targets. Membrane proteins, the targets of well over 50% of marketed pharmaceuticals, present a particular challenge. As they are not naturally abundant, they must be produced recombinantly for the structural biology that is a prerequisite to structure-based drug design. Unfortunately, however, obtaining high yields of functional, recombinant membrane proteins remains a major bottleneck in contemporary bioscience. While repeated rounds of trial-and-error optimization have not (and cannot) reveal mechanistic details of the biology of recombinant protein production, examination of the host response has provided new insights. To this end, we published an early transcriptome analysis that identified genes implicated in high-yielding yeast cell factories, which has enabled the engineering of improved production strains. These advances offer hope that the bottleneck of membrane protein production can be relieved rationally.

Facile synthesis of poly(3-hexylthiophene)-block-poly(ethylene oxide) copolymers via Steglich esterification

Poly(ethylene oxide) has been coupled to poly(3-hexylthiophene) using esterification to produce pure diblock copolymers, highly relevant for use in organic electronic devices. The new synthetic route described herein uses a metal-free coupling step, for the first time, to afford well-defined polymers in high yields following facile purification.

The synthesis and properties of some hydrazines

A new synthetic method, applicable to the preparation of a wide range of hydrazine derivatives, is described. This involves the diborane reduction of a hydrazone, or, more conveniently, the reductive-condensation of a hydrazine and the appropriate aldehyde (or ketone). The method gives high yields and provides a particularly simple route to the relatively inaccessible 1,2-disubstituted hydrazines bearing a different group on each nitrogen. The new method has also been applied to the preparation of 1,2-disubstituted hydrazines with the same group on both nitrogens (via the azine), the very rare 1 ,2-disubstituted hydrazines bearing a tert-butyl group, trisubstituted hydrazines and monosubstituted hydrazines. Application of the reaction to the preparation of diaziridines has also been investigated. A mechanism for the reduction, supported by the isolation of a boron-containing intermediate, is suggested. Some limitations of the procedure are discussed. A general i.r. method of distinguishing the isomeric disubstituted hydrazines, as stable salts, has been developed. This has the advantages of speed and simplicity over previous methods. The mass spectra of a series of monosubstituted hydrazines, a series of 1,2-disubstituted hydrazines and some 1-benzoyl 2-alkylhydrazines have been examined in detail. The spectra are generally dominated byα -cleavage processes and the compounds show a variety of interesting rearrangement reactions. The mass spectra of some 1, 1-disubstituted hydrazines and some trisubstituted hydrazines have also been examined. Rearrangement processes occurring in the mass spectrum of tropylium fluoroborate have been examined. Similar rearrangements have been found in the spectrum of trityl fluoroborate and may be of general occurrence in the mass spectra of aromatic fluoroborates. Chemical shift values for some groups on hydrazine nitrogen are recorded and the results of tumour inhibitory tests on some hydrazines are also given.

Synthesis of hydrazine by the fixation process

A critical review of the literature concerning organic derivatives of hydrazine, the ammonia-chlorine reaction and the electrolytic formation of hydrazine has been carried out. Apparatus was constructed to study the electrolysis of liquid ammonia, the formation of chloramine and the fixation of chloramine with a ketone to form an isohydrazone. In the latter case the reaction was carried out in a 3" diameter stirred tank and also in a 1" diameter, 2' high column reactor where the liquid phase was continuously recirculated. Two methods of analysis of azines and isohydrazones in a ketone solution have been developed. One is a colorimetric technique using p-dimethylaminobenzaldehyde and the other involves the hydrolysis of the organic derivative to hydrazine sulphate. Hydrazine was detected in low concentration in some of the electrolytic experiments carried out but it was concluded that this method did not show sufficient promise to warrant further investigation. The gas phase formation of chloramine and acetone isohydrazone has also been studied but in this system difficulties were encountered with the chlorine jet blocking with ammonium chloride. The formation of isohydrazones in a stirred tank reactor has been investigated in some detail and the effect of several parameters was determined. The yield was found to be extremely sensitive to chlorine concentration and in order to obtain yields of more than 90 per cent, the molar concentration of chlorine in the gas phase had to be of the order of 5 per cent. An optimum temperature in the region of 0°C was also detected. These results disagree with those quoted in previous studies but extensive experimental work has confirmed the information presented in this thesis. It has also been shown that at high yields the chloramine formation reaction took place in the gas phase.