Protein Sources (Heterologous expression of proteins)

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1 Protein Sources (Heterologous expression of proteins) Adrian Suarez Covarrubias Before starting out - why? what? when? where? Recombinant expression? if so, choice of host: prokaryote? eukaryote? modification needed? modified from Sherry Mowbray 1

2 Before Starting Out (I) Why? Why do I need the protein? Source Purity Cost Industrial application Therapeutics/drugs /vaccines Source: less important? Purity: less important? - want bulk quantities Cost: important - need huge amounts => need efficient and cheap source Source: endogenous protein best? Purity: very important - no pathogens, antigens Cost: less important? - high cost, lower yield often OK Basic research Source: often important Purity: usually very important Cost: generally higher, for amount produced 2

3 Before Starting Out (II) What? What kind of protein do I need? What do I know about it? Natural (or very similar) protein? Homologous expression - expression in natural host Heterologous expression - expression in other organism (need to clone) New variants, e.g. mutations? - recombinant technology Literature/databases/bioinformatics - is the gene sequenced? - what else is known? 3

4 Before Starting Out (III) When? When do you need the protein? Research: fast - usually small amount -> overall low cost ( Just do it. ) Drug development: can take 10 years - usually larger amounts, many preps -> higher overall cost (worth optimizing) Where? Where will you use the protein? E.g.: need a thermally or odd-ph stable protein? 4

5 Recombinant DNA technology today Gene source Which? Sequence known? Isolate the gene Screen cdna library (degenerate primers?) RT-PCR (degenerate primers?) Screen expression library (antibody to YFP) Synthetic gene Express and purify Choose organism Clone Choose expression vector Mutations or other changes? 5

6 Chromosomal DNA Isolation and cloning your gene (generally) Source? Gene of interest Eco R1 Isolate gene/pcr/cdna (Cut with restriction enzymes?) Hind III Expression vector? Insert gene into cloning vector Host? Cloned gene Eco R1 Hind III Plasmid Transform into host Yeast Bacteria Animals Plants 6

7 Plan for expression, purification Example: Promoter Operator (strong) (e.g. laco) Ribosome binding site (strong) His-tag Coding region High copy plasmid Extract from bacteria carrying plasmid After induction (lots of protein X) Nickel affinity column Wash His HisHis His His His HisHis Elute His His 7

8 Fungi Expression hosts Bacteria Yeast Aspergillus Eukaryotic cell lines E. coli Streptomyces L. lactis Mammalian cells Transgenic Animals Insect cells Transgenic Plants Sheep Cow Mice Plants 8

9 Choice of host Considerations Amount: industry large amounts; basic research much less Purity: industry lower OK; drugs - very high needed Biological integrity: post-translational modifications Toxicity: drugs and food non-pathogenic, non-toxic GRAS: Generally Recognized As Safe according to FDA (U.S. Food and Drug Administration) For e.g. food additives GRAS organisms: Yeast e.g. Saccharomyces cervisiae Bacteria e.g. Bacillus subtilis Fungi e.g. Aspergillus 9

10 Expression host comparison - Source Mammalian Insect Yeast E. coli Protein folding and purification optimal Low Poor Poor Post-translational modification yes Low Low No Authenticity and Bioactivity Native & Active Poor Poor Very Poor Time and Cost High High Low Low 10

11 Expression host comparison - Source Expression host Publications for host Escherichia coli Spodoptera frugiperda 1234 Trichoplusia ni 363 Pichia pastoris 344 Cricetulus griseus (CHO) 267 Based on the wwpdb data set as of July 29,

12 Microorganisms are common hosts - Why? yeast fungi bacteria Cultured in large quantities in short time Abundant and constant supply of desired proteins Proteins usually more stable than from plant/animal Genetic manipulation usually easy Proteins can be directed to cytoplasm, membrane, secreted 12

13 Heterologous expression in E. coli Gram negative bacteria Advantages Genetically well characterized Many cloning vectors Controlled gene expression Easy and inexpensive to grow Disadvantages Inclusion bodies may result Endotoxins may be an issue No (or different) posttranslational modifications High yields (up to 50% of total) Secretion possible Protease deficient strains Success stories: Many!!! e.g. insulin - unlimited supply 13

14 Heterologous expression in yeast (I) Saccharomyces cervisiae Advantages Genetically well-characterized Easy to grow Naturally occuring plasmids - vectors Post-translational modifications No endotoxins GRAS Disadvantages Gene expression less easily controlled Glycosylation pattern different from mammals Many proteases 14

15 Heterologous expression in yeast (II) Pichia pastoris Advantages compared to S. cervisiae Much higher ( fold) expression up to grams/l! Large number of correctly modified proteins - may not be hyperglycosylated Success story Hepatitis B virus surface antigen (HbsAg) - assembles into the same multi-subunit complex that occurs in infected humans. 240 liters gives 9x10 6 doses of vaccine. 15

16 Heterologous expression in insect cells Baculovirus in Autographa californica (moth) Advantages Protein processing and modifications Safe - only few hosts High levels of expression - up to 50% of total protein Shuttle vectors (bacmids) Disadvantages Glycosylation mechanism poorly understood Product not always functional Relatively slow growth Contamination is easy More than 500 heterologous proteins produced Over 95% with the correct post-translational modifications 16

17 Heterologous expression in mammalian cells e.g. Chinese hamster ovary (CHO) and baby hamster kidney (BHK) Advantages Same modification/activity Expression vectors available Large scale cultures Have been used to produce monoclonal antibodies, vaccines, interferons etc Disadvantages Can be difficult/expensive to grow Slow growth Can be genetically unstable Low productivity Contamination 17

18 Heterologous expression in plants Advantages Easy to grow Stable integration Processing, assembly similar to animals Disadvantages No constant supply - seasonal growth Protein often denatured during purification Different glycosylation - immunogenic? Low transformation efficiency Not commonly used as bioreactors - microorganisms overall are cheaper/more convenient 18

19 Making transgenic plants Transgenic: organism carrying an alien gene Certain bacteria are plant parasites (e.g. Agrobacterium tumefaciens) A. tumefaciens carries a conjugative plasmid Plasmid DNA is transferred into plant cells Any DNA can be transferred by conjugation This DNA is integrated into plant s chromosomes Wounds infected Chromosome T-DNA Bacteria Ti-plasmid Only T-DNA segment transferred to plant cells T-DNA normally responsible for tumor growth Crown gall tumour Foreign genes can be cloned into T-DNA Thus, foreign genes are integrated into plant DNA Creates a transgenic plant 19

20 Heterologous expression in animals - transgenic animals (I) mice, goats, sheep, cows, pigs Advantages Milk is renewable No side effects on animal Post-translational modifications similar to humans Disadvantages Ethical considerations Time-consuming Technically difficult Purification straightforward 20

21 Heterologous expression in animals - transgenic animals (II) 21

22 Cell-free protein expression Useful for relatively small quantities of protein: 1. E. coli, wheat germ, insect and mammalian systems are commercially available 2. Circumvent issues of cellular toxicity 3. Can readily incorporate non-amino acids 4. Can use PCR products as template 5. Still too expensive, but getting cheaper 22

23 Production of a protein in a heterologous system: always a risk you will run into trouble One can run into problems at the level of: 1. Expression (more protein is not always better protein) 2. Folding (E. coli can produce inclusion bodies) 3. Other properties of the protein produced 23

24 Some explanations for poor expression in E. coli Expression of heterologous genes, e.g. human genes in E. coli, common problems due to, e.g.: Clusters of bad (in the host) codon usage Inhibitory sequences Strong RNA secondary structural elements Short lifetime of expressed protein 24

25 Possible explanations: bad codon usage 1. The presence of a XGG among the first 6 codons. 2. Bad combination of codons close to the start codon ATG. Optimal combinations are Kozak consensus ATG GCT A/T richness of the region (12 nts) following the initiation codon plays a significant role in E. coli gene expression. 3. Bad codon usage in clusters and in combination with an alternative translation initiation sequence is especially problematic. 4. Clusters of bad codon usage will result in too many arrests of the ribosome, that is, it may fall off the gene. Experiments to try: Use cell lines with extra trnas that can recognise the problematic codons (e.g. Rosetta). Exchange problematic sequences for synthetic DNA with optimal codons. 25

26 Possible explanations: inhibitory sequences A-rich inhibitory sequences have been identified for mammalian cells. (The situation in E. coli is not yet clear.) Clusters of C s and G s may lead to strong base pairing. Consider: Identify possible problematic sequences. Exchange for synthetic sequences where they are changed. Try different lengths of constructs, extending from N- terminus, see where it stops. 26

27 Possible explanations: Strong RNA secondary structure elements Strong RNA secondary structural elements (e.g. hairpin loop structures) can inhibit transcription. Experiments to try: Identify using prediction software. Exchange for synthetic sequences. 27

28 Short life-time of the expressed product: The N-terminal rule 28

29 Folding of a protein in a heterologous system The folding process is complicated, and happening in the presence of high concentrations of other proteins. (Protein concentration in E. coli is mg/ml, i.e. 5-8 mm!) Might need assistance of factors such as: 1. Metals 2. Co-factors 3. A different cellular location (periplasm?) 4. Disulfide-forming enzymes 5. Chaperones, which help with hydrophobic sequences 29

30 Possible problems: toxic The expressed product could be highly toxic to the bacterial host cell. If the expression system is not turned off completely during cloning and cell growth, this may cause selection for damaged DNA. Or kill the cells when the gene is induced. Experiments to try: Use an expression system that is tightly controlled. Grow cells to relatively high density before inducing. Never allow cell cultures to reach stationary phase of growth. Perform ligation into the expression vector in a nondirectional way. 50% of the of clones should have the insert in the opposite direction. Any deviation from this indicates toxic properties. 30

31 Take-home messages No expression system meets all needs; the final requirements for products will govern the initial choice of cloning system, and what you do afterwards! Be prepared to experiment! 31