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: Genetic engineering in budding yeast
Budding yeast lends itself well to genetic engineering as it is functionally haploid (at least lab strains are), and has very efficient homologous recombination. Novel sequences can be introduced between two short regions of homology, and the rate of unwanted rearrangements is low.
A genetic modification cassette takes this form:
Left flank New sequence Right flank
The Left and Right flanks are between 45 and a few hundred base pairs long and define the insertion points. The New sequence is inserted between the flanks, and whatever was originally there is removed.
Because the flanks can be as little as 45bp, they can be added as part of a primer in a PCR reaction, so to create the above cassette, PCR amplify the New sequence region with the flanks attached to the primers (this makes long oligos of ~65bp, but this does not effect the PCR). The un-purified PCR product may be directly transformed into yeast using the TRAFO protocol.
After transformation, the insertion is tested by PCR. Appropriate PCR primers for this are described with each example below.
A wide variety of plasmids have been created containing sequence cassettes that can be amplified and inserted into the genome, and the most commonly used vectors (at least in our lab) are the pFA6a series.
The pFA6a plasmids
These were designed ADDIN EN.CITE Longtine19981007(Longtine et al., 1998)100717Longtine, M. S.McKenzie, A., 3rdDemarini, D. J.Shah, N. G.Wach, A.Brachat, A.Philippsen, P.Pringle, J. R.Department of Biology, University of North Carolina, Chapel Hill 27599-3280, USA. mlunc@isis.unc.eduAdditional modules for versatile and economical PCR-based gene deletion and modification in Saccharomyces cerevisiaeYeastYeast953-611410DNA PrimersGene DeletionGene ExpressionGenetic VectorsGreen Fluorescent ProteinsLuminescent ProteinsMolecular Biology/*methods*Plasmids*Polymerase Chain ReactionRecombinant Fusion ProteinsReproducibility of ResultsSaccharomyces cerevisiae/*geneticsTransformation, Genetic1998Jul9717241http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9717241 (Longtine et al., 1998) to form a library of different markers and tagging constructs that can all be amplified with the same set of primers.
The original pFA6a plasmids contained three selectable markers: KAN, HIS3, and TRP1, and for each of these a variety of plasmids was constructed for deletion, tagging or promoter fusions. We have obtained or made additional markers for deletion including NAT, HYG, URA3, LEU2 and MET25 at time of writing, and these have then been cloned into tagging constructs as required sub-cloning markers is easy as there are lots of unique restriction sites in the backbone. Similarly, additional tags and promoter fusions plasmids have been and continue to be made.
Note that the original primers recommended in Longtine et al do not work very well, so modifications are recommended (see below).
Some examples of genetic manipulations, involving your favourite gene YFG1:
Deletion
For deletion of any region, in this case your favourite gene (YFG1):
The deletion cassette contains a marker gene (here Kan, for G418 resistance), with a promotor and terminator. The whole cassette is called KanMX6.
This cassette is amplified with oligos F1 and R1, fused to 45bp sequences homologous to the flanks around YFG1. A single 40ul PCR with Takara LA is normally used, and the is transformed unpurified into yeast using the TRAFO protocol (after 3ul are run on a gel to confirm amplification).
F1: CGGATCCCCGGGTTAATTAAG
R1: GAATTCGAGCTCGTTTAAAC
Confirmation by PCR
Not all colonies containing the marker have the construct in the correct place, so single colonies are re-streaked then tested by colony PCR.
Two PCR reactions can be used to confirm that the cassette has integrated in the correct place. Oligos C and D only amplify a product in the parental strain, Oligos MX 4-6 F and D only amplify a product in the correct deletion strain. NOTE WELL: oligo MX 4-6 F only works for some markers, see descriptions of individual markers below for the correct primer.
In the above example, as long as the products of C to D and MX4-6 F to D are different sizes (by at least 100bp), it is possible to test for both possibilities in a single PCR reaction. Simply use all three oligos (C, D and MX4-6 F) in a single PCR reaction. This is very useful as the PCR always gives a product whether the strain is positive or negative (unless the PCR fails).
C- terminal tagging
Very similar to deletion, but in this case the 5 oligo consists of the 45bp upstream of the stop codon fused to oligo F2 (above). Note that it is important that the reading frame is maintained into the tag, and that the original stop codon is removed. The reading frame is indicated by clusters of three nucleotides in the F2 oligo sequence. The same strategy for confirming the inserts used for deletions is appropriate here, and it is wise to further check successful tagging using a western blot for the tag.
F2 for tagging with 3HA, 13Myc or GFP:
CGG ATC CCC GGG TTA ATT AAC (3 base clusters show reading frame)
F2 for tagging with GST:
CGG ATC CCC GGG TTA ATT AAT ATG (clusters show reading frame)
R1: GAATTCGAGCTCGTTTAAAC
Promotor fusion
Promotor fusions are usually used for essential genes that cannot be deleted. The most commonly used promotor is that of GAL1, which expresses highly in galactose medium, and at very low levels in glucose.
Most promotor fusions include an N terminal tag that can be used to follow the depletion of the protein by western blot. Fuse 45bp from ~100bp 5 of the start codon to primer F4, and the complement of the 45bp downstream of the start codon (including the start codon) to R5 (or appropriate R primer for the tag, be careful to maintain the open reading frame). These primers are described in ADDIN EN.CITE Longtine19981007(Longtine et al., 1998)100717Longtine, M. S.McKenzie, A., 3rdDemarini, D. J.Shah, N. G.Wach, A.Brachat, A.Philippsen, P.Pringle, J. R.Department of Biology, University of North Carolina, Chapel Hill 27599-3280, USA. mlunc@isis.unc.eduAdditional modules for versatile and economical PCR-based gene deletion and modification in Saccharomyces cerevisiaeYeastYeast953-611410DNA PrimersGene DeletionGene ExpressionGenetic VectorsGreen Fluorescent ProteinsLuminescent ProteinsMolecular Biology/*methods*Plasmids*Polymerase Chain ReactionRecombinant Fusion ProteinsReproducibility of ResultsSaccharomyces cerevisiae/*geneticsTransformation, Genetic1998Jul9717241http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9717241 (Longtine et al., 1998).
Check the insertion using oligos A, B and MX4-6 F. Note that in the pFA6a PGAL1 vectors, the marker cassettes are reversed compared to the C-terminal tagging constructs.
Problems with the pFA6a plasmids
Close examination of the pFA6a plasmids will reveal similarities; plasmids containing His, Kan, Nat and Hyg share the same promoters and terminators. Therefore, inserting more than one pFA6a based mutation in a strain is more difficult not only can recombination occur at the desired site, it can occur between the old and the new cassette, resulting in a marker swap. Therefore, on the second round of transformation select for both markers to avoid marker swapped transformants. The second transformation will also be less efficient.
Other pFA6a plasmids do not have this problem since they have different promoters and terminators (although the same F1 and R1 primers work to amplify the cassette). There are many variants containing the TRP1 gene, although this marker cannot be used in the lab standard BY4741 strain. We have pFA6a plasmids containing URA3, LEU2 and MET25 markers which can be used instead and do not have homologous sequence.
Individual markers
KanMX6
Resistance to G418 (often called Kan)
Can marker swap with NatMX6, HygMX6, HisMX6
Plate transformations overnight on YPD before replica plating on plates containing G418
Note well: G418 is NOT the same as kanamycin (used for bacteria)
Use at 200ug/ml in YPD or 400ug/ml in synthetic media
G418 plates (often labelled Kan) last for many years at 4
Test oligos:
MX4-6F: CCTCGACATCATCTGCCCAGAT
MX4-6R: TGCAGCGAGGAGCCGTAAT
NatMX6
Resistance to Nourseothricin (NAT)
Can marker swap with KanMX6, HygMX6, HisMX6
Plate transformations overnight on YPD before replica plating on plates containing Nourseothricin
Nourseothricin is purchased from Werner bioagents
Use at 100ug/ml in YPD or 200ug/ml in synthetic media
NAT plates last for many years at 4
Test oligos:
MX4-6F: CCTCGACATCATCTGCCCAGAT
MX4-6R: TGCAGCGAGGAGCCGTAAT
HygMX6 (or HphMX6)
Resistance to Hygromycin (HYG)
Can marker swap with KanMX6, NatMX6, HisMX6
Plate transformations overnight on YPD before replica plating on plates containing Hygromycin
Hygromycin is expensive and very toxic, so use only if Kan and Nat are not an option
Use at 450ug/ml in YPD or 900ug/ml in synthetic media
HYG plates will last 6 months to a year at 4
Test oligos:
MX4-6F: CCTCGACATCATCTGCCCAGAT
MX4-6R: TGCAGCGAGGAGCCGTAAT
HIS3MX6
Allows growth on synthetic HIS plates
Can marker swap with KanMX6, NatMX6, HygMX6
Plate transformations overnight on -His and replica onto a second His plate the next day (in theory not necessary but reduces background)
Auxotrophic markers modify the gene expression profile and metabolism. For genome wide experiments eg: RNA-seq, it is wise to make ensure all strains compared have the same auxotrophic markers
-HIS plates will last years at 4
Test oligos:
MX4-6F: CCTCGACATCATCTGCCCAGAT
MX4-6R: TGCAGCGAGGAGCCGTAAT
TRP1
Allows growth on synthetic TRP plates
Does not marker swap, but can insert at the endogenous TRP1 locus in strains like W303 with trp1 point mutations. Some S288C derived strains (eg: MEP) have TRP1 deletions and work well, but BY4741 is TRP1 wild-type.
Plate transformations directly on -TRP
Auxotrophic markers modify the gene expression profile and metabolism. For genome wide experiments eg: RNA-seq, it is wise to make ensure all strains compared have the same auxotrophic markers
-TRP plates will last years at 4
Test oligo:
TRP1 F1 (JH571): GGAGACAAATGGTGTAAAAGACTCT
URA3
Allows growth on synthetic URA plates
Does not marker swap, but can insert at the endogenous URA3 locus in strains like W303 with ura3 point mutations. S288C-derived strains such as BY4741 and MEP are URA3 deleted so this is not a problem
Plate transformations directly on -URA
Auxotrophic markers modify the gene expression profile and metabolism. For genome wide experiments eg: RNA-seq, it is wise to make ensure all strains compared have the same auxotrophic markers
-URA plates will last years at 4
Test oligo:
URA3 F12 (CC4): GCTGGGAAGCATATTTGAGAAG
klLEU2
Allows growth on synthetic LEU plates
Derived from k. lactis so works in strains with leu2 point mutations
Plate transformations directly on -LEU
Auxotrophic markers modify the gene expression profile and metabolism. For genome wide experiments eg: RNA-seq, it is wise to make ensure all strains compared have the same auxotrophic markers
-LEU plates will last years at 4
Test oligo:
KL LEU2 F1 (JH432): TGGTGATACAAGTTTCAACAATG
MET25
Allows growth on synthetic MET plates
Complements met25, met17, met15 deletions (all are same gene)
Plate transformations directly on MET
Works as selective marker but does not completely complement
Auxotrophic markers modify the gene expression profile and metabolism. For genome wide experiments eg: RNA-seq, it is wise to make ensure all strains compared have the same auxotrophic markers
-MET plates will last years at 4
Test oligo:
MET25 F2 (JH399): CCTCTAACCTCGATGACATCTTC
Non-pFA6a plasmids
There are a lot of useful plasmids in this set:
Janke et al A versatile toolbox for PCR-based tagging of yeast genes: new fluorescent proteins, more markers and promoter substitution cassettes, Yeast 2004; 21: 947962
For tagging with a tandem affinity purification tag (TAP-tag), amplify from pRS1539 (URA3 marker) or pRS1479 (TRP1 marker) using the following primers fused to homologous regions:
F TCC ATG GAA AAG AGA AG (note the reading frame)
R TACGACTCACTATAGGG
Working with autonomous plasmids
Yeast can carry autonomously replicating plasmids, either single copy or high copy. Plasmids are unstable and strains carrying plasmids must be grown on plates and in liquid media that selects for the auxotrophic marker on the plasmid.
Single copy plasmids have a centromere (CEN) and a replication origin (ARS) along with a selectable marker. The pRS31X and 41X series are commonly used, X varies depending on the selectable marker (URA3, HIS3, TRP1, MET25, LYS2, ADE2, LEU2 are available)
Multi-copy plasmids have a 2 micron (2u or 2mu) element from the natural yeast parasitic plasmid 2 micron. They are maintained at tens of copies for cell. The pRS42X series are commonly used.
Plasmid shuffle
A common trick cells are transformed with a plasmid carrying a URA3 marker, then transformed with another plasmid carrying a different marker (eg: HIS3) and plated on plates that select for the new plasmid and also FOA to select against the old plasmid.
Curing or removing endogenous 2u plasmids
All lab strains (that I have encountered) carry endogenous 2u plasmids at high copy, which are normally harmless but can have effects when looking at eg: circular DNA.
This protocol removes these:
Transform with pBIS GAL-kFLP-URA (JH357 or Addgene 49460), plate on URA
Restreak single colony on GALACTOSE URA
Restreak single colony on GALACTOSE URA
Restreak single colony on FOA
Check by PCR for 2u using PCR primers JH1302-1305 (0.9kb product in parental but not in cured strains)
References
ADDIN EN.REFLIST Longtine, M.S., McKenzie, A., 3rd, Demarini, D.J., Shah, N.G., Wach, A., Brachat, A., Philippsen, P., and Pringle, J.R. (1998). Additional modules for versatile and economical PCR-based gene deletion and modification in Saccharomyces cerevisiae. Yeast 14, 953-961.
Rigaut, G., Shevchenko, A., Rutz, B., Wilm, M., Mann, M. and Seraphin, B (1999). A generic protein purification method for protein complex characterization and proteome exploration. Nat Biotechnol 17, 1030-1032.
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