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I was interested in obtaining a yeast strain without the enzyme farnesyltransferase (Which catalyses conversion of FPP to Squalene). The Euroscraf database has thousands of yeast strains with individual genes deleted but when I search for "farnesyltransferase" I get a couple of hits that I am not being able to interpret.

Here's the link: http://www.euroscarf.de/search.php?search=farnesyltransferase&project=

What are all these different strains? In particular how does one interpret notation like which seems to be describing a particular strain:

BY4743; MATa/MATα; ura3Δ0/ura3Δ0; leu2Δ0/leu2Δ0; his3Δ1/his3Δ1; met15Δ0/MET15; LYS2/lys2Δ0; YKL019w/YKL019w::kanMX4
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    $\begingroup$ Seems like you should have searched for erg9 instead... $\endgroup$ – MattDMo Apr 4 '16 at 19:45
  • $\begingroup$ @MattDMo Ah! That explains it. Thanks! So what's the difference between these two strains that it throws up SC2489 and Y22884: euroscarf.de/search.php?search=ERG9&project= Are they both Squalene blocked strains? I still cannot interpret the "Genotype" goblydygook that the database entry has....... $\endgroup$ – curious_cat Apr 4 '16 at 19:56
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    $\begingroup$ Well, the genotype is simply describing what variants of certain genes the strain has - what mating type it is (MATa/MATα), what nutrients it requires in the medium and what it can synthesize for itself, and the type of mutation that occurred (or was engineered) to make the strain deficient for the gene you are interested in. You'll need to talk to someone much more familiar with yeast genetics than me to determine exactly what each notation means - I'm just remembering all this stuff from grad school 13 or 14 years ago... $\endgroup$ – MattDMo Apr 4 '16 at 20:05
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Yeast strains have two mating types MATa (since it secretes a pheromone named 'a factor'), MATα (secretes pheromone 'α factor'). Both MATa and MATα strains are haploid and when they fuse together they form diploid zygote. A haploid yeast has only one set of genes and utilize chemicals like histidine and tryptophan (amino acids) and adenine (part of DNA, ATP and other molecules) for growing. Yeast strains mutant with any of genes to make these chemicals they will not grow unless they can get these chemicals from their food (yeast media) or allowed to mate with strain having normal genes.

Interpreting the strain notation:

BY4743; MATa/MATα; ura3Δ0/ura3Δ0; leu2Δ0/leu2Δ0; his3Δ1/his3Δ1; Met15Δ0/MET15; LYS2/lys2Δ0; YKL019w/YKL019w::kanMX4

Strain name: BY4743 Genotype: MATa/MATα; ura3Δ0/ura3Δ0; leu2Δ0/leu2Δ0; his3Δ1/his3Δ1; Met15Δ0/MET15; LYS2/lys2Δ0; YKL019w/YKL019w::kanMX4

To understand clearly, you can dissect the genotype in individual strains

BY4743;MATa;ura3Δ0;leu2Δ0;his3Δ1;met15Δ0;LYS2;YKL019w/YKL019w

BY4743;MATα;ura3Δ0;leu2Δ0;his3Δ1;MET15;lys2Δ0;kanMX4

Yeast genetics nomenclature:

  1. Normal or wildtype genes are written in capitalized form - MET15 in MATα

  2. Mutated genes are symbolized with small letter and Δ - ura3Δ0

  3. ura3Δ0/ura3Δ0 - allelic mutation: mutation in same genes of both strains (MATa/MATα) - They are two mutant alleles in the same gene locus. Both alleles of same gene are knocked out, so even both strains mate, they need external source of uracil in media to grow. Defect in one strain is NOT complemented by the other.

  4. Met15Δ0/MET15 & LYS2/lys2Δ0 - Non-allelic mutation: Defect in one strain is complemented by the other. MATa has Met15Δ0 (mutation in methionine gene) and MATα has wildtype MET15 gene, capable of met synthesis. Complementation works here.

  5. YKL019w/YKL019w::kanMX4 - Critical aspect of yeast strain in functional complementation assays. In all commercially available yeast strains, one gene will be double knocked out (both alleles of same gene) and replaced with an auxotrophic markers like antibiotics - tetracycline, kanamycin, ampicillin - for selecting the diploid cells after mating two strains. It is similar to plating Kanamycin mixed LB media to pick E.coli colonies harboring Kanamycin resistance vector in it.

The gene that is replaced is the gene of interest, i.e. if I am looking to study role of putative PGPS in Plasmodium falciparum, I get yeast strain knocked out with yeast PGPS (pgsΔ). When I do complementation test, I provide external DNA template cloned with Plasmodium falciparum's PGPS to check whether it complements in yeast genome and yeast grows - gene essentiality study.

I am not sure of the gene YKL019w/YKL019w, but it implies that wildtype of YKL019 is replaced with Kanamycin - kanMX4.

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  • $\begingroup$ Wow! That was an amazing answer. Thank you very much. I am still trying to digest all of it! $\endgroup$ – curious_cat Apr 6 '16 at 16:36

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