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Yeast strains - description of mutations :)

yeast strains mutations mating cells

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#1 freud

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Posted 06 February 2015 - 08:18 AM

Hello there!

I'm doing some homework about 6 yeast strains, that we're supposed to work with on my university in a couple of weeks.

I'd like to be well prepared, but i haven't been able to figure out what the different mutations in these strains mean for their abilities to grow on different mediums etc..

Here they are:

1. MATa ade2-n(deltaNdel) LYS2 leu2-3,112 trp1-1 his3::natMX4 met22:KIURA3

 

2. MATalpha ade2-1 leu2,3-112 ura3-1 trp1-1 LYS2 srs2::HIS3 rad52-R70A

 

3. MATalpha ade2-1 his3-11,15 leu2-? LYS2 ura3-1 trp1-1 rad52-C180A srs2::HIS3

 

4. MATα ade2-ISceI lys2::GAL-ISceI trp1-1 his3::hphMX4 RAD5

 

5. MATa ade2-1 his3-11,15 leu2-3,112 lys2Δ TRP1 rad52-R70A srs2::HIS3

 

6. MATa ade2-1 his3-11,15 leu2-3,112 LYS trp1-1 rad52-C180A srs2::HIS3

 

I know that MATa and MATalpha are the type of mating cell. Also, i know that rad52-R70A and rad52-C180A are mutations in the Rad52 gene, meaning that some function of Rad52 will be affected.

However; the rest of the nomenclature confuses me and i'm not sure what it means. Could someone please clarify? :-)

Thanks a lot!



#2 pito

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Posted 20 February 2015 - 01:54 PM

Hello there!

I'm doing some homework about 6 yeast strains, that we're supposed to work with on my university in a couple of weeks.

I'd like to be well prepared, but i haven't been able to figure out what the different mutations in these strains mean for their abilities to grow on different mediums etc..

Here they are:

1. MATa ade2-n(deltaNdel) LYS2 leu2-3,112 trp1-1 his3::natMX4 met22:KIURA3

 

2. MATalpha ade2-1 leu2,3-112 ura3-1 trp1-1 LYS2 srs2::HIS3 rad52-R70A

 

3. MATalpha ade2-1 his3-11,15 leu2-? LYS2 ura3-1 trp1-1 rad52-C180A srs2::HIS3

 

4. MATα ade2-ISceI lys2::GAL-ISceI trp1-1 his3::hphMX4 RAD5

 

5. MATa ade2-1 his3-11,15 leu2-3,112 lys2Δ TRP1 rad52-R70A srs2::HIS3

 

6. MATa ade2-1 his3-11,15 leu2-3,112 LYS trp1-1 rad52-C180A srs2::HIS3

 

I know that MATa and MATalpha are the type of mating cell. Also, i know that rad52-R70A and rad52-C180A are mutations in the Rad52 gene, meaning that some function of Rad52 will be affected.

However; the rest of the nomenclature confuses me and i'm not sure what it means. Could someone please clarify? :-)

Thanks a lot!

What is it exactly that you need to know?

 

For example: in some strains you can already see that the his3 gene has been mutated by putting another gene in it.. so the strain is auxotrophic for histidine...


If you don't know it, then ask it! Better to ask and look foolish to some than not ask and stay stupid.


#3 freud

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Posted 24 February 2015 - 07:05 AM

 

!

 

What is it exactly that you need to know?

 

For example: in some strains you can already see that the his3 gene has been mutated by putting another gene in it.. so the strain is auxotrophic for histidine...

 

Sorry for not responding - i had given up on the thread! biggrin.png

What i need is basically an idea of what the different "signs/nomenclature" mean.
Like, ::  and : and some kind of overview on how mutations are generally written down - general rules/guidelines/something. It's like it's written in a language that i don't understand.

Examples:

It's difficult to tell (for me) whether or not the mutation "srs2::HIS3" means that the srs2-gene has ben inserted into HIS3, or that the HIS3 gene has  been inserted into the srs2 gene for example.
I know Delta means the gene has been deleted - so i'm guessing "ade2-n(deltaNdel)" means a deletion of the ade2-n gene, but i'm not sure.
LYS2 means... what? A mutation in the LYS-biopathway, or is it just to signify WT LYS? Would LYS2 make a strain auxotrophic for lysine?

Why sometimes the capital letters and sometimes not? 
Like "LYS2"       vs.    "lys2::GAL-IsceI"    - both include lys2, but differ in the way it's written. And i'm not sure what the "lys2::GAL-IsceI" even means, too. :D


Anyhow, it's all just terribly confusing to me biggrin.png

Thanks in advance for your help.



 


Edited by freud, 24 February 2015 - 07:07 AM.


#4 pito

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Posted 25 February 2015 - 05:20 AM

 

 

!

 

What is it exactly that you need to know?

 

For example: in some strains you can already see that the his3 gene has been mutated by putting another gene in it.. so the strain is auxotrophic for histidine...

 

Sorry for not responding - i had given up on the thread! biggrin.png

What i need is basically an idea of what the different "signs/nomenclature" mean.
Like, ::  and : and some kind of overview on how mutations are generally written down - general rules/guidelines/something. It's like it's written in a language that i don't understand.

Examples:

It's difficult to tell (for me) whether or not the mutation "srs2::HIS3" means that the srs2-gene has ben inserted into HIS3, or that the HIS3 gene has  been inserted into the srs2 gene for example.
I know Delta means the gene has been deleted - so i'm guessing "ade2-n(deltaNdel)" means a deletion of the ade2-n gene, but i'm not sure.
LYS2 means... what? A mutation in the LYS-biopathway, or is it just to signify WT LYS? Would LYS2 make a strain auxotrophic for lysine?

Why sometimes the capital letters and sometimes not? 
Like "LYS2"       vs.    "lys2::GAL-IsceI"    - both include lys2, but differ in the way it's written. And i'm not sure what the "lys2::GAL-IsceI" even means, too. biggrin.png


Anyhow, it's all just terribly confusing to me biggrin.png

Thanks in advance for your help.



 

 

 

This might already help (I have not a lot of time now): 

(most important link is at at the bottom btw, in my explanation)

 

http://en.wikipedia....ne_nomenclature

 

http://www.yeastgeno..._cerevisiae.pdf

 

http://www.yeastgeno...ure-conventions

 

http://onlinelibrary...28cdfa01fb01adf

 

http://openwetware.o...st_Nomenclature

 

http://faculty.bsc.e...anson_week2.pdf

 

https://www.unifr.ch...astGenetics.pdf

 

 

Just check for the parts dealing with nomenclature.

 

 

 

To answer your questions quickly: the :: means that the gene in front of the :: has been partly replaced by the gene behind the ::

 

so X::Y means that Y was inserted in gene X

 

delta does indeed mean deleted.

 

LYS2 just means its there and depending on how its written its the wild type or not or... (see link below)

 

Check for sure this : https://www.unifr.ch...astGenetics.pdf

download this book ! Its a very good guide! and check the part on the nomenclature, it will already help a lot!!!

(together with this: http://wiki.yeastgen...y_used_strains)


If you don't know it, then ask it! Better to ask and look foolish to some than not ask and stay stupid.






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