What do they mean

[Dotte]

Hallo all,

 

I am checking a website (to check protein-protein interactions) and I have a problem understand what they mean with "genetic" vs "physical "interactions.

 

See, for example, http://www.yeastgenome.org/locus/S000002706/interaction

You can see a list with interaction and an interaction overview.

But I have troubles understanding what they mean with "physical" and "genetic" interactions.

The physical ones, I get: protein protein interactions in the cell as they are.

But the "genetic" one, I am not 100% sure I get it.

They explain it like this:

(http://www.yeastgenome.org/help/function-help/interactions)

Physical interactions are defined as the direct physical binding of two proteins, or co-existence in a stable complex, whereas genetic interactions are interactions between two or more mutants. For more details about BioGRID's curation process, see here.

 

So what does this mean? A genetic interaction is an interaction proven after mutating one gene (protein) this first protein has another (stranger/other) effect after they changed a second gene as well.

So by mutating a second gene they notice that the first one is also acting different compared to when its not mutated or mutated alone.

Is this correct or ?

 

 

Anyone that can elaborate on this?

 

Thanks in advance

Edited October 9, 2015 by Dotte

[CharonY]

From what they wrote it appears that they compare single mutants with double mutants in order to elucidate interactions.

[Dotte]

From what they wrote it appears that they compare single mutants with double mutants in order to elucidate interactions.

But what does that mean?

[CharonY]

Well, I am not sure what parameters they measure, but as an example, you got your mutant A and measure some parameter (could be expression, could be something else). Then, they look at mutant B and do the same. Finally they look at mutants with deletion in A and B. Say, they look at expression. If you delete A, B goes up, if they delete B A goes up (and in that case AB would just be a negative control).

 

Looking at their definitions they would consider that a genetic interaction (could be direct or indirect via different regulators). The same could be done by looking at other parameters, such as a different target gene could be used.

They use a very broad definition for genetic interaction (as opposed to physical ones).

[Dotte]

Well, I am not sure what parameters they measure, but as an example, you got your mutant A and measure some parameter (could be expression, could be something else). Then, they look at mutant B and do the same. Finally they look at mutants with deletion in A and B. Say, they look at expression. If you delete A, B goes up, if they delete B A goes up (and in that case AB would just be a negative control).

 

Looking at their definitions they would consider that a genetic interaction (could be direct or indirect via different regulators). The same could be done by looking at other parameters, such as a different target gene could be used.

They use a very broad definition for genetic interaction (as opposed to physical ones).

Ah yes, I see what you mean.

 

It does mean that they have an effect on eachother, but it does not mean (necessary) that the proteins interact wich eachother (physically)?

Edited October 9, 2015 by Dotte

[CharonY]

From what I saw on the website this seems to be the case. Part of the description makes me think that they do not even need to affect each other, They only say that there are interactions on the level of mutants. For example, mutation in either A or B has little effect, but A/B at the same time is lethal. That would indicate that they have some common function, but as long as one is active the organism survives.

As I said, it is a very broad definition essentially only meaning that on one level or another, the functions of gene A and B have some sort of intersection. Thus, A/B mutations will look different than mutations in A and B alone (in my example).

 

The issue I have with that point of view is that if we take a global perspective (say, genome or proteome-wide) pretty much everything intersects at some level with something else. There are very few (if any) pathways that are so specialized and isolated that there are no effects whatsoever. More likely it is just not observed under a given test condition (e.g. in laboratory culture).

[Dotte]

From what I saw on the website this seems to be the case. Part of the description makes me think that they do not even need to affect each other, They only say that there are interactions on the level of mutants. For example, mutation in either A or B has little effect, but A/B at the same time is lethal. That would indicate that they have some common function, but as long as one is active the organism survives.

As I said, it is a very broad definition essentially only meaning that on one level or another, the functions of gene A and B have some sort of intersection. Thus, A/B mutations will look different than mutations in A and B alone (in my example).

 

The issue I have with that point of view is that if we take a global perspective (say, genome or proteome-wide) pretty much everything intersects at some level with something else. There are very few (if any) pathways that are so specialized and isolated that there are no effects whatsoever. More likely it is just not observed under a given test condition (e.g. in laboratory culture).

Well indeed.

 

Its a very broad view and I find it weird they add them to the list if "interactions". Its a bit confusing and not very specific.