Gene Limit

[Butters]

Hi. I was just wondering if anybody knew, is there some kind of limit on the possible number of genes that can make up an organism.

 

My understanding is poor, but there are about 25,000 or so making up the human genome I think? Is there any kind of physical reason that there would be a limit on this for other organisms? And if there is an upper limit, what is it?

 

Thanks.

[cypress]

Biological processes in general are functionally efficient. Controls that regulate gene expression tend to switch of expression of non-functional genes and this imposes an artificial and somewhat arbitrary upper limit on the quantity of expressed genes in organisms.

[CharonY]

This is not the question as far as I understood (and is also somewhat inaccurate). The highest number of genes known so far have been recorded in a protist, if I recall correctly, which has more than double the amount of genes than humans.

 

There are certain limitations to genome size, but it is not known where the limit is. For small organisms genome size is a limiting factor for growth speed. In environments where it is crucial to proliferate quickly there tends to be a selection for smaller genomes. On the other hand, more metabolic pathways allow utilization of resources not accessible to others. Good examples are parasites that have access to a lot of resources from their host and therefore often have reduced genomes. One question is of course what functions are really needed. If, for instance, an organisms accumulates a lot genes (for whatever events in their history) but only really utilizes, say, half of it, it means that for the other half there is no real selective pressure to maintain their function. Over time these genes are more likely to accumulate mutations, for instance than the other regions. This can lead to the eventual loss of that particular locus (I refer to it as such as it is not a functional gene anymore). However it may still contribute to e.g. the regulation of the whole genome, just by virtue of being there (i.e. as a spacer between active genes, allowing the DNA to bend in a certain way, etc.). A consequence of that is while the gene size is reduced over time (as the genes eventually lose their functionality) the genome size does not by much, unless there is a strong selective force to maintain small genomes (which is more prevalent in single celled organisms).

 

This is only a very simplified explanation, though.

[Butters]

Okay, thanks for the replies. I clearly have very limited knowledge in this area. I guess what I'm asking is, if we were to develop the technology to make an organism artificially, would there be any physical limit to how mlarge we could make the genome? Whether it is efficient or not, would there be a size where an organism simply could not physically exist?

[Moontanman]

Biological processes in general are functionally efficient. Controls that regulate gene expression tend to switch of expression of non-functional genes and this imposes an artificial and somewhat arbitrary upper limit on the quantity of expressed genes in organisms.

 

 

What would this upper limit be? i see no reason to think there is an arbitrary upper on the genome of any organism.

 

http://en.wikipedia.org/wiki/Genome

[Mr Skeptic]

I think there would be some limit to genome size, but not any arbitrary limit. Eventually it would become too much to handle, but before that such an organism would be straining to live and reproduce with such a large genome. However, I don't think any organism is even close to that limit.

[cypress]

What would this upper limit be? i see no reason to think there is an arbitrary upper on the genome of any organism.

 

http://en.wikipedia.org/wiki/Genome

 

 

As you and skeptic suggest, arbitrary was a poor word choice. Variable might have been better since it depends on many of the factors mentioned by other posters. As far as where this limit lies for any particular organism given the environmental conditions, I don't have enough data to say.

[CharonY]

For the pure physical aspect no limit is currently known. It would require more packing, scaffolding and possibly subdividing into more chromsomes but to my knowledge there is no information that would prohibit a given genome size.

 

And Cypress, you were first talking about gene expression. You do know the difference from what is being asked and discussed, I presume?

Edited July 28, 2010 by CharonY

[Butters]

Thankyou. That answers my question very well. So in summary, although there are a large variety of limiting factors in specific organisms, there is no theoretical limit on the length of a genome. Great news!

[cypress]

And Cypress, you were first talking about gene expression. You do know the difference from what is being asked and discussed, I presume?

 

There is a relationship between gene count contained in an organisms genome and the quantity of genes expressed, and I understand the distinction. Thanks for your concern.

[CharonY]

Actually not necessarily. Organisms with very high number of genes do not express them all at once. In fact, depending on the condition of the cell (and environmental condition of course) the cell may just express genes necessary for basal metabolism and shuts down the majority of its genome (as there is no need for their expression). Thus, the actual transcriptome or proteome of an organism does not correlated directly with its genome size. Of course, one could argue that due to leaky regulation there will always be a few transcripts, but that was not really the question. The point is that the genome is static, the expression is dynamic and the only connection is that a larger genome potentially allows the expression of more genes.

[cypress]

In other words there is indeed a relationship as I said but that relationship is not one to one at any particular time or for any particular cell. Yes, I am also aware of that reality. Again I appreciate your desire to be precise and to ensure that I understand.

[Sisyphus]

The organism with the largest genome yet discovered is Amoeba dubia, a single-celled blob with a genome 230 times as large as humans'.

 

It's not yet clear why:

 

http://en.wikipedia.org/wiki/C-value_enigma

[Butters]

So the genome size tends to be related more to the age of something than to its complexity. As in an older, simpler organism may collect a load of junk over the millenia that serves no purpose and is not actually expressed?

[cypress]

So the genome size tends to be related more to the age of something than to its complexity. As in an older, simpler organism may collect a load of junk over the millenia that serves no purpose and is not actually expressed?

 

No that does not appear to be the case. There is not a relationship between presumed age and genome size. Also it does not appear to be the case that organism populations accumulate any substantial loads of junk over the millennia (although certainly the genome does pick up some nonfunctional noise since some errors do occur. The Junk DNA prediction which reasons that given the process of random genetic errors and natural selection, and in order to provide the raw material for advantageous modifications, genetic junk should accumulate over time. But this idea appears to be false. Recent research indicates that any junk that does accumulate tends to get switched off and eliminated over time in a constrained resource environment.

[Sisyphus]

No that does not appear to be the case. There is not a relationship between presumed age and genome size. Also it does not appear to be the case that organism populations accumulate any substantial loads of junk over the millennia (although certainly the genome does pick up some nonfunctional noise since some errors do occur. The Junk DNA prediction which reasons that given the process of random genetic errors and natural selection, and in order to provide the raw material for advantageous modifications, genetic junk should accumulate over time. But this idea appears to be false. Recent research indicates that any junk that does accumulate tends to get switched off and eliminated over time in a constrained resource environment.

 

So the amoeba doesn't have "junk DNA?"

 

So the genome size tends to be related more to the age of something than to its complexity. As in an older, simpler organism may collect a load of junk over the millenia that serves no purpose and is not actually expressed?

 

It would accumulate "junk," yes, though it might also lose it depending on selection pressures. Bear in mind that the amoeba's lineage is no older than ours. It has certainly had a far larger number of generations, though, and clearly is capable of thriving with such a large genome, while organisms like us might not. So yeah: "older" and "simpler."

 

Also, just because a part of the genome is noncoding doesn't necessarily mean it serves no purpose or has no effect, or that is not subject to natural selection:

 

http://en.wikipedia.org/wiki/Noncoding_DNA

[Mr Skeptic]

So the genome size tends to be related more to the age of something than to its complexity. As in an older, simpler organism may collect a load of junk over the millenia that serves no purpose and is not actually expressed?

 

How so? We haven't had much success getting very ancient DNA. This seems rather like a common misunderstanding. Modern bacteria and modern humans are just as old and just as evolved -- although we humans may have had more changes. Because of the way eukaryotes work, we have more DNA than prokaryotes or viruses. As for junk, there is always a limit to how much junk DNA one can have, since eventually it would become a significant drain of resources and subject to selection pressure for deletion. Also, much non-coding DNA appears to have some function or another, so be careful of the term junk DNA -- it is often used interchangeably with non-coding DNA and may not be referring to actual junk.

[CharonY]

It depends on the selective pressure the organism face to maintain a small genome size. Best example are viruses who only have a very small genome and face physical restrictions in size. Many bacteria also have a selective advantage (faster propagation) when it comes to having smaller size, though there is trade-off with metabolic versatility. More complex eukaryotes have less restriction and therefore are able to maintain larger genomes, even when they serve no immediate purpose. Note that the accumulated "junk" can gain functions at some point as they can serve as a base for genetic variability that organisms with small genomes do not possess. Also they can serve as harmless hot spots for viruses etc.

 

At this point it may be useful to make it clearer what everybody is talking about. For instance whole genome size vs ORFs vs non-coding functional regions vs regions with unknown function.

Or another example is what one means with expressed. E.g. under regulatory control or just dysfunctional in its expression (e.g. by mutation).

Edited August 2, 2010 by CharonY

[Moontanman]

The creatures with the largest genome also happen to the be creatures who are under the most attack by viruses. The amoeba are under constant attack by viruses and continuously take in and emit large amounts of viral material.

 

http://www.sciencedaily.com/releases/2009/12/091230113210.htm