Why Do Certain Genes Vary in Number?

[Drakkith]

So I was reading wikipedia, browsing through various genetics-related articles, when I stumbled across the article for Amylyse, an enzym that breaks down starch into sugars. Apparently humans (and a few other animals) secrete amylyse in their saliva as a result of the expression of a certain gene that was originally expressed only in the pancreas.

My question has to do with the number of copies of this gene. According to the article, populations that have historically consumed higher proportions of carbohydrates in their diet have more copies of this gene (upwards of six) than populations which have a smaller proportion of their diet as carbs (who have 2-3 copies).

How is having more copies of a certain gene beneficial? Does having more copies lead to better expression?

(As as a side note, I just learned about endogenous retroviruses and endogenous viral elements. It's amazing to think that we've evolved to use some of these viral genes)

 

[jedishrfu]

That sounds reasonable.

I found this discussion on researchgate

http://www.researchgate.net/post/Why_do_some_genes_have_multiple_copies_in_a_bacteria_genome_while_some_genes_have_only_one

There they talk about the concentration levels.

 

[Drakkith]

Okay. So what I'm getting is that genes which encode for proteins that are needed in large amounts have multiple copies, enabling the cell to do a sort of 'parallel process' for transcribing the DNA, enabling faster production of these proteins.

 

[atyy]

Okay. So what I'm getting is that genes which encode for proteins that are needed in large amounts have multiple copies, enabling the cell to do a sort of 'parallel process' for transcribing the DNA, enabling faster production of these proteins.

That would seem like it. But the second article you [oops, saw the wrong poster, edited after Drakkith's post below] article that jedishrfu linked to is about bacteria, whereas the Wikipedia article is about people. Wikipedia itself gives as a reference:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2377015/
Perry et al, Diet and the evolution of human amylase gene copy number variation

The way the multiple genes are arranged on chromosomes is given in some detail in:

Groot et al, The human alpha-amylase multigene family consists of haplotypes with variable numbers of genes.
https://www.ncbi.nlm.nih.gov/pubmed/2788608

 

[Drakkith]

Thanks atyy. From the referenced article:

We found that salivary amylase gene (AMY1) copy number is correlated positively with salivary amylase protein levels, and that individuals from populations with high-starch diets have on average more AMY1 copies than those with traditionally low-starch diets.

So it looks like the explanation in Jedi's link is at least plausible.

 

[jim mcnamara]

Hmm. Let's look at plants. Duplicate alleles can be "arrived at" with polyploidy as well as multiple loci.
Wheat genus Triticum at a glance:

Bread wheat (T. aestivum) – hexaploid (6n) species
Spelt (T. spelta) – 6n sometimes clsssified as a subspecies of
T. aestivum.
Durum (T. durum) – (4n) Pasta wheat. With bread wheat
makes up almost all of the modern cultivation of wheat.
Emmer (T. dicoccon) – (4n)
Khorasan (T. turgidum ssp. turanicum) (4n)
Einkorn (T. monococcum) – 2n thought to be a common ancestor of more
modern wheat species.

Yields, number and size of kernels vary with ploidy from 2n (lesser) -> 6n (greater)

Doubling chromosome number has apparently been a useful adaptive trick for grass species -
Panicum virgatum switchgrass has several different choromosome numbers usually localized
to a habitat. Switchgrass grows in all kinds of habitats.
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0038702
https://en.wikipedia.org/wiki/Panicum_virgatum

So what might you expect with cultivated strawberries? The common cultivars are
higher ploidy and so it is. The most commonly grown one is 8n.

And you would expect the wild lesser- ploid species to have smaller fruit - they do.
Mostly. Fragaria virginiana has small fruit but is 8n. Welcome to the wonderful world
of biology where many observations are mostly correct most of the time.

A horticultralists view of polyploidy in strawberries:
http://strawberryplants.org/2011/02/genetics-of-strawberry-plants/

 

[Drakkith]

Welcome to the wonderful world
of biology where many observations are mostly correct most of the time.

Indeed!