Testing hypothesis on the evolutionary forces maintaining gene clusters

A test of the coordinated expression hypothesis for the origin and maintenance of the GAL cluster in yeast.
Lang GI and Botstein D. 2011. PLoS ONE. Sep 22; 10.1371/journal.pone.0025290. [PDF]

[Motivation]

What is the evolutionary force that favors the clustering of genes functioning in the same pathway?

[Hypothesis]

1. coordinated expression, perhaps to facilitate “channeling” of toxic intermediates in metabolic pathways
2. to utilize the genetic linkage to preserve co-adapted genes.
3. reflect a history with frequent horizontal transfers.

[Results]

• It seems to me that the results are quite inconclusive, despite the question being highly motivating. Their test for the first hypothesis, namely the clustering is favored because it contributes to coordinated expression, is achieved by tagging two genes in the pathway by different fluorescence proteins. Importantly, in a diploid cell, they only tag one copy of the gene and as a result, there are two ways of tagging: tagging the two genes on the same chromosome or two that are on different chromosomes. The hypothesis, therefore, can be tested by reading the expression correlation between the two genes tagged either in cis (same chromosome) or trans (on different chromosome).

  While this is all good, I think there is a possibility that one or both of the genes might harbor some self-regulating abilities. Let’s look at the trans case. Although the two genes whose expression are being monitored are on different chromosomes, each of them does have another copy non-tagged. If their expression are partially self-regulated, then having one untagged copy in cis could potentially coordinate the expression of the two copies. While this may sound absurd, given that no explicit mechanism for coordinated expression is being offered and tested here, we could envision any possible mechanism.

  To circumvent this problem, I would like to see this experiment redesigned with some elements borrowed from the second experiment, namely knocking out one copy (the untagged) and leave just one. This should eliminate the self-regulation concern. Given that they had done the second experiment, the additional experiments should be feasible.

• Concerning the test for the second hypothesis, my concern is that they don’t see a fitness difference not because there is not or it is too small for them to see in their experiments, but that the experiment design has fault that prevents them from seeing the effect. My reasoning is that the fitness difference, if any, should result from incompatibility between gene pairs that have each co-adapted with their native partners and when brought together behave less fit than either wildtype. The assumption here is that there has been co-evolution. In this case, I think it is crucial to pick two strains that are reasonably diverged — either two closely related species that can still make hybrids, or two distant strains within a species that harbor different ecological niches with regard to the function of the GAL pathway. In absence of that (the authors mentioned that all strains used in this experiment are derived from the same strain), I don’t see how this experiment can test the hypothesis.