OT:Appearance and disappearance of genes tracked over 300 million years, fungi

[Guest guest]

Appearance and disappearance of genes tracked over 300 million years

September 05, 2007

Ars Technica - Boston,MA*

By Timmer

http://arstechnica.com/journals/science.ars/2007/09/05/appearance-

and-disappearance-of-genes-tracked-over-300-million-years?bub

It's been thought for a while that gene duplications play a key role

in fostering evolutionary novelty. With an extra copy of a gene, the

original can keep performing its normal function, while the new copy

can change in a way that allows novel or specialized activities.

Some examples of this behavior have been identified over the years,

but there were lingering questions about whether those examples

represented the typical behavior. The completion of genome sequences

from a variety of related species has now allowed these questions to

be explored in a systematic manner.

A paper that will appear today in Nature takes advantage of 17

different genome sequences in a group of related fungi (the

Ascomycota) to compile a natural history of all the genes present,

including duplication events, gene losses, and a single whole-genome

duplication event. The reconstruction spans 300 million years' worth

of evolution, and precisely identifies when new genes appeared

relative to speciation events.

Most of the genes essential for basic organismal function are

ancestral, appearing throughout these fungi; for example, in baker's

yeast, 96 percent of essential genes are ancestral. Many novel

groups of genes have appeared within this time scale, most of them

related to significant lifestyle adaptations, such as sporulation

and sexual reproduction. Gene loss also occurred, often associated

with adaptation to a pathenogic lifestyle.

A number of results provide us with a much greater perspective on

how changes in gene copy numbers fit into the big evolutionary

picture. When it comes to the basic biology of the cell, it looks

like additional gene copy numbers may be unhelpful or actually

harmful, as they don't last long in the genome: there were far fewer

changes in gene dose for genes involved in growth and metabolism. In

contrast, genes involved in stress response, development, and

sensing environmental changes were frequently duplicated.

The analysis also looked at how the extra copies of genes picked up

new functions by comparing the activities of the new and old copies

using a number of assays: physical interactions between the gene

product and other proteins, genetic interactions with other genes,

and common regulation by the same transcription factor(s). The

authors suggest that changes in physical interactions indicate

different function has come about via biochemical changes in the

protein itself. In contrast, changes in regulation indicate that new

regulatory information has evolved to allow the two copies to

perform different functions.

In the end, the data suggests that regulatory differences seem to be

key. The authors conclude, " Our analysis shows that paralogues

[duplicated genes] diversify most frequently at the level of

regulation, less frequently through changes in their cellular

component, biological process or molecular interactions, and rarely

in biochemical function. " In the ongoing argument about the

importance of regulatory changes in evolution, this paper clearly

sides with those who argue that these differences are key.

There are a lot of other notable details in the results, but I'll

end this report by backing out and looking at the big picture. The

computational tools the authors developed for this analysis are

general, rather than specific to the fungal genomes. They should

work just as well with any collection of organisms (say, all the

vertebrate genomes), and the analysis can be redone as new genomes

are completed. So, we can look forward to these tools providing us

with further insights in the future.

Nature, 2007. 10.1038/nature06107