New research shows how gene function drives natural selection in important class

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New research shows how gene function drives natural selection in

important class of genetic elements

http://www.eurekalert.org/pub_releases/2008-12/uog-nrs121008.php

Transposons are the Kents of a genome. Apparently mild-mannered

and inconsequential but with sudden bursts of activity, these free-

floating bits of genetic material have for millions of years been

sneaking into the genetic maps of plants and animals, dramatically

increasing a genome's size.

For years, researchers thought that most of this DNA was

passive " junk " and knew little about it. New findings, however, are

peeling back the odd and baffling world of transposons. Now,

researchers at the University of Georgia have just found that natural

selection on gene function is driving the evolution of one kind of

transposable element called the LTR retrotransposon. (LTR refers to

the " long terminal repeat " —a repetition of a recognizable sequence of

nucleotides, the chemical bases that make up strands of DNA.)

" The lab of Professor Jeff Bennetzen at UGA discovered that this

class of mobile DNA comprises more than half of most plant genomes

and has led the way in determining the extraordinary rates of both

amplification and removal of this type of repetitive element, " said

Regina Baucom, a genetics post-doctoral research assistant at UGA and

lead author of the research.

Understanding the evolutionary pressures between host genome and

transposable element will in the future be of interest to those

studying retroviruses, which evolved from retrotransposons. There are

a number of animal and human diseases caused by retroviruses

including HIV/AIDS, avian leukosis and feline leukemia.

" Because LTR retrotransposons are abundant and impact host genomes,

we wanted to determine the influence of natural selection on their

evolution, " said Baucom. " We find that the genes involved in their

replication are subject to Darwinian evolution—the same evolutionary

processes that affect species. "

Other authors of the paper just published in the online version of

the journal Genome Research, were Jeff Bennetzen, in whose genetics

lab Baucom is a research associate; and Estill and Jim Leebens-

Mack in UGA's department of plant biology.

A " retrotransposon " is an element that copies itself and then pastes

copies back into genomes at multiple places. It does this by

initially copying itself into RNA, but this RNA element is then

copied into DNA by an enzyme called reverse transcriptase.

" In this study, we specifically wanted to assess the pattern of

selection on these elements—a pattern that could derive from the

effect of the elements on the host genome, or the effect of host

silencing mechanisms on the elements, " Baucom said. " Our expectation

was that if the elements are adapting to the host genome, we should

see evidence of positive selection in the genes involved in

transposition. "

The researchers examined selection pressure on retrotransposons using

Oryza sativa—rice—as a model plant genome. They analyzed more than

1,000 LTR retrotransposon sequences from 14 separate families that

varied in both the dates they were inserted into the rice genome and

the numbers of copies that were inserted.

" Overwhelmingly, we found that LTR retrotransposons are under

significant evolutionary constraint, by finding strong purifying

selection on genes involved in their replication and life-cycle,

regardless of the family that any the LTR retrotransposon sequences

might belong, " says Baucom.

This evidence of so-called " purifying selection " across all gene

regions is important in understanding how retrotransposons work. But

the research also shows there are rare episodes of positive selection

and even adaption to a host genome when these Kents get busy.

It has been known for a long time that the insertion of transposable

elements can harm the host, but few studies have been done to

determine if there is evidence of selection pressure on LTR

retrotransposons.

What the scientists found helps explain why these elements can, while

lying quiet for millions of years, suddenly amplify within genomes

while not causing more long-term harm than to take up space. And yet

the observation that a tiny percentage of the elements actually

become active parts of genomes provides an intriguing glimpse into

how these twin evolutionary pressures can, in rare cases, " sign an

armistice. "