Biologists Probe Mystery of Ancient Gene -- and Implications for Junk DNA

UNIVERSITY OF UTAH MEDIA RELEASE

Embargoed by the journal Proceedings of the National Academy of Sciences for release at 3 p.m. MST Mon. Jan. 28, 2002

Contacts:-- Baldomero Olivera, professor of biology - (801) 581-8370, [email protected] -- Pradip Bandyopadhyay, biologist - (801) 581-5907, [email protected] -- Lee Siegel, science news specialist, University of Utah - office (801) 581-8993, cell (801) 244-5399, [email protected]

BIOLOGISTS PROBE MYSTERY OF ANCIENT GENEIt Helps Clot Human Blood and Make Snail Venom;What Did It Do 540 Million Years Ago?

Jan. 28, 2002 - A gene that makes human blood clot also is found in bloodless fruit flies and helps venomous cone snails produce an experimental drug against epilepsy. University of Utah biologists discovered the gene existed a half billion years ago, raising a mystery over its ancient role in the primitive ancestors of people, insects and snails.

The finding also supports the notion that "junk DNA" - portions of the genetic code that are within genes but have no apparent function - arose early in evolution, namely more than 500 million years ago, rather than later, as some have argued.

The new study - published in the Jan. 29 online edition of the journal Proceedings of the National Academy of Sciences - involves a gene that helps humans, fruit flies and cone snails make an enzyme named gamma-glutamyl carboxylase or GGC.

All three groups of animals now use the gene and enzyme for different purposes, although their use in fruit flies is unknown. Fruit flies and cone snails lack blood, and humans don't make venom, which the cone snails use to paralyze and capture fish they eat.

The ancestors of humans, fruit flies and predatory, ocean-dwelling cone snails diverged onto different branches of the evolutionary tree at least 540 million years ago, so "there must have been a common reason why this enzyme was present early in all three groups," said University of Utah biology professor Baldomero "Toto" Olivera.

"This enzyme has very well defined uses in these two widely different species [humans and cone snails], and has been preserved a long period of time," said the study's first author, Pradip Bandyopadhyay, (pronounced Bon-doh-pod-thai), a research assistant professor of biology. "We want to know what it did originally."

The enzyme may have played some yet-undetermined role in helping embryos develop, Olivera and Bandyopadhyay said.

Olivera and his laboratory team study cone snails - which have stung to death a few dozen human divers and swimmers around the world - because the snail venoms have potential as medicines for nervous system and cardiovascular disorders.

The GGC enzyme plays a key role in helping the venomous cone snail Conus geographus produce a substance named conantokin-G. Cognetix Inc., a Salt Lake City company co-founded by Olivera in 1996, now is developing CGX-1007 - a compound derived from conantokin-G - as a possible treatment to control seizures in patients with intractable epilepsy. Phase I clinical trials to determine the compound's safety were completed last year.

In humans, the GGC enzyme is required for blood clotting. Blood-thinning drugs such as coumarin work by indirectly counteracting the enzyme Bandyopadhyay showed in previous research that the enzyme also is present in fruit flies, although how they use it is not known.

In the new study, the researchers compared introns - nicknamed "junk DNA" - in the GGC gene in all three groups of animals. Despite the nickname, researchers in recent years have come to suspect that even though introns are not genes, they may play a role in coordinating the actions of genes.

Humans have 14 introns or segments of junk DNA in the sequence of amino acids that includes the gene for the GGC enzyme. The researchers so far examined eight introns associated with the same gene in cone snails, and found they are in the same location as they are in the human genetic blueprint. Fruit flies have only two of the introns left - the others were lost during evolution - but those two also are in the same location in the genetic sequence as their counterparts in humans.

Chordates (the group that includes humans and other vertebrate animals), mollusks (including cone snails) and arthropods (including fruit flies and other insects) branched from a common ancestor more than 500 million years ago. So the similarity of the DNA within the three groups indicates the GGC enzyme and the gene that produces it originated before that branch in the evolutionary tree.

"It says the enzyme is very ancient, that it must have been present in groups of animals that diverged from each other before 540 million years ago," Olivera said. "But what really surprised us was that the junk DNA is in exactly the same place in the gene for humans and in the gene for the snails."

That suggests junk DNA (deoxyribonucleic acid) originated early in evolution, contrary to those who think it evolved more recently, he added.

The "introns early" theory holds that junk DNA's origins stem from the so-called "RNA world," a time before the existence of modern genes, which are made of DNA and order the production of proteins and enzymes that carry out all the functions within living organisms. Early in evolution, RNA is believed to have had a dual role: carrying the genetic code like modern DNA, and also carrying out the functions of living cells, like enzymes and other proteins do today.

For RNA to act like a gene, a strand of RNA would have to unfold so it could be copied as organisms reproduced. To act like a protein, the RNA would have to fold up in a very ordered way because the structure of a protein helps determine what job it performs. Olivera said the early intron theory holds that pieces of junk RNA existed early in the genetic code - when the code was made of RNA instead of DNA - to make it physically possible for the RNA strands to fold or unfold, as needed, to perform a dual role as genes and proteins. The junk RNA essentially was a space holder to make folding and unfolding possible. As modern DNA and genes evolved, pieces of so-called junk persisted but were made of DNA.

Olivera said the opposing theory is that early genes contained only non-junk or useful DNA that ordered the production of proteins, and that junk DNA arose later - perhaps when bacteria infected early cells. DNA from the infecting bacteria could have become the junk DNA within the infected cell's genetic blueprint.

The new study provides more evidence that junk DNA originated early in evolution, and that junk DNA in the human genetic blueprint is an ancient remnant rather than "being added all the time to our DNA for some reason we don't know about," he said.

Finding great similarities in the junk DNA of three kinds of animals that evolved along different paths starting 540 million years ago indicates the junk DNA in the human GGC gene is ancient, and implies "almost all human junk [DNA] might be old junk," Olivera said.

Although the GGC enzyme now helps human blood clot, helps cone snails make venom and plays an unknown role in fruit flies, the enzyme also still may play its mysterious ancient role in all three groups of animals, he added.

"There is a hint it may play a role in development" of embryos into newborn organisms, perhaps in sending chemical signals that help early embryonic cells change or "differentiate" into different kinds of cells needed to make up various tissues within a living organism, Olivera said.

He said scientists are interested in the origin of junk DNA and of the GGC enzyme because "one wants to know about the origins of life, and what happened" as it evolved.

Bandyopadhyay added: "Why should we care what happened in Egypt 3,000 years ago? It [the origin of GGC and junk DNA] is a similar kind of thing. It's part of our history. 'Biology is a historical science to help make sense of why things are the way they are.' Figuring out what really happened is part of figuring out who we are."

Olivera and Bandyopadhyay conducted the study with James E. Garrett, a molecular biologist at Cognetix, and three University of Utah biology students: undergraduates Reshma Shetty and Tyler Keate and graduate student Craig S. Walker.

Baldomero Olivera's web site is at:http://www.biology.utah.edu/faculty2.php?inum=7

The Cognetix web site is at:http://www.cognetix.com

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