Individual gene changes in complex structure traced, proving Darwin theory
GAINESVILLE, Fla. — The protein that gave the Incredible Hulk his distinctive green hue has provided University of Florida researchers the tool they needed to demonstrate for the first time in nature an evolutionary theory that even its originator, Charles Darwin, found troubling.
By studying the green fluorescent protein in the great star coral, UF researchers were able to trace the evolutionary changes in individual genes that give rise to its complex diversity of colors. The results of the research, funded in part by the National Institutes of Health, will be published in the Sept. 3 issue of the journal Science.
Demonstrated previously only in computer simulations, the discovery also is the first to reveal in the natural world Darwin’s principle that complex structures – such as the spectacular colors of a coral reef or the keen eye of an eagle – evolve through an accumulation of small improvements over time. Though he anticipated this was the case, UF researchers say Darwin himself considered the evolution of “organs of extreme perfection and complication” one of the major difficulties of his theory.
The scientists were able to achieve this by resurrecting and characterizing the ancestral coral genes that went extinct as long ago as 300 million years, using statistical methods to infer their DNA sequences, and then actually synthesizing them in the lab and making them work in a bacteria to produce the ancestral proteins.
“For us, the major significance of this study lies in the field of basic evolutionary theory. We stumbled upon this system in which we can trace the evolution of complex features to the level of individual mutations in the genes,” said Mikhail Matz, a research assistant professor at UF’s Whitney Laboratory for Marine Bioscience, and in the department of molecular genetics and microbiology.
“Darwin said it was very difficult to imagine how such a complex structure as the eye of an eagle would arise as a result of random modifications, so he proposed that these kinds of structures would evolve … through small improvements. And we are the first to manage to find a model in which we can see it really happening,” Matz said.
The finding also sheds light on the mechanisms of the green fluorescent protein, or GFP. The use of the GFP holds promise in the fields of medicine, particularly in the areas of genetics and biotechnology, and the conservation of coral reefs, which provide key ecosystems for a variety of marine life, said Matz, who conducted the research with Juan Ugalde, an undergraduate intern from the University of Chile in Santiago, and Belinda Chang, a zoologist at the University of Toronto.
The first gene for GFP was isolated in a crystal jelly jellyfish in 1992. In perhaps the most infamous use of gene-swapping technology, that jellyfish made its big-screen debut in the opening credits of the 2003 movie “Hulk,” which showed the character’s scientist father jabbing a large syringe into the jellyfish to extract the protein, Matz said.
In the real world, scientists quickly realized the possibilities for the GFP, which is uniquely coded for by a single gene, Matz said. All other fluorescent proteins, such as pigments in plants and animals, are much more intricate, involving complicated production pathways and a host of proteins and genes.
These green fluorescent proteins are “very cute, small, can be easily expressed in transgenic animals, (and are) very stable,” Matz said. “It looks almost like this gene family was made to be a model gene family, so we’re taking advantage of that.”
Working to understand the function of coral’s color diversity and what maintains it in evolutionary terms, the researchers followed the ancestral lines leading to three different colors – cyan, red and green – displayed in the great star coral. The red color is the most complex because it performs an additional reaction to synthesize its fluorescent structure, Matz said.
The team discovered the common ancestral gene was green, not red. This essentially proved that the great star coral and related species evolved their color diversity independently from other corals, which means the molecular complexity of red has more than one evolutionary origin, Matz said. Moreover, it turned out that the more complex red color evolved from green through small incremental transitions, according to the paper.
The depth of their finding was a surprise, even to the researchers.
“We thought that we would be just able to determine the color of the common ancestor and that would be excellent results, and we didn’t expect anything more than that,” Matz said. This additional finding was a “real big surprise and very unexpected results. It could have been expected according to the Darwin principles, but nobody (had) ever seen that.”
The simplicity and easily identifiable fluorescent color also make GFPs ideal for medical applications, Matz said. The proteins can be substituted for, or attached to, genes of interest – such as those that may be malfunctioning in cancer or other diseases – which make them visible so researchers can trace their activity, he said.
The research also may aid in helping to preserve coral reefs, many of which have been in decline worldwide because of human and global threats, such as pollution and climate change.
“We’re trying to figure out what you can learn about coral’s well-being or its life history by just looking at its coloration,” he said. “If you can just devise an optical method which could be based on the fluorescence – the color of these proteins – that could really tell you something about the health or the life history of coral, that’d be great and that’s actually the goal.”
The research also was funded by the U.S. Department of Defense, the Natural Sciences and Engineering Research Council of Canada, and the Grass Foundation.