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Press Release
Resurrection of extinct enzymes reveals evolutionary strategy for the invention of new functions
Wednesday, December 12, 2012


How does evolution innovate? We exist because our ancestors have had the ability to adapt successfully to changes in their environment; however, merely examining present-day organisms can limit our understanding of the actual evolutionary processes because the crucial events have been masked by the passage of aeons – what we need is a time machine. Scientists from VIB, KU Leuven, University of Ghent and Harvard have done the next-best thing; by reconstructing DNA and proteins from prehistoric yeast cells, they were able to directly examine the evolutionary forces that have acted over the last 100 million years to shape modern-day enzymes – biological catalysts that enable organisms to manipulate molecules to their will.

The scientists set out to explore how new genes emerge, how they contribute to the survival of the evolving organism, and how, after a humble start, evolution then refines the function of new genes and hones the efficiency of the enzymes that they encode. One of the richest sources of such new genes is the chance duplication of existing genes. One copy of the gene can then continue to encode the original enzyme, allowing it to perform its original task, while the other is free to change and to perhaps take on a new function; alternatively, the two new enzymes might sub-divide the original task.

Although this pattern of innovation is known to have happened many thousands of times during evolution, the way in which it occurs hasn't been clear. In a paper published December 11 in the online Open Access journal PLOS Biology, Karin Voordeckers, Chris Brown and Kevin Verstrepen from VIB in Leuven, together with Steven Maere from VIB and the University of Ghent, tackled this problem, focusing their attention on the evolution of enzymes that have allowed yeast to exploit changing food sources over the last 100 million years of evolution.

The scientists 'resuscitated' ancestral yeast genes, allowing them to examine the properties of enzymes that existed tens of millions of years ago. The original enzyme originally enabled the yeast cells to survive on a diet of maltose, a common sugar, but duplications of their genes gave rise to new enzymes which opened up the possibility of feeding off other types of sugar in the environment. The resurrection of these enzymes meant that the scientist could build up a detailed picture of their atomic structure and directly determine their ability to break down different types of sugars. Armed with this information, they could work out exactly how the enzymes had changed their specificity and how evolution drove their optimisation.

"We used sequence reconstruction algorithms to predict the DNA sequence of ancestral genes from dozens of present-day DNA sequences. This enabled us to rebuild the corresponding ancestral proteins and compare them with those present today", said Steven Maere.

"We searched very specifically for how the yeast adapted to break down various sources of sugar. We found that the primal gene that codes for the protein for the digestion of maltose – a sugar in grain – was copied a number of times during evolution. The DNA of some copies changed slightly, resulting in new proteins that could break down different sugars. By modeling these changes in the corresponding proteins, we now understand how just a few changes in the DNA can lead to the development of a completely new activity in the corresponding proteins", said Karin Voordeckers.

"New functional DNA does not appear out of thin air, but is built up gradually from a copy of an existing segment of functional DNA. By reconstructing a piece of prehistoric DNA that was copied several times during evolution, we were able to investigate in detail which changes occur in each of the copies and gradually lead to new functions. As such, our results provide a unique and detailed view into the molecular details of Darwinian evolution" says Kevin Verstrepen.

The scientists propose that the events observed here in the yeast cell's quest for sugar may reflect a general strategy widely used for innovation in evolution.

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Public Library of Science: http://www.plos.org



Thanks to Public Library of Science for this article.

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Babu G. Ranganathan
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Fri, Aug 09, 2013, 9:22 am CDT
PROTEIN MOLECULES VS. CHANCE ORIGINS: Mathematicians have said that any event with odds of 10 to the 50th power or greater is impossible even within the entire time frame of the supposed billions of years popularly assigned for the age of the universe. Consider that the total number of atoms in the entire universe is 10 to the 23rd power.

The odds of an average protein molecule coming into existence by chance are 10 to the 65th power. That's just one protein molecule! Even the simplest cell is composed of millions of them. The odds of entire cell coming into existence by chance is 10 to the 40, 000th power! (calculated by famous British scientist Frederick Hoyle).

Protein molecules are made of smaller molecules known as amino acids. In order for a protein molecule to work the amino acids have to be together in a precise sequence, just like the letters in a sentence. If they are not in the right sequence then the protein molecule won't work.

It has been shown that the basic building blocks of life, such as amino acid molecules, can come into existence by chance, but it has never been shown that these basic building blocks can come together into a sequence by chance to form protein molecules.

Once there is a complete and living cell then the genetic code (or program) and biological mechanisms exist to direct the formation of more cells with their own DNA and protein molecules. The problem is how did DNA, RNA, proteins, and life come about when no directing code and mechanisms existed in nature.

Time is no help to chance. For every good accident there will be thousands of bad ones with the net result, over time, being deleterious, not beneficial. A partially evolved cell (an oxymoron) that is unprotected by a fully functioning cell membrane would disintegrate in the open environment long before it could evolve into a complete and living cell.

MOST SCIENTISTS ARE ATHEISTS because of personal bias alone, not because of science. True science shows it’s not rational to believe we’re here by chance, even within the evolutionary time frame of billions of years. True science shows that the universe is not eternal and could not have come from nothing by natural processes.

EXPLAINING HOW AN AIRPLANE WORKS doesn't mean no one made the airplane. Explaining how life or the universe works doesn't mean there was no Maker behind them. Natural laws may explain how the order in the universe works and operates, but mere undirected natural laws cannot explain the origin of that order. Once you have a complete and living cell then the genetic code and biological machinery exist to direct the formation of more cells, but how could life or the cell have naturally originated when no directing code and mechanisms existed in nature? Read my Internet article: HOW FORENSIC SCIENCE REFUTES ATHEISM.

WHAT IS SCIENCE? Science simply is knowledge based on observation. No one observed the universe coming by chance or by design, by creation or by evolution. These are positions of faith. The issue is which faith the scientific evidence best supports.

Visit my latest Internet site: THE SCIENCE SUPPORTING CREATION . I discuss: Punctuated Equilibria, "Junk DNA," genetics, mutations, natural selection, fossils, dinosaur “feathers,” the genetic and biological similarities between various species, etc., etc.

Babu G. Ranganathan*
B.A. Bible/Biology

Author of popular Internet article, TRADITIONAL DOCTRINE OF HELL EVOLVED FROM GREEK ROOTS

*I have given successful lectures (with question and answer period afterwards) defending creation before evolutionist science faculty and students at various colleges and universities. I've been privileged to be recognized in the 24th edition of Marquis "Who's Who in The East" for my writings on religion and science.
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