University of Illionois graduate student Elijah Roberts led the new study, developing the computer programs for it. He was assisted by his chemistry professor Zaida Luthey-Schulten (standing),  (Source: L. Brian Stauffer, U. of I. News Bureau)

Professor Carl Woese was a pioneer in using ribosome RNA to study evolution. His work predates computer analysis, but he has rode the wave of breakthroughs that computer analysis has yielded.  (Source: Jason Lindsay)
Skepticism aside, evolution is steadily being verified and analyzed thanks to cutting edge computing

Evolution in its earliest days was derided by some for what they believed was a lack of observable evidence.  However, a major piece of supporting evidence for evolution has come from computer analysis of cellular compounds.  By examining minute details in organisms’ genomes, we have observed how traits were transferred to descendants and how other traits arose at different points in the evolutionary ladder.

The University of Illinois completed a major study on the ribosome that provides documentary evidence of the path of evolution and to help us better understand the differences between domains, the broadest classification level of living organisms.  The research was an extension of the work of Illinois microbiology professor Carl Woese, who was one of the first to examine the consistent differences in ribosomal RNA and proteins, which offers insight into evolution.

Ribosomes, the body's protein factories, are made up of two subunits partly composed of RNA, similar to DNA, but with one differing molecule.  Ribosomal RNA is called rRNA for short, as there are many types of RNA in the cell.  Ribosomes are also partially composed of proteins, which form a scaffold-like support of the RNA, helping it catalyze the reaction.  Messenger RNA, mRNA, carries the genetic message from DNA to the ribosome.  The floating ribosome then makes a polypeptide, which will become a protein, the basic functional unit in a living organism.

What researchers have found is that a domain of extremely primitive microbes known as archaea actually are closer to eukarya than bacteria in its ribosomal genetics; eukarya being the branch of life that humans and all other vertebrates are part of.  These similarities indicate that archaea are a closer "relative" to us on the evolutionary tree than bacteria.

To offer full insight into the ribosome, the researchers examined both the peptide (protein) sequences and the RNA sequences which composed it.  They also examined the 3D structure of the ribosome and the orientation of proteins with respect to each other.  Graduate student Elijah Roberts led the study and wrote computer programs that combed through thousands of organism's ribosomal sequences.  Whenever a difference between organisms was found, it was cataloged and the program then examined if the difference was exclusive to the organism's domain.

Illinois chemistry professor Zaida Luthey-Schulten, one of the senior professors participating in the study describes, "The evolution of cells and the evolution of translation are really linked to one another.  To be a molecular signature a sequence has to be common to all members of a single domain of life, but not another."

Using 3D models for some bacteria and archaea, researchers were able to take the analysis a step further, examining where on the 3D ribosome the differences occurred.  Mr. Roberts explains, "Until the 2000s, when these structures became available, you weren't able to correlate where these signatures were with what was touching them in 3-D space."

What the team found was that a mere 5 percent of the ribsome's RNA contains 50 percent of the domain-specific differences between bacteria and archaea.  Interestingly, this domain is an area critical to the function of the ribosome as a protein factory.  They also found that the differences in RNA were correlated structurally to differences in proteins, indicating that rRNA and ribosomal proteins coevolved.

Professor Luthey-Schulten describes, "The ramifications of this work are it gives you a much better way to probe how this universal machinery changes from one organism to another."

Professor Woese adds, "In that the ribosome constitutes the core of the cellular translation mechanism, which is the sine qua non of gene expression, which is the essence of life as we know it, these findings constitute a major step in understanding the evolution of life, which is still a journey of a thousand miles."

Professor Luthey-Schulten says that by identifying domain-specific critical rRNA segments, manmade drugs can be developed to attack these regions.  This can lead to ultra-effective antibiotics, beyond even today's best drugs.

The new research will be published in the journal Proceedings of the National Academy of Sciences this week.

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