They also looked at the three-dimensional structures of the ribosomal RNA and proteins and their proximity to each other.
Graduate student Elijah Roberts, lead author on the study, developed computer programs to analyze the ribosomal sequences of different organisms. Whenever he found a ribosomal RNA or protein sequence that differed between bacteria and archaea, he screened the database to determine whether a sequence was unique to a given domain.
"To be a molecular signature a sequence has to be common to all members of a single domain of life, but not another," Luthey-Schulten said.
Using the three-dimensional structures available for some bacterial and archaeal ribosomes, the researchers were also able to determine where in the ribosome these molecular signatures occurred.
"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," Roberts said. "So nobody had ever done this sort of analysis before."
The researchers found that 50 percent of the signatures distinguishing the archaeal and bacterial ribosomes is located in five percent of the ribosomal RNA sequence. Most of these molecular signatures occur in regions that are critical to ribosomal function.
They also found correlations between some ribosomal protein and RNA signatures, which they say is evidence that the ribosomal RNA and proteins co-evolved.
"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," Luthey-Schulten said.
"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," Woese said.
|Contact: Diana Yates|
University of Illinois at Urbana-Champaign