April 30, 2009
By literally turning up the heat, a team of scientists has uncovered an enzyme that modifies genetic sequences in an ancient heat-loving organism. The research underscores the widespread nature of RNA editing, a process that helps explain how organisms as complex as humans could be constructed from only 20,000 genes.
For decades, scientists thought that each gene comprised the instructions to make one protein. Now they know better. From one gene, the body can often make several related proteins.
Structure of M. kandleri’s cytidine deaminase. The enzyme is formed when two identical subunits, shown in red and brown, mesh together. In this view, the upper part of the enzyme recognizes the tRNA target, while the smaller region below converts the cytidine (C) at position 8 into a uridine (U). The yellow sphere in the lower portion represents a zinc atom, which is necessary for the enzyme’s activity. Source: Lennart Randau and Dieter Soll
The first step in making proteins is to transcribe the information in a gene into a matching strand of RNA. Then the body can create several different versions of the RNA by adding, removing or interchanging its basic building blocks, a process called RNA editing.
In humans, the process generates slightly altered versions of certain proteins for use in specialized ways in different parts of the body. It is also partly responsible for the tremendous diversity in antibody structures, which helps protect us from the wide variety of pathogens that infect us.
The scientists, led by researcher Dieter Soll, Ph.D., of Yale University, describe their newly discovered RNA editing enzyme in the May 1, 2009, issue of Science.
Their work in the area began years earlier.
In 2002, Soll was looking at the newly sequenced genome of Methanopyrus kandleri, a primitive organism that flourishes in boiling vents under the sea. He noticed an unusual feature in the genes that encode a class of molecules called tRNAs.
tRNAs, or transfer RNAs, are evolutionarily ancient molecules found in all life forms. They help assemble protein building blocks into full length molecules.
Like the proteins they help construct, tRNAs are made of a specific sequence of chemical units that forms a chain that twists and turns itself into a characteristic structure. The four types of units that make up tRNAs are guanosine (G), adenosine (A), cytidine (C) and uridine (U).
In looking at M. kandleri’s genome sequence, Soll noticed that 30 out of the 34 tRNA genes called for the tRNA to have a C at position 8. This was surprising because previous studies had shown that tRNAs need to have U at position 8 to work properly. Some of these studies even linked having C at position 8 with growth problems and muscle disorders in people.
So what was going on? How could M. kandleri function with its abnormal tRNAs?
While many scientists remained puzzled, Soll had a hypothesis. He suspected that the organism somehow converts its maverick C into the correct U.
“I knew there had to be a cytidine deaminase,” Soll recalled. Cytidine deaminase is an enzyme known to convert Cs to Us in other organisms, including humans.
Methanopyrus kandleri, a primitive organism that lives in thermal vents in the ocean. Source: Wikimedia
But with no obvious cytidine deaminase genes in the M. kandleri genome, Soll put the project on hold—until one of his postdoctoral researchers, Lennart Randau, made a surprising discovery.
For an unrelated project, Randau was sequencing tRNAs from various species when he noticed a curious thing. He knew Soll had previously observed that the genetic (DNA) instructions for M. kandleri’s tRNAs coded for the aberrant Cs. But his sequence data revealed that the tRNAs themselves had standard Us at position 8.
So Soll’s initial hunch must be right: M. kandleri has got to have a cytidine deaminase to switch the Cs encoded in the gene into Us.
Randau scrutinized M. kandleri’s genome for genes with any similarity to known cytidine deaminases. But when he finally found a candidate and tested it, there was no biochemical activity, suggesting that the gene was a false lead.
Then he remembered that M. kandleri lives in boiling thermal vents, so many of its biochemical reactions work optimally at high temperatures. When he cranked up the heat on the enzymatic reactions, Randau saw the enzyme come to life and efficiently convert the chemical units.
“While RNA editing has been reported across the evolutionary spectrum, it’s been most often observed in complex multi-cellular organisms including humans,” said Michael Bender, Ph.D., of the National Institute of General Medical Sciences, which partially supported the work. “The discovery of this elusive cytidine deaminase suggests that there may be other as yet undiscovered RNA editing enzymes in simple organisms like M. kandleri.”
In the past, discoveries of enzymes in primitive organisms have led to important scientific advances, such as those that led to DNA fingerprinting, gene-based disease tests, and key biotechnology tools. Only time will tell if the heat-activated RNA enzyme—or any other molecule or process in M. kandleri—will yield similar applications.
With the mystery of M. kandleri’s anomalous tRNAs finally solved, Soll’s team is raising new questions. Prime among them is why M. kandleri did not evolve to simply encode a U at the genetic level like most other organisms.
“This is the question that everyone, including me, is asking,” says Randau. It is possible, he said, that the tRNA gene with the C makes the organism more resistant to harmful DNA elements or viruses, or enables it to survive extreme environmental conditions.
“This work not only changes our views about the origins of RNA editing but it reminds us that genes do not tell us the whole story, said NIGMS’s Bender. “Even in the primitive M. kandleri, RNA editing expands on the information encoded in the genome, producing more complexity than was evident at first glance.”
This is just one example of how answers to a single, basic, biological question bring us closer to understanding the vast complexity of biology—and opens up entire new areas to explore.