ATHENS, Ga. — University of Georgia researchers studying rice genomes, under a National Science Foundation Plant Genome Research Program award, have identified the species’ first active DNA transposons, or “jumping genes.”
In collaboration with researchers from Cornell, Washington University and Japan, a research group headed by geneticist Susan Wessler also discovered the first active “miniature inverted-repeat transposable element,” or MITE, of any organism.
“This is of particular interest because of recent reports of two draft genome sequences for rice by public and private groups and with 40 percent of these sequences derived from transposable elements,” said Wessler. “Since rice is the most important source of human calories, any discoveries in this plant are of international interest.”
The research findings were just published in the Jan. 9 edition of the journal Nature. Major contributors to the study include Ning Jiang from Wessler’s lab at UGA and Zhirong Bao from Washington University in St. Louis.
Until about 50 years ago, scientists thought that all the genetic material of an organism contributed to its form, function and well-being. Then a researcher named Barbara McClintock showed that in addition to genes there is a class of mobile pieces of DNA that came to be called transposable elements or transposons. These elements have been found in vast numbers in virtually every organism studied by researchers.
Wessler and her research group played a key role in developing a new understanding of the role of transposons, which may help in shaping plant genomes and creating the modified gene functions required for evolution. As a postdoctoral fellow in the department of embryology at the Carnegie Institution, Wessler cloned transposons called Ac and Ds and subsequently went on to study the effect of Ac and Ds insertions on gene function.
Wessler’s group also discovered a new class of transposons called miniature inverted repeat transposable elements (MITEs), which are the predominant class of transposons associated with plant genes and are found in several animal genomes, including humans. MITEs could represent one of the most significant forces creating the genetic variation that has fueled plant evolution. Wessler’s group has also shed new light on both the nature and evolution of gene regulation in maize.
Rice (Oryza sativa), an important food crop worldwide, has the smallest genome of all cereals at 430 million base pairs. About 40 percent of the rice genome comprises repetitive DNA that does not code for proteins and thus has no obvious function for the plant. A significant fraction of this repetitive sequence appears to be transposons similar to MITEs. But like most genomes studied to date, including the human genome, the function of this highly repeated so-called “junk DNA” has been a mystery. The discovery of active transposons in rice provides new insights into how genomes change and what role transposons may play in the process.
Although genomes are comprised largely of transposable elements, virtually all of these are either inactive or turned off by the host. Wessler’s group took advantage of the availability of the genome sequence of rice (including all TE sequences) using a computational approach to first identify potentially active TEs (based on DNA sequence characteristics) then to test these elements for activity in the lab.
Active DNA transposons can move new copies of DNA to different places in the genome. To hunt for active DNA transposons, the researchers made use of the publicly available genome sequences for two subspecies of rice, japonica and indica. The researchers reasoned that in plants where such transposons move actively there would be multiple copies of an almost identical sequence. If they could find the conserved sequences in the two rice genomes, then they could test for transposon movement in cell cultures because the number of elements should have increased over time.
“Despite the identifications of hundreds of thousands of MITEs in a variety of organisms, mPing was the first active MITE identified,” said Wessler.
Using this approach, the researchers found a repeated sequence of 430 base pairs that was identified as a candidate for an active MITE because of the high degree of sequence conservation among the copies. Recognizing that it shared common size and other characteristics with MITEs, they named it “mPing” for “miniature Ping.” When they looked in indica rice cell cultures, the number of mPing elements increased, suggesting that it was indeed actively transposing.
It was puzzling to understand how mPing could transpose because MITEs are very small and do not code for any proteins and are thus unable to move on their own. The researchers reasoned that there must be a protein-encoding transposon (called “autonomous”) in the rice genome that encodes the enzyme transposase necessary to enable itself and other related elements to move. To find this autonomous element, the researchers compared the mPing sequence with the japonica and indica rice genome sequences to look for longer, related elements.
They found two candidates: a long version called the “Ping” sequence and another sequence they named “Pong.” The authors believe that Ping lacks a functional coding sequence. On the other hand, Pong contained appropriate coding sequences, and also increased in number along with mPing during cell culture. This led the researchers to suspect that Pong, not Ping, is the autonomous element that causes mPing to transpose. It is also possible, the researchers speculate, that Ping and Pong may co-activate mPing in some cases.
The new findings show that researchers can use a computational approach to identify active candidates from any genome when abundant DNA sequences are available. Even more important is the fact that these elements are actively diversifying the rice genome and may have been activated by stress conditions associated with the domestication of rice in temperate climates.
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