Fertilizers shape plant genomes

Spraying plants with nitrogen-rich fertilizers does more than just make crops grow bigger; it also molds the chemical composition of their genomes and proteomes, according to a linkurl:study;http://mbe.oxfordjournals.org/cgi/content/abstract/msp038 published online last week (Mar. 2) in the journal __Molecular Biology & Evolution__. "This tells us how modifications in the environment can have a big effect on a species and its genome, and how quickly it can happen," said linkurl:Sudhir Kumar,;http://www.kumarlab.net/ an evolutionary biologist at Arizona State University's Biodesign Institute in Tempe who led the study. Nitrogen is a scant resource in nature. So Kumar and his postdoc linkurl:Claudia Acquisti;http://www.kumarlab.net/personnel/acquisti_claudia.html set out to test whether plants conserve the essential element by opting to use nitrogen-poor nucleic acids such as thymine, which only contains two nitrogen atoms, as opposed to guanine with its whopping five N atoms. All told, an AT nucleotide combo equates to a single nitrogen molecule "savings" compared to a GC duo. Thus, if nitrogen limitation has shaped plant genomes, one would expect to find more AT-rich regions, especially in highly transcribed parts of the genome, which use a lot of molecular resources. Kumar and Acquisti analyzed the __Arabidopsis__ genome and found that 95% of the transcribed genome had lower nitrogen content than the genome-wide average. In contrast, humans and fruit flies, which get plenty of nitrogen from their diets, had near-identical nitrogen compositions genome-wide and in their transcribed regions. The researchers then compared the genomes of __Arabidopsis__, a wild weed, and domestic rice (__Oryza sativa__), the world's third largest crop, and showed that the rice genome had significantly more nitrogen-rich nucleic acids, although still less than animals. The researchers also inspected the proteomes of seven other plant species and found that domesticated species, as well as plants harboring nitrogen-fixing bacteria, used more nitrogen-rich amino acids. Because nitrogen is no longer a limiting resource when humans introduce fertilizers into the soil, "there is a release of selection pressure for nitrogen conservation" in farmed plants, Acquisti told __The Scientist__. Researchers have known for centuries that strong selection "leads to tremendous changes in phenotypes," noted Kumar. And now it's becoming apparent that "it can lead to tremendous changes in the genome as a whole." "If it's true, then it's really interesting because it ties in something as fundamental as genome structure with diet," said linkurl:Michael Purugganan,;http://biology.as.nyu.edu/object/MichaelPurugganan a plant genome researcher at New York University who was not involved in the study. He noted, however, that he "would have liked to have seen more comparisons" -- for example, between wild rice and cultivated rice species. That would confirm whether the rice genomic nitrogen content has, indeed, shifted over the course of less than 20,000 generations of domestication, or whether rice differs from __Arabidopsis__ for other reasons. Purugganan and others are currently working to sequence and annotate parts of the wild rice genome, so "in less than a year that comparison can be made," he said. Purugganan was also "intrigued" that Acquisti and Kumar may have discovered a reason why plant introns are much more AT-rich than animal introns. This difference "has been known for 20 years, but no on had an explanation," said Purugganan. "[The finding] will fuel a lot of debate into whether it's real or not, and really open the way for more comparisons," he added.
**__Related stories:__***linkurl:A UK lawn turns 150;http://www.the-scientist.com/article/display/24839/
[October 2006] *linkurl:Integrating plant 'omics';http://www.the-scientist.com/article/display/22227/
[15th June 2004]*linkurl:The genome that feeds the world;http://www.the-scientist.com/article/display/20310/
[5th April 2002]

Fertilizers shape plant genomes

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