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,"

By | March 10, 2009

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]

Comments

Avatar of: Matthew Grossman

Matthew Grossman

Posts: 27

March 12, 2009

Very interesting result, looking forward to more!
Avatar of: Daniel Gaston

Daniel Gaston

Posts: 3

March 12, 2009

Count me in with the "more comparisons should have been made" in order to determine if the extra nitrogen presence is a primary cause for the shift in AT content versus some other requirement. There are other evolutionary pressures that shape AT content of genomes beyond just availability of nitrogen, look at what is going on with parasitic organisms for instance. Comparing wild cultivars to closely related domestic strains across a variety of species would be very helpful.\n\nThis still seems like a very interesting study
Avatar of: anonymous poster

anonymous poster

Posts: 7

March 12, 2009

apples to oranges ?
Avatar of: roberto papa

roberto papa

Posts: 1

March 13, 2009

very nice and interesting

March 13, 2009

The results are interesting as well as intriguing.If fertilizers can affect the genome then scientists have a wonderful tool to work in this field.It may also lend more credit to organic farming.\nGian Singh Aulakh\n

March 14, 2009

Really an interesting and important breakthrough, it will definitely leads to a good amount of works to pin the influence of plant nutrients on genome. \nA well beginning\n
Avatar of: Jag Rawat

Jag Rawat

Posts: 2

March 16, 2009

I, as a the-then-International Coordinator of 'International Network of Students for Environment, Education and Development (www.angelfire.com/pa/INSEED/) had a spirited debate within Department of Evolutionary Biology of Liverpool Univrsity (1998 probably) on the issue of 'NPK working as selection pressure on plant varieties and therefore, it could have been exerting a selection pressure and varieities eventually were selected, could be categorised as 'NPK intensive varieities or cultivars'. In this selection, those which would have rather responded to organic sources of supply of nutrients, got rejected. \n\nMaking this hypothesis, I argued that "In this way, all cultivars resposnive to NPK were being selected over all these years and those responding to organic sources, got ignored by mainstraam plant breeding research". \n\nThat kind of historical bias brought all such NPK intensive cultivars and varieities leading to polluted soils on one hand, while rejection of 'organic responsive varieties', led the researchers to only research for NPK intensive varieites. \n\nAt that time, I said it was a great tragedy of our times and we launched 'Strengthening Organic Farming Initiative' or SOFI at that time. That was the time, I being veterinarian, still got intrigued and interested in the field of evolutionary biology and thought that there could be something which I needed to do to bring all those 'organic responsive cultivars' back into reckoning of plant breeding research, improve them and then, challenge all NPK-intensive varieties. Could we do that? Answer has been rather positive and resounding success.\n\nWell, a that time also, my spirited debate convinced the Professor in Liverpool university on the rationality of the thought but still he was not sure of any evidence of my hypothesis.\n\nNow, that hypothesis stands confirmed and still more work would have to be done to know that so much alteration and shaping of genome has happened that we would have to take recourse to original or wildtype genomic sources and trace those varieties which would be responsive to organic or sustainable inputs. That kind of approach would not only solve productivity problems but also sustaiabability.\n\nOur own success in that field has been tremendous over some 8 years and our cultivars have been selected precisely on this premise.\n\nOur not-for-profit organisation named HABITAT INDIA (www.meragaonmeradesh.co.cc) has a very good reservoir of such cultivars for rice, wheat and Arhar.\n\nI think we would be happy to work in field situations and further establish some of the other issues which are getting more and more understood in the light of the above discovery.\n\nKudos to Dr Sudhir Kumar!\n\nJagveer Rawat\nAssociate Professor, CCS Haryana Agri University, Hisar INDIA\nand Chief Advisor\nHABITAT INDIA (www.meragaonmeradesh.co.cc)
Avatar of: null null

null null

Posts: 44

March 16, 2009

This leaves a lot of unexplored explanations. \nThe most obvious rejoinder is that genome size and so total nitrogen (and phosphorus) requirement varies enormously between species, by factors of 10 and 100, and would have a much bigger effect on nitrogen requirement than a small change in AT:GC ratio. That aside, there are other confounding factors.\n1/ C.G is more stable (higher melting temperature) than A.T so a higher GC ratio might be predicted in organisms living at a higher temperature (mammals and e.coli for example).\n2/ Mammals, at least, are well known for having CpG islands at the start of about half their genes and in mammals the CG content of coding regions is much higher than in regions with low gene density. This seems to contradict the comparison referred to above.\n3/ cytosine is often methylated to 5methyl cytosine which deaminates to uracil which can be repaired to thymine and leads to a transition from C.G to T.A, reducing the frequency of GC in the parts of the genome where such mutations are not harmful.\n4/ Plants are known to use repeat induced gene silencing (RIGS) to mutate and inactivate transposable elements. This involves systematic methylation of cytosine in repeated sequences facilitating deamination of C to U and then replacement by T. This could help explain the high level of AT in plant transposons. It predicts more AT in larger genomes with more junk transposons.\n5/ Animals that feed exclusively on plants, most obviously aphids, are as nitrogen-limited as their food. The hypothesis predicts that wheat aphids will have more CG than their relatives restricted to wild-grass.\n \nMaybe I could go on, but this research so far has barely scratched the surface, and while it is entirely plausible, it certainly does not support any valid conclusions.\nHugh Fletcher.

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