New way to regulate nitrate uptake in plants

The micro RNA switch controls a gene that regulates nitrate uptake, root development and stress tolerance.

Researchers led by the Nation­al Cen­ter of Bio­log­i­cal Sci­ences, Tata Insti­tute of Fun­da­men­tal Research, Ben­galu­ru (NCBS-TIFR) have found a new path­way that reg­u­lates nitrate uptake in plants.

The MADS27 gene, which reg­u­lates nitrate uptake, root devel­op­ment and stress tol­er­ance, is acti­vat­ed by the micro-RNA miR444 and there­fore offers a way to con­trol these plant traits.

The researchers stud­ied this mech­a­nism in both rice (mono­cotyle­do­nous) and tobac­co (dicotyle­do­nous) plants. The research is pub­lished in Jour­nal of Exper­i­men­tal Botany.

Nitro­gen is one of the most impor­tant macronu­tri­ents need­ed for a plant to devel­op. It is a com­po­nent of chloro­phyll, amino acids and nucle­ic acids, among oth­er things. It is main­ly obtained from the soil, where it is tak­en up by the roots, main­ly in the form of nitrates and ammo­ni­um. Nitrates also play a role in con­trol­ling genome-wide gene expres­sion, which in turn reg­u­lates root sys­tem archi­tec­ture, flow­er­ing time, leaf devel­op­ment, etc.

So while much hap­pens in the roots to absorb nitro­gen and turn it into use­ful nitrates, the absorbed nitrates in turn reg­u­late plant devel­op­ment, besides being use­ful as a macronutrient.

Nitrate Over-exploita­tion

The pres­ence of nitrates is there­fore impor­tant for plant devel­op­ment and also for grain pro­duc­tion. How­ev­er, exces­sive use of nitrates in fer­til­iz­ers, for exam­ple, can lead to nitrate dump­ing in soil, lead­ing to accu­mu­la­tion of nitrates in water and soil. This accu­mu­la­tion con­tributes to soil and water pol­lu­tion and an increased con­tri­bu­tion to green­house gases.

To avoid this, nitrates should be used opti­mal­ly. Since the entire process of nitrate uptake takes place in the roots, a well-devel­oped root sys­tem is required for this to work optimally.

On one lev­el, the hor­mone aux­in is known to be respon­si­ble for well-devel­oped roots in all plants. A num­ber of genes are known to aid in aux­in pro­duc­tion, enhanced nitrate trans­port and assim­i­la­tion in plants.

Regulatory Switches

In addi­tion to this path­way, sev­er­al gene reg­u­la­to­ry switch­es are known in mono­cots such as rice, which reg­u­late nitrate uptake and root devel­op­ment, such as the micro-RNA miR444.

“The micro-RNA ‘miR444’ is spe­cif­ic for mono­cots. When this is not the case, its tar­get, MADS27, is pro­duced in greater quan­ti­ty and it improves the biosyn­the­sis and trans­port of the hor­mone aux­in, which is cru­cial for root devel­op­ment and its branch­ing,” says Dr. PV Shiv­aprasad, who led the researchers at Nation­al Cen­ter for Bio­log­i­cal Sci­ences, Tata Insti­tute of Fun­da­men­tal Research, Ben­galu­ru (NCBS-TIFR).

This miR444 reg­u­la­to­ry switch is known to turn off at least five genes called the MADS box tran­scrip­tion fac­tor genes. What is spe­cial about the MADS box tran­scrip­tion fac­tors is that they work like their own con­trol box­es. They bind to their pre­ferred spe­cif­ic DNA sequences and turn on the neigh­bor­ing genes.

Tri­par­tite Effect

The researchers exam­ined a tar­get gene of miR444 called MADS27, a tran­scrip­tion fac­tor that has not been well studied.

They found that this tran­scrip­tion fac­tor has a triple effect on the plant.

First, it reg­u­lates nitrate uptake by “turn­ing on” the pro­teins involved in this process. Sec­ond, it leads to bet­ter root devel­op­ment by reg­u­lat­ing the pro­duc­tion and trans­port of aux­in hor­mones. Final­ly, and some­what sur­pris­ing­ly for the researchers, it helps with abi­ot­ic stress tol­er­ance by keep­ing key stress-play­er pro­teins “switched on.”

“This is a new find­ing with a triple impact and offers an alter­na­tive means of reg­u­lat­ing and opti­miz­ing nitrate intake,” says Dr. Shivaprasad.

Dicotyle­do­nous Plants

In order to test this in dicotyle­do­nous plants as well, the researchers also car­ried out the study on tobac­co plants. “We real­ized that MADS27 works to improve three fac­tors — nitrate absorp­tion, root devel­op­ment and stress tol­er­ance — using RNA analy­sis and after we found which part of the genome this tran­scrip­tion fac­tor binds to,” explains Dr. Shivaprasad.

Accord­ing to the researchers, the MADS27 gene seems to be an excel­lent can­di­date to mod­i­fy to devel­op nitro­gen use effi­cien­cy, which helps the plant absorb more nitrates, and to devel­op abi­ot­ic stress tolerance.

“Tweak­ing MADS27 expres­sion through genome edit­ing is the next step so that the mod­i­fied plants can be used direct­ly,” he adds. The over­all goal of this study is to under­stand the role of epi­ge­net­ics in reg­u­lat­ing the expres­sion of such impor­tant genes.