Discovery of an Unusual Protein Playing a Significant Role in Earth’s Nitrogen Cycle

Anammox Bacteria Bioreactor

One of the bioreactors that Kartal and his colleagues used to grow cells of K. stuttgartiensis in the lab. Anammox bacteria are packed with heme-containing proteins, including the enzymes that perform the key reactions of the anammox process, making the cells remarkably red. Credit: Boran Kartal

Scientists from Bremen discover an unusual protein playing a significant role in the Earth’s nitrogen cycle. The novel heme-containing cytochrome is involved in the anammox process, which is responsible for producing half of the dinitrogen gas in the atmosphere and important in greenhouse gas regulation.

Ni­tro­gen is an es­sen­tial com­pon­ent of life. For ex­ample, it is re­quired for the pro­duc­tion of pro­teins.

Boran Kartal, head of the Microbial Physiology group at the Max Planck In­sti­tute for Mar­ine Mi­cro­bi­o­logy in Bre­men, stud­ies ni­tro­gen-cyc­ling mi­croor­gan­isms, which con­trol the bioavail­ab­il­ity of this vi­tal re­source.

A par­tic­u­larly in­ter­est­ing part of the ni­tro­gen cycle is the anam­mox pro­cess, short for an­aer­obic am­monium ox­id­a­tion. Here, ni­trite or nitric ox­ide and am­monium are con­ver­ted dir­ectly into dinitro­gen gas.

Now Kartal and his col­leagues dis­covered a pro­tein in­volved in the anam­mox pro­cess that might have some sur­prises. Their res­ults are pub­lished in the Novem­ber is­sue of Journal of Biological Chemistry.

Too un­usual to be no­ticed up to now

This pro­tein, a heme-con­tain­ing cyto­chrome, is in­volved in the con­ver­sion of am­monium and nitric ox­ide to hy­drazine. “Heme pro­teins have pro­found func­tions in life, like hemo­globin in our blood that car­ries oxy­gen. Heme struc­tures in gen­eral re­semble a spider web with an iron atom sit­ting in its cen­ter. Throughout the tree of life, we can re­cog­nize where this spider web binds to the rest of a pro­tein from a pat­tern typ­ic­ally formed by five amino acids,” Kartal ex­plains. “Sur­pris­ingly, the pro­tein we dis­covered has a very un­usual and un­ex­pec­ted struc­ture. It forms this pat­tern with only four amino acids, and was there­fore over­looked in stud­ies up to now.”

Anammox, short for anaerobic ammonium oxidation, is a globally important microbial process of the nitrogen cycle. It takes place in many natural and man-made environments. In the process, nitrite and ammonium ions are converted directly into dinitrogen and water and nitrate.

Anammox is responsible for approximately half of the N2 gas produced in the oceans. It thus removes large amounts of bioavailable nitrogen from the seas. This nutrient nitrogen is then no longer available to other organisms; this way anammox can control oceanic primary productivity.

The anammox process is also of interest in wastewater treatment. Removing nitrogen compounds with the help of anammox bacteria is significantly cheaper than traditional methods and reduces emissions of the greenhouse gas CO2.

Re­duc­tion of cli­mate-act­ive gases

The new pro­tein is in the cen­ter of a very ex­cit­ing and rel­ev­ant pro­cess. Anam­mox bac­teria pro­duce only at­mo­spheric ni­tro­gen (N2) from ni­trite or nitric ox­ide (NO) and am­monium, as Kartal previously showed.

Un­like many mi­croor­gan­isms, they do not con­vert nitric ox­ide to the green­house gas ni­trous ox­ide (N2O). Con­sequently, each mo­lecule of NO that is trans­formed into N2 in­stead of N2O is one less mo­lecule adding to cli­mate change. Anam­mox bac­teria re­duce the amount of NO avail­able for N2O pro­duc­tion, and there­fore, the amount of re­leased green­house gas.

A sur­pris­ingly com­mon pat­tern

With this rel­ev­ance in mind, Kartal and his col­leagues car­ried out a data­base search to in­vest­ig­ate how wide­spread pro­teins with the newly dis­covered pat­tern are in nature. “Re­mark­ably, this pat­tern is very com­mon,” says Kartal. Pro­teins with the four-amino-acid pat­tern are present in a large vari­ety of mi­croor­gan­isms throughout the bac­terial and ar­chaeal do­mains. “It is found in many dif­fer­ent groups of mi­croor­gan­isms such as meth­an­o­trophs, that live on meth­ane, and metal de­graders,” Kartal con­tin­ues.

The full po­ten­tial of pro­teins with the four-amino-acid pat­tern is com­pletely un­ex­plored. “In the anam­mox bac­teria, it is found in a pro­tein that shuttles elec­trons.” Kartal says, “In other or­gan­isms this pat­tern might con­fer spe­cial prop­er­ties to the pro­teins it is in. This is def­in­itely something to in­vest­ig­ate fur­ther.”

Reference: “Discovery of a functional, contracted heme-binding motif within a multiheme cytochrome” by Christina Ferousi, Simon Lindhoud, Frauke Baymann, Eric R. Hester, Joachim Reimann and Boran Kartal, 3 October 2019, The Journal of Biological Chemistry.
DOI: 10.1074/jbc.RA119.010568

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