The Nitro­plast, a Ni­tro­­gen-Fix­ing Or­ganelle

by Me­chas

Ni­tro­gen is the most abun­dant el­e­ment in the at­mos­phere as well as an es­sen­tial el­e­ment in all of life. As nicely ex­plained in pre­vi­ous posts, ni­tro­gen is needed to syn­the­size nu­cleic acids and pro­teins. Yet de­spite mak­ing up ap­prox­i­mately 78% of our at­mos­phere, we hu­mans (like the vast ma­jor­ity of liv­ing forms) are un­able to uti­lize this ni­tro­gen gas (N₂). We rely on a few mi­crobes that fix ni­tro­gen by re­duc­ing N₂ to am­mo­nia (NH₃), which is the form uti­lized by the re­main­ing or­gan­isms on planet Earth. This ca­pac­ity to fix ni­tro­gen was thought to be a unique prop­erty of a lim­ited num­ber of di­a­zotrophic bac­te­ria and ar­chaea. Un­til now.

The rel­e­vance of bi­o­log­i­cal ni­tro­gen fix­a­tion to our bios­phere is un­der­scored by the var­i­ous sym­bi­otic in­ter­ac­tions that en­able eu­kary­otes — in­clud­ing an­i­mals, plants, fungi, and pro­tists – to ben­e­fit from the am­mo­nia pro­duced by ni­tro­gen-fix­ing mi­crobes. Many ter­res­trial plants as­so­ciate with rhi­zo­bia bac­te­ria to form nod­ules where the bac­te­ria fix and trans­fer ni­tro­gen to the host in an en­vi­ron­ment that pro­tects the ni­tro­ge­nase en­zyme from the dam­ag­ing ef­fects of oxy­gen. Lichens, them­selves a sym­bio­sis be­tween a fun­gus and a pho­to­syn­thetic alga or bac­terium, also ob­tain ni­tro­gen from as­so­ci­ated ni­tro­gen-fix­ing bac­te­ria. Other ex­am­ples in­clude as­so­ci­a­tions be­tween pro­tists, such as al­gae, and ni­tro­gen-fix­ing cyanobac­te­ria. A re­cent study by Coale and col­lab­o­ra­tors an­a­lyzed one such as­so­ci­a­tion and demon­strated that in­tra­cel­lu­lar "cyanobac­te­ria" (which in fact, are no longer com­plete cyanobac­te­ria) con­sti­tute a novel ni­tro­gen-fix­ing or­ganelle: the ni­tro­plast.

Coale and col­leagues fo­cused on the alga Braaru­dosphaera bigelowii, which car­ries out oxy­genic pho­to­syn­the­sis dur­ing day­light hours. This alga plays an im­por­tant role in ma­rine ni­tro­gen fix­a­tion through the ac­tion of its en­dosym­biont UCYN‑A, aka Can­di­da­tus Atelo­cyanobacterium tha­lassa. The en­dosym­bi­otic UCYN‑A is re­lated to cyanobac­te­ria but, un­like all known cyanobac­te­ria, it lacks the genes for car­bon fix­a­tion (i.e., pho­to­syn­the­sis). How­ever, UCYN‑A does have the nif genes for ni­tro­gen fix­a­tion. At the out­set, it was un­clear whether the as­so­ci­a­tion be­tween B. bigelowii and UCYN‑A rep­re­sented a sym­bio­sis or a new case of evo­lu­tion that goes be­yond sym­bio­sis and to­wards the for­ma­tion of an or­ganelle. To solve this puz­zle, the au­thors probed this sys­tem for bi­o­log­i­cal fea­tures that are in­dica­tive of or­ganelles, like co­or­di­nated cell di­vi­sion, im­port of pro­teins by the en­dosym­biont, and pos­si­ble gene ex­change be­tween part­ner cells.

Fig. 1 B. bigelowii / UCYN‑A or­ga­ni­za­tion. Struc­tural char­ac­ter­i­za­tion dur­ing the light cy­cle: (Left) Dif­fer­en­tial in­ter­fer­ence con­trast (DIC) mi­cro­graph dis­plays the whole alga and show­cases UCYN‑A spher­oid body (SB) and plas­tids (Pls) in the FR21 cul­ture; the cor­re­spon­dent 4′,6‑diamidino-2-phenylindole (DAPI) stain­ing re­veals the cell nu­cleus (Nu). In both im­ages, the UCYN‑A spher­oid body (SB) is iden­ti­fied above the nu­cleus. Scale bars, 5 mm. (Right) Or­thoslice from soft X‑ray to­mog­ra­phy (SXT) data; color-coded 3D ren­der­ings of sub­cel­lu­lar com­po­nents. Adapted from Source. Frontispiece:A ni­tro­plast in­side B. bigelowii (coc­col­iths re­moved), marked by a black ar­row. Like other hap­to­phytes, the cell has 2 un­equal fla­gella. Source 

By us­ing soft X‑ray to­mog­ra­phy to im­age in­di­vid­ual spec­i­mens, the au­thors gen­er­ated 3D maps of cells and quan­ti­fied or­ganelle changes through­out the cell cy­cle. The im­ages show that UCYN‑A is dis­tinctly po­si­tioned be­tween two en­ergy-pro­vid­ing chloro­plasts. UCYN‑A also fol­lows a pre­cise se­quence of di­vi­sion events, co­or­di­nated with al­gal cell growth and di­vi­sion, which im­plies con­trol of its di­vi­sion by the B. bigelowii host. Such con­trol over di­vi­sion en­sures the ver­ti­cal trans­mis­sion of UCYN‑A to daugh­ter cells and rep­re­sents an im­por­tant step along the tra­jec­tory from an en­dosym­biont to an or­ganelle.

The au­thors also car­ried out dif­fer­en­tial genomic/proteomic analy­ses to de­ter­mine which pro­teins were en­coded in the B. bigelowii  genome yet lo­cal­ized in iso­lated UCYN‑A bod­ies. At peak hours of ni­tro­gen fix­a­tion (dur­ing day­light), nearly 30% of the pro­teins present in UCYN‑A came from genes en­coded in the B. bigelowiigenome. These pro­teins are pre­sum­ably im­ported onto UCYN‑A from the B. bigelowii host cell cy­to­plasm via a tran­sit pep­tide found in most of them, anal­o­gous to what oc­curs in chloro­plasts and mi­to­chon­dria.

Fig. 2. Evo­lu­tion and func­tion of the ni­tro­plast. B. bigelowii chloro­plast fixes in­or­ganic car­bon to pro­duce glu­cose, which feeds the res­pi­ra­tory chain in mi­to­chon­dria that pro­duces adeno­sine triphos­phate (ATP), which fu­els ni­tro­gen fix­a­tion in the ni­tro­plast. Glu­cose, am­mo­nia, and ATP gen­er­ated by the or­ganelles, to­gether with ex­ter­nally in­cor­po­rated com­pounds (phos­pho­rous, min­eral nu­tri­ents, and vi­t­a­mins), are the build­ing blocks for cell me­tab­o­lism, re­sult­ing in cell growth and di­vi­sion. Adapted from Source.

As with many en­dosym­bionts and or­ganelles, the genome of UCYN‑A has un­der­gone sub­stan­tial re­duc­tion when com­pared to closely re­lated cyanobac­te­ria. This gene loss re­sults in in­com­plete meta­bolic path­ways. Nicely enough, pro­teins im­ported from B. bigelowii com­ple­ment some of these in­com­plete path­ways, such as the syn­the­sis of amino acids like thre­o­nine, pro­line and ser­ine, nu­cleotides, vi­t­a­mins, and co­fac­tors. Other pro­teins were pre­dicted to par­tic­i­pate in cel­lu­lar ac­tiv­i­ties by re­pair­ing ox­ida­tive dam­age, reg­u­lat­ing UCYN‑A tran­scrip­tion and trans­la­tion, and co­or­di­nat­ing cir­ca­dian cy­cles by cryp­tochromes. Thus, UCYN‑A de­pends on its host for nu­mer­ous meta­bolic processes.

Dis­tin­guish­ing be­tween en­dosym­biont and or­ganelle is no easy task. There are only a few known cases of or­ganelles that have evolved from pri­mary sym­bionts, the prime ex­am­ples be­ing the mi­to­chon­drion and chloro­plast which carry out res­pi­ra­tion and pho­to­syn­the­sis in eu­kary­otes, re­spec­tively. An­other case in­volves the in­de­pen­dent ac­qui­si­tion of a pho­to­syn­thetic chro­matophore re­sult­ing from the en­dosym­bio­sis be­tween the amoeba Paulinella and a cyanobac­terium. The study by Coale and col­lab­o­ra­tors ex­pands the list to in­clude the ni­tro­plast, which has evolved be­yond an en­dosym­biont and is in an early stage of or­ganel­lo­ge­n­e­sis.

With its re­duced genome size, meta­bolic de­pen­dency, and syn­chro­nous di­vi­sion, the ni­tro­plast is now an in­trin­sic part of the B. bigelowii cell ar­chi­tec­ture. It also of­fers an­other beau­ti­ful ex­am­ple of how time and evo­lu­tion pro­vide the fab­ric for con­tin­u­ous bi­o­log­i­cal in­no­va­tions.

 

Note from the archive: STC had two posts deal­ing with Braaru­dosphaera bigelowii and its UCYN‑A sym­biont ear­lier, here and here.

 

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