TABLE 12.1 ‘The major processes of the biogeochenical nitrogen cycle Process Definition (8g yr-te Industialfication Indust conversion of molecular nitrogen to ammonia) 0 ‘Amesphericfhation Lightning and hotocheméal comersion of molecularnitrogen tonitnte 10 Bologicafhation _Prckaryotic conwerion of molecular ntogen to armenia 170 Pant acquisition Plant absomption ard assimilation of ammonium or nitate 1200 Inmebitration Microbial aaceptien and ascinilation of ammoniim ox nitrate Ne ‘mmonifcaton Bacterial and fungal carabellsm of sol organic mater to anmanium NC Nuircation Bacterial (Ntrosomya sp oxKdaton of ammonium to nitite and subsequent bacterial Ntvebactersp) oxidation of nitita to ntrats Ne Mineralization Bacterial and fungal catabolism of soll organic mater to mineral nitrogen through ‘ammonifcation Fntifation NC \latiization Physical loss of gaseous ammonia tothe atmosphere 100 ‘Ammonium fuation Physical embedding of ammonium into sol particles 0 Denitrification Bacterial conversion ofitateto nitrous onde and malecuar trogen 210 uate leaching Physicl fw of nitatedisolvad in grcundwater cut o the topsolland eventually into te oceans 26 Rote Terasiorganians th aa the axorecorain about 10 9 510% gand S107 grepecivayoforgenicitogen tla ‘aiveinthe ode letuming thatthe aman of stnosahone Ny revirecoteary ng utp the mesh redencotne the Were te atsntyogeninekzule chan eigane eta sbeut S70 years fol ae taaon npubs o> 10g sos Toe gaa wey Ts 1D gyely os 10g yr Shenger NT SU/Cnoteaeuted Asrmoephari nitrogen a uw 2 se I j Z 4 a Denieifiern 1 4 pawn Gane I. trate SS titcation =] Froe-lving Na fxee ( or bytseene 2” > [orgntemaner | \ Eee pantaten Nitrite Loss by Wo . leshing on _ — FIGURE 12.1. Nitrogen cycles through the atmosphese asi changes froma gaseous formto sstuced tens before being incorporated into organic compounds in living ‘nganiame. Some of the steps involred.n the nitrogen sycle ate shown,High pie Membrane: ow ple Stroma, matrix, Yi tame, intermembrane es es Or oy off e a ee es "2 on || we eon 2 seem \ es eel “ | t Achigh ALN? MHismenbrane NM reach oa) [emanceaig) Galena: Pedue nie’ Sikleeaboe te tags nome caiet FIGURE !2.2_NH,* toxicity can dissipate pH gredionte, Tho lef side represents the stroma, matrix or ertoplasm, where the pH in high; the right sido roprosent ths kamen, tntor= ‘membrane space, or vacuole, where the pH is lowe and the membrane reprecintethe thylakoid ianer mitochondrial, or {enoplast membrane fr a calorcplast mitechondrion, oF root eel, respectively: The net reat of the reaction shown is that bof the OFF concentration on the letside and the HT” concenteationon the rich side have boon diminished that Js the pH gradient has been dissipated. (After Bloom 1997) oy <— 5] — fe] — a «a Nitrate rekuctace FIGURE 123A model ofthe nitrate reductase dimer ils trating the three binding domains whose polypeptide Sequences are similar in eubargoton molybslonum complex (MoCo), heme, and FAD. The NADH binds athe FAD- bincling mgion af och subunit and initiator a we-locteon ‘transfer fiom the carboxs(C) terminus, through each of the electron tranefr componiant to tho amino (N) termi thus, Nitrate is reduced atthe molybdenum complec nett the omine terminus The polypeptide sequences of the hhinge regions ae aighly variable among species, FIGURE 12.4. Stimulation of nitrate wea tae sctivty follows the inductien f nikrate reductase mRNA in shoots and rootsof barley giv, grams fish welght (Geom Kbinhois ota 1089) Shoot Folatve nate reductase mRNA (%) pat Time after duction (hours) 2048s) ‘eShpeland anLight Feredoxin (reduced) \, nor Neve eee yD oe 25) S > theme —_ Tre redactare nag Feerdoxin Ammonia (ocdized FGURE 125 Model for ccupling of photosynthetic electron flow, via ferredoxin, to the reduction of nitrite bynitrite recuctase, The enzyme contains two prosthetic groups, Fe S, and heme, which participate in the reduction ef nitrite t ammonium, | Stefaria medi (—————T] White ever Perl fvtkoss FT ox ESET Impatiens | a | Barley. ee a es | Bean Ss Bread bean Ld Pea Ce Radish a a a white bine 7 Nitrogen in aylem exudate (9) [S hitrte amides [1 Amino acids EEE Ureides FIGURE 12.6 Relative amounts of nitrate and other nitrogen compounds ir the xylem exudate of various plant species ‘The plaats wire grown with their toots exposed to nitrate solutions. and xylem sap wascollected by severngof the Stem, Note the presence of ursides, specalized nitmgen compounds, inesn and pea (which will be discussed Tater Inthe text). (After Pate 983.)w lear ee + 0 (GOGAT, yc _6) + He — a, eo Or Gr nadHon Mao ory oe ue ao Fl iy Oe eo 4 ! Glutamate Ghaamine 20xodlutarte 2lutsmates o Glutamste Geek dehydregenase_cooH i ‘so i y * ; ‘Ammanim om i pe i i 2Oxoglutarate Glutamate ° Aepartte SImitransferase cOOM itp ee ra im Glutamate Ovaloscetate Aspartate 2-Oxoglitarate ° Asparaine cook ymthetase. GOON 20H T i as) Glutamine Aspartate Asparagine Glutamate FIGURE 127. Strusture and pathways of compounds involved in mmoniam metabolisnArmmonism cin be assimilated by one ‘of sever processes, (A) The GS COGAT pathyray that forme shitamine and glutamate. A reduced cofactor is rai foe the fection: ferredenn in goon leaves and NADH in Rorphotonyn {heii teste (B) The GDH pathnvay that forms glutamate using NADH or NADPH as aredustant (C) lanstoro! the amino soup fiom gistamate to oxaloacetate to form aspartate (ca Siyaai by aspartate aminotranstere) (D) Syntatsof Ssparagine by transer ofan amino acié group from ghitamsine tobepartte atalyzod by asparagine smth).TABLE 12.2 Examples of organisms that can carry out nitrogen fixation Symbiotic nitegenfixtion Host plant Leguminauslagumes,Parasponie ‘Actinothizak alder (tee), Ceanothus (shrub), Casuarina (tree), Datica (shrub) Gunners ‘Aol water fern) Sugarcane fixing symbionts ‘Azerhizebium Bradyrhizobium, Phetorizeblum = Rhizobium, Sinorhizobium Frankia Nostoc ‘naboena Acetobacter Free-living nivogen fuation Type. ‘Gjanobactera (blue-green algae) Other bactata Aerobic Facutative Anaerobic Nonphctosyrthetic Protosythat TABLE 12.3 Associations between host plants and rhizobi Plinthest Parasponia (a nonleguie, formerly called Tera) Soybean (Giyainemax) Alfa (Mediago sativa) Seibania (aquatic) Bean (Phaseolus) {Clover totam) Pea (Pisum sativum) ‘Aeicheromere aquatic) ing genera “Anabaena, Calon, NOsTOC ‘Azospilun, Azoiobacter Blerinkia,Dersia Bacis Keio ostium Methanococcus (archaebacterium) hromatiun, Rhadospritumm Rhizabial symbiont ‘Bradhtzcblum spp. ‘Brad hizeblum japonicum (slow-growing type; Shnomizebium fied fast-growing t=) Sineshizotium meio Azoitizobium (fms both rot and stern nodules; testers have adventitous roots) ‘Rhizobium equminosarumby. paseo; hzobien tropics Rhizobium et -Bhizoblum laguminasarum bu. efoll ‘Rhizobium leguminosarum bv. viiae Photorhizobium (photosyrthetially active rhizobia that for stem nodules probably associated with adventitious roots)FIGURE 128 Root nodules on soybean, The nodules area result of infection by Rhitobium paponcune,(@ Wally Ekothart/‘Visuals Unlimited.) FIGURE 129. Astersystina fila mento the nitogerfixingcyancoac. terlum Antueno, The thickewalled Theterocysts, nterspaced among Vege lave cally Fave on anaerobic inter hvironment that allows yance itera tof ltragen in acrcic conditions. (© Paul W fokneon/ Biological Photo Service)Hydrogen sultte, fucose, of Zoey fucose \ ot sis Oy J ie as no Fatty add FIGURE 12.10. Ned factors am lipachitin ligossechardos ‘The fatty ace chair typically has 16 to 18 carbons, The number of mpeatod mille covtone (1) ie sally 2 62. (After Stokkermans etal 1995)oct har F Z Rhiobia [Note that the reduction of Nz to 2 NH, a sixelectron transfer, is coupled to the reduction of two protons to evolve Hl. The nitrogenase enzyme complex catalyzes this reacion,| The nitrogenase enzyme complex car be separated into ‘ovo compononts—the Fe protein an tre MoFe protein— either of which has catalytic activ by sell Figure 12.12% + The Fe protein isthe smaller ofthe tvo components Ane has tao identical subunits oF 300 72 KDa each, dlependingom the organiam, Each subunit contains an inon-sulfur cluster {Fe and 4 S™) thet participates in the redox reactions lavolved in the cnversion of Ny, te NH Tho Fe protein is trevorsiblr macuivated by (©, with typical hal decoy times of 2 0 45 seconde (Dixon and Wheeler 1880), cating“ growth +The MoFe protsin has Four subunits, witha total mol fecidar mass of 180 to 235 kDa, depending onthe spociss, Each subunit has two Mo-Fo-Sclurtere, The Mote protein i also inactivated by oxygen, with a hnal.docay time in air of 10 minutos. In the overall nitrogen reduction renction (seo Fire 12.12) feredonin serves as an electron donor tothe Pe pro- ‘ein, which i tum hydrolyzes ATP and reciacos the Moe ‘protein, The Mofe protein then can reduce numerous sub Stratos (Tabb 12.4), although undor satural conditicns it reacts only with Ny and 1", One of the reacts catalyzed. bby mtrogonase, tho redaction of acotylono to ethylene, is use in estimating ntrogenase activity (swe Web Topic 122) “Tho onorgotics oF nitmgon fixation is complex. Tho peo- duction of NE from N, and F3, isan exergenic reactionFGURE 12:12 ‘The soation at Nitrogenase enzyme complex yzed by nittogenaee Fencdonsn, tseluow the Fe protin. Binding End hydric of ATP to the Bo Fe protein oFe protein pprowin isthonght causea cone [Fevedadinon Peale {Brmational change of the Fe pro- Th He tein that falitates the tedox mac ‘tons. The Fe protein recuises the Mote protein and the Moe pro- ‘ein ettuces the (After Dison ang Wheeler 186 and Buchenan sta. 2000,) Babette Faredorine| Neen TABLE 12.4 Reactions catalyzed by nitrogenase Ny NA Molecular nitrogen fration N01, +140 tous odd raducton Ny N+ NH ‘zie reauction Ch CHy Acetylene reduction 2H Hy H, produttion ATP ADP +, ATP hydolyticactiviy ‘Source Aer Bar 197% i hy cmerang coc Allantoic add Allantoin iting FIGLRE 1212 The major uside compounds sad to trane- Fortnitrogen from sites of fixation to sites were their ‘eamination sll provide nitrogen for amine acd and ipneboside syathecisSulotareorace i Adening, = Roo nbn zSipheadenyne 2-thosphondenorine 5 phosphonate OAPs) -Sullated metabolite aD 5 kinase Alan QT abate, qo Nene suite soe adam > oi o- tate SE (ee ees 8 GSH iGO SFdlgy tal \ Sate safe Prrephosphatasey"° ag) Mevesbes-phosphoulate APS) “ S-Seguathione “ setng 2 sce sooner —ccom MEMES yo gy ct coer ee ah ye cont ° 2 nh aceyaerne Mr avian Gia ots th saci Octane trna Oe i eveme yy ta oat I on eal FIGURE 12.14. Structure and pathways compounds involved in sulfur Shitamata assimilation. The enzyme ATP sulfuryiase leaves pyrophosphate from ATP And replaces t with subate Sulfide is produced from APS through reactions é involving reduction by glutithione and ferredonin, The sulfide or thosulfide of Yo reacts with O-acetylsenine toform cystine. Fd, ferredaxin;GSH, ghtathione, reduced; CSS5, glutathione oxidized. Reduced glutathione Glutathione also acts as a signal that coordinates the absorption of sulfate by the roots and the assimilation of sulfate by the shoot.& a w= Be os Ty a Tew i i Tartar cid copper tari scl comple * Chlorophyll i agag0oe © QROKOKRKS, Polygalacturonic eid chain Much ofthe calcium in the eallwal thought tobe hound inthis tsdhion Cakeium fon are bald in the spaces between wo Polrgolacturonc seid para Polygatacturonic acid ‘oondination bond between unshared elections from de Iniogen atm and the tnaghesiaan cation, (2) The "a Slome afa carbon compound donate unshared electron bbow" model of the interaction of peiygalactaronis sch Fain (epresented by dows)toforma bond wilia cation, aaj constluen! of pectin i eell wall and caer fa (A) Copper ions skate clectone with thebyosyd onygnre Abright is an enlargcencnt of «single calcium ion forming 3 ff trterie acid. (B) Magpestum ions aharelectrny with coorlination complex with the hyaeonyl oxygen ofthe [Bitmgen atome in slesephylls Decbed lincorgertoonts galacturonic suid resicce, (Alter Roce 1077) FIGURE 1215 Examples of coonlination (Coomlinatics complexe form en omy (A) Monovalent cation (@) Divalentcation coon cor e007 ton vo von i one ae a See a ae os Joon ison of LO Comper emation — lope Male ait Malte Potassium malte FIGURE 12.16. Faamplos of slectioatatic (lnie) comaloxen. (A) The mance ‘valent cation K” and malate form the complex potassium malate. (E) The Uivalont satin Cot and pectate form tho complow aleium portato Divalent cations can form crosslinks betwsen paralll strnds that contain negatively changed easheryl groups, Calcinm soserlinks play structural te in the cell walls, Calcium pecate ppp _ferteceletae Porphyrin ing FIGURE 12.17 The ferrochelatase reaction. The enzyme ferrochelatase cat- alyzes the insertion of ion into the porphyrin ring te form a coordination ‘complee Ser Figure 77 for illustration ofthe biosynthess of the porphyrin fing,() oexygenase reacten iit Livoxygenase ® fe C 4 & fatyacid 4 $ 4 (©) Diongenese reaction Froblhyéromlaeg Fe, scorbate Kore fers ‘The cionygenaseliponygenase (talse te addtonot two Stom of ongen tothe Cenjugeted fot ac to form STyefoperonde wth pa of Sevroneconugsted douse Bench the hydro perony faryactin thane Aten fatty acdsandether metabolites ‘The cicnyoonase prob oot hyaronyaseentlyzesthe i fcltion ef one angen rom ba peers eee shainto produce indrexarotne. and the addition of one angen to hoa oon Retogiuaratetoproauce Praline boon rarctHydhonypatine Sucinate ——sucinate and CO, Ainpelypentide) arerogltarate tinpdvpentide) (@ Menoaxyaenase reaction ar soon coon (ytochreme PASO usescne i Swan from 03 to by by Fydrexylate craic acl Ty + op + uavpn ene Sechrere aso, I L 9 a Ginnamic acid | FIGURE1219. Example =) FOURE 1219. Summary of theprocesses involved in he [imibion of mineral ntingen in oe lok Nitate fandom Sched fos the mae Guo ‘mesophll cll via one of the nite proton symporters (QIET smo the cptopluen Thowe it i oduced to ait vie ‘nae reactase (NM, Nitto fs talocated ino che ‘roma oth chlcmplaet along with proton, Inthe SMhoma, sie randtced to amu ne ite rece [ard other substrates) and the other oxygen to predce Water NAP ress the Saree of the tro typor of xygonnes actions in calle higher plant. \ ees SS cutamae Ly ouramite "7 asparate > sspaagne| ae | tue otra Saceead Z ai nS ‘00a hs an convert int gata I ela anal unweane gets GS aed ie iyemicaberiel a.” nanan tCOCAR) One acai he ep, Rita basi o spa i pe cae ee A nals pein htt UiSrcomare parents epee pyrene ‘ean of AiBuivabat st phen above sh machenMeasurement conditions * 700 umal matt Cop Se0|imol mat" Coz oal ‘a0 aorta ——Ta0 a0 Fhotcaynthetic active radiation (unl mr") FIGURE 12.20, The asimilatory quotient (AQ = CO, assinl- Iated/0, evohec) ef wheat seedlings a5 a function of light level (photosynthetic active radiation). Nitrate photoasimi- lation is directly related to assmilstory quotient because ‘arisfer of electrons to altrate and nitrite during photoas- imation Incrsses O, evoluten ftom te ight-dependent reactions of protosynthests, while CO, assimilation by the lightandependent reactions continued t similar rates. Therefore, plants that are photoasimllting nitrate exblat Homer AQ. In measurements carrad out at ambient, 369, tmol mat Co, concentrations (red trace), the AQ ‘decreased as s function of Incident radiation, Indleating that photoassmilation rates creased. At elevated (700 mel met CO, Elue trace) the AQ remains constant at all light levels use, indicating thatthe CO,-fxing reactions are competing for reductang, and inhib phstoassmlaton, (After Bloom et a. 2002)