Nitrogen assimilation
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Nitrogen assimilation. Plant Physiol Biotech, Biol 3470 Feb. 28, 2006 Lecture 12 Chapter 8. Nitrogen: an essential element. . Fourth most common element Proteins, NAs, PGRs, chlorophyll,… Bioavailable forms: nitrate ( NO 3 - ) and ammonia ( NH 4 + )

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Nitrogen assimilation

Plant Physiol Biotech, Biol 3470

Feb. 28, 2006

Lecture 12

Chapter 8

Nitrogen: an essential element

  • Fourth most common element

    • Proteins, NAs, PGRs, chlorophyll,…

  • Bioavailable forms: nitrate (NO3-)

    and ammonia (NH4+)

  • Paradox:limiting in environment for growth but plenty available in atmosphere as N2

    • Biologically unavailable!

    • Need prokaryotes to help with this…

The N cycle circulates N in the biosphere

  • 3 major N pools:

    • atmosphere, soil, biomass

  • plants convert inorganic soil N to organic N (amino acids, NAs, etc.)

  • Organic N moves up the chain to animals (they eat plants!)

  • Returns to soil in animal waste and decomposition after death

Nitrification by bacteria


or mineralization

by prokaryotes and fungi

Organic N pools

Fig 8.1

Essential N cycle processes include ammonification, nitrification and denitrification

  • Ammonification by prokaryotes and fungi returns N to soil: organic N  ammonia (NH4+)

  • Make ammonia biologically available by its sequential oxidization to nitrite and nitrate by soil bacteria during nitrification

  • Plants must compete for nitrate with soil bacteria that reduce NO3- to N2: denitrification

    • 93 to 130 Mt / year back to atmosphere

N fixation reduces N2 to NH4+

  • Soil N pool loses N to atmosphere but regains N through action of fixing bacteria

  • N2 NH4+ does not happen spontaneously: highly endergonic = very energetically costly

    Where does the biologically available soil N come from?

  • 10% of N fixed into N oxides: lightning, UV, air pollution

  • 30% via industrial N fixation: make N using fossil fuels via Haver-Bosch process at high T and pressure

  • 60% via biological N fixation by microorganisms: poorly understood but extremely valuable process

Only prokaryotes are nitrogen-fixers

  • Need dinitrogenase (a/k/a nitrogenase) to fix/reduce N2 directly to ammonia

  • Can be free living or symbionts, photosynthetic or heterotrophic bacteria or cyanobacteria

  • All need low/zero O2andhigh C levels: high energy requirement for N fixation slows growth

  • Symbiotic relationship involves metabolic integration between specific bacterial (microsymbiont) and plant (host) species

  • This usually results in forming nodules on the roots/stem

  • This is seen between Rhizobia (bacteria) and legumes (plant)

Fig. 8.2

Only a small number of economically important plants can fix their own organic N

Alfalfa (Medicago sativa)

  • These are legumes

    • “Pea family” (Fabaceae): lupin, clover, alfalfa, field beans and peas

  • Note that the top 5 crops cannot fix N and are reliant on fertilizer for high yields

  • This ability evolved over a long period of time and involves both plant and bacterial genes

  • Engineering this trait into modern crops is thus very difficult but economically desirable

  • Rhizobia exist as biovars that restrict the legume species with whom they can establish symbiotic relationships

Rhizobia multiply and infect multiple plant cells within the developing nodule

  • Bacteria continuously multiply during infection

  • Infection complete when bacteria released into host cells by budding off plasma membrane of infection thread

  • Nodule keeps growing via nodule meristem (rapidly dividing cells)

  • Bacteria multiply and infect new plant cells

  • Establish vascular connections with plant: photoassimilate (C) in, fixed N (ammonia, AAs) out

  • When they start fixing N2 for the plant they are called bacteroids



Fig. 8.3

Fig. 8.5

Oxygen inhibits dinitrogenase

  • Irreversibly denatures both constituent proteins

  • But need cellular respiration to make ATP!

  • Strategies

  • Free living bacteria maintain an anaerobic lifestyle or only fix N2 when under anaerobisis

  • Cyanobacteria structurally isolate nitrogen fixing cells (heterocysts): thick walls, high respiratory capacity limits O2 levels, lack PSII and thus can’t evolve O2

Fig. 8.8

  • Nodules restrict O2 to an O2-binding protein, leghemoglobin

    • Synthesized by host, present in bacteroid infected host cells

    • Keeps respiration high while sequestering O2 from dinitrogenase

Key metabolic step is conversion of fixed ammonia to organic N

  • Most plants can assimilate either NO3- or ammonia

  • Recall that nitrifying bacteria scavenge and convert ammonia to NO3-

    • too bad, NH4+ is the preferred form (already reduced for incorporation into organic molecules)

  • N assimilation is energetically expensive: 2 to 15% of plant’s energy production

  • Let’s examine assimilation of N from these two molecules

N assimilation is reliant on a steady supply of C !!

Fig. 8.7

Nitrogen assimilation is a series of reactions that coordinate C and N metabolism


Biologically unavailable!


(via nitrification by bacteria or fertilizer)




Nitrate reductase

+ nitrite reductase

ADP + Pi



Biologically available but toxic!


(C skeleton from ______ )

  • inhibits N2ase

  • Uncouples ATP synthesis from e- transport

  • Thus, plants use the Glu synthase cycle to rapidly assimilate N into organic molecules

Glutamate synthase cycle


ADP + Pi + NAD+



For export to N sinks

Where does the fixed N go?

  • Primarily exported via xylem: monitor by radiolabeling and examining xylem exudate

  • Temperate legumes export asparagine

  • Asparagine is 2 steps away from Glu and Gln siphoned from glutamate synthase cycle



Glu + OAA  αKG + Asp

Gln + Asp  Glu + Asn

Exported from Glu synthase cycle



Siphoned from Glu synthase cycle


  • Making N into an exportable form consumes ~20% of C allocated to N fixation

  • Want to export organic N with as little C attached as possible (low C:N ratio)

  • Asparagine: 2

NO3- is assimilated by nitrate/nitrite reductase

  • Uptake of nitrate is an energy-dependent process involving a specific transporter protein (like for most inorganic elements!)

  • Some of this carrier is constitutive but most is inducibleupon exposure to NO3- (inhibited by exposure to protein synthesis inhibitors)

  • Can store NO3- in vacuole, assimilate directly in roots, or translocate in xylem to leaves (sinks) for assimilation there

    Nitrate reductase activity coordinates N and C assimilation

  • Its complex regulation includes mechanisms of:

    • light and substrate which implies a requirement for photosynthetic energy (e.g., reducing power to supply e-)

    • phytochrome

    • reversible phosphorylation by a protein kinase/phosphatase

N uptake rate varies with plant age

  • Highest during early rapid growth phase

  • N uptake declines as plant enters reproductive phase

  • Assimilated N directed towards young, developing leaves

  • Leaves reach their maximum N content just before full maturity

  • Then leaves become net N exporters even though they continue to import N

    • a/k/a N cycling

  • Developing seeds are strong N sinks: requirement cannot be met by soil uptake alone

  • Steal (reallocate) N from mature leaves

Fig. 8.12

Metabolic consequences of N cycling

  • Most soluble leaf N is tied up in one protein: __________ !

  • This protein is thus an N storage protein

  • Plants mobilize N to storage in seeds, which may reduce photosynthetic capacity

  • In legumes, a lowered C assimilation rate reduces the capacity for N assimilation

    • Major limiting factor for seed yield in legumes

  • Perennials (e.g., trees) mobilize leaf N (rubisco, chlorophyll) in the autumn and store it in the roots as storage protein

    • N is too precious to discard with leaves!

Agricultural productivity is directly dependent on bioavailable N

… which depends on soil pH, temp., O2, H2O

  • Influence activity of microorganisms responsible for N assimilation

  • N is removed with the crop each year!

  • Farmers want to maximize productivity: most crops linearly increase yield with N applied until the critical concentration is reached

Fig. 8.13

N fertilizers are costly

  • Energetically: 1.5 kg oil per kg fixed N

    • 1/3 of energy cost of a crop of maize is N fertilizer

  • Financially for farmers

  • Without added N, yield on a plot eventually declines to a stable, base level

    Natural ecosystems are also N limited

  • 2/3 contribution from N fixers, 1/3 from atmosphere (deposition of NxOs)

  • Most N retained in forest canopy or degraded from litter and

    • Leached into the soil, or

    • Degraded by bacteria, fungi etc.

  • Finally convert organic N to inorganic N (NO3-, NH4+) via mineralization(e.g., ammonification)

  • Accompanied by immobilization: retention and use of N by decomposing organisms

  • Net mineralization (mineralized N minus immobilized N) is available to plants

Rate of natural nitrification varies with environmental conditions

  • Nitrification by bacteria = rate of adding N to soil bioavailable pool (as NO3-, NH4+)

  • Varies with temperature, pH, moisture, oxygen

  • Needs a lot of O2 because this process is energy dependent

  • Nitrification is likely a significant source of bioavailable N; difficult to show because plants keep soil N levels low!

  • Stored N in perennials helps plants overcome low soil NO3- levels

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