Assimilation and fixation of nitrogen

1. Assimilation and fixation of nitrogen

2. Plants are: • Capable of making all necessary organic compounds from inorganic compounds and elements in the environment (autotrophic) • Required to compete with other organisms for these nutrients • Required to employ complex energetic pathways to convert macronutrients to useable forms

3. Nitrogen in the environment • Many biochemical compounds present in plant cells contain nitrogen • Nucleoside phosphates • Amino acids • These form the building blocks of nucleic acids and protein respectively • Only carbon, hydrogen, and oxygen are nor abundant in plants than nitrogen

4. Nitrogen in the environment • Present in many forms • 78% of atmosphere is N2 • Most of this is NOT available to living organisms • Getting N2 for the atmosphere requires breaking the triple bond between N2 gas to produce: • Ammonia (NH3) • Nitrate (NO3-) • So, N2 has to be fixed from the atmosphere so plants can use it

5. Nitrogen in the environment • This occurs naturally by:-Lightning: • 8%: splits H2O: the free O and H attack N2 – forms HNO3 (nitric acid) which fall to ground with rain • Photochemical reactions: • 2%: photochemical reactions between NO gas and O3 to give HNO3 • Nitrogen fixation: • 90%: biological – bacteria fix N2 to ammonium (NH4+)

6. Nitrogen in the environment

7. Nitrogen in the environment • Once fixed in ammonium or nitrate :- • N2 enters biochemical cycle • Passes through several organic or inorganic forms before it returns to molecular nitrogen • The ammonium (NH4+) and nitrate (NO3-) ions generated via fixation are the object of fierce competition between plants and microorganisms • Plants have developed ways to get these from the soil as fast as possible

8. Root uptake soon depletes nutrients near the roots • Formation of a nutrient depletion zone in the region of the soil near the plant root • Forms when rate of nutrient uptake exceeds rate of replacement in soil by diffusion in the water column • Root associations with Mycorrhizal fungi help the plant overcome this problem

9. Mycorrhizal associations • Not unusual • 83% of dicots, 79% of monocots and all gymnosperms • Ectotrophic Mycorrhizal fungi • Form a thick sheath around root. Some mycelium penetrates the cortex cells of the root • Root cortex cells are not penetrated, surrounded by a zone of hyphae called Hartig net • The capacity of the root system to absorb nutrients improved by this association – the fungal hyphae are finer than root hairs and can reach beyond nutrient-depleted zones in the soil near the root

10. Mycorrhizal associations • Vesicular arbuscular mycorrhizal fungi • Hyphae grow in dense arrangement , both within the root itself and extending out from the root into the soil • After entering root, either by root hair or through epidermis hyphae move through regions between cells and penetrate individual cortex cells. • Within cells form oval structures – vesicles – and branched structures – arbuscules (site of nutrient transfer) • P, Cu, & Zn absorption improved by hyphae reaching beyond the nutrient-depleted zones in the soil near the root

11. Nutrients move from fungi to root cells • Ectotrophic Mycorrhizal • Occurs by simple diffusion from the hyphae in the hartig net to the root cells • Vesicular arbuscular mycorrhizal fungi • Occurs by simple diffusion from the arbuscules to the root cells • Also, as arbuscules are degenerating as new ones are forming, the nutrients may be released directly into the host cell

12. Stored ammonium can be toxic • Plants can store high levels of nitrate or translocate it via the phloem without any effect. • However, high levels of ammonium are toxic • Dissipates transmembrane proton gradients required for both photosynthetic and respiratoryelectron transport • AND movement of metabolites to vacuoles.

13. Stored ammonium can be toxic • At high pH in stroma, matrix or cytoplasm: • Ammonium reacts with OH- to produce NH3. • NH3 is membrane permeable and diffuses freely across a membrane down a concentration gradient • At low pH in intermembrane space, lumen, or vacuole: • NH3 reacts with H+ to form ammonium

14. Remember: Nitrogen – the most important mineral nutrient in the soil • Nitrogen is frequently limiting in in terrestrial systems terrestrial systems • Microbial activity is continually converting N to lower energy forms • Conversion to organic form requires raising N to higher energy levels

15. Nitrate Assimilation

16. Deficiency Symptoms - N • General chlorosis. • Chlorosis progresses from light green to yellow. • Entire plant becomes yellow under prolonged stress. • Growth is immediately restricted and plants soon become spindly and drop older leaves. http://plantsci.sdstate.edu/woodardh/soilfert/Nutrient_Deficiency_Pages/soy_def/SOY-N1.JPG

17. Nitrogen assimilation NO3 NO2 NH4+ amino acids nitrate nitrite ammonium • Requires large input of energy • Forms toxic intermediates • Mediated by specialized enzymes that are closely regulated are closely regulated • Doesn’t have to start at the beginning

18. Nitrogen assimilation • Plants assimilate most of the nitrate absorbed by their roots into organic nitrogen compounds. • The first step of this process is the reduction of nitrate to nitrite in the cytosol by the enzyme nitrate reductase.

19. Nitrogen assimilation NAD(P)H induces NADH or NADPH • The most common form of nitrate reductase uses only NADH as an electron donor • The nitrate reductases of higher plants are composed of two identical sub-units, each containing three prosthetic groups • FAD—flavin adenine dinucleotide • Heme • Molybdenum—organic molecule called pterion

20. Nitrate Assimilation • Nitrate reductase is the main molybdenum containing protein in vegetative tissues • Nitrate levels, light intensity, and concentration of carbohydrates all influence the activity of nitrate reductases at the transcription and translation levels • These factors stimulate a protein, phosphatase, that dephosphorylates several serine residues on the nitrate reductase protein thereby activating the enzyme • This dephosphorylation/phosphorylation cycle provides more rapid control over this enzyme than degredation/synthesis of new enzyme would achieve • ( minutes versus hours)

21. Nitrite Reductase Converts Nitrite to Ammonium • Nitrite (NO2-)is highly reactive • Plant cells immediately transport the nitrite generated by nitrite reduction from the cytosol into chloroplasts in leaves and plastids in roots • In these organelles, nitrite reductase reduces nitrite to ammonium

22. Nitrite Reductase Converts Nitrite to Ammonium • Chloroplast and root plastids contain different forms of the enzyme, but both forms consist of a single polypeptide containing an iron sulfur cluster and a specialized heme group • The heme does redox reactions and electron flow, just like the reaction sites of chlorophyll

23. Nitrite Reductase Converts Nitrite to Ammonium • Nitrite is highly reactive • Plant cells immediately transport the nitrite generated by nitrite reduction from the cytosol into chloroplasts in leaves and plastids in roots • In these organelles, nitrite reductase reduces nitrite to ammonium • Chloroplast and root plastids contain different forms of the enzyme, but both forms consist of a single polypeptide containing an iron sulfur cluster and a specialized heme group • The heme does redox reactions and electron flow, just like the reaction sites of chlorophyll

24. Plants assimilate nitrate in both roots and shoots • In many plants, when the roots receive small amounts of nitrate, this nitrate is reduced primarily in the roots • As nitrate supply increases, a greater proportion of the absorbed nitrate is translocated to the shoot and assimilated there • Generally, species native to temperate rely more heavily on nitrate assimilation by the roots than do species of tropical or subtropical origins

25. Ammonium Assimilation • Plants cells avoid ammonium toxicity by rapidly converting the ammonium generated from nitrate assimilation or photorespiration into amino acids • This requires the action of two enzymes • Glutamine synthetase – combines ammonium with glutamate to form glutamine • Glutamate synthase – stimulated by elevated levels of glutamine synthetase • Transfers the amino group of glutamine to an intermediate yielding two molecules of glutamate

26. Transamination Reaction Transfer Nitrogen • Once assimilated into glutamine and glutamate, nitrogen is incorporated into other amino acids via transamination reactions • The enzymes involved in these reactions are known as aminotransferases • Best known — aspartate aminotransferase • The amino group of glutamate is transferred to the carboxyl atom of aspartate • Aspartate is the amino acid which shuttles reducing agents from the mitochondrion and chloroplast into the cytosol and in the transport of carbon from mesophyll to bundle sheath of C4 carbon fixation • All this requires vitamin B6 to act as a cofactor

27. Biological nitrogen Fixation • This accounts for most of the fixation of atmospheric N2 into ammonium • Represents the key entry point of molecular nitrogen into the biogeochemical cycle of nitrogen • Free living and symbiotic bacteria are responsible for converting atmospheric nitrogen into ammonium • Most of these are free living in the soil, a few form symbiotic associations with higher plants • The prokaryote directly provides the host plant with nitrogen in exchange for other nutrients and carbohydrates • The most common association is between members of the plant family leguminosae and bacteria of the genera Azorhizobium

28. Nitrogen Fixation Requires Anaerobic Conditions • As oxygen irreversibly inactivates the nitrogenase enzymes involved in nitrogen fixation, nitrogen must be fixed under anaerobic conditions • Therefore each of the nitrogen-fixing organisms either functions under natural anaerobic conditions or can create an internal anaerobic environment in the presence of oxygen

29. Nitrogen Fixation Requires Anaerobic Conditions • In cyanobacteria, anaerobic conditions are created in specialized cells called heterocysts • These are thick-walled cells which lack photosystem II—the oxygen producing photosystem of chloroplasts • Cyanobacteria can fix nitrogen under anarobic conditions such as those that occur in flooded fields • In Asian countries, nitrogen fixing cyanobacteria of both the heterocyst and non-heterocyst types are the major means of maintaining an adequate nitrogen supply in rice fields • They fix nitrogen when the fields are flooded, and die as the fields dry, releasing the fixed nitrogen into the soil

30. Symbiotic Nitrogen Fixation Occurs in Specialized Structures • Symbiotic nitrogen-fixing prokaryotes dwell within nodules • Special organs of the plant host that enclose the nitrogen-fixing bacteria • Grasses can also develop symbiotic relationships with nitrogen-fixing organisms, but these associations do not lead to the formation of root nodules • Nitrogen-fixing bacteria seem to colonize plant tissues or anchor to the root surface, mainly around the elongation zone and the root hairs • Known as actinorhizal plants

31. Symbiotic Nitrogen Fixation Occurs in Specialized Structures • Both legumes and actinorhizal plants regulated gas permeability in their root nodules • Maintaining a level of oxygen within the nodule that can support cellular respiration for the bacteria, but still sufficiently low to avoid inactivation of the nitrogenase Nodules Contain an oxygen binding heme protein—leghemoglobin Leghemoglobin produces a pink color Helps transport oxygen to the respiring symbiotic bacteria cells in a manner analogous to hemoglobin transporting oxygen to respiring tissues in animals

32. Establishing Symbiosis Requires a Change of Signals • Legumes seedlings germinate without any association to rhizobia • Under nitrogen limiting conditions, the plant and the bacteria seek each other out by an elaborate exchange of signals • Plant genes specific to nodules are called nodulin (nod) genes • Rhizobial genes that participate in nodule formation are called nodulation (nod) genes • The nod genes are classified as common nod genes or host specific nod genes

33. Establishing Symbiosis Requires a Change of Signals • Common nod genes • nodA, nodB, and nodC found in all rhizobial strains • Host specific non genes • nodP, nodQ, nodH, nodE, and nodF differ among rhizobial species and determine the host range • The first stage of the association is the migration of the bacteria through the soil towards the host plant

34. Nod Factors produces by bacteria act as signals for symbiosis • nodD is constitutively expressed—has a role in the activation of all other nod genes by signaling the formation of nod factors • Lipochitin oligosacharides with a chitin-b-1,4 linked N-acetyl-D-glucosamine • nodA, nodB, and nodC encode for the formation of this structure

35. Nodule formation involves several phytohormones • During root nodule formation, two process occur simultaneously • Infection and Nodule Organogenesis • (A) Rhizobia attach to the root hairs and release nod factors that produce a pronounced curling of the root hair cell • (B) Rhizobia get caught and curl, degrade the root hair cell wall allowing the bacterial cells direct access to the outer surface of the plant plasma membrane

36. Nodule formation involves several phytohormones • (C) Then the infection thread forms • Formed from Golgi depositing material at the tip at the site of infection. Local degradation of root hair cell wall also occurs • (D) Infection thread reaches the end of the cell, and thread plasma membrane fuses with plasma membrane of root hair cell • Then bacterial cells are released into the fused plasma membranes

37. Nodule formation involves several phytohormones • (E) Rhizobia are released into the apoplast and enter the middle lamella, • This leads to the formation of a new infection thread, which forms an open channel with the first • (F) Infection thread expands and branches until it reaches target cells • Vesicles composed of plant membrane enclose bacterial cells and they are released into the cytoplasm

38. Nodule formation involves several phytohormones • At first bacteria continue to grow with vesicles expanding by fusing with smaller vesicles • Following an as yet determined chemical signal from the plant, bacteria stop dividing and differentiate • Forms nitrogen-fixing organelles called bacteroids • The nodule itself develops a vascular system • To exchange fixed nitrogen for nutrients from the plant • And a layer of cells to exclude O2 from the rood nodule interior

39. The nitrogenase enzyme complex fixes N2 • Biological nitrogen fixation produces ammonium (NH3) from molecular nitrogen. • N2 + 8e- + 8H+ + 16 ATP 2NH3 + H2+ 16 ADP + 16 Pi • Note that the reduction of N2 to 2NH3 is a six-electron transfer, and is coupled to the reduction of two protons to evolve H2 • This reaction is catalyzed by nitrogenase enzyme complex

40. The nitrogenase enzyme complex fixes N2 • Can be separated into two components • The Fe protein • The MoFe protein • Neither of which has catalytic activity by itself

41. The nitrogenase enzyme complex fixes N2 • Ferredoxin reduces the Fe protein • Binding and hydrolysis of ATP to the Fe protein is thought to cause a conformational change of the Fe protein that facilitates the REDOX reactions • The Fe protein reduces the MoFe protein, and the MoFe protein reduces the N2

42. The MoFe protein can reduce many substances • The MoFe protein can reduce many substrates • Although under natural conditions the MoFe only reacts with N2 and H+.

43. Summary • Nutrient assimilation is the process by which nutrients acquired by plants are incorporated into the carbon constituents necessary for growth and development. • For Nitrogen: • Assimilation is but one in a series of steps that constitute the nitrogen cycle. • The principal sources of nitrogen available to plants are nitrate (NO3-) and ammonia (NH4+). • Nitrate absorbed by roots is assimilated in either shoots or roots • depending on nitrate availability and plant species

44. Summary • In nitrate assimilation, nitrate (NO3-) is reduced to nitrite (NO2-) in the cytosol via the enzyme nitrate reductase. • Then nitrite is reduced to ammonium (NH4+) in roots by nitrite reductase. • Ammonium (NH4+) from either root absorption or generated through nitrate assimilation or photorespiration is converted glutamine or glutamate through the sequential actions of glutamine synthase and glutamate synthase. • Once assimilated into either glutamine or glutamate, nitrogen mat be transferred to many other organic compounds • Via transaminatation reactions

45. Summary • Many plants form a symbiotic relationship with nitrogen fixing bacteria that contain an enzyme complex, nitrogenase, that can reduce atmospheric nitrogen to ammonia. • Legumes and actinorhizal plants form associations with rhizobia. • These associations result from a finely tuned interaction between the bacteria and the host plant • Involves the recognition of specific signals between the symbiotic bacteria and the host plant

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