1. Lipid Metabolism

General membrane functions:

• compartmentalization

• barrier from surrounding

• diffusion barriers

• gradients (e.g. charge)

• …

Curvature

Fluidity

• kinks can be produced by introducing cis-double bonds or adding methyl groups (bacteria/plastids)

  • methyl groups: less reactive, more resistant to oxidation (e.g. due to reactive oxygen species)

Width

• adjustment either by introducing longer chains or sterols

• important for transmembrane proteins (there are proteins that can only be inserted into membranes of a specific width

• important for insulation (electric charges)

  • example: axons

Surface charge

Packing defects

Fatty acid synthesis - chloroplast

• different in animals: located in cytosol, one of the largest molecular machineries

Lipid synthesis - membranes

Fatty acid modification - ER

Fatty acid degradation - polysomes/glyoxysomes

• different in animals: located in mitochondria

Plant fatty acid biosynthesis is comparable to bacterial fatty acid biosynthesis.

Differences between eukaryotic and prokaryotic fatty acid biosynthesis:

• Prokaryotes have single enzymes for all steps of the pathway. Eukaryotes have multifunctional proteins with different domains for different reactions, originating from the fusion of open reading frames.

• ER (eukaryotic) vs. chloroplast/plastid envelope (procaryotic)

• Acyl transferases

  • Substate specificity: C16 for plastids, C18 for ER

  • Substrate: acyl-ACP in the plastid/in procaryotes, in ER acyl-CoA is used

• Head group transfer

  • Prokaryotes: CDP-DAG pathway (activation of phosphatidic acid with CDP, then head group addition)

  • Eukaryotes: DAG pathway

Some metabolic pathways of plants are similar to those in (pathogenic) bacteria and therefore bear potential for drug development.

• Leaves: generation of energy

  • many chloroplasts, therefore many plastid lipids

• Roots: no photosynthesis

  • few plastids, many cytosolic phospholipids

• Seeds: energy storage

  • mainly triacyglycerols

This describes a fatty acid with a chain length of 18. It has two double bonds at positions 9 and 12 (counted from the acid group end).

In addition to the delta nomenclature (counting from the acid group end), there is the omega nomenclature, counting from the aliphatic end.

In all domains of life, the first double bond is introduced at delta 9 and then two Cs to either side (the second one must be an even-number position).

Fatty acid examples:

Properties to be modified:

• chain length

• number and position of double bonds

• additional functional groups (hydroxy/epoxy/… groups)

Reason for diversity:

Plants cannot move and need to adjust to different conditions such as temperature.

Head groups

Phosphoglycerolipids

Glycoglycerolipids

check Hölzl and Dörmann Annu Rev Plant Biol, 2019

for names

• SQDG and GlcADG are anionic head groups

  • important for plants because they can substitute phosphate groups of phospholipids

  • this is very useful because phosphate is the limiting resource for plants (and life on earth in general) to grow

  • the additional phosphate can be used in RNA/DNA etc.

Eruric acid (22:1Δ13) (a former major component in rapeseed oil but we cannot digest it)

• Synthesis of 18:0 (stearic acid)

• Desaturation to 18:1Δ9 (oleic acid)

  • In Arabidopsis via FAB2 in the chloroplast (stromal stearoyl-ACP desaturase)

• Chain elongation (ER)

  • 2 elongation cycles

  • (oleoyl-CoA and malonyl-CoA are “fused” by membrane-bound elongases in the cytosol (no ACP involved)

  • for more information check 8.5.4)

Ricinolic acid (12-OH-18:1Δ9) (castor oil/ricinus oil, used for plastic)

• Biosynthesis of oleic acid

• Oleate Δ12-hydroxylase adds OH group

Vernolic acid (12,13-Epoxy-18:1Δ9) (used for plastic production, found in esterase(?), toxic for insects (and for us)

• Biosynthesis of oleic acid

• Epoxygenase

DAG: activation of headgroup

CDP-DAG: activation of phosphatidate

Not every pathway is used for every headgroup; prokaryotic lipids are produced by CDP-DAG, eukarytic lipids are produced by DAG pathway (check which lipids are pro- and which eukaryotric)

CTP is the main energy carrier molecule for lipid biosynthesis.

Prokaryotic pathway in Plastid: CDP-DAG. This pathway is normally only used for synthesis of a few lipids in Eukaryotes. Lipid molecule (PA: Phosphatidic acid) enters, CTP binds and activates at phosphate, and the backbone is attached to CTP. Maximum length of FA is C18. (FAS-II-Pathway)

The DAG-Route (in ER) is the major route for lipid biosynthesis. CTP activates future headgroup (eg. choline), this is attached to pre existing backbone.

In plants not every pathway is used for every lipid. PC, PE, PS usually synthesised by DAG.

Lands-Cycle: Exchange of FA in Phospholipids. LPC-AT (Acyltransferase) exchanges FA on existing Phospholipids to accomodate changing demands.

(Lecture: Every Phospholipid, transformed by Phospholipase A (PLA) that cleaves off FA, this FA is activated by Acyl-CoA, Liso-PC (LPC) is formed, then any headgroup specific Acyl-transferase (LPCAT) introduces a new FA to form a new Phospholipid)

Kennedy pathway: Synthesis of Phosphatidylcholine. Choline is phosphorilated by ATP via choline kinase, then CTP binds and activates molecule via CCT, then Phosphatidyl group binds via CPT (choline phosphotransferase)

Mevalonate Pathway: The mevalonate pathway begins with acetyl-CoA and ends with the production of IPP and DMAPP.

Further examples: Sphingolipid-biosynthesis, phospholipid BS, alkene pathway… etc.

Lipoxygenase Pathway: JA production

Wax biosynthesis

Key enzymes:

Isocitrate lyase (isocitrate —> glyoxylate + succinate), necessary to bypass decarboxylation steps of the TCA cycle

Malate synthase (glyoxylate + acetyl-CoA —> malate)

This is important during germination to activate the energy stored in TAGs.

Fatty acid synthesis in the plastid. Export to cytosol, incorporated through the Kennedy pathways into glycerolipids in the ER, DAG-pathway: choline or ethanolamine is added, transport to plasmamembrane.

Biosynthesis of saturated fatty acids of normal length (Chloroplast):

• Acetyl-CoA is produced from pyruvate by pyruvate dehydrogenase in plastids

• Acetyl-CoA is converted into malonyl-CoA

• Carrier system exchange: CoA is replaced by ACP (acyl carrier protein)

• Four reactions that are repeated in a cycle:

  • Condensation: Malonyl-ACP/unfinished fatty acid-ACP and acetyl-CoA (KASIII)

  • Reduction: 3’-keto group is reduced to OH

  • Dehydration: Elimination of OH results in double bond in alpha-position

  • Reduction: double bond is reduced

• Result: C16 or C18 fatty acid (KAS I until C16, KAS II for C18)

Desaturation by a desaturase in the plastid (only 18:0 to 18:1Δ9)

Acyl-ACP can be used within the plastid for the synthesis of plastid membrane lipids OR exported to the cytosol (carrier exchange to CoA)

Synthesis of glycerolipids in the plastid or the ER by transfer of the fatty acid to glycerol-3-phosphate à diacylglycerin (DAG)

Headgroup is bound via DAG pathway (activation of head group with phosphate and CDP, Kennedy pathway, major route in eukaryotes) or CDP-DAG pathway (activation of the DAG with CDP)

Further desaturation by acyllipid desaturases and elongation by elongases in the ER membrane (only react with esterified fatty acids)

Transport of lipids via the ER to the respective organelles/membranes (e.g., plasmamembrane)

Synthesis:

• Cytosol: The synthesis of PC begins in the cytosol where the Kennedy pathway takes place. This pathway involves the conversion of glycerol-3-phosphate to phosphatidic acid (PA) through a series of enzymatic reactions.

• Endoplasmic Reticulum (ER): PA is then transported to the ER, where it is converted to diacylglycerol (DAG) by the action of phosphatidic acid phosphohydrolase. DAG is then converted to PC through the action of CDP-choline diacylglycerol choline phosphotransferase

Degradation:

• takes place during phosphate starvation

• phospholipase D (location: extraplastidial membranes)

  • PC —> head group + DAG-P (phosphatidic acid)

• phosphatidic acid phosphatase (location: extraplastidial membranes)

  • DAG-P —> DAG + P

• DAG is split into glycerol and fatty acids by lipases.

• Fatty acids are degraded via beta-oxidation (peroxysomes).

https://doi.org/10.1007/s40502-021-00624-x

Synthesis:

• Different pathways (4) possible (ER membrane).

• Synthesis by double acylation of glycerol-3-phosphate, then hydrolysis of the phosphate and acylation of the third position. Synthesis of PC, then desaturation of the fatty acids and cleavage of the headgroup (à DAG), acylation of the third position.

• Alternative: Formation of PA via Kennedy pathway in the cytosol, followed by transport to the ER. Dephosphorylation yields DAG, which is then converted to TAG (by acyl-CoA-diacylglycerol acyltransferase (DGAT)).

TAGs are stored in oil bodies (enclosed by a monolayer of phospholipids and hydrophilic proteins).

Degradation:

• Lipases: hydrolysis of TAGs into glycerol and fatty acids (in the oil bodies/glyoxysomes)

• Beta-oxidation of fatty acids in peroxysomes —> acetyl-CoA

  
  

• Generally for sphingolipids:

  • C-C bond instead of ester bond (general for sphingolipids)

  • More trans than cis double bonds, good for tight packing (general for sphingolipids)

  • OH groups (alpha position) allow “sealing” of the membrane and make it even more impenetrable

• LCB: long-chain base sphingolipids

  • Amino group (base) instead of the middle OH group in glycerol

  • Mostly C18 in length

• Ceramides

  • Very long chains (C20-C36)

  • Often only 1 DB

  • Used to increase the width of membranes

• Glucosyl ceramides (GlcCers)

• Glycosyl inositol phosphorylceramides (GIPCs)

Metabolism:

• Palmitoyl coa and serine à LCBs

• LCBs are converted into ceramides by forming an amide bond with a fatty acid

• Ceramides are branching point

  • Hexose: Glc ceramides

  • Phosphoinositol: towards GIPCs and IPCs

• Glycosidic bond formation of ceramide and glucose leads to formation of glucosyl ceramide

• Headgroup attachment is specific to the headgroup

Connection: LCB by palmotyl coa and serine, FA attached to LCB is Ceramide, then Glucose attached for GlcCer and then more sugars to headgroup for GIPC

“I will not ask that question because we have not discussed it here”.

• Defense regulation

• Development (root, flower,…)

• Biotic stress tolerance and UV stress tolerance

• Coronatine mimics the function of jasmonate-isoleucine

• Produced by pathogenic bacteria (pseudomonas) to suppress/modify plant defense mechanisms (by binding to the same receptors as jasmonate-isoleucine)

• Cutin forms a wax layer on top of the cell wall of epidermal plant cells

  • Pathogen defense, drought stress barrier, general protective layer

• Suberin forms a layer underneath the cell wall, between the plasmamembrane and the cell wall

  • Barrier against drought stress

Cutin above ground, complex structures/meshes, suberin below ground, forms layers instead of meshes

Esterified hydroxylated fatty acids (length 16-18 C)

Desaturases have mutated a lot throughout evolution and can now introduce other groups than only double bonds.

Desaturases are located in the ER (?).