Indoles & Indole Acetic Acids
Ascorbic Acid
Abscissic Acid
Sulfur Compounds
Volatiles / Gases
See also the opposites of Hormones: Allelopathy in Plants

Phytohormones are plant hormones which govern the way the plant grows in some aspect or other. There are many differing kinds of phytohormones, with various modus-operandi. Auxins are a certain class of phytohormones, based upon Indole Acetic Acid and analogues. There are many other classes.

Signalling Molecules are usually volatile compounds which are able to travel through the air to other plants, where they may variously stimulate the growth of nearby similar plants, or suppress the growth of competing plants, or alert nearby plants of the same species to the fact that the plant emitting the volatile substance(s) is doing so because it is under attack from some pathogen and is signalling nearby similar plants to prepare defences against the pathogen(s). There may also be other circumstances where signalling molecules are emitted.

Some signalling molecules go through the soil or the root system to nearby plants or through the hyphae of fungi to other plants, with similar motives.


There are not many naturally occurring organochlorides in the plant world, but there are some. Perhaps the most abundant organochloride in the plant world is that contained in one of the four indole plant growth hormones, 4-chloro-IndoleAcetic acid (4-Cl-IAA), which is bio-synthesized in members of the Pea Family such as green peas, lentils, vetch, various beans and other peas. Alongside it is the non-chlorinated version, another auxin. The potency of the growth hormone function of the chlorinated version is 100-fold stronger than that of the normal version, Indole-3-Acetic Acid (IAA). However, it has been found to be far too strong to be of much use as a growth promoter in the plants that synthesize it: pea cuttings treated with it at first rooted profusely, but for seven days started producing large amounts of the gas ethylene, a senescence inducer and almost died, whereas normal non-chlorinated auxins only initiate production of Ethylene for one day. It is the ethylene which also stimulates growth, but it can also over-stimulate growth, resulting in death. It is theorised that the plant may produce chlorinated auxins which they then use as the often observed (but so far un-identified) 'death hormone' produced by the seeds during their development which eventually kills the mother plant thereby giving the seedling a much better survival chance.

Control of the shape of leaves is accomplished by the concentration of auxins in certain areas encouraging higher growth whilst the concentration from locality to locality of anti-auxins reduces or inhibiting growth in other areas. By this means leaves can be made flat, cusped, crinkled, cup-shaped or have pointed ends, rounded ends, spines or teeth on the edge, etc.

Sunflowers (and several other flowers) are heliotropic (pointing towards the sun and following its progress across the sky) only when in the bud stage and not when in flower. When they set flower they affix themselves to point in one direction only, usually towards the morning Sun. The seeds are thus protected from the full blaze of the midday sun. The heliotropic response is mediated by one of the plant hormones, Indole-3-Acetic Acid (aka 3-Indolylacetic Acid or IAA) which is a heteroauxin or Plant Growth Regulator. Indole-3-Acetic Acid is a light sensitive hormone which causes the cell to grow in an asymmetric fashion, elongating it. It is this aligned elongation which causes the flower to turn, nominally towards the source of the strong light, the sun. This is a case of Photonasty (light stimulated movements of plants) It seems that another auxin, Indole-3-acetonitrile (aka 3-Indolylacetonitrile or IAN), which has an inhibitory effect on asymmetrical cell growth may also be involved.

Two other native Auxins produced by plants are (Indole-3-Butyric Acid IBA) and 2-PhenylAcetic Acid (PAA), the latter not being an Indole but it behaves similarly so is classed as an auxin.

Indole-3-Butyric Acid (IBA) is present in Maize and also the non-native Tea Plant (Camellia sinensis) and in all Willow Trees (Salix) but it is not widely found elsewhere. It is a phytohormone belonging to the Auxin family which includes such members as Indole Acetic Acid (IAA) and the far more potent (by a 100-fold) 4-Chloro-IndoleAcetic Acid (4-Cl-IAA). It is used commercially as a plant hormone and was once thought to be non-natural until it was discovered in several species of plants. Its modus operandi is contentious, with some scientists suggesting Indole-3-Butyric Acid is converted into IndoleAcetic Acid before being and effective hormone whilst other researches suggest that it acts as an auxin in its own right.

PhenylAcetic Acid (PAA) is a non-indole Auxin which possesses hormonal effects in plants similar to those induced by Indole-3-Acetic Acid (IAA) but is several times less potent. It was once thought not to be found in plants but it has been found in the most-studied of plants, Thale Cress (Arabidopsis thaliana) and has since been found in Tobacco - at several times the concentration that the more potent IAA. It is now known to be widely distributed in both vascular and non-vascular plants (those with and without vessels for transporting fluids). Synthetically-derived PAA has been used since 1975 as a phytohormone.

There are many other indole-based hormones which are produced synthetically in the laboratory.


Melatonin (not to be confused with Melanin, a black pigment made in the skin of dark-skin people and which is also responsible for sun-tan caused by exposing the skin to sunlight or UV radiation) is a hormone produced by the pineal gland in mammals which regulates sleep/wake patterns in response to the bright light of daylight. It synchronises their circadian rhythms, which otherwise free-run at a period slightly longer than a day (about 25 hours, rather than the 24 hours of a day). Melatonin is also involved in the mechanism by which certain amphibians and reptiles can change the colour of their skin, such as can chameleons. It was discovered in 1958.

Up until 2005 no one ever suspected that Melatonin would also be found in a great many plants (in all plants that have so far been screened). It occurs in all parts of the plants, roots, stems, leaves, flowers, fruits and seeds, in varying proportions. Some species of plant have very high amounts of it, varying from several µg/g to just pico g/g. The highest amounts are found in tea, coffee, beer, barley, corn, rice, oats and wheat. It is synthesized in response to stress, the higher the stress the plant is under, the more it generates. The stress could be a fungal infection, insect damage, water deficiency, extremes of temperature, toxins, heavy metals, or soil salinity, for example. It performs so many diverse functions within the plants that it is difficult to classify. It co-opts a plethora of co-enzymes and other substances to help it perform these tasks. Researchers still do not fully understand all of the interactions of melatonins within plants; study is still on-going. Its effects are fairly widespread including auxin-like effects. It is also capable of chelating heavy metal elements forming complexes, such as with cadmium and many other so-called heavy metals.

Melatonin is involved during the following plant conditions: seed ripening, fruit ripening, flower buds and other development stages, leaf senescence, intense sunlight (especially ultraviolet), heat, cold, drought, high salinity, bacterial pathogens and by chemicals which cause stress in plants. It is also involved in growth regulation and in photosynthesis, but so far no one has been able to establish with certainty any hormonal activity. Only limited evidence (in certain plants only) has any light-induced circadian rhythm generation been found.

The melatonin (and the plethora of other co-enzymes, etc involved in response to the stimuli) initiate the following responses to those plant conditions mentioned above: Increases in resistance to osmotic stress and to oxidative stress; increases in cold resilience - increases in the cold and drought responsive genes; increased thermotolerance - increases in production of heat-shock proteins and other heat-shock substances; increases in pathogen resistance; increases in seed viability and seed germination capability; preservation of chlorophyll which delays cell senescence; increases in anti-oxidant enzymes, increases in low-molecular weight anti-oxidants leading to more scavenging of free radicals and singlet oxygen moieties; increases in photo-protection and strong-sunlight tolerance. This is quite some list, especially since Melatonin was only recently discovered in plants.

It is a powerful free-radical scavenger and anti-oxidant. In order to conduct and orchestrate all these diverse effects the Melatonin can also be hydroxylated non-enzymatically by its eager interaction with free radicals, for example with hydroxy radicals. By these means and others the following related substances are also created from Melatonin within plants:



A Butenolide of great importance to both mammals and plants is Ascorbic Acid, better known as Vitamin C (which is not a single compound, but refers to a number of compounds having Vitamin C activity - but to work well, they are converted to the most active form of the vitamer, DehydroAscorbic Acid). Between them, Gibberellic Acid and its antagonist Ascorbic Acid act in anti-concert regarding their roles in seed germination, the first encouraging germination, the second discouraging it. When the relative concentrations of the two tip towards Gibberellic Acid, then the seed sets about germinating, but otherwise if the proportion is tipped towards Ascorbic Acid, then germination is delayed until conditions are just right. A differential mechanism, a balancing act which has far more refined response than that of a trigger point set to the concentration of a single substance. Temperature, rainfall and sunlight-hours could all have their say on the balance between the two mutually antagonistic compounds in ways not yet fully understood.


Abscisic Acid is an ubiquitous and multi-functional plant hormone discovered in 1961 to 1963 in Cotton plants and Lupin by several researchers. It has since been found to be vital for the growth of most (if not all?) plants. It is a stereoisomeric molecule which can exist in two forms, the (S)-cis-Abscisic Acid and (R)-cis Abscisic Acid forms, of which only the former exhibits hormonal activity in plants.

Since Cotton is non-native to the UK, your Author has put it under Lupin, but it occurs in most (all?) plants. It was named Abscisic Acid because it was first thought to be only involved with abscission in plants (the shedding of parts of a plant, such as seeds, leaves, fruit, flower etc) but it is now known to be involved in a great many other ways in which plants grow and senesce. ABA is also produced by some plant pathogenic fungi for nefarious reasons.

It is now known that Abscisic Acid promotes seed dormancy, assists tolerance to desiccation, and inhibits precocious germination during seed development. It also enhances root growth unless they are stressed by shortage of water in which case it inhibits root growth. It also boosts closure of the stomata to help preserve internal water and accelerates leaf senescence.

ABA is located everywhere in the plant; but concentrations of it vary from 1 to 15nM in the xylem, or up to 3000nM within water-stressed leaves.

Abscisic Acid is synthesized within plants from Zeaxanthin via trans-ViolaXanthene to produce first Xanthoxin (not to be confused with Xanthotoxin) which is eventually transformed into Abscisic Acid.

Abscisic Acid is 'in-activated' by being transformed into either Phaseic Acid (itself a hormone found in plants) or to its -β-D-Glucose-Ester. But Phaseic Acid is also a plant hormone which is associated with arresting of photosynthesis and abscission (the shedding of parts of a plant, such as seeds, leaves, fruit, flower etc). High levels of Phaseic Acid impede the closure of stomata (the opposite effect to Abscisic Acid) and to reduce photosynthesis (at least in Thale Cress). Therefore the two hormones Abscisic Acid and its decomposition product Phaseic Acid act partly in opposition to each other, providing a finer level of control that is possible from differential systems, such as in the Ascorbic Acid/Gibberellic Acid (which are both hormones) differential ratio as described on the Danish Scurvygrass page.

See the Violaxanthin Cycle where the balance of Violaxanthin, Antheraxanthin and Zeaxanthin helps protect plants from excess sunlight, which is another balanced cycle.

KARRIKINS - plant growth regulators

Hot forest fires (and any burning plant material as long as it is hot enough) will generate substances called Karrikins, which are wafted around in the smoke. Karrikins are lactones. The karrikins are created by the partial burning of cellulose, which is present not only in trees, but in straw and virtually all other plant material. It is just that, when burning, trees burn at higher temperatures (because they are taller) than lowish plants, and it is in this hotter heat where karrikins are synthesized. Karrikins are Plant Growth Regulators (in particular KAR1) which are stable but volatile molecules. They encourage and promote the germination of seedlings, which would be especially useful to the continued growth of plants razed to the ground by a forest fire, as long it didn't get too hot below the soil to damage the seed. These could be the seeds of trees burnt, or other seeds belonging to other plants that were also scorched. The triggering of seed germination by Karrikins requires the synthesis of Gibberellic Acid (another plant hormone - described below) and the presence of light. In effect, the seeds become more sensitive to sunlight, and emerge from the ground even with reduced exposure to sunlight. They also seem to make the plants more resistant to stress (such as drought). This is an adaptation by plants; they have 'learned' that there is a lot of sunshine that can percolate to ground level after a forest fire, and that this would now be an opportune time to germinate and dominate the scorched and razed land once more. They use the Karrikins which were within the smoke but may have been picked up by any rain-drops which rained on and watered any scattered seeds helping them to germinate. Karrikins are key germination triggers for many plant species prone to forest or grassland fires in hot climates, such as in the centre of large landmasses. Karrikins are able to trigger germination of certain plants such as Thale Cress (Arabidopsis thaliana) far more effectively than can the related and previously known phyto-hormones: the Strigolactones.

There are four known Karrikins (which are butenolides - [a five membered ring and lactone] which is fused to a 4H-Pyran (aka Oxine) ring [a six-membered ring]). They are known as KAR1, KAR2, KAR3 and KAR4. KAR2 is the simplest, lacking any additional methyl side-groups and chemically is a FuroPyranone; KAR3 and KAR4 possess two methyl side-groups.

The word 'karrikin' is derived from karrik, meaning smoke in the language of the Noongar natives from Western Australia. The Noongar people divided their year into 6 distinct seasons which determined when they migrate, hunt, or propagate plants for food.

These next two paragraphs apply mostly to very hot regions such as California or Australia where wild forest fires are a somewhat regular occurrence. It is also interesting to note, that for certain species of plant, fire (and smoke) are essential for germination - such as plants of the Ceanothus genera and Lodgepole Pine, Eucalyptus trees and Banksia species - the latter three having serotinous cones or fruits which are completely sealed with resin and can only release their seeds after a fire has melted or burnt away the resin. Some trees have such incredibly thick protective barks, such as the Larch and Giant Sequoia, that they only succumb to the most intense of forest fires, surviving in lesser fires. Other trees only grow branches at the very top of the (tall) tree, shedding branches lower down as they grow, in order to help it survive a forest fire and also to try not to give as much fuel to any forest fire.

Some other species of trees, shrubs and annual plants require the chemical signals released from burning plant matter before their dormant seeds will germinate at all.

The recent (2018) intense and unprecedented wild forest fires (some of which were started deliberately and have razed to the ground several towns and villages in their spread) have also, in its aftermath, given rise to vast scapes of richly-coloured flowers on the rolling hills of California in March 2019. Here there are large swathes of red, deep blue, purple, deep orange and bright yellow flowers - all reawakened from very long dormancy by the karrikins released in the smoke. This Californian bloom happens only very rarely, and only after an intense forest fire.

Natural fire is an utterly essential part in the conservation of ecosystems, not only of grass fires but also of forest fires. Lightning is the main cause of wild fires, despite the often deliberate setting alight of heather moorlands by gamekeepers and grassy hillsides by mischievous children (and some adults).

Wild fires are also essential for stabilising the concentration of oxygen in Earths' atmosphere and have been doing so ever since the level of oxygen reached 21% in the atmosphere. Oxygen is generated in the atmosphere by plants during photosynthesis. Before plants arose, atmospheric oxygen levels were far lower, but slowly climbed up to 21% after plants had entered the scene. Plants began 420My ago followed by forests 360My ago, but although oxygen levels rose during this time, natural forest fires only began 10My later when oxygen levels had reached about perhaps 21%. The fires burned through the carboniferous period then more fiercely in the Permian when oxygen levels reached above 21%. [The first flowering plants only appeared about 70My ago from fossilised remains found in the charcoal which was created then]. See  Geological History of Oxygen

The likelihood of lightning starting a fire and it being self-sustaining over great swathes of land is highly dependant upon the atmospheric concentration of oxygen. If the concentration of oxygen rose higher than 21% the likelihood of fires is much higher, and when one starts, is much more intense, with both the likelihood and ferocity increasing disproportionately with atmospheric oxygen concentration. Conversely, below 21% oxygen concentrations, wild fires are much less likely and burn with much less vigour, easily fizzling out. Thus the level of oxygen in the air is controlled by a balancing system exhibiting negative feedback. The level of oxygen at 21% has thus remained constant for aeons by this self-controlling feedback mechanism; plants create it, fires consume it.

The problem arises when people build houses near, or even within natural forests! Naturally they do not want their house to burn down in a wild fire so they douse out the flames or they might cut down some trees in the forest and leave them in-situ. This extra combustible material which grows over time only helps any later wild fire gather pace!

With temperatures set to rise by up to maybe 5°C over the coming centuries (as global warming progresses through increased carbon dioxide emissions and other global-warming gases) any wild fires will become ever fiercer as the timber is desiccated by the increased air temperatures. The different climatic conditions are also likely to set the Oxygen Level point to a differing level other than 21% as has happened in the past during the Permian.


Gibberellic Acid (aka Gibberellin A3, GA or GA3) is not a Karrikin but a potent plant hormone which acts in synergy with the Karrikins (when they are around, which is not often - only after a hot forest fire) to help germinate seeds. They accomplish this far more effectively than can Gibberellic Acid acting alone (see text above). Gibberellic Acid is a pentacyclic diterpene which lacks the heterocyclic oxygen atoms within the rings of the Karrikins.

Gibberellic Acid is based on the skeletal structure of ent-Gibberellane, which is similar to that of ent-Kaurane (but that exchanges the 5 membered ring for one of six members with a few other rearrangements or omissions of side-groups). Both are diterpenoids found in plants.

There are a large number of other Gibberellins, 126 as of 2003, found in various living organisms such as plants, fungi and bacteria. All those with 19 carbon atoms are, in general, bio-active, whereas those with 20 carbon atoms are not. Gibberellic Acid is dihydroxylated Gibberellin A1 (not shown). They are based upon the skeleton of ent-Gibberellane but synthesized from ent-Kaurene which possesses a 6-membered ring in place of the 5-membered ring of Gibberelanes.


Jasmonic Acid, and its metabolites, is a plant hormone and is derived from Linolenic Acid. It plays roles in regulating plant development and growth, including growth inhibition, senescence, tendril coiling (but obviously not in Lodgepole Pines), seed germination, flower development, flower form, flowering time, flower opening, the number of open flowers, and leaf fall. It also has a hand in tuber formation of potatoes, yams and onions.

It also plays a role in the wounding response and systemic acquired resistance. It acts as a defence chemical against insects, interfering with their digestive processes.

Jasmonic Acid can be converted into the ester Methyl Jasmonate within the plant, which plays similar roles in plant defence as Jasmonic Acid. Plants produce both chemicals in response to stress or damage. Methyl Jasmonate also signals to remoter parts of the plant (via propagation through the air since it is both aromatic and volatile) forearming them against similar damage or attack, so that they are prepared. It is thus also a signalling molecule. But Methyl Jasmonate is a gas which is not very active in plants, but as a gas is able to waft over to nearby plants whereupon it diffuses into the pores of the leaves of nearby un-damaged plants, where, acted upon by water, it gets converted into the water-soluble Jasmonic Acid. The Jasmonic Acid then attaches itself to specific receptors in cells triggering the leafs' defence mechanism.

Methyl Jasmonate can also induce ethylene formation. Ethylene, H2C=CH2, is a gas and plant hormone that enhances the ripening of nearby fruits which is used extensively in green-house agriculture.

Ethylene is involved in the ripening of fruits, leaf abscission (leaf dropping off) and the senescence of plants.

When a plant is wounded, infected, flooded with water or otherwise under some stress, ethylene is produced and released into the air as a signalling response. The plant responds to this ethylene in various ways which help it cope.


PHYTOCHROME B - a signalling molecule

Thale Cress is the most studied plant in history because it is relatively easy to perform experiments with it. Thale Cress has been found to channel light from the sun/sky down through the plant stems and along the roots, as though they were optical fibres. When that light gets to the roots it triggers photoreceptors detectors in the roots (just like it triggers photoreceptors in the stems) which stimulates gravitotropic rot growth, directing roots downwards. Only certain wavelengths of light are propagated along stems and roots and it is these wavelengths to which Phytochrome B responds, in turn activating Elongated Hypocotyl 5 (Hy5 in shorthand), a transcription factor mediating the gravitotropic response.

Alas, both Phytochrome B and Hy5 are complex biological molecules which are too big to be drawn or shown on this website.

There are a variety of other light-sensitive photoproteins:
PhytoChromes are sensitive to red light, whilst CryptoChromes and PhotoTropins are sensitive to blue and ultraviolet-A light.

Further References:
 Phytochrome Signalling Mechanisms


Putrescine, Spermidine and Spermine are all poly-amines found in all plant cells. Both bind to the phosphate backbone of nucleic acids. The polyamines are crucial to cell migration, proliferation and differentiation in both plants and animals, so are tightly regulated within cells. Spermidine stimulates the enzyme T7-RNA polymerase. Spermine stabilises the helical structure of RNA, particularly of virii. Both Spermine and Spermidine were first discovered in human semen. Both are now used in skin-care beauty creams. Spermidine and Spermine are derivatives of Putrescine, which smells putrid and is excreted by cells as a means of discarding polyamines. It might be no coincidence that Spermidine and Spermine are present in semen because semen also needs a supply of zinc to function efficiently, and both, being polyamines, are capable of binding to zinc.

Indeed, both Spermidine and 24-epi-Brassinolide (aka Brassinolide) are Plant Growth Regulators (but Brassinolide is not universally present in all plants, only a select few such as those belonging to the Brassicaceae (Cabbage) family). The toxic effects of salt or zinc metal stress on Mung Bean Vigna radiata (a Cabbage Family member) plants are completely overcome by the combination of these two Plant Growth Regulators. Zinc is in itself an essential micronutrient in all plants responsible for their normal growth and development, and all plants are capable of easily absorbing it. However too much zinc in the soil or water results in zinc toxicity in many plants not equipped to deal with this toxic influx. Plants unable to deal with an excess of zinc in the soil or water suffer inhibition of root-growth and stem-growth resulting in chlorosis and necrosis of leaves, damage to the photosynthetic machinery, significantly altered mitotic cell division as well as altered membrane integrity and permeability. Zinc kills cells in plants ill-equipped to deal with unwanted high concentrations in the soil or water. The presence of Spermidine or other polyamines and 24-epi-Brassionolide (a phytosterol present in many Brassicaceae plants) helps some plants to deal with excess zinc. Many others succumb to the toxic effects of zinc and will not grow in its excess presence.

Polyamines play a large role in managing stress in plants posed by adverse environmental conditions such as drought-stress or stress due to water salinity. They also protect the plant from damaging heavy elements in the soil. There are other polyamines present in (some) plants, namely NorSpermine and NorSpermidine, which are slightly shortened versions of each, with one CH2 moiety removed from the (CH2)4 section making all of the sections (CH2)3.

ThermoSpermine is yet another polyamine and is a positional (aka structural) isomer of Spermine, but whereas Spermine has the four CH2 moieties in the centre, ThermoSpermine has it near one of the ends. It is a new type of Plant Growth Regulator with widespread presence in the plant kingdom. Unlike Spermine, ThermoSpermine is essential for the normal development of plants. Spermidine can be converted within plants to ThermoSpermine by the enzyme Thermospermine Synthase (TSPMS).

ThermoSpermine is involved in the regulation of stem elongation in (at least) Thale Cress (upon which most research is now based since it has a very small genome), and without it severe dwarfism and over-proliferation of xylem vessels results. The growth hormone Auxin and ThermoSpermine operate against each other, in yet another negative-feedback balancing arrangement. The levels of the polyamines within plants is also highly regulated by the plant, and only increases in response to environmental stress. The hormone Abscisic Acid (ABA) also plays a role in managing stress due to drought conditions.

The interconnectedness of all things is all cross-connected in accordance with the writer Douglas Adams.

Another polyamine Xylemin (CH2)4NH2 (CH2)4NH2 promotes xylem differentiation by the act of inhibiting the synthesis of ThermoSpermine.

Polyamines tend to associate themselves with the macro-molecule RNA until they are required to perform some purpose. There is still a great deal yet to discover about polyamines and their multitudinous roles in both plants and animals. The above just scratches the surface of the plethora of ways they might interact with other metabolites.


Cytokinins are a class of phytohormones which promote cell growth by division (cytokinesis). There are several natural Cytokinins divided into two groups, the Adenine-type (such as Kinetin (originally discovered in Millet), Zeatin (first found in Zea Mays) and 6-BenzylAminoPurine (a synthetic cytokinin) and those based on phenylurea such as N-N'-DiPhenylUrea (found in coconut milk) and the synthetic Thidiazuron which is used extensively in tissue culture and rooting hormones.

Zeatin is one of the Cytokinins aka plant hormones. It was initially found in species of Zea, and is present in Zea Maize. It is derived from the purine base Adenine, which has similarities to other Purines such as Guanine and the Xanthines: Theophylline, Caffeine and Theobromine.

Zeatin (not to be confused with Zeathanthin) belongs to the family of plant-growth hormones called Cytokinins (which modulate cell division and shoot formation) and is also found in Coconut milk. It promotes the growth of lateral buds and can be applied artificially by spraying on to the meristems of plants where it induces cell division leading to bushier plants. Cytokinins are highly synergistic with Auxins, augmenting each other. The ratios of these two groups of plant hormones control most of the main growth periods over a plants lifetime with the cytokinins countering some of the effects of the auxins. The ratio of the two govern where growth occurs, increased cytokinin induces more shoot growth whilst more auxin induces root formation.

Kinetin, a cytokinin first found in Millet, but in 1996 was found to naturally exist in the DNA of cells from almost every organism tested so far. It is thus ubiquitous and is thought to be produced from Furfural (aka Furfuraldehyde) which is derived as an oxidation product from the DeOxyRibose sugar in DNA, and then furfurals further reaction with the Adenine bases in DNA.

STRIGOLACTONES - plant growth hormones

Strigolactones are double-lactones

5-DeoxyStrigol is the pre-cursor to the Strigolactones produced within Chameleon. Strigolactones are Plant Hormones which stimulate the growth of symbiotic mycorrhizal fungi. They also inhibit the formation of branches on established plants whilst at the same time promoting the germination of nearby seedlings. The seedlings then germinate and have more room around them allowing more sunlight to dance upon their fledgling leaves. These Strigolactones are produced within Chameleon itself and are derived from Carotenoids.

Sorgomol is another Strigolactone produced not only in Chameleon but also in Sorghum from which it derives its name. It is a potent germination stimulant for seeds of the root-parasitic weeds of Great Millet (Sorghum bicolor) and is probably instrumental in the propensity for Chameleon to spread rampantly. One Strigolactone (not as [far as your author knows] produced by Chameleon) is called Sorgolactone, which gets its name from the Sorghum plants it helps germinate. Another is (+)-Orobanchol (which is also not reportedly produced by Chameleon), presumably so-called from plants of the genus Orobanche (Broomrapes) it helps to germinate.

Strigone has been isolated from root extracts of Chameleon and is also a potent seed germination stimulant, depending upon the four possible stereoisometric arrangements of the compound, some of which will not be produced naturally.

Karrikins (shown above) are structurally similar to Strigolactones, but much simpler. They are produced naturally in the smoke from forest fires when plant matter burns at high temperature and are much more effective plant hormones, helping seeds to germinate after a fire, than are the Strigolactones themselves.

TWO SALICYLATES - hormone and signalling molecules

Aspirin, or Acetyl Salicylic Acid, is also found in plants, being a plant hormone (phytohormone) which not only helps the plant grow but also is involved in a pathway signalling the presence of plant pathogens and mediating the plant defence against the pathogens.

Once activated by a pathogen, it is also involved in inducing resistance to the pathogen in parts of the plant not yet infected. The signalling process also invokes the conversion of salicylic acid into the volatile ester, methyl salicylate, whereupon it can then drift through the air to other nearby plants to prime them against the presence of a nearby pathogen or pest, warning of their proximity by remote control. Methyl Salicylate is also called Oil of Wintergreen, and is indeed produced by the Wintergreen plants, such as Round-Leaved Wintergreen, some species of Gaultheria, most members of the Pyrolaceae Family, some species of plants of the Genus Betula and all species of plants of the Spiraea family, including Dropwort and Meadowsweet

To humans Methyl Salicylate, aka Oil of Wintergreen, being an ester, smells sweet, hence the name Meadowsweet. Methyl Salicylate is, however, not only toxic but also an insect pheromone. By this means the plant is also able to attract beneficial insects that will help kill the invading herbivorous insect pests. It is commercially extracted not from any Wintergreen plant, but from twigs of the Sweet Birch tree (Betula Lenta. Oil of wintergreen is used a fragrance in certain products not necessarily including perfumes, and in deep-heat liniments and in trace amounts as a flavour in some chewing gums, candies and mouth-washes as an alternative to spearmint and peppermint for it is also an anti-septic. Like most essential oils, it is poisonous in greater amounts.

BRASSINOLIDE - growth enhancer

Brassinolide looks similar to a steroidal compound, but actually on closer examination has a 7-membered lactone ring in place of a 6-membered carbon ring. This was first isolated from the pollen from Oil-seed Rape and it turns out to be a plant hormone or Auxin capable of enhancing the growth of Oil-seed Rape (by this means, and possibly by others, once established, Oil-seed Rape is able to block out all competitors).

TURGORINS - a hormone and signalling molecules

Turgorins are auxins, plant hormones (phytohormones), which are involved in the thigmonastic response of plants. Turgorin itself is one such Turgorin, being the Sulfate of the Glucoside of Gallic Acid. In Mimosa pudica the Glucoside of Gallic Acid is sulfated by the enzyme Sulfotransferase (ST) which transfers a sulfate moiety from 3'-PhosphoAdenoside-5'-PhosphoSulfate (PAPS) to the Glucoside of Gallic Acid.

Another Turgorin is Turgorin LMF1 (Turgorin Leaf Movement Factor 1) which is the double Glycoside of Gentisic Acid (rather than of Gallic Acid as for Turgorin itself). One of the glycosides (the pentose) is related to DeoxyRibose. Both Turgorins are involved in the leaf movements in Sensitive Plant (Mimosa pudica). These same phytohormones are involved both in the tactile and the diurnal closing of its leaves.

The Turgorins are very likely also involved in the mechanism for opening and closing the stomata whereby plants are able to transpire. Thus they are probably involved not only in the regulation of temperature of the plant but also for the transportation of themselves throughout the plant via the sap.

(possibly some signalling molecules)

It has only recently been discovered that when the Sensitive Plant Mimosa pudica is touched it emits a cocktail of volatile and odorous compounds, many containing sulfur, both organic and inorganic compounds, some of which smell foul. They include Sulfur Dioxide (SO2), 2-AminoThioPhenol, PhenoThiazine, MethaneSulfonic Acid, Pyruvic Acid, Sulfinic Acid, EthaneSulfinic Acid, PropylSulfenic Acid, 2-AminoThioPhenol, S-propyl Propane-1-Thiosulfinate, and ThioFormaldehyde - the latter being a fleeting and highly unstable compound which has never before been found to be emitted by a plant. This response to touch involves Thigmorphogenesis whereby parts of the genome are altered to facilitate the synthesis of these compounds, which consumes energy the plant could better spend on growing.

The foul-odour compounds are PropaneSulfenic Acid, 2-AminoThioPhenol and S-propyl Propane-1-ThioSulfinate. These compounds are not, as was once thought, produced by microbes, but are produced within the roots of the plant and emitted when the roots are agitated by touch - either by human skin or by moving soil, but not by touching the roots with other materials such as by glass or metal objects. Some of these sulfur compounds are to be found in onions and garlics.

There are microscopic sac-like protuberances or hairs just 0.5mm long on the roots which contain a higher proportion of potassium K+ and Chlorine Cl- ions than surrounding tissue, and when the hairs are stimulated they release the highly potent odour substances. The levels of these ions both drop and the sacs deflate having expelled their odorous compounds. (The sacs are reminiscent of glandular trichomes as found on Stinging Nettles) These ions are involved in the initiation of the emission of the odorous substances. Only a tiny amount of the odorous compounds is necessary to fill a room with a disgusting smell. It is not known whether the smell is targeted at predators and scavengers or to fend off the roots of competing plants. They do seem to be signalling molecules, but to what target or end is unknown. It may be that the smell (to humans and other mammals) is irrelevant.

Glandular root hairs which secrete small organic molecules have also been found on Sorghum plants and on Apple trees.

Sensitive Plant is not the only plant in the Mimosaceae family to emit smells when disturbed; 40 species from nine genera within the Mimosoidae sub-family produce Carbon Disulfide, CS2 and 19 of those 40 produce Carbonyl Sulfide, S=C=O (normally but incorrectly written as 'COS). However, Sensitive Plant is not one of the 40 Mimosaceae species to emit Carbon Disulfide. Carbon Disulfide is a flammable gas with an unpleasant smell which, in the presence of any water vapour contained in the air (due to humidity), decomposes into Carbon Dioxide CO2 and another toxic flammable gas with obnoxious odour, Hydrogen Sulfide H2S. Carbonyl Sulfide is released by deep ocean vents, volcanoes and by organisms in the ocean. Some is oxidized in the atmosphere to Sulfuric Acid H2SO4. Because it is continually created and destroyed, Carbonyl Sulfide exists in the atmosphere in a    secular equilibrium - indeed it is the most abundant sulfur compound present in the air (at about 0.5ppb ± 10%) since. Carbonyl Sulfide is also given off by some cheese and by cooked vegetables from the Brassicaceae family (Cabbage).

It is thought, but not proven, that both Carbon Disulfide and Carbonyl Sulfide are produced when the non-proteinogenic amino acid (NPAA) Djenkolic Acid (present in the plant) is cleaved with the aid of an enzyme, yielding Cysteine, ThioFormaldehyde and a Pyridinium ion, hydrolysis of which produces first 2-Amino-Acrylate (aka α-Amino-Acrylate), then Pyruvate and Ammonia (NH3).

The pyruvate is present as a salt of Pyruvic Acid.

Djenkolic Acid is yet another NPAA (non-proteinogenic amino acid) which also contains two atoms of sulfur. It is a near-dimer, with two symmetrical parts sharing only a central carbon atom, being Cysteine radicals. It is toxic causing nephrotoxicity and is found in the non-native Jengkol beans, a legume (from the Fabanaceae family) found in South-East Asia. It is toxic because of its insolubility which precipitates sharp needle crystals of Djenkolic Acid in the renal tract. It is thus a mechanical toxin rather than one which uses its chemistry to interact with the body. As such, it has a similar modus operandi to the raphides (sharp needle crystals) of Calcium Oxalate found in species of Oxalis (Wood-Sorrel) and in Rhubarb. If the beans are boiled before consumption this tragedy is avoided. Djenkolic Acid is also found in the seeds of other Legumes, such as Leucaena esculenta and Pithocolobium ondulatum, both non-native to the UK.

(hormones and/or signalling molecules)

Nitric Oxide, NO and Hydrogen Peroxide H2O2 or HO-OH are two other gases (besides Ethylene, HC=CH, discussed above) that are used extensively by plants as signalling molecules. Both Hydrogen peroxide and Nitric Oxide are generated by a wide range of biological and non-biological stress processes. However, the means by which nitric oxide are generated by biological means has not yet been elucidated. The cell response to both hydrogen peroxide and to nitric oxide are both complex and little understood, but they seem to be manifold. The responses of plants to both signalling molecules is also manifold, but it is known that hydrogen peroxide is involved in cell-death.

The subject is so complicated and so little is known about the actions or of the modus-operandi of either substance that your Author directs those interested to a 2001 research paper in pdf format by Neill, Desikan, Clarke, Hurst and Hancock from the Journal of Experimental Botany:  H2O2 & NO as signalling molecules in plants (pdf).

Small molecules tend to have a great many effects and interactions with other molecules, so it is little wonder that both NO and H2O2 have such diverse and little-understood effects when their interactions are manifold. Unlike many much larger molecules, which sometimes are specific to only certain plants, these small molecules can effect changes and responses in a great many different plants and organisms. They are ubiquitous if not universal messengers and initiators.

Nitric Oxide is functional in many biological systems including mammals and humans where, amongst other effects, it modulates the flow of blood. In plants it is now known to affect seed germination. It may also be involved in Nitrogen Fixation in the root nodules of plants belonging to (mainly) the Pea Family. NO is pivotal in the control of stomatal openings in plants (which are used by the plant to control the release of oxygen or of water vapour and to control the ingress of carbon dioxide which the plant requires in order to grow). Nitric Oxide is also produced when plants are under attack from some pathogen suggesting a role in defence. It is hugely important in the control of reactive oxygen species (ROS - which includes hydrogen peroxide) generated when the plant during metabolism, particularly in regard to Glutathione a major anti-oxidant in plants. There are many other at present little understood roles of NO in plants.

Hydrogen Peroxide is one of those reactive oxygen species (ROS) produced in plants during metabolism. It is also produced at the site of a wound in plants in order to hyper-sensitize damaged cells to undergo cell-death (apoptosis) and also to stiffen cell-walls. It is active in plants exposed to UV-B light protecting them from damage by activating several cell pathways, via gene expression. There are similarly many other at present little understood roles of H2O2 in plants.

Ethylene is a gas and almost universal hormone for the ripening of all sorts of fruit. Ethylene is produced within the plants cells and especially when they are rapidly growing and multiplying (dividing), even more so in the dark. Both new growth and newly germinated seedlings produce elevated levels of ethylene. The gas escapes from the plant where it can influence other parts of the same plant such as leaf stalks, which start to bend more upright when the lower surfaces grow faster than the upper surfaces (like a bimetallic strip this forces it to bend): a hyponastic response.

As the parts grow taller and reach more light, the extra light causes phytochrome to assume a differing form which then dampens down the production of ethylene gas allowing the leaf to grow again.

For seedlings that are still underground (which receive no light) ethylene production is greatly ramped up thickening up the stem to give it more rigidity and then able to force its way through to the surface, sometimes through tarmac or other obstacle! but if it still cannot get through the stem ceases growing upwards and grows around the obstacle until it can reach the surface. .


Clathrin is a protein in plants which is involved in defensive plant-signalling and execution in plants. Your Author cannot show these large molecules because they will not fit on the pages, and in any case, they are so large that mistakes in drawing are likely. Moreover, Clathrin is not just one large molecule, it can be quite a few differing ones.

The first step to response by signalling molecules is on the surface of the plant. In Thale Cress there are about 600 of these Receptor-like Kinases which are encoded in the genome, and it is these which allow plants to react swiftly to airborne signalling molecules. From there-on within the plant the response to these received signals complex, involving many pathways and assisting molecules which your Author cannot start to understand. Clathrin is called such because it resembles a clathrate or cage-like molecule which can trap smaller molecules within it. It is not a single molecule, there are 3 shapes it can adopt, each one has 12 pentagons but may have a variable number of hexagons - either 4, 8 or 20. Each shape may be constructed from several differing 3-spoked molecules. Some structures are open-cage whilst others closed-cages. Altogether Clathrin is a large molecule, over n-times 215 kDaltons. As a closed-cage entity it can capture another molecule within it like a trap.

For more details it is best to see  Clathrin

These are C-shaped molecules, or, rather, shaped like a thick metal washer (without the screw) but with 1/4 of it missing. CLAVATA1 (CLV1) is one of the most studied LRRs (in Thale Cress - but what happens in Thale Cress is turning out to be representative of many other plants.

Mutations in CLAVATA1 which inactivate CLAVATA1 (CLV1) cause both the shoot and the floral meristems to grow larger which in turn causes both extra floral organs and the stem-cells to enlarge. This causes deformities in growth patterns of stems, leaves and flowers. In other words this causes Fasciation and Proliferation.

Another (small) protein, CLAVATA3 (CLV3) is thought to be a signalling molecule. When CLV3 binds to its receptor protein CLV1, meristem growth is suppressed instead, which either inhibits cell division(?) or more likely, stimulates cell differentiation.

Mutations in yet another protein which has gene-regulating properties result in the opposite effect to mutations which inactivate CLV1, namely to greatly reduce cell division in the shoot meristem, making the flower produce too few organs.

But much is still to be discovered about all these proteins and their complex modus-operandi and interactions both with each other and other molecules.


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