Common symbiosis signaling pathway

To accurately recognize the infection thread of a different species of organism, and to establish a mutually beneficial association requires robust signaling.[3] AM fungi are also fatty acid auxotrophs;[4][2] therefore they depend on plant for supply of fatty acid supply.[5]

At the pre-symbiotic signaling; both symbionts release chemical factors in their surroundings so that the partners can find each other.[6]' Plant root exudates play role in complex microbial interaction,[7] by releasing a lot of versatile materials.[7][8][9] among which strigolactone has been identified to facilitate both AMF colonisation and pathogen infection.[8]

It is seen that phosphate starvation in plant induces strigolactone production as well as AMF colonisation.[8] Plants release strigolactone, a class of caroteinoid-based plant hormone which also attracts the fungal symbionts and stimulate the fungal oxidative metabolism and also growth and branching of the fungal partner [2] Strigolactone promotes hyphal branching in germinating AMF spores [9] It plays role in intense ramification of the AMF hyphae at the vicinity of root and then colonization [10]

The common symbiosis signalling pathway is called so because it has common components for fungal symbiosis as well as rhizobial symbiosis. The common signalling pathway probably evolved when the existing pathway for arbuscular mycorrhizae was exploited by rhizobia,.[2][11]

The perception happens when fungal Myc factor is detected by plant. Myc factors are comparable to rhizobial nod factors. The chemical nature of Myc factor has recently been revealed as lipo-chito-oligosaccharide (Myc-LCOs) and chito-oligosaccharides (Myc-COs) that work as symbiotic signal,[10][12][13]

Presence of Strigolactone enhances the production of Myc-CO production by AMF [10]

Myc factor receptor (MFR) is still putative, however However, another protein DMI2 (or SYMRK) that have prominent role in perception process and it is thought to be a co-receptor of MFR. Rice plant probably show a different mechanism using OsCERK1 and OsCEBiP which probably detect chitin oligomers[2][14][15]

The transmission happens when the signal transmitted after detection to the gene expression stage. This process is mediated by two nucleoporins NUP85 and NUP133,[11] Alternatively, another hypothesis says HMG-CoA reductase is activated on perception, which then converts HMG-CoA into mevalonate, this mevalonate acts as a second messenger and activates a nuclear K+ cation channel (DMI-1 or Pollux).[2][16] The transmission stage ends by creating a ‘calcium spike’ into the nucleus [17]

The transcription stage starts when a Calcium and Calmodulin dependent kinase (CCaMK) is activated.[2] then it stimulates a target protein CYCLOPS.[2] CCaMK and CYCLOPS probably forms a complex that along with DELLA protein, regulates the expression of RAM1 (Reduced Arbuscular Mycorrhyza1) gene expression.[2]

The accommodation process is the extensive remodelling of host cortical cells. This includes invagination of host plasmalemma, proliferation of endoplasmic reticulum, golgi apparatus, trans-golgi network and secretary vesicles. Plastids multiply and form “stromules”. Vacuoles also goes through extensive reorganization [11]

Rhizobial bacteria and Arbuscular mycorrhizal fungi : two different kinds of symbionts elicite a similar signaling pathway

A TEM section of root nodule showing symbiosome made by Rhizobia, a kind of nitrogen fixing bacteria, in this case Bradyrhizobium japonicum in soybean root.	An arbuscle formed by Arbuscular mycorrhizal fungus Rhizophagus irregularis in Maize root, stained with WGA-Alexa fluor, seen using fluorescence microscopy.

Chemical signalling starts prior to two symbionts come into contact. From the host plant's side, it synthesizes and releases a range of caroteinoid based phytohormone, called strigolactones.[2] They have a conserved tricyclic lactone structure also known as ABC rings.[18] Strigolactone biosynthesis occurs mainly in plastid,[19] where D27 (Rice DWARF 27; Arabidopsis ortholog ATD27), an Iron binding beta-carotene isomerase works at upstream of strigolactone biosynthesis [19] Then carotenoid cleavage dioxygenase enzyme CCD7 and CCD8 modifies the structure, which has following orthologs:

The alpha/beta fold hydrolase D3 and also D14L (D14-Like) (Later one has Arabidopsis ortholog KAI2, or KARRIKIN INSENSITIVE-2) is reported to have important roles in mycorrhizal symbiosis [3], notably, D3, D14 and D14L are localised in nucleus.[2]

NOPE1 or 'NO PERCEPTION 1', newly discovered transporter protein in Rice (Oryza sativa) and Maize (Zea mays), also required for the priming stage for colonisation by the fungus. NOPE1 is a member of Major Facilitator Super family of transport proteins, capable of N-acetylglucosamine transport. Since nope1 mutant's root exudates fail to elicited transcriptional responses in fungi, it strongly seems NOPE1 secretes something (not yet characterised) that promotes fungal response [2]

The chemical structure of MycRi-IV (C16:0,S), a Myc factor of Rhizophagus irregularis as indicated in Maillet, F et al. (2011) "Fungal lipochitooligosaccharide symbiotic signals in arbuscular mycorrhiza." Nature 469:58–63.The factor was first identified by Fabienne Maillet and coworkers  in a groundbreaking work published in Nature, where they have extracted three hundred litre mycorrhized carrot roots and exudates from 40 million germinating spores of Rhizophagus irregularis and purified the active fraction. They demonstrated this active principle is lipo-chito-oligosaccharide in nature.

There are two main type of root symbiosis; one is root nodule symbiosis by Rhizobia (RN-type) and another is Arbuscular Mycorrhiza (AM-type). There are common genes involved in between these two pathways.[20] these key common components, form the Common Symbiosis pathway (CSP or CSSP).[20] It has been proposed that, RN symbiosis has originated from AM symbiosis.[11] The perception of presence of fungal symbiont, takes place mainly through fungal chemical secretions generally termed as Myc factors. Receptors for Myc factors are yet to be identified. However, DMI2/SYMRK probably acts as a co-receptor of Myc factor receptor (MFR). The AM fungal secreted materials relevant to symbiosis are Myc-LCOs, Myc-COs, N-Acetylglucosamine [2][21]

Cell Surface Receptors

Different families of LYSM Receptors

Some SYM genes respond to both RN and AM symbiosis. Some variants exclusively respond to any 1 type of the symbioses.

There are multiple families of pattern recognition receptors and co-receptors involved in recognition of microbial pathogens and symbionts. Some of the relevant families involved in CSSP, are Membrane bound LysMs (LYM), Soluble LysM Receptor like Protein, LYK (LysM receptors with active Kinase domain), LYR (LysM proteins with inactive kinase domain), etc. (ref)

Seemingly, different combinations of a LYK and LYR generates differential signals, such as some combinations generate a pathogen recognition signal whereas some combinations rise to the symbiotic signal [22][23][24][25]

LysM receptor-like kinase

Lysin Motif (LysM) receptor-like kinase are a subfamily related to membrane bound Receptor like kinase (RLKs) with an extracellular region consisting of 3 Lysine motifs. They have some important orthologs in different plants, that vary in their function. (In some plant they are involved in AM symbiosis, in some plants they are not). Tomato (Solanum lycopersicum), a non-legume dicot, also have a similar LysM receptor, SlLYK10 that Promotes AM symbiosis. There are some co-receptors of Myc-factor receptor viz., OsCEBiP in Rice, a LysM membrane protein can function as a co-receptor of OsCERK1 but it works in a different pathway.[29][30][31]

Most of these kinases are Serine/Threonine kinase, some are Tyrosine kinase.[32] Also they are type-1 transmembrane proteins, that indicates their N-terminal domain towards the outside of the cell, and the C-terminal domain is towards inside of the cell.[24]

Cell surface receptors may work differently in different combinations. Same receptor can perform multiple function. Such as Oryza sativa CERK1 Receptor may trigger a PTI response (Pathogen triggered immunity) with Oryza sativa CEBiP as a co-receptor; in presence of  CO8 Chitooligosaccharide. Whereas the same receptor CERK1 can play role in recognition of symbiotic signal, in presence of CO4 Chito-oligosaccharide,  using SYMRK as a Co-receptor.

Important cell surface receptots involved in molecular pattern recognition[32]

					Medicago truncatula	Lotus japonicus	Pisum sativum (pea)	Prunus persica	Arabidopsis thalliana	Brassica rapa	Solanum lycopersicum (Tomato)	Brachypodium distachyon	Oryza sativa (Rice)
	Lysine Motif Receptor-Like Kinase and Lysine Motif Receptor like Protein	LYM		LYMI	LYM1			PpLYM1	AtLYM1 AtLYM3		SlLYM1	BdLYM1 BdLYM3	OsLYP6 OsLYP5, OsLYP4
				LYMII	LYM2			PpLYM3 PpLYM2	AtLYM2		SlLYM3 SlLYM2	BdLYM2 BdLYM4	OsCEBiP OsLYP3
		LYR	LYR 1	LYRIA	MtNFP MtLYR1	LjNFR5 LjLYS11		PpLYR1			SlLyk10	Bd LYR1	OsNFR5
				LYRIB	MtLYR8			PpLYR2			SlLYK9	Bd LYR2
			LYR 2	LIRIIA	MtLYR10	LjLYS16		PpLYR6	AtLYK2		SlLYK2
				LYRIIB	MtLYR9	LjLYS15		PpLYR7			SlLYK15
			LYR 3	LYRIIIA	MtLYR3	LjLYS12		PpLYR3	AtLYK4		SlLYK4	Bd LYR4	OsLYK6
				LYRIIIB	MtLYR2			PpLYR4			SlLYK7 SlLYK6
				LYRIIIC	MtLYR4 MtLYR7	LjLYS13 LjLYS14			AtLYK5			Bd LYR3	OsLYK3 OsLYK2, OsLYK4
			LYR 4	LYRIV	MtLYR5 MtLYR6	LjLYS20		PpLYR5
		LYK		LYKI	LYK1, LYK4, LYK5, LYK6, LYK7, LYK2, LYK3, LYK9, LYK8	LjLYS2 LjLYS1, LjNFR1, LjLYS6, LjLYS7		PpLYK2 PpLyk1	AtLYK1/ AtCERK1		SlLYK13 SlLYK1/ SlBti9, SlLYK12, SlLYK11	BdLYK1	OsCERK1
				LYKII	LYK10	LjLYS3/ EPR3		PpLYK3 PpLYK4
				LYKII				PpLYK5	AtLYK3		SlLYK3	BdLYK3
	Receptor like Kinase			RLK	Mt-DMI2/ Mt-NORK	Lj-SYMRK	Ps-SYM19						OsSYMRK

The transmission of signal cascades into nucleus is not well understood. However, this transmission includes carrying the message up to the nuclear membrane and generation of a calcium wave.[33] Some elements involved in this process are as follows:

Calmodulin is a widespread regulatory protein that functions along with Ca²⁺ in various biological processes. In AM symbiosis signalling it modulates the CCaMK.[36]  CCaMK or DMI3 is a calcium-and-calmodulin-dependent kinase (CCaMK) is thought to be a key decoder of Ca²⁺ oscillation and an important regulatory kinase protein. Nuclear Ca²⁺ spiking promotes binding of Ca²⁺ calmodulin with CCaMK.[36] Binding of Ca²⁺ calmodulin with CCaMK causes conformational change of CCaMK that stimulates a target protein CYCLOPS which has different orthologs.[36] CYCLOPS is a coiled coil domain containing protein [36] possibly form a complex with CCaMK[36] that works along with DELLA proteins. DELLA proteins are kind of GRAS-domain protein and were originally identified as repressors of Gibberellin signalling pathway, however now it is seen that DELLA provides a mechanism for crosstalk between many signalling pathways.[39]  There are two DELLA proteins in Medicago trancatula and Pisum sativum play role in symbiosis whereas in rice plant only one DELLA protein fulfils this task.[36] Reduced Arbuscular Mycorrhiza or RAM1[36] is a GRAS[40] protein whose gene is directly regulated by DELLA and CCaMK/ CYCLOPS.[36] Using Chromatin immune precipitation assay it has been shown that RAM1 binds to RAM2 gene promoter.[36] RAM1 also play role in many of the fungal accommodation genes directly or indirectly.

A bunch of GRAS proteins play role in AM symbiosis whose roles are not yet fully understood. These includes RAD1 (REQUIRED FOR ARBUSCLE DEVELOPMENT 1), MIG1 (MYCORRHIZA INDUCED GRAS1), NSP1, NSP2 etc.[36] WRKY transcription factor genes are thought to play very important roles in establishment of mycorrhizal symbiosis and they perhaps work through regulating plant defense genes.[41]

Huge reorganization of cortex cells takes place in order to make accommodation for the fungal endosymbiont. The pre-penetration apparatus (PPA) like structure and the peri-arbuscular membrane have to form and the cytoplasm have to retract,[34] so, the vacuole retract in size, the nucleus and nucleolus enlarge in size and chromatin decondense indicating heightened transcriptional activity,[34] Plastids multiply and stay connected with “stromulus”.[34] Furthermore, it was suggested that the apoplastic longitudinal hyphal growth is probably regulated by plant genes such as taci1 and CDPK1.[42]

AM fungi and plants co-evolved and developed a very complex interaction that allow the plant accommodate the AM-fungal host [46][47][48] It has been proposed that, RN symbiosis has originated from AM symbiosis[34][35]

• Receptor tyrosine kinase
• Serine threonine kinase
• Pattern recognition receptors
• Monoglyceride
• Strigolactone
• Plant intelligence
• cell signalling
• Signal transduction
• Pathogen Associated Molecular Pattern
• Microbe Associated Molecular Pattern
• Mutualism
• Karrikin signaling
• Mevalonate pathway