The Eukaryotic Linear Motif resource for
Functional Sites in Proteins
Accession:
Functional site class:
Phytohormone-dependent SCF-LRR-binding degrons
Functional site description:
Several plant-specific degrons mediate phytohormone-dependent binding of regulatory proteins to F-box proteins that function as substrate recognition subunits of the SCF (Skp1-Cul1-Rbx1-Fbox protein) E3 ubiquitin ligase, which targets its substrates for subsequent proteasomal degradation. An auxin-dependent degron motif is present in Aux/IAA proteins and mediates binding of these transcriptional repressors to TIR1/AFB F-box proteins. Similarly, a jasmonate-dependent degron motif is present in JAZ proteins and mediates binding of these transcriptional repressors to the COI1 F-box protein. Binding of these degrons to the leucine-rich repeats (LRRs) of their respective F-box proteins is hormone-dependent, as binding of a hormone molecule to the F-box protein results in the formation of a composite binding site for the substrate degron sequence. The resulting tripartite complex allows high-affinity binding of the substrate protein to the F-box protein.
ELMs with same func. site: DEG_SCF_COI1_1  DEG_SCF_TIR1_1 
ELM Description:
Binding of the JAZ degron to the jasmonate-bound leucine-rich repeats (LRRs) of COI1 involves an N-terminal motif region that binds in an extended conformation on top of the binding pocket for isoleucine-conjugated jasmonic acid (JA-Ile) on COI1. In addition, the C-terminal part of the peptide forms an alpha-helix that binds on top of the LRR domain, adjacent to the hormone-binding site (3OGL) (Sheard,2010). The C-terminal part is highly conserved among the JAZ proteins. Evidence indicates that this helix mediates low-affinity docking to COI1 and functions cooperatively with the N-terminal part of the degron to confer high-affinity binding of COI1, the substrate JAZ protein and the hormone (3OGK) (Sheard,2010). Hydrophobic contacts between the helix and COI1 are provided by the invariant leucine in position 7 of the motif, the invariant phenylalanine in position 10, and the hydrophobic residue, predominantly leucine or phenylalanine, in position 11. Conserved basic residues surrounding these hydrophobic sites provide additional contacts for this motif region. The N-terminal region of the degron peptide is less conserved, which might allow the different JAZ proteins to have distinct responsiveness to JA-Ile (Sheard,2010). This part of the motif confers hormone-dependent binding of the degron. The two first residues are mostly hydrophobic and directly bind to JA-Ile. Two highly conserved basic residues in positions 3 and 4 also play an important role in motif function. The residue in position 3 directly binds to a loop on COI1 while the residue in position 4 inserts deeply into the central cavity of the COI1 LRR domain, where it interacts with the hormone (Sheard,2010). The JA-Ile molecule inserted in the cavity at the degron-COI1 interface stabilizes the interaction between JAZ and COI1 and increases the affinity by interacting with both binding partners. Some JAZ proteins show slight deviations from this canonical degron definition (TIFY5A/B), which might indicate an altered specificity.
Pattern: ..[RK][RK].SL..F[FLM].[RK]R[HRK].[RK].
Pattern Probability: 3.626e-11
Present in taxon: Viridiplantae
Interaction Domain:
LRR (SM00370) Leucine-rich repeats, outliers (Stochiometry: 1 : 1)
PDB Structure: 3OGL
o See 9 Instances for DEG_SCF_COI1_1
o Abstract
Phytohormones are a diverse set of endogenous chemicals that control many different aspects of plant development and growth. Some well-studied plant hormones include auxins, ethylene, gibberellins, jasmonates and abscisic acid. Their activity depends on hormone synthesis, transport, conjugation to other substances, and degradation, as well as extensive cross talk between the different hormones (Garay-Arroyo,2012).
The auxin family of plant hormones, with indole-3-acetic acid (IAA) as the most important member, plays a key role in plant development and growth by acting as a signal for cell division, elongation and differentiation. This hormone regulates a wide variety of processes, including embryogenesis, root formation, apical dominance and tropic responses to light and gravity (Mockaitis,2008, Hayashi,2012). Local auxin abundance is determined by the coordinated control of regulatory pathways involved in the metabolism and transport of auxin. Responses to auxin are mediated by a variety of signalling mechanisms that control the expression of specific sets of genes or trigger transcription-independent responses. Genes transcriptionally activated by auxin include GH3 genes involved in synthesis of inactive IAA-amino acid conjugates, the Small Auxin-Up RNA (SAUR) genes of unknown function, and the Aux/IAA genes. Important mediators of the transcriptional response to auxin are the auxin response factor (ARF) transcription factors that directly bind to the promoters of auxin-responsive genes to regulate their expression. The auxin-responsiveness of the ARFs depends on the Aux/IAA proteins, transcriptional repressors that heterodimerize with ARF proteins, thereby inactivating ARF activity and blocking transcription of auxin-responsive genes. In the presence of auxin, the Aux/IAA repressors are targeted for ubiquitin-dependent proteasomal degradation by the SCF (Skp1-Cul1-Rbx1-Fbox protein) E3 ubiquitin ligase. The auxin-dependent degradation of the Aux/IAAs relieves inhibition of ARF activity and results in expression of auxin-responsive genes. As these genes also include the Aux/IAA-encoding genes, this mechanism provides a negative feedback loop for control of auxin signalling (Mockaitis,2008, Hayashi,2012).
Degradation of the Aux/IAA proteins by the SCF complex depends on the Transport Inhibitor Response 1 (TIR1) and Auxin signalling F-Box (AFB) proteins that function as auxin receptors and substrate recognition subunits of the SCF. The Aux/IAAs are recruited to the SCF by a TIR1/AFB F-box protein, subsequently ubiquitylated by the SCF, and thereby marked for degradation by the proteasome. Binding to the F-box subunit is mediated by the auxin-dependent SCF-TIR1-binding degron motif. Auxin promotes an increase of Aux/IAA degradation by enhancing the interaction between the motif and TIR1/AFB (Parry,2006, Calderon-Villalobos,2010). The components of this transcriptional auxin response are conserved in plants, although some Aux/IAA proteins appear to lack a functional TIR1-binding degron motif (Dreher,2006, Paponov,2009).
The oxylipin jasmonic acid (JA) and its metabolites constitute a family of plant hormones collectively referred to as jasmonates. Production of the major bioactive isoform of the hormone, N-[(3R,7S)-(+)-7-iso-Jasmonoyl]-(S)-isoleucine (JA-Ile), requires conjugation of the JA prohormone to isoleucine (Fonseca,2009). Jasmonates play an important role in normal plant development and growth processes, including root growth, including inhibition of root growth and seed germination and stimulation of senescence. In addition, they mediate defensive responses to biotic and abiotic stress signals such as pathogenic infection, wounding and UV irradiation (Wasternack,2007). Jasmonate-induced responses depend on signalling mechanisms that control the expression of specific sets of genes. An important mediator of the transcriptional response to jasmonates is the transcription factor MYC2/RAP1, which directly binds to the promoters of JA-responsive genes. Genes regulated by MYC2 include wound-responsive genes and genes involved in redox signalling (Dombrecht,2007). The JA-responsiveness of MYC2 and the related transcription factors MYC3 and MYC4 depends on the JAZ/TIFY proteins that function as transcriptional repressors and inhibit positive regulation of gene expression by MYC2. In the absence of bioactive jasmonates, the JAZ proteins bind to MYC2 through their C-terminal region. The inhibitory function of JAZ proteins depends on their ZIM domain that binds to the adaptor protein NINJA, which in turn recruits the general corepressor TOPLESS (Pauwels,2011, Kombrink,2012). In the presence of active JA, the JAZ proteins are targeted for ubiquitin-dependent proteasomal degradation by the SCF (Skp1-Cul1-Rbx1-Fbox protein) E3 ubiquitin ligase. The JA-dependent degradation of the JAZ proteins relieves inhibition of MYC2 activity and results in expression of JA-responsive genes. As these genes also include the JAZ-encoding genes, this mechanism provides a negative feedback loop for control of jasmonate signalling (Fonseca,2009).
Degradation of the JAZ proteins by the SCF complex depends on the Coronatine-insensitive protein 1 (COI1), which functions as a JA receptor and substrate recognition subunit of the SCF. The JAZ proteins are recruited to the SCF by the COI1 F-box protein, subsequently ubiquitylated by the SCF, and thereby marked for degradation by the proteasome. Binding to the F-box subunit is mediated by the JA-dependent SCF-COI1-binding degron motif located in the Jas domain, which mediates binding to MYC2. JA-Ile promotes an increase of JAZ degradation by enhancing the interaction between the motif and COI1 (Gfeller,2010, Kombrink,2012). The components of this transcriptional JA response are conserved in higher plants, although some JAZ proteins appear to lack a functional COI1-binding degron motif (Pauwels,2011, Shyu,2012).
o 6 selected references:

o 7 GO-Terms:

o 9 Instances for DEG_SCF_COI1_1
(click table headers for sorting; Notes column: =Number of Switches, =Number of Interactions)
Acc., Gene-, NameStartEndSubsequenceLogic#Ev.OrganismNotes
Q9LDU5 TIFY11A
TI11A_ARATH
182 199 RIARRASLHRFFAKRKDRAV U 1 Arabidopsis thaliana (Thale cress)
Q93ZM9 TIFY9
TIF9_ARATH
169 186 PIARRKSLQRFLEKRKERLV U 1 Arabidopsis thaliana (Thale cress)
Q9C9E3 TIFY11B
TI11B_ARATH
186 203 RIARRASLHRFFAKRKDRAV U 1 Arabidopsis thaliana (Thale cress)
B2XVS2 Jasmonate ZIM-domain protein 3
B2XVS2_SOLLC
251 268 PQARKASLARFLEKRKERVM TP 3 Solanum lycopersicum (Tomato)
1 
A7XXZ0 LOC100134911
A7XXZ0_SOLLC
199 216 PIARRNSLTRFLEKRKDRVT TP 5 Solanum lycopersicum (Tomato)
1 
Q9S7M2 TIFY10B
TI10B_ARATH
205 222 PIARRASLHRFLEKRKDRIT TP 1 Arabidopsis thaliana (Thale cress)
1 
Q8W4J8 TIFY7
TIF7_ARATH
221 238 PQARKASLARFLEKRKERLM TP 3 Arabidopsis thaliana (Thale cress)
1 
Q9LMA8 TIFY10A
TI10A_ARATH
203 220 PIARRASLHRFLEKRKDRVT TP 7 Arabidopsis thaliana (Thale cress)
1 
Q9LVI4 TIFY6B
TIF6B_ARATH
303 320 PLARKASLARFLEKRKERVT TP 6 Arabidopsis thaliana (Thale cress)
1 
Please cite: ELM 2016-data update and new functionality of the eukaryotic linear motif resource. (PMID:26615199)

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