Ubiquitin-Mediated Control of Plant Hormone Signaling
Year: 2012
Type: article
Abstract: The ubiquitin-proteasome system (UPS) plays a role in nearly every aspect of plant biology. The wealth of emerging data demonstrates that regulated protein degradation rivals the well-studied area of transcriptional regulation for importance in cellular regulation. In this Update, we will highlight current research findings that illustrate the contributions of the UPS to phytohormone signaling. We will also consider outstanding questions and discuss possible experimental approaches that will increase our understanding of regulated protein degradation. UPS activity involves a three-step enzymatic cascade between E1, E2, and E3 enzymes that results in the covalent transfer of ubiquitin to target proteins. This process can result in different outcomes, including (1) proteolytic degradation by the 26S proteasome or reversible, nonproteolytic regulatory events. Current plant genome annotations indicate that most species can produce over 1,000 different UPS components; E3 ligase family proteins are the most abundant (Du et al., 2009; Vierstra, 2009). Thus, the potential scope of the UPS is extensive. E3 ligases provide specificity by directly controlling the transfer of ubiquitin to the target substrate and have been classified into four groups based on their complex composition and modes of action: HECT, RING, U-box, and cullin-RING ligases (CRLs; Vierstra, 2009). CRLs are multisubunit ligases that can be further subdivided into four groups based on a variable target recognition module: (1) F-box proteins in the case of S-phase kinase-associated protein1-cullin1-F-box (SCF) ligases; (2) bric-a-brac-tramtrak-broad complex (BTB) proteins that define the BTB group of E3s; (3) the DNA damage-binding (DDB) class that utilizes WD40 domain-containing DWD proteins; and (4) the anaphase-promoting complex category that contains several interchangeable recognition proteins (Vierstra, 2009). Altogether, these enzymatic modules are incredibly diverse, and many of their targets are currently unknown. The phytohormones are small molecule regulators that collectively impact every aspect of plant growth and development. They regulate genetically determined aspects of development such as organ development as well as pathogen response, integration of environmental cues such as light and temperature, and regulation of circadian clock output (Ho et al., 2008; Vierstra, 2009; Lee and Lee, 2012). Recent discoveries highlight the particular importance of UPS action in phytohormone signaling. In fact, UPS-mediated protein degradation has been implicated or demonstrated for every plant hormone, including abscisic acid (ABA), auxin, brassinosteroid (BR), cytokinin, ethylene, GA, jasmonic acid (JA), and strigolactone (SL). Notably, the UPS is also very important for steroid hormone signaling in humans (Lee and Lee, 2012). While some plant hormones undergo long-distance transport and thus have different sites of synthesis and action (e.g. auxin, SL), others appear to be synthesized and function in the same tissue (e.g. BR). As we will discuss in more detail below, one of the major functions of UPS pathways in hormone signaling is the selective destruction of proteins whose concentrations must vary with time and alterations in the state of the cell. UPS action appears to regulate hormone biosynthesis, transport, and perception and thus provides a direct mechanism to control the magnitude and duration of hormone signaling (Figs. 1 and 2). Detailed studies of UPS function in phytohormone pathways have revealed a number of patterns. First, most of the hormone-related UPS targets described to date are proteins associated with transcription. Furthermore, many of the known target transcription factors are classified as repressors and contain ETHYLENE RESPONSE FACTOR-associated amphiphilic repression domains. This includes the auxin/indole-3-acetic acid (Aux/IAA; auxin), jasmonate-ZIM domain (JAZ; JA), and BRASSINAZOLE RESISTANT1 (BZR1; BR) proteins (Kagale et al., 2010). Second, a number of hormones directly control ligase-substrate interactions (e.g. auxin, JA, and GA). The protein degradation mechanisms involved in auxin, JA, and GA signaling are strikingly similar (Fig. 1, A, D, and E). Additionally, in the case of both auxin and JA, the F-box proteins responsible for target proteolysis are themselves part of the hormone receptor complex. UPS components controlling BR and ethylene signaling also appear to be superficially similar. We will describe the types of E3 ligases and their target proteins (when known) that are active in Arabidopsis (Arabidopsis thaliana) in more detail below. The hormones are organized with the aim of highlighting the mechanistic similarities and differences of UPS action. Conservation of these pathways in other plant species is discussed separately at the end of the article. Conserved and diverse UPS degradation mechanisms control hormone signaling (ABA is considered separately due to the abundance of UPS components; see Fig. 2). SCF-type E3 ligases are shown as orange pentagons, RING-type ligases are shown as yellow pentagons, and CRL3-based ligases are depicted as pink pentagons. Unknown ligases are in gray, with a question mark. Known (or unknown) target proteins are shown in blue (transcription factors) or green (kinases and transporters) pie wedges. Transcription factors that are directly bound by SCF target substrates are shown as yellow circles. A, An auxin efflux carrier, PIN2, is degraded in a ubiquitin-dependent manner. In the presence of high auxin concentrations, SCFTIR1/AFB E3 ligases direct the degradation of Aux/IAA transcriptional repressors, releasing bound ARF transcription factors and thus inducing auxin-mediated transcription. B, In the presence of JA-Ile, SCFCOI1 directs the degradation of JAZ transcriptional repressors, releasing bound transcription factors and thus inducing JA-mediated transcription. C, Nucleus-localized growth-repressive DELLA proteins are targeted for degradation by SCFSLY1/SNZ E3 ligases in response to GA perception. D, Ethylene biosynthesis enzymes are degraded by the proteasome. Type-II ACS proteins are targeted by BTBETO1/EOL, while ACS7 is ubiquitylated by XBAT32. In the absence of ethylene, ETP1/2 directs the degradation of the membrane-bound protein EIN2. Degradation of the ETHYLENE INSENSITIVE3 (EIN3) transcription factor is controlled by EBF1 and EBF2 and is inversely correlated with ethylene levels. Thus, as ethylene levels rise, both EIN2 and EIN3 accumulate and ethylene-regulated transcription is stimulated. E, In the absence of SA, the transcription factor NPR1 is targeted for degradation by the NPR4 CUL3-based ligase. The presence of SA reduces the affinity of CUL3NPR4 for NPR1 and thus allows the accumulation of NPR1 and induced resistance. F, Two key components of BR signaling, BIN2 kinase and the transcription factor BZR1, are targets of regulated proteolysis in response to BR via unknown ligase activity. G, The F-box protein MAX2 has been implicated in SL signaling. H, AUF1 may control levels of a cytokinin (represented here by kinetin) response regulator. E3 ligases involved in ABA signaling. The schematic of known UPS components in ABA signaling illustrates that there is regulation of a single substrate (ABI5) by multiple E3 ligases and a number of different classes of E3s act at multiple levels in the ABA pathway, including biosynthesis and downstream gene regulation. RING-type E3 ligases are shown as yellow pentagons, U-box-type E3 ligases as dark orange pentagons, CRL E3 ligases as orange pentagons, and CRL3-based E3 ligases as pink pentagons. AFP is depicted is a green square, and COP1 is a gray triangle. Known (or unknown) ligase substrates are blue pie wedges. Almost every aspect of plant growth and development is controlled by auxin signaling (Stewart and Nemhauser, 2010). The role of UPS activity in the auxin response has been extensively studied and is well established (Santner et al., 2009; Shan et al., 2012). A small family of six F-box proteins, TRANSPORT INHIBITOR RESPONSE1 (TIR1) and AUXIN SIGNALING F-BOX1 (AFB1) to AFB5, act as auxin receptors (Dharmasiri et al., 2005; Greenham et al., 2011). In the presence of auxin, members of the TIR1/AFB1 to -5 family can direct the polyubiquitylation and proteasomal degradation of Aux/IAA transcriptional repressors. There are 29 Aux/IAA proteins in Arabidopsis, and 23 of these are thought to be substrates of SCFTIR1/AFB (Fig. 1A; Calderón Villalobos et al., 2012). Auxin is directly bound by both TIR1/AFB and an Aux/IAA protein simultaneously and thus creates a “coreceptor” complex (Calderón Villalobos et al., 2012). Additionally, the binding affinity of auxin appears to be predominantly controlled by the Aux/IAA proteins and not the TIR1/AFB proteins (Calderón Villalobos et al., 2012). A 13-amino acid motif known as the degron located within domain II of Aux/IAA proteins (Ramos et al., 2001) contributes to substrate stability and turnover rates that range from approximately 10 to 80 min (Dreher et al., 2006). The varied protein-protein interaction affinities between TIR1/AFB proteins and Aux/IAA proteins (Calderón Villalobos et al., 2012) combined with distinct spatiotemporal patterns of accumulation (Parry et al., 2009; Vernoux et al., 2011) may contribute to the broad role of auxin in diverse growth processes. Under low-auxin conditions, members of the Aux/IAA family participate in repressive transcriptional complexes containing an AUXIN RESPONSE FACTOR (Mansfield et al., 2004) transcription factor and TOPLESS (TPL) corepressor protein (Szemenyei et al., 2008). When auxin levels increase, Aux/IAA proteins are targeted for proteasomal degradation. Thus, the specific degradation of the Aux/IAA protein by SCFTIR1/AFB1-5 will result in the disassembly of the repressive complex. It is worth noting that degradation of ARF1 by the proteasome occurs independently of SCFTIR1/AFB1-5, suggesting that ARF protein levels may also be tightly controlled (Salmon et al., 2008). Auxin transport is also regulated by the UPS through proteasomal degradation of the auxin efflux carrier protein PIN-FORMED2 (PIN2; Leitner et al., 2012). Ubiquitylation of PIN2 leads to endocytosis and vacuolar targeting of PIN2 in response to auxin and gravity, which affects auxin distribution within the root (Leitner et al., 2012). It will be interesting to determine which E3 ligase(s) catalyzes the ubiquitylation of PIN2; often, endocytic sorting of a target protein involves multiple E3s (Polo, 2012). Recent studies indicate that UPS action during the jasmonate response parallels what occurs during auxin signaling. JA-Ile (Fig. 1B) is a lipid-derived hormone known to regulate plant development and response to environmental stresses. The F-box protein CORONATINE-INSENSITIVE1 (COI1) acts as a JA-Ile receptor and directs the degradation of JAZ proteins, a small family of transcriptional repressors (Fig. 1B; Shan et al., 2012). A number of JAZ proteins (e.g. JAZ1) contain a degron motif that facilitates binding to COI1 (Grunewald et al., 2009; Pauwels et al., 2010; Sheard et al., 2010). Similar to the situation for auxin, COI and the JAZ protein act as coreceptors for JA-Ile; thus, JA-Ile directly stabilizes SCFCOI1 interactions with some JAZ proteins (Sheard et al., 2010). Some JAZ proteins can form complexes with TPL through the adapter protein NOVEL INTERACTOR OF JAZ (Pauwels et al., 2010), whereas the ETHYLENE RESPONSE FACTOR-associated amphiphilic repression domain-containing JAZ proteins (e.g. JAZ8) interact directly with TPL or other corepressors to inhibit JA responses (Shyu et al., 2012). This JAZ-based complex acts to repress the activity of transcription factors such as MYC2 and MYB21/24 (Pauwels et al., 2010; Song et al., 2011). In the presence of JA-Ile, JAZ proteins are degraded, JAZ-mediated repression is relieved, and early JA-responsive genes are rapidly expressed (Pauwels et al., 2010). Similar to the Aux/IAA proteins, sequence variation in the degron motif alters the stability and repressive action of JAZ proteins (Shyu et al., 2012). Similar SCF-mediated regulation has been shown for GA signaling (Fig. 1C; Gao et al., 2011). The effects of GA include promotion of seed germination, stimulation of organ elongation, and induction of flowering. GA is perceived by a protein called GIBBERELLIN INSENSITIVE DWARF1 (GID1). GA binding to GID1 results in binding to nucleus-localized growth repressors called DELLA proteins (Ueguchi-Tanaka et al., 2005; Nakajima et al., 2006; Willige et al., 2007). This tripartite GID-GA-DELLA complex is subsequently targeted for ubiquitylation by SCFSLY1/SNZ E3 ligases, resulting in degradation of the DELLAs (Gao et al., 2011). This scenario is reminiscent of UPS action during auxin and JA-Ile signaling, because DELLA proteins bind and repress the activity of transcription factors such as the PHYTOCHROME INTERACTING FACTORs (de Lucas et al., 2008; Feng et al., 2008). Thus, this scenario is reminiscent of UPS action during auxin and JA signaling because hormone perception results in the degradation of proteins involved in transcriptional repression. However, while protein degradation is directly involved in GA perception, it is different compared with auxin and JA receptor systems, where the receptors are themselves part of E3 ligase complexes. Ethylene functions as a critical growth regulator and is also important for biotic and abiotic stress responses (Schaller, 2012). Many aspects of ethylene signaling are tightly controlled by the UPS (Fig. 1D). First, a number of enzymes involved in ethylene biosynthesis are targeted for proteasomal degradation. This includes (1) type-2 1-aminocyclopropane-1-carboxylic acid synthase proteins (ACS4, ACS5, and ACS9), which are ubiquitylated by ETO1 and ETO-like1/2 BTB ligases (Wang et al., 2004; Yoshida et al., 2005; Christians et al., 2009), and (2) ACS7, a type-3 ACS enzyme that is ubiquitylated by the RING-type E3 ligase XBAT32 (Lyzenga et al., 2012). These degradation mechanisms provide a rapid way to change ethylene concentrations in planta. In the absence of ethylene, a pair of F-box proteins, EIN2-TARGETING PROTEIN1 (ETP1) and ETP2, promote the degradation of the ethylene signaling protein ETHYLENE INSENSITIVE2 (EIN2), reducing the ethylene response (Qiao et al., 2009). In the presence of ethylene, ETP expression is repressed, allowing the accumulation of EIN2. Downstream of EIN2 lies EIN3 and EIN3-like1 (EIL1), transcription factors that directly target ethylene-responsive genes. At low ethylene levels, EIN3 and EIL1 are targeted for ubiquitylation and degradation by another pair of F-box proteins, EIN3-BINDING F-BOX1 (EBF1) and EBF2, which are also subject to proteasomal degradation (Guo and Ecker, 2003; Potuschak et al., 2003; An et al., 2010). As ethylene levels increase, the stability of EBF1/2 decreases, leading to a buildup of EIN3 and EIL1, thus inducing transcription (An et al., 2010). Salicylic acid (SA) is a secondary metabolite produced by a wide range of organisms, and salicylates have been used by humans for pain relief for centuries (An and Mou, 2011). In plants, SA functions as a plant hormone required for innate immunity (Vlot et al., 2009). Two paralogous receptors were recently identified for SA, NPR1-LIKE PROTEIN3 (NPR3) and NPR4, which are BTB-CUL3 ligases (Fu et al., 2012). CUL3NPR3/4 direct the degradation of NONEXPRESSOR OF PR GENES1 (NPR1), a master transcriptional regulator of plant defense (Fu et al., 2012). NPR1 interacts with other transcription factors in the nucleus to mediate pathogen resistance (Fu et al., 2012). Thus, the perception of SA (Fig. 1E) parallels other UPS-controlled hormone signaling mechanisms (Fig. 1). To what extent (and how) UPS activity plays a role in BR, SL, and cytokinin signaling is not clear at present (Fig. 1, F–H). A of key components of BR signaling appear to be degraded by the 26S proteasome in response to BR by unknown ligases (Fig. the INSENSITIVE2 kinase is regulated by protein degradation et al., 2008). Additionally, the transcription factor is by BIN2 and rapidly degraded by the proteasome to mediate the of several BR genes et al., A also demonstrated that the protein degradation levels of the BR receptor via a ubiquitin et al., 2012). UPS activity is implicated in SL signaling because an F-box protein et al., A direct role for the UPS in cytokinin action has not been However, the of AUXIN PROTEIN1 in interactions between cytokinin and auxin et al., 2011). the extent of protein degradation for other the of MAX2 and targets to be The number of E3 ligases involved (or in ABA signaling is more for other hormone to As a many aspects of ABA are controlled by protein degradation (Fig. 2). ABA plays important in many including seed and stress both biotic and The current understanding of ABA signaling, from receptors to includes many and is complex et al., 2010; 2012). At one ligase has been shown to directly impact ABA E3 the levels of an enzyme that abscisic to ABA et al., 2009). gene that has been shown to ABA levels is which a domain-containing protein that can interact with UPS components in including the F-box et al., 2006). The levels of ABA a transcription are regulated by at different classes of E3 ligases, including a RING-type and WD40 PROTEIN1 and CRLs et al., 2006; Lee et al., 2010). The nucleus-localized family appears to promote degradation in in with the protein it is not clear this process occurs et al., Additionally, such as and of may also a role in degradation of et al., 2003; et al., 2009). The regulation of a single substrate by multiple E3 ligases has been well in the transcription factor targeted for ubiquitylation and degradation by E3 ligases et al., 2010). a mechanism may rapidly different to control the of a key transcription factor leading to the Additionally, a RING-type acts to control transcription factor abundance and downstream ABA signaling et al., A small family of CUL3-based E3 ligases have recently been to a key role in ABA signaling by the proteasomal degradation of the class transcription factor et al., 2011). Furthermore, six proteins can interact with different transcription factors and suggesting that this family of E3 ligases may regulate other as well et al., 2011). A with identified an protein with et al., which may act as part of a CUL3-based ligase et al., Additionally, the E3 ligase can the activity of an A of protein by leading to and of seed et al., 2006). A number of other classes of E3 ligases have been shown to function during ABA signaling, their targets (and direct in protein have not been established These include the F-box proteins et al., and PROTEIN3 et al., et al., and RING-type et al., and et al., 2006). growth and development involves the integration of many different hormone at both the cellular and organ levels. to UPS activity and the there are a number of emerging such may TPL proteins are corepressors that both auxin and JA signaling pathways through the interaction with specific transcription factors (e.g. Aux/IAA and JAZ There are also of one hormone inducing an E3 ligase that acts on a target active in another hormone signaling AUF1 is expressed in response to auxin and affects levels et al., 2011). The interaction of JAZ and DELLA proteins is an of protein-protein interactions directly distinct hormone pathways et al., 2010; Arabidopsis and et al., 2012). As protein-protein interactions to be in plants, we the of to increase The number of UPS components in that the ubiquitin has a broad role in cellular regulation (Vierstra, 2009). what is known from Arabidopsis, it is that many pathways will be in other However, there are also to be some In fact, of the UPS components and protein-protein interactions involved in auxin signaling, including the F-box coreceptors and appear to be in the et al., 2010; et al., 2012). plant are at et al., for in of UPS components for further Additionally, a of UPS proteins, called is at (Du et al., 2009). many proteins are by ubiquitin and degraded by the This is currently a major outstanding question in plant biology. of ubiquitylated proteins in Arabidopsis have identified proteins that are by including known E3 target proteins such as EIN3 and et al., et al., 2009). The recently a specific for proteins et al., 2011). this on ubiquitin a similar be in to ubiquitylated proteins for by data target substrates for known ubiquitin ligases (Figs. 1 and and also proteins that are UPS these with hormone and receptor the role of the UPS in It is worth noting that a three-step combined with identified proteins by small in Arabidopsis and Vierstra, 2011). of the proteins are involved in transcription and suggesting that of may be an important for gene regulation. While the degradation are known for Aux/IAA and JAZ proteins, we not what other contribute to ligase-substrate interactions and protein These are and be identified in due to a of sequence and because the of ubiquitin to substrates may not be to (Dreher et al., 2006; et al., 2008). In fact, we have very of ubiquitylation sites on substrates for well-studied proteins the The of combined with is one to such Additionally, degron may be of hormone action within and A of Aux/IAA domain II which contains the degron for this family of SCFTIR1/AFB1-5 has been used to auxin in the root and et al., et al., 2012). potential area of involves the for E3 Aux/IAA and JAZ proteins rapid degradation within the range of approximately 1 to 80 min (Dreher et al., 2006; Pauwels et al., 2010), we not the stability of other target proteins. studies from have shown a very between levels and protein abundance et al., 2010; et al., et al., and 2012). Additionally, it is clear that many proteins are and we not currently to what extent as a role in UPS-mediated in of of the and proteins discussed here (Figs. 1 and are present in the current et al., 2011). Thus, we to and approaches in to determine protein abundance and in more A number of protein-protein have been used to ligase-substrate most E3 ligases in Arabidopsis are currently A be to ubiquitylation targets in an Arabidopsis Arabidopsis 2011). that a number of known E3 targets are transcription factors (Figs. 1 and with a transcription et al., 2009; et al., et al., 2011) be very also be for the of UPS protein-protein interactions were described based on a between a Aux/IAA protein and a transcription et al., 2010). target proteins are a number of can be used to that are ubiquitylated by ubiquitylation have been recently et al., and et al., 2011). It is an time to be ubiquitylation and protein degradation in plants, as there are many questions and to DNA and provide the proteins are the of into the regulation of protein with to plant hormone signaling, have potential to impact many of plant ubiquitin-proteasome system cullin-RING ligase abscisic acid brassinosteroid jasmonic acid strigolactone acid
Source: PLANT PHYSIOLOGY
Authors: Dior R. Kelley, Mark Estelle
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
Award: G4540028961
OpenAlex ID: W2073224077