Protein degrons and degradation: Exploring substrate recognition and pathway selection in plants.

Proteome composition is dynamic and influenced by many internal and external cues, including developmental signals, light availability, or environmental stresses. Protein degradation, in synergy with protein biosynthesis, allows cells to respond to various stimuli and adapt by reshaping the proteome. Protein degradation mediates the final and irreversible disassembly of proteins, which is important for protein quality control and to eliminate misfolded or damaged proteins, as well as entire organelles. Consequently, it contributes to cell resilience by buffering against protein or organellar damage caused by stresses. Moreover, protein degradation plays important roles in cell signaling, as well as transcriptional and translational events. The intricate task of recognizing specific proteins for degradation is achieved by specialized systems that are tailored to the substrate's physicochemical properties and subcellular localization. These systems recognize diverse substrate cues collectively referred to as "degrons," which can assume a range of configurations. They are molecular surfaces recognized by E3 ligases of the ubiquitin-proteasome system but can also be considered as general features recognized by other degradation systems, including autophagy or even organellar proteases. Here we provide an overview of the newest developments in the field, delving into the intricate processes of protein recognition and elucidating the pathways through which they are recruited for degradation.

The plant-unique protein DRIF1 coordinates with sorting nexin 1 to regulate membrane protein homeostasis.

Membrane protein homeostasis is fine-tuned by the cellular pathways for vacuolar degradation and recycling, which ultimately facilitate plant growth and cell-environment interactions. The endosomal sorting complex required for transport (ESCRT) machinery plays important roles in regulating intraluminal vesicle (ILV) formation and membrane protein sorting to vacuoles. We previously showed that the plant-specific ESCRT component FYVE DOMAIN PROTEIN REQUIRED FOR ENDOSOMAL SORTING1 (FREE1) performs multiple functions in plants, although the underlying mechanisms remain elusive. In this study, we performed a suppressor screen of the FREE1-RNAi mutant and identified and characterized 2 suppressor of free1 (sof) mutants in Arabidopsis (Arabidopsis thaliana). These mutants, sof10 and sof641, result in a premature stop codon or a missense mutation in AT5G10370, respectively. This gene was named DEAH and RING domain-containing protein as FREE1 suppressor 1 (DRIF1). DRIF1 has a homologous gene, DRIF2, in the Arabidopsis genome with 95% identity to DRIF1. The embryos of drif1 drif2 mutants arrested at the globular stage and formed enlarged multivesicular bodies (MVBs) with an increased number of ILVs. DRIF1 is a membrane-associated protein that coordinates with retromer component sorting nexin 1 to regulate PIN-FORMED2 recycling to the plasma membrane. Altogether, our data demonstrate that DRIF1 is a unique retromer interactor that orchestrates FREE1-mediated ILV formation of MVBs and vacuolar sorting of membrane proteins for degradation in plants.

K63-linked ubiquitin chains are a global signal for endocytosis and contribute to selective autophagy in plants.

In contrast to other eukaryotic model organisms, the closely related ubiquitin (Ub)-conjugating enzymes UBC35 and UBC36 are the main sources of K63-linked Ub chains in Arabidopsis.1 Although K63-linked chains have been associated with the regulation of vesicle trafficking, definitive proof for their role in endocytosis was missing. We show that the ubc35 ubc36 mutant has pleiotropic phenotypes related to hormone and immune signaling. Specifically, we reveal that ubc35-1 ubc36-1 plants have altered turnover of integral membrane proteins including FLS2, BRI1, and PIN1 at the plasma membrane. Our data indicates that K63-Ub chains are generally required for endocytic trafficking in plants. In addition, we show that in plants K63-Ub chains are involved in selective autophagy through NBR1, the second major pathway delivering cargoes to the vacuole for degradation. Similar to autophagy-defective mutants, ubc35-1 ubc36-1 plants display an accumulation of autophagy markers. Moreover, autophagy receptor NBR1 interacts with K63-Ub chains, which are required for its delivery to the lytic vacuole.2 Together, we show that K63-Ub chains act as a general signal required for the two main pathways delivering cargo to the vacuole and thus, to maintain proteostasis.

Identification and Characterization of Physiological Pairing of E2 Ubiquitin-Conjugating Enzymes and E3 Ubiquitin Ligases.

The posttranslational attachment of the small protein modifier ubiquitin (Ub) is best known for its function in targeting proteins for degradation by the proteasome. However, ubiquitination also serves as a signal determining protein localization, activity, and interaction. Ubiquitination requires the sequential activity of E1 ubiquitin-activating enzyme (UBA), E2 ubiquitin-conjugating enzyme (UBC), and E3 ubiquitin ligase. Recognition of a target protein by an Ub-E2-E3 complex can result in its mono-ubiquitination (attachment of a single Ub moiety) or poly-ubiquitination, i.e., attachment of Ub chains. While the E3 ligase is important for the reaction specificity, the E2s catalyze the attachment of Ub to the target and to Ub itself to generate chains. In Arabidopsis thaliana, there are two E1s, 37 UBCs (and two ubiquitin-like conjugating enzymes) and more than 1400 E3 ligases, working in a combinatorial way. Therefore, in order to understand E3 ligase function, it is important to frame it within its possible E2s interactors. In this chapter, we propose a two-step identification and characterization of physiological E2-E3 pairs. In a first step, in vivo interacting E2s are identified through bimolecular fluorescence complementation (BiFC) using transient expression in Arabidopsis protoplast. In the second step, the activity of E2-E3 pairs is analyzed by a synthetic biology approach in which autoubiquitination is reconstituted in bacteria.

The Arabidopsis E3 ubiquitin ligase PUB4 regulates BIK1 and is targeted by a bacterial type-III effector.

Plant immunity is tightly controlled by a complex and dynamic regulatory network, which ensures optimal activation upon detection of potential pathogens. Accordingly, each component of this network is a potential target for manipulation by pathogens. Here, we report that RipAC, a type III-secreted effector from the bacterial pathogen Ralstonia solanacearum, targets the plant E3 ubiquitin ligase PUB4 to inhibit pattern-triggered immunity (PTI). PUB4 plays a positive role in PTI by regulating the homeostasis of the central immune kinase BIK1. Before PAMP perception, PUB4 promotes the degradation of non-activated BIK1, while after PAMP perception, PUB4 contributes to the accumulation of activated BIK1. RipAC leads to BIK1 degradation, which correlates with its PTI-inhibitory activity. RipAC causes a reduction in pathogen-associated molecular pattern (PAMP)-induced PUB4 accumulation and phosphorylation. Our results shed light on the role played by PUB4 in immune regulation, and illustrate an indirect targeting of the immune signalling hub BIK1 by a bacterial effector.

Plant proteostasis: a proven and promising target for crop improvement.

The Green Revolution of the 1960s accomplished dramatic increases in crop yields through genetic improvement, chemical fertilisers, irrigation, and mechanisation. However, the current trajectory of population growth, against a backdrop of climate change and geopolitical unrest, predicts that agricultural production will be insufficient to ensure global food security in the next three decades. Improvements to crops that go beyond incremental gains are urgently needed. Plant biology has also undergone a revolution in recent years, through the development and application of powerful technologies including genome sequencing, a pantheon of 'omics techniques, precise genome editing, and step changes in structural biology and microscopy. Proteostasis - the collective processes that control the protein complement of the cell, comprising synthesis, modification, localisation, and degradation - is a field that has benefitted from these advances. This special issue presents a selection of the latest research in this vibrant field, with a particular focus on protein degradation. In the current article, we highlight the diverse and widespread contributions of plant proteostasis to agronomic traits, suggest opportunities and strategies to manipulate different elements of proteostatic mechanisms for crop improvement, and discuss the challenges involved in bringing these ideas into practice.

E2 ubiquitin-conjugating enzymes (UBCs): drivers of ubiquitin signalling in plants.

Most research in the field of ubiquitination has focused on E3 ubiquitin ligases because they are the specificity determinants of the ubiquitination process. Nevertheless, E2s are responsible for the catalysis during ubiquitin transfer, and are therefore, at the heart of the ubiquitination process. Arabidopsis has 37 ubiquitin E2s with additional ones mediating the attachment of ubiquitin-like proteins (e.g. SUMO, Nedd8 and ATG8). Importantly, E2s largely determine the type of ubiquitin chain built, and therefore, the type of signal that decides over the fate of the modified protein, such as degradation by the proteasome (Lys48-linked ubiquitin chains) or relocalization (Lys63-linked ubiquitin chains). Moreover, new regulatory layers impinging on E2s activity, including post-translational modifications or cofactors, are emerging that highlight the importance of E2s.

Analysis of Immunity-Related Oxidative Bursts by a Luminol-Based Assay.

The rapid production of reactive oxygen species (ROS) in response to biotic and abiotic cues is a conserved hallmark of plant responses. The detection and quantification of ROS generation during immune responses is an excellent readout to analyze signaling triggered by the perception of pathogens. The assay described here is easy to employ and versatile, allowing its use in a multitude of variations. For example, ROS production can be analyzed using different tissues including whole seedlings, roots, leaves, protoplasts, and cultured cells, which can originate from different ecotypes or mutants. Samples can be tested in combination with any ROS-inducing elicitors, such as the FLS2-activating peptide flg22, but also lipids or even abiotic stresses. Furthermore, early (PAMP-triggered) and late (effector-triggered) ROS production induced by virulent and avirulent bacteria, respectively, can also be assayed.

Coexpression and Reconstitution of Enzymatic Cascades in Bacteria Using UbiGate.

Coexpression of multiple genes of interest (GOIs) is advantageous for many purposes including the elucidation of protein complexes, reconstitution of enzymatic cascades that mediate the biosynthesis of compounds, the study of signaling cascades, or the elucidation of posttranslational modification. Additional advantages of coexpressing proteins is increased solubility and stability of proteins. For this purpose we developed UbiGate, a modular system based on Golden Gate cloning that enables the generation of polycistronic expression cassettes. Their generation is achieved in four simple steps: (1) GOIs are amplified via PCR, (2) and restriction-ligated into level 0 cloning vectors. Next, (3) the GOIs in a level 0 vector are restriction-ligated into a dedicated set of level 1 vectors that define the position of the GOI within the operon. In the last step (4), level 1 vectors are cloned into a modified pET28-GG expression vector. The resulting modules at each step can be reused to generate fusions with different tags in any desired order and orientation, to include up to six different proteins representing a useful tool facilitating the study of plant metabolic and signaling pathways.

Evolution and Functions of Plant U-Box Proteins: From Protein Quality Control to Signaling.

Posttranslational modifications add complexity and diversity to cellular proteomes. One of the most prevalent modifications across eukaryotes is ubiquitination, which is orchestrated by E3 ubiquitin ligases. U-box-containing E3 ligases have massively expanded in the plant kingdom and have diversified into plant U-box proteins (PUBs). PUBs likely originated from two or three ancestral forms, fusing with diverse functional subdomains that resulted in neofunctionalization. Their emergence and diversification may reflect adaptations to stress during plant evolution, reflecting changes in the needs of plant proteomes to maintain cellular homeostasis. Through their close association with protein kinases, they are physically linked to cell signaling hubs and activate feedback loops by dynamically pairing with E2-ubiquitin-conjugating enzymes to generate distinct ubiquitin polymers that themselves act as signals. Here, we complement current knowledgewith comparative genomics to gain a deeper understanding of PUB function, focusing on their evolution and structural adaptations of key U-box residues, as well as their various roles in plant cells.

The Pleiades are a cluster of fungal effectors that inhibit host defenses.

Biotrophic plant pathogens secrete effector proteins to manipulate the host physiology. Effectors suppress defenses and induce an environment favorable to disease development. Sequence-based prediction of effector function is impeded by their rapid evolution rate. In the maize pathogen Ustilago maydis, effector-coding genes frequently organize in clusters. Here we describe the functional characterization of the pleiades, a cluster of ten effector genes, by analyzing the micro- and macroscopic phenotype of the cluster deletion and expressing these proteins in planta. Deletion of the pleiades leads to strongly impaired virulence and accumulation of reactive oxygen species (ROS) in infected tissue. Eight of the Pleiades suppress the production of ROS upon perception of pathogen associated molecular patterns (PAMPs). Although functionally redundant, the Pleiades target different host components. The paralogs Taygeta1 and Merope1 suppress ROS production in either the cytoplasm or nucleus, respectively. Merope1 targets and promotes the auto-ubiquitination activity of RFI2, a conserved family of E3 ligases that regulates the production of PAMP-triggered ROS burst in plants.

Phosphorylation-dependent subfunctionalization of the calcium-dependent protein kinase CPK28.

Calcium (Ca2+)-dependent protein kinases (CDPKs or CPKs) are a unique family of Ca2+ sensor/kinase-effector proteins with diverse functions in plants. In Arabidopsis thaliana, CPK28 contributes to immune homeostasis by promoting degradation of the key immune signaling receptor-like cytoplasmic kinase BOTRYTIS-INDUCED KINASE 1 (BIK1) and additionally functions in vegetative-to-reproductive stage transition. How CPK28 controls these seemingly disparate pathways is unknown. Here, we identify a single phosphorylation site in the kinase domain of CPK28 (Ser318) that is differentially required for its function in immune homeostasis and stem elongation. We show that CPK28 undergoes intermolecular autophosphorylation on Ser318 and can additionally be transphosphorylated on this residue by BIK1. Analysis of several other phosphorylation sites demonstrates that Ser318 phosphorylation is uniquely required to prime CPK28 for Ca2+ activation at physiological concentrations of Ca2+, possibly through stabilization of the Ca2+-bound active state as indicated by intrinsic fluorescence experiments. Together, our data indicate that phosphorylation of Ser318 is required for the activation of CPK28 at low intracellular [Ca2+] to prevent initiation of an immune response in the absence of infection. By comparison, phosphorylation of Ser318 is not required for stem elongation, indicating pathway-specific requirements for phosphorylation-based Ca2+-sensitivity priming. We additionally provide evidence for a conserved function for Ser318 phosphorylation in related group IV CDPKs, which holds promise for biotechnological applications by generating CDPK alleles that enhance resistance to microbial pathogens without consequences to yield.

Ubiquitin signalling: controlling the message of surface immune receptors.

Microbial attack is first detected by immune receptors located at the plasma membrane. Their activation triggers a plethora of signalling cascades that culminate in the immune response. Ubiquitin and ubiquitin-like protein modifiers play key roles in controlling signalling amplitude and intensity, as well as in buffering proteome imbalances caused by pathogen attack. Here I highlight some of the important advances in the field, which are starting to reveal an intertwined and complex signalling circuitry, which regulates cellular dynamics and protein degradation to maintain homeostasis.

Exocyst subunit Exo70B2 is linked to immune signaling and autophagy.

During the immune response, activation of the secretory pathway is key to mounting an effective response, while gauging its output is important to maintain cellular homeostasis. The Exo70 subunit of the exocyst functions as a spatiotemporal regulator by mediating numerous interactions with proteins and lipids. However, a molecular understanding of the exocyst regulation remains challenging. We show that, in Arabidopsis thaliana, Exo70B2 behaves as a bona fide exocyst subunit. Conversely, treatment with the salicylic acid (SA) defence hormone analog benzothiadiazole (BTH), or the immunogenic peptide flg22, induced Exo70B2 transport into the vacuole. We reveal that Exo70B2 interacts with AUTOPHAGY-RELATED PROTEIN 8 (ATG8) via two ATG8-interacting motives (AIMs) and its transport into the vacuole is dependent on autophagy. In line with its role in immunity, we discovered that Exo70B2 interacted with and was phosphorylated by the kinase MPK3. Mimicking phosphorylation had a dual impact on Exo70B2: first, by inhibiting localization at sites of active secretion, and second, it increased the interaction with ATG8. Phosphonull variants displayed higher effector-triggered immunity (ETI) and were hypersensitive to BTH, which induce secretion and autophagy. Our results suggest a molecular mechanism by which phosphorylation diverts Exo70B2 from the secretory into the autophagy pathway for its degradation, to dampen secretory activity.

A phosphoinositide 5-phosphatase from Solanum tuberosum is activated by PAMP-treatment and may antagonize phosphatidylinositol 4,5-bisphosphate at Phytophthora infestans infection sites.

Potato (Solanum tuberosum) plants susceptible to late blight disease caused by the oomycete Phytophthora infestans display enhanced resistance upon infiltration with the pathogen-associated molecular pattern (PAMP), Pep-13. Here, we characterize a potato gene similar to Arabidopsis 5-phosphatases which was identified in transcript arrays performed to identify Pep-13 regulated genes, and termed StIPP. Recombinant StIPP protein specifically dephosphorylated the D5-position of phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P2 ) in vitro. Other phosphoinositides or soluble inositolpolyphosphates were not converted. When transiently expressed in tobacco (Nicotiana tabacum) pollen tubes, a StIPP-YFP fusion localized to the subapical plasma membrane and antagonized PtdIns(4,5)P2 -dependent effects on cell morphology, indicating in vivo functionality. Phytophthora infestans-infection of N. benthamiana leaf epidermis cells resulted in relocalization of StIPP-GFP from the plasma membrane to the extra-haustorial membrane (EHM). Colocalizion with the effector protein RFP-AvrBlb2 at infection sites is consistent with a role of StIPP in the plant-oomycete interaction. Correlation analysis of fluorescence distributions of StIPP-GFP and biosensors for PtdIns(4,5)P2 or phosphatidylinositol 4-phosphate (PtdIns4P) indicate StIPP activity predominantly at the EHM. In Arabidopsis protoplasts, expression of StIPP resulted in the stabilization of the PAMP receptor, FLAGELLIN-SENSITIVE 2, indicating that StIPP may act as a PAMP-induced and localized antagonist of PtdIns(4,5)P2 -dependent processes during plant immunity.

Efectividad de un apósito de hidrofibra reforzada, con plata iónica al 1,2%, potenciado con EDTA y cloruro de bencetonio: casos de estudio.

Objetivo: Se realizó un estudio prospectivo, observacional, de seguimiento de casos en el servicio de cirugía plástica del hospital El Tunal, Bogotá, Colombia, para evaluar la efectividad de un apósito de hidrofibra reforzada, con plata iónica al 1,2%, potenciado con ácido etilendiaminotetraacético (EDTA) y cloruro de bencetonio en pacientes con heridas de difícil cicatrización. Método: Se incluyeron 23 pacientes con heridas de diferentes etiologías, signos locales de infección, presencia de exudado e indicadores visuales o indirectos de biofilm. Los pacientes fueron divididos en tres grupos: heridas que requerían cicatrización por segunda intención (n=10) (grupo 1), heridas con absceso (n=4) (grupo 2) y heridas en las que se requería preparar el lecho para cobertura quirúrgica (n=9) (grupo 3). El seguimiento de cada caso duró tres meses. Resultados: El grupo 1 demostró una disminución de exudado, infección y signos indirectos de biofilm, así como una reducción significativa de la superficie de la herida con cierre total en ocho de los 10 casos pertenecientes a este grupo. El grupo 2 logró el control de exudado y cierre de la cavidad en un promedio de 21 días. El grupo 3 obtuvo adecuada preparación del lecho de la herida y alcanzó una cobertura quirúrgica en 15 días, en promedio. No se encontraron efectos adversos en los pacientes tratados. Conclusión: Los resultados muestran que el apósito estudiado es efectivo para controlar exudado, infección y signos indirectos de biofilm, así como para disminuir el tamaño de la herida, lograr el cierre de heridas con absceso y preparar el lecho para una cobertura quirúrgica definitiva.Objective: A prospective, observational, case-series study evaluated the efficacy of a hydrofiber dressing with ionic silver, ethylenediaminetetraacetic acid and benzethonium chloride in patients with hard-to-heal wounds at El Tunal hospital in Bogota, Colombia. Method: A total of 23 patients with wounds of different aetiologies, local signs of infection, exudate and biofilm were recruited. Patients were divided into three groups: wounds for secondary intention healing (group 1), abscesses (group 2) and wounds for surgical coverage (group 3). Patients were followed up for 3 months. Results: Group 1 showed a reduction in exudate and infection levels, and a decrease in indirect signs of biofilm. There was also a significant reduction in wound surface, with eight out of 10 patients in this group achieving complete wound closure. Group 2 obtained exudate control and wound closure in 21 days, on average. Group 3 demonstrated an adequate wound bed preparation for surgical coverage in 15 days, on average. No side effects were observed. Conclusion: The results showed that the hydrofiber dressing could be effective in controlling exudate and infection levels, and managing the indirect signs of biofilm, as well as reducing the wound surface, achieving wound closure in abscesses and performing wound bed preparation for surgical coverage.

[Case studies: efficacy of a hydrofiber dressing with ionic silver, ethylenediaminetetraacetic acid and benzethonium chloride]. / Efectividad de un apósito de hidrofibra reforzada, con plata iónica al 1,2%, potenciado con EDTA y cloruro de bencetonio: casos de estudio.

SINOPSIS: Objetivo: Se realizó un estudio prospectivo, observacional, de seguimiento de casos en el servicio de cirugía plástica del hospital El Tunal, Bogotá, Colombia, para evaluar la efectividad de un apósito de hidrofibra reforzada, con plata iónica al 1,2%, potenciado con ácido etilendiaminotetraacético (EDTA) y cloruro de bencetonio en pacientes con heridas de difícil cicatrización. Método: Se incluyeron 23 pacientes con heridas de diferentes etiologías, signos locales de infección, presencia de exudado e indicadores visuales o indirectos de biofilm. Los pacientes fueron divididos en tres grupos: heridas que requerían cicatrización por segunda intención (n=10) (grupo 1), heridas con absceso (n=4) (grupo 2) y heridas en las que se requería preparar el lecho para cobertura quirúrgica (n=9) (grupo 3). El seguimiento de cada caso duró tres meses. Resultados: El grupo 1 demostró una disminución de exudado, infección y signos indirectos de biofilm, así como una reducción significativa de la superficie de la herida con cierre total en ocho de los 10 casos pertenecientes a este grupo. El grupo 2 logró el control de exudado y cierre de la cavidad en un promedio de 21 días. El grupo 3 obtuvo adecuada preparación del lecho de la herida y alcanzó una cobertura quirúrgica en 15 días, en promedio. No se encontraron efectos adversos en los pacientes tratados. Conclusión: Los resultados muestran que el apósito estudiado es efectivo para controlar exudado, infección y signos indirectos de biofilm, así como para disminuir el tamaño de la herida, lograr el cierre de heridas con absceso y preparar el lecho para una cobertura quirúrgica definitiva. ABSTRACT: Objective: A prospective, observational, case-series study evaluated the efficacy of a hydrofiber dressing with ionic silver, ethylenediaminetetraacetic acid and benzethonium chloride in patients with hard-to-heal wounds at El Tunal hospital in Bogota, Colombia. Method: A total of 23 patients with wounds of different aetiologies, local signs of infection, exudate and biofilm were recruited. Patients were divided into three groups: wounds for secondary intention healing (group 1), abscesses (group 2) and wounds for surgical coverage (group 3). Patients were followed up for 3 months. Results: Group 1 showed a reduction in exudate and infection levels, and a decrease in indirect signs of biofilm. There was also a significant reduction in wound surface, with eight out of 10 patients in this group achieving complete wound closure. Group 2 obtained exudate control and wound closure in 21 days, on average. Group 3 demonstrated an adequate wound bed preparation for surgical coverage in 15 days, on average. No side effects were observed. Conclusion: The results showed that the hydrofiber dressing could be effective in controlling exudate and infection levels, and managing the indirect signs of biofilm, as well as reducing the wound surface, achieving wound closure in abscesses and performing wound bed preparation for surgical coverage.