Peptides interfering with protein-protein interactions in the ethylene signaling pathway delay tomato fruit ripening

Peptide design to control protein-protein interactions

Targeting of protein-protein interactions has become of huge interest in every aspect of medicinal and biological sciences. The control of protein interactions selectively offers the opportunity to control biological processes while limiting off target effects. This interest has massively increased with the development of cryo-EM and protein structure prediction with tools such as RosettaFold and AlphaFold. When designing molecules to control protein interactions, either inhibition or stabilisation, a starting point is commonly peptide design. This tutorial review describes that process, highlighting the selection of an initial sequence with and without structural information. Subsequently, methods for how the sequence can be analysed for key residues and how this information can be used to optimise the ligand efficiency are highlighted. Finally a discussion on how peptides can be further modified to increase their affinity and cell permeability, improving their drug-like properties, is presented.

Exploring the world of small proteins in plant biology and bioengineering

Small proteins are ubiquitous in all kingdoms of life. MicroProteins, initially characterized as small proteins with protein interaction domains that enable them to interact with larger multidomain proteins, frequently modulate the function of these proteins. The study of these small proteins has contributed to a greater comprehension of protein regulation. In addition to sequence homology, sequence-divergent small proteins have the potential to function as microProtein mimics, binding to structurally related proteins. Moreover, a multitude of other small proteins encoded by short open reading frames (sORFs) and peptides, derived from diverse sources such as long noncoding RNAs (lncRNAs) and miRNAs, contribute to a variety of biological processes. The potential of small proteins is evident, offering promising avenues for bioengineering that could revolutionize crop performance and reduce reliance on agrochemicals in future agriculture.

Synthesis and evaluation of catecholamine derivatives as amyloid-beta aggregation inhibitors

Effectively inhibition of amyloid β (Aβ) aggregation is considered an important method for treatment of the Alzheimer's disease. Herein, inspired by the ability of trans-clovamide to effectively inhibit Aβ aggregation, we synthesized a series of structurally related catecholamine derivatives and tested them as Aβ aggregation inhibitors using the Thioflavin T assay. The results show that they demonstrated a higher inhibitory rate against Aβ aggregation. Furthermore, these compounds exhibited high water solubilities and low cytotoxicities. Additionally, transmission electron microscopy images and dynamic light scattering of their Aβ aggregations were observed. Docking simulations revealed that the catechol moiety of the synthesized compounds can form hydrogen bonds with the key regions of Aβ and thereby inhibit Aβ aggregation.

Phytosulfokine promotes fruit ripening and quality via phosphorylation of transcription factor DREB2F in tomato

Phytosulfokine (PSK), a plant peptide hormone with a wide range of biological functions, is recognized by its receptor PHYTOSULFOKINE RECEPTOR 1 (PSKR1). Previous studies have reported that PSK plays important roles in plant growth, development, and stress responses. However, the involvement of PSK in fruit development and quality formation remains largely unknown. Here, using tomato (Solanum lycopersicum) as a research model, we show that exogenous application of PSK promotes the initiation of fruit ripening and quality formation, while these processes are delayed in pskr1 mutant fruits. Transcriptomic profiling revealed that molecular events and metabolic pathways associated with fruit ripening and quality formation are affected in pskr1 mutant lines and transcription factors are involved in PSKR1-mediated ripening. Yeast screening further identified that DEHYDRATION-RESPONSIVE ELEMENT BINDING PROTEIN 2F (DREB2F) interacts with PSKR1. Silencing of DREB2F delayed the initiation of fruit ripening and inhibited the promoting effect of PSK on fruit ripening. Moreover, the interaction between PSKR1 and DREB2F led to phosphorylation of DREB2F. PSK improved the efficiency of DREB2F phosphorylation by PSKR1 at the tyrosine-30 site, and the phosphorylation of this site increased the transcription level of potential target genes related to the ripening process and functioned in promoting fruit ripening and quality formation. These findings shed light on the involvement of PSK and its downstream signaling molecule DREB2F in controlling climacteric fruit ripening, offering insights into the regulatory mechanisms governing ripening processes in fleshy fruits.

Proteoform of Arabidopsis seed storage protein identified by functional proteomics approach exhibits acyl hydrolase activity during germination

Lipases play a crucial role in the life cycle of seed plants and the oil content of the seed is highly regulated by the lipase activity. Hence, understanding the role of lipases during germination and post-germination will provide insights into lipid mobilization. However, to date, no lipase gene has been identified in seeds except, Sugar-dependent-1 in Arabidopsis. Hence, in the present study, we employed a functional proteomic approach for the identification of seed-specific lipase. Activity-Based Proteome Profiling (ABPP) of Arabidopsis mature and germinating seeds revealed the expression of a functional serine hydrolase exclusively during germination. The mass-spectrometry analysis reveals the identity and amino acid sequence of the protein correspond to AT4G28520 gene, a canonical 12S Seed Storage Protein (SSP). Interestingly, the identified SSP was a proteoform of AT4G28520 (SL-AT4G28520) and exhibited >90% identity with the canonical AT4G28520 (FL-AT4G28520). Heterologous expression and enzyme assays indicated that SL-AT4G28520 protein indeed possesses monoacylglycerol lipase activity, while the FL-AT4G28520 protein didn't exhibit any detectable activity. Functional proteomics and lipidomics analysis demonstrated a catalytic function of this SSP. Collectively, this is the first report, which suggests that SL-AT4G28520 encodes a lipase, and the activity is depending on the physiological condition.

Interfering Peptides Targeting Protein-Protein Interactions in the Ethylene Plant Hormone Signaling Pathway as Tools to Delay Plant Senescence

Interfering peptides (iPs) have been recognized as valuable substances to specifically target protein-protein interactions (PPIs) in senescence and disease. Although the concept of iPs has been validated for several PPIs in medical and pharmaceutical research, little attention so far has been paid to the enormous potential iPs that may provide to target and control plant growth and developmental processes or plant environmental responses. However, recent research on PPIs in the ethylene signaling pathway has identified the synthetic peptide NOP-1 derived from the nuclear localization signal of ethylene regulator EIN2 as an efficient inhibitor of typical ethylene responses such as ripening, aging, and senescence. Biophysical and biochemical studies on purified recombinant proteins of the ethylene receptor family from various plant species demonstrate that the synthetic peptide binds in the nM-μM range at the plant target. Here, we describe methods to evaluate and quantify the effect of the NOP-1 peptide on flower senescence as a typical ethylene response in the intact plant system. This approach will help to systematically advance our technological capability to delay plant ethylene responses and to expand shelf-life or vase life of fruits and flowers.

Ethylene signaling in rice and Arabidopsis: New regulators and mechanisms

Ethylene is a gaseous hormone which plays important roles in both plant growth and development and stress responses. Based on studies in the dicot model plant species Arabidopsis, a linear ethylene signaling pathway has been established, according to which ethylene is perceived by ethylene receptors and transduced through CONSTITUTIVE TRIPLE RESPONSE 1 (CTR1) and ETHYLENE-INSENSITIVE 2 (EIN2) to activate transcriptional reprogramming. In addition to this canonical signaling pathway, an alternative ethylene receptor-mediated phosphor-relay pathway has also been proposed to participate in ethylene signaling. In contrast to Arabidopsis, rice, a monocot, grows in semiaquatic environments and has a distinct plant structure. Several novel regulators and/or mechanisms of the rice ethylene signaling pathway have recently been identified, indicating that the ethylene signaling pathway in rice has its own unique features. In this review, we summarize the latest progress and compare the conserved and divergent aspects of the ethylene signaling pathway between Arabidopsis and rice. The crosstalk between ethylene and other plant hormones is also reviewed. Finally, we discuss how ethylene regulates plant growth, stress responses and agronomic traits. These analyses should help expand our knowledge of the ethylene signaling mechanism and could further be applied for agricultural purposes.

Ethylene signaling in plants

Ethylene is a gaseous phytohormone and the first of this hormone class to be discovered. It is the simplest olefin gas and is biosynthesized by plants to regulate plant development, growth, and stress responses via a well-studied signaling pathway. One of the earliest reported responses to ethylene is the triple response. This response is common in eudicot seedlings grown in the dark and is characterized by reduced growth of the root and hypocotyl, an exaggerated apical hook, and a thickening of the hypocotyl. This proved a useful assay for genetic screens and enabled the identification of many components of the ethylene-signaling pathway. These components include a family of ethylene receptors in the membrane of the endoplasmic reticulum (ER); a protein kinase, called constitutive triple response 1 (CTR1); an ER-localized transmembrane protein of unknown biochemical activity, called ethylene-insensitive 2 (EIN2); and transcription factors such as EIN3, EIN3-like (EIL), and ethylene response factors (ERFs). These studies led to a linear model, according to which in the absence of ethylene, its cognate receptors signal to CTR1, which inhibits EIN2 and prevents downstream signaling. Ethylene acts as an inverse agonist by inhibiting its receptors, resulting in lower CTR1 activity, which releases EIN2 inhibition. EIN2 alters transcription and translation, leading to most ethylene responses. Although this canonical pathway is the predominant signaling cascade, alternative pathways also affect ethylene responses. This review summarizes our current understanding of ethylene signaling, including these alternative pathways, and discusses how ethylene signaling has been manipulated for agricultural and horticultural applications.

Transmission blockage of an orthotospovirus using synthetic peptides

Orthotospoviruses are acquired by thrips during feeding on infected tissue. Virions travel through the foregut and enter midgut epithelial cells through the interaction between the viral glycoproteins and cellular receptors. Glycoprotein RGD motifs and N-linked glycosylation sites have been predicted to mediate receptor binding or play important roles in virus entry into host cells, yet their function needs to be validated. In this study, peptides derived from the soybean vein necrosis virus N glycoprotein were utilized to identify critical regions in virus-vector interactions. Transmission mediated by single Neohydatothrips variabilis dropped by more than 2/3 when thrips were fed on peptide NASIAAAHEVSQE or the combination of NASIRGDHEVSQE and RLTGECNITKVSLTN when compared to the controls; indicating that this strategy could significantly reduce transmission efficiency, opening new avenues in the control of diseases caused by orthotospoviruses.

Influence of the ethylene-related signal-inhibiting octapeptide NOP-1 on postharvest ripening and quality of 'Golden Delicious' apples

BACKGROUND

Processes extending the shelf life of climacteric fruit play an important role in terms of a sustainable global food supply. In a previous study, a synthetic octapeptide (NOP-1) was shown to inhibit the interaction between ethylene receptor (ETR) and ethylene insensitive-2 (EIN2), and in consequence delay tomato ripening. We investigated for the first time the effect of NOP-1 on inhibiting the ripening of apples ('Golden Delicious') during postharvest.

RESULTS

Using purified recombinant proteins from a bacterial expression system, we demonstrate here that EIN2 also interacts tightly (K_d  = 136 ± 29 nmol L^-1 ) with the corresponding apple ETR MdETR1. In line with previous binding studies on tomato ETRs, the ripening-delaying peptide NOP-1 clearly binds to the purified apple ETR. An NOP-1 solution (1000 µmol L^-1 ) was applied with a brush or microdispenser and compared with apples treated with 1-methylcyclopropene (1-MCP) (SmartFresh™, Agrofresh) applied as gaseous treatment or untreated control fruits. NOP-1 inhibited colour development and chlorophyll degradation during shelf life. These effects were more pronounced with the brush application (surface film) than with microdroplets application (mimicking a sprayable formulation). NOP-1 did not alter ethylene release or respiration rate, whereas 1-MCP expectedly strongly suppressed both. There were no differences in quality parameters evaluated.

CONCLUSION

Our study shows that NOP-1 binds to MdETR1 which results in delaying of ethylene-dependent ripening developments of skin colour and chlorophyll. Besides application methods, possible reasons for the weak effect of NOP-1 in comparison with previous tomato experiments could be different receptor affinity and penetration differences. © 2019 Society of Chemical Industry.

The NOP-1 peptide derived from the central regulator of ethylene signaling EIN2 delays floral senescence in cut flowers

The plant hormone ethylene was identified as important triggering factor and primary regulator of flower senescence in many species. Consequently, application of chemical inhibitors of ethylene biosynthesis and action is used to extend the longevity of ethylene-sensitive flowers. Here, we show that the peptide NOP-1, a biological derived from the nuclear localization signal of ethylene regulator EIN2 tightly binds to the ethylene receptor of carnation plants - a model to study flower senescence. When applied on cut flowers the peptide biological delays petal senescence similar to previously identified and currently used chemical inhibitors, but offers significant advances to these chemicals in biodegradability, sustainability and ecotoxicity. Our bioinformatic analysis of a wide range of ethylene receptors indicates complete sequence conservation of the anticipated NOP-1 binding site in flower species supporting a widespread use of the peptide on flowering ornamentals to delay senescence and decay in cut flowers. We anticipate our innovative approach to extend flower longevity by a new class of biomolecules such as peptides, peptide analogues and peptide mimetics will significantly advance our technological capability to delay flower senescence and expand vase-life of cut flowers in a sustainable and environmentally friendly manner.

Molecular Analysis of Protein-Protein Interactions in the Ethylene Pathway in the Different Ethylene Receptor Subfamilies

Signal perception and transmission of the plant hormone ethylene are mediated by a family of receptor histidine kinases located at the Golgi-ER network. Similar to bacterial and other plant receptor kinases, these receptors work as dimers or higher molecular weight oligomers at the membrane. Sequence analysis and functional studies of different isoforms suggest that the ethylene receptor family is classified into two subfamilies. In Arabidopsis, the type-I subfamily has two members (ETR1 and ERS1) and the type-II subfamily has three members (ETR2, ERS2, and EIN4). Whereas subfamily-I of the Arabidopsis receptors and their interactions with downstream elements in the ethylene pathway has been extensively studied in the past; related information on subfamily-II is sparse. In order to dissect the role of type-II receptors in the ethylene pathway and to decode processes associated with this receptor subfamily on a quantitative molecular level, we have applied biochemical and spectroscopic studies on purified recombinant receptors and downstream elements of the ethylene pathway. To this end, we have expressed purified ETR2 as a prototype of the type-II subfamily, ETR1 for the type-I subfamily and downstream ethylene pathway proteins CTR1 and EIN2. Functional folding of the purified receptors was demonstrated by CD spectroscopy and autokinase assays. Quantitative analysis of protein-protein interactions (PPIs) by microscale thermophoresis (MST) revealed that ETR2 has similar affinities for CTR1 and EIN2 as previously reported for the subfamily-I prototype ETR1 suggesting similar roles in PPI-mediated signal transfer for both subfamilies. We also used in planta fluorescence studies on transiently expressed proteins in Nicotiana benthamiana leaf cells to analyze homo- and heteromer formation of receptors. These studies show that type-II receptors as well as the type-I receptors form homo- and heteromeric complexes at these conditions. Notably, type-II receptor homomers and type-II:type-I heteromers are more stable than type-I homomers as indicated by their lower dissociation constants obtained in microscale thermophoresis studies. The enhanced stability of type-II complexes emphasizes the important role of type-II receptors in the ethylene pathway.

Ethylene receptors and related proteins in climacteric and non-climacteric fruits

Fruits have been traditionally classified into two categories based on their capacity to produce and respond to ethylene during ripening. Fruits whose ripening is associated to a peak of ethylene production and a respiration burst are referred to as climacteric, while those that are not are referred to as non-climacteric. However, an increasing body of literature supports an important role for ethylene in the ripening of both climacteric and non-climacteric fruits. Genome and transcriptomic data have become available across a variety of fruits and we leverage these data to compare the structure and transcriptional regulation of the ethylene receptors and related proteins. Through the analysis of four economically important fruits, two climacteric (tomato and apple), and two non-climacteric (grape and citrus), this review compares the structure and transcriptional regulation of the ethylene receptors and related proteins in both types of fruit, establishing a basis for the annotation of ethylene-related genes. This analysis reveals two interesting differences between climacteric and non-climacteric fruit: i) a higher number of ETR genes are found in climacteric fruits, and ii) non-climacteric fruits are characterized by an earlier ETR expression peak relative to sugar accumulation.

Inhibitors of protein-protein interactions (PPIs): an analysis of scaffold choices and buried surface area

Protein-protein interactions (PPI) were once considered 'undruggable', but clinical successes, driven by advanced methods in drug discovery, have challenged that notion. Here, we review the last three years of literature on PPI inhibitors to understand what is working and why. From the 66 recently reported PPI inhibitors, we found that the average molecular weight was significantly greater than 500Da, but that this trend was driven, in large part, by the contribution of peptide-based compounds. Despite differences in average molecular weight, we found that compounds based on small molecules or peptides were almost equally likely to be potent inhibitors (K_D<1μM). Finally, we found PPIs with buried surface area (BSA) less than 2000Ų were more likely to be inhibited by small molecules, while PPIs with larger BSA values were typically inhibited by peptides. PPIs with BSA values over 4000Ų seemed to create a particular challenge, especially for orthosteric small molecules. Thus, it seems important to choose the inhibitor scaffold based on the properties of the target interaction. Moreover, this survey suggests a (more nuanced) conclusion to the question of whether PPIs are good drug targets; namely, that some PPIs are readily 'druggable' given the right choice of scaffold, while others still seem to deserve the 'undruggable' moniker.

Parallel online determination of ethylene release rate by Shaken Parsley cell cultures using a modified RAMOS device

BACKGROUND

Ethylene is an important plant hormone that controls many physiological processes in plants. Conventional methods for detecting ethylene include gas chromatographs or optical mid-infrared sensors, which are expensive and, in the case of gas chromatographs, are hardly suitable for automated parallelized online measurement. Electrochemical ethylene sensors are cheap but often suffer from poor resolution, baseline drifting, and target gas oxidation. Thus, measuring ethylene at extremely low levels is challenging.

RESULTS

This report demonstrates the integration of electrochemical ethylene sensors into a respiration activity monitoring system (RAMOS) that measures, in addition to the oxygen transfer rate, the ethylene transfer rate in eight parallel shake flasks. A calibration method is presented that is not prone to baseline drifting and considers target gas oxidation at the sensor. In this way, changes in ethylene transfer rate as low as 4 nmol/L/h can be resolved. In confirmatory experiments, the overall accuracy of the method was similar to that of gas chromatography-mass spectrometry (GC/MS) measurements. The RAMOS-based ethylene determination method was exemplified with parsley suspension-cultured cells that were primed for enhanced defense by pretreatment with salicylic acid, methyl jasmonate or 4-chlorosalicylic acid and challenged with the microbial pattern Pep13. Ethylene release into the headspace of the shake flask was observed upon treatment with salicylic acid and methyl jasmonate was further enhanced, in case of salicylic acid and 4-chlorosalicylic acid, upon Pep13 challenge.

CONCLUSION

A conventional RAMOS device was modified for simultaneous measurement of the ethylene transfer rate in eight parallel shake flasks at nmol/L/h resolution. For the first time electrochemical sensors are used to provide a medium-throughput method for monitoring ethylene release by plants. Currently, this can only be achieved by costly laser-based detection systems and automated gas chromatographs. The new method is particularly suitable for plant cell suspension cultures. However, the method may also be applicable to intact plants, detached leaves or other plant tissues. In addition, the general principle of the technology is likely extendable to other volatiles or gases as well, such as nitric oxide or hydrogen peroxide.

Cutting in the middleman: hidden substrates at the interface between proteases and plant development

Contents Summary 916 I. Introduction 916 II. DEK1: towards identification of protease substrates 917 III. Separases: when proteolytic modules attain nonproteolytic functions 918 IV. The peculiar case of a nonredundant subtilisin 919 V. Towards a solution to the protease redundancy problem 920 VI. Matters arising and closing remarks 921 Acknowledgements 921 References 921 SUMMARY: Proteases are integral components of proteome remodelling networks that regulate turnover of proteins and expand their functional diversity. Accumulating evidence highlights the importance of proteases as being central hubs of developmental programs. Yet the molecular pathways that many proteases act on, their natural substrates and their putative nonproteolytic functions remain largely elusive. Here, we discuss recent findings on proteases with functions that converge into plant development regulation, such as DEFECTIVE KERNEL 1 (DEK1), separase and subtilisins, to highlight conspicuous but unexplored aspects of protease biology. We also suggest an exploratory framework for addressing protease functions.

Recognition motif and mechanism of ripening inhibitory peptides in plant hormone receptor ETR1

Synthetic peptides derived from ethylene-insensitive protein 2 (EIN2), a central regulator of ethylene signalling, were recently shown to delay fruit ripening by interrupting protein-protein interactions in the ethylene signalling pathway. Here, we show that the inhibitory peptide NOP-1 binds to the GAF domain of ETR1 - the prototype of the plant ethylene receptor family. Site-directed mutagenesis and computational studies reveal the peptide interaction site and a plausible molecular mechanism for the ripening inhibition.

Regulatory Peptides in Plants

Many different peptides regulating cell differentiation, growth, and development are found in plants. Peptides participate in regulation of plant ontogenesis starting from pollination, pollen tube growth, and the very early stages of embryogenesis, including formation of embryo and endosperm. They direct differentiation of meristematic stem cells, formation of tissues and individual organs, take part in regulation of aging, fruit maturation, and abscission of plant parts associated with apoptosis. Biological activity of peptides is observed at very low concentrations, and it has mainly signal nature and hormonal character. "Mature" peptides appear mainly due to processing of protein precursors with (or without) additional enzymatic modifications. Plant peptides differ in origin, structure, and functional properties. Their specific action is due to binding with respective receptors and interactions with various proteins and other factors. Peptides can also regulate physiological functions by direct peptide-protein interactions. Peptide action is coordinated with the action of known phytohormones (auxins, cytokinins, and others); thus, peptides control phytohormonal signal pathways.

Novel Protein-Protein Inhibitor Based Approach to Control Plant Ethylene Responses: Synthetic Peptides for Ripening Control

Ethylene signaling is decisive for many plant developmental processes. Among these, control of senescence, abscission and fruit ripening are of fundamental relevance for global agriculture. Consequently, detailed knowledge of the signaling network along with the molecular processes of signal perception and transfer are expected to have high impact on future food production and agriculture. Recent advances in ethylene research have demonstrated that signaling of the plant hormone critically depends on the interaction of the ethylene receptor family with the NRAMP-like membrane protein ETHYLENE INSENSITIVE 2 (EIN2) at the ER membrane, phosphorylation-dependent proteolytic processing of ER-localized EIN2 and subsequent translocation of the cleaved EIN2 C-terminal polypeptide (EIN2-CEND) to the nucleus. EIN2 nuclear transport, but also interaction with the receptors sensing the ethylene signal, both, depend on a nuclear localization signal (NLS) located at the EIN2 C-terminus. Loss of the tight interaction between receptors and EIN2 affects ethylene signaling and impairs plant ethylene responses. Synthetic peptides derived from the NLS sequence interfere with the EIN2-receptor interaction and have utility in controlling plant ethylene responses such as ripening. Here, we report that a synthetic peptide (NOP-1) corresponding to the NLS motif of Arabidopsis EIN2 (aa 1262-1269) efficiently binds to tomato ethylene receptors LeETR4 and NR and delays ripening in the post-harvest phase when applied to the surface of sampled green fruits pre-harvest. In particular, degradation of chlorophylls was delayed by several days, as monitored by optical sensors and confirmed by analytical methods. Similarly, accumulation of β-carotene and lycopene in the fruit pulp after NOP-1 application was delayed, without having impact on the total pigment concentration in the completely ripe fruits. Likewise, the peptide had no negative effects on fruit quality. Our molecular and phenotypic studies reveal that peptide biologicals could contribute to the development of a novel family of ripening inhibitors and innovative ripening control in climacteric fruit.