Analysis of unfolded protein response in Arabidopsis

Mechanism of action of the toxic proline mimic azetidine 2-carboxylic acid in plants

Plants have an amazing capacity to outcompete neighboring organisms for space and resources. Toxic metabolites are major players in these interactions, which can have a broad range of effectiveness by targeting conserved molecular mechanisms, such as protein biosynthesis. However, lack of knowledge about defensive metabolite pathways, their mechanisms of action, and resistance mechanisms limits our ability to manipulate these pathways for enhanced crop resilience. Nonproteogenic amino acids (NPAAs) are a structurally diverse class of metabolites with a variety of functions but are typically not incorporated during protein biosynthesis. Here, we investigate the mechanism of action of the NPAA azetidine-2-carboxylic acid (Aze), an analog of the amino acid proline (Pro). Using a combination of plate-based assays, metabolite feeding, metabolomics, and proteomics, we show that Aze inhibits the root growth of Arabidopsis and other plants. Aze-induced growth reduction was restored by supplementing L-, but not D-Pro, and nontargeted proteomics confirm that Aze is misincorporated for Pro during protein biosynthesis, specifically on cytosolically translated proteins. Gene expression analysis, free amino acid profiling, and proteomics show that the unfolded protein response is upregulated during Aze treatment implicating that Aze misincorporation results in accumulation of misfolded proteins triggering a global stress response. This study demonstrates the mechanism of action of Aze in plants and provides a foundation for understanding the biological functions of proteotoxic metabolites.

Unfolded Protein Response in Arabidopsis

The unfolded protein response (UPR) is a highly regulated signaling pathway that is largely conserved across eukaryotes. It is essential for cell homeostasis under environmental and physiological conditions that perturb the protein folding in the endoplasmic reticulum (ER). Arabidopsis is one of the outstanding multicellular model systems in which to investigate the UPR. Here, we described a protocol to induce the UPR in plants, specifically Arabidopsis, and to estimate their ability to cope with ER stress through the quantification of physiological parameters.

Stress response proteins NRP1 and NRP2 are pro-survival factors that inhibit cell death during ER stress

Environmental stresses cause an increased number of unfolded or misfolded proteins to accumulate in the endoplasmic reticulum (ER), resulting in ER stress. To restore ER homeostasis and survive, plants initiate an orchestrated signaling pathway known as the unfolded protein response (UPR). Asparagine-rich protein (NRP) 1 and NRP2, two homologous proteins harboring a Development and Cell Death domain, are associated with various stress responses in Arabidopsis (Arabidopsis thaliana), but the relevant molecular mechanism remains obscure. Here, we show that NRP1 and NRP2 act as key pro-survival factors during the ER stress response and that they inhibit cell death. Loss-of-function of NRP1 and NRP2 results in decreased tolerance to the ER stress inducer tunicamycin (TM), accelerating cell death. NRP2 is constitutively expressed while NRP1 is induced in plants under ER stress. In Arabidopsis, basic leucine zipper protein (bZIP) 28 and bZIP60 are important transcription factors in the UPR that activates the expression of many ER stress-related genes. Notably, under ER stress, bZIP60 activates NRP1 by directly binding to the UPRE-I element in the NRP1 promoter. These findings reveal a pro-survival strategy in plants wherein the bZIP60-NRPs cascade suppresses cell death signal transmission, improving survival under adverse conditions.

A Quantitative Arabidopsis IRE1a Ribonuclease-Dependent in vitro mRNA Cleavage Assay for Functional Studies of Substrate Splicing and Decay Activities

The unfolded protein response (UPR) is an adaptive eukaryotic reaction that controls the protein folding capacities of the endoplasmic reticulum (ER). The most ancient and well-conserved component of the UPR is Inositol-Requiring Enzyme 1 (IRE1). Arabidopsis IRE1a (AtIRE1) is a transmembrane sensor of ER stress equipped with dual protein kinase and ribonuclease (RNase) activities, encoded by its C-terminal domain. In response to both physiological stresses and pathological perturbations, AtIRE1a directly cleaves bZIP60 (basic leucine zipper 60) mRNA. Here, we developed a quantitative in vitro cleavage assay that combines recombinant AtIRE1a protein that is expressed in Nicotiana benthamiana and total RNA isolated from Arabidopsis leaves. Wild-type AtIRE1a as well as its variants containing point mutations in the kinase or RNase domains that modify its cleavage activity were employed to demonstrate their contributions to cleavage activity levels. We show that, when exposed to total RNA in vitro, the AtIRE1a protein cleaves bZIP60 mRNA. Depletion of the bZIP60 transcript in the reaction mixture can be precisely quantified by a qRT-PCR-mediated assay. This method facilitates the functional studies of novel plant IRE1 variants by allowing to quickly and precisely assess the effects of protein mutations on the substrate mRNA cleavage activity before advancing to more laborious, stable transgenic approaches in planta. Moreover, this method is readily adaptable to other plant IRE1 paralogs and orthologs, and can also be employed to test additional novel mRNA substrates of plant IRE1, such as transcripts undergoing degradation through the process of regulated IRE1-dependent decay (RIDD). Finally, this method can also be modified and expanded to functional testing of IRE1 interactors and inhibitors, as well as for studies on the molecular evolution of IRE1 and its substrates, providing additional insights into the mechanistic underpinnings of IRE1-mediated ER stress homeostasis in plant tissues.

Tomato bZIP60 mRNA undergoes splicing in endoplasmic reticulum stress and in response to environmental stresses

Environmental stresses activate endoplasmic reticulum (ER) stress response pathways, collectively known as the unfolded protein response (UPR). IRE1/bZIP60 pathway is the most conserved of all UPR pathways from yeast to plants. Transcription factor bZIP60 is activated by the cytoplasmic splicing of its mRNA by Inositol Requiring Enzyme1 (IRE1) protein. bZIP60 mRNA has a typical stem-loop structure that is required for its splicing by IRE1 ribonuclease. We identified the tomato bZIP60 (SlbZIP60) and secondary structure prediction showed that it has the conserved stem-loop structure. Further, we demonstrate that SlbZIP60 is spliced upon treatment with an ER stress-inducing agent, tunicamycin. Tunicamycin also upregulated the expression of SlbZIP60. Finally, we show that SlbZIP60 undergo physiologically activated splicing in certain tissues of the plant and respond to environmental stresses, heat, and virus infection. This study will help for a deeper understanding of ER stress pathways and how they contribute to the stress tolerance of tomato, one of the important vegetable crops, cultivated under varied environmental conditions.

ATI1 (ATG8-interacting protein 1) and ATI2 define a plant starvation-induced reticulophagy pathway and serve as MSBP1/MAPR5 cargo receptors

Reticulophagy, the selective autophagy of endoplasmic reticulum (ER) components, is known to operate in eukaryotes from yeast and unicellular algae to animals and plants. Thus far, only ER-stress induced reticulophagy was reported and analyzed in plants. In this study we characterize a reticulophagy pathway in Arabidopsis thaliana that is triggered by dark-induced starvation but not by ER stress. This pathway is defined by the previously reported ATG8-interacting proteins, ATI1 and ATI2. We further identified the ER-localized MSBP1 (Membrane Steroid Binding Protein 1) as an ATI1- and ATI2-interacting protein and an autophagy cargo, and show that ATI1 and ATI2 serve as its cargo receptors. Together, these findings expand our knowledge on plant responses during energy deprivation and highlight the role of this special type of reticulophagy in this process.Abbreviations: AGO1: ARGONAUTE 1; ATI: ATG8-Interacting Protein; BiFC: Bimolecular Fluorescence Complementation; BR: brassinosteroid; conA: concanamycin A; DMSO: dimethyl sulfoxid; DTT: dithiothreitol; ER: endoplasmic reticulum; GFP: green fluorescent protein; MAPR: Membrane-Associated Progesterone Binding Protein; MSBP: Membrane Steroid Binding Protein; SD: standard deviation; SE: standard error; TM: tunicamycin; TOR: target of rapamycin; Y2H: yeast two-hybrid.

A high-throughput screening method to identify proteins involved in unfolded protein response of the endoplasmic reticulum in plants

BACKGROUND

The unfolded protein response (UPR) is a highly conserved process in eukaryotic organisms that plays a crucial role in adaptation and development. While the most ubiquitous components of this pathway have been characterized, current efforts are focused on identifying and characterizing other UPR factors that play a role in specific conditions, such as developmental changes, abiotic cues, and biotic interactions. Considering the central role of protein secretion in plant pathogen interactions, there has also been a recent focus on understanding how pathogens manipulate their host's UPR to facilitate infection.

RESULTS

We developed a high-throughput screening assay to identify proteins that interfere with UPR signaling in planta. A set of 35 genes from a library of secreted proteins from the maize pathogen Ustilago maydis were transiently co-expressed with a reporter construct that upregulates enhanced yellow fluorescent protein (eYFP) expression upon UPR stress in Nicotiana benthamiana plants. After UPR stress induction, leaf discs were placed in 96 well plates and eYFP expression was measured. This allowed us to identify a previously undescribed fungal protein that inhibits plant UPR signaling, which was then confirmed using the classical but more laborious qRT-PCR method.

CONCLUSIONS

We have established a rapid and reliable fluorescence-based method to identify heterologously expressed proteins involved in UPR stress in plants. This system can be used for initial screens with libraries of proteins and potentially other molecules to identify candidates for further validation and characterization.

NADPH oxidase activity is required for ER stress survival in plants

In all eukaryotes, the unfolded protein response (UPR) relieves endoplasmic reticulum (ER) stress, which is a potentially lethal condition caused by the accumulation of misfolded proteins in the ER. In mammalian and yeast cells, reactive oxygen species (ROS) generated during ER stress attenuate the UPR, negatively impacting cell survival. In plants, the relationship between the UPR and ROS is less clear. Although ROS develop during ER stress, the sources of ROS linked to ER stress responses and the physiological impact of ROS generation on the survival from proteotoxic stress are yet unknown. Here we show that in Arabidopsis thaliana the respiratory burst oxidase homologs, RBOHD and RBOHF, contribute to the production of ROS during ER stress. We also demonstrate that during ER stress RBOHD and RBOHF are necessary to properly mount the adaptive UPR and overcome temporary and chronic ER stress situations. These results ascribe a cytoprotective role to RBOH-generated ROS in the defense from proteotoxic stress in an essential organelle, and support a plant-specific feature of the UPR management among eukaryotes.

Loss of Arabidopsis p24 function affects ERD2 trafficking and Golgi structure, and activates the unfolded protein response

The p24 family of proteins (also known as the TMED family) are key regulators of protein trafficking along the secretory pathway, but very little is known about their functions in plants. A quadruple loss-of-function mutant affecting the p24 genes from the δ-1 subclass of the p24δ subfamily (p24δ3δ4δ5δ6) showed alterations in the Golgi, suggesting that these p24 proteins play a role in the organization of the compartments of the early secretory pathway in Arabidopsis Loss of p24δ-1 proteins also induced the accumulation of the K/HDEL receptor ERD2a (ER lumen protein-retaining receptor A) at the Golgi and increased secretion of BiP family proteins, ER chaperones containing an HDEL signal, probably due to an inhibition of COPI-dependent Golgi-to-ER transport of ERD2a and thus retrieval of K/HDEL ligands. Although the p24δ3δ4δ5δ6 mutant showed enhanced sensitivity to salt stress, it did not show obvious phenotypic alterations under standard growth conditions. Interestingly, this mutant showed a constitutive activation of the unfolded protein response (UPR) and the transcriptional upregulation of the COPII subunit gene SEC31A, which may help the plant to cope with the transport defects seen in the absence of p24 proteins.

Recovery from temporary endoplasmic reticulum stress in plants relies on the tissue-specific and largely independent roles of bZIP28 and bZIP60, as well as an antagonizing function of BAX-Inhibitor 1 upon the pro-adaptive signaling mediated by bZIP28

The unfolded protein response (UPR) is an ancient signaling pathway that commits to life-or-death outcomes in response to proteotoxic stress in the endoplasmic reticulum (ER). In plants, the membrane-tethered transcription factor bZIP28 and the ribonuclease-kinase IRE1 along with its splicing target, bZIP60, govern the two cytoprotective UPR signaling pathways known to date. The conserved ER membrane-associated BAX inhibitor 1 (BI1) modulates ER stress-induced programmed cell death through yet-unknown mechanisms. Despite the significance of the UPR for cell homeostasis, in plants the regulatory circuitry underlying ER stress resolution is still largely unmapped. To gain insights into the coordination of plant UPR strategies, we analyzed the functional relationship of the UPR modulators through the analysis of single and higher order mutants of IRE1, bZIP60, bZIP28 and BI1 in experimental conditions causing either temporary or chronic ER stress. We established a functional duality of bZIP28 and bZIP60, as they exert partially independent tissue-specific roles in recovery from ER stress, but redundantly actuate survival strategies in chronic ER stress. We also discovered that BI1 attenuates the pro-survival function of bZIP28 in ER stress resolution and, differently to animal cells, it does not temper the ribonuclease activity of inositol-requiring enzyme 1 (IRE1) under temporary ER stress. Together these findings reveal a functional independence of bZIP28 and bZIP60 in plant UPR, and identify an antagonizing role of BI1 in the pro-adaptive signaling mediated by bZIP28, bringing to light the distinctive complexity of the unfolded protein response (UPR) in plants.

Unfolded Protein Response in Arabidopsis

The unfolded protein response (UPR) is a highly regulated signaling pathway that is largely conserved across eukaryotes. It is essential for cell homeostasis under environmental and physiological conditions that perturb the protein folding in the endoplasmic reticulum (ER). Arabidopsis is one of the outstanding multicellular model systems in which to investigate the UPR. Here, we described a protocol to induce the UPR in plants, specifically arabidopsis, and to estimate their ability to cope with ER stress through the quantification of physiological parameters.

An endoplasmic reticulum-localized Coffea arabica BURP domain-containing protein affects the response of transgenic Arabidopsis plants to diverse abiotic stresses

The Coffea arabica BURP domain-containing gene plays an important role in the response of transgenic Arabidopsis plants to abiotic stresses via regulating the level of diverse proteins. Although the functions of plant-specific BURP domain-containing proteins (BDP) have been determined for a few plants, their roles in the growth, development, and stress responses of most plant species, including coffee plant (Coffea arabica), are largely unknown. In this study, the function of a C. arabica BDP, designated CaBDP1, was investigated in transgenic Arabidopsis plants. The expression of CaBDP1 was highly modulated in coffee plants subjected to drought, cold, salt, or ABA. Confocal analysis of CaBDP1-GFP fusion proteins revealed that CaBDP1 is localized in the endoplasmic reticulum. The ectopic expression of CaBDP1 in Arabidopsis resulted in delayed germination of the transgenic plants under abiotic stress and in the presence of ABA. Cotyledon greening and seedling growth of the transgenic plants were inhibited in the presence of ABA due to the upregulation of ABA signaling-related genes like ABI3, ABI4, and ABI5. Proteome analysis revealed that the levels of several proteins are modulated in CaBDP1-expressing transgenic plants. The results of this study underscore the importance of BURP domain proteins in plant responses to diverse abiotic stresses.

The IRE1/bZIP60 Pathway and Bax Inhibitor 1 Suppress Systemic Accumulation of Potyviruses and Potexviruses in Arabidopsis and Nicotiana benthamiana Plants

The inositol requiring enzyme (IRE1) is an endoplasmic reticulum (ER) stress sensor. When activated, it splices the bZIP60 mRNA, producing a truncated transcription factor that upregulates genes involved in the unfolded protein response. Bax inhibitor 1 (BI-1) is another ER stress sensor that regulates cell death in response to environmental assaults. The potyvirus 6K2 and potexvirus TGB3 proteins are known to reside in the ER, serving, respectively, as anchors for the viral replicase and movement protein complex. This study used green fluorescent protein (GFP)-tagged Turnip mosaic virus (TuMV), Plantago asiatica mosaic virus (PlAMV), Potato virus Y (PVY), and Potato virus X (PVX) to determine that the IRE1/bZIP60 pathway and BI-1 machinery are induced early in virus infection in Arabidopsis thaliana, Nicotiana benthamiana, and Solanum tuberosum. Agrodelivery of only the potyvirus 6K2 or TGB3 genes into plant cells activated bZIP60 and BI-1 expression in Arabidopsis thaliana, N. benthamiana, and S. tuberosum. Homozygous ire1a-2, ire1b-4, and ire1a-2/ire1b-4 mutant Arabidopsis plants were inoculated with TuMV-GFP or PlAMV-GFP. PlAMV accumulates to a higher level in ire1a-2 or ire1a-2/ire1b-4 mutant plants than in ire1b-4 or wild-type plants. TuMV-GFP accumulates to a higher level in ire1a-2, ire1b-4, or ire1a-2/ire1b-4 compared with wild-type plants, suggesting that both isoforms contribute to TuMV-GFP infection. Gene silencing was used to knock down bZIP60 and BI-1 expression in N. benthamiana. PVX-GFP and PVY-GFP accumulation was significantly elevated in these silenced plants compared with control plants. This study demonstrates that two ER stress pathways, namely IRE1/bZIP60 and the BI-1 pathway, limit systemic accumulation of potyvirus and potexvirus infection. Silencing BI-1 expression also resulted in systemic necrosis. These data suggest that ER stress-activated pathways, led by IRE1 and BI-1, respond to invading potyvirus and potexviruses to restrict virus infection and enable physiological changes enabling plants to tolerate virus assault.

Conserved and plant-unique strategies for overcoming endoplasmic reticulum stress

Stress caused by environmental conditions or physiological growth can lead to an accumulation of unfolded proteins in the endoplasmic reticulum (ER) causing ER stress, which in turn triggers a cytoprotective mechanism termed the unfolded protein response (UPR). Under mild-short stress conditions the UPR can restore ER functioning and cell growth, such as reducing the load of unfolded proteins through the upregulation of genes involved in protein folding and in degrading mis-folded proteins, and through autophagy activation, but it can also lead to cell death under prolonged and severe stress conditions. A diversified suite of sensors has been evolved in the eukaryotic lineages to orchestrate the UPR most likely to suit the cell's necessity to respond to the different kinds of stress in a conserved as well as species-specific manner. In plants three UPR sensors cooperate with non-identical signaling pathways: the protein kinase inositol-requiring enzyme (IRE1), the ER-membrane-associated transcription factor bZIP28, and the GTP-binding protein β1 (AGB1). In this mini-review, we show how plants differ from the better characterized metazoans and fungi, providing an overview of the signaling pathways of the UPR, and highlighting the overlapping and the peculiar roles of the different UPR branches in light of evolutionary divergences in eukaryotic kingdoms.