Role of Cop9 Signalosome Subunits in the Environmental and Hormonal Balance of Plant

Exploiting DNA methylation in cassava under water deficit for crop improvement

DNA methylation plays a key role in the development and plant responses to biotic and abiotic stresses. This work aimed to evaluate the DNA methylation in contrasting cassava genotypes for water deficit tolerance. The varieties BRS Formosa (bitter) and BRS Dourada (sweet) were grown under greenhouse conditions for 50 days, and afterwards, irrigation was suspended. The stressed (water deficit) and non-stressed plants (negative control) consisted the treatments with five plants per variety. The DNA samples of each variety and treatment provided 12 MethylRAD-Seq libraries (two cassava varieties, two treatments, and three replicates). The sequenced data revealed methylated sites covering 18 to 21% of the Manihot esculenta Crantz genome, depending on the variety and the treatment. The CCGG methylated sites mapped mostly in intergenic regions, exons, and introns, while the CCNGG sites mapped mostly intergenic, upstream, introns, and exons regions. In both cases, methylated sites in UTRs were less detected. The differentially methylated sites analysis indicated distinct methylation profiles since only 12% of the sites (CCGG and CCNGG) were methylated in both varieties. Enriched gene ontology terms highlighted the immediate response of the bitter variety to stress, while the sweet variety appears to suffer more potential stress-damages. The predicted protein-protein interaction networks reinforced such profiles. Additionally, the genomes of the BRS varieties uncovered SNPs/INDELs events covering genes stood out by the interactomes. Our data can be useful in deciphering the roles of DNA methylation in cassava drought-tolerance responses and adaptation to abiotic stresses.

OsJAB1 Positively Regulates Ascorbate Biosynthesis and Negatively Regulates Salt Tolerance Due to Inhibiting Early-Stage Salt-Induced ROS Accumulation in Rice

Reactive oxygen species (ROS) play dual roles in plant stress response, but how plants modulate the dual roles of ROS in stress response is still obscure. OsJAB1 (JUN-activation-domain-binding protein 1) encodes the rice CSN5 (COP9 signalsome subunit 5). This study showed that, similar to the Arabidopsis homolog gene CSN5B, OsJAB1-overexpressing (driven by a CaMV 35S promoter) plants (OEs) impaired rice salt stress tolerance; in contrast, OsJAB1-inhibited-expression (using RNA-interfering technology) plants (RIs) enhanced rice salt stress tolerance. Differing from CSN5B that negatively regulated ascorbate (Asc) biosynthesis, Asc content increased in OEs and decreased in RIs. ROS analysis showed that RIs clearly increased, but OEs inhibited ROS accumulation at the early stage of salt treatment; in contrast, RIs clearly decreased, but OEs promoted ROS accumulation at the late stage of salt treatment. The qPCR revealed that OEs decreased but RIs enhanced the expressions of ROS-scavenging genes. This indicated that OsJAB1 negatively regulated rice salt stress tolerance by suppressing the expression of ROS-scavenging genes. This study provided new insights into the CSN5 homologous protein named OsJAB1 in rice, which developed different functions during long-term evolution. How OsJAB1 regulates the Asc biosynthesis that coordinates the balance between cell redox signaling and ROS scavenging needs to be investigated in the future.

Plant deubiquitinases: from structure and activity to biological functions

This article attempts to provide comprehensive review of plant deubiquitinases, paying special attention to recent advances in their biochemical activities and biological functions. Proteins in eukaryotes are subjected to post-translational modifications, in which ubiquitination is regarded as a reversible process. Cellular deubiquitinases (DUBs) are a key component of the ubiquitin (Ub)-proteasome system responsible for cellular protein homeostasis. DUBs recycle Ub by hydrolyzing poly-Ub chains on target proteins, and maintain a balance of the cellular Ub pool. In addition, some DUBs prefer to cleave poly-Ub chains not linked through the conventional K48 residue, which often alter the substrate activity instead of its stability. In plants, all seven known DUB subfamilies have been identified, namely Ub-binding protease/Ub-specific protease (UBP/USP), Ub C-terminal hydrolase (UCH), Machado-Joseph domain-containing protease (MJD), ovarian-tumor domain-containing protease (OTU), zinc finger with UFM1-specific peptidase domain protease (ZUFSP), motif interacting with Ub-containing novel DUB family (MINDY), and JAB1/MPN/MOV34 protease (JAMM). This review focuses on recent advances in the structure, activity, and biological functions of plant DUBs, particularly in the model plant Arabidopsis.

Genome-wide association study in two-row spring barley landraces identifies QTL associated with plantlets root system architecture traits in well-watered and osmotic stress conditions

Water availability is undoubtedly one of the most important environmental factors affecting crop production. Drought causes a gradual deprivation of water in the soil from top to deep layers and can occur at diverse stages of plant development. Roots are the first organs that perceive water deficit in soil and their adaptive development contributes to drought adaptation. Domestication has contributed to a bottleneck in genetic diversity. Wild species or landraces represent a pool of genetic diversity that has not been exploited yet in breeding program. In this study, we used a collection of 230 two-row spring barley landraces to detect phenotypic variation in root system plasticity in response to drought and to identify new quantitative trait loci (QTL) involved in root system architecture under diverse growth conditions. For this purpose, young seedlings grown for 21 days in pouches under control and osmotic-stress conditions were phenotyped and genotyped using the barley 50k iSelect SNP array, and genome-wide association studies (GWAS) were conducted using three different GWAS methods (MLM GAPIT, FarmCPU, and BLINK) to detect genotype/phenotype associations. In total, 276 significant marker-trait associations (MTAs; p-value (FDR)< 0.05) were identified for root (14 and 12 traits under osmotic-stress and control conditions, respectively) and for three shoot traits under both conditions. In total, 52 QTL (multi-trait or identified by at least two different GWAS approaches) were investigated to identify genes representing promising candidates with a role in root development and adaptation to drought stress.

A Subunit of the COP9 Signalosome, MoCsn6, Is Involved in Fungal Development, Pathogenicity, and Autophagy in Rice Blast Fungus

The COP9 signalosome (CSN) is a highly conserved protein complex in eukaryotes, affecting various development and signaling processes. To date, the biological functions of the COP9 signalosome and its subunits have not been determined in Magnaporthe oryzae. In this study, we characterized the CSN in M. oryzae (which we named MoCsn6) and analyzed its biological functions. MoCsn6 is involved in fungal development, autophagy, and plant pathogenicity. Compared with the wild-type strain 70-15, ΔMocsn6 mutants showed a significantly reduced growth rate, sporulation rate, and germ tube germination rate. Pathogenicity assays showed that the ΔMocsn6 mutants did not cause or significantly reduced the number of disease spots on isolated barley leaves. After the MoCSN6 gene was complemented into the ΔMocsn6 mutant, vegetative growth, sporulation, and pathogenicity were restored. The Osm1 and Pmk1 phosphorylation pathways were also disrupted in the ΔMocsn6 mutants. Furthermore, we found that MoCsn6 participates in the autophagy pathway by interacting with the autophagy core protein MoAtg6 and regulating its ubiquitination level. Deletion of MoCSN6 resulted in rapid lipidation of MoAtg8 and degradation of the autophagic marker protein green fluorescent protein-tagged MoAtg8 under nutrient and starvation conditions, suggesting that MoCsn6 negatively regulates autophagic activity. Taken together, our results demonstrate that MoCsn6 plays a crucial role in regulating fungal development, pathogenicity, and autophagy in M. oryzae. IMPORTANCE Magnaporthe oryzae, a filamentous fungus, is the cause of many cereal diseases. Autophagy is involved in fungal development and pathogenicity. The COP9 signalosome (CSN) has been extensively studied in ubiquitin pathways, but its regulation of autophagy has rarely been reported in plant-pathogenic fungi. Investigations on the relationship between CSN and autophagy will deepen our understanding of the pathogenic mechanism of M. oryzae and provide new insights into the development of new drug targets to control fungal diseases. In this study, the important function of Csn6 in the autophagy regulation pathway and its impact on the pathogenicity of M. oryzae were determined. We showed that Csn6 manages autophagy by interacting with the autophagy core protein Atg6 and regulating its ubiquitination level. Furthermore, future investigations that explore the function of CSN will deepen our understanding of autophagy mechanisms in rice blast fungus.

A novel small open reading frame gene, IbEGF, enhances drought tolerance in transgenic sweet potato

Small open reading frames (sORFs) can encode functional polypeptides or act as cis-translational regulators in stress responses in eukaryotes. Their number and potential importance have only recently become clear in plants. In this study, we identified a novel sORF gene in sweet potato, IbEGF, which encoded the 83-amino acid polypeptide containing an EGF_CA domain. The expression of IbEGF was induced by PEG6000, H₂O₂, abscisic acid (ABA), methyl-jasmonate (MeJA) and brassinosteroid (BR). The IbEGF protein was localized to the nucleus and cell membrane. Under drought stress, overexpression of IbEGF enhanced drought tolerance, promoted the accumulation of ABA, MeJA, BR and proline and upregulated the genes encoding superoxide dismutase (SOD), catalase (CAT) and peroxidase (POD) in transgenic sweet potato. The IbEGF protein was found to interact with IbCOP9-5α, a regulator in the phytohormone signalling pathways. These results suggest that IbEGF interacting with IbCOP9-5α enhances drought tolerance by regulating phytohormone signalling pathways, increasing proline accumulation and further activating reactive oxygen species (ROS) scavenging system in transgenic sweet potato.

Comparative proteomic analysis of chromosome segment substitution lines of Thai jasmine rice KDML105 under short-term salinity stress

Heat shock proteins, ROS detoxifying enzymes, and ion homeostasis proteins, together with proteins in carbohydrate metabolism, cell structure, brassinosteroids, and carotenoid biosynthesis pathway were up-regulated in CSSLs under salinity stress. Rice is one of the most consumed staple foods worldwide. Salinity stress is a serious global problem affecting rice productivity. Many attempts have been made to select or produce salinity-tolerant rice varieties. Genetics and biochemical approaches were used to study the salinity-responsive pathway in rice to develop salinity tolerant strains. This study investigated the proteomic profiles of chromosome segment substitution lines (CSSLs) developed from KDML105 (Khao Dawk Mali 105, a Thai jasmine rice cultivar) under salinity stress. The CSSLs showed a clear resistant phenotype in response to 150 mM NaCl treatment compared to the salinity-sensitive line, IR29. Liquid chromatography-tandem mass spectrometry using the Ultimate 3000 Nano/Capillary LC System coupled to a Hybrid Quadrupole Q-Tof Impact II™ equipped with a nano-captive spray ion source was applied for proteomic analysis. Based on our criteria, 178 proteins were identified as differentially expressed proteins under salinity stress. Protein functions in DNA replication and transcription, and stress and defense accounted for the highest proportions in response to salinity stress, followed by protein transport and trafficking, carbohydrate metabolic process, signal transduction, and cell structure. The protein interaction network among the 75 up-regulated proteins showed connections between proteins involved in cell wall synthesis, transcription, translation, and in defense responses.

Regulatory Mechanism of the Constitutive Photomorphogenesis 9 Signalosome Complex in Response to Abiotic Stress in Plants

The constitutive photomorphogenesis 9 (COP9) signalosome (CSN) is a highly conserved protein complex that regulates signaling pathways in plants under abiotic stress. We discuss the potential molecular mechanisms of CSN under abiotic stress, including oxidative stress with reactive oxygen species signaling, salt stress with jasmonic acid, gibberellic acid, and abscisic acid signaling, high-temperature stress with auxin signaling, and optical radiation with DNA damage and repair response. We conclude that CSN likely participates in affecting antioxidant biosynthesis and hormone signaling by targeting receptors, kinases, and transcription factors in response to abiotic stress, which potentially provides valuable information for engineering stress-tolerant crops.

Expression of the pyrroline-5-carboxylate reductase (P5CR) gene from the wild grapevine Vitis yeshanensis promotes drought resistance in transgenic Arabidopsis

Proline accumulation is one of the most common reactions in plants under drought stress. Pyrroline-5-carboxylate reductase (P5CR) is the final enzyme and plays an important role in proline biosynthesis. The Chinese wild grapevine Vitis yeshanensis J.X. Chen accession 'Yanshan-1' is highly resistant to drought, but the genetic and molecular mechanisms associated with this resistance have not been elucidated. Here, we cloned a VyP5CR gene (Genbank ID: MZ226960) from 'Yanshan-1', and evaluated its transcriptional response to drought, NaCl, cold, as well as exogenous ABA, MeJA and SA. Tissue specific analysis showed that VyP5CR could be expressed in various organs and was highly expressed in roots. To gain insight into the roles of VyP5CR, we overexpressed VyP5CR in Arabidopsis thaliana (Arabidopsis). Transgenic Arabidopsis plants expressing VyP5CR showed enhanced survival rate, smaller stomata in response to severe drought, as well as stronger root growth on a medium containing mannitol. Under drought stress, VyP5CR-OE plants showed reduced levels of MDA, H2O2 and O2-, and higher proline content, SOD and POD activity. In addition, VyP5CR-OE plants showed increased induction of the drought-related genes COR15A, COR47, DREB2A, KIN1, NCED3 and RD29A. Taken together, these experiments reveal that VyP5CR can promote the drought tolerance of transgenic Arabidopsis. Besides, an interacting protein with VyP5CR, VyCSN5B (COP9 signalosome complex subunit 5b), was screened out by yeast two-hybrid and verified by bimolecular fluorescence complementation assay.

Mutant Presenilin 1 Dysregulates Exosomal Proteome Cargo Produced by Human-Induced Pluripotent Stem Cell Neurons

The accumulation and propagation of hyperphosphorylated tau (p-Tau) is a neuropathological hallmark occurring with neurodegeneration of Alzheimer's disease (AD). Extracellular vesicles, exosomes, have been shown to initiate tau propagation in the brain. Notably, exosomes from human-induced pluripotent stem cell (iPSC) neurons expressing the AD familial A246E mutant form of presenilin 1 (mPS1) are capable of inducing tau deposits in the mouse brain after in vivo injection. To gain insights into the exosome proteome cargo that participates in propagating tau pathology, this study conducted proteomic analysis of exosomes produced by human iPSC neurons expressing A246E mPS1. Significantly, mPS1 altered the profile of exosome cargo proteins to result in (1) proteins present only in mPS1 exosomes and not in controls, (2) the absence of proteins in the mPS1 exosomes which were present only in controls, and (3) shared proteins which were upregulated or downregulated in the mPS1 exosomes compared to controls. These results show that mPS1 dysregulates the proteome cargo of exosomes to result in the acquisition of proteins involved in the extracellular matrix and protease functions, deletion of proteins involved in RNA and protein translation systems along with proteasome and related functions, combined with the upregulation and downregulation of shared proteins, including the upregulation of amyloid precursor protein. Notably, mPS1 neuron-derived exosomes displayed altered profiles of protein phosphatases and kinases involved in regulating the status of p-tau. The dysregulation of exosome cargo proteins by mPS1 may be associated with the ability of mPS1 neuron-derived exosomes to propagate tau pathology.

CSN5A Subunit of COP9 Signalosome Is Required for Resetting Transcriptional Stress Memory after Recurrent Heat Stress in Arabidopsis

In nature, plants are exposed to several environmental stresses that can be continuous or recurring. Continuous stress can be lethal, but stress after priming can increase the tolerance of a plant to better prepare for future stresses. Reports have suggested that transcription factors are involved in stress memory after recurrent stress; however, less is known about the factors that regulate the resetting of stress memory. Here, we uncovered a role for Constitutive Photomorphogenesis 5A (CSN5A) in the regulation of stress memory for resetting transcriptional memory genes (APX2 and HSP22) and H3K4me3 following recurrent heat stress. Furthermore, CSN5A is also required for the deposition of H3K4me3 following recurrent heat stress. Thus, CSN5A plays an important role in the regulation of histone methylation and transcriptional stress memory after recurrent heat stress.

SAP130 and CSN1 interact and regulate male gametogenesis in Arabidopsis thaliana

COP9 signalosome (CSN) is a nuclear complex composed of eight distinct subunits that governs vast developmental processes in Arabidopsis thaliana (L.) Heynh. The null alleles of csn mutants display pleiotropic phenotypes that result in seedling lethality. To date, several partially complemented transgenic plants, expressing the particular CSN subunit in its corresponding null mutant allele, were utilized to bypass seedling lethality and investigate CSN regulation at later stages of development. One such transgenic plant corresponding to CSN1 subunit, fus6/CSN1-3-4, accumulates wild-type level of CSN1 and displays normal plant architecture at vegetative stage. Here we show through histological analyses that fus6/CSN1-3-4 plants display impairment of pollen development at the bicellular stage. This defect is identical to that observed in RNAi plants of SAP130, encoding a subunit of the multiprotein splicing factor SF3b. We further dissected the previously reported interaction between CSN1 and SAP130, to reveal that approximately 100 amino-acid residues located at the N-terminal end of CSN1 (CSN1NN) were essential for this interaction. In silico structure modeling demonstrated that CSN1NN could swing out towards SAP130 to dock onto its Helical Insertion protruding from the structure. These results support our model that CSN1 embeds itself within CSN protein complex through its C-terminal half and reaches out to targets through its N-terminal portion of the protein. Taken together, this is the first report to document the identical loss-of-function phenotypes of CSN1 and SAP130 during male gametogenesis. Thus, we propose that SAP130 and CSN1 coordinately regulate development of male reproductive organs.

Molecular Mechanisms of DUBs Regulation in Signaling and Disease

The large family of deubiquitinating enzymes (DUBs) are involved in the regulation of a plethora of processes carried out inside the cell by protein ubiquitination. Ubiquitination is a basic pathway responsible for the correct protein homeostasis in the cell, which could regulate the fate of proteins through the ubiquitin–proteasome system (UPS). In this review we will focus on recent advances on the molecular mechanisms and specificities found for some types of DUBs enzymes, highlighting illustrative examples in which the regulatory mechanism for DUBs has been understood in depth at the molecular level by structural biology. DUB proteases are responsible for cleavage and regulation of the multiple types of ubiquitin linkages that can be synthesized inside the cell, known as the ubiquitin-code, which are tightly connected to specific substrate functions. We will display some strategies carried out by members of different DUB families to provide specificity on the cleavage of particular ubiquitin linkages. Finally, we will also discuss recent progress made for the development of drug compounds targeting DUB proteases, which are usually correlated to the progress of many pathologies such as cancer and neurodegenerative diseases.

Dynamic architecture and regulatory implications of the miRNA network underlying the response to stress in melon

miRNAs are small RNAs that regulate mRNAs at both transcriptional and posttranscriptional level. In plants, miRNAs are involved in the regulation of different processes including development and stress-response. Elucidating how stress-responsive miRNAs are regulated is key to understand the global response to stress but also to develop efficient biotechnological tools that could help to cope with stress. Here, we describe a computational approach based on sRNA sequencing, transcript quantification and degradome data to analyse the accumulation, function and structural organization of melon miRNAs reactivated under seven biotic and abiotic stress conditions at two and four days post-treatment. Our pipeline allowed us to identify fourteen stress-responsive miRNAs (including evolutionary conserved such as miR156, miR166, miR172, miR319, miR398, miR399, miR894 and miR408) at both analysed times. According to our analysis miRNAs were categorized in three groups showing a broad-, intermediate- or narrow- response range. miRNAs reactive to a broad range of environmental cues appear as central components in the stress-response network. The strictly coordinated response of miR398 and miR408 (broad response-range) to the seven stress treatments during the period analysed here reinforces this notion. Although both, the amplitude and diversity of the miRNA-related response to stress changes during the exposition time, the architecture of the miRNA-network is conserved. This organization of miRNA response to stress is also conserved in rice and soybean supporting the conservation of miRNA-network organization in other crops. Overall, our work sheds light into how miRNA networks in plants organize and function during stress.

The dynamic responses of plant physiology and metabolism during environmental stress progression

At adverse environmental conditions, plants produce various kinds of primary and secondary metabolites to protect themselves. Both primary and secondary metabolites play a significant role during the heat, drought, salinity, genotoxic and cold conditions. A multigene response is activated during the progression of these stresses in the plants which stimulate changes in various signaling molecules, amino acids, proteins, primary and secondary metabolites. Plant metabolism is perturbed because of either the inhibition of metabolic enzymes, shortage of substrates, excess demand for specific compounds or a combination of these factors. In this review, we aim to present how plants synthesize different kinds of natural products during the perception of various abiotic stresses. We also discuss how time-scale variable stresses influence secondary metabolite profiles, could be used as a stress marker in plants. This article has the potential to get the attention of researchers working in the area of quantitative trait locus mapping using metabolites as well as metabolomics genome-wide association.

CSN5A Subunit of COP9 Signalosome Temporally Buffers Response to Heat in Arabidopsis

The COP9 (constitutive photomorphogenesis 9) signalosome (CSN) is an evolutionarily conserved protein complex which regulates various growth and developmental processes. However, the role of CSN during environmental stress is largely unknown. Using Arabidopsis as model organism, we used CSN hypomorphic mutants to study the role of the CSN in plant responses to environmental stress and found that heat stress specifically enhanced the growth of csn5a-1 but not the growth of other hypomorphic photomorphogenesis mutants tested. Following heat stress, csn5a-1 exhibits an increase in cell size, ploidy, photosynthetic activity, and number of lateral roots and an upregulation of genes connected to the auxin response. Immunoblot analysis revealed an increase in deneddylation of CUL1 but not CUL3 following heat stress in csn5a-1, implicating improved CUL1 activity as a basis for the improved growth of csn5a-1 following heat stress. Studies using DR5::N7-VENUS and DII-VENUS reporter constructs confirm that the heat-induced growth is due to an increase in auxin signaling. Our results indicate that CSN5A has a specific role in deneddylation of CUL1 and that CSN5A is required for the recovery of AUX/IAA repressor levels following recurrent heat stress to regulate auxin homeostasis in Arabidopsis.

Are Inositol Polyphosphates the Missing Link in Dynamic Cullin RING Ligase Regulation by the COP9 Signalosome?

The E3 ligase activity of Cullin RING Ligases (CRLs) is controlled by cycles of neddylation/deneddylation and intimately regulated by the deneddylase COP9 Signalosome (CSN), one of the proteasome lid-CSN-initiation factor 3 (PCI) domain-containing “Zomes” complex. Besides catalyzing the removal of stimulatory Cullin neddylation, CSN also provides a docking platform for other proteins that might play a role in regulating CRLs, notably protein kinases and deubiquitinases. During the CRL activity cycle, CRL–CSN complexes are dynamically assembled and disassembled. Mechanisms underlying complex dynamics remain incompletely understood. Recently, the inositol polyphosphate metabolites (IP6, IP7) and their metabolic enzymes (IP5K, IP6K) have been discovered to participate in CRL–CSN complex formation as well as stimulus-dependent dissociation. Here we discuss these mechanistic insights in light of recent advances in elucidating structural basis of CRL–CSN complexes.