Arabidopsis OTU1, a linkage-specific deubiquitinase, is required for endoplasmic reticulum-associated protein degradation

β-N-methylamino-L-alanine production, photosynthesis and transcriptional expression in a possible mutation strain and a wild strain of Thalassiosira minima

The neurotoxin β-N-methylamino-L-alanine (BMAA) produced by marine diatoms has been implicated as an important environmental trigger of neurodegenerative diseases in humans. However, the biosynthesis mechanism of BMAA in marine diatoms is still unknown. In the present study, the strain of diatom Thalassiosira minima almost lost the biosynthesis ability for BMAA after a long-term subculture in our laboratory. The production of BMAA-containing proteins in the mutant strain of T. minima reduced to 18.2 % of that in the wild strain, meanwhile the cell size decreased but pigment content increased in the mutant strain. Take consideration of our previous transcriptional data on the mixed diatom and cyanobacterium cultures, the current transcriptome analysis showed four identical and highly correlated KEGG pathways associated with the accumulation of misfolded proteins in diatom, including ribosome, proteasome, SNARE interactions in vesicle transport, and protein processing in the endoplasmic reticulum. Analysis of amino acids and transcriptional information suggested that amino acid synthesis and degradation are associated with the biosynthesis of BMAA-containing proteins. In addition, a reduction in the precision of ubiquitination-mediated protein hydrolysis and vesicular transport by the COPII system will exacerbate the accumulation of BMAA-containing proteins in diatoms.

CDC48 in plants and its emerging function in plant immunity

Protein homeostasis, namely the balance between protein synthesis and degradation, must be finely controlled to ensure cell survival, notably through the ubiquitin-proteasome system (UPS). In all species, including plants, homeostasis is disrupted by biotic and abiotic stresses. A key player in the maintenance of protein balance, the protein CDC48, shows emerging functions in plants, particularly in response to biotic stress. In this review on CDC48 in plants, we detail its highly conserved structure, describe a gene expansion that is only present in Viridiplantae, discuss its various functions and regulations, and finally highlight its recruitment, still not clear, during the plant immune response.

An apicoplast-localized deubiquitinase contributes to the cell growth and apicoplast homeostasis of Toxoplasma gondii

Toxoplasma gondii is among the most important parasites worldwide. The apicoplast is a unique organelle shared by all Apicomplexan protozoa. Increasing lines of evidence suggest that the apicoplast possesses its own ubiquitination system. Deubiquitination is a crucial step executed by deubiquitinase (DUB) during protein ubiquitination. While multiple components of ubiquitination have been identified in T. gondii, the deubiquitinases involved remain unknown. The aim of the current study was to delineate the localization of TgOTU7 and elucidate its functions. TgOTU7 was specifically localized at the apicoplast, and its expression was largely regulated during the cell cycle. Additionally, TgOTU7 efficiently breaks down ubiquitin chains, exhibits linkage-nonspecific deubiquitinating activity and is critical for the lytic cycle and apicoplast biogenesis, similar to the transcription of the apicoplast genome and the nuclear genes encoding apicoplast-targeted proteins. Taken together, the results indicate that the newly described deubiquitinase TgOTU7 specifically localizes to the apicoplast and affects the cell growth and apicoplast homeostasis of T. gondii.

Genome-wide association mapping of genomic regions associated with drought stress tolerance at seedling and reproductive stages in bread wheat

Understanding the genetic architecture of drought stress tolerance in bread wheat at seedling and reproductive stages is crucial for developing drought-tolerant varieties. In the present study, 192 diverse wheat genotypes, a subset from the Wheat Associated Mapping Initiative (WAMI) panel, were evaluated at the seedling stage in a hydroponics system for chlorophyll content (CL), shoot length (SLT), shoot weight (SWT), root length (RLT), and root weight (RWT) under both drought and optimum conditions. Following that, a genome-wide association study (GWAS) was carried out using the phenotypic data recorded during the hydroponics experiment as well as data available from previously conducted multi-location field trials under optimal and drought stress conditions. The panel had previously been genotyped using the Infinium iSelect 90K SNP array with 26,814 polymorphic markers. Using single as well as multi-locus models, GWAS identified 94 significant marker-trait associations (MTAs) or SNPs associated with traits recorded at the seedling stage and 451 for traits recorded at the reproductive stage. The significant SNPs included several novel, significant, and promising MTAs for different traits. The average LD decay distance for the whole genome was approximately 0.48 Mbp, ranging from 0.07 Mbp (chromosome 6D) to 4.14 Mbp (chromosome 2A). Furthermore, several promising SNPs revealed significant differences among haplotypes for traits such as RLT, RWT, SLT, SWT, and GY under drought stress. Functional annotation and in silico expression analysis revealed important putative candidate genes underlying the identified stable genomic regions such as protein kinases, O-methyltransferases, GroES-like superfamily proteins, NAD-dependent dehydratases, etc. The findings of the present study may be useful for improving yield potential, and stability under drought stress conditions.

The Arabidopsis Deubiquitylase OTU5 Suppresses Flowering by Histone Modification-Mediated Activation of the Major Flowering Repressors FLC, MAF4, and MAF5

Distinct phylogeny and substrate specificities suggest that 12 Arabidopsis Ovarian Tumor domain-containing (OTU) deubiquitinases participate in conserved or plant-specific functions. The otu5-1 null mutant displayed a pleiotropic phenotype, including early flowering, mimicking that of mutants harboring defects in subunits (e.g., ARP6) of the SWR1 complex (SWR1c) involved in histone H2A.Z deposition. Transcriptome and RT-qPCR analyses suggest that downregulated FLC and MAF4-5 are responsible for the early flowering of otu5-1. qChIP analyses revealed a reduction and increase in activating and repressive histone marks, respectively, on FLC and MAF4-5 in otu5-1. Subcellular fractionation, GFP-fusion expression, and MNase treatment of chromatin showed that OTU5 is nucleus-enriched and chromatin-associated. Moreover, OTU5 was found to be associated with FLC and MAF4-5. The OTU5-associated protein complex(es) appears to be distinct from SWR1c, as the molecular weights of OTU5 complex(es) were unaltered in arp6-1 plants. Furthermore, the otu5-1 arp6-1 double mutant exhibited synergistic phenotypes, and H2A.Z levels on FLC/MAF4-5 were reduced in arp6-1 but not otu5-1. Our results support the proposition that Arabidopsis OTU5, acting independently of SWR1c, suppresses flowering by activating FLC and MAF4-5 through histone modification. Double-mutant analyses also indicate that OTU5 acts independently of the HUB1-mediated pathway, but it is partially required for FLC-mediated flowering suppression in autonomous pathway mutants and FRIGIDA-Col.

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.

A Plasmodium falciparum ubiquitin-specific protease (PfUSP) is essential for parasite survival and its disruption enhances artemisinin efficacy

Proteins associated with ubiquitin-proteasome system (UPS) are potential drug targets in the malaria parasite. The ubiquitination and deubiquitination are key regulatory processes for the functioning of UPS. In this study, we have characterized the biochemical and functional role of a novel ubiquitin-specific protease (USP) domain-containing protein of the human malaria parasite Plasmodium falciparum (PfUSP). We have shown that the PfUSP is an active deubiquitinase associated with parasite endoplasmic reticulum (ER). Selection linked integration (SLI) method for C-terminal tagging and GlmS-ribozyme mediated inducible knock-down (iKD) of PfUSP was utilized to assess its functional role. Inducible knockdown of PfUSP resulted in a remarkable reduction in parasite growth and multiplication; specifically, PfUSP-iKD disrupted ER morphology and development, blocked the development of healthy schizonts, and hindered proper merozoite development. PfUSP-iKD caused increased ubiquitylation of specific proteins, disrupted organelle homeostasis and reduced parasite survival. Since the mode of action of artemisinin and the artemisinin-resistance are shown to be associated with the proteasome machinery, we analyzed the effect of dihydroartemisinin (DHA) on PfUSP-iKD parasites. Importantly, the PfUSP-knocked-down parasite showed increased sensitivity to dihydroartemisinin (DHA), whereas no change in chloroquine sensitivity was observed, suggesting a role of PfUSP in combating artemisinin-induced cellular stress. Together, the results show that Plasmodium PfUSP is an essential protease for parasite survival, and its inhibition increases the efficacy of artemisinin-based drugs. Therefore, PfUSP can be targeted to develop novel scaffolds for developing new antimalarials to combat artemisinin resistance.

Lipid-mediated activation of plasma membrane-localized deubiquitylating enzymes modulate endosomal trafficking

The abundance of plasma membrane-resident receptors and transporters has to be tightly regulated by ubiquitin-mediated endosomal degradation for the proper coordination of environmental stimuli and intracellular signaling. Arabidopsis OVARIAN TUMOR PROTEASE (OTU) 11 and OTU12 are plasma membrane-localized deubiquitylating enzymes (DUBs) that bind to phospholipids through a polybasic motif in the OTU domain. Here we show that the DUB activity of OTU11 and OTU12 towards K63-linked ubiquitin is stimulated by binding to lipid membranes containing anionic lipids. In addition, we show that the DUB activity of OTU11 against K6- and K11-linkages is also stimulated by anionic lipids, and that OTU11 and OTU12 can modulate the endosomal degradation of a model cargo and the auxin efflux transporter PIN2-GFP in vivo. Our results suggest that the catalytic activity of OTU11 and OTU12 is tightly connected to their ability to bind membranes and that OTU11 and OTU12 are involved in the fine-tuning of plasma membrane proteins in Arabidopsis.

Functions and mechanisms of the Ubc13-UEV complex and lysine 63-linked polyubiquitination in plants

Ubiquitination is one of the best-known post-translational modifications in eukaryotes, in which different linkage types of polyubiquitination result in different outputs of the target proteins. Distinct from the well-characterized K48-linked polyubiquitination that usually serves as a signal for degradation of the target protein, K63-linked polyubiquitination often requires a unique E2 heterodimer Ubc13-UEV and alters the target protein activity instead of marking it for degradation. This review focuses on recent advances on the roles of Ubc13-UEV-mediated K63-linked polyubiquitination in plant growth, development, and response to environmental stresses.

Met1-specific motifs conserved in OTUB subfamily of green plants enable rice OTUB1 to hydrolyse Met1 ubiquitin chains

Linear (Met1-linked) ubiquitination is involved inflammatory and innate immune signaling. Previous studies have characterized enzymes regulating the addition and removal of this modification in mammalian systems. However, only a few plant-derived deubiquitinases targeting Met1-linked ubiquitin chains have been reported and their mechanism of action remains elusive. Here, using a dehydroalanine-bearing Met1-diubiquitin suicide probe, we discover OTUB1 from Oryza sativa (OsOTUB1) as a Met1-linked ubiquitin chain-targeting deubiquitinase. By solving crystal structures of apo OsOTUB1 and an OsOTUB1/Met1-diubiquitin complex, we find that Met1 activity is conferred by Met1-specific motifs in the S1’ pocket of OsOTUB1. Large-scale sequence alignments and hydrolysis experiments provide evidence that these motifs are a general determinant of Met1 activity in the OTUB subfamily across species. Analysis of the species distribution of OTUBs capable of hydrolysing Met1-linked ubiquitin chains shows that this activity is conserved in green plants (Viridiplantae) and does not exist in metazoans, providing insights into the evolutionary differentiation between primitive plants and animals.

Deubiquitinases (DUBs) targeting Met1-linked ubiquitin chains have important functions in mammals but are barely studied in plants. Here, the authors identify rice OTUB1 as a Met1-targeting DUB, characterize the structural determinants of this activity, and show that these features are conserved in green plants.

CDC48B facilitates the intercellular trafficking of SHORT-ROOT during radial patterning in roots

CELL DIVISION CONTROL PROTEIN48 (CDC48) is essential for membrane fusion, protein degradation, and other cellular processes. Here, we revealed the crucial role of CDC48B in regulating periclinal cell division in roots by analyzing the recessive gen1 mutant. We identified the GEN1 gene through map-based cloning and verified that GEN1 encodes CDC48B. gen1 showed severely inhibited root growth, increased periclinal cell division in the endodermis, defective middle cortex (MC) formation, and altered ground tissue patterning in roots. Consistent with these phenotypes, CYCLIND 6;1(CYCD6;1), a periclinal cell division marker, was upregulated in gen1 compared to Col-0. The ratio of SHR_pro :SHR-GFP fluorescence in pre-dividing nuclei versus the adjacent stele decreased by 33% in gen1, indicating that the trafficking of SHORT-ROOT (SHR) decreased in gen1 when endodermal cells started to divide. These findings suggest that the loss of function of CDC48B inhibits the intercellular trafficking of SHR from the stele to the endodermis, thereby decreasing SHR accumulation in the endodermis. These findings shed light on the crucial role of CDC48B in regulating periclinal cell division in roots.

Genome-Wide Identification and Gene Expression Analysis of the OTU DUB Family in Oryza sativa

Ovarian tumor domain (OTU)-containing deubiquitinating enzymes (DUBs) are an essential DUB to maintain protein stability in plants and play important roles in plant growth development and stress response. However, there is little genome-wide identification and analysis of the OTU gene family in rice. In this study, we identified 20 genes of the OTU family in rice genome, which were classified into four groups based on the phylogenetic analysis. Their gene structures, conserved motifs and domains, chromosomal distribution, and cis elements in promoters were further studied. In addition, OTU gene expression patterns in response to plant hormone treatments, including SA, MeJA, NAA, BL, and ABA, were investigated by RT-qPCR analysis. The results showed that the expression profile of OsOTU genes exhibited plant hormone-specific expression. Expression levels of most of the rice OTU genes were significantly changed in response to rice stripe virus (RSV), rice black-streaked dwarf virus (RBSDV), Southern rice black-streaked dwarf virus (SRBSDV), and Rice stripe mosaic virus (RSMV). These results suggest that the rice OTU genes are involved in diverse hormone signaling pathways and in varied responses to virus infection, providing new insights for further functional study of OsOTU genes.

Endoplasmic Reticulum Stress and Unfolded Protein Response Signaling in Plants

Plants are sensitive to a variety of stresses that cause various diseases throughout their life cycle. However, they have the ability to cope with these stresses using different defense mechanisms. The endoplasmic reticulum (ER) is an important subcellular organelle, primarily recognized as a checkpoint for protein folding. It plays an essential role in ensuring the proper folding and maturation of newly secreted and transmembrane proteins. Different processes are activated when around one-third of newly synthesized proteins enter the ER in the eukaryote cells, such as glycosylation, folding, and/or the assembling of these proteins into protein complexes. However, protein folding in the ER is an error-prone process whereby various stresses easily interfere, leading to the accumulation of unfolded/misfolded proteins and causing ER stress. The unfolded protein response (UPR) is a process that involves sensing ER stress. Many strategies have been developed to reduce ER stress, such as UPR, ER-associated degradation (ERAD), and autophagy. Here, we discuss the ER, ER stress, UPR signaling and various strategies for reducing ER stress in plants. In addition, the UPR signaling in plant development and different stresses have been discussed.

Reducing expression of TaOTUB1s decreases tiller number in wheat

Tiller number is an important agronomic trait that affects crop yield. The roles of OTUB1 in regulating tiller numbers in rice have been reported. However, the roles of OTUB1 in wheat remain elusive. In this study, TaOTUB1s were identified in wheat. TaOTUB1 proteins were localized in the nucleus and cytoplasm. Compared with wild-type Fielder, TaOTUB1-RNAi transgenic wheat plants had fewer tillers. Similar to OTUB1 in rice, the yeast double hybrid indicated that the TaOTUB1-A protein could interact with TaSPL17 and TaUBC13 proteins. The results of quantitative real-time polymerase chain reaction revealed that the expression levels of TaOTUB1s decreased while those of TaSPL17 significantly improved in TaOTUB1-RNAi lines. These findings suggested that TaOTUB1s influenced tiller number in wheat.

Protein Quality Control in Plant Organelles: Current Progress and Future Perspectives

The endoplasmic reticulum, chloroplasts, and mitochondria are major plant organelles for protein synthesis, photosynthesis, metabolism, and energy production. Protein homeostasis in these organelles, maintained by a balance between protein synthesis and degradation, is essential for cell functions during plant growth, development, and stress resistance. Nucleus-encoded chloroplast- and mitochondrion-targeted proteins and ER-resident proteins are imported from the cytosol and undergo modification and maturation within their respective organelles. Protein folding is an error-prone process that is influenced by both developmental signals and environmental cues; a number of mechanisms have evolved to ensure efficient import and proper folding and maturation of proteins in plant organelles. Misfolded or damaged proteins with nonnative conformations are subject to degradation via complementary or competing pathways: intraorganelle proteases, the organelle-associated ubiquitin-proteasome system, and the selective autophagy of partial or entire organelles. When proteins in nonnative conformations accumulate, the organelle-specific unfolded protein response operates to restore protein homeostasis by reducing protein folding demand, increasing protein folding capacity, and enhancing components involved in proteasome-associated protein degradation and autophagy. This review summarizes recent progress on the understanding of protein quality control in the ER, chloroplasts, and mitochondria in plants, with a focus on common mechanisms shared by these organelles during protein homeostasis.

Histone Deubiquitinase OTU1 Epigenetically Regulates DA1 and DA2, Which Control Arabidopsis Seed and Organ Size

Seeds are central to plant life cycle and to human nutrition, functioning as the major supplier of human population energy intake. To understand better the roles of enzymic writers and erasers of the epigenetic marks, in particular, histone ubiquitylation and the corresponding histone modifiers, involved in control of seed development, we identified the otubain-like cysteine protease OTU1 as a histone deubiquitinase involved in transcriptional repression of the DA1 and DA2 genes known to regulate seed and organ size in Arabidopsis. Loss-of-function mutants of OTU1 accumulate H2B monoubiquitylation and such euchromatic marks as H3 trimethylation and hyperacetylation in the DA1 and DA2 chromatin. These data advance our knowledge about epigenetic regulation of the DA1 and DA2 genes by recognizing OTU1 as a member of a putative repressor complex that negatively regulates their transcription.

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Histone ubiquitylation regulates transcription of DA1/DA2 that control seed/organ size

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OTU1 deubiquitinase is involved in deubiquitylation of the DA1/DA2 chromatin

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OTU1 acts as an epigenetic transcriptional repressor of the DA1/DA2 genes

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OTU1 is nucleocytoplasmic, indicating involvement in nuclear and cytoplasmic processes