Ubiquitin genes are differentially regulated in protoplast-derived cultures of Nicotiana sylvestris and in response to various stresses

Contrasting Impacts of Ubiquitin Overexpression on Arabidopsis Growth and Development

In plants, the ubiquitin (Ub)-26S proteasome system (UPS) regulates numerous biological functions by selectively targeting proteins for ubiquitylation and degradation. However, the regulation of Ub itself on plant growth and development remains unclear. To demonstrate a possible impact of Ub supply, as seen in animals and flies, we carefully analyzed the growth and developmental phenotypes of two different poly-Ub (UBQ) gene overexpression plants of Arabidopsis thaliana. One is transformed with hexa-6His-UBQ (designated 6HU), driven by the cauliflower mosaic virus 35S promoter, while the other expresses hexa-6His-TEV-UBQ (designated 6HTU), driven by the endogenous promoter of UBQ10. We discovered that 6HU and 6HTU had contrasting seed yields. Compared to wildtype (WT), the former exhibited a reduced seed yield, while the latter showed an increased seed production that was attributed to enhanced growth vigor and an elevated silique number per plant. However, reduced seed sizes were common in both 6HU and 6HTU. Differences in the activity and size of the 26S proteasome assemblies in the two transgenic plants were also notable in comparison with WT, suggestive of a contributory role of UBQ expression in proteasome assembly and function. Collectively, our findings demonstrated that exogenous expression of recombinant Ub may optimize plant growth and development by influencing the UPS activities via structural variance, expression patterns, and abundance of free Ub supply.

GhVIM28, a negative regulator identified from VIM family genes, positively responds to salt stress in cotton

The VIM (belonged to E3 ubiquitin ligase) gene family is crucial for plant growth, development, and stress responses, yet their role in salt stress remains unclear. We analyzed phylogenetic relationships, chromosomal localization, conserved motifs, gene structure, cis-acting elements, and gene expression patterns of the VIM gene family in four cotton varieties. Our findings reveal 29, 29, 17, and 14 members in Gossypium hirsutum (G.hirsutum), Gossypium barbadense (G.barbadense), Gossypium arboreum (G.arboreum), and Gossypium raimondii (G. raimondii), respectively, indicating the maturity and evolution of this gene family. motifs among GhVIMs genes were observed, along with the presence of stress-responsive, hormone-responsive, and growth-related elements in their promoter regions. Gene expression analysis showed varying patterns and tissue specificity of GhVIMs genes under abiotic stress. Silencing GhVIM28 via virus-induced gene silencing revealed its role as a salt-tolerant negative regulator. This work reveals a mechanism by which the VIM gene family in response to salt stress in cotton, identifying a potential negative regulator, GhVIM28, which could be targeted for enhancing salt tolerance in cotton. The objective of this study was to explore the evolutionary relationship of the VIM gene family and its potential function in salt stress tolerance, and provide important genetic resources for salt tolerance breeding of cotton.

Tobacco NtUBC1 and NtUBQ2 enhance salt tolerance by reducing sodium accumulation and oxidative stress through proteasome activation in Arabidopsis

The ubiquitin/proteasome system plays a crucial role in the regulation of plant responses to environmental stress. Here, we studied the involvement of the UBC1 and UBQ2 genes encoding a ubiquitin conjugating enzyme (E2) and ubiquitin extension protein, respectively, in the response to salt stress. Our results showed that the constitutive expression of tobacco NtUBC1 and NtUBQ2 in Arabidopsis thaliana improved salt tolerance, along with the lower Na+ level and higher K+/Na+ ratio compared to control plants. Moreover, the expression levels of sodium transporters, including AtHKT1 (High-Affinity K+ Transporter1) and AtSOS1 (Salt Overly Sensitive 1), were higher in NtUBC1- and NtUBQ2-Arabidopsis. However, the transcript level of AtNHX1 (Na+/H+ Exchanger 1) was similar between control and transgenic plants. After salt exposure, the activity of the 26S proteasome markedly increased in NtUBC1- and NtUBQ2-expressing plants; however, ubiquitinated protein levels decreased compared to control plants. Furthermore, higher activity of antioxidant enzymes and lower ROS production were observed in UBC1- and UBQ2-expressing plants. We further challenged atubc1, atubc2, and atubq2 single mutants and atubc1ubc2 double mutant lines with salt stress; interestingly, the salt sensitivity and sodium levels of the studied mutants were enhanced, while the potassium levels were reduced. However, the atubc1ubc2 double mutant illustrated a more severe phenotype than the single mutants, probably due to the redundant function of UBC1 and UBC2 in Arabidopsis. Taken together, NtUBC1 and NtUBQ2 enhance salt tolerance by enhancing 26S proteasome activity and reducing Na+ accumulation, ROS, and ubiquitinated/salt-denatured proteins.

Current perspectives of ubiquitination and SUMOylation in abiotic stress tolerance in plants

Post-translational modification (PTM) is a critical and rapid mechanism to regulate all the major cellular processes through the modification of diverse protein substrates. Substrate-specific covalent attachment of ubiquitin and Small Ubiquitin-Like Modifier (SUMO) with the target proteins, known as ubiquitination and SUMOylation, respectively, are crucial PTMs that regulate almost every process in the cell by modulating the stability and fidelity of the proteins. Ubiquitination and SUMOylation play a very significant role to provide tolerance to the plants in adverse environmental conditions by activating/deactivating the pre-existing proteins to a great extent. We reviewed the importance of ubiquitination and SUMOylation in plants, implicating its prospects in various abiotic stress regulations. An exhaustive study of molecular mechanisms of ubiquitination and SUMOylation of plant proteins and their role will contribute to the understanding of physiology underlying mitigation of the abiotic stresses and survival in plants. It will be helpful to strategize the improvement of crops for abiotic stress tolerance.

Conserved and Unique Roles of Chaperone-Dependent E3 Ubiquitin Ligase CHIP in Plants

Protein quality control (PQC) is essential for maintaining cellular homeostasis by reducing protein misfolding and aggregation. Major PQC mechanisms include protein refolding assisted by molecular chaperones and the degradation of misfolded and aggregated proteins using the proteasome and autophagy. A C-terminus of heat shock protein (Hsp) 70-interacting protein [carboxy-terminal Hsp70-interacting protein (CHIP)] is a chaperone-dependent and U-box-containing E3 ligase. CHIP is a key molecule in PQC by recognizing misfolded proteins through its interacting chaperones and targeting their degradation. CHIP also ubiquitinates native proteins and plays a regulatory role in other cellular processes, including signaling, development, DNA repair, immunity, and aging in metazoans. As a highly conserved ubiquitin ligase, plant CHIP plays an important role in response to a broad spectrum of biotic and abiotic stresses. CHIP protects chloroplasts by coordinating chloroplast PQC both outside and inside the important photosynthetic organelle of plant cells. CHIP also modulates the activity of protein phosphatase 2A (PP2A), a crucial component in a network of plant signaling, including abscisic acid (ABA) signaling. In this review, we discuss the structure, cofactors, activities, and biological function of CHIP with an emphasis on both its conserved and unique roles in PQC, stress responses, and signaling in plants.

Proteasomal Degradation of Proteins Is Important for the Proper Transcriptional Response to Sulfur Deficiency Conditions in Plants

Plants are continuously exposed to different abiotic and biotic stresses; therefore, to protect themselves, they depend on the fast reprogramming of large gene repertoires to prioritize the expression of a given stress-induced gene set over normal cellular household genes. The activity of the proteasome, a large proteolytic complex that degrades proteins, is vital to coordinate the expression of such genes. Proteins are labeled for degradation by the action of E3 ligases that site-specifically alter their substrates by adding chains of ubiquitin. Recent publications have revealed an extensive role of ubiquitination in the utilization of nutrients. This study presents the transcriptomic profiles of sulfur-deficient rosettes and roots of Arabidopsis thaliana rpt2a mutant with proteasomal malfunction. We found that genes connected with sulfur metabolism are regulated to the lesser extent in rpt2a mutant while genes encoding transfer RNAs and small nucleolar RNAs are highly upregulated. Several genes encoding E3 ligases are specifically regulated by sulfur deficiency. Furthermore, we show that a key transcription factor of sulfur deficiency response, Sulfur LIMitation1, undergoes proteasomal degradation and is able to interact with F-box protein, EBF1.

A Quantitative Proteomics Study of Early Heat-Regulated Proteins by Two-Dimensional Difference Gel Electrophoresis Identified OsUBP21 as a Negative Regulator of Heat Stress Responses in Rice

To understand the early heat shock (HS)-regulated cellular responses that influence the tolerance of rice plant to high environmental temperatures, two-dimensional difference gel electrophoresis (2D-DIGE) is performed to explore the early HS-regulated proteome. Multiple proteins that show abundance changes after 1 and 5 min of HS treatment are identified. Of the early HS-regulated proteins identified, the abundance of a ubiquitin-specific protease, OsUBP21, and its Arabidopsis homolog, AtUBP13, is found to be upregulated by 5 min of HS treatment. Further, knocking the expression of OsUBP21 or AtUBP13 down or out increases the tolerance of rice and Arabidopsis plants to HS stress, suggesting that the function of these ubiquitin-specific proteases in regulating plant HS responses is conserved between monocots and dicots. 2D-DIGE showed a group of proteins are differentially regulated in wild-type and ubp21 mutant after 30 min of HS treatment. Among these proteins, 11 are found to interact directly with OsUBP21; thus, they may be targets of OsUBP21. Future analyses of the roles of these OsUBP21-interacting proteins in plant HS responses will help reveal the protein ubiquitination/deubiquitination-regulated cellular responses induced by HS in rice.

MPSR1 is a cytoplasmic PQC E3 ligase for eliminating emergent misfolded proteins in Arabidopsis thaliana

The essential roles of cytoplasmic E3 ligases in the protein quality control (PQC) pathways have been increasingly highlighted in yeast and animal studies. However, in plants, only CHIP E3 ligase has been characterized, while the knowledge of cytoplasmic PQC E3 ligases remains rudimentary. Misfolded Protein Sensing RING E3 ligase 1 (MPSR1), a self-regulatory sensor system that functions only in the occurrence of misfolded proteins, is an identified cytoplasmic PQC E3 ligase in plants that directly recognizes emergent misfolded proteins independently of chaperones. In addition, MPSR1 sustains the integrity and activity of the 26S proteasome under proteotoxic stress. Given that MPSR1 RING E3 ligase is well conserved in eukaryotes, this study sheds light on a PQC pathway that is present particularly in plants and beyond.

Ubiquitin E3 ligases are crucial for eliminating misfolded proteins before they form cytotoxic aggregates that threaten cell fitness and survival. However, it remains unclear how emerging misfolded proteins in the cytoplasm can be selectively recognized and eliminated by E3 ligases in plants. We found that Misfolded Protein Sensing RING E3 ligase 1 (MPSR1) is an indispensable E3 ligase required for plant survival after protein-damaging stress. Under no stress, MPSR1 is prone to rapid degradation by the 26S proteasome, concealing its protein quality control (PQC) E3 ligase activity. Upon proteotoxic stress, MPSR1 directly senses incipient misfolded proteins and tethers ubiquitins for subsequent degradation. Furthermore, MPSR1 sustains the structural integrity of the proteasome complex at the initial stage of proteotoxic stress. Here, we suggest that the MPSR1 pathway is a constitutive mechanism for proteostasis under protein-damaging stress, as a front-line surveillance system in the cytoplasm.

Responses of Plant Proteins to Heavy Metal Stress-A Review

Plants respond to environmental pollutants such as heavy metal(s) by triggering the expression of genes that encode proteins involved in stress response. Toxic metal ions profoundly affect the cellular protein homeostasis by interfering with the folding process and aggregation of nascent or non-native proteins leading to decreased cell viability. However, plants possess a range of ubiquitous cellular surveillance systems that enable them to efficiently detoxify heavy metals toward enhanced tolerance to metal stress. As proteins constitute the major workhorses of living cells, the chelation of metal ions in cytosol with phytochelatins and metallothioneins followed by compartmentalization of metals in the vacuoles as well as the repair of stress-damaged proteins or removal and degradation of proteins that fail to achieve their native conformations are critical for plant tolerance to heavy metal stress. In this review, we provide a broad overview of recent advances in cellular protein research with regards to heavy metal tolerance in plants. We also discuss how plants maintain functional and healthy proteomes for survival under such capricious surroundings.

Manipulation of monoubiquitin improves chilling tolerance in transgenic tobacco (Nicotiana tabacum)

Ubiquitin (Ub) is a multifunctional protein that mainly functions to tag proteins for selective degradation by the 26S proteasome. We cloned an Ub gene TaUb2 from wheat (Triticum aestivum L.) previously. To study the function of TaUB2 in chilling stress, sense and antisense Ub transgenic tobacco plants (Nicotiana tabacum L.), as well as wild type (WT) and vector control β-glucuronidase (T-GUS) plants, were used. Under stress, leaf wilting in sense plants was significantly less than in controls, but more severe in antisense plants. Meanwhile, the net photosynthetic rate (Pn) and the maximal photochemical efficiency of PSII (Fv/Fm) in sense plants were greater than controls, but lower in antisense plants during chilling stress and recovery. Less wilting in sense plants resulted from improved water status, which may be related to the accumulation of proline and solute sugar. Furthermore, as indicated by electrolyte leakage, membrane damage under stress was less in sense plants and more severe in antisense plants than controls. Consistent with electrolyte leakage, the malondialdehyde (MDA) content was less in sense plants, but more in antisense plants compared to controls. Meanwhile, the less accumulation of reactive oxygen species (ROS) and the greater antioxidant enzyme activity in sense plants implied the improved antioxidant competence by the overexpression of monoubiquitin gene Ta-Ub2 from wheat. We suggest that overexpressing Ub is a useful strategy to promote chilling tolerance. The improvement of ROS scavenging may be an important mechanism underlying the role of Ub in promoting plants tolerant to chilling stress.

E3 ubiquitin ligase CHIP and NBR1-mediated selective autophagy protect additively against proteotoxicity in plant stress responses

Plant stress responses require both protective measures that reduce or restore stress-inflicted damage to cellular structures and mechanisms that efficiently remove damaged and toxic macromolecules, such as misfolded and damaged proteins. We have recently reported that NBR1, the first identified plant autophagy adaptor with a ubiquitin-association domain, plays a critical role in plant stress tolerance by targeting stress-induced, ubiquitinated protein aggregates for degradation by autophagy. Here we report a comprehensive genetic analysis of CHIP, a chaperone-associated E3 ubiquitin ligase from Arabidopsis thaliana implicated in mediating degradation of nonnative proteins by 26S proteasomes. We isolated two chip knockout mutants and discovered that they had the same phenotypes as the nbr1 mutants with compromised tolerance to heat, oxidative and salt stresses and increased accumulation of insoluble proteins under heat stress. To determine their functional interactions, we generated chip nbr1 double mutants and found them to be further compromised in stress tolerance and in clearance of stress-induced protein aggregates, indicating additive roles of CHIP and NBR1. Furthermore, stress-induced protein aggregates were still ubiquitinated in the chip mutants. Through proteomic profiling, we systemically identified heat-induced protein aggregates in the chip and nbr1 single and double mutants. These experiments revealed that highly aggregate-prone proteins such as Rubisco activase and catalases preferentially accumulated in the nbr1 mutant while a number of light-harvesting complex proteins accumulated at high levels in the chip mutant after a relatively short period of heat stress. With extended heat stress, aggregates for a large number of intracellular proteins accumulated in both chip and nbr1 mutants and, to a greater extent, in the chip nbr1 double mutant. Based on these results, we propose that CHIP and NBR1 mediate two distinct but complementary anti-proteotoxic pathways and protein's propensity to aggregate under stress conditions is one of the critical factors for pathway selection of protein degradation.

Environmental stresses such as heat cause generation of misfolded and damaged proteins, which are highly toxic and must be efficiently removed. In plants, NBR1, the first isolated autophagy receptor with an ubiquitin-association domain, plays a critical role in plant stress tolerance by targeting ubiquitinated protein aggregates under stress conditions for degradation by autophagy. To study how stress-induced misfolded and damaged proteins are detected and ubiquitinated in plant cells, we analyzed the chaperone-associated E3 ubiquitin ligase CHIP from Arabidopsis thaliana for its role in protection against proteotoxicity in plant stress responses. Disruption of Arabidopsis CHIP caused increased sensitivity to a spectrum of abiotic stresses as found in the Arabidopsis nbr1 mutants. Disruption of both Arabidopsis CHIP and NBR1 further compromised plant stress tolerance, indicating that their roles are additive. Furthermore, in the chip nbr1 double mutant, compromised heat tolerance was associated with increased accumulation of insoluble proteins derived mostly from heat-sensitive but biologically important proteins such as Rubisco activase, catalases and proteins required for protein synthesis and folding. Importantly, stress-induced protein aggregates were still highly ubiquitinated in the chip mutants. These results strongly suggest that CHIP and NBR1 function in two distinct but complementary anti-proteotoxic pathways in plant stress responses.

The role of ubiquitin and the 26S proteasome in plant abiotic stress signaling

Ubiquitin is a small, highly conserved, ubiquitously expressed eukaryotic protein with immensely important and diverse regulatory functions. A well-studied function of ubiquitin is its role in selective proteolysis by the ubiquitin-proteasome system (UPS). The UPS has emerged as an integral player in plant response and adaptation to environmental stresses such as drought, salinity, cold and nutrient deprivation. The UPS has also been shown to influence the production and signal transduction of stress-related hormones such as abscisic acid. Understanding UPS function has centered mainly on defining the role of E3 ubiquitin ligases, which are the substrate-recruiting component of the ubiquitination pathway. The recent identification of stress signaling/regulatory proteins that are the subject of ubiquitin-dependent degradation has increased our knowledge of how the UPS facilitates responses to adverse environmental conditions. A brief overview is provided on role of the UPS in modulating protein stability during abiotic stress signaling. E3 ubiquitin ligases for which stress-related substrate proteins have been identified are discussed.

Proteomic analysis of the low mutation rate of diploid male gametes induced by colchicine in Ginkgo biloba L

Colchicine treatment of G. biloba microsporocytes results in a low mutation rate in the diploid (2n) male gamete. The mutation rate is significantly lower as compared to other tree species and impedes the breeding of new economic varieties. Proteomic analysis was done to identify the proteins that influence the process of 2n gamete formation in G. biloba. The microsporangia of G. biloba were treated with colchicine solution for 48 h and the proteins were analyzed using 2-D gel electrophoresis and compared to protein profiles of untreated microsporangia. A total of 66 proteins showed difference in expression levels. Twenty-seven of these proteins were identified by mass spectrometry. Among the 27 proteins, 14 were found to be up-regulated and the rest 13 were down-regulated. The identified proteins belonged to five different functional classes: ATP generation, transport and carbohydrate metabolism; protein metabolism; ROS scavenging and detoxifying enzymes; cell wall remodeling and metabolism; transcription, cell cycle and signal transduction. The identification of these differentially expressed proteins and their function could help in analysing the mechanism of lower mutation rate of diploid male gamete when the microsporangium of G. biloba was induced by colchicine.

Shotgun label-free quantitative proteomics of water-deficit-stressed midmature peanut (Arachis hypogaea L.) seed

Legume seeds and peanuts, in particular, are an inexpensive source of plant proteins and edible oil. A comprehensive understanding of seed metabolism and the effects of water-deficit stress on the incorporation of the main storage reserves in seeds, such as proteins, fatty acids, starch, and secondary metabolites, will enhance our ability to improve seed quality and yield through molecular breeding programs. In the present study, we employed a label-free quantitative proteomics approach to study the functional proteins altered in the midmature (65-70 days postanthesis) peanut seed grown under water-deficit stress conditions. We created a pod-specific proteome database and identified 93 nonredundant, statistically significant, and differentially expressed proteins between well-watered and drought-stressed seeds. Mapping of these differential proteins revealed three candidate biological pathways (glycolysis, sucrose and starch metabolism, and fatty acid metabolism) that were significantly altered due to water-deficit stress. Differential accumulation of proteins from these pathways provides insight into the molecular mechanisms underlying the observed physiological changes, which include reductions in pod yield and biomass, reduced germination, reduced vigor, decreased seed membrane integrity, increase in storage proteins, and decreased total fatty acid content. Some of the proteins encoding rate limiting enzymes of biosynthetic pathways could be utilized by breeders to improve peanut seed production during water-deficit conditions in the field. The data have been deposited to the ProteomeXchange with identifier PXD000308.

A novel method of transgene delivery into triticale plants using the Agrobacterium transferred DNA-derived nano-complex

Genetic transformation of monocotyledonous plants still presents a challenge for plant biologists and biotechnologists because monocots are difficult to transform with Agrobacterium tumefaciens, whereas other transgenesis methods, such as gold particle-mediated transformation, result in poor transgene expression because of integration of truncated DNA molecules. We developed a method of transgene delivery into monocots. This method relies on the use of an in vitro-prepared nano-complex consisting of transferred DNA, virulence protein D2, and recombination protein A delivered to triticale microspores with the help of a Tat2 cell-penetrating peptide. We showed that this approach allowed for single transgene copy integration events and prevented degradation of delivered DNA, thus leading to the integration of intact copies of the transgene into the genome of triticale plants. This resulted in transgene expression in all transgenic plants regenerated from microspores transfected with the full transferred DNA/protein complex. This approach can easily substitute the bombardment technique currently used for monocots and will be highly valuable for plant biology and biotechnology.

Abiotic stress tolerance mediated by protein ubiquitination

Plant growth and development is largely influenced by ubiquitin-mediated regulation of protein stability. Specificity of the ubiquitination pathway is controlled mainly by the substrate-recruiting E3 ubiquitin ligases, and consequently, E3 ligases control numerous cellular processes. Recent evidence that ubiquitination plays a critical role in regulating plant responses to abiotic stresses has launched intensive efforts to identify E3 ligases that mediate plant tolerance of adverse environmental conditions. Most stress-related E3 ligases identified to date facilitate responses to environmental stimuli by modulating the abundance of key downstream stress-responsive transcription factors. In this review, the regulatory roles of ubiquitin during the plant's response to abiotic stress are summarized and highlighted.

A redox-mediated modulation of stem bolting in transgenic Nicotiana sylvestris differentially expressing the external mitochondrial NADPH dehydrogenase

Cytosolic NADPH can be directly oxidized by a calcium-dependent NADPH dehydrogenase, NDB1, present in the plant mitochondrial electron transport chain. However, little is known regarding the impact of modified cytosolic NADPH reduction levels on growth and metabolism. Nicotiana sylvestris plants overexpressing potato (Solanum tuberosum) NDB1 displayed early bolting, whereas sense suppression of the same gene led to delayed bolting, with consequential changes in flowering time. The phenotype was dependent on light irradiance but not linked to any change in biomass accumulation. Whereas the leaf NADPH/NADP(+) ratio was unaffected, the stem NADPH/NADP(+) ratio was altered following the genetic modification and strongly correlated with the bolting phenotype. Metabolic profiling of the stem showed that the NADP(H) change affected relatively few, albeit central, metabolites, including 2-oxoglutarate, glutamate, ascorbate, sugars, and hexose-phosphates. Consistent with the phenotype, the modified NDB1 level also affected the expression of putative floral meristem identity genes of the SQUAMOSA and LEAFY types. Further evidence for involvement of the NADPH redox in stem development was seen in the distinct decrease in the stem apex NADPH/NADP(+) ratio during bolting. Additionally, the potato NDB1 protein was specifically detected in mitochondria, and a survey of its abundance in major organs revealed that the highest levels are found in green stems. These results thus strongly suggest that NDB1 in the mitochondrial electron transport chain can, by modifying cell redox levels, specifically affect developmental processes.

Drought tolerance through overexpression of monoubiquitin in transgenic tobacco

Ubiquitin (Ub) is present in all eukaryotic species examined. It is a multifunctional protein and one of its main known functions is to tag proteins for selective degradation by the 26S proteasome. In this study, Ta-Ub2, a cDNA sequence containing a single Ub repeat and a 3' non-coding region of a polyubiquitin gene, was isolated from wheat (Triticum aestivum) by reverse transcription-polymerase chain reaction (RT-PCR). A PBI sense vector with Ta-Ub2 was constructed and transformed into tobacco plants. Ub expression in wheat leaves, monitored by semi-quantitative RT-PCR, responded to drought stress. In transgenic tobacco, determined by protein gel blot analysis, we found higher amounts of Ub-protein conjugates than in control (tobacco carrying a PBI GUS vector without Ta-Ub2) and wild-type (WT) lines. However, free Ub levels did not significantly differ in the 3 genotypes. Seeds from transgenic, Ub-overexpressing tobacco germinated faster and seedlings grew more vigorously than control and WT samples, both under drought and non-drought conditions. Furthermore, CO(2) assimilation of transgenic plants was significantly higher under drought stress. Our results indicate that Ub may be involved in the response of plants to drought stress and that overexpression of monoubiquitin might be an effective strategy for enhancing drought tolerance.

Induction of a polyubiquitin gene promoter by dehydration stresses in transformed rice cells

The expression of the maize polyubiquitin gene promoter UBI1 in rice cells has been used to study the involvement of ubiquitin in cell protection responses to dehydration caused by osmotic, saline or freezing stress. The effect of these stresses on UBI1 activity was investigated by the use of stably transformed rice calli (UBI1:GUS), as well as by transient expression experiments performed with cell lines with high or low tolerance to each type of stress. The theoretical analysis of the UBI1 promoter shows several putative stress-regulated boxes that could account for the stress-related UBI1 induction pattern described in this work. We suggest that the study of the differential UBI1 promoter-driven expression in rice cell lines with different level of tolerance to stress might be useful to elucidate complex signal transduction pathways in response to dehydration stresses in monocots.

20S proteasome and accumulation of oxidized and ubiquitinated proteins in maize leaves subjected to cadmium stress

In order to examine the possible involvement of the 20S proteasome in degradation of oxidized proteins, the effects of different cadmium concentrations on its activities, protein abundance and oxidation level were studied using maize (Zea mays L.) leaf segments. The accumulation of carbonylated and ubiquitinated proteins was also investigated. Treatment with 50 microM CdCl(2) increased both trypsin- and PGPH-like activities of the 20S proteasome. The incremental changes in 20S proteasome activities were probably caused by an increased level of 20S proteasome oxidation, with this being responsible for degradation of the oxidized proteins. When leaf segments were treated with 100 microM CdCl(2), the chymotrysin- and trypsin-like activities of the 20S proteasome also decreased, with a concomitant increase in accumulation of carbonylated and ubiquitinated proteins. With both Cd(2+) concentrations, the abundance of the 20S proteasome protein remained similar to the control experiments. These results provide evidence for the involvement of this proteolytic system in cadmium-stressed plants.

Expression of asparagine synthetase genes in sunflower (Helianthus annuus) under various environmental stresses

In sunflower, asparagine synthetase (AS; EC 6.3.5.4) is encoded by a small family of three genes (HAS1, HAS1.1 and HAS2) that are differentially regulated by light, carbon and nitrogen availability. In this study, the response of each gene to various stress conditions was examined by Northern analysis with gene-specific probes in leaves and roots. The expression of HAS1 and HAS1.1 genes was induced by osmotic stress (300 mM mannitol), salt stress (150 mM NaCl), and heavy-metal stress (20 microM CuSO(4)), more in roots than in leaves. The expression of HAS2 was not significantly altered by stress treatments. The positive response of HAS1 and HAS1.1 genes to osmotic and salt stresses occurred in the light, in contrast to that previously found in unstressed plants. Measurements of sucrose and total free amino acid contents in leaves and roots indicate that the expression of root HAS1 and HAS1.1 genes in stressed plants is not under metabolic control by the intracellular C/N ratio, suggesting the involvement of some specific stress factor(s). Growth of plants at 40 degrees C for 12h negatively affected the expression of HAS1 and HAS1.1 but not that of HAS2.

Uptake and toxicity of Cr(III) in celery seedlings

The present study shows that in celery Cr(III) induces deleterious effects on seedling development and morphology, and a number of metabolic responses related to stress. Exogenous CrCl3 from 0.01 to 1 mM increasingly inhibited seed germination and hypocotyl elongation, or completely blocked it (10 mM), while the root apparatus was dramatically damaged even at the lowest dose. Seedlings took up exogenous Cr(III) in a dose-dependent manner, roots being the site of major metal accumulation; translocation towards the hypocotyl and cotyledonary leaves was also detected. Either total or chlorophyll a content was significantly reduced by chromium as low as 0.01 mM. A large accumulation of free and, to a lesser extent, conjugated polyamines occurred in all segments of treated plants. A dose-dependent relationship linking actual amounts of Cr(III) recovered in the entire seedling or organ and the respective polyamine titre was evidenced. Free putrescine, in particular, was the polyamine exhibiting the highest rate of increase, and cotyledonary leaves the organ where the major response occurred. A marked increase in ubiquitin-protein conjugates after Cr(III) treatment was also observed, particularly in roots. Thus, the study suggests for the first time a possible relationship between ubiquitination and Cr(III)-stress. The putative function of polyamines as a stress response, and the recruitment of the ubiquitin pathway to remove damaged or aberrant proteins which might have been produced in metal-treated seedlings are discussed.

Comparative microarray analysis of programmed cell death induced by proteasome malfunction and hypersensitive response in plants

Programmed cell death (PCD) plays a pivotal role in the elimination of injured or unwanted cells during diverse physiological and developmental conditions in organisms. However in contrast to the animal system, signaling pathways and molecular mechanism of PCD are largely unknown in plants. We previously reported that silencing of NbPAF encoding the alpha6 subunit of 20S proteasome by virus-induced gene silencing activated programmed cell death in plants by inactivating proteasome function. In this study, we analyzed global gene expression profile of PCD induced by suppression of NbPAF expression, in comparison with that of hypersensitive response (HR)-induced PCD, using a cDNA microarray representing 4685 hot pepper genes. HR is a well-characterized PCD program in plants, which occurs in response to pathogen infection. The microarray analyses identified 247 genes whose gene expression was differentially modulated during PCD activated by NbPAF depletion or HR. Most of the genes that were up-regulated during the NbPAF-mediated PCD, including the ubiquitin/proteasome pathway-related genes, were down-regulated during HR cell death. In contrast, transcription of many defense-related genes, transcription factor genes, and photosynthesis-related genes remained unchanged or repressed during NbPAF-mediated PCD, while it was highly induced during HR cell death. Only a small number of genes including antioxidant-related genes and proteases were found to be up-regulated during induction of PCD by both proteasome inactivation and HR. Based on these results, these two PCD pathways appear to be differentially regulated, but some overlapping mechanism exists, which involves core regulators of plant PCD.

Biochemical identification of proteasome-associated endonuclease activity in sunflower

Proteasomes have been purified from sunflower hypocotyles. They elute with a molecular mass of 600 kDa from gel filtration columns and two-dimensional gel electrophoresis indicates that the complex contains at least 20 different protein subunits. Peptide microsequencing revealed the presence of four subunits homologous to subunits Beta2, Beta6, Alpha5 and Alpha6 of plant proteasomes. These proteasomes have chymotrypsin-like activity and the highly purified fraction of this complex is associated with an endonuclease activity hydrolyzing Tobacco mosaic virus RNA and Lettuce mosaic virus RNA with a cleavage pattern showing fragments of well-defined size. This is the first evidence of a RNA endonuclease activity associated with plant proteasomes.

Ubiquitin- and proteasome-dependent proteolysis in plants

In recent years it has become obvious that protein degradation is an important catabolic process during development in plants and animals. One very conserved degradative system is the ubiquitin- and proteasome-dependent proteolytic pathway, which is found in all eukaryotes from yeast to mammals and plants. The pathway consists of two parts, one in which chains of ubiquitin are conjugated to substrate proteins, and one in which these substrate proteins are either degraded by the 26S proteasome or are de-ubiquitinated. The ubiquitin- and proteasome-dependent pathway degrades a wide range of proteins in the nucleus and cytoplasm. It is highly specific, but controls a large number of cellular events due to the diversity in the conjugating enzymes. This pathway is important for removal of abnormal/damaged proteins that have had their recognition sites exposed as well as for control of specific transcription factors and cell cycle regulators. In plants, ubiquitin- and proteasome-dependent proteolysis is known to be involved in regulation of the cell cycle and transcription factors as well as endoplasmic reticulum-associated protein degradation, stress response and developmental processes, such as xylogenesis and senescence.

Structure, expression and promoter activity of two polyubiquitin genes from rice (Oryza sativa L.)

We have isolated two rice polyubiquitin genes designated as RUBQ1 and RUBQ2 by screening a Bacterial Artificial Chromosome (BAC) genomic library with a 32P-labeled ubiquitin cDNA probe. DNA sequence data revealed that both genes contained an open reading frame encoding a hexameric precursor ubiquitin and an intron immediate upstream of the initiation codon. The deduced amino acid sequences of both genes were identical to each other and to other plant ubiquitin sequences. Several putative regulatory elements such as enhancer core and heat shock consensus sequences were found in the 5'-upstream regions of both genes. Northern blot analyses using the 3'-untranslated region as gene specific probes showed that both genes were actively expressed in all rice plant tissues tested. Differential expression was observed in roots where RUBQ2 appeared to be predominantly expressed. Chimeric genes containing the 5'-upstream region including the intron of RUBQ1 or RUBQ2 and the beta-glucuronidase (GUS) coding region were constructed and transferred into rice suspension cells via particle bombardment. GUS activity from constructs containing RUBQ1 and RUBQ2 promoters in rice suspension cells was ten to 15-fold greater than those using the Cauliflower Mosaic Virus 35S (CaMV 35S) promoter, and two to threefold greater than constructs with the maize polyubiquitin Ubi1 promoter. The results demonstrate the potential usefulness of the two rice polyubiquitin promoters in rice or other monocot transformation systems.

Characterization and expression of a heptaubiquitin gene from tomato

Ubiquitin is highly conserved 76 amino acid protein involved, among other functions, in the selective degradation of proteins in the cell. From a tomato (Lycopersicon esculentum Mill. cv. Craigella) genomic library, we have isolated a clone encoding a polyubiquitin gene, designated ubq1-1 comprising seven repeats of ubiquitin and two C-terminal extension amino acids. The ubq1-1 gene contains an intron of 1128bp immediately upstream of the translation start codon. DNA sequence comparison revealed that the 5' and 3' non-coding regions of the tomato ubq1-1 gene are nearly identical to the sequence of a polyubiquitin cDNA clone isolated from potato (Garbarino et al., 1992; Plant Mol. Biol. 20, 235-244). The ubq1-1 gene is expressed in leaves to rather low levels in tomato, and the abundance of ubq1-1 transcripts is increased under heat shock conditions. For functional analyses, a chimeric gene construct containing the intron and 1.6kb of ubq1-1 sequence 5' to the intron fused to the gus reporter gene was introduced into the tobacco genome. In leaves of transgenic tobacco plants, reporter gene expression was generally lower from the ubq1-1 promoter than from the cauliflower mosaic virus 35S RNA promoter. In addition, the tomato ubq1-1 promoter was not found to respond to heat shock in transgenic tobacco plants. Histochemical analysis of the plants demonstrated localization of gus reporter gene activity in the vascular systems of the leaves and the roots. Deletion of the intron from the reporter gene construct markedly reduced reporter gene expression in transformed tobacco plants, thus suggesting that the intron may influence transcript levels deriving from the ubq1-1 promoter.

Induction of HSP70 and polyubiquitin expression associated with plant virus replication

By examining the front of virus invasion in immature pea embryos infected with pea seed-borne mosaic virus (PSbMV), the selective control of different host genes has been observed. From our observations, the early responses to PSbMV replication can be grouped into three classes, inhibited host gene expression, induced host gene expression, and no effect on a normal host function. The expression of two heat-inducible genes encoding HSP70 and polyubiquitin was induced coordinately with the onset of virus replication and the down-regulation of two other genes encoding lipoxygenase and heat shock cognate protein. The down-regulation was part of a general suppression of host gene expression that may be achieved through the degradation of host transcripts. We discuss the possibilities of whether the induction of HSP70 and polyubiquitin genes represents a requirement for the respective protein products by the virus or is merely a consequence of the depletion of other host transcripts. The former is feasible, as the induction of both genes does result in increased HSP70 and ubiquitin accumulation. This also indicates that, in contrast to some animal virus infections, there is not a general inhibition of translation of host mRNAs following PSbMV infection. This selective control of host gene expression was observed in all cell types of the embryo and identifies mechanisms of cellular disruption that could act as triggers for symptom expression.

Proteolysis in plants: mechanisms and functions

Proteolysis is essential for many aspects of plant physiology and development. It is responsible for cellular housekeeping and the stress response by removing abnormal/misfolded proteins, for supplying amino acids needed to make new proteins, for assisting in the maturation of zymogens and peptide hormones by limited cleavages, for controlling metabolism, homeosis, and development by reducing the abundance of key enzymes and regulatory proteins, and for the programmed cell death of specific plant organs or cells. It also has potential biotechnological ramifications in attempts to improve crop plants by modifying protein levels. Accumulating evidence indicates that protein degradation in plants is a complex process involving a multitude of proteolytic pathways with each cellular compartment likely to have one or more. Many of these have homologous pathways in bacteria and animals. Examples include the chloroplast ClpAP protease, vacuolar cathepsins, the KEX2-like proteases of the secretory system, and the ubiquitin/26S proteasome system in the nucleus and cytoplasm. The ubiquitin-dependent pathway requires that proteins targeted for degradation become conjugated with chains of multiple ubiquitins; these chains then serve as recognition signals for selective degradation by the 26S proteasome, a 1.5 MDa multisubunit protease complex. The ubiquitin pathway is particularly important for developmental regulation by selectively removing various cell-cycle effectors, transcription factors, and cell receptors such as phytochrome A. From insights into this and other proteolytic pathways, the use of phosphorylation/dephosphorylation and/or the addition of amino acid tags to selectively mark proteins for degradation have become recurring themes.

The cDNA for the ubiquitin-52-amino-acid fusion protein from rat encodes a previously unidentified 60 S ribosomal subunit protein

Rat cDNAs for a 52-amino-acid ribosomal protein (CEP52) that is typically formed as a ubiquitin fusion protein, were cloned following reverse transcription and PCR amplification. CEP52 sequence conservation is demonstrated by the similarity of the human and rat cDNA sequences and the identity of the predicted proteins. Amplification of rat cDNA with a primer specific for the 3' non-coding region of the CEP52 gene, in combination with a consensus primer for the 5' end of the ubiquitin coding sequence, provided evidence that the rat CEP52 gene is fused to a ubiquitin reading frame. Direct sequence analysis of this PCR product confirmed the in-frame fusion of a ubiquitin coding sequence to the rat CEP52 gene. Antibodies against a synthetic CEP52 peptide were used to show that expressed CEP52 is associated with the 60 S ribosomal subunit, and that is is not linked to ubiquitin. The quantity of CEP52 found in different tissues is quite variable, but appears to correspond to the amount of ribosomes present. Although the human, Arabidopsis thaliana and Nicotiana tabacum CEP52 genes contain introns within the CEP52 coding region, the rat CEP52 coding sequence appears to lack insertions.

Accumulation of cytosolic glyceraldehyde-3-phosphate dehydrogenase RNA under biological stress conditions and elicitor treatments in potato

Plants respond to pathogen infection and environmental stress by regulating the coordinate expression of many stress-related genes. In plants, the expression of the glycolytic enzyme glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is induced under environmental stress. This work was aimed at investigating whither the expression pattern of cytosolic GAPDH is also modulated upon infection of potato plants (Solanum tuberosum L.) with the late blight fungal agent Phytophthora infestans. Northern blot analysis showed the accumulation of the GAPDH gene transcripts in leaves and stems of inoculated potato plants. When tuber discs were treated with eicosapentaenoic acid (EPA), an elicitor found in P. infestans, GAPDH gene transcripts level increased. The increase was parallel to that of the hydroxymethyl glutharyl coenzyme A reductase (HMGR), an enzyme involved in pathogen defense reactions. Glucans obtained from P. infestans cell wall acts synergistically with EPA on GAPDH and HMGR gene induction. Salicylic acid, an endogenous signal for inducing systemic acquired resistance, was also effective in stimulating the GAPDH transcript accumulation in potato leaves. These experiments suggest that related multi-component factors, which are part of both primary and secondary metabolism, are probably regulated by similar signal transduction pathways when they are induced under biotic or abiotic stress conditions.

Characterization, chromosomal mapping, and expression of different ubiquitin fusion protein genes in tissues from control and heat-shocked maize seedlings

Organisms possess at least two multigene families of ubiquitins: the polyubiquitins, with few to several repeat units, which encode a ubiquitin monomer, and the ubiquitin fusion (or extension) protein genes, which encode a single ubiquitin monomer and a specific protein. This report provides details about two ubiquitin fusion protein genes in maize referred to as MubG7 (uwo 1) and MubG10 (uwo 2). Each has one nearly identical ubiquitin coding unit fused without an intervening nucleotide to an unrelated, 237-nucleotide sequence that encodes for a 79 amino acid protein. The derived amino acid sequences of the two fusion proteins show that they differ by five amino acids (substitution by either a serine or threonine). MubG7 maps to chromosome 8L162 and MubG10 maps to chromosome 1L131. Analyses of the role(s) of these genes in response to heat shock (1 h at 42.5 degrees C) reveal that the level of these fusion protein mRNAs in the radicles or plumules from 2-day-old seedlings does not change; however, heat shock does cause a marked reduction in the accumulation of these same gene-specific mRNAs in the radicles and plumules of 5-day-old seedlings. These data confirm the suggestion from our earlier work that there is precise modulation, in a gene-specific manner, of the response to developmental as well as environmental signals.

A novel wound-inducible extensin gene is expressed early in newly isolated protoplasts of Nicotiana sylvestris

A cDNA clone (6PExt 1.2) encoding a novel extensin was isolated from a cDNA library made from 6 h old mesophyll protoplasts of Nicotiana sylvestris. The screening was performed with a heterologous probe from carrot. The encoded polypeptide showed features characteristic of hydroxyproline-rich glycoproteins such as Ser-(Pro)4 repeats and a high content in Tyr and Lys residues. The presence of four Tyr-X-Tyr-Lys motifs suggests the possibility for intramolecular isodityrosine cross-links whereas three Val-Tyr-Lys motifs may participate in intermolecular cross-links. The analysis of genomic DNA gel blots using both the N. sylvestris and the carrot clones as probes showed that the 6PExt 1.2 gene belongs to a complex multigene family encoding extensin and extensin-related polypeptides in N. sylvestris as well as in related Nicotianeae including a laboratory hybrid. This was confirmed by the analysis of RNA gel blots: a set of mRNAs ranging in size from 0.3 kb to 3.5 kb was found by the carrot extensin probe. The 6PExt 1.2 probe found a 1.2 kb mRNA in protoplasts and in wounded tissues as well as a 0.9 kb mRNA which seemed to be stem-specific. The gene encoding 6PExt 1.2 was induced by wounding in protoplasts, in leaf strips and after Agrobacterium tumefaciens infection of stems.

Expression of Agrobacterium rhizogenes auxin biosynthesis genes in transgenic tobacco plants

Plant oncogenes aux1 and aux2 carried by the TR-DNA of Agrobacterium rhizogenes strain A4 encode two enzymes involved in the auxin biosynthesis pathway in transformed plant cells. The short divergent promoter region between the two aux-coding sequences contains the main regulatory elements. This region was fused to the uidA reporter gene and introduced into Nicotiana tabacum in order to investigate the regulation and the tissue specificity of these genes. Neither wound nor hormone induction could be detected on transgenic leaf discs. However, phytohormone concentration and auxin/cytokinin balance controlled the expression of the chimaeric genes in transgenic protoplasts. The expression was localised in apical meristems, root tip meristems, lateral root primordia, in cells derived from transgenic protoplasts and in transgenic calli. Histological analysis showed that the expression was located in cells reactivated by in vitro culture. Experiments using cell-cycle inhibitors such as hydroxyurea or aphidicolin on transgenic protoplast cultures highly decreased the beta-glucuronidase activity of the chimaeric genes. These results as well as the histological approach suggest a correlation between expression of the aux1 and aux2 genes and cell division.

Non-systemic expression of a stress-responsive maize polyubiquitin gene (Ubi-1) in transgenic rice plants

We have used the promoter, 1st exon and 1st intron of the maize polyubiquitin gene (Ubi-1) for rice transformation experiments and revealed the characteristic expression of Ubi-1 gene: (1) Ubi-1 gene is not regulated systemically but rather individual cells respond independently to the heat or physical stress; (2) Ubi-1 gene changes its tissue-specific expression in response to stress treatment; (3) the expression of Ubi-1 gene is dependent on cell cycle.

Structure and promoter activity of a stress and developmentally regulated polyubiquitin-encoding gene of Nicotiana tabacum

A polyubiquitin-encoding gene was identified from a Nicotiana tabacum genomic library using a specific probe spanning the 3' untranslated region of the corresponding cDNA. The gene, Ubi.U4, is expressed in various amounts in the whole plant, except in just-fully-expanded leaves. Genomic blots indicate that it originates from N. tomentosiformis. Sequence analyses reveal that the gene consists of four ubiquitin monomers extended by a fifth truncated subunit. It is disrupted by a single 457-bp intron in close proximity to the start codon of translation. Primer extension experiments localized the transcription start point (tsp). Transient gene expression in N. tabacum protoplasts indicates that the deletion of the intron has no significant influence on gene expression. Mutagenesis on putative cis-regulatory elements indicates at least three important motifs in the proximal promoter: an 'ACGT' core element, an A + T-rich sequence and a less clearly defined cis-element located between bp -162 and -113.

Differential expression of several E2-type ubiquitin carrier protein genes at different developmental stages in Arabidopsis thaliana and Nicotiana sylvestris

We characterized three genes encoding different E2-type ubiquitin carrier proteins involved in the ubiquitin-mediated proteolytic pathway: UbcAt3 shows homologies to the yeast CDC34 gene and Ub-cAt4a and UbcAt4b are two different genes homologous to the Ubc1/4/5 subfamily in yeast. Their accumulation was analysed and compared with that of the different families encoding polyubiquitins, as well as the monoubiquitin fusion protein, which is considered as a marker for cell division, during various developmental stages including G0/S transition and senescence of higher plant cells. Our results imply that these Ubc genes are under the control of complex mechanisms, and are differentially regulated, but not necessarily co-regulated with ubiquitin genes. Even the closely related UbcAt4a and UbcAt4b genes of the same multigene subfamily are controlled by distinct regulatory mechanisms.

Activity of a maize ubiquitin promoter in transgenic rice

We have used the maize ubiquitin 1 promoter, first exon and first intron (UBI) for rice (Oryza sativa L. cv. Taipei 309) transformation experiments and studied its expression in transgenic calli and plants. UBI directed significantly higher levels of transient gene expression than other promoter/intron combinations used for rice transformation. We exploited these high levels of expression to identify stable transformants obtained from callus-derived protoplasts co-transfected with two chimeric genes. The genes consisted of UBI fused to the coding regions of the uidA and bar marker genes (UBI:GUS and UBI:BAR). UBI:GUS expression increased in response to thermal stress in both transfected protoplasts and transgenic rice calli. Histochemical localization of GUS activity revealed that UBI was most active in rapidly dividing cells. This promoter is expressed in many, but not all, rice tissues and undergoes important changes in activity during the development of transgenic rice plants.

Why are quiescent mesophyll protoplasts from Nicotiana sylvestris able to re-enter into the cell cycle and re-initiate a mitotic activity?

Mesophyll protoplasts of Nicotiana sylvestris incubated in an adequate culture medium re-enter very rapidly into the cell cycle and divide. The transition G0/G1 is accompanied by a complete reversion of the program of gene expression. The program of the photosynthetic differentiated mesophyll cell is abolished whereas a new multipartite program of a highly stressed but ready-to-divide cell is established. Some genes encode proteins which structure suggests they may play key roles in these events. Most of the induced genes are under multiple controls: stress and/or development. Stress response and cellular re-organization might thus be closely related events that cannot be dissociated. It is probable that the re-entry of a protoplast into the cell cycle, ie the initial step of totipotency, closely depends on the coordinated activation of a set of genes that share common regulatory mechanisms.