A histochemical and ultrastructural study of yucca seed proteins

Embryos and nutritive tissues in ungerminated Yucca seeds of 4 species contain many spherical bodies which stain positively for proteins. Two distinct morphological types were observed at both the light and electron microscope levels. A meshwork-type consists of electron-dense and electron-transparent regions in which are embedded slightly birefringent inclusions. The second type, named the core-type, consists of a core surrounded by a matrix in which the inclusions are embedded. A single unit membrane surrounds each protein body. Both types are present in the embryo while only the core-type protein body appears in the surrounding nutritive tissue (perisperm). All regions in each of the two protein body types, except the inclusions, stain histochemically for proteins. Seeds were planted at 2-day intervals and allowed to germinate through 14 days. As germination commences (day 0) protein bodies in the embryo begin to break down. By day 4 the bodies are depleted in embryos of 3 of the 4 species. About day 4, protein bodies in perisperm surrounding the embryo begin to break down and this process continues outward to the seed coat until day 14 when all seed proteins have disappeared. During germination the protein bodies in the embryo and perisperm of 3 species coalesce and then undergo breakdown. In a fourth species, there is no appreciable increase in size of the bodies, but an erosion of the periphery and possibly internally as well takes place, followed by ultimate dissolution.     

Biochemical and Morphological Changes in Protein Bodies during Germination of Lentil Seeds

Alvarez, J. and Guerra, H. 1985. Biochemical and morphologicalchanges in protein bodies during germination of lentil seeds.—J.exp. BoL 36: 1296–1303. Protein bodies were extracted from lentil (Lens culinaris Medilk,var. castellana) seeds. Proteins from the protein bodies weredegraded during the first 7 d of germination. In some casesthis mobilization of proteins was accompanied by fusion of theprotein bodies into a large central vacuole. The loss of proteinswas paralleled by an increase in the activity of an enzyme systemthat hydrolysed casein. The different kinds of protein bodiesexhibited structural differences; some displayed uniform material,others coagulated or semi-coagulated material and the thirdkind displayed inclusions. Key words: Lentil, protein bodies, seed germination     

Carbonylated proteins accumulated as vitality decreases during long-term storage of beech (Fagus sylvatica L.) seeds

Key message

Carbonylation of proteins associated with a stress response may contribute to the lowered viability of naturally aged beech seeds, especially the desiccation tolerance-associated proteins and USP-like protein.

Abstract

Proteins are modified by a large number of reactions that involve reactive oxygen species-mediated oxidation. The direct oxidation of amino acids produces 2,4-dinitrophenylhydrazine-detectable protein products. Carbonylation is irreversible, and carbonylated proteins are marked for proteolysis or can escape degradation and form high molecular weight aggregates, which accumulate with age. Beech (Fagus sylvatica L.) seeds stored under optimal conditions for different periods of time, ranging from 2 to 13 years, were analyzed. Protein carbonylation was examined as a potential cause for the loss of viability of beech seeds, and the characteristic spots of protein carbonyls were identified. Here, we present and discuss the role of carbonylation in the proteome of beech seeds that contribute to the loss of seed viability during natural aging. The long-term storage of beech seeds is intricate because their germination capacity decreases with age and is negatively correlated with the level of protein carbonyls that accumulate in the seeds. We establish that protein synthesis, folding and degradation are the most affected biochemical traits in long-term stored beech seeds. In addition, we suggest that proteins associated with the stress response may have contributed to the lowered viability of beech seeds, especially the desiccation tolerance-associated proteins that include T-complex protein 1 and the universal stress protein (USP)-like protein, which is identified as carbonylated for first time here.     

New protein isoforms identified within Arabidopsis thaliana seed oil bodies combining chymotrypsin/trypsin digestion and peptide fragmentation analysis

Plant seed oil bodies, subcellular lipoprotein inclusions providing storage reserves, are composed of a neutral lipid core surrounded by a phospholipid monolayer with several integrated proteins that play a significant role in stabilization of the particles and probably also in lipid mobilization. Oil bodies' proteins are generally very hydrophobic, due to the long uncharged sequences anchoring them into the lipid core, which makes them extremely difficult to handle and to digest successfully. Although oil bodies have been intensively studied during last decades, not all their proteins have been identified yet. To overcome the problems connected with their identification, a method based on SDS-PAGE, in-gel digestion and LC-MS/MS analysis was used. Digestion was carried out with trypsin and chymotrypsin, single or in combination, which increased significantly the number of identified peptides, namely the hydrophobic ones. Thanks to this methodology it was possible to achieve an extensive coverage of proteins studied, to analyze their N-terminal modifications and moreover, to detect four new oil bodies' protein isoforms, which demonstrates the complexity of oil bodies' protein composition.     

The reserve proteins in the cells of mature cotyledons ofLupinus albus var.Lucky. I. Quantitative ultrastructural study of the protein bodies

Summary A quantitative ultrastructural study of the protein bodies of the lupin cotyledonary cells was performed to determine the protein content per cell. Two kinds of protein body were observed by transmission and scanning electron microscopy whatever the cellular type within the cotyledon. Some of these were conventional spherical structures, entirely filled with a dense protein matrix, others exhibited one large or several small light inclusions within the dense matrix. Even when a few light areas contained globoids, the majority remained of unknown nature, but could not be considered proteinaceous since they never reacted with specific protein dyes. The reserve protein content per cell was determined by image analysis on two seeds (L₁ and L₂) selected because they had a markedly different total protein content. The volume occupied by the dense matrix of the intracellular protein bodies was considered representative of the reserve protein quantity. The protein content per cell increased from the periphery to the centre of the cotyledon in the two seeds studied. The protein content per cell of the L₂ seed was generally found to be greater than the L₁ seed, in particular in the abaxial zone where it was markedly higher. The difference in total protein content of the two seeds was demonstrated to be primarily due to a differential alveolation of the protein bodies. These results will be used to study the relationship between the protein content of the cotyledonary cells and their nuclear DNA content.     

棉花种子萌发过程中子叶蛋白体变化

对棉花种子萌发过程中子叶细胞内蛋白体的变化进行了详细的观察。干种子内存在仅由蛋白质基质组成无内含物的蛋白体,含有球状晶体的蛋白体和无含球状晶体和拟晶体的蛋白体。种子萌发过程中蛋白体逐渐液泡化,其降解方式可分为三种类型：（１）内部降解类型：（２）周边降解类型;（３）内部和周边同时降解类型。文中还一步进行了不同降解类型与酶的分布,蛋白体存在部位和萌发时间进程之间的关系。     

Interactions between lectins and other components of leguminous protein bodies

Previous work from this laboratory had shown that Leguminosa seed extracts contain lectin-bound proteins. In the present paper, the isolation of protein bodies from the seeds of 7 Leguminosa species (Canavalia ensiformis, Lens culinaris, Pisum sativum, Glycine max, Sophora japonica, Wisteria floribunda and Phaseolus vulgaris) is described. Protein bodies were characterized microscopically and by their constituents, storage proteins, lectins and some glycosidases. From the protein bodies, lectin-bound proteins were isolated and were shown to be identical with those from whole seed extracts. This indicates a common localization of lectin-bound proteins and of lectins. Lectin-bound proteins belong to the storage proteins and to the proteins with glycosidase activity. The common localization of these proteins and interactions between them suggest a biological role of seed lectins: during maturation they may act as a packaging aid for storage proteins and enzymes into developing protein bodies. Lectins thus may contribute to an ordered construction and degradation of protein bodies.     

Eukaryotic lipid body proteins in oleogenous actinomycetes and their targeting to intracellular triacylglycerol inclusions: Impact on models of lipid body biogenesis

Bacterial neutral lipid inclusions are structurally related to eukaryotic lipid bodies. These lipid inclusions are composed of a matrix of triacylglycerols (TAGs) or wax esters surrounded by a monolayer of phospholipids. Whereas the monolayers of lipid bodies from animal and plant cells harbor specific classes of proteins which are involved in the structure of the inclusions and lipid homoestasis, no such proteins are known to be associated with bacterial lipid inclusions. The present study was undertaken to reveal whether the mammalian lipid body proteins perilipin A, adipose differentiation-related protein, and tail-interacting protein of 47 kDa (TIP47), which comprise the so called PAT family proteins, and the maize (Zea mays L.) oleosin are targeted to prokaryotic TAG bodies in vivo. When fused to enhanced green fluorescent protein, all proteins except the oleosin were mainly located at the surfaces of lipid inclusions when heterologously expressed in the recombinant actinomycetes Rhodococcus opacus PD630 and Mycobacterium smegmatis mc(2)155. A more detailed intracellular distribution analysis of TIP47 in recombinant R. opacus cells by immunocytochemical labeling of ultrathin cryosections and freeze fracture replicas revealed a substantial amount of TIP47 protein also pervading the cores of the inclusions. We discuss the impact of these results on the current model of lipid body biogenesis in prokaryotes.     

Protein bodies of seeds: Ultrastructure,biochemistry, biosynthesis and degradation

Typical organelles for protein storage occur in seeds, protein bodies are found in haploid, diploid or triploid tissues and are single membrane bound. In some plants, they exhibit inclusions (globoid and crystalloid), but not in Gramineae endosperm or in Leguminosae cotyledons. A relationship between species and protein body ultrastructure can be put forward. The chemical composition is based mainly on storage proteins and phytic acid but, hydrolytic enzymes(protease and phytase), cations and ribonucleic acids are also present. Other minor biochemical components include oxalic acid, carbohydrates (excluding starch) and lipids. The locations of the storage proteins, enzymes and phytin are described. Protein body ontogeny during seed maturation has given rise to much controversy: are they plastidic or vacuolar? Recent studies on the location of proteosynthesis show that protein bodies are probably synthesized in endoplasmic reticulum lumen and that the Golgi apparatus plays an important role in storage protein synthesis. During germination protein bodies swell and fuse, giving rise to the cell central vacuole, while the integrity of the membrane is maintained. Protein bodies may be considered as being an example of tonoplast origin from endo-plasmic reticulum.     

Ontogeny, Structure and Breakdown of Protein Bodies in Linum usitatissimum Linn.

In Linum usitatissimum protein bodies are observed in the cellsof endosperm and embryo. They originate in vacuoles. Proteinbodies have both crystalloid and globoid inclusions. The breakdownoccurs by vacuolization and fragmentation. Linum usitatissimum, seed, embryo, endosperm, protein bodies     

Chaperone proteins identified from synthetic proteasome inhibitor-induced inclusions in PC12 cells by proteomic analysis

Chaperone proteins are significant in Lewy bodies, but the profile of chaperone proteins is incompletely unraveled. Proteomic analysis is used to determine protein candidates for further study. Here, to identify potential chaperone proteins from agent-induced inclusions, we carried out proteomic analysis of artificially synthetic proteasome inhibitor (PSI)-induced inclusions formed in PC12 cells exposed to 10 μM PSI for 48 h. Using biochemical fractionation, 2-D electrophoresis, and identification through peptide mass fingerprints searched against multiple protein databases, we repeatedly identified eight reproducible chaperone proteins from the PSI-induced inclusions. Of these, 58 kDa glucose regulated protein, 75 kDa glucose regulated protein, and calcium-binding protein 1 were newly identified. The other five had been reported to be consistent components of Lewy bodies. These findings suggested that the three potential chaperone proteins might be recruited to PSI-induced inclusions in PC12 cells under proteasome inhibition.     

Ubiquitination of alpha-synuclein and autophagy in Parkinson's disease

alpha-Synuclein is mutated in Parkinson's disease (PD) and is found in cytosolic inclusions, called Lewy bodies, in sporadic forms of the disease. A fraction of alpha-synuclein purified from Lewy bodies is monoubiquitinated, but the role of this monoubiquitination has been obscure. We now review recent data indicating a role of alpha-synuclein monoubiquitination in Lewy body formation and implicating the autophagic pathway in regulating these processes. The E3 ubiquitin-ligase SIAH is present in Lewy bodies and monoubiquitinates alpha-synuclein at the same lysines that are monoubiquitinated in Lewy bodies. Monoubiquitination by SIAH promotes the aggregation of alpha-synuclein into amorphous aggregates and increases the formation of inclusions within dopaminergic cells. Such effect is observed even at low monoubiquitination levels, suggesting that monoubiquitinated alpha-synuclein may work as a seed for aggregation. Accumulation of monoubiquitinated alpha-synuclein and formation of cytosolic inclusions is promoted by autophagy inhibition and to a lesser extent by proteasomal and lysosomal inhibition. Monoubiquitinated alpha-synuclein inclusions are toxic to cells and recruit PD-related proteins, such as synphilin-1 and UCH-L1. Altogether, the new data indicate that monoubiquitination might play an important role in Lewy body formation. Decreasing alpha- synuclein monoubiquitination, by preventing SIAH function or by stimulating autophagy, constitutes a new therapeutic strategy for Parkinson's disease.     

Seed Nutrient Reserves of Proteaceae with Special Reference to Protein Bodies and their Inclusions

The storage reserves of seeds of a wide taxonomic range of Proteaceaewere examined by chemical analyses for macronutrients, proteinand non-protein-N composition, by light microscopy of cotyledonarytissue for morphological and histochemical study of proteinbodies and their inclusions, and by X-ray point microanalysisfor determining the elemental composition of the various typesof inclusions. The 70 species from 30 genera showed higher levelsof N, P and Mg but not of Ca and K in seed dry matter in comparisonwith a similarly sized sample of non-proteaceous species. Small-seededProteaceae tended to have seed dry matter significantly moreenriched with minerals than large-seeded species. Protein levelsranged from 18 to 89 per cent of embryo dry weight (mean for32 species 39.5 per cent). Protein and ethanol soluble N fractionsof many species were exceptionally rich in arginine. Oil wasabundant in most species, starch universally absent. Seven typesof protein body inclusions were identified on the basis of size,shape and reaction to toluidine blue. Mineral composition ofthe inclusions differed significantly, particularly in ratiosof Ca to P and of P to S and Mg. All genera and certain speciescould be distinguished one from another on the basis of distributionand frequency of inclusion types within tissues of the cotyledonsand staining patterns of protein bodies to amido black. Thetaxonomic significance of the data is evaluated. Seed reserves, Proteaceae, protein bodies, protein body inclusions, mineral composition, taxonomy     

The UPS and autophagy in chronic neurodegenerative disease: Six of one and half a dozen of the other—Or not?

In the past twenty years, evidence has accumulated to show that ubiquitinated proteins are a consistent feature of the intraneuronal protein aggregates (inclusions) that characterize chronic neurodegenerative disease. These findings may indicate that age-related dysfunction of the 26S proteasome may be central to disease pathogenesis. The aggregate-prone proteins can also be eliminated by autophagy. We have used the Cre-recombinase/loxP genetic approach to ablate the proteasomal psmc1 ATPase gene and deplete 26S proteasomes in neurons in different regions of the brain to mimic neurodegeneration. Deletion of the gene in dopaminergic neurons in the substantia nigra generates a new model of Parkinson’s disease. Ablation of the gene in the forebrain creates the first model of dementia with Lewy bodies. In both neuroanatomical regions, gene ablation causes the formation of Lewy-like inclusions together with extensive neurodegeneration. There is some evidence for neuronal autophagy in areas adjacent to inclusions. The models indicate that neuronal loss in neurodegenerative diseases can be attributed to proteasomal malfunction accompanied by Lewy-like inclusions as seen in dementia with Lewy bodies and Parkinson’s disease.     

Ubiquitin conjugation triggers misfolded protein sequestration into quality control foci when Hsp70 chaperone levels are limiting

Ubiquitin accumulation in amyloid plaques is a pathological marker observed in the vast majority of neurodegenerative diseases, yet ubiquitin function in these inclusions is controversial. It has been suggested that ubiquitylated proteins are directed to inclusion bodies under stress conditions, when both chaperone-mediated refolding and proteasomal degradation are compromised or overwhelmed. Alternatively, ubiquitin and chaperones may be recruited to preformed inclusions to promote their elimination. We address this issue using a yeast model system, based on expression of several mildly misfolded degradation substrates in cells with altered chaperone content. We find that the heat shock protein 70 (Hsp70) chaperone pair Ssa1/Ssa2 and the Hsp40 cochaperone Sis1 are essential for degradation. Substrate ubiquitylation is strictly dependent on Sis1, whereas Ssa1 and Ssa2 are dispensable. Remarkably, in Ssa1/Ssa2-depleted cells, ubiquitylated substrates are sequestered into detergent-insoluble, Hsp42-positive inclusion bodies. Unexpectedly, sequestration is abolished by preventing substrate ubiquitylation. We conclude that Hsp40 is required for the targeting of misfolded proteins to the ubiquitylation machinery, whereas the decision to degrade or sequester ubiquitylated proteins is mediated by the Hsp70s. Accordingly, diminished Hsp70 levels, as observed in aging or certain pathological conditions, might be sufficient to trigger ubiquitin-dependent sequestration of partially misfolded proteins into inclusion bodies.     

TorsinA and heat shock proteins act as molecular chaperones: suppression of alpha-synuclein aggregation

TorsinA, a protein with homology to yeast heat shock protein104, has previously been demonstrated to colocalize with alpha-synuclein in Lewy bodies, the pathological hallmark of Parkinson's disease. Heat shock proteins are a family of chaperones that are both constitutively expressed and induced by stressors, and that serve essential functions for protein refolding and/or degradation. Here, we demonstrate that, like torsinA, specific molecular chaperone heat shock proteins colocalize with alpha-synuclein in Lewy bodies. In addition, using a cellular model of alpha-synuclein aggregation, we demonstrate that torsinA and specific heat shock protein molecular chaperones colocalize with alpha-synuclein immunopositive inclusions. Further, overexpression of torsinA and specific heat shock proteins suppress alpha-synuclein aggregation in this cellular model, whereas mutant torsinA has no effect. These data suggest that torsinA has chaperone-like activity and that the disease-associated GAG deletion mutant has a loss-of-function phenotype. Moreover, these data support a role for chaperone proteins, including torsinA and heat shock proteins, in cellular responses to neurodegenerative inclusions.     

Parkin ubiquitinates the alpha-synuclein-interacting protein, synphilin-1: implications for Lewy-body formation in Parkinson disease

Parkinson disease is a common neurodegenerative disorder characterized by the loss of dopaminergic neurons and the presence of intracytoplasmic-ubiquitinated inclusions (Lewy bodies). Mutations in alpha-synuclein (A53T, A30P) and parkin cause familial Parkinson disease. Both these proteins are found in Lewy bodies. The absence of Lewy bodies in patients with parkin mutations suggests that parkin might be required for the formation of Lewy bodies. Here we show that parkin interacts with and ubiquitinates the alpha-synuclein-interacting protein, synphilin-1. Co-expression of alpha-synuclein, synphilin-1 and parkin result in the formation of Lewy-body-like ubiquitin-positive cytosolic inclusions. We further show that familial-linked mutations in parkin disrupt the ubiquitination of synphilin-1 and the formation of the ubiquitin-positive inclusions. These results provide a molecular basis for the ubiquitination of Lewy-body-associated proteins and link parkin and alpha-synuclein in a common pathogenic mechanism through their interaction with synphilin-1.     

Assembly and transport of seed storage proteins

Plant seeds store nitrogen by accumulating storage proteins in protein bodies within various compartments of the endomembrane system. The prolamin storage proteins of some cereal species are normally retained and assembled into protein bodies within the ER. Yet, these proteins lack a C-terminal KDEL/HDEL signal, suggesting that their retention is regulated by novel mechanisms. Furthermore, in other cereal species, such protein bodies formed within the ER may be subsequently internalized into vacuoles by a special route that does not utilize the Golgi complex. Thus, studies of the routing of seed storage proteins are revealing novel mechanisms of protein assembly and transport in the endomembrane system.     

Deletion of the fiber gene induces the storage of hexon and penton base proteins in PML/Sp100-containing inclusions during adenovirus infection

The present study has documented changes in the in situ distribution of viral DNA and capsid proteins in 293 cells infected with fiber gene-deleted adenoviruses. It shows that infection results in the intense production of progeny viruses which appear morphologically intact although they are devoid of fiber-coding sequence in their genome and hence of fiber protein in their capsid. The data confirm, therefore, that fiber protein is not essential for the assembly of progeny viruses. The main contribution of our observations concerns specific intranuclear structures induced by infection with either wild-type or fiber gene-deleted viruses. These clear amorphous inclusions contain two cellular proteins, PML and Sp100, which in non-infected cells co-localize to a special type of nuclear bodies. PML and Sp100 nuclear bodies appear to directly modulate or to be altered in a wide variety of situations including viral infections, cell death and transformation. In cells infected with fiber gene-deleted viruses, the clear amorphous inclusions now accumulate non-used hexon and penton base proteins, whereas the absence of fiber protein prevents the assembly of capsid proteins in crystallin arrays. Taken together, the data suggest that the clear amorphous inclusions may correspond to storage sites of structural and regulatory proteins. Consequently, these virus-induced structures may promote the productive cycle of adenoviruses by regulating the amount of over-produced viral proteins and the shutoff of the host cell metabolism.