Crop seed oil bodies: From challenges in protein identification to an emerging picture of the oil body proteome

Oleaginous seeds store lipids in specialized structures called oil bodies (OBs). These organelles consist of a core of neutral lipids bound by proteins embedded in a phospholipid monolayer. OB proteins are well conserved in plants and have long been grouped into only two categories: structural proteins or enzymes. Recent work, however, which identified other classes of proteins associated with OBs, clearly shows that this classification is obsolete. Proteomics‐mediated OB protein identification is facilitated in plants for which the genome is sequenced and annotated. However, it is not clear whether this knowledge can be dependably transposed to less well‐characterized plants, including the well‐established commercial sources of seed oil as well as the many others being proposed as novel sources for biodiesel, especially in Africa and Asia. Toward an update of the current data available on OB proteins this review discusses (i) the specific difficulties for proteomic studies of organelles; (ii) a 2012 census of the proteins found in seed OBs from various crops; (iii) the oleosin composition of OBs and their role in organelle stability; (iv) PTM of OB proteins as an emerging field of investigation; and finally we describe the emerging model of the OB proteome from oilseed crops.     

In vitro culture of Lambdina fiscellaria lugubrosa nucleopolyhedrovirus in heterologous cell lines

Infections of two heterologous insect cell lines derived from Malacosoma disstria (Md108) and Choristoneura fumiferana (Cf70) by the Lambdina fiscellaria lugubrosa nucleopolyhedrovirus (LafiNPV-W) were characterized. Cytopathic effects characteristic of LafiNPV-W infection, including rounding of cells, nuclear hypertrophy, and occlusion body (OB) production, were observed in both cell lines. Budded virus titers were slightly higher in Md108 cells than Cf70 cells (5.8?×?10⁷ versus 3.1?×?10⁷ TCID₅₀ units mL^?1). Viral replication kinetics and cytopathic effects induced by LafiNPV-W infection were very similar in both cell lines. Actin rearrangements and redistribution of heterochromatin and euchromatin were observed within 24 h post-inoculation (hpi), and large quantities of nucleocapsids and virions were observed by electron microscopy at 48 hpi in both cell lines. Cf70 cultures produced OBs with numerous embedded virions, while OBs in Md108 cultures contained few virions or were empty with nucleocapsids packed in the nucleoplasm between OBs. In bioassays against second instar L. fiscellaria lugubrosa, OBs derived from LafiNPV-W-infected Md108 cells induced significantly lower levels of mortality than OBs derived from LafiNPV-W-infected Cf70 cells or from infected L. fiscellaria fiscellaria larvae.     

Cool-textured diets for use in baculovirus production

The incorporation of baculovirus into semi-synthetic diets has been used for the inoculation of large batches of insect larvae reared under gregarious conditions. The preparation of most artificial diets involves heating to dissolve the agar gelling agent followed by cooling to ～55–60°C whereupon virus occlusion bodies (OBs) are incorporated into the diet. To avoid exposure of thermolabile OBs to high temperatures, a cool-textured diet using soy fiber was evaluated as a simple method to inoculate batches of larvae with the baculovirus OBs. Spodoptera exigua larvae that fed on a diet with 120, 140 or 160?g/l of soy fiber, as a substitute for agar, had a similar weight gain over a 24?h period than larvae that consumed a standard agar diet. The larval weight gain with cool-textured diets with 140?g/l of soy fiber was not improved by the addition of chlorophyll, green food dye colour, or by the removal of ascorbic acid, sodium benzoate and potassium sorbate. Preliminary tests performed to determine the optimal OBs concentration needed for the inoculation of groups of four instar larvae in agar and soy fiber diets revealed no virus inactivation in heated diets with a similar optimal concentration of 36?OBs?mg^?1 for both diets. Moreover, no significant differences were observed in OB production when each type of diet was used to inoculate groups of 250 larvae reared gregariously in plastic containers. Cool-textured diets could be of interest for the production of baculoviruses that require a diet that can be prepared quickly and easily.     

The lipidome and proteome of microsomes from the methylotrophic yeast Pichia pastoris

The methylotrophic yeast Pichia pastoris is a popular yeast expression system for the production of heterologous proteins in biotechnology. Interestingly, cell organelles which play an important role in this process have so far been insufficiently investigated. For this reason, we started a systematic approach to isolate and characterize organelles from P. pastoris. In this study, we present a procedure to isolate microsomal membranes at high purity. These samples represent endoplasmic reticulum (ER) fractions which were subjected to molecular analysis of lipids and proteins. Organelle lipidomics included a detailed analysis of glycerophospholipids, fatty acids, sterols and sphingolipids. The microsomal proteome analyzed by mass spectrometry identified typical proteins of the ER known from other cell types, especially Saccharomyces cerevisiae, but also a number of unassigned gene products. The lipidome and proteome analysis of P. pastoris microsomes are prerequisite for a better understanding of functions of this organelle and for modifying this compartment for biotechnological applications.     

In-depth proteome analysis of the rubber particle of Hevea brasiliensis (para rubber tree)

The rubber particle is a special organelle in which natural rubber is synthesised and stored in the laticifers of Hevea brasiliensis. To better understand the biological functions of rubber particles and to identify the candidate rubber biosynthesis-related proteins, a comprehensive proteome analysis was performed on H. brasiliensis rubber particles using shotgun tandem mass spectrometry profiling approaches—resulting in a thorough report on the rubber particle proteins. A total of 186 rubber particle proteins were identified, with a range in relative molecular mass of 3.9–194.2 kDa and in isoelectric point values of 4.0–11.2. The rubber particle proteins were analysed for gene ontology and could be categorised into eight major groups according to their functions: including rubber biosynthesis, stress- or defence-related responses, protein processing and folding, signal transduction and cellular transport. In addition to well-known rubber biosynthesis-related proteins such as rubber elongation factor (REF), small rubber particle protein (SRPP) and cis-prenyl transferase (CPT), many proteins were firstly identified to be on the rubber particles, including cyclophilin, phospholipase D, cytochrome P450, small GTP-binding protein, clathrin, eukaryotic translation initiation factor, annexin, ABC transporter, translationally controlled tumour protein, ubiquitin-conjugating enzymes, and several homologues of REF, SRPP and CPT. A procedure of multiple reaction monitoring was established for further protein validation. This comprehensive proteome data of rubber particles would facilitate investigation into molecular mechanisms of biogenesis, self-homeostasis and rubber biosynthesis of the rubber particle, and might serve as valuable biomarkers in molecular breeding studies of H. brasiliensis and other alternative rubber-producing species.     

生物质谱与蛋白质组学

蛋白质组学是后基因组学时代最受关注的研究领域之一,其核心的鉴定技术——生物质谱近年来在仪器设计以及鉴定通量、分辨率和灵敏度等各方面均有质的飞跃,促进了蛋白质表达谱作图、定量蛋白质组分析、亚细胞器蛋白质组作图、蛋白质翻译后修饰以及蛋白质相互作用等蛋白质组研究各个领域的飞速发展。本综述了生物质谱技术的最新进展,及其在蛋白质组学研究中的应用。     

A novel informatics concept for high-throughput shotgun lipidomics based on the molecular fragmentation query language

Shotgun lipidome profiling relies on direct mass spectrometric analysis of total lipid extracts from cells, tissues or organisms and is a powerful tool to elucidate the molecular composition of lipidomes. We present a novel informatics concept of the molecular fragmentation query language implemented within the LipidXplorer open source software kit that supports accurate quantification of individual species of any ionizable lipid class in shotgun spectra acquired on any mass spectrometry platform.     

Pilot-scale supercritical carbon dioxide extractions for the recovery of triacylglycerols from microalgae: a practical tool for algal biofuels research

We describe the preliminary extractions from a pilot-scale supercritical carbon dioxide (SC-CO₂) extractor for the isolation of algal lipids suitable for small-scale conversion to liquid hydrocarbon fuels. Flowable oils were recovered from SC-CO₂ extractions of lyophilized Nannochloropsis granulata. The extracted oils were determined to be composed primarily of triacylglycerols (TAG) by liquid chromatography–mass spectrometry analysis. Gravimetric lipid yield was increased significantly from 15.56 to 28.45 mg g^?1 ash-free dry weight (AFDW) with an increase in temperature from 50°C to 70°C, at 35 MPa over 270 min. Varying pressure had no significant effect on lipid yield. Liquid chromatography–mass spectrometry analysis of the SC-SO₂ extracts indicated that the TAG profile remained constant regardless of extraction pressure, and analysis of fatty acid methyl esters (FAME) revealed a uniform profile throughout all extraction conditions. Our optimized gravimetric lipid yields from N. granulata (28.45 mg g^?1 AFDW) were approximately half of the yields obtained by Soxhlet extraction with hexane (57.53 mg g^?1 AFDW); however, the FAME yields were similar regardless of extraction technique (18.23 mg FAME g^?1 and 17.35 mg FAME g^?1 AFDW from SC-CO₂ extraction and hexane extraction, respectively). Further extractions with Botryococcus braunii indicated that fatty acid extraction by SC-CO₂ was as efficient as hexane extraction. These results highlight the suitability of SC-CO₂ for large-scale oil extraction of microalgae for biofuel or biojet analyses due to its selectivity for TAG extraction.     

Deletion Genotypes Reduce Occlusion Body Potency but Increase Occlusion Body Production in a Colombian Spodoptera frugiperda Nucleopolyhedrovirus Population

A Colombian field isolate (SfCOL-wt) of Spodoptera frugiperda multiple nucleopolyhedrovirus (SfMNPV) is a mixture of different genotypes. To evaluate the insecticidal properties of the different genotypic variants, 83 plaque purified virus were characterized. Ten distinct genotypes were identified (named A through J). SfCOL-A was the most prevalent (71±2%; mean ± SE) showing a PstI restriction profile indistinguishable to that of SfCOL-wt. The remaining nine genotypes presented genomic deletions of 3.8 - 21.8 Kb located mainly between nucleotides 11,436 and 33,883 in the reference genome SfMNPV-B, affecting the region between open reading frames (ORFs) sf20 and sf33. The insecticidal activity of each genotype from SfCOL-wt and several mixtures of genotypes was compared to that of SfCOL-wt. The potency of SfCOL-A occlusion bodies (OBs) was 4.4-fold higher than SfCOL-wt OBs, whereas the speed of kill of SfCOL-A was similar to that of SfCOL-wt. Deletion genotype OBs were similarly or less potent than SfCOL-wt but six deletion genotypes were faster killing than SfCOL-wt. The potency of genotype mixtures co-occluded within OBs were consistently reduced in two-genotype mixtures involving equal proportions of SfCOL-A and one of three deletion genotypes (SfCOL-C, -D or -F). Speed of kill and OB production were improved only when the certain genotype mixtures were co-occluded, although OB production was higher in the SfCOL-wt isolate than in any of the component genotypes, or mixtures thereof. Deleted genotypes reduced OB potency but increased OB production of the SfCOL-wt population, which is structured to maximize the production of OBs in each infected host.     

Insecticidal properties and microbial contaminants in a Spodoptera exigua multiple nucleopolyhedrovirus (Baculoviridae) formulation stored at different temperatures

The Spodoptera exigua (Hübner) multiple nucleopolyhedrovirus (SeMNPV) is currently being tested as a biological insecticide for use in greenhouse crops in southern Spain. We performed a study in which semipurified SeMNPV occlusion bodies (OBs) were formulated in phosphate-buffered saline, pH 6.5, with 5% (vol:vol) glycerol and 0.15% (wt:vol) sorbic acid, and they were stored at -20, 4, or 25 degrees C during 18 mo. Initial aerobic counts (+/-SE) averaged 1.4 (+/-0.17) x 10(7) colony-forming units/ml after 17-h incubation at 37 degrees C. Aerobic counts of microorganisms that contaminated OB formulations stored at 250C decreased markedly over the period of the study, whereas only small decreases were observed in counts from OBs stored at 4 or -20 degrees C. The principal microbial contaminants of OB suspensions were Enterococcus spp., Enterobacteriaceae, and yeasts. Potential human pathogens (Salmonella, Shigella, and Vibrio species) were not detected, and populations of Staphylococcus aureus and Bacillus cereus were extremely low. Compared with newly formulated OBs, the estimated LD50 values of OBs stored at 25 degrees C increased by >16,666-fold over the 18 mo of storage, whereas LD50 values were not greatly affected by storage at 4 or -20 degrees C. Significant changes over time in OB concentrations were only observed in the 25 degrees C treatment. Complete degradation of viral DNA was observed at 25 degrees C but not in refrigerated or frozen OBs. We conclude that OB formulation with bacteriostatic or antioxidant additives, together with storage and distribution in refrigerated conditions, will likely result in an SeMNPV biopesticide shelf life that exceeds 18 mo.     

Solubilization and Identification of Hen Eggshell Membrane Proteins During Different Times of Chicken Embryo Development Using the Proteomic Approach

A fertilized chicken egg is a unit of life. During hatching, transport of nutrients, including calcium, have been reported from the egg components to the developing embryo. Calcium is mobilized from the eggshell with the involvement of Ca²⁺-binding proteins. In addition, other unknown proteins may also play some important roles during embryo developing process. Therefore identification and prediction of biological functions of eggshell membrane (ESM) proteins during chick embryo development was conducted by proteome analysis. Comparison of different lysis solutions indicated that the highest ability to extract ESM proteins could be obtained with 1 % sodium dodecyl sulfate in 5 mM Tris–HCl buffer pH 8.8 containing 0.1 % 2-mercaptoethanol. In this study fertilized Cornish chicken eggs were incubated at 37 °C in humidified incubators for up to 21 days. At selected times (days 1, 9, 15 and 21), samples were taken and the ESMs were carefully separated by hand, washed with distilled water, and air-dried at room temperature. The ESM proteins were then solubilized and analyzed by proteome analysis. Sodium dodecyl sulfate polyacrylamide gel electrophoresis combined with high performance liquid chromatography and mass spectrometry revealed 62 proteins in the ESM; only keratin is known ESM protein, 8 of which are egg white proteins and related while 53 others have not previously been reported. Some differences in the types of proteins and their molecular functions were noted in ESM at different incubation times. One protein which was present only at days 15 and 21 of egg incubation was identified as a calcium binding protein i.e. EGF like repeats and discoidin I like domain 3 (EDIL3 homologous protein).     

Linear fusigen as the major hydroxamate siderophore of the ectomycorrhizal Basidiomycota Laccaria laccata and Laccaria bicolor

A screening for siderophores produced by the ectomycorrhizal fungi Laccaria laccata and Laccaria bicolor in synthetic low iron medium revealed the release of several different hydroxamate siderophores of which four major siderophores could be identified by high resolution mass spectrometry. While ferricrocin, coprogen and triacetylfusarinine C were assigned as well as other known fungal siderophores, a major peak of the siderophore mixture revealed an average molecular mass of 797 for the iron-loaded compound. High resolution mass spectrometry indicated an absolute mass of m/z = 798.30973 ([M + H]⁺). With a relative error of Δ = 0.56 ppm this corresponds to linear fusigen (C₃₃H₅₂N₆O₁₃Fe; MW = 797.3). The production of large amounts of linear fusigen by these basidiomycetous mycorrhizal fungi may possibly explain the observed suppression of plant pathogenic Fusarium species. For comparative purposes Fusarium roseum was included in this study as a well known producer of cyclic and linear fusigen.     

A Chrysodeixis chalcites Single-Nucleocapsid Nucleopolyhedrovirus Population from the Canary Islands Is Genotypically Structured To Maximize Survival

A Chrysodeixis chalcites single-nucleocapsid nucleopolyhedrovirus wild-type isolate from the Canary Islands, Spain, named ChchSNPV-TF1 (ChchTF1-wt), appears to have great potential as the basis for a biological insecticide for control of the pest. An improved understanding of the genotypic structure of this wild-type strain population should facilitate the selection of genotypes for inclusion in a bioinsecticidal product. Eight genetically distinct genotypes were cloned in vitro: ChchTF1-A to ChchTF1-H. Quantitative real-time PCR (qPCR) analysis confirmed that ChchTF1-A accounted for 36% of the genotypes in the wild-type population. In bioassays, ChchTF1-wt occlusion bodies (OBs) were significantly more pathogenic than any of the component single-genotype OBs, indicating that genotype interactions were likely responsible for the pathogenicity phenotype of wild-type OBs. However, the wild-type population was slower killing and produced higher OB yields than any of the single genotypes alone. These results strongly suggested that the ChchTF1-wt population is structured to maximize its transmission efficiency. Experimental OB mixtures and cooccluded genotype mixtures containing the most abundant and the rarest genotypes, at frequencies similar to those at which they were isolated, revealed a mutualistic interaction that restored the pathogenicity of OBs. In OB and cooccluded mixtures containing only the most abundant genotypes, ChchTF1-ABC, OB pathogenicity was even greater than that of wild-type OBs. The ChchTF1-ABC cooccluded mixture killed larvae 33 h faster than the wild-type population and remained genotypically and biologically stable throughout five successive passages in vivo. In conclusion, the ChchTF1-ABC mixture shows great potential as the active ingredient of a bioinsecticide to control C. chalcites in the Canary Islands.     

Proteomics of Secretory and Endocytic Organelles in Giardia lamblia

Giardia lamblia is a flagellated protozoan enteroparasite transmitted as an environmentally resistant cyst. Trophozoites attach to the small intestine of vertebrate hosts and proliferate by binary fission. They access nutrients directly via uptake of bulk fluid phase material into specialized endocytic organelles termed peripheral vesicles (PVs), mainly on the exposed dorsal side. When trophozoites reach the G2/M restriction point in the cell cycle they can begin another round of cell division or encyst if they encounter specific environmental cues. They induce neogenesis of Golgi-like organelles, encystation-specific vesicles (ESVs), for regulated secretion of cyst wall material. PVs and ESVs are highly simplified and thus evolutionary diverged endocytic and exocytic organelle systems with key roles in proliferation and transmission to a new host, respectively. Both organelle systems physically and functionally intersect at the endoplasmic reticulum (ER) which has catabolic as well as anabolic functions. However, the unusually high degree of sequence divergence in Giardia rapidly exhausts phylogenomic strategies to identify and characterize the molecular underpinnings of these streamlined organelles. To define the first proteome of ESVs and PVs we used a novel strategy combining flow cytometry-based organelle sorting with in silico filtration of mass spectrometry data. From the limited size datasets we retrieved many hypothetical but also known organelle-specific factors. In contrast to PVs, ESVs appear to maintain a strong physical and functional link to the ER including recruitment of ribosomes to organelle membranes. Overall the data provide further evidence for the formation of a cyst extracellular matrix with minimal complexity. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium with the dataset identifier PXD000694.     

Effects of high-fat diet and age on the blood lipidome and circulating endocannabinoids of female C57BL/6 mice

Alterations in lipid metabolism play a significant role in the pathogenesis of obesity-associated disorders, and dysregulation of the lipidome across multiple diseases has prompted research to identify novel lipids indicative of disease progression. To address the significant gap in knowledge regarding the effect of age and diet on the blood lipidome, we used shotgun lipidomics with electrospray ionization-mass spectrometry (ESI-MS). We analyzed blood lipid profiles of female C57BL/6 mice following high-fat diet (HFD) and low-fat diet (LFD) consumption for short (6 weeks), long (22 weeks), and prolonged (36 weeks) periods. We examined endocannabinoid levels, plasma esterase activity, liver homeostasis, and indices of glucose tolerance and insulin sensitivity to compare lipid alterations with metabolic dysregulation. Multivariate analysis indicated differences in dietary blood lipid profiles with the most notable differences after 6 weeks along with robust alterations due to age. HFD altered phospholipids, fatty acyls, and glycerolipids. Endocannabinoid levels were affected in an age-dependent manner, while HFD increased plasma esterase activity at all time points, with the most pronounced effect at 6 weeks. HFD-consumption also altered liver mRNA levels of PPARα, PPARγ, and CD36. These findings indicate an interaction between dietary fat consumption and aging with widespread effects on the lipidome, which may provide a basis for identification of female-specific obesity- and age-related lipid biomarkers.     

A simultaneous extraction method for metabolome and lipidome and its application in cry1Ac and sck-transgenic rice leaf treated with insecticide based on LC–MS analysis

Abiotic stress caused by insecticide treatment is an interesting and challenging topic in plant research. Here a simultaneous extraction method with methyl tert-butyl ether for metabolomics and lipidomics analysis by using rapid resolution liquid chromatography quadrupole time-of-flight mass spectrometry was developed and validated. The extraction efficiency of lipidome and metabolome based on the current developed method showed an obvious improvement compared with literatures. About 300 metabolites were identified in rice leaf. Method validation was performed and analytical properties including the linearity (R², 0.991–1.000), repeatability (over 87 % peaks with CV < 20 % accounting for over 92 % of total response) and recovery (74.4–119.6 %) were satisfactory. The method was then applied to investigate time-course changes caused by insecticide treatment in transgenic rice with cry1Ac and sck genes and its wild counterpart. Antioxidants including ferulic acid and sinapic acid were down-regulated at 24 h after insecticide treatment. Signaling metabolites including salicylic acid and nicotinamide adenine dinucleotide were significantly up-regulated at 12–24 h after treatment in transgenic rice. More flavonoids were significantly changed in transgenic plants. Results indicated that gene transformation affected the metabolic response of rice to insecticide stress.     

A proteomic analysis to identify cold acclimation associated proteins in wild wheat (Triticum urartu L.)

To gain a better understanding of cold acclimation process in wheat, we applied a 2-DE based proteomic approach to discover changes in proteome profile of a diploid wild wheat (Triticum urartu L.) during prolonged cold stress treatment. To this end, plants were grown in pots and the growing seedlings (4-leaf stage) were exposed to cold stress. After 4 weeks of cold acclimation (4–6 °C) and subsequent treatment for 12 h at ?2 °C, samples were collected from control and stressed plants and were subjected to proteome pattern analysis. Among approximately 450 reproducible protein spots displayed in each given 2-DE gels, 34 proteins changed significantly in abundance in response to cold stress. Among them, 25 and 9 proteins were up and down-regulated under stress condition, respectively. Analysis by matrix-assisted laser desorption ionization time of flight/time of flight mass spectrometry coupled with non-redundant protein database search allowed the identification of 20 cold-induced proteins. Integrated proteomic and database survey resulted in identification of several cold stress related proteins such as pathogenesis related protein, cold regulated protein, cold-responsive LEA/RAB-related COR protein, oxygen-evolving enhancer protein and oxalate oxidase. The presumed functions of the identified proteins were mostly related to cold acclimation, oxidative stress and photosynthesis. The possible implications of differentially accumulated proteins in acquiring systemic tolerance to freezing stress following exposure to prolonged low temperature will be discussed.     

Variability of low-molecular-weight serum subproteome in healthy humans under the conditions of normal vital activity

To study interindividual variability of the low-molecular-weight serum subproteome in healthy humans, the proteome profiles of blood sera were studied in subjects divided into three age groups: from 20 to 30 years (36 subjects), from 30 to 40 years (11 subjects), and from 40 to 50 years (11 subjects). Serum samples were fractionated by MB WCX magnetic beads using a ClintProt robot prior to the mass spectrometry based profiling. The mass spectra have been obtained using an Autoflex III time-of-flight mass spectrometer (Bruker Daltonics) in the automated mode. The low-molecular-weight serum subproteome in healthy humans was found to be characterized by significant interindividual variability: 21% of all the peaks in the proteome profiles had a coefficient of variation of more than 50%, and 29% of all the peaks had a low variance (CV < 30%). Therefore, the majority of the peaks in the proteome profile had a moderate group variation (the CV was in the interval from 30 to 50%). Fragments of high-molecular-weight kininogen, inter-α-trypsin inhibitor, C3 and C4a complement components, CI apolipoprotein, platelet factor IV, β2-microglobulin, and C cystatin were shown to display a wide variation among the tested groups of healthy humans. The peak area variance of high-molecular-weight kininogen, inter-α-trypsin inhibitor, AII and CIII apolipoproteins increased with age.