Silvia Mazzuca

Establishing research strategies, methodologies and technologies to link genomics and proteomics to seagrass productivity, community metabolism, and ecosystem carbon fluxes

A complete understanding of the mechanistic basis of marine ecosystem functioning is only possible through integrative and interdisciplinary research. This enables the prediction of change and possibly the mitigation of the consequences of anthropogenic impacts. One major aim of the European Cooperation in Science and Technology (COST) Action ES0609 “Seagrasses productivity. From genes to ecosystem management,” is the calibration and synthesis of various methods and the development of innovative techniques and protocols for studying seagrass ecosystems. During 10 days, 20 researchers representing a range of disciplines (molecular biology, physiology, botany, ecology, oceanography, and underwater acoustics) gathered at The Station de Recherches Sous-marines et Océanographiques (STARESO, Corsica) to study together the nearby Posidonia oceanica meadow. STARESO is located in an oligotrophic area classified as “pristine site” where environmental disturbances caused by anthropogenic pressure are exceptionally low. The healthy P. oceanica meadow, which grows in front of the research station, colonizes the sea bottom from the surface to 37 m depth. During the study, genomic and proteomic approaches were integrated with ecophysiological and physical approaches with the aim of understanding changes in seagrass productivity and metabolism at different depths and along daily cycles. In this paper we report details on the approaches utilized and we forecast the potential of the data that will come from this synergistic approach not only for P. oceanica but for seagrasses in general.

Acclimation to different depths by the marine angiosperm Posidonia oceanica: transcriptomic and proteomic profiles

For seagrasses, seasonal and daily variations in light and temperature represent the mains factors driving their distribution along the bathymetric cline. Changes in these environmental factors, due to climatic and anthropogenic effects, can compromise their survival. In a framework of conservation and restoration, it becomes crucial to improve our knowledge about the physiological plasticity of seagrass species along environmental gradients. Here, we aimed to identify differences in transcriptomic and proteomic profiles, involved in the acclimation along the depth gradient in the seagrass Posidonia oceanica, and to improve the available molecular resources in this species, which is an important requisite for the application of eco-genomic approaches. To do that, from plant growing in shallow (−5 m) and deep (−25 m) portions of a single meadow, (i) we generated two reciprocal Expressed Sequences Tags (EST) libraries using a Suppressive Subtractive Hybridization (SSH) approach, to obtain depth/specific transcriptional profiles, and (ii) we identified proteins differentially expressed, using the highly innovative USIS mass spectrometry methodology, coupled with 1D-SDS electrophoresis and labeling free approach. Mass spectra were searched in the open source Global Proteome Machine (GPM) engine against plant databases and with the X!Tandem algorithm against a local database. Transcriptional analysis showed both quantitative and qualitative differences between depths. EST libraries had only the 3% of transcripts in common. A total of 315 peptides belonging to 64 proteins were identified by mass spectrometry. ATP synthase subunits were among the most abundant proteins in both conditions. Both approaches identified genes and proteins in pathways related to energy metabolism, transport and genetic information processing, that appear to be the most involved in depth acclimation in P. oceanica. Their putative rules in acclimation to depth were discussed.

Oleuropein-Specific-β-Glucosidase Activity Marks the Early Response of Olive Fruits (Olea europaea) to Mimed Insect Attack

Olive fruits are seriously deteriorated by pre and postharvest damage due to the attack of insects, such as Bactrocera olaea, which strongly alters the quality of olives. Defence response in olive fruits injured both by pathogens and by mechanical damages has been associated with the enzyme β-glucosidase, which specifically hydrolyses oleuropein, producing highly reactive aldehyde molecules. In situ detection of β-glucosidase activity in olive fruit tissues following injury, which simulates Bactrocera oleae punctures, is reported. The assay was performed in two cultivars showing different degrees of susceptibilities to fly infestation. In both cultivars, the histochemical assay for β-glucosidase showed that within 20 min after the injury, a strong β-glucosidase activity could be observed in the damaged tissues. Thereafter a progressive enzyme inactivation occurred starting from tissues around the boundary of the injury with decrease of the enzyme activity and stopped after 3 h. Whereas the mass of active cells reached a distance of (300 ± 50) μm from the edge of the injury. Biochemical analyses showed that in extracts of the injured fruit, β-glucosidase activity rapidly increased within 20 min from injury, thereafter decreasing and reaching values comparable with those in intact fruits. Following puncture, the oleuropein contents did not change significantly in the high susceptibility cultivar, whereas it rapidly decreased in the cultivar showing low susceptibility. The results strongly suggest that olive fruits susceptible towards fly infestation could be related to the ability of the oleuropein-degrading-β-glucosidase to produce the highly reactive molecules in the damaged tissues. As a consequence of puncture, high level of peroxidase activity was detected. This feature also suggested that this enzyme could play a key role in the defence response against insect injuries.

Proteome from Lemon Fruit Flavedo Reveals That This Tissue Produces High Amounts of the Cit s1 Germin-like Isoforms

A multistep procedure has been developed and applied to extract and purify proteins from lemon fruit flavedo. 2DE, LC-ESI-MS/MS, and bioinformatics were used to detect the high abundance of the germin-like glycoprotein Cit s1, a powerful allergen in humans. Peptide alignments against Citrus EST repositories gave the best scores with the C. sinensis cDNA (gi|188354270/EY710037), annotated as unknown sweet orange fruit protein; additional BLAST of peptides against NCBI databases gave high sequence identities with sequence of orange Cit s1 (gi|52782810/P84159), suggesting that the unknown sweet orange fruit protein is consistent with the Cit s1 protein. Peptides of Cit s1 were detected in 17 spots ranging from 120 to 20 kDa, pointing out that in the flavedo of lemon the Cit s1 may be expressed as several isoforms of which the 120 kDa isoform is the largest monomer and the 20 kDa is the smallest one. This finding adds information about the features of Cit s1, because it has been previously reported as a unique monomeric glycoprotein of 24 kDa.

Depth-specific fluctuations of gene expression and protein abundance modulate the photophysiology in the seagrass Posidonia oceanica

Here we present the results of a multiple organizational level analysis conceived to identify acclimative/adaptive strategies exhibited by the seagrass Posidonia oceanica to the daily fluctuations in the light environment, at contrasting depths. We assessed changes in photophysiological parameters, leaf respiration, pigments, and protein and mRNA expression levels. The results show that the diel oscillations of P. oceanica photophysiological and respiratory responses were related to transcripts and proteins expression of the genes involved in those processes and that there was a response asynchrony between shallow and deep plants probably caused by the strong differences in the light environment. The photochemical pathway of energy use was more effective in shallow plants due to higher light availability, but these plants needed more investment in photoprotection and photorepair, requiring higher translation and protein synthesis than deep plants. The genetic differentiation between deep and shallow stands suggests the existence of locally adapted genotypes to contrasting light environments. The depth-specific diel rhythms of photosynthetic and respiratory processes, from molecular to physiological levels, must be considered in the management and conservation of these key coastal ecosystems.

The modulation of leaf metabolism plays a role in salt tolerance of Cymodocea nodosa exposed to hypersaline stress in mesocosms

Applying proteomics, we tested the physiological responses of the euryhaline seagrass Cymodocea nodosa to deliberate manipulation of salinity in a mesocosm system. Plants were subjected to a chronic hypersaline condition (43 psu) to compare protein expression and plant photochemistry responses after 15 and 30 days of exposure with those of plants cultured under normal/ambient saline conditions (37 psu). Results showed a general decline in the expression level of leaf proteins in hypersaline stressed plants, with more intense reductions after long-lasting exposure. Specifically, the carbon-fixing enzyme RuBisCo displayed a lower accumulation level in stressed plants relative to controls. In contrast, the key enzymes involved in the regulation of glycolysis, cytosolic glyceraldehyde-3-phosphate dehydrogenase, enolase 2 and triose-phosphate isomerase, showed significantly higher accumulation levels. These responses suggested a shift in carbon metabolism in stressed plants. Hypersaline stress also induced a significant alteration of the photosynthetic physiology of C. nodosa by means of a down-regulation in structural proteins and enzymes of both PSII and PSI. However we found an over-expression of the cytochrome b559 alpha subunit of the PSII initial complex, which is a receptor for the PSII core proteins involved in biogenesis or repair processes and therefore potentially involved in the absence of effects at the photochemical level of stressed plants. As expected hypersalinity also affects vacuolar metabolism by increasing the leaf cell turgor pressure and enhancing the up-take of Na+ by over-accumulating the tonoplast specific intrinsic protein pyrophosphate-energized inorganic pyrophosphatase (H(+)-PPase) coupled to the Na+/H+-antiporter. The modulation of carbon metabolism and the enhancement of vacuole capacity in Na+ sequestration and osmolarity changes are discussed in relation to salt tolerance of C. nodosa.

2-DE polypeptide mapping of Posidonia oceanica leaves, a molecular tool for marine environment studies

Abstract The aim of this research is to provide a molecular tool based on polypeptide mapping to investigate the flowering marine plant Posidonia oceanica. This plant is very vulnerable to contaminants; thus it is considered a valuable bio-indicator of water quality in bio-monitoring of coastal environments. Posidonia oceanica was found to be recalcitrant to the common protein extraction methods. In the present work, three different extraction procedures were compared to obtain high yield and quality protein extracts suitable for mono-dimensional and bi-dimensional electrophoresis (1-DE and 2-DE). Proteins were extracted from juvenile, intermediate and adult leaves in order to assess the influence of tissue differentiation on protein yield. The highest protein yield was obtained with 20% trichloroacetic acid (TCA) precipitation of proteins. The best extraction efficiency was found in juvenile leaves as compared with intermediate and adult ones. However, as a large amount of juvenile leaves is required for obtaining sufficiently large protein samples, these were considered not suitable for the electrophoretic analysis. Extensive sampling could introduce further damage in the meadows under study. High quality 2-DE polypeptide mappings were obtained only from intermediate and adult leaves; the good reproducibility of protein patterns indicates that this approach could be used to explore changes in protein expression of P. oceanica in response to altered environmental conditions.

Magnetic field affects meristem activity and cell differentiation in Zea mays roots

Abstract Exposure of Zea mays seedlings to a continuous electromagnetic field (EMF) for 30 h induced a 30% stimulation in the rate of root elongation compared with the controls. It also resulted in a significant increase of cell expansion, in both the acropetal (metaxylem cell lineage) and basipetal (root cap cells) direction. In addition, in EMF-exposed roots a precocious structural disorder was observed both in differentiating metaxylem cells and root cap cells. All these features may be consistent with an advanced differentiation of root cells that are programmed to die. EMF treatment also resulted in a significant reduction in the size of the quiescent centre in the root apical meristem. The extent to which these responses are causally linked is discussed.

The Citrus clementina Putative Allergens: From Proteomic Analysis to Structural Features

Several allergens have been identified and characterized in the genus Citrus, which belongs to the germin-like proteins (GPLs), profilins, and non-specific lipid transfer proteins (nsLTPs). In this work, in silico sequence analysis, protein purification, mass spectrometry identification, and the spectral counting method were integrated to identify new putative allergens of Citrus clementina and their expression level in the fruit peel. The in silico analysis revealed fifteen new sequences belonging to GLPs (Cit cl 1), and two more belonging to nsLTPs (Cit cl 3). No other new sequences were found as regards profilins (Cit cl 2). Each putative allergen from fruit peel was obtained using different protein extraction methods, and the protein sequences of the putative allergens were identified by means of LTQ-Orbitrap XL mass spectrometer. The spectral counting strategy revealed that Cit cl 1 had a higher expression level than Cit cl 2 and Cit cl 3. To predict the quaternary structure and deduced function of Cit cl 1, its primary sequence was used as a template to search a homologous protein structure in the RCSB PDB Database, getting high correspondence with the oxalate oxidase protein in barley.

Purification of intact chloroplasts from marine plant Posidonia oceanica suitable for organelle proteomics

Posidonia oceanica is a marine angiosperm, or seagrass, adapted to grow to the underwater life from shallow waters to 50 m depth. This raises questions of how their photosynthesis adapted to the attenuation of light through the water column and leads to the assumption that biochemistry and metabolism of the chloroplast are the basis of adaptive capacity. In the present study, we described a protocol that was adapted from those optimized for terrestrial plants, to extract chloroplasts from as minimal tissue as possible. We obtained the best balance between tissue amount/intact chloroplasts yield using one leaf from one plant. After isopynic separations, the chloroplasts purity and integrity were evaluated by biochemical assay and using a proteomic approach. Chloroplast proteins were extracted from highly purified organelles and resolved by 1DE SDS‐PAGE. Proteins were sequenced by nLC‐ESI‐IT‐MS/MS of 1DE gel bands and identified against NCBInr green plant databases, Dr. Zompo database for seagrasses in a local customized dataset. The curated localization of proteins in sub‐plastidial compartments (i.e. envelope, stroma and thylakoids) was retrieved in the AT_CHLORO database. This purification protocol and the validation of compartment markers may serve as basis for sub‐cellular proteomics in P. oceanica and other seagrasses.