Poplar woody root proteome during the transition dormancy-active growth

Woody plants living in temperate climates finely regulate their growth and development in relation to seasonal changes; their transition from vegetative to dormancy phase represents an adaptation to their environment. Events occurring in the shoot during onset/release from dormancy have been largely investigated, whereas in woody roots they remain completely unknown. In recent years, we have been interested in understanding the molecular and physiological events occurring in poplar woody root during release from dormancy. Here, we propose the results of a comparative analysis of the proteome of poplar woody root sampled at different time points: T0 (dormancy condition), T1 (release from dormancy), and T2 (full vegetative condition). This study identified proteins that may be involved in the long-term survival of a dormant root or landmarking a specific time point

Proteomic analysis of apricot fruit during ripening

Ripening of climacteric fruits involves a complex network of biochemical and metabolic changes that make them palatable and rich in nutritional and health-beneficial compounds. Since fruit maturation has a profound impact on human nutrition, it has been recently the object of increasing research activity by holistic approaches, especially on model species. Here we report on the original proteomic characterization of ripening in apricot, a widely cultivated species of temperate zones appreciated for its taste and aromas, whose cultivation is yet hampered by specific limitations. Fruits of Prunus armeniaca cv. Vesuviana were harvested at three ripening stages and proteins extracted and resolved by 1D and 2D electrophoresis. Whole lanes from 1D gels were subjected to shot-gun analysis that identified 245 gene products, showing preliminary qualitative differences between maturation stages. In parallel, differential analysis of 2D proteomic maps highlighted 106 spots as differentially represented among variably ripen fruits. Most of these were further identified by means of MALDI-TOF-PMF and nanoLC–ESI–LIT–MS/MS as enzymes involved in main biochemical processes influencing metabolic/structural changes occurring during maturation, i.e. organic acids, carbohydrates and energy metabolism, ethylene biosynthesis, cell wall restructuring and stress response, or as protein species linkable to peculiar fruit organoleptic characteristics. In addition to originally present preliminary information on the main biochemical changes that characterize apricot ripening, this study also provides indications for future marker-assisted selection breeding programs aimed to ameliorate fruit quality

Impairment of enzymatic antioxidant defenses is associated with bilirubin-induced neuronal cell death in the cerebellum of Ugt1 KO mice

Severe hyperbilirubinemia is toxic during central nervous system development. Prolonged and uncontrolled high levels of unconjugated bilirubin lead to bilirubin-induced encephalopathy and eventually death by kernicterus. Despite extensive studies, the molecular and cellular mechanisms of bilirubin toxicity are still poorly defined. To fill this gap, we investigated the molecular processes underlying neuronal injury in a mouse model of severe neonatal jaundice, which develops hyperbilirubinemia as a consequence of a null mutation in the Ugt1 gene. These mutant mice show cerebellar abnormalities and hypoplasia, neuronal cell death and die shortly after birth because of bilirubin neurotoxicity. To identify protein changes associated with bilirubin-induced cell death, we performed proteomic analysis of cerebella from Ugt1 mutant and wild-type mice. Proteomic data pointed-out to oxidoreductase activities or antioxidant processes as important intracellular mechanisms altered during bilirubin-induced neurotoxicity. In particular, they revealed that down-representation of DJ-1, superoxide dismutase, peroxiredoxins 2 and 6 was associated with hyperbilirubinemia in the cerebellum of mutant mice. Interestingly, the reduction in protein levels seems to result from post-translational mechanisms because we did not detect significant quantitative differences in the corresponding mRNAs. We also observed an increase in neuro-specific enolase 2 both in the cerebellum and in the serum of mutant mice, supporting its potential use as a biomarker of bilirubin-induced neurological damage. In conclusion, our data show that different protective mechanisms fail to contrast oxidative burst in bilirubin-affected brain regions, ultimately leading to neurodegeneration. \ua9 2015 Macmillan Publishers Limited All rights reserved

A genomic, transcriptomic and proteomic look at the GE2270 producer Planobispora rosea, an uncommon actinomycete

We report the genome sequence of Planobispora rosea ATCC 53733, a mycelium-forming soil-dweller belonging to one of the lesser studied genera of Actinobacteria and producing the thiopeptide GE2270. The P. rosea genome presents considerable convergence in gene organization and function with other members in the family Streptosporangiaceae, with a significant number (44%) of shared orthologs. Patterns of gene expression in P. rosea cultures during exponential and stationary phase have been analyzed using whole transcriptome shotgun sequencing and by proteome analysis. Among the differentially abundant proteins, those involved in protein metabolism are particularly represented, including the GE2270-insensitive EF-Tu. Two proteins from the pbt cluster, directing GE2270 biosynthesis, slightly increase their abundance values over time. While GE2270 production starts during the exponential phase, most pbt genes, as analyzed by qRT-PCR, are down-regulated. The exception is represented by pbtA, encoding the precursor peptide of the ribosomally synthesized GE2270, whose expression reached the highest level at the entry into stationary phase. Copyright

Characterisation of Bombyx mori odorant-binding proteins reveals that a general odorant-binding protein discriminates between sex pheromone components

In many insect species, odorant-binding proteins (OBPs) are thought to be responsible for the transport of pheromones and other semiochemicals across the sensillum lymph to the olfactory receptors (ORs) within the antennal sensilla. In the silkworm Bombyx mori, the OBPs are subdivided into three main subfamilies; pheromone-binding proteins (PBPs), general odorant-binding proteins (GOBPs) and antennal-binding proteins (ABPs). We used the MotifSearch algorithm to search for genes encoding putative OBPs in B. mori and found 13, many fewer than are found in the genomes of fruit flies and mosquitoes. The 13 genes include seven new ABP-like OBPs as well as the previously identified PBPs (three), GOBPs (two) and ABPx. Quantitative examination of transcript levels showed that BmorPBP1, BmorGOBP1, BmorGOBP2 and BmorABPx are expressed at very high levels in the antennae and so could be involved in olfaction. A new two-phase binding assay, along with other established assays, showed that BmorPBP1, BmorPBP2, BmorGOBP2 and BmorABPx all bind to the B. mori sex pheromone component (10E,12Z)-hexadecadien-1-ol (bombykol). BmorPBP1, BmorPBP2 and BmorABPx also bind the pheromone component (10E,12Z)-hexadecadienal (bombykal) equally well, whereas BmorGOBP2 can discriminate between bombykol and bombykal. X-ray structures show that when bombykol is bound to BmorGOBP2 it adopts a different conformation from that found when it binds to BmorPBP1. Binding to BmorGOBP2 involves hydrogen bonding to Arg110 rather than to Ser56 as found for BmorPBP1

Biochar Administration to San Marzano Tomato Plants Cultivated Under Low-Input Farming Increases Growth, Fruit Yield, and Affects Gene Expression

Biochar is a rich-carbon charcoal obtained by pyrolysis of biomasses, which was used since antiquity as soil amendant. Its storage in soils was demonstrated contributing to abate the effects of climate changes by sequestering carbon, also providing bioenergy, and improving soil characteristics and crop yields. Despite interest in this amendant, there is still poor information on its effects on soil fertility and plant growth. Considerable variation in the plant response has been reported, depending on biomass source, pyrolysis conditions, crop species, and cultivation practices. Due to these conflicting evidences, this work was aimed at studying the effects of biochar from pyrolyzed wood at 550 degrees C, containing 81.1% carbon and 0.91% nitrogen, on growth and yield of tomato plants experiencing low-input farming conditions. San Marzano ecotype from Southern Italy was investigated, due to its renowned quality and adaptability to sustainable farming practices. Biochar administration improved vegetative growth and berry yield, while affecting gene expression and protein repertoire in berries. Different enzymes of carbon metabolism and photosynthesis were over-represented, whereas various stress-responsive and defense proteins were down-represented. Molecular results are here discussed in relation to estimated agronomic parameters to provide a rationale justifying the growth-promoting effect of this soil amendant

A Genotyping Method for Detecting Foreign Buffalo Material in Mozzarella di Bufala Campana Cheese Using Allele-Specific- and Single-Tube Heminested-Polymerase Chain Reaction.

Mozzarella di Bufala Campana (MdBC) cheese is a Protected Designation of Origin (PDO) product that is important for the economy and cultural heritage of the Campania region. Food fraud can undermine consumers' trust in this dairy product and harm the livelihood of local producers. The current methods for detecting adulteration in MdBC cheese due to the use of buffalo material from foreign countries could exhibit limitations associated with the required use of expensive equipment, time-consuming procedures, and specialized personnel. To address these limits here, we propose a rapid, reliable, and cost-effective genotyping method that can detect foreign buffalo milk in a counterpart from the PDO area and in MdBC cheese, ensuring the quality and authenticity of the latter dairy product. This method is based on dedicated allele-specific and single-tube heminested polymerase chain reaction procedures. By using allele-specific primers that are designed to detect the nucleotide g.472G>C mutation of the CSN1S1Bbt allele, we distinguished an amplicon of 330 bp in the amplification product of DNA when extracted from milk and cheese, which is specific to the material originating from foreign countries. By spiking foreign milk samples with known amounts of the counterpart from the PDO area, the sensitivity of this assay was determined to be 0.01% v/v foreign to PDO milk. Based on a rough estimate of its simplicity, reliability, and cost, this method could be a valuable tool for identifying adulterated buffalo PDO dairy products

Mono-dimensional blue native-PAGE and bi-dimensional blue native/urea-PAGE or /SDS-PAGE combined with nLC-ESI-LIT-MS/MS unveil membrane protein heteromeric and homomeric complexes in streptococcus thermophilus

Protein interactions are essential elements for the biological machineries underlying biochemical and physiological mechanisms indispensable for microorganism life. By using mono-dimensional blue native polyacrylamide gel electrophoresis (1D-BN-PAGE), two-dimensional blue native/urea-PAGE (2D-BN/urea-PAGE) and two-dimensional blue native/SDS-PAGE (2D-BN/SDS-PAGE), membrane protein complexes of Streptococcus thermophilus were resolved and visualized. Protein complex and oligomer constituents were then identified by nLC-ESI-LIT-MS/MS. In total, 65 heteromeric and 30 homomeric complexes were observed, which were then associated with 110 non-redundant bacterial proteins. Protein machineries involved in polysaccharide biosynthesis, molecular uptake, energy metabolism, cell division, protein secretion, folding and chaperone activities were highly represented in electrophoretic profiles; a number of homomeric moonlighting proteins were also identified. Information on hypothetical proteins was also derived. Parallel genome sequencing unveiled that the genes coding for the enzymes involved in exopolysaccharide biosynthesis derive from two separate clusters, generally showing high variability between bacterial strains, which contribute to a unique, synchronized and active synthetic module. The approach reported here paves the way for a further functional characterization of these protein complexes and will facilitate future studies on their assembly and composition during various growth conditions and in different mutant backgrounds, with important consequences for biotechnological applications of this bacterium in dairy productions. Biological significance Combined proteomic procedures have been applied to the characterization of heteromultimeric and homomeric protein complexes from the membrane fraction of S. thermophilus. Protein machineries involved in polysaccharide biosynthesis, molecular uptake, energy metabolism, cell division, protein secretion, folding and chaperone activities were identified; information on hypothetical and moonlighting proteins were also derived. This study is original in the lactic bacteria context and maybe considered as preliminary to a deeper functional characterization of the corresponding protein complexes. Due to the large use of S. thermophilus as a starter for dairy productions, the data reported here may facilitate future investigations on protein complex assembly and composition under different experimental conditions or for bacterial strains having specific biotechnological applications