A distinctive protein signature induced by lysophosphatidic acid receptor 6 (LPAR6) expression in hepatocellular carcinoma cells.

Hepatocellular carcinoma (HCC) is the most commonly diagnosed liver malignancy, ranking third in the overall global cancer-related mortality. A complex network of interacting proteins controls HCC growth and progression. Lysophosphatidic acid receptors (LPAR) are commonly overexpressed in HCC. In particular, we have previously reported that the expression of LPAR6 sustains tumorigenesis and growth of HCC and results in a poor prognosis in HCC patients. Here, we applied a comparative proteomic approach to compare protein expression in both LPAR6 expressing (HLE-LPAR6) and nonexpressing HCC cells (HLE-neo). We found changes in the expression levels of 19 proteins, which include carbohydrate metabolism enzymes, redox and detoxification enzymes, and gene-expression regulatory proteins. Our findings support the role of LPAR6 in controlling the expression of a distinctive protein signature in HCC cells, which can offer a valuable resource for the identification of potential theranostic biomarkers.

Decreased amount of vimentin N-terminal truncated proteolytic products in parkin-mutant skin fibroblasts.

Vimentin, a member of cytoskeleton intermediate filaments proteins, plays a critical role in cell structure and dynamics. The present proteomic study reveals reduced amount of six different lengths, N-terminal truncated proteolytic products of vimentin, in the primary skin fibroblasts from two unrelated PD patients, as compared to control fibroblasts. The decreased amount of N-terminal truncated forms of vimentin in parkin-mutant fibroblasts, could contribute to impairment of cellular function, potentially contributing to the pathogenesis of Parkinson disease.

Proteomics for the Investigation of Surface-Exposed Proteins in Probiotics.

Probiotics are commensal microorganisms that are present in the intestinal tract and in many fermented foods and positively affect human health, promoting digestion and uptake of dietary nutrients, strengthening intestinal barrier function, modulating immune response, and enhancing antagonism toward pathogens. The proteosurfaceome, i.e., the complex set of proteins present on the bacterial surface, is directly involved as leading actor in the dynamic communication between bacteria and host. In the last decade, the biological relevance of surface-exposed proteins prompted research activities exploiting the potentiality of proteomics to define the complex network of proteins that are involved in the molecular mechanisms at the basis of the adaptation to gastrointestinal environment and the probiotic effects. These studies also took advantages of the recent technological improvements in proteomics, mass spectrometry and bioinformatics that triggered the development of ad hoc designed innovative strategies to characterize the bacterial proteosurfaceome. This mini-review is aimed at describing the key role of proteomics in depicting the cell wall protein architecture and the involvement of surface-exposed proteins in the intimate and dynamic molecular dialogue between probiotics and intestinal epithelial and immune cells.

Impact of aerobic and respirative life-style on Lactobacillus casei N87 proteome.

Lactic acid bacteria (LAB) are used as starter, adjunct and/or probiotic cultures in fermented foods. Several species are recognized as oxygen-tolerant anaerobes, and aerobic and respiratory cultivations may provide them with physiological and technological benefits. In this light, mechanisms involved in the adaptation to aerobic and respiratory (supplementation with heme and menaquinone) growth conditions of the O2-tolerant strain Lactobacillus casei N87 were investigated by proteomics. In fact, in this bacterial strain, respiration induced an increase in biomass yield and robustness to oxidative, long-term starvation and freeze-drying stresses, while high concentrations of dissolved O2 (dO2 60%) negatively affected its growth and cell survival. Proteomic results well paralleled with physiological and metabolic features and clearly showed that aerobic life-style led to a higher abundance of several proteins involved in carbohydrate metabolism and stress response mechanisms and, concurrently, impaired the biosynthesis of proteins involved in nucleic acid formation and translation processes, thus providing evidence at molecular level of the significant damage to L.casei N87 fitness. On the contrary, the activation of respiratory pathways due to heme and menaquinone supplementation, led to a decreased amount of chaperones and other stress related proteins. These findings confirmed that respiration reduced oxidative stress condition, allowing to positively modulate the central carbohydrate and energy metabolism and improve growth and stress tolerance features. Results of this study could be potentially functional to develop competitive adjunct and probiotic cultures effectively focused on the improvement of quality of fermented foods and the promotion of human health.

Lactobacillus acidophilus-Rutin Interplay Investigated by Proteomics.

Dietary polyphenols are bioactive molecules that beneficially affect human health, due to their anti-oxidant, anti-inflammatory, cardio-protective and chemopreventive properties. They are absorbed in a very low percentage in the small intestine and reach intact the colon, where they are metabolized by the gut microbiota. Although it is well documented a key role of microbial metabolism in the absorption of polyphenols and modulation of their biological activity, molecular mechanisms at the basis of the bacteria-polyphenols interplay are still poorly understood. In this context, differential proteomics was applied to reveal adaptive response mechanisms that enabled a potential probiotic Lactobacillus acidophilus strain to survive in the presence of the dietary polyphenol rutin. The response to rutin mainly modulated the expression level of proteins involved in general stress response mechanisms and, in particular, induced the activation of protein quality control systems, and affected carbohydrate and amino acid metabolism, protein synthesis and cell wall integrity. Moreover, rutin triggered the expression of proteins involved in oxidation-reduction processes.This study provides a first general view of the impact of dietary polyphenols on metabolic and biological processes of L. acidophilus.

Altered protein expression pattern in skin fibroblasts from parkin-mutant early-onset Parkinson's disease patients.

Parkinson's disease (PD) is the most common neurodegenerative movement disorder caused primarily by selective degeneration of the dopaminergic neurons in substantia nigra. In this work the proteomes extracted from primary fibroblasts of two unrelated, hereditary cases of PD patients, with different parkin mutations, were compared with the proteomes extracted from commercial adult normal human dermal fibroblasts (NHDF) and primary fibroblasts from the healthy mother of one of the two patients. The results show that the fibroblasts from the two different cases of parkin-mutant patients display analogous alterations in the expression level of proteins involved in different cellular functions, like cytoskeleton structure-dynamics, calcium homeostasis, oxidative stress response, protein and RNA processing.

Comparative secretome analysis of four isogenic Bacillus clausii probiotic strains.

BACKGROUND: The spore-bearing alkaliphilic Bacillus species constitute a large, heterogeneous group of microorganisms, important for their ability to produce enzymes, antibodies and metabolites of potential medical use. Some Bacillus species are currently being used for manufacturing probiotic products consisting of bacterial spores, exhibiting specific features (colonization, immune-stimulation and antimicrobial activity) that can account for their claimed probiotic properties. In the present work a comparative proteomic study was performed aimed at characterizing the secretome of four closely related isogenic O/C, SIN, N/R and T B. clausii strains, already marketed in a pharmaceutical mixture as probiotics. RESULTS: Proteomic analyses revealed a high degree of concordance among the four secretomes, although some proteins exhibited considerable variations in their expression level in the four strains. Among these, some proteins with documented activity in the interaction with host cells were identified, such as the glycolytic enzyme enolase, with a putative plasminogen-binding activity, GroEL, a molecular chaperone shown to be able to bind to mucin, and flagellin protein, a structural flagella protein and a putative immunomodulation agent. CONCLUSION: This study shows, for the first time, differences in the secretome of the OC, SIN, NR and T B. clausii strains. These differences indicate that specific secretome features characterize each of the four strains despite their genotypic similarity. This could confer to the B. clausii strains specific probiotic functions associated with the differentially expressed proteins and indicate that they can cooperate as probiotics as the secretome components of each strain could contribute to the overall activity of a mixed probiotic preparation.

Comparative proteomic analysis of four Bacillus clausii strains: proteomic expression signature distinguishes protein profile of the strains.

A comparative proteomic approach, using two dimensional gel electrophoresis and mass spectrometry, has been developed to compare and elucidate the differences among the cellular proteomes of four closely related isogenic O/C, SIN, N/R and T, B. clausii strains during both exponential and stationary phases of growth. Image analysis of the electropherograms reveals a high degree of concordance among the four proteomes, some proteins result, however, differently expressed. The proteins spots exhibiting high different expression level were identified, by mass-spectrometry analysis, as alcohol dehydrogenase (ADHA, EC1.2.1.3; ABC0046 isoform) aldehyde dehydrogenase (DHAS, EC 1.2.1.3; ABC0047 isoform) and flagellin-protein of B. clausii KSM-k16. The different expression levels of the two dehydrogenases were confirmed by quantitative RT-PCR and dehydrogenases enzymatic activity. The different patterns of protein expression can be considered as cell proteome signatures of the different strains.

A two-dimensional electrophoresis and mass spectrometry protein analysis of the antibiotic producer Nonomuraea sp. ATCC 39727 in different growth conditions.

Nonomuraea sp. ATCC 39727 is an aerobic actinomycete, industrially important as a producer of the glycopeptide A40926, which is used as a precursor of the semi-synthetic antibiotic dalbavancin. Previous studies showed that the production of A40926 is depressed by calcium, but promoted by l-glutamine or l-asparagine. In this study, the protein expression changes of Nonomuraea sp. ATCC 39727 in these two different growth and antibiotic-production conditions have been investigated by two-dimensional electrophoresis and mass spectrometry (MS) analysis. Few protein spots show statistically significant expression changes, and, among this group of proteins, malate dehydrogenase (MDH) shows a significant decrease in the overproduction condition. The decrease of MDH is of particular interest because it is the first described significant change in the expression levels of enzymes of the central metabolism related with A40926 overproduction.