CNR Institute of Biomembrane and Bioenergetics

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CNR Institute of Biomembrane and Bioenergetics

Italy
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D'Onorio De Meo P.,Consorzio Interuniversitario Per Le Applicazioni Of Supercalcolo Per University cerca | D'Antonio M.,University of Bari | Griggio F.,University of Milan | Lupi R.,University of Milan | And 6 more authors.
Nucleic Acids Research | Year: 2012

The MITOchondrial genome database of metaZOAns (MitoZoa) is a public resource for comparative analyses of metazoan mitochondrial genomes (mtDNA) at both the sequence and genomic organizational levels. The main characteristics of the MitoZoa database are the careful revision of mtDNA entry annotations and the possibility of retrieving gene order and non-coding region (NCR) data in appropriate formats. The MitoZoa retrieval system enables basic and complex queries at various taxonomic levels using different search menus. MitoZoa 2.0 has been enhanced in several aspects, including: a re-annotation pipeline to check the correctness of protein-coding gene predictions; a standardized annotation of introns and of precursor ORFs whose functionality is post-transcriptionally recovered by RNA editing or programmed translational frameshifting; updates of taxon-related fields and a BLAST sequence similarity search tool. Database novelties and the definition of standard mtDNA annotation rules, together with the user-friendly retrieval system and the BLAST service, make MitoZoa a valuable resource for comparative and evolutionary analyses as well as a reference database to assist in the annotation of novel mtDNA sequences. MitoZoa is freely accessible at http://www.caspur.it/mitozoa. © The Author(s) 2011. Published by Oxford University Press.


Megli F.M.,CNR Institute of Biomembrane and Bioenergetics | Conte E.,CNR Institute of Biomembrane and Bioenergetics | Russo L.,Ospedale di Matera
Biochimica et Biophysica Acta - Biomembranes | Year: 2010

A 3-doxylcholestane spin label was employed in addition to 5-doxylstearoyl lecithin for a more detailed study of the different effects exerted by variously oxidized lecithins on fatty acid alignment in phospholipid planar bilayers. Either spin label was enclosed in oriented PLPC planar samples also containing in turn a variety of conjugated-dienes lecithins and cleaved chain lecithins, in order to monitor EPR spectral angular dependence loss. Data obtained by use of arachidonoyl-hydroxystearoyl-PC and palmitoyl-hydroxylinoleoyl-PC confirm that the 5-DSPC nitroxide ring almost completely retains its orientation in CD-PCs-containing planar membranes, in contrast with angular dependence loss observed in the presence of the CC-PC molecular species palmitoyl-oxononanoyl-PC and palmitoyl-oxovaleroyl-PC, already seen with cleaved-chain palmitoyl-glutaroyl-PC and palmitoyl-azelaoyl-PC. However, the 3-DC nitroxide ring also loses its orientation with CD-PCs, in addition to being disoriented by cleaved chain-lecithins, similarly to 5DSPC. Joint information from the two spin labels will help to clarify whether OXPC-related disordering involved the whole bilayer structure or only the hydrophobic core. In addition, the propensity of different OXPCs to form bilayer vesicles in water suspension was also determined by Sepharose 4B gel-chromatography. The results suggest that CD-PCs might yield SPB bilayer structures with a disordered hydrophobic core, while pure CC-PC more probably forms non-bilayer disordered structures, possibly micelles or mixed micelle/bilayers. © 2010 Elsevier B.V.


de Bari L.,CNR Institute of Biomembrane and Bioenergetics | Valenti D.,CNR Institute of Biomembrane and Bioenergetics | Atlante A.,CNR Institute of Biomembrane and Bioenergetics | Passarella S.,University of Molise
FEBS Letters | Year: 2010

In order to ascertain whether and how mitochondria can produce hydrogen peroxide (H2O2) as a result of l-lactate addition, we monitored H2O2 generation in rat liver mitochondria and in submitochondrial fractions free of peroxisomal and cytosolic contamination. We found that H2O2 is produced independently on the respiratory chain with 1:1 stoichiometry with pyruvate, due to a putative flavine-dependent l-lactate oxidase restricted to the intermembrane space. The l-lactate oxidase reaction shows a hyperbolic dependence on l-lactate concentration and is inhibited by NAD+ in a competitive manner, being the enzyme different from the l-lactate dehydrogenase isoenzymes as shown by their pH profiles. © 2010 Federation of European Biochemical Societies.


Bobba A.,CNR Institute of Biomembrane and Bioenergetics | Amadoro G.,CNR Institute of Neuroscience | Valenti D.,CNR Institute of Biomembrane and Bioenergetics | Corsetti V.,European Brain Research Institute EBRI | And 2 more authors.
Mitochondrion | Year: 2013

Here we investigate the effect of β-amyloid on mitochondrial respiratory function, i.e.mitochondrial oxygen consumption and membrane potential generation as well as the individual activities of both the mitochondrial Complexes I-IV, that compose mitochondrial electron transport chain, and the ATP synthase, by using homogenate from cerebellar granule cells, treated with low concentrations of β-amyloid, and Alzheimer synaptic-enriched brain samples. We found that β-amyloid caused both a selective defect in Complex I activity associated with an increase (5 fold) of intracellular reactive oxygen species and an impairment of Complex IV likely due to membrane lipid peroxidation. In addition, a 130% increase of the GSSG/GSH ratio was measured in Alzheimer brains with respect to age-matched controls. Knowing the mechanisms of action of β-amyloid could allow to mitigate or even to interrupt the toxic cascade that leads a cell to death. The results of this study represent an important innovation because they offer the possibility to act at mitochondrial level and on specific sites to protect cells, for example by preventing the interaction of β-amyloid with the identified targets, by stabilizing or by restoring mitochondrial function or by interfering with the energy metabolism. © 2013 Elsevier B.V. and Mitochondria Research Society.


Guaragnella N.,CNR Institute of Biomembrane and Bioenergetics | Antonacci L.,University of Molise | Passarella S.,University of Molise | Marra E.,CNR Institute of Biomembrane and Bioenergetics | Giannattasio S.,CNR Institute of Biomembrane and Bioenergetics
Biochemical Society Transactions | Year: 2011

The use of non-mammalian model organisms, including yeast Saccharomyces cerevisiae, can provide new insights into eukaryotic PCD (programmed cell death) pathways. In the present paper, we report recent achievements in the elucidation of the events leading to PCD that occur as a response to yeast treatment with AA (acetic acid). In particular, ROS (reactive oxygen species) generation, cyt c (cytochrome c) release and mitochondrial function and proteolytic activity will be dealt with as they vary along the AA-PCD time course by using both wild-type andmutant yeast cells. Two AA-PCD pathways are described sharing common features, but distinct from one another with respect to the role of ROS andmitochondria, the former in which YCA1 acts upstream of cyt c release and caspase-like activation in a ROS-dependent manner and the latter in which cyt c release does not occur, but caspase-like activity increases, in a ROS-independent manner. ©The Authors Journal compilation ©2011 Biochemical Society.


Guaragnella N.,CNR Institute of Biomembrane and Bioenergetics | Passarella S.,University of Molise | Marra E.,CNR Institute of Biomembrane and Bioenergetics | Giannattasio S.,CNR Institute of Biomembrane and Bioenergetics
FEBS Letters | Year: 2010

To gain further insight into yeast acetic acid-induced programmed cell death (AA-PCD) we analyzed the effects of the antioxidant N-acetyl-l-cysteine (NAC) on cell viability, hydrogen peroxide (H2O2) production, DNA fragmentation, cytochrome c (cyt c) release and caspase-like activation in wild type (wt) and metacaspase and/or cyt c-lacking cells. We found that NAC prevents AA-PCD in wt cells, by scavenging H2O2 and by inhibiting both cyt c release and caspase-like activation. This shows the occurrence of a reactive oxygen species (ROS)-dependent AA-PCD. Contrarily no NAC dependent change in AA-PCD of mutant cells was detectable, showing that a ROS-independent AA-PCD can also occur. © 2010 Federation of European Biochemical Societies.


De Bari L.,CNR Institute of Biomembrane and Bioenergetics | Moro L.,CNR Institute of Biomembrane and Bioenergetics | Passarella S.,University of Molise
FEBS Letters | Year: 2013

Although d-lactate metabolism has been shown to occur in a variety of mitochondria, the metabolic fate of d-lactate in cancer cells has never been investigated, as it is believed to be exported to the extracellular phase. We show that mitochondria from both cancer (PC-3) and normal (PNT1A) prostate cells can metabolize d-lactate in an energy competent manner. This is due to the mitochondrial d-lactate dehydrogenase, a membrane flavoprotein, the activity and protein level of which are higher in PC-3 than in PNT1A cells, as detected by both kinetic and immunological analysis. d-Lactate can enter prostate mitochondria and cause the export of newly synthesized malate in a carrier-mediated manner, with the rate of malate efflux from mitochondria twofold higher in cancer. © 2013 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.


Zambelli F.,University of Milan | Prazzoli G.M.,University of Milan | Pesole G.,CNR Institute of Biomembrane and Bioenergetics | Pesole G.,University of Bari | Pavesi G.,University of Milan
Nucleic Acids Research | Year: 2012

The regulation of transcription of eukaryotic genes is a very complex process, which involves interactions between transcription factors (TFs) and DNA, as well as other epigenetic factors like histone modifications, DNA methylation, and so on, which nowadays can be studied and characterized with techniques like ChIP-Seq. Cscan is a web resource that includes a large collection of genome-wide ChIP-Seq experiments performed on TFs, histone modifications, RNA polymerases and others. Enriched peak regions from the ChIP-Seq experiments are crossed with the genomic coordinates of a set of input genes, to identify which of the experiments present a statistically significant number of peaks within the input genes' loci. The input can be a cluster of co-expressed genes, or any other set of genes sharing a common regulatory profile. Users can thus single out which TFs are likely to be common regulators of the genes, and their respective correlations. Also, by examining results on promoter activation, transcription, histone modifications, polymerase binding and so on, users can investigate the effect of the TFs (activation or repression of transcription) as well as of the cell or tissue specificity of the genes' regulation and expression. The web interface is free for use, and there is no login requirement. Available at: http://www.beaconlab.it/cscan. © 2012 The Author(s).


Valenti D.,CNR Institute of Biomembrane and Bioenergetics | Manente G.A.,University of Piemonte Orientale | Moro L.,University of Piemonte Orientale | Marra E.,CNR Institute of Biomembrane and Bioenergetics | Vacca R.A.,CNR Institute of Biomembrane and Bioenergetics
Biochemical Journal | Year: 2011

DS (Down's syndrome) is the most common human aneuploidy associated with mental retardation and early neurodegeneration. Mitochondrial dysfunction has emerged as a crucial factor in the pathogenesis of numerous neurological disorders including DS, but the cause of mitochondrial damage remains elusive. In the present study, we identified new molecular events involved in mitochondrial dysfunction which could play a role in DS pathogenesis. We analysed mitochondrial respiratory chain function in DS-HSFs (Down's syndrome human foetal skin fibroblasts; human foetal skin fibroblasts with chromosome 21 trisomy) and found a selective deficit in the catalytic efficiency of mitochondrial complex I. The complex I deficit was associated with a decrease in cAMP-dependent phosphorylation of the 18 kDa subunit of the complex, due to a decrease in PKA (protein kinase A) activity related to reduced basal levels of cAMP. Consistently, exposure of DS-HSFs to db-cAMP (dibutyryl-cAMP), a membrane-permeable cAMP analogue, stimulated PKA activity and consequently rescued the deficit of both the cAMP-dependent phosphorylation and the catalytic activity of complex I; conversely H89, a specific PKA inhibitor, suppressed these cAMP-dependent activations. Furthermore, in the present paperwe report a 3-fold increase in cellular levels of ROS (reactive oxygen species), in particular superoxide anion, mainly produced by DS-HSF mitochondria. ROS accumulation was prevented by db-cAMP-dependent activation of complex I, suggesting its involvement in ROS production. Taken together, the results of the present study suggest that the drastic decrease in basal cAMP levels observed in DS-HSFs participates in the complex I deficit and overproduction of ROS by DS-HSF mitochondria. © The Authors Journal compilation © 2011 Biochemical Society.


Giannattasio S.,CNR Institute of Biomembrane and Bioenergetics | Guaragnella N.,CNR Institute of Biomembrane and Bioenergetics | Zdralevic M.,CNR Institute of Biomembrane and Bioenergetics | Marra E.,CNR Institute of Biomembrane and Bioenergetics
Frontiers in Microbiology | Year: 2013

Beyond its classical biotechnological applications such as food and beverage production or as a cell factory, the yeast Saccharomyces cerevisiae is a valuable model organism to study fundamental mechanisms of cell response to stressful environmental changes. Acetic acid is a physiological product of yeast fermentation and it is a well-known food preservative due to its antimicrobial action. Acetic acid has recently been shown to cause yeast cell death and aging. Here we shall focus on the molecular mechanisms of S. cerevisiae stress adaptation and programmed cell death in response to acetic acid. We shall elaborate on the intracellular signaling pathways involved in the cross-talk of pro-survival and pro-death pathways underlying the importance of understanding fundamental aspects of yeast cell homeostasis to improve the performance of a given yeast strain in biotechnological applications. © 2013 Giannattasio, Guaragnella, Ždralević and Marra.

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