[Show abstract][Hide abstract] ABSTRACT: Respiratory complex I (NADH:ubiquinone oxidoreductase) is a ubiquitous bioenergetic enzyme formed by over 40 subunits in eukaryotes
and a minimum of 11 subunits in bacteria. Recently, crystal structures have greatly advanced our knowledge of complex I but
have not clarified the details of its reaction with ubiquinone (Q). This reaction is essential for bioenergy production and
takes place in a large cavity embedded within a conserved module that is homologous to the catalytic core of Ni-Fe hydrogenases.
However, how a hydrogenase core has evolved into the protonmotive Q reductase module of complex I has remained unclear. This
work has exploited the abundant genomic information that is currently available to deduce structure-function relationships
in complex I that indicate the evolutionary steps of Q reactivity and its adaptation to natural Q substrates. The results
provide answers to fundamental questions regarding various aspects of complex I reaction with Q and help re-defining the old
concept that this reaction may involve two Q or inhibitor sites. The re-definition leads to a simplified classification of
the plethora of complex I inhibitors while throwing a new light on the evolution of the enzyme function.
Preview · Article · Nov 2015 · Genome Biology and Evolution
[Show abstract][Hide abstract] ABSTRACT: Apoptosis has been reported to induce changes in the remodelling of membrane lipids; after death receptor engagement, specific changes of lipid composition occur not only at the plasma membrane, but also in intracellular membranes. This paper focuses on one important aspect of apoptotic changes in cellular lipids, namely, the redistribution of the mitochondria-specific phospholipid, cardiolipin (CL). CL predominantly resides in the inner mitochondrial membrane, even if the rapid remodelling of its acyl chains and the subsequent degradation occur in other membrane organelles. After death receptor stimulation, CL appears to concentrate into mitochondrial “raft-like” microdomains at contact sites between inner and outer mitochondrial membranes, leading to local oligomerization of proapoptotic proteins, including Bid. Clustering of Bid in CL-enriched contacts sites is interconnected with pathways of CL remodelling that intersect membrane traffic routes dependent upon actin. In addition, CL association with cytoskeleton protein vimentin was observed. Such novel association also indicated that CL molecules may be expressed at the cell surface following apoptotic stimuli. This observation adds a novel implication of biomedical relevance. The association of CL with vimentin at the cell surface may represent a “new” target antigen in the context of the apoptotic origin of anti-vimentin/CL autoantibodies in Antiphospholipid Syndrome.
Full-text · Article · Sep 2015 · Journal of Immunology Research
[Show abstract][Hide abstract] ABSTRACT: Lymphocyte functions triggered by antigen recognition and co-stimulation signals are associated with a rapid and intense cell division, and hence with metabolism adaptation. The nucleotide cytidine 5' triphosphate (CTP) is a precursor required for the metabolism of DNA, RNA and phospholipids. CTP originates from two sources: a salvage pathway and a de novo synthesis pathway that depends on two enzymes, the CTP synthases (or synthetases) 1 and 2 (CTPS1 with CTPS2); the respective roles of these two enzymes are not known. CTP synthase activity is a potentially important step for DNA synthesis in lymphocytes. Here we report the identification of a loss-of-function homozygous mutation (rs145092287) in CTPS1 in humans that causes a novel and life-threatening immunodeficiency, characterized by an impaired capacity of activated T and B cells to proliferate in response to antigen receptor-mediated activation. In contrast, proximal and distal T-cell receptor (TCR) signalling events and responses were only weakly affected by the absence of CTPS1. Activated CTPS1-deficient cells had decreased levels of CTP. Normal T-cell proliferation was restored in CTPS1-deficient cells by expressing wild-type CTPS1 or by addition of exogenous CTP or its nucleoside precursor, cytidine. CTPS1 expression was found to be low in resting T cells, but rapidly upregulated following TCR activation. These results highlight a key and specific role of CTPS1 in the immune system by its capacity to sustain the proliferation of activated lymphocytes during the immune response. CTPS1 may therefore represent a therapeutic target of immunosuppressive drugs that could specifically dampen lymphocyte activation.
[Show abstract][Hide abstract] ABSTRACT: The ancestors of mitochondria, or proto-mitochondria, played a crucial role in the evolution of eukaryotic cells and derived from symbiotic α-proteobacteria which merged with other microorganisms - the basis of the widely accepted endosymbiotic theory. However, the identity and relatives of proto-mitochondria remain elusive. Here we show that methylotrophic α-proteobacteria could be the closest living models for mitochondrial ancestors. We reached this conclusion after reconstructing the possible evolutionary pathways of the bioenergy systems of proto-mitochondria with a genomic survey of extant α-proteobacteria. Results obtained with complementary molecular and genetic analyses of diverse bioenergetic proteins converge in indicating the pathway stemming from methylotrophic bacteria as the most probable route of mitochondrial evolution. Contrary to other α-proteobacteria, methylotrophs show transition forms for the bioenergetic systems analysed. Our approach of focusing on these bioenergetic systems overcomes the phylogenetic impasse that has previously complicated the search for mitochondrial ancestors. Moreover, our results provide a new perspective for experimentally re-evolving mitochondria from extant bacteria and in the future produce synthetic mitochondria.
[Show abstract][Hide abstract] ABSTRACT: Acetic acid bacteria (AAB) live in sugar rich environments including food matrices, plant tissues and the gut of sugar-feeding insects. By comparing the newly sequenced genomes of Asaia platycodi and Saccharibacter sp., symbionts of Anopheles stephensi and Apis mellifera respectively, with those of 14 other AAB, we provide a genomic view of the evolutionary pattern of this bacterial group and clues on traits that explain the success of AAB as insect symbionts. A specific pre-adaptive trait, cytochrome bo3 ubiquinol oxidase, appears ancestral in AAB and shows a phylogeny that is congruent with that of the genomes. The functional properties of this terminal oxidase might have allowed AAB to adapt to the diverse oxygen levels of arthropod guts.
Full-text · Article · Mar 2014 · Genome Biology and Evolution
[Show abstract][Hide abstract] ABSTRACT: Peripheral nerve injuries (PNI) are continuing to be an ever-growing socio-economic burden affecting mainly the young working population and the current clinical treatments to PNI provide a poor clinical outcome involving significant loss of sensation. Thus, our understanding of the underlying factors responsible for the extensive loss of the sensory cutaneous subpopulation in the dorsal root ganglia (DRG) that occurs following injury needs to be improved. The current investigations focus in identifying visual cues of mitochondria-related apoptotic events in the various subpopulations of sensory cutaneous neurons. Sensory neuronal subpopulations were identified using FastBlue retrograde labelling following axotomy. Specialised fluorogenic probes, MitoTracker Red and MitoTracker Orange, were employed to visualise the dynamic changes of the mitochondrial population of neurons. The results reveal a fragmented mitochondrial network in sural neurons following apoptosis, whereas a fused elongated mitochondrial population is present in sensory proprioceptive muscle neurons following tibial axotomy. We also demonstrate the neuroprotective properties of NAC and ALCAR therapy in vitro. The dynamic mitochondrial network breaks down following oxidative exposure to hydrogen peroxide (H(2)O(2)), but reinitiates fusion after NAC and ALCAR therapy. In conclusion, this study provides both qualitative and quantitative evidence of the susceptibility of sensory cutaneous sub-population in apoptosis and of the neuroprotective effects of NAC and ALCAR treatment on H(2)O(2)-challenged neurons.
No preview · Article · Sep 2012 · Experimental Brain Research
[Show abstract][Hide abstract] ABSTRACT: Acyl coenzyme A (acyl-CoA) thioesterases hydrolyze thioester bonds in acyl-CoA metabolites. The majority of mammalian thioesterases
are α/β-hydrolases and have been studied extensively. A second class of Hotdog-fold enzymes has been less well described.
Here, we present a structural and functional analysis of a new mammalian mitochondrial thioesterase, Them5. Them5 and its
paralog, Them4, adopt the classical Hotdog-fold structure and form homodimers in crystals. In vitro, Them5 shows strong thioesterase activity with long-chain acyl-CoAs. Loss of Them5 specifically alters the remodeling process
of the mitochondrial phospholipid cardiolipin. Them5−/− mice show deregulation of lipid metabolism and the development of fatty liver, exacerbated by a high-fat diet. Consequently,
mitochondrial morphology is affected, and functions such as respiration and β-oxidation are impaired. The novel mitochondrial
acyl-CoA thioesterase Them5 has a critical and specific role in the cardiolipin remodeling process, connecting it to the development
of fatty liver and related conditions.
Full-text · Article · May 2012 · Molecular and Cellular Biology
[Show abstract][Hide abstract] ABSTRACT: Cell-to-cell communication is a fundamental process for development and maintenance of multicellular organisms. Diverse mechanisms for the exchange of molecular information between cells have been documented, such as the exchange of membrane fragments (trogocytosis), formation of tunneling nanotubes (TNTs) and release of microvesicles (MVs). In this study we assign to Fas signalling a pivotal role for intercellular communication in CD4+ T cells. Binding of membrane-bound FasL to Fas expressing target cells triggers a well-characterized pro-apoptotic signalling cascade. However, our results, pairing up flow cytometric studies with confocal microscopy data, highlight a new social dimension for Fas/FasL interactions between CD4+ T cells. Indeed, FasL enhances the formation of cell conjugates (8 fold of increase) in an early time-frame of stimulation (30 min), and this phenomenon appears to be a crucial step to prime intercellular communication. Our findings show that this communication mainly proceeds along a cytosolic material exchange (ratio of exchange >10, calculated as ratio of stimulated cells signal divided by that recorded in control cells) via TNTs and MVs release. In particular, inhibition of TNTs genesis by pharmacological agents (Latruculin A and Nocodazole) markedly reduced this exchange (inhibition percentage: >40% and >50% respectively), suggesting a key role for TNTs in CD4+ T cells communication. Although MVs are present in supernatants from PHA-activated T cells, Fas treatment also leads to a significant increase in the amount of released MVs. In fact, the co-culture performed between MVs and untreated cells highlights a higher presence of MVs in the medium (1.4 fold of increase) and a significant MVs uptake (6 fold of increase) by untreated T lymphocytes. We conclude that Fas signalling induces intercellular communication in CD4+ T cells by different mechanisms that seem to start concomitantly with the main pathway (programmed cell death) promoted by FasL.
[Show abstract][Hide abstract] ABSTRACT: In this paper an extension of the Lintner model  is considered: the problem of portfolio optimization is studied when short-selling is allowed through the mechanism of margin requirements. This induces a non-linear constraint on the wealth. When interest on deposited margin is present, Lintner ingeniously solved the problem by recovering the unique optimal solution of the linear model (no margin requirements). In this paper an alternative and more realistic approach is explored: the nonlinear constraint is maintained but no interest is perceived on the money deposited against short-selling. This leads to a fully non-linear problem which admits multiple and unstable solutions very different among themselves but corresponding to similar risk levels. Our analysis is built on a seminal idea by Galluccio, Bouchaud and Potters , who have re-stated the problem of finding solutions of the portfolio optimization problem in futures markets in terms of a spin glass problem. In order to get the best portfolio (i.e. the one lying on the efficiency frontier), we have to implement a two-step procedure. A worked example with real data is presented.
No preview · Article · Nov 2011 · International Journal of Theoretical and Applied Finance
[Show abstract][Hide abstract] ABSTRACT: Mitochondrial dysfunction often leads to cell death and disease. We can now draw correlations between the dysfunction of one of the most important mitochondrial enzymes, NADH:ubiquinone reductase or complex I, and its structural organization thanks to the recent advances in the X-ray structure of its bacterial homologs. The new structural information on bacterial complex I provide essential clues to finally understand how complex I may work. However, the same information remains difficult to interpret for many scientists working on mitochondrial complex I from different angles, especially in the field of cell death. Here, we present a novel way of interpreting the bacterial structural information in accessible terms. On the basis of the analogy to semi-automatic shotguns, we propose a novel functional model that incorporates recent structural information with previous evidence derived from studies on mitochondrial diseases, as well as functional bioenergetics.
Full-text · Article · Oct 2011 · Cell Death & Disease
[Show abstract][Hide abstract] ABSTRACT: In a previous article (Degli Esposti and Geraci. Bulletin of Italian Politics, 2011), we presented an historical survey of
the university reform laws that took place in Italy in the last 30 years. On that occasion, we stressed how important is merit
evaluation for academics and their institutions, especially in view of the much debated but not yet implemented ‘Gelmini’
reform with its long awaited new regulation for accessing academic positions (concorsi) and for determining individual weight in financial resource allocation among universities. Here, we present and compare
several rankings used to evaluate the prestige and merit of Italian universities. We also consider alternative approaches
to academic rankings that highlight peculiar aspects of the universities in Italy which cannot be reasonably accounted for
by other international rankings. Finally, we propose a new approach that combines both national and international standing
of Italian universities. It is hoped that this study will provide practical guidance to policy makers for establishing the
criteria upon which merit should be assessed.
[Show abstract][Hide abstract] ABSTRACT: The localization and control of Bcl-2 proteins on mitochondria is essential for the intrinsic pathway of apoptosis. Anti-apoptotic Bcl-2 proteins reside on the outer mitochondrial membrane (OMM) and prevent apoptosis by inhibiting the activation of the pro-apoptotic family members Bax and Bak. The Bcl-2 subfamily of BH3-only proteins can either inhibit the anti-apoptotic proteins or directly activate Bax or Bak. How these proteins interact with each other, the mitochondrial surface and within the OMM are complex processes we are only beginning to understand. However, these interactions are fundamental for the transduction of apoptotic signals to mitochondria and the subsequent release of caspase activating factors into the cytosol. In this review we will discuss our knowledge of how Bcl-2 proteins are directed to mitochondria in the first place, a crucial but poorly understood aspect of their regulation. This article is part of a Special Issue entitled Mitochondria: the deadly organelle.
Preview · Article · Nov 2010 · Biochimica et Biophysica Acta
[Show abstract][Hide abstract] ABSTRACT: The vacuolating cytotoxin (VacA) is an important virulence factor of Helicobacter pylori with pleiotropic effects on mammalian cells, including the ability to trigger mitochondria-dependent apoptosis. However, the mechanism by which VacA exerts its apoptotic function is unclear. Using a genetic approach, in this study we show that killing by VacA requires the proapoptotic Bcl-2 family members BAX and BAK at the mitochondrial level, but not adequate endoplasmic reticulum Ca²(+) levels, similarly controlled by BAX and BAK. A combination of subcellular fractionation and imaging shows that wild-type VacA, but not mutants in its channel-forming region, induces the accumulation of BAX on endosomes and endosome-mitochondria juxtaposition that precedes the retrieval of active BAX on mitochondria. It is noteworthy that in Bax- and Bak-deficient cells, VacA is unable to cause endosome-mitochondria juxtaposition and is not retrieved in mitochondria. Thus, VacA causes BAX/BAK-dependent juxtaposition of endosomes and mitochondria early in the process of cell death, revealing a new function for these proapoptotic proteins in the regulation of relative position of organelles.
Full-text · Article · Nov 2010 · Cell death and differentiation
[Show abstract][Hide abstract] ABSTRACT: The entropy of an ergodic source is the limit of properly rescaled 1-block
entropies of sources obtained applying successive non-sequential recursive
pairs substitutions (see P. Grassberger 2002 ArXiv:physics/0207023 and D.
Benedetto, E. Caglioti and D. Gabrielli 2006 Jour. Stat. Mech. Theo. Exp. 09
doi:10.1088/1742.-5468/2006/09/P09011). In this paper we prove that the cross
entropy and the Kullback-Leibler divergence can be obtained in a similar way.
Full-text · Article · Sep 2010 · Journal of Statistical Mechanics Theory and Experiment
[Show abstract][Hide abstract] ABSTRACT: Apoptosis is an active and tightly regulated form of cell death, which can also be considered a stress-induced process of cellular communication. Recent studies reveal that the lipid network within cells is involved in the regulation and propagation of death signalling. Despite the vast growth of our current knowledge on apoptosis, little is known of the specific role played by lipid molecules in the central event of apoptosis-the piercing of mitochondrial membranes. Here we review the information regarding changes in mitochondrial lipids that are associated with apoptosis and discuss whether they may be involved in the permeabilization of mitochondria to release their apoptogenic factors, or just lie downstream of this permeabilization leading to the amplification of caspase activation. We focus on the earliest changes that physiological apoptosis induces in mitochondrial membranes, which may derive from an upstream alteration of phospholipid metabolism that reverberates on the mitochondrial re-modelling of their characteristic lipid, cardiolipin. Hopefully, this review will lead to an increased understanding of the role of mitochondrial lipids in apoptosis and also help revealing new stress sensing mechanisms in cells. This article is part of a Special Issue entitled Mitochondria: the deadly organelle.