A coupled spectrophotometric enzyme assay for methyltransferases

Adenosine deaminase (EC 3.5.4.4), purified from Aspergillus oryzae, is active in deaminating S-adenosylhomocysteine and its related thioethers, whereas the related sulfonium compound, S-adenosylmethionine, is not deaminated. By taking advantage of the different reactivity of the two compounds, a coupled optical enzyme assay for methyl transfer reactions has been developed. The amount of Ado-Hcy formed is calculated from the decrease in optical density at 265 nm, after addition of an excess of adenosine deaminase. The validity of the method has been tested with three purified enzymes, i.e., homocysteine methyltransferase, histamine methylase, and acetylserotonin methyltransferase. Some kinetic constants of these enzymes have been obtained. The procedure is highly accurate, reproducible, and relatively simple compared to the conventional radio-chemical methods currently in use.     

Habitat selection of European pine marten in Central Italy: from a tree dependent to a generalist species

Studies at small spatial scale are often fundamental to highlight the behavioural plasticity of a species and thus have important implications for conservation planning, in particular for species usually considered as habitat specialists. We investigated second-order habitat selection of the European pine marten in an area dominated by deciduous oak forest and open fields in central Italy, by radio-tracking 16 pine martens (eight males, eight females). Pine martens placed home ranges in areas with more open field than in the study area, whereas woodland (oak and conifer forests) comprised a smaller portion of the home range than predominant forest character of the studied area. Although the presence of the species in the open habitats has been documented, to our knowledge, our results provide the first evidence of home range establishment in this cover type by pine marten at population level. The combination of low predation risk and high availability of resources could allow pine martens to occupy open fields in our study area. We highlighted different individual strategies of habitat selection, with some individuals placing home ranges in areas with high forest coverage while others occupying open areas. We found no effects of sex and body condition on habitat selection, and this could indicate that in the study area, both forested and non-forested cover types, such as open fields, shrub and anthropic areas, can provide adequate food, overhead cover and resting sites for all individuals. Pine marten ability to occupy open fields seems thus more related to the behavioural flexibility of the species, rather than to the need to supplement dens and forage from complementary lower quality habitat. The high quality of the Mediterranean continental area studied could also explain the selection of open areas by the pine marten. Our results offer useful information on pine marten ecology and may be helpful for conservation management of this species in southern Europe.     

Post-translational modifications of VDAC1 and VDAC2 cysteines from rat liver mitochondria

VDACs three isoforms (VDAC1, VDAC2, VDAC3) are integral proteins of the outer mitochondrial membrane whose primary function is to permit the communication and exchange of molecules related to the mitochondrial functions. We have recently reported about the peculiar over-oxidation of VDAC3 cysteines. In this work we have extended our analysis, performed by tryptic and chymotryptic proteolysis and UHPLC/High Resolution ESI-MS/MS, to the other two isoforms VDAC1 and VDAC2 from rat liver mitochondria, and we have been able to find also in these proteins over-oxidation of cysteines. Further PTM of cysteines as succination has been found, while the presence of selenocysteine was not detected. Unfortunately, a short sequence stretch containing one genetically encoded cysteine was not covered both in VDAC2 and in VDAC3, raising the suspect that more, unknown modifications of these proteins exist. Interestingly, cysteine over-oxidation appears to be an exclusive feature of VDACs, since it is not present in other transmembrane mitochondrial proteins eluted by hydroxyapatite. The assignment of a functional role to these modifications of VDACs will be a further step towards the full understanding of the roles of these proteins in the cell.     

Differential toxicity of TAR DNA‐binding protein 43 isoforms depends on their submitochondrial localization in neuronal cells

TAR DNA ‐binding protein 43 (TDP ‐43) is an RNA ‐binding protein and a major component of protein aggregates found in amyotrophic lateral sclerosis and several other neurodegenerative diseases. TDP ‐43 exists as a full‐length protein and as two shorter forms of 25 and 35 kD a. Full‐length mutant TDP ‐43s found in amyotrophic lateral sclerosis patients re‐localize from the nucleus to the cytoplasm and in part to mitochondria, where they exert a toxic role associated with neurodegeneration. However, induction of mitochondrial damage by TDP ‐43 fragments is yet to be clarified. In this work, we show that the mitochondrial 35 kD a truncated form of TDP ‐43 is restricted to the intermembrane space, while the full‐length forms also localize in the mitochondrial matrix in cultured neuronal NSC ‐34 cells. Interestingly, the full‐length forms clearly affect mitochondrial metabolism and morphology, possibly via their ability to inhibit the expression of Complex I subunits encoded by the mitochondrial‐transcribed mRNA s, while the 35 kD a form does not. In the light of the known differential contribution of the full‐length and short isoforms to generate toxic aggregates, we propose that the presence of full‐length TDP ‐43s in the matrix is a primary cause of mitochondrial damage. This in turn may cause oxidative stress inducing toxic oligomers formation, in which short TDP ‐43 forms play a major role.

     

Reduced mitochondrial Ca2+ transients stimulate autophagy in human fibroblasts carrying the 13514A>G mutation of the ND5 subunit of NADH dehydrogenase

Mitochondrial disorders are a group of pathologies characterized by impairment of mitochondrial function mainly due to defects of the respiratory chain and consequent organellar energetics. This affects organs and tissues that require an efficient energy supply, such as brain and skeletal muscle. They are caused by mutations in both nuclear- and mitochondrial DNA (mtDNA)-encoded genes and their clinical manifestations show a great heterogeneity in terms of age of onset and severity, suggesting that patient-specific features are key determinants of the pathogenic process. In order to correlate the genetic defect to the clinical phenotype, we used a cell culture model consisting of fibroblasts derived from patients with different mutations in the mtDNA-encoded ND5 complex I subunit and with different severities of the illness. Interestingly, we found that cells from patients with the 13514A>G mutation, who manifested a relatively late onset and slower progression of the disease, display an increased autophagic flux when compared with fibroblasts from other patients or healthy donors. We characterized their mitochondrial phenotype by investigating organelle turnover, morphology, membrane potential and Ca²⁺ homeostasis, demonstrating that mitochondrial quality control through mitophagy is upregulated in 13514A>G cells. This is due to a specific downregulation of mitochondrial Ca²⁺ uptake that causes the stimulation of the autophagic machinery through the AMPK signaling axis. Genetic and pharmacological manipulation of mitochondrial Ca²⁺ homeostasis can revert this phenotype, but concurrently decreases cell viability. This indicates that the higher mitochondrial turnover in complex I deficient cells with this specific mutation is a pro-survival compensatory mechanism that could contribute to the mild clinical phenotype of this patient.Mitochondrial disorders include a wide range of pathological conditions characterized by defects in organelle homoeostasis and energy metabolism, in particular in the electron transport chain (ETC) complexes. They are mostly caused by mutations in nuclear- or mtDNA-encoded genes of the respiratory chain complexes leading to a variety of clinical manifestations, ranging from lesions in specific tissues, such as in Leber''s hereditary optic neuropathy, to complex multisystem syndromes, such as myoclonic epilepsy with ragged-red fibers, Leigh syndrome or the mitochondrial encephalomyopathy, lactic acidosis and stroke-like episodes syndrome (MELAS).^{1, 2} Despite the detailed knowledge of the molecular defects in these diseases, their pathogenesis remains poorly understood. The heterogeneity of signs and symptoms depends on the diversity of the genetic background and on patient-specific compensatory mechanisms. Several studies investigated the consequences of nuclear DNA mutations on intracellular organelle physiology and Ca²⁺ homeostasis.^{3, 4} Here we analyzed a cohort of patients with mutations in the mtDNA-encoded ND5 subunit of NADH dehydrogenase in order to correlate the clinical phenotype with relevant intracellular parameters involved in mitochondrial physiology, such as the rate of autophagy and mitophagy fluxes, mitochondrial Ca²⁺ dynamics, mitochondrial membrane potential and their functional relationship.Mitochondrial Ca²⁺ is a key regulator of organelle physiology, and impairment of cation homeostasis is a general feature of many pathological conditions, including mitochondrial diseases.⁵ In addition, Ca²⁺ uptake in this organelle has recently been demonstrated to be a fundamental regulator of autophagy.^{6, 7} Autophagy is involved in physiological organelle turnover and in the removal of damaged or non-functional mitochondria by autophagy (called ‘mitophagy'')^{8, 9, 10, 11} and is critical for organelle quality control. Given the pivotal role of mitochondrial Ca²⁺ in the adaptation of adenosine triphosphate (ATP) production to cellular energy demand, the recent identification of the channel responsible for Ca²⁺ entry into the organelle, the mitochondrial Ca²⁺ uniporter (MCU), is instrumental for the understanding of the regulation of mitochondrial Ca²⁺ transport in both physiological and pathological conditions. MCU was identified in 2011,^{12, 13} and in the following years, molecular insight on its complex regulatory mechanism was obtained. The pore region is composed of MCU, its isoform MCUb¹⁴ and essential MCU regulator (EMRE).¹⁵ The channel is gated by the Ca²⁺-sensitive proteins mitochondrial Ca²⁺ uptake 1 (MICU1) and MICU2^{16, 17, 18, 19} and further regulated by the SLC25A23 protein.²⁰ As to its cellular function, mitochondrial Ca²⁺ has been shown to stimulate ATP production by positive regulation of three key dehydrogenases of the tricarboxylic acid cycle²¹ and of the ETC.²² In parallel, unregulated and sustained organelle Ca²⁺ overload can also lead to the opening of the mitochondrial permeability transition pore,^{23, 24} with consequent dissipation of mitochondrial membrane potential (ΔΨ_mt), release of caspase cofactors and activation of the apoptotic cascade.⁵ Despite the significant molecular understanding of all these cellular processes, their role in the pathogenesis of mitochondrial diseases is still poorly understood. Here we investigated the interplay of these pathways and the possibility of their contribution to determine the severity of the pathology in a cellular model consisting of fibroblasts from patients carrying mutations in the mitochondrial ND5 gene.     

Tim/Timeless,a member of the replication fork protection complex,operates with the Warsaw breakage syndrome DNA helicase DDX11 in the same fork recovery pathway

We present evidence that Tim establishes a physical and functional interaction with DDX11, a super-family 2 iron-sulfur cluster DNA helicase genetically linked to the chromosomal instability disorder Warsaw breakage syndrome. Tim stimulates DDX11 unwinding activity on forked DNA substrates up to 10-fold and on bimolecular anti-parallel G-quadruplex DNA structures and three-stranded D-loop approximately 4–5-fold. Electrophoretic mobility shift assays revealed that Tim enhances DDX11 binding to DNA, suggesting that the observed stimulation derives from an improved ability of DDX11 to interact with the nucleic acid substrate. Surface plasmon resonance measurements indicate that DDX11 directly interacts with Tim. DNA fiber track assays with HeLa cells exposed to hydroxyurea demonstrated that Tim or DDX11 depletion significantly reduced replication fork progression compared to control cells; whereas no additive effect was observed by co-depletion of both proteins. Moreover, Tim and DDX11 are epistatic in promoting efficient resumption of stalled DNA replication forks in hydroxyurea-treated cells. This is consistent with the finding that association of the two endogenous proteins in the cell extract chromatin fraction is considerably increased following hydroxyurea exposure. Overall, our studies provide evidence that Tim and DDX11 physically and functionally interact and act in concert to preserve replication fork progression in perturbed conditions.     

Porphyromonas gingivalis prevalence related to other micro-organisms in adult refractory periodontitis.

Forty-six adult periodontal patients, selected on the basis of clinical examination, and 46 adult healthy subjects were examined. The subgingival plaque samples from one inflammatory and one non-inflammatory site of each periodontal patient were studied to determine Porphyromonas gingivalis prevalence related to other periodontal micro-organisms and to periodontal tissue destruction. The results showed Porphyromonas gingivalis as the main pathogenic micro-organism isolated in the inflammatory sites together with Bacteroides forsythus. Peptostreptococcus sp., Actinomyces sp. and Prevotella sp. were found as a normal oral flora in the healthy subjects. Fusobacterium nucleatum, Prevotella intermedia, Campylobacter rectus and Eikenella corrodens were detected both in inflammatory and in non-inflammatory sites of periodontal patients as well as in the healthy subjects.