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Di Noia MA, Scarcia P, Agrimi G, Ocheja OB, Wahid E, Pisano I, Paradies E, Palmieri L, Guaragnella C, Guaragnella N. Inactivation of HAP4 Accelerates RTG-Dependent Osmoadaptation in Saccharomyces cerevisiae. Int J Mol Sci 2023; 24:ijms24065320. [PMID: 36982394 PMCID: PMC10049445 DOI: 10.3390/ijms24065320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 01/31/2023] [Accepted: 02/24/2023] [Indexed: 03/14/2023] Open
Abstract
Mitochondrial RTG (an acronym for ReTroGrade) signaling plays a cytoprotective role under various intracellular or environmental stresses. We have previously shown its contribution to osmoadaptation and capacity to sustain mitochondrial respiration in yeast. Here, we studied the interplay between RTG2, the main positive regulator of the RTG pathway, and HAP4, encoding the catalytic subunit of the Hap2-5 complex required for the expression of many mitochondrial proteins that function in the tricarboxylic acid (TCA) cycle and electron transport, upon osmotic stress. Cell growth features, mitochondrial respiratory competence, retrograde signaling activation, and TCA cycle gene expression were comparatively evaluated in wild type and mutant cells in the presence and in the absence of salt stress. We showed that the inactivation of HAP4 improved the kinetics of osmoadaptation by eliciting both the activation of retrograde signaling and the upregulation of three TCA cycle genes: citrate synthase 1 (CIT1), aconitase 1 (ACO1), and isocitrate dehydrogenase 1 (IDH1). Interestingly, their increased expression was mostly dependent on RTG2. Impaired respiratory competence in the HAP4 mutant does not affect its faster adaptive response to stress. These findings indicate that the involvement of the RTG pathway in osmostress is fostered in a cellular context of constitutively reduced respiratory capacity. Moreover, it is evident that the RTG pathway mediates peroxisomes–mitochondria communication by modulating the metabolic function of mitochondria in osmoadaptation.
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Affiliation(s)
- Maria Antonietta Di Noia
- Department of Biosciences, Biotechnologies and Environment, University of Bari “Aldo Moro”, 70125 Bari, Italy
| | - Pasquale Scarcia
- Department of Biosciences, Biotechnologies and Environment, University of Bari “Aldo Moro”, 70125 Bari, Italy
| | - Gennaro Agrimi
- Department of Biosciences, Biotechnologies and Environment, University of Bari “Aldo Moro”, 70125 Bari, Italy
| | - Ohiemi Benjamin Ocheja
- Department of Biosciences, Biotechnologies and Environment, University of Bari “Aldo Moro”, 70125 Bari, Italy
| | - Ehtisham Wahid
- Department of Electrical and Information Engineering, Politecnico di Bari, 70125 Bari, Italy
| | - Isabella Pisano
- Department of Biosciences, Biotechnologies and Environment, University of Bari “Aldo Moro”, 70125 Bari, Italy
| | - Eleonora Paradies
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, 70126 Bari, Italy
| | - Luigi Palmieri
- Department of Biosciences, Biotechnologies and Environment, University of Bari “Aldo Moro”, 70125 Bari, Italy
| | - Cataldo Guaragnella
- Department of Electrical and Information Engineering, Politecnico di Bari, 70125 Bari, Italy
| | - Nicoletta Guaragnella
- Department of Biosciences, Biotechnologies and Environment, University of Bari “Aldo Moro”, 70125 Bari, Italy
- Correspondence:
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Miniero DV, Monné M, Di Noia MA, Palmieri L, Palmieri F. Evidence for Non-Essential Salt Bridges in the M-Gates of Mitochondrial Carrier Proteins. Int J Mol Sci 2022; 23:ijms23095060. [PMID: 35563451 PMCID: PMC9104175 DOI: 10.3390/ijms23095060] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 04/28/2022] [Accepted: 04/29/2022] [Indexed: 01/05/2023] Open
Abstract
Mitochondrial carriers, which transport metabolites, nucleotides, and cofactors across the mitochondrial inner membrane, have six transmembrane α-helices enclosing a translocation pore with a central substrate binding site whose access is controlled by a cytoplasmic and a matrix gate (M-gate). The salt bridges formed by the three PX[DE]XX[RK] motifs located on the odd-numbered transmembrane α-helices greatly contribute to closing the M-gate. We have measured the transport rates of cysteine mutants of the charged residue positions in the PX[DE]XX[RK] motifs of the bovine oxoglutarate carrier, the yeast GTP/GDP carrier, and the yeast NAD+ transporter, which all lack one of these charged residues. Most single substitutions, including those of the non-charged and unpaired charged residues, completely inactivated transport. Double mutations of charged pairs showed that all three carriers contain salt bridges non-essential for activity. Two double substitutions of these non-essential charge pairs exhibited higher transport rates than their corresponding single mutants, whereas swapping the charged residues in these positions did not increase activity. The results demonstrate that some of the residues in the charged residue positions of the PX[DE]XX[KR] motifs are important for reasons other than forming salt bridges, probably for playing specific roles related to the substrate interaction-mediated conformational changes leading to the M-gate opening/closing.
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Affiliation(s)
- Daniela Valeria Miniero
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Via E. Orabona 4, 70125 Bari, Italy; (D.V.M.); (M.M.); (M.A.D.N.)
| | - Magnus Monné
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Via E. Orabona 4, 70125 Bari, Italy; (D.V.M.); (M.M.); (M.A.D.N.)
- Department of Sciences, University of Basilicata, Via Ateneo Lucano 10, 85100 Potenza, Italy
| | - Maria Antonietta Di Noia
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Via E. Orabona 4, 70125 Bari, Italy; (D.V.M.); (M.M.); (M.A.D.N.)
| | - Luigi Palmieri
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Via E. Orabona 4, 70125 Bari, Italy; (D.V.M.); (M.M.); (M.A.D.N.)
- CNR Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), 70126 Bari, Italy
- Correspondence: (L.P.); (F.P.)
| | - Ferdinando Palmieri
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Via E. Orabona 4, 70125 Bari, Italy; (D.V.M.); (M.M.); (M.A.D.N.)
- CNR Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), 70126 Bari, Italy
- Correspondence: (L.P.); (F.P.)
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Shahroor MA, Lasorsa FM, Porcelli V, Dweikat I, Di Noia MA, Gur M, Agostino G, Shaag A, Rinaldi T, Gasparre G, Guerra F, Castegna A, Todisco S, Abu-Libdeh B, Elpeleg O, Palmieri L. PNC2 (SLC25A36) Deficiency Associated With the Hyperinsulinism/Hyperammonemia Syndrome. J Clin Endocrinol Metab 2022; 107:1346-1356. [PMID: 34971397 DOI: 10.1210/clinem/dgab932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Indexed: 11/19/2022]
Abstract
CONTEXT The hyperinsulinism/hyperammonemia (HI/HA) syndrome, the second-most common form of congenital hyperinsulinism, has been associated with dominant mutations in GLUD1, coding for the mitochondrial enzyme glutamate dehydrogenase, that increase enzyme activity by reducing its sensitivity to allosteric inhibition by GTP. OBJECTIVE To identify the underlying genetic etiology in 2 siblings who presented with the biochemical features of HI/HA syndrome but did not carry pathogenic variants in GLUD1, and to determine the functional impact of the newly identified mutation. METHODS The patients were investigated by whole exome sequencing. Yeast complementation studies and biochemical assays on the recombinant mutated protein were performed. The consequences of stable slc25a36 silencing in HeLa cells were also investigated. RESULTS A homozygous splice site variant was identified in solute carrier family 25, member 36 (SLC25A36), encoding the pyrimidine nucleotide carrier 2 (PNC2), a mitochondrial nucleotide carrier that transports pyrimidine as well as guanine nucleotides across the inner mitochondrial membrane. The mutation leads to a 26-aa in-frame deletion in the first repeat domain of the protein, which abolishes transport activity. Furthermore, knockdown of slc25a36 expression in HeLa cells caused a marked reduction in the mitochondrial GTP content, which likely leads to a hyperactivation of glutamate dehydrogenase in our patients. CONCLUSION We report for the first time a mutation in PNC2/SLC25A36 leading to HI/HA and provide functional evidence of the molecular mechanism responsible for this phenotype. Our findings underscore the importance of mitochondrial nucleotide metabolism and expand the role of mitochondrial transporters in insulin secretion.
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Affiliation(s)
- Maher A Shahroor
- Department of Pediatrics and Genetics, Al Makassed Hospital and Al-Quds University, 95908 Jerusalem, Palestine
- Department of Neonatology, Sunnybrook Health Sciences Center, University of Toronto, M4N 3M5 Toronto, Canada
| | - Francesco M Lasorsa
- Laboratory of Biochemistry and Molecular Biology, Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari Aldo Moro, 70125 Bari, Italy
- CNR Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, 70125 Bari, Italy
| | - Vito Porcelli
- Laboratory of Biochemistry and Molecular Biology, Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari Aldo Moro, 70125 Bari, Italy
| | - Imad Dweikat
- Metabolic Unit, An-Najah National University, P467 Nablus, Palestine
| | - Maria Antonietta Di Noia
- Laboratory of Biochemistry and Molecular Biology, Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari Aldo Moro, 70125 Bari, Italy
| | - Michal Gur
- Department of Genetics, Hadassah, Hebrew University Medical Center, 91120 Jerusalem, Israel
| | - Giulia Agostino
- Laboratory of Biochemistry and Molecular Biology, Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari Aldo Moro, 70125 Bari, Italy
| | - Avraham Shaag
- Department of Genetics, Hadassah, Hebrew University Medical Center, 91120 Jerusalem, Israel
| | - Teresa Rinaldi
- Pasteur Institute-Cenci Bolognetti Foundation, Department of Biology and Biotechnology "Charles Darwin", University of Rome La Sapienza, 00185 Rome, Italy
| | - Giuseppe Gasparre
- Department of Medical and Surgical Sciences (DIMEC), Unit of Medical Genetics and Center for Applied Biomedical Research (CRBA), University of Bologna, 40138 Bologna, Italy
| | - Flora Guerra
- Department of Medical and Surgical Sciences (DIMEC), Unit of Medical Genetics and Center for Applied Biomedical Research (CRBA), University of Bologna, 40138 Bologna, Italy
| | - Alessandra Castegna
- Laboratory of Biochemistry and Molecular Biology, Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari Aldo Moro, 70125 Bari, Italy
- CNR Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, 70125 Bari, Italy
| | - Simona Todisco
- Laboratory of Biochemistry and Molecular Biology, Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari Aldo Moro, 70125 Bari, Italy
| | - Bassam Abu-Libdeh
- Department of Pediatrics and Genetics, Al Makassed Hospital and Al-Quds University, 95908 Jerusalem, Palestine
| | - Orly Elpeleg
- Department of Genetics, Hadassah, Hebrew University Medical Center, 91120 Jerusalem, Israel
| | - Luigi Palmieri
- Laboratory of Biochemistry and Molecular Biology, Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari Aldo Moro, 70125 Bari, Italy
- CNR Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, 70125 Bari, Italy
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Castellaneta A, Losito I, Coniglio D, Leoni B, Santamaria P, Di Noia MA, Palmieri L, Calvano CD, Cataldi TRI. LIPIC: An Automated Workflow to Account for Isotopologue-Related Interferences in Electrospray Ionization High-Resolution Mass Spectra of Phospholipids. J Am Soc Mass Spectrom 2021; 32:1008-1019. [PMID: 33705659 DOI: 10.1021/jasms.1c00008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
In the past decade, hydrophilic interaction liquid chromatography (HILIC) has emerged as an efficient alternative to reversed-phase chromatography (RPC) for the analysis of phospholipid (PL) mixtures based on mass spectrometric detection. Since the separation of PL by HILIC is chiefly based on their headgroup, the mass spectrum of each class can be obtained by spectral averaging under the corresponding HILIC band. Using experimental m/z values resulting from high mass resolution/accuracy instruments, the sum compositions of PL in a specific class can be thus inferred but partial overlapping may occur between signals related to the M + 0 isotopologue of one species and the M + 2/M + 4 isotopologues of species having one/two more C═C bonds in their chemical structures. Here, an automated workflow, named LIPIC (lipid isotopic pattern interference correction), is proposed to account for such interferences. Starting from the experimentally verified assumption that peaks in isotope patterns are Gaussian, LIPIC predicts, as a function of m/z ratio, signal intensities due to M + 2 and M + 4 isotopologues of species with one or two more C = C bonds than the target one and calculates the corrected intensity for the M + 0 isotopologue of the latter. Thanks to an iterative procedure, the suggested algorithm compensates also for slight shifts occurring between experimental and theoretical m/z ratios related to isotopologue peaks. Examples of applications to simulated and experimental mass spectra of two PL classes, i.e., phosphatidylcholines (PC) and cardiolipins (CL), emphasize the increased extent of correction at the increase of molecular masses of involved species.
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Menga A, Serra M, Todisco S, Riera‐Domingo C, Ammarah U, Ehling M, Palmieri EM, Di Noia MA, Gissi R, Favia M, Pierri CL, Porporato PE, Castegna A, Mazzone M. Glufosinate constrains synchronous and metachronous metastasis by promoting anti-tumor macrophages. EMBO Mol Med 2020; 12:e11210. [PMID: 32885605 PMCID: PMC7539200 DOI: 10.15252/emmm.201911210] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 07/31/2020] [Accepted: 08/01/2020] [Indexed: 01/19/2023] Open
Abstract
Glutamine synthetase (GS) generates glutamine from glutamate and controls the release of inflammatory mediators. In macrophages, GS activity, driven by IL10, associates to the acquisition of M2-like functions. Conditional deletion of GS in macrophages inhibits metastasis by boosting the formation of anti-tumor, M1-like, tumor-associated macrophages (TAMs). From this basis, we evaluated the pharmacological potential of GS inhibitors in targeting metastasis, identifying glufosinate as a specific human GS inhibitor. Glufosinate was tested in both cultured macrophages and on mice bearing metastatic lung, skin and breast cancer. We found that glufosinate rewires macrophages toward an M1-like phenotype both at the primary tumor and metastatic site, countering immunosuppression and promoting vessel sprouting. This was also accompanied to a reduction in cancer cell intravasation and extravasation, leading to synchronous and metachronous metastasis growth inhibition, but no effects on primary tumor growth. Glufosinate treatment was well-tolerated, without liver and brain toxicity, nor hematopoietic defects. These results identify GS as a druggable enzyme to rewire macrophage functions and highlight the potential of targeting metabolic checkpoints in macrophages to treat cancer metastasis.
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Affiliation(s)
- Alessio Menga
- Laboratory of Tumor Inflammation and AngiogenesisCenter for Cancer Biology (CCB)VIBLeuvenBelgium
- Laboratory of Tumor Inflammation and AngiogenesisDepartment of OncologyKU LeuvenLeuvenBelgium
- Department of Molecular Biotechnology and Health ScienceMolecular Biotechnology CentreUniversity of TorinoTorinoItaly
- Department of Biosciences, Biotechnologies and BiopharmaceuticsUniversity of BariBariItaly
| | - Marina Serra
- Laboratory of Tumor Inflammation and AngiogenesisCenter for Cancer Biology (CCB)VIBLeuvenBelgium
- Laboratory of Tumor Inflammation and AngiogenesisDepartment of OncologyKU LeuvenLeuvenBelgium
| | - Simona Todisco
- Department of SciencesUniversity of BasilicataPotenzaItaly
| | - Carla Riera‐Domingo
- Laboratory of Tumor Inflammation and AngiogenesisCenter for Cancer Biology (CCB)VIBLeuvenBelgium
- Laboratory of Tumor Inflammation and AngiogenesisDepartment of OncologyKU LeuvenLeuvenBelgium
| | - Ummi Ammarah
- Department of Molecular Biotechnology and Health ScienceMolecular Biotechnology CentreUniversity of TorinoTorinoItaly
| | - Manuel Ehling
- Laboratory of Tumor Inflammation and AngiogenesisCenter for Cancer Biology (CCB)VIBLeuvenBelgium
- Laboratory of Tumor Inflammation and AngiogenesisDepartment of OncologyKU LeuvenLeuvenBelgium
| | - Erika M Palmieri
- Cancer & Inflammation ProgramNational Cancer InstituteFrederickMDUSA
| | | | - Rosanna Gissi
- Department of Biosciences, Biotechnologies and BiopharmaceuticsUniversity of BariBariItaly
| | - Maria Favia
- Department of Biosciences, Biotechnologies and BiopharmaceuticsUniversity of BariBariItaly
| | - Ciro L Pierri
- Department of Biosciences, Biotechnologies and BiopharmaceuticsUniversity of BariBariItaly
| | - Paolo E Porporato
- Department of Molecular Biotechnology and Health ScienceMolecular Biotechnology CentreUniversity of TorinoTorinoItaly
| | - Alessandra Castegna
- Department of Biosciences, Biotechnologies and BiopharmaceuticsUniversity of BariBariItaly
- IBIOM‐CNRInstitute of Biomembranes, Bioenergetics and Molecular BiotechnologiesNational Research CouncilBariItaly
| | - Massimiliano Mazzone
- Laboratory of Tumor Inflammation and AngiogenesisCenter for Cancer Biology (CCB)VIBLeuvenBelgium
- Laboratory of Tumor Inflammation and AngiogenesisDepartment of OncologyKU LeuvenLeuvenBelgium
- Department of Molecular Biotechnology and Health ScienceMolecular Biotechnology CentreUniversity of TorinoTorinoItaly
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Gorgoglione R, Porcelli V, Santoro A, Daddabbo L, Vozza A, Monné M, Di Noia MA, Palmieri L, Fiermonte G, Palmieri F. The human uncoupling proteins 5 and 6 (UCP5/SLC25A14 and UCP6/SLC25A30) transport sulfur oxyanions, phosphate and dicarboxylates. Biochim Biophys Acta Bioenerg 2019; 1860:724-733. [PMID: 31356773 DOI: 10.1016/j.bbabio.2019.07.010] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 06/27/2019] [Accepted: 07/25/2019] [Indexed: 01/07/2023]
Abstract
The human genome encodes 53 members of the solute carrier family 25 (SLC25), also called the mitochondrial carrier family. In this work, two members of this family, UCP5 (BMCP1, brain mitochondrial carrier protein 1 encoded by SLC25A14) and UCP6 (KMCP1, kidney mitochondrial carrier protein 1 encoded by SLC25A30) have been thoroughly characterized biochemically. They were overexpressed in bacteria, purified and reconstituted in phospholipid vesicles. Their transport properties and kinetic parameters demonstrate that UCP5 and UCP6 transport inorganic anions (sulfate, sulfite, thiosulfate and phosphate) and, to a lesser extent, a variety of dicarboxylates (e.g. malonate, malate and citramalate) and, even more so, aspartate and (only UCP5) glutamate and tricarboxylates. Both carriers catalyzed a fast counter-exchange transport and a very low uniport of substrates. Transport was saturable and inhibited by mercurials and other mitochondrial carrier inhibitors at various degrees. The transport affinities of UCP5 and UCP6 were higher for sulfate and thiosulfate than for any other substrate, whereas the specific activity of UCP5 was much higher than that of UCP6. It is proposed that a main physiological role of UCP5 and UCP6 is to catalyze the export of sulfite and thiosulfate (the H2S degradation products) from the mitochondria, thereby modulating the level of the important signal molecule H2S.
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Affiliation(s)
- Ruggiero Gorgoglione
- Department of Biosciences, Biotechnologies and Biopharmaceutics, Laboratory of Biochemistry and Molecular Biology, University of Bari Aldo Moro, Via E. Orabona 4, 70125 Bari, Italy
| | - Vito Porcelli
- Department of Biosciences, Biotechnologies and Biopharmaceutics, Laboratory of Biochemistry and Molecular Biology, University of Bari Aldo Moro, Via E. Orabona 4, 70125 Bari, Italy
| | - Antonella Santoro
- Department of Biosciences, Biotechnologies and Biopharmaceutics, Laboratory of Biochemistry and Molecular Biology, University of Bari Aldo Moro, Via E. Orabona 4, 70125 Bari, Italy
| | - Lucia Daddabbo
- Department of Biosciences, Biotechnologies and Biopharmaceutics, Laboratory of Biochemistry and Molecular Biology, University of Bari Aldo Moro, Via E. Orabona 4, 70125 Bari, Italy
| | - Angelo Vozza
- Department of Biosciences, Biotechnologies and Biopharmaceutics, Laboratory of Biochemistry and Molecular Biology, University of Bari Aldo Moro, Via E. Orabona 4, 70125 Bari, Italy; Center of Excellence in Comparative Genomics, University of Bari, via Orabona 4, 70125 Bari, Italy
| | - Magnus Monné
- Department of Biosciences, Biotechnologies and Biopharmaceutics, Laboratory of Biochemistry and Molecular Biology, University of Bari Aldo Moro, Via E. Orabona 4, 70125 Bari, Italy; Department of Sciences, University of Basilicata, Via Ateneo Lucano 10, 85100 Potenza, Italy
| | - Maria Antonietta Di Noia
- Department of Biosciences, Biotechnologies and Biopharmaceutics, Laboratory of Biochemistry and Molecular Biology, University of Bari Aldo Moro, Via E. Orabona 4, 70125 Bari, Italy
| | - Luigi Palmieri
- Department of Biosciences, Biotechnologies and Biopharmaceutics, Laboratory of Biochemistry and Molecular Biology, University of Bari Aldo Moro, Via E. Orabona 4, 70125 Bari, Italy; Center of Excellence in Comparative Genomics, University of Bari, via Orabona 4, 70125 Bari, Italy; CNR Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), 70126 Bari, Italy
| | - Giuseppe Fiermonte
- Department of Biosciences, Biotechnologies and Biopharmaceutics, Laboratory of Biochemistry and Molecular Biology, University of Bari Aldo Moro, Via E. Orabona 4, 70125 Bari, Italy; Center of Excellence in Comparative Genomics, University of Bari, via Orabona 4, 70125 Bari, Italy.
| | - Ferdinando Palmieri
- Department of Biosciences, Biotechnologies and Biopharmaceutics, Laboratory of Biochemistry and Molecular Biology, University of Bari Aldo Moro, Via E. Orabona 4, 70125 Bari, Italy; Center of Excellence in Comparative Genomics, University of Bari, via Orabona 4, 70125 Bari, Italy; CNR Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), 70126 Bari, Italy
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Bochicchio A, Cefola R, Choppin S, Colobert F, Di Noia MA, Funicello M, Hanquet G, Pisano I, Todisco S, Chiummiento L. Selective Claisen rearrangement and iodination for the synthesis of polyoxygenated allyl phenol derivatives. Tetrahedron Lett 2016. [DOI: 10.1016/j.tetlet.2016.07.079] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Todisco S, Di Noia MA, Onofrio A, Parisi G, Punzi G, Redavid G, De Grassi A, Pierri CL. Identification of new highly selective inhibitors of the human ADP/ATP carriers by molecular docking and in vitro transport assays. Biochem Pharmacol 2015; 100:112-32. [PMID: 26616220 DOI: 10.1016/j.bcp.2015.11.019] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 11/18/2015] [Indexed: 12/16/2022]
Abstract
Mitochondrial carriers are proteins that shuttle a variety of metabolites, nucleotides and coenzymes across the inner mitochondrial membrane. The mitochondrial ADP/ATP carriers (AACs) specifically translocate the ATP synthesized within mitochondria to the cytosol in exchange for the cytosolic ADP, playing a key role in energy production, in promoting cell viability and regulating mitochondrial permeability transition pore opening. In Homo sapiens four genes code for AACs with different tissue distribution and expression patterns. Since AACs are dysregulated in several cancer types, the employment of known and new AAC inhibitors might be crucial for inducing mitochondrial-mediated apoptosis in cancer cells. Albeit carboxyatractyloside (CATR) and bongkrekic acid (BKA) are known to be powerful and highly selective AAC inhibitors, able to induce mitochondrial dysfunction at molecular level and poisoning at physiological level, we estimated here for the first time their affinity for the human recombinant AAC2 by in vitro transport assays. We found that the inhibition constants of CATR and BKA are 4 nM and 2.0 μM, respectively. For finding new AAC inhibitors we also performed a docking-based virtual screening of an in-house developed chemical library and we identified about 100 ligands showing high affinity for the AAC2 binding region. By testing 13 commercially available molecules, out of the 100 predicted candidates, we found that 2 of them, namely suramin and chebulinic acid, are competitive AAC2 inhibitors with inhibition constants 0.3 μM and 2.1 μM, respectively. We also demonstrated that chebulinic acid and suramin are "highly selective" AAC2 inhibitors, since they poorly inhibit other human mitochondrial carriers (namely ORC1, APC1 and AGC1).
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Affiliation(s)
- Simona Todisco
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Via Orabona 4, 70125 Bari, Italy; Department of Sciences, University of Basilicata, Via N. Sauro 85, 85100 Potenza, Italy
| | - Maria Antonietta Di Noia
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Via Orabona 4, 70125 Bari, Italy
| | - Angelo Onofrio
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Via Orabona 4, 70125 Bari, Italy
| | - Giovanni Parisi
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Via Orabona 4, 70125 Bari, Italy
| | - Giuseppe Punzi
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Via Orabona 4, 70125 Bari, Italy
| | - Giandomenico Redavid
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Via Orabona 4, 70125 Bari, Italy
| | - Anna De Grassi
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Via Orabona 4, 70125 Bari, Italy
| | - Ciro Leonardo Pierri
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Via Orabona 4, 70125 Bari, Italy.
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Onofrio A, Parisi G, Punzi G, Todisco S, Di Noia MA, Bossis F, Turi A, De Grassi A, Pierri CL. Distance-dependent hydrophobic-hydrophobic contacts in protein folding simulations. Phys Chem Chem Phys 2015; 16:18907-17. [PMID: 25083519 DOI: 10.1039/c4cp01131g] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Successful prediction of protein folding from an amino acid sequence is a challenge in computational biology. In order to reveal the geometric constraints that drive protein folding, highlight those constraints kept or missed by distinct lattices and for establishing which class of intra- and inter-secondary structure element interactions is the most relevant for the correct folding of proteins, we have calculated inter-alpha carbon distances in a set of 42 crystal structures consisting of mainly helix, sheet or mixed conformations. The inter-alpha carbon distances were also calculated in several lattice "hydrophobic-polar" models built from the same protein set. We found that helix structures are more prone to form "hydrophobic-hydrophobic" contacts than beta-sheet structures. At a distance lower than or equal to 3.8 Å (very short-range interactions), "hydrophobic-hydrophobic" contacts are almost absent in the native structures, while they are frequent in all the analyzed lattice models. At distances in-between 3.8 and 9.5 Å (short-/medium-range interactions), the best performing lattice for reproducing mainly helix structures is the body-centered-cubic lattice. If protein structures contain sheet portions, lattice performances get worse, with few exceptions observed for double-tetrahedral and body-centered-cubic lattices. Finally, we can observe that ab initio protein folding algorithms, i.e. those based on the employment of lattices and Monte Carlo simulated annealings, can be improved simply and effectively by preventing the generation of "hydrophobic-hydrophobic" contacts shorter than 3.8 Å, by monitoring the "hydrophobic-hydrophobic/polar-polar" contact ratio in short-/medium distance ranges and by using preferentially a body-centered-cubic lattice.
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Affiliation(s)
- Angelo Onofrio
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Via Orabona 4, 70125, Bari, Italy.
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Di Noia MA, Todisco S, Cirigliano A, Rinaldi T, Agrimi G, Iacobazzi V, Palmieri F. The human SLC25A33 and SLC25A36 genes of solute carrier family 25 encode two mitochondrial pyrimidine nucleotide transporters. J Biol Chem 2014; 289:33137-48. [PMID: 25320081 DOI: 10.1074/jbc.m114.610808] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The human genome encodes 53 members of the solute carrier family 25 (SLC25), also called the mitochondrial carrier family, many of which have been shown to transport inorganic anions, amino acids, carboxylates, nucleotides, and coenzymes across the inner mitochondrial membrane, thereby connecting cytosolic and matrix functions. Here two members of this family, SLC25A33 and SLC25A36, have been thoroughly characterized biochemically. These proteins were overexpressed in bacteria and reconstituted in phospholipid vesicles. Their transport properties and kinetic parameters demonstrate that SLC25A33 transports uracil, thymine, and cytosine (deoxy)nucleoside di- and triphosphates by an antiport mechanism and SLC25A36 cytosine and uracil (deoxy)nucleoside mono-, di-, and triphosphates by uniport and antiport. Both carriers also transported guanine but not adenine (deoxy)nucleotides. Transport catalyzed by both carriers was saturable and inhibited by mercurial compounds and other inhibitors of mitochondrial carriers to various degrees. In confirmation of their identity (i) SLC25A33 and SLC25A36 were found to be targeted to mitochondria and (ii) the phenotypes of Saccharomyces cerevisiae cells lacking RIM2, the gene encoding the well characterized yeast mitochondrial pyrimidine nucleotide carrier, were overcome by expressing SLC25A33 or SLC25A36 in these cells. The main physiological role of SLC25A33 and SLC25A36 is to import/export pyrimidine nucleotides into and from mitochondria, i.e. to accomplish transport steps essential for mitochondrial DNA and RNA synthesis and breakdown.
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Affiliation(s)
- Maria Antonietta Di Noia
- From the Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, via Orabona 4, 70125 Bari, Italy, Department of Sciences, University of Basilicata, via N. Sauro 85, 85100 Potenza, Italy
| | - Simona Todisco
- From the Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, via Orabona 4, 70125 Bari, Italy
| | - Angela Cirigliano
- Pasteur Institute-Cenci Bolognetti Foundation, Department of Biology and Biotechnology "Charles Darwin," University of Rome La Sapienza, 00185 Rome, Italy, Associazione Gian Franco Lupo "Un Sorriso alla Vita," ASM Azienda Sanitaria Locale di Matera, via Montescaglioso 75100 Matera, Italy, and
| | - Teresa Rinaldi
- Pasteur Institute-Cenci Bolognetti Foundation, Department of Biology and Biotechnology "Charles Darwin," University of Rome La Sapienza, 00185 Rome, Italy
| | - Gennaro Agrimi
- From the Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, via Orabona 4, 70125 Bari, Italy
| | - Vito Iacobazzi
- From the Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, via Orabona 4, 70125 Bari, Italy, Center of Excellence in Comparative Genomics, University of Bari, via Orabona 4, 70125 Bari, Italy
| | - Ferdinando Palmieri
- From the Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, via Orabona 4, 70125 Bari, Italy, Center of Excellence in Comparative Genomics, University of Bari, via Orabona 4, 70125 Bari, Italy
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Todisco S, Di Noia MA, Castegna A, Lasorsa FM, Paradies E, Palmieri F. The Saccharomyces cerevisiae gene YPR011c encodes a mitochondrial transporter of adenosine 5'-phosphosulfate and 3'-phospho-adenosine 5'-phosphosulfate. Biochim Biophys Acta 2013; 1837:326-34. [PMID: 24296033 DOI: 10.1016/j.bbabio.2013.11.013] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Revised: 11/15/2013] [Accepted: 11/21/2013] [Indexed: 11/19/2022]
Abstract
The genome of Saccharomyces cerevisiae contains 35 members of the mitochondrial carrier family, nearly all of which have been functionally characterized. In this study, the identification of the mitochondrial carrier for adenosine 5'-phosphosulfate (APS) is described. The corresponding gene (YPR011c) was overexpressed in bacteria. The purified protein was reconstituted into phospholipid vesicles and its transport properties and kinetic parameters were characterized. It transported APS, 3'-phospho-adenosine 5'-phosphosulfate, sulfate and phosphate almost exclusively by a counter-exchange mechanism. Transport was saturable and inhibited by bongkrekic acid and other inhibitors. To investigate the physiological significance of this carrier in S. cerevisiae, mutants were subjected to thermal shock at 45°C in the presence of sulfate and in the absence of methionine. At 45°C cells lacking YPR011c, engineered cells (in which APS is produced only in mitochondria) and more so the latter cells, in which the exit of mitochondrial APS is prevented by the absence of YPR011cp, were less thermotolerant. Moreover, at the same temperature all these cells contained less methionine and total glutathione than wild-type cells. Our results show that S. cerevisiae mitochondria are equipped with a transporter for APS and that YPR011cp-mediated mitochondrial transport of APS occurs in S. cerevisiae under thermal stress conditions.
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Affiliation(s)
- Simona Todisco
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, via Orabona 4, 70125 Bari, Italy; Center of Excellence in Comparative Genomics, University of Bari, Italy
| | | | - Alessandra Castegna
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, via Orabona 4, 70125 Bari, Italy; Center of Excellence in Comparative Genomics, University of Bari, Italy
| | - Francesco Massimo Lasorsa
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, via Orabona 4, 70125 Bari, Italy; CNR Institute of Biomembranes and Bioenergetics, via Amendola 165/A, 70126 Bari, Italy
| | - Eleonora Paradies
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, via Orabona 4, 70125 Bari, Italy; CNR Institute of Biomembranes and Bioenergetics, via Amendola 165/A, 70126 Bari, Italy
| | - Ferdinando Palmieri
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, via Orabona 4, 70125 Bari, Italy; Center of Excellence in Comparative Genomics, University of Bari, Italy.
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Di Noia MA, Van Driesche S, Palmieri F, Yang LM, Quan S, Goodman AI, Abraham NG. Heme oxygenase-1 enhances renal mitochondrial transport carriers and cytochrome C oxidase activity in experimental diabetes. J Biol Chem 2006; 281:15687-93. [PMID: 16595661 DOI: 10.1074/jbc.m510595200] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Up-regulation of heme oxygenase (HO-1) by either cobalt protoporphyrin (CoPP) or human gene transfer improves vascular and renal function by several mechanisms, including increases in antioxidant levels and decreases in reactive oxygen species (ROS) in vascular and renal tissue. The purpose of the present study was to determine the effect of HO-1 overexpression on mitochondrial transporters, cytochrome c oxidase, and anti-apoptotic proteins in diabetic rats (streptozotocin, (STZ)-induced type 1 diabetes). Renal mitochondrial carnitine, deoxynucleotide, and ADP/ATP carriers were significantly reduced in diabetic compared with nondiabetic rats (p < 0.05). The citrate carrier was not significantly decreased in diabetic tissue. CoPP administration produced a robust increase in carnitine, citrate, deoxynucleotide, dicarboxylate, and ADP/ATP carriers and no significant change in oxoglutarate and aspartate/glutamate carriers. The increase in mitochondrial carriers (MCs) was associated with a significant increase in cytochrome c oxidase activity. The administration of tin mesoporphyrin (SnMP), an inhibitor of HO-1 activity, prevented the restoration of MCs in diabetic rats. Human HO-1 cDNA transfer into diabetic rats increased both HO-1 protein and activity, and restored mitochondrial ADP/ATP and deoxynucleotide carriers. The increase in HO-1 by CoPP administration was associated with a significant increase in the phosphorylation of AKT and levels of BcL-XL proteins. These observations in experimental diabetes suggest that the cytoprotective mechanism of HO-1 against oxidative stress involves an increase in the levels of MCs and anti-apoptotic proteins as well as in cytochrome c oxidase activity.
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