150 results on '"Ballario P"'
Search Results
52. Cloning of a yeast gene coding for the glutamate synthase small subunit (GUS2) by complementation ofSaccharomyces cerevisiaeandEscherichia coliglutamate auxotrophs
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Gonzàlez, A., primary, Membrillo-Hernández, J., additional, Olivera, H., additional, Aranda, C., additional, Macino, G., additional, and Ballario, P., additional
- Published
- 1992
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53. A Novel Histone Acetyltransferase Inhibitor Modulating Gcn5 Network: Cyclopentylidene-[4-(4′-chlorophenyl)thiazol-2-yl)hydrazone.
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Franco Chimenti, Bruna Bizzarri, Elias Maccioni, Daniela Secci, Adriana Bolasco, Paola Chimenti, Rossella Fioravanti, Arianna Granese, Simone Carradori, Federica Tosi, Paola Ballario, Stefano Vernarecci, and Patrizia Filetici
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- 2009
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54. The Neurospora crassa carotenoid biosynthetic gene (albino 3) reveals highly conserved regions among prenyltransferases.
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Carattoli, A, primary, Romano, N, additional, Ballario, P, additional, Morelli, G, additional, and Macino, G, additional
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- 1991
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55. CBM1, a Neurospora crassa genomic cosmid library in pAC3 and its use for walking on the right arm of linkage group VII
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CABIBBO, A., primary, SPORENO, E., additional, MACINO, G., additional, and BALLARIO, P., additional
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- 1991
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56. A cloud chamber observation of a single charged unstable fragment
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Alexander, G., Ballario, C., Bizzarri, B., Brunelli, B., Demarco, A., Michblini, A., Moneti, G. C., Zavattini, E., Zichichi, A., and Astbury, J. P.
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- 1956
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57. In vivo mutagenesis of the N. Crassa carotenoid biosynthetic gene(al-3)
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ROMANO, N, primary, BALLARIO, P, additional, MORELLI, G, additional, CARATTOLI, A, additional, and MACINO, G, additional
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- 1990
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58. Molecular cloning of carotenoid biosynthetic gene (al-3)
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CARATTOLI, A, primary, ROMANO, N, additional, SPORENO, E, additional, MORELLI, G, additional, BALLARIO, P, additional, and MACINO, G, additional
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- 1990
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59. Photoregulated expression of the gene of
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MORELLI, G, primary, BAIMA, S, additional, BALLARIO, P, additional, CARATTOLI, A, additional, and MACINO, G, additional
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- 1990
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60. Physical association of the WC-1 photoreceptor and the histone acetyltransferase NGF-1 is required for blue light signal transduction in Neurospora crassa
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Brenna, Andrea, Grimaldi, Benedetto, Filetici, Patrizia, and Ballario, Paola
- Abstract
Neurosporaand higher eukaryotes share a common mechanism for the signal transduction of environmental stimuli. A scenario is given in which the NeurosporaWC-1 photoreceptor represents a function orthologous to that of vertebrate nuclear receptors, acting through the association with the HAT NGF-1 via a vertebrate-like LXXLL motif.
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- 2012
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61. Cloning of a yeast gene coding for the glutamate synthase small subunit (GUS2) by complementation of Saccharomyces cerevisiae and Escherichia coli glutamate auxotrophs.
- Author
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González, A., Membrillo-Hernández, J., Olivera, H., Aranda, C., Macino, G., and Ballario, P.
- Subjects
SACCHAROMYCES cerevisiae ,YEAST ,GENES ,CLONING ,ESCHERICHIA coli - Abstract
A Saccharomyces cerevisiae glutamate auxotroph, lacking NADP-glutamate dehydrogenase (NADPGDH) and glutamate synthase (GOGAT) activities, was complemented with a yeast genomic library. Clones were obtained which still lacked NADP-GDH but showed GOGAT activity. Northern analysis revealed that the DNA fragment present in the complementing plasmids coded for a 1.5kb mRNA. Since the only GOGAT enzyme so far purified from S. cerevisiae is made up of a small and a large subunit, the size of the mRNA suggested that the cloned DNA fragment could code for the GOGAT small subunit. Plasmids were purified and used to transform Escherichia coli glutamate auxotrophs. Transformants were only recovered when the recipient strain was an E. coli GDH-less mutant lacking the small GOGAT subunit. These data show that we have cloned the structural gene coding for the yeast small subunit (GUS2). Evidence is also presented indicating that the GOGAT enzyme which is synthesized in the E. coli transformants is a hybrid comprising the large E. coli subunit and the small S. cerevisiae subunit. [ABSTRACT FROM AUTHOR]
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- 1992
62. The Neurospora crassaWhite Collar-1 dependent Blue Light Response Requires Acetylation of Histone H3 Lysine 14 by NGF-1
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Grimaldi, Benedetto, Coiro, Pierluca, Filetici, Patrizia, Berge, Emanuela, Dobosy, Joseph R., Freitag, Michael, Selker, Eric U., and Ballario, Paola
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Blue light-induced transcription in Neurospora crassais regulated by the White Collar-1 (WC-1) photoreceptor. We report that residue K14 of histone H3 associated with the light-inducible albino-3(al-3) promoter becomes transiently acetylated after photoinduction. This acetylation depends on WC-1. The relevance of this chromatin modification was directly evaluated in vivo by construction of a Neurosporastrain with a mutated histone H3 gene (hH3K14Q). This strain phenocopies a wc-1blind mutant and shows a strong reduction of light-induced transcriptional activation of both al-3and vivid(vvd), another light-inducible gene. We mutated Neurospora GCN Five (ngf-1), which encodes a homologue of the yeast HAT Gcn5p, to generate a strain impaired in H3 K14 acetylation and found that it was defective in photoinduction. Together, our findings reveal a direct link between histone modification and light signaling in Neurosporaand contribute to the developing understanding of the molecular mechanisms operating in light-inducible gene activation.
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- 2006
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63. The Neurospora crassa White Collar-1 dependent Blue Light Response Requires Acetylation of Histone H3 Lysine 14 by NGF-1
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Grimaldi, Benedetto, Coiro, Pierluca, Filetici, Patrizia, Berge, Emanuela, Dobosy, Joseph R., Freitag, Michael, Selker, Eric U., and Ballario, Paola
- Abstract
Blue light-induced transcription in Neurospora crassa is regulated by the White Collar-1 (WC-1) photoreceptor. We report that residue K14 of histone H3 associated with the light-inducible albino-3 (al-3) promoter becomes transiently acetylated after photoinduction. This acetylation depends on WC-1. The relevance of this chromatin modification was directly evaluated in vivo by construction of a Neurospora strain with a mutated histone H3 gene (hH3K14Q). This strain phenocopies a wc-1 blind mutant and shows a strong reduction of light-induced transcriptional activation of both al-3 and vivid (vvd), another light-inducible gene. We mutated Neurospora GCN Five (ngf-1), which encodes a homologue of the yeast HAT Gcn5p, to generate a strain impaired in H3 K14 acetylation and found that it was defective in photoinduction. Together, our findings reveal a direct link between histone modification and light signaling in Neurospora and contribute to the developing understanding of the molecular mechanisms operating in light-inducible gene activation.
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- 2006
64. Evaluation of P53 Protein Overexpression, Ki67 Proliferative Activity and Mitotic Index as Markers of Tumour Recurrence in Superficial Transitional Cell Carcinoma of the Bladder
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Gontero, P., Casetta, G., Zitella, A., Ballario, R., Pacchioni, D., Magnani, C., Muir, G.H., and Tizzani, A.
- Abstract
Objectives:To confirm the interrelationship between p53, ki67, mitotic index with others known prognostic factors such us stage, grade, multifocality, tumour size, history of recurrence in transitional cell carcinoma (TCC) of the bladder and to determine the prognostic impact of p53, Ki67 and mitotic index in predicting recurrence in superficial bladder cancer.Methods:Two hundred and fourteen patients with apparently superficial TCC of the bladder underwent TURBT and the 192 histologically Ta–T1 were divided into 104 primary lesions (group 1, mean follow–up 26 months) and 88 recurrent tumours (group 2, mean follow–up 28 months). Data concerning focality, tumour size, number of recurrences and recurrence–free survival were considered in each patients. All samples were immunohistochemically stained with p53 and Ki67 monoclonal antibodies. Mitotic index (MI) was calculated on haematoxylin and eosin stained sections.Results:Recurrence–free survival was significantly lower in superficial recurrent tumours (group 2) compared with primary tumours (group 1). P53 staining was correlated with grade and stage for both 5 and 20% positivity thresholds. Ki67 and MI were significantly different over strata defined by stage, grade and focality in both patients groups but only Ki67 showed a correlation with p53 status. Recurrence–free survival could not be predicted either by p53 status or MI. A 20% cut–off level of Ki67 staining resulted a good predictor of recurrence in group 1 Ta–T1/G1–G2 tumours (p = 0.03). Only Ki67 and multifocality were found to be independent prognostic factors of recurrence in multivariate analysis. Stratifying Ta–T1/G1–G2 patients according to these variables, Ki67 provided a useful tool to predict early recurrence in monofocal lesions from both groups.Conclusions:P53 and MI despite a fairly good correlation with traditional prognostic factors in bladder TCC seem to play no role in the prediction of tumoural recurrence. A Ki67 index over 20% predicts those single well–differentiated (Ta–T1/G1–G2) tumours which are likely to recur within one year of treatment
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- 2000
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65. The bromodomain of Gcn5p interacts in vitrowith specific residues in the N terminus of histone H411Edited by T. Richmond
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Ornaghi, Prisca, Ballario, Paola, Lena, Anna Maria, Gonzàlez, Alicia, and Filetici, Patrizia
- Abstract
Whereas the histone acetyltransferase activity of yeast Gcn5p has been widely studied, its structural interactions with the histones and the role of the carboxy-terminal bromodomain are still unclear. Using a glutathione S-transferase pull down assay we show that Gcn5p binds the amino-terminal tails of histones H3 and H4, but not H2A and H2B. The deletion of bromodomain abolishes this interaction and bromodomain alone is able to interact with the H3 and H4 N termini. The amino acid residues of the H4 N terminus involved in the binding with Gcn5p have been studied by site-directed mutagenesis. The substitution of amino acid residues R19 or R23 of the H4 N terminus with a glutamine (Q) abolishes the interaction with Gcn5p and the bromodomain. These residues differ from those known to be acetylated or to be involved in binding the SIR proteins. This evidence and the known dispensability of the bromodomain for Gcn5p acetyltransferase activity suggest a new structural role for the highly evolutionary conserved bromodomain.
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- 1999
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66. Ty1 extrachromosomal circular copies in Saccharomyces cerevisiae
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Ballario, Paola, Filetici, Patrizia, Junakovic, Nikolaj, and Pedone, Francesco
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The eukaryotic transposable element Ty1 is present in about 20–30 integrated copies per yeast aploid genome, variably localized in different strains. Here, we report the presence in yeast of circular extrachromosomal molecules homologous to Ty1, 6 kilobases in size (the same as integrated copies) present in about 1 circular copy/250–300 cells. This finding shows another analogy between eurkaryotic-transposable elements and the pro-viral integrative form of retroviruses.
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- 1983
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67. Effect of Extracellular Alkali Metal Salts on the Electric Parameters of Human Erythrocytes in Normal and Pathological Conditions (Homozygous β-Thalassemia)
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Ballario, C., Bonincontro, A., Cametti, C., Rosi, A., and Sportelli, L.
- Abstract
The conductivity of human erythrocyte cells dispersed in various uni-univalent electrolyte solutions (NaCl, KCl, LiCl, CsCl; 0.15 ᴍ) have been measured in the frequency range from 10 KHz to 100 MHz at five temperatures between 5 and 45 °C. The results were analyzed in the light of the theory of conductivity polarization of a suspension of ellipsoidal particles covered with two confocal shells.
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- 1984
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68. White collar proteins: PASsing the light signal in Neurospora crassa
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Ballario, P. and Macino, G.
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- 1997
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69. Conductivity of Normal and Pathological Human Erythrocytes (Homozygous β-Thalassemia) at Radiowave Frequencies
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Ballario, C., Bonincontro, A., Cametti, C., Rosi, A., and Sportelli, L.
- Abstract
The conductivity of normal and homozygous β-thalassemic erythrocyte suspensions has been measured over the frequency range from 5 KHz to 100 MHz in the temperature interval from 5 to 45 °C.
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- 1984
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70. Apparatus for Carbon-14 Dating
- Author
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Ballario, C., Beneventano, M., De Marco, A., Magistrelli, F., Cortesi, C., and Mantovani, T.
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- 1955
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71. Role of Shock wave Therapy in Peyronie's Disease
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Aresu, L., Ballario, R., Beltrami, P., Ruggera, L., Schiavone, D., and Artibani, W.
- Abstract
Shock wave therapy (ESWT) for the treatment of Peyronie's Disease (PD) is still controversial. The aim of this study is to evaluate the efficacy of shock wave therapy in patients candidates for surgical treatment of stable PD for at least 12 months.238 patients affected by PD were treated with ESWT since January 2000. We selected those patients (65 cases) who were having a stable disease for at least 12 months, previously treated unsuccessfully with different therapy (pharmacological, ionophoresis or infiltrations), and with an adequate follow-up. The parameters considered were the size modification of the lesion, the reduction of the penile deviation and the overall satisfaction for reaching an adequate sexual activity after the ESWT treatment. All patients received a 3000 shock waves treatment in 4 occasions during 2 weeks according to the institutional protocol.All the study patients reported to have an inadequate sexual function before the ESWT treatment. The mean age was 57 years, the penile deviation varied between 30° and 90° and the average follow-up was 18 months. In 43 cases (66%) the ultrasounds revealed a significant reduction of the penile deviation and 39 patients (60%) reported to have reached an adequate sexual activity after the ESWT treatment.ESWT represents a valid option in the treatment of PD considering that the patients’ main goal is to regain a satisfactory sexual activity. Therefore this non-invasive treatment should be included in the therapeutic guidelines of PD together with other non-surgical treatments.
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- 2006
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72. IN VITRO TRANSCRIPTION OF YEAST 2 μm DNA BY HOMOLOGOUS RNA POLYMERASE II. MAPPING OF INITIATION SITES AND EFFECTS OF PROTEIN FACTORS ON THE SELECTIVITY OF TRANSCRIPTION
- Author
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Ballario, P., primary, Buongiorno-Nardelli, M., additional, Carnevali, F., additional, Di Mauro, E., additional, and Pedone, F., additional
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- 1981
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73. Cosmids from the Vollmer-Yanofsky library identified with a chromosome VII probe.
- Author
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Ballario, P., primary, Morelli, G., additional, Sporeno, E., additional, and Macino, G., additional
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- 1989
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74. Life time estimate of λ° and θ° particles
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Ballario, C., Bizzarri, K., Brunelli, B., De Marco, A., Di Capua, E., Michelini, A., Moneti, G. C., Zavattini, E., and Zichichi, A.
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- 1949
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75. An Optical System for the Illumination of a Deep Wilson Chamber
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Ballario, C., Beneventano, M., Brunelli, B., and De Marco, A.
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- 1954
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76. Selective in vitro transcription by purified yeast RNA polymerase II on cloned 2 {micro}m DNA
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Ballario, Paola, Buongiorno-Nardelli, Mario, Carnevali, Francesca, Di Mauro, Ernesto, and Pedone, Francesco
- Abstract
The
in vitro transcription properties of purified yeast RNA polymerase II have been analyzed on prokaryotic plasmids (pBR322 and pBR313) and chimaeric plasmids bearing yeast 2 μm sequences (BTYP1, BTYH2 and BTYH3). Conditions for selective transcription of the 2μm DNA sequences in chimaeric plasmids have been determined. pBR322 and pBR313 are not transcribed by the purified RNA polymerase II when not bearing eukaryotic inserts. We show that the agarose gel electrophoretic analysis of ternary transcription complexes allows the localization of nascent RNA chains. The RNA produced has been visualized by electron microscopy (nascent RNA hybridization loops) and by gel electrophoretic analysis. All the observed properties are shared by RNA polymerase II purified by a conventional method (1) and by a rapid alternative procedure described herein. The peculiar properties of a partially purified form of RNA polymerase II are reported.- Published
- 1981
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77. Photoregulated expression of the al-3gene of Neurospora crassa
- Author
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Morelli, Giorgio, Baima, Simona, Ballario, Paola, Carattoli, Alessandra, and Macino, Giuseppe
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- 1990
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78. Molecular cloning of Neurospora crassacarotenoid biosynthetic gene (al-3)
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Carattoli, Alessandra, Romano, Nicoletta, Sporeno, Elisabetta, Morelli, Giorgio, Ballario, Paola, and Macino, Giuseppe
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- 1990
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79. Yeast RNA polymerase II transcription of circular DNA at different degrees of supercoiling
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Pedone, Francesco, Filetici, Patrizia, and Ballario, Paola
- Abstract
Purified yeast RNA polymerase II was tested for transcriptional activity as a function of the degree of circular DNA supercoiling. Chimaeric plasmids P30 and P31 both containing inserts from the yeast transposable element TY1 cloned in pBR322 and the vector pBR322 were used as templates. For pBR322 the transcriptional activity increases about 4 fold from the fully relaxed covalently closed circles to the native supercoiled forms, further supercoiling having no effect on transcription. P30 shows a 5 fold increase of transcriptional activity reaching a plateau at the native supercoiled conformation. However, at an intermediate degree of supercoiling {σ=0.024), transcription decreases to a value close to zero. P31 too exhibits a conformation (σ=0.014) in which there is a drop of transcriptional activity. Furthermore, a 10 fold increase of transcription is obtained at the higher values of superhelix density. Both kinetic and autoradiographic experiments confirm the existence of DNA conformations that can inhibit “in vitro” transcription.
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- 1982
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80. Périgord black truffle genome uncovers evolutionary origins and mechanisms of symbiosis
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Francis Martin, Annegret Kohler, Claude Murat, Raffaella Balestrini, Pedro M. Coutinho, Olivier Jaillon, Barbara Montanini, Emmanuelle Morin, Benjamin Noel, Riccardo Percudani, Bettina Porcel, Andrea Rubini, Antonella Amicucci, Joelle Amselem, Véronique Anthouard, Sergio Arcioni, François Artiguenave, Jean-Marc Aury, Paola Ballario, Angelo Bolchi, Andrea Brenna, Annick Brun, Marc Buée, Brandi Cantarel, Gérard Chevalier, Arnaud Couloux, Corinne Da Silva, France Denoeud, Sébastien Duplessis, Stefano Ghignone, Benoît Hilselberger, Mirco Iotti, Benoît Marçais, Antonietta Mello, Michele Miranda, Giovanni Pacioni, Hadi Quesneville, Claudia Riccioni, Roberta Ruotolo, Richard Splivallo, Vilberto Stocchi, Emilie Tisserant, Arturo Roberto Viscomi, Alessandra Zambonelli, Elisa Zampieri, Bernard Henrissat, Marc-Henri Lebrun, Francesco Paolocci, Paola Bonfante, Simone Ottonello, Patrick Wincker, Interactions Arbres-Microorganismes (IAM), Université de Lorraine (UL)-Institut National de la Recherche Agronomique (INRA), Istituto per la Protezione Sostenibile delle Piante (CNR-IPSP), UOS Torino, Architecture et fonction des Macromolécules Biologiques - UMR 6098 (AFMB), Université de Provence - Aix-Marseille 1-Centre National de la Recherche Scientifique (CNRS), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Dipartimento di Biochimica e Biologia Molecolare, Università degli studi di Parma [Parme, Italie], Chimie Et Interdisciplinarité : Synthèse, Analyse, Modélisation (CEISAM), Université de Nantes - Faculté des Sciences et des Techniques, Université de Nantes (UN)-Université de Nantes (UN)-Centre National de la Recherche Scientifique (CNRS), Consiglio Nazionale delle Ricerche [Milano] (CNR), Dipartimento di Scienze Biomolecolari Universita di Urbino (DISB), Università degli Studi di Urbino 'Carlo Bo', Institut National de la Recherche Agronomique (INRA), Génomique métabolique (UMR 8030), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Dipartimento di Genetica e Biologia Molecolare, Università degli Studi di Roma 'La Sapienza' [Rome], Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Università degli Studi di Bologna, Dipartimento di Biologia Vegetale, Università degli studi di Torino (UNITO), Dipartimento di Biologia di Base ed Applicata, Aquila University, Università degli Studi dell'Aquila [L'Aquila] (UNIVAQ.IT), Unité de Recherche Génomique Info (URGI), CNR IGV, Consiglio Nazionale delle Ricerche (CNR), University of Goettingen, Consiglio Nazionale delle Ricerche [Torino] (CNR), Architecture et fonction des macromolécules biologiques (AFMB), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), BIOlogie et GEstion des Risques en agriculture (BIOGER), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Istituto di Scienze e Tecnologie Molecolari = Institute of Molecular Science and Technologies (ISTM-CNR [Perugia - Milano]), ANR-06-BLAN-0399,FungEffector,A genome-wide survey of secreted proteins as effectors of symbiosis and pathogenicity in plant-associated fungi(2006), European Project: 33958,EVOLTREE, Martin, Francis, Murat-Furminieux, Claude, Martin F., Kohler A., Murat C., Balestrini R., Coutinho P.M., Jaillon O., Montanini B., Morin E., Noel B., Percudani R., Porcel B., Rubini A., Amicucci A., Amselem J., Anthouard V., Arcioni S., Artiguenave F., Aury J.M., Ballario P., Bolchi A., Brenna A., Brun A., Buée M., Cantarel B., Chevalier G., Couloux A., Da Silva C., Denoeud F., Duplessis S., Ghignone S., Hilselberger B., Iotti M., Mello M., Miranda M., Pacioni G., Quesneville H., Riccioni C., Ruotolo R., Splivallo R., Stocchi V., Tisserant E., Viscomi A.R., Zambonelli A., Zampieri E., Henrissat B., Lebrun M.H., Paolocci F., Bonfante P., Ottonello S., Wincker P., Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), CNR Istituto per la Protezione Sostenibile delle Piante [Torino, Italia] (IPSP), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Università degli studi di Parma = University of Parma (UNIPR), Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Università degli Studi di Roma 'La Sapienza' = Sapienza University [Rome] (UNIROMA), Alma Mater Studiorum Università di Bologna [Bologna] (UNIBO), Università degli studi di Torino = University of Turin (UNITO), Università degli Studi dell'Aquila = University of L'Aquila (UNIVAQ), Georg-August-University = Georg-August-Universität Göttingen, Centre National de la Recherche Scientifique (CNRS)-Université de Provence - Aix-Marseille 1, University of Parma = Università degli studi di Parma [Parme, Italie], Université de Nantes (UN)-Université de Nantes (UN)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Università degli Studi di Roma 'La Sapienza' = Sapienza University [Rome], Università degli Studi dell'Aquila (UNIVAQ), University of Göttingen - Georg-August-Universität Göttingen, Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), and AgroParisTech-Institut National de la Recherche Agronomique (INRA)
- Subjects
0106 biological sciences ,Tuber melanosporum ,tuber ,ectomycorrhizal fungi ,TRUFFE NOIRE DU PERIGORD ,[SDV]Life Sciences [q-bio] ,Genes, Fungal ,Molecular Sequence Data ,TRUFFE BLANCHE DU PIEMONT ,Carbohydrates ,Genomics ,Haploidy ,01 natural sciences ,Genome ,Ectosymbiosis ,Evolution, Molecular ,03 medical and health sciences ,truffe ,Symbiosis ,Ascomycota ,Tuber aestivum ,champignon comestible ,Fruiting Bodies, Fungal ,030304 developmental biology ,2. Zero hunger ,Genetics ,0303 health sciences ,Multidisciplinary ,Truffle ,biology ,génome ,Fungal genetics ,Sequence Analysis, DNA ,biology.organism_classification ,DNA Transposable Elements ,fungal genoma ,Genome, Fungal ,europe ,symbiose ,Sulfur ,010606 plant biology & botany - Abstract
Letter; International audience; The Périgord black truffle ($Tuber\ melanosporum$ Vittad.) and the Piedmont white truffle dominate today's truffle market. The hypogeous fruiting body of $T.\ melanosporum$ is a gastronomic delicacy produced by an ectomycorrhizal symbiont endemic to calcareous soils in southern Europe. The worldwide demand for this truffle has fuelled intense efforts at cultivation. Identification of processes that condition and trigger fruit body and symbiosis formation, ultimately leading to efficient crop production, will be facilitated by a thorough analysis of truffle genomic traits. In the ectomycorrhizal $Laccaria\ bicolor$, the expansion of gene families may have acted as a 'symbiosis toolbox'. This feature may however reflect evolution of this particular taxon and not a general trait shared by all ectomycorrhizal species. To get a better understanding of the biology and evolution of the ectomycorrhizal symbiosis, we report here the sequence of the haploid genome of $T.\ melanosporum$, which at $\sim$125 megabases is the largest and most complex fungal genome sequenced so far. This expansion results from a proliferation of transposable elements accounting for $\sim$58% of the genome. In contrast, this genome only contains $\sim$7,500 protein-coding genes with very rare multigene families. It lacks large sets of carbohydrate cleaving enzymes, but a few of them involved in degradation of plant cell walls are induced in symbiotic tissues. The latter feature and the upregulation of genes encoding for lipases and multicopper oxidases suggest that $T.\ melanosporum$ degrades its host cell walls during colonization. Symbiosis induces an increased expression of carbohydrate and amino acid transporters in both $L.\ bicolor$ and $T.\ melanosporum$, but the comparison of genomic traits in the two ectomycorrhizal fungi showed that genetic predispositions for symbiosis $-$'the symbiosis toolbox'$-$ evolved along different ways in ascomycetes and basidiomycetes
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- 2010
81. Photoreceptors in the dark: A functional white collar-like complex and other putative light-sensing components encoded by the genome of the subterranean fungus Tuber melanosporum.
- Author
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Gerace R, Montanini B, Proietto M, Levati E, De Luca C, Brenna A, Filetici P, Kohler A, Ottonello S, and Ballario P
- Subjects
- Computational Biology, Ascomycota genetics, Genome, Fungal, Photoreceptors, Microbial genetics
- Abstract
Light is perceived and transduced by fungi, where it modulates processes as diverse as growth and morphogenesis, sexual development and secondary metabolism. A special case in point is that of fungi with a subterranean, light-shielded habitat such as Tuber spp. Using as reference the genome sequence of the black truffle Tuber melanosporum, we used bioinformatic prediction tools and expression data to gain insight on the photoreceptor systems of this hypogeous ectomycorrhizal fungus. These include a chromophore-less opsin, a putative red-light-sensing phytochrome not expressed at detectable levels in any of the examined lifecycle stages, and a nearly canonical two-component (WC-1/WC-2) photoreceptor system similar to the Neurospora white collar complex (WCC). Multiple evidence, including expression at relatively high levels in all lifecycle stages except for fruiting-bodies and the results of heterologous functional complementation experiments conducted in Neurospora, suggests that the Tuber WCC is likely functional and capable of responding to blue-light. The other putative T. melanosporum photoreceptor components, especially the chromophore-less opsin and the likely non-functional phytochrome, may instead represent signatures of adaptation to a hypogeous (light-shielded) lifestyle., (Copyright © 2016 British Mycological Society. Published by Elsevier Ltd. All rights reserved.)
- Published
- 2017
- Full Text
- View/download PDF
82. SAGA DUB-Ubp8 Deubiquitylates Centromeric Histone Variant Cse4.
- Author
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Canzonetta C, Vernarecci S, Iuliani M, Marracino C, Belloni C, Ballario P, and Filetici P
- Subjects
- Alleles, Centromere metabolism, Endopeptidases genetics, Gene Deletion, Mitosis, Mutation, Peptide Elongation Factors metabolism, Protein Binding, Protein Multimerization, Protein Transport, Proteolysis, Ubiquitin-Protein Ligases metabolism, Ubiquitination, Chromosomal Proteins, Non-Histone metabolism, DNA-Binding Proteins metabolism, Endopeptidases metabolism, Saccharomyces cerevisiae Proteins metabolism, Trans-Activators metabolism
- Abstract
Aneuploidy, the unbalanced segregation of chromosomes during cell division, is recurrent in many tumors and the cause of birth defects and genetic diseases. Centromeric chromatin represents the chromosome attachment site to the mitotic spindle, marked by specialized nucleosomes containing a specific histone variant, CEN-H3/Cse4, in yeast. Mislocalization of Cse4 outside the centromere is deleterious and may cause aberrant chromosome behavior and mitotic loss. For this reason, ubiquitylation by the E3-ubiquitin ligase Psh1 and subsequent proteolysis tightly regulates its restricted localization. Among multiproteic machineries, the SAGA complex is not merely engaged in acetylation but also directly involved in deubiquitylation. In this study, we investigated the role of SAGA-DUB's Ubp8-driven deubiquitylation of the centromeric histone variant Cse4 in budding yeast. We found that Ubp8 works in concert with the E3-ubiquitin ligase Psh1, and that its loss causes defective deubiquitylation and the accumulation of a short ubiquitin oligomer on Cse4. We also show that lack of Ubp8 and defective deubiquitylation increase mitotic instability, cause faster Cse4 proteolysis and induce mislocalization of the centromeric histone outside the centromere. Our data provide evidence for a fundamental role of DUB-Ubp8 in deubiquitylation and the stability of the centromeric histone in budding yeast., (Copyright © 2016 Canzonetta et al.)
- Published
- 2015
- Full Text
- View/download PDF
83. Epigenetic and Posttranslational Modifications in Light Signal Transduction and the Circadian Clock in Neurospora crassa.
- Author
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Proietto M, Bianchi MM, Ballario P, and Brenna A
- Subjects
- Chromatin metabolism, Circadian Clocks radiation effects, Epigenesis, Genetic radiation effects, Light Signal Transduction radiation effects, Neurospora crassa radiation effects, Protein Processing, Post-Translational radiation effects, Circadian Clocks genetics, Light Signal Transduction genetics, Neurospora crassa genetics, Protein Processing, Post-Translational genetics
- Abstract
Blue light, a key abiotic signal, regulates a wide variety of physiological processes in many organisms. One of these phenomena is the circadian rhythm presents in organisms sensitive to the phase-setting effects of blue light and under control of the daily alternation of light and dark. Circadian clocks consist of autoregulatory alternating negative and positive feedback loops intimately connected with the cellular metabolism and biochemical processes. Neurospora crassa provides an excellent model for studying the molecular mechanisms involved in these phenomena. The White Collar Complex (WCC), a blue-light receptor and transcription factor of the circadian oscillator, and Frequency (FRQ), the circadian clock pacemaker, are at the core of the Neurospora circadian system. The eukaryotic circadian clock relies on transcriptional/translational feedback loops: some proteins rhythmically repress their own synthesis by inhibiting the activity of their transcriptional factors, generating self-sustained oscillations over a period of about 24 h. One of the basic mechanisms that perpetuate self-sustained oscillations is post translation modification (PTM). The acronym PTM generically indicates the addition of acetyl, methyl, sumoyl, or phosphoric groups to various types of proteins. The protein can be regulatory or enzymatic or a component of the chromatin. PTMs influence protein stability, interaction, localization, activity, and chromatin packaging. Chromatin modification and PTMs have been implicated in regulating circadian clock function in Neurospora. Research into the epigenetic control of transcription factors such as WCC has yielded new insights into the temporal modulation of light-dependent gene transcription. Here we report on epigenetic and protein PTMs in the regulation of the Neurospora crassa circadian clock. We also present a model that illustrates the molecular mechanisms at the basis of the blue light control of the circadian clock.
- Published
- 2015
- Full Text
- View/download PDF
84. Synthesis of a novel series of thiazole-based histone acetyltransferase inhibitors.
- Author
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Secci D, Carradori S, Bizzarri B, Bolasco A, Ballario P, Patramani Z, Fragapane P, Vernarecci S, Canzonetta C, and Filetici P
- Subjects
- Acetylation, Cell Line, Tumor, HeLa Cells, Humans, Thiazoles chemistry, Histone Acetyltransferases antagonists & inhibitors, Histone Acetyltransferases chemical synthesis, Thiazoles chemical synthesis
- Abstract
Acetylation, which targets a broad range of histone and non-histone proteins, is a reversible mechanism and plays a critical role in eukaryotic genes activation/deactivation. Acetyltransferases are very well conserved through evolution. This allows the use of a simple model organism, such as budding yeast, for the study of their related processes and to discover specific inhibitors. Following a simple yeast-based chemogenetic approach, we have identified a novel HAT (histone acetyltransferase) inhibitor active both in vitro and in vivo. This new synthetic compound, 1-(4-(4-chlorophenyl)thiazol-2-yl)-2-(propan-2-ylidene)hydrazine, named BF1, showed substrate selectivity for histone H3 acetylation and inhibitory activity in vitro on recombinant HAT Gcn5 and p300. Finally, we tested BF1 on human cells, HeLa as control and two aggressive cancer cell lines: a neuroblastoma from neuronal tissue and glioblastoma from brain tumour. Both global acetylation of histone H3 and specific acetylation at lysine 18 (H3AcK18) were lowered by BF1 treatment. Collectively, our results show the efficacy of this novel HAT inhibitor and propose the utilization of BF1 as a new, promising tool for future pharmacological studies., (Copyright © 2014 Elsevier Ltd. All rights reserved.)
- Published
- 2014
- Full Text
- View/download PDF
85. Chemogenomic profiling of the cellular effects associated with histone H3 acetylation impairment by a quinoline-derived compound.
- Author
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Ruotolo R, Tosi F, Vernarecci S, Ballario P, Mai A, Filetici P, and Ottonello S
- Subjects
- Acetylation drug effects, Gene Deletion, Histone Acetyltransferases metabolism, Histones drug effects, Histones genetics, Histones metabolism, Microbial Sensitivity Tests methods, Multiprotein Complexes genetics, Multiprotein Complexes metabolism, Quinolines chemistry, Saccharomyces cerevisiae enzymology, Saccharomyces cerevisiae genetics, Saccharomyces cerevisiae Proteins genetics, Saccharomyces cerevisiae Proteins metabolism, Gene Expression Profiling, Histone Acetyltransferases antagonists & inhibitors, Histone Acetyltransferases genetics, Mutation drug effects, Quinolines pharmacology, Saccharomyces cerevisiae drug effects
- Abstract
We report the results of a chemogenomic profiling aimed to explore the mode of action of a quinolic analogue of the p300 histone acetyltransferase (HAT) inhibitor anacardic acid, named MC1626. This compound reduced histone H3 acetylation in a dose-dependent manner and the HATs Gcn5 and Rtt109, which specifically target H3 lysines, were the only ones that caused chemical-genetic synthetic sickness with MC1626 when mutated. Deletion of specific Gcn5 (e.g., Ada1) and Rtt109 (e.g., Asf1) multiprotein complex components also enhanced MC1626 sensitivity. In addition to N-terminal H3 lysines, MC1626 inhibits H3-K56 acetylation, a histone modification that, in yeast, is exclusively supported by Rtt109 and indirectly influences DNA integrity. Several DNA repair mutants were found to be sensitive to MC1626. Functional links between histone acetylation impairment by MC1626 and mitochondrion as well as cytoskeleton functionality were also revealed, thus extending the range of non-nuclear processes that are influenced by histone acetylation., (Copyright © 2010 Elsevier Inc. All rights reserved.)
- Published
- 2010
- Full Text
- View/download PDF
86. Périgord black truffle genome uncovers evolutionary origins and mechanisms of symbiosis.
- Author
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Martin F, Kohler A, Murat C, Balestrini R, Coutinho PM, Jaillon O, Montanini B, Morin E, Noel B, Percudani R, Porcel B, Rubini A, Amicucci A, Amselem J, Anthouard V, Arcioni S, Artiguenave F, Aury JM, Ballario P, Bolchi A, Brenna A, Brun A, Buée M, Cantarel B, Chevalier G, Couloux A, Da Silva C, Denoeud F, Duplessis S, Ghignone S, Hilselberger B, Iotti M, Marçais B, Mello A, Miranda M, Pacioni G, Quesneville H, Riccioni C, Ruotolo R, Splivallo R, Stocchi V, Tisserant E, Viscomi AR, Zambonelli A, Zampieri E, Henrissat B, Lebrun MH, Paolocci F, Bonfante P, Ottonello S, and Wincker P
- Subjects
- Carbohydrates, DNA Transposable Elements genetics, Fruiting Bodies, Fungal metabolism, Genes, Fungal genetics, Genomics, Haploidy, Molecular Sequence Data, Sequence Analysis, DNA, Sulfur metabolism, Ascomycota genetics, Evolution, Molecular, Genome, Fungal genetics, Symbiosis genetics
- Abstract
The Périgord black truffle (Tuber melanosporum Vittad.) and the Piedmont white truffle dominate today's truffle market. The hypogeous fruiting body of T. melanosporum is a gastronomic delicacy produced by an ectomycorrhizal symbiont endemic to calcareous soils in southern Europe. The worldwide demand for this truffle has fuelled intense efforts at cultivation. Identification of processes that condition and trigger fruit body and symbiosis formation, ultimately leading to efficient crop production, will be facilitated by a thorough analysis of truffle genomic traits. In the ectomycorrhizal Laccaria bicolor, the expansion of gene families may have acted as a 'symbiosis toolbox'. This feature may however reflect evolution of this particular taxon and not a general trait shared by all ectomycorrhizal species. To get a better understanding of the biology and evolution of the ectomycorrhizal symbiosis, we report here the sequence of the haploid genome of T. melanosporum, which at approximately 125 megabases is the largest and most complex fungal genome sequenced so far. This expansion results from a proliferation of transposable elements accounting for approximately 58% of the genome. In contrast, this genome only contains approximately 7,500 protein-coding genes with very rare multigene families. It lacks large sets of carbohydrate cleaving enzymes, but a few of them involved in degradation of plant cell walls are induced in symbiotic tissues. The latter feature and the upregulation of genes encoding for lipases and multicopper oxidases suggest that T. melanosporum degrades its host cell walls during colonization. Symbiosis induces an increased expression of carbohydrate and amino acid transporters in both L. bicolor and T. melanosporum, but the comparison of genomic traits in the two ectomycorrhizal fungi showed that genetic predispositions for symbiosis-'the symbiosis toolbox'-evolved along different ways in ascomycetes and basidiomycetes.
- Published
- 2010
- Full Text
- View/download PDF
87. A novel histone acetyltransferase inhibitor modulating Gcn5 network: cyclopentylidene-[4-(4'-chlorophenyl)thiazol-2-yl)hydrazone.
- Author
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Chimenti F, Bizzarri B, Maccioni E, Secci D, Bolasco A, Chimenti P, Fioravanti R, Granese A, Carradori S, Tosi F, Ballario P, Vernarecci S, and Filetici P
- Subjects
- Acetylation, Catalysis, Enzyme Inhibitors chemistry, Glutamic Acid genetics, Histone Acetyltransferases drug effects, Histone Acetyltransferases genetics, Histone Acetyltransferases metabolism, Histones metabolism, Hydrazones chemistry, Mutation, Saccharomyces cerevisiae Proteins genetics, Saccharomyces cerevisiae Proteins metabolism, Thiazoles chemistry, Enzyme Inhibitors pharmacology, Histone Acetyltransferases antagonists & inhibitors, Hydrazones pharmacology, Saccharomyces cerevisiae Proteins drug effects, Thiazoles pharmacology
- Abstract
Acetylation is a key modulator of genome accessibility through decondensation of the chromatin structure. The balance between acetylation and opposite deacetylation is, in fact, a prerequisite for several cell functions and differentiation. To find modulators of the histone acetyltransferase Gcn5p, we performed a phenotypic screening on a set of newly synthesized molecules derived from thiazole in budding yeast Saccharomyces cerevisiae. We selected compounds that induce growth inhibition in yeast strains deleted in genes encoding known histone acetyltransferases. A novel molecule CPTH2, cyclopentylidene-[4-(4'-chlorophenyl)thiazol-2-yl)hydrazone, was selected based on its inhibitory effect on the growth of a gcn5Delta strain. We demonstrated a specific chemical-genetic interaction between CPTH2 and HAT Gcn5p, indicating that CPTH2 inhibits the Gcn5p dependent functional network. CPTH2 inhibited an in vitro HAT reaction, which is reverted by increasing concentration of histone H3. In vivo, it decreased acetylation of bulk histone H3 at the specific H3-AcK14 site. On the whole, our results demonstrate that CPTH2 is a novel HAT inhibitor modulating Gcn5p network in vitro and in vivo.
- Published
- 2009
- Full Text
- View/download PDF
88. Gcn5p plays an important role in centromere kinetochore function in budding yeast.
- Author
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Vernarecci S, Ornaghi P, Bâgu A, Cundari E, Ballario P, and Filetici P
- Subjects
- Adaptor Proteins, Signal Transducing, Cell Cycle, Mitosis, Multiprotein Complexes physiology, Nucleosomes, Saccharomyces cerevisiae chemistry, Trans-Activators physiology, Centromere ultrastructure, Histone Acetyltransferases physiology, Kinetochores physiology, Saccharomyces cerevisiae cytology, Saccharomyces cerevisiae Proteins metabolism, Saccharomyces cerevisiae Proteins physiology, Trans-Activators metabolism
- Abstract
We report that the histone acetyltransferase Gcn5p is involved in cell cycle progression, whereas its absence induces several mitotic defects, including inefficient nuclear division, chromosome loss, delayed G(2) progression, and spindle elongation. The fidelity of chromosome segregation is finely regulated by the close interplay between the centromere and the kinetochore, a protein complex hierarchically assembled in the centromeric DNA region, while disruption of GCN5 in mutants of inner components results in sick phenotype. These synthetic interactions involving the ADA complex lay the genetic basis for the critical role of Gcn5p in kinetochore assembly and function. We found that Gcn5p is, in fact, physically linked to the centromere, where it affects the structure of the variant centromeric nucleosome. Our findings offer a key insight into a Gcn5p-dependent epigenetic regulation at centromere/kinetochore in mitosis.
- Published
- 2008
- Full Text
- View/download PDF
89. The role of loop ZA and Pro371 in the function of yeast Gcn5p bromodomain revealed through molecular dynamics and experiment.
- Author
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Pizzitutti F, Giansanti A, Ballario P, Ornaghi P, Torreri P, Ciccotti G, and Filetici P
- Subjects
- Acetylation, Amino Acid Motifs, Amino Acid Sequence, Conserved Sequence, Crystallography, X-Ray, Histones chemistry, Models, Molecular, Molecular Sequence Data, Mutation, Protein Binding, Protein Structure, Tertiary, Saccharomyces cerevisiae growth & development, Sequence Alignment, Histone Acetyltransferases chemistry, Histone Acetyltransferases metabolism, Histones metabolism, Proline physiology, Saccharomyces cerevisiae metabolism, Saccharomyces cerevisiae Proteins chemistry, Saccharomyces cerevisiae Proteins metabolism
- Abstract
Biological experiments were combined with molecular dynamics simulations to understand the importance of amino acidic residues present in the bromodomain of the yeast histone acetyltransferase Gcn5p. It was found that residue Pro371 plays an important role in the molecular recognition of the acetylated histone H4 tail by Gcn5p bromodomain. Crystallographic analysis of the complex showed that this residue does not directly interact with the histone substrate. It has been demonstrated that a double mutation Pro371Thr and Met372Ala in the Gcn5p bromodomain impairs chromatin remodeling activity. It is demonstrated here that, in this double mutant and in the fully deleted bromodomain strain, there is lower growth under amino acid deprivation conditions. By in vitro surface plasmon resonance (Biacore) experiments it is shown that the binding affinity of the double mutation to acetyl lysine 16 histone H4 peptide decreases. Molecular dynamics simulations were used to explain this loss in acetyl lysine-Gcn5p bromodomain affinity, in the double mutant. By comparing nanosecond molecular dynamics trajectories of the native as well as the single and doubly mutated bromodomain, it is concluded that the presence of Pro371 is important to the functionality of the Gcn5p bromodomain. In the simulation a point mutation involving this highly conserved residue induced an increase in the flexibility of the ZA loop, which in turn modulated the exposure of the binding pocket to the acetyl lysine. The combined double mutations (Pro371Thr-Met372Ala) not only markedly perturb the motion of the ZA loop but also destabilize the entire structure of the bromodomain., (Copyright 2005 John Wiley & Sons, Ltd.)
- Published
- 2006
- Full Text
- View/download PDF
90. The bromodomain: a chromatin browser?
- Author
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Filetici P, P O, and Ballario P
- Subjects
- Acetyltransferases chemistry, Acetyltransferases metabolism, Amino Acid Sequence, Animals, Chromatin genetics, Histone Acetyltransferases, Humans, Lysine metabolism, Molecular Sequence Data, Mutation, Neoplasms genetics, Oncogene Proteins, Fusion physiology, Protein Structure, Tertiary, Sequence Homology, Amino Acid, Transcription, Genetic, Chromatin metabolism, Lysine analogs & derivatives, Nuclear Proteins chemistry, Nuclear Proteins physiology, Saccharomyces cerevisiae Proteins
- Abstract
Reversible modification of histone tails is a regulatory step in chromatin remodeling. The N-terminal tails of histones are signaling platforms that carry amino acid residues for post-translational modification and contribute to chromosomal higher order structure. These modifications are performed by a number of chromatin modulators such as histone (h) acetyltransferase, h-deacetylase, h-methyltransferase and h-kinase. Large numbers of these enzymes as well as other chromatin-associated proteins share the bromodomain, a signature protein motif. Structural studies reveal not only wide structural conservation of bromodomains but also envision a possible role of this domain in the recognition of specific modified residues in the histone tails. The widespread presence of bromodomains in leukemogenic and cancer genes has provided a fundamental tool for studies of the role of epigenetic and chromatin remodeling in malignant diseases.
- Published
- 2001
- Full Text
- View/download PDF
91. The bromodomain of Gcn5p interacts in vitro with specific residues in the N terminus of histone H4.
- Author
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Ornaghi P, Ballario P, Lena AM, González A, and Filetici P
- Subjects
- Acetyltransferases genetics, Acetyltransferases metabolism, Amino Acid Sequence, Arginine, Binding Sites, Cell Cycle Proteins, Evolution, Molecular, Glutamine, Histone Acetyltransferases, Models, Biological, Peptide Fragments genetics, Peptide Fragments metabolism, Protein Binding, Recombinant Fusion Proteins metabolism, Sequence Deletion, Trans-Activators genetics, Transcription Factors, p300-CBP Transcription Factors, Conserved Sequence, Histones metabolism, Saccharomyces cerevisiae Proteins, Trans-Activators metabolism
- Abstract
Whereas the histone acetyltransferase activity of yeast Gcn5p has been widely studied, its structural interactions with the histones and the role of the carboxy-terminal bromodomain are still unclear. Using a glutathione S-transferase pull down assay we show that Gcn5p binds the amino-terminal tails of histones H3 and H4, but not H2A and H2B. The deletion of bromodomain abolishes this interaction and bromodomain alone is able to interact with the H3 and H4 N termini. The amino acid residues of the H4 N terminus involved in the binding with Gcn5p have been studied by site-directed mutagenesis. The substitution of amino acid residues R19 or R23 of the H4 N terminus with a glutamine (Q) abolishes the interaction with Gcn5p and the bromodomain. These residues differ from those known to be acetylated or to be involved in binding the SIR proteins. This evidence and the known dispensability of the bromodomain for Gcn5p acetyltransferase activity suggest a new structural role for the highly evolutionary conserved bromodomain., (Copyright 1998 Academic Press.)
- Published
- 1999
- Full Text
- View/download PDF
92. Roles in dimerization and blue light photoresponse of the PAS and LOV domains of Neurospora crassa white collar proteins.
- Author
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Ballario P, Talora C, Galli D, Linden H, and Macino G
- Subjects
- Amino Acid Sequence, Binding Sites, DNA-Binding Proteins genetics, Dimerization, Light, Molecular Sequence Data, Mutation, Neurospora crassa genetics, Phenotype, Transcription Factors genetics, DNA-Binding Proteins physiology, Fungal Proteins, Neurospora crassa physiology, Transcription Factors physiology
- Abstract
The genes coding for white collar-1 and white collar-2 (wc-1 and wc-2) have been isolated previously, and their products characterized as Zn-finger transcription factors involved in the control of blue light-induced genes. Here, we show that the PAS dimerization domains present in both proteins enable the WC-1 and WC-2 proteins to dimerize in vitro. Homodimers and heterodimers are formed between the white collar (WC) proteins. A computer analysis of WC-1 reveals a second domain, called LOV, also identified in NPH1, a putative blue light photoreceptor in plants and conserved in redox-sensitive proteins and in the phytochromes. The WC-1 LOV domain does not dimerize with canonical PAS domains, but it is able to self-dimerize. The isolation of three blind wc-1 strains, each with a single amino acid substitution only in the LOV domain, reveals that this region is essential for blue light responses in Neurospora. The demonstration that the WC-1 proteins in these LOV mutants are still able to self-dimerize suggests that this domain plays an additional role, essential in blue light signal transduction.
- Published
- 1998
- Full Text
- View/download PDF
93. Regulation of expression of GLT1, the gene encoding glutamate synthase in Saccharomyces cerevisiae.
- Author
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Valenzuela L, Ballario P, Aranda C, Filetici P, and González A
- Subjects
- Base Sequence, Glutamate Synthase chemistry, Molecular Sequence Data, Saccharomyces cerevisiae genetics, Transformation, Genetic, Fungal Proteins genetics, Gene Expression Regulation, Fungal, Glutamate Synthase genetics, Promoter Regions, Genetic genetics, Saccharomyces cerevisiae enzymology
- Abstract
Saccharomyces cerevisiae glutamate synthase (GOGAT) is an oligomeric enzyme composed of three 199-kDa identical subunits encoded by GLT1. In this work, we analyzed GLT1 transcriptional regulation. GLT1-lacZ fusions were prepared and GLT1 expression was determined in a GDH1 wild-type strain and in a gdh1 mutant derivative grown in the presence of various nitrogen sources. Null mutants impaired in GCN4, GLN3, GAT1/NIL1, or UGA43/DAL80 were transformed with a GLT1-lacZ fusion to determine whether the above-mentioned transcriptional factors had a role in GLT1 expression. A collection of increasingly larger 5' deletion derivatives of the GLT1 promoter was constructed to identify DNA sequences that could be involved in GLT1 transcriptional regulation. The effect of the lack of GCN4, GLN3, or GAT1/NIL1 was also tested in the pertinent 5' deletion derivatives. Our results indicate that (i) GLT1 expression is negatively modulated by glutamate-mediated repression and positively regulated by Gln3p- and Gcn4p-dependent transcriptional activation; (ii) two cis-acting elements, a CGGN15CCG palindrome and an imperfect poly(dA-dT), are present and could play a role in GLT1 transcriptional activation; and (iii) GLT1 expression is moderately regulated by GCN4 under amino acid deprivation. Our results suggest that in a wild-type strain grown on ammonium, GOGAT constitutes an ancillary pathway for glutamate biosynthesis.
- Published
- 1998
- Full Text
- View/download PDF
94. GCN5, a yeast transcriptional coactivator, induces chromatin reconfiguration of HIS3 promoter in vivo.
- Author
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Filetici P, Aranda C, Gonzàlez A, and Ballario P
- Subjects
- DNA, Fungal, Fungal Proteins genetics, Gene Expression Regulation, Fungal, Histone Acetyltransferases, Models, Genetic, Mutation, Nucleosomes, Protein Kinases genetics, Transcriptional Activation, Yeasts, Chromatin ultrastructure, DNA-Binding Proteins, Fungal Proteins metabolism, Hydro-Lyases genetics, Promoter Regions, Genetic, Protein Kinases metabolism, Saccharomyces cerevisiae Proteins, Transcription Factors metabolism
- Abstract
Gcn5p, the nuclear histone acetyltransferase (HAT A), is a component of the multiprotein adaptor complex, ADA. Its role as a transcriptional coactivator is required for full induction of most of the genes regulated by GCN4. In this study we present experimental evidence demonstrating that, during gene activation, the nuclease sensitive region of HIS3 promoter, harbouring the poly (dA:dT) and the GCN4 binding site, is invaded by nucleosomes in a gcn5 disrupted strain. These data demonstrate, for the first time, that Gcn5p affects directly the chromatin organization of a chromosomal gene during its transcriptional activation.
- Published
- 1998
- Full Text
- View/download PDF
95. Blue light regulation in Neurospora crassa.
- Author
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Linden H, Ballario P, and Macino G
- Subjects
- Color, Gene Expression Regulation, Fungal, Light, Neurospora crassa genetics, Promoter Regions, Genetic, Signal Transduction genetics, Neurospora crassa radiation effects
- Abstract
The fungus Neurospora crassa has been shown to be a paradigm for photobiological, biochemical, and genetic studies of blue light perception and signal transduction. Several different developmental and morphological processes of Neurospora are regulated by blue light and can be divided into early and late blue light responses. The characterization of two central regulator proteins of blue light signal transduction in Neurospora crassa, WC1 and WC2, and the isolation of light-regulated genes, indicate transcriptional control as a central step in blue light signalling., (Copyright 1997 Academic Press.)
- Published
- 1997
- Full Text
- View/download PDF
96. Sequence of the GLT1 gene from Saccharomyces cerevisiae reveals the domain structure of yeast glutamate synthase.
- Author
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Filetici P, Martegani MP, Valenzuela L, González A, and Ballario P
- Subjects
- Amino Acid Sequence, Base Sequence, Cloning, Molecular, Cysteine genetics, Electronic Data Processing, Escherichia coli genetics, Flavin Mononucleotide genetics, Medicago sativa genetics, Molecular Sequence Data, NAD genetics, Sequence Analysis, Sequence Homology, Amino Acid, Zea mays genetics, Glutamate Synthase genetics, Saccharomyces cerevisiae genetics
- Abstract
Glutamate synthase (GOGAT) and glutamine synthetase play a crucial role in ammonium assimilation and glutamate biosynthesis in the yeast Saccharomyces cerevisiae. The GOGAT enzyme has been purified and the GOGAT structural gene (GLT1) has been cloned, showing that this enzyme is a homotrimeric protein with a monomeric size of 199 kDa. We report the GLT1 nucleotide sequence and the amino acid sequence of its deduced protein product. Our results show that there is a high conservation with the corresponding genes of Escherichia coli, Medicago sativa (alfalfa) and Zea mais (maize). Binding domains for glutamine, cofactors (FMN and NADH) and the cysteine clusters (which comprise the iron-sulfur centres) were tentatively identified on the basis of sequence comparison with GOGAT sequences from E. coli, alfalfa and maize.
- Published
- 1996
- Full Text
- View/download PDF
97. Photoregulated carotenoid biosynthetic genes of Neurospora crassa.
- Author
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Morelli G, Nelson MA, Ballario P, and Macino G
- Subjects
- Amino Acid Sequence, Blotting, Northern, Cloning, Molecular methods, Farnesyltranstransferase, Molecular Sequence Data, Neurospora crassa genetics, Neurospora crassa radiation effects, RNA, Fungal genetics, RNA, Fungal isolation & purification, Restriction Mapping, Sequence Homology, Amino Acid, Spheroplasts metabolism, Transcription, Genetic, Alkyl and Aryl Transferases, Carotenoids biosynthesis, Gene Expression Regulation, Fungal radiation effects, Genes, Fungal drug effects, Light, Neurospora crassa metabolism, Transferases genetics
- Published
- 1993
- Full Text
- View/download PDF
98. Binding of sea-urchin RNA polymerase II on homologous histone genes.
- Author
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Buongiorno-Nardelli M, Ballario P, and Di Mauro E
- Subjects
- Animals, Binding Sites, Cloning, Molecular, Microscopy, Electron, Protein Binding, Sea Urchins enzymology, DNA, Recombinant metabolism, DNA-Directed RNA Polymerases genetics, Genes, Histones genetics, RNA Polymerase II genetics
- Published
- 1981
- Full Text
- View/download PDF
99. Circular extrachromosomal copia-like transposable elements in Drosophila tissue culture cells.
- Author
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Junakovic N and Ballario P
- Subjects
- Animals, Cells, Cultured, DNA, Circular isolation & purification, DNA Transposable Elements, DNA, Circular genetics, Drosophila melanogaster genetics, Extrachromosomal Inheritance
- Abstract
We find that in the circular extrachromosomal DNA from Drosophila tissue culture cells the transposable elements copia, 412, 297, and mdg 1 are present in variable amounts. There is no detectable circular DNA homologous to B104 . From the relationship between the intra- and extrachromosomal forms it appears that the amount of different circular elements is not related to the amount of the respective chromosomal elements.
- Published
- 1984
- Full Text
- View/download PDF
100. Purification of sea-urchin RNA polymerase II. Characterization by template requirements and sensitivity to inhibitors.
- Author
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Ballario P, Di Mauro E, Giuliani C, and Pedone F
- Subjects
- Amanitins pharmacology, Animals, Gastrula enzymology, Heparin pharmacology, Methods, RNA Polymerase II antagonists & inhibitors, RNA Polymerase II metabolism, Rifamycins pharmacology, Sea Urchins enzymology, Templates, Genetic, DNA-Directed RNA Polymerases isolation & purification, RNA Polymerase II isolation & purification
- Abstract
The purification of RNA polymerase II from gastrulae of Paracentrotus lividus is described. The enzyme obtained is homogeneous as judged by electrophoresis under non-denaturing conditions. It is able to transcribe both native high-Mr P. lividus DNA and Psammechinus miliaris h22 histone DNA, although single-stranded and nicked DNAs are better templates. P. lividus RNA polymerase II forms with homologous native DNA stable binary complexes that are able to initiate RNA chains after exposure to heparin. Heparin-resistant complexes do not form on nicks of DNA molecules. Sensitivity of sea-urchin RNA polymerase II to rifamycin derivatives and alpha-amanitin has been determined.
- Published
- 1980
- Full Text
- View/download PDF
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