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Puzzi L, Marchetti L, Peverali FA, Biamonti G, Giacca M. DNA-protein interaction dynamics at the Lamin B2 replication origin. Cell Cycle 2015; 14:64-73. [PMID: 25483070 PMCID: PMC4352957 DOI: 10.4161/15384101.2014.973337] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Accepted: 09/30/2014] [Indexed: 12/24/2022] Open
Abstract
To date, a complete understanding of the molecular events leading to DNA replication origin activation in mammalian cells still remains elusive. In this work, we report the results of a high resolution chromatin immunoprecipitation study to detect proteins interacting with the human Lamin B2 replication origin. In addition to the pre-RC component ORC4 and to the transcription factors USF and HOXC13, we found that 2 components of the AP-1 transcription factor, c-Fos and c-Jun, are also associated with the origin DNA during the late G1 phase of the cell cycle and that these factors interact with ORC4. Both DNA replication and AP-1 factor binding to the origin region were perturbed by cell treatment with merbarone, a topoisomerase II inhibitor, suggesting that DNA topology is essential for determining origin function.
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Affiliation(s)
- Luca Puzzi
- Molecular Biology Laboratory; Scuola Normale Superiore; Pisa, Italy
- Molecular Medicine Laboratory; International Centre for Genetic Engineering and Biotechnology (ICGEB); Trieste, Italy
| | - Laura Marchetti
- NEST; Scuola Normale Superiore and Istituto Nanoscienze-CNR; Pisa, Italy
| | - Fiorenzo A Peverali
- Istituto di Genetica Molecolare (IGM); Consiglio Nazionale delle Ricerche (CNR); Pavia, Italy
| | - Giuseppe Biamonti
- Istituto di Genetica Molecolare (IGM); Consiglio Nazionale delle Ricerche (CNR); Pavia, Italy
| | - Mauro Giacca
- Molecular Medicine Laboratory; International Centre for Genetic Engineering and Biotechnology (ICGEB); Trieste, Italy
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Wu Y, Peng C, Xu L, Zheng X, Liao M, Yan Y, Jin Y, Zhou J. Proteome dynamics in primary target organ of infectious bursal disease virus. Proteomics 2012; 12:1844-59. [PMID: 22623289 DOI: 10.1002/pmic.201100479] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Viruses induce dramatic changes in target tissue during pathogenesis, including host cellular responses that either limit or support the pathogen. The infectious bursal disease virus (IBDV) targets primarily the bursa of Fabricius (BF) of chickens, causing severe immunodeficiency. Here, we characterized the cellular proteome changes of the BF caused by IBDV replication in vivo using 2DE followed MALDI-TOF MS identification. Comparative analysis of multiple 2DE gels revealed that the majority of protein expression changes appeared between 24 and 96 h after IBDV infection. MS identified 54 altered cell proteins, 12 of which were notably upregulated by IBDV infection. Meanwhile, the other 42 cellular proteins were considerably suppressed by IBDV infection and are involved in protein degradation, energy metabolism, stress response, host macromolecular biosynthesis, and transport process. The upregulation of β-actin and downregulation of dynamin during IBDV infection were also confirmed by Western blot and immunofluorescence analysis. These altered protein expressions provide a response profile of chicken BF to virulent IBDV infection. Further functional study on these altered proteins may lead to better understanding of pathogenic mechanisms of virulent IBDV infection and to new potential therapeutic targets.
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Affiliation(s)
- Yongping Wu
- Key Laboratory of Animal Virology of Ministry of Agriculture, Zhejiang University, Hangzhou, P. R. China
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Marchetti L, Comelli L, D'Innocenzo B, Puzzi L, Luin S, Arosio D, Calvello M, Mendoza-Maldonado R, Peverali F, Trovato F, Riva S, Biamonti G, Abdurashidova G, Beltram F, Falaschi A. Homeotic proteins participate in the function of human-DNA replication origins. Nucleic Acids Res 2010; 38:8105-19. [PMID: 20693533 PMCID: PMC3001063 DOI: 10.1093/nar/gkq688] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2010] [Revised: 07/16/2010] [Accepted: 07/22/2010] [Indexed: 01/15/2023] Open
Abstract
Recent evidence points to homeotic proteins as actors in the crosstalk between development and DNA replication. The present work demonstrates that HOXC13, previously identified as a new member of human DNA replicative complexes, is a stable component of early replicating chromatin in living cells: it displays a slow nuclear dynamics due to its anchoring to the DNA minor groove via the arginine-5 residue of the homeodomain. HOXC13 binds in vivo to the lamin B2 origin in a cell-cycle-dependent manner consistent with origin function; the interaction maps with nucleotide precision within the replicative complex. HOXC13 displays in vitro affinity for other replicative complex proteins; it interacts also in vivo with the same proteins in a cell-cycle-dependent fashion. Chromatin-structure modifying treatments, disturbing origin function, reduce also HOXC13-origin interaction. The described interactions are not restricted to a single origin nor to a single homeotic protein (also HOXC10 binds the lamin B2 origin in vivo). Thus, HOX complexes probably contribute in a general, structure-dependent manner, to origin identification and assembly of replicative complexes thereon, in presence of specific chromatin configurations.
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Affiliation(s)
- Laura Marchetti
- NEST, Scuola Normale Superiore and Istituto Nanoscienze-CNR, Laboratorio di Biologia Molecolare, Scuola Normale Superiore, Pisa, Italy.
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Kusic J, Tomic B, Divac A, Kojic S. Human initiation protein Orc4 prefers triple stranded DNA. Mol Biol Rep 2010; 37:2317-22. [PMID: 19690980 DOI: 10.1007/s11033-009-9735-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2009] [Accepted: 08/04/2009] [Indexed: 12/18/2022]
Abstract
In higher eukaryotes mechanism of DNA replication origin recognition and binding by origin recognition complex (ORC) is still unknown. Origin transfer studies have shown that origin sites are genetically determined, containing functionally interchangeable modules. One of such modules from the human lamin B2 origin of replication has the ability to adopt unorthodox structure partly composed of intramolecular triplex. Sequences involved in triplex formation coincide with ORC binding sites both in vitro and in vivo. To explore potential significance of unorthodox DNA structures in origin recognition by ORC, we tested DNA binding properties of human ORC subunit 4 (HsOrc4) which has independent DNA binding activity in vitro and similar binding characteristics as ORC holocomplex. Our results demonstrated that DNA binding activity of HsOrc4 depends on length and structure of DNA with triplex being the protein's preferred binding target. Such feature could play part in origin selection through directing ORC to DNA sequence prone to adopt unorthodox structure.
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Affiliation(s)
- J Kusic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11000 Belgrade, Serbia.
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Stefanovic D, Kusic J, Divac A, Tomic B. Formation of noncanonical DNA structures mediated by human ORC4, a protein component of the origin recognition complex. Biochemistry 2008; 47:8760-7. [PMID: 18652488 DOI: 10.1021/bi800684f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Many genomic sequences, DNA replication origins included, contain specific structural motifs prone to alternative base pairing. Structural rearrangements of DNA require specific environmental conditions and could be favored by chemical agents or proteins. To improve our understanding of alternative conformations of origins and the manner in which they form, we have investigated the effect of DNA-binding, AAA+ protein human ORC4 on single-stranded origin DNA or various oligonucleotides. Here we demonstrate that human ORC4 stimulated formation of inter- and intramolecular T.A.T triplexes and created novel structures, such as homoadenine duplexes. Adenine-based structures were held together by Hoogsteen hydrogen bonds, as demonstrated on 7-deaza-dAMP- or dAMP-containing substrates, and characterized by increased thermal stability. Adenine pairing occurred only in the presence of human ORC4, in a neutral buffer supplemented with ATP and Mg (2+) ions. The protein mutant that could not bind ATP was inactive in this reaction. Since the action of human ORC4 could be biologically important, its potential impact on DNA replication is discussed.
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Affiliation(s)
- Dragana Stefanovic
- Institute of Molecular Genetics and Genetic Engineering, Vojvode Stepe 444a, P.O. Box 23, 11010 Belgrade, Serbia.
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Abdurashidova G, Radulescu S, Sandoval O, Zahariev S, Danailov MB, Demidovich A, Santamaria L, Biamonti G, Riva S, Falaschi A. Functional interactions of DNA topoisomerases with a human replication origin. EMBO J 2007; 26:998-1009. [PMID: 17290216 PMCID: PMC1852844 DOI: 10.1038/sj.emboj.7601578] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2006] [Accepted: 01/04/2007] [Indexed: 01/22/2023] Open
Abstract
The human DNA replication origin, located in the lamin B2 gene, interacts with the DNA topoisomerases I and II in a cell cycle-modulated manner. The topoisomerases interact in vivo and in vitro with precise bonds ahead of the start sites of bidirectional replication, within the pre-replicative complex region; topoisomerase I is bound in M, early G1 and G1/S border and topoisomerase II in M and the middle of G1. The Orc2 protein competes for the same sites of the origin bound by either topoisomerase in different moments of the cell cycle; furthermore, it interacts on the DNA with topoisomerase II during the assembly of the pre-replicative complex and with DNA-bound topoisomerase I at the G1/S border. Inhibition of topoisomerase I activity abolishes origin firing. Thus, the two topoisomerases are closely associated with the replicative complexes, and DNA topology plays an essential functional role in origin activation.
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Affiliation(s)
- Gulnara Abdurashidova
- Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Sorina Radulescu
- Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Oscar Sandoval
- Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Sotir Zahariev
- Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | | | | | - Laura Santamaria
- Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Giuseppe Biamonti
- Molecular Biology Section, Istituto di Genetica Molecolare, CNR, Pavia, Italy
| | - Silvano Riva
- Molecular Biology Section, Istituto di Genetica Molecolare, CNR, Pavia, Italy
| | - Arturo Falaschi
- Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
- Molecular Biology Laboratory, Scuola Normale Superiore, Pisa, Italy
- Laboratory of Gene and Molecular Therapy, Istituto di Fisiologia Clinica, CNR, Pisa, Italy
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Hegele RA, Cao H, Liu DM, Costain GA, Charlton-Menys V, Rodger NW, Durrington PN. Sequencing of the reannotated LMNB2 gene reveals novel mutations in patients with acquired partial lipodystrophy. Am J Hum Genet 2006; 79:383-9. [PMID: 16826530 PMCID: PMC1559499 DOI: 10.1086/505885] [Citation(s) in RCA: 155] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2006] [Accepted: 05/12/2006] [Indexed: 01/31/2023] Open
Abstract
The etiology of acquired partial lipodystrophy (APL, also called "Barraquer-Simons syndrome") is unknown. Genomic DNA mutations affecting the nuclear lamina protein lamin A cause inherited partial lipodystrophy but are not found in patients with APL. Because it also encodes a nuclear lamina protein (lamin B2) and its genomic structure was recently reannotated, we sequenced LMNB2 as a candidate gene in nine white patients with APL. In four patients, we found three new rare mutations in LMNB2: intron 1 -6G-->T, exon 5 c.643G-->A (p.R215Q; in two patients), and exon 8 c.1218G-->A (p.A407T). The combined frequency of these mutations was 0.222 in the patients with APL, compared with 0.0018 in a multiethnic control sample of 1,100 subjects (P = 2.1 x 10-7) and 0.0045 in a sample of 330 white controls (P = 1.2 x 10-5). These novel heterozygous mutations are the first reported for LMNB2, are the first reported among patients with APL, and indicate how sequencing of a reannotated candidate gene can reveal new disease-associated mutations.
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Affiliation(s)
- Robert A Hegele
- Robarts Research Institute, 406-100 Perth Drive, London, Ontario, Canada N6A 5K8.
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