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Seul A, Brasilès S, Petitpas I, Lurz R, Campanacci V, Cambillau C, Weise F, Zairi M, Tavares P, Auzat I. Biogenesis of a Bacteriophage Long Non-Contractile Tail. J Mol Biol 2021; 433:167112. [PMID: 34153288 DOI: 10.1016/j.jmb.2021.167112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 05/22/2021] [Accepted: 06/15/2021] [Indexed: 10/21/2022]
Abstract
Siphoviruses are main killers of bacteria. They use a long non-contractile tail to recognize the host cell and to deliver the genome from the viral capsid to the bacterial cytoplasm. Here, we define the molecular organization of the Bacillus subtilis bacteriophage SPP1 ~ 6.8 MDa tail and uncover its biogenesis mechanisms. A complex between gp21 and the tail distal protein (Dit) gp19.1 is assembled first to build the tail cap (gp19.1-gp21Nter) connected by a flexible hinge to the tail fiber (gp21Cter). The tip of the gp21Cter fiber is loosely associated to gp22. The cap provides a platform where tail tube proteins (TTPs) initiate polymerization around the tape measure protein gp18 (TMP), a reaction dependent on the non-structural tail assembly chaperones gp17.5 and gp17.5* (TACs). Gp17.5 is essential for stability of gp18 in the cell. Helical polymerization stops at a precise tube length followed by binding of proteins gp16.1 (TCP) and gp17 (THJP) to build the tail interface for attachment to the capsid portal system. This finding uncovers the function of the extensively conserved gp16.1-homologs in assembly of long tails. All SPP1 tail components, apart from gp22, share homology to conserved proteins whose coding genes' synteny is broadly maintained in siphoviruses. They conceivably represent the minimal essential protein set necessary to build functional long tails. Proteins homologous to SPP1 tail building blocks feature a variety of add-on modules that diversify extensively the tail core structure, expanding its capability to bind host cells and to deliver the viral genome to the bacterial cytoplasm.
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Affiliation(s)
- Anait Seul
- Unité de Virologie Moléculaire et Structurale, Centre de Recherche de Gif, CNRS UPR 3296 and IFR115, CNRS, Gif-sur-Yvette, France
| | - Sandrine Brasilès
- Unité de Virologie Moléculaire et Structurale, Centre de Recherche de Gif, CNRS UPR 3296 and IFR115, CNRS, Gif-sur-Yvette, France; Institute for Integrative Biology of the Cell, Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette, France
| | - Isabelle Petitpas
- Unité de Virologie Moléculaire et Structurale, Centre de Recherche de Gif, CNRS UPR 3296 and IFR115, CNRS, Gif-sur-Yvette, France
| | - Rudi Lurz
- Max Planck Institute for Molecular Genetics, D-14195 Berlin, Germany
| | - Valérie Campanacci
- Institute for Integrative Biology of the Cell, Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette, France; Architecture et Fonction des Macromolécules Biologiques, UMR 6098 CNRS and Universités d'Aix-Marseille I & II, Campus de Luminy, Marseille, France
| | - Christian Cambillau
- Architecture et Fonction des Macromolécules Biologiques, UMR 6098 CNRS and Universités d'Aix-Marseille I & II, Campus de Luminy, Marseille, France
| | - Frank Weise
- Max Planck Institute for Molecular Genetics, D-14195 Berlin, Germany
| | - Mohamed Zairi
- Unité de Virologie Moléculaire et Structurale, Centre de Recherche de Gif, CNRS UPR 3296 and IFR115, CNRS, Gif-sur-Yvette, France
| | - Paulo Tavares
- Unité de Virologie Moléculaire et Structurale, Centre de Recherche de Gif, CNRS UPR 3296 and IFR115, CNRS, Gif-sur-Yvette, France; Institute for Integrative Biology of the Cell, Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette, France.
| | - Isabelle Auzat
- Unité de Virologie Moléculaire et Structurale, Centre de Recherche de Gif, CNRS UPR 3296 and IFR115, CNRS, Gif-sur-Yvette, France; Institute for Integrative Biology of the Cell, Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette, France.
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2
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Lorenzo-Díaz F, Fernández-López C, Lurz R, Bravo A, Espinosa M. Crosstalk between vertical and horizontal gene transfer: plasmid replication control by a conjugative relaxase. Nucleic Acids Res 2017; 45:7774-7785. [PMID: 28525572 PMCID: PMC5737340 DOI: 10.1093/nar/gkx450] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 05/09/2017] [Indexed: 01/09/2023] Open
Abstract
Horizontal gene transfer is a key process in the evolution of bacteria and also represents a source of genetic variation in eukaryotes. Among elements participating in gene transfer, thousands of small (<10 kb) mobile bacterial plasmids that replicate by the rolling circle mechanism represent a driving force in the spread of antibiotic resistances. In general, these plasmids are built as genetic modules that encode a replicase, an antibiotic-resistance determinant, and a relaxase that participates in their conjugative mobilization. Further, they control their relatively high copy number (∼30 copies per genome equivalent) by antisense RNAs alone or combined with a repressor protein. We report here that the MobM conjugative relaxase encoded by the promiscuous plasmid pMV158 participates in regulation of the plasmid copy number by transcriptional repression of the antisense RNA, thus increasing the number of plasmid molecules ready to be horizontally transferred (mobilization) and/or vertically inherited (replication). This type of crosstalk between genetic modules involved in vertical and horizontal gene flow has not been reported before.
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Affiliation(s)
- Fabián Lorenzo-Díaz
- Departamento de Bioquímica, Microbiología, Biología Celular y Genética, Universidad de La Laguna. Av. Astrofísico Francisco Sánchez s/n, 38071 Santa Cruz de Tenerife, Spain.,Unidad de Investigación, Hospital Universitario Nuestra Señora de Candelaria, 38010 Santa Cruz de Tenerife, Spain
| | - Cris Fernández-López
- Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu, 9, 28040 Madrid, Spain
| | - Rudi Lurz
- Max-Plank Institut für molekulare Genetik, Ihnestrasse 63-73, D-14195 Berlin, Germany
| | - Alicia Bravo
- Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu, 9, 28040 Madrid, Spain
| | - Manuel Espinosa
- Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu, 9, 28040 Madrid, Spain
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3
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Molina-García L, Gasset-Rosa F, Moreno-del Álamo M, Fernández-Tresguerres ME, Moreno-Díaz de la Espina S, Lurz R, Giraldo R. Functional amyloids as inhibitors of plasmid DNA replication. Sci Rep 2016; 6:25425. [PMID: 27147472 PMCID: PMC4857107 DOI: 10.1038/srep25425] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 04/12/2016] [Indexed: 12/24/2022] Open
Abstract
DNA replication is tightly regulated to constrain the genetic material within strict spatiotemporal boundaries and copy numbers. Bacterial plasmids are autonomously replicating DNA molecules of much clinical, environmental and biotechnological interest. A mechanism used by plasmids to prevent over-replication is 'handcuffing', i.e. inactivating the replication origins in two DNA molecules by holding them together through a bridge built by a plasmid-encoded initiator protein (Rep). Besides being involved in handcuffing, the WH1 domain in the RepA protein assembles as amyloid fibres upon binding to DNA in vitro. The amyloid state in proteins is linked to specific human diseases, but determines selectable and epigenetically transmissible phenotypes in microorganisms. Here we have explored the connection between handcuffing and amyloidogenesis of full-length RepA. Using a monoclonal antibody specific for an amyloidogenic conformation of RepA-WH1, we have found that the handcuffed RepA assemblies, either reconstructed in vitro or in plasmids clustering at the bacterial nucleoid, are amyloidogenic. The replication-inhibitory RepA handcuff assembly is, to our knowledge, the first protein amyloid directly dealing with DNA. Built on an amyloid scaffold, bacterial plasmid handcuffs can bring a novel molecular solution to the universal problem of keeping control on DNA replication initiation.
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Affiliation(s)
- Laura Molina-García
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas – CSIC, E28040 Madrid, Spain
| | - Fátima Gasset-Rosa
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas – CSIC, E28040 Madrid, Spain
| | - María Moreno-del Álamo
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas – CSIC, E28040 Madrid, Spain
| | | | | | - Rudi Lurz
- Max Planck Institute for Molecular Genetics, D14195 Berlin, Germany
| | - Rafael Giraldo
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas – CSIC, E28040 Madrid, Spain
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4
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Kearns S, Lurz R, Orlova EV, Okorokov AL. Two p53 tetramers bind one consensus DNA response element. Nucleic Acids Res 2016; 44:6185-99. [PMID: 27034469 PMCID: PMC5291249 DOI: 10.1093/nar/gkw215] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 03/20/2016] [Indexed: 01/28/2023] Open
Abstract
p53 tumor suppressor is a transcription factor that controls cell cycle and genetic integrity. In response to genotoxic stress p53 activates DNA repair, cell cycle arrest, apoptosis or senescence, which are initiated via p53 binding to its specific DNA response elements (RE). The consensus p53 DNA RE consists of two decameric palindromic half-site sequences. Crystallographic studies have demonstrated that two isolated p53 DNA-binding core domains interact with one half-site of the p53 DNA REs suggesting that one p53 tetramer is bound to one RE. However, our recent 3D cryo-EM studies showed that the full-length p53 tetramer is bound to only one half-site of RE. Here, we have used biochemical and electron microscopy (EM) methods to analyze DNA-binding of human and murine p53 tetramers to various p53 DNA REs. Our new results demonstrate that two p53 tetramers can interact sequence-specifically with one DNA RE at the same time. In particular, the EM structural analysis revealed that two p53 tetramers bind one DNA RE simultaneously with DNA positioned between them. These results demonstrate a mode different from that assumed previously for the p53-DNA interaction and suggest important biological implications on p53 activity as a transcriptional regulator of cellular response to stress.
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Affiliation(s)
- Sinéad Kearns
- Institute for Structural and Molecular Biology, School of Biological Sciences, Birkbeck College, London WC1E 7HX, UK Wolfson Institute for Biomedical Research, Division of Medicine, University College London, London WC1E 6BT, UK
| | - Rudi Lurz
- Max Planck Institute for Molecular Genetics, Ihnestrasse, Berlin 14195, Germany
| | - Elena V Orlova
- Institute for Structural and Molecular Biology, School of Biological Sciences, Birkbeck College, London WC1E 7HX, UK
| | - Andrei L Okorokov
- Wolfson Institute for Biomedical Research, Division of Medicine, University College London, London WC1E 6BT, UK
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5
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Kunkel F, Lurz R, Weinhold E. A 7-Deazaadenosylaziridine Cofactor for Sequence-Specific Labeling of DNA by the DNA Cytosine-C5 Methyltransferase M.HhaI. Molecules 2015; 20:20805-22. [PMID: 26610450 PMCID: PMC6332214 DOI: 10.3390/molecules201119723] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 11/03/2015] [Accepted: 11/10/2015] [Indexed: 12/30/2022] Open
Abstract
DNA methyltransferases (MTases) catalyze the transfer of the activated methyl group of the cofactor S-adenosyl-l-methionine (AdoMet or SAM) to the exocyclic amino groups of adenine or cytosine or the C5 ring atom of cytosine within specific DNA sequences. The DNA adenine-N6 MTase from Thermus aquaticus (M.TaqI) is also capable of coupling synthetic N-adenosylaziridine cofactor analogues to its target adenine within the double-stranded 5′-TCGA-3′ sequence. This M.TaqI-mediated coupling reaction was exploited to sequence-specifically deliver fluorophores and biotin to DNA using N-adenosylaziridine derivatives carrying reporter groups at the 8-position of the adenine ring. However, these 8-modified aziridine cofactors were poor substrates for the DNA cytosine-C5 MTase from Haemophilus haemolyticus (M.HhaI). Based on the crystal structure of M.HhaI in complex with a duplex oligodeoxynucleotide and the cofactor product, we synthesized a stable 7-deazaadenosylaziridine derivative with a biotin group attached to the 7-position via a flexible linker. This 7-modified aziridine cofactor can be efficiently used by M.HhaI for the direct, quantitative and sequence-specific delivery of biotin to the second cytosine within 5′-GCGC-3′ sequences in short duplex oligodeoxynucleotides and plasmid DNA. In addition, we demonstrate that biotinylation by M.HhaI depends on the methylation status of the target cytosine and, thus, could provide a method for cytosine-C5 DNA methylation detection in mammalian DNA.
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Affiliation(s)
- Falk Kunkel
- Institute of Organic Chemistry, RWTH Aachen University, Landoltweg 1, Aachen D-52056, Germany.
| | - Rudi Lurz
- Max-Planck-Institute for Molecular Genetics, Ihnestrasse 73, Berlin D-14195, Germany.
| | - Elmar Weinhold
- Institute of Organic Chemistry, RWTH Aachen University, Landoltweg 1, Aachen D-52056, Germany.
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6
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Lioy VS, Volante A, Soberón NE, Lurz R, Ayora S, Alonso JC. ParAB Partition Dynamics in Firmicutes: Nucleoid Bound ParA Captures and Tethers ParB-Plasmid Complexes. PLoS One 2015; 10:e0131943. [PMID: 26161642 PMCID: PMC4498918 DOI: 10.1371/journal.pone.0131943] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 06/08/2015] [Indexed: 11/17/2022] Open
Abstract
In Firmicutes, small homodimeric ParA-like (δ2) and ParB-like (ω2) proteins, in concert with cis-acting plasmid-borne parS and the host chromosome, secure stable plasmid inheritance in a growing bacterial population. This study shows that (ω:YFP)2 binding to parS facilitates plasmid clustering in the cytosol. (δ:GFP)2 requires ATP binding but not hydrolysis to localize onto the cell’s nucleoid as a fluorescent cloud. The interaction of (δ:CFP)2 or δ2 bound to the nucleoid with (ω:YFP)2 foci facilitates plasmid capture, from a very broad distribution, towards the nucleoid and plasmid pairing. parS-bound ω2 promotes redistribution of (δ:GFP)2, leading to the dynamic release of (δ:GFP)2 from the nucleoid, in a process favored by ATP hydrolysis and protein-protein interaction. (δD60A:GFP)2, which binds but cannot hydrolyze ATP, also forms unstable complexes on the nucleoid. In the presence of ω2, (δD60A:GFP)2 accumulates foci or patched structures on the nucleoid. We propose that (δ:GFP)2 binding to different nucleoid regions and to ω2-parS might generate (δ:GFP)2 gradients that could direct plasmid movement. The iterative pairing and unpairing cycles may tether plasmids equidistantly on the nucleoid to ensure faithful plasmid segregation by a mechanism compatible with the diffusion-ratchet mechanism as proposed from in vitro reconstituted systems.
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Affiliation(s)
- Virginia S Lioy
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, Darwin Str. 3, 28049 Madrid, Spain
| | - Andrea Volante
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, Darwin Str. 3, 28049 Madrid, Spain
| | - Nora E Soberón
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, Darwin Str. 3, 28049 Madrid, Spain
| | - Rudi Lurz
- Max Planck Institute for Molecular Genetics, Ihnestrasse 73, D-1000 Berlin, Germany
| | - Silvia Ayora
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, Darwin Str. 3, 28049 Madrid, Spain
| | - Juan C Alonso
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, Darwin Str. 3, 28049 Madrid, Spain
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7
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Hammerl JA, Roschanski N, Lurz R, Johne R, Lanka E, Hertwig S. The Molecular Switch of Telomere Phages: High Binding Specificity of the PY54 Cro Lytic Repressor to a Single Operator Site. Viruses 2015; 7:2771-93. [PMID: 26043380 PMCID: PMC4488713 DOI: 10.3390/v7062746] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [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: 04/13/2015] [Accepted: 05/28/2015] [Indexed: 11/16/2022] Open
Abstract
Temperate bacteriophages possess a molecular switch, which regulates the lytic and lysogenic growth. The genomes of the temperate telomere phages N15, PY54 and ϕKO2 harbor a primary immunity region (immB) comprising genes for the prophage repressor, the lytic repressor and a putative antiterminator. The roles of these products are thought to be similar to those of the lambda proteins CI, Cro and Q, respectively. Moreover, the gene order and the location of several operator sites in the prototype telomere phage N15 and in ϕKO2 are also reminiscent of lambda-like phages. By contrast, in silico analyses revealed the presence of only one operator (OR3) in PY54. The purified PY54 Cro protein was used for EMSA studies demonstrating that it exclusively binds to a 16-bp palindromic site (OR3) upstream of the prophage repressor gene. The OR3 operator sequences of PY54 and ϕKO2/N15 only differ by their peripheral base pairs, which are responsible for Cro specificity. PY54 cI and cro transcription is regulated by highly active promoters initiating the synthesis of a homogenious species of leaderless mRNA. The location of the PY54 Cro binding site and of the identified promoters suggests that the lytic repressor suppresses cI transcription but not its own synthesis. The results indicate an unexpected diversity of the growth regulation mechanisms in lambda-related phages.
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Affiliation(s)
- Jens Andre Hammerl
- Bundesinstitut für Risikobewertung (Federal Institute for Risk Assessment), Department of Biological Safety, Diedersdorfer Weg 1, D-12277 Berlin, Germany.
| | - Nicole Roschanski
- Free University Berlin, Institute of Animal Hygiene and Environmental Health, Robert-von-Ostertag-Str. 7-13, D-14163 Berlin, Germany.
| | - Rudi Lurz
- Max-Planck-Institut für Molekulare Genetik, Ihnestraße 63-73, D-14195 Berlin, Germany.
| | - Reimar Johne
- Bundesinstitut für Risikobewertung (Federal Institute for Risk Assessment), Department of Biological Safety, Diedersdorfer Weg 1, D-12277 Berlin, Germany.
| | - Erich Lanka
- Max-Planck-Institut für Molekulare Genetik, Ihnestraße 63-73, D-14195 Berlin, Germany.
| | - Stefan Hertwig
- Bundesinstitut für Risikobewertung (Federal Institute for Risk Assessment), Department of Biological Safety, Diedersdorfer Weg 1, D-12277 Berlin, Germany.
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Kim KP, Born Y, Lurz R, Eichenseher F, Zimmer M, Loessner MJ, Klumpp J. Inducible Clostridium perfringens bacteriophages ΦS9 and ΦS63: Different genome structures and a fully functional sigK intervening element. Bacteriophage 2014; 2:89-97. [PMID: 23050219 PMCID: PMC3442830 DOI: 10.4161/bact.21363] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Two inducible temperate bacteriophages ΦS9 and ΦS63 from Clostridium perfringens were sequenced and analyzed. Isometric heads and long non-contractile tails classify ΦS9 and ΦS63 in the Siphoviridae family, and their genomes consist of 39,457 bp (ΦS9) and 33,609 bp (ΦS63) linear dsDNA, respectively. ΦS63 has 3′-overlapping cohesive genome ends, whereas ΦS9 is the first Clostridium phage featuring an experimentally proven terminally redundant and circularly permuted genome. A total of 50 and 43 coding sequences were predicted for ΦS9 and ΦS63, respectively, organized into 6 distinct lifestyle-associated modules typical for temperate Siphoviruses. Putative functions could be assigned to 26 gene products of ΦS9, and to 25 of ΦS63. The ΦS9 attB attachment and insertion site is located in a non-coding region upstream of a putative phosphorylase gene. Interestingly, ΦS63 integrates into the 3′ part of sigK in C. perfringens, and represents the first functional skin-element-like phage described for this genus. With respect to possible effects of lysogeny, we did not obtain evidence that ΦS9 may influence sporulation of a lysogenized host. In contrast, interruption of sigK, a sporulation associated gene in various bacteria, by the ΦS63 prophage insertion is more likely to affect sporulation of its carrier.
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Affiliation(s)
- Kwang-Pyo Kim
- Department of Food Science and Technology; Chonbuk National University; Jeonbuk, South Korea ; Institute of Food; Nutrition and Health; ETH Zurich; Zurich, Switzerland
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Barucker C, Harmeier A, Weiske J, Fauler B, Albring KF, Prokop S, Hildebrand P, Lurz R, Heppner FL, Huber O, Multhaup G. Nuclear translocation uncovers the amyloid peptide Aβ42 as a regulator of gene transcription. J Biol Chem 2014; 289:20182-91. [PMID: 24878959 DOI: 10.1074/jbc.m114.564690] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Although soluble species of the amyloid-β peptide Aβ42 correlate with disease symptoms in Alzheimer disease, little is known about the biological activities of amyloid-β (Aβ). Here, we show that Aβ peptides varying in lengths from 38 to 43 amino acids are internalized by cultured neuroblastoma cells and can be found in the nucleus. By three independent methods, we demonstrate direct detection of nuclear Aβ42 as follows: (i) biochemical analysis of nuclear fractions; (ii) detection of biotin-labeled Aβ in living cells by confocal laser scanning microscopy; and (iii) transmission electron microscopy of Aβ in cultured cells, as well as brain tissue of wild-type and transgenic APPPS1 mice (overexpression of amyloid precursor protein and presenilin 1 with Swedish and L166P mutations, respectively). Also, this study details a novel role for Aβ42 in nuclear signaling, distinct from the amyloid precursor protein intracellular domain. Chromatin immunoprecipitation showed that Aβ42 specifically interacts as a repressor of gene transcription with LRP1 and KAI1 promoters. By quantitative RT-PCR, we confirmed that mRNA levels of the examined candidate genes were exclusively decreased by the potentially neurotoxic Aβ42 wild-type peptide. Shorter peptides (Aβ38 or Aβ40) and other longer peptides (nontoxic Aβ42 G33A substitution or Aβ43) did not affect mRNA levels. Overall, our data indicate that the nuclear translocation of Aβ42 impacts gene regulation, and deleterious effects of Aβ42 in Alzheimer disease pathogenesis may be influenced by altering the expression profiles of disease-modifying genes.
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Affiliation(s)
- Christian Barucker
- From the Institut fuer Chemie und Biochemie, Freie Universitaet Berlin, 14195 Berlin, Germany, the Department of Pharmacology and Therapeutics, Faculty of Medicine, McGill University, Montreal, Quebec H3G 0B1, Canada
| | - Anja Harmeier
- From the Institut fuer Chemie und Biochemie, Freie Universitaet Berlin, 14195 Berlin, Germany
| | - Joerg Weiske
- the Institute of Clinical Chemistry and Pathobiochemistry, Charite-Campus Benjamin Franklin, 12203 Berlin, Germany
| | - Beatrix Fauler
- the Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Kai Frederik Albring
- the Institute of Clinical Chemistry and Pathobiochemistry, Charite-Campus Benjamin Franklin, 12203 Berlin, Germany, the Institute of Biochemistry II, Jena University Hospital, Friedrich Schiller University, 07743 Jena, Germany, and
| | | | - Peter Hildebrand
- Institute of Medical Physics and Biophysics, Charite-Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Rudi Lurz
- the Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | | | - Otmar Huber
- the Institute of Clinical Chemistry and Pathobiochemistry, Charite-Campus Benjamin Franklin, 12203 Berlin, Germany, the Institute of Biochemistry II, Jena University Hospital, Friedrich Schiller University, 07743 Jena, Germany, and
| | - Gerhard Multhaup
- From the Institut fuer Chemie und Biochemie, Freie Universitaet Berlin, 14195 Berlin, Germany, the Department of Pharmacology and Therapeutics, Faculty of Medicine, McGill University, Montreal, Quebec H3G 0B1, Canada,
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Auzat I, Petitpas I, Lurz R, Weise F, Tavares P. A touch of glue to complete bacteriophage assembly: the tail-to-head joining protein (THJP) family. Mol Microbiol 2014; 91:1164-78. [DOI: 10.1111/mmi.12526] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/18/2014] [Indexed: 12/21/2022]
Affiliation(s)
- Isabelle Auzat
- Laboratoire de Virologie Moléculaire et Structurale; Centre de Recherche de Gif; CNRS UPR 3296 and IFR115; 91198 Gif-sur-Yvette France
| | - Isabelle Petitpas
- Laboratoire de Virologie Moléculaire et Structurale; Centre de Recherche de Gif; CNRS UPR 3296 and IFR115; 91198 Gif-sur-Yvette France
| | - Rudi Lurz
- Max Planck Institute for Molecular Genetics; Ihnestraße 63-73 D-14195 Berlin Germany
| | - Frank Weise
- Max Planck Institute for Molecular Genetics; Ihnestraße 63-73 D-14195 Berlin Germany
| | - Paulo Tavares
- Laboratoire de Virologie Moléculaire et Structurale; Centre de Recherche de Gif; CNRS UPR 3296 and IFR115; 91198 Gif-sur-Yvette France
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11
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Evrin C, Fernández-Cid A, Riera A, Zech J, Clarke P, Herrera MC, Tognetti S, Lurz R, Speck C. The ORC/Cdc6/MCM2-7 complex facilitates MCM2-7 dimerization during prereplicative complex formation. Nucleic Acids Res 2013; 42:2257-69. [PMID: 24234446 PMCID: PMC3936773 DOI: 10.1093/nar/gkt1148] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The replicative mini-chromosome-maintenance 2–7 (MCM2-7) helicase is loaded in Saccharomyces cerevisiae and other eukaryotes as a head-to-head double-hexamer around origin DNA. At first, ORC/Cdc6 recruits with the help of Cdt1 a single MCM2-7 hexamer to form an ‘initial’ ORC/Cdc6/Cdt1/MCM2-7 complex. Then, on ATP hydrolysis and Cdt1 release, the ‘initial’ complex is transformed into an ORC/Cdc6/MCM2-7 (OCM) complex. However, it remains unclear how the OCM is subsequently converted into a MCM2-7 double-hexamer. Through analysis of MCM2-7 hexamer-interface mutants we discovered a complex competent for MCM2-7 dimerization. We demonstrate that these MCM2-7 mutants arrest during prereplicative complex (pre-RC) assembly after OCM formation, but before MCM2-7 double-hexamer assembly. Remarkably, only the OCM complex, but not the ‘initial’ ORC/Cdc6/Cdt1/MCM2-7 complex, is competent for MCM2-7 dimerization. The MCM2-7 dimer, in contrast to the MCM2-7 double-hexamer, interacts with ORC/Cdc6 and is salt-sensitive, classifying the arrested complex as a helicase-loading intermediate. Accordingly, we found that overexpression of the mutants cause cell-cycle arrest and dominant lethality. Our work identifies the OCM complex as competent for MCM2-7 dimerization, reveals MCM2-7 dimerization as a limiting step during pre-RC formation and defines critical mechanisms that explain how origins are licensed.
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Affiliation(s)
- Cecile Evrin
- DNA Replication Group, MRC Clinical Sciences Centre, Imperial College, Du Cane Road, London W12 0NN, UK and Microscopy Unit, Max Planck Institute for Molecular Genetics, Berlin 14195, Germany
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12
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Fernández-López C, Lorenzo-Díaz F, Pérez-Luque R, Rodríguez-González L, Boer R, Lurz R, Bravo A, Coll M, Espinosa M. Nicking activity of the pMV158 MobM relaxase on cognate and heterologous origins of transfer. Plasmid 2013; 70:120-30. [DOI: 10.1016/j.plasmid.2013.03.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Revised: 03/22/2013] [Accepted: 03/25/2013] [Indexed: 10/27/2022]
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13
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Solano-Collado V, Lurz R, Espinosa M, Bravo A. The pneumococcal MgaSpn virulence transcriptional regulator generates multimeric complexes on linear double-stranded DNA. Nucleic Acids Res 2013; 41:6975-91. [PMID: 23723245 PMCID: PMC3737547 DOI: 10.1093/nar/gkt445] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
The MgaSpn transcriptional regulator contributes to the virulence of Streptococcus pneumoniae. It is thought to be a member of the Mga/AtxA family of global regulators. MgaSpn was shown to activate in vivo the P1623B promoter, which is divergent from the promoter (Pmga) of its own gene. This activation required a 70-bp region (PB activation region) located between both promoters. In this work, we purified an untagged form of the MgaSpn protein, which formed dimers in solution. By gel retardation and footprinting assays, we analysed the binding of MgaSpn to linear double-stranded DNAs. MgaSpn interacted with the PB activation region when it was placed at internal position on the DNA. However, when it was positioned at one DNA end, MgaSpn recognized preferentially the Pmga promoter placed at internal position. In both cases, and on binding to the primary site, MgaSpn spread along the adjacent DNA regions generating multimeric protein–DNA complexes. When both MgaSpn-binding sites were located at internal positions on longer DNAs, electron microscopy experiments demonstrated that the PB activation region was the preferred target. DNA molecules totally or partially covered by MgaSpn were also visualized. Our results suggest that MgaSpn might recognize particular DNA conformations to achieve DNA-binding specificity.
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Affiliation(s)
- Virtu Solano-Collado
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, E-28040 Madrid, Spain
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14
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Evrin C, Fernández-Cid A, Zech J, Herrera MC, Riera A, Clarke P, Brill S, Lurz R, Speck C. In the absence of ATPase activity, pre-RC formation is blocked prior to MCM2-7 hexamer dimerization. Nucleic Acids Res 2013; 41:3162-72. [PMID: 23376927 PMCID: PMC3597701 DOI: 10.1093/nar/gkt043] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The origin recognition complex (ORC) of Saccharomyces cerevisiae binds origin DNA and cooperates with Cdc6 and Cdt1 to load the replicative helicase MCM2–7 onto DNA. Helicase loading involves two MCM2–7 hexamers that assemble into a double hexamer around double-stranded DNA. This reaction requires ORC and Cdc6 ATPase activity, but it is unknown how these proteins control MCM2–7 double hexamer formation. We demonstrate that mutations in Cdc6 sensor-2 and Walker A motifs, which are predicted to affect ATP binding, influence the ORC–Cdc6 interaction and MCM2–7 recruitment. In contrast, a Cdc6 sensor-1 mutant affects MCM2–7 loading and Cdt1 release, similar as a Cdc6 Walker B ATPase mutant. Moreover, we show that Orc1 ATP hydrolysis is not involved in helicase loading or in releasing ORC from loaded MCM2–7. To determine whether Cdc6 regulates MCM2–7 double hexamer formation, we analysed complex assembly. We discovered that inhibition of Cdc6 ATPase restricts MCM2–7 association with origin DNA to a single hexamer, while active Cdc6 ATPase promotes recruitment of two MCM2–7 hexamer to origin DNA. Our findings illustrate how conserved Cdc6 AAA+ motifs modulate MCM2–7 recruitment, show that ATPase activity is required for MCM2–7 hexamer dimerization and demonstrate that MCM2–7 hexamers are recruited to origins in a consecutive process.
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Affiliation(s)
- Cecile Evrin
- DNA Replication Group, MRC Clinical Sciences Centre, Imperial College, London W12 0NN, UK
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15
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Donczew R, Weigel C, Lurz R, Zakrzewska-Czerwinska J, Zawilak-Pawlik A. Helicobacter pylori oriC--the first bipartite origin of chromosome replication in Gram-negative bacteria. Nucleic Acids Res 2012; 40:9647-60. [PMID: 22904070 PMCID: PMC3479198 DOI: 10.1093/nar/gks742] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Binding of the DnaA protein to oriC leads to DNA melting within the DNA unwinding element (DUE) and initiates replication of the bacterial chromosome. Helicobacter pylori oriC was previously identified as a region localized upstream of dnaA and containing a cluster of DnaA boxes bound by DnaA protein with a high affinity. However, no unwinding within the oriC sequence has been detected. Comprehensive in silico analysis presented in this work allowed us to identify an additional region (oriC2), separated from the original one (oriC1) by the dnaA gene. DnaA specifically binds both regions, but DnaA-dependent DNA unwinding occurs only within oriC2. Surprisingly, oriC2 is bound exclusively as supercoiled DNA, which directly shows the importance of the DNA topology in DnaA-oriC interactions, similarly as previously presented only for initiator-origin interactions in Archaea and some Eukaryota. We conclude that H. pylori oriC exhibits bipartite structure, being the first such origin discovered in a Gram-negative bacterium. The H. pylori mode of initiator-oriC interactions, with the loop formation between the subcomplexes of the discontinuous origin, resembles those discovered in Bacillus subtilis chromosome and in many plasmids, which might suggest a similar way of controlling initiation of replication.
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Affiliation(s)
- Rafał Donczew
- Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Department of Microbiology, Weigla 12, 53-114 Wrocław, Poland
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16
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Kaden D, Harmeier A, Weise C, Munter LM, Althoff V, Rost BR, Hildebrand PW, Schmitz D, Schaefer M, Lurz R, Skodda S, Yamamoto R, Arlt S, Finckh U, Multhaup G. Novel APP/Aβ mutation K16N produces highly toxic heteromeric Aβ oligomers. EMBO Mol Med 2012; 4:647-59. [PMID: 22514144 PMCID: PMC3407951 DOI: 10.1002/emmm.201200239] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2011] [Revised: 03/01/2012] [Accepted: 03/02/2012] [Indexed: 12/04/2022] Open
Abstract
Here, we describe a novel missense mutation in the amyloid precursor protein (APP) causing a lysine-to-asparagine substitution at position 687 (APP770; herein, referred to as K16N according to amyloid-β (Aβ) numbering) resulting in an early onset dementia with an autosomal dominant inheritance pattern. The K16N mutation is located exactly at the α-secretase cleavage site and influences both APP and Aβ. First, due to the K16N mutation APP secretion is affected and a higher amount of Aβ peptides is being produced. Second, Aβ peptides carrying the K16N mutation are unique in that the peptide itself is not harmful to neuronal cells. Severe toxicity, however, is evident upon equimolar mixture of wt and mutant peptides, mimicking the heterozygous state of the subject. Furthermore, Aβ42 K16N inhibits fibril formation of Aβ42 wild-type. Even more, Aβ42 K16N peptides are protected against clearance activity by the major Aβ-degrading enzyme neprilysin. Thus the mutation characterized here harbours a combination of risk factors that synergistically may contribute to the development of early onset Alzheimer disease.
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Affiliation(s)
- Daniela Kaden
- Institut fuer Chemie und Biochemie, Freie Universitaet, Berlin, Germany
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17
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Müller I, Lurz R, Geider K. Tasmancin and lysogenic bacteriophages induced from Erwinia tasmaniensis strains. Microbiol Res 2012; 167:381-7. [PMID: 22381912 DOI: 10.1016/j.micres.2012.01.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2011] [Revised: 01/16/2012] [Accepted: 01/22/2012] [Indexed: 11/29/2022]
Abstract
Mitomycin C treatment of Erwinia tasmaniensis strains from Australia induced prophages and the expression of bacteriocins. The bacteriocin named tasmancin inhibited E. tasmaniensis strains from South Africa and Germany. A gene cluster with a klebicin-related operon and an immunity protein was detected on plasmid pET46 from E. tasmaniensis strain Et1/99. PCR reactions using primers directed to this region produced signals for several strains originating from Australia, but not for strains isolated in South Africa and Germany. The latter isolates lacked plasmid pET46. Bacteriophages were induced from E. tasmaniensis strains Et88 and Et14/99, both isolates from South-Eastern Australia. These phages formed plaques on several other strains from this region, as well as on E. tasmaniensis strains from South Africa and Germany. Sequencing revealed similarity of phages ϕEt88 and ϕEt14, which shared the host range on E. tasmaniensis strains. Bacteriophages and tasmancin may interfere with the viability of several related E. tasmaniensis strains in the environment of carrier strains.
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Affiliation(s)
- Ina Müller
- Julius Kühn-Institut, Institut für Pflanzenschutz in Obst- und Weinbau, Schwabenheimer Str. 101, 69221 Dossenheim, Germany
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18
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Vinga I, Baptista C, Auzat I, Petipas I, Lurz R, Tavares P, Santos MA, São-José C. Role of bacteriophage SPP1 tail spike protein gp21 on host cell receptor binding and trigger of phage DNA ejection. Mol Microbiol 2011; 83:289-303. [DOI: 10.1111/j.1365-2958.2011.07931.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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19
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Bieschke J, Herbst M, Wiglenda T, Friedrich RP, Boeddrich A, Schiele F, Kleckers D, Lopez del Amo JM, Grüning BA, Wang Q, Schmidt MR, Lurz R, Anwyl R, Schnoegl S, Fändrich M, Frank RF, Reif B, Günther S, Walsh DM, Wanker EE. Small-molecule conversion of toxic oligomers to nontoxic β-sheet–rich amyloid fibrils. Nat Chem Biol 2011; 8:93-101. [DOI: 10.1038/nchembio.719] [Citation(s) in RCA: 355] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2011] [Accepted: 09/02/2011] [Indexed: 11/09/2022]
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20
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Prigione A, Hossini AM, Lichtner B, Serin A, Fauler B, Megges M, Lurz R, Lehrach H, Makrantonaki E, Zouboulis CC, Adjaye J. Mitochondrial-associated cell death mechanisms are reset to an embryonic-like state in aged donor-derived iPS cells harboring chromosomal aberrations. PLoS One 2011; 6:e27352. [PMID: 22110631 PMCID: PMC3215709 DOI: 10.1371/journal.pone.0027352] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2011] [Accepted: 10/14/2011] [Indexed: 01/05/2023] Open
Abstract
Somatic cells reprogrammed into induced pluripotent stem cells (iPSCs) acquire features of human embryonic stem cells (hESCs) and thus represent a promising source for cellular therapy of debilitating diseases, such as age-related disorders. However, reprogrammed cell lines have been found to harbor various genomic alterations. In addition, we recently discovered that the mitochondrial DNA of human fibroblasts also undergoes random mutational events upon reprogramming. Aged somatic cells might possess high susceptibility to nuclear and mitochondrial genome instability. Hence, concerns over the oncogenic potential of reprogrammed cells due to the lack of genomic integrity may hinder the applicability of iPSC-based therapies for age-associated conditions. Here, we investigated whether aged reprogrammed cells harboring chromosomal abnormalities show resistance to apoptotic cell death or mitochondrial-associated oxidative stress, both hallmarks of cancer transformation. Four iPSC lines were generated from dermal fibroblasts derived from an 84-year-old woman, representing the oldest human donor so far reprogrammed to pluripotency. Despite the presence of karyotype aberrations, all aged-iPSCs were able to differentiate into neurons, re-establish telomerase activity, and reconfigure mitochondrial ultra-structure and functionality to a hESC-like state. Importantly, aged-iPSCs exhibited high sensitivity to drug-induced apoptosis and low levels of oxidative stress and DNA damage, in a similar fashion as iPSCs derived from young donors and hESCs. Thus, the occurrence of chromosomal abnormalities within aged reprogrammed cells might not be sufficient to over-ride the cellular surveillance machinery and induce malignant transformation through the alteration of mitochondrial-associated cell death. Taken together, we unveiled that cellular reprogramming is capable of reversing aging-related features in somatic cells from a very old subject, despite the presence of genomic alterations. Nevertheless, we believe it will be essential to develop reprogramming protocols capable of safeguarding the integrity of the genome of aged somatic cells, before employing iPSC-based therapy for age-associated disorders.
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Affiliation(s)
- Alessandro Prigione
- Molecular Embryology and Aging Group, Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Amir M. Hossini
- Departments of Dermatology, Venereology, Allergology and Immunology, Dessau Medical Center, Dessau, Germany
| | - Björn Lichtner
- Molecular Embryology and Aging Group, Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Akdes Serin
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Beatrix Fauler
- Electron Microscopy Group, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Matthias Megges
- Molecular Embryology and Aging Group, Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Rudi Lurz
- Electron Microscopy Group, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Hans Lehrach
- Molecular Embryology and Aging Group, Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Eugenia Makrantonaki
- Departments of Dermatology, Venereology, Allergology and Immunology, Dessau Medical Center, Dessau, Germany
- Institute of Clinical Pharmacology and Toxicology, Charité University Medicine, Berlin, Germany
| | - Christos C. Zouboulis
- Departments of Dermatology, Venereology, Allergology and Immunology, Dessau Medical Center, Dessau, Germany
| | - James Adjaye
- Molecular Embryology and Aging Group, Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany
- The Stem Cell Unit, Department of Anatomy, College of Medicine, King Saud University, Riyadh, Saudi Arabia
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21
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Müller I, Lurz R, Kube M, Quedenau C, Jelkmann W, Geider K. Molecular and physiological properties of bacteriophages from North America and Germany affecting the fire blight pathogen Erwinia amylovora. Microb Biotechnol 2011; 4:735-45. [PMID: 21791029 PMCID: PMC3815410 DOI: 10.1111/j.1751-7915.2011.00272.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2011] [Revised: 05/09/2011] [Accepted: 05/19/2011] [Indexed: 12/05/2022] Open
Abstract
For possible control of fire blight affecting apple and pear trees, we characterized Erwinia amylovora phages from North America and Germany. The genome size determined by electron microscopy (EM) was confirmed by sequence data and major coat proteins were identified from gel bands by mass spectroscopy. By their morphology from EM data, φEa1h and φEa100 were assigned to the Podoviridae and φEa104 and φEa116 to the Myoviridae. Host ranges were essentially confined to E. amylovora, strains of the species Erwinia pyrifoliae, E. billingiae and even Pantoea stewartii were partially sensitive. The phages φEa1h and φEa100 were dependent on the amylovoran capsule of E. amylovora, φEa104 and φEa116 were not. The Myoviridae efficiently lysed their hosts and protected apple flowers significantly better than the Podoviridae against E. amylovora and should be preferred in biocontrol experiments. We have also isolated and partially characterized E. amylovora phages from apple orchards in Germany. They belong to the Podoviridae or Myoviridae with a host range similar to the phages isolated in North America. In EM measurements, the genome sizes of the Podoviridae were smaller than the genomes of the Myoviridae from North America and from Germany, which differed from each other in corresponding nucleotide sequences.
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Affiliation(s)
- Ina Müller
- Julius Kühn‐Institut, Institut für Pflanzenschutz in Obst‐ und Weinbau, Schwabenheimer Str. 101, 69221 Dossenheim, Germany
| | - Rudi Lurz
- Max‐Planck‐Institut für Molekulare Genetik, Ihnestr. 63, 14195 Berlin, Germany
| | - Michael Kube
- Max‐Planck‐Institut für Molekulare Genetik, Ihnestr. 63, 14195 Berlin, Germany
| | - Claudia Quedenau
- Max‐Planck‐Institut für Molekulare Genetik, Ihnestr. 63, 14195 Berlin, Germany
| | - Wilhelm Jelkmann
- Julius Kühn‐Institut, Institut für Pflanzenschutz in Obst‐ und Weinbau, Schwabenheimer Str. 101, 69221 Dossenheim, Germany
| | - Klaus Geider
- Julius Kühn‐Institut, Institut für Pflanzenschutz in Obst‐ und Weinbau, Schwabenheimer Str. 101, 69221 Dossenheim, Germany
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22
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Born Y, Fieseler L, Marazzi J, Lurz R, Duffy B, Loessner MJ. Novel virulent and broad-host-range Erwinia amylovora bacteriophages reveal a high degree of mosaicism and a relationship to Enterobacteriaceae phages. Appl Environ Microbiol 2011; 77:5945-54. [PMID: 21764969 PMCID: PMC3165370 DOI: 10.1128/aem.03022-10] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [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: 12/24/2010] [Accepted: 07/05/2011] [Indexed: 12/16/2022] Open
Abstract
A diverse set of 24 novel phages infecting the fire blight pathogen Erwinia amylovora was isolated from fruit production environments in Switzerland. Based on initial screening, four phages (L1, M7, S6, and Y2) with broad host ranges were selected for detailed characterization and genome sequencing. Phage L1 is a member of the Podoviridae, with a 39.3-kbp genome featuring invariable genome ends with direct terminal repeats. Phage S6, another podovirus, was also found to possess direct terminal repeats but has a larger genome (74.7 kbp), and the virus particle exhibits a complex tail fiber structure. Phages M7 and Y2 both belong to the Myoviridae family and feature long, contractile tails and genomes of 84.7 kbp (M7) and 56.6 kbp (Y2), respectively, with direct terminal repeats. The architecture of all four phage genomes is typical for tailed phages, i.e., organized into function-specific gene clusters. All four phages completely lack genes or functions associated with lysogeny control, which correlates well with their broad host ranges and indicates strictly lytic (virulent) lifestyles without the possibility for host lysogenization. Comparative genomics revealed that M7 is similar to E. amylovora virus ΦEa21-4, whereas L1, S6, and Y2 are unrelated to any other E. amylovora phage. Instead, they feature similarities to enterobacterial viruses T7, N4, and ΦEcoM-GJ1. In a series of laboratory experiments, we provide proof of concept that specific two-phage cocktails offer the potential for biocontrol of the pathogen.
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Affiliation(s)
- Yannick Born
- Agroscope Changins-Wädenswil ACW, Swiss National Competence Center for Fire Blight, 8820 Wädenswil, Switzerland
- Institute of Food, Nutrition, and Health, ETH Zürich, 8092 Zürich, Switzerland
| | - Lars Fieseler
- Institute of Food, Nutrition, and Health, ETH Zürich, 8092 Zürich, Switzerland
| | - Janine Marazzi
- Institute of Food, Nutrition, and Health, ETH Zürich, 8092 Zürich, Switzerland
| | - Rudi Lurz
- Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Brion Duffy
- Agroscope Changins-Wädenswil ACW, Swiss National Competence Center for Fire Blight, 8820 Wädenswil, Switzerland
| | - Martin J. Loessner
- Institute of Food, Nutrition, and Health, ETH Zürich, 8092 Zürich, Switzerland
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23
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Aramayo R, Sherman MB, Brownless K, Lurz R, Okorokov AL, Orlova EV. Quaternary structure of the specific p53-DNA complex reveals the mechanism of p53 mutant dominance. Nucleic Acids Res 2011; 39:8960-71. [PMID: 21764777 PMCID: PMC3203597 DOI: 10.1093/nar/gkr386] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The p53 tumour suppressor is a transcriptional activator that controls cell fate in response to various stresses. p53 can initiate cell cycle arrest, senescence and/or apoptosis via transactivation of p53 target genes, thus preventing cancer onset. Mutations that impair p53 usually occur in the core domain and negate the p53 sequence-specific DNA binding. Moreover, these mutations exhibit a dominant negative effect on the remaining wild-type p53. Here, we report the cryo electron microscopy structure of the full-length p53 tetramer bound to a DNA-encoding transcription factor response element (RE) at a resolution of 21 A. While two core domains from both dimers of the p53 tetramer interact with DNA within the complex, the other two core domains remain available for binding another DNA site. This finding helps to explain the dominant negative effect of p53 mutants based on the fact that p53 dimers are formed co-translationally before the whole tetramer assembles; therefore, a single mutant dimer would prevent the p53 tetramer from binding DNA. The structure indicates that the Achilles' heel of p53 is in its dimer-of-dimers organization, thus the tetramer activity can be negated by mutation in only one allele followed by tumourigenesis.
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Affiliation(s)
- Ricardo Aramayo
- Crystallography, Institute for Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, Malet Street, London, WC1E 7HX, UK
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24
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Harmeier A, Gensler M, Barucker C, Rost B, Zhuang W, Beyermann M, Hildebrand PW, Schmitz D, Lurz R, Rabe JP, Multhaup G. P2‐215: Aggregation of Aß42 is strongly influenced by Gly33 of the GxxxG motif and an inhibitor peptide which mimics Gly33 substitutions. Alzheimers Dement 2011. [DOI: 10.1016/j.jalz.2011.05.1098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
| | | | | | | | - W. Zhuang
- Humboldt Uiversität BerlinBerlinGermany
| | | | | | | | - Rudi Lurz
- Max Plank Institute for Molecular GeneticsBerlinGermany
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25
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Prigione A, Fauler B, Lurz R, Lehrach H, Adjaye J. The senescence-related mitochondrial/oxidative stress pathway is repressed in human induced pluripotent stem cells. Stem Cells 2010; 28:721-33. [PMID: 20201066 DOI: 10.1002/stem.404] [Citation(s) in RCA: 477] [Impact Index Per Article: 34.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The ability of stem cells to propagate indefinitely is believed to occur via the fine modulation of pathways commonly involved in cellular senescence, including the telomerase, the p53, and the mitochondrial/oxidative stress pathways. Induced pluripotent stem cells (iPSCs) are a novel stem cell population obtained from somatic cells through forced expression of a set of genes normally expressed in embryonic stem cells (ESCs). These reprogrammed cells acquire self-renewal properties and appear almost undistinguishable from ESCs in terms of morphology, gene expression, and differentiation potential. Accordingly, iPSCs exhibit alterations of the senescence-related telomerase and p53 signaling pathways. However, although treatments with antioxidants have been recently shown to enhance cellular reprogramming, detailed information regarding the state of the mitochondrial/oxidative stress pathway in iPSCs is still lacking. Mitochondria undergo specific changes during organismal development and aging. Thus, addressing whether somatic mitochondria within iPSCs acquire ESC-like features or retain the phenotype of the parental cell is an unanswered but relevant question. Herein, we demonstrate that somatic mitochondria within human iPSCs revert to an immature ESC-like state with respect to organelle morphology and distribution, expression of nuclear factors involved in mitochondrial biogenesis, content of mitochondrial DNA, intracellular ATP level, oxidative damage, and lactate generation. Upon differentiation, mitochondria within iPSCs and ESCs exhibited analogous maturation and anaerobic-to-aerobic metabolic modifications. Overall, the data highlight that human iPSCs and ESCs, although not identical, share similar mitochondrial properties and suggest that cellular reprogramming can modulate the mitochondrial/oxidative stress pathway, thus inducing a rejuvenated state capable of escaping cellular senescence.
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Affiliation(s)
- Alessandro Prigione
- Department of Vertebrate Genomics, Molecular Embryology and Aging Group, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, D-14195 Berlin, Germany
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26
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Lurz R. Geburtenhäufigkeit und Kindersterblichkeit bei den Rundi in Deutsch-Ostafrika. IV. (Schluß aus Nr. 48.). Dtsch Med Wochenschr 2009. [DOI: 10.1055/s-0028-1136284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Lurz R. Bäder und Chinin bei chronischer Malaria1). Dtsch Med Wochenschr 2009. [DOI: 10.1055/s-0029-1193078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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28
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Aranda-Orgillés B, Aigner J, Kunath M, Lurz R, Schneider R, Schweiger S. Active transport of the ubiquitin ligase MID1 along the microtubules is regulated by protein phosphatase 2A. PLoS One 2008; 3:e3507. [PMID: 18949047 PMCID: PMC2568803 DOI: 10.1371/journal.pone.0003507] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2008] [Accepted: 10/02/2008] [Indexed: 11/18/2022] Open
Abstract
Mutations in the MID1 protein have been found in patients with Opitz BBB/G syndrome (OS), which is characterised by multiple malformations of the ventral midline. MID1 is a microtubule-associated protein that stabilizes microtubules and, in association with the regulatory subunit of protein phosphatase 2A (PP2A), alpha4, provides ubiquitin ligase activity for the ubiquitin-specific modification of PP2A. Using Fluorescence Recovery After Photobleaching (FRAP) technology, we show here that MID1 is actively and bi-directionally transported along the microtubules, and that this movement is directly linked to its MAP kinase and PP2A-mediated phosphorylation status. Intact transport depends on both kinesins and dyneins and is inhibited upon colcemide treatments. MID1 proteins carrying missense mutations in the alpha4 binding domain still bind the microtubules but cannot be actively transported. Likewise, knock-down of the alpha4 protein, inhibition of PP2A activity by okadaic acid and fostriecin or the simulation of permanent phosphorylation at Ser96 in MID1 stop the migration of MID1-GFP, while preserving its microtubule-association. In summary, our data uncover an unexpected and novel function for PP2A, its regulatory subunit alpha4 and PP2A/alpha4/mTOR signaling in the active transport of the MID1 ubiquitin ligase complex along the cytoskeleton. Furthermore, a failure in the microtubule directed transport of this protein complex would be an attractive mechanism underlying the pathogenesis of OS in patients with B-box1 mutations.
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Affiliation(s)
| | - Johanna Aigner
- Max-Planck Institute for Molecular Genetics, Berlin, Germany
| | - Melanie Kunath
- Max-Planck Institute for Molecular Genetics, Berlin, Germany
| | - Rudi Lurz
- Max-Planck Institute for Molecular Genetics, Berlin, Germany
| | - Rainer Schneider
- Institute of Biochemistry, University Innsbruck, Innsbruck, Austria
| | - Susann Schweiger
- Max-Planck Institute for Molecular Genetics, Berlin, Germany
- Division of Pathology and Neuroscience, Ninewells Hospital, University of Dundee, Dundee, United Kingdom
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Lange M, Kaynak B, Forster UB, Tönjes M, Fischer JJ, Grimm C, Schlesinger J, Just S, Dunkel I, Krueger T, Mebus S, Lehrach H, Lurz R, Gobom J, Rottbauer W, Abdelilah-Seyfried S, Sperling S. Regulation of muscle development by DPF3, a novel histone acetylation and methylation reader of the BAF chromatin remodeling complex. Genes Dev 2008; 22:2370-84. [PMID: 18765789 DOI: 10.1101/gad.471408] [Citation(s) in RCA: 163] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Chromatin remodeling and histone modifications facilitate access of transcription factors to DNA by promoting the unwinding and destabilization of histone-DNA interactions. We present DPF3, a new epigenetic key factor for heart and muscle development characterized by a double PHD finger. DPF3 is associated with the BAF chromatin remodeling complex and binds methylated and acetylated lysine residues of histone 3 and 4. Thus, DPF3 may represent the first plant homeodomains that bind acetylated lysines, a feature previously only shown for the bromodomain. During development Dpf3 is expressed in the heart and somites of mouse, chicken, and zebrafish. Morpholino knockdown of dpf3 in zebrafish leads to incomplete cardiac looping and severely reduced ventricular contractility, with disassembled muscular fibers caused by transcriptional deregulation of structural and regulatory proteins. Promoter analysis identified Dpf3 as a novel downstream target of Mef2a. Taken together, DPF3 adds a further layer of complexity to the BAF complex by representing a tissue-specific anchor between histone acetylations as well as methylations and chromatin remodeling. Furthermore, this shows that plant homeodomain proteins play a yet unexplored role in recruiting chromatin remodeling complexes to acetylated histones.
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Affiliation(s)
- Martin Lange
- Group Cardiovascular Genetics, Department Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin 14195, Germany
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Abstract
The majority of bacteriophages have a long non-contractile tail (Siphoviridae) that serves as a conduit for viral DNA traffic from the phage capsid to the host cell at the beginning of infection. The 160-nm-long tail tube of Bacillus subtilis bacteriophage SPP1 is shown to be composed of two major tail proteins (MTPs), gp17.1 and gp17.1*, at a ratio of about 3:1. They share a common amino-terminus, but the latter species has approximately 10 kDa more than gp17.1. A CCC.UAA sequence with overlapping proline codons at the 3' end of gene 17.1 drives a programmed translational frameshift to another open reading frame. The recoding event generates gp17.1*. Phages carrying exclusively gp17.1 or gp17.1* are viable, but tails are structurally distinct. gp17.1 and the carboxyl-terminus of gp17.1* have a distinct evolutionary history correlating with different functions: the polypeptide sequence identical in the two proteins is responsible for assembly of the tail tube while the additional module of gp17.1* shields the structure exterior exposed to the environment. The carboxyl-terminal extension is an elaboration present in some tailed bacteriophages. Different extensions were found to combine in a mosaic fashion with the MTP essential module in a subset of Siphoviridae genomes.
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Affiliation(s)
- Isabelle Auzat
- Unité de Virologie Moléculaire et Structurale, CNRS UMR 2472, INRA UMR1157 and IFR 115, Bâtiment 14B, CNRS, 91198 Gif-sur-Yvette, France
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31
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Kaesler I, Graeber I, Borchert MS, Pape T, Dieckmann R, von Dohren H, Nielsen P, Lurz R, Michaelis W, Szewzyk U. Spongiispira norvegica gen. nov., sp. nov., a marine bacterium isolated from the boreal sponge Isops phlegraei. Int J Syst Evol Microbiol 2008; 58:1815-20. [DOI: 10.1099/ijs.0.65439-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Harmeier A, Munter L, Wozny C, Rost B, Zhuang W, Gensler M, Beyermann M, Lurz R, Rabe J, Schmitz D, Multhaup G. P1‐427: The GxxxG motif of the Aβ sequence unlinks Aβ aggregation from toxicity. Alzheimers Dement 2008. [DOI: 10.1016/j.jalz.2008.05.1009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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33
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Graeber I, Kaesler I, Borchert MS, Dieckmann R, Pape T, Lurz R, Nielsen P, von Döhren H, Michaelis W, Szewzyk U. Spongiibacter marinus gen. nov., sp. nov., a halophilic marine bacterium isolated from the boreal sponge Haliclona sp. 1. Int J Syst Evol Microbiol 2008; 58:585-90. [PMID: 18319460 DOI: 10.1099/ijs.0.65438-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain HAL40b(T) was isolated from the marine sponge Haliclona sp. 1 collected at the Sula Ridge off the Norwegian coast and characterized by physiological, biochemical and phylogenetic analyses. The isolate was a small rod with a polar flagellum. It was aerobic, Gram-negative and oxidase- and catalase-positive. Optimal growth was observed at 20-30 degrees C, pH 7-9 and in 3 % NaCl. Substrate utilization tests were positive for arabinose, Tween 40 and Tween 80. Enzyme tests were positive for alkaline phosphatase, esterase lipase (C8), leucine arylamidase, acid phosphatase, naphthol-AS-BI-phosphohydrolase and N-acetyl-beta-glucosaminidase. The predominant cellular fatty acid was C(17 : 1) omega8, followed by C(17 : 0) and C(18 : 1) omega7. Analysis by matrix-assisted laser desorption/ionization time-of-flight MS was used to characterize the strain, producing a characteristic low-molecular-mass protein pattern that could be used as a fingerprint for identification of members of this species. The DNA G+C content was 69.1 mol%. Phylogenetic analysis supported by 16S rRNA gene sequence comparison classified the strain as a member of the class Gammaproteobacteria. Strain HAL40b(T) was only distantly related to other marine bacteria including Neptunomonas naphthovorans and Marinobacter daepoensis (type strain sequence similarity >90 %). Based on its phenotypic, physiological and phylogenetic characteristics, it is proposed that the strain should be placed into a new genus as a representative of a novel species, Spongiibacter marinus gen. nov., sp. nov.; the type strain of Spongiibacter marinus is HAL40b(T) (=DSM 17750(T) =CCUG 54896(T)).
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Affiliation(s)
- Ingeborg Graeber
- Berlin University of Technology, Environmental Microbiology Group, Franklinstrasse 29, Sekr. FR 1-2, D-10587 Berlin, Germany.
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Pratto F, Cicek A, Weihofen WA, Lurz R, Saenger W, Alonso JC. Streptococcus pyogenes pSM19035 requires dynamic assembly of ATP-bound ParA and ParB on parS DNA during plasmid segregation. Nucleic Acids Res 2008; 36:3676-89. [PMID: 18477635 PMCID: PMC2441792 DOI: 10.1093/nar/gkn170] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The accurate partitioning of Firmicute plasmid pSM19035 at cell division depends on ATP binding and hydrolysis by homodimeric ATPase δ2 (ParA) and binding of ω2 (ParB) to its cognate parS DNA. The 1.83 Å resolution crystal structure of δ2 in a complex with non-hydrolyzable ATPγS reveals a unique ParA dimer assembly that permits nucleotide exchange without requiring dissociation into monomers. In vitro, δ2 had minimal ATPase activity in the absence of ω2 and parS DNA. However, stoichiometric amounts of ω2 and parS DNA stimulated the δ2 ATPase activity and mediated plasmid pairing, whereas at high (4:1) ω2 : δ2 ratios, stimulation of the ATPase activity was reduced and δ2 polymerized onto DNA. Stimulation of the δ2 ATPase activity and its polymerization on DNA required ability of ω2 to bind parS DNA and its N-terminus. In vivo experiments showed that δ2 alone associated with the nucleoid, and in the presence of ω2 and parS DNA, δ2 oscillated between the nucleoid and the cell poles and formed spiral-like structures. Our studies indicate that the molar ω2 : δ2 ratio regulates the polymerization properties of (δ•ATP•Mg2+)2 on and depolymerization from parS DNA, thereby controlling the temporal and spatial segregation of pSM19035 before cell division.
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Affiliation(s)
- Florencia Pratto
- Department of Microbial Biotechnology, National Centre of Biotechnology, CSIC, 28049 Madrid, Spain
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35
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Poh SL, el Khadali F, Berrier C, Lurz R, Melki R, Tavares P. Oligomerization of the SPP1 scaffolding protein. J Mol Biol 2008; 378:551-64. [PMID: 18377930 DOI: 10.1016/j.jmb.2008.02.028] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2007] [Revised: 02/11/2008] [Accepted: 02/12/2008] [Indexed: 11/29/2022]
Abstract
Viral scaffolding proteins direct polymerization of major capsid protein subunits into icosahedral procapsid structures. The scaffolding protein of bacteriophage SPP1 was engineered with a C-terminal hexahistidine tag (gp11-His(6)) and purified. The protein is an alpha-helical-rich molecule with a very elongated shape as found for internal scaffolding proteins from other phages. It is a 3.3 S tetramer of 93.6 kDa at micromolar concentrations. Intersubunit cross-linking of these tetramers generated preferentially covalently bound dimers, revealing that gp11-His(6) is structurally a dimer of dimers. Incubation at temperatures above 37 degrees C correlated with a reduction of its alpha-helical content and a less effective intersubunit cross-linking. Complete loss of secondary structure was observed at temperatures above 60 degrees C. Refolding of gp11-His(6) thermally denatured at 65 degrees C led to reacquisition of the protein native ellipticity spectrum but the resulting population of molecules was heterogeneous. Its hydrodynamic behavior was compatible with a mix of 3.3 S elongated tetramers (approximately 90%) and a smaller fraction of 2.4 S dimers (approximately 10%). This population of gp11-His(6) was competent to direct polymerization of the SPP1 major capsid protein gp13 into procapsid-like structures in a newly developed assembly assay in vitro. Although native tetramers were active in assembly, refolded gp11-His(6) showed enhanced binding to gp13 revealing a more active species for interaction with the major capsid protein than native gp11-His(6).
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Affiliation(s)
- Siew Lay Poh
- Unité de Virologie Moléculaire et Structurale, UMR CNRS 2472, UMR INRA 1157 and IFR 115, Bât. 14B, Avenue de la Terrasse, 91198 Gif-sur-Yvette Cedex, France
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36
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Gasset-Rosa F, Díaz-López T, Lurz R, Prieto A, Fernández-Tresguerres ME, Giraldo R. Negative regulation of pPS10 plasmid replication: origin pairing by zipping-up DNA-bound RepA monomers. Mol Microbiol 2008; 68:560-72. [PMID: 18284592 DOI: 10.1111/j.1365-2958.2008.06166.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In many plasmid replicons of gram-negative bacteria, Rep protein dimers are transcriptional self-repressors of their genes, whereas monomers are initiators of DNA replication. Switching between both functions implies conformational remodelling of Rep, and is promoted by Rep binding to the origin DNA repeats (iterons) or chaperones. Rep proteins play another key role: they bridge together two iteron DNA stretches, found either on the same or on different plasmid molecules. These so-called, respectively, 'looped' and 'handcuffed' complexes are thought to be negative regulators of plasmid replication. Although evidence for Rep-dependent plasmid handcuffing has been found in a number of replicons, the structure of these Rep-DNA assemblies is still unknown. Here, by a combination of proteomics, electron microscopy, genetic analysis and modelling, we provide insight on a possible three-dimensional structure for two handcuffed arrays of the iterons found at the origin of pPS10 replicon. These are brought together in parallel register by zipping-up DNA-bound RepA monomers. We also present evidence for a distinct role of RepA dimers in DNA looping. This work defines a new regulatory interface in Rep proteins.
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Affiliation(s)
- Fátima Gasset-Rosa
- Department of Molecular Microbiology, Centro de Investigaciones Biológicas-CSIC, Madrid, Spain
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37
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Affiliation(s)
- Goran Pljevaljcić
- Present address: Department of Molecular Biology, MB19, The Scripps Research Institute, 10550 N. Torrey Pines Rd. La Jolla, CA 92037, USA
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Zawilak-Pawlik A, Kois A, Stingl K, Boneca IG, Skrobuk P, Piotr J, Lurz R, Zakrzewska-Czerwińska J, Labigne A. HobA ? a novel protein involved in initiation of chromosomal replication in Helicobacter pylori. Mol Microbiol 2007; 65:979-94. [PMID: 17645450 DOI: 10.1111/j.1365-2958.2007.05853.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Replication of the bacterial chromosome is initiated by the binding of the DnaA protein to a unique DNA region, called oriC. Many regulatory factors in numerous species act by controlling the ability of DnaA to bind and unwind DNA, but the Helicobacter pylori genome does not contain homologues to any of these factors. Here, we describe HobA, a novel protein essential for initiation of H. pylori chromosome replication, which is conserved among, and unique to, epsilon proteobacteria. We demonstrate that HobA interacts specifically via DnaA with the oriC-DnaA complex. We postulate that HobA is essential for correct formation and stabilization of the orisome by facilitating the spatial positioning of DnaA at oriC. Consistent with its function, overexpression of hobA had no effect on growth of H. pylori, whereas depletion of HobA led to growth arrest and failure to initiate replication. In conclusion, HobA may be the first identified of a new group of initiation factors common to epsilon proteobacteria.
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Affiliation(s)
- Anna Zawilak-Pawlik
- Institut Pasteur, Unité de Pathogénie Bactérienne des Muqueuses, 75724-Paris Cedex 15, France.
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Zemojtel T, Kolanczyk M, Kossler N, Stricker S, Lurz R, Mikula I, Duchniewicz M, Schuelke M, Ghafourifar P, Martasek P, Vingron M, Mundlos S. Corrigendum to “Mammalian mitochondrial nitric oxide synthase: Characterization of a novel candidate” [FEBS Lett. 580 (2006) 455-462]. FEBS Lett 2007. [DOI: 10.1016/j.febslet.2007.04.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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40
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Vinga I, Lurz R, Tavares P. [DNA ejection from single phage particles]. Virologie (Montrouge) 2007; 11:154-155. [PMID: 37012836 DOI: 10.1684/vir.2011.8929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
Affiliation(s)
- I Vinga
- Unité de virologie moléculaire et structurale, CNRS UMR 2472, INRA UMR1157 and IFR 115, Bâtiment 14B, CNRS, 91198 Gif-sur-Yvette
| | - R Lurz
- Max-Planck Institut fur Molekulare Genetik, Ihnestraße 73, D-14195 Berlin, Allemagne
| | - P Tavares
- Unité de virologie moléculaire et structurale, CNRS UMR 2472, INRA UMR1157 and IFR 115, Bâtiment 14B, CNRS, 91198 Gif-sur-Yvette
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Ruiz-Masó JA, Lurz R, Espinosa M, del Solar G. Interactions between the RepB initiator protein of plasmid pMV158 and two distant DNA regions within the origin of replication. Nucleic Acids Res 2007; 35:1230-44. [PMID: 17267412 PMCID: PMC1851628 DOI: 10.1093/nar/gkl1099] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Plasmids replicating by the rolling circle mode usually possess a single site for binding of the initiator protein at the origin of replication. The origin of pMV158 is different in that it possesses two distant binding regions for the initiator RepB. One region was located close to the site where RepB introduces the replication-initiating nick, within the nic locus; the other, the bind locus, is 84 bp downstream from the nick site. Binding of RepB to the bind locus was of higher affinity and stability than to the nic locus. Contacts of RepB with the bind and nic loci were determined through high-resolution footprinting. Upon binding of RepB, the DNA of the bind locus follows a winding path in its contact with the protein, resulting in local distortion and bending of the double-helix. On supercoiled DNA, simultaneous interaction of RepB with both loci favoured extrusion of the hairpin structure harbouring the nick site while causing a strong DNA distortion around the bind locus. This suggests interplay between the two RepB binding sites, which could facilitate loading of the initiator protein to the nic locus and the acquisition of the appropriate configuration of the supercoiled DNA substrate.
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Affiliation(s)
- José A. Ruiz-Masó
- Centro de Investigaciones Biológicas, CSIC. Ramiro de Maeztu, 9. E-28040-Madrid, Spain and Max Planck Institute for Molecular Genetics. Ihnestrasse 73, D-14195 Berlin, Germany
| | - Rudi Lurz
- Centro de Investigaciones Biológicas, CSIC. Ramiro de Maeztu, 9. E-28040-Madrid, Spain and Max Planck Institute for Molecular Genetics. Ihnestrasse 73, D-14195 Berlin, Germany
| | - Manuel Espinosa
- Centro de Investigaciones Biológicas, CSIC. Ramiro de Maeztu, 9. E-28040-Madrid, Spain and Max Planck Institute for Molecular Genetics. Ihnestrasse 73, D-14195 Berlin, Germany
| | - Gloria del Solar
- Centro de Investigaciones Biológicas, CSIC. Ramiro de Maeztu, 9. E-28040-Madrid, Spain and Max Planck Institute for Molecular Genetics. Ihnestrasse 73, D-14195 Berlin, Germany
- * To whom correspondence should be addressed. Tel: +34 918373112; Fax: +34 915360432; E-mail:
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Herbst M, Bieschke J, Wang Q, Lurz R, Boeddrich A, Otto A, Anwyl R, Walsh DM, Wanker EE. Induction of fibril-like beta-amyloid aggregates by a natural substance decreases soluble oligomers and protects from neurotoxicity. Akt Neurol 2007. [DOI: 10.1055/s-2007-987948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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43
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Lioy VS, Martín MT, Camacho AG, Lurz R, Antelmann H, Hecker M, Hitchin E, Ridge Y, Wells JM, Alonso JC. pSM19035-encoded zeta toxin induces stasis followed by death in a subpopulation of cells. Microbiology (Reading) 2006; 152:2365-2379. [PMID: 16849801 DOI: 10.1099/mic.0.28950-0] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The toxin-antitoxin operon of pSM19035 encodes three proteins: the omega global regulator, the epsilon labile antitoxin and the stable zeta toxin. Accumulation of zeta toxin free of epsilon antitoxin induced loss of cell proliferation in both Bacillus subtilis and Escherichia coli cells. Induction of a zeta variant (zetaY83C) triggered stasis, in which B. subtilis cells were viable but unable to proliferate, without selectively affecting protein translation. In E. coli cells, accumulation of free zeta toxin induced stasis, but this was fully reversed by expression of the epsilon antitoxin within a defined time window. The time window for reversion of zeta toxicity by expression of epsilon antitoxin was dependent on the initial cellular level of zeta. After 240 min of constitutive expression, or inducible expression of high levels of zeta toxin for 30 min, expression of epsilon failed to reverse the toxic effect exerted by zeta in cells growing in minimal medium. Under the latter conditions, zeta inhibited replication, transcription and translation and finally induced death in a fraction (approximately 50 %) of the cell population. These results support the view that zeta interacts with its specific target and reversibly inhibits cell proliferation, but accumulation of zeta might lead to cell death due to pleiotropic effects.
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Affiliation(s)
- Virginia S Lioy
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CSIC, 28049 Madrid, Spain
| | - M Teresa Martín
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CSIC, 28049 Madrid, Spain
| | - Ana G Camacho
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CSIC, 28049 Madrid, Spain
| | - Rudi Lurz
- Max-Planck-Institut für molekulare Genetik, D-14195 Berlin, Germany
| | - Haike Antelmann
- Institut für Mikrobiologie, Ernst-Moritz-Arndt-Universität, D-17487 Greifswald, Greifswald, Germany
| | - Michael Hecker
- Institut für Mikrobiologie, Ernst-Moritz-Arndt-Universität, D-17487 Greifswald, Greifswald, Germany
| | - Ed Hitchin
- Department of Food Safety Science, BBSRC Institute of Food Research, Norwich Laboratory, Colney Lane, Norwich Research Park, Colney, Norwich NR4 7UA, UK
| | - Yvonne Ridge
- Department of Food Safety Science, BBSRC Institute of Food Research, Norwich Laboratory, Colney Lane, Norwich Research Park, Colney, Norwich NR4 7UA, UK
| | - Jerry M Wells
- University of Amsterdam, Swammerdam Institute of Life Sciences, 1018 WV Amsterdam, The Netherlands
- Department of Food Safety Science, BBSRC Institute of Food Research, Norwich Laboratory, Colney Lane, Norwich Research Park, Colney, Norwich NR4 7UA, UK
| | - Juan C Alonso
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CSIC, 28049 Madrid, Spain
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Vinga I, Dröge A, Stiege AC, Lurz R, Santos MA, Daugelavicius R, Tavares P. The minor capsid protein gp7 of bacteriophage SPP1 is required for efficient infection of Bacillus subtilis. Mol Microbiol 2006; 61:1609-21. [PMID: 16899078 DOI: 10.1111/j.1365-2958.2006.05327.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Gp7 is a minor capsid protein of the Bacillus subtilis bacteriophage SPP1. Homologous proteins are found in numerous phages but their function remained unknown. Deletion of gene 7 from the SPP1 genome yielded a mutant phage (SPP1del7) with reduced burst-size. SPP1del7 infections led to normal assembly of virus particles whose morphology, DNA and protein composition was undistinguishable from wild-type virions. However, only approximately 25% of the viral particles that lack gp7 were infectious. SPP1del7 particles caused a reduced depolarization of the B. subtilis membrane in infection assays suggesting a defect in virus genome traffic to the host cell. A higher number of SPP1del7 DNA ejection events led to abortive release of DNA to the culture medium when compared with wild-type infections. DNA ejection in vitro showed that no detectable gp7 is co-ejected with the SPP1 genome and that its presence in the virion correlated with anchoring of released DNA to the phage particle. The release of DNA from wild-type phages was slower than that from SPP1del7 suggesting that gp7 controls DNA exit from the virion. This feature is proposed to play a central role in supporting correct routing of the phage genome from the virion to the cell cytoplasm.
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Affiliation(s)
- Inês Vinga
- Unité de Virologie Moléculaire et Structurale, CNRS UMR 2472, INRA UMR1157 and IFR 115, Bâtiment 14B, CNRS, 91198 Gif-sur-Yvette, France
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45
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São-José C, Lhuillier S, Lurz R, Melki R, Lepault J, Santos MA, Tavares P. The Ectodomain of the Viral Receptor YueB Forms a Fiber That Triggers Ejection of Bacteriophage SPP1 DNA. J Biol Chem 2006; 281:11464-70. [PMID: 16481324 DOI: 10.1074/jbc.m513625200] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The irreversible binding of bacteriophages to their receptor(s) in the host cell surface triggers release of the naked genome from the virion followed by transit of viral DNA to the host cell cytoplasm. We have purified, for the first time, a receptor from a Gram-positive bacterium that is active to trigger viral DNA ejection in vitro. This extracellular region ("ectodomain") of the Bacillus subtilis protein YueB (YueB780) was a 7 S elongated dimer forming a 36.5-nm-long fiber. YueB780 bound to the tail tip of bacteriophage SPP1. Although a stable receptor-phage interaction occurred between 0 and 37 degrees C, complete blocking of phage DNA release or partial ejection events were observed at temperatures below 15 degrees C. We also showed that the receptor was exposed to the B. subtilis surface. YueB differed structurally from phage receptors from Gram-negative bacteria. Its properties revealed a fiber spanning the full length of the 30-nm-thick peptidoglycan layer. The fiber is predicted to be anchored in the cell membrane through transmembrane segments. These features, highly suitable for a virus receptor in Gram-positive bacteria, are very likely shared by a large number of phage receptors.
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Affiliation(s)
- Carlos São-José
- Faculdade de Ciências de Lisboa, Instituto de Ciência Aplicada e Tecnologia e Departamento de Biologia Vegetal, 1749-016 Lisboa, Portugal.
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46
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Boeddrich A, Gaumer S, Haacke A, Tzvetkov N, Albrecht M, Evert BO, Müller EC, Lurz R, Breuer P, Schugardt N, Plaßmann S, Xu K, Warrick JM, Suopanki J, Wüllner U, Frank R, Hartl UF, Bonini NM, Wanker EE. An arginine/lysine-rich motif is crucial for VCP/p97-mediated modulation of ataxin-3 fibrillogenesis. EMBO J 2006; 25:1547-58. [PMID: 16525503 PMCID: PMC1440312 DOI: 10.1038/sj.emboj.7601043] [Citation(s) in RCA: 128] [Impact Index Per Article: 7.1] [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: 09/28/2005] [Accepted: 02/21/2006] [Indexed: 11/09/2022] Open
Abstract
Arginine/lysine-rich motifs typically function as targeting signals for the translocation of proteins to the nucleus. Here, we demonstrate that such a motif consisting of four basic amino acids in the polyglutamine protein ataxin-3 (Atx-3) serves as a recognition site for the interaction with the molecular chaperone VCP. Through this interaction, VCP modulates the fibrillogenesis of pathogenic forms of Atx-3 in a concentration-dependent manner, with low concentrations of VCP stimulating fibrillogenesis and excess concentrations suppressing it. No such effect was observed with a mutant Atx-3 variant, which does not contain a functional VCP interaction motif. Strikingly, a stretch of four basic amino acids in the ubiquitin chain assembly factor E4B was also discovered to be critical for VCP binding, indicating that arginine/lysine-rich motifs might be generally utilized by VCP for the targeting of proteins. In vivo studies with Drosophila models confirmed that VCP selectively modulates aggregation and neurotoxicity induced by pathogenic Atx-3. Together, these results define the VCP-Atx-3 association as a potential target for therapeutic intervention and suggest that it might influence the progression of spinocerebellar ataxia type 3.
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Affiliation(s)
- Annett Boeddrich
- Department of Neuroproteomics, Max Delbrueck Center for Molecular Medicine (MDC), Berlin, Germany
- These two authors contributed equally to this work
| | - Sébastien Gaumer
- Department of Biology, Howard Hughes Medical Institute, University of Pennsylvania, Philadelphia, PA, USA
- These two authors contributed equally to this work
- Present address: Universite de Versailles Saint-Quentin-en-Yvelines, 45 avenue des Etats-Unis, F-78035 Versailles cedex, France
| | - Annette Haacke
- Max-Planck-Institute for Biochemistry, Martinsried, Germany
| | | | - Mario Albrecht
- Max-Planck-Institute for Informatics, Saarbrücken, Germany
| | - Bernd O Evert
- Department of Neurology, University of Bonn, Bonn, Germany
| | - Eva C Müller
- Department of Neuroproteomics, Max Delbrueck Center for Molecular Medicine (MDC), Berlin, Germany
| | - Rudi Lurz
- Max-Planck-Institute for Molecular Genetics, Berlin, Germany
| | - Peter Breuer
- Max-Planck-Institute for Biochemistry, Martinsried, Germany
| | - Nancy Schugardt
- Department of Neuroproteomics, Max Delbrueck Center for Molecular Medicine (MDC), Berlin, Germany
| | - Stephanie Plaßmann
- Department of Neuroproteomics, Max Delbrueck Center for Molecular Medicine (MDC), Berlin, Germany
| | - Kexiang Xu
- Department of Biology, Howard Hughes Medical Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - John M Warrick
- Department of Biology, Howard Hughes Medical Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Jaana Suopanki
- Department of Neuroproteomics, Max Delbrueck Center for Molecular Medicine (MDC), Berlin, Germany
| | | | - Ronald Frank
- Department of Chemical Biology, GBF, Braunschweig, Germany
- These are senior authors
| | - Ulrich F Hartl
- Max-Planck-Institute for Biochemistry, Martinsried, Germany
- These are senior authors
| | - Nancy M Bonini
- Department of Biology, Howard Hughes Medical Institute, University of Pennsylvania, Philadelphia, PA, USA
- These are senior authors
| | - Erich E Wanker
- Department of Neuroproteomics, Max Delbrueck Center for Molecular Medicine (MDC), Berlin, Germany
- These are senior authors
- Department of Neuroproteomics, Max Delbrueck Center for Molecular Medicine (MDC), Robert-Roessle-Straße 10, 13092 Berlin, Germany. Tel.: +49 30 9406 2157; Fax: +49 30 9406 2552; E-mail:
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Zemojtel T, Kolanczyk M, Kossler N, Stricker S, Lurz R, Mikula I, Duchniewicz M, Schuelke M, Ghafourifar P, Martasek P, Vingron M, Mundlos S. Mammalian mitochondrial nitric oxide synthase: Characterization of a novel candidate. FEBS Lett 2005; 580:455-62. [PMID: 16380119 DOI: 10.1016/j.febslet.2005.12.038] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [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] [Received: 10/24/2005] [Revised: 12/05/2005] [Accepted: 12/13/2005] [Indexed: 02/07/2023]
Abstract
Recently a novel family of putative nitric oxide synthases, with AtNOS1, the plant member implicated in NO production, has been described. Here we present experimental evidence that a mammalian ortholog of AtNOS1 protein functions in the cellular context of mitochondria. The expression data suggest that a candidate for mammalian mitochondrial nitric oxide synthase contributes to multiple physiological processes during embryogenesis, which may include roles in liver haematopoesis and bone development.
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Affiliation(s)
- Tomasz Zemojtel
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, D-14195 Berlin, Germany.
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Abstract
The Bacillus subtilis RecU protein is able to catalyze in vitro DNA strand annealing and Holliday-junction resolution. The interaction between the RecA and RecU proteins, in the presence or absence of a single-stranded binding (SSB) protein, was studied. Substoichiometric amounts of RecU enhanced RecA loading onto single-stranded DNA (ssDNA) and stimulated RecA-catalyzed D-loop formation. However, RecU inhibited the RecA-mediated three-strand exchange reaction and ssDNA-dependent dATP or rATP hydrolysis. The addition of an SSB protein did not reverse the negative effect exerted by RecU on RecA function. Annealing of circular ssDNA and homologous linear 3′-tailed double-stranded DNA by RecU was not affected by the addition of RecA both in the presence and in the absence of SSB. We propose that RecU modulates RecA activities by promoting RecA-catalyzed strand invasion and inhibiting RecA-mediated branch migration, by preventing RecA filament disassembly, and suggest a potential mechanism for the control of resolvasome assembly.
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Affiliation(s)
- Begoña Carrasco
- Departmento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSICC/Darwin 3, Campus Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Silvia Ayora
- Departmento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSICC/Darwin 3, Campus Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Departamento de Biología MolecularC/Darwin 2, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Rudi Lurz
- Max-Planck-Institut für molekulare GenetikIhnestrasse 73, D-14195, Germany
| | - Juan C. Alonso
- Departmento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSICC/Darwin 3, Campus Universidad Autónoma de Madrid, 28049 Madrid, Spain
- To whom correspondence should be addressed. Tel: +34 91585 4546; Fax: +34 91585 4506;
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Ziegelin G, Tegtmeyer N, Lurz R, Hertwig S, Hammerl J, Appel B, Lanka E. The repA gene of the linear Yersinia enterocolitica prophage PY54 functions as a circular minimal replicon in Escherichia coli. J Bacteriol 2005; 187:3445-54. [PMID: 15866931 PMCID: PMC1111997 DOI: 10.1128/jb.187.10.3445-3454.2005] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Yersinia enterocolitica prophage PY54 replicates as a linear DNA molecule with covalently closed ends. For replication of a circular PY54 minimal replicon that has been derived from a linear minireplicon, two phage-encoded loci are essential in Escherichia coli: (i) the reading frame of the replication initiation gene repA and (ii) its 212-bp origin located within the 3' portion of repA. The RepA protein acts in trans on the origin since we have physically separated the PY54 origin and repA onto a two-plasmid origin test system. For this trans action, the repA 3' end carrying the origin is dispensable. Mutagenesis by alanine scan demonstrated that the motifs for primase and for nucleotide binding present in the protein are essential for RepA activity. The replication initiation functions of RepA are replicon specific. The replication initiation proteins DnaA, DnaG, and DnaB of the host are unable to promote origin replication in the presence of mutant RepA proteins that carry single residue exchanges in these motifs. The proposed origins of the known related hairpin prophages PY54, N15, and PKO2 are all located toward the 3' end of the corresponding repA genes, where several structure elements are conserved. Origin function depends on the integrity of these elements.
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50
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Korn C, Scholz SR, Gimadutdinow O, Lurz R, Pingoud A, Meiss G. Interaction of DNA Fragmentation Factor (DFF) with DNA Reveals an Unprecedented Mechanism for Nuclease Inhibition and Suggests That DFF Can Be Activated in a DNA-bound State. J Biol Chem 2005; 280:6005-15. [PMID: 15572351 DOI: 10.1074/jbc.m413035200] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
DNA fragmentation factor (DFF) is a complex of the DNase DFF40 (CAD) and its chaperone/inhibitor DFF45 (ICAD-L) that can be activated during apoptosis to induce DNA fragmentation. Here, we demonstrate that DFF directly binds to DNA in vitro without promoting DNA cleavage. DNA binding by DFF is mediated by the nuclease subunit, which can also form stable DNA complexes after release from DFF. Recombinant and reconstituted DFF is catalytically inactive yet proficient in DNA binding, demonstrating that the nuclease subunit in DFF is inhibited in DNA cleavage but not in DNA binding, revealing an unprecedented mode of nuclease inhibition. Activation of DFF in the presence of naked DNA or isolated nuclei stimulates DNA degradation by released DFF40 (CAD). In transfected HeLa cells transiently expressed DFF associates with chromatin, suggesting that DFF could be activated during apoptosis in a DNA-bound state.
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Affiliation(s)
- Christian Korn
- Institute of Biochemistry, Justus-Liebig-University Giessen, 35392 Giessen, Germany
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