1
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Fatalska A, Stepinac E, Richter M, Kovacs L, Pietras Z, Puchinger M, Dong G, Dadlez M, Glover DM. The dimeric Golgi protein Gorab binds to Sas6 as a monomer to mediate centriole duplication. eLife 2021; 10:e57241. [PMID: 33704067 PMCID: PMC8009671 DOI: 10.7554/elife.57241] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 03/11/2021] [Indexed: 12/30/2022] Open
Abstract
The duplication and ninefold symmetry of the Drosophila centriole requires that the cartwheel molecule, Sas6, physically associates with Gorab, a trans-Golgi component. How Gorab achieves these disparate associations is unclear. Here, we use hydrogen-deuterium exchange mass spectrometry to define Gorab's interacting surfaces that mediate its subcellular localization. We identify a core stabilization sequence within Gorab's C-terminal coiled-coil domain that enables homodimerization, binding to Rab6, and thereby trans-Golgi localization. By contrast, part of the Gorab monomer's coiled-coil domain undergoes an antiparallel interaction with a segment of the parallel coiled-coil dimer of Sas6. This stable heterotrimeric complex can be visualized by electron microscopy. Mutation of a single leucine residue in Sas6's Gorab-binding domain generates a Sas6 variant with a sixteenfold reduced binding affinity for Gorab that cannot support centriole duplication. Thus, Gorab dimers at the Golgi exist in equilibrium with Sas6-associated monomers at the centriole to balance Gorab's dual role.
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Affiliation(s)
- Agnieszka Fatalska
- Department of Genetics, University of CambridgeCambridgeUnited Kingdom
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
- Institute of Biochemistry and Biophysics, Polish Academy of SciencesWarsawPoland
| | - Emma Stepinac
- Department of Medical Biochemistry, Max Perutz Labs, Medical University of ViennaViennaAustria
| | - Magdalena Richter
- Department of Genetics, University of CambridgeCambridgeUnited Kingdom
| | - Levente Kovacs
- Department of Genetics, University of CambridgeCambridgeUnited Kingdom
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
| | - Zbigniew Pietras
- Institute of Biochemistry and Biophysics, Polish Academy of SciencesWarsawPoland
| | - Martin Puchinger
- Department of Structural and Computational Biology, Max Perutz Labs, University of ViennaViennaAustria
| | - Gang Dong
- Department of Medical Biochemistry, Max Perutz Labs, Medical University of ViennaViennaAustria
| | - Michal Dadlez
- Institute of Biochemistry and Biophysics, Polish Academy of SciencesWarsawPoland
| | - David M Glover
- Department of Genetics, University of CambridgeCambridgeUnited Kingdom
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
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2
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Kotrys AV, Cysewski D, Czarnomska SD, Pietras Z, Borowski LS, Dziembowski A, Szczesny RJ. Quantitative proteomics revealed C6orf203/MTRES1 as a factor preventing stress-induced transcription deficiency in human mitochondria. Nucleic Acids Res 2019; 47:7502-7517. [PMID: 31226201 PMCID: PMC6698753 DOI: 10.1093/nar/gkz542] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [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: 02/04/2019] [Revised: 06/05/2019] [Accepted: 06/13/2019] [Indexed: 12/18/2022] Open
Abstract
Maintenance of mitochondrial gene expression is crucial for cellular homeostasis. Stress conditions may lead to a temporary reduction of mitochondrial genome copy number, raising the risk of insufficient expression of mitochondrial encoded genes. Little is known how compensatory mechanisms operate to maintain proper mitochondrial transcripts levels upon disturbed transcription and which proteins are involved in them. Here we performed a quantitative proteomic screen to search for proteins that sustain expression of mtDNA under stress conditions. Analysis of stress-induced changes of the human mitochondrial proteome led to the identification of several proteins with poorly defined functions among which we focused on C6orf203, which we named MTRES1 (Mitochondrial Transcription Rescue Factor 1). We found that the level of MTRES1 is elevated in cells under stress and we show that this upregulation of MTRES1 prevents mitochondrial transcript loss under perturbed mitochondrial gene expression. This protective effect depends on the RNA binding activity of MTRES1. Functional analysis revealed that MTRES1 associates with mitochondrial RNA polymerase POLRMT and acts by increasing mitochondrial transcription, without changing the stability of mitochondrial RNAs. We propose that MTRES1 is an example of a protein that protects the cell from mitochondrial RNA loss during stress.
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Affiliation(s)
- Anna V Kotrys
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Warsaw 02-106, Poland
| | - Dominik Cysewski
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Warsaw 02-106, Poland
| | - Sylwia D Czarnomska
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Warsaw 02-106, Poland
| | - Zbigniew Pietras
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Warsaw 02-106, Poland.,Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Warsaw 02-109, Poland
| | - Lukasz S Borowski
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Warsaw 02-106, Poland.,Faculty of Biology, Institute of Genetics and Biotechnology, University of Warsaw, Warsaw 02-106, Poland
| | - Andrzej Dziembowski
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Warsaw 02-106, Poland.,Faculty of Biology, Institute of Genetics and Biotechnology, University of Warsaw, Warsaw 02-106, Poland
| | - Roman J Szczesny
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Warsaw 02-106, Poland
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3
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Wycisk K, Tarczewska A, Kaus-Drobek M, Dadlez M, Hołubowicz R, Pietras Z, Dziembowski A, Taube M, Kozak M, Orłowski M, Ożyhar A. Intrinsically disordered N-terminal domain of the Helicoverpa armigera Ultraspiracle stabilizes the dimeric form via a scorpion-like structure. J Steroid Biochem Mol Biol 2018; 183:167-183. [PMID: 29944921 DOI: 10.1016/j.jsbmb.2018.06.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 06/18/2018] [Accepted: 06/18/2018] [Indexed: 12/31/2022]
Abstract
Nuclear receptors (NRs) are a family of ligand-dependent transcription factors activated by lipophilic compounds. NRs share a common structure comprising three domains: a variable N-terminal domain (NTD), a highly conserved globular DNA-binding domain and a ligand-binding domain. There are numerous papers describing the molecular details of the latter two globular domains. However, very little is known about the structure-function relationship of the NTD, especially as an intrinsically disordered fragment of NRs that may influence the molecular properties and, in turn, the function of globular domains. Here, we investigated whether and how an intrinsically disordered NTD consisting of 58 amino acid residues affects the functions of the globular domains of the Ultraspiracle protein from Helicoverpa armigera (HaUsp). The role of the NTD was examined for two well-known and easily testable NR functions, i.e., interactions with specific DNA sequences and dimerization. Electrophoretic mobility shift assays showed that the intrinsically disordered NTD influences the interaction of HaUsp with specific DNA sequences, apparently by destabilization of HaUsp-DNA complexes. On the other hand, multi-angle light scattering and sedimentation velocity analytical ultracentrifugation revealed that the NTD acts as a structural element that stabilizes HaUsp homodimers. Molecular models based on small-angle X-ray scattering indicate that the intrinsically disordered NTD may exert its effects on the tested HaUsp functions by forming an unexpected scorpion-like structure, in which the NTD bends towards the ligand-binding domain in each subunit of the HaUsp homodimer. This structure may be crucial for specific NTD-dependent regulation of the functions of globular domains in NRs.
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Affiliation(s)
- Krzysztof Wycisk
- Department of Biochemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland.
| | - Aneta Tarczewska
- Department of Biochemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Magdalena Kaus-Drobek
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106 Warsaw, Poland
| | - Michał Dadlez
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106 Warsaw, Poland
| | - Rafał Hołubowicz
- Department of Biochemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Zbigniew Pietras
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106 Warsaw, Poland
| | - Andrzej Dziembowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106 Warsaw, Poland
| | - Michał Taube
- Department of Macromolecular Physics, Faculty of Physics, Adam Mickiewicz University, Umultowska 85, 61-614 Poznań, Poland
| | - Maciej Kozak
- Department of Macromolecular Physics, Faculty of Physics, Adam Mickiewicz University, Umultowska 85, 61-614 Poznań, Poland
| | - Marek Orłowski
- Department of Biochemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Andrzej Ożyhar
- Department of Biochemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland.
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4
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Pietras Z, Wojcik MA, Borowski LS, Szewczyk M, Kulinski TM, Cysewski D, Stepien PP, Dziembowski A, Szczesny RJ. Controlling the mitochondrial antisense - role of the SUV3-PNPase complex and its co-factor GRSF1 in mitochondrial RNA surveillance. Mol Cell Oncol 2018; 5:e1516452. [PMID: 30525095 PMCID: PMC6276855 DOI: 10.1080/23723556.2018.1516452] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Revised: 08/21/2018] [Accepted: 08/23/2018] [Indexed: 12/30/2022]
Abstract
Transcription of the human mitochondrial genome produces a vast amount of non-coding antisense RNAs. These RNA species can form G-quadraplexes (G4), which affect their decay. We found that the mitochondrial degradosome, a complex of RNA helicase SUPV3L1 (best known as SUV3) and the ribonuclease PNPT1 (also known as PNPase), together with G4-melting protein GRSF1, is a key player in restricting antisense mtRNAs.
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Affiliation(s)
- Zbigniew Pietras
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics Polish Academy of Sciences, Warsaw, Poland.,Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Magdalena A Wojcik
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics Polish Academy of Sciences, Warsaw, Poland.,Faculty of Biology, Institute of Genetics and Biotechnology, University of Warsaw, Warsaw, Poland
| | - Lukasz S Borowski
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics Polish Academy of Sciences, Warsaw, Poland.,Faculty of Biology, Institute of Genetics and Biotechnology, University of Warsaw, Warsaw, Poland
| | - Maciej Szewczyk
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics Polish Academy of Sciences, Warsaw, Poland.,Faculty of Biology, Institute of Genetics and Biotechnology, University of Warsaw, Warsaw, Poland
| | - Tomasz M Kulinski
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics Polish Academy of Sciences, Warsaw, Poland
| | - Dominik Cysewski
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics Polish Academy of Sciences, Warsaw, Poland
| | - Piotr P Stepien
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics Polish Academy of Sciences, Warsaw, Poland.,Faculty of Biology, Institute of Genetics and Biotechnology, University of Warsaw, Warsaw, Poland
| | - Andrzej Dziembowski
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics Polish Academy of Sciences, Warsaw, Poland.,Faculty of Biology, Institute of Genetics and Biotechnology, University of Warsaw, Warsaw, Poland
| | - Roman J Szczesny
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics Polish Academy of Sciences, Warsaw, Poland
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5
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Kalisiak K, Kuliński TM, Tomecki R, Cysewski D, Pietras Z, Chlebowski A, Kowalska K, Dziembowski A. A short splicing isoform of HBS1L links the cytoplasmic exosome and SKI complexes in humans. Nucleic Acids Res 2018; 45:2068-2080. [PMID: 28204585 PMCID: PMC5389692 DOI: 10.1093/nar/gkw862] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [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] [Received: 04/18/2016] [Revised: 08/25/2016] [Accepted: 09/20/2016] [Indexed: 12/18/2022] Open
Abstract
The exosome complex is a major eukaryotic exoribonuclease that requires the SKI complex for its activity in the cytoplasm. In yeast, the Ski7 protein links both complexes, whereas a functional equivalent of the Ski7 has remained unknown in the human genome. Proteomic analysis revealed that a previously uncharacterized short splicing isoform of HBS1L (HBS1LV3) is the long-sought factor linking the exosome and SKI complexes in humans. In contrast, the canonical HBS1L variant, HBS1LV1, which acts as a ribosome dissociation factor, does not associate with the exosome and instead interacts with the mRNA surveillance factor PELOTA. Interestingly, both HBS1LV1 and HBS1LV3 interact with the SKI complex and HBS1LV1 seems to antagonize SKI/exosome supercomplex formation. HBS1LV3 contains a unique C-terminal region of unknown structure, with a conserved RxxxFxxxL motif responsible for exosome binding and may interact with the exosome core subunit RRP43 in a way that resembles the association between Rrp6 RNase and Rrp43 in yeast. HBS1LV3 or the SKI complex helicase (SKI2W) depletion similarly affected the transcriptome, deregulating multiple genes. Furthermore, half-lives of representative upregulated mRNAs were increased, supporting the involvement of HBS1LV3 and SKI2W in the same mRNA degradation pathway, essential for transcriptome homeostasis in the cytoplasm.
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Affiliation(s)
- Katarzyna Kalisiak
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Tomasz M. Kuliński
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Rafał Tomecki
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Dominik Cysewski
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Zbigniew Pietras
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
- International Institute of Molecular and Cell Biology in Warsaw, Ks. Trojdena 4, 02-109 Warsaw, Poland
| | - Aleksander Chlebowski
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Katarzyna Kowalska
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Andrzej Dziembowski
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
- To whom correspondence should be addressed. Tel: +48 22 5922033; Fax: +48 22 6584176;
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6
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Pietras Z, Wojcik MA, Borowski LS, Szewczyk M, Kulinski TM, Cysewski D, Stepien PP, Dziembowski A, Szczesny RJ. Dedicated surveillance mechanism controls G-quadruplex forming non-coding RNAs in human mitochondria. Nat Commun 2018; 9:2558. [PMID: 29967381 PMCID: PMC6028389 DOI: 10.1038/s41467-018-05007-9] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [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: 12/01/2017] [Accepted: 06/08/2018] [Indexed: 12/13/2022] Open
Abstract
The GC skew in vertebrate mitochondrial genomes results in synthesis of RNAs that are prone to form G-quadruplexes (G4s). Such RNAs, although mostly non-coding, are transcribed at high rates and are degraded by an unknown mechanism. Here we describe a dedicated mechanism of degradation of G4-containing RNAs, which is based on cooperation between mitochondrial degradosome and quasi-RNA recognition motif (qRRM) protein GRSF1. This cooperation prevents accumulation of G4-containing transcripts in human mitochondria. In vitro reconstitution experiments show that GRSF1 promotes G4 melting that facilitates degradosome-mediated decay. Among degradosome and GRSF1 regulated transcripts we identified one that undergoes post-transcriptional modification. We show that GRSF1 proteins form a distinct qRRM group found only in vertebrates. The appearance of GRSF1 coincided with changes in the mitochondrial genome, which allows the emergence of G4-containing RNAs. We propose that GRSF1 appearance is an evolutionary adaptation enabling control of G4 RNA.
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Affiliation(s)
- Zbigniew Pietras
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Laboratory of RNA Biology and Functional Genomics, Pawinskiego 5A, 02-106, Warsaw, Poland.,International Institute of Molecular and Cell Biology, Laboratory of Protein Structure, Ks. Trojdena 4, 02-109, Warsaw, Poland
| | - Magdalena A Wojcik
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Laboratory of RNA Biology and Functional Genomics, Pawinskiego 5A, 02-106, Warsaw, Poland.,Faculty of Biology, Institute of Genetics and Biotechnology, University of Warsaw, Pawinskiego 5A, 02-106, Warsaw, Poland
| | - Lukasz S Borowski
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Laboratory of RNA Biology and Functional Genomics, Pawinskiego 5A, 02-106, Warsaw, Poland.,Faculty of Biology, Institute of Genetics and Biotechnology, University of Warsaw, Pawinskiego 5A, 02-106, Warsaw, Poland
| | - Maciej Szewczyk
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Laboratory of RNA Biology and Functional Genomics, Pawinskiego 5A, 02-106, Warsaw, Poland.,Faculty of Biology, Institute of Genetics and Biotechnology, University of Warsaw, Pawinskiego 5A, 02-106, Warsaw, Poland
| | - Tomasz M Kulinski
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Laboratory of RNA Biology and Functional Genomics, Pawinskiego 5A, 02-106, Warsaw, Poland
| | - Dominik Cysewski
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Laboratory of RNA Biology and Functional Genomics, Pawinskiego 5A, 02-106, Warsaw, Poland
| | - Piotr P Stepien
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Laboratory of RNA Biology and Functional Genomics, Pawinskiego 5A, 02-106, Warsaw, Poland.,Faculty of Biology, Institute of Genetics and Biotechnology, University of Warsaw, Pawinskiego 5A, 02-106, Warsaw, Poland
| | - Andrzej Dziembowski
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Laboratory of RNA Biology and Functional Genomics, Pawinskiego 5A, 02-106, Warsaw, Poland. .,Faculty of Biology, Institute of Genetics and Biotechnology, University of Warsaw, Pawinskiego 5A, 02-106, Warsaw, Poland.
| | - Roman J Szczesny
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Laboratory of RNA Biology and Functional Genomics, Pawinskiego 5A, 02-106, Warsaw, Poland. .,Faculty of Biology, Institute of Genetics and Biotechnology, University of Warsaw, Pawinskiego 5A, 02-106, Warsaw, Poland.
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7
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Kowalczyk J, Palusinska M, Wroblewska-Swiniarska A, Pietras Z, Szewc L, Dolata J, Jarmolowski A, Swiezewski S. Alternative Polyadenylation of the Sense Transcript Controls Antisense Transcription of DELAY OF GERMINATION 1 in Arabidopsis. Mol Plant 2017; 10:1349-1352. [PMID: 28782720 DOI: 10.1016/j.molp.2017.07.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 07/04/2017] [Accepted: 07/27/2017] [Indexed: 05/22/2023]
Affiliation(s)
- Justyna Kowalczyk
- Department of Protein Biosynthesis, Institute of Biochemistry of Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Malgorzata Palusinska
- Department of Protein Biosynthesis, Institute of Biochemistry of Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Agata Wroblewska-Swiniarska
- Department of Protein Biosynthesis, Institute of Biochemistry of Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Zbigniew Pietras
- Department of Protein Biosynthesis, Institute of Biochemistry of Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Lukasz Szewc
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland
| | - Jakub Dolata
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland
| | - Artur Jarmolowski
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland
| | - Szymon Swiezewski
- Department of Protein Biosynthesis, Institute of Biochemistry of Biophysics, Polish Academy of Sciences, Warsaw, Poland.
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8
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Cyrek M, Fedak H, Ciesielski A, Guo Y, Sliwa A, Brzezniak L, Krzyczmonik K, Pietras Z, Kaczanowski S, Liu F, Swiezewski S. Seed Dormancy in Arabidopsis Is Controlled by Alternative Polyadenylation of DOG1. Plant Physiol 2016; 170:947-55. [PMID: 26620523 PMCID: PMC4734566 DOI: 10.1104/pp.15.01483] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 11/25/2015] [Indexed: 05/19/2023]
Abstract
DOG1 (Delay of Germination 1) is a key regulator of seed dormancy in Arabidopsis (Arabidopsis thaliana) and other plants. Interestingly, the C terminus of DOG1 is either absent or not conserved in many plant species. Here, we show that in Arabidopsis, DOG1 transcript is subject to alternative polyadenylation. In line with this, mutants in RNA 3' processing complex display weakened seed dormancy in parallel with defects in DOG1 proximal polyadenylation site selection, suggesting that the short DOG1 transcript is functional. This is corroborated by the finding that the proximally polyadenylated short DOG1 mRNA is translated in vivo and complements the dog1 mutant. In summary, our findings indicate that the short DOG1 protein isoform produced from the proximally polyadenylated DOG1 mRNA is a key player in the establishment of seed dormancy in Arabidopsis and characterizes a set of mutants in RNA 3' processing complex required for production of proximally polyadenylated functional DOG1 transcript.
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Affiliation(s)
- Malgorzata Cyrek
- Institute of Biochemistry and Biophysics, Department of Protein Biosynthesis, Pawinskiego 5a, 02-106 Warsaw, Poland (M.C., H.F., A.C., Y.G., A.S., L.B., K.K., Z.P., S.K., S.S.); Warsaw University, Department of Chemistry, Pasteura 1, 02-093 Warsaw, Poland (A.C.); andQueen's University Belfast, School of Biological Sciences, Belfast BT9 7BL, Northern Ireland (F.L.)
| | - Halina Fedak
- Institute of Biochemistry and Biophysics, Department of Protein Biosynthesis, Pawinskiego 5a, 02-106 Warsaw, Poland (M.C., H.F., A.C., Y.G., A.S., L.B., K.K., Z.P., S.K., S.S.); Warsaw University, Department of Chemistry, Pasteura 1, 02-093 Warsaw, Poland (A.C.); andQueen's University Belfast, School of Biological Sciences, Belfast BT9 7BL, Northern Ireland (F.L.)
| | - Arkadiusz Ciesielski
- Institute of Biochemistry and Biophysics, Department of Protein Biosynthesis, Pawinskiego 5a, 02-106 Warsaw, Poland (M.C., H.F., A.C., Y.G., A.S., L.B., K.K., Z.P., S.K., S.S.); Warsaw University, Department of Chemistry, Pasteura 1, 02-093 Warsaw, Poland (A.C.); andQueen's University Belfast, School of Biological Sciences, Belfast BT9 7BL, Northern Ireland (F.L.)
| | - Yanwu Guo
- Institute of Biochemistry and Biophysics, Department of Protein Biosynthesis, Pawinskiego 5a, 02-106 Warsaw, Poland (M.C., H.F., A.C., Y.G., A.S., L.B., K.K., Z.P., S.K., S.S.); Warsaw University, Department of Chemistry, Pasteura 1, 02-093 Warsaw, Poland (A.C.); andQueen's University Belfast, School of Biological Sciences, Belfast BT9 7BL, Northern Ireland (F.L.)
| | - Aleksandra Sliwa
- Institute of Biochemistry and Biophysics, Department of Protein Biosynthesis, Pawinskiego 5a, 02-106 Warsaw, Poland (M.C., H.F., A.C., Y.G., A.S., L.B., K.K., Z.P., S.K., S.S.); Warsaw University, Department of Chemistry, Pasteura 1, 02-093 Warsaw, Poland (A.C.); andQueen's University Belfast, School of Biological Sciences, Belfast BT9 7BL, Northern Ireland (F.L.)
| | - Lien Brzezniak
- Institute of Biochemistry and Biophysics, Department of Protein Biosynthesis, Pawinskiego 5a, 02-106 Warsaw, Poland (M.C., H.F., A.C., Y.G., A.S., L.B., K.K., Z.P., S.K., S.S.); Warsaw University, Department of Chemistry, Pasteura 1, 02-093 Warsaw, Poland (A.C.); andQueen's University Belfast, School of Biological Sciences, Belfast BT9 7BL, Northern Ireland (F.L.)
| | - Katarzyna Krzyczmonik
- Institute of Biochemistry and Biophysics, Department of Protein Biosynthesis, Pawinskiego 5a, 02-106 Warsaw, Poland (M.C., H.F., A.C., Y.G., A.S., L.B., K.K., Z.P., S.K., S.S.); Warsaw University, Department of Chemistry, Pasteura 1, 02-093 Warsaw, Poland (A.C.); andQueen's University Belfast, School of Biological Sciences, Belfast BT9 7BL, Northern Ireland (F.L.)
| | - Zbigniew Pietras
- Institute of Biochemistry and Biophysics, Department of Protein Biosynthesis, Pawinskiego 5a, 02-106 Warsaw, Poland (M.C., H.F., A.C., Y.G., A.S., L.B., K.K., Z.P., S.K., S.S.); Warsaw University, Department of Chemistry, Pasteura 1, 02-093 Warsaw, Poland (A.C.); andQueen's University Belfast, School of Biological Sciences, Belfast BT9 7BL, Northern Ireland (F.L.)
| | - Szymon Kaczanowski
- Institute of Biochemistry and Biophysics, Department of Protein Biosynthesis, Pawinskiego 5a, 02-106 Warsaw, Poland (M.C., H.F., A.C., Y.G., A.S., L.B., K.K., Z.P., S.K., S.S.); Warsaw University, Department of Chemistry, Pasteura 1, 02-093 Warsaw, Poland (A.C.); andQueen's University Belfast, School of Biological Sciences, Belfast BT9 7BL, Northern Ireland (F.L.)
| | - Fuquan Liu
- Institute of Biochemistry and Biophysics, Department of Protein Biosynthesis, Pawinskiego 5a, 02-106 Warsaw, Poland (M.C., H.F., A.C., Y.G., A.S., L.B., K.K., Z.P., S.K., S.S.); Warsaw University, Department of Chemistry, Pasteura 1, 02-093 Warsaw, Poland (A.C.); andQueen's University Belfast, School of Biological Sciences, Belfast BT9 7BL, Northern Ireland (F.L.)
| | - Szymon Swiezewski
- Institute of Biochemistry and Biophysics, Department of Protein Biosynthesis, Pawinskiego 5a, 02-106 Warsaw, Poland (M.C., H.F., A.C., Y.G., A.S., L.B., K.K., Z.P., S.K., S.S.); Warsaw University, Department of Chemistry, Pasteura 1, 02-093 Warsaw, Poland (A.C.); andQueen's University Belfast, School of Biological Sciences, Belfast BT9 7BL, Northern Ireland (F.L.)
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9
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Abstract
Members of the DEAD-box family of RNA helicases contribute to virtually every aspect of RNA metabolism, in organisms from all domains of life. Many of these helicases are constituents of multicomponent assemblies, and their interactions with partner proteins within the complexes underpin their activities and biological function. In Escherichia coli the DEAD-box helicase RhlB is a component of the multienzyme RNA degradosome assembly, and its interaction with the core ribonuclease RNase E boosts the ATP-dependent activity of the helicase. Earlier studies have identified the regulator of ribonuclease activity A (RraA) as a potential interaction partner of both RNase E and RhlB. We present structural and biochemical evidence showing how RraA can bind to, and modulate the activity of RhlB and another E. coli DEAD-box enzyme, SrmB. Crystallographic structures are presented of RraA in complex with a portion of the natively unstructured C-terminal tail of RhlB at 2.8-Å resolution, and in complex with the C-terminal RecA-like domain of SrmB at 2.9 Å. The models suggest two distinct mechanisms by which RraA might modulate the activity of these and potentially other helicases.
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Affiliation(s)
- Zbigniew Pietras
- From the Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, United Kingdom and
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10
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Deshayes C, Bielecka MK, Cain RJ, Scortti M, de las Heras A, Pietras Z, Luisi BF, Núñez Miguel R, Vázquez-Boland JA. Allosteric mutants show that PrfA activation is dispensable for vacuole escape but required for efficient spread and Listeria survival in vivo. Mol Microbiol 2012; 85:461-77. [PMID: 22646689 PMCID: PMC3443378 DOI: 10.1111/j.1365-2958.2012.08121.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [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: 12/18/2022]
Abstract
The transcriptional regulator PrfA controls key virulence determinants of the facultative intracellular pathogen Listeria monocytogenes. PrfA-dependent gene expression is strongly induced within host cells. While the basis of this activation is unknown, the structural homology of PrfA with the cAMP receptor protein (Crp) and the finding of constitutively activated PrfA* mutants suggests it may involve ligand-induced allostery. Here, we report the identification of a solvent-accessible cavity within the PrfA N-terminal domain that may accommodate an activating ligand. The pocket occupies a similar position to the cAMP binding site in Crp but lacks the cyclic nucleotide-anchoring motif and has its entrance on the opposite side of the β-barrel. Site-directed mutations in this pocket impaired intracellular PrfA-dependent gene activation without causing extensive structural/functional alterations to PrfA. Two substitutions, L48F and Y63W, almost completely abolished intracellular virulence gene induction and thus displayed the expected phenotype for allosteric activation-deficient PrfA mutations. Neither PrfA(allo) substitution affected vacuole escape and initial intracellular growth of L. monocytogenes in epithelial cells and macrophages but caused defective cell-to-cell spread and strong attenuation in mice. Our data support the hypothesis that PrfA is allosterically activated during intracellular infection and identify the probable binding site for the effector ligand. They also indicate that PrfA allosteric activation is not required for early intracellular survival but is essential for full Listeria virulence and colonization of host tissues.
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Affiliation(s)
- Caroline Deshayes
- Centres for Infectious Diseases and Immunity, Infection & Evolution, University of Edinburgh, Edinburgh, UK
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11
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Abstract
RNA and DNA helicases manipulate or translocate along single strands of nucleic acids by grasping them using a conserved structural motif. We have examined the available crystal structures of helicases of the two principal superfamilies, SF1 and SF2, and observed that the most conserved interactions with the nucleic acid occur between the phosphosugar backbone of a trinucleotide and the three strand-helix loops within a (beta-strand/alpha-helix)(3) structural module. At the first and third loops is a conserved hydrogen-bonded feature called a thr-motif, often seen at alpha-helical N-termini, with the threonine as the N-cap residue. These loops can be aligned with few insertions or deletions, and their main chain atoms are structurally congruent amongst the family members and between the two modules found as tandem pairs in all SF1 and SF2 proteins. The other highly conserved interactions with nucleic acid involve main chain NH groups, often at the helical N-termini, interacting with phosphate groups. We comment on how the sequence motifs that are commonly used to identify helicases map to locations on the module and discuss the implications of the conserved orientation of nucleic acid on the surface of the module for directional stepping along DNA or RNA.
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Affiliation(s)
- E James Milner-White
- Institute of Biomedical and Life Sciences, University of Glasgow, Glasgow, United Kingdom.
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12
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Górna MW, Pietras Z, Tsai YC, Callaghan AJ, Hernández H, Robinson CV, Luisi BF. The regulatory protein RraA modulates RNA-binding and helicase activities of the E. coli RNA degradosome. RNA 2010; 16:553-562. [PMID: 20106955 PMCID: PMC2822920 DOI: 10.1261/rna.1858010] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2009] [Accepted: 12/03/2009] [Indexed: 05/28/2023]
Abstract
The Escherichia coli endoribonuclease RNase E is an essential enzyme having key roles in mRNA turnover and the processing of several structured RNA precursors, and it provides the scaffold to assemble the multienzyme RNA degradosome. The activity of RNase E is inhibited by the protein RraA, which can interact with the ribonuclease's degradosome-scaffolding domain. Here, we report that RraA can bind to the RNA helicase component of the degradosome (RhlB) and the two RNA-binding sites in the degradosome-scaffolding domain of RNase E. In the presence of ATP, the helicase can facilitate the exchange of RraA for RNA stably bound to the degradosome. Our data suggest that RraA can affect multiple components of the RNA degradosome in a dynamic, energy-dependent equilibrium. The multidentate interactions of RraA impede the RNA-binding and ribonuclease activities of the degradosome and may result in complex modulation and rerouting of degradosome activity.
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Affiliation(s)
- Maria W Górna
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
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13
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Pietras Z, Lin HT, Surade S, Luisi B, Slattery O, Pos KM, Moreno A. The use of novel organic gels and hydrogels in protein crystallization. J Appl Crystallogr 2010. [DOI: 10.1107/s0021889809051917] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
The use of an organic solvent-based gel prepared from polyethylene oxide and a polyvinyl alcohol hydrogel for protein crystallization was investigated. The preparation, properties and application of the gels for protein crystallization are described, and the advantages and limitations of the approach are discussed. The gels are compared with agar, which is a popular aqueous gel used for protein crystallization. The growth behaviour and diffraction quality of crystals prepared in these gel media were evaluated for two model soluble proteins, thaumatin and lysozyme, and for two bacterial membrane proteins, TolC and AcrB.
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14
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Godlewska R, Wiśniewska K, Pietras Z, Jagusztyn-Krynicka EK. Peptidoglycan-associated lipoprotein (Pal) of Gram-negative bacteria: function, structure, role in pathogenesis and potential application in immunoprophylaxis. FEMS Microbiol Lett 2009; 298:1-11. [PMID: 19519769 DOI: 10.1111/j.1574-6968.2009.01659.x] [Citation(s) in RCA: 143] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The protein Pal (peptidoglycan-associated lipoprotein) is anchored in the outer membrane (OM) of Gram-negative bacteria and interacts with Tol proteins. Tol-Pal proteins form two complexes: the first is composed of three inner membrane Tol proteins (TolA, TolQ and TolR); the second consists of the TolB and Pal proteins linked to the cell's OM. These complexes interact with one another forming a multiprotein membrane-spanning system. It has recently been demonstrated that Pal is essential for bacterial survival and pathogenesis, although its role in virulence has not been clearly defined. This review summarizes the available data concerning the structure and function of Pal and its role in pathogenesis.
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Affiliation(s)
- Renata Godlewska
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
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15
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Pietras Z, Bavro VN, Furnham N, Pellegrini-Calace M, Milner-White EJ, Luisi BF. Structure and mechanism of drug efflux machinery in Gram negative bacteria. Curr Drug Targets 2008; 9:719-28. [PMID: 18781919 DOI: 10.2174/138945008785747743] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In Gram-negative bacteria, multi-component machines that span the inner and outer membranes actively extrude drugs and other toxic small compounds. Many of these machines are assembled principally from three different types of components: i) an outer membrane protein that acts as a channel and opens from a sealed resting state during the transport process, ii) an inner membrane protein that transduces proton electrochemical energy into vectorial displacement of the transported compounds, and iii) a bridging, periplasmic component that links the inner and outer membrane proteins. The pumps may assemble transiently, and the association of components is favoured by engaged substrate and the trans-membrane electrochemical potential. We describe recent structural and functional studies on the individual pump components and discuss models that explain how they associate in the dynamic, active assembly. Based on the available data, we suggest that the assembly of these multi-drug efflux pumps is accompanied by induced fit of the outer membrane component driven mainly by accommodation of the periplasmic component.
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Affiliation(s)
- Zbigniew Pietras
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK
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16
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Bavro VN, Pietras Z, Furnham N, Pérez-Cano L, Fernández-Recio J, Pei XY, Misra R, Luisi B. Assembly and channel opening in a bacterial drug efflux machine. Mol Cell 2008; 30:114-21. [PMID: 18406332 PMCID: PMC2292822 DOI: 10.1016/j.molcel.2008.02.015] [Citation(s) in RCA: 138] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2007] [Revised: 01/18/2008] [Accepted: 02/04/2008] [Indexed: 01/07/2023]
Abstract
Drugs and certain proteins are transported across the membranes of Gram-negative bacteria by energy-activated pumps. The outer membrane component of these pumps is a channel that opens from a sealed resting state during the transport process. We describe two crystal structures of the Escherichia coli outer membrane protein TolC in its partially open state. Opening is accompanied by the exposure of three shallow intraprotomer grooves in the TolC trimer, where our mutagenesis data identify a contact point with the periplasmic component of a drug efflux pump, AcrA. We suggest that the assembly of multidrug efflux pumps is accompanied by induced fit of TolC driven mainly by accommodation of the periplasmic component.
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Affiliation(s)
- Vassiliy N Bavro
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
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Kawalec M, Pietras Z, Daniłowicz E, Jakubczak A, Gniadkowski M, Hryniewicz W, Willems RJL. Clonal structure of Enterococcus faecalis isolated from Polish hospitals: characterization of epidemic clones. J Clin Microbiol 2006; 45:147-53. [PMID: 17093020 PMCID: PMC1828945 DOI: 10.1128/jcm.01704-06] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
To study the population structure of Enterococcus faecalis from Polish hospitals, 291 isolates were typed by pulsed-field gel electrophoresis and a novel multilocus sequence typing scheme (P. Ruiz-Garbajosa et al., J. Clin. Microbiol. 44:2220-2228, 2006). The isolates originated from geographically widespread medical institutions and were recovered during a 10-year period (1996 to 2005) from different clinical sources. The analysis grouped the isolates into five epidemic and 71 sporadic clones. The importance of the previously identified global clonal complexes CC2 and CC9 was corroborated by our findings that two of the Polish epidemic clones, A and J, were classified into these clonal complexes (CCs). However, the two most predominant clones, C (ST40) and F (CC87), did not cluster in the aforementioned CCs and may represent novel epidemic CCs. These clones may have emerged in Central Europe. Clone F, carrying glycopeptide resistance determinants of VanA or VanB phenotypes, caused several outbreaks in hematology units and appeared to be the most prevalent clone in recent years in Poland. Antimicrobial susceptibility testing and additional tests for pathogenicity-related phenotypes (hemolysin and gelatinase production) and genes (asa1 and esp) were performed to further characterize these epidemic clones. Multidrug resistance, glycopeptide resistance, presence of asa1, and production of hemolysin appeared to be statistically significant features related to epidemicity. Production of gelatinase was significant for two of the epidemic clones, whereas presence of the esp gene was not specific for the epidemic clones.
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Affiliation(s)
- Magdalena Kawalec
- Department of Molecular Microbiology, National Institute of Public Health, Chełmska 30/34, 00-725 Warsaw, Poland.
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