1
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ComFC mediates transport and handling of single-stranded DNA during natural transformation. Nat Commun 2022; 13:1961. [PMID: 35414142 PMCID: PMC9005727 DOI: 10.1038/s41467-022-29494-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 03/17/2022] [Indexed: 11/09/2022] Open
Abstract
The ComFC protein is essential for natural transformation, a process that plays a major role in the spread of antibiotic resistance genes and virulence factors across bacteria. However, its role remains largely unknown. Here, we show that Helicobacter pylori ComFC is involved in DNA transport through the cell membrane, and is required for the handling of the single-stranded DNA once it is delivered into the cytoplasm. The crystal structure of ComFC includes a zinc-finger motif and a putative phosphoribosyl transferase domain, both necessary for the protein's in vivo activity. Furthermore, we show that ComFC is a membrane-associated protein with affinity for single-stranded DNA. Our results suggest that ComFC provides the link between the transport of the transforming DNA into the cytoplasm and its handling by the recombination machinery.
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2
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Natural transformation protein ComFA exhibits single-stranded DNA translocase activity. J Bacteriol 2022; 204:e0051821. [PMID: 35041498 DOI: 10.1128/jb.00518-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Natural transformation is one of the major mechanisms of horizontal gene transfer in bacterial populations and has been demonstrated in numerous species of bacteria. Despite the prevalence of natural transformation, much of the molecular mechanism remains unexplored. One major outstanding question is how the cell powers DNA import, which is rapid and highly processive. ComFA is one of a handful of proteins required for natural transformation in gram-positive bacteria. Its structural resemblance to the DEAD-box helicase family has led to a long-held hypothesis that ComFA acts as a motor to help drive DNA import into the cytosol. Here, we explored the helicase and translocase activity of ComFA to address this hypothesis. We followed the DNA-dependent ATPase activity of ComFA and, combined with mathematical modeling, demonstrated that ComFA likely translocates on single-stranded DNA from 5' to 3'. However, this translocase activity does not lead to DNA unwinding in the conditions we tested. Further, we analyzed the ATPase cycle of ComFA and found that ATP hydrolysis stimulates the release of DNA, providing a potential mechanism for translocation. These findings help define the molecular contribution of ComFA to natural transformation and support the conclusion that ComFA plays a key role in powering DNA uptake. Importance Competence, or the ability of bacteria to take up and incorporate foreign DNA in a process called natural transformation, is common in the bacterial kingdom. Research in several bacterial species suggests that long, contiguous stretches of DNA are imported into cells in a processive manner, but how bacteria power transformation remains unclear. Our finding that ComFA, a DEAD-box helicase required for competence in gram-positive bacteria, translocates on single-stranded DNA from 5' to 3', supports the long held hypothesis that ComFA may be the motor powering DNA transport during natural transformation. Moreover, ComFA may be a previously unidentified type of DEAD-box helicase-one with the capability of extended translocation on single-stranded DNA.
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3
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Hahn J, DeSantis M, Dubnau D. Mechanisms of Transforming DNA Uptake to the Periplasm of Bacillus subtilis. mBio 2021; 12:e0106121. [PMID: 34126763 PMCID: PMC8262900 DOI: 10.1128/mbio.01061-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 05/05/2021] [Indexed: 11/20/2022] Open
Abstract
We demonstrate here that the acquisition of DNase resistance by transforming DNA, often assumed to indicate transport to the cytoplasm, reflects uptake to the periplasm, requiring a reevaluation of conclusions about the roles of several proteins in transformation. The new evidence suggests that the transformation pilus is needed for DNA binding to the cell surface near the cell poles and for the initiation of uptake. The cellular distribution of the membrane-anchored ComEA of Bacillus subtilis does not dramatically change during DNA uptake as does the unanchored ComEA of Vibrio and Neisseria. Instead, our evidence suggests that ComEA stabilizes the attachment of transforming DNA at localized regions in the periplasm and then mediates uptake, probably by a Brownian ratchet mechanism. Following that, the DNA is transferred to periplasmic portions of the channel protein ComEC, which plays a previously unsuspected role in uptake to the periplasm. We show that the transformation endonuclease NucA also facilitates uptake to the periplasm and that the previously demonstrated role of ComFA in the acquisition of DNase resistance derives from the instability of ComGA when ComFA is deleted. These results prompt a new understanding of the early stages of DNA uptake for transformation. IMPORTANCE Transformation is a widely distributed mechanism of bacterial horizontal gene transfer that plays a role in the spread of antibiotic resistance and virulence genes and more generally in evolution. Although transformation was discovered nearly a century ago and most, if not all the proteins required have been identified in several bacterial species, much remains poorly understood about the molecular mechanism of DNA uptake. This study uses epifluorescence microscopy to investigate the passage of labeled DNA into the compartment between the cell wall and the cell membrane of Bacillus subtilis, a necessary early step in transformation. The roles of individual proteins in this process are identified, and their modes of action are clarified.
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Affiliation(s)
- Jeanette Hahn
- Public Health Research Institute, Rutgers University, Newark, New Jersey, USA
- Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, New Jersey, USA
| | - Micaela DeSantis
- Public Health Research Institute, Rutgers University, Newark, New Jersey, USA
- Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, New Jersey, USA
| | - David Dubnau
- Public Health Research Institute, Rutgers University, Newark, New Jersey, USA
- Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, New Jersey, USA
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4
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Silale A, Lea SM, Berks BC. The DNA transporter ComEC has metal-dependent nuclease activity that is important for natural transformation. Mol Microbiol 2021; 116:416-426. [PMID: 33772889 PMCID: PMC8579336 DOI: 10.1111/mmi.14720] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 03/22/2021] [Accepted: 03/23/2021] [Indexed: 12/25/2022]
Abstract
In the process of natural transformation bacteria import extracellular DNA molecules for integration into their genome. One strand of the incoming DNA molecule is degraded, whereas the remaining strand is transported across the cytoplasmic membrane. The DNA transport channel is provided by the protein ComEC. Many ComEC proteins have an extracellular C-terminal domain (CTD) with homology to the metallo-β-lactamase fold. Here we show that this CTD binds Mn2+ ions and exhibits Mn2+ -dependent phosphodiesterase and nuclease activities. Inactivation of the enzymatic activity of the CTD severely inhibits natural transformation in Bacillus subtilis. These data suggest that the ComEC CTD is a nuclease responsible for degrading the nontransforming DNA strand during natural transformation and that this process is important for efficient DNA import.
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Affiliation(s)
- Augustinas Silale
- Department of Biochemistry, University of Oxford, Oxford, UK.,Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Susan M Lea
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Ben C Berks
- Department of Biochemistry, University of Oxford, Oxford, UK
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5
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Abstract
Transformation is a widespread mechanism of horizontal gene transfer in bacteria. DNA uptake to the periplasmic compartment requires a DNA-uptake pilus and the DNA-binding protein ComEA. In the gram-negative bacteria, DNA is first pulled toward the outer membrane by retraction of the pilus and then taken up by binding to periplasmic ComEA, acting as a Brownian ratchet to prevent backward diffusion. A similar mechanism probably operates in the gram-positive bacteria as well, but these systems have been less well characterized. Transport, defined as movement of a single strand of transforming DNA to the cytosol, requires the channel protein ComEC. Although less is understood about this process, it may be driven by proton symport. In this review we also describe various phenomena that are coordinated with the expression of competence for transformation, such as fratricide, the kin-discriminatory killing of neighboring cells, and competence-mediated growth arrest.
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Affiliation(s)
- David Dubnau
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, New Jersey 07103, USA;
| | - Melanie Blokesch
- Laboratory of Molecular Microbiology, Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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6
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Engholm DH, Kilian M, Goodsell DS, Andersen ES, Kjærgaard RS. A visual review of the human pathogen Streptococcus pneumoniae. FEMS Microbiol Rev 2018; 41:854-879. [PMID: 29029129 DOI: 10.1093/femsre/fux037] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 09/04/2017] [Indexed: 11/12/2022] Open
Abstract
Being the principal causative agent of bacterial pneumonia, otitis media, meningitis and septicemia, the bacterium Streptococcus pneumoniae is a major global health problem. To highlight the molecular basis of this problem, we have portrayed essential biological processes of the pneumococcal life cycle in eight watercolor paintings. The paintings are done to a consistent nanometer scale based on currently available data from structural biology and proteomics. In this review article, the paintings are used to provide a visual review of protein synthesis, carbohydrate metabolism, cell wall synthesis, cell division, teichoic acid synthesis, virulence, transformation and pilus synthesis based on the available scientific literature within the field of pneumococcal biology. Visualization of the molecular details of these processes reveals several scientific questions about how molecular components of the pneumococcal cell are organized to allow biological function to take place. By the presentation of this visual review, we intend to stimulate scientific discussion, aid in the generation of scientific hypotheses and increase public awareness. A narrated video describing the biological processes in the context of a whole-cell illustration accompany this article.
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Affiliation(s)
- Ditte Høyer Engholm
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
| | - Mogens Kilian
- Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark
| | - David S Goodsell
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.,Rutgers, the State University of New Jersey, NJ 08901, USA
| | - Ebbe Sloth Andersen
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark.,Interdisciplinary Nanoscience Center, Aarhus University, 8000 Aarhus, Denmark
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7
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Diallo A, Foster HR, Gromek KA, Perry TN, Dujeancourt A, Krasteva PV, Gubellini F, Falbel TG, Burton BM, Fronzes R. Bacterial transformation: ComFA is a DNA-dependent ATPase that forms complexes with ComFC and DprA. Mol Microbiol 2017; 105:741-754. [DOI: 10.1111/mmi.13732] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/13/2017] [Indexed: 12/28/2022]
Affiliation(s)
- Amy Diallo
- Institut Pasteur, G5 Groupe Biologie Structurale de la Sécrétion Bactérienne; Paris France
- CNRS, UMR3528, Institut Pasteur; 25-28 rue du Docteur Roux, Paris F-75015 France
- Université Pierre et Marie Curie; Paris France
| | | | | | - Thomas N. Perry
- Institut Pasteur, G5 Groupe Biologie Structurale de la Sécrétion Bactérienne; Paris France
- CNRS, UMR3528, Institut Pasteur; 25-28 rue du Docteur Roux, Paris F-75015 France
| | - Annick Dujeancourt
- Institut Pasteur, G5 Groupe Biologie Structurale de la Sécrétion Bactérienne; Paris France
- CNRS, UMR3528, Institut Pasteur; 25-28 rue du Docteur Roux, Paris F-75015 France
| | - Petya V. Krasteva
- Institut Pasteur, G5 Groupe Biologie Structurale de la Sécrétion Bactérienne; Paris France
- CNRS, UMR3528, Institut Pasteur; 25-28 rue du Docteur Roux, Paris F-75015 France
| | - Francesca Gubellini
- Institut Pasteur, G5 Groupe Biologie Structurale de la Sécrétion Bactérienne; Paris France
- CNRS, UMR3528, Institut Pasteur; 25-28 rue du Docteur Roux, Paris F-75015 France
| | | | | | - Rémi Fronzes
- Institut Pasteur, G5 Groupe Biologie Structurale de la Sécrétion Bactérienne; Paris France
- CNRS, UMR3528, Institut Pasteur; 25-28 rue du Docteur Roux, Paris F-75015 France
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8
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Mitra SD, Afonina I, Kline KA. Right Place, Right Time: Focalization of Membrane Proteins in Gram-Positive Bacteria. Trends Microbiol 2016; 24:611-621. [PMID: 27117048 DOI: 10.1016/j.tim.2016.03.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 03/03/2016] [Accepted: 03/24/2016] [Indexed: 11/25/2022]
Abstract
Membrane proteins represent a significant proportion of total bacterial proteins and perform vital cellular functions ranging from exchanging metabolites and genetic material, secretion and sorting, sensing signal molecules, and cell division. Many of these functions are carried out at distinct foci on the bacterial membrane, and this subcellular localization can be coordinated by a number of factors, including lipid microdomains, protein-protein interactions, and membrane curvature. Elucidating the mechanisms behind focal protein localization in bacteria informs not only protein structure-function correlation, but also how to disrupt the protein function to limit virulence. Here we review recent advances describing a functional role for subcellular localization of membrane proteins involved in genetic transfer, secretion and sorting, cell division and growth, and signaling.
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Affiliation(s)
- Sumitra D Mitra
- Singapore Centre for Environmental Life Sciences Engineering, School of Biological Sciences, Nanyang Technological University, Singapore
| | - Irina Afonina
- Singapore Centre for Environmental Life Sciences Engineering, School of Biological Sciences, Nanyang Technological University, Singapore
| | - Kimberly A Kline
- Singapore Centre for Environmental Life Sciences Engineering, School of Biological Sciences, Nanyang Technological University, Singapore.
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9
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Matthey N, Blokesch M. The DNA-Uptake Process of Naturally Competent Vibrio cholerae. Trends Microbiol 2015; 24:98-110. [PMID: 26614677 DOI: 10.1016/j.tim.2015.10.008] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Revised: 10/05/2015] [Accepted: 10/22/2015] [Indexed: 10/22/2022]
Abstract
The sophisticated DNA-uptake machinery used during natural transformation is still poorly characterized, especially in Gram-negative bacteria where the transforming DNA has to cross two membranes as well as the peptidoglycan layer before entering the cytoplasm. The DNA-uptake machinery was hypothesized to take the form of a pseudopilus, which, upon repeated cycles of extension and retraction, would pull external DNA towards the cell surface or into the periplasmic space, followed by translocation across the cytoplasmic membrane. In this review, we summarize recent advances on the DNA-uptake machinery of V. cholerae, highlighting the presence of an extended competence-induced pilus and the contribution of a conserved DNA-binding protein that acts as a ratchet and reels DNA into the periplasm.
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Affiliation(s)
- Noémie Matthey
- Laboratory of Molecular Microbiology, Global Health Institute, School of Life Sciences, Station 19, EPFL-SV-UPBLO, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Melanie Blokesch
- Laboratory of Molecular Microbiology, Global Health Institute, School of Life Sciences, Station 19, EPFL-SV-UPBLO, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland.
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10
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Mann JM, Carabetta VJ, Cristea IM, Dubnau D. Complex formation and processing of the minor transformation pilins of Bacillus subtilis. Mol Microbiol 2013; 90:1201-15. [PMID: 24164455 PMCID: PMC5687075 DOI: 10.1111/mmi.12425] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/04/2013] [Indexed: 01/06/2023]
Abstract
Transformation in most bacteria is dependent on orthologues of Type 2 secretion and Type 4 pilus system proteins. In each system, pilin proteins (major and minor) are required to make the pilus structure and are essential to the process, although the precise roles of the minor pilins remain unclear. We have explored protein-protein interactions among the competence minor pilins of Bacillus subtilis through in vitro binding studies, immunopurification and mass spectrometry. We demonstrate that the minor pilins directly interact, and the minor pilin ComGG interacts with most of the known proteins required for transformation. We find that ComGG requires other ComG proteins for its stabilization and for processing by the pre-pilin peptidase. These observations, C-terminal mutations in ComGG that prevent processing and the inaccessibility of pre-ComGG to externally added protease suggest a model in which pre-ComGG must be associated with other minor pilins for processing to take place. We propose that ComGG does not become a transmembrane protein until after processing. These behaviours contrast with that of pre-ComGC, the major pilin, which is accessible to externally added protease and requires only the peptidase to be processed. The roles of the pilins and of the pilus in transformation are discussed.
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Affiliation(s)
- Jessica M. Mann
- Department of Microbiology and Molecular Genetics, New Jersey Medical School, Rutgers University, 225 Warren Street, Newark, NJ 07103, USA
| | - Valerie J. Carabetta
- Public Health Research Institute, New Jersey Medical School, Rutgers University, 225 Warren Street, Newark, NJ 07103, USA
| | - Ileana M. Cristea
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - David Dubnau
- Department of Microbiology and Molecular Genetics, New Jersey Medical School, Rutgers University, 225 Warren Street, Newark, NJ 07103, USA
- Public Health Research Institute, New Jersey Medical School, Rutgers University, 225 Warren Street, Newark, NJ 07103, USA
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11
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Bergé MJ, Kamgoué A, Martin B, Polard P, Campo N, Claverys JP. Midcell recruitment of the DNA uptake and virulence nuclease, EndA, for pneumococcal transformation. PLoS Pathog 2013; 9:e1003596. [PMID: 24039578 PMCID: PMC3764208 DOI: 10.1371/journal.ppat.1003596] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Accepted: 07/19/2013] [Indexed: 12/02/2022] Open
Abstract
Genetic transformation, in which cells internalize exogenous DNA and integrate it into their chromosome, is widespread in the bacterial kingdom. It involves a specialized membrane-associated machinery for binding double-stranded (ds) DNA and uptake of single-stranded (ss) fragments. In the human pathogen Streptococcus pneumoniae, this machinery is specifically assembled at competence. The EndA nuclease, a constitutively expressed virulence factor, is recruited during competence to play the key role of converting dsDNA into ssDNA for uptake. Here we use fluorescence microscopy to show that EndA is uniformly distributed in the membrane of noncompetent cells and relocalizes at midcell during competence. This recruitment requires the dsDNA receptor ComEA. We also show that under ‘static’ binding conditions, i.e., in cells impaired for uptake, EndA and ComEA colocalize at midcell, together with fluorescent end-labelled dsDNA (Cy3-dsDNA). We conclude that midcell clustering of EndA reflects its recruitment to the DNA uptake machinery rather than its sequestration away from this machinery to protect transforming DNA from extensive degradation. In contrast, a fraction of ComEA molecules were located at cell poles post-competence, suggesting the pole as the site of degradation of the dsDNA receptor. In uptake-proficient cells, we used Cy3-dsDNA molecules enabling expression of a GFP fusion upon chromosomal integration to identify transformed cells as GFP producers 60–70 min after initial contact between DNA and competent cells. Recording of images since initial cell-DNA contact allowed us to look back to the uptake period for these transformed cells. Cy3-DNA foci were thus detected at the cell surface 10–11 min post-initial contact, all exclusively found at midcell, strongly suggesting that active uptake of transforming DNA takes place at this position in pneumococci. We discuss how midcell uptake could influence homology search, and the likelihood that midcell uptake is characteristic of cocci and/or the growth phase-dependency of competence. Natural genetic transformation, a programmed mechanism for horizontal gene transfer, permits the passage of environmental double-stranded (ds) DNA through the bacterial membrane and its subsequent integration into the recipient chromosome by homology. In the human pathogen Streptococcus pneumoniae, it requires development of a physiological state termed competence, which develops transiently in nearly all cells of an exponentially growing culture. Expression of a specific set of genes then allows assembly of a large membrane-associated machinery for binding exogenous dsDNA and internalizing single-stranded (ss) DNA fragments. The key role of converting dsDNA into ssDNA is fulfilled by EndA, a membrane-located endonuclease which is also a pneumococcal virulence factor pre-existing in noncompetent cells. Here, we report that EndA is uniformly distributed in the membrane of noncompetent cells and relocates into clusters during competence. We show that this relocalization is dependent upon the dsDNA-receptor ComEA and that ComEA and EndA are preferentially located at midcell in cultures exhibiting maximal transformation proficiency. Finally, using fluorescence microscopy, we visualize the transformation process in living cells providing evidence that DNA binding and presumably uptake occur at midcell.
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Affiliation(s)
- Matthieu J. Bergé
- Centre National de la Recherche Scientifique, LMGM-UMR5100, Toulouse, France
- Université de Toulouse, Université Paul Sabatier, Laboratoire de Microbiologie et Génétique Moléculaires, Toulouse, France
| | - Alain Kamgoué
- Université de Toulouse, Université Paul Sabatier, Laboratoire de Microbiologie et Génétique Moléculaires, Toulouse, France
- Centre National de la Recherche Scientifique, LBME-UMR5099, Toulouse, France
| | - Bernard Martin
- Centre National de la Recherche Scientifique, LMGM-UMR5100, Toulouse, France
- Université de Toulouse, Université Paul Sabatier, Laboratoire de Microbiologie et Génétique Moléculaires, Toulouse, France
| | - Patrice Polard
- Centre National de la Recherche Scientifique, LMGM-UMR5100, Toulouse, France
- Université de Toulouse, Université Paul Sabatier, Laboratoire de Microbiologie et Génétique Moléculaires, Toulouse, France
| | - Nathalie Campo
- Centre National de la Recherche Scientifique, LMGM-UMR5100, Toulouse, France
- Université de Toulouse, Université Paul Sabatier, Laboratoire de Microbiologie et Génétique Moléculaires, Toulouse, France
- * E-mail: (NC); (JPC)
| | - Jean-Pierre Claverys
- Centre National de la Recherche Scientifique, LMGM-UMR5100, Toulouse, France
- Université de Toulouse, Université Paul Sabatier, Laboratoire de Microbiologie et Génétique Moléculaires, Toulouse, France
- * E-mail: (NC); (JPC)
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12
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Kovács AT, Smits WK, Mirończuk AM, Kuipers OP. Ubiquitous late competence genes in Bacillus species indicate the presence of functional DNA uptake machineries. Environ Microbiol 2009; 11:1911-22. [PMID: 19453701 DOI: 10.1111/j.1462-2920.2009.01937.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Natural competence for genetic transformation, i.e. the ability to take up DNA and stably integrate it in the genome, has so far only been observed in the bacterial kingdom (both in gram-negative and gram-positive species) and may contribute to survival under adverse growth conditions. Bacillus subtilis, the model organism for the Bacillus genus, possesses a well-characterized competence machinery. Phylogenetic analysis of several genome sequences of different Bacillus species reveals the presence of many, but not all genes potentially involved in competence and its regulation. The recent demonstration of functional DNA uptake by B. cereus supports the significance of our genome analyses and shows that the ability for functional DNA uptake might be widespread among Bacilli.
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Affiliation(s)
- Akos T Kovács
- Department of Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9751 NN Haren, The Netherlands
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13
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Allemand JF, Maier B. Bacterial translocation motors investigated by single molecule techniques. FEMS Microbiol Rev 2009; 33:593-610. [PMID: 19243443 DOI: 10.1111/j.1574-6976.2009.00166.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Translocation of DNA and protein fibers through narrow constrictions is a ubiquitous and crucial activity of bacterial cells. Bacteria use specialized machines to support macromolecular movement. A very important step toward a mechanistic understanding of these translocation machines is the characterization of their physical properties at the single molecule level. Recently, four bacterial transport processes have been characterized by nanomanipulation at the single molecule level, DNA translocation by FtsK and SpoIIIE, DNA import during transformation, and the related process of a type IV pilus retraction. With all four processes, the translocation rates, processivity, and stalling forces were remarkably high as compared with single molecule experiments with other molecular motors. Although substrates of all four processes proceed along a preferential direction of translocation, directionality has been shown to be controlled by distinct mechanisms.
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14
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Abstract
Proteins required for transformation of Bacillus subtilis and other competent bacteria are associated with the membrane or reside in the cytosol. Previous work has shown that RecA, ComGA, ComFA and SsbB are directed to the cell poles in competent cells, and that the uptake of transforming DNA occurs preferentially at the poles. We show that ComGA, ComFA, DprA (Smf), SsbB (YwpH), RecA and YjbF (CoiA) are located at the cell poles, where they appear to colocalize. Using fluorescence resonance energy transfer, we have shown that these six competent (Com) proteins reside in close proximity to one another. This conclusion was supported by the effects of com gene knockouts on the stabilities of Com proteins. Data obtained from the com gene knockout studies, as well as information from other sources, extend the list of proteins in the transformation complex to include ComEC and ComEA. Because ComGA and ComFA are membrane-associated, while DprA, SsbB, RecA and YjbF are soluble, a picture emerges of a large multiprotein polar complex, involving both cytosolic and membrane proteins. This complex mediates the binding and uptake of single-stranded DNA, the protection of this DNA from cellular nucleases and its recombination with the recipient chromosome.
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Affiliation(s)
- Naomi Kramer
- Public Health Research Institute, 225 Warren Street, Newark, NJ 07103, USA
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15
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Abstract
Transformation and conjugation permit the passage of DNA through the bacterial membranes and represent dominant modes for the transfer of genetic information between bacterial cells or between bacterial and eukaryotic cells. As such, they are responsible for the spread of fitness-enhancing traits, including antibiotic resistance. Both processes usually involve the recognition of double-stranded DNA, followed by the transfer of single strands. Elaborate molecular machines are responsible for negotiating the passage of macromolecular DNA through the layers of the cell surface. All or nearly all the machine components involved in transformation and conjugation have been identified, and here we present models for their roles in DNA transport.
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Affiliation(s)
- Inês Chen
- Public Health Research Institute, 225 Warren Street, Newark, NJ 07103, USA
| | - Peter J. Christie
- Department of Microbiology and Molecular Genetics, University of Texas Medical School at Houston, Houston, TX 77030, USA
| | - David Dubnau
- Public Health Research Institute, 225 Warren Street, Newark, NJ 07103, USA
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16
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Hahn J, Maier B, Haijema BJ, Sheetz M, Dubnau D. Transformation proteins and DNA uptake localize to the cell poles in Bacillus subtilis. Cell 2005; 122:59-71. [PMID: 16009133 PMCID: PMC4442496 DOI: 10.1016/j.cell.2005.04.035] [Citation(s) in RCA: 114] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2005] [Revised: 04/08/2005] [Accepted: 04/30/2005] [Indexed: 11/29/2022]
Abstract
The Gram-positive, rod-forming bacterium Bacillus subtilis efficiently binds and internalizes transforming DNA. The localization of several competence proteins, required for DNA uptake, has been studied using fluorescence microscopy. At least three proteins (ComGA, ComFA, and YwpH) are preferentially associated with the cell poles and appear to colocalize. This association is dynamic; the proteins accumulate at the poles as transformability develops and then delocalize as transformability wanes. DNA binding and uptake also occur preferentially at the cell poles, as shown using fluorescent DNA and in single-molecule experiments with laser tweezers. In addition to the prominent polar sites, the competence proteins also localize as foci in association with the lateral cell membrane, but this distribution does not exhibit the same temporal changes as the polar accumulation. The results suggest the regulated assembly and disassembly of a DNA-uptake machine at the cell poles.
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Affiliation(s)
- Jeanette Hahn
- Public Health Research Institute, 225 Warren Street, Newark, New Jersey 07103
| | - Berenike Maier
- Department of Biological Sciences, Columbia University, New York, New York 10027
| | - Bert Jan Haijema
- Public Health Research Institute, 225 Warren Street, Newark, New Jersey 07103
| | - Michael Sheetz
- Department of Biological Sciences, Columbia University, New York, New York 10027
| | - David Dubnau
- Public Health Research Institute, 225 Warren Street, Newark, New Jersey 07103
- Correspondence:
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Provvedi R, Chen I, Dubnau D. NucA is required for DNA cleavage during transformation of Bacillus subtilis. Mol Microbiol 2001; 40:634-44. [PMID: 11359569 DOI: 10.1046/j.1365-2958.2001.02406.x] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We have re-examined the roles of nucA and nin, in the transformation of Bacillus subtilis as conflicting accounts have been presented concerning the importance of these genes for transformation. The present report demonstrates that nucA deficiency lowers the rate of DNA transport and that NucA is needed for the double-strand cleavage of transforming DNA, probably acting directly as an endonuclease. A relative paucity of DNA termini, resulting from the absence of this endonuclease activity, most probably accounts for the decreased transport rate. NucA is a bitopic integral membrane protein, with its C-terminus external to the membrane where it is appropriately located to effect the cleavage of bound transforming DNA. We have also investigated the roles of the known competence genes in the DNA processing that accompanies transformation in B. subtilis. The genes that are required for DNA transport (comEA, comEC and comFA) are also required for the degradation of the non-transforming strand that accompanies internalization, but comEC and comFA are not needed for the double-strand cleavage that occurs external to the cell membrane.
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Affiliation(s)
- R Provvedi
- Public Health Research Institute, 455 First Avenue, New York 10016, USA
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18
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Abstract
The yjzA open reading frame, along with med, constitutes an operon. Disruption of yjzA caused a five-fold enhancement of comG expression, thereby leading to a three-fold-higher transformation efficiency. The expression of comK and the other three late competence operons was not affected significantly in the yjzA-deficient mutant.
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Affiliation(s)
- M Ogura
- Department of Marine Science and Technology, Tokai University, 3-20-1 Orido, Shimizu, Shizuoka 424, Japan.
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19
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Abstract
The steps involved in the transformation of Bacillus subtilis are reviewed. These include the initial binding, processing and passage of DNA across the cell wall and transport across the plasma membrane. Our understanding of the roles of the proteins known to be required for these steps is reviewed.
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Affiliation(s)
- D Dubnau
- Public Health Research Institute, New York, NY 10016, USA.
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20
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Abstract
Natural competence is widespread among bacterial species. The mechanism of DNA uptake in both gram-positive and gram-negative bacteria is reviewed. The transformation pathways are discussed, with attention to the fate of donor DNA as it is processed by the competent cell. The proteins involved in mediating various steps in these pathways are described, and models for the transformation mechanisms are presented. Uptake of DNA across the inner membrane is probably similar in gram-positive and gram-negative bacteria, and at least some of the required proteins are orthologs. The initial transformation steps differ, as expected, from the presence of an outer membrane only in the gram-negative organisms. The similarity of certain essential competence proteins to those required for the assembly of type-4 pili and for type-2 protein secretion is discussed. Finally several hypotheses for the biological role of transformation are presented and evaluated.
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Affiliation(s)
- D Dubnau
- Public Health Research Institute, New York, NY 10016, USA.
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21
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Piazza F, Tortosa P, Dubnau D. Mutational analysis and membrane topology of ComP, a quorum-sensing histidine kinase of Bacillus subtilis controlling competence development. J Bacteriol 1999; 181:4540-8. [PMID: 10419951 PMCID: PMC103584 DOI: 10.1128/jb.181.15.4540-4548.1999] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
ComP is a sensor histidine kinase of Bacillus subtilis required for the signal transduction pathway that initiates the development of competence for genetic transformation. It is believed that ComP senses the presence of ComX, a modified extracellular peptide pheromone, and donates a phosphate to ComA, thereby activating this transcription factor for binding to the srfA promoter. In the present study, fusions to the Escherichia coli proteins PhoA and LacZ and analysis of its susceptibility to the protease kallikrein were used to probe the membrane topology of ComP. These data suggest that ComP contains six or eight membrane-spanning segments and two large extracytoplasmic loops in its N-terminal membrane-associated domain. Deletions were introduced involving the large extracellular loops to explore the role of the N-terminal domain of ComP in signal transduction. The absence of the second loop conferred a phenotype in which ComP was active in the absence of ComX. The implications of these data are discussed.
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Affiliation(s)
- F Piazza
- Public Health Research Institute, New York, New York 10016, USA
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22
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Roos S, Lindgren S, Jonsson H. Autoaggregation of Lactobacillus reuteri is mediated by a putative DEAD-box helicase. Mol Microbiol 1999; 32:427-36. [PMID: 10231497 DOI: 10.1046/j.1365-2958.1999.01363.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We have cloned and sequenced a gene from Lactobacillus reuteri that encodes a 56 kDa protein, which mediates autoaggregation of the bacteria. Using an antiserum raised against extracellular proteins from the pig intestinal isolate L. reuteri 1063, we screened a genomic lambda library derived from the same strain. Affinity purification of recombinant protein from the isolated lambda clones showed that one type of clone expressed a protein that efficiently aggregated the parental strain when added to the bacteria. Subcloning and introduction of the corresponding gene, here denoted aggHinto the L. reuteri type strain markedly enhanced aggregation. Furthermore, insertional inactivation of aggH in strain 1063 resulted in an autoaggregation-deficient phenotype. Finally, an affinity-purified and cleaved fusion of AggH protein and the maltose-binding protein, MBP, strongly promoted aggregation of L. reuteri 1063, whereas the uncleaved fusion protein was inactive. Sequencing of aggH revealed that the corresponding protein has extensive sequence homology to the large family of ATP-dependent DEAD-box helicases. These results are intriguing in view of earlier data on the promotion of genetic exchange in Lactobacillus by aggregation.
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Affiliation(s)
- S Roos
- Department of Microbiology, Swedish University of Agricultural Sciences, Box 7025, S-750 07 Uppsala, Sweden
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23
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Abstract
Competent cells of Bacillus subtilis efficiently bind and internalize DNA. ComEA and the seven proteins encoded by the comG operon are required in vivo for the binding step. We show here that ComEA, a bitopic membrane protein, is itself capable of high-affinity DNA binding. A domain necessary for DNA binding is located at the C-terminus of ComEA. Proteins with similar 60-80 amino acid residue domains are widespread among bacteria and higher organisms. ComEA shows a marked preference for double-stranded DNA and can bind to oligomers as small as 22 bp in length. DNA binding by ComEA exhibits no apparent base sequence specificity. Using a membrane vesicle DNA-binding assay system we show that in the absence of cell wall, ComEA is still required for DNA binding, whereas the requirement for the ComG proteins is bypassed. We conclude that the ComG proteins are needed in vivo to provide access of the binding domain of ComEA to exogenous DNA. Possible specific roles for the ComG proteins are discussed.
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Affiliation(s)
- R Provvedi
- Public Health Research Institute, New York, NY 10016, USA
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24
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Dubnau D. Binding and transport of transforming DNA by Bacillus subtilis: the role of type-IV pilin-like proteins--a review. Gene 1997; 192:191-8. [PMID: 9224890 DOI: 10.1016/s0378-1119(96)00804-9] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The pathway for binding, processing and transport of transforming DNA into competent cells of Bacillus subtilis is described. The known proteins involved in mediating these processes are reviewed in turn, including several that resemble proteins required for type-IV pilus assembly and function, and those involved in protein secretion. Based on the phenotypes of null mutations in the cognate genes for these proteins, on similarities to other proteins and on membrane localization and topology data, proposals are made for the roles of the individual proteins in the transformation process. A dynamic model is suggested for the presentation of transforming DNA to the transport apparatus.
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Affiliation(s)
- D Dubnau
- Public Health Research Institute, New York, NY 10016, USA.
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25
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Inamine GS, Dubnau D. ComEA, a Bacillus subtilis integral membrane protein required for genetic transformation, is needed for both DNA binding and transport. J Bacteriol 1995; 177:3045-51. [PMID: 7768800 PMCID: PMC176991 DOI: 10.1128/jb.177.11.3045-3051.1995] [Citation(s) in RCA: 126] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The competence-related phenotypes of mutations in each of the four open reading frames associated with the comE locus of Bacillus subtilis are described. comEA and comEC are required for transformability, whereas the products of comEB and of the overlapping comER, which is transcribed in the reverse direction, are dispensable. Loss of the comEA product decreases the binding of DNA to the competent cell surface and the internalization of DNA, in addition to exhibiting a profound effect on transformability. The comEC product is required for internalization but is dispensable for DNA binding. ComEA is shown to be an integral membrane protein, as predicted from hydropathy analysis, with its C-terminal domain outside the cytoplasmic membrane. This C-terminal domain possesses a sequence with similarity to those of several proteins known to be involved in nucleic acid transactions including UvrC and a human protein that binds to the replication origin of the Epstein-Barr virus.
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Affiliation(s)
- G S Inamine
- Public Health Research Institute, New York, New York 10016, USA
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26
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Chung YS, Dubnau D. ComC is required for the processing and translocation of comGC, a pilin-like competence protein of Bacillus subtilis. Mol Microbiol 1995; 15:543-51. [PMID: 7783624 DOI: 10.1111/j.1365-2958.1995.tb02267.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
ComGC is a cell surface-localized protein required for DNA binding during transformation in Bacillus subtilis. It resembles type IV prepilins in its N-terminal domain, particularly in the amino acid sequence surrounding the processing cleavage sites of these proteins. ComC is another protein required for DNA binding, which resembles the processing proteases that cleave type IV prepilins. We show here that ComGC is processed in competent cells and that this processing requires ComC. We also demonstrate that the PilD protein of Neisseria gonorrhoeae, a ComC homologue, can process ComGC in Escherichia coli, and that the ComC protein itself is the only B. subtilis protein needed to accomplish cleavage of ComGC in the latter organism. Based on NaOH-solubility studies, we have shown that in the absence of ComC, but in the presence of all other competence proteins, B. subtilis is incapable of correctly translocating ComGC to the outer face of the cell membrane. Finally, we show that ComGC can be cross-linked to yield a form with higher molecular mass, possibly a dimer, and present evidence suggesting that formation of the higher mass complex takes place in the membrane, prior to translocation. Formation of this complex does not require ComC or any of the comG products, other than ComGC itself.
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Affiliation(s)
- Y S Chung
- Public Health Research Institute, New York, New York 10016, USA
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