1
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George JL, Agbavor C, Cabo LF, Cahoon LA. Streptococcus pneumoniae secretion chaperones PrsA, SlrA, and HtrA are required for competence, antibiotic resistance, colonization, and invasive disease. Infect Immun 2024; 92:e0049023. [PMID: 38226817 PMCID: PMC10863415 DOI: 10.1128/iai.00490-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 12/19/2023] [Indexed: 01/17/2024] Open
Abstract
Streptococcus pneumoniae is a Gram-positive bacterium and a significant health threat with the populations most at risk being children, the elderly, and the immuno-compromised. To colonize and transition into an invasive infectious organism, S. pneumoniae secretes virulence factors that are translocated across the bacterial membrane and destined for surface exposure, attachment to the cell wall, or secretion into the host. The surface exposed protein chaperones PrsA, SlrA, and HtrA facilitate S. pneumoniae protein secretion; however, the distinct roles contributed by each of these secretion chaperones have not been well defined. Tandem Mass-Tagged Mass Spectrometry and virulence, adhesion, competence, and cell wall integrity assays were used to interrogate the individual and collective contributions of PrsA, SlrA, and HtrA to multiple aspects of S. pneumoniae physiology and virulence. PrsA, SlrA, and HtrA were found to play critical roles in S. pneumoniae host cell infection and competence, and the absence of each of these secretion chaperones significantly altered the S. pneumoniae secretome in distinct ways. PrsA and SlrA were additionally found to contribute to cell wall assembly and resistance to cell wall-active antimicrobials and were important for enabling S. pneumoniae host cell adhesion during colonization and invasive infection. These findings serve to further illustrate the pivotal contributions of PrsA, SlrA, and HtrA to S. pneumoniae protein secretion and virulence.
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Affiliation(s)
- Jada L. George
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Charles Agbavor
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Leah F. Cabo
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Laty A. Cahoon
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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2
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Morgene F, Rizoug Zeghlache C, Feng SY, Hauck Y, Mirouze N. Natural transformation and cell division delay in competent Staphylococcus aureus. Microbiol Spectr 2023; 11:e0280723. [PMID: 37831481 PMCID: PMC10714784 DOI: 10.1128/spectrum.02807-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 09/01/2023] [Indexed: 10/14/2023] Open
Abstract
IMPORTANCE Natural transformation, considered one of the three main mechanisms leading to horizontal gene transfer in bacteria, is able to promote genomic plasticity and foster antibiotic resistance spreading. Conserved machinery and actors required to perform natural transformation have been shown to accumulate at different cellular localizations depending on the model organism considered. Here, we show in the human pathogen Staphylococcus aureus that DNA binding, uptake, and recombination are spatially and temporally coordinated to ensure S. aureus natural transformation. We also reveal that localization of natural transformation proteins occurs in the vicinity of the division septum allowing S. aureus competent cells to block cell division to ensure the success of natural transformation before the final constriction of the cytokinetic ring.
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Affiliation(s)
- Fedy Morgene
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Célia Rizoug Zeghlache
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Shi Yuan Feng
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Yolande Hauck
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Nicolas Mirouze
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
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3
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Milly TA, Renshaw CP, Tal-Gan Y. Developing multispecies quorum-sensing modulators based on the Streptococcus mitis competence-stimulating peptide. J Biol Chem 2023; 299:105448. [PMID: 37951305 PMCID: PMC10714334 DOI: 10.1016/j.jbc.2023.105448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 10/26/2023] [Accepted: 10/30/2023] [Indexed: 11/13/2023] Open
Abstract
Bacteria utilize quorum sensing (QS) to coordinate many group behaviors. As such, QS has attracted significant attention as a potential mean to attenuate bacterial infectivity without introducing selective pressure for resistance development. Streptococcus mitis, a human commensal, acts as a genetic diversity reservoir for Streptococcus pneumoniae, a prevalent human pathogen. S. mitis possesses a typical comABCDE competence regulon QS circuitry; however, the competence-stimulating peptide (CSP) responsible for QS activation and the regulatory role of the competence regulon QS circuitry in S. mitis are yet to be explored. We set out to delineate the competence regulon QS circuitry in S. mitis, including confirming the identity of the native CSP signal, evaluating the molecular mechanism that governs CSP interactions with histidine kinase receptor ComD leading to ComD activation, and defining the regulatory roles of the competence regulon QS circuitry in initiating various S. mitis phenotypes. Our analysis revealed important structure-activity relationship insights of the CSP signal and facilitated the development of novel CSP-based QS modulators. Our analysis also revealed the involvement of the competence regulon in modulating competence development and biofilm formation. Furthermore, our analysis revealed that the native S. mitis CSP signal can modulate QS response in S. pneumoniae. Capitalizing on this crosstalk, we developed a multispecies QS modulator that activates both the pneumococcus ComD receptors and the S. mitis ComD-2 receptor with high potencies. The novel scaffolds identified herein can be utilized to evaluate the effects temporal QS modulation has on S. mitis as it inhabits its natural niche.
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Affiliation(s)
- Tahmina A Milly
- Department of Chemistry, University of Nevada, Reno, Reno, Nevada, USA
| | - Clay P Renshaw
- Department of Chemistry, University of Nevada, Reno, Reno, Nevada, USA
| | - Yftah Tal-Gan
- Department of Chemistry, University of Nevada, Reno, Reno, Nevada, USA.
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4
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Maziero M, Lane D, Polard P, Bergé M. Fever-like temperature bursts promote competence development via an HtrA-dependent pathway in Streptococcus pneumoniae. PLoS Genet 2023; 19:e1010946. [PMID: 37699047 PMCID: PMC10516426 DOI: 10.1371/journal.pgen.1010946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 09/22/2023] [Accepted: 08/30/2023] [Indexed: 09/14/2023] Open
Abstract
Streptococcus pneumoniae (the pneumococcus) is well known for its ability to develop competence for natural DNA transformation. Competence development is regulated by an autocatalytic loop driven by variations in the basal level of transcription of the comCDE and comAB operons. These genes are part of the early gene regulon that controls expression of the late competence genes known to encode the apparatus of transformation. Several stressful conditions are known to promote competence development, although the induction pathways are remain poorly understood. Here we demonstrate that transient temperature elevation induces an immediate increase in the basal expression level of the comCDE operon and early genes that, in turn, stimulates its full induction, including that of the late competence regulon. This thermal regulation depends on the HtrA chaperone/protease and its proteolytic activity. We find that other competence induction stimulus, like norfloxacin, is not conveyed by the HtrA-dependent pathway. This finding strongly suggests that competence can be induced by at least two independent pathways and thus reinforces the view that competence is a general stress response system in the pneumococcus.
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Affiliation(s)
- Mickaël Maziero
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), UMR5100, Centre de Biologie Intégrative (CBI), Centre Nationale de la Recherche Scientifique (CNRS), Toulouse, France
- Université Paul Sabatier (Toulouse III), Toulouse, France
| | - David Lane
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), UMR5100, Centre de Biologie Intégrative (CBI), Centre Nationale de la Recherche Scientifique (CNRS), Toulouse, France
- Université Paul Sabatier (Toulouse III), Toulouse, France
| | - Patrice Polard
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), UMR5100, Centre de Biologie Intégrative (CBI), Centre Nationale de la Recherche Scientifique (CNRS), Toulouse, France
- Université Paul Sabatier (Toulouse III), Toulouse, France
| | - Mathieu Bergé
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), UMR5100, Centre de Biologie Intégrative (CBI), Centre Nationale de la Recherche Scientifique (CNRS), Toulouse, France
- Université Paul Sabatier (Toulouse III), Toulouse, France
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5
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Johnston CHG, Hope R, Soulet AL, Dewailly M, De Lemos D, Polard P. The RecA-directed recombination pathway of natural transformation initiates at chromosomal replication forks in the pneumococcus. Proc Natl Acad Sci U S A 2023; 120:e2213867120. [PMID: 36795748 PMCID: PMC9974461 DOI: 10.1073/pnas.2213867120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 12/09/2022] [Indexed: 02/17/2023] Open
Abstract
Homologous recombination (HR) is a crucial mechanism of DNA strand exchange that promotes genetic repair and diversity in all kingdoms of life. Bacterial HR is driven by the universal recombinase RecA, assisted in the early steps by dedicated mediators that promote its polymerization on single-stranded DNA (ssDNA). In bacteria, natural transformation is a prominent HR-driven mechanism of horizontal gene transfer specifically dependent on the conserved DprA recombination mediator. Transformation involves internalization of exogenous DNA as ssDNA, followed by its integration into the chromosome by RecA-directed HR. How DprA-mediated RecA filamentation on transforming ssDNA is spatiotemporally coordinated with other cellular processes remains unknown. Here, we tracked the localization of fluorescent fusions to DprA and RecA in Streptococcus pneumoniae and revealed that both accumulate in an interdependent manner with internalized ssDNA at replication forks. In addition, dynamic RecA filaments were observed emanating from replication forks, even with heterologous transforming DNA, which probably represent chromosomal homology search. In conclusion, this unveiled interaction between HR transformation and replication machineries highlights an unprecedented role for replisomes as landing pads for chromosomal access of tDNA, which would define a pivotal early HR step for its chromosomal integration.
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Affiliation(s)
- Calum H. G. Johnston
- Laboratoire de Microbiologie et Génétique Moléculaires, UMR5100, Centre de Biologie Intégrative, Centre Nationale de la Recherche Scientifique, 31062Toulouse, France
- Université Paul Sabatier (Toulouse III), 31062Toulouse, France
| | - Rachel Hope
- Laboratoire de Microbiologie et Génétique Moléculaires, UMR5100, Centre de Biologie Intégrative, Centre Nationale de la Recherche Scientifique, 31062Toulouse, France
- Université Paul Sabatier (Toulouse III), 31062Toulouse, France
- Department of Life Sciences, Imperial College, SW7 2AZLondon, UK
| | - Anne-Lise Soulet
- Laboratoire de Microbiologie et Génétique Moléculaires, UMR5100, Centre de Biologie Intégrative, Centre Nationale de la Recherche Scientifique, 31062Toulouse, France
- Université Paul Sabatier (Toulouse III), 31062Toulouse, France
| | - Marie Dewailly
- Laboratoire de Microbiologie et Génétique Moléculaires, UMR5100, Centre de Biologie Intégrative, Centre Nationale de la Recherche Scientifique, 31062Toulouse, France
- Université Paul Sabatier (Toulouse III), 31062Toulouse, France
| | - David De Lemos
- Laboratoire de Microbiologie et Génétique Moléculaires, UMR5100, Centre de Biologie Intégrative, Centre Nationale de la Recherche Scientifique, 31062Toulouse, France
- Université Paul Sabatier (Toulouse III), 31062Toulouse, France
| | - Patrice Polard
- Laboratoire de Microbiologie et Génétique Moléculaires, UMR5100, Centre de Biologie Intégrative, Centre Nationale de la Recherche Scientifique, 31062Toulouse, France
- Université Paul Sabatier (Toulouse III), 31062Toulouse, France
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6
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Studying the Interaction of Neutrophils and Glaesserella Parasuis Indicates a Serotype Independent Benefit from Degradation of NETs. Pathogens 2022; 11:pathogens11080880. [PMID: 36015001 PMCID: PMC9415231 DOI: 10.3390/pathogens11080880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/28/2022] [Accepted: 08/01/2022] [Indexed: 02/04/2023] Open
Abstract
Glaesserella (G.) parasuis is one of the most important porcine pathogens causing Glaesser’s disease. Neutrophil granulocytes are the major counteracting cell type of the innate immune system, which contribute to the host defense by phagocytosis or the formation of neutrophil extracellular traps (NETs). Recently, NET-formation has been shown to facilitate the survival of bacteria from the Pasteurellaceae family. However, the interaction of NETs and G. parasuis is unclear so far. In this study, we investigated the interplay of three G. parasuis serotypes with porcine neutrophils. The production of reactive oxygen species by neutrophils after G. parasuis infection varied slightly among the serotypes but was generally low and not significantly influenced by the serotypes. Interestingly, we detected that independent of the serotype of G. parasuis, NET formation in neutrophils was induced to a small but significant extent. This phenomenon occurred despite the ability of G. parasuis to release nucleases, which can degrade NETs. Furthermore, the growth of Glaesserella was enhanced by external DNases and degraded NETs. This indicates that Glaesserella takes up degraded NET components, supplying them with nicotinamide adenine dinucleotide (NAD), as this benefit was diminished by inhibiting the 5′-nucleotidase, which metabolizes NAD. Our results indicate a serotype-independent interaction of Glaesserella with neutrophils by inducing NET-formation and benefiting from DNA degradation.
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7
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Gibson PS, Bexkens E, Zuber S, Cowley LA, Veening JW. The acquisition of clinically relevant amoxicillin resistance in Streptococcus pneumoniae requires ordered horizontal gene transfer of four loci. PLoS Pathog 2022; 18:e1010727. [PMID: 35877768 PMCID: PMC9352194 DOI: 10.1371/journal.ppat.1010727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 08/04/2022] [Accepted: 07/05/2022] [Indexed: 11/18/2022] Open
Abstract
Understanding how antimicrobial resistance spreads is critical for optimal application of new treatments. In the naturally competent human pathogen Streptococcus pneumoniae, resistance to β-lactam antibiotics is mediated by recombination events in genes encoding the target proteins, resulting in reduced drug binding affinity. However, for the front-line antibiotic amoxicillin, the exact mechanism of resistance still needs to be elucidated. Through successive rounds of transformation with genomic DNA from a clinically resistant isolate, we followed amoxicillin resistance development. Using whole genome sequencing, we showed that multiple recombination events occurred at different loci during one round of transformation. We found examples of non-contiguous recombination, and demonstrated that this could occur either through multiple D-loop formation from one donor DNA molecule, or by the integration of multiple DNA fragments. We also show that the final minimum inhibitory concentration (MIC) differs depending on recipient genome, explained by differences in the extent of recombination at key loci. Finally, through back transformations of mutant alleles and fluorescently labelled penicillin (bocillin-FL) binding assays, we confirm that pbp1a, pbp2b, pbp2x, and murM are the main resistance determinants for amoxicillin resistance, and that the order of allele uptake is important for successful resistance evolution. We conclude that recombination events are complex, and that this complexity contributes to the highly diverse genotypes of amoxicillin-resistant pneumococcal isolates.
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Affiliation(s)
- Paddy S. Gibson
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Evan Bexkens
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Sylvia Zuber
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Lauren A. Cowley
- Department of Biology & Biochemistry, Milner Centre for Evolution, University of Bath, Bath, United Kingdom
| | - Jan-Willem Veening
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
- * E-mail:
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8
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Di Giacomo S, Toussaint F, Ledesma-García L, Knoops A, Vande Capelle F, Fremaux C, Horvath P, Ladrière JM, Ait-Abderrahim H, Hols P, Mignolet J. OUP accepted manuscript. FEMS Microbiol Rev 2022; 46:6543703. [PMID: 35254446 PMCID: PMC9300618 DOI: 10.1093/femsre/fuac014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 02/14/2022] [Accepted: 03/01/2022] [Indexed: 11/14/2022] Open
Abstract
Nowadays, the growing human population exacerbates the need for sustainable resources. Inspiration and achievements in nutrient production or human/animal health might emanate from microorganisms and their adaptive strategies. Here, we exemplify the benefits of lactic acid bacteria (LAB) for numerous biotechnological applications and showcase their natural transformability as a fast and robust method to hereditarily influence their phenotype/traits in fundamental and applied research contexts. We described the biogenesis of the transformation machinery and we analyzed the genome of hundreds of LAB strains exploitable for human needs to predict their transformation capabilities. Finally, we provide a stepwise rational path to stimulate and optimize natural transformation with standard and synthetic biology techniques. A comprehensive understanding of the molecular mechanisms driving natural transformation will facilitate and accelerate the improvement of bacteria with properties that serve broad societal interests.
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Affiliation(s)
- Stefano Di Giacomo
- Biochemistry and Genetics of Microorganisms (BGM), Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Croix du Sud 4-5, (box L7.07.06), B-1348 Louvain-la-Neuve, Belgium
| | - Frédéric Toussaint
- Biochemistry and Genetics of Microorganisms (BGM), Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Croix du Sud 4-5, (box L7.07.06), B-1348 Louvain-la-Neuve, Belgium
| | - Laura Ledesma-García
- Biochemistry and Genetics of Microorganisms (BGM), Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Croix du Sud 4-5, (box L7.07.06), B-1348 Louvain-la-Neuve, Belgium
| | - Adrien Knoops
- Biochemistry and Genetics of Microorganisms (BGM), Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Croix du Sud 4-5, (box L7.07.06), B-1348 Louvain-la-Neuve, Belgium
| | - Florence Vande Capelle
- Biochemistry and Genetics of Microorganisms (BGM), Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Croix du Sud 4-5, (box L7.07.06), B-1348 Louvain-la-Neuve, Belgium
| | - Christophe Fremaux
- Health and Biosciences, IFF Danisco France SAS, CS 10010, F-86220 Dangé-Saint-Romain, France
| | - Philippe Horvath
- Health and Biosciences, IFF Danisco France SAS, CS 10010, F-86220 Dangé-Saint-Romain, France
| | - Jean-Marc Ladrière
- Health and Biosciences, IFF Danisco France SAS, CS 10010, F-86220 Dangé-Saint-Romain, France
| | | | - Pascal Hols
- Corresponding author: Biochemistry and Genetics of Microorganisms, Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Croix du Sud 4-5 (box L7.07.06), B-1348 Louvain-La-Neuve, Belgium. Tel: +3210478896; Fax: +3210472825; E-mail:
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9
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Lam T, Ellison CK, Eddington DT, Brun YV, Dalia AB, Morrison DA. Competence pili in Streptococcus pneumoniae are highly dynamic structures that retract to promote DNA uptake. Mol Microbiol 2021; 116:381-396. [PMID: 33754381 DOI: 10.1111/mmi.14718] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 03/11/2021] [Accepted: 03/17/2021] [Indexed: 01/11/2023]
Abstract
The competence pili of transformable Gram-positive species are phylogenetically related to the diverse and widespread class of extracellular filamentous organelles known as type IV pili. In Gram-negative bacteria, type IV pili act through dynamic cycles of extension and retraction to carry out diverse activities including attachment, motility, protein secretion, and DNA uptake. It remains unclear whether competence pili in Gram-positive species exhibit similar dynamic activity, and their mechanism of action for DNA uptake remains unclear. They are hypothesized to either (1) leave transient cavities in the cell wall that facilitate DNA passage, (2) form static adhesins to enrich DNA near the cell surface for subsequent uptake by membrane-embedded transporters, or (3) play an active role in translocating bound DNA via dynamic activity. Here, we use a recently described pilus labeling approach to demonstrate that competence pili in Streptococcus pneumoniae are highly dynamic structures that rapidly extend and retract from the cell surface. By labeling the principal pilus monomer, ComGC, with bulky adducts, we further demonstrate that pilus retraction is essential for natural transformation. Together, our results suggest that Gram-positive competence pili in other species may also be dynamic and retractile structures that play an active role in DNA uptake.
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Affiliation(s)
- Trinh Lam
- Department of Bioengineering, University of Illinois at Chicago, Chicago, IL, USA
| | - Courtney K Ellison
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.,Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - David T Eddington
- Department of Bioengineering, University of Illinois at Chicago, Chicago, IL, USA
| | - Yves V Brun
- Department of Biology, Indiana University, Bloomington, IN, USA.,Département de microbiologie, infectiologie et immunologie, Université de Montréal, Montréal, QC, Canada
| | - Ankur B Dalia
- Department of Biology, Indiana University, Bloomington, IN, USA
| | - Donald A Morrison
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, USA
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10
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Johnston CH, Soulet AL, Bergé M, Prudhomme M, De Lemos D, Polard P. The alternative sigma factor σ X mediates competence shut-off at the cell pole in Streptococcus pneumoniae. eLife 2020; 9:62907. [PMID: 33135635 PMCID: PMC7665891 DOI: 10.7554/elife.62907] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 10/31/2020] [Indexed: 12/22/2022] Open
Abstract
Competence is a widespread bacterial differentiation program driving antibiotic resistance and virulence in many pathogens. Here, we studied the spatiotemporal localization dynamics of the key regulators that master the two intertwined and transient transcription waves defining competence in Streptococcus pneumoniae. The first wave relies on the stress-inducible phosphorelay between ComD and ComE proteins, and the second on the alternative sigma factor σX, which directs the expression of the DprA protein that turns off competence through interaction with phosphorylated ComE. We found that ComD, σX and DprA stably co-localize at one pole in competent cells, with σX physically conveying DprA next to ComD. Through this polar DprA targeting function, σX mediates the timely shut-off of the pneumococcal competence cycle, preserving cell fitness. Altogether, this study unveils an unprecedented role for a transcription σ factor in spatially coordinating the negative feedback loop of its own genetic circuit.
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Affiliation(s)
- Calum Hg Johnston
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM ; UMR5100), Centre de Biologie Intégrative (CBI), Centre Nationale de la Recherche Scientifique (CNRS), Toulouse, France.,Université Paul Sabatier (Toulouse III), Toulouse, France
| | - Anne-Lise Soulet
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM ; UMR5100), Centre de Biologie Intégrative (CBI), Centre Nationale de la Recherche Scientifique (CNRS), Toulouse, France.,Université Paul Sabatier (Toulouse III), Toulouse, France
| | - Matthieu Bergé
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM ; UMR5100), Centre de Biologie Intégrative (CBI), Centre Nationale de la Recherche Scientifique (CNRS), Toulouse, France.,Université Paul Sabatier (Toulouse III), Toulouse, France.,Dept. Microbiology and Molecular Medicine, Institute of Genetics & Genomics in Geneva (iGE3), Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Marc Prudhomme
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM ; UMR5100), Centre de Biologie Intégrative (CBI), Centre Nationale de la Recherche Scientifique (CNRS), Toulouse, France.,Université Paul Sabatier (Toulouse III), Toulouse, France
| | - David De Lemos
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM ; UMR5100), Centre de Biologie Intégrative (CBI), Centre Nationale de la Recherche Scientifique (CNRS), Toulouse, France.,Université Paul Sabatier (Toulouse III), Toulouse, France
| | - Patrice Polard
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM ; UMR5100), Centre de Biologie Intégrative (CBI), Centre Nationale de la Recherche Scientifique (CNRS), Toulouse, France.,Université Paul Sabatier (Toulouse III), Toulouse, France
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11
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Liu M, Huang M, Wang M, Zhu D, Jia R, Chen S, Zhang L, Pan L, Cheng A. The Clustered Regularly Interspaced Short Palindromic Repeat System and Argonaute: An Emerging Bacterial Immunity System for Defense Against Natural Transformation? Front Microbiol 2020; 11:593301. [PMID: 33193265 PMCID: PMC7642515 DOI: 10.3389/fmicb.2020.593301] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 09/23/2020] [Indexed: 12/21/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeat (CRISPR) systems and prokaryotic Argonaute proteins (Agos) have been shown to defend bacterial and archaeal cells against invading nucleic acids. Indeed, they are important elements for inhibiting horizontal gene transfer between bacterial and archaeal cells. The CRISPR system employs an RNA-guide complex to target invading DNA or RNA, while Agos target DNA using single stranded DNA or RNA as guides. Thus, the CRISPR and Agos systems defend against exogenous nucleic acids by different mechanisms. It is not fully understood how antagonization of these systems occurs during natural transformation, wherein exogenous DNA enters a host cell as single stranded DNA and is then integrated into the host genome. In this review, we discuss the functions and mechanisms of the CRISPR system and Agos in cellular defense against natural transformation.
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Affiliation(s)
- Mafeng Liu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Mi Huang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Mingshu Wang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Dekang Zhu
- Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Renyong Jia
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Shun Chen
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Ling Zhang
- Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Leichang Pan
- Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Anchun Cheng
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
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12
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Kurushima J, Campo N, van Raaphorst R, Cerckel G, Polard P, Veening JW. Unbiased homeologous recombination during pneumococcal transformation allows for multiple chromosomal integration events. eLife 2020; 9:e58771. [PMID: 32965219 PMCID: PMC7567608 DOI: 10.7554/elife.58771] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 09/22/2020] [Indexed: 01/25/2023] Open
Abstract
The spread of antimicrobial resistance and vaccine escape in the human pathogen Streptococcus pneumoniae can be largely attributed to competence-induced transformation. Here, we studied this process at the single-cell level. We show that within isogenic populations, all cells become naturally competent and bind exogenous DNA. We find that transformation is highly efficient and that the chromosomal location of the integration site or whether the transformed gene is encoded on the leading or lagging strand has limited influence on recombination efficiency. Indeed, we have observed multiple recombination events in single recipients in real-time. However, because of saturation and because a single-stranded donor DNA replaces the original allele, transformation efficiency has an upper threshold of approximately 50% of the population. The fixed mechanism of transformation results in a fail-safe strategy for the population as half of the population generally keeps an intact copy of the original genome.
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Affiliation(s)
- Jun Kurushima
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of LausanneLausanneSwitzerland
| | - Nathalie Campo
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI)ToulouseFrance
| | - Renske van Raaphorst
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of LausanneLausanneSwitzerland
| | - Guillaume Cerckel
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of LausanneLausanneSwitzerland
| | - Patrice Polard
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI)ToulouseFrance
| | - Jan-Willem Veening
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of LausanneLausanneSwitzerland
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13
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Mortier-Barrière I, Polard P, Campo N. Direct Visualization of Horizontal Gene Transfer by Transformation in Live Pneumococcal Cells Using Microfluidics. Genes (Basel) 2020; 11:E675. [PMID: 32575751 PMCID: PMC7350252 DOI: 10.3390/genes11060675] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 06/13/2020] [Accepted: 06/16/2020] [Indexed: 12/21/2022] Open
Abstract
Natural genetic transformation is a programmed mechanism of horizontal gene transfer in bacteria. It requires the development of competence, a specialized physiological state during which proteins involved in DNA uptake and chromosomal integration are produced. In Streptococcus pneumoniae, competence is transient. It is controlled by a secreted peptide pheromone, the competence-stimulating peptide (CSP) that triggers the sequential transcription of two sets of genes termed early and late competence genes, respectively. Here, we used a microfluidic system with fluorescence microscopy to monitor pneumococcal competence development and transformation, in live cells at the single cell level. We present the conditions to grow this microaerophilic bacterium under continuous flow, with a similar doubling time as in batch liquid culture. We show that perfusion of CSP in the microfluidic chamber results in the same reduction of the growth rate of individual cells as observed in competent pneumococcal cultures. We also describe newly designed fluorescent reporters to distinguish the expression of competence genes with temporally distinct expression profiles. Finally, we exploit the microfluidic technology to inject both CSP and transforming DNA in the microfluidic channels and perform near real time-tracking of transformation in live cells. We show that this approach is well suited to investigating the onset of pneumococcal competence together with the appearance and the fate of transformants in individual cells.
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Affiliation(s)
| | | | - Nathalie Campo
- Laboratoire de Microbiologie et Génétique Moléculaires, Centre de Biologie Intégrative (CBI), Centre National de la Recherche Scientifique (CNRS), Université de Toulouse, UPS, F-31000 Toulouse, France; (I.M.-B.); (P.P.)
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14
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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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15
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Liu Y, Zeng Y, Huang Y, Gu L, Wang S, Li C, Morrison DA, Deng H, Zhang JR. HtrA-mediated selective degradation of DNA uptake apparatus accelerates termination of pneumococcal transformation. Mol Microbiol 2019; 112:1308-1325. [PMID: 31396996 DOI: 10.1111/mmi.14364] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/06/2019] [Indexed: 02/06/2023]
Abstract
Natural transformation mediates horizontal gene transfer, and thereby promotes exchange of antibiotic resistance and virulence traits among bacteria. Streptococcus pneumoniae, the first known transformable bacterium, rapidly activates and then terminates the transformation state, but it is unclear how the bacterium accomplishes this rapid turn-around at the protein level. This work determined the transcriptomic and proteomic dynamics during the window of pneumococcal transformation. RNA sequencing revealed a nearly uniform temporal pattern of rapid transcriptional activation and subsequent shutdown for the genes encoding transformation proteins. In contrast, mass spectrometry analysis showed that the majority of transformation proteins were substantially preserved beyond the window of transformation. However, ComEA and ComEC, major components of the DNA uptake apparatus for transformation, were completely degraded at the end of transformation. Further mutagenesis screening revealed that the membrane-associated serine protease HtrA mediates selective degradation of ComEA and ComEC, strongly suggesting that breakdown of the DNA uptake apparatus by HtrA is an important mechanism for termination of pneumococcal transformation. Finally, our mutagenesis analysis showed that HtrA inhibits natural transformation of Streptococcus mitis and Streptococcus gordonii. Together, this work has revealed that HtrA regulates the level and duration of natural transformation in multiple streptococcal species.
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Affiliation(s)
- Yanni Liu
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing, China
| | - Yuna Zeng
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing, China
| | - Yijia Huang
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing, China
| | - Lixiao Gu
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Shaolin Wang
- College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Chunhao Li
- Department of Oral and Craniofacial Molecular Biology, School of Dentistry, Virginia Commonwealth University, Richmond, VA, USA
| | - Donald A Morrison
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | - Haiteng Deng
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Jing-Ren Zhang
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing, China
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16
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Abstract
The ability of Streptococcus pneumoniae (the pneumococcus) to transform is particularly convenient for genome engineering. Several protocols relying on sequential positive and negative selection strategies have been described to create directed markerless modifications, including deletions, insertions, or point mutations. Transformation with DNA fragments carrying long flanking homology sequences is also used to generate mutations without selection but it requires high transformability. Here, we present an optimized version of this method. As an example, we construct a strain harboring a translational fusion ftsZ-mTurquoise at the ftsZ locus. We provide instructions to produce a linear DNA fragment containing the chimeric construction and give details of the conditions to obtain optimal pneumococcal transformation efficiencies.
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17
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Keller LE, Rueff AS, Kurushima J, Veening JW. Three New Integration Vectors and Fluorescent Proteins for Use in the Opportunistic Human Pathogen Streptococcus pneumoniae. Genes (Basel) 2019; 10:genes10050394. [PMID: 31121970 PMCID: PMC6562690 DOI: 10.3390/genes10050394] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 05/09/2019] [Accepted: 05/20/2019] [Indexed: 12/20/2022] Open
Abstract
Here, we describe the creation of three integration vectors, pPEPX, pPEPY and pPEPZ, for use with the opportunistic human pathogen Streptococcus pneumoniae. The constructed vectors, named PEP for Pneumococcal Engineering Platform (PEP), employ an IPTG-inducible promoter and BglBrick and BglFusion compatible multiple cloning sites allowing for fast and interchangeable cloning. PEP plasmids replicate in Escherichia coli and harbor integration sites that have homology in a large set of pneumococcal strains, including recent clinical isolates. In addition, several options of antibiotic resistance markers are available, even allowing for selection in multidrug resistant clinical isolates. The transformation efficiency of these PEP vectors as well as their ability to be expressed simultaneously was tested. Two of the three PEP vectors share homology of the integration regions with over half of the S. pneumoniae genomes examined. Transformation efficiency varied among PEP vectors based on the length of the homology regions, but all were highly transformable and can be integrated simultaneously in strain D39V. Vectors used for pneumococcal cloning are an important tool for researchers for a wide range of uses. The PEP vectors described are of particular use because they have been designed to allow for easy transfer of genes between vectors as well as integrating into transcriptionally silent areas of the chromosome. In addition, we demonstrate the successful production of several new spectrally distinct fluorescent proteins (mTurquoise2, mNeonGreen and mScarlet-I) from the PEP vectors. The PEP vectors and newly described fluorescent proteins will expand the genetic toolbox for pneumococcal researchers and aid future discoveries.
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Affiliation(s)
- Lance E Keller
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Biophore Building, CH-1015 Lausanne, Switzerland.
| | - Anne-Stéphanie Rueff
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Biophore Building, CH-1015 Lausanne, Switzerland.
| | - Jun Kurushima
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Biophore Building, CH-1015 Lausanne, Switzerland.
| | - Jan-Willem Veening
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Biophore Building, CH-1015 Lausanne, Switzerland.
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18
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Tan A, Li WS, Verderosa AD, Blakeway LV, D Mubaiwa T, Totsika M, Seib KL. Moraxella catarrhalis NucM is an entry nuclease involved in extracellular DNA and RNA degradation, cell competence and biofilm scaffolding. Sci Rep 2019; 9:2579. [PMID: 30796312 PMCID: PMC6384898 DOI: 10.1038/s41598-019-39374-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 01/18/2019] [Indexed: 11/10/2022] Open
Abstract
Moraxella catarrhalis is a host-adapted bacterial pathogen that causes otitis media and exacerbations of chronic obstructive pulmonary disease. This study characterises the conserved M. catarrhalis extracellular nuclease, a member of the ββα metal finger family of nucleases, that we have named NucM. NucM shares conserved sequence motifs from the ββα nuclease family, including the DRGH catalytic core and Mg2+ co-ordination site, but otherwise shares little primary sequence identity with other family members, such as the Serratia Nuc and pneumococcal EndA nucleases. NucM is secreted from the cell and digests linear and circular nucleic acid. However, it appears that a proportion of NucM is also associated with the cell membrane and acts as an entry nuclease, facilitating transformation of M. catarrhalis cells. This is the first example of a ββα nuclease in a Gram negative bacteria that acts as an entry nuclease. In addition to its role in competence, NucM affects cell aggregation and biofilm formation by M. catarrhalis, with ΔnucM mutants having increased biofilm biomass. NucM is likely to increase the ability of cells to survive and persist in vivo, increasing the virulence of M. catarrhalis and potentially affecting the behaviour of other pathogens that co-colonise the otorhinolaryngological niche.
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Affiliation(s)
- Aimee Tan
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, 4215, Australia
| | - Wing-Sze Li
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, 4215, Australia
| | - Anthony D Verderosa
- Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, 4006, Australia
| | - Luke V Blakeway
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, 4215, Australia
| | - Tsitsi D Mubaiwa
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, 4215, Australia
| | - Makrina Totsika
- Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, 4006, Australia
| | - Kate L Seib
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, 4215, Australia.
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19
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Salvadori G, Junges R, Åmdal HA, Chen T, Morrison DA, Petersen FC. High-resolution profiles of the Streptococcus mitis CSP signaling pathway reveal core and strain-specific regulated genes. BMC Genomics 2018; 19:453. [PMID: 29898666 PMCID: PMC6001120 DOI: 10.1186/s12864-018-4802-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 05/18/2018] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND In streptococci of the mitis group, competence for natural transformation is a transient physiological state triggered by competence stimulating peptides (CSPs). Although low transformation yields and the absence of a widespread functional competence system have been reported for Streptococcus mitis, recent studies revealed that, at least for some strains, high efficiencies can be achieved following optimization protocols. To gain a deeper insight into competence in this species, we used RNA-seq, to map the global CSP response of two transformable strains: the type strain NCTC12261T and SK321. RESULTS All known genes induced by ComE in Streptococcus pneumoniae, including sigX, were upregulated in the two strains. Likewise, all sets of streptococcal SigX core genes involved in extracellular DNA uptake, recombination, and fratricide were upregulated. No significant differences in the set of induced genes were observed when the type strain was grown in rich or semi-defined media. Five upregulated operons unique to S. mitis with a SigX-box in the promoter region were identified, including two specific to SK321, and one specific to NCTC12261T. Two of the strain-specific operons coded for different bacteriocins. Deletion of the unique S. mitis sigX regulated genes had no effect on transformation. CONCLUSIONS Overall, comparison of the global transcriptome in response to CSP shows the conservation of the ComE and SigX-core regulons in competent S. mitis isolates, as well as species and strain-specific genes. Although some S. mitis exhibit truncations in key competence genes, this study shows that in transformable strains, competence seems to depend on the same core genes previously identified in S. pneumoniae.
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Affiliation(s)
- G Salvadori
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Postboks 1052, Blindern, 0316, Oslo, Norway
| | - R Junges
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Postboks 1052, Blindern, 0316, Oslo, Norway
| | - H A Åmdal
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Postboks 1052, Blindern, 0316, Oslo, Norway
| | - T Chen
- Department of Microbiology, The Forsyth Institute, Cambridge, MA, USA
| | - D A Morrison
- Department of Biological Sciences, College of Liberal Arts and Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | - F C Petersen
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Postboks 1052, Blindern, 0316, Oslo, Norway.
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20
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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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21
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Nguyen LTT, Takemura AJ, Ohniwa RL, Saito S, Morikawa K. Sodium Polyanethol Sulfonate Modulates Natural Transformation of SigH-Expressing Staphylococcus aureus. Curr Microbiol 2017; 75:499-504. [DOI: 10.1007/s00284-017-1409-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 11/29/2017] [Indexed: 11/28/2022]
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22
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A programmed cell division delay preserves genome integrity during natural genetic transformation in Streptococcus pneumoniae. Nat Commun 2017; 8:1621. [PMID: 29158515 PMCID: PMC5696345 DOI: 10.1038/s41467-017-01716-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 10/11/2017] [Indexed: 11/22/2022] Open
Abstract
Competence for genetic transformation is a differentiation program during which exogenous DNA is imported into the cell and integrated into the chromosome. In Streptococcus pneumoniae, competence develops transiently and synchronously in all cells during exponential phase, and is accompanied by a pause in growth. Here, we reveal that this pause is linked to the cell cycle. At least two parallel pathways impair peptidoglycan synthesis in competent cells. Single-cell analyses demonstrate that ComM, a membrane protein induced during competence, inhibits both initiation of cell division and final constriction of the cytokinetic ring. Competence also interferes with the activity of the serine/threonine kinase StkP, the central regulator of pneumococcal cell division. We further present evidence that the ComM-mediated delay in division preserves genomic integrity during transformation. We propose that cell division arrest is programmed in competent pneumococcal cells to ensure that transformation is complete before resumption of cell division, to provide this pathogen with the maximum potential for genetic diversity and adaptation. In Streptococcus pneumoniae, competence for genetic transformation is accompanied by a pause in growth. Here, Bergé et al. show that this pause is linked to the cell cycle via at least two pathways that impair peptidoglycan synthesis and preserve genomic integrity during transformation.
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23
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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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24
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Barnes AMT, Dale JL, Chen Y, Manias DA, Greenwood Quaintance KE, Karau MK, Kashyap PC, Patel R, Wells CL, Dunny GM. Enterococcus faecalis readily colonizes the entire gastrointestinal tract and forms biofilms in a germ-free mouse model. Virulence 2016; 8:282-296. [PMID: 27562711 DOI: 10.1080/21505594.2016.1208890] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The mammalian gastrointestinal (GI) tract is a complex organ system with a twist-a significant portion of its composition is a community of microbial symbionts. The microbiota plays an increasingly appreciated role in many clinically-relevant conditions. It is important to understand the details of biofilm development in the GI tract since bacteria in this state not only use biofilms to improve colonization, biofilm bacteria often exhibit high levels of resistance to common, clinically relevant antibacterial drugs. Here we examine the initial colonization of the germ-free murine GI tract by Enterococcus faecalis-one of the first bacterial colonizers of the naïve mammalian gut. We demonstrate strong morphological similarities to our previous in vitro E. faecalis biofilm microcolony architecture using 3 complementary imaging techniques: conventional tissue Gram stain, immunofluorescent imaging (IFM) of constitutive fluorescent protein reporter expression, and low-voltage scanning electron microscopy (LV-SEM). E. faecalis biofilm microcolonies were readily identifiable throughout the entire lower GI tract, from the duodenum to the colon. Notably, biofilm development appeared to occur as discrete microcolonies directly attached to the epithelial surface rather than confluent sheets of cells throughout the GI tract even in the presence of high (>109) fecal bacterial loads. An in vivo competition experiment using a pool of 11 select E. faecalis mutant strains containing sequence-defined transposon insertions showed the potential of this model to identify genetic factors involved in E. faecalis colonization of the murine GI tract.
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Affiliation(s)
- Aaron M T Barnes
- a Departments of Microbiology & Immunology , University of Minnesota Medical School , Minneapolis , MN , USA
| | - Jennifer L Dale
- a Departments of Microbiology & Immunology , University of Minnesota Medical School , Minneapolis , MN , USA
| | - Yuqing Chen
- a Departments of Microbiology & Immunology , University of Minnesota Medical School , Minneapolis , MN , USA
| | - Dawn A Manias
- a Departments of Microbiology & Immunology , University of Minnesota Medical School , Minneapolis , MN , USA
| | - Kerryl E Greenwood Quaintance
- b Department of Laboratory Medicine and Pathology , Division of Clinical Microbiology, Mayo Clinic , Rochester , MN , USA
| | - Melissa K Karau
- b Department of Laboratory Medicine and Pathology , Division of Clinical Microbiology, Mayo Clinic , Rochester , MN , USA
| | - Purna C Kashyap
- c Division of Gastroenterology , Department of Medicine , Mayo Clinic , Rochester , MN , USA
| | - Robin Patel
- b Department of Laboratory Medicine and Pathology , Division of Clinical Microbiology, Mayo Clinic , Rochester , MN , USA.,d Department of Medicine , Division of Infectious Disease, Mayo Clinic , Rochester , MN , USA
| | - Carol L Wells
- a Departments of Microbiology & Immunology , University of Minnesota Medical School , Minneapolis , MN , USA.,e Laboratory Medicine and Pathology , University of Minnesota Medical School , Minneapolis , MN , USA
| | - Gary M Dunny
- a Departments of Microbiology & Immunology , University of Minnesota Medical School , Minneapolis , MN , USA
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25
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Corbinais C, Mathieu A, Kortulewski T, Radicella JP, Marsin S. Following transforming DNA inHelicobacter pylorifrom uptake to expression. Mol Microbiol 2016; 101:1039-53. [DOI: 10.1111/mmi.13440] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/11/2016] [Indexed: 12/22/2022]
Affiliation(s)
- Christopher Corbinais
- CEA; Institute of Molecular and Cellular Radiobiology; F-92265 Fontenay aux Roses France
- INSERM, U967, F-92265 Fontenay-aux-Roses, France
- Universités Paris Diderot et Paris Sud; UMR967, F-92265 Fontenay-aux-Roses France
| | - Aurélie Mathieu
- CEA; Institute of Molecular and Cellular Radiobiology; F-92265 Fontenay aux Roses France
| | - Thierry Kortulewski
- CEA; Institute of Molecular and Cellular Radiobiology; F-92265 Fontenay aux Roses France
- INSERM, U967, F-92265 Fontenay-aux-Roses, France
- Universités Paris Diderot et Paris Sud; UMR967, F-92265 Fontenay-aux-Roses France
| | - J. Pablo Radicella
- CEA; Institute of Molecular and Cellular Radiobiology; F-92265 Fontenay aux Roses France
- INSERM, U967, F-92265 Fontenay-aux-Roses, France
- Universités Paris Diderot et Paris Sud; UMR967, F-92265 Fontenay-aux-Roses France
| | - Stéphanie Marsin
- CEA; Institute of Molecular and Cellular Radiobiology; F-92265 Fontenay aux Roses France
- INSERM, U967, F-92265 Fontenay-aux-Roses, France
- Universités Paris Diderot et Paris Sud; UMR967, F-92265 Fontenay-aux-Roses France
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Addiction of Hypertransformable Pneumococcal Isolates to Natural Transformation for In Vivo Fitness and Virulence. Infect Immun 2016; 84:1887-1901. [PMID: 27068094 DOI: 10.1128/iai.00097-16] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 04/06/2016] [Indexed: 12/25/2022] Open
Abstract
Natural genetic transformation of Streptococcus pneumoniae, an important human pathogen, mediates horizontal gene transfer for the development of drug resistance, modulation of carriage and virulence traits, and evasion of host immunity. Transformation frequency differs greatly among pneumococcal clinical isolates, but the molecular basis and biological importance of this interstrain variability remain unclear. In this study, we characterized the transformation frequency and other associated phenotypes of 208 S. pneumoniae clinical isolates representing at least 30 serotypes. While the vast majority of these isolates (94.7%) were transformable, the transformation frequency differed by up to 5 orders of magnitude between the least and most transformable isolates. The strain-to-strain differences in transformation frequency were observed among many isolates producing the same capsule types, indicating no general association between transformation frequency and serotype. However, a statistically significant association was observed between the levels of transformation and colonization fitness/virulence in the hypertransformable isolates. Although nontransformable mutants of all the selected hypertransformable isolates were significantly attenuated in colonization fitness and virulence in mouse infection models, such mutants of the strains with relatively low transformability had no or marginal fitness phenotypes under the same experimental settings. This finding strongly suggests that the pneumococci with high transformation capability are "addicted" to a "hypertransformable" state for optimal fitness in the human host. This work has thus provided an intriguing hint for further investigation into how the competence system impacts the fitness, virulence, and other transformation-associated traits of this important human pathogen.
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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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28
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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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29
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Fontaine L, Wahl A, Fléchard M, Mignolet J, Hols P. Regulation of competence for natural transformation in streptococci. INFECTION GENETICS AND EVOLUTION 2015; 33:343-60. [DOI: 10.1016/j.meegid.2014.09.010] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2014] [Revised: 08/28/2014] [Accepted: 09/07/2014] [Indexed: 02/02/2023]
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30
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de Buhr N, Stehr M, Neumann A, Naim HY, Valentin-Weigand P, von Köckritz-Blickwede M, Baums CG. Identification of a novel DNase of Streptococcus suis (EndAsuis) important for neutrophil extracellular trap degradation during exponential growth. MICROBIOLOGY-SGM 2015; 161:838-50. [PMID: 25667008 DOI: 10.1099/mic.0.000040] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 01/27/2015] [Indexed: 12/25/2022]
Abstract
The porcine and human pathogen Streptococcus suis induces and degrades neutrophil extracellular traps (NETs) in vitro. In this study, we investigated the working hypothesis that NET degradation is mediated not only by the known secreted S. suis nuclease A (SsnA) but also by a so-far undescribed putative endonuclease A of S. suis (designated EndAsuis) homologous to the pneumococcal endonuclease A (EndA). Comparative analysis was conducted to identify differences in localization, expression and function of EndAsuis and SsnA. In contrast to ssnA, endAsuis RNA expression was not substantially different during exponential and stationary growth. Modelling of the 3D structure confirmed a putative DRGH-motif-containing ββα-metal finger catalytic core in EndAsuis. Accordingly, nuclease activity of recombinant EndAsuis with a point-mutated H165 was rescued through imidazol treatment. In accordance with a putative membrane anchor, nuclease activity caused by endAsuis was not detectable in the supernatant. Importantly, endAsuis determined nuclease activity of S. suis prominently during exponential growth. This activity depended on the presence of Mg(2+) but, in contrast to SsnA activity, not on Ca(2+). A pH of 5.4 did not inhibit endAsuis-encoded nuclease activity during exponential growth. NET degradation of S. suis harvested during exponential growth was significantly attenuated in the endAsuis mutant. In contrast to SsnA, mutagenesis of endAsuis did not result in a significantly higher susceptibility against the antimicrobial effect mediated by NETs. As degradation of bacterial DNA caused by S. suis depended on ssnA and endAsuis, further functions of both factors in the host-pathogen interaction might be envisioned.
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Affiliation(s)
- Nicole de Buhr
- Institute for Microbiology, Department of Infectious Diseases, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Matthias Stehr
- Institute for Microbiology, Department of Infectious Diseases, University of Veterinary Medicine Hannover, Hannover, Germany LIONEX Diagnostics and Therapeutics GmbH, Braunschweig, Germany
| | - Ariane Neumann
- Department of Physiological Chemistry, Department of Infectious Diseases, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Hassan Y Naim
- Department of Physiological Chemistry, Department of Infectious Diseases, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Peter Valentin-Weigand
- Institute for Microbiology, Department of Infectious Diseases, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Maren von Köckritz-Blickwede
- Department of Physiological Chemistry, Department of Infectious Diseases, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Christoph G Baums
- Institute for Microbiology, Department of Infectious Diseases, University of Veterinary Medicine Hannover, Hannover, Germany Institute for Bacteriology and Mycology, Centre for Infectious Diseases, College of Veterinary Medicine, University of Leipzig, Leipzig, Germany
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31
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Muschiol S, Balaban M, Normark S, Henriques-Normark B. Uptake of extracellular DNA: competence induced pili in natural transformation of Streptococcus pneumoniae. Bioessays 2015; 37:426-35. [PMID: 25640084 PMCID: PMC4405041 DOI: 10.1002/bies.201400125] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Transport of DNA across bacterial membranes involves complex DNA uptake systems. In Gram-positive bacteria, the DNA uptake machinery shares fundamental similarities with type IV pili and type II secretion systems. Although dedicated pilus structures, such as type IV pili in Gram-negative bacteria, are necessary for efficient DNA uptake, the role of similar structures in Gram-positive bacteria is just beginning to emerge. Recently two essentially very different pilus structures composed of the same major pilin protein ComGC were proposed to be involved in transformation of the Gram-positive bacterium Streptococcus pneumoniae – one is a long, thin, type IV pilus-like fiber with DNA binding capacity and the other one is a pilus structure that was thicker, much shorter and not able to bind DNA. Here we discuss how competence induced pili, either by pilus retraction or by a transient pilus-related opening in the cell wall, may mediate DNA uptake in S. pneumoniae.
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Affiliation(s)
- Sandra Muschiol
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden; Department of Laboratory Medicine, Division of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
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32
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Ardissone S, Fumeaux C, Bergé M, Beaussart A, Théraulaz L, Radhakrishnan SK, Dufrêne YF, Viollier PH. Cell cycle constraints on capsulation and bacteriophage susceptibility. eLife 2014; 3. [PMID: 25421297 PMCID: PMC4241560 DOI: 10.7554/elife.03587] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 10/21/2014] [Indexed: 12/28/2022] Open
Abstract
Despite the crucial role of bacterial capsules in pathogenesis, it is still unknown if systemic cues such as the cell cycle can control capsule biogenesis. In this study, we show that the capsule of the synchronizable model bacterium Caulobacter crescentus is cell cycle regulated and we unearth a bacterial transglutaminase homolog, HvyA, as restriction factor that prevents capsulation in G1-phase cells. This capsule protects cells from infection by a generalized transducing Caulobacter phage (φCr30), and the loss of HvyA confers insensitivity towards φCr30. Control of capsulation during the cell cycle could serve as a simple means to prevent steric hindrance of flagellar motility or to ensure that phage-mediated genetic exchange happens before the onset of DNA replication. Moreover, the multi-layered regulatory circuitry directing HvyA expression to G1-phase is conserved during evolution, and HvyA orthologues from related Sinorhizobia can prevent capsulation in Caulobacter, indicating that alpha-proteobacteria have retained HvyA activity.
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Affiliation(s)
- Silvia Ardissone
- Department of Microbiology and Molecular Medicine, Institute of Genetics and Genomics in Geneva, University of Geneva, Geneva, Switzerland
| | - Coralie Fumeaux
- Department of Microbiology and Molecular Medicine, Institute of Genetics and Genomics in Geneva, University of Geneva, Geneva, Switzerland
| | - Matthieu Bergé
- Department of Microbiology and Molecular Medicine, Institute of Genetics and Genomics in Geneva, University of Geneva, Geneva, Switzerland
| | - Audrey Beaussart
- Institute of Life Sciences, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Laurence Théraulaz
- Department of Microbiology and Molecular Medicine, Institute of Genetics and Genomics in Geneva, University of Geneva, Geneva, Switzerland
| | - Sunish Kumar Radhakrishnan
- Department of Microbiology and Molecular Medicine, Institute of Genetics and Genomics in Geneva, University of Geneva, Geneva, Switzerland
| | - Yves F Dufrêne
- Institute of Life Sciences, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Patrick H Viollier
- Department of Microbiology and Molecular Medicine, Institute of Genetics and Genomics in Geneva, University of Geneva, Geneva, Switzerland
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33
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Straume D, Stamsås GA, Håvarstein LS. Natural transformation and genome evolution in Streptococcus pneumoniae. INFECTION GENETICS AND EVOLUTION 2014; 33:371-80. [PMID: 25445643 DOI: 10.1016/j.meegid.2014.10.020] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Revised: 10/16/2014] [Accepted: 10/23/2014] [Indexed: 01/30/2023]
Abstract
Streptococcus pneumoniae is a frequent colonizer of the human nasopharynx that has the potential to cause severe infections such as pneumonia, bacteremia and meningitis. Despite considerable efforts to reduce the burden of pneumococcal disease, it continues to be a major public health problem. After the Second World War, antimicrobial therapy was introduced to fight pneumococcal infections, followed by the first effective vaccines more than half a century later. These clinical interventions generated a selection pressure that drove the evolution of vaccine-escape mutants and strains that were highly resistant against antibiotics. The remarkable ability of S. pneumoniae to acquire drug resistance and evade vaccine pressure is due to its recombination-mediated genetic plasticity. S. pneumoniae is competent for natural genetic transformation, a property that enables the pneumococcus to acquire new traits by taking up naked DNA from the environment and incorporating it into its genome through homologous recombination. In the present paper, we review current knowledge on pneumococcal transformation, and discuss how the pneumococcus uses this mechanism to adapt and survive under adverse and fluctuating conditions.
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Affiliation(s)
- Daniel Straume
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, NO-1432 Ås, Norway
| | - Gro Anita Stamsås
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, NO-1432 Ås, Norway
| | - Leiv Sigve Håvarstein
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, NO-1432 Ås, Norway.
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34
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Abstract
The field of plasmid biology has historically focused on bacteria growing in liquid culture. Surface attached communities of bacterial biofilms have recently been understood to be the normal environment of bacteria in the natural world. Thus, studies examining plasmid replication, maintenance, and transfer in biofilms are essential for a true understanding of bacterial plasmid biology. This chapter reviews the current knowledge of the interplay between bacterial biofilms and plasmids, focusing on the role of plasmids in biofilm development and the role of biofilms in plasmid maintenance, copy number control, and transfer. The studies examined herein highlight the importance of biofilms as an important ecological niche in which bacterial plasmids play an essential role.
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Affiliation(s)
| | - Gary M. Dunny
- Department of Microbiology, University of Minnesota, 1460 Mayo Bldg., MMC196, 420 Delaware St., SE, Minneapolis MN, 55455
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35
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Fagerlund A, Granum PE, Håvarstein LS. Staphylococcus aureus competence genes: mapping of the SigH, ComK1 and ComK2 regulons by transcriptome sequencing. Mol Microbiol 2014; 94:557-79. [PMID: 25155269 DOI: 10.1111/mmi.12767] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/21/2014] [Indexed: 01/17/2023]
Abstract
Staphylococcus aureus is a major human pathogen. Hospital infections caused by methicillin-resistant strains (MRSA), which have acquired resistance to a broad spectrum of antibiotics through horizontal gene transfer (HGT), are of particular concern. In S. aureus, virulence and antibiotic resistance genes are often encoded on mobile genetic elements that are disseminated by HGT. Conjugation and phage transduction have long been known to mediate HGT in this species, but it is unclear whether natural genetic transformation contributes significantly to the process. Recently, it was reported that expression of the alternative sigma factor SigH induces the competent state in S. aureus. The transformation efficiency obtained, however, was extremely low, indicating that the optimal conditions for competence development had not been found. We therefore used transcriptome sequencing to determine whether the full set of genes known to be required for competence in other naturally transformable bacteria is part of the SigH regulon. Our results show that several essential competence genes are not controlled by SigH. This presumably explains the low transformation efficiency previously reported, and demonstrates that additional regulating mechanisms must be involved. We found that one such mechanism involves ComK1, a transcriptional activator that acts synergistically with SigH.
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Affiliation(s)
- Annette Fagerlund
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
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36
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DNA transport across the outer and inner membranes of naturally transformable Vibrio cholerae is spatially but not temporally coupled. mBio 2014; 5:mBio.01409-14. [PMID: 25139903 PMCID: PMC4147865 DOI: 10.1128/mbio.01409-14] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The physiological state of natural competence for transformation allows certain bacteria to take up free DNA from the environment and to recombine such newly acquired DNA into their chromosomes. However, even though conserved components that are required to undergo natural transformation have been identified in several naturally competent bacteria, our knowledge of the underlying mechanisms of the DNA uptake process remains very limited. To better understand these mechanisms, we investigated the competence-mediated DNA transport in the naturally transformable pathogen Vibrio cholerae. Previously, we used a cell biology-based approach to experimentally address an existing hypothesis, which suggested the competence protein ComEA plays a role in the DNA uptake process across the outer membrane of Gram-negative bacteria. Here, we extended this knowledge by investigating the dynamics of DNA translocation across both membranes. More precisely, we indirectly visualized the transfer of the external DNA from outside the cell into the periplasm followed by the shuttling of the DNA into the cytoplasm. Based on these data, we conclude that for V. cholerae, the DNA translocation across the outer and inner membranes is spatially but not temporally coupled. As a mode of horizontal gene transfer, natural competence for transformation has contributed substantially to the plasticity of genomes and to bacterial evolution. Natural competence is often a tightly regulated process and is induced by diverse environmental cues. This is in contrast to the mechanistic aspects of the DNA translocation event, which are most likely conserved among naturally transformable bacteria. However, the DNA uptake process is still not well understood. We therefore investigated how external DNA reaches the cytosol of the naturally transformable bacterium V. cholerae. More specifically, we provide evidence that the DNA translocation across the membranes is spatially but not temporally coupled. We hypothesize that this model also applies to other competent Gram-negative bacteria and that our study contributes to the general understanding of this important biological process.
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37
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Concerted spatio-temporal dynamics of imported DNA and ComE DNA uptake protein during gonococcal transformation. PLoS Pathog 2014; 10:e1004043. [PMID: 24763594 PMCID: PMC3999279 DOI: 10.1371/journal.ppat.1004043] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Accepted: 02/17/2014] [Indexed: 01/28/2023] Open
Abstract
Competence for transformation is widespread among bacterial species. In the case of Gram-negative systems, a key step to transformation is the import of DNA across the outer membrane. Although multiple factors are known to affect DNA transport, little is known about the dynamics of DNA import. Here, we characterized the spatio-temporal dynamics of DNA import into the periplasm of Neisseria gonorrhoeae. DNA was imported into the periplasm at random locations around the cell contour. Subsequently, it was recruited at the septum of diplococci at a time scale that increased with DNA length. We found using fluorescent DNA that the periplasm was saturable within minutes with ∼40 kbp DNA. The DNA-binding protein ComE quantitatively governed the carrying capacity of the periplasm in a gene-dosage-dependent fashion. As seen using a fluorescent-tagged derivative protein, ComE was homogeneously distributed in the periplasm in the absence of external DNA. Upon addition of external DNA, ComE was relocalized to form discrete foci colocalized with imported DNA. We conclude that the periplasm can act as a considerable reservoir for imported DNA with ComE governing the amount of DNA stored potentially for transport through the inner membrane. Bacterial transformation is the import and inheritable integration of external DNA. As such, it is believed to be a major evolutionary force. A key step is the import of DNA through the outer membrane. Here, we have characterized the spatio-temporal dynamics of DNA during import and residence in the periplasm of the Gram-negative pathogen Neisseria gonorrhoeae. We found that the periplasm can serve as a reservoir for imported DNA that can fill within five minutes by importing DNA from the environment. The amount of imported DNA roughly corresponds to the size of a phage genome. The periplasmic DNA-binding protein ComE is homogeneously distributed in the periplasm in the absence of extracellular DNA. It relocates rapidly to imported DNA when external DNA is added to competent gonococci. As ComE governs the carrying capacity of the periplasm, we propose that it might condense DNA, thus linking DNA uptake to its compaction. Although the import through the outer membrane was localized all around the cell contour, the major part of the imported DNA relocated to the septum at the center of diplococci. Our findings strongly support the idea that the periplasm masses DNA independently of transport through the inner membrane.
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38
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Johnston C, Martin B, Fichant G, Polard P, Claverys JP. Bacterial transformation: distribution, shared mechanisms and divergent control. Nat Rev Microbiol 2014; 12:181-96. [DOI: 10.1038/nrmicro3199] [Citation(s) in RCA: 402] [Impact Index Per Article: 40.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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39
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Metzger LC, Blokesch M. Composition of the DNA-uptake complex of Vibrio cholerae.. Mob Genet Elements 2014; 4:e28142. [PMID: 24558639 PMCID: PMC3919817 DOI: 10.4161/mge.28142] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Revised: 02/05/2014] [Accepted: 02/06/2014] [Indexed: 12/20/2022] Open
Abstract
Natural competence for transformation is a developmental program that allows certain bacteria to take up free extracellular DNA from the environment and integrate this DNA into their genome. Thereby, natural transformation acts as mode of horizontal gene transfer and impacts bacterial evolution. The number of genes induced upon competence induction varies significantly between organisms. However, all of the naturally competent bacteria possess competence genes that encode so-called DNA-uptake machineries. Some components of these multi-protein complexes resemble subunits of type IV pili and type II secretion systems. However, knowledge on the mechanistic aspects of such DNA-uptake complexes is still very limited. Here, we discuss some new findings regarding the DNA-uptake machinery of the naturally transformable human pathogen Vibrio cholerae. The potential of this organism to initiate the competence program was discovered less than a decade ago. However, recent studies have provided new insight into both the regulatory pathways of competence induction and into the DNA uptake dynamics.
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Affiliation(s)
- Lisa C Metzger
- Global Health Institute; School of Life Sciences; Swiss Federal Institute of Technology Lausanne (Ecole Polytechnique Fédérale de Lausanne, EPFL); Lausanne, Switzerland
| | - Melanie Blokesch
- Global Health Institute; School of Life Sciences; Swiss Federal Institute of Technology Lausanne (Ecole Polytechnique Fédérale de Lausanne, EPFL); Lausanne, Switzerland
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40
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Johnston C, Campo N, Bergé MJ, Polard P, Claverys JP. Streptococcus pneumoniae, le transformiste. Trends Microbiol 2014; 22:113-9. [PMID: 24508048 DOI: 10.1016/j.tim.2014.01.002] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Revised: 01/09/2014] [Accepted: 01/09/2014] [Indexed: 10/25/2022]
Abstract
Streptococcus pneumoniae (the pneumococcus) is an important human pathogen. Natural genetic transformation, which was discovered in this species, involves internalization of exogenous single-stranded DNA and its incorporation into the chromosome. It allows acquisition of pathogenicity islands and antibiotic resistance and promotes vaccine escape via capsule switching. This opinion article discusses how recent advances regarding several facets of pneumococcal transformation support the view that the process has evolved to maximize plasticity potential in this species, making the pneumococcus le transformiste of the bacterial kingdom and providing an advantage in the constant struggle between this pathogen and its host.
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Affiliation(s)
- Calum Johnston
- Centre National de la Recherche Scientifique, LMGM-UMR5100, F-31000 Toulouse, France; Université de Toulouse, UPS, Laboratoire de Microbiologie et Génétique Moléculaires, F-31000 Toulouse, France
| | - Nathalie Campo
- Centre National de la Recherche Scientifique, LMGM-UMR5100, F-31000 Toulouse, France; Université de Toulouse, UPS, Laboratoire de Microbiologie et Génétique Moléculaires, F-31000 Toulouse, France
| | - Matthieu J Bergé
- Centre National de la Recherche Scientifique, LMGM-UMR5100, F-31000 Toulouse, France; Université de Toulouse, UPS, Laboratoire de Microbiologie et Génétique Moléculaires, F-31000 Toulouse, France
| | - Patrice Polard
- Centre National de la Recherche Scientifique, LMGM-UMR5100, F-31000 Toulouse, France; Université de Toulouse, UPS, Laboratoire de Microbiologie et Génétique Moléculaires, F-31000 Toulouse, France
| | - Jean-Pierre Claverys
- Centre National de la Recherche Scientifique, LMGM-UMR5100, F-31000 Toulouse, France; Université de Toulouse, UPS, Laboratoire de Microbiologie et Génétique Moléculaires, F-31000 Toulouse, France.
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41
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Seitz P, Pezeshgi Modarres H, Borgeaud S, Bulushev RD, Steinbock LJ, Radenovic A, Dal Peraro M, Blokesch M. ComEA is essential for the transfer of external DNA into the periplasm in naturally transformable Vibrio cholerae cells. PLoS Genet 2014; 10:e1004066. [PMID: 24391524 PMCID: PMC3879209 DOI: 10.1371/journal.pgen.1004066] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Accepted: 11/12/2013] [Indexed: 11/18/2022] Open
Abstract
The DNA uptake of naturally competent bacteria has been attributed to the action of DNA uptake machineries resembling type IV pilus complexes. However, the protein(s) for pulling the DNA across the outer membrane of Gram-negative bacteria remain speculative. Here we show that the competence protein ComEA binds incoming DNA in the periplasm of naturally competent Vibrio cholerae cells thereby promoting DNA uptake, possibly through ratcheting and entropic forces associated with ComEA binding. Using comparative modeling and molecular simulations, we projected the 3D structure and DNA-binding site of ComEA. These in silico predictions, combined with in vivo and in vitro validations of wild-type and site-directed modified variants of ComEA, suggested that ComEA is not solely a DNA receptor protein but plays a direct role in the DNA uptake process. Furthermore, we uncovered that ComEA homologs of other bacteria (both Gram-positive and Gram-negative) efficiently compensated for the absence of ComEA in V. cholerae, suggesting that the contribution of ComEA in the DNA uptake process might be conserved among naturally competent bacteria. Horizontal gene transfer (HGT) plays a key role in transferring genetic information from one organism to another. Natural competence for transformation is one of three modes of HGT used by bacteria to promote the uptake of free DNA from the surrounding. The human pathogen Vibrio cholerae enters such a competence state upon growth on chitinous surfaces, which represent its natural niche in the aquatic environment. Whereas we have gained a reasonable understanding on how the competence phenotype is regulated in V. cholerae we are only at the beginning of deciphering the mechanistic aspects of the DNA uptake process. In this study, we characterize the competence protein ComEA. We show that ComEA is transported into the periplasm of V. cholerae and that it is required for the uptake of DNA across the outer membrane. We demonstrate that ComEA aggregates around incoming DNA in vivo and that the binding of DNA is dependent on specific residues within a conserved helix-hairpin-helix motif. We propose a model indicating that the DNA uptake process across the outer membrane might be driven through ratcheting and entropic forces associated with ComEA binding.
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Affiliation(s)
- Patrick Seitz
- Laboratory of Molecular Microbiology, Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Hassan Pezeshgi Modarres
- Laboratory for Biomolecular Modeling, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Sandrine Borgeaud
- Laboratory of Molecular Microbiology, Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Roman D. Bulushev
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Lorenz J. Steinbock
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Aleksandra Radenovic
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Matteo Dal Peraro
- Laboratory for Biomolecular Modeling, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Melanie Blokesch
- Laboratory of Molecular Microbiology, Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- * E-mail:
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