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Mårli MT, Oppegaard O, Porcellato D, Straume D, Kjos M. Genetic modification of Streptococcus dysgalactiae by natural transformation. mSphere 2024; 9:e0021424. [PMID: 38904369 PMCID: PMC11288034 DOI: 10.1128/msphere.00214-24] [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: 03/18/2024] [Accepted: 05/13/2024] [Indexed: 06/22/2024] Open
Abstract
Streptococcus dysgalactiae is an emerging human and animal pathogen. Functional studies of genes involved in virulence of S. dysgalactiae and other pyogenic group streptococci are often hampered by limited genetic tractability. It is known that pyogenic streptococci carry genes required for competence for natural transformation; however, in contrast to other streptococcal subgroups, there is limited evidence for gene transfer by natural transformation in these bacteria. In this study, we systematically assessed the genomes of 179 S. dysgalactiae strains of both human and animal origins (subsp. equisimilis and dysgalactiae, respectively) for the presence of genes required for natural transformation. While a considerable fraction of the strains contained inactive genes, the majority (64.2%) of the strains had an intact gene set. In selected strains, we examined the dynamics of competence activation after addition of competence-inducing pheromones using transcriptional reporter assays and exploratory RNA-seq. Based on these findings, we were able to establish a protocol allowing us to utilize natural transformation to construct deletion mutants by allelic exchange in several S. dysgalactiae strains of both subspecies. As part of the work, we deleted putative lactose utilization genes to study their role in growth on lactose. The data presented here provide new knowledge on the potential of horizonal gene transfer by natural transformation in S. dysgalactiae and, importantly, demonstrates the possibility to exploit natural transformation for genetic engineering in these bacteria. IMPORTANCE Numerous Streptococcus spp. exchange genes horizontally through natural transformation, which also facilitates efficient genetic engineering in these organisms. However, for the pyogenic group of streptococci, including the emerging pathogen Streptococcus dysgalactiae, there is limited experimental evidence for natural transformation. In this study, we demonstrate that natural transformation in vitro indeed is possible in S. dysgalactiae strains under optimal conditions. We utilized this method to perform gene deletion through allelic exchange in several strains, thereby paving the way for more efficient gene engineering methods in pyogenic streptococci.
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Affiliation(s)
- Marita Torrissen Mårli
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Oddvar Oppegaard
- Haukeland University Hospital, University of Bergen, Bergen, Norway
| | - Davide Porcellato
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Daniel Straume
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Morten Kjos
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
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Prudhomme M, Johnston CHG, Soulet AL, Boyeldieu A, De Lemos D, Campo N, Polard P. Pneumococcal competence is a populational health sensor driving multilevel heterogeneity in response to antibiotics. Nat Commun 2024; 15:5625. [PMID: 38987237 PMCID: PMC11237056 DOI: 10.1038/s41467-024-49853-2] [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: 12/14/2023] [Accepted: 06/21/2024] [Indexed: 07/12/2024] Open
Abstract
Competence for natural transformation is a central driver of genetic diversity in bacteria. In the human pathogen Streptococcus pneumoniae, competence exhibits a populational character mediated by the stress-induced ComABCDE quorum-sensing (QS) system. Here, we explore how this cell-to-cell communication mechanism proceeds and the functional properties acquired by competent cells grown under lethal stress. We show that populational competence development depends on self-induced cells stochastically emerging in response to stresses, including antibiotics. Competence then propagates through the population from a low threshold density of self-induced cells, defining a biphasic Self-Induction and Propagation (SI&P) QS mechanism. We also reveal that a competent population displays either increased sensitivity or improved tolerance to lethal doses of antibiotics, dependent in the latter case on the competence-induced ComM division inhibitor. Remarkably, these surviving competent cells also display an altered transformation potential. Thus, the unveiled SI&P QS mechanism shapes pneumococcal competence as a health sensor of the clonal population, promoting a bet-hedging strategy that both responds to and drives cells towards heterogeneity.
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Affiliation(s)
- 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
| | - Calum H G 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
| | - Anne Boyeldieu
- 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
| | - Nathalie Campo
- 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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Oh MW, Lin J, Chong SY, Lew SQ, Alam T, Lau GW. Time-resolved RNA-seq analysis to unravel the in vivo competence induction by Streptococcus pneumoniae during pneumonia-derived sepsis. Microbiol Spectr 2024; 12:e0305023. [PMID: 38305162 PMCID: PMC10913500 DOI: 10.1128/spectrum.03050-23] [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: 08/08/2023] [Accepted: 01/09/2024] [Indexed: 02/03/2024] Open
Abstract
Competence development in Streptococcus pneumoniae (pneumococcus) is tightly intertwined with virulence. In addition to genes encoding genetic transformation machinery, the competence regulon also regulates the expression of allolytic factors, bacteriocins, and cytotoxins. Pneumococcal competence system has been extensively interrogated in vitro where the short transient competent state upregulates the expression of three distinct phases of "early," "late," and "delayed" genes. Recently, we have demonstrated that the pneumococcal competent state develops naturally in mouse models of pneumonia-derived sepsis. To unravel the underlying adaptive mechanisms driving the development of the competent state, we conducted a time-resolved transcriptomic analysis guided by the spatiotemporal live in vivo imaging system of competence induction during pneumonia-derived sepsis. Mouse lungs infected by the serotype 2 strain D39 expressing a competent state-specific reporter gene (D39-ssbB-luc) were subjected to RNA sequencing guided by monitoring the competence development at 0, 12, 24, and, at the moribund state, >40 hours post-infection (hpi). Transcriptomic analysis revealed that the competence-specific gene expression patterns in vivo were distinct from those under in vitro conditions. There was significant upregulation of early, late, and some delayed phase competence-specific genes as early as 12 hpi, suggesting that the pneumococcal competence regulon is important for adaptation to the lung environment. Additionally, members of the histidine triad (pht) gene family were sharply upregulated at 12 hpi followed by a steep decline throughout the rest of the infection cycle, suggesting that Pht proteins participate in the early adaptation to the lung environment. Further analysis revealed that Pht proteins execute a metal ion-dependent regulatory role in competence induction.IMPORTANCEThe induction of pneumococcal competence for genetic transformation has been extensively studied in vitro but poorly understood during lung infection. We utilized a combination of live imaging and RNA sequencing to monitor the development of a competent state during acute pneumonia. Upregulation of competence-specific genes was observed as early as 12 hour post-infection, suggesting that the pneumococcal competence regulon plays an important role in adapting pneumococcus to the stressful lung environment. Among others, we report novel finding that the pneumococcal histidine triad (pht) family of genes participates in the adaptation to the lung environment and regulates pneumococcal competence induction.
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Affiliation(s)
- Myung Whan Oh
- Department of Pathobiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Jingjun Lin
- Department of Pathobiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Sook Yin Chong
- Department of Pathobiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Shi Qian Lew
- Department of Pathobiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Tauqeer Alam
- Department of Pathobiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Gee W. Lau
- Department of Pathobiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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Jim KK, Aprianto R, Koning R, Domenech A, Kurushima J, van de Beek D, Vandenbroucke-Grauls CMJE, Bitter W, Veening JW. Pneumolysin promotes host cell necroptosis and bacterial competence during pneumococcal meningitis as shown by whole-animal dual RNA-seq. Cell Rep 2022; 41:111851. [PMID: 36543127 PMCID: PMC9794515 DOI: 10.1016/j.celrep.2022.111851] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 07/16/2022] [Accepted: 11/28/2022] [Indexed: 12/24/2022] Open
Abstract
Pneumolysin is a major virulence factor of Streptococcus pneumoniae that plays a key role in interaction with the host during invasive disease. How pneumolysin influences these dynamics between host and pathogen interaction during early phase of central nervous system infection in pneumococcal meningitis remains unclear. Using a whole-animal in vivo dual RNA sequencing (RNA-seq) approach, we identify pneumolysin-specific transcriptional responses in both S. pneumoniae and zebrafish (Danio rerio) during early pneumococcal meningitis. By functional enrichment analysis, we identify host pathways known to be activated by pneumolysin and discover the importance of necroptosis for host survival. Inhibition of this pathway using the drug GSK'872 increases host mortality during pneumococcal meningitis. On the pathogen's side, we show that pneumolysin-dependent competence activation is crucial for intra-host replication and virulence. Altogether, this study provides new insights into pneumolysin-specific transcriptional responses and identifies key pathways involved in pneumococcal meningitis.
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Affiliation(s)
- Kin Ki Jim
- Amsterdam UMC Location Vrije Universiteit Amsterdam, Department of Medical Microbiology and Infection Prevention, De Boelelaan 1117, Amsterdam, the Netherlands; Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands; Amsterdam UMC Location University of Amsterdam, Department of Neurology, Meibergdreef 9, Amsterdam, the Netherlands; Amsterdam Neuroscience, Amsterdam, the Netherlands
| | - Rieza Aprianto
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Biophore Building, 1015 Lausanne, Switzerland
| | - Rutger Koning
- Amsterdam UMC Location University of Amsterdam, Department of Neurology, Meibergdreef 9, Amsterdam, the Netherlands; Amsterdam Neuroscience, Amsterdam, the Netherlands
| | - Arnau Domenech
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Biophore Building, 1015 Lausanne, Switzerland
| | - Jun Kurushima
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Biophore Building, 1015 Lausanne, Switzerland
| | - Diederik van de Beek
- Amsterdam UMC Location University of Amsterdam, Department of Neurology, Meibergdreef 9, Amsterdam, the Netherlands; Amsterdam Neuroscience, Amsterdam, the Netherlands
| | - Christina M J E Vandenbroucke-Grauls
- Amsterdam UMC Location Vrije Universiteit Amsterdam, Department of Medical Microbiology and Infection Prevention, De Boelelaan 1117, Amsterdam, the Netherlands; Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands
| | - Wilbert Bitter
- Amsterdam UMC Location Vrije Universiteit Amsterdam, Department of Medical Microbiology and Infection Prevention, De Boelelaan 1117, Amsterdam, the Netherlands; Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands; Section of Molecular Microbiology, Amsterdam Institute for Molecules, Medicines and Systems, VU University Amsterdam, 1081 Amsterdam, the Netherlands
| | - Jan-Willem Veening
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Biophore Building, 1015 Lausanne, Switzerland.
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Oh MW, Lella M, Kuo SH, Tal-Gan Y, Lau GW. Pharmacological Evaluation of Synthetic Dominant-Negative Peptides Derived from the Competence-Stimulating Peptide of Streptococcus pneumoniae. ACS Pharmacol Transl Sci 2022; 5:299-305. [PMID: 35592433 PMCID: PMC9112410 DOI: 10.1021/acsptsci.2c00037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Indexed: 11/28/2022]
Abstract
The competence regulon of Streptococcus pneumoniae (pneumococcus) is a quorum-sensing circuitry that regulates the ability of this pathogen to acquire antibiotic resistance or perform serotype switching, leading to vaccine-escape serotypes, via horizontal gene transfer, as well as initiate virulence. Induction of the competence regulon is centered on binding of the competence-stimulating peptide (CSP) to its cognate receptor, ComD. We have recently synthesized multiple dominant-negative peptide analogs capable of inhibiting competence induction and virulence in S. pneumoniae. However, the pharmacodynamics and safety profiles of these peptide drug leads have not been characterized. Therefore, in this study, we compared the biostability of cyanine-7.5-labeled wild-type CSPs versus dominant-negative peptide analogs (dnCSPs) spatiotemporally by using an IVIS Spectrum in vivo imaging system. Moreover, in vitro cytotoxicity and in vivo toxicity were evaluated. We conclude that our best peptide analog, CSP1-E1A-cyc(Dap6E10), is an attractive therapeutic agent against pneumococcal infection with superior safety and pharmacokinetics profiles.
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Affiliation(s)
- Myung Whan Oh
- Department of Pathobiology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61802, United States
| | - Muralikrishna Lella
- Department of Chemistry, University of Nevada, Reno, 1664 North Virginia Street, Reno, Nevada 89557, United States
| | - Shanny Hsuan Kuo
- Department of Pathobiology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61802, United States
| | - Yftah Tal-Gan
- Department of Chemistry, University of Nevada, Reno, 1664 North Virginia Street, Reno, Nevada 89557, United States
| | - Gee W Lau
- Department of Pathobiology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61802, United States
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Caraway HE, Lau JZ, Maron B, Oh MW, Belo Y, Brill A, Malach E, Ismail N, Hayouka Z, Lau GW. Antimicrobial Random Peptide Mixtures Eradicate Acinetobacter baumannii Biofilms and Inhibit Mouse Models of Infection. Antibiotics (Basel) 2022; 11:antibiotics11030413. [PMID: 35326876 PMCID: PMC8944503 DOI: 10.3390/antibiotics11030413] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 03/07/2022] [Accepted: 03/16/2022] [Indexed: 12/11/2022] Open
Abstract
Antibiotic resistance is one of the greatest crises in human medicine. Increased incidents of antibiotic resistance are linked to clinical overuse and overreliance on antibiotics. Among the ESKAPE pathogens, Acinetobacter baumannii, especially carbapenem-resistant isolates, has emerged as a significant threat in the context of blood, urinary tract, lung, and wound infections. Therefore, new approaches that limit the emergence of antibiotic resistant A. baumannii are urgently needed. Recently, we have shown that random peptide mixtures (RPMs) are an attractive alternative class of drugs to antibiotics with strong safety and pharmacokinetic profiles. RPMs are antimicrobial peptide mixtures produced by incorporating two amino acids at each coupling step, rendering them extremely diverse but still defined in their overall composition, chain length, and stereochemistry. The extreme diversity of RPMs may prevent bacteria from evolving resistance rapidly. Here, we demonstrated that RPMs rapidly and efficiently kill different strains of A. baumannii, inhibit biofilm formation, and disrupt mature biofilms. Importantly, RPMs attenuated bacterial burden in mouse models of acute pneumonia and soft tissue infection and significantly reduced mouse mortality during sepsis. Collectively, our results demonstrate RPMs have the potential to be used as powerful therapeutics against antibiotic-resistant A. baumannii.
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Affiliation(s)
- Hannah E. Caraway
- Department of Pathobiology, University of Illinois at Urbana-Champaign, Urbana, IL 61802, USA; (H.E.C.); (J.Z.L.); (M.W.O.)
| | - Jonathan Z. Lau
- Department of Pathobiology, University of Illinois at Urbana-Champaign, Urbana, IL 61802, USA; (H.E.C.); (J.Z.L.); (M.W.O.)
| | - Bar Maron
- Institute of Biochemistry, Food Science and Nutrition, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel; (B.M.); (Y.B.); (A.B.); (E.M.)
| | - Myung Whan Oh
- Department of Pathobiology, University of Illinois at Urbana-Champaign, Urbana, IL 61802, USA; (H.E.C.); (J.Z.L.); (M.W.O.)
| | - Yael Belo
- Institute of Biochemistry, Food Science and Nutrition, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel; (B.M.); (Y.B.); (A.B.); (E.M.)
| | - Aya Brill
- Institute of Biochemistry, Food Science and Nutrition, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel; (B.M.); (Y.B.); (A.B.); (E.M.)
| | - Einav Malach
- Institute of Biochemistry, Food Science and Nutrition, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel; (B.M.); (Y.B.); (A.B.); (E.M.)
| | - Nahed Ismail
- Department of Pathology, College of Medicine, University of Illinois at Chicago, 840 South Wood Street, Chicago, IL 60612, USA;
| | - Zvi Hayouka
- Institute of Biochemistry, Food Science and Nutrition, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel; (B.M.); (Y.B.); (A.B.); (E.M.)
- Correspondence: (Z.H.); (G.W.L.)
| | - Gee W. Lau
- Department of Pathobiology, University of Illinois at Urbana-Champaign, Urbana, IL 61802, USA; (H.E.C.); (J.Z.L.); (M.W.O.)
- Correspondence: (Z.H.); (G.W.L.)
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Colonization of the Murine Oropharynx by Streptococcus pyogenes Is Governed by the Rgg2/3 Quorum Sensing System. Infect Immun 2020; 88:IAI.00464-20. [PMID: 32747598 DOI: 10.1128/iai.00464-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 07/27/2020] [Indexed: 12/12/2022] Open
Abstract
Streptococcus pyogenes is a human-restricted pathogen most often found in the human nasopharynx. Multiple bacterial factors are known to contribute to persistent colonization of this niche, and many are important in mucosal immunity and vaccine development. In this work, mice were infected intranasally with transcriptional regulator mutants of the Rgg2/3 quorum sensing (QS) system-a peptide-based signaling system conserved in sequenced isolates of S. pyogenes Deletion of the QS system's transcriptional activator (Δrgg2) dramatically diminished the percentage of colonized mice, while deletion of the transcriptional repressor (Δrgg3) increased the percentage of colonized mice compared to that of the wild type (WT). Stimulation of the QS system using synthetic pheromones prior to inoculation did not significantly increase the percentage of animals colonized, indicating that QS-dependent colonization is responsive to the intrinsic conditions within the host upper respiratory tract. Bacterial RNA extracted directly from oropharyngeal swabs and evaluated by quantitative reverse transcription-PCR (qRT-PCR) subsequently confirmed QS upregulation within 1 h of inoculation. In the nasal-associated lymphoid tissue (NALT), a muted inflammatory response to the Δrgg2 bacteria suggests that their rapid elimination failed to elicit the previously characterized response to intranasal inoculation of GAS. This work identifies a new transcriptional regulatory system governing the ability of S. pyogenes to colonize the nasopharynx and provides knowledge that could help lead to decolonization therapeutics.
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