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Kurushima J, Tomita H. Advances of genetic engineering in Streptococci and Enterococci. Microbiol Immunol 2022; 66:411-417. [PMID: 35703039 DOI: 10.1111/1348-0421.13015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 06/09/2022] [Accepted: 06/11/2022] [Indexed: 11/26/2022]
Abstract
In the post-genome era, reverse genetic engineering is an indispensable methodology for experimental molecular biology to provide a deeper understanding of the principal relationship between genomic features and biological phenotypes. Technically, genetic engineering is carried out through allele replacement of a target genomic locus with a designed nucleotide sequence, so called site-directed mutagenesis. To artificially manipulate allele replacement through homologous recombination, researchers have improved various methodologies that are optimized to the bacterial species of interest. Here, we review widely used genetic engineering technologies, particularly for streptococci and enterococci, and recent advances that enable more effective and flexible manipulation. The development of genetic engineering has been promoted by synthetic biology approaches based on basic biology knowledge of horizontal gene transfer systems, such as natural conjugative transfer, natural transformation, and the CRISPR/Cas system. Therefore, this review also describes basic insights into molecular biology that underlie improvements in genetic engineering technology. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Jun Kurushima
- Department of Bacteriology, Gunma University Graduate School of Medicine, 3-39-22, Showa-machi, Maebashi-shi, Gunma, 371-8511, Japan
| | - Haruyoshi Tomita
- Department of Bacteriology, Gunma University Graduate School of Medicine, 3-39-22, Showa-machi, Maebashi-shi, Gunma, 371-8511, Japan.,Laboratory of Bacterial Drug Resistance, Gunma University Graduate School of Medicine, 3-39-22, Showa-machi, Maebashi-shi, Gunma, 371-8511, Japan
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Pandey SD, Biswas I. Clp ATPases differentially affect natural competence development in Streptococcus mutans. Microbiologyopen 2022; 11:e1288. [PMID: 35765180 PMCID: PMC9108599 DOI: 10.1002/mbo3.1288] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 04/27/2022] [Indexed: 11/25/2022] Open
Abstract
In naturally competent bacteria, DNA transformation through horizontal gene transfer is an evolutionary mechanism to receive extracellular DNA. Bacteria need to maintain a state of competence to accept foreign DNA, and this is an energy-driven phenomenon that is tightly controlled. In Streptococcus, competence development is a complex process that is not fully understood. In this study, we used Streptococcus mutans, an oral bacterium, to determine how cell density affects competence development. We found that in S. mutans the transformation efficiency is maximum when the transforming DNA was added at low cell density and incubated for 2.5 h before selecting for transformants. We also found that S. mutans cells remain competent until the mid-logarithmic phase, after which the competence decreases drastically. Surprisingly, we observed that individual components of Clp proteolytic complexes differentially regulate competence. If the transformation is carried out at the early growth phase, both ClpP protease and ClpX ATPase are needed for competence. In contrast, we found that both ClpC and ClpE negatively affect competence. We also found that if the transformation is carried out at the mid-logarithmic growth phase ClpX is still required for competence, but ClpP negatively affects competence. While the exact reason for this differential effect of ClpP and ClpX on transformation is currently unknown, we found that both ClpC and ClpE have a negative effect on transformation, which was not reported before.
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Affiliation(s)
- Satya D. Pandey
- Department of MicrobiologyUniversity of Kansas Medical CenterKansas CityKansasUSA
| | - Indranil Biswas
- Department of MicrobiologyUniversity of Kansas Medical CenterKansas CityKansasUSA
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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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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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