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Zhang Y, Zhang J, Xiao J, Wang H, Yang R, Guo X, Zheng Y, Yin Y, Zhang X. comCDE (Competence) Operon Is Regulated by CcpA in Streptococcus pneumoniae D39. Microbiol Spectr 2023; 11:e0001223. [PMID: 37036382 PMCID: PMC10269683 DOI: 10.1128/spectrum.00012-23] [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: 01/06/2023] [Accepted: 02/16/2023] [Indexed: 04/11/2023] Open
Abstract
Natural transformation plays an important role in the formation of drug-resistant bacteria. Exploring the regulatory mechanism of natural transformation can aid the discovery of new antibacterial targets and reduce the emergence of drug-resistant bacteria. Competence is a prerequisite of natural transformation in Streptococcus pneumoniae, in which comCDE operon is the core regulator of competence. To date, only ComE has been shown to directly regulate comCDE transcription. In this study, a transcriptional regulator, the catabolite control protein A (CcpA), was identified that directly regulated comCDE transcription. We confirmed that CcpA binds to the cis-acting catabolite response elements (cre) in the comCDE promoter region to regulate comCDE transcription and transformation. Moreover, CcpA can coregulate comCDE transcription with phosphorylated and dephosphorylated ComE. Regulation of comCDE transcription and transformation by CcpA was also affected by carbon source signals. Together, these insights demonstrate the versatility of CcpA and provide a theoretical basis for reducing the emergence of drug-resistant bacteria. IMPORTANCE Streptococcus pneumoniae is a major cause of bacterial infections in humans, such as pneumonia, bacteremia, meningitis, otitis media, and sinusitis. Like most streptococci, S. pneumoniae is naturally competent and employs this ability to augment its adaptive evolution. The current study illustrates CcpA, a carbon catabolite regulator, can participate in the competence process by regulating comCDE transcription, and this process is regulated by different carbon source signals. These hidden abilities are likely critical for adaptation and colonization in the environment.
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Affiliation(s)
- Yapeng Zhang
- Key Laboratory of Diagnostic Medicine Designated by the Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, China
| | | | - Jiangming Xiao
- Key Laboratory of Diagnostic Medicine Designated by the Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, China
| | - Hanyi Wang
- Key Laboratory of Diagnostic Medicine Designated by the Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, China
| | - Rui Yang
- Key Laboratory of Diagnostic Medicine Designated by the Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, China
| | - Xinlin Guo
- Department of Medicine Laboratory, Children’s Hospital of Chongqing Medical University, Chongqing, China
| | - Yuqiang Zheng
- Department of Medicine Laboratory, Children’s Hospital of Chongqing Medical University, Chongqing, China
| | - Yibing Yin
- Key Laboratory of Diagnostic Medicine Designated by the Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, China
| | - Xuemei Zhang
- Key Laboratory of Diagnostic Medicine Designated by the Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, China
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2
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Markerless Genome Editing in Competent Streptococci. Methods Mol Biol 2023; 2588:201-216. [PMID: 36418690 DOI: 10.1007/978-1-0716-2780-8_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Selective markers employed in classical mutagenesis methods using natural genetic transformation can affect gene expression, risk phenotypic effects, and accumulate as unwanted genes during successive mutagenesis cycles. In this chapter, we present a protocol for markerless genome editing in Streptococcus mutans and Streptococcus pneumoniae achieved with an efficient method for natural transformation. High yields of transformants are obtained by combining the unimodal state of competence developed after treatment of S. mutans with sigX-inducing peptide pheromone (XIP) in a chemically defined medium (CDM) or of S. pneumoniae with the competence-stimulating peptide (CSP) together with use of a donor amplicon carrying extensive flanking homology. This combination ensures efficient and precise integration of a new allele by the recombination machinery present in competent cells.
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3
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Solano-Collado V, Ruiz-Cruz S, Lorenzo-Díaz F, Pluta R, Espinosa M, Bravo A. Recognition of Streptococcal Promoters by the Pneumococcal SigA Protein. Front Mol Biosci 2021; 8:666504. [PMID: 34250014 PMCID: PMC8264293 DOI: 10.3389/fmolb.2021.666504] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 06/14/2021] [Indexed: 11/13/2022] Open
Abstract
Promoter recognition by RNA polymerase is a key step in the regulation of gene expression. The bacterial RNA polymerase core enzyme is a complex of five subunits that interacts transitory with one of a set of sigma factors forming the RNA polymerase holoenzyme. The sigma factor confers promoter specificity to the RNA polymerase. In the Gram-positive pathogenic bacterium Streptococcus pneumoniae, most promoters are likely recognized by SigA, a poorly studied housekeeping sigma factor. Here we present a sequence conservation analysis and show that SigA has similar protein architecture to Escherichia coli and Bacillus subtilis homologs, namely the poorly conserved N-terminal 100 residues and well-conserved rest of the protein (domains 2, 3, and 4). Further, we have purified the native (untagged) SigA protein encoded by the pneumococcal R6 strain and reconstituted an RNA polymerase holoenzyme composed of the E. coli core enzyme and the sigma factor SigA (RNAP-SigA). By in vitro transcription, we have found that RNAP-SigA was able to recognize particular promoters, not only from the pneumococcal chromosome but also from the S. agalactiae promiscuous antibiotic-resistance plasmid pMV158. Specifically, SigA was able to direct the RNA polymerase to transcribe genes involved in replication and conjugative mobilization of plasmid pMV158. Our results point to the versatility of SigA in promoter recognition and its contribution to the promiscuity of plasmid pMV158.
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Affiliation(s)
| | - Sofía Ruiz-Cruz
- School of Microbiology, University College Cork, Cork, Ireland
| | - Fabián Lorenzo-Díaz
- Departamento de Bioquímica, Microbiología, Biología Celular y Genética, Universidad de La Laguna, Tenerife, Spain
| | - Radoslaw Pluta
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Manuel Espinosa
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Alicia Bravo
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
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4
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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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5
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Inniss NL, Morrison DA. ComWΔ6 Stimulates Transcription of Pneumococcal Competence Genes in vitro. Front Mol Biosci 2020; 7:61. [PMID: 32435654 PMCID: PMC7218084 DOI: 10.3389/fmolb.2020.00061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 03/24/2020] [Indexed: 11/28/2022] Open
Abstract
The alternative streptococcal σ-factor and master competence regulator, σX, stimulates transcription from competence promoters, in vitro. As the only known alternative σ-factor in streptococci, σX expression is tightly controlled in each species and has a specific physiological role. Pneumococcal transformation also requires the DNA binding activity of ComW, a known σX activator and stabilizer. Mutations to the housekeeping σ factor, σA, partially alleviate the ComW requirement, suggesting that ComW is a key player in the σ factor swap during the pneumococcal competence response. However, there is no evidence of a direct ComW - RNA polymerase interaction. Furthermore, if and how ComW functions directly at combox promoters is still unknown. Here we report that a DNA-binding ComW variant, ComΔ6, can stimulate transcription from σX promoters in vitro.
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Affiliation(s)
| | - Donald A. Morrison
- Department of Biological Sciences, The University of Illinois at Chicago, Chicago, IL, United States
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6
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Inniss NL, Prehna G, Morrison DA. The pneumococcal σ X activator, ComW, is a DNA-binding protein critical for natural transformation. J Biol Chem 2019; 294:11101-11118. [PMID: 31160340 DOI: 10.1074/jbc.ra119.007571] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 05/19/2019] [Indexed: 11/06/2022] Open
Abstract
Natural genetic transformation via horizontal gene transfer enables rapid adaptation to dynamic environments and contributes to both antibiotic resistance and vaccine evasion among bacterial populations. In Streptococcus pneumoniae (pneumococcus), transformation occurs when cells enter competence, a transient state in which cells express the competence master regulator, SigX (σΧ), an alternative σ factor (σ), and a competence co-regulator, ComW. Together, ComW and σX facilitate expression of the genes required for DNA uptake and genetic recombination. SigX activity depends on ComW, as ΔcomW cells transcribe late genes and transform at levels 10- and 10,000-fold below that of WT cells, respectively. Previous findings suggest that ComW functions during assembly of the RNA polymerase-σX holoenzyme to help promote transcription from σX-targeted promoters. However, it remains unknown how ComW facilitates holoenzyme assembly. As ComW seems to be unique to Gram-positive cocci and has no sequence similarity with known transcriptional activators, here we used Rosetta to generate an ab initio model of pneumococcal ComW's 3D-structure. Using this model as a basis for further biochemical, biophysical, and genetic investigations into the molecular features important for its function, we report that ComW is a predicted globular protein and that it interacts with DNA, independently of DNA sequence. We also identified conserved motifs in ComW and show that key residues in these motifs contribute to DNA binding. Lastly, we provide evidence that ComW's DNA-binding activity is important for transformation in pneumococcus. Our findings begin to fill the gaps in understanding how ComW regulates σΧ activity during bacterial natural transformation.
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Affiliation(s)
- Nicole L Inniss
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois 60607
| | - Gerd Prehna
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Donald A Morrison
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois 60607
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7
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Salvadori G, Junges R, Morrison DA, Petersen FC. Competence in Streptococcus pneumoniae and Close Commensal Relatives: Mechanisms and Implications. Front Cell Infect Microbiol 2019; 9:94. [PMID: 31001492 PMCID: PMC6456647 DOI: 10.3389/fcimb.2019.00094] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 03/15/2019] [Indexed: 12/21/2022] Open
Abstract
The mitis group of streptococci comprises species that are common colonizers of the naso-oral-pharyngeal tract of humans. Streptococcus pneumoniae and Streptococcus mitis are close relatives and share ~60–80% of orthologous genes, but still present striking differences in pathogenic potential toward the human host. S. mitis has long been recognized as a reservoir of antibiotic resistance genes for S. pneumoniae, as well as a source for capsule polysaccharide variation, leading to resistance and vaccine escape. Both species share the ability to become naturally competent, and in this context, competence-associated killing mechanisms such as fratricide are thought to play an important role in interspecies gene exchange. Here, we explore the general mechanism of natural genetic transformation in the two species and touch upon the fundamental clinical and evolutionary implications of sharing similar competence, fratricide mechanisms, and a large fraction of their genomic DNA.
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Affiliation(s)
- Gabriela Salvadori
- Faculty of Dentistry, Institute of Oral Biology, University of Oslo, Oslo, Norway
| | - Roger Junges
- Faculty of Dentistry, Institute of Oral Biology, University of Oslo, Oslo, Norway
| | - Donald A Morrison
- Department of Biological Sciences, College of Liberal Arts and Sciences, University of Illinois at Chicago, Chicago, IL, United States
| | - Fernanda C Petersen
- Faculty of Dentistry, Institute of Oral Biology, University of Oslo, Oslo, Norway
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8
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Function of BriC peptide in the pneumococcal competence and virulence portfolio. PLoS Pathog 2018; 14:e1007328. [PMID: 30308062 PMCID: PMC6181422 DOI: 10.1371/journal.ppat.1007328] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 09/10/2018] [Indexed: 02/07/2023] Open
Abstract
Streptococcus pneumoniae (pneumococcus) is an opportunistic pathogen that causes otitis media, sinusitis, pneumonia, meningitis and sepsis. The progression to this pathogenic lifestyle is preceded by asymptomatic colonization of the nasopharynx. This colonization is associated with biofilm formation; the competence pathway influences the structure and stability of biofilms. However, the molecules that link the competence pathway to biofilm formation are unknown. Here, we describe a new competence-induced gene, called briC, and demonstrate that its product promotes biofilm development and stimulates colonization in a murine model. We show that expression of briC is induced by the master regulator of competence, ComE. Whereas briC does not substantially influence early biofilm development on abiotic surfaces, it significantly impacts later stages of biofilm development. Specifically, briC expression leads to increases in biofilm biomass and thickness at 72h. Consistent with the role of biofilms in colonization, briC promotes nasopharyngeal colonization in the murine model. The function of BriC appears to be conserved across pneumococci, as comparative genomics reveal that briC is widespread across isolates. Surprisingly, many isolates, including strains from clinically important PMEN1 and PMEN14 lineages, which are widely associated with colonization, encode a long briC promoter. This long form captures an instance of genomic plasticity and functions as a competence-independent expression enhancer that may serve as a precocious point of entry into this otherwise competence-regulated pathway. Moreover, overexpression of briC by the long promoter fully rescues the comE-deletion induced biofilm defect in vitro, and partially in vivo. These findings indicate that BriC may bypass the influence of competence in biofilm development and that such a pathway may be active in a subset of pneumococcal lineages. In conclusion, BriC is a part of the complex molecular network that connects signaling of the competence pathway to biofilm development and colonization. Pneumococcal biofilms occur in chronic otitis media, chronic rhinosinusitis, and nasopharyngeal colonization. These biofilms are an important component of pneumococcal epidemiology, particularly in influencing transmission, maintenance of asymptomatic colonization, and development of disease. The transcriptional program initiated via signaling of the competence pathway is critical for productive biofilm formation and is a strong contributor of pneumococcal infection and adaptation. In this study, we have identified BriC, a previously uncharacterized peptide that serves as a bridge between the competence pathway and biofilm development. We show that briC is induced by ComE, the master regulator of competence, and promotes biofilm development. Moreover, our studies in the murine model demonstrate that BriC is a novel colonization enhancer. Our studies of briC regulation capture an instance of genomic plasticity, where natural variation in the briC promoter sequence reveals the existence of an additional competence-independent regulatory unit. This natural variation may be able to modify the extent to which competence contributes to biofilm development and to nasopharyngeal colonization across different pneumococcal lineages. In summary, this study introduces a colonization factor and reveals a molecular link between competence and biofilm development.
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9
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Obszańska K, Kern-Zdanowicz I, Sitkiewicz I. Efficient construction of Streptococcus anginosus mutants in strains of clinical origin. J Appl Genet 2018; 59:515-523. [PMID: 30259345 DOI: 10.1007/s13353-018-0468-z] [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: 06/26/2018] [Revised: 08/28/2018] [Accepted: 09/13/2018] [Indexed: 10/28/2022]
Abstract
Streptococcus anginosus group (SAG) is Gram-positive bacteria responsible for a number of purulent human infections such as brain and liver abscesses, which have been on the rise for last few decades. Although some virulence factors of SAG are described, they are mostly undefined and there are almost no methods for genetic manipulations of clinical SAG. Therefore, we presented various approaches to produce engineered strains of this poorly known group of streptococci. We developed a procedure of transformation characterized by transformation efficiency at the level of 104 per 1 μg DNA for certain strains. Moreover, mutagenesis for many SAG strain is possible based on the process of natural transformation. However, the usefulness of methods and their effectiveness are strain dependent.
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Affiliation(s)
- Katarzyna Obszańska
- Department of Microbial Biochemistry, Institute of Biochemistry and Biophysics PAS, Warsaw, Poland
| | - Izabella Kern-Zdanowicz
- Department of Microbial Biochemistry, Institute of Biochemistry and Biophysics PAS, Warsaw, Poland
| | - Izabela Sitkiewicz
- Department of Drug Biotechnology and Bioinformatics, National Medicines Institute, Chełmska 30/34, 00-725, Warsaw, Poland.
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10
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Streptococcus pneumoniae two-component regulatory systems: The interplay of the pneumococcus with its environment. Int J Med Microbiol 2018; 308:722-737. [DOI: 10.1016/j.ijmm.2017.11.012] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 11/21/2017] [Accepted: 11/24/2017] [Indexed: 02/06/2023] Open
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11
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Weyder M, Prudhomme M, Bergé M, Polard P, Fichant G. Dynamic Modeling of Streptococcus pneumoniae Competence Provides Regulatory Mechanistic Insights Into Its Tight Temporal Regulation. Front Microbiol 2018; 9:1637. [PMID: 30087661 PMCID: PMC6066662 DOI: 10.3389/fmicb.2018.01637] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 06/30/2018] [Indexed: 12/31/2022] Open
Abstract
In the human pathogen Streptococcus pneumoniae, the gene regulatory circuit leading to the transient state of competence for natural transformation is based on production of an auto-inducer that activates a positive feedback loop. About 100 genes are activated in two successive waves linked by a central alternative sigma factor ComX. This mechanism appears to be fundamental to the biological fitness of S. pneumoniae. We have developed a knowledge-based model of the competence cycle that describes average cell behavior. It reveals that the expression rates of the two competence operons, comAB and comCDE, involved in the positive feedback loop must be coordinated to elicit spontaneous competence. Simulations revealed the requirement for an unknown late com gene product that shuts of competence by impairing ComX activity. Further simulations led to the predictions that the membrane protein ComD bound to CSP reacts directly to pH change of the medium and that blindness to CSP during the post-competence phase is controlled by late DprA protein. Both predictions were confirmed experimentally.
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Affiliation(s)
| | - Marc Prudhomme
- Laboratoire de Microbiologie et Génétique Moléculaires, Centre de Biologie Intégrative, Université de Toulouse, CNRS, Université Toulouse III Paul Sabatier, Toulouse, France
| | | | | | - Gwennaele Fichant
- Laboratoire de Microbiologie et Génétique Moléculaires, Centre de Biologie Intégrative, Université de Toulouse, CNRS, Université Toulouse III Paul Sabatier, Toulouse, France
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12
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Kinetics of drug-ribosome interactions defines the cidality of macrolide antibiotics. Proc Natl Acad Sci U S A 2017; 114:13673-13678. [PMID: 29229833 DOI: 10.1073/pnas.1717168115] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Antibiotics can cause dormancy (bacteriostasis) or induce death (cidality) of the targeted bacteria. The bactericidal capacity is one of the most important properties of antibacterial agents. However, the understanding of the fundamental differences in the mode of action of bacteriostatic or bactericidal antibiotics, especially those belonging to the same chemical class, is very rudimentary. Here, by examining the activity and binding properties of chemically distinct macrolide inhibitors of translation, we have identified a key difference in their interaction with the ribosome, which correlates with their ability to cause cell death. While bacteriostatic and bactericidal macrolides bind in the nascent peptide exit tunnel of the large ribosomal subunit with comparable affinities, the bactericidal antibiotics dissociate from the ribosome with significantly slower rates. The sluggish dissociation of bactericidal macrolides correlates with the presence in their structure of an extended alkyl-aryl side chain, which establishes idiosyncratic interactions with the ribosomal RNA. Mutations or chemical alterations of the rRNA nucleotides in the drug binding site can protect cells from macrolide-induced killing, even with inhibitor concentrations that significantly exceed those required for cell growth arrest. We propose that the increased translation downtime due to slow dissociation of the antibiotic may damage cells beyond the point where growth can be reinitiated upon the removal of the drug due to depletion of critical components of the gene-expression pathway.
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13
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Quorum Sensing Regulation of Competence and Bacteriocins in Streptococcus pneumoniae and mutans. Genes (Basel) 2017; 8:genes8010015. [PMID: 28067778 PMCID: PMC5295010 DOI: 10.3390/genes8010015] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 12/25/2016] [Accepted: 12/27/2016] [Indexed: 11/17/2022] Open
Abstract
The human pathogens Streptococcus pneumoniae and Streptococcus mutans have both evolved complex quorum sensing (QS) systems that regulate the production of bacteriocins and the entry into the competent state, a requirement for natural transformation. Natural transformation provides bacteria with a mechanism to repair damaged genes or as a source of new advantageous traits. In S. pneumoniae, the competence pathway is controlled by the two-component signal transduction pathway ComCDE, which directly regulates SigX, the alternative sigma factor required for the initiation into competence. Over the past two decades, effectors of cellular killing (i.e., fratricides) have been recognized as important targets of the pneumococcal competence QS pathway. Recently, direct interactions between the ComCDE and the paralogous BlpRH pathway, regulating bacteriocin production, were identified, further strengthening the interconnections between these two QS systems. Interestingly, a similar theme is being revealed in S. mutans, the primary etiological agent of dental caries. This review compares the relationship between the bacteriocin and the competence QS pathways in both S. pneumoniae and S. mutans, and hopes to provide clues to regulatory pathways across the genus Streptococcus as a potential tool to efficiently investigate putative competence pathways in nontransformable streptococci.
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14
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Junges R, Khan R, Tovpeko Y, Åmdal HA, Petersen FC, Morrison DA. Markerless Genome Editing in Competent Streptococci. Methods Mol Biol 2017; 1537:233-247. [PMID: 27924598 DOI: 10.1007/978-1-4939-6685-1_14] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Selective markers employed in classical mutagenesis methods using natural genetic transformation can affect gene expression, risk phenotypic effects, and accumulate as unwanted genes during successive mutagenesis cycles. In this chapter, we present a protocol for markerless genome editing in Streptococcus mutans and Streptococcus pneumoniae achieved with an efficient method for natural transformation. High yields of transformants are obtained by combining the unimodal state of competence developed after treatment of S. mutans with sigX-inducing peptide pheromone (XIP) in a chemically defined medium (CDM) or of S. pneumoniae with the competence-stimulating peptide (CSP) together with use of a donor amplicon carrying extensive flanking homology. This combination ensures efficient and precise integration of a new allele by the recombination machinery present in competent cells.
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Affiliation(s)
- Roger Junges
- Department of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - Rabia Khan
- Department of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - Yanina Tovpeko
- Department of Biological Sciences, College of Liberal Arts and Sciences, University of Illinois at Chicago, 845 West Taylor Street, (MC 066), Chicago, IL, 60607, USA
| | - Heidi A Åmdal
- Department of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - Fernanda C Petersen
- Department of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - Donald A Morrison
- Department of Biological Sciences, College of Liberal Arts and Sciences, University of Illinois at Chicago, 845 West Taylor Street, (MC 066), Chicago, IL, 60607, USA.
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15
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Competence for Genetic Transformation in Streptococcus pneumoniae: Mutations in σA Bypass the ComW Requirement for Late Gene Expression. J Bacteriol 2016; 198:2370-8. [PMID: 27353650 DOI: 10.1128/jb.00354-16] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 06/20/2016] [Indexed: 01/23/2023] Open
Abstract
UNLABELLED Streptococcus pneumoniae is able to integrate exogenous DNA into its genome by natural genetic transformation. Transient accumulation of high levels of the only S. pneumoniae alternative σ factor is insufficient for development of full competence without expression of a second competence-specific protein, ComW. The ΔcomW mutant is 10(4)-fold deficient in the yield of recombinants, 10-fold deficient in the amount of σ(X) activity, and 10-fold deficient in the amount of σ(X) protein. The critical role of ComW during transformation can be partially obviated by σ(A) mutations clustered on surfaces controlling affinity for core RNA polymerase (RNAP). While strains harboring σ(A) mutations in the comW mutant background were transforming at higher rates, the mechanism of transformation restoration was not clear. To investigate the mechanism of transformation restoration, we measured late gene expression in σ(A)* suppressor strains. Restoration of late gene expression was observed in ΔcomW σ(A)* mutants, indicating that a consequence of the σ(A)* mutations is, at least, to restore σ(X) activity. Competence kinetics were normal in ΔcomW σ(A)* strains, indicating that strains with restored competence exhibit the same pattern of transience as wild-type (WT) strains. We also identified a direct interaction between ComW and σ(X) using the yeast two-hybrid (Y2H) assay. Taken together, these data are consistent with the idea that ComW increases σ(X) access to core RNAP, pointing to a direct role of ComW in σ factor exchange during genetic transformation. However, the lack of late gene shutoff in ΔcomW mutants also points to a potential new role for ComW in competence shutoff. IMPORTANCE The sole alternative sigma factor of the streptococci, SigX, regulates development of competence for genetic transformation, a widespread mechanism of adaptation by horizontal gene transfer in this genus. The transient appearance of this sigma factor is strictly controlled at the levels of transcription and stability. This report shows that it is also controlled at the point of its substitution for SigA by a second transient competence-specific protein, ComW.
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Genome editing by natural genetic transformation in Streptococcus mutans. J Microbiol Methods 2015; 119:134-41. [PMID: 26481669 DOI: 10.1016/j.mimet.2015.09.023] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Revised: 09/21/2015] [Accepted: 09/21/2015] [Indexed: 11/20/2022]
Abstract
Classical mutagenesis strategies using selective markers linked to designed mutations are powerful and widely applicable tools for targeted mutagenesis via natural genetic transformation in bacteria and archaea. However, the markers that confer power are also potentially problematic as they can be cumbersome, risk phenotypic effects of the inserted genes, and accumulate as unwanted genes during successive mutagenesis cycles. Alternative mutagenesis strategies use temporary plasmid or cassette insertions and can in principle achieve equally flexible mutation designs, but design of suitable counter-selected markers can be complex. All these drawbacks are eased by use of direct genome editing. Here we describe a strategy for directly editing the genome of S. mutans, which is applied to the widely studied reference strain UA159 (ATCC 700610) and has the advantage of extreme simplicity, requiring construction of only one synthetic donor amplicon and a single transformation step, followed by a simple PCR screen among a few dozen clones to identify the desired mutant. The donor amplicon carries the mutant sequence and extensive flanking segments of homology, which ensure efficient and precise integration by the recombination machinery specific to competent cells. The recipients are highly competent cells, in a state achieved by treatment with a synthetic competence pheromone.
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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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