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Drummond IY, DePaolo A, Krieger M, Driscoll H, Eckstrom K, Spatafora GA. Small regulatory RNAs are mediators of the Streptococcus mutans SloR regulon. J Bacteriol 2023; 205:e0017223. [PMID: 37695854 PMCID: PMC10521355 DOI: 10.1128/jb.00172-23] [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: 05/31/2023] [Accepted: 08/08/2023] [Indexed: 09/13/2023] Open
Abstract
Dental caries is among the most prevalent chronic diseases worldwide. Streptococcus mutans, the chief causative agent of caries, uses a 25-kDa manganese-dependent SloR protein to coordinate the uptake of essential manganese with the transcription of its virulence attributes. Small non-coding RNAs (sRNAs) can either enhance or repress gene expression, and reports in the literature ascribe an emerging role for sRNAs in the environmental stress response. Herein, we focused our attention on 18-50 nt sRNAs as mediators of the S. mutans SloR and manganese regulons. Specifically, the results of RNA sequencing revealed 19 sRNAs in S. mutans, which were differentially transcribed in the SloR-proficient UA159 and SloR-deficient GMS584 strains, and 10 sRNAs that were differentially expressed in UA159 cells grown in the presence of low vs high manganese. We describe SmsR1532 and SmsR1785 as SloR- and manganese-responsive sRNAs that are processed from large transcripts and that bind SloR directly in their promoter regions. The predicted targets of these sRNAs include regulators of metal ion transport, growth management via a toxin-antitoxin operon, and oxidative stress tolerance. These findings support a role for sRNAs in coordinating intracellular metal ion homeostasis with virulence gene control in an important oral cariogen. IMPORTANCE Small regulatory RNAs (sRNAs) are critical mediators of environmental signaling, particularly in bacterial cells under stress, but their role in Streptococcus mutans is poorly understood. S. mutans, the principal causative agent of dental caries, uses a 25-kDa manganese-dependent protein, called SloR, to coordinate the regulated uptake of essential metal ions with the transcription of its virulence genes. In the present study, we identified and characterized sRNAs that are both SloR and manganese responsive. Taken together, this research can elucidate the details of regulatory networks that engage sRNAs in an important oral pathogen and that can enable the development of an effective anti-caries therapeutic.
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Affiliation(s)
| | | | - Madeline Krieger
- Department of Restorative Dentistry, School of Dentistry, Oregon Health and Science University, Portland, Oregon, USA
| | - Heather Driscoll
- Department of Biology, Vermont Biomedical Research Network, Norwich University, Northfield, Vermont, USA
| | - Korin Eckstrom
- Department of Microbiology and Molecular Genetics, The Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, Vermont, USA
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Drummond IY, DePaolo A, Krieger M, Driscoll H, Eckstrom K, Spatafora GA. Small regulatory RNAs are mediators of the Streptococcus mutans SloR regulon. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.02.543485. [PMID: 37398324 PMCID: PMC10312646 DOI: 10.1101/2023.06.02.543485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Dental caries is among the most prevalent chronic infectious diseases worldwide. Streptococcus mutans , the chief causative agent of caries, uses a 25 kDa manganese dependent SloR protein to coordinate the uptake of essential manganese with the transcription of its virulence attributes. Small non-coding RNAs (sRNAs) can either enhance or repress gene expression and reports in the literature ascribe an emerging role for sRNAs in the environmental stress response. Herein, we identify 18-50 nt sRNAs as mediators of the S. mutans SloR and manganese regulons. Specifically, the results of sRNA-seq revealed 56 sRNAs in S. mutans that were differentially transcribed in the SloR-proficient UA159 and SloR-deficient GMS584 strains, and 109 sRNAs that were differentially expressed in UA159 cells grown in the presence of low versus high manganese. We describe SmsR1532 and SmsR1785 as SloR- and/or manganese-responsive sRNAs that are processed from large transcripts, and that bind SloR directly in their promoter regions. The predicted targets of these sRNAs include regulators of metal ion transport, growth management via a toxin-antitoxin operon, and oxidative stress tolerance. These findings support a role for sRNAs in coordinating intracellular metal ion homeostasis with virulence gene control in an important oral cariogen. IMPORTANCE Small regulatory RNAs (sRNAs) are critical mediators of environmental signaling, particularly in bacterial cells under stress, but their role in Streptococcus mutans is poorly understood. S. mutans, the principal causative agent of dental caries, uses a 25 kDa manganese-dependent protein, called SloR, to coordinate the regulated uptake of essential metal ions with the transcription of its virulence genes. In the present study, we identified and characterize sRNAs that are both SloR- and manganese-responsive. Taken together, this research can elucidate the details of regulatory networks that engage sRNAs in an important oral pathogen, and that can enable the development of an effective anti-caries therapeutic.
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Okamoto K, Kudo D, Phuong DND, Iwamoto Y, Watanabe K, Yoshioka Y, Ariyoshi W, Yamasaki R. Magnesium Hydroxide Nanoparticles Inhibit the Biofilm Formation of Cariogenic Microorganisms. NANOMATERIALS (BASEL, SWITZERLAND) 2023; 13:nano13050864. [PMID: 36903742 PMCID: PMC10005196 DOI: 10.3390/nano13050864] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 02/24/2023] [Accepted: 02/24/2023] [Indexed: 06/01/2023]
Abstract
Although various caries-preventive agents have been developed, dental caries is still a leading global disease, mostly caused by biological factors such as mutans streptococci. Magnesium hydroxide nanoparticles have been reported to exhibit antibacterial effects; however, they are rarely used in oral care practical applications. In this study, we examined the inhibitory effect of magnesium hydroxide nanoparticles on biofilm formation by Streptococcus mutans and Streptococcus sobrinus-two typical caries-causing bacteria. Three different sizes of magnesium hydroxide nanoparticles (NM80, NM300, and NM700) were studied, all of which inhibited biofilm formation. The results showed that the nanoparticles were important for the inhibitory effect, which was not influenced by pH or the presence of magnesium ions. We also determined that the inhibition process was mainly contact inhibition and that medium (NM300) and large (NM700) sizes were particularly effective in this regard. The findings of our study demonstrate the potential applications of magnesium hydroxide nanoparticles as caries-preventive agents.
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Affiliation(s)
- Kentaro Okamoto
- Division of Infections and Molecular Biology, Department of Health Promotion, Kyushu Dental University, Kitakyushu, Fukuoka 803-8580, Japan
- Division of Developmental Stomatognathic Function Science, Department of Health Promotion, Kyushu Dental University, Kitakyushu, Fukuoka 803-8580, Japan
| | - Daisuke Kudo
- SETOLAS Holdings Inc., Hayashida-cho, Sakaide, Kagawa 762-0012, Japan
| | | | - Yoshihito Iwamoto
- SETOLAS Holdings Inc., Hayashida-cho, Sakaide, Kagawa 762-0012, Japan
| | - Koji Watanabe
- Division of Developmental Stomatognathic Function Science, Department of Health Promotion, Kyushu Dental University, Kitakyushu, Fukuoka 803-8580, Japan
| | - Yoshie Yoshioka
- Division of Infections and Molecular Biology, Department of Health Promotion, Kyushu Dental University, Kitakyushu, Fukuoka 803-8580, Japan
| | - Wataru Ariyoshi
- Division of Infections and Molecular Biology, Department of Health Promotion, Kyushu Dental University, Kitakyushu, Fukuoka 803-8580, Japan
| | - Ryota Yamasaki
- Division of Infections and Molecular Biology, Department of Health Promotion, Kyushu Dental University, Kitakyushu, Fukuoka 803-8580, Japan
- Collaborative Research Centre for Green Materials on Environmental Technology, Kyushu Institute of Technology, 1-1 Sensui-chou, Tobata-ku, Kitakyushu, Fukuoka 804-8550, Japan
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Okamoto M, Naito M, Miyanohara M, Imai S, Nomura Y, Saito W, Momoi Y, Takada K, Miyabe-Nishiwaki T, Tomonaga M, Hanada N. Complete genome sequence of Streptococcus troglodytae TKU31 isolated from the oral cavity of a chimpanzee (Pan troglodytes). Microbiol Immunol 2017; 60:811-816. [PMID: 27921343 DOI: 10.1111/1348-0421.12453] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 11/21/2016] [Accepted: 11/24/2016] [Indexed: 11/27/2022]
Abstract
Streptococcus troglodytae TKU31 was isolated from the oral cavity of a chimpanzee (Pan troglodytes) and was found to be the most closely related species of the mutans group streptococci to Streptococcus mutans. The complete sequence of TKU31 genome consists of a single circular chromosome that is 2,097,874 base pairs long and has a G + C content of 37.18%. It possesses 2082 coding sequences (CDSs), 65 tRNAs and five rRNA operons (15 rRNAs). Two clustered regularly interspaced short palindromic repeats, six insertion sequences and two predicted prophage elements were identified. The genome of TKU31 harbors some putative virulence associated genes, including gtfB, gtfC and gtfD genes encoding glucosyltransferase and gbpA, gbpB, gbpC and gbpD genes encoding glucan-binding cell wall-anchored protein. The deduced amino acid identity of the rhamnose-glucose polysaccharide F gene (rgpF), which is one of the serotype determinants, is 91% identical with that of S. mutans LJ23 (serotype k) strain. However, two other virulence-associated genes cnm and cbm, which encode the collagen-binding proteins, were not found in the TKU31 genome. The complete genome sequence of S. troglodytae TKU31 has been deposited at DDBJ/European Nucleotide Archive/GenBank under the accession no. AP014612.
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Affiliation(s)
- Masaaki Okamoto
- Department of Translational Research, Tsurumi University School of Dental Medicine
| | - Mariko Naito
- Division of Microbiology and Oral Infection, Department of Molecular Microbiology and Immunology, Nagasaki University Graduate School of Biomedical Sciences, 1-7-1 Sakamoto, Nagasaki 852-8588
| | - Mayu Miyanohara
- Department of Translational Research, Tsurumi University School of Dental Medicine
| | - Susumu Imai
- Department of Translational Research, Tsurumi University School of Dental Medicine
| | - Yoshiaki Nomura
- Department of Translational Research, Tsurumi University School of Dental Medicine
| | - Wataru Saito
- Department of Operative Dentistry, 2-1-3, Tsurumi, Tsurumi-ku, Yokohama 230-8501
| | - Yasuko Momoi
- Department of Operative Dentistry, 2-1-3, Tsurumi, Tsurumi-ku, Yokohama 230-8501
| | - Kazuko Takada
- Department of Oral Microbiology, Nihon University School of Dentistry at Matsudo, 2-870-1 Sakaecho-Nishi, Matsudo, Chiba, 271-8587
| | | | - Masaki Tomonaga
- Language and Intelligence Section, Primate Research Institute, Kyoto University, Inuyama, Aichi 484-8506, Japan
| | - Nobuhiro Hanada
- Department of Translational Research, Tsurumi University School of Dental Medicine
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Highly Variable Streptococcus oralis Strains Are Common among Viridans Streptococci Isolated from Primates. mSphere 2016; 1:mSphere00041-15. [PMID: 27303717 PMCID: PMC4863584 DOI: 10.1128/msphere.00041-15] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 02/06/2016] [Indexed: 12/11/2022] Open
Abstract
Streptococcus pneumoniae is a rare example of a human-pathogenic bacterium among viridans streptococci, which consist of commensal symbionts, such as the close relatives Streptococcus mitis and S. oralis. We have shown that S. oralis can frequently be isolated from primates and a variety of other viridans streptococci as well. Genes and genomic islands which are known pneumococcal virulence factors are present in S. oralis and S. mitis, documenting the widespread occurrence of these compounds, which encode surface and secreted proteins. The frequent occurrence of CRISP-Cas gene clusters and a surprising variation of a set of small noncoding RNAs are factors to be considered in future research to further our understanding of mechanisms involved in the genomic diversity driven by horizontal gene transfer among viridans streptococci. Viridans streptococci were obtained from primates (great apes, rhesus monkeys, and ring-tailed lemurs) held in captivity, as well as from free-living animals (chimpanzees and lemurs) for whom contact with humans is highly restricted. Isolates represented a variety of viridans streptococci, including unknown species. Streptococcus oralis was frequently isolated from samples from great apes. Genotypic methods revealed that most of the strains clustered on separate lineages outside the main cluster of human S. oralis strains. This suggests that S. oralis is part of the commensal flora in higher primates and evolved prior to humans. Many genes described as virulence factors in Streptococcus pneumoniae were present also in other viridans streptococcal genomes. Unlike in S. pneumoniae, clustered regularly interspaced short palindromic repeat (CRISPR)–CRISPR-associated protein (Cas) gene clusters were common among viridans streptococci, and many S. oralis strains were type PI-2 (pilus islet 2) variants. S. oralis displayed a remarkable diversity of genes involved in the biosynthesis of peptidoglycan (penicillin-binding proteins and MurMN) and choline-containing teichoic acid. The small noncoding cia-dependent small RNAs (csRNAs) controlled by the response regulator CiaR might contribute to the genomic diversity, since we observed novel genomic islands between duplicated csRNAs, variably present in some isolates. All S. oralis genomes contained a β-N-acetyl-hexosaminidase gene absent in S. pneumoniae, which in contrast frequently harbors the neuraminidases NanB/C, which are absent in S. oralis. The identification of S. oralis-specific genes will help us to understand their adaptation to diverse habitats. IMPORTANCEStreptococcus pneumoniae is a rare example of a human-pathogenic bacterium among viridans streptococci, which consist of commensal symbionts, such as the close relatives Streptococcus mitis and S. oralis. We have shown that S. oralis can frequently be isolated from primates and a variety of other viridans streptococci as well. Genes and genomic islands which are known pneumococcal virulence factors are present in S. oralis and S. mitis, documenting the widespread occurrence of these compounds, which encode surface and secreted proteins. The frequent occurrence of CRISP-Cas gene clusters and a surprising variation of a set of small noncoding RNAs are factors to be considered in future research to further our understanding of mechanisms involved in the genomic diversity driven by horizontal gene transfer among viridans streptococci.
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Okamoto M, Imai S, Miyanohara M, Saito W, Momoi Y, Nomura Y, Ikawa T, Ogawa T, Miyabe-Nishiwaki T, Kaneko A, Watanabe A, Watanabe S, Hayashi M, Tomonaga M, Hanada N. Streptococcus panodentissp. nov. from the oral cavities of chimpanzees. Microbiol Immunol 2015; 59:526-32. [DOI: 10.1111/1348-0421.12290] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Revised: 07/15/2015] [Accepted: 07/29/2015] [Indexed: 11/28/2022]
Affiliation(s)
| | | | | | | | | | | | - Tomoko Ikawa
- Department of Fixed Prosthodontics; Tsurumi University School of Dental Medicine, 2-1-3, Tsurumi; Tsurumi-ku Yokohama 230-8501
| | - Takumi Ogawa
- Department of Fixed Prosthodontics; Tsurumi University School of Dental Medicine, 2-1-3, Tsurumi; Tsurumi-ku Yokohama 230-8501
| | | | | | | | | | - Misato Hayashi
- Language and Intelligence Section; Primate Research Institute, Kyoto University; Inuyama Aichi 484-8506, Japan
| | - Masaki Tomonaga
- Language and Intelligence Section; Primate Research Institute, Kyoto University; Inuyama Aichi 484-8506, Japan
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