Transcriptomic Stress Response in Streptococcus mutans following Treatment with a Sublethal Concentration of Chlorhexidine Digluconate
Abstract
:1. Introduction
2. Materials and Methods
2.1. Chlorhexidine Digluconate
2.2. Bacterial Culture and Treatment
2.3. RNA Extraction, Library Preparation and RNA Sequencing
2.4. RNA Sequencing Data Analysis
2.5. Primer Design and qRT-PCR
3. Results
3.1. Sublethal Concentration of CHX
3.2. RNA-Seq and Analysis of Differentially Expressed Genes
3.3. Pathway Enrichment Analysis with Differentially Expressed Genes
3.4. Validation of RNA-Seq Data Using qRT-PCR
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Target Gene | Sequence 5′-3′ (F = Forward; R = Reverse) | Product Size |
---|---|---|
gyrB | F: GCACAAGAGTACGATGCCAGT | 119 bp |
R: TCCCAAACAAGGTGATGCAGC | ||
D820_RS03005 | F: CGTGGTTATCAAGTATCGTGTGA | 148 bp |
R: AAAGAATTGGTCCTGCATCCA | ||
D820_RS09005 | F: CAGTAGGTGCCGCTCAAACT | 128 bp |
R: AAGTCCGCCGCCAAACATAT | ||
glgA | F: GTGCCTTGCCCAAATCCCTT | 145 bp |
R: ACATATTCACGACGCCAGCC | ||
ssrS | F: CGGAAGCAACTAAAGTCAGAGCG | 80 bp |
R: TGGCACCGATGATTCACGTT |
Gene ID | Gene Name | Product | Log2 FC | padj |
---|---|---|---|---|
D820_RS03005 | NA | PTS fructose transporter subunit IIB | −3.2 | 1.60 × 10−6 |
D820_RS01705 | NA | tRNA-Thr | −3.1 | 2.46 × 10−4 |
D820_RS03010 | NA | PTS mannitol/fructose, IIC component | −3.0 | 2.26 × 10−5 |
D820_RS03000 | NA | PTS mannitol transporter subunit IIB | −3.0 | 6.57 × 10−6 |
D820_RS02990 | lacC | Tagatose-6-phosphate kinase | −3.0 | 2.40 × 10−5 |
D820_RS02995 | lacD | Tagatose-bisphosphate aldolase | −2.9 | 6.31 × 10−6 |
D820_RS08540 | NA | tRNA-Ser | −2.8 | 6.90 × 10−3 |
D820_RS02980 | lacA | Galactose-6-phosphate isomerase | −2.7 | 1.24 × 10−4 |
D820_RS02985 | lacB | Galactose-6-phosphate isomerase | −2.7 | 1.43 × 10−4 |
D820_RS03015 | NA | Lactose-specific phosphotransferase enzyme IIA component | −2.6 | 2.85 × 10−8 |
D820_RS02805 | glgA | Glycogen synthase | 3.9 | 0.00 |
D820_RS04685 | NA | ABC transporter (ATP-binding protein) | 4.0 | 0.00 |
D820_RS06900 | NA | Hypothetical protein | 4.0 | 0.00 |
D820_RS01630 | NA | 16S ribosomal RNA | 4.1 | 2.44 × 10−7 |
D820_RS02745 | NA | ABC transporter (ATP-binding protein) | 4.1 | 0.00 |
D820_RS02750 | NA | ABC transporter permease | 4.2 | 0.00 |
D820_RS06905 | lrgB | Antiholin | 4.4 | 0.00 |
D820_RS07700 | pflB | Formate C-acetyltransferase | 4.5 | 0.00 |
D820_RS0109785 | NA | 23S ribosomal RNA | 5.0 | 1.79 × 10−6 |
D820_RS0109610 | NA | 23S ribosomal RNA | 6.5 | 5.73 × 10−6 |
Gene ID | Gene Name | Product | Log2 FC | padj |
---|---|---|---|---|
D820_RS06120 | ahpC | Peroxiredoxin | 1.1 | 1.50 × 10−6 |
D820_RS06115 | ahpF | Alkyl hydroperoxide reductase subunit F | 1.8 | 6.00 × 10−17 |
D820_RS06685 | sod | Superoxide dismutase | 1.6 | 1.71 × 10−6 |
D820_RS07435 | trxB | Thioredoxin disulfide reductase | 1.1 | 5.15 × 10−4 |
D820_RS05415 | tpx | 2-Cys-peroxiredoxine | 1.0 | 1.02 × 10−2 |
D820_RS07050 | NA | DNA protection protein | 1.9 | 2.41 × 10−12 |
D820_RS00990 | groES | Co-Chaperone GroES | 1.1 | 8.15 × 10−6 |
D820_RS00995 | groEL | Chaperone GroEL | 1.5 | 0.00 |
D820_RS05270 | NA | ATP-dependent Clp protease ATP-binding subunit | 1.1 | 1.04 × 10−7 |
D820_RS03310 | clpB | Clp proteinase ATP-binding subunit ClpB | 2.4 | 4.29 × 10−15 |
D820_RS06955 | NA | ATP-dependent Clp protease ATP-binding subunit | 1.4 | 3.43 × 10−10 |
D820_RS08310 | aguA | Agmatine deiminase | 1.3 | 1.27 × 10−14 |
D820_RS08960 | mleP | Malate permease | 3.7 | 0.00 |
Pathway | Genes Involved in Pathway (Ensemble IDs) | p-Value | |
---|---|---|---|
Upregulated | |||
Carboxylate degradation | D820_RS00885, D820_RS07700, D820_RS07305, D820_RS08215, D820_RS08265, D820_RS08275, D820_RS08270, D820_RS04975, D820_RS04980, D820_RS08965 | 5.00 × 10−5 | |
5-Aminoimidazole ribonucleotide biosynthesis | D820_RS09340, D820_RS09355, D820_RS09335, D820_RS09300, D820_RS09345 | 2.00 × 10−3 | |
Glycan pathway | D820_RS07040, D820_RS02810, D820_RS02685, D820_RS02800, D820_RS02795, D820_RS02790, D820_RS02805 | 3.00 × 10−3 | |
L-ascorbate degradation | D820_RS08215, D820_RS08265, D820_RS08275, D820_RS08270 | 6.00 × 10−3 | |
L-histidine biosynthesis | D820_RS03965, D820_RS03970, D820_RS03955, D820_RS03950, D820_RS03960, D820_RS03940, D820_RS03930 | 7.00 × 10−3 | |
Purine nucleotide biosynthesis | D820_RS04105, D820_RS04110, D820_RS04100, D820_RS09285, D820_RS09290, D820_RS09325, D820_RS09250, D820_RS08295, D820_RS09340, D820_RS09355, D820_RS09335, D820_RS09300, D820_RS09345 | 1.00 × 10−2 | |
Inosine-5’-phosphate biosynthesis | D820_RS09285, D820_RS09290, D820_RS09325, D820_RS09250 | 2.00 × 10−2 | |
Downregulated | |||
Lactose degradation | D820_RS02995, D820_RS02980, D820_RS02985, D820_RS03025, D820_RS02990 | 4.00 × 10−6 | |
Galactose degradation | D820_RS02995, D820_RS02980, D820_RS02985, D820_RS03025, D820_RS02990 | 4.00 × 10−6 | |
Protein modification | D820_RS05715, D820_RS02255, D820_RS08010 | 2.00 × 10−2 | |
L-phenylalanine biosynthesis | D820_RS03740, D820_RS07095 | 2.00 × 10−2 |
Gene | RNA-Seq | qRT-PCR |
---|---|---|
D820_RS03005 | −3.2 | −2.4 |
D820_RS09005 | 3.3 | 3.4 |
ssrS | 3.4 | 2.5 |
glgA | 3.9 | 4.0 |
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Muehler, D.; Mao, X.; Czemmel, S.; Geißert, J.; Engesser, C.; Hiller, K.-A.; Widbiller, M.; Maisch, T.; Buchalla, W.; Al-Ahmad, A.; et al. Transcriptomic Stress Response in Streptococcus mutans following Treatment with a Sublethal Concentration of Chlorhexidine Digluconate. Microorganisms 2022, 10, 561. https://doi.org/10.3390/microorganisms10030561
Muehler D, Mao X, Czemmel S, Geißert J, Engesser C, Hiller K-A, Widbiller M, Maisch T, Buchalla W, Al-Ahmad A, et al. Transcriptomic Stress Response in Streptococcus mutans following Treatment with a Sublethal Concentration of Chlorhexidine Digluconate. Microorganisms. 2022; 10(3):561. https://doi.org/10.3390/microorganisms10030561
Chicago/Turabian StyleMuehler, Denise, Xiaojun Mao, Stefan Czemmel, Janina Geißert, Christina Engesser, Karl-Anton Hiller, Matthias Widbiller, Tim Maisch, Wolfgang Buchalla, Ali Al-Ahmad, and et al. 2022. "Transcriptomic Stress Response in Streptococcus mutans following Treatment with a Sublethal Concentration of Chlorhexidine Digluconate" Microorganisms 10, no. 3: 561. https://doi.org/10.3390/microorganisms10030561