Investigating Extracellular DNA Release in Staphylococcus xylosus Biofilm In Vitro
Abstract
:1. Introduction
2. Materials and Methods
2.1. Bacterial Strain and Biofilm Formation
2.2. Confocal Laser Scanning Microscopy Analyses of the Biofilms
2.3. Phage Induction and Transmission Electron Microscopy
2.4. RNA Extraction, Labeling and Microarray Analyses
3. Results and Discussion
3.1. Evidence of Extracellular DNA by CLSM Analyses
3.2. Cell Lysis
3.3. Slow Cellular Process in the Mature Biofilm
3.4. DNA/RNA, Protein Repair Systems
3.5. Pyrimidine and Purine Salvage
3.6. Amino Sugar Catabolism
3.7. Amino Acid Synthesis
3.8. Cofactor, Vitamin Synthesis
3.9. Inorganic Ion Transport
3.10. Response to Stress
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Mean Ratio of Expression | ||||
---|---|---|---|---|
Gene ID | Gene Name | Description | 24 h/9 h | 48 h/9 h |
CELL LYSIS | ||||
SXYL_01051 | Phage integrase | 7.2 | 17.9 | |
SXYL_01054-66 | Phage proteins | 5.7 * | 12.4 * | |
SXYL_01727-84 | Phage proteins | 3.8 * | 3.1 * | |
SXYL_00365-66 | cidAB | Holin-like protein CidA and CidB | 2.7 * | 13.5 * |
SXYL_00367 | cidC | Pyruvate oxidase | 9.2 | |
SXYL_00431 | budA | Alpha-acetolactate decarboxylase | 8.3 | 4.9 |
SXYL_00873-74 | ilvNB | Acetolactate synthase | 2.1 * | |
INFORMATION STORAGE, PROCESSING, CELLULAR PROCESSES | ||||
Replication, recombination | ||||
SXYL_01294 | dnaG | DNA primase | 2.2 | 2.1 |
SXYL_00005-06 | gyrBA | DNA gyrase subunits B,A | 2.1 * | |
Transcription | ||||
SXYL_00212 | Transcriptional regulator | 2.1 | 2.6 | |
SXYL_00418 | marR | MarR-family transcriptional regulator | 4.1 | 4.5 |
SXYL_00690 | MarR family transcriptional regulator | 3.2 | 5.1 | |
SXYL_00457 | Acetyltransferase | 2.5 | ||
SXYL_00523 | PadR-like family transcriptional regulator | 5.9 | 7.0 | |
SXYL_00786 | Transcriptional regulator, GntR family | 5.1 | ||
SXYL_00904 | Transcriptional regulator, GntR family | 2.3 | ||
SXYL_02403 | Transcriptional regulator, GntR family | 4.3 | 5.8 | |
SXYL_01239 | mnmA | tRNA-specific 2-thiouridylase MnmA | 2.4 | 2.8 |
SXYL_01352 | AraC-family transcriptional regulator | 2.3 | ||
SXYL_02345 | LacI-family transcriptional regulator | 2.3 | 2.1 | |
SXYL_02663 | Transcriptional regulator, LacI family | 2.3 | ||
SXYL_02482 | Transcriptional regulator, MerR family | 2.1 | ||
SXYL_02549 | Transcriptional regulator | 5.1 | 5.1 | |
SXYL_02596 | HxlR family transcriptional regulator | 3.1 | ||
SXYL_00022 | walK | Sensor protein kinase walK | 2.1 | |
SXYL_00323 | isaA | Probable transglycosylase IsaA | 2.8 | |
SXYL_00116 | sceD2 | Probable transglycosylase SceD 2 | 8.7 | 18.6 |
SXYL_00117 | sceD1 | Probable transglycosylase SceD1 | 13.7 | 21.7 |
Translation, ribosomal biogenesis | ||||
SXYL_01279-80 | prmA | Ribosomal protein L11 methyltransferase | 3.6 * | 3.5 * |
SXYL_01281 | rpsU | 30S ribosomal protein S21 | 2.1 | 2.0 |
SXYL_01549 | rpsN | 30S ribosomal protein S14 | 3.5 | 3.5 |
SXYL_01550 | rpmG2 | 50S ribosomal protein L33 2 | 2.0 | |
SXYL_01615 | infB | Translation initiation factor IF-2 | 2.0 | |
SXYL_01619 | rimP | Ribosome maturation factor RimP | 2.2 | |
SXYL_01673 | Peptide deformylase-like | 2.1 | ||
SXYL_02139 | queC | 7-cyano-7-deazaguanine synthase | 3.2 | 3.3 |
SXYL_02689 | rsmG | Ribosomal RNA small subunit methyltransferase G | 2.8 | 2.5 |
SXYL_02690-91 | mnmGE | tRNA uridine 5-carboxymethylaminomethyl, GTPase | 2.9 * | 2.6 * |
DNA/RNA repair | ||||
SXYL_00942 | dinB | DNA polymerase IV | 2.8 | 3.7 |
SXYL_00004 | recF | DNA replication and repair protein RecF | 2.1 | |
SXYL_01201 | tag | DNA-3-methyladenine glycosylase | 2.1 | |
SXYL_01206 | DNA repair RadC family protein | 2.8 | ||
SXYL_02062 | rnr | Ribonuclease R | 2.1 | |
SXYL_01796 | uvrC | UvrABC system protein C | 3.7 | 2.1 |
SXYL_02088-89 | uvrAB | UvrABC system protein A, B | 4.3 * | 3.5 * |
SXYL_00943 | Putative exonuclease | 2.3 | 3.0 | |
SXYL_02241 | Endonuclease III | 2.2 | ||
Protein turnover | ||||
SXYL_02399 | ctsR | Transcriptional regulator CtsR | 5.4 | 6.1 |
SXYL_02396 | clpC | ATP-dependent Clp protease ATP-binding subunit ClpC | 4.9 | 4.8 |
SXYL_01946 | clpB | Chaperone protein ClpB | 10.8 | 13.4 |
SXYL_00898 | groS | 10 kDa chaperonin | 2.1 | |
SXYL_01275 | hrcA | Heat-inducible transcription repressor HrcA | 3.8 | 4.6 |
SXYL_01276 | grpE | Protein GrpE | 3.9 | 4.8 |
SXYL_01277 | dnaK | Chaperone protein DnaK | 3.4 | 3.7 |
SXYL_01278 | dnaJ | Chaperone protein dnaJ | 3.9 | 3.9 |
SXYL_01192 | clpX | ATP-dependent Clp protease ATP-binding subunit ClpX | 2.2 | 2.1 |
SXYL_01933 | mecA | Adapter protein MecA | 2.0 | |
SXYL_02418 | hslO | 33 kDa chaperonin | 2.5 | 2.1 |
SXYL_00548 | Heat shock protein Hsp20 | 7.6 | 7.3 | |
SXYL_00549 | Heat shock protein Hsp20 | 9.5 | 8.8 | |
SXYL_00505 | Membrane protein insertase, YidC/Oxa1 family | 2.2 | ||
PYRIMIDINE, PURINES SALVAGE | ||||
Pyrimidine | ||||
SXYL_00796 | pdp | Pyrimidine-nucleoside phosphorylase | 2.1 | |
SXYL_01688-91 | pyrCBPR | Pyrimidine synthesis | 8.2 * | |
SXYL_01407 | Nucleoside-diphosphate-sugar epimerase | 2.1 | ||
SXYL_02117-18 | nrdFE | Ribonucleoside-diphosphate reductase | 2.8 * | |
Purine | ||||
SXYL_00017 | purA | Adenylosuccinate synthetase | 2.2 | |
SXYL_01548 | guaC | GMP reductase | 2.5 | 3.0 |
SXYL_02435 | purR | Pur operon repressor | 2.0 | |
CARBOHYDRATE CATABOLISM | ||||
Amino sugar catabolism | ||||
SXYL_00403 | nanE | N-acetylmannosamine-6-phosphate 2-epimerase | 2.5 | |
SXYL_00404 | RpiR family transcriptional regulator | 2.1 | ||
SXYL_00405 | nanK | N-acetylmannosamine kinase | 2.5 | |
SXYL_00406 | nanA | N-acetylneuraminate lyase | 3.9 | 2.7 |
SXYL_00254 | Glucosamine-6-phosphate deaminase | 3.4 | ||
Glycolysis | ||||
SXYL_00773-76 | mtlDFA | PTS system mannitol | 4.1 * | 5.4 * |
SXYL_00253 | PTS system, glucose-specific IIBC component | 4.7 | 2.7 | |
SXYL_01179 | gapA2 | Glyceraldehyde-3-phosphate dehydrogenase 2 | 2.7 | |
SXYL_00207 | ppsA | Pyruvate phosphate dikinase | 5.6 | 5.6 |
SXYL_00208 | Putative pyruvate, phosphate dikinase regulatory protein | 6.3 | 7.3 | |
Pentose, glucuronate | ||||
SXYL_01454 | Xylose isomerase-like protein | 2.3 | ||
SXYL_00123 | araB | l-ribulokinase | 2.1 | |
SXYL_00124 | araD | l-ribulose-5-phosphate 4-epimerase | 2.2 | 2.4 |
SXYL_02343 | 2-keto-3-deoxygluconate kinase | 2.6 | 5.4 | |
Energy | ||||
SXYL_01849-50 | cydBA | Cytochrome bd-type quinol oxidase | 2.5 * | |
AMINO ACID METABOLISM | ||||
Transport | ||||
SXYL_00264-66 | Amino acid ABC transporter | 4.1 * | ||
SXYL_02464 | Ammonia permease | 2.7 | 4.3 | |
SXYL_00661-65 | ABC-type amino acid transport system, Glutamate ABC transporter | 2.7 * | ||
Glutamate/glutamine | ||||
SXYL_02459 | gltD | NADH-glutamate synthase small unit | 2.4 | |
SXYL_02460 | gltB | Glutamate synthase large subunit | 2.9 | 2.3 |
SXYL_02461 | gltC | Transcription activator of glutamate synthase operon | 3.6 | |
SXYL_01568-69 | glnA1R | Glutamine synthetase, repressor | 3.4 * | |
SXYL_00107-08 | glnA2 | Glutamine synthetase, Aldehyde dehydrogenase | 6.7 * | 4.5 * |
SXYL_01686-87 | carBA | Carbamoyl-phosphate synthase | 4.1 * | |
Histidine | ||||
SXYL_00008 | hutH | Histidine ammonia-lyase (Histidase) | 6.4 | 5.0 |
SXYL_00617-18 | hutUI | Urocanate hydratase, Imidazolonepropionase | 2.9 * | 3.1 * |
Valine/leucine/isoleucine | ||||
SXYL_00867-74 | ilvADCBACNB | Valine, leucine, isoleucine synthesis | 2.7 * | |
Glycine/serine/threonine | ||||
SXYL_01317-19 | gcvTPAPB | Aminomethyltransferase, probable glycine dehydrogenase | 3.0 * | 2.3 * |
Cysteine/methionine | ||||
SXYL_02417 | cysK | Cysteine synthase | 2.3 | |
SXYL_02636-37 | cysIJ | Sulfite reductase (NADPH) hemoprotein | 3.3 * | |
SXYL_01238 | Putative cysteine desulfurase | 2.5 | 3.2 | |
SXYL_01672 | fmt | Methionyl-tRNA formyltransferase | 2.2 | |
Alanine/lysine | ||||
SXYL_01473 | lysA | Diaminopimelate decarboxylase | 5.3 | 3.3 |
SXYL_01474 | alr2 | Alanine racemase 2 | 11.9 | 7.6 |
SXYL_01475 | Uncharacterized hydrolase | 12.1 | 7.6 | |
SXYL_01476-78 | dapHBA | 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-acetyltransferase, | 4.1 * | 2.5 * |
4-hydroxy-tetrahydrodipicolinate reductase, synthase | ||||
SXYL_02665 | Dihydrodipicolinate synthase | 2.0 | 3.2 | |
SXYL_00325 | ldhD | d-lactate dehydrogenase | 10.3 | 11.9 |
COFACTOR, VITAMIN SYNTHESIS | ||||
SXYL_01097-100 | ribDEBAH | Riboflavin biosynthesis | 2.8 * | 3.7 * |
SXYL_00734-35 | ecfA2T | Energy-coupling factor transporter | 2.2 * | |
SXYL_01194 | hemA | Glutamyl-tRNA reductase | 2.0 | |
SXYL_01196 | hemC | Porphobilinogen deaminase | 2.5 | |
SXYL_02635 | cobA | Uroporphyrin-III C-methyltransferase | 2.0 | 2.9 |
SXYL_00839 | thiD | Hydroxymethylpyrimidine/phosphomethylpyrimidine kinase | 2.0 | |
SXYL_01231 | HesA/MoeB/ThiF family protein | 2.1 | 2.0 | |
SXYL_01893 | menF | Isochorismate synthase | 2.0 | 2.4 |
SXYL_02295 | folE2 | GTP cyclohydrolase FolE2 | 2.2 | |
INORGANIC ION TRANSPORT | ||||
Phosphate | ||||
SXYL_01484-86 | pstSCA | ABC-type phosphate transport system | 2.4 * | |
Fe | ||||
SXYL_01359 | fur | Ferric uptake regulation protein | 2.3 | 2.1 |
SXYL_02216-18 | sitABC | ABC metal ion transport system, Iron/manganese/zinc | 2.0 * | 4.7 * |
SXYL_00561-63 | Oxidoreductase, Monooxygenase, Transporter | 5.6 * | 12.4 * | |
SXYL_00793 | dps | Dps family protein | 3.6 | 3.7 |
Mn, Co, Zn, Cu | ||||
SXYL_02659-60 | mtsC | Metal ion ABC transporter, manganese | 3.4 * | |
SXYL_00416 | Putative ABC-type Mn Zn transport system periplasmic | 2.2 | ||
SXYL_00783-84 | czrA | Co Zn Cd efflux system component, Zn, Co transport repressor CzrA | 11.6 * | 11.8 * |
SXYL_00326-27 | copZA | Copper chaperone CopZ, Copper-exporting P-type ATPase A | 10.0 * | 13.2 * |
SXYL_00512 | Putative cation efflux family protein | 4.5 | 3.4 | |
RESPONSE TO STRESS | ||||
Osmotic | ||||
SXYL_00223 | cudT | Choline transporter | 2.4 | |
SXYL_00224 | cudC | Putative transcriptional regulator | 4.9 | 5.6 |
SXYL_00225 | cudA | Glycine betaine aldehyde dehydrogenase | 21.1 | 21.4 |
SXYL_00226 | betA | Oxygen-dependent choline dehydrogenase | 13.4 | 12.3 |
SXYL_02221-26 | mnhF2E2D2C2B2A2 | Na(+)/H(+) antiporter | 2.7 * | |
SXYL_02219 | Putative NhaP-type Na+ H+ and K+ H+ antiporter | 2.1 | ||
SXYL_00425 | Na(+)/H(+) exchanger | 2.1 | ||
SXYL_00407 | Sodium:solute symporter family protein | 4.0 | 2.3 | |
Oxidative | ||||
SXYL_01551 | katB | Catalase B | 2.4 | |
SXYL_02505 | katA | Catalase A | 4.2 | 5.7 |
SXYL_01797 | trxA | Thioredoxin | 2.6 | |
SXYL_02083 | trxB | Thioredoxin reductase | 2.3 | 2.3 |
SXYL_02534-35 | ahpCF | Alkyl hydroperoxide reductase | 4.2 * | 4.2 * |
SXYL_00895 | Nitroreductase family protein | 4.9 | 4.1 |
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Leroy, S.; Lebert, I.; Andant, C.; Micheau, P.; Talon, R. Investigating Extracellular DNA Release in Staphylococcus xylosus Biofilm In Vitro. Microorganisms 2021, 9, 2192. https://doi.org/10.3390/microorganisms9112192
Leroy S, Lebert I, Andant C, Micheau P, Talon R. Investigating Extracellular DNA Release in Staphylococcus xylosus Biofilm In Vitro. Microorganisms. 2021; 9(11):2192. https://doi.org/10.3390/microorganisms9112192
Chicago/Turabian StyleLeroy, Sabine, Isabelle Lebert, Carine Andant, Pierre Micheau, and Régine Talon. 2021. "Investigating Extracellular DNA Release in Staphylococcus xylosus Biofilm In Vitro" Microorganisms 9, no. 11: 2192. https://doi.org/10.3390/microorganisms9112192
APA StyleLeroy, S., Lebert, I., Andant, C., Micheau, P., & Talon, R. (2021). Investigating Extracellular DNA Release in Staphylococcus xylosus Biofilm In Vitro. Microorganisms, 9(11), 2192. https://doi.org/10.3390/microorganisms9112192