Influence of Redox Imbalances on the Transposition of Insertion Sequences in Deinococcus geothermalis
Abstract
:1. Introduction
2. Materials and Methods
2.1. Bacterial Strains and Culture Conditions
2.2. Non-Pigmented Colonies and Streptomycin-Resistant Selection
2.3. Detection of Insertion Sequence Transposition
2.4. Transcriptomic Analysis by RNA-Seq
2.5. Quantitative Real-Time (qRT)-PCR
3. Results
3.1. Physiological Properties of Target Gene Disrupted and Complemented Mutants
3.2. Major Gene Categories Differentially Expressed in the Cystine Importer-Disrupted Mutant
3.3. Detection of IS Transposition
3.4. Streptomycin-Resistant Phenotypic Mutation
3.5. Gene Expression Levels of Redox Control-Related Genes and Transposases
4. Discussion
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
BSH | bacillithiol |
Dps | DNA-binding protein for DNA protection in starved cell |
IS | insertion sequence |
MSH | mycothiol |
RES | reactive electrophilic species |
RONS | reactive oxygen/nitrogen species |
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Category | Gene | Fold Change | Function |
---|---|---|---|
Transposase (ISDge5, IS701 family) | dgeo_0308 | 4.82 | Transposase |
dgeo_0464 | 3.71 | Transposase | |
dgeo_0925 | 3.74 | Transposase | |
dgeo_1807 | 6.15 | Transposase | |
dgeo_2205 | 3.92 | Transposase | |
dgeo_2430 | 4.93 | Transposase | |
dgeo_2823 | 4.55 | Transposase | |
dgeo_2659 | 4.65 | Transposase | |
Sigma factor | dgeo_1346 | 4.13 | Sigma 70 |
dgeo_1519 | 3.26 | Sigma factor | |
Regulator | dgeo_0527 | 3.35 | HxlR family |
dgeo_1148 | 3.18 | MarR family | |
dgeo_1956 | 6.36 | SugE family | |
dgeo_2329 | 8.36 | AraC family | |
ABC transporter | dgeo_0543 | 3.34 | ABC transporter |
dgeo_0647-48 | 6.96–7.06 | ABC transporter | |
dgeo_0954-56 | 4.20–9.76 | Chromate transporter | |
dgeo_1413 | 5.91 | ABC transporter | |
dgeo_1805 | 8.03 | ABC transporter | |
dgeo_2443 | 4.69 | Iron permease | |
dgeo_2581-82 | 3.60–3.25 | cation transporter | |
MFS transporter | dgeo_0249 | 3.75 | MFS transporter |
dgeo_0530 | 6.41 | MFS efflux | |
dgeo_1968 | 5.57 | MFS transporter | |
dgeo_2330 | 3.22 | MFS efflux pump | |
GCN5 family | dgeo_0369-70 | 9.60–12.53 | GCN5 family regulator |
dgeo_2125 | 3.73 | GCN5 family acetyltransferase | |
dgeo_2313 | 11.2 | GCN5 family acetyltransferase | |
Enzyme | dgeo_0071 | 5.01 | Peptidase M29 |
dgeo_0334 | 4.68 | Carboxypeptidase | |
dgeo_0431 | 5 | Phage integrase | |
dgeo_0528 | 8.8 | NADH dehydrogenase | |
dgeo_0570 | 3.68 | Proline tRNA ligase | |
dgeo_0824 | 3.34 | Exonuclease | |
dgeo_0909 | 3.45 | NADH-quinone oxidoreductase | |
dgeo_1337 | 6.43 | Methylenetetrahydrofolate reductase | |
dgeo_1407-08 | 7.49–9.32 | Ferredoxin nitrite reductase/sulfate adenylyltransferase | |
dgeo_1714 | 10.78 | Cysteine tRNA ligase | |
dgeo_2583 | 3.49 | NrdH redoxin | |
dgeo_2681 | 3.63 | Zn dependent hydrolase | |
dgeo_2801 | 3.14 | WYL domain protein |
Loci | Gene | Fold | Function |
---|---|---|---|
Chromosome | dgeo_1056 | 0.22 | Nuclease inhibitor |
dgeo_1081 | 0.27 | 3-hydroxyisobutyrate dehydrogenase | |
dgeo_1535-36 | 0.17 | Thioesterase/pterin dehydratase | |
dgeo_2122 | 0.07 | Peptide ABC transporter | |
dgeo_2245 | 0.27 | Citrate synthase | |
Plasmid 1 | dgeo_2704 | 0.25 | Cytochrome D subunit |
dgeo_2619 | 0.2 | RpiR family regulator | |
dgeo_2561 | 0.25 | Peptidase C39 | |
dgeo_2515 | 0.29 | DNA binding protein | |
Plasmid 2 | dgeo_3003-04 | 0.12 | Thiamine biosynthesis/ferric reductase |
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Ye, Q.; Lee, C.; Shin, E.; Lee, S.-J. Influence of Redox Imbalances on the Transposition of Insertion Sequences in Deinococcus geothermalis. Antioxidants 2021, 10, 1623. https://doi.org/10.3390/antiox10101623
Ye Q, Lee C, Shin E, Lee S-J. Influence of Redox Imbalances on the Transposition of Insertion Sequences in Deinococcus geothermalis. Antioxidants. 2021; 10(10):1623. https://doi.org/10.3390/antiox10101623
Chicago/Turabian StyleYe, Qianying, Chanjae Lee, Eunjung Shin, and Sung-Jae Lee. 2021. "Influence of Redox Imbalances on the Transposition of Insertion Sequences in Deinococcus geothermalis" Antioxidants 10, no. 10: 1623. https://doi.org/10.3390/antiox10101623