Transcriptomic Analysis Reveals Key Roles of (p)ppGpp and DksA in Regulating Metabolism and Chemotaxis in Yersinia enterocolitica
Abstract
1. Introduction
2. Results
2.1. (p)ppGpp- and DksA-Dependent Genes in Y. enterocolitica Identified Using RNA-Seq
2.2. (p)ppGpp- and DksA- Dependent Cell Functions in Y. enterocolitica
2.3. DksA and (p)ppGpp Inhibit Ribosomal Synthesis and Regulate Metabolic Networks
2.4. DksA and (p)ppGpp Are Required for Amino Acid Transport and Utilization
2.5. DksA and ppGpp Positively Affect Bacterial Chemotaxis
3. Discussion
4. Material and Methods
4.1. Bacterial Strains and Growth Conditions
4.2. RNA Extraction, Library Construction, and Sequencing
4.3. Gene Annotation and Data Analysis
4.4. RT-qPCR
4.5. In Vitro Bacterial Growth
4.6. Swim Plate and Competitive Capillary Assays for Chemotaxis
4.7. Statistical Analysis
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Samples | Genetic Number | Ratios | Number of DEGs | DEGs | |
---|---|---|---|---|---|
Upregulated | Downregulated | ||||
WT | 3651 | 84.65% | 0 | 0 | 0 |
ΔdksA | 3644 | 84.49% | 801 | 384 | 417 |
ΔrelAΔspoT | 3434 | 79.62% | 1437 | 695 | 742 |
ΔdksAΔrelAΔspoT | 3614 | 83.79% | 1059 | 560 | 499 |
Strain | Genotype | Sources |
---|---|---|
WT | Y. enterocolitica ATCC 23715; Serotype O:8; Biotype 1B; pYV- | Lab stored |
ΔdksA | Y. enterocolitica ATCC 23715 derived, Δ dksA | Lab stored |
ΔrelAΔspoT | Y. enterocolitica ATCC 23715 derived, Δ relA Δ spoT | Lab stored |
ΔdksAΔrelAΔspoT | ΔrelAΔspoT derived, Δ dksA | Lab stored |
ΔdksA(dksA) | ΔdksA harboring pBAD24—dksA, AMPr | Lab stored |
ΔrelAΔspoT(spoT) | ΔrelAΔspoT harboring pBAD24—spoT, AMPr | Lab stored |
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Huang, C.; Li, W.; Chen, J. Transcriptomic Analysis Reveals Key Roles of (p)ppGpp and DksA in Regulating Metabolism and Chemotaxis in Yersinia enterocolitica. Int. J. Mol. Sci. 2023, 24, 7612. https://doi.org/10.3390/ijms24087612
Huang C, Li W, Chen J. Transcriptomic Analysis Reveals Key Roles of (p)ppGpp and DksA in Regulating Metabolism and Chemotaxis in Yersinia enterocolitica. International Journal of Molecular Sciences. 2023; 24(8):7612. https://doi.org/10.3390/ijms24087612
Chicago/Turabian StyleHuang, Can, Wenqian Li, and Jingyu Chen. 2023. "Transcriptomic Analysis Reveals Key Roles of (p)ppGpp and DksA in Regulating Metabolism and Chemotaxis in Yersinia enterocolitica" International Journal of Molecular Sciences 24, no. 8: 7612. https://doi.org/10.3390/ijms24087612
APA StyleHuang, C., Li, W., & Chen, J. (2023). Transcriptomic Analysis Reveals Key Roles of (p)ppGpp and DksA in Regulating Metabolism and Chemotaxis in Yersinia enterocolitica. International Journal of Molecular Sciences, 24(8), 7612. https://doi.org/10.3390/ijms24087612