Maturation of UTR-Derived sRNAs Is Modulated during Adaptation to Different Growth Conditions
Abstract
:1. Introduction
2. Results
2.1. Identification of Five Novel UTR-Derived sRNAs
2.2. Global Prediction of UTR-Derived sRNA Generation Mechanisms
2.3. Several Enzymes Account for The Maturation and Processing of UTR-Derived sRNAs In Vivo
2.4. Growth Conditions Impact the UTR-Derived sRNA Levels
2.4.1. Uds’ Abundances Are Growth Phase Dependent
2.4.2. External Stressors Affect the sRNA Abundances
3. Discussion
4. Material and Methods
4.1. Bacterial Strains and Growth Conditions
4.2. Construction of a rppH and a ybeY Deletion Strain
4.3. Promoter Activity Assay
4.4. Reverse Transcription (RT) PCR
4.5. Northern Blot Analysis
4.6. Bioinformatical Analysis
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
CDS | coding sequence |
OD | optical density |
OG | outgrowth |
RT | reverse transcription |
TEX | terminator 5-phosphate dependent 5-to-3 exoribonuclease |
TSS | transcription start site |
UTR | untranslated region |
Uds | UTR-derived sRNA |
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sRNA | Origin | Predicted 5 End | Predicted 3 End | Involvement of RNases/Hfq In Vivo |
---|---|---|---|---|
UdsA | 5 UTR | TSS | RNase E | RNase III, RppH, PNPase |
UdsB | 3 UTR | RNase E | terminator | RNase E, PNPase |
UdsC | 3 UTR | RNase E | terminator | RNase III, RNase E, PNPase, Hfq |
UdsD | 3 UTR | RNase E | terminator/PNPase | PNPase |
UdsE | 5 UTR | TSS | unknown | RNase E, PNPase |
UdsF | 5 UTR | TSS | unknown | Hfq, PNPase |
UdsG | 5 UTR | TSS | RNase E | PNPase |
UdsH | 3 UTR | RNase E | terminator | RNase III, RNase J, RNase E, PNPase |
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Spanka, D.-T.; Klug, G. Maturation of UTR-Derived sRNAs Is Modulated during Adaptation to Different Growth Conditions. Int. J. Mol. Sci. 2021, 22, 12260. https://doi.org/10.3390/ijms222212260
Spanka D-T, Klug G. Maturation of UTR-Derived sRNAs Is Modulated during Adaptation to Different Growth Conditions. International Journal of Molecular Sciences. 2021; 22(22):12260. https://doi.org/10.3390/ijms222212260
Chicago/Turabian StyleSpanka, Daniel-Timon, and Gabriele Klug. 2021. "Maturation of UTR-Derived sRNAs Is Modulated during Adaptation to Different Growth Conditions" International Journal of Molecular Sciences 22, no. 22: 12260. https://doi.org/10.3390/ijms222212260