The Fate and Functionality of Alien tRNA Fragments in Culturing Medium and Cells of Escherichia coli
Abstract
:1. Introduction
2. Results
2.1. Assessing Interspecies Relations of E. coli with Prevotella copri (P. copri) and Rhodospirillum rubrum (R. rubrum)
2.2. Search for RNAs Secreted by P. copri or R. rubrum with a Potential Effect on E. coli
2.3. Assessing Fragmentation of Selected RNAs in the Medium of Mixed Populations
2.4. Dual Effects Exerted by Synthetic Analogs of Model RNAs on the Growth of E. coli
2.5. Fragmentation of Synthetic Analogs of Model tRFs in Culture Medium
2.6. Alien tRFs Underwent Additional Structural Changes upon Entry into E. coli Cells but Partially Retain the Pattern of Extracellular Nuclease Cleavage
2.7. Permutation of Synthetic Oligonucleotides Indicates Self-Ligation and Nuclease Cleavage of the Intermediate Circular Isoform in the Culture Medium
3. Discussion
4. Materials and Methods
4.1. Bacterial Strains and Growth Conditions
4.2. Cultivation of E. coli in Conditioned LB Media
4.3. Co-Culturing of Bacteria in Membrane-Separated Compartments
4.4. Effect of Exogenous Oligonucleotides on E. coli Growth
4.5. Evaluating the Effects Posed by E. coli on the Integrity of Exogenous Oligonucleotides
4.6. RNA Isolation
4.7. Preparation of Sequencing Libraries and Sequencing
4.8. Data Processing
4.9. Bioinformatics Analysis
4.9.1. Search for RNAs Secreted by P. copri or R. rubrum and Imported by E. coli
4.9.2. Evaluation of the Relative Sizes of E. coli, P. copri and R. rubrum Secretomes in Mixed Populations
4.9.3. Assessing Fragmentation of Selected RNAs in the Medium of Mixed Populations
4.9.4. Assessing Fragmentation of Synthetic Analogs of Model tRFs in the Cells and Medium of E. coli Monoculture
4.9.5. Evaluating Circular Permutations of Synthetic Analogs and RNA Fragments of E. coli
4.10. Statistics
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Shavkunov, K.S.; Markelova, N.Y.; Glazunova, O.A.; Kolzhetsov, N.P.; Panyukov, V.V.; Ozoline, O.N. The Fate and Functionality of Alien tRNA Fragments in Culturing Medium and Cells of Escherichia coli. Int. J. Mol. Sci. 2023, 24, 12960. https://doi.org/10.3390/ijms241612960
Shavkunov KS, Markelova NY, Glazunova OA, Kolzhetsov NP, Panyukov VV, Ozoline ON. The Fate and Functionality of Alien tRNA Fragments in Culturing Medium and Cells of Escherichia coli. International Journal of Molecular Sciences. 2023; 24(16):12960. https://doi.org/10.3390/ijms241612960
Chicago/Turabian StyleShavkunov, Konstantin S., Natalia Yu. Markelova, Olga A. Glazunova, Nikolay P. Kolzhetsov, Valery V. Panyukov, and Olga N. Ozoline. 2023. "The Fate and Functionality of Alien tRNA Fragments in Culturing Medium and Cells of Escherichia coli" International Journal of Molecular Sciences 24, no. 16: 12960. https://doi.org/10.3390/ijms241612960