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Altering translation allows E. coli to overcome chemically stabilized G-quadruplexes.

ABSTRACT: G-quadruplex (G4) structures can form in guanine-rich DNA or RNA and have been found to modulate cellular processes including replication, transcription, and translation. Many studies on the cellular roles of G4s have focused on eukaryotic systems, with far fewer probing bacterial G4s. Using a chemical-genetic approach, we identified genes in Escherichia coli that are important for growth in G4-stabilizing conditions. Reducing levels of elongation factor Tu or slowing translation elongation with chloramphenicol suppress the effects of G4 stabilization. In contrast, reducing expression of certain translation termination or ribosome recycling proteins is detrimental to growth in G4-stabilizing conditions. Proteomic and transcriptomic analyses demonstrate that ribosome assembly factors and other proteins involved in translation are less abundant in G4-stabilizing conditions. Our integrated systems approach allowed us to propose a model for how RNA G4s can present barriers to E. coli growth and that reducing the rate of translation can compensate for G4-related stress.

SUBMITTER: Cueny RR

PROVIDER: S-EPMC11343134 | biostudies-literature | 2024 Aug

REPOSITORIES: biostudies-literature

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Altering translation allows <i>E. coli</i> to overcome chemically stabilized G-quadruplexes.

Cueny Rachel R RR Voter Andrew F AF McKenzie Aidan M AM Morgenstern Marcel M Myers Kevin S KS Place Michael M MM Peters Jason M JM Coon Joshua J JJ Keck James L JL

bioRxiv : the preprint server for biology 20240812

G-quadruplex (G4) structures can form in guanine-rich DNA or RNA and have been found to modulate cellular processes including replication, transcription, and translation. Many studies on the cellular roles of G4s have focused on eukaryotic systems, with far fewer probing bacterial G4s. Using a chemical-genetic approach, we identified genes in <i>Escherichia coli</i> that are important for growth in G4-stabilizing conditions. Reducing levels of elongation factor Tu or slowing translation elongati ...[more]

PMID: 39185182

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Project description:One of the significant issues persisting in the study of soil stabilization is the establishment of the optimum proportions of the quantity of stabilizer to be added to the soil. Determining optimum solutions or the most feasible remedies for the utilization of stabilizing products in terms of their dose rates has become a significant concern in major civil engineering design projects. Using the response surface methodology, this study primarily focused on investigating the optimal levels of reinforcement fiber length (FL), fiber dosage (FD), and curing time (CT) for geotechnical parameters of stabilized soil. To realize this objective, an experimental study was undertaken on the California bearing ratio (CBR) and unconfined compressive strength (UCS). Hydraulic conductivity (HC) tests were also performed, with stabilizer proportions of 6-12 mm for the FL and 0.2-0.6% for the FD calculated for the total dry weight of soil and 6% lime (total weight of dry soil). The curing times used for testing were 0, 7, and 14 days for the CBR tests; 60, 210, and 360 days for the UCS tests; and 7, 17, and 28 days for the HC tests. All practical experiments were conducted with experimental techniques using stabilizer proportions and curing times. The FL, FD, CT, CBR, UCS, and HC response factors were determined using the central composite design. The results point toward a statistically significant model constructed (p ≤ 0.05) using the analysis of variance. The results from this optimization procedure show that the optimal values for the FL, FD, and CT were 11.1 mm, 0.5%, and 13.2 days, respectively, as these provided the maximum values for the CBR; 11.7 mm for the FL, 0.3% for the FD, and 160 days for the CT corresponded to the maximum values for the UCS; and 10.5 mm for the FL, 0.5% for the FD, and 15 days for the CT led to the minimum value for the HC. In practice, the suggested values may be useful for experiments, especially for preliminary assessments prior to stabilization.

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Altering translation allows E. coli to overcome chemically stabilized G-quadruplexes.

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Altering translation allows <i>E. coli</i> to overcome chemically stabilized G-quadruplexes.

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Altering translation allows E. coli to overcome chemically stabilized G-quadruplexes.

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Altering translation allows &lt;i&gt;E. coli&lt;/i&gt; to overcome chemically stabilized G-quadruplexes.

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Altering translation allows <i>E. coli</i> to overcome chemically stabilized G-quadruplexes.