Genome-wide proximity between RNA polymerase and DNA topoisomerase I supports transcription in Streptococcus pneumoniae

Ferrándiz, Marı́a José; Hernández, Pablo; Campa, Adela G. de la

doi:10.1371/journal.pgen.1009542

Cited by 16 publications

(37 citation statements)

References 50 publications

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“…We find the model to account for our experimental data only when TopoI and gyrase are allowed to act specifically. In line with previous works on gyrase [30, 50] and TopoI [33, 50, 51] in various bacteria, including E. coli , our results thus demonstrate that these topoisomerases are essential facilitators of transcription. Our analysis further reveals that the production rate of supercoils is lower for TopoI than for gyrase.…”

Section: Discussionsupporting

confidence: 93%

Assessingin vivothe impact of gene context on transcription through DNA supercoiling

Boulas

Rimsky

Espéli

et al. 2022

Preprint

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Gene context can have significant impact on gene expression but is currently not integrated in quantitative models of gene regulation despite known biophysical principles and quantitative in vitro measurements. Conceptually, the simplest gene context consists of a single gene framed by two topological barriers, known as the twin transcriptional-loop model, which illustrates the interplay between transcription and DNA supercoiling. In vivo, DNA supercoiling is additionally modulated by topoisomerases, whose modus operandi remains to be quantified. Here, we bridge the gap between theory and in vivo properties by realizing in Escherichia coli the twin transcriptional-loop model and by measuring how gene expression varies with promoters and distances to the topological barriers. We find that gene expression depends on the distance to the upstream barrier but not to the downstream barrier, with a promoter-dependent intensity. We rationalize these findings with a first-principle biophysical model of DNA transcription. The model integrates binding, initiation and elongation of RNA polymerases parametrized with available in vitro measurements, as well as the action of topoisomerases for which parameters are constrained by our experimental results. By comparing it with the data, our biophysical model supports that TopoI and gyrase must both act specifically, respectively upstream and downstream the gene, and predicts TopoI to be less active than gyrase. It also highlights antagonistic effects of TopoI, which both facilitates elongation and tends to repress initiation. Altogether, our work sets the foundations for a systematic and quantitative description of the impact of gene context on gene regulation.

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Section: Discussionsupporting

confidence: 93%

Assessingin vivothe impact of gene context on transcription through DNA supercoiling

Boulas

Rimsky

Espéli

et al. 2022

Preprint

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“…Since CTD does not influence transcription elongation, the results support the existence of an RNAP:EcTopoI complex that is formed during transcription initiation and persists during transcription elongation in vivo. In contrast to E. coli, enrichment of streptococcal SpTopoI is abolished by Rif, possibly indicating a distinct mechanism of RNAP:TopoI interaction (Ferrandiz, Hernandez and de la Campa, 2021).…”

Section: Ectopoi Interacts With Rnap In Vivomentioning

confidence: 90%

“…Streptococcus pneumoniae (Ferrandiz, Hernandez and de la Campa, 2021). It was hypothesized that association with RNAP enables TopoI to rapidly relax negative DNA supercoils forming behind the elongating RNAP, thereby preventing the R-loops formation (Cheng et al, 2003;Yang et al, 2015).…”

Section: Introductionmentioning

confidence: 99%

“…Kirkegaard, Pflugfelder and Wang, 1983). Recently, the genome-wide distribution of TopoI from M. tuberculosis (MtTopoI), M. smegmatis (MsTopoI), and S. pneumoniae (SpTopoI) was investigated using ChIP-Seq (Ahmed et al, 2017;Rani and Nagaraja, 2018;Ferrandiz, Hernandez and de la Campa, 2021). In all cases, the topoisomerase was shown to associate with actively transcribed genes with particular enrichment upstream of RNAP peaks at promoter regions.…”

Section: Introductionmentioning

confidence: 99%

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Interaction Between Transcribing RNA Polymerase and Topoisomerase I Prevents R-loop Formation in E. coli

Sutormin

Galivondzhyan

Musharova

et al. 2021

Preprint

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Bacterial topoisomerase I (TopoI) removes excessive negative supercoiling and is thought to relax DNA molecules during transcription, replication and other processes. Using ChIP-Seq, we show that TopoI of Escherichia coli (EcTopoI) is co-localized, genome-wide, with RNA polymerase (RNAP) in transcription units. Treatment with transcription elongation inhibitor rifampicin leads to EcTopoI relocation to promoter regions, where RNAP also accumulates. When a 14 kDa RNAP-binding EcTopoI C-terminal domain (CTD) is overexpressed, co-localization of EcTopoI and RNAP along the transcription units is reduced. Pull-down experiments directly show that the two enzymes interact in vivo. Using ChIP-Seq and Topo-Seq, we demonstrate that EcTopoI is enriched and in and upstream (within up to 12-15 Kbs) of highly-active transcription units, indicating that EcTopoI relaxes negative supercoiling generated by transcription. Uncoupling of the RNAP-EcTopoI interaction by either overexpression of EcTopoI CTD or deletion of EcTopoI domains involved in the interaction is toxic for cells and leads to excessive negative plasmid supercoiling. Moreover, the CTD overexpression leads to R-loops accumulation genome-wide, indicating that the RNAP-EcTopoI interaction is required for prevention of R-loops formation.Article HighlightsTopoI colocalizes genome-wide and interacts with RNAP in E. coliDisruption of the interaction between TopoI and RNAP decreases cells viability, leads to hypernegative DNA supercoiling, and R-loops accumulationTopoI and DNA gyrase are enriched, respectively, upstream and downstream of transcription units in accordance with twin-domain model of Liu and WangTopoI recognizes its cleavage sites through a specific motif and by sensing negative supercoiling

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“…Topo I has an essential role in supporting transcription in S. pneumonia e. We have shown that Topo I and RNA polymerase physically interact in vitro and colocalize at gene promoters in vivo. Binding of each of these enzymes to promoters was prevented by the specific inhibition of the other enzyme, either by rifampicin (RNA polymerase) or by SCN (Topo I), supporting a role for Topo I in RNA polymerase transcription [ 50 ]. These results allowed envisaging SCN as a new drug for the treatment of diseases caused by infection with multi-drug resistant strains of S. pneumoniae .…”

Section: Discussionmentioning

confidence: 99%

Seconeolitsine, the Novel Inhibitor of DNA Topoisomerase I, Protects against Invasive Pneumococcal Disease Caused by Fluoroquinolone-Resistant Strains

et al. 2021

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Antibiotic resistance in Streptococcus pneumoniae has increased worldwide, making fluoroquinolones an alternative therapeutic option. Fluoroquinolones inhibit the type II DNA topoisomerases (topoisomerase IV and gyrase). In this study we have evaluated the in vivo activity of seconeolitsine, an inhibitor of topoisomerase I. Levofloxacin (12.5 to 50 mg/kg) or seconeolitsine (5 to 40 mg/kg) were administered every 12 h during two days in mice infected with a serotype 8-resistant strain. At 48 h, a 70% protection was obtained with seconeolitsine (40 mg/kg; p < 0.001). However, survival with levofloxacin was 20%, regardless of the dose. In addition, seconeolitsine decreased bacteremia efficiently. Levofloxacin had higher levels in serum than seconeolitsine (Cmax of 14.7 vs. 1.6; p < 0.01) and higher values of area under the serum concentration-time curve (AUC0-12h of 17.3 vs. 5; p < 0.01). However, seconeolitsine showed higher levels of time to peak concentration and elimination half-life. This is consistent with the higher binding of seconeolitsine to plasma proteins (40% and 80% when used at 1 µg/mL and 50 µg/mL, respectively) in comparison to levofloxacin (12% at 5 µg/mL and 33% at 50 µg/mL). Our results suggest that seconeolitsine would be a promising therapeutic alternative against pneumococcal isolates with high fluoroquinolone resistance levels.

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Genome-wide proximity between RNA polymerase and DNA topoisomerase I supports transcription in Streptococcus pneumoniae

Cited by 16 publications

References 50 publications

Assessingin vivothe impact of gene context on transcription through DNA supercoiling

Assessingin vivothe impact of gene context on transcription through DNA supercoiling

Interaction Between Transcribing RNA Polymerase and Topoisomerase I Prevents R-loop Formation in E. coli

Seconeolitsine, the Novel Inhibitor of DNA Topoisomerase I, Protects against Invasive Pneumococcal Disease Caused by Fluoroquinolone-Resistant Strains

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