Regulation of DNA Replication Initiation by Chromosome Structure

Magnan, David; Bates, David

doi:10.1128/jb.00446-15

Cited by 30 publications

(28 citation statements)

References 101 publications

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“…Similarly, its been shown that high transcriptional activity also gives rise to net negative chromosomal supercoiling, especially near the origin of replication where several highly-expressed rRNA genes reside. This supercoiling should facilitate DNA melting, again leading to earlier replication times [41]. In light of these considerations, we anticipated lower ρ ( k t , t r ) values than were in fact observed among our best-performing matrices.…”

Section: Finding Extrinsic Noise Correlations That Fit Experimentmentioning

confidence: 83%

Careful accounting of extrinsic noise in protein expression reveals correlations among its sources

Cole

Luthey‐Schulten

2017

Phys. Rev. E

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In order to grow and replicate, living cells must express a diverse array of proteins, but the process by which proteins are made includes a great deal of inherent randomness. Understanding this randomness—whether it arises from the discrete stochastic nature of chemical reactivity (“intrinsic” noise), or from cell-to-cell variability in the concentrations of molecules involved in gene expression or the timings of important cell-cycle events like DNA replication or cell division (“extrinsic” noise)—remains a challenge. In this article we analyze a model of gene expression that accounts for several extrinsic sources of noise, including those associated with chromosomal replication, cell division, and variability in the numbers of RNA polymerase, ribonuclease E, and ribosomes. We then attempt to fit our model to a large proteomics and transcriptomics data set, and find that only through the introduction of a few key correlations among the extrinsic noise sources can we accurately recapitulate the experimental data. These include significant correlations between the rate of mRNA degradation (mediated by ribonuclease E) and the rates of both transcription (RNA polymerase) and translation (ribosomes), and strikingly, an anticorrelation between the transcription and translation rates themselves.

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Section: Finding Extrinsic Noise Correlations That Fit Experimentmentioning

confidence: 83%

Careful accounting of extrinsic noise in protein expression reveals correlations among its sources

Cole

Luthey‐Schulten

2017

Phys. Rev. E

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“…En effet, en se liant à des séquences opératrices (les boîtes DnaA) qui sont présentes aux abords de l'origine de réplication, DnaA, liée à l'ATP, stimule l'ouverture de la double hélice d'ADN et facilite l'accès à la machinerie de réplication d'ADN appelée réplisome [2]. Réguler la quantité totale de DnaA, ou la proportion de DnaA liée à l'ATP, constitue donc un moyen efficace pour les bactéries de contrô-ler précisément l'initiation de la réplication d'ADN.…”

Section: Contrôle Métabolique De La Réplication D'adn Initiation De Lunclassified

Métabolisme et cycle cellulaire, deux processus interconnectés chez les bactéries

Hallez

2016

Med Sci (Paris)

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Afin d’optimiser les chances de survie d’une cellule dans son environnement, le métabolisme et le cycle cellulaire doivent nécessairement être interconnectés. En effet, les cellules possèdent des mécanismes leur permettant, d’une part, de vérifier leur état métabolique avant d’initier l’une ou l’autre étape du cycle cellulaire souvent énergivore et, d’autre part, d’achever certaines étapes du cycle cellulaire avant d’éventuellement modifier leur métabolisme. Parce que les bactéries ne dérogent pas à cette règle, un nombre croissant d’exemples de connexions entre le métabolisme et le cycle cellulaire a émergé ces dernières années. L’identification d’enzymes métaboliques comme messagers coordonnant métabolisme et cycle cellulaire, permet d’ajouter une nouvelle dimension aux cartes métaboliques. La très grande conservation de ces mêmes cartes métaboliques, des bactéries jusqu’à l’homme, permet également d’imaginer des recherches sur les cellules tumorales qui ont un cycle cellulaire débridé et un appétit vorace.

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“…As discussed above, DnaA and λ O utilize the protein-induced ΔLk to open/melt the AT-rich DUE of replication origins to initiate DNA replication Grimwade 2009, 2015;Magnan and Bates 2015;Rajewska et al 2012;Wolanski et al 2014). Additionally, the nucleoprotein complexes by these replication initiators functioning as a DNA topological barrier (Leng et al 2004(Leng et al , 2011Leng and McMacken 2002) block, confine, and capture transcription-coupled DNA supercoiling, which helps open/melt DUE of replication origins and facilitates DNA replication initiation (Chung 1996).…”

Section: Conclusion and Biological Effectsmentioning

confidence: 99%

“…Nevertheless, DnaAmediated DNA wrapping (winding or unwinding/ΔLk) is critical for the opening of DUE (Duderstadt et al 2011). Other factors such as (−) supercoiling and HU may also help melt/open DUE of OriC (Hwang and Kornberg 1992;Magnan and Bates 2015).…”

Section: Bacterial Dna Replication Initiators: λ O and Dnaamentioning

confidence: 99%

Protein-induced DNA linking number change by sequence-specific DNA binding proteins and its biological effects

Leng

2016

Biophys Rev

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Sequence-specific DNA-binding proteins play essential roles in many fundamental biological events such as DNA replication, recombination, and transcription. One common feature of sequence-specific DNA-binding proteins is to introduce structural changes to their DNA recognition sites including DNA-bending and DNA linking number change (ΔLk). In this article, I review recent progress in studying protein-induced ΔLk by several sequence-specific DNAbinding proteins, such as E. coli cAMP receptor protein (CRP) and lactose repressor (LacI). It was demonstrated recently that protein-induced ΔLk is an intrinsic property for sequence-specific DNA-binding proteins and does not correlate to protein-induced other structural changes, such as DNA bending. For instance, although CRP bends its DNA recognition site by 90°, it was not able to introduce a ΔLk to it. However, LacI was able to simultaneously bend and introduce a ΔLk to its DNA binding sites. Intriguingly, LacI also constrained superhelicity within LacI-lac O1 complexes if (−) supercoiled DNA templates were provided. I also discuss how protein-induced ΔLk help sequence-specific DNA-binding proteins regulate their biological functions. For example, it was shown recently that LacI utilizes the constrained superhelicity (ΔLk) in LacI-lac O1 complexes and serves as a topological barrier to constrain free, unconstrained (−) supercoils within the 401-bp DNA loop. These constrained (−) supercoils enhance LacI's binding affinity and therefore the repression of the lac promoter. Other biological functions include how DNA replication initiators λ O and DnaA use the induced ΔLk to open/melt bacterial DNA replication origins.

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Regulation of DNA Replication Initiation by Chromosome Structure

Cited by 30 publications

References 101 publications

Careful accounting of extrinsic noise in protein expression reveals correlations among its sources

Careful accounting of extrinsic noise in protein expression reveals correlations among its sources

Métabolisme et cycle cellulaire, deux processus interconnectés chez les bactéries

Protein-induced DNA linking number change by sequence-specific DNA binding proteins and its biological effects

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