Changing Perspectives on the Role of DnaA-ATP in Orisome Function and Timing Regulation

Leonard, Alan C.; Rao, Prassanna; Kadam, Rohit Pradip; Grimwade, Julia E.

doi:10.3389/fmicb.2019.02009

Cited by 28 publications

(29 citation statements)

References 105 publications

(174 reference statements)

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“…The R-type DnaA boxes (consensus 5′-TTATMCACA-3′) are bound by DnaA complexed with ATP or ADP (ATP–DnaA or ADP–DnaA) and serve as anchors for subsequent DnaA-binding low-affinity boxes [ 20 , 21 ]. The low-affinity sites are bound by ATP–DnaA, which is important for the synchronization and/or regulation of chromosome replication [ 22 , 23 , 24 ]. The low-affinity ATP–DnaA boxes differ by 3–6 bases from the R-type DnaA box [ 19 , 25 ].…”

Section: Introductionmentioning

confidence: 99%

Putative Cooperative ATP–DnaA Binding to Double-Stranded DnaA Box and Single-Stranded DnaA-Trio Motif upon Helicobacter pylori Replication Initiation Complex Assembly

Jaworski

Żyła-Uklejewicz

Nowaczyk-Cieszewska

et al. 2021

IJMS

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oriC is a region of the bacterial chromosome at which the initiator protein DnaA interacts with specific sequences, leading to DNA unwinding and the initiation of chromosome replication. The general architecture of oriCs is universal; however, the structure of oriC and the mode of orisome assembly differ in distantly related bacteria. In this work, we characterized oriC of Helicobacter pylori, which consists of two DnaA box clusters and a DNA unwinding element (DUE); the latter can be subdivided into a GC-rich region, a DnaA-trio and an AT-rich region. We show that the DnaA-trio submodule is crucial for DNA unwinding, possibly because it enables proper DnaA oligomerization on ssDNA. However, we also observed the reverse effect: DNA unwinding, enabling subsequent DnaA–ssDNA oligomer formation—stabilized DnaA binding to box ts1. This suggests the interplay between DnaA binding to ssDNA and dsDNA upon DNA unwinding. Further investigation of the ts1 DnaA box revealed that this box, together with the newly identified c-ATP DnaA box in oriC1, constitute a new class of ATP–DnaA boxes. Indeed, in vitro ATP–DnaA unwinds H. pylori oriC more efficiently than ADP–DnaA. Our results expand the understanding of H. pylori orisome formation, indicating another regulatory pathway of H. pylori orisome assembly.

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Section: Introductionmentioning

confidence: 99%

Putative Cooperative ATP–DnaA Binding to Double-Stranded DnaA Box and Single-Stranded DnaA-Trio Motif upon Helicobacter pylori Replication Initiation Complex Assembly

Jaworski

Żyła-Uklejewicz

Nowaczyk-Cieszewska

et al. 2021

IJMS

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“…In the following, the most important aspects of the ATP-DnaA dependent initiation step of DNA replication is shortly summarized. For further details on this complex field, see expert reviews ( Leonard and Grimwade, 2010 ; Katayama et al., 2017 ; Hansen and Atlung, 2018 ; Leonard et al., 2019 ).…”

Section: Does the Prevention Of Atp-dnaa-dependent Initiation Of Dna mentioning

confidence: 99%

Persistence of Intracellular Bacterial Pathogens—With a Focus on the Metabolic Perspective

Eisenreich

Rudel

Heesemann

et al. 2021

Front. Cell. Infect. Microbiol.

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Persistence has evolved as a potent survival strategy to overcome adverse environmental conditions. This capability is common to almost all bacteria, including all human bacterial pathogens and likely connected to chronic infections caused by some of these pathogens. Although the majority of a bacterial cell population will be killed by the particular stressors, like antibiotics, oxygen and nitrogen radicals, nutrient starvation and others, a varying subpopulation (termed persisters) will withstand the stress situation and will be able to revive once the stress is removed. Several factors and pathways have been identified in the past that apparently favor the formation of persistence, such as various toxin/antitoxin modules or stringent response together with the alarmone (p)ppGpp. However, persistence can occur stochastically in few cells even of stress-free bacterial populations. Growth of these cells could then be induced by the stress conditions. In this review, we focus on the persister formation of human intracellular bacterial pathogens, some of which belong to the most successful persister producers but lack some or even all of the assumed persistence-triggering factors and pathways. We propose a mechanism for the persister formation of these bacterial pathogens which is based on their specific intracellular bipartite metabolism. We postulate that this mode of metabolism ultimately leads, under certain starvation conditions, to the stalling of DNA replication initiation which may be causative for the persister state.

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“…The interplay between DnaA and oriC culminates in the formation of a structured orisome, promoting the opening of the replication bubble (Leonard et al . 2019 ).…”

Section: The Cell Cycle Pacemakers and The Checkpoint Paradigmmentioning

confidence: 99%

Bacterial cell proliferation: from molecules to cells

Meunier

Cornet

Campos

2020

FEMS Microbiology Reviews

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Bacterial cell proliferation is highly efficient, both because bacteria grow fast and multiply with a low failure rate. This efficiency is underpinned by the robustness of the cell cycle and its synchronization with cell growth and cytokinesis. Recent advances in bacterial cell biology brought about by single cell physiology in microfluidic chambers suggest a series of simple phenomenological models at the cellular scale, coupling cell size and growth with the cell cycle. We contrast the apparent simplicity of these mechanisms based on the addition of a constant size between cell cycle events (e.g. two consecutive initiation of DNA replication or cell division) with the complexity of the underlying regulatory networks. Beyond the paradigm of cell cycle checkpoints, the coordination between the DNA and division cycles and cell growth is largely mediated by a wealth of other mechanisms. We propose our perspective on these mechanisms, through the prism of the known crosstalk between DNA replication and segregation, cell division and cell growth or size. We argue that the precise knowledge of these molecular mechanisms is critical to integrate the diverse layers of controls at different time and space scales into synthetic and verifiable models.

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Changing Perspectives on the Role of DnaA-ATP in Orisome Function and Timing Regulation

Cited by 28 publications

References 105 publications

Putative Cooperative ATP–DnaA Binding to Double-Stranded DnaA Box and Single-Stranded DnaA-Trio Motif upon Helicobacter pylori Replication Initiation Complex Assembly

Putative Cooperative ATP–DnaA Binding to Double-Stranded DnaA Box and Single-Stranded DnaA-Trio Motif upon Helicobacter pylori Replication Initiation Complex Assembly

Persistence of Intracellular Bacterial Pathogens—With a Focus on the Metabolic Perspective

Bacterial cell proliferation: from molecules to cells

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