Direct observation of helicase–topoisomerase coupling within reverse gyrase

Yang, Xi; Garnier, Florence; Débat, Hélène; Strick, Térence; Nadal, Marc

doi:10.1073/pnas.1921848117

Cited by 11 publications

(13 citation statements)

References 64 publications

(70 reference statements)

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“…It is noteworthy that the DNA-binding protein Sso7d is able to constrain negative supercoils of DNA and consequently inhibits reverse gyrase ( Napoli et al, 2002 ). This inhibition might be the consequence of the decrease of the unwinding capability of DNA, which is required for the activity of the reverse gyrase, as we evidenced previously ( Yang et al, 2020 ).…”

Section: Type I Dna-topoisomerasessupporting

confidence: 61%

“…After ATP-binding, this unwinding decreased to 10 base pairs, reflecting a conformational change into the protein that probably induces a particular shape to the DNA before the cleavage and the strand passage reaction. It is this particular DNA conformation that leads to an increase of the linking number by one after the DNA resealing ( Yang et al, 2020 ). Even though nearly all reverse gyrases have a monomeric structure with two domains, it is noteworthy that in Nanoarchaeum equitans , the two domains of the reverse gyrase are naturally split into two polypeptides ( Capp et al, 2010 ).…”

Section: Type I Dna-topoisomerasesmentioning

confidence: 99%

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Archaea: A Gold Mine for Topoisomerase Diversity

et al. 2021

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The control of DNA topology is a prerequisite for all the DNA transactions such as DNA replication, repair, recombination, and transcription. This global control is carried out by essential enzymes, named DNA-topoisomerases, that are mandatory for the genome stability. Since many decades, the Archaea provide a significant panel of new types of topoisomerases such as the reverse gyrase, the type IIB or the type IC. These more or less recent discoveries largely contributed to change the understanding of the role of the DNA topoisomerases in all the living world. Despite their very different life styles, Archaea share a quasi-homogeneous set of DNA-topoisomerases, except thermophilic organisms that possess at least one reverse gyrase that is considered a marker of the thermophily. Here, we discuss the effect of the life style of Archaea on DNA structure and topology and then we review the content of these essential enzymes within all the archaeal diversity based on complete sequenced genomes available. Finally, we discuss their roles, in particular in the processes involved in both the archaeal adaptation and the preservation of the genome stability.

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Section: Type I Dna-topoisomerasessupporting

confidence: 61%

Section: Type I Dna-topoisomerasesmentioning

confidence: 99%

Archaea: A Gold Mine for Topoisomerase Diversity

et al. 2021

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“…To determine how the C-terminal domain affects the turnover kinetics of TOP3B, we carried out single-molecule measurements 50 – 52 comparing DNA relaxation by TOP3B and the TOP3Bcore (Fig. 4h ).…”

Section: Resultsmentioning

confidence: 99%

Structural and biochemical basis for DNA and RNA catalysis by human Topoisomerase 3β

et al. 2022

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In metazoans, topoisomerase 3β (TOP3B) regulates R-loop dynamics and mRNA translation, which are critical for genome stability, neurodevelopment and normal aging. As a Type IA topoisomerase, TOP3B acts by general acid-base catalysis to break and rejoin single-stranded DNA. Passage of a second DNA strand through the transient break permits dissipation of hypernegative DNA supercoiling and catenation/knotting. Additionally, hsTOP3B was recently demonstrated as the human RNA topoisomerase, required for normal neurodevelopment and proposed to be a potential anti-viral target upon RNA virus infection. Here we elucidate the biochemical mechanisms of human TOP3B. We delineate the roles of divalent metal ions, and of a conserved Lysine residue (K10) in the differential catalysis of DNA and RNA. We also demonstrate that three regulatory factors fine-tune the catalytic performance of TOP3B: the TOP3B C-terminal tail, its protein partner TDRD3, and the sequence of its DNA/RNA substrates.

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“…[129]. Optical (OT) [130,131], and magnetic tweezers (MT) [132][133][134][135][136] probing protein function (not unfolding, ROS: reactive oxygen species). Surface immobilized smFRET in confocal [137], or TIRF mode with CMOS [138] or EMCCD [2] detectors.…”

Section: Single-molecule Techniques Side By Sidementioning

confidence: 99%

Nanopores: a versatile tool to study protein dynamics

Schmid

Dekker

2021

Essays in Biochemistry

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Proteins are the active workhorses in our body. These biomolecules perform all vital cellular functions from DNA replication and general biosynthesis to metabolic signaling and environmental sensing. While static 3D structures are now readily available, observing the functional cycle of proteins – involving conformational changes and interactions – remains very challenging, e.g., due to ensemble averaging. However, time-resolved information is crucial to gain a mechanistic understanding of protein function. Single-molecule techniques such as FRET and force spectroscopies provide answers but can be limited by the required labelling, a narrow time bandwidth, and more. Here, we describe electrical nanopore detection as a tool for probing protein dynamics. With a time bandwidth ranging from microseconds to hours, nanopore experiments cover an exceptionally wide range of timescales that is very relevant for protein function. First, we discuss the working principle of label-free nanopore experiments, various pore designs, instrumentation, and the characteristics of nanopore signals. In the second part, we review a few nanopore experiments that solved research questions in protein science, and we compare nanopores to other single-molecule techniques. We hope to make electrical nanopore sensing more accessible to the biochemical community, and to inspire new creative solutions to resolve a variety of protein dynamics – one molecule at a time.

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Direct observation of helicase–topoisomerase coupling within reverse gyrase

Cited by 11 publications

References 64 publications

Archaea: A Gold Mine for Topoisomerase Diversity

Archaea: A Gold Mine for Topoisomerase Diversity

Structural and biochemical basis for DNA and RNA catalysis by human Topoisomerase 3β

Nanopores: a versatile tool to study protein dynamics

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