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Article: Archaea: A Gold Mine for Topoisomerase Diversity.

Garnier, Florence / Couturier, Mohea / Débat, Hélène / Nadal, Marc

2021 Volume 12, Page(s) 661411

Abstract: 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 ... ...

Abstract	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.
Language	English
Publishing date	2021-05-25
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2587354-4
ISSN	1664-302X
ISSN	1664-302X
DOI	10.3389/fmicb.2021.661411
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Article ; Online: Structural basis of DNA crossover capture by

Vayssières, Marlène / Marechal, Nils / Yun, Long / Lopez Duran, Brian / Murugasamy, Naveen Kumar / Fogg, Jonathan M / Zechiedrich, Lynn / Nadal, Marc / Lamour, Valérie

Science (New York, N.Y.)

2024 Volume 384, Issue 6692, Page(s) 227–232

Abstract: DNA supercoiling must be precisely regulated by topoisomerases to prevent DNA entanglement. The interaction of type IIA DNA topoisomerases with two DNA molecules, enabling the transport of one duplex through the transient double-stranded break of the ... ...

Abstract	DNA supercoiling must be precisely regulated by topoisomerases to prevent DNA entanglement. The interaction of type IIA DNA topoisomerases with two DNA molecules, enabling the transport of one duplex through the transient double-stranded break of the other, remains elusive owing to structures derived solely from single linear duplex DNAs lacking topological constraints. Using cryo-electron microscopy, we solved the structure of
MeSH term(s)	Cryoelectron Microscopy ; DNA/chemistry ; DNA Gyrase/chemistry ; DNA Gyrase/metabolism ; DNA, Superhelical ; Escherichia coli/enzymology ; Escherichia coli/genetics ; Escherichia coli Proteins/chemistry ; Escherichia coli Proteins/metabolism ; Protein Domains
Chemical Substances	DNA (9007-49-2) ; DNA Gyrase (EC 5.99.1.3) ; DNA, Superhelical ; Escherichia coli Proteins
Language	English
Publishing date	2024-04-11
Publishing country	United States
Document type	Journal Article
ZDB-ID	128410-1
ISSN	1095-9203 ; 0036-8075
ISSN (online)	1095-9203
ISSN	0036-8075
DOI	10.1126/science.adl5899
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Article: Reverse gyrase: an insight into the role of DNA-topoisomerases.

Nadal, Marc

Biochimie

2007 Volume 89, Issue 4, Page(s) 447–455

Abstract: Reverse gyrase was discovered more than twenty years ago. Recent biochemical and structural results have greatly enhanced our understanding of their positive supercoiling mechanism. In addition to new biochemical properties, a fine tuning of reverse ... ...

Abstract	Reverse gyrase was discovered more than twenty years ago. Recent biochemical and structural results have greatly enhanced our understanding of their positive supercoiling mechanism. In addition to new biochemical properties, a fine tuning of reverse gyrase regulation in response to DNA damaging agents has been recently described. These data give us a new insight in the cellular role of reverse gyrase. Moreover, it has been proposed that reverse gyrase has been implicated in genome stability.
MeSH term(s)	DNA Damage ; DNA Topoisomerases/genetics ; DNA Topoisomerases/metabolism ; DNA Topoisomerases, Type I/genetics ; DNA Topoisomerases, Type I/metabolism ; DNA, Superhelical/metabolism ; Genome ; Kinetics
Chemical Substances	DNA, Superhelical ; DNA Topoisomerases (EC 5.99.1.-) ; DNA reverse gyrase (EC 5.99.1.-) ; DNA Topoisomerases, Type I (EC 5.99.1.2)
Language	English
Publishing date	2007-04
Publishing country	France
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	120345-9
ISSN	0300-9084
ISSN	0300-9084
DOI	10.1016/j.biochi.2006.12.010
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Article ; Online: The reverse gyrase TopR1 is responsible for the homeostatic control of DNA supercoiling in the hyperthermophilic archaeon Sulfolobus solfataricus.

Couturier, Mohea / Gadelle, Danièle / Forterre, Patrick / Nadal, Marc / Garnier, Florence

Molecular microbiology

2019 Volume 113, Issue 2, Page(s) 356–368

Abstract: Maintaining an appropriate DNA topology with DNA-based processes (DNA replication, transcription and recombination) is crucial for all three domains of life. In bacteria, the homeostatic regulation for controlling DNA supercoiling relies on antagonistic ... ...

Abstract	Maintaining an appropriate DNA topology with DNA-based processes (DNA replication, transcription and recombination) is crucial for all three domains of life. In bacteria, the homeostatic regulation for controlling DNA supercoiling relies on antagonistic activities of two DNA topoisomerases, TopoI and gyrase. In hyperthermophilic crenarchaea, the presence of such a regulatory system is suggested as two DNA topoisomerases, TopoVI and reverse gyrase, catalyze antagonistic activities. To test this hypothesis, we estimated and compared the number of the TopoVI with that of the two reverse gyrases, TopR1 and TopR2, in Sulfolobus solfataricus cells maintained either at 80 or at 88°C, or reciprocally shifted from one temperature to the other. From the three DNA topoisomerases, TopR1 is the only one exhibiting significant quantitative variations in response to the up- and down-shifts. In addition, the corresponding intrinsic activities of these three DNA topoisomerases were tested in vitro at both temperatures. Although temperature modulates the three DNA topoisomerases activities, TopR1 is the sole topoisomerase able to function at high temperature. Altogether, results presented in this study demonstrate, for the first time, that the DNA topological state of a crenarchaeon is regulated via a homeostatic control, which is mainly mediated by the fine-tuning of TopR1.
MeSH term(s)	Archaea/genetics ; Archaea/metabolism ; Archaeal Proteins/metabolism ; DNA Topoisomerases/metabolism ; DNA Topoisomerases, Type II/metabolism ; DNA, Bacterial ; DNA, Superhelical ; Homeostasis ; Hot Temperature ; Sulfolobus solfataricus/genetics ; Sulfolobus solfataricus/metabolism
Chemical Substances	Archaeal Proteins ; DNA, Bacterial ; DNA, Superhelical ; DNA Topoisomerases (EC 5.99.1.-) ; DNA topoisomerase VI (EC 5.99.1.-) ; DNA Topoisomerases, Type II (EC 5.99.1.3)
Language	English
Publishing date	2019-12-04
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	619315-8
ISSN	1365-2958 ; 0950-382X
ISSN (online)	1365-2958
ISSN	0950-382X
DOI	10.1111/mmi.14424
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Article ; Online: Direct observation of helicase-topoisomerase coupling within reverse gyrase.

Yang, Xi / Garnier, Florence / Débat, Hélène / Strick, Terence R / Nadal, Marc

Proceedings of the National Academy of Sciences of the United States of America

2020 Volume 117, Issue 20, Page(s) 10856–10864

Abstract: Reverse gyrases (RGs) are the only topoisomerases capable of generating positive supercoils in DNA. Members of the type IA family, they do so by generating a single-strand break in substrate DNA and then manipulating the two single strands to generate ... ...

Abstract	Reverse gyrases (RGs) are the only topoisomerases capable of generating positive supercoils in DNA. Members of the type IA family, they do so by generating a single-strand break in substrate DNA and then manipulating the two single strands to generate positive topology. Here, we use single-molecule experimentation to reveal the obligatory succession of steps that make up the catalytic cycle of RG. In the initial state, RG binds to DNA and unwinds ∼2 turns of the double helix in an ATP-independent fashion. Upon nucleotide binding, RG then rewinds ∼1 turn of DNA. Nucleotide hydrolysis and/or product release leads to an increase of 2 units of DNA writhe and resetting of the enzyme, for a net change of topology of +1 turn per cycle. Final dissociation of RG from DNA results in rewinding of the 2 turns of DNA that were initially disrupted. These results show how tight coupling of the helicase and topoisomerase activities allows for induction of positive supercoiling despite opposing torque.
MeSH term(s)	Adenosine Triphosphate/metabolism ; DNA/metabolism ; DNA Helicases/metabolism ; DNA Topoisomerases/metabolism ; DNA Topoisomerases, Type I/metabolism ; DNA, Bacterial/metabolism ; DNA-Binding Proteins/metabolism ; Models, Molecular ; Protein Conformation ; Protein Domains ; Thermus/genetics
Chemical Substances	DNA, Bacterial ; DNA-Binding Proteins ; Adenosine Triphosphate (8L70Q75FXE) ; DNA (9007-49-2) ; DNA Helicases (EC 3.6.4.-) ; DNA Topoisomerases (EC 5.99.1.-) ; DNA reverse gyrase (EC 5.99.1.-) ; DNA Topoisomerases, Type I (EC 5.99.1.2)
Language	English
Publishing date	2020-05-05
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.1921848117
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Article ; Online: Type IA DNA Topoisomerases: A Universal Core and Multiple Activities.

Garnier, Florence / Debat, Hélène / Nadal, Marc

Methods in molecular biology (Clifton, N.J.)

2017 Volume 1703, Page(s) 1–20

Abstract: All the type IA topoisomerases display universal characteristics relying on a core region basically responsible for the transesterification and the strand passage reaction. First limited to the bacterial domain for a long time, these enzymes were further ...

Abstract	All the type IA topoisomerases display universal characteristics relying on a core region basically responsible for the transesterification and the strand passage reaction. First limited to the bacterial domain for a long time, these enzymes were further retrieved in Archaea and Eukarya as well. This is representative of an extremely ancient origin, probably due to an inheritance from the RNA world. As remaining evidence, some current topoisomerases IA have retained a RNA topoisomerase activity. Despite the presence of this core region in all of these TopoIAs, some differences exist and are originated from variable regions, located essentially within both extremities, conferring on them their specificities. During the last 2 decades the evidence of multiple activities and dedicated roles highlighted the importance of the topoisomerases IA. It is now obvious that topoisomerases IA are key enzymes involved in the maintenance of the genome stability. The discovery of these new activities was done thanks to the use of more accurate assays, based on new sophisticated DNA substrates.
MeSH term(s)	Catalytic Domain ; DNA Topoisomerases, Type I/chemistry ; DNA Topoisomerases, Type I/metabolism ; Esterification ; Models, Molecular ; Protein Conformation ; Protein Domains
Chemical Substances	DNA Topoisomerases, Type I (EC 5.99.1.2)
Language	English
Publishing date	2017-11-25
Publishing country	United States
Document type	Journal Article
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-4939-7459-7_1
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Article ; Online: The trigger enzyme PepA (aminopeptidase A) of Escherichia coli, a transcriptional repressor that generates positive supercoiling.

Nguyen Le Minh, Phu / Nadal, Marc / Charlier, Daniel

FEBS letters

2016 Volume 590, Issue 12, Page(s) 1816–1825

Abstract: Escherichia coli aminopeptidase A (PepA) is a trigger enzyme endowed with catalytic activity and DNA-binding properties prominent in transcriptional regulation and site-specific DNA recombination. The current work demonstrates that PepA is a repressor in ...

Abstract	Escherichia coli aminopeptidase A (PepA) is a trigger enzyme endowed with catalytic activity and DNA-binding properties prominent in transcriptional regulation and site-specific DNA recombination. The current work demonstrates that PepA is a repressor in its own right, capable of specifically inhibiting transcription initiation at promoter P1 of the carAB operon, encoding carbamoylphosphate synthase. Furthermore, in vitro topology studies performed with DNA minicircles demonstrate that PepA binding constrains a single positive supercoil in the carP1 control region. Such a topological event is understood to constitute an impediment to transcription initiation and may serve as a mechanism to regulate gene expression.
MeSH term(s)	DNA, Bacterial/genetics ; DNA, Bacterial/metabolism ; DNA, Superhelical/genetics ; DNA, Superhelical/metabolism ; Escherichia coli/genetics ; Escherichia coli/metabolism ; Escherichia coli Proteins/genetics ; Escherichia coli Proteins/metabolism ; Gene Expression Regulation, Bacterial/physiology ; Glutamyl Aminopeptidase/genetics ; Glutamyl Aminopeptidase/metabolism ; Operon/physiology ; Repressor Proteins/genetics ; Repressor Proteins/metabolism ; Transcriptional Activation/physiology
Chemical Substances	DNA, Bacterial ; DNA, Superhelical ; Escherichia coli Proteins ; PepA protein, E coli ; Repressor Proteins ; Glutamyl Aminopeptidase (EC 3.4.11.7)
Language	English
Publishing date	2016
Publishing country	England
Document type	Letter ; Research Support, Non-U.S. Gov't
ZDB-ID	212746-5
ISSN	1873-3468 ; 0014-5793
ISSN (online)	1873-3468
ISSN	0014-5793
DOI	10.1002/1873-3468.12224
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Article ; Online: A specific proteomic response of Sulfolobus solfataricus P2 to gamma radiations.

Larmony, Sharon / Garnier, Florence / Hoste, Astrid / Nadal, Marc

Biochimie

2015 Volume 118, Page(s) 270–277

Abstract: Sulfolobus solfataricus is an acidophilic hyperthermophilic crenarchaeon living at 80 °C in aerobic conditions. As other thermophilic organisms, S. solfataricus is resistant to gamma irradiation and we studied the response of this microorganism to this ... ...

Abstract	Sulfolobus solfataricus is an acidophilic hyperthermophilic crenarchaeon living at 80 °C in aerobic conditions. As other thermophilic organisms, S. solfataricus is resistant to gamma irradiation and we studied the response of this microorganism to this ionizing irradiation by monitoring cell growth, DNA integrity and proteome variations. In aerobic conditions, the S. solfataricus genome was fragmented due to the multiple DNA double strand breakages induced by γ-rays and was fully restored within a couple of hours. Comparison of irradiated and unirradiated cell proteomes indicated that only few proteins changed. The proteins identified by mass spectrometry are involved in different cellular pathways including DNA replication, recombination and repair. Interestingly, we observed that some proteins are irradiation dose-specific while others are common to the cell response regardless of the irradiation dose. Most of the proteins highlighted in these conditions seem to act together to allow an efficient cell response to γ-irradiation.
MeSH term(s)	Archaeal Proteins/metabolism ; DNA Breaks, Double-Stranded/radiation effects ; DNA Repair/physiology ; Electrophoresis, Gel, Two-Dimensional ; Gamma Rays/adverse effects ; Mass Spectrometry ; Proteome/radiation effects ; Sulfolobus solfataricus/metabolism ; Sulfolobus solfataricus/radiation effects
Chemical Substances	Archaeal Proteins ; Proteome
Language	English
Publishing date	2015-11
Publishing country	France
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	120345-9
ISSN	1638-6183 ; 0300-9084
ISSN (online)	1638-6183
ISSN	0300-9084
DOI	10.1016/j.biochi.2015.06.014
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Article ; Online: Transcriptional analysis of the two reverse gyrase encoding genes of Sulfolobus solfataricus P2 in relation to the growth phases and temperature conditions.

Garnier, Florence / Nadal, Marc

Extremophiles : life under extreme conditions

2008 Volume 12, Issue 6, Page(s) 799–809

Abstract: Sulfolobus solfataricus, a hyperthermophilic crenarchaeon, contains two genes encoding reverse gyrases, topR1 and topR2. The steady-state level of their transcripts were quantified during the growth phases for cells maintained either at 72, or 80 degrees ...

Abstract	Sulfolobus solfataricus, a hyperthermophilic crenarchaeon, contains two genes encoding reverse gyrases, topR1 and topR2. The steady-state level of their transcripts were quantified during the growth phases for cells maintained either at 72, or 80 degrees C, and after temperature changes from one to the other temperature. The transcripts of both genes are weakly expressed, but the highest level is observed in actively dividing cells, and is almost undetectable in cells in decline phase. During the temperature shift experiments, there is no significant topR2 variation. By contrast, there is a maximum 2.4-fold increase in topR1 transcripts within 30 min after the downshift. After 1 h, the transcript level reaches the level characteristic of cells adapted to the new temperature. After an upward shift, the topR1 expression pattern is inversely regulated with a transient decrease with the same time course. The topR1 expression profile is completely different from that of topR2 after temperature shift experiments; this suggests a different regulation process for the two reverse gyrase genes. The fine tuning of the topR1 transcript expression within a short interval of time after a temperature shift illustrates a rapid adaptation response to temperature change.
MeSH term(s)	Base Sequence ; Blotting, Northern ; DNA Gyrase/genetics ; DNA Primers ; Genes, Archaeal ; Hot Temperature ; RNA, Messenger/genetics ; Sulfolobus solfataricus/genetics ; Sulfolobus solfataricus/growth & development ; Transcription, Genetic
Chemical Substances	DNA Primers ; RNA, Messenger ; DNA Gyrase (EC 5.99.1.3)
Language	English
Publishing date	2008-09-06
Publishing country	Germany
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1481278-2
ISSN	1433-4909 ; 1431-0651
ISSN (online)	1433-4909
ISSN	1431-0651
DOI	10.1007/s00792-008-0186-2
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Article: Transcriptional analysis of the two reverse gyrase encoding genes of Sulfolobus solfataricus P2 in relation to the growth phases and temperature conditions

Garnier, Florence / Nadal, Marc

Extremophiles life under extreme conditions. 2008 Nov., v. 12, no. 6

2008

Abstract	Sulfolobus solfataricus, a hyperthermophilic crenarchaeon, contains two genes encoding reverse gyrases, topR1 and topR2. The steady-state level of their transcripts were quantified during the growth phases for cells maintained either at 72, or 80°C, and after temperature changes from one to the other temperature. The transcripts of both genes are weakly expressed, but the highest level is observed in actively dividing cells, and is almost undetectable in cells in decline phase. During the temperature shift experiments, there is no significant topR2 variation. By contrast, there is a maximum 2.4-fold increase in topR1 transcripts within 30 min after the downshift. After 1 h, the transcript level reaches the level characteristic of cells adapted to the new temperature. After an upward shift, the topR1 expression pattern is inversely regulated with a transient decrease with the same time course. The topR1 expression profile is completely different from that of topR2 after temperature shift experiments; this suggests a different regulation process for the two reverse gyrase genes. The fine tuning of the topR1 transcript expression within a short interval of time after a temperature shift illustrates a rapid adaptation response to temperature change.
Language	English
Dates of publication	2008-11
Size	p. 799-809.
Publisher	Springer Japan
Publishing place	Japan
Document type	Article
ZDB-ID	1481278-2
ISSN	1433-4909 ; 1431-0651
ISSN (online)	1433-4909
ISSN	1431-0651
DOI	10.1007/s00792-008-0186-2
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