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Article: Le complexe de réplication des poxvirus : cible potentielle de molécules antivirales.

Tarbouriech, Nicolas / Burmeister, Wim P / Bersch, Beate / Iseni, Frédéric

2024 Volume 28, Issue 1, Page(s) 23–35

Abstract: In the spring of 2022, an epidemic due to human monkeypox virus (MPXV) of unprecedented magnitude spread across all continents. Although this event was surprising in its suddenness, the resurgence of a virus from the Poxviridae family is not surprising ... ...

Title translation	Poxvirus-encoded DNA replication proteins: potential targets for antivirals.
Abstract	In the spring of 2022, an epidemic due to human monkeypox virus (MPXV) of unprecedented magnitude spread across all continents. Although this event was surprising in its suddenness, the resurgence of a virus from the Poxviridae family is not surprising in a world population that has been largely naïve to these viruses since the eradication of the smallpox virus in 1980 and the concomitant cessation of vaccination. Since then, a vaccine and two antiviral compounds have been developed to combat a possible return of smallpox. However, the use of these treatments during the 2022 MPXV epidemic showed certain limitations, indicating the importance of continuing to develop the therapeutic arsenal against these viruses. For several decades, efforts to understand the molecular mechanisms involved in the synthesis of the DNA genome of these viruses have been ongoing. Although many questions remain unanswered up to now, the three-dimensional structures of essential proteins, and in particular of the DNA polymerase holoenzyme in complex with DNA, make it possible to consider the development of a model for poxvirus DNA replication. In addition, these structures are valuable tools for the development of new antivirals targeting viral genome synthesis. This review will first present the molecules approved for the treatment of poxvirus infections, followed by a review of our knowledge of the replication machinery of these viruses. Finally, we will describe how these proteins could be the target of new antiviral compounds.
MeSH term(s)	Humans ; Poxviridae/genetics ; Variola virus/genetics ; Mpox (monkeypox) ; DNA ; DNA Replication ; Antiviral Agents/pharmacology ; Antiviral Agents/therapeutic use
Chemical Substances	DNA (9007-49-2) ; Antiviral Agents
Language	French
Publishing date	2024-03-07
Publishing country	France
Document type	Review ; English Abstract ; Journal Article
ZDB-ID	2118387-9
ISSN	1950-6961 ; 1267-8694
ISSN (online)	1950-6961
ISSN	1267-8694
DOI	10.1684/vir.2024.1033
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Selection of Primer-Template Sequences That Bind with Enhanced Affinity to Vaccinia Virus E9 DNA Polymerase.

DeStefano, Jeffrey J / Iseni, Frédéric / Tarbouriech, Nicolas

Viruses

2022 Volume 14, Issue 2

Abstract: A modified SELEX (Systematic Evolution of Ligands by Exponential Enrichment) pr,otocol (referred to as PT SELEX) was used to select primer-template (P/T) sequences that bound to the vaccinia virus polymerase catalytic subunit (E9) with enhanced affinity. ...

Abstract	A modified SELEX (Systematic Evolution of Ligands by Exponential Enrichment) pr,otocol (referred to as PT SELEX) was used to select primer-template (P/T) sequences that bound to the vaccinia virus polymerase catalytic subunit (E9) with enhanced affinity. A single selected P/T sequence (referred to as E9-R5-12) bound in physiological salt conditions with an apparent equilibrium dissociation constant (K
MeSH term(s)	Avian Myeloblastosis Virus/genetics ; Avian Myeloblastosis Virus/metabolism ; Base Sequence ; DNA, Viral/biosynthesis ; DNA-Directed DNA Polymerase/genetics ; DNA-Directed DNA Polymerase/metabolism ; HIV Reverse Transcriptase/genetics ; HIV Reverse Transcriptase/metabolism ; Moloney murine leukemia virus/genetics ; Moloney murine leukemia virus/metabolism ; Protein Binding ; SELEX Aptamer Technique ; Vaccinia virus/enzymology ; Vaccinia virus/genetics ; Viral Proteins/genetics ; Viral Proteins/metabolism ; Virus Replication
Chemical Substances	DNA, Viral ; Viral Proteins ; DNA polymerase, vaccinia virus (EC 2.7.7.-) ; HIV Reverse Transcriptase (EC 2.7.7.49) ; DNA-Directed DNA Polymerase (EC 2.7.7.7)
Language	English
Publishing date	2022-02-10
Publishing country	Switzerland
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v14020369
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Article: Human viruses, ancient, recent and zoonosis: a never ending story?

Ruigrok, Rob W H / Drouet, Emmanuel / Morand, Patrice / Tarbouriech, Nicolas

Virologie (Montrouge, France)

2022 Volume 26, Issue 3, Page(s) 240–252

Abstract: For the past three years, the nature and evolution of human viruses have been taught in University Grenoble-Alpes without relying on the systematic list of all virus families. A «historical» approach allows to define three main categories of viruses ... ...

Title translation	Virus humains anciens, récents et zoonotiques : une histoire sans fin ?
Abstract	For the past three years, the nature and evolution of human viruses have been taught in University Grenoble-Alpes without relying on the systematic list of all virus families. A «historical» approach allows to define three main categories of viruses following if they have co-evolved with humans for a very long time (ancient human viruses), if they began to infect humans in the Neolithic or later (recent human viruses) or if they are still animal viruses that are transmitted to humans sporadically (zoonotic viruses). We present below the principles and some examples of this pedagogic separation which has not the pretention to replace the classical taxonomic classification based on morphological and sequence similarity (ICTV classification) or on the form and replication mode of the viral genome (Baltimore classification). It helps grouping of viruses with similar effects even if their evolution is different. We show where human viruses come from and how they can cause human diseases. This approach was tested with Biology students, and then extended to Medicine and Pharmacy students to ensure that teaching was based on the same concepts in the three Faculties. In the end, all the students were very receptive and interested in this approach. Of course, different teaching methods can work, but this way of presenting things is also more fun for teachers and promotes cooperation between speakers.
MeSH term(s)	Animals ; Baltimore ; Genome, Viral ; Humans ; Viruses/genetics ; Zoonoses
Language	French
Publishing date	2022-08-09
Publishing country	France
Document type	Journal Article
ZDB-ID	2118387-9
ISSN	1950-6961 ; 1267-8694
ISSN (online)	1950-6961
ISSN	1267-8694
DOI	10.1684/vir.2022.0957
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Article: Selection of Primer–Template Sequences That Bind with Enhanced Affinity to Vaccinia Virus E9 DNA Polymerase

DeStefano, Jeffrey J. / Iseni, Frédéric / Tarbouriech, Nicolas

Viruses. 2022 Feb. 10, v. 14, no. 2

2022

Abstract: A modified SELEX (Systematic Evolution of Ligands by Exponential Enrichment) pr,otocol (referred to as PT SELEX) was used to select primer–template (P/T) sequences that bound to the vaccinia virus polymerase catalytic subunit (E9) with enhanced affinity. ...

Abstract	A modified SELEX (Systematic Evolution of Ligands by Exponential Enrichment) pr,otocol (referred to as PT SELEX) was used to select primer–template (P/T) sequences that bound to the vaccinia virus polymerase catalytic subunit (E9) with enhanced affinity. A single selected P/T sequence (referred to as E9-R5-12) bound in physiological salt conditions with an apparent equilibrium dissociation constant (KD,ₐₚₚ) of 93 ± 7 nM. The dissociation rate constant (kₒff) and binding half-life (t₁/₂) for E9-R5-12 were 0.083 ± 0.019 min⁻¹ and 8.6 ± 2.0 min, respectively. The values indicated a several-fold greater binding ability compared to controls, which bound too weakly to be accurately measured under the conditions employed. Loop-back DNA constructs with 3′-recessed termini derived from E9-R5-12 also showed enhanced binding when the hybrid region was 21 nucleotides or more. Although the sequence of E9-R5-12 matched perfectly over a 12-base-pair segment in the coding region of the virus B20 protein, there was no clear indication that this sequence plays any role in vaccinia virus biology, or a clear reason why it promotes stronger binding to E9. In addition to E9, five other polymerases (HIV-1, Moloney murine leukemia virus, and avian myeloblastosis virus reverse transcriptases (RTs), and Taq and Klenow DNA polymerases) have demonstrated strong sequence binding preferences for P/Ts and, in those cases, there was biological or potential evolutionary relevance. For the HIV-1 RT, sequence preferences were used to aid crystallization and study viral inhibitors. The results suggest that several other DNA polymerases may have P/T sequence preferences that could potentially be exploited in various protocols.
Keywords	Avian myeloblastosis virus ; DNA ; DNA-directed DNA polymerase ; Murine leukemia virus ; Vaccinia virus ; crystallization ; dissociation ; half life ; hybrids ; nucleotides ; protein subunits ; systematic evolution of ligands by exponential enrichment ; viruses
Language	English
Dates of publication	2022-0210
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
ZDB-ID	2516098-9
ISSN	1999-4915
ISSN	1999-4915
DOI	10.3390/v14020369
Database	NAL-Catalogue (AGRICOLA)

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Article: La synthèse du génome des poxvirus.

Tarbouriech, Nicolas / Flusin, Olivier / Sele, Céleste / Iseni, Frédéric

Virologie (Montrouge, France)

2020 Volume 16, Issue 4, Page(s) 210–224

Abstract: Poxviruses are distinguished from other DNA viruses by replicating exclusively in the cytoplasm of the infected host cell. Replication of the linear double-stranded DNA genome takes place in the perinuclear area, in cytoplasmic foci called viral ... ...

Title translation	La synthèse du génome des poxvirus.
Abstract	Poxviruses are distinguished from other DNA viruses by replicating exclusively in the cytoplasm of the infected host cell. Replication of the linear double-stranded DNA genome takes place in the perinuclear area, in cytoplasmic foci called viral factories. Poxvirus genome organization evolved in order to prevent the virus from being dependent on nuclear enzymes. Therefore, they encode most, if not all, of the proteins required for efficient replication of their genome. Some of these proteins are essential for virus growth (i.e., enzymes directly involved in DNA synthesis). In contrast, others are dispensable for virus propagation in cell culture (i.e., proteins involved in nucleotide metabolism). Most of our knowledge concerning poxvirus replication comes from studies performed on vaccinia virus, the virus used as vaccine to eradicate smallpox more than 30 years ago. This article reviews our current knowledge of the molecular mechanisms governing poxvirus genome synthesis, with a particular focus on the viral proteins involved in this process. A working model for poxvirus DNA replication is also presented.
Language	English
Publishing date	2020-09-11
Publishing country	France
Document type	Journal Article
ZDB-ID	2118387-9
ISSN	1950-6961 ; 1267-8694
ISSN (online)	1950-6961
ISSN	1267-8694
DOI	10.1684/vir.2012.0456
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Article ; Online: Analysis of SEC-SAXS data via EFA deconvolution and Scatter.

Tully, Mark D / Tarbouriech, Nicolas / Rambo, Robert P / Hutin, Stephanie

Journal of visualized experiments : JoVE

2021 , Issue 167

Abstract: BioSAXS is a popular technique used in molecular and structural biology to determine the solution structure, particle size and shape, surface-to-volume ratio and conformational changes of macromolecules and macromolecular complexes. A high quality SAXS ... ...

Abstract	BioSAXS is a popular technique used in molecular and structural biology to determine the solution structure, particle size and shape, surface-to-volume ratio and conformational changes of macromolecules and macromolecular complexes. A high quality SAXS dataset for structural modeling must be from monodisperse, homogeneous samples and this is often only reached by a combination of inline chromatography and immediate SAXS measurement. Most commonly, size-exclusion chromatography is used to separate samples and exclude contaminants and aggregations from the particle of interest allowing SAXS measurements to be made from a well-resolved chromatographic peak of a single protein species. Still, in some cases, even inline purification is not a guarantee of monodisperse samples, either because multiple components are too close to each other in size or changes in shape induced through binding alter perceived elution time. In these cases, it may be possible to deconvolute the SAXS data of a mixture to obtain the idealized SAXS curves of individual components. Here, we show how this is achieved and the practical analysis of SEC-SAXS data is performed on ideal and difficult samples. Specifically, we show the SEC-SAXS analysis of the vaccinia E9 DNA polymerase exonuclease minus mutant.
MeSH term(s)	Algorithms ; Chromatography, Gel ; DNA/chemistry ; Data Analysis ; Proteins/chemistry ; Scattering, Small Angle ; X-Ray Diffraction
Chemical Substances	Proteins ; DNA (9007-49-2)
Language	English
Publishing date	2021-01-28
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Video-Audio Media
ZDB-ID	2259946-0
ISSN	1940-087X ; 1940-087X
ISSN (online)	1940-087X
ISSN	1940-087X
DOI	10.3791/61578
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Article ; Online: Solution Structure of the C-terminal Domain of A20, the Missing Brick for the Characterization of the Interface between Vaccinia Virus DNA Polymerase and its Processivity Factor.

Bersch, Beate / Tarbouriech, Nicolas / Burmeister, Wim P / Iseni, Frédéric

Journal of molecular biology

2021 Volume 433, Issue 13, Page(s) 167009

Abstract: Poxviruses are enveloped viruses with a linear, double-stranded DNA genome. Viral DNA synthesis is achieved by a functional DNA polymerase holoenzyme composed of three essential proteins. For vaccinia virus (VACV) these are E9, the catalytic subunit, a ... ...

Abstract	Poxviruses are enveloped viruses with a linear, double-stranded DNA genome. Viral DNA synthesis is achieved by a functional DNA polymerase holoenzyme composed of three essential proteins. For vaccinia virus (VACV) these are E9, the catalytic subunit, a family B DNA polymerase, and the heterodimeric processivity factor formed by D4 and A20. The A20 protein links D4 to the catalytic subunit. High-resolution structures have been obtained for the VACV D4 protein in complex with an N-terminal fragment of A20 as well as for E9. In addition, biochemical studies provided evidence that a poxvirus-specific insertion (insert 3) in E9 interacts with the C-terminal residues of A20. Here, we provide solution structures of two different VACV A20 C-terminal constructs containing residues 304-426, fused at their C-terminus to either a BAP (Biotin Acceptor Peptide)-tag or a short peptide containing the helix of E9 insert 3. Together with results from titration studies, these structures shed light on the molecular interface between the catalytic subunit and the processivity factor component A20. The interface comprises hydrophobic residues conserved within the Chordopoxvirinae subfamily. Finally, we constructed a HADDOCK model of the VACV A20
MeSH term(s)	Amino Acid Sequence ; Catalytic Domain/genetics ; Crystallography, X-Ray ; DNA, Viral/chemistry ; DNA, Viral/genetics ; DNA, Viral/metabolism ; DNA-Directed DNA Polymerase/chemistry ; DNA-Directed DNA Polymerase/genetics ; DNA-Directed DNA Polymerase/metabolism ; Holoenzymes/chemistry ; Holoenzymes/genetics ; Holoenzymes/metabolism ; Models, Molecular ; Peptides/chemistry ; Peptides/genetics ; Peptides/metabolism ; Protein Binding ; Protein Domains ; Sequence Homology, Amino Acid ; Solutions/chemistry ; Vaccinia virus/enzymology ; Vaccinia virus/genetics ; Viral Proteins/chemistry ; Viral Proteins/genetics ; Viral Proteins/metabolism ; Virus Replication/genetics
Chemical Substances	DNA, Viral ; Holoenzymes ; Peptides ; Solutions ; Viral Proteins ; DNA polymerase, vaccinia virus (EC 2.7.7.-) ; DNA-Directed DNA Polymerase (EC 2.7.7.7)
Language	English
Publishing date	2021-04-24
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	80229-3
ISSN	1089-8638 ; 0022-2836
ISSN (online)	1089-8638
ISSN	0022-2836
DOI	10.1016/j.jmb.2021.167009
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Article: Analysis of sec-saxs data via efa deconvolution and scatter

Tully, Mark D / Tarbouriech, Nicolas / Rambo, Robert P / Hutin, Stephanie

Journal of visualized experiments. 2021 Jan. 28, , no. 167

2021

Abstract	BioSAXS is a popular technique used in molecular and structural biology to determine the solution structure, particle size and shape, surface-to-volume ratio and conformational changes of macromolecules and macromolecular complexes. A high quality SAXS dataset for structural modeling must be from monodisperse, homogeneous samples and this is often only reached by a combination of inline chromatography and immediate SAXS measurement. Most commonly, size-exclusion chromatography is used to separate samples and exclude contaminants and aggregations from the particle of interest allowing SAXS measurements to be made from a well-resolved chromatographic peak of a single protein species. Still, in some cases, even inline purification is not a guarantee of monodisperse samples, either because multiple components are too close to each other in size or changes in shape induced through binding alter perceived elution time. In these cases, it may be possible to deconvolute the SAXS data of a mixture to obtain the idealized SAXS curves of individual components. Here, we show how this is achieved and the practical analysis of SEC-SAXS data is performed on ideal and difficult samples. Specifically, we show the SEC-SAXS analysis of the vaccinia E9 DNA polymerase exonuclease minus mutant.
Keywords	DNA-directed DNA polymerase ; data collection ; gel chromatography ; mutants ; particle size ; structural biology
Language	English
Dates of publication	2021-0128
Size	p. e61578.
Publishing place	Journal of Visualized Experiments
Document type	Article
Note	NAL-AP-2-clean
ZDB-ID	2259946-0
ISSN	1940-087X
ISSN	1940-087X
DOI	10.3791/61578
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Article: Solution Structure of the C-terminal Domain of A20, the Missing Brick for the Characterization of the Interface between Vaccinia Virus DNA Polymerase and its Processivity Factor

Bersch, Beate / Tarbouriech, Nicolas / Burmeister, Wim P / Iseni, Frédéric

Journal of molecular biology. 2021 June 25, v. 433, no. 13

2021

Abstract	Poxviruses are enveloped viruses with a linear, double-stranded DNA genome. Viral DNA synthesis is achieved by a functional DNA polymerase holoenzyme composed of three essential proteins. For vaccinia virus (VACV) these are E9, the catalytic subunit, a family B DNA polymerase, and the heterodimeric processivity factor formed by D4 and A20. The A20 protein links D4 to the catalytic subunit. High-resolution structures have been obtained for the VACV D4 protein in complex with an N-terminal fragment of A20 as well as for E9. In addition, biochemical studies provided evidence that a poxvirus-specific insertion (insert 3) in E9 interacts with the C-terminal residues of A20. Here, we provide solution structures of two different VACV A20 C-terminal constructs containing residues 304–426, fused at their C-terminus to either a BAP (Biotin Acceptor Peptide)-tag or a short peptide containing the helix of E9 insert 3. Together with results from titration studies, these structures shed light on the molecular interface between the catalytic subunit and the processivity factor component A20. The interface comprises hydrophobic residues conserved within the Chordopoxvirinae subfamily. Finally, we constructed a HADDOCK model of the VACV A20₃₀₄₋₄₂₆-E9 complex, which is in excellent accordance with previous experimental data.
Keywords	DNA ; DNA replication ; DNA-directed DNA polymerase ; Vaccinia virus ; amino acid sequences ; biotin ; bricks ; genome ; hydrophobicity ; models ; molecular biology ; peptides ; protein subunits ; titration
Language	English
Dates of publication	2021-0625
Publishing place	Elsevier Ltd
Document type	Article
Note	NAL-AP-2-clean
ZDB-ID	80229-3
ISSN	1089-8638 ; 0022-2836
ISSN (online)	1089-8638
ISSN	0022-2836
DOI	10.1016/j.jmb.2021.167009
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: The Vaccinia Virus DNA Helicase Structure from Combined Single-Particle Cryo-Electron Microscopy and AlphaFold2 Prediction.

Hutin, Stephanie / Ling, Wai Li / Tarbouriech, Nicolas / Schoehn, Guy / Grimm, Clemens / Fischer, Utz / Burmeister, Wim P

Viruses

2022 Volume 14, Issue 10

Abstract: Poxviruses are large DNA viruses with a linear double-stranded DNA genome circularized at the extremities. The helicase-primase D5, composed of six identical 90 kDa subunits, is required for DNA replication. D5 consists of a primase fragment flexibly ... ...

Abstract	Poxviruses are large DNA viruses with a linear double-stranded DNA genome circularized at the extremities. The helicase-primase D5, composed of six identical 90 kDa subunits, is required for DNA replication. D5 consists of a primase fragment flexibly attached to the hexameric C-terminal polypeptide (res. 323-785) with confirmed nucleotide hydrolase and DNA-binding activity but an elusive helicase activity. We determined its structure by single-particle cryo-electron microscopy. It displays an AAA+ helicase core flanked by N- and C-terminal domains. Model building was greatly helped by the predicted structure of D5 using AlphaFold2. The 3.9 Å structure of the N-terminal domain forms a well-defined tight ring while the resolution decreases towards the C-terminus, still allowing the fit of the predicted structure. The N-terminal domain is partially present in papillomavirus E1 and polyomavirus LTA helicases, as well as in a bacteriophage NrS-1 helicase domain, which is also closely related to the AAA+ helicase domain of D5. Using the Pfam domain database, a D5_N domain followed by DUF5906 and Pox_D5 domains could be assigned to the cryo-EM structure, providing the first 3D structures for D5_N and Pox_D5 domains. The same domain organization has been identified in a family of putative helicases from large DNA viruses, bacteriophages, and selfish DNA elements.
MeSH term(s)	DNA Primase/chemistry ; DNA Primase/genetics ; DNA Primase/metabolism ; Cryoelectron Microscopy ; Vaccinia virus/genetics ; DNA Helicases/genetics ; DNA ; DNA Replication ; Nucleotides
Chemical Substances	DNA Primase (EC 2.7.7.-) ; DNA Helicases (EC 3.6.4.-) ; DNA (9007-49-2) ; Nucleotides
Language	English
Publishing date	2022-10-07
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v14102206
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