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Article ; Online: Translation of SARS-CoV-2 gRNA Is Extremely Efficient and Competitive despite a High Degree of Secondary Structures and the Presence of an uORF.

Condé, Lionel / Allatif, Omran / Ohlmann, Théophile / de Breyne, Sylvain

2022 Volume 14, Issue 7

Abstract: The SARS-CoV-2 infection generates up to nine different sub-genomic mRNAs (sgRNAs), in addition to the genomic RNA (gRNA). The 5'UTR of each viral mRNA shares the first 75 nucleotides (nt.) at their 5'end, called the leader, but differentiates by a ... ...

Abstract	The SARS-CoV-2 infection generates up to nine different sub-genomic mRNAs (sgRNAs), in addition to the genomic RNA (gRNA). The 5'UTR of each viral mRNA shares the first 75 nucleotides (nt.) at their 5'end, called the leader, but differentiates by a variable sequence (0 to 190 nt. long) that follows the leader. As a result, each viral mRNA has its own specific 5'UTR in term of length, RNA structure, uORF and Kozak context; each one of these characteristics could affect mRNA expression. In this study, we have measured and compared translational efficiency of each of the ten viral transcripts. Our data show that most of them are very efficiently translated in all translational systems tested. Surprisingly, the gRNA 5'UTR, which is the longest and the most structured, was also the most efficient to initiate translation. This property is conserved in the 5'UTR of SARS-CoV-1 but not in MERS-CoV strain, mainly due to the regulation imposed by the uORF. Interestingly, the translation initiation mechanism on the SARS-CoV-2 gRNA 5'UTR requires the cap structure and the components of the eIF4F complex but showed no dependence in the presence of the poly(A) tail in vitro. Our data strongly suggest that translation initiation on SARS-CoV-2 mRNAs occurs via an unusual cap-dependent mechanism.
MeSH term(s)	5' Untranslated Regions ; Genomics ; Nucleic Acid Conformation ; Protein Biosynthesis ; RNA, Messenger/genetics ; SARS-CoV-2/genetics
Chemical Substances	5' Untranslated Regions ; RNA, Messenger
Language	English
Publishing date	2022-07-08
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v14071505
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Article ; Online: Focus on Translation Initiation of the HIV-1 mRNAs.

de Breyne, Sylvain / Ohlmann, Théophile

International journal of molecular sciences

2018 Volume 20, Issue 1

Abstract: To replicate and disseminate, viruses need to manipulate and modify the cellular machinery for their own benefit. We are interested in translation, which is one of the key steps of gene expression and viruses that have developed several strategies to ... ...

Abstract	To replicate and disseminate, viruses need to manipulate and modify the cellular machinery for their own benefit. We are interested in translation, which is one of the key steps of gene expression and viruses that have developed several strategies to hijack the ribosomal complex. The type 1 human immunodeficiency virus is a good paradigm to understand the great diversity of translational control. Indeed, scanning, leaky scanning, internal ribosome entry sites, and adenosine methylation are used by ribosomes to translate spliced and unspliced HIV-1 mRNAs, and some require specific cellular factors, such as the DDX3 helicase, that mediate mRNA export and translation. In addition, some viral and cellular proteins, including the HIV-1 Tat protein, also regulate protein synthesis through targeting the protein kinase PKR, which once activated, is able to phosphorylate the eukaryotic translation initiation factor eIF2α, which results in the inhibition of cellular mRNAs translation. Finally, the infection alters the integrity of several cellular proteins, including initiation factors, that directly or indirectly regulates translation events. In this review, we will provide a global overview of the current situation of how the HIV-1 mRNAs interact with the host cellular environment to produce viral proteins.
MeSH term(s)	Gene Expression Regulation, Viral ; HIV Infections/virology ; HIV-1/physiology ; Host-Pathogen Interactions/immunology ; Humans ; Immunity, Innate ; Internal Ribosome Entry Sites ; Peptide Chain Initiation, Translational ; Protein Biosynthesis ; RNA Splicing ; RNA, Messenger/genetics ; RNA, Messenger/metabolism ; RNA, Viral/genetics
Chemical Substances	Internal Ribosome Entry Sites ; RNA, Messenger ; RNA, Viral
Keywords	covid19
Language	English
Publishing date	2018-12-28
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms20010101
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Article ; Online: Focus on Translation Initiation of the HIV-1 mRNAs

Sylvain de Breyne / Théophile Ohlmann

International Journal of Molecular Sciences, Vol 20, Iss 1, p

2018 Volume 101

Abstract	To replicate and disseminate, viruses need to manipulate and modify the cellular machinery for their own benefit. We are interested in translation, which is one of the key steps of gene expression and viruses that have developed several strategies to hijack the ribosomal complex. The type 1 human immunodeficiency virus is a good paradigm to understand the great diversity of translational control. Indeed, scanning, leaky scanning, internal ribosome entry sites, and adenosine methylation are used by ribosomes to translate spliced and unspliced HIV-1 mRNAs, and some require specific cellular factors, such as the DDX3 helicase, that mediate mRNA export and translation. In addition, some viral and cellular proteins, including the HIV-1 Tat protein, also regulate protein synthesis through targeting the protein kinase PKR, which once activated, is able to phosphorylate the eukaryotic translation initiation factor eIF2α, which results in the inhibition of cellular mRNAs translation. Finally, the infection alters the integrity of several cellular proteins, including initiation factors, that directly or indirectly regulates translation events. In this review, we will provide a global overview of the current situation of how the HIV-1 mRNAs interact with the host cellular environment to produce viral proteins.
Keywords	HIV-1 ; unspliced mRNA ; translation initiation ; RNA helicases ; IRES ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
Language	English
Publishing date	2018-12-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
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Article: Translation of SARS-CoV-2 gRNA Is Extremely Efficient and Competitive despite a High Degree of Secondary Structures and the Presence of an uORF

Condé, Lionel / Allatif, Omran / Ohlmann, Théophile / de Breyne, Sylvain

Viruses. 2022 July 08, v. 14, no. 7

2022

Abstract: The SARS-CoV-2 infection generates up to nine different sub-genomic mRNAs (sgRNAs), in addition to the genomic RNA (gRNA). The 5′UTR of each viral mRNA shares the first 75 nucleotides (nt.) at their 5′end, called the leader, but differentiates by a ... ...

Abstract	The SARS-CoV-2 infection generates up to nine different sub-genomic mRNAs (sgRNAs), in addition to the genomic RNA (gRNA). The 5′UTR of each viral mRNA shares the first 75 nucleotides (nt.) at their 5′end, called the leader, but differentiates by a variable sequence (0 to 190 nt. long) that follows the leader. As a result, each viral mRNA has its own specific 5′UTR in term of length, RNA structure, uORF and Kozak context; each one of these characteristics could affect mRNA expression. In this study, we have measured and compared translational efficiency of each of the ten viral transcripts. Our data show that most of them are very efficiently translated in all translational systems tested. Surprisingly, the gRNA 5′UTR, which is the longest and the most structured, was also the most efficient to initiate translation. This property is conserved in the 5′UTR of SARS-CoV-1 but not in MERS-CoV strain, mainly due to the regulation imposed by the uORF. Interestingly, the translation initiation mechanism on the SARS-CoV-2 gRNA 5′UTR requires the cap structure and the components of the eIF4F complex but showed no dependence in the presence of the poly(A) tail in vitro. Our data strongly suggest that translation initiation on SARS-CoV-2 mRNAs occurs via an unusual cap-dependent mechanism.
Keywords	Coronavirus infections ; Severe acute respiratory syndrome coronavirus ; Severe acute respiratory syndrome coronavirus 2 ; gene expression ; genomics ; nucleotides
Language	English
Dates of publication	2022-0708
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
ZDB-ID	2516098-9
ISSN	1999-4915
ISSN	1999-4915
DOI	10.3390/v14071505
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Translational control of coronaviruses.

de Breyne, Sylvain / Vindry, Caroline / Guillin, Olivia / Condé, Lionel / Mure, Fabrice / Gruffat, Henri / Chavatte, Laurent / Ohlmann, Théophile

Nucleic acids research

2021 Volume 48, Issue 22, Page(s) 12502–12522

Abstract: Coronaviruses represent a large family of enveloped RNA viruses that infect a large spectrum of animals. In humans, the severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) is responsible for the current COVID-19 pandemic and is genetically ... ...

Abstract	Coronaviruses represent a large family of enveloped RNA viruses that infect a large spectrum of animals. In humans, the severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) is responsible for the current COVID-19 pandemic and is genetically related to SARS-CoV and Middle East respiratory syndrome-related coronavirus (MERS-CoV), which caused outbreaks in 2002 and 2012, respectively. All viruses described to date entirely rely on the protein synthesis machinery of the host cells to produce proteins required for their replication and spread. As such, virus often need to control the cellular translational apparatus to avoid the first line of the cellular defense intended to limit the viral propagation. Thus, coronaviruses have developed remarkable strategies to hijack the host translational machinery in order to favor viral protein production. In this review, we will describe some of these strategies and will highlight the role of viral proteins and RNAs in this process.
MeSH term(s)	Animals ; COVID-19/epidemiology ; COVID-19/prevention & control ; COVID-19/virology ; Gene Expression Regulation, Viral ; Genome, Viral/genetics ; Humans ; Pandemics ; Protein Biosynthesis/genetics ; RNA, Viral/genetics ; SARS-CoV-2/genetics ; SARS-CoV-2/physiology ; Virus Replication
Chemical Substances	RNA, Viral
Language	English
Publishing date	2021-01-18
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkaa1116
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Article ; Online: Two ribosome recruitment sites direct multiple translation events within HIV1 Gag open reading frame.

Deforges, Jules / de Breyne, Sylvain / Ameur, Melissa / Ulryck, Nathalie / Chamond, Nathalie / Saaidi, Afaf / Ponty, Yann / Ohlmann, Theophile / Sargueil, Bruno

Nucleic acids research

2017 Volume 45, Issue 12, Page(s) 7538

Language	English
Publishing date	2017-05-02
Publishing country	England
Document type	Journal Article ; Published Erratum
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkx401
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Article ; Online: HIV-1 sequences isolated from patients promote expression of shorter isoforms of the Gag polyprotein.

Daudé, Christelle / Décimo, Didier / Trabaud, Mary-Anne / André, Patrice / Ohlmann, Théophile / de Breyne, Sylvain

Archives of virology

2016 Volume 161, Issue 12, Page(s) 3495–3507

Abstract: Human immunodeficiency virus type 1 (HIV-1) unspliced mRNA drives the expression of both Gag and Gag-Pol polyproteins by using both cap- and internal ribosome entry site (IRES)-dependent translation initiation mechanisms. An IRES has been described in ... ...

Abstract	Human immunodeficiency virus type 1 (HIV-1) unspliced mRNA drives the expression of both Gag and Gag-Pol polyproteins by using both cap- and internal ribosome entry site (IRES)-dependent translation initiation mechanisms. An IRES has been described in the matrix coding region that is involved in the production of shorter isoforms of Gag. However, up to now, this has only been shown with sequences derived from the HIV-1 laboratory strains (NL4.3 and HXB2) and never from clinical HIV-1 isolates. We have isolated ~70 sequences from HIV-1-positive patients that we have sequenced and cloned into an expression vector to monitor their ability to drive translation of Gag p55 and the shorter isoforms both in vitro and ex vivo. The results indicate that (1) the translational efficiency from the AUG-p55 varies significantly among the different isolates; (2) expression initiated at AUG-p40 codon is independent of translation initiation at the AUG-p55 triplet; and (3) all sequences promote expression of shorter Gag isoforms, in particular in Jurkat T cells, in which internal initiation occurs exclusively and directly at the AUG-p40 codon. The composition of the first ~800 nucleotides of the HIV-1 unspliced mRNA modulates the expression initiated both at the AUG-p55 and AUG-p40 codons and may impact viral production and replication. Interestingly, the AUG-p40 codon and its surrounding nucleotide context are conserved amongst clinical isolates and are used as a translation initiation site to produce a shorter Gag isoform.
MeSH term(s)	Cloning, Molecular ; Female ; Gene Expression ; HIV Infections/virology ; HIV-1/genetics ; HIV-1/isolation & purification ; Humans ; Jurkat Cells ; Male ; Protein Biosynthesis ; Protein Isoforms/genetics ; RNA, Viral/genetics ; Sequence Analysis, DNA ; gag Gene Products, Human Immunodeficiency Virus/genetics
Chemical Substances	Protein Isoforms ; RNA, Viral ; gag Gene Products, Human Immunodeficiency Virus
Language	English
Publishing date	2016-12
Publishing country	Austria
Document type	Journal Article
ZDB-ID	7491-3
ISSN	1432-8798 ; 0304-8608
ISSN (online)	1432-8798
ISSN	0304-8608
DOI	10.1007/s00705-016-3073-7
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Article ; Online: Two ribosome recruitment sites direct multiple translation events within HIV1 Gag open reading frame.

Deforges, Jules / de Breyne, Sylvain / Ameur, Melissa / Ulryck, Nathalie / Chamond, Nathalie / Saaidi, Afaf / Ponty, Yann / Ohlmann, Theophile / Sargueil, Bruno

Nucleic acids research

2017 Volume 45, Issue 12, Page(s) 7382–7400

Abstract: In the late phase of the HIV virus cycle, the unspliced genomic RNA is exported to the cytoplasm for the necessary translation of the Gag and Gag-pol polyproteins. Three distinct translation initiation mechanisms ensuring Gag production have been ... ...

Abstract	In the late phase of the HIV virus cycle, the unspliced genomic RNA is exported to the cytoplasm for the necessary translation of the Gag and Gag-pol polyproteins. Three distinct translation initiation mechanisms ensuring Gag production have been described with little rationale for their multiplicity. The Gag-IRES has the singularity to be located within Gag ORF and to directly interact with ribosomal 40S. Aiming at elucidating the specificity and the relevance of this interaction, we probed HIV-1 Gag-IRES structure and developed an innovative integrative modelling strategy to take into account all the gathered information. We propose a novel Gag-IRES secondary structure strongly supported by all experimental data. We further demonstrate the presence of two regions within Gag-IRES that independently and directly interact with the ribosome. Importantly, these binding sites are functionally relevant to Gag translation both in vitro and ex vivo. This work provides insight into the Gag-IRES molecular mechanism and gives compelling evidence for its physiological importance. It allows us to propose original hypotheses about the IRES physiological role and conservation among primate lentiviruses.
MeSH term(s)	Genes, Reporter ; HIV-1/genetics ; HIV-1/metabolism ; Humans ; Internal Ribosome Entry Sites ; Jurkat Cells ; Kinetics ; Luciferases/genetics ; Luciferases/metabolism ; Models, Molecular ; Nucleic Acid Conformation ; Open Reading Frames ; Peptide Chain Initiation, Translational ; Ribosome Subunits, Small, Eukaryotic/metabolism ; Ribosome Subunits, Small, Eukaryotic/ultrastructure ; gag Gene Products, Human Immunodeficiency Virus/genetics ; gag Gene Products, Human Immunodeficiency Virus/metabolism
Chemical Substances	Internal Ribosome Entry Sites ; gag Gene Products, Human Immunodeficiency Virus ; Luciferases (EC 1.13.12.-)
Language	English
Publishing date	2017-04-28
Publishing country	England
Document type	Journal Article
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkx303
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Article ; Online: HSP90 Chaperoning in Addition to Phosphoprotein Required for Folding but Not for Supporting Enzymatic Activities of Measles and Nipah Virus L Polymerases.

Bloyet, Louis-Marie / Welsch, Jérémy / Enchery, François / Mathieu, Cyrille / de Breyne, Sylvain / Horvat, Branka / Grigorov, Boyan / Gerlier, Denis

Journal of virology

2016 Volume 90, Issue 15, Page(s) 6642–6656

Abstract: Unlabelled: Nonsegmented negative-stranded RNA viruses, or members of the order Mononegavirales, share a conserved gene order and the use of elaborate transcription and replication machinery made up of at least four molecular partners. These partners ... ...

Abstract	Unlabelled: Nonsegmented negative-stranded RNA viruses, or members of the order Mononegavirales, share a conserved gene order and the use of elaborate transcription and replication machinery made up of at least four molecular partners. These partners have coevolved with the acquisition of the permanent encapsidation of the entire genome by the nucleoprotein (N) and the use of this N-RNA complex as a template for the viral polymerase composed of the phosphoprotein (P) and the large enzymatic protein (L). Not only is P required for polymerase function, but it also stabilizes the L protein through an unknown underlying molecular mechanism. By using NVP-AUY922 and/or 17-dimethylaminoethylamino-17-demethoxygeldanamycin as specific inhibitors of cellular heat shock protein 90 (HSP90), we found that efficient chaperoning of L by HSP90 requires P in the measles, Nipah, and vesicular stomatitis viruses. While the production of P remains unchanged in the presence of HSP90 inhibitors, the production of soluble and functional L requires both P and HSP90 activity. Measles virus P can bind the N terminus of L in the absence of HSP90 activity. Both HSP90 and P are required for the folding of L, as evidenced by a luciferase reporter insert fused within measles virus L. HSP90 acts as a true chaperon; its activity is transient and dispensable for the activity of measles and Nipah virus polymerases of virion origin. That the cellular chaperoning of a viral polymerase into a soluble functional enzyme requires the assistance of another viral protein constitutes a new paradigm that seems to be conserved within the Mononegavirales order. Importance: Viruses are obligate intracellular parasites that require a cellular environment for their replication. Some viruses particularly depend on the cellular chaperoning apparatus. We report here that for measles virus, successful chaperoning of the viral L polymerase mediated by heat shock protein 90 (HSP90) requires the presence of the viral phosphoprotein (P). Indeed, while P protein binds to the N terminus of L independently of HSP90 activity, both HSP90 and P are required to produce stable, soluble, folded, and functional L proteins. Once formed, the mature P+L complex no longer requires HSP90 to exert its polymerase functions. Such a new paradigm for the maturation of a viral polymerase appears to be conserved in several members of the Mononegavirales order, including the Nipah and vesicular stomatitis viruses.
MeSH term(s)	Animals ; Chlorocebus aethiops ; DNA-Directed RNA Polymerases/metabolism ; HSP90 Heat-Shock Proteins/chemistry ; HSP90 Heat-Shock Proteins/metabolism ; HeLa Cells ; Henipavirus Infections/metabolism ; Henipavirus Infections/virology ; Humans ; Measles/metabolism ; Measles/virology ; Measles virus/physiology ; Mice ; Nipah Virus/physiology ; Nucleoproteins/metabolism ; Phosphoproteins/metabolism ; Protein Binding ; Protein Folding ; Rhabdoviridae Infections/metabolism ; Rhabdoviridae Infections/virology ; Vero Cells ; Vesiculovirus/physiology ; Viral Proteins/metabolism ; Virion/physiology ; Virus Replication
Chemical Substances	HSP90 Heat-Shock Proteins ; Nucleoproteins ; Phosphoproteins ; Viral Proteins ; L protein, Nipah virus (EC 2.7.7.-) ; DNA-Directed RNA Polymerases (EC 2.7.7.6) ; L polymerase protein, Vesicular stomatitis-Indiana virus (EC 2.7.7.6)
Language	English
Publishing date	2016-07-11
Publishing country	United States
Document type	Comparative Study ; Journal Article
ZDB-ID	80174-4
ISSN	1098-5514 ; 0022-538X
ISSN (online)	1098-5514
ISSN	0022-538X
DOI	10.1128/JVI.00602-16
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Article ; Online: Translation initiation is driven by different mechanisms on the HIV-1 and HIV-2 genomic RNAs.

de Breyne, Sylvain / Soto-Rifo, Ricardo / López-Lastra, Marcelo / Ohlmann, Théophile

Virus research

2013 Volume 171, Issue 2, Page(s) 366–381

Abstract: The human immunodeficiency virus (HIV) unspliced full length genomic RNA possesses features of an eukaryotic cellular mRNA as it is capped at its 5' end and polyadenylated at its 3' extremity. This genomic RNA is used both for the production of the viral ...

Abstract	The human immunodeficiency virus (HIV) unspliced full length genomic RNA possesses features of an eukaryotic cellular mRNA as it is capped at its 5' end and polyadenylated at its 3' extremity. This genomic RNA is used both for the production of the viral structural and enzymatic proteins (Gag and Pol, respectively) and as genome for encapsidation in the newly formed viral particle. Although both of these processes are critical for viral replication, they should be controlled in a timely manner for a coherent progression into the viral cycle. Some of this regulation is exerted at the level of translational control and takes place on the viral 5' untranslated region and the beginning of the gag coding region. In this review, we have focused on the different initiation mechanisms (cap- and internal ribosome entry site (IRES)-dependent) that are used by the HIV-1 and HIV-2 genomic RNAs and the cellular and viral factors that can modulate their expression. Interestingly, although HIV-1 and HIV-2 share many similarities in the overall clinical syndrome they produce, in some aspects of their replication cycle, and in the structure of their respective genome, they exhibit some differences in the way that ribosomes are recruited on the gag mRNA to initiate translation and produce the viral proteins; this will be discussed in the light of the literature.
MeSH term(s)	Animals ; HIV Infections/virology ; HIV-1/genetics ; HIV-1/metabolism ; HIV-2/genetics ; HIV-2/metabolism ; Humans ; Protein Biosynthesis ; RNA, Viral/genetics ; RNA, Viral/metabolism ; Viral Proteins/genetics ; Viral Proteins/metabolism ; Virus Replication
Chemical Substances	RNA, Viral ; Viral Proteins
Language	English
Publishing date	2013-02
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	605780-9
ISSN	1872-7492 ; 0168-1702
ISSN (online)	1872-7492
ISSN	0168-1702
DOI	10.1016/j.virusres.2012.10.006
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