Bipartite promoters and RNA editing of paramyxoviruses and filoviruses

Mercier, Philippe Le; Kolakofsky, Daniel

doi:10.1261/rna.068825.118

Cited by 17 publications

(10 citation statements)

References 29 publications

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“…Substitution of nt −13 to −36 was neutral and nucleotide identities at positions −37 to −44 immediately preceding the TSS were not essential for transcription, although contributing to transcription activity (McGivern et al 2005). Current models of bipartite 3 ′ -leader promoters, developed for paramyxoviruses (Murphy et al 1998;Tapparel et al 1998; for reviews, see Noton and Fearns 2015;le Mercier and Kolakofsky 2019), predict that 3 ′ -terminal and internal promoter elements (resembling PE1 and PE2, Fig 1B) need to be juxtaposed on the same vertical face of the nucleocapsid helix for concerted recognition by the viral polymerase. This model is based on the finding that the paramyxoviral nucleocapsid contains 13 NP molecules per helical turn and NP molecules 14-16 (counted from the 3 ′ -end) bind to the three PE2 hexamers (3 ′ -CN 5 in the case of Sendai virus [SeV]).…”

Section: Discussionmentioning

confidence: 99%

Hexamer phasing governs transcription initiation in the 3′-leader of Ebola virus

Bach

Biedenkopf

Grünweller

et al. 2020

RNA

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The genomic, bipartite replication promoter of Ebola virus (EBOV) consists of elements 1 (PE1) and 2 (PE2). PE1 (55 nt at the 3 ′ ′ ′ ′ ′ -terminus) is separated from PE2 (harboring eight 3 ′ ′ ′ ′ ′ -UN 5 hexamers) by the transcription start sequence (TSS) of the first nucleoprotein (NP) gene plus a spacer sequence. Insertions or deletions in the spacer were reported to support genome replication if comprising 6 or 12, but not 1/2/3/5/9 nt. This gave rise to the formulation of the "rule of 6" for the EBOV replication promoter. Here, we studied the impact of such hexamer phasing on viral transcription using a series of replication-competent and -deficient monocistronic minigenomes, in which the spacer of the NP gene was mutated or replaced with that of internal EBOV genes and mutated variants thereof. Beyond reporter gene assays, we conducted qRT-PCR to determine the levels of mRNA, genomic and antigenomic RNA. We demonstrate that hexamer phasing is also essential for viral transcription, that UN 5 hexamer periodicity extends into PE1 and that the spacer region can be expanded by 48 nt without losses of transcriptional activity. Making the UN 5 hexamer phasing continuous between PE1 and PE2 enhanced the efficiency of transcription and replication. We show that the 2 nt preceding the TSS are essential for transcription. We further propose a role for UN 5 hexamer phasing in positioning NP during initiation of RNA synthesis, or in dissociation/reassociation of NP from the template RNA strand while threading the RNA through the active site of the elongating polymerase during replication and transcription.

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Section: Discussionmentioning

confidence: 99%

Hexamer phasing governs transcription initiation in the 3′-leader of Ebola virus

Bach

Biedenkopf

Grünweller

et al. 2020

RNA

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“…Each nucleocapsid protein binds six nucleotides of RNA ( Alayyoubi et al 2015 ; Gutsche et al 2015 ; Jamin and Yabukarski 2017 ; Webby et al 2019 ), and paramyxoviral genomes always conform to the ‘rule of six’ whereby genome length is some multiple of six ( Calain and Roux 1993 ; Kolakofsky et al 1998 , 2005 ). This is hypothesized to result from the requirement to position the promoter sequences required for initiation of RNA synthesis in the correct register, or phase, with respect to the nucleocapsid protein ( Le Mercier and Kolakofsky 2019 ).…”

Section: Paramyxoviral Rna Synthesis and The Rule Of Sixmentioning

confidence: 99%

Evolutionary history of cotranscriptional editing in the paramyxoviral phosphoprotein gene

2021

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The phosphoprotein gene of the paramyxoviruses encodes multiple protein products. The P, V, and W proteins are generated by transcriptional slippage. This process results in the insertion of non-templated guanosine nucleosides into the mRNA at a conserved edit site. The P protein is an essential component of the viral RNA polymerase, and is encoded by a faithful copy of the gene in the majority of paramyxoviruses. However, in some cases the non essential V protein is encoded by default and guanosines must be inserted into the mRNA in order to encode P. The number of guanosines inserted into the P gene can be described by a probability distribution which varies between viruses. In this article we review the nature of these distributions, which can be inferred from mRNA sequencing data, and reconstruct the evolutionary history of cotranscriptional editing in the paramyxovirus family. Our model suggests that, throughout known history of the family, the system has switched from a P default to a V default mode four times; complete loss of the editing system has occurred twice, the canonical zinc finger domain of the V protein has been deleted or heavily mutated a further two times, and the W protein has independently evolved a novel function three times. Finally, we review the physical mechanisms of cotranscriptional editing via slippage of the viral RNA polymerase.

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“…These viruses share a common architecture of their genomes. The RNA genome length varies between 12 (RSV, VSV) and 19 (filoviruses) kb in length and contains essential untranslated regions (UTRs) at their 3 -(leader) and 5 -(trailer) terminal ends important for viral transcription, replication, and encapsidation [61][62][63][64][65]. While the number of genes encoded by nsNSV varies among its families (from 5 to 10), the organization and relative position of the structural genes is highly conserved: 3'-leader-Nucleoprotein N-Phosphoprotein P-Matrix protein (M)-Glycoprotein (G)-RNA-dependent RNA polymerase (L for large protein)-trailer-5 (Figure 2A,B).…”

Section: Viral Replication Cycle Of Negative Strand Rna Viruses (Nsv)mentioning

confidence: 99%

New Perspectives on the Biogenesis of Viral Inclusion Bodies in Negative-Sense RNA Virus Infections

Dolnik

Gerresheim

Biedenkopf

2021

Cells

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Infections by negative strand RNA viruses (NSVs) induce the formation of viral inclusion bodies (IBs) in the host cell that segregate viral as well as cellular proteins to enable efficient viral replication. The induction of those membrane-less viral compartments leads inevitably to structural remodeling of the cellular architecture. Recent studies suggested that viral IBs have properties of biomolecular condensates (or liquid organelles), as have previously been shown for other membrane-less cellular compartments like stress granules or P-bodies. Biomolecular condensates are highly dynamic structures formed by liquid-liquid phase separation (LLPS). Key drivers for LLPS in cells are multivalent protein:protein and protein:RNA interactions leading to specialized areas in the cell that recruit molecules with similar properties, while other non-similar molecules are excluded. These typical features of cellular biomolecular condensates are also a common characteristic in the biogenesis of viral inclusion bodies. Viral IBs are predominantly induced by the expression of the viral nucleoprotein (N, NP) and phosphoprotein (P); both are characterized by a special protein architecture containing multiple disordered regions and RNA-binding domains that contribute to different protein functions. P keeps N soluble after expression to allow a concerted binding of N to the viral RNA. This results in the encapsidation of the viral genome by N, while P acts additionally as a cofactor for the viral polymerase, enabling viral transcription and replication. Here, we will review the formation and function of those viral inclusion bodies upon infection with NSVs with respect to their nature as biomolecular condensates.

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Bipartite promoters and RNA editing of paramyxoviruses and filoviruses

Cited by 17 publications

References 29 publications

Hexamer phasing governs transcription initiation in the 3′-leader of Ebola virus

Hexamer phasing governs transcription initiation in the 3′-leader of Ebola virus

Evolutionary history of cotranscriptional editing in the paramyxoviral phosphoprotein gene

New Perspectives on the Biogenesis of Viral Inclusion Bodies in Negative-Sense RNA Virus Infections

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