Elsevier

Virus Research

Volume 162, Issues 1–2, December 2011, Pages 126-137
Virus Research

Review
Structural insights into the rhabdovirus transcription/replication complex

https://doi.org/10.1016/j.virusres.2011.09.025Get rights and content

Abstract

The rhabdoviruses have a non-segmented single stranded negative-sense RNA genome. Their multiplication in a host cell requires three viral proteins in addition to the viral RNA genome. The nucleoprotein (N) tightly encapsidates the viral RNA, and the N–RNA complex serves as the template for both transcription and replication. The viral RNA-dependent RNA polymerase is a two subunit complex that consists of a large subunit, L, and a non-catalytic cofactor, the phosphoprotein, P. P also acts as a chaperone of nascent RNA-free N by forming a N0–P complex that prevents N from binding to cellular RNAs and from polymerizing in the absence of RNA. Here, we discuss the recent molecular and structural studies of individual components and multi-molecular complexes that are involved in the transcription/replication complex of these viruses with regard to their implication in viral transcription and replication.

Section snippets

The rhabdoviruses

The Rhabdoviridae is a family of enveloped viruses that have a non-segmented genome ((−)RNA) made of a single stranded negative-sense RNA molecule. The Rhabdoviridae family is grouped in the order Mononegavirales (MNV) (the name is a composition of three elements: Mono – single; nega – negative sense; virales – virus) with the Filoviridae (Ebola and Marburg viruses), the Paramyxoviridae (measles, mumps, respiratory syncytial viruses) and the Bornaviridae (Borna disease virus). All these

The viral transcription/replication machinery

The genome of the Rhabdoviridae is of 9–18 kb in length and comprises up to ten genes flanked by untranslated leader (le) and trailer (tr) RNA regions. RAV and VSV genomes contain only five genes that are common to all members of the MNV and encode successively from the 3′ terminus, the nucleoprotein (N), the phosphoprotein (P), the matrix protein (M), the glycoprotein (G) and the large subunit of the RNA-dependent RNA polymerase (L) (Fig. 1A).

The replication cycle of both RAV and VSV occurs

The nucleoprotein and the N–RNA complex

In rhabdovirus NCs, each N molecule binds nine nucleotides (Iseni et al., 1998, Thomas et al., 1985). The number of N molecules present in a virion of VSV (1250 N) (Ge et al., 2010, Thomas et al., 1985) corresponds closely to the theoretical number required for covering the entire genome (VSV: 11161 nt → 1240 N), although the length of the genomic RNA molecule is not an entire multiple of nine nucleotides. By contrast, in Paramyxoviridae each N molecule binds six nucleotides and the length of

The phosphoprotein

Early studies showed that P contains independent functional regions (Das et al., 1997, Takacs et al., 1993) and its hydrodynamic properties suggested that it is a non-globular molecule (Gérard et al., 2007). These characteristic features are explained by the recent findings that P is made of concatenated disordered regions and structured domains. The structure and functions of rhabdovirus phosphoproteins have been reviewed recently (Leyrat et al., 2010, Leyrat et al., 2011b), and therefore,

Complexes between the nucleoprotein and the phosphoprotein

During the replication cycle, P forms two different complexes with N, the N0–P complex and the N–RNA–P complex. These interactions are independent of each other, and the recent structural characterization of these two complexes reveals the molecular origin of the dual behavior of P.

The L subunit of the viral polymerase

The L protein is a 250 kDa multi-enzymatic protein, which catalyzes RNA synthesis as well as mRNA capping, methylation and polyadenylation. Its sequence is well conserved among all non-segmented (−)RNA viruses, and sequence alignments revealed the existence of six conserved regions, numbered I–VI (Poch et al., 1990). The conserved region III contains different motives involved in the RNA-dependent RNA polymerase activity, while the conserved regions V and VI carry out mRNA capping. The capping

The viral particle

Animal rhabdoviruses have an overall bullet shape with one conical end and one flat end, while plant rhabdoviruses have a bacillus shape with two conical ends. Fig. 6A and B shows negative-staining electron micrographs of RAV and VSV particles. Recently, the cryo-electron microscopy (EM) reconstruction of the virion of VSV, revealed the molecular organization of the viral proteins in three concentric layers (Ge et al., 2010). The outer shell is a host cell-derived lipid membrane decorated with

Future work

The recent progress made in the preparation of highly purified components of the rhabdovirus transcription/replication complex and in the characterization of their stoichiometry, size, shape and structure opens new avenues for deciphering the molecular mechanisms of this machinery and the subtleties of their regulations. In the near future, it should be possible to reconstitute a functional system from purified components and to test hypotheses concerning the motion of the polymerase on its

Acknowledgments

Research activities in the authors’ laboratory were supported by grants from the French ANR (ANR-07–001-01 (ANRAGE)), the FINOVI foundation and Lyonbiopôle. Ivan Ivanov was supported by a PhD fellowship from the ILL and Filip Yabukarski was supported by a MENRT fellowship from the French government. We thank Guy Schoehn and Leandro Estrozi for their help in preparing Fig. 2, Fig. 6, our colleagues for extensive discussions and the Partnership for Structural Biology for the excellent structural

References (133)

  • C. Ferrer-Orta et al.

    A comparison of viral RNA-dependent RNA polymerases

    Curr. Opin. Struct. Biol.

    (2006)
  • M. Fuxreiter et al.

    Preformed structural elements feature in partner recognition by intrinsically unstructured proteins

    J. Mol. Biol.

    (2004)
  • Y. Gaudin et al.

    Aggregation of VSV M protein is reversible and mediated by nucleation sites: implications for viral assembly

    Virology

    (1995)
  • F.C.A. Gérard et al.

    Modular organization of rabies virus phosphoprotein

    J. Mol. Biol.

    (2009)
  • C.A. Hanlon et al.

    Efficacy of rabies biologics against new Lyssaviruses from Eurasia

    Virus Res.

    (2005)
  • T. Hemachudha et al.

    Human rabies: a disease of complex neuropathogenetic mechanisms and diagnostic challenges

    Lancet Neurol.

    (2002)
  • N. Hercyk et al.

    The vesicular stomatitis virus L protein possesses the mRNA methyltransferase activities

    Virology

    (1988)
  • L.E. Iverson et al.

    Localized attenuation and discontinuous synthesis during vesicular stomatitis virus transcription

    Cell

    (1981)
  • D. Kolakofsky et al.

    Viral RNA polymerase scanning and the gymnastics of sendai virus RNA synthesis

    Virology

    (2004)
  • J. Lenard

    Host cell protein kinases in nonsegmented negative-strand virus (mononegavirales) infection

    Pharmacol. Ther.

    (1999)
  • B.D. Lichty et al.

    Vesicular stomatitis virus: re-inventing the bullet

    Trends Mol. Med.

    (2004)
  • M. Luo et al.

    Conserved characteristics of the rhabdovirus nucleoprotein

    Virus Res.

    (2007)
  • M. Mavrakis et al.

    Isolation and characterisation of the rabies virus N degrees–P complex produced in insect cells

    Virology

    (2003)
  • M. Mavrakis et al.

    Structure and function of the C-terminal domain of the polymerase cofactor of rabies virus

    J. Mol. Biol.

    (2004)
  • M. Mavrakis et al.

    Rabies virus chaperone: identification of the phosphoprotein peptide that keeps nucleoprotein soluble and free from non-specific RNA

    Virology

    (2006)
  • S.A. Moyer et al.

    Messenger RNA species synthesized in vitro by the virion-associated RNA polymerase of vesicular stomatitis virus

    Cell

    (1975)
  • T. Ogino et al.

    Unconventional mechanism of mRNA capping by the RNA-dependent RNA polymerase of vesicular stomatitis virus

    Mol. Cell

    (2007)
  • G. Abraham et al.

    Sequential transcription of the genes of vesicular stomatitis virus

    Proc. Natl. Acad. Sci. U.S.A.

    (1976)
  • M. Ahmed et al.

    Ability of the matrix protein of vesicular stomatitis virus to suppress beta interferon gene expression is genetically correlated with the inhibition of host RNA and protein synthesis

    J. Virol.

    (2003)
  • A.A. Albertini et al.

    Isolation and crystallization of a unique size category of recombinant rabies virus nucleoprotein–RNA rings

    J. Struct. Biol.

    (2006)
  • A.A. Albertini et al.

    Structural aspects of rabies virus replication

    Cell Mol. Life Sci.

    (2008)
  • A.A. Albertini et al.

    Crystal structure of the rabies virus nucleoprotein–RNA complex

    Science

    (2006)
  • L.A. Ball et al.

    Order of transcription of genes of vesicular stomatitis virus

    Proc. Natl. Acad. Sci. U.S.A.

    (1976)
  • A. Barge et al.

    Vesicular stomatitis virus M protein may be inside the ribonucleocapsid coil

    J. Virol.

    (1993)
  • J.N. Barr et al.

    Polymerase slippage at vesicular stomatitis virus gene junctions to generate poly(A) is regulated by the upstream 3′-AUAC-5′ tetranucleotide: implications for the mechanism of transcription termination

    J. Virol.

    (2001)
  • J.N. Barr et al.

    cis-Acting signals involved in termination of vesicular stomatitis virus mRNA synthesis include the conserved AUAC and the U7 signal for polyadenylation

    J. Virol.

    (1997)
  • S. Basak et al.

    Reviewing Chandipura: a vesiculovirus in human epidemics

    Biosci. Rep.

    (2007)
  • B.M. Blumberg et al.

    Intracellular vesicular stomatitis virus leader RNAs are found in nucleocapsid structures

    J. Virol.

    (1981)
  • G. Castel et al.

    Peptides that mimic the amino-terminal end of the rabies virus phosphoprotein have antiviral activity

    J. Virol.

    (2009)
  • M. Chen et al.

    Interaction of vesicular stomatitis virus P and N proteins: identification of two overlapping domains at the N-terminus of P that are involved in N0–P complex formation and encapsidation of viral genome RNA

    J. Virol.

    (2007)
  • M. Chenik et al.

    Mapping the interacting domains between the rabies virus polymerase and phosphoprotein

    J. Virol.

    (1998)
  • J.L. Chuang et al.

    Initiation of vesicular stomatitis virus mutant polR1 transcription internally at the N gene in vitro

    J. Virol.

    (1997)
  • S. Cleaveland et al.

    Estimating human rabies mortality in the United Republic of Tanzania from dog bite injuries

    Bull. World Health Organ.

    (2002)
  • J.H. Connor et al.

    Vesicular stomatitis virus infection alters the eIF4F translation initiation complex and causes dephosphorylation of the eIF4E binding protein 4E-BP1

    J. Virol.

    (2002)
  • J. Curran

    A role for the Sendai virus P protein trimer in RNA synthesis

    J. Virol.

    (1998)
  • O. Delmas et al.

    The structure of the nucleoprotein binding domain of Lyssavirus phosphoprotein reveals a structural relationship between the N–RNA binding domains of Rhabdoviridae and Paramyxoviridae

    RNA Biol.

    (2010)
  • B. Dietzschold et al.

    Concepts in the pathogenesis of rabies

    Future Virol.

    (2008)
  • P.J. Dillon et al.

    Early steps in the assembly of vesicular stomatitis virus nucleocapsids in infected cells

    J. Virol.

    (1988)
  • H. Ding et al.

    Crystal structure of the oligomerization domain of the phosphoprotein of vesicular stomatitis virus

    J. Virol.

    (2006)
  • H. Ding et al.

    Crystallization and preliminary X-ray analysis of a proteinase-K-resistant domain within the phosphoprotein of vesicular stomatitis virus (Indiana)

    Acta Crystallogr. D: Biol. Crystallogr.

    (2004)
  • Cited by (0)

    View full text