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Review
. 2014 Sep:109:97-109.
doi: 10.1016/j.antiviral.2014.06.013. Epub 2014 Jul 1.

Accessory proteins of SARS-CoV and other coronaviruses

Ding Xiang Liu  1 , To Sing Fung  2 , Kelvin Kian-Long Chong  2 , Aditi Shukla  3 , Rolf Hilgenfeld  3
Affiliations
Review

Accessory proteins of SARS-CoV and other coronaviruses

Ding Xiang Liu et al. Antiviral Res. 2014 Sep.

Abstract

The huge RNA genome of SARS coronavirus comprises a number of open reading frames that code for a total of eight accessory proteins. Although none of these are essential for virus replication, some appear to have a role in virus pathogenesis. Notably, some SARS-CoV accessory proteins have been shown to modulate the interferon signaling pathways and the production of pro-inflammatory cytokines. The structural information on these proteins is also limited, with only two (p7a and p9b) having their structures determined by X-ray crystallography. This review makes an attempt to summarize the published knowledge on SARS-CoV accessory proteins, with an emphasis on their involvement in virus-host interaction. The accessory proteins of other coronaviruses are also briefly discussed. This paper forms part of a series of invited articles in Antiviral Research on "From SARS to MERS: 10 years of research on highly pathogenic human coronaviruses" (see Introduction by Hilgenfeld and Peiris (2013)).

Keywords: Accessory proteins; Other coronaviruses; SARS-CoV; Structure and function.

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Figures

Fig. 1
Fig. 1
Schematic diagram showing the genome organization of the severe acute respiratory syndrome coronavirus (SARS-CoV). The eight accessory proteins (3a, 3b, 6, 7a, 7b, 8a, 8b, and 9b) are shown as colored boxes. The 5′ leader sequence (black box), open reading frames (ORFs 1a, 1b) encoding components of the replication/transcription complex, the structural genes spike (S), membrane (M), envelope (E), and nucleo-capsid (N) are also indicated (not drawn to scale).
Fig. 2
Fig. 2
Schematic diagram showing motifs and domains within SARS-CoV accessory proteins p3a and p6. TM, transmembrane domain.
Fig. 3
Fig. 3
Schematic diagram showing the known topological and structural features of SARS-CoV accessory proteins. N-terminus (N) and C-terminus (C) are indicated. α-Helices are represented by blue columns and β-strands are represented by red arrows. The topological or structural features of p3b, p8a, and p8b are not well understood. Ribbon diagrams for p7a and p9b are adapted from Nelson et al. (2005) and Meier et al., 2006, respectively.
Fig. 4
Fig. 4
Phylogenetic analysis of coronaviruses based on pp1ab using Kalign multiple sequence alignment and TreeDyn tree viewer (Chevenet et al., 2006, Lassmann and Sonnhammer, 2005). Next to the branch, the virus name is indicated, along with the previously defined viral lineages, i.e. group 1 for Alphacoronavirus members, 2a, 2b, 2c, 2d for Betacoronavirus members, and 3 for the member of the genus Gammacoronavirus. Scale bar indicates nucleotide substitutions per site.
Fig. 5
Fig. 5
Genome organization of members of Betacoronavirus lineages a–d, as well as of the genera Alphacoronavirus and Gammacoronavirus, showing structural and accessory genes downstream of the orf1a/1b gene. The 5′ leader sequence (black box), open reading frames (ORFs 1a, 1b) encoding components of the replication/transcription complex, the genes encoding the structural proteins spike (S), membrane (M), envelope (E), and nucleocapsid (N) are also indicated in gray. Interspersed between (or within) them are the genes coding for putative accessory proteins (not drawn to scale). The following coronavirus genomes are illustrated (GenBank accession numbers in brackets): (1) Bovine coronavirus (NC_003045), (2) Mouse Hepatitis Virus (AC_000192), (3) Human coronavirus HKU1 (NC_006577), (4) Human coronavirus OC43 (NC_005147), (5) Severe Acute Respiratory Syndrome coronavirus (NC_004718), (6) Tylonycteris bat coronavirus HKU4 (NC_009019), (7) Pipistrellus bat coronavirus HKU5 (NC_009020), (8) MERS coronavirus (NC_019843), (9) Rousettus bat coronavirus HKU9 (NC_009021). (10) Feline infectious peritonitis virus (NC_002306), (11) Porcine respiratory coronavirus (DQ811787), (12) Transmissible gastroenteritis virus (DQ811788), (13) Human coronavirus 229E (NC_002645), (14) Infectious Bronchitis Virus (NC_001451).
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