The molecular biology of coronaviruses

Abstract

Coronaviruses are large, enveloped RNA viruses of both medical and veterinary importance. Interest in this viral family has intensified in the past few years as a result of the identification of a newly emerged coronavirus as the causative agent of severe acute respiratory syndrome (SARS). At the molecular level, coronaviruses employ a variety of unusual strategies to accomplish a complex program of gene expression. Coronavirus replication entails ribosome frameshifting during genome translation, the synthesis of both genomic and multiple subgenomic RNA species, and the assembly of progeny virions by a pathway that is unique among enveloped RNA viruses. Progress in the investigation of these processes has been enhanced by the development of reverse genetic systems, an advance that was heretofore obstructed by the enormous size of the coronavirus genome. This review summarizes both classical and contemporary discoveries in the study of the molecular biology of these infectious agents, with particular emphasis on the nature and recognition of viral receptors, viral RNA synthesis, and the molecular interactions governing virion assembly.

Fig 1

Schematic of the coronavirus virion, with the minimal set of structural proteins.

Fig 2

The spike (S) protein. At the right is a linear map of the protein, denoting the amino‐terminal S1 and the carboxy‐terminal S2 portions of the molecule. The arrowhead marks the site of cleavage for those S proteins that become cleaved by cellular protease(s). The signal peptide and regions of mapped receptor‐binding domains (RBDs) are shown in S1. The heptad repeat regions (HR1 and HR2), putative fusion peptide (F), transmembrane domain, and endodomain are indicated in S2. At the left is a model for the S protein trimer.

Fig 3

The membrane (M), envelope (E), and nucleocapsid (N) proteins. At the right are linear maps of the proteins, denoting known regions of importance, including transmembrane (tm) domains. At the left are models for the three proteins.

Fig 4

Coronavirus genomic organization. The layout of the MHV genome is shown as an example. All coronavirus genomes have a 5′ cap and 3′ poly(A) tail. The invariant order of the canonical genes is replicase‐S‐E‐M‐N. The replicase contains two ORFs, 1a and 1b, complete expression of which is accomplished via ribosomal frameshifting. Accessory proteins (2a, HE, 4, 5a, and I, in the case of MHV) occur at various positions among the canonical genes.

Fig 5

The coronavirus life cycle.

Fig 6

Coronavirus RNA synthesis. The nested set of positive‐ and negative‐strand RNAs produced during replication and transcription are shown, using MHV as an example. The inset shows details of the arrangement of leader and body copies of the transcription‐regulating sequence (TRS).

Fig 7

Model for discontinuous negative‐strand transcription. Negative‐strand sgRNAs are initiated at the 3′ end of the gRNA template. Elongation proceeds as far as a body copy of a transcription‐regulating sequence (TRS). A strand‐switching event then occurs, pairing the newly transcribed negative‐sense body TRS with the leader copy of the TRS, from which point transcription resumes. A complex of the (+)gRNA and the (−)sgRNA then serves as the template for synthesis of multiple (+)sgRNAs.

Fig 8

RNA elements required for ribosomal frameshifting. The expanded region shows RNA sequences and secondary structures that program the frameshift, using IBV as an example.

Fig 9

Protein products of the replicase gene. Cleavage sites and processed products of pp1a (nsp1–nsp11) and of pp1ab (nsp1–nsp10, nsp12–nsp16) are shown. Predicted and/or experimentally demonstrated activities are indicated.