The role of programmed-1 ribosomal frameshifting in coronavirus propagation

Abstract

Coronaviruses have the potential to cause significant economic, agricultural and health problems. The severe acute respiratory syndrome (SARS) associated coronavirus outbreak in late 2002, early 2003 called attention to the potential damage that coronaviruses could cause in the human population. The ensuing research has enlightened many to the molecular biology of coronaviruses. A programmed -1 ribosomal frameshift is required by coronaviruses for the production of the RNA dependent RNA polymerase which in turn is essential for viral replication. The frameshifting signal encoded in the viral genome has additional features that are not essential for frameshifting. Elucidation of the differences between coronavirus frameshift signals and signals from other viruses may help our understanding of these features. Here we summarize current knowledge and add additional insight regarding the function of the programmed -1 ribosomal frameshift signal in the coronavirus lifecycle.

Figure 1

Coronavirus Lifecycle. Viral entry is mediated by a spike-receptor interaction and cathepsin L mediated membrane fusion or endocytosis (A). After endocytosis the viral genome is released (B). The first phase of translation results in the production of two polyproteins (C.) The polyproteins are processed (D) and form double membraned vesicles (DMV). The DMV is the site of both minus- and plus-strand replication (E). A second phase of translation occurs from which proteins encoded in the subgenomic RNAs are made (F). New genomic RNA is packaged by nucleocapid protein. The structural proteins are processed in the ERGIC (G). The new viral particles exit the cell via exocytosis (H). See the main text for additional detail.

Figure 2

SARS Coronavirus Genome Organization. (A) There are nine major open reading frames in the SARS-CoV genome. The first is divided into two overlapping parts, ORF1a and ORF1b, and comprises two thirds of the genome. In addition to the full length genomic RNA, 5′ nested subgenomic RNAs are present in infected cells. The sgRNAs contain the same 5′ non-coding region (bold line) as the full length genomic RNA. Two polyproteins are produced from the full length RNA (shaded boxes). They are subsequently processed into functional units, non-structural proteins nsp1 through nsp16. The structural and accessory proteins are translated from the sgRNAs (shaded boxes). See text for additional detail.

Figure 3

Programmed -1 Ribosomal Frameshifting. During translation features intrinsic to the mRNA being decoded manipulate the ribosome such that the reading frame is altered. (A) The ribosome pauses over a heptameric slippery site (UUUAAAC in coronaviruses). The aminoacyl-tRNA (with the filled circle) and the peptidyl-tRNA (with open circles) are positioned in the zero frame in the A- and P-sites of the ribosome. The pause and curbing of ribosome fidelity is stimulated by a 3′ RNA structure. (B) Both peptidyl- and aminoacyl-tRNAs un-pair from the mRNA and re-pair in the -1 reading frame. This is facilitated by the anticodons being able to base pair at the non-wobble positions in the new reading frame. The pseudoknot structure is resolved and translation continues in the new reading frame.

Figure 4

Coronavirus Frameshift Signals. Two to three RNA stems following a heptameric slippery site comprise the coronavirus frameshift signal. The slippery site is underlined. The proposed IBV, SARS-CoV and HCoV-229E pseudoknot structures are shown (A to C respectively). The IBV structure has two stems, the SARS-CoV structure contains an additional internal stem, and the HCoV-229E structure is formed by two ‘kissing’ stem-loops. See text for additional detail.