Phylogeny of the SARS Coronavirus

Eickmann, Markus; Becker, Stephan; Klenk, Hans‐Dieter; Doerr, Hans Wilhelm; Stadler, Konrad; Censini, Stefano; Guidotti, Silvia; Masignani, Vega; Scarselli, María; Mora, Marirosa; Donati, Claudio; Han, Jang H.; Song, Hyun Chul; Abrignani, Sergio; Covacci, Antonello; Rappuoli, Rino

doi:10.1126/science.302.5650.1504b

Cited by 90 publications

(38 citation statements)

References 6 publications

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“…The SARS–CoV lineage has been proposed to cluster with Group 2 (44,45). To further analyse conservation patterns within the S3 element in a broader context, we aligned 28 complete genomic CoV sequences (summarized in Supplementary Table S1).…”

Section: Resultsmentioning

confidence: 99%

RNA dimerization plays a role in ribosomal frameshifting of the SARS coronavirus

Ishimaru

Plant

Sims

et al. 2012

Nucleic Acids Research

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Messenger RNA encoded signals that are involved in programmed -1 ribosomal frameshifting (-1 PRF) are typically two-stemmed hairpin (H)-type pseudoknots (pks). We previously described an unusual three-stemmed pseudoknot from the severe acute respiratory syndrome (SARS) coronavirus (CoV) that stimulated -1 PRF. The conserved existence of a third stem–loop suggested an important hitherto unknown function. Here we present new information describing structure and function of the third stem of the SARS pseudoknot. We uncovered RNA dimerization through a palindromic sequence embedded in the SARS-CoV Stem 3. Further in vitro analysis revealed that SARS-CoV RNA dimers assemble through ‘kissing’ loop–loop interactions. We also show that loop–loop kissing complex formation becomes more efficient at physiological temperature and in the presence of magnesium. When the palindromic sequence was mutated, in vitro RNA dimerization was abolished, and frameshifting was reduced from 15 to 5.7%. Furthermore, the inability to dimerize caused by the silent codon change in Stem 3 of SARS-CoV changed the viral growth kinetics and affected the levels of genomic and subgenomic RNA in infected cells. These results suggest that the homodimeric RNA complex formed by the SARS pseudoknot occurs in the cellular environment and that loop–loop kissing interactions involving Stem 3 modulate -1 PRF and play a role in subgenomic and full-length RNA synthesis.

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Section: Resultsmentioning

confidence: 99%

RNA dimerization plays a role in ribosomal frameshifting of the SARS coronavirus

Ishimaru

Plant

Sims

et al. 2012

Nucleic Acids Research

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“…The S-protein drives entry into target cells CoVs are subdivided into three phylogenetic groups; human CoVs are found in groups I (229E and NL63) and II (OC43). Depending on the method of sequence analysis used, SARS-CoV either constitutes a new phylogenetic group or a subgroup of group II CoVs [10,11]. The organization of the positive-stranded RNA genome of SARS-CoV, which is 29.7 kb in size, resembles that of other coronaviruses and harbors open-reading frames (ORFs) that encode a large polyprotein required for genome replication, four structural proteins and eight additional polypeptides of unclear function ( Figure 1) [1].…”

Section: Cellular Entry Of the Sars Coronavirus Heike Hofmann And Stementioning

confidence: 99%

Cellular entry of the SARS coronavirus

Hofmann

Pöhlmann

2004

Trends in Microbiology

239

228

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“…The SARS-CoV S glycoprotein is a 1255-amino acid precursor polypeptide as deduced from the published genome sequence and has 23 potential N -linked glycosylation sites (Eickmann et al, 2003; Marra et al, 2003; Rota et al, 2003; Xiao et al, 2003). Previous studies have demonstrated that several of these sites are occupied and possess both complex-type and high-mannose type N -glycans (Krokhin et al, 2003; Song et al, 2004; Ying et al, 2004).…”

Section: Introductionmentioning

confidence: 99%

Identification of N-linked carbohydrates from severe acute respiratory syndrome (SARS) spike glycoprotein

Ritchie¹,

Harvey²,

et al. 2010

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N-glycans were released from the SARS coronavirus (SARS-CoV) spike glycoprotein produced in Vero E6 cells and their structures were determined by a combination of matrix-assisted laser desorption/ionization (MALDI) mass spectrometry, negative ion electrospray collision-induced dissociation time-of-flight mass spectrometry and normal-phase high-performance liquid chromatography with exoglycosidase digestion. Major glycans were high-mannose (Man5–9GlcNAc2), hybrid and bi-, tri- and tetra-antennary complex with and without bisecting GlcNAc and core fucose. Complex glycans with fewer than the full complement of galactose residues were present and sialylation was negligible. Treatment with the glucosidase inhibitor N-butyl-deoxynojirimycin (NB-DNJ) inhibited N-glycan processing as evidenced by the appearance of glycans of composition Glc3Man7–9GlcNAc2. However, some complex glycans remained suggesting the presence of an α-endomannosidase. Our data in tissue culture indicate that inhibition of N-glycan processing may be considered as a therapeutic strategy against SARS CoV infections.

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Phylogeny of the SARS Coronavirus

Cited by 90 publications

References 6 publications

RNA dimerization plays a role in ribosomal frameshifting of the SARS coronavirus

RNA dimerization plays a role in ribosomal frameshifting of the SARS coronavirus

Cellular entry of the SARS coronavirus

Identification of N-linked carbohydrates from severe acute respiratory syndrome (SARS) spike glycoprotein

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