Coronavirus genome: prediction of putative functional domains in the non-structural polyprotein by comparative amino acid sequence analysis.
Amino acid sequences of 2 giant non-structural polyproteins (F1 and F2) of infectious bronchitis virus (IBV), a member of Coronaviridae, were compared, by computer-assisted methods, to sequences of a number of other positive strand RNA viral and cellular proteins. By this approach, juxtaposed putative RNA-dependent RNA polymerase, nucleic acid binding ("finger"-like) and RNA helicase domains were identified in F2. Together, these domains might constitute the core of the protein complex involved in the primer-dependent transcription, replication and recombination of coronaviruses. In F1, two cysteine protease-like domains and a growth factor-like one were revealed. One of the putative proteases of IBV is similar to 3C proteases of picornaviruses and related enzymes of como- nepo- and potyviruses. Search of IBV F1 and F2 sequences for sites similar to those cleaved by the latter proteases and intercomparison of the surrounding sequence stretches revealed 13 dipeptides Q/S(G) which are probably cleaved by the coronavirus 3C-like protease. Based on these observations, a partial tentative scheme for the functional organization and expression strategy of the non-structural polyproteins of IBV was proposed. It implies that, despite the general similarity to other positive strand RNA viruses, and particularly to potyviruses, coronaviruses possess a number of unique structural and functional features.
Gorbalenya
A E
AE
Institute of Poliomyelitis and Viral Encephalitides, USSR Academy of Medical Sciences, Moscow.
Koonin
E V
EV
Donchenko
A P
AP
Blinov
V M
VM
D000595:Amino Acid Sequence; D002213:Capsid / Q000235:genetics* / Q000502:physiology; D003332:Coronaviridae / Q000235:genetics*; D003545:Cysteine / Q000502:physiology; D003546:Cysteine Endopeptidases / Q000235:genetics / Q000502:physiology; D005814:Genes, Viral; D008969:Molecular Sequence Data; D012324:RNA-Dependent RNA Polymerase / Q000235:genetics / Q000302:isolation & purification; D012689:Sequence Homology, Nucleic Acid; D014758:Viral Core Proteins / Q000235:genetics* / Q000502:physiology; D017361:Viral Nonstructural Proteins
D014758:Viral Core Proteins; D017361:Viral Nonstructural Proteins; D012324:RNA-Dependent RNA Polymerase; D003546:Cysteine Endopeptidases; D003545:Cysteine