Coronavirus genome: prediction of putative functional domains in the non-structural polyprotein by comparative amino acid sequence analysis

• Published in: Nucleic Acids Research Vol. 17; no. 12; pp. 4847 - 4861
• Main Authors: Gorbalenya, A.E, Koonin, E.V, Donchenko, A.P, Blinov, V.M
• Format: Journal Article Web Resource
• Language: English
• Published: Oxford Oxford University Press 26.06.1989
• Subjects: Amino Acid Sequence; amino acid sequences; binding proteins; binding sites; Biological and medical sciences; Capsid - genetics; Capsid - physiology; computer analysis; Coronaviridae; Coronaviridae - genetics; Coronavirus; Cysteine - physiology; Cysteine Endopeptidases - genetics; Cysteine Endopeptidases - physiology; DNA-directed RNA polymerase; Fundamental and applied biological sciences. Psychology; Genes, Viral; Infectious bronchitis virus; Molecular and cellular biology; Molecular genetics; Molecular Sequence Data; nucleic acids; proteinases; proteolysis; RNA helicase; RNA Replicase - genetics; RNA Replicase - isolation & purification; RNA-directed RNA polymerase; Sequence Homology, Nucleic Acid; Transcription. Transcription factor. Splicing. Rna processing; Viral Core Proteins - genetics; Viral Core Proteins - physiology; Viral Nonstructural Proteins; viral proteins; Recombination; Molecular structure; Transcription; Zinc finger structure; Cysteine proteinase; Homology; Avian infectious bronchitis virus; Secondary structure; Virus; Coronavirus; Domain structure; DNA; Replication; Coronaviridae; Aminoacid sequence; Computer aided analysis; Growth factor
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/17.12.4847

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.