Compositional diversity and evolutionary pattern of coronavirus accessory proteins
Autor: | Na Han, Hangyu Zhou, Yousong Peng, Liang Li, Taijiao Jiang, Ziyi Chen, Jingzhe Shang, Chengyang Ji, Aiping Wu, Jing Meng |
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Rok vydání: | 2020 |
Předmět: |
AcademicSubjects/SCI01060
compositional diversity Genes Viral viruses coronavirus Computational biology Biology medicine.disease_cause Open Reading Frames Viral Proteins 03 medical and health sciences 0302 clinical medicine Viral life cycle Transcription (biology) evolution medicine Humans Protein Interaction Maps 030212 general & internal medicine Molecular Biology 030304 developmental biology Coronavirus 0303 health sciences Case Study SARS-CoV-2 COVID-19 virus diseases Molecular Sequence Annotation Genome project Biological Evolution Open reading frame Regulatory sequence accessory proteins Host adaptation Information Systems |
Zdroj: | Briefings in Bioinformatics |
ISSN: | 1477-4054 1467-5463 |
Popis: | Accessory proteins play important roles in the interaction between coronaviruses and their hosts. Accordingly, a comprehensive study of the compositional diversity and evolutionary patterns of accessory proteins is critical to understanding the host adaptation and epidemic variation of coronaviruses. Here, we developed a standardized genome annotation tool for coronavirus (CoroAnnoter) by combining open reading frame prediction, transcription regulatory sequence recognition and homologous alignment. Using CoroAnnoter, we annotated 39 representative coronavirus strains to form a compositional profile for all of the accessary proteins. Large variations were observed in the number of accessory proteins of 1–10 for different coronaviruses, with SARS-CoV-2 and SARS-CoV having the most (9 and 10, respectively). The variation between SARS-CoV and SARS-CoV-2 accessory proteins could be traced back to related coronaviruses in other hosts. The genomic distribution of accessory proteins had significant intra-genus conservation and inter-genus diversity and could be grouped into 1, 4, 2 and 1 types for alpha-, beta-, gamma-, and delta-coronaviruses, respectively. Evolutionary analysis suggested that accessory proteins are more conservative locating before the N-terminal of proteins E and M (E-M), while they are more diverse after these proteins. Furthermore, comparison of virus-host interaction networks of SARS-CoV-2 and SARS-CoV accessory proteins showed that they share multiple antiviral signaling pathways, those involved in the apoptotic process, viral life cycle and response to oxidative stress. In summary, our study provides a tool for coronavirus genome annotation and builds a comprehensive profile for coronavirus accessory proteins covering their composition, classification, evolutionary pattern and host interaction. |
Databáze: | OpenAIRE |
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