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Acquisition of new protein domains by coronaviruses: analysis of overlapping genes coding for proteins N and 9b in SARS coronavirus

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Abstract

Acquisition of new proteins by viruses usually occurs through horizontal gene transfer or through gene duplication, but another, less common mechanism is the usage of completely or partially overlapping reading frames. A case of acquisition of a completely new protein through introduction of a start codon in an alternative reading frame is the protein encoded by open reading frame (orf) 9b of SARS coronavirus. This gene completely overlaps with the nucleocapsid (N) gene (orf9a). Our findings indicate that the orf9b gene features a discordant codon-usage pattern. We analyzed the evolution of orf9b in concert with orf9a using sequence data of betacoronavirus-lineage b and found that orf9b, which encodes the overprinting protein, evolved largely independent of the overprinted orf9a. We also examined the protein products of these genomic sequences for their structural flexibility and found that it is not necessary for a newly acquired, overlapping protein product to be intrinsically disordered, in contrast to earlier suggestions. Our findings contribute to characterizing sequence properties of newly acquired genes making use of overlapping reading frames.

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Acknowledgments

We thank Dr. Zhengli Shi of the Wuhan Institute of Virology, Chinese Academy of Sciences, for sharing the sequence of the SL-CoV WIV1 nucleocapsid gene with us prior to publication. This project has been supported by the “Graduate School for Computing in Medicine & Life Sciences” funded by Germany’s Excellence Initiative [DFG GSC 235/2].

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  1. Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, 23538, Lübeck, Germany

    Aditi Shukla & Rolf Hilgenfeld

  2. Graduate School for Computing in Medicine & Life Sciences, University of Lübeck, Lübeck, Germany

    Aditi Shukla

  3. German Center for Infection Research (DZIF), University of Lübeck, Lübeck, Germany

    Rolf Hilgenfeld

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  1. Aditi Shukla
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Correspondence to Rolf Hilgenfeld.

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Shukla, A., Hilgenfeld, R. Acquisition of new protein domains by coronaviruses: analysis of overlapping genes coding for proteins N and 9b in SARS coronavirus. Virus Genes 50, 29–38 (2015). https://doi.org/10.1007/s11262-014-1139-8

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