GC usage of SARS-CoV-2 genes might adapt to the environment of human lung expressed genes
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ORIGINAL ARTICLE
GC usage of SARS‑CoV‑2 genes might adapt to the environment of human lung expressed genes Yue Li1 · Xinai Yang1 · Na Wang1 · Haiyan Wang1 · Bin Yin1 · Xiaoping Yang1 · Wenqing Jiang1 Received: 19 June 2020 / Accepted: 20 August 2020 © Springer-Verlag GmbH Germany, part of Springer Nature 2020
Abstract Understanding how SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) efficiently reproduces itself by taking resources from the human host could facilitate the development of drugs against the virus. SARS-CoV-2 translates its own proteins by using the host tRNAs, so that its GC or codon usage should fit that of the host cells. It is necessary to study both the virus and human genomes in the light of evolution and adaptation. The SARS-CoV-2 virus has significantly lower GC content and GC3 as compared to human. However, when we selected a set of human genes that have similar GC properties to SARS-CoV-2, we found that these genes were enriched in particular pathways. Moreover, these human genes have the codon composition perfectly correlated with the SARS-CoV-2, and were extraordinarily highly expressed in human lung tissues, demonstrating that the SARS-CoV-2 genes have similar GC usage as compared to the lung expressed human genes. RSCU (relative synonymous codon usage) and CAI (codon adaptation index) profiles further support the matching between SARS-CoV-2 and lungs. Our study indicates that SARS-CoV-2 might have adapted to the human lung environment by observing the high correlation between GC usage of SARS-CoV-2 and human lung genes, which suggests the GC content of SARS-CoV-2 is optimized to take advantage of human lung tissues. Keywords SARS-CoV-2 · GC content · Lung expressed genes · Adaptation
Introduction The recent outbreak of SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) has caused severe damage to China especially the Hubei province (Cowling and Leung 2020; Hui et al. 2020; Wang et al. 2020). It is urgent to find ways to control its transmission and cure the infected patients (Edelstein and Heymann 2015; Sheahan and Baric 2018; Wang et al. 2020). Particularly, understanding how SARSCoV-2 achieved rapid reproduction in the human host might be helpful in developing antivirus drugs. Notably, SARSCoV-2 translates its own proteins using the host tRNAs, which indicates that the codon composition of SARS-CoV-2 should have adapted to that of the human hosts. Therefore, it
Communicated by Stefan Hohmann. * Wenqing Jiang [email protected] 1
Department of Respiratory Diseases, Qingdao Haici Hospital, Qingdao, China
is rational to study both the virus and human genomes from the perspective of evolution and adaptation. It is well established that the viruses themselves do not survive alone, and they could only translate and reproduce their own proteins by using the resources from host cells (Taghinezhad et al. 2017). Proteins commonly consist of 20 amino acids, which are encoded by specific codons. The host cells do not equally use each amino acid and codon (Plotkin a
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