Journal of Microbiology

Journal Article

Hepatitis B virus (HBV) codon adapts well to the gene expression profile of liver cancer: an evolutionary explanation for HBV’s oncogenic role: Chunpeng Yu , Jian Li , Qun Li , Shuai Chang , Yufeng Cao , Hui Jiang , Lingling Xie , Gang Fan , Song Wang; J. Microbiol. 2022;60(11):1106-1112. Published online October 17, 2022; DOI: https://doi.org/10.1007/s12275-022-2371-x

Abstract: Due to the evolutionary arms race between hosts and viruses, viruses must adapt to host translation systems to rapidly synthesize viral proteins. Highly expressed genes in hosts have a codon bias related to tRNA abundance, the primary RNA translation rate determinant. We calculated the relative synonymous codon usage (RSCU) of three hepatitis viruses (HAV, HBV, and HCV), SARS-CoV-2, 30 human tissues, and hepatocellular carcinoma (HCC). After comparing RSCU between viruses and human tissues, we calculated the codon adaptation index (CAI) of viral and human genes. HBV and HCV showed the highest correlations with HCC and the normal liver, while SARS-CoV-2 had the strongest association with lungs. In addition, based on HCC RSCU, the CAI of HBV and HCV genes was the highest. HBV and HCV preferentially adapt to the tRNA pool in HCC, facilitating viral RNA translation. After an initial trigger, rapid HBV/HCV translation and replication may change normal liver cells into HCC cells. Our findings reveal a novel perspective on virus-mediated oncogenesis.

Research Support, Non-U.S. Gov't

Factors Influencing Preferential Utilization of RNA Polymerase Containing Sigma-38 in Stationary-Phase Gene Expression in Escherichia coli: Eun Young Kim , Min-Sang Shin , Joon Haeng Rhee , Hyon E. Choy; J. Microbiol. 2004;42(2):103-110.; DOI: https://doi.org/2037 [pii]

Abstract: In order to understand the molecular basis of selective expression of stationary-phase genes by RNA polymerase containing [sigma]^38 (E[sigma]^38) in Escherichia coli, we examined transcription from the stationaryphase promoters, katEP, bolAP, hdeABP, csgBAP, and mcbP, in vivo and in vitro. Although these promoters are preferentially recognized in vivo by E[sigma]^38, they are transcribed in vitro by both E[sigma]^38 and E[sigma]^70 containing the major exponential [sigma], [sigma]^70. In the presence of high concentrations of glutamate salts, however, only E[sigma]^38 was able to efficiently transcribe from these promoters, which supports the concept that the promoter selectivity of [sigma]^38 -containing RNA polymerase is observed only under specific reaction conditions. The examination of 6S RNA, which is encoded by the ssr1 gene in vivo, showed that it reduced E[sigma]^70 activity during the stationary phase, but this reduction of activity did not result in the elevation of E[sigma]^38 activity. Thus, the preferential expression of stationary-phase genes by E[sigma]^38 is unlikely the consequence of selective inhibition of E[sigma]^70 by 6S RNA.

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