Ribosome Pausing at Inefficient Codons at the End of the Replicase Coding Region Is Important for Hepatitis C Virus Genome Replication
Hepatitis C virus (HCV) infects liver cells and often causes chronic infection, also leading to liver cirrhosis and cancer. In the cytoplasm, the viral structural and non-structural (NS) proteins are directly translated from the plus strand HCV RNA genome. The viral proteins NS3 to NS5B proteins con...
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| Format: | Article |
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MDPI AG
2020-09-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/21/18/6955 |
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| author | Gesche K. Gerresheim Carolin S. Hess Lyudmila A. Shalamova Markus Fricke Manja Marz Dmitri E. Andreev Ivan N. Shatsky Michael Niepmann |
| author_facet | Gesche K. Gerresheim Carolin S. Hess Lyudmila A. Shalamova Markus Fricke Manja Marz Dmitri E. Andreev Ivan N. Shatsky Michael Niepmann |
| author_sort | Gesche K. Gerresheim |
| collection | DOAJ |
| description | Hepatitis C virus (HCV) infects liver cells and often causes chronic infection, also leading to liver cirrhosis and cancer. In the cytoplasm, the viral structural and non-structural (NS) proteins are directly translated from the plus strand HCV RNA genome. The viral proteins NS3 to NS5B proteins constitute the replication complex that is required for RNA genome replication via a minus strand antigenome. The most C-terminal protein in the genome is the NS5B replicase, which needs to initiate antigenome RNA synthesis at the very 3′-end of the plus strand. Using ribosome profiling of cells replicating full-length infectious HCV genomes, we uncovered that ribosomes accumulate at the HCV stop codon and about 30 nucleotides upstream of it. This pausing is due to the presence of conserved rare, inefficient Wobble codons upstream of the termination site. Synonymous substitution of these inefficient codons to efficient codons has negative consequences for viral RNA replication but not for viral protein synthesis. This pausing may allow the enzymatically active replicase core to find its genuine RNA template in <i>cis</i>, while the protein is still held in place by being stuck with its C-terminus in the exit tunnel of the paused ribosome. |
| first_indexed | 2024-03-10T16:08:58Z |
| format | Article |
| id | doaj.art-abfa222c058044f9ab2bbc0b3914873b |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-10T16:08:58Z |
| publishDate | 2020-09-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-abfa222c058044f9ab2bbc0b3914873b2023-11-20T14:38:58ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672020-09-012118695510.3390/ijms21186955Ribosome Pausing at Inefficient Codons at the End of the Replicase Coding Region Is Important for Hepatitis C Virus Genome ReplicationGesche K. Gerresheim0Carolin S. Hess1Lyudmila A. Shalamova2Markus Fricke3Manja Marz4Dmitri E. Andreev5Ivan N. Shatsky6Michael Niepmann7Inst. of Biochemistry, Medical Faculty, Justus-Liebig-University, 35392 Giessen, GermanyInst. of Biochemistry, Medical Faculty, Justus-Liebig-University, 35392 Giessen, GermanyInst. of Virology, Faculty of Veterinary Medicine, Justus-Liebig-University, 35392 Giessen, GermanyGenevention GmbH, 37079 Göttingen, GermanyRNA Bioinformatics and High Throughput Analysis, Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, 07743 Jena, GermanyLomonosov Moscow State University, Belozersky Inst. of Physico-Chemical Biology, Moscow 119234, RussiaLomonosov Moscow State University, Belozersky Inst. of Physico-Chemical Biology, Moscow 119234, RussiaInst. of Biochemistry, Medical Faculty, Justus-Liebig-University, 35392 Giessen, GermanyHepatitis C virus (HCV) infects liver cells and often causes chronic infection, also leading to liver cirrhosis and cancer. In the cytoplasm, the viral structural and non-structural (NS) proteins are directly translated from the plus strand HCV RNA genome. The viral proteins NS3 to NS5B proteins constitute the replication complex that is required for RNA genome replication via a minus strand antigenome. The most C-terminal protein in the genome is the NS5B replicase, which needs to initiate antigenome RNA synthesis at the very 3′-end of the plus strand. Using ribosome profiling of cells replicating full-length infectious HCV genomes, we uncovered that ribosomes accumulate at the HCV stop codon and about 30 nucleotides upstream of it. This pausing is due to the presence of conserved rare, inefficient Wobble codons upstream of the termination site. Synonymous substitution of these inefficient codons to efficient codons has negative consequences for viral RNA replication but not for viral protein synthesis. This pausing may allow the enzymatically active replicase core to find its genuine RNA template in <i>cis</i>, while the protein is still held in place by being stuck with its C-terminus in the exit tunnel of the paused ribosome.https://www.mdpi.com/1422-0067/21/18/6955HCVtranslationribosome pausingrare codonWobble codonreplication |
| spellingShingle | Gesche K. Gerresheim Carolin S. Hess Lyudmila A. Shalamova Markus Fricke Manja Marz Dmitri E. Andreev Ivan N. Shatsky Michael Niepmann Ribosome Pausing at Inefficient Codons at the End of the Replicase Coding Region Is Important for Hepatitis C Virus Genome Replication International Journal of Molecular Sciences HCV translation ribosome pausing rare codon Wobble codon replication |
| title | Ribosome Pausing at Inefficient Codons at the End of the Replicase Coding Region Is Important for Hepatitis C Virus Genome Replication |
| title_full | Ribosome Pausing at Inefficient Codons at the End of the Replicase Coding Region Is Important for Hepatitis C Virus Genome Replication |
| title_fullStr | Ribosome Pausing at Inefficient Codons at the End of the Replicase Coding Region Is Important for Hepatitis C Virus Genome Replication |
| title_full_unstemmed | Ribosome Pausing at Inefficient Codons at the End of the Replicase Coding Region Is Important for Hepatitis C Virus Genome Replication |
| title_short | Ribosome Pausing at Inefficient Codons at the End of the Replicase Coding Region Is Important for Hepatitis C Virus Genome Replication |
| title_sort | ribosome pausing at inefficient codons at the end of the replicase coding region is important for hepatitis c virus genome replication |
| topic | HCV translation ribosome pausing rare codon Wobble codon replication |
| url | https://www.mdpi.com/1422-0067/21/18/6955 |
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