{"doi":"10.1128/jvi.01559-06","title":"Translation of the Flavivirus Kunjin NS3 Gene in\n            <i>cis</i>\n            but Not Its RNA Sequence or Secondary Structure Is Essential for Efficient RNA Packaging","abstract":"<jats:title>ABSTRACT</jats:title>\n          <jats:p>\n            Our previous studies using\n            <jats:italic>trans</jats:italic>\n            -complementation analysis of Kunjin virus (KUN) full-length cDNA clones harboring in-frame deletions in the NS3 gene demonstrated the inability of these defective complemented RNAs to be packaged into virus particles (W. J. Liu, P. L. Sedlak, N. Kondratieva, and A. A. Khromykh, J. Virol.\n            <jats:bold>76:</jats:bold>\n            10766-10775). In this study we aimed to establish whether this requirement for NS3 in RNA packaging is determined by the secondary RNA structure of the NS3 gene or by the essential role of the translated NS3 gene product. Multiple silent mutations of three computer-predicted stable RNA structures in the NS3 coding region of KUN replicon RNA aimed at disrupting RNA secondary structure without affecting amino acid sequence did not affect RNA replication and packaging into virus-like particles in the packaging cell line, thus demonstrating that the predicted conserved RNA structures in the NS3 gene do not play a role in RNA replication and/or packaging. In contrast, double frameshift mutations in the NS3 coding region of full-length KUN RNA, producing scrambled NS3 protein but retaining secondary RNA structure, resulted in the loss of ability of these defective RNAs to be packaged into virus particles in complementation experiments in KUN replicon-expressing cells. Furthermore, the more robust complementation-packaging system based on established stable cell lines producing large amounts of complemented replicating NS3-deficient replicon RNAs and infection with KUN virus to provide structural proteins also failed to detect any secreted virus-like particles containing packaged NS3-deficient replicon RNAs. These results have now firmly established the requirement of KUN NS3 protein translated in\n            <jats:italic>cis</jats:italic>\n            for genome packaging into virus particles.\n          </jats:p>","journal":"Journal of Virology","year":2006,"id":35007,"datarank":1.8165653434286457,"base_score":3.6109179126442243,"endowment":3.6109179126442243,"self_citation_contribution":0.5416376868966337,"citation_network_contribution":1.274927656532012,"self_endowment_contribution":0.5416376868966337,"citer_contribution":1.274927656532012,"corpus_percentile":null,"corpus_rank":null,"citation_count":36,"citer_count":33,"citers_with_citation_signal":29,"citers_with_endowment":29,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":180223,"name":"Natasha Kondratieva","orcid":null,"position":1,"is_corresponding":false},{"id":180224,"name":"Alexander A. Khromykh","orcid":null,"position":2,"is_corresponding":false},{"id":170986,"name":"Gorben P. Pijlman","orcid":null,"position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"base_score":3.6109179126442243,"endowment":3.6109179126442243,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"16971441","pmcid":"PMC1642170","openalex_id":"https://openalex.org/W2065628597","authors":[],"funders":[],"total_grants":0,"fwci":3.5712,"citation_percentile":0.91897875,"influential_citations":0,"citation_trend":[{"year":2012,"count":4},{"year":2013,"count":1},{"year":2014,"count":1},{"year":2015,"count":4},{"year":2016,"count":3},{"year":2017,"count":2},{"year":2018,"count":3},{"year":2020,"count":1},{"year":2021,"count":1},{"year":2022,"count":1},{"year":2024,"count":1}],"oa_status":"green","license":"https://journals.asm.org/non-commercial-tdm-license","oa_locations":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/1642170","host_type":"repository"},{"url":"https://doi.org/10.1128/jvi.01559-06","host_type":"GREEN"},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/1642170","host_type":"repository"},{"url":"https://journals.asm.org/doi/pdf/10.1128/JVI.01559-06","host_type":"publisher"},{"url":"https://pubmed.ncbi.nlm.nih.gov/16971441","host_type":"repository"},{"url":"http://europepmc.org/pmc/articles/PMC1642170","host_type":"repository"},{"url":"https://research.wur.nl/en/publications/translation-of-the-flavivirus-kunjin-ns3-gene-in-cis-but-not-its-","host_type":"repository"}],"fields_of_study":["Mosquito-borne diseases and control","Viral Infections and Vectors","Insect symbiosis and bacterial influences","Medicine","Biology","Animals","Chlorocebus aethiops","Frameshift Mutation","Genes, Reporter","Mutation","Nucleic Acid Conformation","Protein Biosynthesis","RNA Helicases","RNA, Viral","Serine Endopeptidases","Transcription, Genetic","Vero Cells","Viral Nonstructural Proteins","Virus Assembly","West Nile virus","beta-Galactosidase","Nucleoside-Triphosphatase","DEAD-box RNA Helicases","Viral Proteases"],"mesh_terms":["Viral Proteases","Animals","beta-Galactosidase","Chlorocebus aethiops","Mutation","Nucleic Acid Conformation","RNA, Viral","Serine Endopeptidases","Transcription, Genetic","Protein Biosynthesis","Vero Cells","West Nile virus","Frameshift Mutation","Viral Nonstructural Proteins","Genes, Reporter","Virus Assembly","RNA Helicases","Nucleoside-Triphosphatase","DEAD-box RNA Helicases"],"keywords":["Replicon","Biology","RNA","NS3","Complementation","Non-coding RNA","Intron","RNA-dependent RNA polymerase","Gene","Flavivirus","Coding region","Viral replication","Virology","Molecular biology","Genetics","Virus","Plasmid","Hepatitis C virus"],"sdg_mappings":[],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[{"name":"gen"}],"source":"live","citation_network_status":"fetched"},"created_at":"2026-06-09T23:11:40.974728Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}