{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,5]],"date-time":"2026-07-05T10:26:55Z","timestamp":1783247215978,"version":"3.54.6"},"reference-count":33,"publisher":"American Society for Microbiology","issue":"5","license":[{"start":{"date-parts":[[2024,5,2]],"date-time":"2024-05-02T00:00:00Z","timestamp":1714608000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2024,5,2]],"date-time":"2024-05-02T00:00:00Z","timestamp":1714608000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"DOI":"10.13039\/100009619","name":"Japan Agency for Medical Research and Development","doi-asserted-by":"publisher","award":["23fk0108687h0001"],"award-info":[{"award-number":["23fk0108687h0001"]}],"id":[{"id":"10.13039\/100009619","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100007449","name":"Takeda Science Foundation","doi-asserted-by":"crossref","award":["2020"],"award-info":[{"award-number":["2020"]}],"id":[{"id":"10.13039\/100007449","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100004051","name":"Kato Memorial Bioscience Foundation","doi-asserted-by":"crossref","award":["2023"],"award-info":[{"award-number":["2023"]}],"id":[{"id":"10.13039\/501100004051","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100012014","name":"Kieikai Research Foundation","doi-asserted-by":"crossref","award":["2023"],"award-info":[{"award-number":["2023"]}],"id":[{"id":"10.13039\/501100012014","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["Microbiol Spectr"],"published-print":{"date-parts":[[2024,5,2]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n          <jats:sec>\n            <jats:title\/>\n            <jats:p>\n              Paramyxo- and filovirus genomes are equipped with bipartite promoters at their 3\n              <jats:italic>'<\/jats:italic>\n              ends to initiate RNA synthesis. The two elements, the primary promoter element 1 (PE1) and the secondary promoter element 2 (PE2), are separated by a spacer region that must be precisely a multiple of 6 nucleotides (nts), indicating these viruses adhere to the \u201crule of six.\u201d However, our knowledge of PE2 has been limited to a narrow spectrum of virus species. In this study, a comparative analysis of 1,647 paramyxoviral genomes from a public database revealed that the paramyxovirus PE2 can be clearly categorized into two distinct subcategories: one marked by C repeats at every six bases (exclusive to the subfamily\n              <jats:italic>Orthoparamyxovirinae<\/jats:italic>\n              ) and another characterized by CG repeats every 6 nts (observed in the subfamilies\n              <jats:italic>Avulavirinae<\/jats:italic>\n              and\n              <jats:italic>Rubulavirinae<\/jats:italic>\n              ). This unique pattern collectively mirrors the evolutionary lineage of these subfamilies. Furthermore, we showed that PE2 of the\n              <jats:italic>Rubulavirinae<\/jats:italic>\n              , with the exception of mumps virus, serves as part of the gene-coding region. This may be due to the fact that the\n              <jats:italic>Rubulavirinae<\/jats:italic>\n              are the only paramyxoviruses that cannot propagate without RNA editing. Filoviruses have three to eight consecutive uracil repeats every six bases (UN\n              <jats:sub>5<\/jats:sub>\n              ) in PE2, which is located in the 3\n              <jats:italic>'<\/jats:italic>\n              end region of the genome. We obtained PE2 sequences from 2,195 filoviruses in a public database and analyzed the sequence conservation among virus species. Our results indicate that the continuity of UN\n              <jats:sub>5<\/jats:sub>\n              hexamers is consistently maintained with a high degree of conservation across virus species.\n            <\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>IMPORTANCE<\/jats:title>\n            <jats:p>\n              The genomic intricacies of paramyxo- and filoviruses are highlighted by the bipartite promoters\u2014promoter element 1 (PE1) and promoter element 2 (PE2)\u2014at their 3\n              <jats:italic>'<\/jats:italic>\n              termini. The spacer region between these elements follows the \u201crule of six,\u201d crucial for genome replication. By a comprehensive analysis of paramyxoviral genome sequences, we identified distinct subcategories of PE2 based on C and CG repeats that were specific to\n              <jats:italic>Orthoparamyxovirinae<\/jats:italic>\n              and\n              <jats:italic>Avulavirinae<\/jats:italic>\n              \/\n              <jats:italic>Rubulavirinae<\/jats:italic>\n              , respectively, mirroring their evolutionary lineages. Notably, the PE2 of\n              <jats:italic>Rubulavirinae<\/jats:italic>\n              is integrated into the gene-coding region, a unique trait potentially linked to its strict dependence on RNA editing for virus growth. This study also focused on the PE2 sequences in filovirus genomes. The strict conservation of the continuity of UN\n              <jats:sub>5<\/jats:sub>\n              among virus species emphasizes its crucial role in viral genome replication.\n            <\/jats:p>\n          <\/jats:sec>","DOI":"10.1128\/spectrum.00417-24","type":"journal-article","created":{"date-parts":[[2024,4,12]],"date-time":"2024-04-12T13:00:47Z","timestamp":1712926847000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":9,"title":["Phylogenetic analysis of the promoter element 2 of paramyxo- and filoviruses"],"prefix":"10.1128","volume":"12","author":[{"given":"Shoichi","family":"Ashida","sequence":"first","affiliation":[{"name":"Transboundary Animal Diseases Research Center, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shohei","family":"Kojima","sequence":"additional","affiliation":[{"name":"Genome Immunobiology RIKEN Hakubi Research Team, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Takashi","family":"Okura","sequence":"additional","affiliation":[{"name":"Department of Virology 3, National Institute of Infectious Diseases, Tokyo, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fumihiro","family":"Kato","sequence":"additional","affiliation":[{"name":"Department of Virology 3, National Institute of Infectious Diseases, Tokyo, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7163-6960","authenticated-orcid":true,"given":"Wakako","family":"Furuyama","sequence":"additional","affiliation":[{"name":"National Research Center for the Control and Prevention of Infectious Diseases (CCPID), Nagasaki University, Nagasaki, 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