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dc.contributor.authorWei, Y
dc.contributor.authorSilke, JR
dc.contributor.authorXia, X
dc.date.accessioned2020-12-17T04:22:25Z
dc.date.available2020-12-17T04:22:25Z
dc.date.issued2017-12-15
dc.identifierpii: 10.1038/s41598-017-17918-6
dc.identifier.citationWei, Y., Silke, J. R. & Xia, X. (2017). Elucidating the 16S rRNA 3 ' boundaries and defining optimal SD/aSD pairing in Escherichia coli and Bacillus subtilis using RNA-Seq data. SCIENTIFIC REPORTS, 7 (1), https://doi.org/10.1038/s41598-017-17918-6.
dc.identifier.issn2045-2322
dc.identifier.urihttp://hdl.handle.net/11343/255280
dc.description.abstractBacterial translation initiation is influenced by base pairing between the Shine-Dalgarno (SD) sequence in the 5' UTR of mRNA and the anti-SD (aSD) sequence at the free 3' end of the 16S rRNA (3' TAIL) due to: 1) the SD/aSD sequence binding location and 2) SD/aSD binding affinity. In order to understand what makes an SD/aSD interaction optimal, we must define: 1) terminus of the 3' TAIL and 2) extent of the core aSD sequence within the 3' TAIL. Our approach to characterize these components in Escherichia coli and Bacillus subtilis involves 1) mapping the 3' boundary of the mature 16S rRNA using high-throughput RNA sequencing (RNA-Seq), and 2) identifying the segment within the 3' TAIL that is strongly preferred in SD/aSD pairing. Using RNA-Seq data, we resolve previous discrepancies in the reported 3' TAIL in B. subtilis and recovered the established 3' TAIL in E. coli. Furthermore, we extend previous studies to suggest that both highly and lowly expressed genes favor SD sequences with intermediate binding affinity, but this trend is exclusive to SD sequences that complement the core aSD sequences defined herein.
dc.languageEnglish
dc.publisherNATURE PUBLISHING GROUP
dc.titleElucidating the 16S rRNA 3 ' boundaries and defining optimal SD/aSD pairing in Escherichia coli and Bacillus subtilis using RNA-Seq data
dc.typeJournal Article
dc.identifier.doi10.1038/s41598-017-17918-6
melbourne.affiliation.departmentMedical Biology (W.E.H.I.)
melbourne.source.titleScientific Reports
melbourne.source.volume7
melbourne.source.issue1
dc.rights.licenseCC BY
melbourne.elementsid1334097
melbourne.contributor.authorSilke, John
dc.identifier.eissn2045-2322
melbourne.accessrightsOpen Access


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