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Here, we show that ribosomes purified from Flavobacterium johnsoniae, a representative of the Bacteroidetes, fail to recognize the SD sequence of mRNA in vitro. A cryo-electron microscopy structure of the complete 70S ribosome from F. johnsoniae at 2.8 \u00c5 resolution reveals that the ASD is sequestered by ribosomal proteins bS21, bS18 and bS6, explaining the basis of ASD inhibition. The structure also uncovers a novel ribosomal protein\u2014bL38. Remarkably, in F. johnsoniae and many other Flavobacteriia, the gene encoding bS21 contains a strong SD, unlike virtually all other genes. A subset of Flavobacteriia have an alternative ASD, and in these organisms the fully complementary sequence lies upstream of the bS21 gene, indicative of natural covariation. In other Bacteroidetes classes, strong SDs are frequently found upstream of the genes for bS21 and\/or bS18. We propose that these SDs are used as regulatory elements, enabling bS21 and bS18 to translationally control their own production.<\/jats:p>","DOI":"10.1093\/nar\/gkaa1195","type":"journal-article","created":{"date-parts":[[2020,11,24]],"date-time":"2020-11-24T19:16:14Z","timestamp":1606245374000},"page":"547-567","source":"Crossref","is-referenced-by-count":39,"title":["Structural basis of sequestration of the anti-Shine-Dalgarno sequence in the Bacteroidetes ribosome"],"prefix":"10.1093","volume":"49","author":[{"given":"Vikash","family":"Jha","sequence":"first","affiliation":[{"name":"Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec H3A 0C7, Canada"},{"name":"Centre for Structural Biology, McGill University, Montreal, Quebec H3G 0B1, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bappaditya","family":"Roy","sequence":"additional","affiliation":[{"name":"Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA"},{"name":"Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dushyant","family":"Jahagirdar","sequence":"additional","affiliation":[{"name":"Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec H3A 0C7, Canada"},{"name":"Centre for Structural Biology, McGill University, Montreal, Quebec H3G 0B1, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zakkary A","family":"McNutt","sequence":"additional","affiliation":[{"name":"Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA"},{"name":"Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elan\u00a0A","family":"Shatoff","sequence":"additional","affiliation":[{"name":"Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA"},{"name":"Department of Physics, The Ohio State University, Columbus, OH 43210, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bethany L","family":"Boleratz","sequence":"additional","affiliation":[{"name":"Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dean E","family":"Watkins","sequence":"additional","affiliation":[{"name":"Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6699-8614","authenticated-orcid":false,"given":"Ralf","family":"Bundschuh","sequence":"additional","affiliation":[{"name":"Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA"},{"name":"Department of Physics, The Ohio State University, Columbus, OH 43210, USA"},{"name":"Department of Chemistry & Biochemistry, Division of Hematology, The Ohio State University, Columbus, OH 43210, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kaustuv","family":"Basu","sequence":"additional","affiliation":[{"name":"Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec H3A 0C7, Canada"},{"name":"Centre for Structural Biology, McGill University, Montreal, Quebec H3G 0B1, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9423-3344","authenticated-orcid":false,"given":"Joaquin","family":"Ortega","sequence":"additional","affiliation":[{"name":"Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec H3A 0C7, Canada"},{"name":"Centre for Structural Biology, McGill University, Montreal, Quebec H3G 0B1, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kurt","family":"Fredrick","sequence":"additional","affiliation":[{"name":"Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA"},{"name":"Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA"},{"name":"Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2020,12,16]]},"reference":[{"key":"2021011005250517500_B1","doi-asserted-by":"crossref","first-page":"1342","DOI":"10.1073\/pnas.71.4.1342","article-title":"The 3\u2032-terminal sequence of Escherichia coli 16S ribosomal RNA: complementarity to nonsense triplets and ribosome binding sites","volume":"71","author":"Shine","year":"1974","journal-title":"Proc. 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