A bacterial riboswitch class for the thiamin precursor HMP-PP employs a terminator-embedded aptamer
We recently implemented a bioinformatics pipeline that can uncover novel, but rare, riboswitch candidates as well as other noncoding RNA structures in bacteria. A prominent candidate revealed by our initial search efforts was called the ‘thiS motif’ because of its frequent association with a gene co...
| Main Authors: | , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
eLife Sciences Publications Ltd
2019-04-01
|
| Series: | eLife |
| Subjects: | |
| Online Access: | https://elifesciences.org/articles/45210 |
| _version_ | 1811181104872292352 |
|---|---|
| author | Ruben M Atilho Gayan Mirihana Arachchilage Etienne B Greenlee Kirsten M Knecht Ronald R Breaker |
| author_facet | Ruben M Atilho Gayan Mirihana Arachchilage Etienne B Greenlee Kirsten M Knecht Ronald R Breaker |
| author_sort | Ruben M Atilho |
| collection | DOAJ |
| description | We recently implemented a bioinformatics pipeline that can uncover novel, but rare, riboswitch candidates as well as other noncoding RNA structures in bacteria. A prominent candidate revealed by our initial search efforts was called the ‘thiS motif’ because of its frequent association with a gene coding for the ThiS protein, which delivers sulfur to form the thiazole moiety of the thiamin precursor HET-P. In the current report, we describe biochemical and genetic data demonstrating that thiS motif RNAs function as sensors of the thiamin precursor HMP-PP, which is fused with HET-P ultimately to form the final active coenzyme thiamin pyrophosphate (TPP). HMP-PP riboswitches exhibit a distinctive architecture wherein an unusually small ligand-sensing aptamer is almost entirely embedded within an otherwise classic intrinsic transcription terminator stem. This arrangement yields remarkably compact genetic switches that bacteria use to tune the levels of thiamin precursors during the biosynthesis of this universally distributed coenzyme. |
| first_indexed | 2024-04-11T09:14:06Z |
| format | Article |
| id | doaj.art-922d4cb28a1848f4ab8bfbb84ae854fe |
| institution | Directory Open Access Journal |
| issn | 2050-084X |
| language | English |
| last_indexed | 2024-04-11T09:14:06Z |
| publishDate | 2019-04-01 |
| publisher | eLife Sciences Publications Ltd |
| record_format | Article |
| series | eLife |
| spelling | doaj.art-922d4cb28a1848f4ab8bfbb84ae854fe2022-12-22T04:32:25ZengeLife Sciences Publications LtdeLife2050-084X2019-04-01810.7554/eLife.45210A bacterial riboswitch class for the thiamin precursor HMP-PP employs a terminator-embedded aptamerRuben M Atilho0Gayan Mirihana Arachchilage1Etienne B Greenlee2Kirsten M Knecht3Ronald R Breaker4https://orcid.org/0000-0002-2165-536XDepartment of Molecular Biophysics and Biochemistry, Yale University, New Haven, United StatesHoward Hughes Medical Institute, Yale University, New Haven, United StatesDepartment of Molecular, Cellular and Developmental Biology, Yale University, New Haven, United StatesDepartment of Molecular Biophysics and Biochemistry, Yale University, New Haven, United StatesDepartment of Molecular Biophysics and Biochemistry, Yale University, New Haven, United States; Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, United StatesWe recently implemented a bioinformatics pipeline that can uncover novel, but rare, riboswitch candidates as well as other noncoding RNA structures in bacteria. A prominent candidate revealed by our initial search efforts was called the ‘thiS motif’ because of its frequent association with a gene coding for the ThiS protein, which delivers sulfur to form the thiazole moiety of the thiamin precursor HET-P. In the current report, we describe biochemical and genetic data demonstrating that thiS motif RNAs function as sensors of the thiamin precursor HMP-PP, which is fused with HET-P ultimately to form the final active coenzyme thiamin pyrophosphate (TPP). HMP-PP riboswitches exhibit a distinctive architecture wherein an unusually small ligand-sensing aptamer is almost entirely embedded within an otherwise classic intrinsic transcription terminator stem. This arrangement yields remarkably compact genetic switches that bacteria use to tune the levels of thiamin precursors during the biosynthesis of this universally distributed coenzyme.https://elifesciences.org/articles/45210gene regulationpseudoknotRNA transcriptionthiamin pyrophosphate |
| spellingShingle | Ruben M Atilho Gayan Mirihana Arachchilage Etienne B Greenlee Kirsten M Knecht Ronald R Breaker A bacterial riboswitch class for the thiamin precursor HMP-PP employs a terminator-embedded aptamer eLife gene regulation pseudoknot RNA transcription thiamin pyrophosphate |
| title | A bacterial riboswitch class for the thiamin precursor HMP-PP employs a terminator-embedded aptamer |
| title_full | A bacterial riboswitch class for the thiamin precursor HMP-PP employs a terminator-embedded aptamer |
| title_fullStr | A bacterial riboswitch class for the thiamin precursor HMP-PP employs a terminator-embedded aptamer |
| title_full_unstemmed | A bacterial riboswitch class for the thiamin precursor HMP-PP employs a terminator-embedded aptamer |
| title_short | A bacterial riboswitch class for the thiamin precursor HMP-PP employs a terminator-embedded aptamer |
| title_sort | bacterial riboswitch class for the thiamin precursor hmp pp employs a terminator embedded aptamer |
| topic | gene regulation pseudoknot RNA transcription thiamin pyrophosphate |
| url | https://elifesciences.org/articles/45210 |
| work_keys_str_mv | AT rubenmatilho abacterialriboswitchclassforthethiaminprecursorhmpppemploysaterminatorembeddedaptamer AT gayanmirihanaarachchilage abacterialriboswitchclassforthethiaminprecursorhmpppemploysaterminatorembeddedaptamer AT etiennebgreenlee abacterialriboswitchclassforthethiaminprecursorhmpppemploysaterminatorembeddedaptamer AT kirstenmknecht abacterialriboswitchclassforthethiaminprecursorhmpppemploysaterminatorembeddedaptamer AT ronaldrbreaker abacterialriboswitchclassforthethiaminprecursorhmpppemploysaterminatorembeddedaptamer AT rubenmatilho bacterialriboswitchclassforthethiaminprecursorhmpppemploysaterminatorembeddedaptamer AT gayanmirihanaarachchilage bacterialriboswitchclassforthethiaminprecursorhmpppemploysaterminatorembeddedaptamer AT etiennebgreenlee bacterialriboswitchclassforthethiaminprecursorhmpppemploysaterminatorembeddedaptamer AT kirstenmknecht bacterialriboswitchclassforthethiaminprecursorhmpppemploysaterminatorembeddedaptamer AT ronaldrbreaker bacterialriboswitchclassforthethiaminprecursorhmpppemploysaterminatorembeddedaptamer |