Specific structural elements of the T-box riboswitch drive the two-step binding of the tRNA ligand
T-box riboswitches are cis-regulatory RNA elements that regulate the expression of proteins involved in amino acid biosynthesis and transport by binding to specific tRNAs and sensing their aminoacylation state. While the T-box modular structural elements that recognize different parts of a tRNA have...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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eLife Sciences Publications Ltd
2018-09-01
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| Series: | eLife |
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| Online Access: | https://elifesciences.org/articles/39518 |
| _version_ | 1811200736837500928 |
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| author | Jiacheng Zhang Bhaskar Chetnani Eric D Cormack Dulce Alonso Wei Liu Alfonso Mondragón Jingyi Fei |
| author_facet | Jiacheng Zhang Bhaskar Chetnani Eric D Cormack Dulce Alonso Wei Liu Alfonso Mondragón Jingyi Fei |
| author_sort | Jiacheng Zhang |
| collection | DOAJ |
| description | T-box riboswitches are cis-regulatory RNA elements that regulate the expression of proteins involved in amino acid biosynthesis and transport by binding to specific tRNAs and sensing their aminoacylation state. While the T-box modular structural elements that recognize different parts of a tRNA have been identified, the kinetic trajectory describing how these interactions are established temporally remains unclear. Using smFRET, we demonstrate that tRNA binds to the riboswitch in two steps, first anticodon recognition followed by the sensing of the 3’ NCCA end, with the second step accompanied by a T-box riboswitch conformational change. Studies on site-specific mutants highlight that specific T-box structural elements drive the two-step binding process in a modular fashion. Our results set up a kinetic framework describing tRNA binding by T-box riboswitches, and suggest such binding mechanism is kinetically beneficial for efficient, co-transcriptional recognition of the cognate tRNA ligand. |
| first_indexed | 2024-04-12T02:08:44Z |
| format | Article |
| id | doaj.art-31ea41cbdfdd4781a946d6e0dd8a7d47 |
| institution | Directory Open Access Journal |
| issn | 2050-084X |
| language | English |
| last_indexed | 2024-04-12T02:08:44Z |
| publishDate | 2018-09-01 |
| publisher | eLife Sciences Publications Ltd |
| record_format | Article |
| series | eLife |
| spelling | doaj.art-31ea41cbdfdd4781a946d6e0dd8a7d472022-12-22T03:52:27ZengeLife Sciences Publications LtdeLife2050-084X2018-09-01710.7554/eLife.39518Specific structural elements of the T-box riboswitch drive the two-step binding of the tRNA ligandJiacheng Zhang0https://orcid.org/0000-0002-8671-5888Bhaskar Chetnani1Eric D Cormack2Dulce Alonso3Wei Liu4Alfonso Mondragón5https://orcid.org/0000-0002-0423-6323Jingyi Fei6https://orcid.org/0000-0002-9775-3820Institute for Biophysical Dynamics, University of Chicago, Chicago, United StatesDepartment of Molecular Biosciences, Northwestern University, Evanston, United StatesUniversity of Chicago College, Chicago, United StatesDepartment of Molecular Biosciences, Northwestern University, Evanston, United StatesDepartment of Biochemistry and Molecular Biology, University of Chicago, Chicago, United StatesDepartment of Molecular Biosciences, Northwestern University, Evanston, United StatesInstitute for Biophysical Dynamics, University of Chicago, Chicago, United States; Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, United StatesT-box riboswitches are cis-regulatory RNA elements that regulate the expression of proteins involved in amino acid biosynthesis and transport by binding to specific tRNAs and sensing their aminoacylation state. While the T-box modular structural elements that recognize different parts of a tRNA have been identified, the kinetic trajectory describing how these interactions are established temporally remains unclear. Using smFRET, we demonstrate that tRNA binds to the riboswitch in two steps, first anticodon recognition followed by the sensing of the 3’ NCCA end, with the second step accompanied by a T-box riboswitch conformational change. Studies on site-specific mutants highlight that specific T-box structural elements drive the two-step binding process in a modular fashion. Our results set up a kinetic framework describing tRNA binding by T-box riboswitches, and suggest such binding mechanism is kinetically beneficial for efficient, co-transcriptional recognition of the cognate tRNA ligand.https://elifesciences.org/articles/39518riboswitchT-boxsmFRETgene regulation |
| spellingShingle | Jiacheng Zhang Bhaskar Chetnani Eric D Cormack Dulce Alonso Wei Liu Alfonso Mondragón Jingyi Fei Specific structural elements of the T-box riboswitch drive the two-step binding of the tRNA ligand eLife riboswitch T-box smFRET gene regulation |
| title | Specific structural elements of the T-box riboswitch drive the two-step binding of the tRNA ligand |
| title_full | Specific structural elements of the T-box riboswitch drive the two-step binding of the tRNA ligand |
| title_fullStr | Specific structural elements of the T-box riboswitch drive the two-step binding of the tRNA ligand |
| title_full_unstemmed | Specific structural elements of the T-box riboswitch drive the two-step binding of the tRNA ligand |
| title_short | Specific structural elements of the T-box riboswitch drive the two-step binding of the tRNA ligand |
| title_sort | specific structural elements of the t box riboswitch drive the two step binding of the trna ligand |
| topic | riboswitch T-box smFRET gene regulation |
| url | https://elifesciences.org/articles/39518 |
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