Cargando…

Differential Assembly of Catalytic Interactions within the Conserved Active Sites of Two Ribozymes

Molecular recognition is central to biology and a critical aspect of RNA function. Yet structured RNAs typically lack the preorganization needed for strong binding and precise positioning. A striking example is the group I ribozyme from Tetrahymena, which binds its guanosine substrate (G) orders of...

Descripción completa

Detalles Bibliográficos
Autores principales: van Schie, Sabine N. S., Sengupta, Raghuvir N., Herschlag, Daniel
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4976970/
https://www.ncbi.nlm.nih.gov/pubmed/27501145
http://dx.doi.org/10.1371/journal.pone.0160457
_version_ 1782446947317055488
author van Schie, Sabine N. S.
Sengupta, Raghuvir N.
Herschlag, Daniel
author_facet van Schie, Sabine N. S.
Sengupta, Raghuvir N.
Herschlag, Daniel
author_sort van Schie, Sabine N. S.
collection PubMed
description Molecular recognition is central to biology and a critical aspect of RNA function. Yet structured RNAs typically lack the preorganization needed for strong binding and precise positioning. A striking example is the group I ribozyme from Tetrahymena, which binds its guanosine substrate (G) orders of magnitude slower than diffusion. Binding of G is also thermodynamically coupled to binding of the oligonucleotide substrate (S) and further work has shown that the transition from E•G to E•S•G accompanies a conformational change that allows G to make the active site interactions required for catalysis. The group I ribozyme from Azoarcus has a similarly slow association rate but lacks the coupled binding observed for the Tetrahymena ribozyme. Here we test, using G analogs and metal ion rescue experiments, whether this absence of coupling arises from a higher degree of preorganization within the Azoarcus active site. Our results suggest that the Azoarcus ribozyme forms cognate catalytic metal ion interactions with G in the E•G complex, interactions that are absent in the Tetrahymena E•G complex. Thus, RNAs that share highly similar active site architectures and catalyze the same reactions can differ in the assembly of transition state interactions. More generally, an ability to readily access distinct local conformational states may have facilitated the evolutionary exploration needed to attain RNA machines that carry out complex, multi-step processes.
format Online
Article
Text
id pubmed-4976970
institution National Center for Biotechnology Information
language English
publishDate 2016
publisher Public Library of Science
record_format MEDLINE/PubMed
spelling pubmed-49769702016-08-25 Differential Assembly of Catalytic Interactions within the Conserved Active Sites of Two Ribozymes van Schie, Sabine N. S. Sengupta, Raghuvir N. Herschlag, Daniel PLoS One Research Article Molecular recognition is central to biology and a critical aspect of RNA function. Yet structured RNAs typically lack the preorganization needed for strong binding and precise positioning. A striking example is the group I ribozyme from Tetrahymena, which binds its guanosine substrate (G) orders of magnitude slower than diffusion. Binding of G is also thermodynamically coupled to binding of the oligonucleotide substrate (S) and further work has shown that the transition from E•G to E•S•G accompanies a conformational change that allows G to make the active site interactions required for catalysis. The group I ribozyme from Azoarcus has a similarly slow association rate but lacks the coupled binding observed for the Tetrahymena ribozyme. Here we test, using G analogs and metal ion rescue experiments, whether this absence of coupling arises from a higher degree of preorganization within the Azoarcus active site. Our results suggest that the Azoarcus ribozyme forms cognate catalytic metal ion interactions with G in the E•G complex, interactions that are absent in the Tetrahymena E•G complex. Thus, RNAs that share highly similar active site architectures and catalyze the same reactions can differ in the assembly of transition state interactions. More generally, an ability to readily access distinct local conformational states may have facilitated the evolutionary exploration needed to attain RNA machines that carry out complex, multi-step processes. Public Library of Science 2016-08-08 /pmc/articles/PMC4976970/ /pubmed/27501145 http://dx.doi.org/10.1371/journal.pone.0160457 Text en © 2016 van Schie et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
van Schie, Sabine N. S.
Sengupta, Raghuvir N.
Herschlag, Daniel
Differential Assembly of Catalytic Interactions within the Conserved Active Sites of Two Ribozymes
title Differential Assembly of Catalytic Interactions within the Conserved Active Sites of Two Ribozymes
title_full Differential Assembly of Catalytic Interactions within the Conserved Active Sites of Two Ribozymes
title_fullStr Differential Assembly of Catalytic Interactions within the Conserved Active Sites of Two Ribozymes
title_full_unstemmed Differential Assembly of Catalytic Interactions within the Conserved Active Sites of Two Ribozymes
title_short Differential Assembly of Catalytic Interactions within the Conserved Active Sites of Two Ribozymes
title_sort differential assembly of catalytic interactions within the conserved active sites of two ribozymes
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4976970/
https://www.ncbi.nlm.nih.gov/pubmed/27501145
http://dx.doi.org/10.1371/journal.pone.0160457
work_keys_str_mv AT vanschiesabinens differentialassemblyofcatalyticinteractionswithintheconservedactivesitesoftworibozymes
AT senguptaraghuvirn differentialassemblyofcatalyticinteractionswithintheconservedactivesitesoftworibozymes
AT herschlagdaniel differentialassemblyofcatalyticinteractionswithintheconservedactivesitesoftworibozymes